Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold341
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: 1349338
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 9
Found at i:163674 original size:33 final size:32
Alignment explanation
Indices: 163637--163708 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
163627 AATTTATTTT
*
163637 TTATTTTGATTTTAAAAATATTAAAAATAAATA
1 TTATTTT-AATTTAAAAATATTAAAAATAAATA
*** *
163670 TTATTTTAATTTAATGGTATTGAAAATAAATA
1 TTATTTTAATTTAAAAATATTAAAAATAAATA
163702 TTATTTT
1 TTATTTT
163709 TAAAATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 27 0.79
33 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (32 bp):
TTATTTTAATTTAAAAATATTAAAAATAAATA
Found at i:163779 original size:28 final size:30
Alignment explanation
Indices: 163739--163798 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 30
163729 TTTAAAATAT
*
163739 AATTGTTAGAGATAATTTTTTATTTT-TAA
1 AATTGTTAAAGATAATTTTTTATTTTCTAA
163768 AATT-TTAAAGATAATTTTTTATTTTCTAA
1 AATTGTTAAAGATAATTTTTTATTTTCTAA
163797 AA
1 AA
163799 ATAATTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (30 bp):
AATTGTTAAAGATAATTTTTTATTTTCTAA
Found at i:164372 original size:21 final size:21
Alignment explanation
Indices: 164311--164363 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
164301 TTTCATCCAG
164311 ATGTATCGATAGATATTTTTC
1 ATGTATCGATAGATATTTTTC
*
164332 ATGTATCAATAGATATTTTTC
1 ATGTATCGATAGATATTTTTC
164353 ATGTATCGATA
1 ATGTATCGATA
164364 CAAAGTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (21 bp):
ATGTATCGATAGATATTTTTC
Found at i:166661 original size:19 final size:19
Alignment explanation
Indices: 166622--166670 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
166612 TCTTTATCAA
* * *
166622 TCTTTTTTTCTCTTTCTTT
1 TCTTTCTTTCTCTCTCCTT
166641 TCTTTCTTTCTCTCTCCTT
1 TCTTTCTTTCTCTCTCCTT
*
166660 TCCTTCTTTCT
1 TCTTTCTTTCT
166671 TTCATTTCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
TCTTTCTTTCTCTCTCCTT
Found at i:167317 original size:4 final size:4
Alignment explanation
Indices: 167308--167369 Score: 56
Period size: 4 Copynumber: 16.0 Consensus size: 4
167298 TTTTATTCTT
* * * *
167308 TTTC TTTC TTTC CTT- TTTC TTTT TTTC -CTC TTTC TTTT TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
167354 TTTC TCTC TTTT TTTC
1 TTTC TTTC TTTC TTTC
167370 ACCTTTGCCC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
3 4 0.09
4 40 0.91
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:167325 original size:15 final size:15
Alignment explanation
Indices: 167305--167364 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
167295 ATTTTTTATT
167305 CTTTTTCTTTCTTTC
1 CTTTTTCTTTCTTTC
*
167320 CTTTTTCTTTTTTTC
1 CTTTTTCTTTCTTTC
* *
167335 CTCTTTCTTTTTTTC
1 CTTTTTCTTTCTTTC
* *
167350 TTTCTTTCTCTCTTT
1 CTT-TTTCTTTCTTT
167365 TTTTCACCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
15 29 0.76
16 9 0.24
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
CTTTTTCTTTCTTTC
Found at i:167450 original size:2 final size:2
Alignment explanation
Indices: 167443--167469 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
167433 TGTAATAGAT
167443 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 T
167470 GTATGTATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:168235 original size:3 final size:3
Alignment explanation
Indices: 168227--168269 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
168217 AAATGCTTCT
168227 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
168270 CATTTAAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:168884 original size:20 final size:19
Alignment explanation
Indices: 168859--168909 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
168849 CATAATGAAT
*
168859 ATAATTATTTACTAAATTTA
1 ATAATTATTTACTAAA-ATA
*
168879 ATAATTAATTTATTAAAATA
1 ATAATT-ATTTACTAAAATA
*
168899 TTAATTATTTA
1 ATAATTATTTA
168910 AAAAGTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.19
20 13 0.48
21 9 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAATTATTTACTAAAATA
Found at i:169579 original size:16 final size:17
Alignment explanation
Indices: 169558--169589 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
169548 TATGCTTTGA
169558 TTTTA-TCTAAATAAAT
1 TTTTATTCTAAATAAAT
169574 TTTTATTCTAAATAAA
1 TTTTATTCTAAATAAA
169590 AAGTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTATTCTAAATAAAT
Found at i:169673 original size:21 final size:22
Alignment explanation
Indices: 169642--169688 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
169632 TAAAGATTTT
169642 TTTAGTATAAAT-TAAATAAAAA
1 TTTAGTATAAATATAAAT-AAAA
*
169664 TTTA-TATAAATATAAATTAAA
1 TTTAGTATAAATATAAATAAAA
169685 TTTA
1 TTTA
169689 AATATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TTTAGTATAAATATAAATAAAA
Found at i:171010 original size:23 final size:23
Alignment explanation
Indices: 170958--171010 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
170948 CAACTTCAAT
*
170958 TATATACTTATATCTAAGTTAAG
1 TATATACTTATATCTAAGTTAAA
170981 TATATACTTATATCTAAGTTTAAA
1 TATATACTTATATCTAAG-TTAAA
171005 TA-ATAC
1 TATATAC
171011 AGGGATACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (23 bp):
TATATACTTATATCTAAGTTAAA
Found at i:171747 original size:10 final size:9
Alignment explanation
Indices: 171731--171755 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
171721 TATTGAGACT
171731 TAAAAAAAA
1 TAAAAAAAA
171740 TAAAAAAAA
1 TAAAAAAAA
171749 TAAAAAA
1 TAAAAAA
171756 TATAGATGAA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:175781 original size:23 final size:23
Alignment explanation
Indices: 175741--175797 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
175731 TTACAAGAGA
* * *
175741 AAAAATAATTA-TATTTAAATATT
1 AAAAA-AATTATTAATTAAAAAAT
175764 AAAAAAATTATTAATTAAAAAAT
1 AAAAAAATTATTAATTAAAAAAT
*
175787 AAATAAATTAT
1 AAAAAAATTAT
175798 CAACATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAAAATTATTAATTAAAAAAT
Found at i:178883 original size:2 final size:2
Alignment explanation
Indices: 178876--178914 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
178866 TAAATAATTG
178876 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
178915 CATGCTATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:179528 original size:17 final size:17
Alignment explanation
Indices: 179496--179529 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
179486 ATTTAAATTG
179496 AATTATTTTAAATATTT
1 AATTATTTTAAATATTT
179513 AATT-TTTTAAATTATTT
1 AATTATTTTAAA-TATTT
179530 TTAGGTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTATTTTAAATATTT
Found at i:179555 original size:17 final size:17
Alignment explanation
Indices: 179516--179555 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
179506 AATATTTAAT
179516 TTTTTAAATTATTTTTA
1 TTTTTAAATTATTTTTA
** *
179533 GGTTTAGATTATTTTTA
1 TTTTTAAATTATTTTTA
179550 TTTTTA
1 TTTTTA
179556 CTTTTTTAAA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (17 bp):
TTTTTAAATTATTTTTA
Found at i:179578 original size:16 final size:16
Alignment explanation
Indices: 179559--179610 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
179549 ATTTTTACTT
179559 TTTTAAATTTCGATCA
1 TTTTAAATTTCGATCA
*
179575 TTTT-GATTTCGGATCA
1 TTTTAAATTTC-GATCA
179591 TTTTAAA-TTCGAGTCA
1 TTTTAAATTTCGA-TCA
179607 TTTT
1 TTTT
179611 GGTTTTACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 7 0.23
16 23 0.74
17 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.52
Consensus pattern (16 bp):
TTTTAAATTTCGATCA
Found at i:180570 original size:25 final size:24
Alignment explanation
Indices: 180507--180570 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 24
180497 TATTTATTTT
*
180507 TTATATAATAAAAATGACATAACA
1 TTATATAATAAAAATGACATAAAA
*
180531 -TATATAAATACAAAATTA-ATATAAA
1 TTATAT-AATA-AAAATGACATA-AAA
180556 TTATATAATTAAAAA
1 TTATATAA-TAAAAA
180571 GGGATTAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
23 5 0.15
24 7 0.21
25 14 0.42
26 7 0.21
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (24 bp):
TTATATAATAAAAATGACATAAAA
Found at i:180798 original size:17 final size:16
Alignment explanation
Indices: 180765--180800 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
180755 TTCGAATTCG
*
180765 AATCATTTGAAATTTA
1 AATCATTTAAAATTTA
180781 AATCATTTAAAGATTTA
1 AATCATTTAAA-ATTTA
180798 AAT
1 AAT
180801 TAATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (16 bp):
AATCATTTAAAATTTA
Found at i:181134 original size:24 final size:23
Alignment explanation
Indices: 181106--181170 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
181096 ACTATTTATA
181106 ATTAAAATATTATTTATATTAAT
1 ATTAAAATATTATTTATATTAAT
*
