Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 57 of 255
Found at i:16359718 original size:22 final size:22
Alignment explanation
Indices: 16359677--16359722 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
16359667 GAAAAGTCGA
*
16359677 AAAAAGAAAAAGTAGAGAAAAG
1 AAAAAGAAAAAGAAGAGAAAAG
16359699 AAAAAGAAAAAGAATG-GAAAAG
1 AAAAAGAAAAAGAA-GAGAAAAG
16359721 AA
1 AA
16359723 GAACTAACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (22 bp):
AAAAAGAAAAAGAAGAGAAAAG
Found at i:16365499 original size:22 final size:21
Alignment explanation
Indices: 16365440--16365500 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
16365430 TTGTTATAAT
*
16365440 ATATATTTTTTAAAATTTTAA
1 ATATATTTTTTAAAATATTAA
16365461 ATATTATTTTTT-AAATATTAA
1 ATA-TATTTTTTAAAATATTAA
16365482 ATATATTTTTTAATAATAT
1 ATATATTTTTTAA-AATAT
16365501 AAAAATTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 8 0.22
21 15 0.42
22 13 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATTTTTTAAAATATTAA
Found at i:16365503 original size:21 final size:20
Alignment explanation
Indices: 16365434--16365503 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 20
16365424 TGAAATTTGT
16365434 TATAATATATATTTTTTAAAA
1 TATAA-ATATATTTTTTAAAA
*
16365455 TTTTAAATATTATTTTTT-AAA
1 -TATAAATA-TATTTTTTAAAA
16365476 TATTAAATATATTTTTTAATAA
1 TA-TAAATATATTTTTTAA-AA
16365498 TATAAA
1 TATAAA
16365504 AATTTAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
20 9 0.21
21 17 0.40
22 16 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATAAATATATTTTTTAAAA
Found at i:16365581 original size:30 final size:29
Alignment explanation
Indices: 16365547--16365623 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 29
16365537 TTTATTATTA
*
16365547 GTTTTATAATATCTTTAATATTTTTAATTT
1 GTTTTATAATAT-TTTAATATTTGTAATTT
*
16365577 GTTTTATAATATTTTTTATATTTGTAATTT
1 GTTTTATAATA-TTTTAATATTTGTAATTT
16365607 GTTTTATAATATTTTAA
1 GTTTTATAATATTTTAA
16365624 ATTATGATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.12
30 37 0.86
31 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (29 bp):
GTTTTATAATATTTTAATATTTGTAATTT
Found at i:16365846 original size:20 final size:20
Alignment explanation
Indices: 16365790--16365846 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
16365780 ATAAATTTAT
*
16365790 TTAAAATATATATGTTAAAAA
1 TTAAAA-ATATATATTAAAAA
* * *
16365811 GTAAAAATTTAAATTAAAAA
1 TTAAAAATATATATTAAAAA
16365831 TTAAAAATATATATTA
1 TTAAAAATATATATTA
16365847 TAATTGGTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
TTAAAAATATATATTAAAAA
Found at i:16366327 original size:20 final size:20
Alignment explanation
Indices: 16366304--16366368 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
16366294 ATAATTTTTT
16366304 AATTTTAGTACACATTCATA
1 AATTTTAGTACACATTCATA
* ** *
16366324 AATTTATA-TATTA-ATTTTTT
1 AATTT-TAGTA-CACATTCATA
16366344 AATTTTAGTACACATTCATA
1 AATTTTAGTACACATTCATA
16366364 AATTT
1 AATTT
16366369 ATATACTTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.49
Consensus pattern (20 bp):
AATTTTAGTACACATTCATA
Found at i:16366339 original size:40 final size:41
Alignment explanation
Indices: 16366295--16366379 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 41
16366285 GTGTTAGTTA
16366295 TAATTTTTTAATTTTAGTACACATTCATAAATTTATATA-T
1 TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
16366335 TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
1 TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
16366376 TAAT
1 TAAT
16366380 ATATATTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 39 0.89
41 5 0.11
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (41 bp):
TAATTTTTTAATTTTAGTACACATTCATAAATTTATATACT
Found at i:16366390 original size:40 final size:40
Alignment explanation
Indices: 16366303--16366390 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
16366293 TATAATTTTT
* *
16366303 TAATTTTAGTACACATTCATAAATTTATATATTAATTTTT
1 TAATTTTAGTACACATTCATAAATTTATATATTAATTATA
16366343 TAATTTTAGTACACATTCATAAATTTATATACTTAA-TATA
1 TAATTTTAGTACACATTCATAAATTTATATA-TTAATTATA
*
16366383 TATTTTTA
1 TAATTTTA
16366391 ATAGGTAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (40 bp):
TAATTTTAGTACACATTCATAAATTTATATATTAATTATA
Found at i:16366651 original size:17 final size:17
Alignment explanation
Indices: 16366583--16366653 Score: 72
Period size: 17 Copynumber: 4.0 Consensus size: 17
16366573 GAAAAAAGGT
16366583 TTTTAAATATATTTAAAA
1 TTTTAAATATA-TTAAAA
*
16366601 TTTTAAA-AAACTTAAAAAA
1 TTTTAAATATA-TT--AAAA
*
16366620 ATTTAAATATATTAAAA
1 TTTTAAATATATTAAAA
*
16366637 TTTTAAATATGTTAAAA
1 TTTTAAATATATTAAAA
16366654 GAAAATGTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
17 23 0.52
18 7 0.16
19 12 0.27
20 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTTAAATATATTAAAA
Found at i:16366745 original size:22 final size:24
Alignment explanation
Indices: 16366696--16366753 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
16366686 TTAATATATA
* *
16366696 TTAATATATTATTACTTATTTAAT
1 TTAATATATTATAACTTATTTAAG
*
16366720 TTAATATATTA-AACTT-TTTAGG
1 TTAATATATTATAACTTATTTAAG
16366742 TTAAT-T-TTATAA
1 TTAATATATTATAA
16366754 AAAAAAGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 3 0.10
21 3 0.10
22 9 0.30
23 4 0.13
24 11 0.37
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (24 bp):
TTAATATATTATAACTTATTTAAG
Found at i:16367932 original size:179 final size:179
Alignment explanation
Indices: 16367632--16367990 Score: 718
Period size: 179 Copynumber: 2.0 Consensus size: 179
16367622 TGTGGATCGG
16367632 TAGTGTTGGCCGCATTGTACTATAAGCTTTGCCGAGCAACAAAACATGGGGTTAGTAACATAGCT
1 TAGTGTTGGCCGCATTGTACTATAAGCTTTGCCGAGCAACAAAACATGGGGTTAGTAACATAGCT
16367697 GGTTGTCTGGGTCTGCTACAATCTTACGCATTATATAAGATGCCGTTTCTAGGCGGCTGTTAAGC
66 GGTTGTCTGGGTCTGCTACAATCTTACGCATTATATAAGATGCCGTTTCTAGGCGGCTGTTAAGC
16367762 ACCAACCATATTCGTTTCCACTTATAAATAGGTAAAAACAAAATTATAC
131 ACCAACCATATTCGTTTCCACTTATAAATAGGTAAAAACAAAATTATAC
16367811 TAGTGTTGGCCGCATTGTACTATAAGCTTTGCCGAGCAACAAAACATGGGGTTAGTAACATAGCT
1 TAGTGTTGGCCGCATTGTACTATAAGCTTTGCCGAGCAACAAAACATGGGGTTAGTAACATAGCT
16367876 GGTTGTCTGGGTCTGCTACAATCTTACGCATTATATAAGATGCCGTTTCTAGGCGGCTGTTAAGC
66 GGTTGTCTGGGTCTGCTACAATCTTACGCATTATATAAGATGCCGTTTCTAGGCGGCTGTTAAGC
16367941 ACCAACCATATTCGTTTCCACTTATAAATAGGTAAAAACAAAATTATAC
131 ACCAACCATATTCGTTTCCACTTATAAATAGGTAAAAACAAAATTATAC
16367990 T
1 T
16367991 TAACATTTAA
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
179 180 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (179 bp):
TAGTGTTGGCCGCATTGTACTATAAGCTTTGCCGAGCAACAAAACATGGGGTTAGTAACATAGCT
GGTTGTCTGGGTCTGCTACAATCTTACGCATTATATAAGATGCCGTTTCTAGGCGGCTGTTAAGC
ACCAACCATATTCGTTTCCACTTATAAATAGGTAAAAACAAAATTATAC
Found at i:16368816 original size:30 final size:30
Alignment explanation
