Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold439
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: 1094049
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 4 of 7
Found at i:496332 original size:79 final size:79
Alignment explanation
Indices: 496223--496370 Score: 199
Period size: 79 Copynumber: 1.9 Consensus size: 79
496213 TTCATTTAAA
* * * * *
496223 AATAAAATAAATTTAATTAAATTTATTTAATTAAGTTAAATTAAATTTATTTATCAAACAAAAAA
1 AATAAAATAAATTTAATCAAATTAACTTAATTAAATTAAATTAAATCTATTTATCAAACAAAAAA
496288 TAAATTTAATTCGT
66 TAAATTTAATTCGT
* * **
496302 AATAAAATTAAA-TTACTCAAATTAACTTAATTAAATTAAATTAAATCTATTTATCTATTAAAAA
1 AATAAAA-TAAATTTAATCAAATTAACTTAATTAAATTAAATTAAATCTATTTATCAAACAAAAA
496366 ATAAA
65 ATAAA
496371 CTCGATTTCC
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
79 55 0.93
80 4 0.07
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (79 bp):
AATAAAATAAATTTAATCAAATTAACTTAATTAAATTAAATTAAATCTATTTATCAAACAAAAAA
TAAATTTAATTCGT
Found at i:496493 original size:16 final size:15
Alignment explanation
Indices: 496472--496516 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
496462 TTAAAAATTT
496472 TAATTAAATTTATAAA
1 TAATTAAATTTA-AAA
496488 TAATTAAATATTAAAA
1 TAATTAAAT-TTAAAA
*
496504 TACTTAAATTTAA
1 TAATTAAATTTAA
496517 TTCGTAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 20 0.74
17 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATTAAATTTAAAA
Found at i:500705 original size:19 final size:19
Alignment explanation
Indices: 500683--500722 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
500673 TTTAATTCAT
500683 TTTAA-TTAATATTATTTAA
1 TTTAATTTAATATTA-TTAA
*
500702 TTTAATTTGATATTATTAA
1 TTTAATTTAATATTATTAA
500721 TT
1 TT
500723 CGAATGAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTAATTTAATATTATTAA
Found at i:500795 original size:17 final size:17
Alignment explanation
Indices: 500769--500812 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
500759 TGGTTCATAG
* * *
500769 TAAAATTAATTTAAATT
1 TAAAAATAATTCAAATA
500786 TAAAAATAATTCAAATA
1 TAAAAATAATTCAAATA
500803 TAAATAATAA
1 TAAA-AATAA
500813 AAAATAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATAATTCAAATA
Found at i:501474 original size:13 final size:11
Alignment explanation
Indices: 501441--501557 Score: 75
Period size: 11 Copynumber: 10.5 Consensus size: 11
501431 ATATTATTGT
501441 TTATATTTTAA
1 TTATATTTTAA
501452 TTATATTTTAA
1 TTATATTTTAA
501463 TTATAAATTTTAA
1 TTAT--ATTTTAA
* *
501476 -AATA-TTAAA
1 TTATATTTTAA
* *
501485 ATATTATTATT-T
1 TTA-TATT-TTAA
501497 TTATATTTT-A
1 TTATATTTTAA
*
501507 TAATATTTTATA
1 TTATATTTTA-A
*
501519 TTATATATTAA
1 TTATATTTTAA
501530 TTAT-TTTTATA
1 TTATATTTTA-A
501541 TTATAATTTT-A
1 TTAT-ATTTTAA
501552 TTATAT
1 TTATAT
501558 AATTATGTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
9 4 0.05
10 18 0.21
11 36 0.43
12 14 0.17
13 12 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:501517 original size:17 final size:17
Alignment explanation
Indices: 501495--501557 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
501485 ATATTATTAT
501495 TTTTATATTTTATAATA
1 TTTTATATTTTATAATA
501512 TTTTATATTATATATTAATTA
1 TTTTATATT-T-TA-TAA-TA
* *
501533 TTTT-TATATTATAATT
1 TTTTATATTTTATAATA
501549 TTATTATAT
1 TT-TTATAT
501558 AATTATGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
16 3 0.08
17 14 0.37
18 6 0.16
19 3 0.08
20 6 0.16
21 6 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTATATTTTATAATA
Found at i:501960 original size:23 final size:24
Alignment explanation
Indices: 501934--501987 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
501924 AAATTATTCA
501934 TAATATTACTT-AAAAATAATATT
1 TAATATTACTTCAAAAATAATATT
* **
501957 TAATA-TATTTCAAATTTAATATT
1 TAATATTACTTCAAAAATAATATT
501980 TAATATTA
1 TAATATTA
501988 TTTTATTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 20 0.77
24 2 0.08
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATATTACTTCAAAAATAATATT
Found at i:502118 original size:3 final size:3
Alignment explanation
Indices: 502106--502156 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
502096 TATATTATTT
*
502106 ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
502155 AT
1 AT
502157 TTTATTTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:502370 original size:28 final size:27
Alignment explanation
Indices: 502312--502382 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
502302 TTTAATTTTT
* * *
502312 TAATAAATTTTTATATTTTATCATACT
1 TAATAAAATTTTATTTTTTATCATACA
*
502339 TAAATAAAATTTTATTTTTTAAT-TTACA
1 T-AATAAAATTTTATTTTTT-ATCATACA
502367 TAA-AAAATTTTATTTT
1 TAATAAAATTTTATTTT
502383 AAATAAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 13 0.34
27 3 0.08
28 20 0.53
29 2 0.05
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
TAATAAAATTTTATTTTTTATCATACA
Found at i:502885 original size:10 final size:10
Alignment explanation
Indices: 502870--502913 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
502860 TTTAAAATAA
502870 AAATAAAATT
1 AAATAAAATT
*
502880 AAATAAATTT
1 AAATAAAATT
* *
502890 TATTAAAATT
1 AAATAAAATT
*
502900 AAATAAAATA
1 AAATAAAATT
502910 AAAT
1 AAAT
502914 TTTAAATATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATAAAATT
Found at i:502898 original size:25 final size:26
Alignment explanation
Indices: 502869--502917 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
502859 TTTTAAAATA
*
502869 AAAATAAAATTAAAT-AAATTTTATT
1 AAAATAAAATAAAATAAAATTTTATT
*
502894 AAAATTAAATAAAATAAAATTTTA
1 AAAATAAAATAAAATAAAATTTTA
502918 AATATTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAATAAAATAAAATAAAATTTTATT
Found at i:502902 original size:26 final size:26
Alignment explanation
Indices: 502867--502917 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
502857 TTTTTTAAAA
*
502867 TAAAAATAAAATTAAAT-AAATTTTAT
1 TAAAAAT-AAATAAAATAAAATTTTAT
*
502893 TAAAATTAAATAAAATAAAATTTTA
1 TAAAAATAAATAAAATAAAATTTTA
502918 AATATTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAAAATAAATAAAATAAAATTTTAT
Found at i:502904 original size:30 final size:30
Alignment explanation
Indices: 502856--502913 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
502846 TAATTTATTT
*
502856 ATTTTTTAAAATAAAAATAAAATTAAATAA
1 ATTTTTTAAAATAAAAATAAAATAAAATAA
*
502886 ATTTTATTAAAAT-TAAATAAAATAAAAT
1 ATTTT-TTAAAATAAAAATAAAATAAAAT
502914 TTTAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
ATTTTTTAAAATAAAAATAAAATAAAATAA
Found at i:502931 original size:35 final size:35
Alignment explanation
Indices: 502864--502931 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
502854 TTATTTTTTA
502864 AAATAAAAATAAAATTAAATAAATTTTATTAAAATT
1 AAATAAAAATAAAATT-AATAAATTTTATTAAAATT
*
502900 AAAT-AAAATAAAATT-TTAAATATTTAGTTAAA
1 AAATAAAAATAAAATTAATAAAT-TTTA-TTAAA
502932 TATTTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 5 0.17
34 4 0.14
35 16 0.55
36 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (35 bp):
AAATAAAAATAAAATTAATAAATTTTATTAAAATT
Found at i:505336 original size:20 final size:20
Alignment explanation
Indices: 505291--505400 Score: 87
Period size: 20 Copynumber: 5.5 Consensus size: 20
505281 ATATTTTCAA
* * *
505291 ATCGATACATTGATGTAATAT
1 ATCGATACATT-ATATATTGT
505312 ATCGATACATTATATATTGT
1 ATCGATACATTATATATTGT
* * *
505332 ATCGATACATTGTGTATTAT
1 ATCGATACATTATATATTGT
* **
505352 ATTGATACATTGCATATTGT
1 ATCGATACATTATATATTGT
* *
505372 ATCGATATATTTTAGTA-TGT
1 ATCGATACATTATA-TATTGT
*
505392 ATCAATACA
1 ATCGATACA
505401 AATGAGGATT
Statistics
Matches: 72, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
20 59 0.82
21 13 0.18
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.43
Consensus pattern (20 bp):
ATCGATACATTATATATTGT
Found at i:505361 original size:40 final size:41
Alignment explanation
Indices: 505291--505378 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 41
505281 ATATTTTCAA
*
505291 ATCGATACATTGATGTAATATATCGATACATTATATATTGT
1 ATCGATACATTGATGTAATATATCGATACATTACATATTGT
* * *
505332 ATCGATACATTG-TGTATTATATTGATACATTGCATATTGT
1 ATCGATACATTGATGTAATATATCGATACATTACATATTGT
505372 ATCGATA
1 ATCGATA
505379 TATTTTAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 31 0.72
41 12 0.28
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (41 bp):
ATCGATACATTGATGTAATATATCGATACATTACATATTGT
Found at i:510634 original size:11 final size:11
Alignment explanation
Indices: 510618--510660 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
510608 TGATAATTTA
510618 TATATTTATAT
1 TATATTTATAT
510629 TATATTTATAT
1 TATATTTATAT
*
510640 TA-ATCTTTTA-
1 TATAT-TTATAT
510650 TATATTTATAT