181129 ATTTAAAATATTA--T-TATTATT
1 A-TTAAAATATTATTTATATTAAT
181150 ATTAAAATATTATTTTATATT
1 ATTAAAATATTA-TTTATATT
181171 TTTTAAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
20 11 0.31
21 7 0.19
22 1 0.03
23 2 0.06
24 15 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTAAAATATTATTTATATTAAT
Found at i:181170 original size:21 final size:21
Alignment explanation
Indices: 181106--181179 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
181096 ACTATTTATA
*
181106 ATTAAAATATTATTTATATTAAT
1 ATTAAAATATTATTT-TA-TATT
*
181129 ATTTAAAATATTATTAT-TATT
1 A-TTAAAATATTATTTTATATT
181150 ATTAAAATATTATTTTATATT
1 ATTAAAATATTATTTTATATT
* *
181171 TTTTAAATA
1 ATTAAAATA
181180 ATAATATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 14 0.32
21 15 0.34
23 2 0.05
24 13 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTAAAATATTATTTTATATT
Found at i:181188 original size:44 final size:43
Alignment explanation
Indices: 181101--181188 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 43
181091 TCTAAACTAT
*
181101 TTATAATTAAAATATTATTTATATTAATATTTAAAATATTATTA
1 TTATAATTAAAATATTATTTATATT-ATATTTAAAATAATATTA
* *
181145 TTATTATTAAAATATTATTTTATATT-T-TTT-AAATAATAATA
1 TTATAATTAAAATATTA-TTTATATTATATTTAAAATAATATTA
181186 TTA
1 TTA
181189 ACATAAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
41 12 0.30
42 3 0.08
43 1 0.03
44 16 0.40
45 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (43 bp):
TTATAATTAAAATATTATTTATATTATATTTAAAATAATATTA
Found at i:181255 original size:15 final size:15
Alignment explanation
Indices: 181237--181295 Score: 70
Period size: 14 Copynumber: 4.1 Consensus size: 15
181227 CTATTTATCA
181237 TTAAACTAATAAT-TT
1 TTAAA-TAATAATATT
*
181252 TT-AATATTAATATT
1 TTAAATAATAATATT
181266 TTAAATAATAATATT
1 TTAAATAATAATATT
*
181281 TT-AATGATAATATT
1 TTAAATAATAATATT
181295 T
1 T
181296 AACGCTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
13 6 0.15
14 18 0.46
15 15 0.38
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAAATAATAATATT
Found at i:181259 original size:28 final size:28
Alignment explanation
Indices: 181228--181285 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 28
181218 TATTAAAAAC
181228 TATT-TATCATTAAACTAATAAT-TTTTAA
1 TATTATAT-ATTAAA-TAATAATATTTTAA
*
181256 TATTAATATTTTAAATAATAATATTTTAA
1 TATT-ATATATTAAATAATAATATTTTAA
181285 T
1 T
181286 GATAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 11 0.42
29 12 0.46
30 3 0.12
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TATTATATATTAAATAATAATATTTTAA
Found at i:181282 original size:29 final size:29
Alignment explanation
Indices: 181237--181295 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
181227 CTATTTATCA
181237 TTAAACTAATAATTTTTAAT-ATTAATATT
1 TTAAACTAATAATTTTTAATGA-TAATATT
181266 TTAAA-TAATAATATTTTAATGATAATATT
1 TTAAACTAATAAT-TTTTAATGATAATATT
181295 T
1 T
181296 AACGCTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 7 0.25
29 20 0.71
30 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (29 bp):
TTAAACTAATAATTTTTAATGATAATATT
Found at i:181383 original size:20 final size:20
Alignment explanation
Indices: 181358--181399 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
181348 TTAAAACATA
181358 ATTAT-ATAAATATTTAAAAT
1 ATTATAATAAATA-TTAAAAT
*
181378 ATTATAATAATTATTAAAAT
1 ATTATAATAAATATTAAAAT
181398 AT
1 AT
181400 CATTTCAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTATAATAAATATTAAAAT
Found at i:181624 original size:29 final size:29
Alignment explanation
Indices: 181543--181624 Score: 71
Period size: 29 Copynumber: 2.8 Consensus size: 29
181533 TATTTATTAT
*
181543 TAAAATATAAATATATTTT-T-TTAATAATAC
1 TAAAATA-AAATAT-TTTTATATT-ATAATAA
** *
181573 TCAAAATAAAATA-TTAAAAATTATAATAA
1 T-AAAATAAAATATTTTTATATTATAATAA
181602 TAAAATAAAATATTTTTATATTA
1 TAAAATAAAATATTTTTATATTA
181625 ATATTTTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
28 13 0.32
29 14 0.34
30 8 0.20
31 6 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAAATAAAATATTTTTATATTATAATAA
Found at i:181673 original size:34 final size:33
Alignment explanation
Indices: 181607--181675 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 33
181597 AATAATAAAA
* * * * *
181607 TAAAATATTTTTATATTAATATTTTAATATTTT
1 TAAAATATTTTTACATTAAAAATTAAAAATTTT
181640 TAAAATATTTTTAACATTAAAAATTAAAAATTTT
1 TAAAATATTTTT-ACATTAAAAATTAAAAATTTT
181674 TA
1 TA
181676 TTAATAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (33 bp):
TAAAATATTTTTACATTAAAAATTAAAAATTTT
Found at i:184308 original size:2 final size:2
Alignment explanation
Indices: 184301--184341 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
184291 AAGCAAACGA
184301 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
184341 A
1 A
184342 GTTAATTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:184877 original size:2 final size:2
Alignment explanation
Indices: 184870--184911 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
184860 TGTTGTCAGC
184870 AT AT AT AT 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 AT AT AT AT
184912 TAGTATGAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:187218 original size:19 final size:20
Alignment explanation
Indices: 187191--187230 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
187181 TACAAAAAAT
* *
187191 AAAATATAAT-ATAATATGA
1 AAAAAATAATAATAACATGA
187210 AAAAAATAATAATAACATGA
1 AAAAAATAATAATAACATGA
187230 A
1 A
187231 TCGAATGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (20 bp):
AAAAAATAATAATAACATGA
Found at i:187384 original size:30 final size:30
Alignment explanation
Indices: 187350--187409 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
187340 CTCCCTTTAT
* *
187350 CACAATTGA-CCCTCAATTATTTGACCTTTG
1 CACAATT-ACCCCTCAATTAATTAACCTTTG
*
187380 CACAATTACCCCTTAATTAATTAACCTTTG
1 CACAATTACCCCTCAATTAATTAACCTTTG
187410 TTATAATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (30 bp):
CACAATTACCCCTCAATTAATTAACCTTTG
Found at i:189390 original size:5 final size:5
Alignment explanation
Indices: 189379--189415 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
189369 TTGGATCATA
*
189379 TTTCT TTCCT TTTCT TTTCT TTTCT TTTCT TTTCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TT
189416 CTTGTGGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:190006 original size:19 final size:21
Alignment explanation
Indices: 189984--190032 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
189974 TTATAATAAA
189984 ATATTAAAAATT-TAT-TTTT
1 ATATTAAAAATTATATATTTT
* *
190003 ATATTAATATTTATATATTTT
1 ATATTAAAAATTATATATTTT
190024 ATAATTAAA
1 AT-ATTAAA
190033 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
20 3 0.12
21 6 0.25
22 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTAAAAATTATATATTTT
Found at i:190022 original size:26 final size:27
Alignment explanation
Indices: 189965--190022 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
189955 CAAATTTCAT
189965 TATTTAATTTTATAATAAAATATTAAA
1 TATTTAATTTTATAATAAAATATTAAA
* * * * *
189992 AATTTATTTTTATATTAATAT-TTATA
1 TATTTAATTTTATAATAAAATATTAAA
190018 TATTT
1 TATTT
190023 TATAATTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTTAATTTTATAATAAAATATTAAA
Found at i:191679 original size:3 final size:3
Alignment explanation
Indices: 191671--191718 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
191661 AATTAACGTT
191671 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
191719 AAATAAAAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:193903 original size:23 final size:23
Alignment explanation
Indices: 193873--193919 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
193863 CAGACAAGAA
193873 TTGTCTGAACAAATAGTTGTGTC
1 TTGTCTGAACAAATAGTTGTGTC
193896 TTGTCTGAACAAATAGTTGTGTC
1 TTGTCTGAACAAATAGTTGTGTC
193919 T
1 T
193920 GTAGGTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (23 bp):
TTGTCTGAACAAATAGTTGTGTC
Found at i:194869 original size:3 final size:3
Alignment explanation
Indices: 194861--194894 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
194851 AGCATGTAAA
194861 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
194895 ACAGATGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:195384 original size:22 final size:21
Alignment explanation
Indices: 195359--195411 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
195349 TAAATAAAAA
195359 TAAAAATTTATTTATTTTTAA-T
1 TAAAAATTTATTTA--TTTAATT
* *
195381 TAAATATCTATTTATTTAATT
1 TAAAAATTTATTTATTTAATT
195402 TAAAAATTTA
1 TAAAAATTTA
195412 AAAAAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.19
21 9 0.35
22 12 0.46
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAAAATTTATTTATTTAATT
