Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold19
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: 2266706
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17655 characters in sequence are not A, C, G, or T
File 4 of 15
Found at i:408928 original size:102 final size:102
Alignment explanation
Indices: 408752--408950 Score: 326
Period size: 102 Copynumber: 2.0 Consensus size: 102
408742 AAAAACCACC
* * *
408752 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGGCAAACCACCAAATCA
* *
408817 CCCATTTAATCAATAATGGTAAGCTACCAAATTTCTT
66 CCCATTTAATCAACAATGGTAAACTACCAAATTTCTT
* * *
408854 ATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGCAAACCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGGCAAACCACCAAATCA
408919 CCCATTTAATCAACAATGGTAAACTACCAAAT
66 CCCATTTAATCAACAATGGTAAACTACCAAAT
408951 CACCATTTAA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 89 1.00
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (102 bp):
ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGGCAAACCACCAAATCA
CCCATTTAATCAACAATGGTAAACTACCAAATTTCTT
Found at i:413419 original size:34 final size:33
Alignment explanation
Indices: 413372--413589 Score: 233
Period size: 34 Copynumber: 6.5 Consensus size: 33
413362 TGGTAAAAAC
*
413372 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
413405 CTACTATTTAATCAACAATGGTAAGCC-ATCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
413439 CACCATTTAATCAATAATGGTAAGCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
** *
413472 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * **
413506 CTCCCATTTAGTCAACAATAGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAAT-GGTAACCTACCAAAT
* * *
413540 CACTCATTTAATCAACAATGATAAACTATCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
413574 CACCATTTAATCAACA
1 CACCATTTAATCAACA
413590 TAAATTAAAA
Statistics
Matches: 155, Mismatches: 22, Indels: 16
0.80 0.11 0.08
Matches are distributed among these distances:
32 1 0.01
33 46 0.30
34 101 0.65
35 7 0.05
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:413481 original size:67 final size:67
Alignment explanation
Indices: 413372--413589 Score: 285
Period size: 67 Copynumber: 3.2 Consensus size: 67
413362 TGGTAAAAAC
* *
413372 CACCATTTAATCAACAATGGCAACCTACCAAATCTACT-ATTTAATCAACAATGGTAAGCCATCA
1 CACCATTTAATCAACAATGGCAAACTACCAAAT-TACTCATTTAATCAACAATGGTAAGCTATCA
413436 AAT
65 AAT
* * * * *
413439 CACCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTATCAA
413504 AT
66 AT
* * * * * * *
413506 CTCCCATTTAGTCAACAATAGCAAACCACCAAATCACTCATTTAATCAACAATGATAAACTATCA
1 C-ACCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTATCA
413571 AAT
65 AAT
413574 CACCATTTAATCAACA
1 CACCATTTAATCAACA
413590 TAAATTAAAA
Statistics
Matches: 129, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
66 3 0.02
67 71 0.55
68 55 0.43
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATTACTCATTTAATCAACAATGGTAAGCTATCAA
AT
Found at i:415079 original size:16 final size:16
Alignment explanation
Indices: 415058--415092 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
415048 CTTTTAATAA
415058 TTTCCTGAGCCACTAT
1 TTTCCTGAGCCACTAT
415074 TTTCCTGAGCCACTAT
1 TTTCCTGAGCCACTAT
415090 TTT
1 TTT
415093 TGGTTTAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.29, G:0.11, T:0.43
Consensus pattern (16 bp):
TTTCCTGAGCCACTAT
Found at i:417383 original size:25 final size:24
Alignment explanation
Indices: 417354--417418 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 24
417344 ATTTATTTTT
*
417354 TTATATGATAAAAATT-ATATAATAA
1 TTATATAATAAAAATTAATAT-AT-A
417379 TTATA-AATATAAAATTAATATATA
1 TTATATAATA-AAAATTAATATATA
417403 TTATATAATTAAAAAT
1 TTATATAA-TAAAAAT
417419 GAGTTGAGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
24 9 0.26
25 20 0.57
26 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TTATATAATAAAAATTAATATATA
Found at i:417852 original size:31 final size:31
Alignment explanation
Indices: 417817--417876 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
417807 TTGTGACTAG
417817 TAAATTCAATTTAAATTTAACTGATGATTAA
1 TAAATTCAATTTAAATTTAACTGATGATTAA
* * *
417848 TAAATTTAATTTAAATTTGATTGATGATT
1 TAAATTCAATTTAAATTTAACTGATGATT
417877 GGTAGTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (31 bp):
TAAATTCAATTTAAATTTAACTGATGATTAA
Found at i:422541 original size:31 final size:31
Alignment explanation
Indices: 422479--422548 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
422469 TTTAGCTAAC
* * *
422479 GGCTGGTAGCTAGGGAATTCAATTTGGATTT
1 GGCTGGTGGCTAAGGAATTCAATTTGAATTT
422510 GGCTGGTGGCTAAGGAATTCAATTCT-AATTT
1 GGCTGGTGGCTAAGGAATTCAATT-TGAATTT
*
422541 GACTGGTG
1 GGCTGGTG
422549 ATTAGAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.34
Consensus pattern (31 bp):
GGCTGGTGGCTAAGGAATTCAATTTGAATTT
Found at i:431438 original size:69 final size:69
Alignment explanation
Indices: 431327--431464 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 69
431317 AAGCCCTGTT
* * * * *
431327 TATGAAGTAATTTCATGAGAAAGCAGCAAAATCTACCGATGTCGGTGAGTTAAGAAACCCAAAAT
1 TATGAAGTAATTTCATAAGAAAGCAACAAAATCTACCGATGTCAGTCACTTAAGAAACCCAAAAT
431392 CAAA
66 CAAA
* * *
431396 TATGAAGTAATTTCATAAGAGAGCAACAAAATCTTCCGATGTCAGTCACTTAAGAAACCCATAAT
1 TATGAAGTAATTTCATAAGAAAGCAACAAAATCTACCGATGTCAGTCACTTAAGAAACCCAAAAT
431461 CAAA
66 CAAA
431465 ATCTGACAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.23
Consensus pattern (69 bp):
TATGAAGTAATTTCATAAGAAAGCAACAAAATCTACCGATGTCAGTCACTTAAGAAACCCAAAAT
CAAA
Found at i:433328 original size:2 final size:2
Alignment explanation
Indices: 433321--433360 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
433311 ATATAAGTAT
433321 TA TA TA TA TA -A TA TA TA TA TA TA TA TA -A 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
433361 ACGAGATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:433337 original size:13 final size:13
Alignment explanation
Indices: 433321--433361 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
433311 ATATAAGTAT
433321 TATATATATAATATA
1 TATATATAT-ATA-A
433336 TATATATATATAA
1 TATATATATATAA
433349 TATATATATATAA
1 TATATATATATAA
433362 CGAGATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 14 0.54
14 3 0.12
15 9 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATATATATATAA
Found at i:433343 original size:17 final size:17
Alignment explanation
Indices: 433321--433360 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
433311 ATATAAGTAT
433321 TATATATATAATATATA
1 TATATATATAATATATA
433338 TATATATATAATATATA
1 TATATATATAATATATA
433355 TATATA
1 TATATA
433361 ACGAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATATATAATATATA
Found at i:433359 original size:15 final size:15
Alignment explanation
Indices: 433311--433361 Score: 70
Period size: 15 Copynumber: 3.4 Consensus size: 15
433301 TGTTAAGTAC
433311 ATATAAGTAT-TATAT
1 ATATAA-TATATATAT
433326 ATATAATATATATAT
1 ATATAATATATATAT
433341 ATAT-ATAATATATAT
1 ATATAAT-ATATATAT
433356 ATATAA
1 ATATAA
433362 CGAGATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.15
15 27 0.82
16 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
ATATAATATATATAT
Found at i:434325 original size:2 final size:2
Alignment explanation
Indices: 434318--434354 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
434308 AACCTTTATT
*
434318 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
434355 TAAATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:435343 original size:11 final size:11
Alignment explanation