1 TATATTTATAT
510661 AAATTTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:511273 original size:14 final size:14
Alignment explanation
Indices: 511254--511283 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
511244 AAGCCTGTAC
511254 ATGATGCGATATCG
1 ATGATGCGATATCG
511268 ATGATGCGATATCG
1 ATGATGCGATATCG
511282 AT
1 AT
511284 TTTATTAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (14 bp):
ATGATGCGATATCG
Found at i:511315 original size:7 final size:7
Alignment explanation
Indices: 511303--511355 Score: 54
Period size: 7 Copynumber: 7.1 Consensus size: 7
511293 TGTTAAATAA
511303 ATTTTTT
1 ATTTTTT
511310 ATTTTTT
1 ATTTTTT
*
511317 ATTTTTA
1 ATTTTTT
511324 ATTTTTT
1 ATTTTTT
511331 -TTAATTATT
1 ATT--TT-TT
511340 ATTTTTTT
1 A-TTTTTT
511348 ATTTTTT
1 ATTTTTT
511355 A
1 A
511356 AATTATATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 2 0.05
7 26 0.67
8 5 0.13
9 4 0.10
11 2 0.05
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:511332 original size:16 final size:14
Alignment explanation
Indices: 511305--511353 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
511295 TTAAATAAAT
511305 TTTTTA-TTTTTTA
1 TTTTTATTTTTTTA
511318 TTTTTAATTTTTTTTAA
1 TTTTT-A-TTTTTTT-A
*
511335 TTATTATTTTTTTA
1 TTTTTATTTTTTTA
511349 TTTTT
1 TTTTT
511354 TAAATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 5 0.17
14 6 0.20
15 7 0.23
16 7 0.23
17 5 0.17
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:511338 original size:20 final size:20
Alignment explanation
Indices: 511315--511381 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
511305 TTTTTATTTT
511315 TTATTTTTAATTTTTTTTAA
1 TTATTTTTAATTTTTTTTAA
**
511335 TTATTATTTTTTTATTTTTTAAA
1 TTATT-TTTAATT-TTTTTT-AA
* * *
511358 TTA-TATTAATATTTTTAAA
1 TTATTTTTAATTTTTTTTAA
511377 TTATT
1 TTATT
511382 AAATTTATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
19 5 0.14
20 11 0.31
21 8 0.22
22 7 0.19
23 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTTTAATTTTTTTTAA
Found at i:511372 original size:26 final size:25
Alignment explanation
Indices: 511335--511397 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 25
511325 TTTTTTTTAA
* * *
511335 TTATT-ATTTTTTTATTTTTTAAAT
1 TTATTAATTTTTTAAATTATTAAAT
511359 TATATTAATATTTTTAAATTATTAAAT
1 T-TATTAAT-TTTTTAAATTATTAAAT
511386 TTATTAATTTTT
1 TTATTAATTTTT
511398 AATTCAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 1 0.03
25 8 0.24
26 9 0.27
27 15 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTATTAATTTTTTAAATTATTAAAT
Found at i:511379 original size:42 final size:38
Alignment explanation
Indices: 511304--511382 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 38
511294 GTTAAATAAA
* *
511304 TTTTTTATTTTTTATTTTTAATTTTTTTTAATTATTAT
1 TTTTTTATTTTTTATTTTTAATATTTTTAAATTATTAT
511342 TTTTTTATTTTTTAAATTATATTAATATTTTTAAATTATTA
1 TTTTTTATTTTTT--ATT-T-TTAATATTTTTAAATTATTA
511383 AATTTATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 13 0.37
40 3 0.09
41 1 0.03
42 18 0.51
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (38 bp):
TTTTTTATTTTTTATTTTTAATATTTTTAAATTATTAT
Found at i:511390 original size:20 final size:21
Alignment explanation
Indices: 511345--511390 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
511335 TTATTATTTT
*
511345 TTTATTTTTTAAATTATATTAA
1 TTTA-TTTTTAAATTATATAAA
511367 --TATTTTTAAATTAT-TAAA
1 TTTATTTTTAAATTATATAAA
511385 TTTATT
1 TTTATT
511391 AATTTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 3 0.14
19 12 0.57
20 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATTTTTAAATTATATAAA
Found at i:511873 original size:14 final size:15
Alignment explanation
Indices: 511840--511872 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
511830 TTTATTATTC
511840 TTTTCTCTTTTTCCA
1 TTTTCTCTTTTTCCA
511855 TTTTCT-TTTTTCTCA
1 TTTTCTCTTTTTC-CA
511870 TTT
1 TTT
511873 CACCATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTCTCTTTTTCCA
Found at i:517617 original size:11 final size:11
Alignment explanation
Indices: 517579--517763 Score: 57
Period size: 11 Copynumber: 16.4 Consensus size: 11
517569 TGAAATATTG
*
517579 ATATTTAAATAT
1 ATATTTTAAT-T
517591 ATATTTT--TT
1 ATATTTTAATT
517600 AATATTTTAATT
1 -ATATTTTAATT
517612 ATA-TTTAA-T
1 ATATTTTAATT
*
517621 ATATTATATATT
1 ATATTTTA-ATT
*
517633 A-ATTTTAA-G
1 ATATTTTAATT
517642 ATA--TTAATT
1 ATATTTTAATT
**
517651 ATTTATTTTATAAA
1 A--TATTTTA-ATT
517665 ATATATTTATATT
1 ATAT-TTTA-ATT
*
517678 AAATATATTATATTT
1 --ATAT-TT-TAATT
*
517693 ATATTATTATTTT
1 ATATT-TTA-ATT
*
517706 ATATTGT-ATT
1 ATATTTTAATT
*
517716 ATATTTTTATT
1 ATATTTTAATT
*
517727 ATATATTAATT
1 ATATTTTAATT
517738 AT-TTTTATATT
1 ATATTTTA-ATT
* *
517749 TTATTTTTATT
1 ATATTTTAATT
517760 ATAT
1 ATAT
517764 AATTATATCA
Statistics
Matches: 132, Mismatches: 19, Indels: 45
0.67 0.10 0.23
Matches are distributed among these distances:
8 4 0.03
9 7 0.05
10 30 0.23
11 35 0.27
12 21 0.16
13 22 0.17
14 2 0.02
15 9 0.07
16 2 0.02
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (11 bp):
ATATTTTAATT
Found at i:517635 original size:33 final size:32
Alignment explanation
Indices: 517579--517752 Score: 96
Period size: 33 Copynumber: 5.5 Consensus size: 32
517569 TGAAATATTG
* *
517579 ATATTTAA-ATATATATTTTTTAATATTTTAATT
1 ATATTTAATATAT-TATATATT-ATATTTTAATT
*
517612 ATATTTAATATATTATATATTA-ATTTTAA-G
1 ATATTTAATATATTATATATTATATTTTAATT
* * * *
517642 ATA-TTAAT-TATT-TATTTTATAAAATATATTT
1 ATATTTAATATATTATATATTAT--ATTTTAATT
* *
517673 ATATTAAATATATTATAT-TTATATTATTATTTT
1 ATATTTAATATATTATATATTATATT-TTA-ATT
* * *
517706 ATATTGTATTATATT-TTTATTATATATTAATT
1 ATATT-TAATATATTATATATTATATTTTAATT
* *
517738 AT-TTTTATATTTTAT
1 ATATTTAATATATTAT
517753 TTTTATTATA
Statistics
Matches: 109, Mismatches: 19, Indels: 28
0.70 0.12 0.18
Matches are distributed among these distances:
27 6 0.06
28 4 0.04
29 5 0.05
30 13 0.12
31 15 0.14
32 11 0.10
33 35 0.32
34 20 0.18
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (32 bp):
ATATTTAATATATTATATATTATATTTTAATT
Found at i:517683 original size:15 final size:15
Alignment explanation
Indices: 517654--517691 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
517644 ATTAATTATT
*
517654 TATTT-TATAAAATA
1 TATTTATATTAAATA
517668 TATTTATATTAAATA
1 TATTTATATTAAATA
517683 TA-TTATATT
1 TATTTATATT
517692 TATATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTATATTAAATA
Found at i:517703 original size:46 final size:46
Alignment explanation
Indices: 517618--517708 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 46
517608 AATTATATTT
* *
517618 AATATATTATATATTAATTTTAAGATATTAATTATTTATTTTATAA
1 AATATATTATATATTAAATATAAGATATTAATTATTTATTTTATAA
**
517664 AATATATT-TATATTAAATATATTATATTTATATTA-TTATTTTATA
1 AATATATTATATATTAAATATAAGATA-TTA-ATTATTTATTTTATA
517709 TTGTATTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
45 14 0.36
46 21 0.54
47 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (46 bp):
AATATATTATATATTAAATATAAGATATTAATTATTTATTTTATAA
Found at i:517716 original size:38 final size:38
Alignment explanation
Indices: 517680--517771 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 38
517670 TTTATATTAA
517680 ATATATTATATT-TATATT-ATTA-TTTTATATTGTATT
1 ATAT-TTATATTATATATTAATTATTTTTATATTGTATT
* *
517716 ATATTTTTATTATATATTAATTATTTTTATATTTTATTT
1 ATATTTATATTATATATTAATTATTTTTATATTGTA-TT
*
517755 TTATTATATAATTATAT
1 ATATT-TAT-ATTATAT
517772 CATATTTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
35 6 0.13
36 10 0.22
37 4 0.09
38 11 0.24
39 6 0.13
40 2 0.04
41 7 0.15
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (38 bp):
ATATTTATATTATATATTAATTATTTTTATATTGTATT
Found at i:517717 original size:18 final size:18
Alignment explanation
Indices: 517666--517769 Score: 78
Period size: 17 Copynumber: 5.9 Consensus size: 18
517656 TTTTATAAAA
* *
517666 TATATTTATATTAAATATAT
1 TATA-TTATATT-ATTATTT
517686 TATATTTATATTATTATTT
1 TATA-TTATATTATTATTT
*
517705 TATATTGTATTA-TATTT
1 TATATTATATTATTATTT
517722 T-TATTATA-TATTAATTAT
1 TATATTATATTATT-ATT-T
517740 T-T-TTATATT-TTATTT
1 TATATTATATTATTATTT
*
517755 T-TATTATATAATTAT
1 TATATTATATTATTAT
517770 ATCATATTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
15 5 0.07
16 16 0.22
17 20 0.27
18 11 0.15
19 9 0.12
20 12 0.16
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (18 bp):
TATATTATATTATTATTT
Found at i:517741 original size:49 final size:47
Alignment explanation
Indices: 517666--517759 Score: 111
Period size: 49 Copynumber: 1.9 Consensus size: 47
517656 TTTTATAAAA
517666 TATATTTATATTAAATATATTATA-TTTATATTATTATTTTATATTGTAT
1 TATATTTATATT-AATATATTATATTTTATATT-TTATTTT-TATTGTAT
