Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold433
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: 558157
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Warning! 7244 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:489298 original size:12 final size:11
Alignment explanation
Indices: 489263--489338 Score: 72
Period size: 11 Copynumber: 7.2 Consensus size: 11
489253 TTAAATAAAA
* *
489263 AAATTTAAATC
1 AAATTTAATTT
*
489274 AAATTAAATTT
1 AAATTTAATTT
489285 AAATTTAATCTT
1 AAATTTAAT-TT
489297 AAATTTAATTT
1 AAATTTAATTT
489308 -AATTT--TTT
1 AAATTTAATTT
489316 -AATTATAATTT
1 AAATT-TAATTT
489327 -AATTTAATTT
1 AAATTTAATTT
489337 AA
1 AA
489339 CCAATAAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
8 7 0.12
9 1 0.02
10 11 0.20
11 26 0.46
12 11 0.20
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:489308 original size:5 final size:5
Alignment explanation
Indices: 489275--489338 Score: 69
Period size: 5 Copynumber: 12.4 Consensus size: 5
489265 ATTTAAATCA
*
489275 AATTA AATTT AAATTT AATCTT AAATTT AATTT AATTT --TTT AATTAT
1 AATTT AATTT -AATTT AAT-TT -AATTT AATTT AATTT AATTT AATT-T
489322 AATTT AATTT AATTT AA
1 AATTT AATTT AATTT AA
489339 CCAATAAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
3 3 0.06
5 32 0.62
6 14 0.27
7 3 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:489772 original size:19 final size:20
Alignment explanation
Indices: 489744--489781 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
489734 TATAATAAAA
489744 ATTAAATAAA-AATAATTTT
1 ATTAAATAAATAATAATTTT
*
489763 ATTAATTAAATAATAATTT
1 ATTAAATAAATAATAATTT
489782 AAGTTTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTAAATAAATAATAATTTT
Found at i:490508 original size:24 final size:21
Alignment explanation
Indices: 490462--490510 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
490452 TAGATGTATT
*
490462 TATATTTATTTTTTAAAAGTA
1 TATACTTATTTTTTAAAAGTA
490483 TATACTTATTTATTTATAAAGTTA
1 TATACTTATTT-TTTA-AAAG-TA
490507 TATA
1 TATA
490511 TTAAGCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 10 0.42
22 4 0.17
23 4 0.17
24 6 0.25
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
TATACTTATTTTTTAAAAGTA
Found at i:492150 original size:16 final size:17
Alignment explanation
Indices: 492129--492179 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 17
492119 AAAAATTATA
492129 ATTATTATTTTA-TAAT
1 ATTATTATTTTATTAAT
492145 ATTATT-TTTTATTAAT
1 ATTATTATTTTATTAAT
*
492161 AATATATATTTTAATTAAT
1 ATTAT-TATTTT-ATTAAT
492180 TATAATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.17
16 14 0.47
17 1 0.03
18 4 0.13
19 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATTATTTTATTAAT
Found at i:492153 original size:14 final size:14
Alignment explanation
Indices: 492124--492152 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
492114 TAAATAAAAA
492124 TTATAATTATTATT
1 TTATAATTATTATT
492138 TTATAA-TATTATT
1 TTATAATTATTATT
492151 TT
1 TT
492153 TTATTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATAATTATTATT
Found at i:492177 original size:19 final size:19
Alignment explanation
Indices: 492140--492189 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
492130 TTATTATTTT
*
492140 ATAATAT-TATTTTTTATTA
1 ATAATATATA-TTTTAATTA
492159 ATAATATATATTTTAATTA
1 ATAATATATATTTTAATTA
*
492178 ATTATAATATAT
1 ATAAT-ATATAT
492190 ATATACACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATAATATATATTTTAATTA
Found at i:492187 original size:22 final size:19
Alignment explanation
Indices: 492138--492191 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 19
492128 AATTATTATT
492138 TTATAATAT-TATTTTTTA
1 TTATAATATATATTTTTTA
492156 TTAATAATATATATTTTAATTAA
1 TT-ATAATATATATTTT--TT-A
492179 TTATAATATATAT
1 TTATAATATATAT
492192 ATACACACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.06
19 7 0.23
20 6 0.19
22 13 0.42
23 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATAATATATATTTTTTA
Found at i:493239 original size:2 final size:2
Alignment explanation
Indices: 493232--493256 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
493222 TTCAATTTTC
493232 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
493257 GAATAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:493310 original size:2 final size:2
Alignment explanation
Indices: 493303--493327 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
493293 TAAATCTTTA
493303 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
493328 AGAACCAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:497742 original size:26 final size:28
Alignment explanation
Indices: 497713--497770 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 28
497703 TAATAAAAAT
497713 ATAATTAAAT-TTAA-AATTTAA-AATTA
1 ATAATTAAATATTAATAA-TTAATAATTA
497739 ATAATTAAATAATTAATAATTAATAATTA
1 ATAATTAAAT-ATTAATAATTAATAATTA
497768 ATA
1 ATA
497771 TTTATATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 10 0.36
28 8 0.29
29 10 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAATTAAATATTAATAATTAATAATTA
Found at i:497744 original size:7 final size:7
Alignment explanation
Indices: 497713--497785 Score: 71
Period size: 7 Copynumber: 10.3 Consensus size: 7
497703 TAATAAAAAT
497713 ATAATTA
1 ATAATTA
*
497720 A-ATTTA
1 ATAATTA
497726 A-AATTTA
1 ATAA-TTA
497733 A-AATTA
1 ATAATTA
497739 ATAATTAA
1 ATAATT-A
497747 ATAATTA
1 ATAATTA
497754 ATAATTA
1 ATAATTA
497761 ATAATTA