Indices: 435324--435395 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
435314 AAGCACGATA
*
435324 ATAATATAAAT
1 ATAAAATAAAT
435335 ATAAAATAAAT
1 ATAAAATAAAT
435346 ATAATAA-AAAT
1 ATAA-AATAAAT
*
435357 A-AGAATAAA-
1 ATAAAATAAAT
435366 ATAAAAT-AAT
1 ATAAAATAAAT
435376 A-ACAACATAAAT
1 ATA-AA-ATAAAT
*
435388 TTAAAATA
1 ATAAAATA
435396 TCAAGATCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
9 6 0.12
10 11 0.22
11 24 0.49
12 7 0.14
13 1 0.02
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.26
Consensus pattern (11 bp):
ATAAAATAAAT
Found at i:435350 original size:22 final size:21
Alignment explanation
Indices: 435323--435374 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
435313 TAAGCACGAT
435323 AATAATATAAATATAA-AATAA
1 AATAATATAAA-ATAAGAATAA
435344 ATATAATA-AAAATAAGAATAA
1 A-ATAATATAAAATAAGAATAA
*
435365 AATAAAATAA
1 AATAATATAA
435375 TAACAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 9 0.33
21 12 0.44
22 6 0.22
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (21 bp):
AATAATATAAAATAAGAATAA
Found at i:435368 original size:5 final size:5
Alignment explanation
Indices: 435323--435374 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
435313 TAAGCACGAT
* *
435323 AATAA TATAA ATATAA AAT-A AATAT AATAAA AATAA GAATAA AATAA
1 AATAA AATAA A-ATAA AATAA AATAA AAT-AA AATAA -AATAA AATAA
435370 AATAA
1 AATAA
435375 TAACAACATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.10
5 21 0.54
6 14 0.36
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (5 bp):
AATAA
Found at i:436101 original size:43 final size:43
Alignment explanation
Indices: 436040--436125 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
436030 TACTTGCAAG
436040 AAATCATTTGCATGCCAAAAATAATATGATAATAGCTCCTAAT
1 AAATCATTTGCATGCCAAAAATAATATGATAATAGCTCCTAAT
*
436083 AAATCATTTGCATGCCAAAAATAATATGATAATGGCTCCTAAT
1 AAATCATTTGCATGCCAAAAATAATATGATAATAGCTCCTAAT
436126 GCTCAAGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.30
Consensus pattern (43 bp):
AAATCATTTGCATGCCAAAAATAATATGATAATAGCTCCTAAT
Found at i:436554 original size:14 final size:15
Alignment explanation
Indices: 436535--436587 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
436525 AAGGTTCAAT
436535 TAAAAA-TTTATATG
1 TAAAAAGTTTATATG
436549 TAAAAAGTTT-TAT-
1 TAAAAAGTTTATATG
*
436562 TAAAAATTTTATATG
1 TAAAAAGTTTATATG
436577 TAAAAAGTTTA
1 TAAAAAGTTTA
436588 GTGATAACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 9 0.26
14 12 0.35
15 13 0.38
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (15 bp):
TAAAAAGTTTATATG
Found at i:436563 original size:27 final size:28
Alignment explanation
Indices: 436533--436586 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
436523 AGAAGGTTCA
436533 ATTAAAAA-TTTATATGTAAAAAGTTTT
1 ATTAAAAATTTTATATGTAAAAAGTTTT
436560 ATTAAAAATTTTATATGTAAAAAGTTT
1 ATTAAAAATTTTATATGTAAAAAGTTT
436587 AGTGATAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (28 bp):
ATTAAAAATTTTATATGTAAAAAGTTTT
Found at i:437887 original size:18 final size:18
Alignment explanation
Indices: 437864--437901 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
437854 ATCATAGATC
*
437864 TATAGAGTTTAGTGTCGA
1 TATAGAGTTTAATGTCGA
437882 TATAGAGTTTAATGTCGA
1 TATAGAGTTTAATGTCGA
437900 TA
1 TA
437902 AAGTTACCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (18 bp):
TATAGAGTTTAATGTCGA
Found at i:440646 original size:3 final size:3
Alignment explanation
Indices: 440638--440683 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
440628 AGTCAACTTT
440638 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
440684 CTTGAAGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:442980 original size:16 final size:15
Alignment explanation
Indices: 442959--442999 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
442949 ATTTACTATA
442959 TTTAAATTTATTTAAT
1 TTTAAATTTATTT-AT
*
442975 TTTAAAATTATTTAT
1 TTTAAATTTATTTAT
*
442990 TTTACATTTA
1 TTTAAATTTA
443000 AATTCTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAAATTTATTTAT
Found at i:449871 original size:21 final size:19
Alignment explanation
Indices: 449832--449876 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
449822 TTCATACTTA
449832 AGAA-AAAAAGAGAGTGAG
1 AGAAGAAAAAGAGAGTGAG
*
449850 AGAAGAAAGAGAGAGCTAGAG
1 AGAAGAAAAAGAGAG-T-GAG
449871 AGAAGA
1 AGAAGA
449877 GAGGATAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 9 0.39
20 1 0.04
21 9 0.39
ACGTcount: A:0.58, C:0.02, G:0.36, T:0.04
Consensus pattern (19 bp):
AGAAGAAAAAGAGAGTGAG
Found at i:451901 original size:19 final size:18
Alignment explanation
Indices: 451861--451911 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
451851 GTTAATTATT
451861 TTTTATATA-TTTTGACA
1 TTTTATATATTTTTGACA
**
451878 TTTTATATATTTTTGTTA
1 TTTTATATATTTTTGACA
451896 TGTTTATATTATTTTT
1 T-TTTATA-TATTTTT
451912 ATATTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 9 0.31
18 7 0.24
19 6 0.21
20 7 0.24
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTTATATATTTTTGACA
Found at i:452208 original size:19 final size:19
Alignment explanation
Indices: 452184--452221 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
452174 ATATTTTGAT
*
452184 ATATTTATGTATTCATATC
1 ATATTTATATATTCATATC
*
452203 ATATTTATATTTTCATATC
1 ATATTTATATATTCATATC
452222 GTGTCGTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (19 bp):
ATATTTATATATTCATATC
Found at i:452448 original size:13 final size:13
Alignment explanation
Indices: 452432--452457 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
452422 TAACAGATAT
452432 TTTAAAACTATTA
1 TTTAAAACTATTA
452445 TTTAAAACTATTA
1 TTTAAAACTATTA
452458 ATTATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAAACTATTA
Found at i:452495 original size:30 final size:32
Alignment explanation
Indices: 452442--452500 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
452432 TTTAAAACTA
**
452442 TTATTTAAAACTATTAATTATAAT-AATATTT
1 TTATTTAAAACTATTAAAGATAATGAATATTT
*
452473 TTATTTAATAC-ATTAAAGATAATGAATA
1 TTATTTAAAACTATTAAAGATAATGAATA
452501 AAATTATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (32 bp):
TTATTTAAAACTATTAAAGATAATGAATATTT
Found at i:454019 original size:14 final size:15
Alignment explanation
Indices: 454002--454032 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
453992 GTATGTAATT
454002 TTTAA-TATAAAAAA
1 TTTAATTATAAAAAA
454016 TTTAATTATAAAAAA
1 TTTAATTATAAAAAA
454031 TT
1 TT
454033 AAAAGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTAATTATAAAAAA
Found at i:454357 original size:17 final size:17
Alignment explanation
Indices: 454323--454357 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
454313 TTTATTTTAA
*
454323 ATTTATTTAGTTAATTT
1 ATTTATTTACTTAATTT
*
454340 ATTTATTTACTTATTTT
1 ATTTATTTACTTAATTT
454357 A
1 A
454358 GATAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTTATTTACTTAATTT
Found at i:467642 original size:3 final size:3
Alignment explanation
Indices: 467634--467662 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
467624 GACTCTTTAT
467634 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
467663 TTTTGAGTTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:470234 original size:20 final size:20
Alignment explanation
Indices: 470211--470259 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
470201 AATTAAACAA
470211 ATTTATTTTAACTCAAATTT
1 ATTTATTTTAACTCAAATTT
* *
470231 ATTTA-TTCAACTTAAATTT
1 ATTTATTTTAACTCAAATTT
*
470250 -TTTTTTTTAA
1 ATTTATTTTAA
470260 TTCGACTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.12
19 16 0.67