*
517715 TATATTTTTATT-ATATATTAATTATTTTTATATTTTATTTTTATT
1 TATATTTATATTAATATATT-A-TA-TTTTATATTTTATTTTTATT
517760 ATATAATTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
47 7 0.17
48 1 0.03
49 17 0.43
50 7 0.17
51 8 0.20
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (47 bp):
TATATTTATATTAATATATTATATTTTATATTTTATTTTTATTGTAT
Found at i:517760 original size:22 final size:22
Alignment explanation
Indices: 517691--517763 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
517681 TATATTATAT
* *
517691 TTATATTATTATTTTATATTGTA
1 TTATATTTTTATTTTAT-TTTTA
* * *
517714 TTATATTTTTATTATATATTAA
1 TTATATTTTTATTTTATTTTTA
517736 TTAT-TTTTATATTTTATTTTTA
1 TTATATTTT-TATTTTATTTTTA
517758 TTATAT
1 TTATAT
517764 AATTATATCA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 4 0.10
22 20 0.50
23 16 0.40
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (22 bp):
TTATATTTTTATTTTATTTTTA
Found at i:526288 original size:14 final size:14
Alignment explanation
Indices: 526269--526338 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
526259 CTATTTTTTA
526269 ATTATATAATATAT
1 ATTATATAATATAT
*
526283 ATTATATAATTTAT
1 ATTATATAATATAT
*
526297 ATAATATAA-A-A-
1 ATTATATAATATAT
526308 A--ATA-AATATAT
1 ATTATATAATATAT
526319 A-TATATAAATATAT
1 ATTATAT-AATATAT
526333 ATTATA
1 ATTATA
526339 ACGTAAACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
8 2 0.04
9 4 0.09
10 1 0.02
11 2 0.04
12 4 0.09
14 29 0.63
15 4 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTATATAATATAT
Found at i:526430 original size:37 final size:35
Alignment explanation
Indices: 526342--526434 Score: 96
Period size: 40 Copynumber: 2.5 Consensus size: 35
526332 TATTATAACG
* **
526342 TAAACATTAAAAAATATATTAAATTATTTATATTT
1 TAAAAATTAAAAAATATATTAAATTAAGTATATTT
* *
526377 TAAAACTTAAATAAAAATTATTAAATTAAAAGTATATATT
1 TAAAAATTAAA-AAATA-TATTAAATT--AAGTATAT-TT
526417 TAAAAATTAAAAAATATA
1 TAAAAATTAAAAAATATA
526435 ATATTAACAT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
35 9 0.20
36 4 0.09
37 9 0.20
38 2 0.04
39 10 0.22
40 12 0.26
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (35 bp):
TAAAAATTAAAAAATATATTAAATTAAGTATATTT
Found at i:527163 original size:16 final size:16
Alignment explanation
Indices: 527144--527179 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
527134 AATTTTAAAA
527144 TATATTCATATTTTAT
1 TATATTCATATTTTAT
**
527160 TATATTTTTATTTTAT
1 TATATTCATATTTTAT
527176 TATA
1 TATA
527180 AGTATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTCATATTTTAT
Found at i:529248 original size:3 final size:3
Alignment explanation
Indices: 529240--529275 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
529230 TAAACAGAAA
529240 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
529276 TGAGATGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:529602 original size:3 final size:3
Alignment explanation
Indices: 529596--529624 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
529586 GTAGATGATG
529596 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
529625 TTGAGAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:532035 original size:19 final size:20
Alignment explanation
Indices: 531995--532037 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
531985 ATATGTTTTG
531995 CATTGTATCGATACATTGCT
1 CATTGTATCGATACATTGCT
532015 CATTGTATCGATACA-TGCT
1 CATTGTATCGATACATTGCT
532034 CATT
1 CATT
532038 TTTCCAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (20 bp):
CATTGTATCGATACATTGCT
Found at i:534666 original size:51 final size:51
Alignment explanation
Indices: 534499--534667 Score: 230
Period size: 51 Copynumber: 3.3 Consensus size: 51
534489 TTATTTTTGA
* * *
534499 GGGGATACTCCAATCCCGATTTTATTTCTAAAATACAAATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTCATAATC
* * * * *
534550 GGGGATACTTCAACTCTGATTTTATTTCCAAAACACTAATTTCTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTCATAATC
* *
534601 GGGGATACTCCAACCCCGATTTTATTTTTAAAACACTAATTTTTTATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTCATAATC
**
534652 AAGGATACTCCAACCC
1 GGGGATACTCCAACCC
534668 TGTTATTTTT
Statistics
Matches: 101, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 101 1.00
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.36
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTCATAATC
Found at i:535997 original size:110 final size:109
Alignment explanation
Indices: 535842--536279 Score: 508
Period size: 111 Copynumber: 4.0 Consensus size: 109
535832 GTAATTTACA
* * * * *
535842 CAAAAAATA-AATTA-CCTTACATAAAGGGCGTTCGTACGCCACTTTATGACTCTAGACGACGAC
1 CAAAAAATAGAATTATCC-TATATAAAAGGCATTCGTACGCCGCTTTATGACTCTAGACGATGAC
* *
535905 CTATTTCGAGGCCAATCTTTTGGTGCCCGAATTTATGTCATTAATG
65 CTATTTCG-GGCCAATCTTTTGGTGCCCGAATTTACGTAATTAATG
* * * *
535951 CAAAAAATAGAATTATCCTATATAAAGGGCATTCGTACACCGCTTTATTACTCTAGATGATGACC
1 CAAAAAATAGAATTATCCTATATAAAAGGCATTCGTACGCCGCTTTATGACTCTAGACGATGACC
*
536016 TATTTCGGGACCAATCTTTTGGTGCCCGAATTTA-GTAATTAAAG
66 TATTTCGGG-CCAATCTTTTGGTGCCCGAATTTACGTAATTAATG
* * **
536060 CAAAAAA-CGAATTATCCTATATAAAAGGCATTCGTATGCCGCTTTATGACTCTAGACGATGATT
1 CAAAAAATAGAATTATCCTATATAAAAGGCATTCGTACGCCGCTTTATGACTCTAGACGATGACC
* *
536124 TATTTCGGGGCTAATCTCTTGGTG-CCGAATATTACGTAATTAATG
66 TATTTC-GGGCCAATCTTTTGGTGCCCGAAT-TTACGTAATTAATG
* * ** * * *
536169 TAAAAAAAATGAATTATCCTATATAAAAGGTGTTCGTACGCCGTTTTATAACTCTAGACGATGAG
1 CAAAAAATA-GAATTATCCTATATAAAAGGCATTCGTACGCCGCTTTATGACTCTAGACGATGAC
* ** * *
536234 TTATTTCGGAATCAATCTTTTGGTGTCCGAATCTACGTAATTAATG
65 CTATTTCGG-GCCAATCTTTTGGTGCCCGAATTTACGTAATTAATG
536280 TAATTAAATT
Statistics
Matches: 286, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
107 6 0.02
108 70 0.24
109 44 0.15
110 78 0.27
111 82 0.29
112 6 0.02
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (109 bp):
CAAAAAATAGAATTATCCTATATAAAAGGCATTCGTACGCCGCTTTATGACTCTAGACGATGACC
TATTTCGGGCCAATCTTTTGGTGCCCGAATTTACGTAATTAATG
Found at i:536241 original size:219 final size:219
Alignment explanation
Indices: 535862--536277 Score: 557
Period size: 218 Copynumber: 1.9 Consensus size: 219
535852 ATTACCTTAC
* * *
535862 ATAAAGGGCGTTCGTACGCCACTTTATGACTCTAGACGACGACCTATTTCGAGGCCAATCTTTTG
1 ATAAAAGGCATTCGTACGCCACTTTATGACTCTAGACGACGACCTATTTCGAGGCCAATCTCTTG
* * * *
535927 GTGCCCGAATTTATGTCATTAATGCAAAAAATAGAATTATCCTATATAAAGGGCATTCGTACACC
66 GTGCCCGAATTTACGTAATTAATGCAAAAAAAAGAATTATCCTATATAAAAGGCATTCGTACACC
* * * *
535992 GCTTTATTACTCTAGATGATGACCTATTTCGGGACCAATCTTTTGGTGCCCGAATTTA-GTAATT
131 GCTTTATAACTCTAGACGATGACCTATTTCGGAACCAATCTTTTGGTGCCCGAATCTACGTAATT
536056 AAAGCAAAAAACGAATTATCCTAT
196 AAAGCAAAAAACGAATTATCCTAT
* * * ** * *
536080 ATAAAAGGCATTCGTATGCCGCTTTATGACTCTAGACGATGATTTATTTCGGGGCTAATCTCTTG
1 ATAAAAGGCATTCGTACGCCACTTTATGACTCTAGACGACGACCTATTTCGAGGCCAATCTCTTG
* ** *
536145 GTG-CCGAATATTACGTAATTAATGTAAAAAAAATGAATTATCCTATATAAAAGGTGTTCGTACG
66 GTGCCCGAAT-TTACGTAATTAATGCAAAAAAAA-GAATTATCCTATATAAAAGGCATTCGTACA
* ** * *
536209 CCGTTTTATAACTCTAGACGATGAGTTATTTCGGAATCAATCTTTTGGTGTCCGAATCTACGTAA
129 CCGCTTTATAACTCTAGACGATGACCTATTTCGGAACCAATCTTTTGGTGCCCGAATCTACGTAA
536274 TTAA
194 TTAA
536278 TGTAATTAAA
Statistics
Matches: 168, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
217 6 0.04
218 77 0.46
219 77 0.46
220 8 0.05
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (219 bp):
ATAAAAGGCATTCGTACGCCACTTTATGACTCTAGACGACGACCTATTTCGAGGCCAATCTCTTG
GTGCCCGAATTTACGTAATTAATGCAAAAAAAAGAATTATCCTATATAAAAGGCATTCGTACACC
GCTTTATAACTCTAGACGATGACCTATTTCGGAACCAATCTTTTGGTGCCCGAATCTACGTAATT
AAAGCAAAAAACGAATTATCCTAT
Found at i:536368 original size:17 final size:16
Alignment explanation
Indices: 536343--536394 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
536333 ACTCATTAAT
536343 AAATAAATACGTAAAAA
1 AAATAAATAC-TAAAAA
*
536360 AAATTAATATCTAAAAA
1 AAATAAATA-CTAAAAA
*
536377 TAATAAATACTAATAAA
1 AAATAAATACTAA-AAA
536394 A
1 A
536395 TTTTTTGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 4 0.14
17 24 0.83
18 1 0.03
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (16 bp):
AAATAAATACTAAAAA
Found at i:538012 original size:28 final size:28
Alignment explanation
Indices: 537975--538101 Score: 114
Period size: 28 Copynumber: 4.5 Consensus size: 28
537965 TACCAGCTAG
* * *
537975 TGTGGACTTTGATTTAGATGCTAACTAG
1 TGTGGGCTTTGACTTAGATGCTAACTAA
* * *
538003 TGTGGGCTTTAACTTAGGTG-TCAACGAA
1 TGTGGGCTTTGACTTAGATGCT-AACTAA
* * *
538031 TGTGGGATTAGACTTATG-TGCTAACGAA
1 TGTGGGCTTTGACTTA-GATGCTAACTAA
* *
538059 TGTGGGCTTTGACTTAGATACCAACTAA
1 TGTGGGCTTTGACTTAGATGCTAACTAA
*
538087 TATGGGCTTTGACTT
1 TGTGGGCTTTGACTT