1 ATAATTA
*
497768 ATATTTA
1 ATAATTA
497775 TATACATTA
1 -ATA-ATTA
497784 AT
1 AT
497786 TAAATCTATT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
6 10 0.18
7 32 0.56
8 12 0.21
9 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (7 bp):
ATAATTA
Found at i:497759 original size:22 final size:22
Alignment explanation
Indices: 497713--497785 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
497703 TAATAAAAAT
*
497713 ATAATTAA-ATTTAAA-ATTTA
1 ATAATTAATAATTAAATATTTA
*
497733 A-AATTAATAATTAAATAATTA
1 ATAATTAATAATTAAATATTTA
497754 ATAATTAATAATT-AATATTTA
1 ATAATTAATAATTAAATATTTA
497775 TATACATTAAT
1 -ATA-ATTAAT
497786 TAAATCTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.13
20 7 0.16
21 12 0.27
22 14 0.31
23 6 0.13
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATTAATAATTAAATATTTA
Found at i:497766 original size:29 final size:29
Alignment explanation
Indices: 497713--497785 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
497703 TAATAAAAAT
497713 ATAATTAAAT--TTAA-AATTTAAAATTA
1 ATAATTAAATAATTAATAATTTAAAATTA
497739 ATAATTAAATAATTAATAA-TTAATAATTA
1 ATAATTAAATAATTAATAATTTAA-AATTA
* *
497768 ATATTTATATACATTAAT
1 ATAATTAAATA-ATTAAT
497786 TAAATCTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 10 0.25
28 8 0.20
29 16 0.40
30 6 0.15
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (29 bp):
ATAATTAAATAATTAATAATTTAAAATTA
Found at i:498506 original size:22 final size:23
Alignment explanation
Indices: 498478--498545 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 23
498468 AATATATTAA
498478 AAATTATTTTCAT-ATT-AATATT
1 AAATTATTTTCATAATTAAAT-TT
498500 AAATTATTTTCATAATTAAATTT
1 AAATTATTTTCATAATTAAATTT
* *
498523 AAATAAATTTTTATTAATTAAAT
1 AAAT-TATTTTCA-TAATTAAAT
498546 AGTAATTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
22 13 0.32
23 9 0.22
24 9 0.22
25 9 0.22
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTATTTTCATAATTAAATTT
Found at i:499395 original size:17 final size:17
Alignment explanation
Indices: 499354--499395 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
499344 GTACAGTTTG
499354 ATAATAATATTTTTAAT
1 ATAATAATATTTTTAAT
**
499371 ATTTTAATATATTTTAA-
1 ATAATAATAT-TTTTAAT
499388 ATAATAAT
1 ATAATAAT
499396 TTGAATCGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAATAATATTTTTAAT
Found at i:499560 original size:16 final size:16
Alignment explanation
Indices: 499541--499588 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
499531 TATACGATGC
499541 AAATTTAAAATAAATT
1 AAATTTAAAATAAATT
* *
499557 AAATATAAAATAATTT
1 AAATTTAAAATAAATT
* *
499573 ATATTTAAAATTAATT
1 AAATTTAAAATAAATT
499589 TTAATTTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATTTAAAATAAATT
Found at i:499990 original size:16 final size:16
Alignment explanation
Indices: 499955--499997 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
499945 ATCATTTTAG
499955 ATATA-ATAATATTAA
1 ATATATATAATATTAA
499970 A-ATATATAATATTAA
1 ATATATATAATATTAA
*
499985 ATATATTTAATAT
1 ATATATATAATAT
499998 ATATTATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 3 0.12
15 12 0.48
16 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATATATAATATTAA
Found at i:501389 original size:23 final size:20
Alignment explanation
Indices: 501358--501401 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 20
501348 AATTTTTATT
501358 TAAATTTAATAATAAAAATATA
1 TAAATTTAAT-ATAAAAA-ATA
501380 TAAATATTAATATAAAAAATA
1 TAAAT-TTAATATAAAAAATA
501401 T
1 T
501402 TTTAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 12 0.57
23 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATTTAATATAAAAAATA
Found at i:501408 original size:23 final size:23
Alignment explanation
Indices: 501354--501410 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
501344 TAAAAATTTT
501354 TATTTAAAT-TTAATAATAAAAA
1 TATTTAAATATTAATAATAAAAA
*
501376 TATATAAATATTAAT-ATAAAAAA
1 TATTTAAATATTAATAAT-AAAAA
*
501399 TATTTTAATATT
1 TATTTAAATATT
501411 TTTAAATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTTAAATATTAATAATAAAAA
Found at i:502304 original size:19 final size:18
Alignment explanation
Indices: 502262--502304 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
502252 ACGAAATATT
*
502262 ATATTTAATTTTTTTTAA
1 ATATTTAAATTTTTTTAA
*
502280 AAATTTAAATTTTTTTATA
1 ATATTTAAATTTTTTTA-A
502299 ATATTT
1 ATATTT
502305 CACACATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTTAAATTTTTTTAA
Found at i:504354 original size:2 final size:2
Alignment explanation
Indices: 504349--504380 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
504339 ACACACACAC
504349 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
504381 GCAATTTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:505312 original size:58 final size:58
Alignment explanation
Indices: 505249--505362 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
505239 CTACCATTGC
505249 AAAGCTGAAGTAGAATCATT-GAAAATTTGTTCTCCATAACACAATCGTTATCATTTGT
1 AAAGCTGAAGTAGAATCATTGGAAAA-TTGTTCTCCATAACACAATCGTTATCATTTGT
* * *
505307 AAAGCTGAAGTAGAGTCGTTGGAAAATTGTTCTTCATAACACAATCGTTATCATTT
1 AAAGCTGAAGTAGAATCATTGGAAAATTGTTCTCCATAACACAATCGTTATCATTT
505363 AATTAATCCT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
58 47 0.90
59 5 0.10
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (58 bp):
AAAGCTGAAGTAGAATCATTGGAAAATTGTTCTCCATAACACAATCGTTATCATTTGT
Found at i:505834 original size:12 final size:12