20 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTATTTTAACTCAAATTT
Found at i:473499 original size:12 final size:12
Alignment explanation
Indices: 473482--473509 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
473472 ATTAGCCAAG
473482 AAAATATGAAAA
1 AAAATATGAAAA
473494 AAAATATGAAAA
1 AAAATATGAAAA
473506 AAAA
1 AAAA
473510 ATTAACAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAATATGAAAA
Found at i:473972 original size:17 final size:15
Alignment explanation
Indices: 473947--474012 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 15
473937 TTTTTCAATC
473947 TTCAATTTTCATTTTT
1 TTCAATTTT-ATTTTT
473963 TTCTAA-TTT-TTTTT
1 TTC-AATTTTATTTTT
473977 TTCAATTTTATTTTTT
1 TTCAATTTTA-TTTTT
*
473993 TTC-ATTTTTTTCTTT
1 TTCAATTTTATT-TTT
474008 TTCAA
1 TTCAA
474013 AGAATCAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
13 2 0.05
14 13 0.30
15 11 0.26
16 15 0.35
17 2 0.05
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.73
Consensus pattern (15 bp):
TTCAATTTTATTTTT
Found at i:473975 original size:14 final size:14
Alignment explanation
Indices: 473958--474003 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
473948 TCAATTTTCA
473958 TTTTTTTCTAATTT
1 TTTTTTTCTAATTT
473972 TTTTTTTC-AATTT
1 TTTTTTTCTAATTT
* *
473985 TATTTTTTTTCATTT
1 T-TTTTTTCTAATTT
474000 TTTT
1 TTTT
474004 CTTTTTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.21
14 17 0.61
15 5 0.18
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTTCTAATTT
Found at i:473983 original size:30 final size:28
Alignment explanation
Indices: 473947--474003 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
473937 TTTTTCAATC
473947 TTCAATTTTCATTTTTTTCTAATTTTTTTT
1 TTCAATTTT-ATTTTTTT-TAATTTTTTTT
*
473977 TTCAATTTTATTTTTTTTCATTTTTTT
1 TTCAATTTTATTTTTTTTAATTTTTTT
474004 CTTTTTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 9 0.35
29 8 0.31
30 9 0.35
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (28 bp):
TTCAATTTTATTTTTTTTAATTTTTTTT
Found at i:474009 original size:15 final size:14
Alignment explanation
Indices: 473969--474011 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
473959 TTTTTTCTAA
473969 TTTTTTTTTTCAATT
1 TTTTTTTTTTC-ATT
473984 TTATTTTTTTTCATT
1 TT-TTTTTTTTCATT
473999 TTTTTCTTTTTCA
1 TTTTT-TTTTTCA
474012 AAGAATCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.12
15 14 0.54
16 9 0.35
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTTCATT
Found at i:475110 original size:41 final size:39
Alignment explanation
Indices: 475052--475192 Score: 158
Period size: 41 Copynumber: 3.5 Consensus size: 39
475042 TAAAAATCAG
*
475052 AAACTCTTGTTTTATAAGACGTGAGCACGTTAAGAAATCGA
1 AAACTCTTGTTTGATAAGACGTGAGCACGTTAAGAAA-C-A
* * *
475093 AAACTCTTATTTGATAAGGCGTGGGCACGTTAAGAAACTAA
1 AAACTCTTGTTTGATAAGACGTGAGCACGTTAAGAAAC--A
* *
475134 AAACTCTTGTTTGATAA-AGCGTAAGCACATTAAGAAAACA
1 AAACTCTTGTTTGATAAGA-CGTGAGCACGTTAAG-AAACA
475174 GAAACTCTTGTTTGATAAG
1 -AAACTCTTGTTTGATAAG
475193 GCATGGACAC
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
40 2 0.02
41 79 0.93
42 4 0.05
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (39 bp):
AAACTCTTGTTTGATAAGACGTGAGCACGTTAAGAAACA
Found at i:475189 original size:82 final size:82
Alignment explanation
Indices: 475052--475203 Score: 209
Period size: 82 Copynumber: 1.9 Consensus size: 82
475042 TAAAAATCAG
* * * * *
475052 AAACTCTTGTTTTATAAGACGTGAGCACGTTAAGAAATCGAAAACTCTTATTTGATAAGGCGTGG
1 AAACTCTTGTTTGATAAGACGTAAGCACATTAAGAAAACGAAAACTCTTATTTGATAAGGCATGG
*
475117 GCACGTTAAGAAACTAA
66 ACACGTTAAGAAACTAA
*
475134 AAACTCTTGTTTGATAA-AGCGTAAGCACATTAAGAAAAC-AGAAACTCTTGTTTGATAAGGCAT
1 AAACTCTTGTTTGATAAGA-CGTAAGCACATTAAGAAAACGA-AAACTCTTATTTGATAAGGCAT
475197 GGACACG
64 GGACACG
475204 CTCTATAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
81 2 0.03
82 59 0.97
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (82 bp):
AAACTCTTGTTTGATAAGACGTAAGCACATTAAGAAAACGAAAACTCTTATTTGATAAGGCATGG
ACACGTTAAGAAACTAA
Found at i:479791 original size:15 final size:17
Alignment explanation
Indices: 479754--479793 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
479744 TTTATCAATC
479754 TCTTTTTTCTCCCTCCTA
1 TCTTTTTTCTCCCT-CTA
479772 T-TTTTTTC-CCCT-TA
1 TCTTTTTTCTCCCTCTA
479786 TCTTTTTT
1 TCTTTTTT
479794 TCCTTTGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.14
15 6 0.29
16 4 0.19
17 7 0.33
18 1 0.05
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.65
Consensus pattern (17 bp):
TCTTTTTTCTCCCTCTA
Found at i:480760 original size:21 final size:22
Alignment explanation
Indices: 480736--480776 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
480726 AAAATATATT
480736 TATTT-TTTATATTTAAAAAAG
1 TATTTATTTATATTTAAAAAAG
*
480757 TATTTATTTATTTTTAAAAA
1 TATTTATTTATATTTAAAAA
480777 TTTAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTTATTTATATTTAAAAAAG
Found at i:480805 original size:29 final size:29
Alignment explanation
Indices: 480710--480807 Score: 119
Period size: 29 Copynumber: 3.3 Consensus size: 29
480700 GATACTCACC
*
480710 TTTTAAAATTTTATAAAAAATATATTTATT
1 TTTTAAAATTTAAT-AAAAATATATTTATT
* *
480740 TTTT-ATATTTAA-AAAAGTATTTATTTATT
1 TTTTAAAATTTAATAAAA--ATATATTTATT
*
480769 TTTAAAAATTTAATAAAAATATATTTATT
1 TTTTAAAATTTAATAAAAATATATTTATT
480798 TTTTAAAATT
1 TTTTAAAATT
480808 ATTATTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.07
29 38 0.67
30 11 0.19
31 4 0.07
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (29 bp):
TTTTAAAATTTAATAAAAATATATTTATT
Found at i:480865 original size:51 final size:45
Alignment explanation
Indices: 480764--480868 Score: 129
Period size: 50 Copynumber: 2.2 Consensus size: 45
480754 AAGTATTTAT
* *
480764 TTATTTTTAAAAATTTAATAAAAATATATTTATTTTTTAAAATTA
1 TTATTTTTAAAAATTTAATAAAAATAAATATATTTTTTAAAATTA
*
480809 TTATTTTTAAATTAATTTTAAATAAAAAATAAATATATTTTTTATTAATTA
1 TTATTTTTAAA--AA-TTT-AAT-AAAAATAAATATATTTTTTA-AAATTA
480860 TTATTTTTA
1 TTATTTTTA
480869 TTTTTTATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
45 11 0.22
47 2 0.04
48 3 0.06
49 3 0.06
50 18 0.35
51 14 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (45 bp):
TTATTTTTAAAAATTTAATAAAAATAAATATATTTTTTAAAATTA
Found at i:480868 original size:16 final size:16
Alignment explanation
Indices: 480847--480889 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
480837 ATAAATATAT
480847 TTTTTATTAATTATTA
1 TTTTTATTAATTATTA
**
480863 TTTTTATTTTTTATTA
1 TTTTTATTAATTATTA
480879 TTTTTACTTAA
1 TTTTTA-TTAA
480890 AAATTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTATTAATTATTA
Found at i:485598 original size:4 final size:4
Alignment explanation
Indices: 485589--485642 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
485579 GGGTACATTA
* * *
485589 ATAT ATAT ATAT ATAT ATAT ATAT ATAT TTAT ATGT ATGT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
485637 TTAT AT
1 ATAT AT
485643 GTATGTATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (4 bp):
ATAT
Found at i:485600 original size:6 final size:6
Alignment explanation
Indices: 485589--485642 Score: 72
Period size: 6 Copynumber: 9.0 Consensus size: 6
485579 GGGTACATTA
* * *
485589 ATATAT ATATAT ATATAT ATATAT ATATTT ATATGT ATGTAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
485637 TTATAT
1 ATATAT
485643 GTATGTATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
ATATAT
Found at i:485604 original size:10 final size:10
Alignment explanation
Indices: 485589--485642 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
485579 GGGTACATTA
485589 ATATATATAT
1 ATATATATAT
