Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001484.1 Hibiscus syriacus cultivar Beakdansim tig00002880_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1039362
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:250357 original size:6 final size:6
Alignment explanation
Indices: 250347--250382 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
250337 CATACTAGAT
*
250347 ATGCCT ATGCCA ATGCCA ATGCCA ATGCCA ATGCCA
1 ATGCCA ATGCCA ATGCCA ATGCCA ATGCCA ATGCCA
250383 TTGCAGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (6 bp):
ATGCCA
Found at i:250505 original size:13 final size:14
Alignment explanation
Indices: 250487--250531 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
250477 GAGAGACGCC
250487 AGAAATTAATAAT-
1 AGAAATTAATAATA
*
250500 AGAAATTAGTATATA
1 AGAAATTAATA-ATA
*
250515 AGAAATTAATAAAA
1 AGAAATTAATAATA
250529 AGA
1 AGA
250532 CTTAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 10 0.37
14 7 0.26
15 10 0.37
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (14 bp):
AGAAATTAATAATA
Found at i:251364 original size:20 final size:20
Alignment explanation
Indices: 251339--251408 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
251329 GTATCGTGAT
*
251339 TTTGTCGTTTGGGATTTAGA
1 TTTGTCGTTTGGGATTTAGC
251359 TTTGTCGTTTGGGATTTAGC
1 TTTGTCGTTTGGGATTTAGC
251379 TTTGTCGTTTGGGATTTAGC
1 TTTGTCGTTTGGGATTTAGC
251399 TTTGTCGTTT
1 TTTGTCGTTT
251409 TATTCATAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.10, C:0.09, G:0.29, T:0.53
Consensus pattern (20 bp):
TTTGTCGTTTGGGATTTAGC
Found at i:251631 original size:26 final size:27
Alignment explanation
Indices: 251590--251644 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
251580 GTTTTTCTAT
*
251590 AAAAATATATAATTTT-AAGTTTTATA
1 AAAAATATATAATTTTAAAATTTTATA
251616 AAAAATATA-AATTTTTAAAATTTTATA
1 AAAAATATATAA-TTTTAAAATTTTATA
251643 AA
1 AA
251645 GACGACACGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 2 0.08
26 13 0.50
27 11 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
AAAAATATATAATTTTAAAATTTTATA
Found at i:255054 original size:18 final size:17
Alignment explanation
Indices: 255022--255055 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
255012 TTCAAAATTT
*
255022 AATTAAAAATTATATAA
1 AATTAAAAATAATATAA
255039 AATTAAAAATAAATATA
1 AATTAAAAAT-AATATA
255056 TTAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATTAAAAATAATATAA
Found at i:256301 original size:42 final size:42
Alignment explanation
Indices: 256169--256318 Score: 137
Period size: 42 Copynumber: 3.5 Consensus size: 42
256159 CTTTTTTATA
* *
256169 TTTATAATTGAGGTCTTAAATCTTTTTCAATCTCACTTTGTACT
1 TTTATAATTGAGGCCTT-AAT-TTTTTCAATCTCACTTTCTACT
* * * *
256213 TTTATAATTAATGCCTCTAATTTTTT-AACCTCACTTTCTACC
1 TTTATAATTGAGGCCT-TAATTTTTTCAATCTCACTTTCTACT
* *
256255 TTTATAATTGAGGCCATTAATGTTTTTCAATATCA-TTT-TATT
1 TTTATAATTGAGGCC-TTAAT-TTTTTCAATCTCACTTTCTACT
*
256297 TTTATAATT-AGACCTCTAATTT
1 TTTATAATTGAGGCCT-TAATTT
256319 AATCATTTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
40 3 0.03
41 8 0.09
42 41 0.47
43 14 0.16
44 21 0.24
45 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (42 bp):
TTTATAATTGAGGCCTTAATTTTTTCAATCTCACTTTCTACT
Found at i:258586 original size:11 final size:11
Alignment explanation
Indices: 258566--258611 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
258556 AATATATTAA
258566 ATTTAAATATT
1 ATTTAAATATT
*
258577 ATTTATATATT
1 ATTTAAATATT
258588 ATATTAAAATATT
1 AT-TT-AAATATT
*
258601 ATTTTAATATT
1 ATTTAAATATT
258612 TTAATATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 18 0.60
12 4 0.13
13 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTAAATATT
Found at i:258611 original size:24 final size:24
Alignment explanation
Indices: 258557--258604 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
258547 CATCTTATCA
*
258557 ATATATTAAATTTAAATATTATTT
1 ATATATTAAATTAAAATATTATTT
*
258581 ATATATTATATTAAAATATTATTT
1 ATATATTAAATTAAAATATTATTT
258605 TAATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATATATTAAATTAAAATATTATTT
Found at i:258622 original size:24 final size:24
Alignment explanation
Indices: 258557--258623 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
258547 CATCTTATCA
*
258557 ATATATTA-AATTTAAATATTATTT
1 ATATATTATAA-TAAAATATTATTT
*
258581 ATATATTATATTAAAATATTATTT
1 ATATATTATAATAAAATATTATTT
* *
258605 -TAATATTTTAATATAATAT
1 AT-ATATTATAATAAAATAT
258624 ATGTTAGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATATATTATAATAAAATATTATTT
Found at i:258638 original size:13 final size:15
Alignment explanation
Indices: 258619--258649 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
258609 ATTTTAATAT
258619 AATATATGTTAGAAA
1 AATATATGTTAGAAA
258634 AATATATGTTAGAAA
1 AATATATGTTAGAAA
258649 A
1 A
258650 GAATGTAATT
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:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (15 bp):
AATATATGTTAGAAA
Found at i:259491 original size:24 final size:24
Alignment explanation
Indices: 259445--259499 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
259435 ATTTTCTCTT
259445 TTTTAATCTATTTAGTGTTTTTTA
1 TTTTAATCTATTTAGTGTTTTTTA
*
259469 TATTTAA-CTTTTTA-TGTTATTTTA
1 T-TTTAATCTATTTAGTGTT-TTTTA
259493 TTTTAAT
1 TTTTAAT
259500 AAATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 9 0.33
24 13 0.48
25 5 0.19
ACGTcount: A:0.24, C:0.04, G:0.05, T:0.67
Consensus pattern (24 bp):
TTTTAATCTATTTAGTGTTTTTTA
Found at i:262463 original size:42 final size:42
Alignment explanation
Indices: 262412--262513 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
262402 AAGATTATTG
262412 TCGTCACAAATCACCAACTAACATTAATGACAAAAACAATTA
1 TCGTCACAAATCACCAACTAACATTAATGACAAAAACAATTA
* * *
262454 TCGTCACAAATCTCCAACTAAGATTAGTGACAAAAACAATTA
1 TCGTCACAAATCACCAACTAACATTAATGACAAAAACAATTA
* *
262496 TTGTCACAAATCATCAAC
1 TCGTCACAAATCACCAAC
262514 AAAGACTGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.24
Consensus pattern (42 bp):
TCGTCACAAATCACCAACTAACATTAATGACAAAAACAATTA
Found at i:267509 original size:32 final size:32
Alignment explanation
Indices: 267468--267531 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
267458 TTTGTTGATT
267468 CAGATTGTAGTGCTTGTCCTGATACTTGACGG
1 CAGATTGTAGTGCTTGTCCTGATACTTGACGG
*
267500 CAGATTGTAGTGCTTGTCCTTATACTTGACGG
1 CAGATTGTAGTGCTTGTCCTGATACTTGACGG
267532 TCTATAACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.36
Consensus pattern (32 bp):
CAGATTGTAGTGCTTGTCCTGATACTTGACGG
Found at i:268948 original size:22 final size:22
Alignment explanation
Indices: 268896--268969 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
268886 TTAAAAATAT
* *
268896 AAATAAAAAATAGTCA-AACGATC
1 AAATAAAACATA-TCATAAAGA-C
*
268919 AAA-AAAACATATCA-AAAGGC
1 AAATAAAACATATCATAAAGAC
268939 ATAATAAAACATATCATAAAGAC
1 A-AATAAAACATATCATAAAGAC
268962 AAATAAAA
1 AAATAAAA
268970 ACGTGTTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.05
21 8 0.18
22 25 0.57
23 9 0.20
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.16
Consensus pattern (22 bp):
AAATAAAACATATCATAAAGAC
Found at i:269040 original size:18 final size:17
Alignment explanation
Indices: 269017--269062 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
269007 TGGACTTATT
269017 AAATATAAAATAAAATAA
1 AAATATAAAATAAAA-AA
*
269035 AAATATAATATAAAAAA
1 AAATATAAAATAAAAAA
*
269052 TAATA-AAAATA
1 AAATATAAAATA
269063 TCAACGATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 5 0.20
17 6 0.24
18 14 0.56
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATATAAAATAAAAAA
Found at i:269045 original size:23 final size:23
Alignment explanation
Indices: 269018--269063 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
269008 GGACTTATTA
269018 AATATAAAATAA-AATAAAAATAT
1 AATATAAAA-AATAATAAAAATAT
269041 AATATAAAAAATAATAAAAATAT
1 AATATAAAAAATAATAAAAATAT
269064 CAACGATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (23 bp):
AATATAAAAAATAATAAAAATAT
Found at i:271694 original size:21 final size:21
Alignment explanation
Indices: 271668--271858 Score: 171
Period size: 21 Copynumber: 9.2 Consensus size: 21
271658 GATTCGTAAC
271668 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
271689 GCGAACTTGGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
271710 GCGATA-GTCGACTATCGCAAT
1 GCGA-ACTTCGACTATCGCAAT
*
271731 GCGAACTTAGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
** *
271752 GCGAA-TATATA-AATCGCAAT
1 GCGAACT-TCGACTATCGCAAT