Alignment explanation
Indices: 505816--505849 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
505806 ATATTCAACC
505816 ATTTTTTCCTTT
1 ATTTTTTCCTTT
*
505828 GTTTTTTCCTTT
1 ATTTTTTCCTTT
*
505840 ACTTTTTCCT
1 ATTTTTTCCT
505850 ATAAAGCAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.21, G:0.03, T:0.71
Consensus pattern (12 bp):
ATTTTTTCCTTT
Found at i:509239 original size:18 final size:18
Alignment explanation
Indices: 509218--509298 Score: 55
Period size: 14 Copynumber: 4.5 Consensus size: 18
509208 ATATTATAAT
509218 AATAGAATAAATATACTA
1 AATAGAATAAATATACTA
*
509236 AATAG----AATATAGTA
1 AATAGAATAAATATACTA
509250 AA-AGAATAAATATAACATA
1 AATAGAATAAATAT-AC-TA
* *
509269 TAATATAATAATAATATAATA
1 -AATAGAAT-A-AATATACTA
509290 AATAGAATA
1 AATAGAATA
509299 GAAAAAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 19
0.67 0.07 0.26
Matches are distributed among these distances:
13 2 0.04
14 10 0.21
17 5 0.10
18 6 0.12
19 3 0.06
20 9 0.19
21 6 0.12
22 2 0.04
23 5 0.10
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.28
Consensus pattern (18 bp):
AATAGAATAAATATACTA
Found at i:509259 original size:31 final size:30
Alignment explanation
Indices: 509199--509279 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
509189 AGAGTGATAT
* * *
509199 TATACTAATATATTATAATAATAGAATAAA
1 TATACTAATAGAATATAATAAAAGAATAAA
*
509229 TATACTAAATAGAATATAGTAAAAGAATAAA
1 TATACT-AATAGAATATAATAAAAGAATAAA
*
509260 TATA--ACATATAATATAATAA
1 TATACTA-ATAGAATATAATAA
509280 TAATATAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 1 0.02
29 12 0.28
30 6 0.14
31 24 0.56
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (30 bp):
TATACTAATAGAATATAATAAAAGAATAAA
Found at i:509346 original size:15 final size:15
Alignment explanation
Indices: 509326--509364 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
509316 GGTATAAAAA
*
509326 AGATAAATAATATAT
1 AGATAAATAATAAAT
*
509341 AGATAAATTATAAAT
1 AGATAAATAATAAAT
*
509356 ATATAAATA
1 AGATAAATA
509365 TTTTTATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (15 bp):
AGATAAATAATAAAT
Found at i:510282 original size:41 final size:41
Alignment explanation
Indices: 510237--510420 Score: 212
Period size: 41 Copynumber: 4.5 Consensus size: 41
510227 AAAACGCCAC
* * * * *
510237 TAATTTGAATTAATTAGCTG-TGTTTTTAATATAAATATCGT
1 TAATTTAAATTAATTAAC-GATATTTTTAATATAAACATCAT
*
510278 TAATTTAAATTAATTAACGATATTTTT-ATATAAATATCAT
1 TAATTTAAATTAATTAACGATATTTTTAATATAAACATCAT
* *
510318 TAATTTAAATTAATTAACGATATTTTTATTATAAACATCTT
1 TAATTTAAATTAATTAACGATATTTTTAATATAAACATCAT
* * *
510359 TAATTTAAATTAATTAAC-AGTATTTTTATTATAAACGTCCT
1 TAATTTAAATTAATTAACGA-TATTTTTAATATAAACATCAT
**
510400 TAATTTTGATTAATTAACGAT
1 TAATTTAAATTAATTAACGAT
510421 GTTTAAAATT
Statistics
Matches: 128, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
40 41 0.32
41 86 0.67
42 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.48
Consensus pattern (41 bp):
TAATTTAAATTAATTAACGATATTTTTAATATAAACATCAT
Found at i:510305 original size:21 final size:21
Alignment explanation
Indices: 510281--510345 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 21
510271 ATATCGTTAA
510281 TTTAAATTAATTAACGATATT
1 TTTAAATTAATTAACGATATT
* * * *
510302 TTTATA-TAAATATC-AT-TAA
1 TTTAAATTAATTAACGATAT-T
510321 TTTAAATTAATTAACGATATT
1 TTTAAATTAATTAACGATATT
510342 TTTA
1 TTTA
510346 TTATAAACAT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
18 1 0.03
19 7 0.22
20 12 0.38
21 11 0.34
22 1 0.03
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (21 bp):
TTTAAATTAATTAACGATATT
Found at i:510372 original size:81 final size:82
Alignment explanation
Indices: 510237--510420 Score: 230
Period size: 81 Copynumber: 2.3 Consensus size: 82
510227 AAAACGCCAC
* * * *
510237 TAATTTGAATTAATTAGCTG-TGTTTTTAATATAAATATCGTTAATTTAAATTAATTAAC-GATA
1 TAATTTAAATTAATTAAC-GATATTTTTAATATAAACATCGTTAATTTAAATTAATTAACAG-TA
*
510300 TTTTTA-TATAAATATCAT
64 TTTTTATTATAAACATCAT
* *
510318 TAATTTAAATTAATTAACGATATTTTTATTATAAACATCTTTAATTTAAATTAATTAACAGTATT
1 TAATTTAAATTAATTAACGATATTTTTAATATAAACATCGTTAATTTAAATTAATTAACAGTATT
* *
510383 TTTATTATAAACGTCCT
66 TTTATTATAAACATCAT
**
510400 TAATTTTGATTAATTAACGAT
1 TAATTTAAATTAATTAACGAT
510421 GTTTAAAATT
Statistics
Matches: 89, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
80 1 0.01
81 59 0.66
82 29 0.33
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.48
Consensus pattern (82 bp):
TAATTTAAATTAATTAACGATATTTTTAATATAAACATCGTTAATTTAAATTAATTAACAGTATT
TTTATTATAAACATCAT
Found at i:513307 original size:27 final size:25
Alignment explanation
Indices: 513256--513307 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
513246 TTTGAAATGT
* *
513256 TTTTTTATGTATTTAAATGTTATTC
1 TTTTTTATGTATTTAAATATGATTC
*
513281 TTTTTTATGTATGTTTGAATATGATTC
1 TTTTTTATGTA--TTTAAATATGATTC
513308 GAACACAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 11 0.50
27 11 0.50
ACGTcount: A:0.23, C:0.04, G:0.12, T:0.62
Consensus pattern (25 bp):
TTTTTTATGTATTTAAATATGATTC
Found at i:513586 original size:25 final size:26
Alignment explanation
Indices: 513558--513606 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
513548 TAAATATTTA
*
513558 TATTTGACAT-ATATTTAAATATAAG
1 TATTGGACATAATATTTAAATATAAG
* *
513583 TATTGGATATAATTTTTAAATATA
1 TATTGGACATAATATTTAAATATA
513607 TGAAAAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (26 bp):
TATTGGACATAATATTTAAATATAAG