485599 ATATATATAT
1 ATATATATAT
*
485609 ATATATATTT
1 ATATATATAT
* *
485619 ATATGTATGT
1 ATATATATAT
*
485629 ATATATATTT
1 ATATATATAT
485639 ATAT
1 ATAT
485643 GTATGTATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (10 bp):
ATATATATAT
Found at i:485643 original size:20 final size:20
Alignment explanation
Indices: 485589--485650 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
485579 GGGTACATTA
* * *
485589 ATATATATATATATATATAT
1 ATATATATTTATATGTATGT
485609 ATATATATTTATATGTATGT
1 ATATATATTTATATGTATGT
485629 ATATATATTTATATGTATGT
1 ATATATATTTATATGTATGT
485649 AT
1 AT
485651 GTGCATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (20 bp):
ATATATATTTATATGTATGT
Found at i:488055 original size:17 final size:16
Alignment explanation
Indices: 488019--488052 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
488009 CTCGTAGTTC
488019 AATTTGATAGATAAAA
1 AATTTGATAGATAAAA
488035 AATTTGATAGATAAAA
1 AATTTGATAGATAAAA
488051 AA
1 AA
488053 ATTAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (16 bp):
AATTTGATAGATAAAA
Found at i:488069 original size:19 final size:21
Alignment explanation
Indices: 488047--488087 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
488037 TTTGATAGAT
488047 AAAAAAATTA-AAAT-TTAAA
1 AAAAAAATTATAAATATTAAA
488066 AAAAAAATTATAAATATTAAA
1 AAAAAAATTATAAATATTAAA
488087 A
1 A
488088 TTTAAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 4 0.20
21 6 0.30
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAAATTATAAATATTAAA
Found at i:488491 original size:2 final size:2
Alignment explanation
Indices: 488486--488538 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
488476 AAATAGAACA
488486 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
488528 AC AC AC AC AC A
1 AC AC AC AC AC A
488539 AAACCCCCAA
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:488862 original size:3 final size:3
Alignment explanation
Indices: 488854--488900 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
488844 CCGTATATTA
488854 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
488901 ATTTTAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:493349 original size:17 final size:17
Alignment explanation
Indices: 493323--493355 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
493313 TATGTTGAAA
493323 TCTTTCTTTTTTCTTTT
1 TCTTTCTTTTTTCTTTT
*
493340 TCTTTTTTTTTTCTTT
1 TCTTTCTTTTTTCTTT
493356 CACTTAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TCTTTCTTTTTTCTTTT
Found at i:493633 original size:3 final size:3
Alignment explanation
Indices: 493625--493652 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
493615 TACCATCATT
493625 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
493653 GAATGCAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:494163 original size:20 final size:20
Alignment explanation
Indices: 494141--494195 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
494131 ATGATTCAAT
*
494141 AAATTAATATCTATTAAAATA
1 AAATT-ATAACTATTAAAATA
**
494162 AAATTATAACTATTATTATA
1 AAATTATAACTATTAAAATA
*
494182 AAA-TATAAATATTA
1 AAATTATAACTATTA
494196 TAACAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 10 0.33
20 15 0.50
21 5 0.17
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATTATAACTATTAAAATA
Found at i:494194 original size:19 final size:20
Alignment explanation
Indices: 494159--494196 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
494149 ATCTATTAAA
*
494159 ATAAAATTATAACTATTATT
1 ATAAAATTATAAATATTATT
494179 ATAAAA-TATAAATATTAT
1 ATAAAATTATAAATATTAT
494197 AACAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAATTATAAATATTATT
Found at i:494203 original size:19 final size:19
Alignment explanation
Indices: 494161--494205 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
494151 CTATTAAAAT
* * *
494161 AAAATTATAACTATTATTAT
1 AAAA-TATAAATATTATAAC
494181 AAAATATAAATATTATAAC
1 AAAATATAAATATTATAAC
494200 AAAATA
1 AAAATA
494206 CCATTATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATATAAATATTATAAC
Found at i:501968 original size:2 final size:2
Alignment explanation
Indices: 501961--501989 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
501951 GAATTTTAAA
501961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
501990 AATTCTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:502421 original size:18 final size:18
Alignment explanation
Indices: 502374--502423 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
502364 AAATCTATAT
* *
502374 ATTACATAAATAATTAAA
1 ATTACATTAATATTTAAA
**
502392 ATTTGTATTAATATTTAAA
1 A-TTACATTAATATTTAAA
502411 ATTACATTAATAT
1 ATTACATTAATAT
502424 AATCTTTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTACATTAATATTTAAA
Found at i:503893 original size:13 final size:13
Alignment explanation
Indices: 503866--503902 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
503856 TATATCAATA
*
503866 TTACTTTTTTTTTT
1 TTAC-TTTTTCTTT
503880 TTACTTTTTCTTT
1 TTACTTTTTCTTT
503893 TTACTTTTTC
1 TTACTTTTTC
503903 AAGTCAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (13 bp):
TTACTTTTTCTTT
Found at i:504113 original size:16 final size:17
Alignment explanation
Indices: 504084--504129 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
504074 TCGATGTGAT
504084 AAATTTTAATAATAA-A
1 AAATTTTAATAATAATA
504100 AAATATTTAA-AATAATA
1 AAAT-TTTAATAATAATA
504117 AAA--TTAATAATAA
1 AAATTTTAATAATAA
504130 AATAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.15
15 5 0.19
16 9 0.33
17 9 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTTAATAATAATA
Found at i:504140 original size:15 final size:15
Alignment explanation
Indices: 504109--504149 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 15
504099 AAAATATTTA
504109 AAATAATAAAAT--T
1 AAATAATAAAATAAT
504122 -AATAATAAAATAAT
1 AAATAATAAAATAAT
504136 AAATAAT-AAATAAT
1 AAATAATAAAATAAT
504150 TTAATCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.44
14 8 0.32
15 6 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAATAAAATAAT
Found at i:504141 original size:7 final size:7
Alignment explanation
Indices: 504109--504149 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
504099 AAAATATTTA
504109 AAATAAT
1 AAATAAT
504116 -AA-AAT
1 AAATAAT
*
504121 TAATAAT
1 AAATAAT
504128 AAAATAAT
1 -AAATAAT
504136 AAATAAT
1 AAATAAT
504143 AAATAAT
1 AAATAAT
504150 TTAATCAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
5 3 0.10
6 4 0.13
7 17 0.57
8 6 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATAAT
Found at i:504147 original size:19 final size:19
Alignment explanation
Indices: 504091--504148 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
504081 GATAAATTTT
* **
504091 AATAATAAAAAATATTTAA
1 AATAATAAATAATAAATAA
504110 AATAATAAAATTAAT-AATAA
1 AATAAT-AAA-TAATAAATAA
504130 AATAATAAATAATAAATAA
1 AATAATAAATAATAAATAA
504149 TTTAATCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.12
19 14 0.42
20 12 0.36
21 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAATAAATAATAAATAA
Found at i:505627 original size:9 final size:9
Alignment explanation
Indices: 505613--505645 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
505603 GCTTTTTATT
505613 ATTAATTTA
1 ATTAATTTA
505622 ATTAATTTA
1 ATTAATTTA
505631 ATT-ATTTGA
1 ATTAATTT-A
505640 ATTAAT
1 ATTAAT
505646 AGGTTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.18
9 16 0.73
10 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
ATTAATTTA
Found at i:505697 original size:21 final size:20
Alignment explanation