Indices: 16368776--16368879 Score: 136
Period size: 30 Copynumber: 3.5 Consensus size: 30
16368766 GTCGTAGAGC
* * * *
16368776 AGTTCCTATCACTCGGACATTGGTGGTTCA
1 AGTTCATATCACCCGGACATAGGTGGTTCG
*
16368806 AGTTCATATCACCCGGACATGGGTGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
* *
16368836 AGTTCATATCACCCAGACATAGGCGGTTCG
1 AGTTCATATCACCCGGACATAGGTGGTTCG
*
16368866 AGTTCATTTCACCC
1 AGTTCATATCACCC
16368880 AGAGCAACCA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (30 bp):
AGTTCATATCACCCGGACATAGGTGGTTCG
Found at i:16372221 original size:9 final size:10
Alignment explanation
Indices: 16372203--16372253 Score: 52
Period size: 11 Copynumber: 5.0 Consensus size: 10
16372193 TATAAAAATT
16372203 ATATTT-AAA
1 ATATTTAAAA
16372212 AT-TTTAAAA
1 ATATTTAAAA
16372221 ATATTTAAAA
1 ATATTTAAAA
*
16372231 TATATATTTAAA
1 -ATAT-TTAAAA
16372243 ATATTATAAAA
1 ATATT-TAAAA
16372254 CAAATAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 3 0.09
9 7 0.20
10 8 0.23
11 12 0.34
12 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATTTAAAA
Found at i:16372239 original size:13 final size:13
Alignment explanation
Indices: 16372221--16372246 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16372211 AATTTTAAAA
16372221 ATATTTAAAATAT
1 ATATTTAAAATAT
16372234 ATATTTAAAATAT
1 ATATTTAAAATAT
16372247 TATAAAACAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTTAAAATAT
Found at i:16372310 original size:25 final size:23
Alignment explanation
Indices: 16372281--16372393 Score: 70
Period size: 24 Copynumber: 4.7 Consensus size: 23
16372271 AGGTCATATC
*
16372281 TTTAAAAATAATATATTTTAAATAA
1 TTTAAAAATAATA-ATTTAAAAT-A
*
16372306 TTTAAAAATCATAATTTAAAATA
1 TTTAAAAATAATAATTTAAAATA
* * *
16372329 TTATAAAAAATTAAAAAATATT-TAAAA
1 TT-T-AAAAA-T-AATAAT-TTAAAATA
16372356 TTT-AAAAT-ATAAATTTAAAATA
1 TTTAAAAATAAT-AATTTAAAATA
*
16372378 TTATAAAACTAATAAT
1 TT-TAAAAATAATAAT
16372394 AAATTTATAA
Statistics
Matches: 68, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
21 3 0.04
22 8 0.12
23 5 0.07
24 20 0.29
25 19 0.28
26 2 0.03
27 9 0.13
28 2 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TTTAAAAATAATAATTTAAAATA
Found at i:16372322 original size:24 final size:24
Alignment explanation
Indices: 16372281--16372391 Score: 79
Period size: 25 Copynumber: 4.5 Consensus size: 24
16372271 AGGTCATATC
*
16372281 TTTAAAAATAATATATTTTAAATAA
1 TTTAAAAATAATATATTTAAAAT-A
*
16372306 TTTAAAAATCATA-ATTTAAAATA
1 TTTAAAAATAATATATTTAAAATA
*
16372329 TTATAAAAAATTAAAAAATATTT-AAA-A
1 TT-T-AAAAA-T--AATATATTTAAAATA
*
16372356 TTT-AAAAT-ATAAATTTAAAATA
1 TTTAAAAATAATATATTTAAAATA
*
16372378 TTATAAAACTAATA
1 TT-TAAAAATAATA
16372392 ATAAATTTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
20 6 0.09
21 3 0.04
22 3 0.04
23 5 0.07
24 17 0.25
25 20 0.29
26 2 0.03
27 3 0.04
28 5 0.07
29 4 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
TTTAAAAATAATATATTTAAAATA
Found at i:16372371 original size:13 final size:13
Alignment explanation
Indices: 16372353--16372378 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16372343 AAAATATTTA
16372353 AAATTTAAAATAT
1 AAATTTAAAATAT
16372366 AAATTTAAAATAT
1 AAATTTAAAATAT
16372379 TATAAAACTA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTTAAAATAT
Found at i:16372375 original size:29 final size:27
Alignment explanation
Indices: 16372343--16372413 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 27
16372333 AAAAAATTAA
*
16372343 AAAATATTTAAAATTTAAAATATAAATTT
1 AAAATATTTAAAA-CTAAAA-ATAAATTT
*
16372372 AAAATATTATAAAACTAATAATAAATTT
1 AAAATATT-TAAAACTAAAAATAAATTT
16372400 ATAAAGTATTTAAA
1 A-AAA-TATTTAAA
16372414 TGTTTTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 9 0.24
29 19 0.51
30 9 0.24
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (27 bp):
AAAATATTTAAAACTAAAAATAAATTT
Found at i:16372474 original size:21 final size:21
Alignment explanation
Indices: 16372341--16372525 Score: 61
Period size: 21 Copynumber: 8.8 Consensus size: 21
16372331 ATAAAAAATT
16372341 AAAA-AATATTTAAAA-TTTA
1 AAAATAATATTTAAAATTTTA
16372360 AAATATAA-ATTTAAAATATTATA
1 AAA-ATAATATTTAAAAT-TT-TA
* *
16372383 AAACTAATA-AT-AAATTTATA
1 AAAATAATATTTAAAATTT-TA
* * * *
16372403 AAGTATTTAAATGTTTTATATTATTA
1 AA--A-AT-AATATTTAAAATT-TTA
* * * *
16372429 AAAATATATATTTGATACTTAA
1 AAAATA-ATATTTAAAATTTTA
16372451 AAAATAATATTTAAAATTTT-
1 AAAATAATATTTAAAATTTTA
**
16372471 AAAA-AATATTTTCAA----A
1 AAAATAATATTTAAAATTTTA
16372487 AAAAT-ATATTTAAAATTTTTA
1 AAAATAATATTTAAAA-TTTTA
16372508 AAAATATATATTATAAAA
1 AAAATA-ATATT-TAAAA
16372526 CATTTCAAAT
Statistics
Matches: 123, Mismatches: 19, Indels: 43
0.66 0.10 0.23
Matches are distributed among these distances:
16 12 0.10
19 12 0.10
20 20 0.16
21 22 0.18
22 16 0.13
23 22 0.18
24 9 0.07
25 1 0.01
26 8 0.07
27 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAATAATATTTAAAATTTTA
Found at i:16372504 original size:23 final size:24
Alignment explanation
Indices: 16372478--16372534 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
16372468 TTTAAAAAAT
16372478 ATTTTCAAAAAAATATATT-TAAA
1 ATTTTCAAAAAAATATATTATAAA
* *
16372501 ATTTTTAAAAATATATATTATAAA
1 ATTTTCAAAAAAATATATTATAAA
*
16372525 ACATTTCAAA
1 A-TTTTCAAA
16372535 TAAACATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 17 0.61
24 5 0.18
25 6 0.21
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (24 bp):
ATTTTCAAAAAAATATATTATAAA
Found at i:16372541 original size:13 final size:13
Alignment explanation
Indices: 16372523--16372548 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16372513 ATATATTATA
16372523 AAACATTTCAAAT
1 AAACATTTCAAAT
16372536 AAACATTTCAAAT
1 AAACATTTCAAAT
16372549 TTTTTAAATT
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
AAACATTTCAAAT
Found at i:16374274 original size:22 final size:22
Alignment explanation
Indices: 16374248--16374292 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
16374238 GTTATAAAAA
16374248 TATTAATGA-TTTATTTAAAATT
1 TATTAATGACTTT-TTTAAAATT
* *
16374270 TATTAGTGACTTTTTTCAAATT
1 TATTAATGACTTTTTTAAAATT
16374292 T
1 T
16374293 TGGGTTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (22 bp):
TATTAATGACTTTTTTAAAATT
Found at i:16377607 original size:56 final size:55
Alignment explanation
Indices: 16377522--16377629 Score: 171
Period size: 56 Copynumber: 1.9 Consensus size: 55
16377512 TTATAGATTG
* * *
16377522 CAAATTAATTATTCATTAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTA
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAATAATGATTTATCATCTTA
*
16377577 CAAATTTAATTATTCATAAGTACTATTCAAATTAAAAATAATGATTTATCATC
1 CAAA-TTAATTATTCATAAGCACTATTCAAATTAAAAATAATGATTTATCATC
16377630 CAATTGATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
55 4 0.08
56 44 0.92
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.40