*
271772 GCGATA-GTCGACTATCGCAAT
1 GCGA-ACTTCGACTATCGCAAT
* *
271793 GCGAACTTGGACTATCGTAAT
1 GCGAACTTCGACTATCGCAAT
* * * *
271814 G-TAAATAT-GTA-AATCGTAAT
1 GCGAACT-TCG-ACTATCGCAAT
271834 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
271855 GCGA
1 GCGA
271859 TAGTCCAAGT
Statistics
Matches: 138, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
20 32 0.23
21 105 0.76
22 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:271788 original size:62 final size:62
Alignment explanation
Indices: 271668--271858 Score: 251
Period size: 62 Copynumber: 3.1 Consensus size: 62
271658 GATTCGTAAC
* * *
271668 GCGAACTTCGACTATCGCAATGCGAACT-TGGACTATCGCAATGCGATAGTCGACTATCGCAAT
1 GCGAACTTAGACTATCGCAATGCGAA-TATGTA-AATCGCAATGCGATAGTCGACTATCGCAAT
*
271731 GCGAACTTAGACTATCGCAATGCGAATATATAAATCGCAATGCGATAGTCGACTATCGCAAT
1 GCGAACTTAGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAAT
* * ** * *
271793 GCGAACTTGGACTATCGTAATGTAAATATGTAAATCGTAATGCGA-ACTTCGACTATCGCAAT
1 GCGAACTTAGACTATCGCAATGCGAATATGTAAATCGCAATGCGATA-GTCGACTATCGCAAT
271855 GCGA
1 GCGA
271859 TAGTCCAAGT
Statistics
Matches: 115, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
61 1 0.01
62 87 0.76
63 27 0.23
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (62 bp):
GCGAACTTAGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAAT
Found at i:271907 original size:35 final size:35
Alignment explanation
Indices: 271854--271921 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
271844 ACTATCGCAA
*
271854 TGCGATAGTCCAAGTTCGCATTGCGATTTATTCGT
1 TGCGATAGTCCAAATTCGCATTGCGATTTATTCGT
* *
271889 TGCGATAGTCGAAATTCGCGTTGCGATTTATTC
1 TGCGATAGTCCAAATTCGCATTGCGATTTATTC
271922 TAAATTCGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (35 bp):
TGCGATAGTCCAAATTCGCATTGCGATTTATTCGT
Found at i:272607 original size:21 final size:20
Alignment explanation
Indices: 272581--272626 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
272571 ATGCAGTCGT
* *
272581 TGCGAATTTGGACTATCGCAA
1 TGCGAATATGGA-AATCGCAA
*
272602 TGCGAATATGTAAATCGCAA
1 TGCGAATATGGAAATCGCAA
272622 TGCGA
1 TGCGA
272627 TAGTCGACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCGAATATGGAAATCGCAA
Found at i:272670 original size:21 final size:20
Alignment explanation
Indices: 272644--272698 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
272634 CTATTACATA
*
272644 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGT-CAAC
*
272665 TTCGCATTGCGATAGTCGAC
1 TTCGCATTGCGATAGTCAAC
272685 TATCGCATTGCGAT
1 T-TCGCATTGCGAT
272699 TTACATATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 3 0.10
21 28 0.90
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCAAC
Found at i:287032 original size:88 final size:89
Alignment explanation
Indices: 286869--287040 Score: 337
Period size: 88 Copynumber: 1.9 Consensus size: 89
286859 GAAGCTCAAC
286869 AATTATTCTCCATATGCCAGTCACCATCAAGTTAACTAAGAACCCATAAATAGATCATCTCTCTG
1 AATTATTCTCCATATGCCAGTCACCATCAAGTTAACTAAGAACCCATAAATAGATCATCTCTCTG
286934 ATGTTTTCAGTATTAACATGCATG
66 ATGTTTTCAGTATTAACATGCATG
286958 AATTATTCTCCATATGCCAGTCACCATCAAGTTAACT-AGAACCCATAAATAGATCATCTCTCTG
1 AATTATTCTCCATATGCCAGTCACCATCAAGTTAACTAAGAACCCATAAATAGATCATCTCTCTG
287022 ATGTTTTCAGTATTAACAT
66 ATGTTTTCAGTATTAACAT
287041 CGCACGATGA
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 46 0.55
89 37 0.45
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (89 bp):
AATTATTCTCCATATGCCAGTCACCATCAAGTTAACTAAGAACCCATAAATAGATCATCTCTCTG
ATGTTTTCAGTATTAACATGCATG
Found at i:289271 original size:29 final size:28
Alignment explanation
Indices: 289237--289317 Score: 99
Period size: 29 Copynumber: 2.9 Consensus size: 28
289227 TCATTAACCT
*
289237 TTAAAACACTTCGATTTTAGCATTTAAC
1 TTAAAACACTTCAATTTTAGCATTTAAC
* *
289265 TTCAAAACACTTCAATTTTAGCCTTAAAC
1 TT-AAAACACTTCAATTTTAGCATTTAAC
* * *
289294 TTTAAACGCTTAAATTTTAGCATT
1 TTAAAACACTTCAATTTTAGCATT
289318 AAATATTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 20 0.44
29 25 0.56
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.40
Consensus pattern (28 bp):
TTAAAACACTTCAATTTTAGCATTTAAC
Found at i:289309 original size:28 final size:29
Alignment explanation
Indices: 289228--289320 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
289218 TCAATTTGAT
* * **
289228 CATTAACCTTTAAAACACTTCGATTTTAG
1 CATTAAACTTCAAAACACTTAAATTTTAG
* *
289257 CATTTAACTTCAAAACACTTCAATTTTAG
1 CATTAAACTTCAAAACACTTAAATTTTAG
* * *
289286 CCTTAAACTT-TAAACGCTTAAATTTTAG
1 CATTAAACTTCAAAACACTTAAATTTTAG
289314 CATTAAA
1 CATTAAA
289321 TATTTTATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 21 0.39
29 33 0.61
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (29 bp):
CATTAAACTTCAAAACACTTAAATTTTAG
Found at i:290558 original size:18 final size:18
Alignment explanation
Indices: 290535--290572 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
290525 TTCGGATCCT
290535 ATGCCCATCCCGAGTTAC
1 ATGCCCATCCCGAGTTAC
*
290553 ATGCCCATCCCTAGTTAC
1 ATGCCCATCCCGAGTTAC
290571 AT
1 AT
290573 AAGTGTTAAC
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:0.24, C:0.37, G:0.13, T:0.26
Consensus pattern (18 bp):
ATGCCCATCCCGAGTTAC
Found at i:292155 original size:20 final size:20
Alignment explanation
Indices: 292132--292183 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
292122 AACGCGATCC
292132 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
292152 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
292172 CCAAAATCGCAA
1 CCAGAATCGCAA
292184 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:292333 original size:20 final size:20
Alignment explanation
Indices: 292239--292607 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
292229 GATTTTCCAT
* ** *
292239 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
292259 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
292279 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
292299 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
292319 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
292339 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
292359 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
292379 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
292399 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
292419 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
292439 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
292459 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
292479 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
292499 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
292519 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
292539 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
292559 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
292579 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
292599 AATCACAAC
1 AATCGCAAC
292608 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:293329 original size:24 final size:24
Alignment explanation
Indices: 293290--293336 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
293280 AAATTTGGTC
293290 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
293314 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
293337 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:293528 original size:12 final size:12
Alignment explanation
Indices: 293511--293535 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
293501 ATATAATCCT
293511 GAAGAAGAAAAA
1 GAAGAAGAAAAA
293523 GAAGAAGAAAAA
1 GAAGAAGAAAAA
293535 G
1 G
293536 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:295335 original size:14 final size:14
Alignment explanation
Indices: 295316--295372 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
295306 GCGAAATGAA
*
295316 AATCGCAACGACAG
1 AATCGCAACGAAAG
295330 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
295347 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
295363 AATCGCAACG
1 AATCGCAACG
295373 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:295343 original size:33 final size:33
Alignment explanation
Indices: 295297--295389 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
295287 GCGAAACCAA
*
295297 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
295330 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
295363 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
295390 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:295354 original size:19 final size:19