Found at i:515410 original size:19 final size:21
Alignment explanation
Indices: 515370--515411 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
515360 ACTAACTTTA
515370 TTTATAAAATATAATAATTTT
1 TTTATAAAATATAATAATTTT
*
515391 TTTAT-AAATA-AATTATTTT
1 TTTATAAAATATAATAATTTT
515410 TT
1 TT
515412 ACATCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 5 0.25
21 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATAAAATATAATAATTTT
Found at i:515923 original size:20 final size:20
Alignment explanation
Indices: 515895--515954 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
515885 ATAATTAAAT
*
515895 TTAAA-AAATTATTATTTTA
1 TTAAATAAATTATTATTTAA
* *
515914 TTAAATAAATAATAATTTAA
1 TTAAATAAATTATTATTTAA
*
515934 TTAAATTAATT-TTATTTAA
1 TTAAATAAATTATTATTTAA
515953 TT
1 TT
515955 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAAATAAATTATTATTTAA
Found at i:516155 original size:21 final size:22
Alignment explanation
Indices: 516109--516170 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 22
516099 TAATTTAATT
*
516109 TAAATTATTATTTATATAATAA
1 TAAATTATTATTTATATAAAAA
*
516131 -AAATTATT-TTTATTTAAAAA
1 TAAATTATTATTTATATAAAAA
516151 TAAA-TATTA---ATATAAAAA
1 TAAATTATTATTTATATAAAAA
516169 TA
1 TA
516171 TATATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 10 0.29
20 14 0.40
21 11 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTATTATTTATATAAAAA
Found at i:517551 original size:6 final size:7
Alignment explanation
Indices: 517529--517577 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
517519 AAAGTATTAA
517529 AAATTTT
1 AAATTTT
517536 AAATTTT
1 AAATTTT
*
517543 AAATTTA
1 AAATTTT
517550 AAATTATT
1 AAATT-TT
*
517558 AAATATT
1 AAATTTT
*
517565 ATATCTTT
1 AAAT-TTT
517573 AAATT
1 AAATT
517578 AATTATATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
7 24 0.71
8 10 0.29
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (7 bp):
AAATTTT
Found at i:518040 original size:2 final size:2
Alignment explanation
Indices: 518033--518065 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
518023 AGATCTAAAC
*
518033 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
518066 GTAAAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:518727 original size:32 final size:31
Alignment explanation
Indices: 518691--518756 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
518681 TTTACTTAAA
518691 TTTAATTATAATTATT-AAT-ATAAAAATAATTT
1 TTTAA-TATAATT-TTAAATAAT-AAAATAATTT
*
518723 TTTAATATTATTTTAAATAATAAAATAATTT
1 TTTAATATAATTTTAAATAATAAAATAATTT
518754 TTT
1 TTT
518757 TCCCATACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
30 2 0.06
31 22 0.71
32 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTAATATAATTTTAAATAATAAAATAATTT
Found at i:521017 original size:15 final size:15
Alignment explanation
Indices: 520983--521033 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
520973 TAATTTAAAA
* *
520983 TTTTTGGATTTAGGT
1 TTTTTGAATTTAAGT
*
520998 CTTTTGAATTTAAGTT
1 TTTTTGAATTTAAG-T
*
521014 TTTTTGAATTTAAAT
1 TTTTTGAATTTAAGT
521029 TTTTT
1 TTTTT
521034 TAAGTTCGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.22, C:0.02, G:0.14, T:0.63
Consensus pattern (15 bp):
TTTTTGAATTTAAGT
Found at i:521034 original size:17 final size:16
Alignment explanation
Indices: 520999--521034 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
520989 GATTTAGGTC
520999 TTTTGAATTTAAGTTT
1 TTTTGAATTTAAGTTT
*
521015 TTTTGAATTTAAATTT
1 TTTTGAATTTAAGTTT
521031 TTTT
1 TTTT
521035 AAGTTCGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (16 bp):
TTTTGAATTTAAGTTT
Found at i:521942 original size:17 final size:17
Alignment explanation
Indices: 521916--521952 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
521906 TCGAGTGTGA
*
521916 GTGTCAGATATGGGTAT
1 GTGTCAGATATGGATAT
*
521933 GTGTCTGATATGGATAT
1 GTGTCAGATATGGATAT
521950 GTG
1 GTG
521953 CAATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.05, G:0.35, T:0.38
Consensus pattern (17 bp):
GTGTCAGATATGGATAT
Found at i:524631 original size:2 final size:2
Alignment explanation
Indices: 524626--524665 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
524616 TATATATATA
524626 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
524666 AAAAGGGCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:525411 original size:14 final size:12
Alignment explanation
Indices: 525369--525521 Score: 61
Period size: 12 Copynumber: 13.1 Consensus size: 12
525359 TTAGTAAAAA
*
525369 TTAAATATAATT
1 TTAAATTTAATT
*
525381 TTATATTTAATT
1 TTAAATTTAATT
525393 TTAAATTTAATTAT
1 TTAAATTTAA-T-T
*
525407 TTAAATTTAA-A
1 TTAAATTTAATT
525418 TTAAA---AATT
1 TTAAATTTAATT
525427 TTAATATTT-ATT
1 TTAA-ATTTAATT
** ** **
525439 AAAAATAAAAAA
1 TTAAATTTAATT
*
525451 TTAAATTAAATT
1 TTAAATTTAATT
* *
525463 TAAAATTTTA-T
1 TTAAATTTAATT
* * *
525474 ATAAATTAAATA
1 TTAAATTTAATT
525486 TTAAATTT-ATT
1 TTAAATTTAATT
* *
525497 TT-ATTTTATAAT
1 TTAAATTTA-ATT
525509 TTAAATTTAATT
1 TTAAATTTAATT
525521 T
1 T
525522 GATAAAGTAT
Statistics
Matches: 98, Mismatches: 31, Indels: 24
0.64 0.20 0.16
Matches are distributed among these distances:
8 2 0.02
9 4 0.04
10 5 0.05
11 18 0.18
12 52 0.53
13 6 0.06
14 11 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATTTAATT
Found at i:525414 original size:6 final size:6
Alignment explanation
Indices: 525369--525518 Score: 53
Period size: 6 Copynumber: 24.7 Consensus size: 6