Consensus pattern (55 bp):
CAAATTAATTATTCATAAGCACTATTCAAATTAAAAATAATGATTTATCATCTTA
Found at i:16380033 original size:43 final size:43
Alignment explanation
Indices: 16379923--16380035 Score: 163
Period size: 43 Copynumber: 2.6 Consensus size: 43
16379913 CATTTTTTAC
* *
16379923 AAACGCCGCTAAAGGTCCTGGTCTTTAGCAGCGCTTTTCCAAA
1 AAACGCCGCTAAAGGTCCTGATCTTTAGCAGCACTTTTCCAAA
* *
16379966 AAACGCCGCTAAAGGTCCTAATCTTTAGCGGCACTTTTCCAAA
1 AAACGCCGCTAAAGGTCCTGATCTTTAGCAGCACTTTTCCAAA
** *
16380009 AAACGCCGCTAAAAATCATGATCTTTA
1 AAACGCCGCTAAAGGTCCTGATCTTTA
16380036 AAAAAATTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCCTGATCTTTAGCAGCACTTTTCCAAA
Found at i:16380084 original size:22 final size:23
Alignment explanation
Indices: 16380056--16380098 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
16380046 TTTATTTTAA
*
16380056 TTAAATAATAT-TTATTTTTATG
1 TTAAATAATATATTATGTTTATG
*
16380078 TTAAATATTATATTATGTTTA
1 TTAAATAATATATTATGTTTA
16380099 ATTTTTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (23 bp):
TTAAATAATATATTATGTTTATG
Found at i:16380277 original size:18 final size:18
Alignment explanation
Indices: 16380254--16380288 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16380244 ATGTAATTTA
16380254 ATACATAAAAACACACAC
1 ATACATAAAAACACACAC
* *
16380272 ATACATAGAGACACACA
1 ATACATAAAAACACACA
16380289 AAGTATTACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.26, G:0.06, T:0.11
Consensus pattern (18 bp):
ATACATAAAAACACACAC
Found at i:16384315 original size:16 final size:16
Alignment explanation
Indices: 16384291--16384335 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
16384281 TAATTTTAAA
*
16384291 TTTATATTTATAATAT
1 TTTAAATTTATAATAT
*
16384307 TTTAAATTTAT-ATTT
1 TTTAAATTTATAATAT
16384322 TTTAAAATTTATAA
1 TTT-AAATTTATAA
16384336 AAAAAAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 18 0.72
17 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAAATTTATAATAT
Found at i:16385199 original size:14 final size:15
Alignment explanation
Indices: 16385182--16385210 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16385172 AACCTTTAAA
16385182 CCCT-AAATCATAAT
1 CCCTAAAATCATAAT
16385196 CCCTAAAATCATAAT
1 CCCTAAAATCATAAT
16385211 TCATCACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (15 bp):
CCCTAAAATCATAAT
Found at i:16385272 original size:21 final size:21
Alignment explanation
Indices: 16385248--16385331 Score: 60
Period size: 21 Copynumber: 3.7 Consensus size: 21
16385238 ACTCTTAAAC
16385248 CTTAAACCCTAAACTATATAT
1 CTTAAACCCTAAACTATATAT
* *
16385269 CTTAAACCATACTTAACTCATAAACCT
1 CTTAAACC---CTAAACT-ATATA--T
* *
16385296 ACTTAAACCCTTAACCATATAT
1 -CTTAAACCCTAAACTATATAT
*
16385318 CTTAAACCATAAAC
1 CTTAAACCCTAAAC
16385332 CTTAAACTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
21 20 0.40
22 1 0.02
24 10 0.20
25 10 0.20
27 1 0.02
28 8 0.16
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (21 bp):
CTTAAACCCTAAACTATATAT
Found at i:16385688 original size:41 final size:41
Alignment explanation
Indices: 16385501--16385678 Score: 254
Period size: 41 Copynumber: 4.4 Consensus size: 41
16385491 GTTATATGAC
*
16385501 TTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* *
16385542 TTTTAGCGGCGATTTAGCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
16385583 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * **
16385623 TTTTAGCGGCGTTTTTTACTAAAA-CACCGCTGTTGCTCT-GT
1 TTTTAGCGGCG--TTTTACCAAAAGCGCCGCTAATGCTCTGGT
16385664 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
16385679 TTGAAAAAAC
Statistics
Matches: 126, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
39 4 0.03
40 13 0.10
41 99 0.79
42 10 0.08
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:16393512 original size:26 final size:26
Alignment explanation
Indices: 16393483--16393590 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
16393473 TGATAAAAAT
*
16393483 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
16393509 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16393535 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
16393561 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16393587 TGAT
1 TGAT
16393591 GGGCATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:16400561 original size:26 final size:26
Alignment explanation
Indices: 16400527--16400633 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
16400517 TTGATAAAAT
*
16400527 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
16400553 TGATAAT-GGTTAGGTAAATATTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
16400578 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
16400604 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16400630 TGAT
1 TGAT
16400634 GGGCATTTCA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
25 22 0.30
26 52 0.70
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:16400582 original size:51 final size:52
Alignment explanation
Indices: 16400527--16400633 Score: 180
Period size: 51 Copynumber: 2.1 Consensus size: 52
16400517 TTGATAAAAT
* *
16400527 TGATAATGGGTTAGGTAAATGTTTCATGATAATGG-TTAGGTAAATATTCTA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATATTCCA
*
16400578 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATATTCCA
16400630 TGAT
1 TGAT
16400634 GGGCATTTCA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 34 0.65
52 18 0.35
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATATTCCA
Found at i:16408458 original size:19 final size:20
Alignment explanation
Indices: 16408434--16408472 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
16408424 TCTCATTTTT
16408434 TATTTGTTTTT-TGTTTTAA
1 TATTTGTTTTTATGTTTTAA
16408453 TATTTGTTTTTATGTTTTAA
1 TATTTGTTTTTATGTTTTAA
16408473 ATGTATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (20 bp):
TATTTGTTTTTATGTTTTAA
Found at i:16408490 original size:25 final size:23
Alignment explanation
Indices: 16408434--16408498 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 23
16408424 TCTCATTTTT
*
16408434 TATTTGTTTTT-TGTTTT-AA--
1 TATTTGTTTTTATATTTTAAATG
*
16408453 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
16408476 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
16408499 ATTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
21 2 0.05
23 6 0.15
24 3 0.08
25 11 0.28
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:16409095 original size:29 final size:30
Alignment explanation
Indices: 16409062--16409122 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
16409052 ATTATATTTG
*
16409062 AATTGATTAACTTTAAT-TTTGTACTTTTA
1 AATTGATTAACTTTAATCTTTATACTTTTA
*
16409091 AATTGATTAATTTTAATCTTTATACTTTTA
1 AATTGATTAACTTTAATCTTTATACTTTTA
16409121 AA
1 AA
16409123 ATATTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (30 bp):