Indices: 505656--505701 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
505646 AGGTTTAATT
505656 AAAATATTTTTAATTATTAA
1 AAAATATTTTTAATTATTAA
505676 AAAATATTTTTAATT-TTATA
1 AAAATATTTTTAATTATTA-A
505696 AAAATA
1 AAAATA
505702 ATAAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAATATTTTTAATTATTAA
Found at i:506025 original size:10 final size:10
Alignment explanation
Indices: 505987--506070 Score: 50
Period size: 10 Copynumber: 8.8 Consensus size: 10
505977 AAATTAAAAG
505987 TTTATATATT
1 TTTATATATT
** *
505997 CATAT-TATA
1 TTTATATATT
506006 TTTATATATT
1 TTTATATATT
*
506016 TTTATGTATT
1 TTTATATATT
* *
506026 ATTAT-TATA
1 TTTATATATT
*
506035 TTTA-AGA-T
1 TTTATATATT
*
506043 ATTATATATT
1 TTTATATATT
* *
506053 TATATAAATT
1 TTTATATATT
506063 TTTATATA
1 TTTATATA
506071 CTAATAATTT
Statistics
Matches: 51, Mismatches: 19, Indels: 8
0.65 0.24 0.10
Matches are distributed among these distances:
8 3 0.06
9 15 0.29
10 33 0.65
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (10 bp):
TTTATATATT
Found at i:506028 original size:21 final size:19
Alignment explanation
Indices: 505987--506134 Score: 70
Period size: 19 Copynumber: 8.2 Consensus size: 19
505977 AAATTAAAAG
*
505987 TTTATATATTCATATTATA
1 TTTATATATTTATATTATA
*
506006 TTTATATATTTTTATGTAT-
1 TTTATATATTTATAT-TATA
*
506025 TATTATTATATTTA-A-GATA
1 T-TTA-TATATTTATATTATA
*
506044 -TTATATATTTATA-TAAA
1 TTTATATATTTATATTATA
* *
506061 TTT-T-TATATACTAATA-A
1 TTTATATATTTA-TATTATA
* *
506078 TTTATATA-ATATA-AAT-
1 TTTATATATTTATATTATA
506094 TTTAATATATTTATATTA-A
1 TTT-ATATATTTATATTATA
*
506113 TTT-TTTATTTTATATTATA
1 TTTATATA-TTTATATTATA
506132 TTT
1 TTT
506135 TAATTATTAT
Statistics
Matches: 101, Mismatches: 11, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
16 17 0.17
17 23 0.23
18 23 0.23
19 24 0.24
20 7 0.07
21 7 0.07
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (19 bp):
TTTATATATTTATATTATA
Found at i:506148 original size:18 final size:19
Alignment explanation
Indices: 506092--506150 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 19
506082 TATAATATAA
506092 ATTTTAATATATTTATATTA-
1 ATTTTAAT-TA-TTATATTAT
*
506112 ATTTTTTATT-TTATATTAT
1 A-TTTTAATTATTATATTAT
506131 ATTTTAATTATTAT-TTAT
1 ATTTTAATTATTATATTAT
506149 AT
1 AT
506151 CGGATGCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 21 0.62
19 5 0.15
20 2 0.06
21 6 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTAATTATTATATTAT
Found at i:506677 original size:19 final size:19
Alignment explanation
Indices: 506653--506741 Score: 65
Period size: 19 Copynumber: 4.5 Consensus size: 19
506643 TAAAATAAAT
506653 ATTAAATATAATATATTTA
1 ATTAAATATAATATATTTA
* *
506672 ATTAAAATATATTTATTTTTA
1 ATT-AAATATA-ATATATTTA
*
506693 A-AAAATTTATAATATATTTA
1 ATTAAA--TATAATATATTTA
* *
506713 A-AAAATTATAATATTTTTA
1 ATTAAA-TATAATATATTTA
*
506732 TTTAAATATA
1 ATTAAATATA
506742 TATCTATTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
19 23 0.40
20 22 0.39
21 12 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAAATATAATATATTTA
Found at i:506680 original size:15 final size:15
Alignment explanation
Indices: 506642--506686 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
506632 TTATTTGAAT
*
506642 TTAAAATAAATATTAA
1 TTAAAATATAT-TTAA
* *
506658 ATATAATATATTTAA
1 TTAAAATATATTTAA
506673 TTAAAATATATTTA
1 TTAAAATATATTTA
506687 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAAATATATTTAA
Found at i:506681 original size:20 final size:18
Alignment explanation
Indices: 506656--506731 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 18
506646 AATAAATATT
506656 AAATATAATATATTTAATTA
1 AAATATAATATATTTAA--A
* *
506676 AAATATATTTATTTTTAAA
1 AAATATA-ATATATTTAAA
506695 AAATTTATAATATATTTAAA
1 AAA--TATAATATATTTAAA
*
506715 AAATTATAATATTTTTA
1 AAA-TATAATATATTTA
506732 TTTAAATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
19 17 0.35
20 19 0.40
21 12 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATATAATATATTTAAA
Found at i:506738 original size:20 final size:19
Alignment explanation
Indices: 506652--506743 Score: 60
Period size: 20 Copynumber: 4.6 Consensus size: 19
506642 TTAAAATAAA
506652 TATTAAA-TATAATATATT
1 TATTAAATTATAATATATT
* * *
506670 TAATTAAAATATATTTATTTT
1 T-ATTAAATTATA-ATATATT
**
506691 TAAAAAATTTATAATATATT
1 TATTAAA-TTATAATATATT
** *
506711 TAAAAAATTATAATATTTT
1 TATTAAATTATAATATATT
506730 TATTTAAATATATA
1 TA-TTAAAT-TATA
506744 TCTATTCATG
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
18 1 0.02
19 19 0.33
20 24 0.41
21 14 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTAAATTATAATATATT
Found at i:520874 original size:3 final size:3
Alignment explanation
Indices: 520866--520899 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
520856 AATTTTATTC
*
520866 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
520900 AAAGTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:522792 original size:16 final size:17
Alignment explanation
Indices: 522771--522813 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
522761 CGGACTCGAT
522771 ATGACTCGAACCT-AAA
1 ATGACTCGAACCTGAAA
* *
522787 ATGACTTGAACTTGAAA
1 ATGACTCGAACCTGAAA
522804 ATGACTCGAA
1 ATGACTCGAA
522814 AATTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (17 bp):
ATGACTCGAACCTGAAA
Found at i:525231 original size:19 final size:18
Alignment explanation
Indices: 525207--525250 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
525197 AATTGCCTAC
525207 TTTTTTATTATTAAATTA
1 TTTTTTATTATTAAATTA
*
525225 TTATTTTATTCTTAAATTA
1 TT-TTTTATTATTAAATTA
525244 TTTTTTA
1 TTTTTTA
525251 AATTCAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTTATTATTAAATTA
Found at i:525925 original size:4 final size:4
Alignment explanation
Indices: 525916--525946 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
525906 ATGTAAAAAC
525916 AAAG AAAG AAAG AAAG AAAG AAAGG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAA-G AAAG AA
525947 TCATAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:527777 original size:17 final size:18
Alignment explanation
Indices: 527746--527785 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
527736 AAAGTAAGAA
527746 AAAAATACAATATTTAAT
1 AAAAATACAATATTTAAT
*
527764 AAAAATATAA-ATTTAAT
1 AAAAATACAATATTTAAT
527781 AAAAA
1 AAAAA
527786 ATTTACAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATACAATATTTAAT
Found at i:527786 original size:18 final size:19
Alignment explanation
Indices: 527745--527787 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
527735 AAAAGTAAGA
527745 AAAAAATACAATATTTAAT
1 AAAAAATACAATATTTAAT
*
527764 -AAAAATATAA-ATTTAAT
1 AAAAAATACAATATTTAAT
527781 AAAAAAT
1 AAAAAAT
527788 TTACAAAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAAATACAATATTTAAT
Found at i:528084 original size:17 final size:18
Alignment explanation
Indices: 528064--528100 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
528054 TGAATAAAGA
528064 AAAAAATAATATT-AATT
1 AAAAAATAATATTAAATT
528081 AAAAAATAATATTAAATT
1 AAAAAATAATATTAAATT
528099 AA
1 AA
528101 TAATTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAAATAATATTAAATT
Found at i:531045 original size:22 final size:21
Alignment explanation
Indices: 531014--531083 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
531004 ATGATTTAAG
531014 TAATTATATAAAATATTAAAAGT
1 TAATT-TATAAAATATTAAAA-T
* *
531037 TTATTTATATAAATAATAAAAT
1 TAATTTATA-AAATATTAAAAT
* *
531059 TAATTT-TAATAAAATTAAAAA
1 TAATTTATAA-AATATTAAAAT
531080 TAAT
1 TAAT
531084 AATGATAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 14 0.36