538102 GTGTGTCAGT
Statistics
Matches: 80, Mismatches: 15, Indels: 8
0.78 0.15 0.08
Matches are distributed among these distances:
27 2 0.03
28 76 0.95
29 2 0.03
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.35
Consensus pattern (28 bp):
TGTGGGCTTTGACTTAGATGCTAACTAA
Found at i:538101 original size:56 final size:56
Alignment explanation
Indices: 537993--538106 Score: 129
Period size: 56 Copynumber: 2.0 Consensus size: 56
537983 TTGATTTAGA
* * * ** *
537993 TGCTAACTAGTGTGGGCTTTAACTTAGGTGTCAACGAATGTGGGATTAGACTTATG
1 TGCTAACGAATGTGGGCTTTAACTTAGATACCAACGAATATGGGATTAGACTTATG
* * * * *
538049 TGCTAACGAATGTGGGCTTTGACTTAGATACCAACTAATATGGGCTTTGACTTGTG
1 TGCTAACGAATGTGGGCTTTAACTTAGATACCAACGAATATGGGATTAGACTTATG
538105 TG
1 TG
538107 TCAGTGAATG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (56 bp):
TGCTAACGAATGTGGGCTTTAACTTAGATACCAACGAATATGGGATTAGACTTATG
Found at i:538116 original size:84 final size:84
Alignment explanation
Indices: 537975--538186 Score: 232
Period size: 84 Copynumber: 2.5 Consensus size: 84
537965 TACCAGCTAG
* * * * * * *
537975 TGTGGACTTTGATTTAGATGCTAACTAGTGTGGGCTTTAACTTAG-GTGTCAACGAATGTGGGAT
1 TGTGGGCTTTGACTTAGATGCCAACTAATATGGGCTTTGACTT-GTGTGTCAACGAATGTAGGAT
* *
538039 TAGACTTATGTGCTAACGAA
65 TAGACTTATGGGCCAACGAA
* ** *
538059 TGTGGGCTTTGACTTAGATACCAACTAATATGGGCTTTGACTTGTGTGTCAGTGAATGTAGGCTT
1 TGTGGGCTTTGACTTAGATGCCAACTAATATGGGCTTTGACTTGTGTGTCAACGAATGTAGGATT
* * *
538124 AGGCTTGTGGGCCAACGAG
66 AGACTTATGGGCCAACGAA
* *
538143 TGTGGGTTTTGACTT--ATGCCAACAAATATGGGCTTTGACTTGTG
1 TGTGGGCTTTGACTTAGATGCCAACTAATATGGGCTTTGACTTGTG
538187 CCAACGAATG
Statistics
Matches: 108, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
82 27 0.25
83 1 0.01
84 80 0.74
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (84 bp):
TGTGGGCTTTGACTTAGATGCCAACTAATATGGGCTTTGACTTGTGTGTCAACGAATGTAGGATT
AGACTTATGGGCCAACGAA
Found at i:538174 original size:26 final size:26
Alignment explanation
Indices: 538145--538229 Score: 116
Period size: 26 Copynumber: 3.3 Consensus size: 26
538135 CCAACGAGTG
* *
538145 TGGGTTTTGACTTATGCCAACAAATA
1 TGGGCTTTGACTTGTGCCAACAAATA
* *
538171 TGGGCTTTGACTTGTGCCAACGAATG
1 TGGGCTTTGACTTGTGCCAACAAATA
* *
538197 TGGGCTTTGACTTGTGTCAACTAATA
1 TGGGCTTTGACTTGTGCCAACAAATA
538223 TGGGCTT
1 TGGGCTT
538230 CGTTTTAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.35
Consensus pattern (26 bp):
TGGGCTTTGACTTGTGCCAACAAATA
Found at i:551436 original size:110 final size:110
Alignment explanation
Indices: 551322--551725 Score: 476
Period size: 109 Copynumber: 3.7 Consensus size: 110
551312 GTTTGTATGT
* *
551322 CACTTTATGACTCTAGACGACGATCTATTTCGAGATCAATCTTTTGGTGCCCGAATTTACGTAAT
1 CACTTTATGACTCTAGACGATGATCTATTTCGAGATCAATCTTTTGATGCCCGAATTTACGTAAT
* *
551387 TAATGTAAAAAATAAAATTATCTTATATAAAAAGCG-TCTGTACGC
66 TAATGCAAAAAATAAAATTATCTTATATAAAAGGCGTTC-GTACGC
* * * * * *
551432 CACTTTATGACTCTAAATGATGACCTATTTCGAGA-CAAATCTTTTGGTGCCTGAATTTA-ATAA
1 CACTTTATGACTCTAGACGATGATCTATTTCGAGATC-AATCTTTTGATGCCCGAATTTACGTAA
* * *
551495 TTAATGCAAAAAAT-AAATTATCCTATATAAAGGGCGTTCATACGTC
65 TTAATGCAAAAAATAAAATTATCTTATATAAAAGGCGTTCGTACG-C
* * * ** * *
551541 CACTTTACGACTCTAGACGATGATTTATTTCGGGGCCAATCTCTTGATGCCCGAATATTAAGTAA
1 CACTTTATGACTCTAGACGATGATCTATTTCGAGATCAATCTTTTGATGCCCGAAT-TTACGTAA
*
551606 TTAATGCAAAAAAAATAAATTATCTTATATAAAAGGCGTTCGTACGC
65 TTAATGCAAAAAATA-AAATTATCTTATATAAAAGGCGTTCGTACGC
* * * * * *
551653 CGCTTTATAACTTTAGATGATAAGT-TATTTCGAGATCAATCTTTTGATGCCCGAATCTACGTAA
1 CACTTTATGACTCTAGACGATGA-TCTATTTCGAGATCAATCTTTTGATGCCCGAATTTACGTAA
551717 TTAATGCAA
65 TTAATGCAA
551726 TTAAATTCTA
Statistics
Matches: 247, Mismatches: 38, Indels: 17
0.82 0.13 0.06
Matches are distributed among these distances:
108 23 0.09
109 64 0.26
110 56 0.23
111 31 0.13
112 45 0.18
113 28 0.11
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (110 bp):
CACTTTATGACTCTAGACGATGATCTATTTCGAGATCAATCTTTTGATGCCCGAATTTACGTAAT
TAATGCAAAAAATAAAATTATCTTATATAAAAGGCGTTCGTACGC
Found at i:551817 original size:17 final size:16
Alignment explanation
Indices: 551797--551840 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
551787 AATAAATACG
551797 TAAAAAAAATTAATAT
1 TAAAAAAAATTAATAT
* *
551813 CTAAAAATAATAAATAT
1 -TAAAAAAAATTAATAT
*
551830 TAACAAAAATT
1 TAAAAAAAATT
551841 TTAATTATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAAAAATTAATAT
Found at i:553059 original size:16 final size:16
Alignment explanation
Indices: 553040--553070 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
553030 TTTTTTTGTA
*
553040 TTTTTGTATTTTTTAT
1 TTTTTATATTTTTTAT
553056 TTTTTATATTTTTTA
1 TTTTTATATTTTTTA
553071 ATTATTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTATATTTTTTAT
Found at i:553078 original size:24 final size:24
Alignment explanation
Indices: 553031--553078 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
553021 AGTGTTCACT
* *
553031 TTTTTTGTATTTTTGTATTTTTTA
1 TTTTTTATATTTTTGTATTATTTA
553055 TTTTTTATATTTTT-TAATTATTTA
1 TTTTTTATATTTTTGT-ATTATTTA
553079 ATTACTCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (24 bp):
TTTTTTATATTTTTGTATTATTTA
Found at i:553109 original size:15 final size:16
Alignment explanation
Indices: 553086--553126 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
553076 TTAATTACTC
*
553086 TTAATTAATTAAATT-
1 TTAAATAATTAAATTA
553101 TTAAATAA-TAAATTA
1 TTAAATAATTAAATTA
*
553116 TTCAATAATTA
1 TTAAATAATTA
553127 TTTTGACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 6 0.27
15 14 0.64
16 2 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAATAATTAAATTA
Found at i:553210 original size:10 final size:12
Alignment explanation
Indices: 553186--553234 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
553176 AAAAACTAAC
553186 TATATATTTATT
1 TATATATTTATT
553198 TATATA-TTA-T
1 TATATATTTATT
553208 TATATTATTTATAT
1 TATA-TATTTAT-T
553222 T-TATATTT-TT
1 TATATATTTATT
553232 TAT
1 TAT
553235 TTGAGATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
10 7 0.22
11 7 0.22
12 14 0.44
13 2 0.06
14 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATATATTTATT
Found at i:553215 original size:15 final size:15
Alignment explanation
Indices: 553186--553228 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
553176 AAAAACTAAC
553186 TATATATTTAT-TTA
1 TATATATTTATATTA
553200 TATAT-TATTATATTA
1 TATATAT-TTATATTA
*
553215 TTTATATTTATATT
1 TATATATTTATATT
553229 TTTTATTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 9 0.36
15 14 0.56
16 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATATTTATATTA
Found at i:553233 original size:15 final size:17
Alignment explanation
Indices: 553188--553234 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 17
553178 AAACTAACTA
553188 TATATTTATTTATATAT
1 TATATTTATTTATATAT
553205 TATTATATTATTTATAT-T
1 TA-TAT-TTATTTATATAT
553223 TATATTT-TTTAT
1 TATATTTATTTAT
553235 TTGAGATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.18
16 2 0.07
17 5 0.18
18 6 0.21
19 10 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATATTTATTTATATAT
Found at i:554416 original size:14 final size:15
Alignment explanation
Indices: 554390--554418 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
554380 TAATATAAAA
554390 TTTTATTTCAATTAT
1 TTTTATTTCAATTAT
554405 TTTTATTT-AATTAT
1 TTTTATTTCAATTAT
554419 GTCCTAAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATTTCAATTAT
Found at i:554870 original size:15 final size:15
Alignment explanation
Indices: 554852--554882 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
554842 TTTAGGTTGG
*
554852 ATCATTTTAGATTAA
1 ATCATTTGAGATTAA
554867 ATCATTTGAGATTAA
1 ATCATTTGAGATTAA
554882 A
1 A
554883 ATTTTCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (15 bp):
ATCATTTGAGATTAA
Found at i:554946 original size:16 final size:16
Alignment explanation
Indices: 554927--554962 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
554917 GATTTAGGTT
554927 ATTTTAAGTTCGAATC
1 ATTTTAAGTTCGAATC
* *
554943 ATTTTGAGTTCGAGTC
1 ATTTTAAGTTCGAATC
554959 ATTT
1 ATTT
554963 CGAGTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (16 bp):
ATTTTAAGTTCGAATC
Found at i:554967 original size:16 final size:16
Alignment explanation
Indices: 554933--554968 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
554923 GGTTATTTTA
*
554933 AGTTCGAATCATTTTG
1 AGTTCGAATCATTTCG
*
554949 AGTTCGAGTCATTTCG
1 AGTTCGAATCATTTCG
554965 AGTT
1 AGTT
554969 TAAATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (16 bp):
AGTTCGAATCATTTCG
Found at i:555814 original size:16 final size:16
Alignment explanation
Indices: 555795--555857 Score: 83