AATTGATTAACTTTAATCTTTATACTTTTA
Found at i:16410610 original size:356 final size:363
Alignment explanation
Indices: 16409938--16410614 Score: 888
Period size: 356 Copynumber: 1.9 Consensus size: 363
16409928 CTTGAGGCTA
* ** *
16409938 AAATCGAGCATAGATACCTTAGGAACAATACATTTACTGTTGAGGGAGTGAGACACTACAAAGTA
1 AAATCGAGCATAGACACCTTAGGAACAATACATCCACTGTTGAAGGAGTGAGACACTACAAAGTA
*
16410003 GATACTTACCCTTAACATAAAAGGTGGCTTTAATGGGTTTGAATCCCACCAAGGCTAAATTATAA
66 GATACTTACCCTTAACATAAAAGATGGCTTTAATGGGTTTGAATCCCACCAAGGCTAAATTATAA
* ** * * * *
16410068 AATATTTTCTTGGTGGACCTAAATGCTTCCACTGAAACTTCTTGAACCCCTTTAAGCTCTCCTCA
131 AACATTAACTTGGCGCACCTAAATGCTTCCACTGAAACTCCTTGAACCACTTTAAGCTCTCCTCA
** * * * * * *
16410133 GGGTATAAAAACCAAAACTCAAGGCTAAGATCGAGCATAGACATCTCGGGAATAATACTTCCACC
196 GAATAGAAAAACCAAAACTCAAGGCTAAAATCAAGCAAAGACATCTCGAGAATAATACCTCCACC
* * ** * * *
16410198 CTTGAGGAAGTGAGGCACTCTAGAGCAAATACTTGCTCTCTACAAGCTTAATGCAAGAACTCCTT
261 CTGGAGGAAGTGAGACACTCTAGAGCAAATACTCACCCTCAACAAGCATAATGCAAGAACTCCTT
16410263 TGGGCTCTCCTCAAAGTAGGAGAGAAAAACCCGATGTT
326 TGGGCTCTCCTCAAAGTAGGAGAGAAAAACCCGATGTT
*
16410301 AAATCGAGCATAGACA-CTCTA-GAACACTACATCCACTGTTGAAGGAGTGAGACACTACAAAGT
1 AAATCGAGCATAGACACCT-TAGGAACAATACATCCACTGTTGAAGGAGTGAGACACTACAAAGT
***
16410364 AGATACTTACCCTTAACAT-AAAGATGGCTTTAATGGGTTTGAATCCGGTCAAGGCTAAATTATA
65 AGATACTTACCCTTAACATAAAAGATGGCTTTAATGGGTTTGAATCCCACCAAGGCTAAATTATA
* * *
16410428 AAACATTAACTTGGCGCACCTAGATGC-TCCACTGAAAC-CCTATGAA-TACTTT-GGCTCTCCT
130 AAACATTAACTTGGCGCACCTAAATGCTTCCACTGAAACTCCT-TGAACCACTTTAAGCTCTCCT
** * *
16410489 C-GAATAGAAAAA-CAAAACTTGAGGTTAAAATCAAGCAAAGACATCTTGAGAATAATACCTCCA
194 CAGAATAGAAAAACCAAAACTCAAGGCTAAAATCAAGCAAAGACATCTCGAGAATAATACCTCCA
* * *
16410552 CCCTGGGGGAAGTGAGACACT-TCAGAGCATATACTCACCCTCAACCAGCATAATGCAAGAACT
259 CCCTGGAGGAAGTGAGACACTCT-AGAGCAAATACTCACCCTCAACAAGCATAATGCAAGAACT
16410615 AATAATAGCA
Statistics
Matches: 270, Mismatches: 41, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
355 1 0.00
356 93 0.34
357 8 0.03
358 9 0.03
359 6 0.02
360 15 0.06
361 62 0.23
362 59 0.22
363 17 0.06
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (363 bp):
AAATCGAGCATAGACACCTTAGGAACAATACATCCACTGTTGAAGGAGTGAGACACTACAAAGTA
GATACTTACCCTTAACATAAAAGATGGCTTTAATGGGTTTGAATCCCACCAAGGCTAAATTATAA
AACATTAACTTGGCGCACCTAAATGCTTCCACTGAAACTCCTTGAACCACTTTAAGCTCTCCTCA
GAATAGAAAAACCAAAACTCAAGGCTAAAATCAAGCAAAGACATCTCGAGAATAATACCTCCACC
CTGGAGGAAGTGAGACACTCTAGAGCAAATACTCACCCTCAACAAGCATAATGCAAGAACTCCTT
TGGGCTCTCCTCAAAGTAGGAGAGAAAAACCCGATGTT
Found at i:16423208 original size:16 final size:17
Alignment explanation
Indices: 16423184--16423221 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
16423174 CGGTTTAGTC
*
16423184 ATTTGTTTATTTC-ATT
1 ATTTATTTATTTCAATT
16423200 ATTTATTTATTTCAATT
1 ATTTATTTATTTCAATT
16423217 ATTTA
1 ATTTA
16423222 ATTTCTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTTATTTATTTCAATT
Found at i:16429448 original size:24 final size:24
Alignment explanation
Indices: 16429428--16429478 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
16429418 AAGATTTAGA
* *
16429428 ATTTATTAGTATAATATATTTAAC
1 ATTTATAAGCATAATATATTTAAC
*
16429452 ATTTATAAGCATAATATATTTGAC
1 ATTTATAAGCATAATATATTTAAC
16429476 ATT
1 ATT
16429479 GATTAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (24 bp):
ATTTATAAGCATAATATATTTAAC
Found at i:16431239 original size:14 final size:14
Alignment explanation
Indices: 16431220--16431251 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16431210 AGGTCATTTA
16431220 GCCCAACCAAACGG
1 GCCCAACCAAACGG
*
16431234 GCCCAACCAAACTG
1 GCCCAACCAAACGG
16431248 GCCC
1 GCCC
16431252 GGTGATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.47, G:0.19, T:0.03
Consensus pattern (14 bp):
GCCCAACCAAACGG
Found at i:16436363 original size:14 final size:14
Alignment explanation
Indices: 16436344--16436375 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16436334 AGGTCATTTA
16436344 GCCCAACCAAACGG
1 GCCCAACCAAACGG
*
16436358 GCCCAACCAAACTG
1 GCCCAACCAAACGG
16436372 GCCC
1 GCCC
16436376 GGTGATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.47, G:0.19, T:0.03
Consensus pattern (14 bp):
GCCCAACCAAACGG
Found at i:16438501 original size:30 final size:31
Alignment explanation
Indices: 16438452--16438514 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
16438442 ACTTATTTTA
16438452 TTGTTAATTATTATTATTATTTTAGAGGCAT
1 TTGTTAATTATTATTATTATTTTAGAGGCAT
*
16438483 TTGTTAATT-TTGTTATTATTTTAGAGGCAT
1 TTGTTAATTATTATTATTATTTTAGAGGCAT
16438513 TT
1 TT
16438515 ACTTGTTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (31 bp):
TTGTTAATTATTATTATTATTTTAGAGGCAT
Found at i:16438527 original size:30 final size:30
Alignment explanation
Indices: 16438455--16438528 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
16438445 TATTTTATTG
* *
16438455 TTAATTATTATTATTATTTTAGAGGCATTTG
1 TTAATTA-TGTTATTATTTTAGAGGCATTTC
*
16438486 TTAATTTTGTTATTATTTTAGAGGCATTTAC
1 TTAATTATGTTATTATTTTAGAGGCATTT-C
*
16438517 TT-GTTATGTTAT
1 TTAATTATGTTAT
16438529 ATCTATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 29 0.78
31 8 0.22
ACGTcount: A:0.26, C:0.04, G:0.14, T:0.57
Consensus pattern (30 bp):
TTAATTATGTTATTATTTTAGAGGCATTTC
Found at i:16439839 original size:25 final size:25
Alignment explanation
Indices: 16439797--16439845 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
16439787 CATAGCTTTA
* *
16439797 ATAAAATAAGGTTGATAATAAATGC
1 ATAAAATAAGGTTCATAACAAATGC
* *
16439822 ATAAAATGATGTTCATAACAAATG
1 ATAAAATAAGGTTCATAACAAATG
16439846 GGAATGTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (25 bp):
ATAAAATAAGGTTCATAACAAATGC
Found at i:16441959 original size:24 final size:24
Alignment explanation
Indices: 16441931--16441994 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
16441921 TTTCTAGAAG
* *
16441931 ATTTAATATTTATTAGTATAAGAT
1 ATTTAACATTTATTAGCATAAGAT
*
16441955 ATTTAACATTTATTAGCATAATAT
1 ATTTAACATTTATTAGCATAAGAT
* *
16441979 ATTTGACATTGATTAG
1 ATTTAACATTTATTAG
16441995 AATTAGGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (24 bp):
ATTTAACATTTATTAGCATAAGAT
Found at i:16446448 original size:24 final size:24
Alignment explanation
Indices: 16446397--16446449 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
16446387 TTTAATATTT
* *
16446397 ATTAGTATAATATATTTAGCATTT
1 ATTAGCATAATATATTTAGCATTG
16446421 ATTAGCATAATATATTT-GACATTG
1 ATTAGCATAATATATTTAG-CATTG
16446445 ATTAG
1 ATTAG
16446450 AATTAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (24 bp):
ATTAGCATAATATATTTAGCATTG
Found at i:16448300 original size:21 final size:21
Alignment explanation
Indices: 16448274--16448315 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16448264 CAACGCCAAT
*
16448274 CTTTGGAGATTGACATTAAAG
1 CTTTGGAGATTGACATCAAAG