22 10 0.26
23 14 0.36
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (21 bp):
TAATTTATAAAATATTAAAAT
Found at i:531048 original size:24 final size:23
Alignment explanation
Indices: 531017--531073 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
531007 ATTTAAGTAA
* *
531017 TTATATAAAATATTAAAAGTTTAT
1 TTATATAAAATAATAAAA-TTAAT
531041 TTATAT-AAATAATAAAATTAAT
1 TTATATAAAATAATAAAATTAAT
531063 TT-TAATAAAAT
1 TTAT-ATAAAAT
531074 TAAAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 1 0.03
22 8 0.28
23 14 0.48
24 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTATATAAAATAATAAAATTAAT
Found at i:531083 original size:15 final size:15
Alignment explanation
Indices: 531047--531085 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
531037 TTATTTATAT
531047 AAATAATAAAATTAA
1 AAATAATAAAATTAA
***
531062 TTTTAATAAAATTAA
1 AAATAATAAAATTAA
531077 AAATAATAA
1 AAATAATAA
531086 TGATAATAAA
Statistics
Matches: 18, Mismatches: 6, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATAATAAAATTAA
Found at i:531132 original size:24 final size:24
Alignment explanation
Indices: 531066--531132 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
531056 AATTAATTTT
* *
531066 AATAAAATTAAAAATAATAATGAT
1 AATAAAATTAAATATAATAATGAA
* *
531090 AATAAAATTAGATATTATAATAGTAA
1 AATAAAATTAAATATAATAAT-G-AA
531116 AATTAAAATTAAATATA
1 AA-TAAAATTAAATATA
531133 TTTTAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 18 0.53
25 1 0.03
26 3 0.09
27 12 0.35
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
AATAAAATTAAATATAATAATGAA
Found at i:531266 original size:39 final size:38
Alignment explanation
Indices: 531217--531431 Score: 144
Period size: 34 Copynumber: 6.0 Consensus size: 38
531207 TATATATATG
531217 ATAAATAATTAAAAATATATTTATATTAAATAATAAAAT
1 ATAAA-AATTAAAAATATATTTATATTAAATAATAAAAT
531256 ATATAAAATT----AT-T-TTTATATTAAATAAT--AAT
1 ATA-AAAATTAAAAATATATTTATATTAAATAATAAAAT
* *
531287 -TAAAAATTATTAAATTATATTTATATTAAGTAA-AAAAT
1 ATAAAAATTA--AAAATATATTTATATTAAATAATAAAAT
* *
531325 AT--AAA-TAAAAGTATATTTATGTTAAATAAT--AAT
1 ATAAAAATTAAAAATATATTTATATTAAATAATAAAAT
* * * * *
531358 -TAAAAATTATTAAAT-TATATATA-TATATTATATAAT
1 ATAAAAATTA-AAAATATATTTATATTAAATAATAAAAT
** *
531394 A-AATTATTAAAATTATATTTATATTAAATAATAAAAT
1 ATAAAAATTAAAAATATATTTATATTAAATAATAAAAT
531431 A
1 A
531432 CATATTAAAA
Statistics
Matches: 135, Mismatches: 19, Indels: 46
0.68 0.09 0.23
Matches are distributed among these distances:
29 6 0.04
30 2 0.01
31 3 0.02
32 1 0.01
33 18 0.13
34 29 0.21
35 14 0.10
36 22 0.16
37 27 0.20
38 3 0.02
39 8 0.06
40 2 0.01
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (38 bp):
ATAAAAATTAAAAATATATTTATATTAAATAATAAAAT
Found at i:531340 original size:104 final size:105
Alignment explanation
Indices: 531221--531431 Score: 263
Period size: 104 Copynumber: 2.0 Consensus size: 105
531211 TATATGATAA
* *
531221 ATAATTAAAAATATATTTATATTAAATAATAAAATATATAAAATTATT-TTTATATTAAATA-AT
1 ATAAATAAAAATATATTTATATTAAATAAT--AAT-TA-AAAATTATTAATTATA-TAAATATAT
*
531284 AAT-TAA-AAATTATT-AAATTATATTTATATTAAGTAA-AAAAT
61 AATATAATAAATTATTAAAATTATATTTATATTAAATAATAAAAT
* * * *
531325 ATAAATAAAAGTATATTTATGTTAAATAATAATTAAAAATTATTAAATTATATATATATATTATA
1 ATAAATAAAAATATATTTATATTAAATAATAATTAAAAATTATT-AATTATATAAATATATAATA
531390 TAATAAATTATTAAAATTATATTTATATTAAATAATAAAAT
65 TAATAAATTATTAAAATTATATTTATATTAAATAATAAAAT
531431 A
1 A
531432 CATATTAAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
100 9 0.10
101 7 0.08
102 12 0.13
103 3 0.03
104 35 0.38
105 21 0.23
106 6 0.06
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (105 bp):
ATAAATAAAAATATATTTATATTAAATAATAATTAAAAATTATTAATTATATAAATATATAATAT
AATAAATTATTAAAATTATATTTATATTAAATAATAAAAT
Found at i:531344 original size:71 final size:69
Alignment explanation
Indices: 531232--531427 Score: 270
Period size: 71 Copynumber: 2.8 Consensus size: 69
531222 TAATTAAAAA
*
531232 TATATTTATATTAAATAATAAAATAT-ATAAAATTATTTTTATATTAAATAATAATTAAAAATTA
1 TATATTTATATT-AATAA-AAAATATAATAAAATTATATTTATATTAAATAATAATTAAAAATTA
531296 TTAAAT
64 TTAAAT
* *
531302 TATATTTATATTAAGTAAAAAATATAAATAAAAGTATATTTATGTTAAATAATAATTAAAAATTA
1 TATATTTATATTAA-TAAAAAATAT-AATAAAATTATATTTATATTAAATAATAATTAAAAATTA
531367 TTAAAT
64 TTAAAT
* *
531373 TATATATATATATTATATAATAAAT-TATTAAAATTATATTTATATTAAATAATAA
1 TATAT-T-TATATTA-ATAAAAAATATAATAAAATTATATTTATATTAAATAATAA
531428 AATACATATT
Statistics
Matches: 113, Mismatches: 7, Indels: 11
0.86 0.05 0.08
Matches are distributed among these distances:
69 9 0.08
70 15 0.13
71 72 0.64
72 2 0.02
73 14 0.12
74 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (69 bp):
TATATTTATATTAATAAAAAATATAATAAAATTATATTTATATTAAATAATAATTAAAAATTATT
AAAT
Found at i:531407 original size:34 final size:31
Alignment explanation
Indices: 531217--531428 Score: 145
Period size: 37 Copynumber: 6.2 Consensus size: 31
531207 TATATATATG
* *
531217 ATAAATAATTAAAAATATATTTATATTAAATA
1 ATAAATTATT-AAATTATATTTATATTAAATA
* *
531249 ATAAAATATATAAAATTATTTTTATATTAAATAATA
1 AT-AAAT-TATTAAATTATATTTATATT--A-AATA
*
531285 ATTAAAAATTATTAAATTATATTTATATTAAGTA
1 A-T--AAATTATTAAATTATATTTATATTAAATA
* * * *
531319 AAAAATATAAATAAAAGTATATTTATGTTAAATAATA
1 ATAAAT-T--ATTAAATTATATTTATATT--A-AATA
*
531356 ATTAAAAATTATTAAATTATATATATATATTATATA
1 A-T--AAATTATTAAATTATAT-T-TATATTAAATA
531392 ATAAATTATTAAAATTATATTTATATTAAATA
1 ATAAATTATT-AAATTATATTTATATTAAATA
531424 ATAAA
1 ATAAA
531429 ATACATATTA
Statistics
Matches: 143, Mismatches: 18, Indels: 38
0.72 0.09 0.19
Matches are distributed among these distances:
31 4 0.03
32 18 0.13
33 27 0.19
34 31 0.22
35 3 0.02
36 10 0.07
37 34 0.24
38 6 0.04
39 6 0.04
40 4 0.03
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (31 bp):
ATAAATTATTAAATTATATTTATATTAAATA
Found at i:531416 original size:25 final size:25
Alignment explanation
Indices: 531381--531430 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
531371 ATTATATATA
*
531381 TATATTATATAATAAATTATTAAAAT
1 TATATTATATAATAAA-TAATAAAAT
*
531407 TATATT-TATATTAAATAATAAAAT
1 TATATTATATAATAAATAATAAAAT
531431 ACATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 8 0.36
26 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TATATTATATAATAAATAATAAAAT
Found at i:531436 original size:25 final size:26
Alignment explanation
Indices: 531365--531438 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
531355 AATTAAAAAT
* *
531365 TATTAAATTAT-ATATATATATTATA
1 TATTAAATAATAAAATATATATTATA
* *
531390 TAATAAATTATTAAAAT-TATATT-TA
1 TATTAAA-TAATAAAATATATATTATA
*
531415 TATTAAATAATAAAATACATATTA
1 TATTAAATAATAAAATATATATTA
531439 AAAACTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
24 8 0.21
25 19 0.50
26 8 0.21
27 3 0.08
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
TATTAAATAATAAAATATATATTATA
Found at i:531481 original size:27 final size:28
Alignment explanation
Indices: 531451--531516 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
531441 AACTAAAAAT
*
531451 AATATTTATGTTAAAAAATAA-T-TTAAA
1 AATATTTATATT-AAAAATAATTATTAAA
531478 AATAATTTATATTAAAAATAATTATTAAA
1 AAT-ATTTATATTAAAAATAATTATTAAA
531507 ATATATTTAT
1 A-ATATTTAT
531517 TATATTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
27 11 0.32
28 9 0.26
29 12 0.35
30 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AATATTTATATTAAAAATAATTATTAAA
Found at i:531492 original size:28 final size:29
Alignment explanation
Indices: 531444--531516 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 29
531434 TATTAAAAAC
*