Alignment explanation
Indices: 295260--295394 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
295250 TAGTTTACTT
* *
295260 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
295280 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
295299 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
295318 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
295332 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
295351 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
295365 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
295384 TCGCAATGCGA
1 TCGCAACGCGA
295395 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:295412 original size:19 final size:19
Alignment explanation
Indices: 295390--295518 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
295380 AAAATCGCAA
295390 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
295409 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
295423 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
295442 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
295456 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
295475 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
295494 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
295514 TGCGA
1 TGCGA
295519 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:295432 original size:33 final size:33
Alignment explanation
Indices: 295390--295481 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
295380 AAAATCGCAA
295390 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
295423 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
295456 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
295482 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:295709 original size:93 final size:93
Alignment explanation
Indices: 295550--296016 Score: 909
Period size: 93 Copynumber: 5.0 Consensus size: 93
295540 GCAAATTGAA
295550 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
295615 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
295643 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
295708 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
295736 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
295801 GCAGAATTGGCATCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
295829 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
295893 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
295921 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
295986 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
296014 ACT
1 ACT
296017 AAGCAATCTA
Statistics
Matches: 370, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 91 0.25
93 279 0.75
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:295986 original size:185 final size:186
Alignment explanation
Indices: 295550--296016 Score: 909
Period size: 185 Copynumber: 2.5 Consensus size: 186
295540 GCAAATTGAA
295550 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
295615 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
295680 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
295736 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
295801 GCAGAATTGGCATCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
295865 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
295921 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
295986 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
296017 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 153 0.55
186 125 0.45
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:297741 original size:14 final size:14
Alignment explanation
Indices: 297722--297812 Score: 74
Period size: 14 Copynumber: 5.7 Consensus size: 14
297712 TTGAAATGAA
297722 AATCGCAACGAGAG
1 AATCGCAACGAGAG
297736 AATCGCAACGAGAG
1 AATCGCAACGAGAG
297750 AATGACTGTCGCAACGAGAG
1 -A--A---TCGCAACGAGAG
*
297770 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
297789 AATCGCAACGAGAG
1 AATCGCAACGAGAG
297803 AATCGCAACG
1 AATCGCAACG
297813 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 22
0.73 0.02 0.25
Matches are distributed among these distances:
14 32 0.50
15 2 0.03
16 2 0.03
17 4 0.06
18 1 0.02
19 11 0.17
20 12 0.19
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:297794 original size:19 final size:19
Alignment explanation
Indices: 297770--297834 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
297760 GCAACGAGAG
297770 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
297789 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
297803 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
297822 AATCGCAATGCGA
1 AATCGCAACGCGA
297835 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:297795 original size:33 final size:33
Alignment explanation
Indices: 297714--297829 Score: 187
Period size: 33 Copynumber: 3.5 Consensus size: 33
297704 TCTTTTGGTT
*
297714 GAAATGAAAATCGCAACGAGAGAATCGCAACGA
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
***
297747 GAGAATGACTGTCGCAACGAGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGAGAGAATCGCAACGC
297781 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
297814 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
297830 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
33 46 0.61
34 29 0.39
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:297878 original size:33 final size:33
Alignment explanation
Indices: 297832--297896 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
297822 AATCGCAATG
**
297832 CGATTTTGGTTTCGCGTTGCGATTCTCTCGTTA
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
297865 CGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTT
297897 GCGACAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.09, C:0.23, G:0.22, T:0.46
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTCTCTCGTTA
Found at i:297908 original size:33 final size:33
Alignment explanation
Indices: 297841--297922 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
297831 GCGATTTTGG
***
297841 TTTCGCGTTGCGATTCTCTCGTTACGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTACGACAGTCA
*
297874 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTACGACAGTCA
*
297907 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
297923 TTCATTTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 31 0.72
34 12 0.28
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTACGACAGTCA
Found at i:298063 original size:33 final size:33
Alignment explanation
Indices: 298021--298091 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
298011 AATACTAACT
*
298021 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
298054 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
298087 TGAAA
1 TGAAA
298092 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:298325 original size:22 final size:22
Alignment explanation
Indices: 298273--298327 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
298263 TGGTTATGAG
**
298273 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
* **
298295 AGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
298317 GGATTTCTTCG
1 GGATTTCTTCG
298328 CCGTAGAGAG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:298498 original size:20 final size:20
Alignment explanation
Indices: 298473--298665 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
298463 CTTTAAATAT
298473 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
298493 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
298515 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
298534 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
298554 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
298574 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
298594 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
298614 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
298634 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
298654 CGCGTTGCGATT
1 CGCGTTGCGATT
298666 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:298660 original size:60 final size:60
Alignment explanation
Indices: 298473--298665 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
298463 CTTTAAATAT
**
298473 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
298534 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
298594 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
298654 CGCGTTGCGATT
1 CGCGTTGCGATT