Period size: 16 Copynumber: 3.9 Consensus size: 16
555785 ATTGTTCGGG
555795 TCATTTTAAGTTCGAA
1 TCATTTTAAGTTCGAA
555811 TCATTTT-AGATTCGAA
1 TCATTTTAAG-TTCGAA
** *
555827 TCATTTCGAGTTCAAA
1 TCATTTTAAGTTCGAA
555843 TCATTTTAAGTTCGA
1 TCATTTTAAGTTCGA
555858 GTTATTTTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 2 0.05
16 36 0.90
17 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (16 bp):
TCATTTTAAGTTCGAA
Found at i:555876 original size:16 final size:16
Alignment explanation
Indices: 555857--555887 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
555847 TTTAAGTTCG
*
555857 AGTTATTTTGGATTTA
1 AGTTATTTGGGATTTA
555873 AGTTATTTGGGATTT
1 AGTTATTTGGGATTT
555888 CGGATCGATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (16 bp):
AGTTATTTGGGATTTA
Found at i:566336 original size:31 final size:30
Alignment explanation
Indices: 566298--566360 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
566288 TTAATTTATC
* *
566298 ATAATTTATATTAATATAAAATATTTTAAAT
1 ATAATTTATAATAATATAAAATA-TATAAAT
* *
566329 ATAATTTATAATATTATATAATATATAAAT
1 ATAATTTATAATAATATAAAATATATAAAT
566359 AT
1 AT
566361 GAAATAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
ATAATTTATAATAATATAAAATATATAAAT
Found at i:566591 original size:18 final size:17
Alignment explanation
Indices: 566570--566621 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
566560 ATTTAGTAAT
566570 TTATATTATTTTTATATA
1 TTATA-TATTTTTATATA
* *
566588 TTATAAATATTTAATATA
1 TTATATAT-TTTTATATA
566606 TTATATA-TTTTATATA
1 TTATATATTTTTATATA
566622 AATTTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 8 0.28
17 2 0.07
18 19 0.66
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATATATTTTTATATA
Found at i:566597 original size:9 final size:10
Alignment explanation
Indices: 566583--566651 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 10
566573 TATTATTTTT
566583 ATATATTATA
1 ATATATTATA
566593 A-ATATT-TA
1 ATATATTATA
566601 ATATATTAT-
1 ATATATTATA
*
566610 ATATTTTAT-
1 ATATATTATA
* *
566619 ATAAATTTTA
1 ATATATTATA
566629 ATATATTAATA
1 ATATATT-ATA
566640 ATTTATATTATA
1 A--TATATTATA
566652 TAAATTTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
8 3 0.06
9 24 0.51
10 8 0.17
11 3 0.06
12 3 0.06
13 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATATATTATA
Found at i:566610 original size:36 final size:37
Alignment explanation
Indices: 566566--566650 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 37
566556 GTAAATTTAG
*
566566 TAATTTATATTATTTT-TATATATTATAAATAT-TTAA
1 TAATTTATATTATTTTATATAAATT-TAAATATATTAA
*
566602 T-ATATTATA-TATTTTATATAAATTTTAATATATTAA
1 TAAT-TTATATTATTTTATATAAATTTAAATATATTAA
566638 TAATTTATATTAT
1 TAATTTATATTAT
566651 ATAAATTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
35 14 0.33
36 23 0.55
37 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (37 bp):
TAATTTATATTATTTTATATAAATTTAAATATATTAA
Found at i:566651 original size:32 final size:34
Alignment explanation
Indices: 566570--566684 Score: 105
Period size: 36 Copynumber: 3.4 Consensus size: 34
566560 ATTTAGTAAT
* * *
566570 TTATATTATTTTTATATATTATAAATATTTAATATA
1 TTATA-TATTTATATAAATT-TTAATATTTAATATA
566606 TTATATATTTTATATAAATTTTAATATATTAATA-A
1 TTATATA-TTTATATAAATTTTAATAT-TTAATATA
566641 TT-TATA-TTATATAAATTTTAATACATTT-ATATA
1 TTATATATTTATATAAATTTTAAT--ATTTAATATA
*
566674 TCA-ATATTTAT
1 TTATATATTTAT
566685 TTTTTATCGT
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
32 19 0.28
33 7 0.10
34 10 0.15
35 11 0.16
36 21 0.31
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (34 bp):
TTATATATTTATATAAATTTTAATATTTAATATA
Found at i:566682 original size:24 final size:23
Alignment explanation
Indices: 566627--566682 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
566617 ATATAAATTT
*
566627 TAATATATTAATAATTTATATTA
1 TAATATTTTAATAATTTATATTA
*
566650 TATAAATTTTAATACATTTATA-TA
1 TA-ATATTTTAATA-ATTTATATTA
566674 TCAATATTT
1 T-AATATTT
566683 ATTTTTTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 2 0.07
24 17 0.63
25 8 0.30
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATATTTTAATAATTTATATTA
Found at i:566740 original size:17 final size:18
Alignment explanation
Indices: 566718--566760 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
566708 TTATATTTTA
566718 ATTATTTTTTATAA-TAT
1 ATTATTTTTTATAAGTAT
566735 ATTATTTTTTATAAGTAT
1 ATTATTTTTTATAAGTAT
566753 ATATATTT
1 AT-TATTT
566761 GACTAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 14 0.58
18 5 0.21
19 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTATTTTTTATAAGTAT
Found at i:568129 original size:10 final size:10
Alignment explanation
Indices: 568116--568165 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
568106 CTAATATATA
568116 TTTTTATTATT
1 TTTTTATTA-T
568127 TTTTTATTAT
1 TTTTTATTAT
568137 TTTTTA-TAT
1 TTTTTATTAT
*
568146 TATATTA-TAT
1 T-TTTTATTAT
*
568156 TTTATATTAT
1 TTTTTATTAT
568166 ACTTTAATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 7 0.21
10 18 0.53
11 9 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:568132 original size:11 final size:11
Alignment explanation
Indices: 568116--568148 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
568106 CTAATATATA
568116 TTTTTATTATT
1 TTTTTATTATT
568127 TTTTTATTATT
1 TTTTTATTATT
568138 TTTTATATTAT
1 TTTT-TATTAT
568149 ATTATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:568151 original size:17 final size:17
Alignment explanation
Indices: 568131--568166 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
568121 ATTATTTTTT
*
568131 TATTATTTTTTATATTA
1 TATTATATTTTATATTA
568148 TATTATATTTTATATTA
1 TATTATATTTTATATTA
568165 TA
1 TA
568167 CTTTAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTATATTTTATATTA
Found at i:568166 original size:12 final size:12
Alignment explanation
Indices: 568112--568163 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
568102 TATACTAATA
568112 TATATTTT-TAT
1 TATATTTTATAT
*
568123 TAT-TTTTTTAT
1 TATATTTTATAT
*
568134 TATTTTTTATAT
1 TATATTTTATAT
* *
568146 TATATTATATTT
1 TATATTTTATAT
568158 TATATT
1 TATATT
568164 ATACTTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 4 0.11
11 9 0.26
12 22 0.63
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:574206 original size:18 final size:18
Alignment explanation
Indices: 574185--574220 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
574175 AAATTGAAGG
574185 AATAAAAA-ATAAGAAAAT
1 AATAAAAAGA-AAGAAAAT
574203 AATAAAAAGAAAGAAAAT
1 AATAAAAAGAAAGAAAAT
574221 GAATTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (18 bp):
AATAAAAAGAAAGAAAAT
Found at i:576604 original size:12 final size:12
Alignment explanation
Indices: 576587--576660 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
576577 AAAAATTGTT
576587 ATTTTAAATATA
1 ATTTTAAATATA
*
576599 ATTTTAAAAAT-
1 ATTTTAAATATA
* *
576610 A-TATAAATATTG
1 ATTTTAAATA-TA
576622 A-TTT-AATATA
1 ATTTTAAATATA
*
576632 ATATTTTAATAT-
1 AT-TTTAAATATA
576644 ATTTTAAATAATA
1 ATTTTAAAT-ATA
576657 ATTT
1 ATTT
576661 GAATGAGCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
10 8 0.16
11 12 0.24
12 20 0.41
13 9 0.18
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (12 bp):
ATTTTAAATATA
Found at i:577298 original size:2 final size:2
Alignment explanation
Indices: 577293--577322 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
577283 TATGTAGTCC
577293 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
577323 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:577327 original size:2 final size:2
Alignment explanation
Indices: 577322--577351 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
577312 TCTCTCTCTC
577322 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
577352 GATGCACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:580124 original size:16 final size:16
Alignment explanation
Indices: 580103--580138 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
580093 AAAGATACCG
*
580103 AAATAATTTTAATTTA
1 AAATAATTTGAATTTA
580119 AAATAATTTGAATTTA
1 AAATAATTTGAATTTA
580135 AAAT
1 AAAT
580139 GATGTTAAAA
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:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATAATTTGAATTTA
Found at i:583437 original size:32 final size:31
Alignment explanation
Indices: 583401--583494 Score: 91
Period size: 32 Copynumber: 3.0 Consensus size: 31
583391 AATTAGACAT
* *
583401 AATTACTCATAAGTTTGATAAATATTATATAA
1 AATTACTCATAAATTTGATAAATATTACA-AA
* * * *
583433 AATTATTCATAACTTTAATAAATATTACACA
1 AATTACTCATAAATTTGATAAATATTACAAA
* * *
583464 AATTACTTATAAAATTGATAATTATTA-AAA
1 AATTACTCATAAATTTGATAAATATTACAAA