525359 TTAGTAAAAA
* * * *
525369 TTAAAT ATAATT TTATAT TTAATT TTAAAT TTAATTAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA--AT TTAAAT TTAAAT
* * ** *
525419 TAAAAATT TTAATAT TT--AT TAAAAAT AAAAAA TTAAA- TTAAAT TTAAAAT
1 T-TAAA-T TTAA-AT TTAAAT T-TAAAT TTAAAT TTAAAT TTAAAT TT-AAAT
* * * *
525469 TT-TAT ATAAA- TTAAAT ATTAAAT TT--AT TTTATT TTATAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTA-AAT TTAAAT
525515 TTAA
1 TTAA
525519 TTTGATAAAG
Statistics
Matches: 106, Mismatches: 22, Indels: 32
0.66 0.14 0.20
Matches are distributed among these distances:
4 7 0.07
5 12 0.11
6 51 0.48
7 27 0.25
8 9 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:525427 original size:19 final size:19
Alignment explanation
Indices: 525385--525460 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 19
525375 ATAATTTTAT
* **
525385 ATTTAATTTTAAATTTAATT
1 ATTTAAATTTAAA-TTAAAA
525405 ATTTAAATTTAAATTAAAA
1 ATTTAAATTTAAATTAAAA
525424 ATTTTAATATTT--ATTAAAA
1 A-TTTAA-ATTTAAATTAAAA
** *
525443 ATAAAAAATTAAATTAAA
1 ATTTAAATTTAAATTAAA
525461 TTTAAAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
17 3 0.07
18 3 0.07
19 19 0.41
20 17 0.37
21 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTAAATTTAAATTAAAA
Found at i:525441 original size:44 final size:42
Alignment explanation
Indices: 525393--525490 Score: 97
Period size: 43 Copynumber: 2.3 Consensus size: 42
525383 ATATTTAATT
** * **
525393 TTAAATTTAATTATTTAAATTTAAATTAAAAATTTTAATATTTA
1 TTAAATTTAAAAAATTAAA-TTAAATTAAAAATTTT-ATATAAA
** *
525437 TTAAAAATAAAAAATTAAATTAAATTTAAAATTTTATATAAA
1 TTAAATTTAAAAAATTAAATTAAATTAAAAATTTTATATAAA
525479 TTAAATATTAAA
1 TTAAAT-TTAAA
525491 TTTATTTTAT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
42 10 0.23
43 19 0.44
44 14 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (42 bp):
TTAAATTTAAAAAATTAAATTAAATTAAAAATTTTATATAAA
Found at i:528226 original size:21 final size:21
Alignment explanation
Indices: 528202--528244 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
528192 TGAGTATATA
528202 TTTAAATATATAAAATAATTT
1 TTTAAATATATAAAATAATTT
528223 TTTAAATATATAAAATAATTT
1 TTTAAATATATAAAATAATTT
528244 T
1 T
528245 AAAAGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAAATATATAAAATAATTT
Found at i:528255 original size:19 final size:21
Alignment explanation
Indices: 528209--528255 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
528199 ATATTTAAAT
* *
528209 ATATAAAATAATTTTTTAAAT
1 ATATAAAATAATTTTTAAAAG
528230 ATATAAAATAA-TTTTAAAAG
1 ATATAAAATAATTTTTAAAAG
528250 AT-TAAA
1 ATATAAA
528256 TAGTAATAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 9 0.38
21 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATATAAAATAATTTTTAAAAG
Found at i:528349 original size:11 final size:12
Alignment explanation
Indices: 528330--528362 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
528320 GATATGAATG
528330 TAATATAAAAAA
1 TAATATAAAAAA
*
528342 TAAT-TAAAATA
1 TAATATAAAAAA
528353 TAATATAAAA
1 TAATATAAAA
528363 TATTATACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TAATATAAAAAA
Found at i:528361 original size:12 final size:12
Alignment explanation
Indices: 528330--528365 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
528320 GATATGAATG
*
528330 TAATATAAAAAA
1 TAATATAAAATA
528342 TAAT-TAAAATA
1 TAATATAAAATA
528353 TAATATAAAATA
1 TAATATAAAATA
528365 T
1 T
528366 TATACGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATATAAAATA
Found at i:528707 original size:14 final size:13
Alignment explanation
Indices: 528681--528721 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
528671 TTATAATAAA
528681 AAATATT-ATTAT
1 AAATATTAATTAT
*
528693 ATAATTTTAATTAT
1 A-AATATTAATTAT
528707 AAATATTAA-TAT
1 AAATATTAATTAT
528719 AAA
1 AAA
528722 AATAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 12 0.48
14 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATATTAATTAT
Found at i:528727 original size:24 final size:25
Alignment explanation
Indices: 528672--528756 Score: 66
Period size: 24 Copynumber: 3.4 Consensus size: 25
528662 TTATTATTTT
* * * *
528672 TATAATAAAAAATATTATTATATAAT
1 TATAATTATAAATATTAATATA-AAA
*
528698 TTTAATTATAAATATTAATATAAAA
1 TATAATTATAAATATTAATATAAAA
* * * *
528723 -ATAATTTTTAATATTATTTTAAAA
1 TATAATTATAAATATTAATATAAAA
528747 TATAA-TATAA
1 TATAATTATAA
528757 GTTGGTGAAT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
24 22 0.48
25 6 0.13
26 18 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTATAAATATTAATATAAAA
Found at i:528788 original size:24 final size:24
Alignment explanation
Indices: 528761--528808 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
528751 ATATAAGTTG
528761 GTGAATTAATTCAACTTAAATCTA
1 GTGAATTAATTCAACTTAAATCTA
528785 GTGAATTAATTCAACTTAAATCTA
1 GTGAATTAATTCAACTTAAATCTA
528809 AACTAAAAAA
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:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (24 bp):
GTGAATTAATTCAACTTAAATCTA
Found at i:529108 original size:22 final size:22
Alignment explanation
Indices: 529076--529129 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
529066 TAAATTTGAT
*
529076 TTTTTTA-TTAATTTTAGTTTAG
1 TTTTTTATTTAA-TTTAATTTAG
529098 -TTTTTATTTAATTTAATTTAG
1 TTTTTTATTTAATTTAATTTAG
529119 TTTTTTATTTA
1 TTTTTTATTTA
529130 TAAATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (22 bp):
TTTTTTATTTAATTTAATTTAG
Found at i:537708 original size:17 final size:16