298666 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:298746 original size:20 final size:20
Alignment explanation
Indices: 298721--298772 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
298711 AAGAATCGCG
*
298721 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
298741 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
298761 TTGCGATTCTGG
1 TTGCGATTCTGG
298773 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:305784 original size:37 final size:36
Alignment explanation
Indices: 305709--305784 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
305699 TTTTTATATT
*
305709 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
305745 TTTAATTTTTTAAATAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
305782 TTT
1 TTT
305785 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:306149 original size:3 final size:3
Alignment explanation
Indices: 306141--306179 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
306131 ACACTTTATC
306141 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
306180 ATTTCATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:308210 original size:60 final size:60
Alignment explanation
Indices: 308146--308277 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 60
308136 CAAATGACTT
* * * * *
308146 TTTTATAAATTTTAATATTC-AAGAGATTCAATAAAGTAATATTCTATAGTTAAAAGATTA
1 TTTTATAAATTTTAATAGTCAAAGA-ATTCAATAAAATAATATTCTATAATCAAAAAATTA
* * * * *
308206 TTTTATAATTTTTAGTAGTGAAAGAATTTAATAAAATAATATTTTATAATCAAAAAATTA
1 TTTTATAAATTTTAATAGTCAAAGAATTCAATAAAATAATATTCTATAATCAAAAAATTA
*
308266 TTTGTGTAAATT
1 TTT-TATAAATT
308278 ACTCTTATTT
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
60 48 0.83
61 10 0.17
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (60 bp):
TTTTATAAATTTTAATAGTCAAAGAATTCAATAAAATAATATTCTATAATCAAAAAATTA
Found at i:317958 original size:24 final size:24
Alignment explanation
Indices: 317926--317973 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
317916 AGAAATGTAT
317926 CCCTAGAGCCAGCTTGATTGCTAG
1 CCCTAGAGCCAGCTTGATTGCTAG
317950 CCCTAGAGCCAGCTTGATTGCTAG
1 CCCTAGAGCCAGCTTGATTGCTAG
317974 AATTTGGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (24 bp):
CCCTAGAGCCAGCTTGATTGCTAG
Found at i:329246 original size:12 final size:12
Alignment explanation
Indices: 329229--329253 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
329219 TTCAACTCGT
329229 TAATAATGAATA
1 TAATAATGAATA
329241 TAATAATGAATA
1 TAATAATGAATA
329253 T
1 T
329254 GATTCTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAATGAATA
Found at i:330925 original size:16 final size:16
Alignment explanation
Indices: 330904--330941 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
330894 CGATTTAAAT
330904 TATTTTT-GTTTCAGAA
1 TATTTTTAGTTT-AGAA
*
330920 TATTTTTAGTTTAGAT
1 TATTTTTAGTTTAGAA
330936 TATTTT
1 TATTTT
330942 AAAAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.24, C:0.03, G:0.11, T:0.63
Consensus pattern (16 bp):
TATTTTTAGTTTAGAA
Found at i:336787 original size:69 final size:69
Alignment explanation
Indices: 336711--336965 Score: 352
Period size: 69 Copynumber: 3.7 Consensus size: 69
336701 ATCTTTCTCG
** * * * *
336711 CAATCAATTTTCTGGAAATATATCTG-TCCTTGAGAGTCTAACATCTCTTAAAACGTTATATCTC
1 CAATCAATTTTCTGGAAATATAGATGCT-CTTAAAAGTCTAACATCTCTTGAAACATTATATCTC
336775 TCTTC
65 TCTTC
336780 CAATCAATTTTCTGGAAATATAGATGCTCTTAAAAGTCTAACATCTCTTGAAACATTAGT-TCTC
1 CAATCAATTTTCTGGAAATATAGATGCTCTTAAAAGTCTAACATCTCTTGAAACATTA-TATCTC
336844 TCTTC
65 TCTTC
* *
336849 CAATCAATTTTCTGGAAATATAGATGCTCTTAAAAGTCTAACATCTCTTGAAACATTAGAACTCT
1 CAATCAATTTTCTGGAAATATAGATGCTCTTAAAAGTCTAACATCTCTTGAAACATTATATCTCT
336914 CTTC
66 CTTC
* * * ** *
336918 CAATCAGTTTTCCGGAAATATTGATGCTCTTAAGGGTCTAGCATCTCT
1 CAATCAATTTTCTGGAAATATAGATGCTCTTAAAAGTCTAACATCTCT
336966 CCAAGACATG
Statistics
Matches: 169, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
69 167 0.99
70 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (69 bp):
CAATCAATTTTCTGGAAATATAGATGCTCTTAAAAGTCTAACATCTCTTGAAACATTATATCTCT
CTTC
Found at i:339180 original size:16 final size:16
Alignment explanation
Indices: 339159--339199 Score: 73
Period size: 16 Copynumber: 2.5 Consensus size: 16
339149 CCGATATTAA
339159 ATATTATAAATTATAT
1 ATATTATAAATTATAT
339175 ATATTATAAATTATAT
1 ATATTATAAATTATAT
339191 ATATATATA
1 ATAT-TATA
339200 TAATCGCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTATAAATTATAT
Found at i:344844 original size:59 final size:59
Alignment explanation
Indices: 344745--344856 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 59
344735 AAGTTATTGA
* * * *
344745 AATGTTCAAAAGTCTGGAGACTAATTTTGAACAAGATTATAGTTTAGGGATGAAATTAG
1 AATGTTCAAAAATCTGAAGACTAATTTAGAACAAGATTATAATTTAGGGATGAAATTAG
* * * *
344804 AATGTTCAAAAAT-TGAAGACTAATTTAGAATGAGGTTTATAATTTGGGGATGA
1 AATGTTCAAAAATCTGAAGACTAATTTAGAA-CAAGATTATAATTTAGGGATGA
344857 GTTTAAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
58 15 0.34
59 29 0.66
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.33
Consensus pattern (59 bp):
AATGTTCAAAAATCTGAAGACTAATTTAGAACAAGATTATAATTTAGGGATGAAATTAG
Found at i:353023 original size:39 final size:39
Alignment explanation
Indices: 352980--353069 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
352970 GCTAAATATG
* *
352980 AAGACTCCATGACTACATGACTTCTTCAGACAAATGAAA
1 AAGACCCCATGACTACATGACATCTTCAGACAAATGAAA
* * * * * * *
353019 AAGACCCCACGATTGCATGTCATCTTCAGGCAAATGGAG
1 AAGACCCCATGACTACATGACATCTTCAGACAAATGAAA
353058 AAGACCCCATGA
1 AAGACCCCATGA
353070 ATGCACGGCG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (39 bp):
AAGACCCCATGACTACATGACATCTTCAGACAAATGAAA
Found at i:353084 original size:39 final size:39
Alignment explanation
Indices: 353002--353088 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 39
352992 CTACATGACT
* * *
353002 TCTTCAGACAAATGAAAAAGACCCCACGATTGCATGTCA
1 TCTTCAGACAAATGAAAAAGACCCCACGAATGCACGGCA
* * * * *
353041 TCTTCAGGCAAATGGAGAAGACCCCATGAATGCACGGCG
1 TCTTCAGACAAATGAAAAAGACCCCACGAATGCACGGCA
353080 TCTTCAGAC
1 TCTTCAGAC
353089 TAATAAGATG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (39 bp):
TCTTCAGACAAATGAAAAAGACCCCACGAATGCACGGCA
Found at i:355119 original size:254 final size:256
Alignment explanation
Indices: 354664--355177 Score: 960
Period size: 254 Copynumber: 2.0 Consensus size: 256
354654 CTTTTGTTTC
354664 TTTAATTGTTGGTTCAATTCAACATGCATGACATAGATAGTAGCTATTCATTTAGCTTTAAAATG
1 TTTAATTGTTGGTTCAATTCAACATGCATGACATAGATAGTAGCTATTCATTTAGCTTTAAAATG
354729 CTAAGATTTTCTATATCAGTTGAAGGTGAATATGGAAAATCACAAAGAATTTAGAATCTTTCTTT
66 CTAAGATTTTCTATATCAGTT----GTGAATATGGAAAATCACAAAGAATTTAGAATCTTTCTTT
*
354794 GTTTTATAGGCTGTTATGCTTAATGCTTCGGTTTTGATAGTTTTTTAAATATTAAATTTGTAGAA
127 GTTTTATAGGCTGTTATGCTTAATGCTTCGGTTTTGATAGTTGTTTAAATATTAAATTTGTAGAA
354859 TTTGGTTAGAAATAGATATTAAATCATTTTCACATATAGTTATTGTAGTAAATGTGGCTATAGAA
192 TTTGGTTAGAAATAGATATTAAATCATTTTCACATATAGTTATTGTAGTAAATGTGGCTATAGAA
354924 TTTAATTGTTGGTTCAATTCAACATGCATGACATAGATAGTAGCTATTCATTTAGCTTTAAAATG
1 TTTAATTGTTGGTTCAATTCAACATGCATGACATAGATAGTAGCTATTCATTTAGCTTTAAAATG
354989 CTAAGATTTTCTATATCAG-T-TGAATATGGAAAATCACAAAGAATTTAGAATCTTTCTTTGTTT
66 CTAAGATTTTCTATATCAGTTGTGAATATGGAAAATCACAAAGAATTTAGAATCTTTCTTTGTTT
*
355052 TATAGGCTGTTATTCTTAATGCTTCGGTTTTGATAGTTGTTTAAATATTAAATTTGTAGAATTTG
131 TATAGGCTGTTATGCTTAATGCTTCGGTTTTGATAGTTGTTTAAATATTAAATTTGTAGAATTTG
355117 GTTAGAAATAGATATTAAATCATTTTCACATATAGTTATTGTAGTAAATGTGGCTATAGAA
196 GTTAGAAATAGATATTAAATCATTTTCACATATAGTTATTGTAGTAAATGTGGCTATAGAA
355178 AGCACACTCT
Statistics
Matches: 252, Mismatches: 2, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
254 167 0.66
259 1 0.00
260 84 0.33
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (256 bp):
TTTAATTGTTGGTTCAATTCAACATGCATGACATAGATAGTAGCTATTCATTTAGCTTTAAAATG
CTAAGATTTTCTATATCAGTTGTGAATATGGAAAATCACAAAGAATTTAGAATCTTTCTTTGTTT
TATAGGCTGTTATGCTTAATGCTTCGGTTTTGATAGTTGTTTAAATATTAAATTTGTAGAATTTG
GTTAGAAATAGATATTAAATCATTTTCACATATAGTTATTGTAGTAAATGTGGCTATAGAA
Found at i:365631 original size:2 final size:2
Alignment explanation
Indices: 365624--365655 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
365614 ATTCAACTGA
365624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
365656 TGTTAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:366015 original size:3 final size:3
Alignment explanation
Indices: 366007--366054 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
365997 CTCTCGTTAA