583494 A
1 A
583495 GTTTTGACCT
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 3 0.06
31 22 0.44
32 25 0.50
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.39
Consensus pattern (31 bp):
AATTACTCATAAATTTGATAAATATTACAAA
Found at i:589650 original size:30 final size:29
Alignment explanation
Indices: 589598--589677 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 29
589588 TCGTATCTTT
589598 TTAATTTTAAATTAAATAAATTAAAATTA
1 TTAATTTTAAATTAAATAAATTAAAATTA
**
589627 TTAATTTTTTATTAAATTAAATTAAAA-TA
1 TTAATTTTAAATTAAA-TAAATTAAAATTA
**
589656 --AA-TTTAAATTCTATAAATTAAA
1 TTAATTTTAAATTAAATAAATTAAA
589678 TGAATTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
25 9 0.20
26 7 0.16
27 2 0.05
29 16 0.36
30 10 0.23
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
TTAATTTTAAATTAAATAAATTAAAATTA
Found at i:591179 original size:29 final size:29
Alignment explanation
Indices: 591124--591180 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
591114 TCATGAATGA
* * *
591124 AATATTTTAGTCTTTATATTATTAAATTT
1 AATATTTTAATCTTTAAATTATGAAATTT
591153 AATATTTTAATCTTATAAATT-TGAAATT
1 AATATTTTAATCTT-TAAATTATGAAATT
591181 ATAACACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (29 bp):
AATATTTTAATCTTTAAATTATGAAATTT
Found at i:591214 original size:20 final size:18
Alignment explanation
Indices: 591189--591237 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
591179 TTATAACACA
591189 TAAAAAATAGTTAATAGTAT
1 TAAAAAATAGTTAA-A-TAT
*
591209 TAAAAAATTATTTAAATAT
1 TAAAAAA-TAGTTAAATAT
591228 TAATAAAATA
1 TAA-AAAATA
591238 CTGATATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 8 0.31
20 12 0.46
21 6 0.23
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (18 bp):
TAAAAAATAGTTAAATAT
Found at i:591226 original size:22 final size:20
Alignment explanation
Indices: 591188--591235 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
591178 ATTATAACAC
591188 ATAAAAAATAGTTAATAGTA
1 ATAAAAAATAGTTAATAGTA
* * *
591208 TTAAAAAATTATTTAAATATTA
1 ATAAAAAA-TAGTT-AATAGTA
591230 ATAAAA
1 ATAAAA
591236 TACTGATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
ATAAAAAATAGTTAATAGTA
Found at i:591490 original size:29 final size:29
Alignment explanation
Indices: 591420--591483 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
591410 TATTTTTATT
*
591420 TATTATAATTTTAAAAATACAAAAATTAAAA
1 TATTA-AA-TTTAAAAATACAAAAACTAAAA
* * *
591451 TGTTAAATTTAAAAATATATAAACTAAAA
1 TATTAAATTTAAAAATACAAAAACTAAAA
591480 TATT
1 TATT
591484 TTATTTATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 22 0.79
30 2 0.07
31 4 0.14
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (29 bp):
TATTAAATTTAAAAATACAAAAACTAAAA
Found at i:592260 original size:19 final size:18
Alignment explanation
Indices: 592232--592273 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
592222 TAATATAATT
*
592232 TTTATTTAAAATTTAAAAA
1 TTTATCTAAAATTT-AAAA
*
592251 TTTATCTAAAATTTTAAA
1 TTTATCTAAAATTTAAAA
592269 TTTAT
1 TTTAT
592274 ATTATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTATCTAAAATTTAAAA
Found at i:593866 original size:24 final size:24
Alignment explanation
Indices: 593839--593892 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
593829 AAACTTTAAT
**
593839 ATTTTTTATTAAAATAAATTTTTA
1 ATTTTTTATTAAAATAAAAATTTA
* *
593863 A-TTTATATTTAAATAAAAATTTA
1 ATTTTTTATTAAAATAAAAATTTA
593886 ATTTTTT
1 ATTTTTT
593893 TATATTTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTTTATTAAAATAAAAATTTA
Found at i:594041 original size:26 final size:28
Alignment explanation
Indices: 593989--594048 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
593979 GATACAAATT
* * *
593989 AAATAATAAAATTTATTTTATATAATAA
1 AAATAATAAAATTTATCTTAAAAAATAA
594017 AAAT-ATAAAATTTA-CTTAAAAAAT-A
1 AAATAATAAAATTTATCTTAAAAAATAA
594042 AAATAAT
1 AAATAAT
594049 TTAACAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 5 0.18
26 9 0.32
27 10 0.36
28 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
AAATAATAAAATTTATCTTAAAAAATAA
Found at i:596735 original size:41 final size:40
Alignment explanation
Indices: 596673--596808 Score: 125
Period size: 41 Copynumber: 3.4 Consensus size: 40
596663 ATTTAATAGG
* * *
596673 TTCACTGT-AAAATGCTGCTAATAGGAAAAAATTAGCGGCA
1 TTCACAGTAAAAATGCTACTAATA-GAAAAAATTAGCGACA
* * *
596713 TTTACTA-TAAAAATGCCACTAATAAAAAAAATTTAGCGACA
1 TTCAC-AGTAAAAATGCTACTAATAGAAAAAA-TTAGCGACA
* * * *
596754 TTCACAGTAAAAACGTTACTAATAGAAAAATTTAGC-AGCG
1 TTCACAGTAAAAATGCTACTAATAGAAAAAATTAGCGA-CA
596794 TTCACAGTAAAAATG
1 TTCACAGTAAAAATG
596809 GCGCTAATAT
Statistics
Matches: 77, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
39 1 0.01
40 32 0.42
41 44 0.57
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.26
Consensus pattern (40 bp):
TTCACAGTAAAAATGCTACTAATAGAAAAAATTAGCGACA
Found at i:596783 original size:40 final size:40
Alignment explanation
Indices: 596690--596832 Score: 112
Period size: 41 Copynumber: 3.5 Consensus size: 40
596680 TAAAATGCTG
* * * *
596690 CTAATAGGAAAAAATTAGCGGCATTTACTA-TAAAAATGCCA
1 CTAATA-GAAAAATTTAGCGACATTCAC-AGTAAAAACGCCA
* **
596731 CTAATAAAAAAAATTTAGCGACATTCACAGTAAAAACGTTA
1 CTAAT-AGAAAAATTTAGCGACATTCACAGTAAAAACGCCA
* * * *
596772 CTAATAGAAAAATTTAGC-AGCGTTCACAGTAAAAATGGCG
1 CTAATAGAAAAATTTAGCGA-CATTCACAGTAAAAACGCCA
*
596812 CTAATATGAATAA-TTAGCGAC
1 CTAATA-GAAAAATTTAGCGAC
596833 GCTTGTAAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
39 1 0.01
40 40 0.48
41 41 0.49
42 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (40 bp):
CTAATAGAAAAATTTAGCGACATTCACAGTAAAAACGCCA
Found at i:598535 original size:115 final size:116
Alignment explanation
Indices: 598317--598527 Score: 255
Period size: 115 Copynumber: 1.8 Consensus size: 116
598307 ACTTTTTTGA
* * * ** *
598317 GTTACTTTAGGTCATTTTTCATGATCTAAGAATTTTTATGTAATTTCACATATTTTAAAGTCATA
1 GTTACTTTAGATCATTCTTCAAGATCTAAGAATTTTTATACAATTTCACATATATTAAAGTCATA
* ** *
598382 TAGGTTATTTTTTATAATCTAAAGATTTTTACATAATTTATGTATATGGCG
66 TAGGTCATTTCCTATAATCTAAAGACTTTTACATAATTTATGTATATGGCG
* * * *
598433 GTTA-TTTAGATCATTCTTCAAGATCTAAGAATTTTTTTACAATTTTATGA-ATATTAAAGTTAT
1 GTTACTTTAGATCATTCTTCAAGATCTAAGAATTTTTATACAATTTCA-CATATATTAAAGTCAT
* *
598496 TTAGGTCATTTCCTATTATCTAAAGACTTTTA
65 ATAGGTCATTTCCTATAATCTAAAGACTTTTA
598528 TGTAATTTCA
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
115 73 0.94
116 5 0.06
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (116 bp):
GTTACTTTAGATCATTCTTCAAGATCTAAGAATTTTTATACAATTTCACATATATTAAAGTCATA
TAGGTCATTTCCTATAATCTAAAGACTTTTACATAATTTATGTATATGGCG
Found at i:599420 original size:31 final size:31
Alignment explanation
Indices: 599384--599445 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
599374 TTTTATTGAT
599384 ATAAATTATATAATA-TATA-AATATAAAAATA
1 ATAAA-TATATAATATTATATAAT-TAAAAATA
* *
599415 ATAAATATTTTATATTATATAATTAAAAATA
1 ATAAATATATAATATTATATAATTAAAAATA
599446 GATCGGATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 7 0.26
31 17 0.63
32 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
ATAAATATATAATATTATATAATTAAAAATA
Found at i:600108 original size:27 final size:27
Alignment explanation
Indices: 600078--600129 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
600068 TAAATTTATA
600078 TTATATAAAT-TATTAATATATTAAAAT
1 TTATATAAATATA-TAATATATTAAAAT
*
600105 TTATATAAATATATAATATTTTAAA
1 TTATATAAATATATAATATATTAAA
600130 TAAGATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTATATAAATATATAATATATTAAAAT
Found at i:600109 original size:25 final size:25
Alignment explanation
Indices: 600050--600203 Score: 90
Period size: 25 Copynumber: 6.2 Consensus size: 25
600040 GATCATAATA
* *
600050 AAAATATATAAATT-TTTATAAATTT
1 AAAATATATAAATTATTAATATA-TT
* *
600075 ATATTATATAAATTATTAATATATT
1 AAAATATATAAATTATTAATATATT
600100 AAAATTTATATAAA-TATATAATAT-TT
1 AAAA--TATATAAATTAT-TAATATATT
* * *
600126 -TAA-ATA-AGATTA-TAATAAATT
1 AAAATATATAAATTATTAATATATT
* * *
600147 AAAATATATAAAATA-TAAAATACAT
1 AAAATATATAAATTATTAATATA-TT
* *
600172 AAAATATATAAATATATTAAAATATA
1 AAAATATATAAAT-TATTAATATATT
600198 AAAATA
1 AAAATA
600204 GTATTTGTGA
Statistics
Matches: 99, Mismatches: 18, Indels: 23
0.71 0.13 0.16
Matches are distributed among these distances:
20 5 0.05
21 4 0.04
22 7 0.07
23 3 0.03
24 9 0.09
25 31 0.31
26 19 0.19
27 21 0.21
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (25 bp):
AAAATATATAAATTATTAATATATT
Found at i:600127 original size:20 final size:20
Alignment explanation
Indices: 600051--600142 Score: 57
Period size: 20 Copynumber: 4.6 Consensus size: 20
600041 ATCATAATAA
600051 AAATATATAA-ATTTT-TAT
1 AAATATATAATATTTTATAT