Found at i:195708 original size:2 final size:2
Alignment explanation
Indices: 195703--195729 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
195693 GAGTTTTTTT
195703 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
195730 TTTTTCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:199904 original size:27 final size:27
Alignment explanation
Indices: 199865--199919 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
199855 TCTCATTAAG
*
199865 GCCTACAGCATGTTCTAGTCCTAAAAT
1 GCCTAAAGCATGTTCTAGTCCTAAAAT
* *
199892 GCCTAAAGTATGTTGTAGTCCTAAAAT
1 GCCTAAAGCATGTTCTAGTCCTAAAAT
199919 G
1 G
199920 AAATTGTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (27 bp):
GCCTAAAGCATGTTCTAGTCCTAAAAT
Found at i:202040 original size:32 final size:32
Alignment explanation
Indices: 202004--202067 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
201994 AATTTTAATT
**
202004 CTTTTATAATGAAATCAAATATAACAAATATA
1 CTTTTATAACAAAATCAAATATAACAAATATA
* *
202036 CTTTTATAACAAAATTAAATGTAACAAATATA
1 CTTTTATAACAAAATCAAATATAACAAATATA
202068 TCGTAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.34
Consensus pattern (32 bp):
CTTTTATAACAAAATCAAATATAACAAATATA
Found at i:203694 original size:21 final size:21
Alignment explanation
Indices: 203661--203700 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
203651 TCATTGATGA
*
203661 TTTATTTAATTATTATTTACT
1 TTTATTTAATTATCATTTACT
**
203682 TTTATTTTTTTATCATTTA
1 TTTATTTAATTATCATTTA
203701 TTTGAATAAA
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:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTATTTAATTATCATTTACT
Found at i:204133 original size:18 final size:18
Alignment explanation
Indices: 204112--204161 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
204102 TATATTTTAA
204112 AATTTATATAATATAAAT
1 AATTTATATAATATAAAT
*
204130 AATTTATATATTA-AAAT
1 AATTTATATAATATAAAT
*
204147 -ATATATA-AATATAAA
1 AATTTATATAATATAAA
204162 AAAACTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 3 0.11
16 9 0.32
17 4 0.14
18 12 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTATATAATATAAAT
Found at i:204163 original size:18 final size:16
Alignment explanation
Indices: 204109--204163 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
204099 ATATATATTT
*
204109 TAAAATTTATATAATA
1 TAAAAATTATATAATA
204125 TAAATAATT-TAT-ATA
1 TAAA-AATTATATAATA
*
204140 TTAAAATATATATAAATA
1 TAAAAAT-TATAT-AATA
204158 TAAAAA
1 TAAAAA
204164 AACTTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 3 0.10
15 7 0.23
16 10 0.32
17 3 0.10
18 8 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAAATTATATAATA
Found at i:205788 original size:17 final size:18
Alignment explanation
Indices: 205758--205792 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
205748 AAAAATTGAT
205758 TTTTTATTACTTTTATAA
1 TTTTTATTACTTTTATAA
*
205776 TTTTTATT-TTTTTATAA
1 TTTTTATTACTTTTATAA
205793 ATAATAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATTACTTTTATAA
Found at i:207564 original size:20 final size:19
Alignment explanation
Indices: 207536--207581 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
207526 AATATTAGTG
207536 ATTAAAAAAAT-AAAAATA
1 ATTAAAAAAATCAAAAATA
207554 ATTCAAAAAAATCAAAAATA
1 ATT-AAAAAAATCAAAAATA
207574 ATTAAAAA
1 ATTAAAAA
207582 TAAGGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.12
19 13 0.50
20 10 0.38
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (19 bp):
ATTAAAAAAATCAAAAATA
Found at i:207582 original size:10 final size:10
Alignment explanation
Indices: 207536--207584 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
207526 AATATTAGTG
207536 ATTAAAAA-A
1 ATTAAAAATA
207545 A-TAAAAATA
1 ATTAAAAATA
207554 ATTCAAAAA-A
1 ATT-AAAAATA
*
207564 ATCAAAAATA
1 ATTAAAAATA
207574 ATTAAAAATA
1 ATTAAAAATA
207584 A
1 A
207585 GGAAAAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
8 6 0.18
9 8 0.24
10 15 0.44
11 5 0.15
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (10 bp):
ATTAAAAATA
Found at i:207590 original size:20 final size:20
Alignment explanation
Indices: 207547--207591 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
207537 TTAAAAAAAT
*
207547 AAAAATAATTCAAAAAAATC
1 AAAAATAATTCAAAAAAAGC
*
207567 AAAAATAATT-AAAAATAAGG
1 AAAAATAATTCAAAAA-AAGC
207587 AAAAA
1 AAAAA
207592 ATCAGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (20 bp):
AAAAATAATTCAAAAAAAGC
Found at i:208640 original size:22 final size:21
Alignment explanation
Indices: 208591--208662 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
208581 GACCCAGAAC
* *
208591 ATAAATTT-TTTAATAAAT-T
1 ATAAATTTAATTAAAAAATAT
208610 AT-AATTTAATTAAAAAATTAT
1 ATAAATTTAATTAAAAAA-TAT
* *
208631 TTAAATTTAATTATAAAATAT
1 ATAAATTTAATTAAAAAATAT
*
208652 ATATATTTAAT
1 ATAAATTTAAT
208663 ATTTTTAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 5 0.12
19 9 0.21
20 1 0.02
21 14 0.33
22 14 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAATTTAATTAAAAAATAT
Found at i:208661 original size:21 final size:20
Alignment explanation
Indices: 208600--208662 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 20
208590 CATAAATTTT
*
208600 TTAATAAAT-TATAATTTAA
1 TTAAAAAATATATAATTTAA
*
208619 TTAAAAAATTATTTAAATTTAA
1 TTAAAAAA-TATAT-AATTTAA
*
208641 TTATAAAATATATATATTTAA
1 TTAAAAAATATATA-ATTTAA
208662 T
1 T
208663 ATTTTTAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 7 0.19
20 2 0.06
21 13 0.36
22 14 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAAAAATATATAATTTAA
Found at i:211730 original size:14 final size:15
Alignment explanation
Indices: 211703--211732 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
211693 CTGGCTCCCT
211703 TCCATTACCTTTCAA
1 TCCATTACCTTTCAA
211718 TCCATTA-CTTTCAA
1 TCCATTACCTTTCAA
211732 T
1 T
211733 TAAATGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (15 bp):
TCCATTACCTTTCAA
Found at i:215948 original size:23 final size:21
Alignment explanation
Indices: 215922--215964 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
215912 TTATTATTTT
*
215922 ATTTGTAATAATTTAATTATAAC
1 ATTTGTAA-AACTTAA-TATAAC
*
215945 ATTTTTAAAACTTAATATAA
1 ATTTGTAAAACTTAATATAA
215965 TAAATTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTGTAAAACTTAATATAAC
Found at i:217722 original size:10 final size:11
Alignment explanation
Indices: 217706--217741 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
217696 TTAATAGGTC
217706 ATTTATATATT
1 ATTTATATATT
217717 -TTTATA-ATT
1 ATTTATATATT
217726 ATTTATAT-TT
1 ATTTATATATT
217736 ATTTAT
1 ATTTAT
217742 TTTGATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 3 0.13
10 20 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTATATATT
Found at i:217735 original size:26 final size:26
Alignment explanation
Indices: 217706--217755 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
217696 TTAATAGGTC
*
217706 ATTTATATATTTTTATAATTATTTAT
1 ATTTATATATTTTGATAATTATTTAT
* *
217732 ATTTATTTATTTTGATTATTATTT
1 ATTTATATATTTTGATAATTATTT
217756 TTTGTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
ATTTATATATTTTGATAATTATTTAT
Found at i:217769 original size:19 final size:20
Alignment explanation
Indices: 217724--217769 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
217714 ATTTTTATAA
217724 TTATTTA-TATTTATTTATT
1 TTATTTATTATTTATTTATT
*
217743 TTGA-TTATTATTT-TTTGTT
1 TT-ATTTATTATTTATTTATT
217762 TTATTTAT
1 TTATTTAT
217770 GTAAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.04
19 16 0.70
20 6 0.26
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (20 bp):
TTATTTATTATTTATTTATT
Found at i:218245 original size:46 final size:46
Alignment explanation
Indices: 218158--218246 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 46
218148 AACGGGTAAC
* * *
218158 TATACACTTTGTAATATAAATATATCATGATATATATATATATATA
1 TATACACTTTGTAAGATAAATATATAATGATATATAAATATATATA
*
218204 TATACACTTTGTAAGAT--ATATAGTAATAATATATAAA-ATATAT
1 TATACACTTTGTAAGATAAATATA-TAATGATATATAAATATATAT
218247 CATGCTTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 11 0.29
45 11 0.29
46 16 0.42
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (46 bp):
TATACACTTTGTAAGATAAATATATAATGATATATAAATATATATA
Found at i:219035 original size:11 final size:10
Alignment explanation
Indices: 219005--219035 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
218995 ATATCAATCA
219005 TATAAAAATT
1 TATAAAAATT
219015 TATAAAAATT
1 TATAAAAATT
219025 TATAAACAATT
1 TATAAA-AATT
219036 AACTTTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (10 bp):
TATAAAAATT
Found at i:219991 original size:15 final size:14
Alignment explanation
Indices: 219956--220003 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
219946 AAAGACAAGG