531444 TAAAAATAATATTTATGTTAAAAAATAATT-
1 TAAAAAT-ATATTTATATT-AAAAATAATTA
531474 TAAAAATA-ATTTATATTAAAAATAATTA
1 TAAAAATATATTTATATTAAAAATAATTA
*
531502 TTAAAATATATTTAT
1 TAAAAATATATTTAT
531517 TATATTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.26
28 15 0.38
29 7 0.18
30 7 0.18
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
TAAAAATATATTTATATTAAAAATAATTA
Found at i:531493 original size:143 final size:143
Alignment explanation
Indices: 531231--531526 Score: 318
Period size: 143 Copynumber: 2.1 Consensus size: 143
531221 ATAATTAAAA
* * *
531231 ATATATTTATATTAAATAATAAAATATATAAAATTATTTTTATATTAAATAATAATTAAAAATTA
1 ATATATATATATTAAATAATAAAATATATAAAATTATATTTATATTAAATAATAAATAAAAATTA
* * * * * * *
531296 TTAAATTATATTTATATTAAGTAAAAAATATAAATAAAAGTATATTTATGTTAAATAATAATTA-
66 TAAAATAAAAATAATATTAAGTAAAAAATATAAATAAAAATATATTTATATTAAA-AATAATTAT
531360 AAAAT-TATTAAATT
130 AAAATATATT-AATT
* * * *
531374 ATATATATATATTATATAATAAATTAT-TAAAATTATATTTATATTAAATAATAAAATACATATT
1 ATATATATATATTAAATAATAAAATATATAAAATTATATTTATATTAAATAAT-AAATAAAAATT
* **
531438 A-AAAACTAAAAATAATATTTATGTTAAAAAATA-ATTTAAAAATA-ATTTATATTAAAAATAAT
65 ATAAAA-TAAAAATAATA-TTAAG-TAAAAAATATAAATAAAAATATATTTATATTAAAAATAAT
*
531500 TATTAAAATATATTTATT
127 TA-TAAAATATATTAATT
531518 ATAT-TATAT
1 ATATATATAT
531527 TTTTATCAAT
Statistics
Matches: 128, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
142 35 0.27
143 56 0.44
144 24 0.19
145 13 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (143 bp):
ATATATATATATTAAATAATAAAATATATAAAATTATATTTATATTAAATAATAAATAAAAATTA
TAAAATAAAAATAATATTAAGTAAAAAATATAAATAAAAATATATTTATATTAAAAATAATTATA
AAATATATTAATT
Found at i:531517 original size:27 final size:26
Alignment explanation
Indices: 531444--531518 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 26
531434 TATTAAAAAC
531444 TAAAAATAATATTTATGTTAAAAAATAATT
1 TAAAAAT-ATATTTA--TT-AAAAATAATT
531474 TAAAAATA-ATTTATATTAAAAATAATT
1 TAAAAATATA-TT-TATTAAAAATAATT
*
531501 ATTAAAATATATTTATTA
1 -TAAAAATATATTTATTA
531519 TATTATATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
27 15 0.38
28 12 0.30
29 4 0.10
30 9 0.22
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (26 bp):
TAAAAATATATTTATTAAAAATAATT
Found at i:531518 original size:14 final size:14
Alignment explanation
Indices: 531487--531528 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
531477 AAATAATTTA
*
531487 TATTAAAA-ATAAT
1 TATTAAAATATATT
531500 TATTAAAATATATT
1 TATTAAAATATATT
* *
531514 TATTATATTATATT
1 TATTAAAATATATT
531528 T
1 T
531529 TTATCAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTAAAATATATT
Found at i:533970 original size:15 final size:15
Alignment explanation
Indices: 533933--533962 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
533923 TTCAATTAAC
533933 AACTAACATATATAA
1 AACTAACATATATAA
533948 AACTAACATATATAA
1 AACTAACATATATAA
533963 CATTAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (15 bp):
AACTAACATATATAA
Found at i:538183 original size:16 final size:16
Alignment explanation
Indices: 538162--538197 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
538152 ACTTCATAAA
* *
538162 AACTAGTCATTACTTT
1 AACTAGGCATTACTTC
538178 AACTAGGCATTACTTC
1 AACTAGGCATTACTTC
538194 AACT
1 AACT
538198 GACCACTAAC
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:0.33, C:0.22, G:0.08, T:0.36
Consensus pattern (16 bp):
AACTAGGCATTACTTC
Found at i:541694 original size:15 final size:15
Alignment explanation
Indices: 541674--541704 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
541664 TGAAAATTTC
541674 AACATGTTGAAGTTA
1 AACATGTTGAAGTTA
541689 AACATGTTGAAGTTA
1 AACATGTTGAAGTTA
541704 A
1 A
541705 TGCATTGCTT
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:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
AACATGTTGAAGTTA
Found at i:541931 original size:3 final size:3
Alignment explanation
Indices: 541925--541949 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
541915 TTCTTTTATT
541925 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
541950 CATTGTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:544063 original size:6 final size:7
Alignment explanation
Indices: 544046--544102 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
544036 ACATATATTT
544046 TTATATA
1 TTATATA
544053 TTATA-A
1 TTATATA
544059 TTATAT-
1 TTATATA
*
544065 TTAAAATA
1 TT-ATATA
544073 TTATATA
1 TTATATA
544080 TTA-ATA
1 TTATATA
*
544086 -TATATT
1 TTATATA
544092 TTAATATA
1 TT-ATATA
544100 TTA
1 TTA
544103 ATAATAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
5 2 0.05
6 13 0.32
7 17 0.43
8 8 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTATATA
Found at i:544094 original size:27 final size:27
Alignment explanation
Indices: 544046--544135 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
544036 ACATATATTT
544046 TTATATATT-ATA-ATTATATTTAAAATA
1 TTATATATTAATATA-TAT-TTTAAAATA
*
544073 TTATATATTAATATATATTTTAATATA
1 TTATATATTAATATATATTTTAAAATA
* * * *
544100 TTA-ATAATAATTTATTTTTTATAAATT
1 TTATATATTAATATATATTTTA-AAATA
544127 TTAATATAT
1 TT-ATATAT
544136 CATGCACTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
26 15 0.29
27 25 0.49
28 7 0.14
29 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTATATATTAATATATATTTTAAAATA
Found at i:544110 original size:26 final size:26
Alignment explanation
Indices: 544049--544117 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
544039 TATATTTTTA
*
544049 TATATTATAATTATA-TTTAAAATAT
1 TATATAATAATTATATTTTAAAATAT
* *
544074 TATATATTAATATATATTTTAATATAT
1 TATATAATAAT-TATATTTTAAAATAT
544101 TA-ATAATAATT-TATTTT
1 TATATAATAATTATATTTT
544118 TTATAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
24 6 0.16
25 10 0.26
26 11 0.29
27 11 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TATATAATAATTATATTTTAAAATAT
Found at i:544119 original size:26 final size:27
Alignment explanation
Indices: 544049--544134 Score: 79
Period size: 26 Copynumber: 3.2 Consensus size: 27
544039 TATATTTTTA
*
544049 TATATTATAAT-TATA-TTTAAAATAT
1 TATATAATAATATATATTTTAAAATAT
* *
544074 TATATATTAATATATATTTTAATATAT
1 TATATAATAATATATATTTTAAAATAT
* * *
544101 TA-ATAATAATTTATTTTTTATAAATTT
1 TATATAATAATATATATTTTA-AAATAT
544128 TAATATA
1 T-ATATA
544135 TCATGCACTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 9 0.19
26 19 0.40
27 16 0.33
28 1 0.02
29 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATATAATAATATATATTTTAAAATAT
Found at i:544206 original size:16 final size:16
Alignment explanation
Indices: 544187--544222 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
544177 ATTTTCTACG
*
544187 TATTGTATTTATATTA
1 TATTATATTTATATTA
*
544203 TATTATGTTTATATTA
1 TATTATATTTATATTA
544219 TATT
1 TATT
544223 TACATCATGA
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:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TATTATATTTATATTA
Found at i:550384 original size:2 final size:2
Alignment explanation
Indices: 550377--550405 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
550367 AATAGAACAA
550377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
550406 AAATCAGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:551817 original size:12 final size:12
Alignment explanation
Indices: 551800--551864 Score: 62
Period size: 12 Copynumber: 5.3 Consensus size: 12
551790 TATTTAGATA
551800 TTATATTATATT
1 TTATATTATATT
* *
551812 TTATATTTTAAT
1 TTATATTATATT
551824 TTATATTATAATT
1 TTATATTAT-ATT
551837 TT-T-TTATATTT
1 TTATATTATA-TT
*
551848 TTATAATATGATT
1 TTATATTAT-ATT
551861 TTAT
1 TTAT