* * **
600069 AAATTTATATTATATAAATTAT
1 AAATATATAATAT-TTTA-TAT
* *
600091 TAATATATTAA-AATTTATAT
1 AAATATA-TAATATTTTATAT
*
600111 AAATATATAATATTTTAAAT
1 AAATATATAATATTTTATAT
600131 AAGAT-TATAATA
1 AA-ATATATAATA
600143 AATTAAAATA
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
18 8 0.15
19 5 0.09
20 26 0.48
21 4 0.07
22 9 0.17
23 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (20 bp):
AAATATATAATATTTTATAT
Found at i:600160 original size:9 final size:9
Alignment explanation
Indices: 600146--600203 Score: 70
Period size: 8 Copynumber: 6.8 Consensus size: 9
600136 TATAATAAAT
600146 TAAAATATA
1 TAAAATATA
600155 T-AAA-ATA
1 TAAAATATA
*
600162 TAAAATACA
1 TAAAATATA
600171 TAAAATATA
1 TAAAATATA
600180 T-AAATATA
1 TAAAATATA
600188 TTAAAATATA
1 -TAAAATATA
600198 -AAAATA
1 TAAAATA
600204 GTATTTGTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
7 4 0.09
8 19 0.44
9 13 0.30
10 7 0.16
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAATATA
Found at i:600161 original size:30 final size:30
Alignment explanation
Indices: 600105--600195 Score: 76
Period size: 30 Copynumber: 2.9 Consensus size: 30
600095 ATATTAAAAT
* * *
600105 TTATATAAATATATAATATTTTAAATAAGA
1 TTATATAAATATAAAATATATAAAATAAGA
*
600135 TTATAATAAAT-TAAAATATATAAAATATAAA
1 TTAT-ATAAATATAAAATATATAAAATA-AGA
* *
600166 ATACATAAAATATATAAATATATTAAAATA
1 TTATAT-AAATATA-AAATATA-TAAAATA
600196 TAAAAATAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
30 19 0.39
31 14 0.29
32 2 0.04
33 7 0.14
34 7 0.14
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (30 bp):
TTATATAAATATAAAATATATAAAATAAGA
Found at i:600167 original size:16 final size:16
Alignment explanation
Indices: 600080--600200 Score: 88
Period size: 16 Copynumber: 7.5 Consensus size: 16
600070 AATTTATATT
* *
600080 ATATAAATTAT-TAAT
1 ATATAAAATATATAAA
*
600095 ATATTAAAATTTATATAA
1 ATA-TAAAATATATA-AA
* * *
600113 ATATATAATATTTTAA
1 ATATAAAATATATAAA
* *
600129 ATA-AGATTATA-ATAA
1 ATATAAAATATATA-AA
600144 AT-TAAAATATATAAA
1 ATATAAAATATATAAA
*
600159 ATATAAAATACATAAA
1 ATATAAAATATATAAA
600175 ATATATAAATATATTAAA
1 ATATA-AAATATA-TAAA
600193 ATATAAAA
1 ATATAAAA
600201 ATAGTATTTG
Statistics
Matches: 82, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
15 22 0.27
16 29 0.35
17 18 0.22
18 13 0.16
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (16 bp):
ATATAAAATATATAAA
Found at i:600186 original size:8 final size:8
Alignment explanation
Indices: 600051--600199 Score: 64
Period size: 8 Copynumber: 18.4 Consensus size: 8
600041 ATCATAATAA
600051 AAATATAT
1 AAATATAT
*
600059 AAATTTTTAT
1 AAA--TATAT
*
600069 AAATTTAT
1 AAATATAT
*
600077 -ATTATAT
1 AAATATAT
600084 AAAT-TAT
1 AAATATAT
*
600091 TAATATATT
1 AAATATA-T
600100 AAAATTTATAT
1 -AAA--TATAT
600111 AAATATAT
1 AAATATAT
*
600119 -AATATTTT
1 AAATA-TAT
600127 AAATA-A-
1 AAATATAT
* *
600133 GATTATAAT
1 AAATAT-AT
600142 AAAT-TA-
1 AAATATAT
600148 AAATATAT
1 AAATATAT
600156 AAA-ATAT
1 AAATATAT
*
600163 AAAATACAT
1 -AAATATAT
600172 AAAATATAT
1 -AAATATAT
600181 AAATATATT
1 AAATATA-T
600190 AAA-ATAT
1 AAATATAT
600197 AAA
1 AAA
600200 AATAGTATTT
Statistics
Matches: 109, Mismatches: 14, Indels: 37
0.68 0.09 0.23
Matches are distributed among these distances:
6 7 0.06
7 26 0.24
8 37 0.34
9 22 0.20
10 12 0.11
11 1 0.01
12 4 0.04
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (8 bp):
AAATATAT
Found at i:600470 original size:20 final size:20
Alignment explanation
Indices: 600455--600491 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
600445 TTTATAAGTT
600455 CTTATA-AATTTATATAACA
1 CTTATATAATTTATATAACA
600474 CTTATATAATTTATATAA
1 CTTATATAATTTATATAA
600492 TATTTTACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (20 bp):
CTTATATAATTTATATAACA
Found at i:601438 original size:19 final size:20
Alignment explanation
Indices: 601414--601456 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
601404 TACATAAAAT
601414 TTTAAAATATAA-AA-AATTA
1 TTTAAAATA-AATAATAATTA
601433 TTT-AAATAAATAATAATTA
1 TTTAAAATAAATAATAATTA
601452 TTTAA
1 TTTAA
601457 TACAGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.10
18 7 0.33
19 11 0.52
20 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTAAAATAAATAATAATTA
Found at i:602502 original size:2 final size:2
Alignment explanation
Indices: 602495--602527 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
602485 ATAGAGTGCA
*
602495 AG AG AG AG AG AG AT AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
602528 AAAGAAAAAA
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:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (2 bp):
AG
Found at i:605476 original size:28 final size:27
Alignment explanation
Indices: 605440--605516 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 27
605430 ATTTTTCACA
* *
605440 ATCGGGGATACTCTAACCCCGTTATTT
1 ATCGAGGATACTCCAACCCCGTTATTT
*
605467 CATCGAGGATACTCCAACCCCATTATTT
1 -ATCGAGGATACTCCAACCCCGTTATTT
605495 -TCGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
605517 GCGTTATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 4 0.09
28 39 0.91
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (27 bp):
ATCGAGGATACTCCAACCCCGTTATTT
Found at i:605572 original size:79 final size:78
Alignment explanation
Indices: 605468--605803 Score: 361
Period size: 79 Copynumber: 4.3 Consensus size: 78
605458 CCGTTATTTC
* * * * *
605468 ATCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGCGTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACCTTATTTCTAAAAC
* *
605533 ATTGATTTCTCACA
66 ATCGATTT-TCATA
* ** * * * *
605547 ATCGGGGATACTCCATCCCTTTTATTTTCGCGAGGATACTCCAACCTCGACCTTATTTCTAAAGC
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACCTTATTTCTAAAAC
605612 ATCGATTTTCCATA
66 ATCGATTTT-CATA
* **
605626 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAATTTTATTT-TCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACCTTATTTCT-AAAA
* *
605690 CACCGATTTTTTATA
65 CATCGA-TTTTCATA
* * * * **
605705 ATCAGGGATACTCCAACTCTGTTATTTTCGAGGGGATACTCCAACCCCAATTTTATTT-TCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACCTTATTTCT-AAAA
*
605769 CATCGATTTTTTATA
65 CATCGA-TTTTCATA
*
605784 ATCGGGGATACTCCAGCCCC
1 ATCGGGGATACTCCAACCCC
605804 ATTGTTATCC
Statistics
Matches: 221, Mismatches: 33, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
78 2 0.01
79 215 0.97
80 4 0.02
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACCTTATTTCTAAAAC
ATCGATTTTCATA
Found at i:605761 original size:158 final size:158
Alignment explanation
Indices: 605468--605806 Score: 412
Period size: 158 Copynumber: 2.1 Consensus size: 158
605458 CCGTTATTTC
* ** *
605468 ATCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGCGTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCAACGTTATTTCTAAAAC
** * * * * * *
605533 ATTGATTTCTCACAATCGGGGATACTCCATCCCTTTTATTTTCGCGAGGATACTCCAACCTCGAC
66 ACCGATTTCTCACAATCAGGGATACTCCAACCCTGTTATTTTCGAGAGGATACTCCAACCCCAAC
*
605598 CTTA-TTTCTAAAGCATCGATTTTCCATA
131 CTTATTTTC-AAAACATCGATTTTCCATA
* **
605626 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAATTTTATTT-TCAAAA
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCAACGTTATTTCT-AAAA
* * * * *
605690 CACCGATTTTTTATAATCAGGGATACTCCAACTCTGTTATTTTCGAGGGGATACTCCAACCCCAA
65 CACCGATTTCTCACAATCAGGGATACTCCAACCCTGTTATTTTCGAGAGGATACTCCAACCCCAA
** **
605755 TTTTATTTTCAAAACATCGATTTTTTATA
130 CCTTATTTTCAAAACATCGATTTTCCATA
*
605784 ATCGGGGATACTCCAGCCCCATT
1 ATCGGGGATACTCCAACCCCATT
605807 GTTATCCCCA
Statistics
Matches: 152, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
157 1 0.01
158 147 0.97
159 4 0.03
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (158 bp):
ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCAACGTTATTTCTAAAAC
ACCGATTTCTCACAATCAGGGATACTCCAACCCTGTTATTTTCGAGAGGATACTCCAACCCCAAC
CTTATTTTCAAAACATCGATTTTCCATA
Found at i:608139 original size:2 final size:2
Alignment explanation
Indices: 608132--608176 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
608122 AATAAAGTGT
608132 TA TA 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 TA TA
608174 TA T
1 TA T
608177 TTTGAACTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:608559 original size:19 final size:18
Alignment explanation
Indices: 608535--608577 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
608525 TATATTTTAA
*
608535 TATATTCGTG-TATTTATGT
1 TATATTCATGTTATTT-T-T
608554 TATATTCATGTTATTTTT
1 TATATTCATGTTATTTTT
608572 TATATT
1 TATATT
608578 GAGCATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.63
Consensus pattern (18 bp):
TATATTCATGTTATTTTT