*
219956 AGAAAAAA-AAAGA
1 AGAAAAAAGGAAGA
219969 AG-AAAAAGGACAGA
1 AGAAAAAAGGA-AGA
*
219983 AGAAAAAAGGAATA
1 AGAAAAAAGGAAGA
219997 AGAAAAA
1 AGAAAAA
220004 CAAATTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 5 0.17
13 3 0.10
14 14 0.47
15 8 0.27
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (14 bp):
AGAAAAAAGGAAGA
Found at i:220366 original size:18 final size:18
Alignment explanation
Indices: 220339--220395 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
220329 GATTCGAAAA
*
220339 TTTTTAAGTTCAATTTTT
1 TTTTTGAGTTCAATTTTT
*
220357 TTTTTGAGTTCAA--GTT
1 TTTTTGAGTTCAATTTTT
* *
220373 ATTTTGAATTCAATTTTT
1 TTTTTGAGTTCAATTTTT
220391 TTTTT
1 TTTTT
220396 AAATTTAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 13 0.42
18 18 0.58
ACGTcount: A:0.21, C:0.05, G:0.09, T:0.65
Consensus pattern (18 bp):
TTTTTGAGTTCAATTTTT
Found at i:220377 original size:17 final size:18
Alignment explanation
Indices: 220338--220397 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 18
220328 AGATTCGAAA
*
220338 ATTTTTAAGTTCAATTTT
1 ATTTTTAAGTTCAATGTT
* *
220356 TTTTTTGAGTTCAA-GTT
1 ATTTTTAAGTTCAATGTT
* *
220373 ATTTTGAA-TTCAATTTT
1 ATTTTTAAGTTCAATGTT
*
220390 TTTTTTAA
1 ATTTTTAA
220398 ATTTAAATAA
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
16 5 0.16
17 15 0.47
18 12 0.38
ACGTcount: A:0.25, C:0.05, G:0.08, T:0.62
Consensus pattern (18 bp):
ATTTTTAAGTTCAATGTT
Found at i:220393 original size:16 final size:16
Alignment explanation
Indices: 220354--220393 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
220344 AAGTTCAATT
*
220354 TTTTTTTTGAGTTCAA
1 TTTTTTTTGAATTCAA
* *
220370 GTTATTTTGAATTCAA
1 TTTTTTTTGAATTCAA
220386 TTTTTTTT
1 TTTTTTTT
220394 TTAAATTTAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.10, T:0.65
Consensus pattern (16 bp):
TTTTTTTTGAATTCAA
Found at i:220411 original size:34 final size:35
Alignment explanation
Indices: 220337--220411 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 35
220327 TAGATTCGAA
* * * *
220337 AATTTTTAAGTTCAATTTTTTTTTTGAGTTCAAGT
1 AATTTTGAAGTTCAATTTTTTTTTTAAATTCAAAT
* *
220372 TATTTTGAA-TTCAATTTTTTTTTTAAATTTAAAT
1 AATTTTGAAGTTCAATTTTTTTTTTAAATTCAAAT
220406 AATTTT
1 AATTTT
220412 TTTATCAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
34 26 0.79
35 7 0.21
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (35 bp):
AATTTTGAAGTTCAATTTTTTTTTTAAATTCAAAT
Found at i:221193 original size:14 final size:14
Alignment explanation
Indices: 221174--221207 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
221164 AATTTTTTTA
221174 AAATTTTTAT-ATT
1 AAATTTTTATAATT
221187 AATATTTTTATAATT
1 AA-ATTTTTATAATT
221202 AAATTT
1 AAATTT
221208 AAAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 12 0.63
15 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AAATTTTTATAATT
Found at i:221223 original size:23 final size:22
Alignment explanation
Indices: 221182--221233 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 22
221172 TAAAATTTTT
*
221182 ATATTAATATTTTTATAATTAA
1 ATATTAAAATTTTTATAATTAA
221204 AT-TTAAAATTTTTAATTAATTAA
1 ATATTAAAATTTTT-A-TAATTAA
221227 ATATTAA
1 ATATTAA
221234 TTCGAATCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 10 0.38
22 3 0.12
23 9 0.35
24 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTAAAATTTTTATAATTAA
Found at i:221235 original size:34 final size:35
Alignment explanation
Indices: 221170--221235 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
221160 TTAAAATTTT
** *
221170 TTTAAAATTTTTATATTAATATTTTTATAATTAAA
1 TTTAAAATTTTTATATTAATAAATATATAATTAAA
221205 TTTAAAATTTTTA-ATTAATTAAATAT-TAATT
1 TTTAAAATTTTTATATTAA-TAAATATATAATT
221236 CGAATCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.37
35 17 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
TTTAAAATTTTTATATTAATAAATATATAATTAAA
Found at i:222562 original size:32 final size:33
Alignment explanation
Indices: 222526--222590 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
222516 ATATTATTAA
*
222526 TTTATATAAATTTTTACATATTAATA-ATTTAT
1 TTTATATAAATTTTAACATATTAATATATTTAT
* *
222558 TTTATATAAATTTTAATATATTCATATATTTAT
1 TTTATATAAATTTTAACATATTAATATATTTAT
222591 AATGTGTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 23 0.79
33 6 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (33 bp):
TTTATATAAATTTTAACATATTAATATATTTAT
Found at i:223439 original size:6 final size:6
Alignment explanation
Indices: 223430--223467 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
223420 CTTTCTCTTC
*
223430 TGCCAT TGCCAT TGCCAT TGCCAT TGCCAT TGCTAT TG
1 TGCCAT TGCCAT TGCCAT TGCCAT TGCCAT TGCCAT TG
223468 TCATCTTCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (6 bp):
TGCCAT
Found at i:224859 original size:2 final size:2
Alignment explanation
Indices: 224854--224883 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
224844 TACTTTTTTC
224854 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
224884 TCATTTAACA
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):
AT
Found at i:235906 original size:11 final size:11
Alignment explanation
Indices: 235860--235921 Score: 72
Period size: 11 Copynumber: 5.5 Consensus size: 11
235850 TTATATTACA
235860 TATATTATATT
1 TATATTATATT
* *
235871 TTTATTATTTTT
1 TATATTA-TATT
235883 TATATTATATT
1 TATATTATATT
235894 TATATTATATT
1 TATATTATATT
*
235905 TAAATT-TATTT
1 TATATTATA-TT
235916 TATATT
1 TATATT
235922 TTATATAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
10 2 0.05
11 32 0.74
12 9 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATATTATATT
Found at i:235917 original size:22 final size:22
Alignment explanation
Indices: 235835--235934 Score: 70
Period size: 23 Copynumber: 4.8 Consensus size: 22
235825 TTTTTTATCT
235835 TATTA-ATAT-ATTT-T-TTTA
1 TATTATATATAATTTATATTTA
* *
235853 TATTACATAT-A-TTATATTTT
1 TATTATATATAATTTATATTTA
* * *
235873 TATTATTTTTTATATTATATTTA
1 TATTATATATAAT-TTATATTTA
*
235896 TATTATATTTAAATTTAT-TTTA
1 TATTATATAT-AATTTATATTTA
*
235918 TATTTTATATAATTTAT
1 TATTATATATAATTTAT
235935 CATAATAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.11
19 6 0.09
20 10 0.15
21 8 0.12
22 12 0.18
23 21 0.32
24 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTATATATAATTTATATTTA
Found at i:235922 original size:11 final size:11
Alignment explanation
Indices: 235818--235922 Score: 55
Period size: 11 Copynumber: 9.8 Consensus size: 11
235808 TTATAGTGTG
235818 TTTATATTT-T
1 TTTATATTTAT
*
235828 TTTAT-CTTAT
1 TTTATATTTAT
*
235838 TAATATATTT-T
1 T-TTATATTTAT
235849 TTTATA-TTA-
1 TTTATATTTAT
**
235858 CATATATTATAT
1 TTTATATT-TAT
235870 TTT-TA-TTAT
1 TTTATATTTAT
*
235879 TTTTTATATTAT
1 TTTATAT-TTAT
235891 ATTTATA-TTAT
1 -TTTATATTTAT
*
235902 ATTTAAATTTAT
1 -TTTATATTTAT
235914 TTTATATTT
1 TTTATATTT
235923 TATATAATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 23
0.68 0.10 0.22
Matches are distributed among these distances:
9 14 0.19
10 15 0.21
11 27 0.38
12 11 0.15
13 5 0.07
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATATTTAT
Found at i:235931 original size:21 final size:21
Alignment explanation
Indices: 235823--235934 Score: 65
Period size: 21 Copynumber: 5.3 Consensus size: 21
235813 GTGTGTTTAT
*
235823 ATTT-TTTTATCTTATTA-ATA
1 ATTTATTTTATATT-TTATATA
**
235843 TATTT-TTTTATATTACATAT-
1 -ATTTATTTTATATTTTATATA
*
235863 ATTATATTTTTATTATTTTTTAT-
1 ATT-TA-TTTTA-TATTTTATATA
* *
235886 A-TTATATTTATATTATATTTAA
1 ATTTAT-TTTATATTTTATAT-A
235908 ATTTATTTTATATTTTATATA
1 ATTTATTTTATATTTTATATA
235929 ATTTAT
1 ATTTAT
235935 CATAATAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.04
20 10 0.14
21 27 0.38
22 19 0.27
23 12 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTATTTTATATTTTATATA
Found at i:235932 original size:17 final size:18
Alignment explanation
Indices: 235864--235927 Score: 71
Period size: 17 Copynumber: 3.7 Consensus size: 18
235854 ATTACATATA
235864 TTATATTTT-TA-TTATT
1 TTATATTTTATATTTATT
* * *
235880 TTTTATATTATATTTATA
1 TTATATTTTATATTTATT
*
235898 TTATA-TTTAAATTTATT
1 TTATATTTTATATTTATT
235915 TTATATTTTATAT
1 TTATATTTTATAT
235928 AATTTATCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 7 0.19
17 16 0.43
18 14 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATATTTTATATTTATT
Found at i:235967 original size:22 final size:20
Alignment explanation
Indices: 235942--235982 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
235932 TATCATAATA
*
235942 ATTTAATTTAAATTATAAATTT
1 ATTT-ATTTAAA-AATAAATTT
235964 ATTTATTTAAAAATAAATT
1 ATTTATTTAAAAATAAATT
235983 ATTATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTATTTAAAAATAAATTT
Found at i:235992 original size:19 final size:19