Alignment explanation
Indices: 537686--537724 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
537676 AATATTTAAT
*
537686 AATTTTAAAATTATTTA
1 AATTTTAAAATT-TATA
*
537703 AATTTTAATATTTATA
1 AATTTTAAAATTTATA
537719 AATTTT
1 AATTTT
537725 TTTAAAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTTAAAATTTATA
Found at i:537715 original size:25 final size:27
Alignment explanation
Indices: 537680--537730 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
537670 TAAAATAATA
537680 TTTAATAATTT-TAAAATTATTTAAAT
1 TTTAATAATTTATAAAATTATTTAAAT
* *
537706 TTTAAT-ATTTATAAATTTTTTTAAA
1 TTTAATAATTTATAAAATTATTTAAA
537731 ATCTTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTAATAATTTATAAAATTATTTAAAT
Found at i:537722 original size:16 final size:16
Alignment explanation
Indices: 537675--537724 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
537665 TTTTATAAAA
537675 TAATATTTA-ATAATTT
1 TAATATTTATA-AATTT
* *
537691 TAAAATTATTTAAATTT
1 TAATATT-TATAAATTT
537708 TAATATTTATAAATTT
1 TAATATTTATAAATTT
537724 T
1 T
537725 TTTAAAATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 15 0.54
17 12 0.43
18 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATATTTATAAATTT
Found at i:539552 original size:12 final size:12
Alignment explanation
Indices: 539530--539559 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
539520 CTAAAAAAAT
539530 TATATAAATATAA
1 TATA-AAATATAA
539543 TATAAAATATAA
1 TATAAAATATAA
539555 TATAA
1 TATAA
539560 GATCAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TATAAAATATAA
Found at i:539942 original size:22 final size:22
Alignment explanation
Indices: 539893--539945 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
539883 ATAATTAATT
** *
539893 TATAAATAA-ATTTATATAATA
1 TATAAATAATATAAATATAAAA
*
539914 TAAAAATAATATAAATATAAAA
1 TATAAATAATATAAATATAAAA
539936 TATAAATAAT
1 TATAAATAAT
539946 TAGGGCCGCG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TATAAATAATATAAATATAAAA
Found at i:540308 original size:33 final size:33
Alignment explanation
Indices: 540271--540346 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
540261 ATTTGATATG
* *
540271 AATATTATTTTTAATTTAACAATATTAAAGATA
1 AATATTCTTTTTAATTTAACAATATTAAAAATA
* * *
540304 AATA-TCGTTTTAATTTAATAGTATTAAAAATA
1 AATATTCTTTTTAATTTAACAATATTAAAAATA
540336 AATATTCTTTT
1 AATATTCTTTT
540347 AAAACTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
32 27 0.75
33 9 0.25
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (33 bp):
AATATTCTTTTTAATTTAACAATATTAAAAATA
Found at i:541070 original size:23 final size:21
Alignment explanation
Indices: 541031--541074 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
541021 AAAAATTTAT
541031 TTTTATATTAATATTAATATAA
1 TTTTATATTAATATTAA-ATAA
541053 TTTTATAATTAA-ATTTAAATAA
1 TTTTAT-ATTAATA-TTAAATAA
541075 AATAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTATATTAATATTAAATAA
Found at i:541401 original size:37 final size:36
Alignment explanation
Indices: 541355--541433 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 36
541345 GAAAGTTTAT
* *
541355 TTTATTATTTA-AAATAATATTAAAATATAAATATATA
1 TTTAATATTTATAAATAA-ATTAAAATAAAAATAT-TA
* * *
541392 TTTAATATTTATAATTAAATTTAAATAAAAATATTT
1 TTTAATATTTATAAATAAATTAAAATAAAAATATTA
541428 TTTAAT
1 TTTAAT
541434 TTAATTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 7 0.19
37 24 0.67
38 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
TTTAATATTTATAAATAAATTAAAATAAAAATATTA
Found at i:542071 original size:21 final size:21
Alignment explanation
Indices: 542026--542071 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
542016 TTATAAAAAT
* * *
542026 TTTAAAAATAATTTTTTATTT
1 TTTAAAAATAATTATTAATTA
*
542047 TTTAAATATAATTATTAATTA
1 TTTAAAAATAATTATTAATTA
542068 TTTA
1 TTTA
542072 TATTTTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAAAAATAATTATTAATTA
Found at i:544216 original size:42 final size:42
Alignment explanation
Indices: 544126--544215 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
544116 TTTAAGCTAA
* *
544126 GATTTTTATATATATTTTTAATTTTTTAATTTTTAGTTATTT
1 GATTTTTATATATATTTTTAATTTTTTAATCTTGAGTTATTT
*
544168 GATTTTTATATCTATTTTTAATTTTTT-ATCTTGA-TTACTTT
1 GATTTTTATATATATTTTTAATTTTTTAATCTTGAGTTA-TTT
*
544209 TATTTTT
1 GATTTTT
544216 TTCATATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 3 0.07
41 14 0.33
42 26 0.60
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.69
Consensus pattern (42 bp):
GATTTTTATATATATTTTTAATTTTTTAATCTTGAGTTATTT
Found at i:544245 original size:15 final size:15
Alignment explanation
Indices: 544227--544257 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
544217 TCATATTTAT
544227 ATTTAAAAAATAAAA
1 ATTTAAAAAATAAAA
544242 ATTTAAAAAATAAAA
1 ATTTAAAAAATAAAA
544257 A
1 A
544258 ATATTCCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATTTAAAAAATAAAA
Found at i:544518 original size:17 final size:19
Alignment explanation
Indices: 544480--544518 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
544470 TTCTAAATAT
544480 ATATAAATAATATTTGAAA
1 ATATAAATAATATTTGAAA
*
544499 ATATTAATAA-ATTT-AAA
1 ATATAAATAATATTTGAAA
544516 ATA
1 ATA
544519 ATATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATATAAATAATATTTGAAA
Found at i:544526 original size:18 final size:18
Alignment explanation
Indices: 544485--544527 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
544475 AATATATATA