16448295 CTTTGGAGATTGACATCAAAG
1 CTTTGGAGATTGACATCAAAG
16448316 AAATGATGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (21 bp):
CTTTGGAGATTGACATCAAAG
Found at i:16450085 original size:26 final size:25
Alignment explanation
Indices: 16450037--16450088 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
16450027 CATTTAAAAC
*
16450037 ATAATTTAAAACTAAAAAAAATAAT
1 ATAATTAAAAACTAAAAAAAATAAT
* *
16450062 ATAATTAAAAATCTAATAATAATAAT
1 ATAATTAAAAA-CTAAAAAAAATAAT
16450088 A
1 A
16450089 AGTTCATTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
ATAATTAAAAACTAAAAAAAATAAT
Found at i:16452084 original size:26 final size:26
Alignment explanation
Indices: 16452038--16452087 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
16452028 GGATGGTGAG
16452038 GACCATCAACTACGAAAAGGGATAAC
1 GACCATCAACTACGAAAAGGGATAAC
* *
16452064 GACCATCGAA-TATGAAGAGGGATA
1 GACCATC-AACTACGAAAAGGGATA
16452088 GCTTCAGCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (26 bp):
GACCATCAACTACGAAAAGGGATAAC
Found at i:16452139 original size:84 final size:86
Alignment explanation
Indices: 16451964--16452173 Score: 232
Period size: 84 Copynumber: 2.4 Consensus size: 86
16451954 CGAGGAGAAT
* * *
16451964 GAAAAGGGATGGTGATGACCATCGAATATGAAAAGGGATAGCTTCCGCTATCATTTATGAAAAGG
1 GAAAAGGGAT-GAGACGACCATCGAATATGAAAAGGGATAGCTTCAGCTATCATTTATGAAAAGG
*
16452029 GATGGTGAGGACCATCAACTAC
65 GATGCTGAGGACCATCAACTAC
*
16452051 GAAAAGGGAT-A-ACGACCATCGAATATGAAGAGGGATAGCTTCAGCTATCGA-TTATGAAAAGG
1 GAAAAGGGATGAGACGACCATCGAATATGAAAAGGGATAGCTTCAGCTATC-ATTTATGAAAAGG
** ** * * *
16452113 GATAGCTTCGG-TTATCGATTAT
65 GAT-GCTGAGGACCATCAACTAC
16452135 GAAAAGGGATGATGACGACCATC-AATTATGAAAAGGGAT
1 GAAAAGGGATGA-GACGACCATCGAA-TATGAAAAGGGAT
16452174 GGTGACGACC
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
84 65 0.62
85 6 0.06
86 2 0.02
87 31 0.30
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.22
Consensus pattern (86 bp):
GAAAAGGGATGAGACGACCATCGAATATGAAAAGGGATAGCTTCAGCTATCATTTATGAAAAGGG
ATGCTGAGGACCATCAACTAC
Found at i:16452163 original size:58 final size:58
Alignment explanation
Indices: 16451962--16452231 Score: 198
Period size: 58 Copynumber: 4.7 Consensus size: 58
16451952 ATCGAGGAGA
* *
16451962 ATGAAAAGGGATGGTGATGACCATCGAA-TATGAAAAGGGATAGCTTCCGCTATC-ATTT
1 ATGAAAAGGGATGGTGACGACCATC-AATTATGAAAAGGGATAGCTTCGGCTATCGA-TT
* * * * * * *
16452020 ATGAAAAGGGATGGTGAGGACCATCAACTACGAAAAGGGATA---ACGACCATCGAAT
1 ATGAAAAGGGATGGTGACGACCATCAATTATGAAAAGGGATAGCTTCGGCTATCGATT
* * * * * *
16452075 ATGAAGAGGGATAGCT-TC-AGCTATCGATTATGAAAAGGGATAGCTTCGGTTATCGATT
1 ATGAAAAGGGAT-GGTGACGA-CCATCAATTATGAAAAGGGATAGCTTCGGCTATCGATT
* * * * *
16452133 ATGAAAAGGGATGATGACGACCATCAATTATGAAAAGGGAT-GGTGACGACCATCGATT
1 ATGAAAAGGGATGGTGACGACCATCAATTATGAAAAGGGATAGCT-TCGGCTATCGATT
* ** *
16452191 AATGAAAGGGGATGGTTTCAACCATCGAA-TATGAAAAGGGA
1 -ATGAAAAGGGATGGTGACGACCATC-AATTATGAAAAGGGA
16452232 CGGTTATGAC
Statistics
Matches: 165, Mismatches: 35, Indels: 23
0.74 0.16 0.10
Matches are distributed among these distances:
54 1 0.01
55 35 0.21
56 3 0.02
57 6 0.04
58 85 0.52
59 33 0.20
60 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.22
Consensus pattern (58 bp):
ATGAAAAGGGATGGTGACGACCATCAATTATGAAAAGGGATAGCTTCGGCTATCGATT
Found at i:16452168 original size:113 final size:115
Alignment explanation
Indices: 16451981--16452231 Score: 321
Period size: 113 Copynumber: 2.2 Consensus size: 115
16451971 GATGGTGATG
* *
16451981 ACCATCGAATATGAAAAGGGATAGCTTCCGCTATCATTTATGAAAAGGGATGGTGAGGACCATCA
1 ACCATCGAATATGAAAAGGGATAGCTTCCGCTATCATTTATGAAAAGGGATGATGACGACCATCA
16452046 ACTACGAAAAGGGA-TAACGACCATCGAAT-ATG-AAGAGGGATAGCTTCA
66 ACTACGAAAAGGGAGTAACGACCATCGAATAATGAAAG-GGGATAGCTTCA
* * * * *
16452094 GCTATCGATTATGAAAAGGGATAGCTTCGGTTATCGA-TTATGAAAAGGGATGATGACGACCATC
1 ACCATCGAATATGAAAAGGGATAGCTTCCGCTATC-ATTTATGAAAAGGGATGATGACGACCATC
* * * * * *
16452158 AATTATGAAAAGGGATGGTGACGACCATCGATTAATGAAAGGGGATGGTTTCA
65 AACTACGAAAAGGGA--GTAACGACCATCGAATAATGAAAGGGGATAGCTTCA
16452211 ACCATCGAATATGAAAAGGGA
1 ACCATCGAATATGAAAAGGGA
16452232 CGGTTATGAC
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
113 68 0.59
114 1 0.01
116 13 0.11
117 31 0.27
118 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.22
Consensus pattern (115 bp):
ACCATCGAATATGAAAAGGGATAGCTTCCGCTATCATTTATGAAAAGGGATGATGACGACCATCA
ACTACGAAAAGGGAGTAACGACCATCGAATAATGAAAGGGGATAGCTTCA
Found at i:16452203 original size:30 final size:29
Alignment explanation
Indices: 16451962--16452245 Score: 179
Period size: 29 Copynumber: 9.9 Consensus size: 29
16451952 ATCGAGGAGA
* *
16451962 ATGAAAAGGGATGGTGATGACCATCGAAT
1 ATGAAAAGGGATGGTGACGACCATCGATT
* ** *
16451991 ATGAAAAGGGATAGCTTCCG-CTATC-ATTT
1 ATGAAAAGGGAT-GGTGACGACCATCGA-TT
* * *
16452020 ATGAAAAGGGATGGTGAGGACCATCAACT
1 ATGAAAAGGGATGGTGACGACCATCGATT
* * *
16452049 ACGAAAAGGGA---TAACGACCATCGAAT
1 ATGAAAAGGGATGGTGACGACCATCGATT
* * * *
16452075 ATGAAGAGGGATAGCT-TC-AGCTATCGATT
1 ATGAAAAGGGAT-GGTGACGA-CCATCGATT
* * ***
16452104 ATGAAAAGGGATAGCT-TCGGTTATCGATT
1 ATGAAAAGGGAT-GGTGACGACCATCGATT
* *
16452133 ATGAAAAGGGATGATGACGACCATCAATT
1 ATGAAAAGGGATGGTGACGACCATCGATT
16452162 ATGAAAAGGGATGGTGACGACCATCGATT
1 ATGAAAAGGGATGGTGACGACCATCGATT
* ** * *
16452191 AATGAAAGGGGATGGTTTCAACCATCGAAT
1 -ATGAAAAGGGATGGTGACGACCATCGATT
* * *
16452221 ATGAAAAGGGACGGTTATGACCATC
1 ATGAAAAGGGATGGTGACGACCATC
16452246 ATTTAGTACA
Statistics
Matches: 200, Mismatches: 43, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
26 20 0.10
28 7 0.04
29 144 0.72
30 29 0.14
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (29 bp):
ATGAAAAGGGATGGTGACGACCATCGATT
Found at i:16452225 original size:59 final size:58
Alignment explanation
Indices: 16452126--16452245 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 58
16452116 AGCTTCGGTT
* *
16452126 ATCGATTATGAAAAGGGATGATGACGACCATCAATTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGATGACAACCATCAATTATGAAAAGGGACGGTGACGACC
* * ** * *
16452184 ATCGATTAATGAAAGGGGATGGTTTCAACCATCGAA-TATGAAAAGGGACGGTTATGACC
1 ATCGATT-ATGAAAAGGGATGATGACAACCATC-AATTATGAAAAGGGACGGTGACGACC
16452243 ATC
1 ATC
16452246 ATTTAGTACA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
58 7 0.13
59 43 0.83
60 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.23
Consensus pattern (58 bp):
ATCGATTATGAAAAGGGATGATGACAACCATCAATTATGAAAAGGGACGGTGACGACC
Found at i:16459941 original size:39 final size:39
Alignment explanation
Indices: 16459887--16459985 Score: 162
Period size: 39 Copynumber: 2.5 Consensus size: 39
16459877 ATGTTTTTGA
16459887 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGG
1 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGG
* *
16459926 GTATTGTGATATATGCTTAAATGTTATGTGGTTATATGT
1 GTATTGTGATATATGCTTAAATGTTATGTGATTATATGG
* *
16459965 GCAATGTGATATATGCTTAAA