Alignment explanation
Indices: 235942--235989 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
235932 TATCATAATA
*
235942 ATTTAATTTAAATTATAAATTT
1 ATTT-ATTTAAA-AATAAA-TT
235964 ATTTATTTAAAAATAAATT
1 ATTTATTTAAAAATAAATT
235983 A-TTATTT
1 ATTTATTT
235990 TAATCATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
19 3 0.12
20 5 0.20
21 7 0.28
22 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTATTTAAAAATAAATT
Found at i:236705 original size:12 final size:12
Alignment explanation
Indices: 236688--236715 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
236678 TTATATAATA
236688 TTTTTTAATTAT
1 TTTTTTAATTAT
236700 TTTTTTAATTAT
1 TTTTTTAATTAT
236712 TTTT
1 TTTT
236716 ATGTCATATC
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:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTAATTAT
Found at i:241641 original size:18 final size:19
Alignment explanation
Indices: 241618--241660 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
241608 TTTTTAAAAG
241618 ATAATATTAAAT-AAATTT
1 ATAATATTAAATAAAATTT
*
241636 ATAATA-TAATTAAAATTT
1 ATAATATTAAATAAAATTT
241654 -TAATATT
1 ATAATATT
241661 TATTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATATTAAATAAAATTT
Found at i:244377 original size:32 final size:33
Alignment explanation
Indices: 244324--244387 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
244314 TAAACTTAAT
*
244324 ATAAATATATAAATATTTTAAAATTTATATAAA
1 ATAAATATATAAATATATTAAAATTTATATAAA
*
244357 ATAAAT-TATTAATATATTAAAATTTATATAA
1 ATAAATATATAAATATATTAAAATTTATATAA
244388 TTATATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 23 0.79
33 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
ATAAATATATAAATATATTAAAATTTATATAAA
Found at i:244392 original size:20 final size:19
Alignment explanation
Indices: 244329--244393 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
244319 TTAATATAAA
*
244329 TATATAAATATTTTAAAATT
1 TATAT-AATATATTAAAATT
244349 TATATAA-A-A-T-AAA-T
1 TATATAATATATTAAAATT
244363 TAT-TAATATATTAAAATT
1 TATATAATATATTAAAATT
244381 TATATAATTATAT
1 TATATAA-TATAT
244394 AATAACTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 3 0.08
14 5 0.14
15 4 0.11
16 2 0.05
17 3 0.08
18 5 0.14
19 5 0.14
20 10 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATAATATATTAAAATT
Found at i:244425 original size:24 final size:24
Alignment explanation
Indices: 244384--244430 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
244374 TAAAATTTAT
*
244384 ATAATTATATAATAACTTAAAAAC
1 ATAATTATATAACAACTTAAAAAC
244408 ATAATTA-ATAACACACTTAAAAA
1 ATAATTATATAACA-ACTTAAAAA
244431 TATGCACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (24 bp):
ATAATTATATAACAACTTAAAAAC
Found at i:245673 original size:31 final size:31
Alignment explanation
Indices: 245635--245701 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
245625 AGCACCACAT
245635 TTCAAAAAACAAATAAATAAAAAATGAATTA
1 TTCAAAAAACAAATAAATAAAAAATGAATTA
* *
245666 TTC-AAAAACAAATAAATCAAAAATGAATTG
1 TTCAAAAAACAAATAAATAAAAAATGAATTA
245696 TTCAAA
1 TTCAAA
245702 GAGATTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 28 0.85
31 5 0.15
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (31 bp):
TTCAAAAAACAAATAAATAAAAAATGAATTA
Found at i:245700 original size:15 final size:15
Alignment explanation
Indices: 245654--245701 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
245644 CAAATAAATA
245654 AAAAATGAATTATTC
1 AAAAATGAATTATTC
** * *
245669 AAAAACAAATAAATC
1 AAAAATGAATTATTC
*
245684 AAAAATGAATTGTTC
1 AAAAATGAATTATTC
245699 AAA
1 AAA
245702 GAGATTGTTT
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.25
Consensus pattern (15 bp):
AAAAATGAATTATTC
Found at i:246160 original size:21 final size:21
Alignment explanation
Indices: 246113--246160 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
246103 TTATTTATTA
*
246113 TAATTTAT-TATAATAATACG
1 TAATATATCTATAATAATACG
*
246133 TATTATATCTATAATAATACAG
1 TAATATATCTATAATAATAC-G
246155 -AATATA
1 TAATATA
246161 ATGCAATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.26
21 16 0.70
22 1 0.04
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (21 bp):
TAATATATCTATAATAATACG
Found at i:246831 original size:27 final size:28
Alignment explanation
Indices: 246798--246859 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
246788 AAATATATAA
246798 AATAAATTAT-TAATATATAAAA-ATTT
1 AATAAATTATATAATATATAAAATATTT
*
246824 ATATAAATT-TATAATATTTAAAATATTT
1 A-ATAAATTATATAATATATAAAATATTT
246852 AA-AAATTA
1 AATAAATTA
246860 ATACAAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 7 0.23
27 19 0.61
28 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AATAAATTATATAATATATAAAATATTT
Found at i:248903 original size:17 final size:16
Alignment explanation
Indices: 248881--248917 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
248871 AATTTGACAC
*
248881 TTAAAAAAATTTAAAT
1 TTAAAAAAATTTAAAA
248897 TTAAAAAAATTTAAAA
1 TTAAAAAAATTTAAAA
248913 TTAAA
1 TTAAA
248918 TACTTGACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAAAAAATTTAAAA
Found at i:250072 original size:11 final size:10
Alignment explanation
Indices: 250058--250096 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
250048 AAATTTTTTT
250058 ATTTAAATATA
1 ATTTAAAT-TA
*
250069 ATTTATATCTA
1 ATTTAAAT-TA
250080 ATTTAAATTA
1 ATTTAAATTA
250090 ATTTAAA
1 ATTTAAA
250097 AATTTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (10 bp):
ATTTAAATTA
Found at i:250105 original size:22 final size:21
Alignment explanation
Indices: 250055--250105 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
250045 TTAAAATTTT
*
250055 TTTATTTAAATATAATTTATA
1 TTTATTTAAATATAATTTAAA
*
250076 TCTAATTTAAAT-TAATTTAAAAA
1 T-TTATTTAAATATAATTT--AAA
250099 TTTATTT
1 TTTATTT
250106 TATTATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 7 0.29
22 14 0.58
23 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATTTAAATATAATTTAAA
Found at i:250247 original size:23 final size:23
Alignment explanation
Indices: 250219--250262 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
250209 AATTAAATGA
250219 TATGACACATAAA-ATTATAAAAT
1 TATGACACA-AAATATTATAAAAT
*
250242 TATGACATAAAATATTATAAA
1 TATGACACAAAATATTATAAA
250263 TATATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.32
Consensus pattern (23 bp):
TATGACACAAAATATTATAAAAT
Found at i:250310 original size:23 final size:22
Alignment explanation
Indices: 250283--250409 Score: 88
Period size: 23 Copynumber: 5.8 Consensus size: 22
250273 AAATTTATAT
250283 AATATAAATTATTAATATATTAA
1 AATATAAATTA-TAATATATTAA
* *
250306 AATATAAA-TATAAAATATCTTA
1 AATATAAATTATAATATAT-TAA
* *
250328 AATAT-AATTATACTATAATAA
1 AATATAAATTATAATATATTAA
*
250349 AATATATAAATATAATATA--AA
1 AATATA-AATTATAATATATTAA
*
250370 TAA-ATAAATTATTAAATATATTCA
1 -AATATAAATTA-T-AATATATTAA
*
250394 AAT-TTAATT-TAATATA
1 AATATAAATTATAATATA
250410 AATTAAATTT
Statistics
Matches: 83, Mismatches: 11, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
20 10 0.12
21 23 0.28
22 24 0.29
23 25 0.30
24 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AATATAAATTATAATATATTAA
Found at i:250320 original size:45 final size:45
Alignment explanation
Indices: 250253--250396 Score: 120
Period size: 45 Copynumber: 3.2 Consensus size: 45
250243 ATGACATAAA
** *
250253 ATATTATAAATATATTTTTAAAATTTATATAATATAAATTATTAAT
1 ATATTA-AAATATAAATATAAAATTTATATAATATAAATTATTAAT
*
250299 ATATTAAAATATAAATATAAAATATCT-TA-AATAT-AATTA-TACT
1 ATATTAAAATATAAATATAAAAT-T-TATATAATATAAATTATTAAT
* * * *
250342 ATAATAAAATATATAA-ATATAATATAAATAA-ATAAATTATTAAAT
1 ATATTAAAATATA-AATATAAAATTTATATAATATAAATTATT-AAT
*
250387 ATATTCAAAT
1 ATATTAAAAT
250397 TTAATTTAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
41 1 0.01
42 3 0.04
43 28 0.35
44 8 0.10
45 29 0.37
46 9 0.11
47 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (45 bp):
ATATTAAAATATAAATATAAAATTTATATAATATAAATTATTAAT
Found at i:250334 original size:22 final size:21
Alignment explanation
Indices: 250248--250388 Score: 72
Period size: 22 Copynumber: 6.4 Consensus size: 21
250238 AAATTATGAC
**
250248 ATAAAATATTATAAATATATTT
1 ATAAAATATTA-AAATATAAAT
*
250270 TTAAAAT-TTATATAATATAAATT
1 ATAAAATATTA-A-AATATAAA-T
*
250293 ATTAATATATTAAAATATAAAT
1 A-TAAAATATTAAAATATAAAT
* *
250315 ATAAAATATCTTAAATATAATT
1 ATAAAATAT-TAAAATATAAAT
** *
250337 ATACTATAATAAAATATATAA-
1 ATAAAATATTAAAATATA-AAT
* *
250358 ATATAATA-TAAATAAATAAATT
1 ATAAAATATTAAA-ATATAAA-T
*
250380 ATTAAATAT
1 ATAAAATAT
250389 ATTCAAATTT
Statistics
Matches: 91, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
20 6 0.07
21 30 0.33
22 37 0.41
23 9 0.10
24 6 0.07
25 3 0.03