551865 TTTTTTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 1 0.02
11 8 0.19
12 20 0.47
13 13 0.30
14 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
TTATATTATATT
Found at i:556426 original size:20 final size:20
Alignment explanation
Indices: 556388--556443 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
556378 ATTTTTATTA
*
556388 ATATTATCTAATT--TAATT
1 ATATTACCTAATTCATAATT
* **
556406 ATTTTATTTAATTCATAATT
1 ATATTACCTAATTCATAATT
556426 ATATTACCTAATTCATAA
1 ATATTACCTAATTCATAA
556444 GTTCAAAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 11 0.35
20 20 0.65
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTACCTAATTCATAATT
Found at i:561239 original size:26 final size:28
Alignment explanation
Indices: 561208--561285 Score: 79
Period size: 32 Copynumber: 2.7 Consensus size: 28
561198 TTATAATATA
561208 AAAATATAAATATTTTAAAT-AATT-AT
1 AAAATATAAATATTTTAAATAAATTAAT
* *
561234 ATAATATAAATTATTTATATATTGAAATTAAT
1 AAAATATAAA-TATTT-TA-AAT-AAATTAAT
561266 AAAATATAAAATATTTTAAA
1 AAAATAT-AAATATTTTAAA
561286 AACAAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 9 0.22
27 5 0.12
28 2 0.05
29 2 0.05
30 1 0.02
31 6 0.15
32 13 0.32
33 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
AAAATATAAATATTTTAAATAAATTAAT
Found at i:565831 original size:15 final size:15
Alignment explanation
Indices: 565811--565887 Score: 71
Period size: 15 Copynumber: 5.7 Consensus size: 15
565801 TTATTAAAAT
565811 ATATTAAATAATTTA
1 ATATTAAATAATTTA
565826 ATATTAAAT-ATTT-
1 ATATTAAATAATTTA
*
565839 AT-TTAATTAA--TA
1 ATATTAAATAATTTA
* *
565851 ATATTATATTATTT-
1 ATATTAAATAATTTA
565865 A-ATT-AATAATTTA
1 ATATTAAATAATTTA
565878 ATATTAAATA
1 ATATTAAATA
565888 TTGTTTAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
11 1 0.02
12 13 0.27
13 12 0.25
14 8 0.17
15 14 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTAAATAATTTA
Found at i:565844 original size:18 final size:17
Alignment explanation
Indices: 565821--565889 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 17
565811 ATATTAAATA
565821 ATTTAATATTAAATATTT
1 ATTTAAT-TTAAATATTT
*
565839 ATTTAATTAATAATA-TT
1 ATTTAATTTA-AATATTT
* * *
565856 ATATT-ATTTAATTAATA
1 AT-TTAATTTAAATATTT
565873 ATTTAATATTAAATATT
1 ATTTAAT-TTAAATATT
565890 GTTTAATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
16 5 0.12
17 15 0.38
18 20 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTAATTTAAATATTT
Found at i:565883 original size:22 final size:22
Alignment explanation
Indices: 565823--565883 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
565813 ATTAAATAAT
*
565823 TTAAT-ATTAAATATTTATTTAA
1 TTAATAATTTAATA-TTATTTAA
565845 TTAATAATATT-ATATTATTTAA
1 TTAATAAT-TTAATATTATTTAA
565867 TTAATAATTTAATATTA
1 TTAATAATTTAATATTA
565884 AATATTGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 2 0.06
22 27 0.77
23 5 0.14
24 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAATAATTTAATATTATTTAA
Found at i:565895 original size:25 final size:24
Alignment explanation
Indices: 565776--565899 Score: 83
Period size: 25 Copynumber: 4.8 Consensus size: 24
565766 TTAGATAAAA
*
565776 ATTAAAT-TTTTTAAATTATATATAATT
1 ATTAAATATTTTT-AA-TA-ATTTAA-T
* *
565803 ATTAAAATATATTAAATAATTTAAT
1 ATT-AAATATTTTTAATAATTTAAT
565828 ATTAAATATTTATT--TAATTAATAAT
1 ATTAAATATTT-TTAATAATT--TAAT
*
565853 ATTATATTATTTAATTAATAATTTAAT
1 ATTA-AATATTT--TTAATAATTTAAT
565880 ATTAAATATTGTTTAATAAT
1 ATTAAATATT-TTTAATAAT
565900 GCTAGGGATA
Statistics
Matches: 80, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
23 5 0.06
24 7 0.09
25 21 0.26
26 16 0.20
27 17 0.21
28 6 0.08
29 8 0.10
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.52
Consensus pattern (24 bp):
ATTAAATATTTTTAATAATTTAAT
Found at i:567123 original size:11 final size:11
Alignment explanation
Indices: 567107--567143 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
567097 AACATATAAA
567107 TTTTTTTC-TT
1 TTTTTTTCTTT
567117 TTTTTTTCTTT
1 TTTTTTTCTTT
*
567128 TCTTTTTCTTT
1 TTTTTTTCTTT
567139 TTTTT
1 TTTTT
567144 CTTTCCCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:567130 original size:15 final size:15
Alignment explanation
Indices: 567107--567147 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
567097 AACATATAAA
567107 TTTTTTTCTTTTT-T
1 TTTTTTTCTTTTTCT
567121 TTTCTTTTCTTTTTCT
1 TTT-TTTTCTTTTTCT
567137 TTTTTTTCTTT
1 TTTTTTTCTTT
567148 CCCTCATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.12
15 18 0.72
16 4 0.16
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTCTTTTTCT
Found at i:567139 original size:20 final size:21
Alignment explanation
Indices: 567109--567147 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
567099 CATATAAATT
567109 TTTTTCTTTTTTTTTCTTTTC
1 TTTTTCTTTTTTTTTCTTTTC
567130 TTTTTC-TTTTTTTTCTTT
1 TTTTTCTTTTTTTTTCTTT
567148 CCCTCATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (21 bp):
TTTTTCTTTTTTTTTCTTTTC
Found at i:567157 original size:21 final size:20
Alignment explanation
Indices: 567116--567165 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
567106 ATTTTTTTCT
* **
567116 TTTTTTTTCTTTTCTTTTTC
1 TTTTTTTTCTTTCCTCATTC
567136 TTTTTTTTCTTTCCCTCATTC
1 TTTTTTTTCTTT-CCTCATTC
567157 TTCTTTTTT
1 TT-TTTTTT
567166 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.48
21 7 0.28
22 6 0.24
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTTTCTTTCCTCATTC
Found at i:568925 original size:23 final size:21
Alignment explanation
Indices: 568871--568914 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
568861 TTATCAATTT
*
568871 TATATTTTGATAATATAATTATA
1 TATATTTTAAT-A-ATAATTATA
568894 TATATTTTAATAATAATTATA
1 TATATTTTAATAATAATTATA
568915 ATTTTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 1 0.05
23 10 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TATATTTTAATAATAATTATA
Found at i:569490 original size:26 final size:26
Alignment explanation
Indices: 569455--569508 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
569445 ATTTGCTTAA
569455 AAAACATATTACATATCTATTTAATT
1 AAAACATATTACATATCTATTTAATT
* *
569481 AAAACATATTATATATTTATTTAATT
1 AAAACATATTACATATCTATTTAATT
569507 AA
1 AA
569509 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAACATATTACATATCTATTTAATT
Found at i:570272 original size:3 final size:3
Alignment explanation
Indices: 570264--570309 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
570254 AAATGTGTTT
* *
570264 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
570310 GTGCTGTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:571094 original size:38 final size:39
Alignment explanation
Indices: 571023--571096 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
571013 TTTATATTTT
*
571023 AATTATATTTAAATAAAAAATAAAATATTAATTTTTTAA
1 AATTATATTTAAATAAAAAATAAAATATCAATTTTTTAA
*
571062 AATT-TATTTAAAT-ATAAATAAAATATACAATTTTT
1 AATTATATTTAAATAAAAAATAAAATAT-CAATTTTT
571097 GTTAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 12 0.38
38 16 0.50
39 4 0.12
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (39 bp):
AATTATATTTAAATAAAAAATAAAATATCAATTTTTTAA
Found at i:579179 original size:15 final size:17
Alignment explanation
Indices: 579147--579184 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
579137 AACACTACTA
*
579147 CAAAAAAGTGTTGTTGT
1 CAAAAAAGTGCTGTTGT
579164 CAAAAAA-TGCTG-TGT
1 CAAAAAAGTGCTGTTGT
579179 CAAAAA
1 CAAAAA
579185 TATATGTGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 4 0.20
17 7 0.35
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (17 bp):
CAAAAAAGTGCTGTTGT
Done.