366007 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
366055 AAGCTAAACC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
TCC
Found at i:366446 original size:29 final size:30
Alignment explanation
Indices: 366373--366446 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
366363 TTTAAAAACA
**
366373 TAAGATACAATCACTTTCGTTTTTATTTAAT
1 TAAGATATGATCA-TTTCGTTTTTATTTAAT
* *
366404 TAAGATGTGGTCATTTCGTTTTTA-TTAAT
1 TAAGATATGATCATTTCGTTTTTATTTAAT
366433 TAAGATATGATCAT
1 TAAGATATGATCAT
366447 CACGGGTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 17 0.46
30 11 0.30
31 9 0.24
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (30 bp):
TAAGATATGATCATTTCGTTTTTATTTAAT
Found at i:400998 original size:6 final size:7
Alignment explanation
Indices: 400976--401004 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
400966 TAAAACAATT
400976 AAATGAA
1 AAATGAA
400983 AAATGAA
1 AAATGAA
400990 AAATGAA
1 AAATGAA
400997 AAAT-AA
1 AAATGAA
401003 AA
1 AA
401005 CGAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (7 bp):
AAATGAA
Found at i:404041 original size:19 final size:19
Alignment explanation
Indices: 404013--404056 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
404003 CATCCGATCT
*
404013 AGATCTTTGCCTGACTCCA
1 AGATCCTTGCCTGACTCCA
404032 AGATCCTTGCCTGACTCCA
1 AGATCCTTGCCTGACTCCA
404051 AGATCC
1 AGATCC
404057 ACGGGAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (19 bp):
AGATCCTTGCCTGACTCCA
Found at i:409307 original size:14 final size:14
Alignment explanation
Indices: 409288--409347 Score: 93
Period size: 14 Copynumber: 4.3 Consensus size: 14
409278 TGTTCGTTTA
* *
409288 CGTTCGTTTACGTC
1 CGTTCGTTTATGTT
409302 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
409316 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
*
409330 CGTTCATTTATGTT
1 CGTTCGTTTATGTT
409344 CGTT
1 CGTT
409348 TATCATTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.08, C:0.18, G:0.20, T:0.53
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:409330 original size:24 final size:24
Alignment explanation
Indices: 409261--409350 Score: 69
Period size: 24 Copynumber: 3.6 Consensus size: 24
409251 TTTATGTTAG
* *
409261 TTTACGTTCATTTAT-TGT-GTTCG
1 TTTACGTTCGTTTATGT-TCGTTCA
*
409284 TTTACGTTCGTTTACGTCCGTTCGTTTA
1 TTTACGTTCGTTTA--T--GTTCGTTCA
409312 TGTT-CGTTCGTTTATGTTCGTTCA
1 T-TTACGTTCGTTTATGTTCGTTCA
*
409336 TTTATGTTCGTTTAT
1 TTTACGTTCGTTTAT
409351 CATTTAAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
23 15 0.28
24 19 0.35
25 1 0.02
26 1 0.02
27 1 0.02
28 15 0.28
29 2 0.04
ACGTcount: A:0.11, C:0.16, G:0.18, T:0.56
Consensus pattern (24 bp):
TTTACGTTCGTTTATGTTCGTTCA
Found at i:421407 original size:76 final size:76
Alignment explanation
Indices: 421281--421424 Score: 279
Period size: 76 Copynumber: 1.9 Consensus size: 76
421271 GAAGGAACAT
421281 AATAGCTAGTGGTGAAAACGCTTCTAAGTGACCTCTAGGCATACTTTGGTATTACCCATGTAATA
1 AATAGCTAGTGGTGAAAACGCTTCTAAGTGACCTCTAGGCATACTTTGGTATTACCCATGTAATA
421346 TGTATGCCATG
66 TGTATGCCATG
*
421357 AATAGTTAGTGGTGAAAACGCTTCTAAGTGACCTCTAGGCATACTTTGGTATTACCCATGTAATA
1 AATAGCTAGTGGTGAAAACGCTTCTAAGTGACCTCTAGGCATACTTTGGTATTACCCATGTAATA
421422 TGT
66 TGT
421425 GCCAGGAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (76 bp):
AATAGCTAGTGGTGAAAACGCTTCTAAGTGACCTCTAGGCATACTTTGGTATTACCCATGTAATA
TGTATGCCATG
Found at i:426500 original size:4 final size:4
Alignment explanation
Indices: 426491--426528 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
426481 TAAATTAGTG
426491 ATTT ATTT ATTT ATTT CGATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT --ATTT ATTT ATTT ATTT ATTT
426529 GAAGGGGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 28 0.88
6 4 0.12
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:426511 original size:18 final size:18
Alignment explanation
Indices: 426490--426524 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
426480 ATAAATTAGT
426490 GATTTATTTATTTATTTC
1 GATTTATTTATTTATTTC
426508 GATTTATTTATTTATTT
1 GATTTATTTATTTATTT
426525 ATTTGAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.69
Consensus pattern (18 bp):
GATTTATTTATTTATTTC
Found at i:426982 original size:14 final size:14
Alignment explanation
Indices: 426963--426998 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
426953 TTATTTATTT
426963 ATTTATTTCAAATA
1 ATTTATTTCAAATA
**
426977 ATTTATTTTGAATA
1 ATTTATTTCAAATA
426991 ATTTATTT
1 ATTTATTT
426999 ATTTATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (14 bp):
ATTTATTTCAAATA
Found at i:427023 original size:21 final size:20
Alignment explanation
Indices: 426997--427050 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
426987 AATAATTTAT
*
426997 TTATTTATTAATTTTAAATA
1 TTATTTATTAATTTCAAATA
427017 TTAATTTATTAATTTCAAATA
1 TT-ATTTATTAATTTCAAATA
*
427038 -TATTTTTTAATTT
1 TTATTTATTAATTT
427051 ATTTGCTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 11 0.35
20 3 0.10
21 17 0.55
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATTTATTAATTTCAAATA
Found at i:430000 original size:23 final size:25
Alignment explanation
Indices: 429960--430008 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
429950 ATTTAATTTT
*
429960 TTAAAAATTAAAAAAATTATTTAGA
1 TTAAAAATTAAAAAAATTATTAAGA
*
429985 TTAAAAA-T-AAACAATTATTAAGA
1 TTAAAAATTAAAAAAATTATTAAGA
430008 T
1 T
430009 ATTTAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 1 0.05
25 7 0.32
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
TTAAAAATTAAAAAAATTATTAAGA
Found at i:431054 original size:21 final size:22
Alignment explanation
Indices: 431030--431075 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
431020 TATAAAAATA
431030 TTCTAATTATATTGT-TTTATT
1 TTCTAATTATATTGTATTTATT
*
431051 TTCTAATTTTATTGTAATTTATT
1 TTCTAATTATATTGT-ATTTATT
431074 TT
1 TT
431076 GAATATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.64
23 8 0.36
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (22 bp):
TTCTAATTATATTGTATTTATT
Found at i:433100 original size:2 final size:2
Alignment explanation
Indices: 433093--433128 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
433083 TTTAATAATT
433093 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
433129 CACACACACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:433432 original size:22 final size:22
Alignment explanation
Indices: 433404--433453 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
433394 GCACTTCTAC
433404 ATTGAAGGGTTAAATTTATTTA
1 ATTGAAGGGTTAAATTTATTTA
433426 ATTGAAGGGTTAAATTTATTTA
1 ATTGAAGGGTTAAATTTATTTA
433448 ATTGAA
1 ATTGAA
433454 TTAAAATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (22 bp):
ATTGAAGGGTTAAATTTATTTA
Found at i:439201 original size:154 final size:153
Alignment explanation
Indices: 438894--439193 Score: 483
Period size: 154 Copynumber: 2.0 Consensus size: 153
438884 TAAATTAGTT
* ** *
438894 AAAAATTTAAAGGTAAATTATTTAAAATATAGGGTAAACTATATTAGTGACCACCTAACAATTTC
1 AAAAATTTAAACGTAAATTATTTAAAATATAGGGTAAACTATACCAGTGACCACCTAACAATTGC
* * *
438959 CCATTTTTATTTTGATCACCATTTTTGAAATTTTATCAATCATGTCATTCAATTATTTAAATGTA
66 CCATTTTCATTTTGATCACCATTTTTGAAATTTTATCAATCATGTCACTCAACTATTTAAATGTA
*
439024 TTCAATTAAGCTACTTACTGTTA
131 TTCAATTAAGCCACTTACTGTTA
* *
439047 AAAAGATTTAAACGTAAATTATTTAAAATATAGGGTAAACTATACCAGTGATCACCTAACTATTG
1 AAAA-ATTTAAACGTAAATTATTTAAAATATAGGGTAAACTATACCAGTGACCACCTAACAATTG
* *
439112 CCCCTTTTCATTTTGATCACTATTTTTGAAATTTTATCAATCATGTCACTCAACTATTTAAATGT
65 CCCATTTTCATTTTGATCACCATTTTTGAAATTTTATCAATCATGTCACTCAACTATTTAAATGT
439177 ATTCAATTAAGCCACTT
130 ATTCAATTAAGCCACTT
439194 GTCGTTAATA
Statistics
Matches: 134, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
153 4 0.03
154 130 0.97
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (153 bp):
AAAAATTTAAACGTAAATTATTTAAAATATAGGGTAAACTATACCAGTGACCACCTAACAATTGC
CCATTTTCATTTTGATCACCATTTTTGAAATTTTATCAATCATGTCACTCAACTATTTAAATGTA
TTCAATTAAGCCACTTACTGTTA
Found at i:443011 original size:12 final size:12
Alignment explanation
Indices: 442994--443018 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
442984 TGATTATCAG
442994 TAAACAACTTCA
1 TAAACAACTTCA
443006 TAAACAACTTCA
1 TAAACAACTTCA
443018 T
1 T
443019 GTATGAACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAACAACTTCA
Found at i:444076 original size:2 final size:2
Alignment explanation
Indices: 444028--444064 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
444018 TATAATCTTT
444028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