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAAATATTAAAATATAAAT
Found at i:250361 original size:8 final size:8
Alignment explanation
Indices: 250284--250390 Score: 57
Period size: 8 Copynumber: 13.5 Consensus size: 8
250274 AATTTATATA
250284 ATATAAAT
1 ATATAAAT
*
250292 -TATTAAT
1 ATATAAAT
250299 ATATTAAA-
1 ATA-TAAAT
250307 ATATAAAT
1 ATATAAAT
250315 ATA-AAAT
1 ATATAAAT
* *
250322 ATCTTAA-
1 ATATAAAT
*
250329 ATATAATT
1 ATATAAAT
*
250337 ATACTATA-
1 ATA-TAAAT
250345 ATA-AAAT
1 ATATAAAT
250352 ATATAAATAT
1 ATAT-AA-AT
250362 AATATAAAT
1 -ATATAAAT
*
250371 AAATAAAT
1 ATATAAAT
250379 -TATTAAAT
1 ATA-TAAAT
250387 ATAT
1 ATAT
250391 TCAAATTTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 26
0.66 0.11 0.23
Matches are distributed among these distances:
6 2 0.03
7 24 0.32
8 29 0.39
9 11 0.15
10 4 0.05
11 4 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAAAT
Found at i:250971 original size:136 final size:129
Alignment explanation
Indices: 250705--251045 Score: 449
Period size: 136 Copynumber: 2.6 Consensus size: 129
250695 TTTTTTAATT
250705 AAAAATAATATTTAATTAAGTTTAAAAAAATTTACATT-ACAAATTAAAATATTAATTA-T-T-T
1 AAAAATAATATTTAATTAAGTTTAAAAAAA-TTACATTAACAAATTAAAATATTAATTATTATGT
* * * *
250766 TTTTAAAATAAAAAAATTTAAATAAAAATAAAAAGGGTTTATTATTATTATTTTTTAATAAAATT
65 TTTTAAAAAAAAAAAATTTAAATAAAAATAAAAAAGGTTTATTATTATTAATTTTTAATAAAATA
* * *
250831 AAAAATAATCTTTAATTAAGTTTTAAAAAATTACATTAATAAATTAAAATATTAATTATTATGTT
1 AAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTATGTT
*
250896 TTTAATAAAAATAACAAATTTCAAAATAAAAAAATACAAAAAGGTTTTTTATTA-TAATTTTTAA
66 TTTAA-AAAAA-AA-AAATTT--AAAT--AAAAATA-AAAAAGGTTTATTATTATTAATTTTTAA
250960 TAAAATA
123 TAAAATA
* * * *
250967 AAAAATAATATTTAATTAAGTTTGAATAATTTATATTAACAAATTAAAATATTAATTATTATGTT
1 AAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTATGTT
*
251032 TTTAAAAAATAAAA
66 TTTAAAAAAAAAAA
251046 GTATTTTTTA
Statistics
Matches: 188, Mismatches: 15, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
125 7 0.04
126 47 0.25
127 1 0.01
128 1 0.01
129 7 0.04
130 4 0.02
131 2 0.01
132 6 0.03
133 2 0.01
134 6 0.03
135 4 0.02
136 86 0.46
137 15 0.08
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (129 bp):
AAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTATGTT
TTTAAAAAAAAAAAATTTAAATAAAAATAAAAAAGGTTTATTATTATTAATTTTTAATAAAATA
Found at i:251201 original size:24 final size:24
Alignment explanation
Indices: 251167--251214 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
251157 TAGATGGTTT
* *
251167 TTTTATTATTATTCAATTAAAAAA
1 TTTTATCATTATTCAAATAAAAAA
251191 TTTTATCATTATTCAAATAAAAAA
1 TTTTATCATTATTCAAATAAAAAA
251215 CCCTTTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTTATCATTATTCAAATAAAAAA
Found at i:255218 original size:22 final size:22
Alignment explanation
Indices: 255182--255244 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
255172 GTAACTCGTG
*
255182 ATTTTTTTAATTTAAAATTTAAA
1 ATTTTTATAA-TTAAAATTTAAA
* *
255205 ATTTTTATAATTAATATTTTAA
1 ATTTTTATAATTAAAATTTAAA
255227 ATTTATATATAA-TAAAAT
1 ATTT-T-TATAATTAAAAT
255245 AAAAATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 14 0.41
23 15 0.44
24 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTTTATAATTAAAATTTAAA
Found at i:255525 original size:41 final size:39
Alignment explanation
Indices: 255480--255557 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 39
255470 TAAAAAATTA
*
255480 TTATTTTAAATAATAATTTTTAATATATTTATATAAAAAAC
1 TTATTTTAAA-AATAATTTTTAA-AAATTTATATAAAAAAC
* *
255521 TTATTTTAAAAATATTTTTTAAAAATTTATTTAAAAA
1 TTATTTTAAAAATAATTTTTAAAAATTTATATAAAAA
255558 TTAAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 13 0.38
40 11 0.32
41 10 0.29
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (39 bp):
TTATTTTAAAAATAATTTTTAAAAATTTATATAAAAAAC
Found at i:255539 original size:12 final size:12
Alignment explanation
Indices: 255524--255559 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
255514 AAAAAACTTA
255524 TTTTAAAAATATT
1 TTTTAAAAAT-TT
255537 TTTTAAAAATTT
1 TTTTAAAAATTT
*
255549 ATTTAAAAATT
1 TTTTAAAAATT
255560 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTTAAAAATTT
Found at i:262238 original size:15 final size:17
Alignment explanation
Indices: 262208--262240 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
262198 GTAAGAATAA
262208 ATTTTTTTCATAATTTT
1 ATTTTTTTCATAATTTT
262225 ATTTTTTT-AT-ATTTT
1 ATTTTTTTCATAATTTT
262240 A
1 A
262241 AATAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTTTCATAATTTT
Found at i:267767 original size:279 final size:280
Alignment explanation
Indices: 267232--267797 Score: 974
Period size: 279 Copynumber: 2.0 Consensus size: 280
267222 AAAATATTCT
* *
267232 AAAAATTCTGAAAAATCACTTTCTGGGAGAACTAAATTCTTGAATTTGGCCCTATTGCAATGCTG
1 AAAAATCCTAAAAAATCACTTTCTGGGAGAACTAAATTCTTGAATTTGGCCCTATTGCAATGCTG
267297 GCAGAGCACGCAAGAGGAAAGGTGTGACAAATTTTGAAAAATCACTTCGGATTCATGTGGTATCA
66 GCAGAGCACGCAAGAGGAAAGGTGTGACAAATTTTGAAAAATCACTTCGGATTCATGTGGTATCA
*
267362 AAAATTGCAAATGATACCTTTCTAGAAAGAGAATTTCATGAACGTTTTAGAGAAATATTTAGAAA
131 AAAATTGCAAATGATACCTTTCTAGAAAGAGAATTTCATGAACGTTTTAAAGAAATATTTAGAAA
* * * * *
267427 ATTTATAAAAATCGTATAGTGTGCCAACATGACTAGATCAGAATGTAATTCATTGATTTTAAGGG
196 ATTTATAAAAATCGTATAGTGTGCCAAAACGACTAGATCAAAATGTAATTCACTAATTTTAAGGG
*
267492 TTCTGAACAGTGTAGGTTTG
261 TTCTGAACAGTGTAGATTTG
*
267512 AAAAATCCTAAAAAATCACTTTCT-GGAGAACTAAATTCTTGAATTTGGCCTTATTGCAATGCTG
1 AAAAATCCTAAAAAATCACTTTCTGGGAGAACTAAATTCTTGAATTTGGCCCTATTGCAATGCTG
*
267576 GCAGAGCACGCAAGAGGAAAGGTGTGACAAATTTTGAAAAATCACTTCGGATTCATTTGGTATCA
66 GCAGAGCACGCAAGAGGAAAGGTGTGACAAATTTTGAAAAATCACTTCGGATTCATGTGGTATCA
* *
267641 AAAATTGCAAATGATACCTTTCT-GAAAAGGGAATTTCATGAACGTTTTAAAGAAATGTTTAGAA
131 AAAATTGCAAATGATACCTTTCTAG-AAAGAGAATTTCATGAACGTTTTAAAGAAATATTTAGAA
* *
267705 AATTTGTAAAAATCGTATAGTGTGCCAAAACGACTAGATCAAAATGTAATTCGCTAATTTTAAGG
195 AATTTATAAAAATCGTATAGTGTGCCAAAACGACTAGATCAAAATGTAATTCACTAATTTTAAGG
267770 GTTCTGAACAGTGTAGATTTG
260 GTTCTGAACAGTGTAGATTTG
267791 AAAAATC
1 AAAAATC
267798 TTAACTCCCT
Statistics
Matches: 270, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
278 1 0.00
279 247 0.91
280 22 0.08
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (280 bp):
AAAAATCCTAAAAAATCACTTTCTGGGAGAACTAAATTCTTGAATTTGGCCCTATTGCAATGCTG
GCAGAGCACGCAAGAGGAAAGGTGTGACAAATTTTGAAAAATCACTTCGGATTCATGTGGTATCA
AAAATTGCAAATGATACCTTTCTAGAAAGAGAATTTCATGAACGTTTTAAAGAAATATTTAGAAA
ATTTATAAAAATCGTATAGTGTGCCAAAACGACTAGATCAAAATGTAATTCACTAATTTTAAGGG
TTCTGAACAGTGTAGATTTG
Found at i:269194 original size:14 final size:14
Alignment explanation
Indices: 269171--269200 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
269161 GCTTCTTTAC
269171 CTCTTCTTTTTTTT
1 CTCTTCTTTTTTTT
269185 CTCTT-TTTTTTTT
1 CTCTTCTTTTTTTT
269198 CTC
1 CTC
269201 GTCACCTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
CTCTTCTTTTTTTT
Found at i:269816 original size:166 final size:166
Alignment explanation
Indices: 269623--269954 Score: 610
Period size: 166 Copynumber: 2.0 Consensus size: 166
269613 ATTTTTTAAT
* *
269623 TTTTTTATATTTTTCAAATAAGTCTAAATTAAAATGCATTAAGCCCAATTAATTTGGATCCAATA
1 TTTTTTATATTTTTCAAATAAGTCTAAATTAAAATGAATTAAGCCCAATTAATTTAGATCCAATA
* *
269688 AATTCATATTAAAGATGACTAGATTAATTGAATTATTTTAAAATAAGTGTCCTAAAAATGGCCGA
66 AATTCATATTAAAGATGACTAGATTAATTGAATTATTTTAAAATAAGTGTCCTAAAAATGACCAA
* *
269753 CCAAAATTTGATGTCTACCGCTGCCCCTCTTTGGCC
131 ACAAAATTTGATGACTACCGCTGCCCCTCTTTGGCC
269789 TTTTTTATATTTTTCAAATAAGTCTAAATTAAAATGAATTAAGCCCAATTAATTTAGATCCAATA
1 TTTTTTATATTTTTCAAATAAGTCTAAATTAAAATGAATTAAGCCCAATTAATTTAGATCCAATA
269854 AATTCATATTAAAGATGACTAGATTAATTGAATTATTTTAAAATAAGTGTCCTAAAAATGACCAA
66 AATTCATATTAAAGATGACTAGATTAATTGAATTATTTTAAAATAAGTGTCCTAAAAATGACCAA
269919 ACAAAATTTGATGACTACCGCTGCCCCTCTTTGGCC
131 ACAAAATTTGATGACTACCGCTGCCCCTCTTTGGCC
269955 GTTGCTGAGT
Statistics
Matches: 160, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
166 160 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (166 bp):
TTTTTTATATTTTTCAAATAAGTCTAAATTAAAATGAATTAAGCCCAATTAATTTAGATCCAATA
AATTCATATTAAAGATGACTAGATTAATTGAATTATTTTAAAATAAGTGTCCTAAAAATGACCAA
ACAAAATTTGATGACTACCGCTGCCCCTCTTTGGCC
Found at i:270248 original size:43 final size:43
Alignment explanation
Indices: 270182--270267 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
270172 AGAAAAATGA
* * *
270182 TAAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGGACT
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCAATATTGGACT
* *
270225 TAAAGGTGCCAATATGCTAATTCAATGCTAGCAATATTGGACT
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCAATATTGGACT
270268 GAAGAATGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTAATTCAAGGCCAGCAATATTGGACT