1 GTATTGTGATATATGCTTAAA
16459986 AATGAATATG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.44
Consensus pattern (39 bp):
GTATTGTGATATATGCTTAAATGTTATGTGATTATATGG
Found at i:16463810 original size:25 final size:25
Alignment explanation
Indices: 16463781--16463858 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
16463771 GAATGGCCAA
16463781 TGTGATGAAAGTGAACATGTATATG
1 TGTGATGAAAGTGAACATGTATATG
* *** *
16463806 TGTGAT-AAAGCCG-A-ATGGCCA-A
1 TGTGATGAAAG-TGAACATGTATATG
*
16463828 TGTGATGAAAGTAAACATGTATATG
1 TGTGATGAAAGTGAACATGTATATG
16463853 TGTGAT
1 TGTGAT
16463859 AAGGCCGAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
22 6 0.16
23 9 0.24
24 9 0.24
25 13 0.35
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.29
Consensus pattern (25 bp):
TGTGATGAAAGTGAACATGTATATG
Found at i:16463832 original size:47 final size:47
Alignment explanation
Indices: 16463740--16464002 Score: 359
Period size: 47 Copynumber: 5.6 Consensus size: 47
16463730 TAATTGAATA
*
16463740 AATGTGAA-AGTGTATATGTGTGAATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATGTGTG-ATAAGGCCGAATGGCCAATGTGATG
* *
16463788 AAAGTGAACATGTATATGTGTGATAAAGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* *
16463835 AAAGTAAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* *
16463882 AATGTGAACATGTGTATGTGTGATAAGGCCGAGTGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * * * *
16463929 AATGTGAGCATGTGTATGTGAGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
**
16463976 AATGTGAA-AGTGTATAAATGTGATAAG
1 AATGTGAACA-TGTATATGTGTGATAAG
16464003 TCCCGAAGGG
Statistics
Matches: 194, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
46 1 0.01
47 173 0.89
48 19 0.10
49 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.27
Consensus pattern (47 bp):
AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:16466017 original size:40 final size:40
Alignment explanation
Indices: 16465960--16466422 Score: 727
Period size: 40 Copynumber: 11.6 Consensus size: 40
16465950 TCGAATGATG
* *
16465960 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TATA
* * * * *
16466000 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCGTGCTAGTGA-TATA
16466040 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
*
16466080 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* *
16466120 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
*
16466160 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
16466200 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
16466240 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
16466280 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
*
16466320 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
*
16466360 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* *
16466400 TCCGTGCTAAATCCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCA
16466423 ATCATGCTGG
Statistics
Matches: 398, Mismatches: 21, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
39 1 0.00
40 377 0.95
41 20 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
Found at i:16470291 original size:25 final size:25
Alignment explanation
Indices: 16470262--16470339 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
16470252 GAATGGCCAA
16470262 TGTGATGAAAGTGAACATGTATATG
1 TGTGATGAAAGTGAACATGTATATG
* *** *
16470287 TGTGAT-AAAGCCG-A-ATGGCCA-A
1 TGTGATGAAAG-TGAACATGTATATG
*
16470309 TGTGATGAAAGTAAACATGTATATG
1 TGTGATGAAAGTGAACATGTATATG
16470334 TGTGAT
1 TGTGAT
16470340 AAGGCCGAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
22 6 0.16
23 9 0.24
24 9 0.24
25 13 0.35
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.29
Consensus pattern (25 bp):
TGTGATGAAAGTGAACATGTATATG
Found at i:16470313 original size:47 final size:47
Alignment explanation
Indices: 16470221--16470483 Score: 359
Period size: 47 Copynumber: 5.6 Consensus size: 47
16470211 TAATTGAATA
*
16470221 AATGTGAA-AGTGTATATGTGTGAATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATGTGTG-ATAAGGCCGAATGGCCAATGTGATG
* *
16470269 AAAGTGAACATGTATATGTGTGATAAAGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* *
16470316 AAAGTAAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* *
16470363 AATGTGAACATGTGTATGTGTGATAAGGCCGAGTGGCCAATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * * * *
16470410 AATGTGAGCATGTGTATGTGAGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
**
16470457 AATGTGAA-AGTGTATAAATGTGATAAG
1 AATGTGAACA-TGTATATGTGTGATAAG
16470484 TCCCGAAGGG
Statistics
Matches: 194, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
46 1 0.01
47 173 0.89
48 19 0.10
49 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.27
Consensus pattern (47 bp):
AATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:16479172 original size:19 final size:18
Alignment explanation
Indices: 16479130--16479180 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 18
16479120 TAAATACTAC
* *
16479130 TTAAAATATTATTATCTT
1 TTAAAATTTTATTTTCTT
16479148 TT--AATTTTATTTTCTT
1 TTAAAATTTTATTTTCTT
16479164 ATTAAAATTTTAATTTT
1 -TTAAAATTTT-ATTTT
16479181 AATAGGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 12 0.44
17 2 0.07
18 2 0.07
19 6 0.22
20 5 0.19
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTAAAATTTTATTTTCTT
Found at i:16486395 original size:50 final size:50
Alignment explanation
Indices: 16486320--16486496 Score: 264
Period size: 50 Copynumber: 3.5 Consensus size: 50
16486310 CCATGGCAAC
** *
16486320 AAGTGATAAGTGATAGCTTCGGCTACGTTTATCTGATCAAGAACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
*
16486370 AAGTGATAAGTGATAGTTTCGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
* * *
16486420 AAGTGATAAGTGATAGCTTCGGTTACACTTATTTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
* *
16486470 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
16486497 CTGATCAGTG
Statistics
Matches: 115, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
50 92 0.80
51 23 0.20
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
Found at i:16486510 original size:31 final size:31
Alignment explanation
Indices: 16486472--16486806 Score: 571
Period size: 31 Copynumber: 10.8 Consensus size: 31
16486462 ACAAATGACA
16486472 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
16486503 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
**
16486534 AGTGAAAAGTGGTAGCTTCGATTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
16486565 AGTGAAAAGTGGTAACTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
16486596 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
16486627 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
16486658 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
16486689 GGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* **