444065 TGTTTAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:447463 original size:24 final size:24
Alignment explanation
Indices: 447436--447489 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
447426 TAAATGATAT
** *
447436 ATGAACACAAATTAACGAATGTAA
1 ATGAACACAAACGAACGAATATAA
447460 ATGAACACAAACGAACGAATATAA
1 ATGAACACAAACGAACGAATATAA
*
447484 ACGAAC
1 ATGAAC
447490 GTAGATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.17, G:0.13, T:0.15
Consensus pattern (24 bp):
ATGAACACAAACGAACGAATATAA
Found at i:447623 original size:10 final size:10
Alignment explanation
Indices: 447608--447632 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
447598 CGGGTCTGGA
447608 GAACATAAAC
1 GAACATAAAC
447618 GAACATAAAC
1 GAACATAAAC
447628 GAACA
1 GAACA
447633 GATTATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.12, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:447726 original size:40 final size:41
Alignment explanation
Indices: 447675--447754 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 41
447665 AACAAGCATT
*
447675 TTATTCGTGTTCATTCATTTAAT-TAAACGAACATAAAATA
1 TTATTCATGTTCATTCATTTAATATAAACGAACATAAAATA
* *
447715 TTATTCATGTTCGTTCGTTTAATAAATAAACGAACATAAA
1 TTATTCATGTTCATTCATTTAAT--ATAAACGAACATAAA
447755 CGAACTTCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 20 0.59
43 14 0.41
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (41 bp):
TTATTCATGTTCATTCATTTAATATAAACGAACATAAAATA
Found at i:449095 original size:20 final size:20
Alignment explanation
Indices: 449070--449110 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
449060 GTCATACAAC
449070 TAATAATAGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
*
449090 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
449110 T
1 T
449111 TGTAAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:453683 original size:21 final size:20
Alignment explanation
Indices: 453659--453700 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
453649 GTCATACAAC
*
453659 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
453680 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
453700 T
1 T
453701 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:461802 original size:14 final size:14
Alignment explanation
Indices: 461785--461832 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
461775 TGGGCTAAAT
461785 ATAAATGAACGAAC
1 ATAAATGAACGAAC
*
461799 ATAAATGAACAAAC
1 ATAAATGAACGAAC
461813 AT--A--AACGAAC
1 ATAAATGAACGAAC
461823 ATAAATGAAC
1 ATAAATGAAC
461833 ATATTACCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 8 0.29
12 2 0.07
14 18 0.64
ACGTcount: A:0.60, C:0.15, G:0.10, T:0.15
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:467571 original size:39 final size:39
Alignment explanation
Indices: 467501--467619 Score: 127
Period size: 39 Copynumber: 3.1 Consensus size: 39
467491 TAGATCTTTT
** *
467501 ATTTATAA-TTC-TAAGATTATTTCACTTTAACATTCTAA
1 ATTTATAATTTCTTAA-ATTATTAAACATTAACATTCTAA
*
467539 ATTTATAATTTCTTAAATTATGTAAACA-TAACATTTTAA
1 ATTTATAATTTCTTAAATTAT-TAAACATTAACATTCTAA
* * **
467578 ATTTTTTATTTCTTAAATTATTTCACATTAACATTCTAA
1 ATTTATAATTTCTTAAATTATTAAACATTAACATTCTAA
467617 ATT
1 ATT
467620 ATTTTTTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
38 12 0.18
39 50 0.74
40 6 0.09
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (39 bp):
ATTTATAATTTCTTAAATTATTAAACATTAACATTCTAA
Found at i:492009 original size:27 final size:27
Alignment explanation
Indices: 491978--492045 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
491968 TCTATTTACA
491978 AAATCATATCTATATAGGAATGATAAC
1 AAATCATATCTATATAGGAATGATAAC
* *
492005 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTATATAGGAATGATAAC
*
492032 AAATCATCTCTATA
1 AAATCATATCTATA
492046 ATTCCTACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATCATATCTATATAGGAATGATAAC
Found at i:498075 original size:23 final size:24
Alignment explanation
Indices: 498035--498081 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
498025 TAAATTTTCT
*
498035 TAAGATCTTTTTTAAAACTTGTGA
1 TAAGATCTTCTTTAAAACTTGTGA
498059 TAAGATC-TCTTTAAAACTTGTGA
1 TAAGATCTTCTTTAAAACTTGTGA
498082 AACTCAAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (24 bp):
TAAGATCTTCTTTAAAACTTGTGA
Found at i:498344 original size:2 final size:2
Alignment explanation
Indices: 498339--498374 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
498329 TGGCCTTTTC
498339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
498375 TTTAAAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:502154 original size:36 final size:37
Alignment explanation
Indices: 502084--502160 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
502074 ATTCCAAATT
502084 AAATTGTAATTAGGCATGATTAGAAAAAATACACTAA
1 AAATTGTAATTAGGCATGATTAGAAAAAATACACTAA
*
502121 AAATTGTAATTAGGTATGATTA-AAAAAATACACTAA
1 AAATTGTAATTAGGCATGATTAGAAAAAATACACTAA
502157 AAAT
1 AAAT
502161 ACGAGAATAC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 18 0.46
37 21 0.54
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (37 bp):
AAATTGTAATTAGGCATGATTAGAAAAAATACACTAA
Found at i:504400 original size:12 final size:12
Alignment explanation
Indices: 504383--504407 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
504373 GATGTTTTCA
504383 CTGAATACAATG
1 CTGAATACAATG
504395 CTGAATACAATG
1 CTGAATACAATG
504407 C
1 C
504408 AGATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (12 bp):
CTGAATACAATG
Found at i:506849 original size:35 final size:38
Alignment explanation
Indices: 506802--506874 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 38
506792 TTTCATTTAG
506802 GGGGAAATCGATACCCCT-CA-GGGGGAATCTGTTCCC
1 GGGGAAATCGATACCCCTCCAGGGGGGAATCTGTTCCC
506838 GGGG-AATCGATACCCCTCCAGGGGGGAATCTGTTCCC
1 GGGGAAATCGATACCCCTCCAGGGGGGAATCTGTTCCC
506875 CCTGCACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 13 0.37
36 6 0.17
37 16 0.46
ACGTcount: A:0.21, C:0.29, G:0.32, T:0.19
Consensus pattern (38 bp):
GGGGAAATCGATACCCCTCCAGGGGGGAATCTGTTCCC
Found at i:513731 original size:35 final size:35
Alignment explanation
Indices: 513685--513754 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
513675 TTCATTTAGG
513685 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
513720 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
513755 CCTGCACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.31, G:0.31, T:0.17
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
Found at i:513756 original size:20 final size:20
Alignment explanation
Indices: 513684--513747 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
513674 TTTCATTTAG
513684 GGGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
*
513704 GGGGGAATCTG-T---TCCC-
1 GGGGGAATC-GATACCCCCCA
513720 -GGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
513739 GGGGGAATC
1 GGGGGAATC
513748 TGTTCCCCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
14 1 0.03
15 9 0.26
17 3 0.09
18 3 0.09
20 18 0.51
21 1 0.03
ACGTcount: A:0.22, C:0.30, G:0.34, T:0.14
Consensus pattern (20 bp):
GGGGGAATCGATACCCCCCA
Found at i:514870 original size:6 final size:6
Alignment explanation
Indices: 514859--514888 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
514849 AACTTTCATC
*
514859 TAGCAT TAGCAT TAGCAT TAACAT TAGCAT
1 TAGCAT TAGCAT TAGCAT TAGCAT TAGCAT
514889 CGAGGAGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (6 bp):
TAGCAT
Found at i:519165 original size:11 final size:11
Alignment explanation
Indices: 519149--519180 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
519139 ATCGGTCTAC
519149 CATTCTGTTTG
1 CATTCTGTTTG
519160 CATTCTGTTTG
1 CATTCTGTTTG
519171 CATTCTGTTT
1 CATTCTGTTT
519181 AACTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.16, T:0.56
Consensus pattern (11 bp):
CATTCTGTTTG
Found at i:521547 original size:2 final size:2
Alignment explanation
Indices: 521540--521571 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
521530 CCATTGACTC
521540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
521572 TTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:526875 original size:48 final size:49
Alignment explanation
Indices: 526782--526879 Score: 171
Period size: 48 Copynumber: 2.0 Consensus size: 49
526772 ATAGCCGATT
*
526782 ATATCTATATATATATTGCTAAATTCCTAGGATTTTGCTTGTTGAAGGA
1 ATATATATATATATATTGCTAAATTCCTAGGATTTTGCTTGTTGAAGGA
*
526831 ATATATATATATATGTTGCTAAATT-CTAGGATTTTGCTTGTTGAAGGA