Found at i:270435 original size:32 final size:31
Alignment explanation
Indices: 270388--270560 Score: 147
Period size: 32 Copynumber: 5.5 Consensus size: 31
270378 TAGAAAGAGA
* *
270388 TGCCACCAACATGTGTGGGCTTTTGAGAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGA-AGGGT
* *
270420 TGCCACTGACTTGTGTGGGCTTTTACAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTT--GAAGGGT
* * * *
270453 TGCCACCGACTTCTGTGAGCTTTAGAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGGGT
* *
270484 TGCCACCAACTTATGTGGGC-TTTGACTAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGA--AGGGT
* *
270516 TGCCACCGAC-T-TGTGAGC-TTTGACTAAGGT
1 TGCCACCGACTTGTGTGGGCTTTTGA--AGGGT
270546 TGCCACCGACTTGTG
1 TGCCACCGACTTGTG
270561 GGCTTTAAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
30 31 0.26
31 24 0.21
32 36 0.31
33 25 0.21
34 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (31 bp):
TGCCACCGACTTGTGTGGGCTTTTGAAGGGT
Found at i:270538 original size:30 final size:32
Alignment explanation
Indices: 270401--270566 Score: 157
Period size: 30 Copynumber: 5.3 Consensus size: 32
270391 CACCAACATG
* * *
270401 TGTGGGCTTTTGA-GAGGGTTGCCACTGACTTG
1 TGTGGGC-TTTGACTAGGGTTGCCACCGACTTA
* * *
270433 TGTGGGCTTTTACAAAGGGTTGCCACCGACTTC
1 TGTGGGCTTTGAC-TAGGGTTGCCACCGACTTA
* * *
270466 TGTGAGCTTTAGA--AAGGTTGCCACCAACTTA
1 TGTGGGCTTT-GACTAGGGTTGCCACCGACTTA
270497 TGTGGGCTTTGACTAGGGTTGCCACCGAC-T-
1 TGTGGGCTTTGACTAGGGTTGCCACCGACTTA
* *
270527 TGTGAGCTTTGACTAAGGTTGCCACCGAC-T-
1 TGTGGGCTTTGACTAGGGTTGCCACCGACTTA
270557 TGTGGGCTTT
1 TGTGGGCTTT
270567 AAAAGGGGTG
Statistics
Matches: 114, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
30 39 0.34
31 29 0.25
32 20 0.18
33 25 0.22
34 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.30, T:0.32
Consensus pattern (32 bp):
TGTGGGCTTTGACTAGGGTTGCCACCGACTTA
Found at i:270656 original size:28 final size:28
Alignment explanation
Indices: 270401--271927 Score: 1184
Period size: 29 Copynumber: 53.0 Consensus size: 28
270391 CACCAACATG
*
270401 TGTGGGCTTTTGAGAGGGTTGCCACTGACTT
1 TGTGGGC-TTTGAAAGGG-TGCCACTGAC-T
* *
270432 GTGTGGGCTTTTACAAAGGGTTGCCACCGACTT
1 -TGTGGGC-TTT-GAAAGGG-TGCCACTGAC-T
* * **
270465 CTGTGAGCTTTAGAAAGGTTGCCACCAACTT
1 -TGTGGGCTTT-GAAAGGGTGCCACTGAC-T
* *
270496 ATGTGGGCTTTGACTAGGGTTGCCACCGACT
1 -TGTGGGCTTTGA-AAGGG-TGCCACTGACT
* * *
270527 TGTGAGCTTTGACTAAGGTTGCCACCGACT
1 TGTGGGCTTTGA--AAGGGTGCCACTGACT
* *
270557 TGTGGGCTTTAAAAGGGGTGCCACTAACT
1 TGTGGGCTTTGAAA-GGGTGCCACTGACT
* * *
270586 TATGGGCTTTAAAAGGG-GCACCACTAACT
1 TGTGGGCTTTGAAAGGGTG--CCACTGACT
* * * *
270615 TATGAG-TTTAAAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
270642 TGCGGACTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
270670 TGTGGGCTTTGAAAAGGGGTGCCACTGACT
1 TGTGGGCTTTG-AAA-GGGTGCCACTGACT
* *
270700 TATGGGCTTTGAAAGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
270728 TATGGGCTTTAAAAAGGGTGCCACTGACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
* *
270757 TGTAGGCTTT-AGAAGGGTGCCATTGACT
1 TGTGGGCTTTGA-AAGGGTGCCACTGACT
*
270785 TGTGGGCTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
270814 TGTGGGCTTTGGAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
270842 TATGGGCTTTGGAA-TGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
270869 TGTGTGCTTTAAAAGGATGGCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
270897 TGTAGGCTTTGAAAGGGGTACCATTGACT
1 TGTGGGCTTTGAAA-GGGTGCCACTGACT
* * *
270926 TGTGAGCTTTAAAAGGGGTGCCACTAACT
1 TGTGGGCTTTGAAA-GGGTGCCACTGACT
* * * *
270955 TGTGAGCTTTGAAAAGGGTGTCACTCACA
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
270984 TGTGGGCTTTAAAAAGAGTGCCATTGACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
* * *
271013 TATGGGCTTTGAAAATGGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
271042 TGTGGGCTTTGAAAAGGTGCTACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
271070 TGT-GGCTTTGAAAAAGGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
271098 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
271126 TATGGGCTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
271155 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
271183 TGTGGGCTTTAAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGG-GTGCCACTGACT
271212 TGTGGGCTTTGGAAA-GGTGCCACTGACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
* * * * * *
271240 TGTGGCCTTTAAAAGGATGCCATTAATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
271268 TGTGTGCTTTGAAAGGGGTGCCATTAACT
1 TGTGGGCTTTGAAA-GGGTGCCACTGACT
* * * * *
271297 TGTGGGCTTTAAAAGGATGCCATTAATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
271325 TGTGTGCTTTGAAAGAGGTGACATTAACT
1 TGTGGGCTTTGAAAG-GGTGCCACTGACT
* * *
271354 TGTGGGCTTTAAAAGGGGTGTCACTAACT
1 TGTGGGCTTTGAAA-GGGTGCCACTGACT
* *
271383 TGTGGG-TTTGAAAAGAGTGCCACT-AAT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* ** * *
271410 ACGTGGGCTTTGAAAAAAGTACCACTAACTT
1 -TGTGGGCTTTG-AAAGGGTGCCACTGAC-T
* ** * * *
271441 TATAAGCTTTGAAAAGTGTACCACTGATT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
271470 TGTGGGCTTTGAAAGGGGTACCACTAACT
1 TGTGGGCTTTGAAA-GGGTGCCACTGACT
* *
271499 TGTGGGCTTTGAAAAGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
271527 TATGGGCTTTGAAAATGGTGCGACTCACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
271556 TGTGGGCTTTAAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
271584 TATGGGCCTTAAAAGGGTACCCCTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
271612 TGTGGGCTTTGGAAA-GGTGCCACTAACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
** * * * *
271640 TGTGAACTTTAAAAGGATGCTACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
271668 TATGGGCTTTTAAAGGGTTCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* **
271696 TGTGGGCTTTAAAAGGGGTGTTACTGACT
1 TGTGGGCTTTGAAA-GGGTGCCACTGACT
* * *
271725 TGTAGGCTTTGAAAAGGGTGCCACTAACA
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* ** *
271754 TATGGGCTTTGAAAAGAATGCCATTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
271783 TGTGGGCTTTAAAAAGGATGCCACTGACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
* * * * *
271812 TGCGGGCTTCG-GAGATGTGCCACTGTCT
1 TGTGGGCTTTGAAAG-GGTGCCACTGACT
271840 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGG-GTGCCACTGACT
* *
271869 TGTGGGTTTTGAAAAGGGTGCCATTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
271898 TGTGGGCTTTAAAAAGGTTGCCACTAACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
271927 T
1 T
271928 ATATGCTTTA
Statistics
Matches: 1226, Mismatches: 223, Indels: 95
0.79 0.14 0.06
Matches are distributed among these distances:
27 51 0.04
28 460 0.38
29 540 0.44
30 95 0.08
31 28 0.02
32 29 0.02
33 23 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:270685 original size:57 final size:57
Alignment explanation
Indices: 270401--271949 Score: 1304
Period size: 57 Copynumber: 26.9 Consensus size: 57
270391 CACCAACATG
* * *
270401 TGTGGGCTTTTGAGAGGGTTGCCACTGACTTGTGTGGGCTTTTACAAAGGGTTGCCACCGACTT
1 TGTGGGC-TTTGAAAGGG-TGCCACTGAC-T-TGTGGGCTTTGA-AAAGGG-TGCCACTGAC-T
* * ** ** *
270465 CTGTGAGCTTTAGAAAGGTTGCCACCAACTTATGTGGGCTTTGACTAGGGTTGCCACCGACT
1 -TGTGGGCTTT-GAAAGGGTGCCACTGAC-T-TGTGGGCTTTGAAAAGGG-TGCCACTGACT
* * * *
270527 TGTGAGCTTTGACTAAGGTTGCCACCGACTTGTGGGCTTT-AAAAGGGGTGCCACTAACT
1 TGTGGGCTTTGA--AAGGGTGCCACTGACTTGTGGGCTTTGAAAA-GGGTGCCACTGACT
* * * * * *
270586 TATGGGCTTTAAAAGGG-GCACCACTAACTTATGAG-TTT-AAAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTG--CCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* *
270642 TGCGGACTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAA-GGGTGCCACTGACT
* * * *
270700 TATGGGCTTTGAAAGGGTACCACTGACTTATGGGCTTTAAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * *
270757 TGTAGGCTTT-AGAAGGGTGCCATTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGA-AAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * * * * *
270814 TGTGGGCTTTGGAAGAGTGCCACTAACTTATGGGCTTTG-GAA-TGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * * * * * * *
270869 TGTGTGCTTTAAAAGGATGGCATTGACTTGTAGGCTTTGAAAGGGGTACCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * * * * *
270926 TGTGAGCTTTAAAAGGGGTGCCACTAACTTGTGAGCTTTGAAAAGGGTGTCACTCACA
1 TGTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * * * *
270984 TGTGGGCTTTAAAAAGAGTGCCATTGACTTATGGGCTTTGAAAATGGTGCCACTAACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * *
271042 TGTGGGCTTTGAAAAGGTGCTACTAACTTGT-GGCTTTGAAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* *
271098 TGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
*
271155 TGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTT-AAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGG-GTGCCACTGACT