Found at i:609796 original size:58 final size:57
Alignment explanation
Indices: 609685--609793 Score: 159
Period size: 56 Copynumber: 1.9 Consensus size: 57
609675 ATTTGCATCG
*
609685 TATCTCAATTCATGACATATTTGTATAATTTATTATAATAATTTAATTTAAAATATCA
1 TATCTCAATTCATGA-ATATTTGTATAATTTATTATAATAATTTAATTAAAAATATCA
* *
609743 TATCTCAATTCATG-AT-TTTTTCATAATTTATTATAGTAATTTAATTAAAAA
1 TATCTCAATTCATGAATATTTGT-ATAATTTATTATAATAATTTAATTAAAAA
609794 AATTTATATT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
55 4 0.09
56 29 0.62
58 14 0.30
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (57 bp):
TATCTCAATTCATGAATATTTGTATAATTTATTATAATAATTTAATTAAAAATATCA
Found at i:610036 original size:13 final size:14
Alignment explanation
Indices: 610019--610094 Score: 52
Period size: 14 Copynumber: 5.4 Consensus size: 14
610009 TTTTTATATG
610019 ATTAAATTTTAATT
1 ATTAAATTTTAATT
*
610033 -TTAAA-TTTATTT
1 ATTAAATTTTAATT
*
610045 ATTAAATTTT-TTT
1 ATTAAATTTTAATT
*
610058 AAATAAATTTT-ATT
1 -ATTAAATTTTAATT
*
610072 AATTATAATTTTATTT
1 -ATTA-AATTTTAATT
610088 AATTAAA
1 -ATTAAA
610095 AATTTTATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
12 6 0.12
13 13 0.25
14 18 0.35
15 8 0.15
16 7 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTAAATTTTAATT
Found at i:610066 original size:14 final size:14
Alignment explanation
Indices: 610033--610094 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 14
610023 AATTTTAATT
*
610033 TTAAATTTATTT-A
1 TTAAATTTTTTTAA
610046 TTAAATTTTTTTAA
1 TTAAATTTTTTTAA
* *
610060 ATAAATTTTATTAA
1 TTAAATTTTTTTAA
610074 TTATAATTTTATTTAA
1 TTA-AATTTT-TTTAA
610090 TTAAA
1 TTAAA
610095 AATTTTATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.27
14 15 0.37
15 8 0.20
16 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAAATTTTTTTAA
Found at i:610135 original size:2 final size:2
Alignment explanation
Indices: 610130--610164 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
610120 AAAAATCTAG
610130 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
610165 CACACGCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:611557 original size:20 final size:19
Alignment explanation
Indices: 611530--611570 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
611520 TTTAGTATTA
*
611530 AATTTATATTATAAAAATT
1 AATTTATATTACAAAAATT
*
611549 AATTGTATATTACCAAAATT
1 AATT-TATATTACAAAAATT
611569 AA
1 AA
611571 GTATTGACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTTATATTACAAAAATT
Found at i:612837 original size:2 final size:2
Alignment explanation
Indices: 612830--612882 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
612820 ACCATGCCAT
612830 TA TA 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 TA TA
612872 TA TA TA TA TA T
1 TA TA TA TA TA T
612883 TAAAACTCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:613185 original size:5 final size:6
Alignment explanation
Indices: 613158--613186 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
613148 TTTTTAGATT
613158 TTTTAA TTTTAA TTTTAA TTTT-A TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
613187 ATAATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:614063 original size:29 final size:29
Alignment explanation
Indices: 613997--614072 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
613987 TTCATTCTCA
*
613997 ATTTTTTATACAAAATTTAAATAAATAATT
1 ATTTTTTA-ATAAAATTTAAATAAATAATT
* * *
614027 ATTATTTAATAAAATTTAATTTAAA-ATTT
1 ATTTTTTAATAAAATTTAA-ATAAATAATT
*
614056 ATTTTTTATTAATAATT
1 ATTTTTTAATAA-AATT
614073 GATTAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 23 0.61
30 15 0.39
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTTTTTAATAAAATTTAAATAAATAATT
Found at i:614399 original size:12 final size:11
Alignment explanation
Indices: 614382--614510 Score: 63
Period size: 10 Copynumber: 12.9 Consensus size: 11
614372 TTTAAATTTG
614382 ATAATATTAGAT
1 ATAATATTA-AT
614394 ATAATATTAAT
1 ATAATATTAAT
*
614405 ATGATA--AA-
1 ATAATATTAAT
*
614413 AAAATAATTAA-
1 ATAAT-ATTAAT
*
614424 A-AATA-TGAT
1 ATAATATTAAT
* *
614433 ATAATATAAAA
1 ATAATATTAAT
*
614444 ATAATATAAAT
1 ATAATATTAAT
614455 ATAATA-TAAT
1 ATAATATTAAT
614465 AT-ATATTAAT
1 ATAATATTAAT
*
614475 AT--T-TTAAA
1 ATAATATTAAT
*
614483 ATTATA-TAAT
1 ATAATATTAAT
614493 ATAA-ATT-AT
1 ATAATATTAAT
614502 -TAATATTAA
1 ATAATATTAA
614511 ATTTTATAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
8 14 0.15
9 15 0.16
10 27 0.29
11 27 0.29
12 9 0.10
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
ATAATATTAAT
Found at i:614439 original size:5 final size:5
Alignment explanation
Indices: 614425--614561 Score: 61
Period size: 5 Copynumber: 27.2 Consensus size: 5
614415 AATAATTAAA
* *
614425 AATAT GATAT AATAT AAAAAT AATAT AAATAT AATAT AATAT -ATATT
1 AATAT AATAT AATAT -AATAT AATAT -AATAT AATAT AATAT AATA-T
* * * * * * *
614472 AATAT --TTT AAAAT TATAT AATAT AA-AT TAT-T AATATT AAATTT TATAA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA-T -AATAT AATAT
* * *
614520 AATAT AAAAT -ATTT AAATAT AATTAT AATAT AATAA AATAT A
1 AATAT AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT A
614562 CCAAGAACAA
Statistics
Matches: 95, Mismatches: 24, Indels: 26
0.66 0.17 0.18
Matches are distributed among these distances:
3 2 0.02
4 11 0.12
5 57 0.60
6 22 0.23
7 3 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:614443 original size:28 final size:27
Alignment explanation
Indices: 614403--614497 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 27
614393 TATAATATTA
* *
614403 ATATGATAAAAAAATAATTAAAAATAT
1 ATATAATATAAAAATAATTAAAAATAT
*
614430 GATATAATATAAAAATAA-TATAAATAT
1 -ATATAATATAAAAATAATTAAAAATAT
* * *
614457 AATATAATATATATTAATATTTTAAAAT-T
1 -ATATAATATA-A-AAATAATTAAAAATAT
614486 ATATAATATAAA
1 ATATAATATAAA
614498 TTATTAATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
27 19 0.35
28 26 0.47
29 5 0.09
30 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
ATATAATATAAAAATAATTAAAAATAT
Found at i:614449 original size:11 final size:11
Alignment explanation
Indices: 614433--614463 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
614423 AAAATATGAT
614433 ATAATATAAAA
1 ATAATATAAAA
*
614444 ATAATATAAAT
1 ATAATATAAAA
614455 ATAATATAA
1 ATAATATAA
614464 TATATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:614492 original size:44 final size:41
Alignment explanation
Indices: 614444--614556 Score: 110
Period size: 37 Copynumber: 2.7 Consensus size: 41
614434 TAATATAAAA
614444 ATAATATAAATATAATATAATATATATTAATATTT-TAAAATTAT
1 ATAATATAAATATAATATAATATATA--AAT-TTTATAAAA-TAT
614488 ATAATATAAAT-T-AT-TAATAT-TAAATTTTATAAAATAT
1 ATAATATAAATATAATATAATATATAAATTTTATAAAATAT
*
614525 AAAATATTTAAATATAATTATAATATAATAAA
1 ATAATA--TAAATATAA-TATAATAT-ATAAA
614557 ATATACCAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 17
0.77 0.01 0.22
Matches are distributed among these distances:
37 11 0.19
38 8 0.14
39 5 0.08
40 3 0.05
41 7 0.12
42 3 0.05
43 7 0.12
44 11 0.19
45 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (41 bp):
ATAATATAAATATAATATAATATATAAATTTTATAAAATAT
Found at i:614500 original size:28 final size:29
Alignment explanation
Indices: 614424--614552 Score: 101
Period size: 27 Copynumber: 4.6 Consensus size: 29
614414 AAATAATTAA
* * *
614424 AAATATGATATAATATAAA--AATAATAT
1 AAATATTATATAATATAAATTAATATTTT
* *
614451 AAATATAATATAATATATATTAATATTTT
1 AAATATTATATAATATAAATTAATATTTT
* *
614480 AAA-ATTATATAATATAAATTATTAATATT
1 AAATATTATATAATATAAATTAAT-ATTTT
* *
614509 AAATTTTATAAAATAT-AA--AATA-TTT
1 AAATATTATATAATATAAATTAATATTTT
*
614534 AAATATAATTATAATATAA
1 AAATATTA-TATAATATAA
614553 TAAAATATAC
Statistics
Matches: 81, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
25 8 0.10
26 8 0.10
27 20 0.25
28 17 0.21
29 18 0.22
30 10 0.12
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
AAATATTATATAATATAAATTAATATTTT
Found at i:614504 original size:23 final size:23
Alignment explanation
Indices: 614444--614561 Score: 72
Period size: 23 Copynumber: 5.3 Consensus size: 23
614434 TAATATAAAA
*
614444 ATAATATAAA-TA-TAATATAAT
1 ATAATATAAATTATTAATATTAT
*
614465 AT-ATATTAATATT-TTAAAATTAT
1 ATAATA-TAA-ATTATTAATATTAT
*
614488 ATAATATAAATTATTAATATTAA
1 ATAATATAAATTATTAATATTAT
** * *
614511 ATTTTATAAAATATAAAATATT-T
1 ATAATATAAATTAT-TAATATTAT
*
614534 A-AATAT-AATTA-TAATATAAT
1 ATAATATAAATTATTAATATTAT
*
614554 AAAATATA
1 ATAATATA
614562 CCAAGAACAA
Statistics
Matches: 73, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
19 5 0.07
20 5 0.07
21 14 0.19
22 7 0.10
23 33 0.45
24 9 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAATATAAATTATTAATATTAT
Done.