1 ATATATATATATATATTGCTAAATTCCTAGGATTTTGCTTGTTGAAGGA
526879 A
1 A
526880 ATAAATGGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 24 0.51
49 23 0.49
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (49 bp):
ATATATATATATATATTGCTAAATTCCTAGGATTTTGCTTGTTGAAGGA
Found at i:529655 original size:41 final size:41
Alignment explanation
Indices: 529609--529694 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
529599 TAATATTTTT
* *
529609 ATATTTTATTAATAACATGATATTATCTTATAATGATATAA
1 ATATTTTAATAATAACATGATATTATCTTATAATGATACAA
*
529650 ATATTTTAATAATAATATGATATTATCTTATAATGATACAA
1 ATATTTTAATAATAACATGATATTATCTTATAATGATACAA
529691 ATAT
1 ATAT
529695 CATCAATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (41 bp):
ATATTTTAATAATAACATGATATTATCTTATAATGATACAA
Found at i:532418 original size:11 final size:10
Alignment explanation
Indices: 532400--532429 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
532390 TACACGAGTA
532400 AAAAAATAAT
1 AAAAAATAAT
532410 AAAATAATAAT
1 AAAA-AATAAT
532421 AAAAAATAA
1 AAAAAATAA
532430 AATCATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:532430 original size:18 final size:17
Alignment explanation
Indices: 532402--532442 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
532392 CACGAGTAAA
532402 AAAATAATAAAATAATAAT
1 AAAA-AATAAAATAAT-AT
*
532421 AAAAAATAAAATCATAT
1 AAAAAATAAAATAATAT
532438 AAAAA
1 AAAAA
532443 TATATATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 10 0.48
19 4 0.19
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAAATAAAATAATAT
Found at i:535407 original size:12 final size:12
Alignment explanation
Indices: 535392--535421 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
535382 TCCAAACAAC
535392 TTTCCAACTTAA
1 TTTCCAACTTAA
535404 TTTCCAACTTAA
1 TTTCCAACTTAA
535416 TTTCCA
1 TTTCCA
535422 GCATTTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (12 bp):
TTTCCAACTTAA
Found at i:537418 original size:2 final size:2
Alignment explanation
Indices: 537409--537441 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
537399 TTATCATTTA
537409 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
537442 TAGTTTAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:542472 original size:9 final size:9
Alignment explanation
Indices: 542458--542482 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
542448 TAAAAACTAG
542458 TCACTTAGA
1 TCACTTAGA
542467 TCACTTAGA
1 TCACTTAGA
542476 TCACTTA
1 TCACTTA
542483 AGGACCAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (9 bp):
TCACTTAGA
Found at i:542877 original size:23 final size:22
Alignment explanation
Indices: 542827--542889 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
542817 AAAATTATGC
*
542827 CACAAAGGCAGAGATAAACGTG
1 CACAAAGGCAGAGATAAACATG
542849 CTACAAAGGCAGAGATAAACATG
1 C-ACAAAGGCAGAGATAAACATG
* *
542872 TCACAAAGACATAGATAA
1 -CACAAAGGCAGAGATAA
542890 CTGTGTCACA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.03
23 34 0.94
24 1 0.03
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.13
Consensus pattern (22 bp):
CACAAAGGCAGAGATAAACATG
Found at i:547796 original size:16 final size:16
Alignment explanation
Indices: 547748--547807 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
547738 AATTTAGCAA
* *
547748 AACCTAAAGCAACCCG
1 AACCGAAAGCAAACCG
* ** *
547764 AATCGAAATTAATCCG
1 AACCGAAAGCAAACCG
*
547780 AACTGAAAGCAAACCG
1 AACCGAAAGCAAACCG
547796 AACCGAAAGCAA
1 AACCGAAAGCAA
547808 CTCGAACCAA
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.48, C:0.27, G:0.15, T:0.10
Consensus pattern (16 bp):
AACCGAAAGCAAACCG
Found at i:547813 original size:16 final size:16
Alignment explanation
Indices: 547778--547835 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
547768 GAAATTAATC
*
547778 CGAACTGAAAGCAAAC-
1 CGAACCGAAAGC-AACT
547794 CGAACCGAAAGCAACT
1 CGAACCGAAAGCAACT
* **
547810 CGAACCAAAATTAACT
1 CGAACCGAAAGCAACT
*
547826 TGAACCGAAA
1 CGAACCGAAA
547836 AAAATTTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 3 0.09
16 32 0.91
ACGTcount: A:0.48, C:0.26, G:0.16, T:0.10
Consensus pattern (16 bp):
CGAACCGAAAGCAACT
Found at i:550166 original size:2 final size:2
Alignment explanation
Indices: 550159--550188 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
550149 ATAGGATGAC
550159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
550189 TAAATAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:552632 original size:83 final size:83
Alignment explanation
Indices: 552493--553363 Score: 789
Period size: 83 Copynumber: 10.5 Consensus size: 83
552483 AAAACTCTAC
* * * * *
552493 CATGTCATAGTTTTTCA-TCTCATCCGAAATGAAATGCACGTTCCAGGAGAAACATTTTCCATTA
1 CATGTCATAGTGTTCCATTC-CATCCGAAATGAAAGGCGCGTTCCAGGAGAAGCATTTTCCATTA
*
552557 TTATTTAGAGAATCTCTGT
65 TTATTCAGAGAATCTCTGT
* * * * ** * ***
552576 CATGTCATAGTGTTTCATTCCATTCGAAATGAAAGGCACATTATAGGGGAAGCATTTTATGTTAT
1 CATGTCATAGTGTTCCATTCCATCCGAAATGAAAGGCGCGTTCCAGGAGAAGCATTTTCCATTAT
* * **
552641 TATTCAGATAATCTTTAC
66 TATTCAGAGAATCTCTGT
* * ** * **
552659 CATATCATAGTGTTCCATCCCATCCGAAATGAAAGGCGCGTTTGAGGGGAAATATTTTCCATTAT
1 CATGTCATAGTGTTCCATTCCATCCGAAATGAAAGGCGCGTTCCAGGAGAAGCATTTTCCATTAT
* *
552724 TATTAAAAGAATCTCTGT
66 TATTCAGAGAATCTCTGT
* * * * * *
552742 CATGTCATACTGTTCCA-TCTCATCCAAAATGAAAGACGCGTTACAAGAGAATCATTTTCCATTA
1 CATGTCATAGTGTTCCATTC-CATCCGAAATGAAAGGCGCGTTCCAGGAGAAGCATTTTCCATTA
* *
552806 TTATTAAGAGAATCTCTGA
65 TTATTCAGAGAATCTCTGT
* * * * * ** ** * * *
552825 CATGTCTTAGTGTTTCA-TCTTATCCAAAATGAAAGACATGTTTTAGGGGAAGCGTTTTCTATTA
1 CATGTCATAGTGTTCCATTC-CATCCGAAATGAAAGGCGCGTTCCAGGAGAAGCATTTTCCATTA
* * *
552889 TTATTCAGAAAATCTATAT
65 TTATTCAGAGAATCTCTGT
* * * * *
552908 CATGTCATAGTGTTCCA-TCTCATCCGAAATGAAAGACGCATTACAGGGGAAGTATTTTCCATTA
1 CATGTCATAGTGTTCCATTC-CATCCGAAATGAAAGGCGCGTTCCAGGAGAAGCATTTTCCATTA
*
552972 TTATTCAAAGAATCTCTGT
65 TTATTCAGAGAATCTCTGT
* * ** * * *
552991 CATGTCATAGTGGTT-CATCCCATCCAAAATGAATTGCGTGTTCCAAGAGAAACATTTTCCATTA
1 CATGTCATAGT-GTTCCATTCCATCCGAAATGAAAGGCGCGTTCCAGGAGAAGCATTTTCCATTA
* * * *
553055 TTATTCAGGGAAGCTTTGC
65 TTATTCAGAGAATCTCTGT
* * * * * *
553074 CATGTCATAGTGTTCCATTCTATCTGAAATGAAAGGTGTGTTCCAGGAGAAGTATTTTCCATTTT
1 CATGTCATAGTGTTCCATTCCATCCGAAATGAAAGGCGCGTTCCAGGAGAAGCATTTTCCATTAT
553139 TATTCAGAGAATCTCTGT
66 TATTCAGAGAATCTCTGT
* * * * * * * *
553157 TATGTCATAGTGTTACATCCCATCCGAAATGAAAGCCGTGTTTCAAGAGAAGTATTTTCCATTAT
1 CATGTCATAGTGTTCCATTCCATCCGAAATGAAAGGCGCGTTCCAGGAGAAGCATTTTCCATTAT
*
553222 TATTCAGAGAATCTCTGA
66 TATTCAGAGAATCTCTGT
* * * * * * *
553240 CATGTCATAGTGTTTCATCCCATCCAAAATGAAAGGCGCGTTCTAGGGGAAACGTTTTCCATTAT
1 CATGTCATAGTGTTCCATTCCATCCGAAATGAAAGGCGCGTTCCAGGAGAAGCATTTTCCATTAT
*
553305 TATTCAGAGAATCTATGT
66 TATTCAGAGAATCTCTGT
* * ** *
553323 CATGCCATAGTGTTCCATCCCATCAAAAATAAAAGGCGCGT
1 CATGTCATAGTGTTCCATTCCATCCGAAATGAAAGGCGCGT
553364 GTTCCACTAT
Statistics
Matches: 640, Mismatches: 143, Indels: 10
0.81 0.18 0.01
Matches are distributed among these distances:
82 4 0.01
83 630 0.98
84 6 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (83 bp):
CATGTCATAGTGTTCCATTCCATCCGAAATGAAAGGCGCGTTCCAGGAGAAGCATTTTCCATTAT
TATTCAGAGAATCTCTGT
Found at i:552934 original size:249 final size:248
Alignment explanation
Indices: 552467--553340 Score: 1009
Period size: 249 Copynumber: 3.5 Consensus size: 248
552457 TGTCATAATG
* ** * * *
552467 TTTTTCATTATT-TTAAAA-AA-CTCTACCATGTCATAGTTTTTCATCTCATCCGAAATGAAATG
1 TTTTCCATTATTATTAAAAGAATCTCTGTCATGTCATAGTGTTTCATCCCATCCAAAATGAAA-G
* * * *
552529 CACGTTCCAGGAGAAACATTTTCCATTATTATTTAGAGAATCTCTGTCATGTCATAGTGTTTCAT
65 CGCGTTCCAAGAGAAACATTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATAGTGTTCCAT
* * ** * * * * *
552594 TCCATTCGAAATGAAAGGCACATTATAGGGGAAGCATTTTATGTTATTATTCAGATAATCTTTAC
130 TCTATCCGAAATGAAAGGCATGTTATAGGGGAAGCATTTTCTATTATTATTCAGAAAATCTATAT
* * * *
552659 CATATCATAGTGTTCCATCCCATCCGAAATGAAAGGCGCGTTTGAGGGGAAATA
195 CATGTCATAGTGTTCCATCCCATCCGAAATGAAAGACGCGTTTCAGGGGAAGTA
* * *
552713 TTTTCCATTATTATTAAAAGAATCTCTGTCATGTCATACTGTTCCATCTCATCCAAAATGAAAGA
1 TTTTCCATTATTATTAAAAGAATCTCTGTCATGTCATAGTGTTTCATCCCATCCAAAATGAAAG-
* * * * * *
552778 CGCGTTACAAGAGAATCATTTTCCATTATTATTAAGAGAATCTCTGACATGTCTTAGTGTTTCA-
65 CGCGTTCCAAGAGAAACATTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATAGTGTTCCAT
* * * *
552842 TCTTATCCAAAATGAAAGACATGTTTTAGGGGAAGCGTTTTCTATTATTATTCAGAAAATCTATA
130 TC-TATCCGAAATGAAAGGCATGTTATAGGGGAAGCATTTTCTATTATTATTCAGAAAATCTATA
* * *