*
544485 AATAATATTTGAAAATATT
1 AATAA-ATTTGAAAATAAT
544504 AATAAATTT-AAAATAAT
1 AATAAATTTGAAAATAAT
544521 ATATAAA
1 A-ATAAA
544528 AATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 9 0.41
19 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AATAAATTTGAAAATAAT
Found at i:544536 original size:14 final size:13
Alignment explanation
Indices: 544475--544560 Score: 50
Period size: 14 Copynumber: 6.3 Consensus size: 13
544465 ATAGATTCTA
*
544475 AATATATATAAAT
1 AATATATAAAAAT
*
544488 AATATTTGAAAATATT
1 AATATAT-AAAA-A-T
* *
544504 AATAAATTTAAAAT
1 AATATA-TAAAAAT
544518 AATATATAAAAAT
1 AATATATAAAAAT
* *
544531 ATATATATTAATAT
1 A-ATATATAAAAAT
544545 CAA-A-ATAAAAAT
1 -AATATATAAAAAT
544557 AATA
1 AATA
544561 AACTCATTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
11 2 0.04
12 7 0.13
13 14 0.25
14 20 0.36
15 3 0.05
16 8 0.15
17 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (13 bp):
AATATATAAAAAT
Found at i:545172 original size:2 final size:2
Alignment explanation
Indices: 545165--545189 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
545155 CCATGAACAT
545165 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
545190 AATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:545196 original size:2 final size:2
Alignment explanation
Indices: 545191--545218 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
545181 ACACACACAA
545191 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
545219 TAATTTCTAG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:547382 original size:29 final size:29
Alignment explanation
Indices: 547345--547416 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
547335 ATAATTTTTT
547345 AAAAA-TATTTTTAAAAACTTTAAAAATA
1 AAAAATTATTTTTAAAAACTTTAAAAATA
* *
547373 AAAAATTATTTATAAAAATTTTAAAAATA
1 AAAAATTATTTTTAAAAACTTTAAAAATA
*
547402 AAAAATTATTCTTAA
1 AAAAATTATTTTTAA
547417 CAATCATCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
AAAAATTATTTTTAAAAACTTTAAAAATA
Found at i:549988 original size:17 final size:18
Alignment explanation
Indices: 549966--550003 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
549956 GATAATTTTA
549966 ATATTAGTATTATAT-TT
1 ATATTAGTATTATATATT
* *
549983 ATATTATTTTTATATATT
1 ATATTAGTATTATATATT
550001 ATA
1 ATA
550004 AATATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
ATATTAGTATTATATATT
Found at i:550049 original size:16 final size:16
Alignment explanation
Indices: 550024--550071 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
550014 AAATATTATT
550024 ATTTATATAAATTTTA
1 ATTTATATAAATTTTA
*
550040 ATTTAAAT-AA-TTT-
1 ATTTATATAAATTTTA
550053 ATATTATATAAATTTTA
1 AT-TTATATAAATTTTA
550070 AT
1 AT
550072 AATTTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
13 2 0.08
14 8 0.31
15 4 0.15
16 10 0.38
17 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTATATAAATTTTA
Found at i:550439 original size:23 final size:23
Alignment explanation
Indices: 550413--550517 Score: 81
Period size: 23 Copynumber: 4.6 Consensus size: 23
550403 AATTTATCAA
550413 TAATATATAAATTTATATATTAT
1 TAATATATAAATTTATATATTAT
* * *
550436 TAATACATCAAATATA-AAATTAT
1 TAATATAT-AAATTTATATATTAT
* * *
550459 GAAT-T-TAACTTTAATATATTAA
1 TAATATATAAATTT-ATATATTAT
*
550481 TAATATATAATTTTATATATTAT
1 TAATATATAAATTTATATATTAT
* *
550504 CAATAAATTAAATT
1 TAATATA-TAAATT
550518 AAATCATCTT
Statistics
Matches: 61, Mismatches: 15, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
20 4 0.07
21 2 0.03
22 8 0.13
23 30 0.49
24 17 0.28
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.46
Consensus pattern (23 bp):
TAATATATAAATTTATATATTAT
Found at i:550439 original size:34 final size:34
Alignment explanation
Indices: 550401--550508 Score: 91
Period size: 34 Copynumber: 3.2 Consensus size: 34
550391 ACGATATAAT
*
550401 TTAATTTATCAATAATATATAAATTTATATATTA
1 TTAATATATCAATAATATATAAATTTATATATTA
*
550435 TTAATACATC-A-AATATA-AAA-TTATGA-ATTTAA
1 TTAATATATCAATAATATATAAATTTAT-ATA-TT-A
* *
550467 CTTTAATATATTAATAATATATAATTTTATATATTA
1 --TTAATATATCAATAATATATAAATTTATATATTA
*
550503 TCAATA
1 TTAATA
550509 AATTAAATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
30 5 0.09
31 6 0.10
32 7 0.12
33 1 0.02
34 21 0.36
35 1 0.02
36 7 0.12
37 5 0.09
38 5 0.09
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (34 bp):
TTAATATATCAATAATATATAAATTTATATATTA
Found at i:551209 original size:10 final size:10
Alignment explanation
Indices: 551181--551252 Score: 58
Period size: 10 Copynumber: 6.9 Consensus size: 10
551171 GAGCCTCTCG
551181 TATTTATATTA
1 TATTTATA-TA
551192 TATTTATATA
1 TATTTATATA
*
551202 TTTTTATATA
1 TATTTATATA
551212 TAATATTA-ATTA
1 T-AT-TTATA-TA
*
551224 TATTTA-AAA
1 TATTTATATA
*
551233 TATTATATATT
1 TATT-TATATA
551244 TATTTATAT
1 TATTTATAT
551253 TTTTTGATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
9 5 0.10
10 23 0.45
11 17 0.33
12 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATTTATATA
Found at i:551210 original size:16 final size:15
Alignment explanation
Indices: 551189--551245 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
551179 CGTATTTATA
551189 TTATATTTATATATTT
1 TTATATTTA-ATATTT
* *
551205 TTATATATAATATTAA
1 TTATATTTAATATT-T
*
551221 TTATATTTAAAATATT
1 TTATATTTAATAT-TT
*
551237 ATATATTTA
1 TTATATTTA
551246 TTTATATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 5 0.15
16 27 0.82
17 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATTTAATATTT
Found at i:551316 original size:17 final size:17
Alignment explanation
Indices: 551291--551335 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
551281 TATATTGAGT
*
551291 TCATCTTAT-TTTTTATA
1 TCATTTTATATTTTT-TA
551308 TCATTTTATATTTTTTA
1 TCATTTTATATTTTTTA
551325 TCATATTTATA
1 TCAT-TTTATA
551336 ATCATATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (17 bp):
TCATTTTATATTTTTTA
Found at i:552146 original size:9 final size:10
Alignment explanation
Indices: 552128--552180 Score: 58
Period size: 9 Copynumber: 5.4 Consensus size: 10
552118 AATTAAAATT
552128 ATTT-ATTAA
1 ATTTAATTAA
552137 ATTTAA-TAA
1 ATTTAATTAA
552146 ATTTAATTTAA
1 ATTTAA-TTAA
*
552157 ATTAAATTAA
1 ATTTAATTAA
552167 ATTT-ATTATA
1 ATTTAATTA-A
552177 ATTT
1 ATTT
552181 TTAAATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 17 0.45
10 13 0.34
11 8 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTAATTAA
Found at i:552179 original size:10 final size:9
Alignment explanation
Indices: 552128--552186 Score: 57
Period size: 9 Copynumber: 6.2 Consensus size: 9
552118 AATTAAAATT
552128 ATTTATTAA
1 ATTTATTAA
*
552137 ATTTAATAA
1 ATTTATTAA
552146 ATTTAATTTAA
1 ATTT-A-TTAA
*
552157 ATTAAATTAA
1 ATT-TATTAA
552167 ATTTATTATA
1 ATTTATTA-A
552177 ATTT-TTAA
1 ATTTATTAA
552185 AT
1 AT
552187 AAAAGACAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
8 3 0.07
9 19 0.45
10 13 0.31
11 7 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATTTATTAA
Found at i:552395 original size:2 final size:2
Alignment explanation
Indices: 552388--552425 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
552378 TATTGATTGT
552388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
552426 AGTAATTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:554678 original size:6 final size:6
Alignment explanation
Indices: 554624--554684 Score: 52
Period size: 6 Copynumber: 9.3 Consensus size: 6
554614 TAAATTAATA
*
554624 ATTTAT ATTATAT ATTTAT ACTTTATT ATATTAT AATTA- ATTTAAAT
1 ATTTAT ATT-TAT ATTTAT A-TTTA-T AT-TTAT ATTTAT ATTT--AT
554671 ATTTAT ATTTAT AT
1 ATTTAT ATTTAT AT
554685 AAATGATAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
5 3 0.07
6 20 0.43
7 14 0.30
8 9 0.20
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (6 bp):
ATTTAT
Found at i:554694 original size:34 final size:34
Alignment explanation
Indices: 554621--554718 Score: 98
Period size: 34 Copynumber: 2.9 Consensus size: 34
554611 ATCTAAATTA
* * *
554621 ATAATTTATATTATATATTTATACTTTAT-TATATT
1 ATAA-TTATATTAAATATTTATA-TTTATATAAATG
554656 ATAATTA-ATTTAAATATTTATATTTATATAAATG
1 ATAATTATA-TTAAATATTTATATTTATATAAATG
554690 ATAA-TATATT-AATAATTTATA-TTATATAA
1 ATAATTATATTAAAT-ATTTATATTTATATAA
554719 TTTTTTTAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
32 11 0.20
33 17 0.30
34 24 0.43
35 4 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (34 bp):
ATAATTATATTAAATATTTATATTTATATAAATG
Found at i:554715 original size:18 final size:18
Alignment explanation
Indices: 554617--554716 Score: 53
Period size: 18 Copynumber: 6.1 Consensus size: 18
554607 TATGATCTAA
554617 ATTAATAATTTATATTAT
1 ATTAATAATTTATATTAT
* *
554635 A-TATTTATACTT-TATTAT
1 ATTA-ATA-ATTTATATTAT
554653 ATT-ATAA-TTA-ATT-T
1 ATTAATAATTTATATTAT
554667 A--AAT-ATTTATATT-T
1 ATTAATAATTTATATTAT
* * *
554681 A-T-ATAAATGATAATAT
1 ATTAATAATTTATATTAT
554697 ATTAATAATTTATATTAT
1 ATTAATAATTTATATTAT
554715 AT
1 AT
554717 AATTTTTTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 24
0.65 0.10 0.26
Matches are distributed among these distances:
12 1 0.02
13 5 0.08
14 9 0.15
15 11 0.18
16 3 0.05
17 5 0.08
18 23 0.38
19 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
ATTAATAATTTATATTAT
Found at i:554720 original size:14 final size:14
Alignment explanation
Indices: 554617--554755 Score: 65
Period size: 14 Copynumber: 10.5 Consensus size: 14
554607 TATGATCTAA
554617 ATTA-ATAATTTAT
1 ATTATATAATTTAT
554630 ATTATAT-ATTTAT
1 ATTATATAATTTAT
*
554643 ACT-T-T-A-TTAT
1 ATTATATAATTTAT
554653 ATTATAATTAATTTAAAT
1 ATTAT-A-TAATTT--AT
554671 ATT-TAT-ATTTAT
1 ATTATATAATTTAT
*
554683 ATAAATGATAA--TAT
1 AT-TAT-ATAATTTAT
554697 ATTA-ATAATTTAT
1 ATTATATAATTTAT
554710 ATTATATAATTT-T
1 ATTATATAATTTAT
* *
554723 TTTAATATCATTTAT
1 ATT-ATATAATTTAT
*
554738 -TTA-ATATTTTAT
1 ATTATATAATTTAT
554750 A-TATAT
1 ATTATAT
554756 TATATTTACA
Statistics
Matches: 98, Mismatches: 8, Indels: 40
0.67 0.05 0.27
Matches are distributed among these distances:
10 6 0.06
11 7 0.07
12 14 0.14
13 26 0.27
14 30 0.31
15 5 0.05
16 4 0.04
17 1 0.01
18 5 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (14 bp):
ATTATATAATTTAT
Found at i:555805 original size:3 final size:3
Alignment explanation
Indices: 555799--555841 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
555789 TTATATCATC
555799 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
555842 GAATCAATAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:557067 original size:28 final size:29
Alignment explanation
Indices: 557035--557089 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
557025 GCATGGTATA
557035 TTACGCTA-GTTATTTTATGAGTTTGACT
1 TTACGCTATGTTATTTTATGAGTTTGACT
* *
557063 TTACGGTATTTTATTTTATGAGTTTGA
1 TTACGCTATGTTATTTTATGAGTTTGA
557090 TTTTTTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.22, C:0.07, G:0.18, T:0.53
Consensus pattern (29 bp):
TTACGCTATGTTATTTTATGAGTTTGACT
Done.