16486720 GGTGAAAAGTGGTAGCTTCAACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
16486751 AGTGAAAAATGGTAGCTTCGGCTGCCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
16486782 AGTGAATAGTGGTAGCTTCAGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
16486807 AAGTGACAAG
Statistics
Matches: 286, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 286 1.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:16492930 original size:13 final size:14
Alignment explanation
Indices: 16492912--16492944 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
16492902 ATTCCATGTC
16492912 TTTTATTTA-AAAT
1 TTTTATTTATAAAT
*
16492925 TTTTATTTATAACT
1 TTTTATTTATAAAT
16492939 TTTTAT
1 TTTTAT
16492945 ATGTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATTTATAAAT
Found at i:16493247 original size:16 final size:18
Alignment explanation
Indices: 16493212--16493249 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
16493202 GTAAAGAATT
*
16493212 ATTAGTAATATTATTTAA
1 ATTAGTAATATTATTAAA
16493230 ATTA-TAATA-TATTAAA
1 ATTAGTAATATTATTAAA
16493246 ATTA
1 ATTA
16493250 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 5 0.26
18 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTAGTAATATTATTAAA
Found at i:16495032 original size:22 final size:23
Alignment explanation
Indices: 16494990--16495034 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
16494980 TCAAATAGCA
16494990 TTTGAATTAGAAGAAAATTTTAC
1 TTTGAATTAGAAGAAAATTTTAC
16495013 TTTGAATTAGAAG-AAATTTTAC
1 TTTGAATTAGAAGAAAATTTTAC
16495035 AACTTTGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (23 bp):
TTTGAATTAGAAGAAAATTTTAC
Found at i:16499706 original size:13 final size:13
Alignment explanation
Indices: 16499688--16499712 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16499678 AGAAATTCGA
16499688 AACACGAAAAATT
1 AACACGAAAAATT
16499701 AACACGAAAAAT
1 AACACGAAAAAT
16499713 CAAAACATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.08, T:0.12
Consensus pattern (13 bp):
AACACGAAAAATT
Found at i:16500398 original size:15 final size:15
Alignment explanation
Indices: 16500378--16500406 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16500368 AAAAAAAAAA
16500378 CCATAAACCCTAATT
1 CCATAAACCCTAATT
16500393 CCATAAACCCTAAT
1 CCATAAACCCTAAT
16500407 ACTAAACACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.24
Consensus pattern (15 bp):
CCATAAACCCTAATT
Found at i:16504763 original size:22 final size:22
Alignment explanation
Indices: 16504735--16504776 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
16504725 CCCAGAACCT
16504735 AAATTGATAATTAATGTAACTA
1 AAATTGATAATTAATGTAACTA
16504757 AAATTGATAATTAATGTAAC
1 AAATTGATAATTAATGTAAC
16504777 CAATTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (22 bp):
AAATTGATAATTAATGTAACTA
Found at i:16506185 original size:60 final size:59
Alignment explanation
Indices: 16506059--16506186 Score: 154
Period size: 60 Copynumber: 2.1 Consensus size: 59
16506049 TAGAGATCAC
* *
16506059 CCAACTATAGTTTTTTTTTTTGTTTGGCCATCTAACTATAAAAAGTTACAAAATGGTTA
1 CCAACTATAGTTTTTTTTTTTGTTTGGCCATCTAACTATAAAAAGTTACAAAATAGTCA
* *
16506118 CCTAACTAT-GTTTTTTTTTCTTTTTTGG--TTGCTCAACTATAAAAAGTTACAAAATAGTCA
1 CC-AACTATAGTTTTTTTTT-TTGTTTGGCCAT-CT-AACTATAAAAAGTTACAAAATAGTCA
16506178 TCCAACTAT
1 -CCAACTAT
16506187 TCAATTTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
58 1 0.02
59 14 0.23
60 43 0.72
61 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (59 bp):
CCAACTATAGTTTTTTTTTTTGTTTGGCCATCTAACTATAAAAAGTTACAAAATAGTCA
Found at i:16506771 original size:30 final size:33
Alignment explanation
Indices: 16506716--16506781 Score: 111
Period size: 30 Copynumber: 2.1 Consensus size: 33
16506706 TTGTAATGAT
16506716 AAAATTATATTTTAATCCTTCTAAAAATTATAA
1 AAAATTATATTTTAATCCTTCTAAAAATTATAA
16506749 AAAATTA-A-TTTAATCC-TCTAAAAATTATAA
1 AAAATTATATTTTAATCCTTCTAAAAATTATAA
16506779 AAA
1 AAA
16506782 TATAAACTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 17 0.52
31 8 0.24
32 1 0.03
33 7 0.21
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (33 bp):
AAAATTATATTTTAATCCTTCTAAAAATTATAA
Found at i:16532857 original size:19 final size:19
Alignment explanation
Indices: 16532820--16532858 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16532810 ATCATCCATT
*
16532820 TTCATTTTCTATATGCATA
1 TTCATTTTCCATATGCATA
16532839 TTCATCTTTCCATAT-CATA
1 TTCAT-TTTCCATATGCATA
16532858 T
1 T
16532859 GAACATATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.51
Consensus pattern (19 bp):
TTCATTTTCCATATGCATA
Found at i:16536315 original size:21 final size:20
Alignment explanation
Indices: 16536289--16536330 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
16536279 GACTAAAATG
16536289 AAAAGTTGTAAAATTTGATGA
1 AAAAGTT-TAAAATTTGATGA
* *
16536310 AAAAGTTTGAAATTTTATGA
1 AAAAGTTTAAAATTTGATGA
16536330 A
1 A
16536331 TACATGTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.36
Consensus pattern (20 bp):
AAAAGTTTAAAATTTGATGA
Found at i:16539958 original size:30 final size:30
Alignment explanation
Indices: 16539912--16539972 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
16539902 ATCCCGAGCC
16539912 TAGGGGCAAAAATGTAAATATGCAAAAATT
1 TAGGGGCAAAAATGTAAATATGCAAAAATT
* * * *
16539942 TAGGGGTAAAATTGTAAATTTGCCAAAATT
1 TAGGGGCAAAAATGTAAATATGCAAAAATT
16539972 T
1 T
16539973 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAAATATGCAAAAATT
Found at i:16540549 original size:93 final size:93
Alignment explanation
Indices: 16540390--16540561 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
16540380 GGATGGTTGA
* * *
16540390 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
16540455 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
16540483 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
16540548 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
16540562 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:16540566 original size:46 final size:46
Alignment explanation
Indices: 16540394--16540568 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
16540384 GGTTGAGCAT
* * *
16540394 CCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * * *
16540440 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
*
16540485 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
16540533 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
16540569 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
45 3 0.03
46 63 0.58
47 27 0.25
48 4 0.04
50 3 0.03
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:16544996 original size:7 final size:7
Alignment explanation
Indices: 16544984--16545022 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
16544974 GCATAATTAA
16544984 TTAAAAT
1 TTAAAAT
16544991 TTAAAAT
1 TTAAAAT
16544998 TTAAAAT
1 TTAAAAT
16545005 TTAAAAT
1 TTAAAAT
16545012 TTAAAAT