552907 TCATGTCATAGTGTTCCATCTCATCCGAAATGAAAGACGCATTACAGGGGAAGTA
194 TCATGTCATAGTGTTCCATCCCATCCGAAATGAAAGACGCGTTTCAGGGGAAGTA
* * *
552962 TTTTCCATTATTATTCAAAGAATCTCTGTCATGTCATAGTGGTTCATCCCATCCAAAATGAATTG
1 TTTTCCATTATTATTAAAAGAATCTCTGTCATGTCATAGTGTTTCATCCCATCCAAAATGAA-AG
* * * * *
553027 CGTGTTCCAAGAGAAACATTTTCCATTATTATTCAGGGAAGCTTTGCCATGTCATAGTGTTCCAT
65 CGCGTTCCAAGAGAAACATTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATAGTGTTCCAT
* ** ** * * * * * * *
553092 TCTATCTGAAATGAAAGGTGTGTTCCAGGAGAAGTATTTTCCATTTTTATTCAGAGAATCTCTGT
130 TCTATCCGAAATGAAAGGCATGTTATAGGGGAAGCATTTTCTATTATTATTCAGAAAATCTATAT
* * * * * *
553157 TATGTCATAGTGTTACATCCCATCCGAAATGAAAGCCGTGTTTCAAGAGAAGTA
195 CATGTCATAGTGTTCCATCCCATCCGAAATGAAAGACGCGTTTCAGGGGAAGTA
* * *
553211 TTTTCCATTATTATTCAGAGAATCTCTGACATGTCATAGTGTTTCATCCCATCCAAAATGAAAGG
1 TTTTCCATTATTATTAAAAGAATCTCTGTCATGTCATAGTGTTTCATCCCATCCAAAATGAAA-G
* * * * * *
553276 CGCGTTCTAGGGGAAACGTTTTCCATTATTATTCAGAGAATCTATGTCATGCCATAGTGTTCCAT
65 CGCGTTCCAAGAGAAACATTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATAGTGTTCCAT
553341 CCCATCAAAA
Statistics
Matches: 532, Mismatches: 88, Indels: 13
0.84 0.14 0.02
Matches are distributed among these distances:
246 11 0.02
247 6 0.01
248 5 0.01
249 507 0.95
250 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (248 bp):
TTTTCCATTATTATTAAAAGAATCTCTGTCATGTCATAGTGTTTCATCCCATCCAAAATGAAAGC
GCGTTCCAAGAGAAACATTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATAGTGTTCCATT
CTATCCGAAATGAAAGGCATGTTATAGGGGAAGCATTTTCTATTATTATTCAGAAAATCTATATC
ATGTCATAGTGTTCCATCCCATCCGAAATGAAAGACGCGTTTCAGGGGAAGTA
Found at i:553486 original size:8 final size:8
Alignment explanation
Indices: 553473--553535 Score: 69
Period size: 8 Copynumber: 8.1 Consensus size: 8
553463 ATCTTTGAAA
553473 TCTCAAAC
1 TCTCAAAC
553481 TCTCAAAC
1 TCTCAAAC
*
553489 T-TTAAAC
1 TCTCAAAC
553496 TCTCAAAC
1 TCTCAAAC
*
553504 T-TTAAAC
1 TCTCAAAC
*
553511 TTTCAAAC
1 TCTCAAAC
553519 T-TCAAAAC
1 TCTC-AAAC
553527 TCTCAAAC
1 TCTCAAAC
553535 T
1 T
553536 AAGAAAATGA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
7 14 0.30
8 31 0.66
9 2 0.04
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.32
Consensus pattern (8 bp):
TCTCAAAC
Found at i:553491 original size:23 final size:22
Alignment explanation
Indices: 553465--553535 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 22
553455 AACTCTGTAT
553465 CTTTGAAATCTCAAACTCTCAAA
1 CTTT-AAATCTCAAACTCTCAAA
*
553488 CTTTAAACTCTCAAACT-TTAAA
1 CTTTAAA-TCTCAAACTCTCAAA
553510 CTTTCAAA-CTTCAAAACTCTCAAA
1 CTTT-AAATC-TC-AAACTCTCAAA
553534 CT
1 CT
553536 AAGAAAATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 1 0.02
22 13 0.32
23 21 0.51
24 6 0.15
ACGTcount: A:0.39, C:0.27, G:0.01, T:0.32
Consensus pattern (22 bp):
CTTTAAATCTCAAACTCTCAAA
Found at i:553497 original size:15 final size:15
Alignment explanation
Indices: 553477--553535 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
553467 TTGAAATCTC
553477 AAACTCTCAAACTTT
1 AAACTCTCAAACTTT
553492 AAACTCTCAAACTTT
1 AAACTCTCAAACTTT
* *
553507 AAACTTTCAAACTTCA
1 AAACTCTCAAACTT-T
553523 AAACTCTCAAACT
1 AAACTCTCAAACT
553536 AAGAAAATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
15 28 0.70
16 12 0.30
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTCTCAAACTTT
Found at i:554981 original size:178 final size:170
Alignment explanation
Indices: 554691--555039 Score: 594
Period size: 178 Copynumber: 2.0 Consensus size: 170
554681 ATGTAACAAA
554691 TATATGCATACATATATGTCGTTACATTCTCTTATATCATTCCTATGATCTCTTATGTCCATTCA
1 TATATGCATACATATATGTCGTTACATTCTCTTATATCATTCCTATGATCTCTTATGTCCATTCA
554756 TATAACAATATACATAACCAATTGCACATATACATATCATGTCGTGTACACTATATATATATACT
66 TATAACAATATACATAACCAATTGCACATATACATATCATGTCGTGTACACTATATATATATACT
554821 ATCATAAAACACGTACACCCAAGCAATTATA-TATCATCT
131 ATCATAAAACACGTACACCCAAGCAATTATATTATCATCT
554860 TATATGCATACATATATGTCGTTATCATTCATATCTCTTATATCATATTCCTATGATCTCTTATG
1 TATATGCATACATATATGTCG-T-T-A--CAT-TCTCTTATATC--ATTCCTATGATCTCTTATG
554925 TCCATATCATATAAC-ATATACCATAACCAATTGCACATATACATATCATGTCGTGTACACTATA
58 TCCAT-TCATATAACAATATA-CATAACCAATTGCACATATACATATCATGTCGTGTACACTATA
554989 TATATATACTATCATAAAACACGTACACCCAAGCAATTATATTATCATCT
121 TATATATACTATCATAAAACACGTACACCCAAGCAATTATATTATCATCT
555039 T
1 T
555040 CATTTCTTTC
Statistics
Matches: 169, Mismatches: 0, Indels: 12
0.93 0.00 0.07
Matches are distributed among these distances:
169 21 0.12
170 1 0.01
171 1 0.01
172 1 0.01
174 3 0.02
175 11 0.07
177 29 0.17
178 93 0.55
179 9 0.05
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (170 bp):
TATATGCATACATATATGTCGTTACATTCTCTTATATCATTCCTATGATCTCTTATGTCCATTCA
TATAACAATATACATAACCAATTGCACATATACATATCATGTCGTGTACACTATATATATATACT
ATCATAAAACACGTACACCCAAGCAATTATATTATCATCT
Found at i:555315 original size:23 final size:23
Alignment explanation
Indices: 555289--555375 Score: 111
Period size: 23 Copynumber: 3.7 Consensus size: 23
555279 TACCACATAT
555289 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCGCGTAG
* *** *
555312 AATTGCACCGTAGTGCCATATAAT
1 AATTGCACCGGAGTGCCGCGT-AG
555336 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCGCGTAG
*
555359 AATTGCACCGTAGTGCC
1 AATTGCACCGGAGTGCC
555376 ATATAATAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 34 0.65
24 18 0.35
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCGCGTAG
Found at i:555341 original size:47 final size:47
Alignment explanation
Indices: 555287--555385 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
555277 AGTACCACAT
555287 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
1 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
555334 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
1 ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
555381 ATAAT
1 ATAAT
555386 GTCCATAAGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (47 bp):
ATAATTGCACCGGAGTGCCGCGTAGAATTGCACCGTAGTGCCATATA
Found at i:555563 original size:103 final size:103
Alignment explanation
Indices: 555392--555609 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
555382 TAATGTCCAT
* *
555392 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
555457 GACTTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
555495 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
555560 GACTTTACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
555598 AAGGACCACATA
1 AAGGACCACATA
555610 GACCCTCGAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:556818 original size:23 final size:24
Alignment explanation
Indices: 556789--556835 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
556779 TATCATCTAA
556789 TAATCAAAACCC-ACCTTAAAATC
1 TAATCAAAACCCAACCTTAAAATC
556812 TAATCAAAACCCAACCTTAAAATC
1 TAATCAAAACCCAACCTTAAAATC
556836 AACAATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (24 bp):
TAATCAAAACCCAACCTTAAAATC
Found at i:559848 original size:2 final size:2
Alignment explanation
Indices: 559836--559881 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
559826 TTCTTATAAC
559836 TA TA T- TA TA TA TA TA TA TA TA TA TA T- 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
559876 TA TA TA
1 TA TA TA
559882 AATTATACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:559854 original size:21 final size:21
Alignment explanation
Indices: 559836--559881 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
559826 TTCTTATAAC
559836 TATATTATATATATATATATA
1 TATATTATATATATATATATA
559857 TATATTATATATATATATATA
1 TATATTATATATATATATATA
559878 TATA
1 TATA
559882 AATTATACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TATATTATATATATATATATA
Found at i:559867 original size:23 final size:23
Alignment explanation
Indices: 559841--559888 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
559831 ATAACTATAT
*
559841 TATATATATATATATATATATTA
1 TATATATATATATATATAAATTA
559864 TATATATATATATATATAAATTA
1 TATATATATATATATATAAATTA
559887 TA
1 TA
559889 CATAAACCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATATATATATATATAAATTA
Found at i:559888 original size:21 final size:22
Alignment explanation
Indices: 559839--559888 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
559829 TTATAACTAT
559839 ATTATATATATATATATATAT-
1 ATTATATATATATATATATATA
559860 ATTATATATATATATATATATAA
1 ATTATATATATATATATATAT-A
559883 ATTATA
1 ATTATA
559889 CATAAACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.78
23 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTATATATATATATATATATA
Done.