* * * * *
271212 TGTGGGCTTTGGAAA-GGTGCCACTGACTTGTGGCCTTT-AAAAGGATGCCATTAATT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * * * * *
271268 TGTGTGCTTTGAAAGGGGTGCCATTAACTTGTGGGCTTT-AAAAGGATGCCATTAATT
1 TGTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * * * *
271325 TGTGTGCTTTGAAAGAGGTGACATTAACTTGTGGGCTTT-AAAAGGGGTGTCACTAACT
1 TGTGGGCTTTGAAAG-GGTGCCACTGACTTGTGGGCTTTGAAAA-GGGTGCCACTGACT
* * * ** * *
271383 TGTGGG-TTTGAAAAGAGTGCCACT-AATACGTGGGCTTTGAAAAAAGTACCACTAACTT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT-TGTGGGCTTTGAAAAGGGTGCCACTGAC-T
* ** * * * * * *
271441 TATAAGCTTTGAAAAGTGTACCACTGATTTGTGGGCTTTGAAAGGGGTACCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * * * *
271499 TGTGGGCTTTGAAAAGGTACCACTGACTTATGGGCTTTGAAAATGGTGCGACTCACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * * * * *
271556 TGTGGGCTTTAAAAGGATGCCACTAACTTATGGGCCTT-AAAAGGGTACCCCTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* ** * * *
271612 TGTGGGCTTTGGAAA-GGTGCCACTAACTTGTGAACTTT-AAAAGGATGCTACTAACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * **
271668 TATGGGCTTTTAAAGGGTTCCACTGACTTGTGGGCTTT-AAAAGGGGTGTTACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAA-GGGTGCCACTGACT
* * * * ** *
271725 TGTAGGCTTTGAAAAGGGTGCCACTAACATATGGGCTTTGAAAAGAATGCCATTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * * * * * *
271783 TGTGGGCTTTAAAAAGGATGCCACTGACTTGCGGGCTTCGGAGA-TGTGCCACTGTCT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* *
271840 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGTTTTGAAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * * ** *
271898 TGTGGGCTTTAAAAAGGTTGCCACTAACTTATATGCTTT-AAAAGGGTACCAC
1 TGTGGGCTTT-GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCAC
271950 GGAGTTATGG
Statistics
Matches: 1213, Mismatches: 233, Indels: 84
0.79 0.15 0.05
Matches are distributed among these distances:
55 60 0.05
56 200 0.16
57 501 0.41
58 286 0.24
59 73 0.06
60 17 0.01
61 11 0.01
62 15 0.01
63 15 0.01
64 24 0.02
65 11 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (57 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
Found at i:271465 original size:59 final size:57
Alignment explanation
Indices: 271389--271522 Score: 151
Period size: 59 Copynumber: 2.3 Consensus size: 57
271379 AACTTGTGGG
*
271389 TTTGAAAAGAGTGCCACTAATACGTGGGCTTTGAAAAAAGTACCACTAACTTTATAAGC
1 TTTGAAAAG-GTACCACTAATACGTGGGCTTTGAAAAAAGTACCACTAAC-TTATAAGC
* ** *** * **
271448 TTTGAAAAGTGTACCACTGATTTGTGGGCTTTGAAAGGGGTACCACTAACTTGTGGGC
1 TTTGAAAAG-GTACCACTAATACGTGGGCTTTGAAAAAAGTACCACTAACTTATAAGC
271506 TTTGAAAAGGTACCACT
1 TTTGAAAAGGTACCACT
271523 GACTTATGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 8 0.12
58 14 0.22
59 42 0.66
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (57 bp):
TTTGAAAAGGTACCACTAATACGTGGGCTTTGAAAAAAGTACCACTAACTTATAAGC
Found at i:271976 original size:27 final size:27
Alignment explanation
Indices: 271935--272050 Score: 117
Period size: 27 Copynumber: 4.3 Consensus size: 27
271925 CTTATATGCT
* * * *
271935 TTAAAAGGGTACCACGGAGTTATGGAT
1 TTAAAAAGGTGCCACGAAGTTATGGAC
*
271962 TTAAAAAGGTGCCACGAAGTTGTGGAC
1 TTAAAAAGGTGCCACGAAGTTATGGAC
* *
271989 TT-AAAAGTGTGCCACGAAGTTGTGAAC
1 TTAAAAAG-GTGCCACGAAGTTATGGAC
** * *
272016 TTAAAATTGTTCCACGGAGTTATGGAC
1 TTAAAAAGGTGCCACGAAGTTATGGAC
272043 TTAAAAAG
1 TTAAAAAG
272051 AAATGCCATT
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
26 5 0.07
27 65 0.89
28 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (27 bp):
TTAAAAAGGTGCCACGAAGTTATGGAC
Found at i:272004 original size:54 final size:54
Alignment explanation
Indices: 271935--272048 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 54
271925 CTTATATGCT
* * * *
271935 TTAAAAGGGTACCACGGAGTTATGGATTTAAAAAGGTGCCACGAAGTTGTGGAC
1 TTAAAAGGGTACCACGAAGTTATGAACTTAAAAAGGTGCCACGAAGTTATGGAC
* * * ** * *
271989 TTAAAAGTGTGCCACGAAGTTGTGAACTTAAAATTGTTCCACGGAGTTATGGAC
1 TTAAAAGGGTACCACGAAGTTATGAACTTAAAAAGGTGCCACGAAGTTATGGAC
272043 TTAAAA
1 TTAAAA
272049 AGAAATGCCA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.27
Consensus pattern (54 bp):
TTAAAAGGGTACCACGAAGTTATGAACTTAAAAAGGTGCCACGAAGTTATGGAC
Found at i:273483 original size:24 final size:22
Alignment explanation
Indices: 273456--273527 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
273446 TTGTTCCTTC
273456 TTTTTGTTTTGCTTTTACATTCTT
1 TTTTTGTTTTGCTTTT-CATT-TT
*
273480 TTTTTGTTTTTCTTTTCATTTT
1 TTTTTGTTTTGCTTTTCATTTT
** * *
273502 TTTGCGCTTTTGCTTTTGAATTT
1 TTTTTG-TTTTGCTTTTCATTTT
273525 TTT
1 TTT
273528 GTCATTTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
22 6 0.15
23 20 0.49
24 15 0.37
ACGTcount: A:0.07, C:0.11, G:0.10, T:0.72
Consensus pattern (22 bp):
TTTTTGTTTTGCTTTTCATTTT
Found at i:280460 original size:10 final size:9
Alignment explanation
Indices: 280439--280468 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
280429 AGTTATCTTG
280439 TTTTTATTT
1 TTTTTATTT
*
280448 TTTTAATTT
1 TTTTTATTT
280457 TTTTTATTT
1 TTTTTATTT
280466 TTT
1 TTT
280469 CATAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTATTT
Found at i:286207 original size:20 final size:20
Alignment explanation
Indices: 286179--286253 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
286169 TCATACCCTG
286179 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
286199 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
286219 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
286239 ATGTATCGATACATT
1 ATGTATCGATACATT
286254 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:286246 original size:40 final size:39
Alignment explanation
Indices: 286179--286256 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
286169 TCATACCCTG
* *
286179 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
286219 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
286257 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:287191 original size:23 final size:23
Alignment explanation
Indices: 287164--287215 Score: 97
Period size: 22 Copynumber: 2.3 Consensus size: 23
287154 AGCCTTTGAC
287164 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
287187 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
287209 CATGCAT
1 CATGCAT
287216 ATTTAACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:290540 original size:4 final size:4
Alignment explanation
Indices: 290533--290559 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
290523 GATGTTCATT
290533 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
290560 TGCTATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:303763 original size:9 final size:9
Alignment explanation
Indices: 303751--303833 Score: 53
Period size: 9 Copynumber: 9.2 Consensus size: 9
303741 CCCACAACCG
303751 CCCACCCAC
1 CCCACCCAC
*
303760 CCCACACAC
1 CCCACCCAC
* *
303769 CCCCCCCCC
1 CCCACCCAC
*
303778 CCCCCCCACC
1 CCCACCCA-C
*
303788 ACCCAACCAC
1 -CCCACCCAC
*
303798 CCC-CACAC
1 CCCACCCAC
* *
303806 CCCCCCCCC
1 CCCACCCAC
*
303815 CCCACCCCC
1 CCCACCCAC
303824 CCCA-CCAC
1 CCCACCCAC
303832 CC
1 CC
303834 TCCCGACATC
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
8 11 0.19
9 39 0.67
10 2 0.03
11 6 0.10
ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00
Consensus pattern (9 bp):
CCCACCCAC
Found at i:303781 original size:38 final size:37
Alignment explanation
Indices: 303739--303817 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 37
303729 CCCACACAAA
* *
303739 CCCCCACAACCGCCCACCCACCCCACACACCCCCCCCC
1 CCCCCACAACCACCCAACCACCCC-CACACCCCCCCCC
* *
303777 CCCCCCCCACCACCCAACCACCCCCACACCCCCCCCC
1 CCCCCACAACCACCCAACCACCCCCACACCCCCCCCC
303814 CCCC
1 CCCC
303818 ACCCCCCCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 17 0.46
38 20 0.54
ACGTcount: A:0.19, C:0.80, G:0.01, T:0.00
Consensus pattern (37 bp):
CCCCCACAACCACCCAACCACCCCCACACCCCCCCCC
Found at i:303786 original size:31 final size:31
Alignment explanation
Indices: 303710--303833 Score: 108
Period size: 31 Copynumber: 4.0 Consensus size: 31
303700 TACCAAATCT
* * **
303710 CCCCCCCCCCCCAACACACCCCACACAAACC
1 CCCCCCCCCCCCCACCCACCCCACACACCCC
* ** *
303741 CCCACAACCGCCCACCCACCCCACACACCCC
1 CCCCCCCCCCCCCACCCACCCCACACACCCC
* *
303772 CCCCCCCCCCCCCA-CCACCCAACCACCCCCAC
1 CCCCCCCCCCCCCACCCACCCCA-CACACCC-C
*
303804 ACCCCCCCCCCCCCACCCCCCCCAC-CACCC
1 -CCCCCCCCCCCCCACCCACCCCACACACCC
303834 TCCCGACATC
Statistics
Matches: 72, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
30 7 0.10
31 39 0.54
32 5 0.07
33 15 0.21
34 6 0.08
ACGTcount: A:0.22, C:0.77, G:0.01, T:0.00
Consensus pattern (31 bp):
CCCCCCCCCCCCCACCCACCCCACACACCCC
Done.