1 TTAAAAT
16545019 TTAA
1 TTAA
16545023 TAGTTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTAAAAT
Found at i:16545029 original size:21 final size:21
Alignment explanation
Indices: 16544984--16545029 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
16544974 GCATAATTAA
*
16544984 TTAAAATTTAAAATTTAAAAT
1 TTAAAATTTAAAATTTAAAAG
*
16545005 TTAAAATTTAAAATTTAATAG
1 TTAAAATTTAAAATTTAAAAG
16545026 TTAA
1 TTAA
16545030 TTTCAGTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAAAATTTAAAATTTAAAAG
Found at i:16546690 original size:59 final size:59
Alignment explanation
Indices: 16546609--16546753 Score: 245
Period size: 59 Copynumber: 2.4 Consensus size: 59
16546599 GCACGTCAGT
16546609 AATATATTTGTACAAAAATATTCAAAAGAACTTATATTTTATTAAATGAAAAAATATAAA
1 AATA-ATTTGTACAAAAATATTCAAAAGAACTTATATTTTATTAAATGAAAAAATATAAA
* * *
16546669 AATAATTAGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTATATTTTATTAAATGAAAAAATATAAA
*
16546728 AACAATTTGTACAAAAATATTCAAAA
1 AATAATTTGTACAAAAATATTCAAAA
16546754 ATAAATCAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 76 0.95
60 4 0.05
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (59 bp):
AATAATTTGTACAAAAATATTCAAAAGAACTTATATTTTATTAAATGAAAAAATATAAA
Found at i:16556083 original size:20 final size:21
Alignment explanation
Indices: 16556058--16556124 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
16556048 TTATTTTAAC
16556058 TTTTTTAAAGATTTTA-AATT
1 TTTTTTAAAGATTTTAGAATT
*
16556078 TTTTTT-ATGTATTCTTTAGAATT
1 TTTTTTAAAG-A-T-TTTAGAATT
* *
16556101 TTTTTAAAAG-TTTTATAATT
1 TTTTTTAAAGATTTTAGAATT
16556121 TTTT
1 TTTT
16556125 AAAAATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 2 0.05
20 19 0.50
21 2 0.05
22 4 0.11
23 9 0.24
24 2 0.05
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.64
Consensus pattern (21 bp):
TTTTTTAAAGATTTTAGAATT
Found at i:16556129 original size:20 final size:20
Alignment explanation
Indices: 16556092--16556129 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16556082 TTATGTATTC
*
16556092 TTTAGAATTTTTTTAAAAGT
1 TTTAGAATTTTTTAAAAAGT
*
16556112 TTTATAATTTTTTAAAAA
1 TTTAGAATTTTTTAAAAA
16556130 TATAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTAGAATTTTTTAAAAAGT
Found at i:16556175 original size:19 final size:20
Alignment explanation
Indices: 16556153--16556199 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
16556143 ATTTTATAAA
*
16556153 TATTTTTAAT-CTTAAAAAT
1 TATTTTGAATACTTAAAAAT
* *
16556172 TATTTTGAATATTTGAAAAT
1 TATTTTGAATACTTAAAAAT
16556192 TATTTTGA
1 TATTTTGA
16556200 CATTTTTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (20 bp):
TATTTTGAATACTTAAAAAT
Found at i:16566416 original size:47 final size:47
Alignment explanation
Indices: 16566363--16566457 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
16566353 TGCTCCCTAT
16566363 GTTGCAACATCAAACTCACTGTGTAGTAGTACAGAGACTAGTATCGA
1 GTTGCAACATCAAACTCACTGTGTAGTAGTACAGAGACTAGTATCGA
16566410 GTTGCAACATCAAACTCACTGTGTAGTAGTACAGAGACTAGTATCGA
1 GTTGCAACATCAAACTCACTGTGTAGTAGTACAGAGACTAGTATCGA
16566457 G
1 G
16566458 CTAGCACACC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (47 bp):
GTTGCAACATCAAACTCACTGTGTAGTAGTACAGAGACTAGTATCGA
Found at i:16567908 original size:40 final size:40
Alignment explanation
Indices: 16567860--16568047 Score: 304
Period size: 40 Copynumber: 4.7 Consensus size: 40
16567850 GCAAACACAT
* * * *
16567860 TTGCCTTCGGGTCTTAACCCAGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
16567900 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
16567940 TTGCCTTCGGGTCTTGGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
16567980 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
16568020 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
16568048 TCCAATGCTC
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 139 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:16576894 original size:42 final size:42
Alignment explanation
Indices: 16576846--16576927 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
16576836 AAGGTCGTGT
16576846 CACATGCCCGTGTGCCATGTCGTGTAACTCTTTGAGTTGCCC
1 CACATGCCCGTGTGCCATGTCGTGTAACTCTTTGAGTTGCCC
16576888 CACATGCCCGTGTGCCATGTCGTGTAACTCTTTGAGTTGC
1 CACATGCCCGTGTGCCATGTCGTGTAACTCTTTGAGTTGC
16576928 ACCTTAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.15, C:0.29, G:0.24, T:0.32
Consensus pattern (42 bp):
CACATGCCCGTGTGCCATGTCGTGTAACTCTTTGAGTTGCCC
Found at i:16591832 original size:28 final size:28
Alignment explanation
Indices: 16591798--16591874 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
16591788 TCATTTACGA
16591798 ATCAATTCAATTTCACTTTTCATCAAT-
1 ATCAATTCAATTTCACTTTTCATCAATC
* * * *
16591825 ATACAATTCAATATCAATACTT-ATCCATC
1 AT-CAATTCAATTTCACT-TTTCATCAATC
16591854 ATCAATTCAATTTC-CTTTTCA
1 ATCAATTCAATTTCACTTTTCA
16591875 ATTCCGTAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 29 0.74
29 4 0.10
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (28 bp):
ATCAATTCAATTTCACTTTTCATCAATC
Found at i:16591940 original size:19 final size:18
Alignment explanation
Indices: 16591913--16591958 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
16591903 TACTTATCAT
* *
16591913 ACATATAATTAAAAATTTA
1 ACATTTAATTAAAAA-ATA
16591932 ACATTTAA-TAAAAAATA
1 ACATTTAATTAAAAAATA
16591949 ACA-TTAATTA
1 ACATTTAATTA
16591959 TAGTAATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.17
17 7 0.29
18 6 0.25
19 7 0.29
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (18 bp):
ACATTTAATTAAAAAATA
Found at i:16592190 original size:23 final size:22
Alignment explanation
Indices: 16592143--16592190 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
16592133 CAATTTAATC
16592143 CTAACTAAATTCACTTACTTTT
1 CTAACTAAATTCACTTACTTTT
*
16592165 CTAACTCAATTCATACTT-CTTTT
1 CTAACTAAATTC--ACTTACTTTT
16592188 CTA
1 CTA
16592191 CTTAATTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
23 8 0.35
24 4 0.17
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.46
Consensus pattern (22 bp):
CTAACTAAATTCACTTACTTTT
Found at i:16609094 original size:29 final size:28
Alignment explanation
Indices: 16609009--16609114 Score: 108
Period size: 29 Copynumber: 3.7 Consensus size: 28
16608999 ACATACATGT
16609009 ATATGGCCCACTAGGCCCAA-TCTTATTC
1 ATATGGCCCACTAGGCCCAATTC-TATTC
* * *
16609037 AAATGGCCCATCT-TGCCCAGTTCATATTC
1 ATATGGCCCA-CTAGGCCCAATTC-TATTC
* *
16609066 TTATGGCCCACTAGGCCTAATTCTCATTC
1 ATATGGCCCACTAGGCCCAATTCT-ATTC
*
16609095 ATATGGCCCATTAGGCCCAA
1 ATATGGCCCACTAGGCCCAA
16609115 ATCATATTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
28 17 0.27
29 45 0.73
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (28 bp):
ATATGGCCCACTAGGCCCAATTCTATTC
Found at i:16609113 original size:58 final size:57
Alignment explanation
Indices: 16609010--16609122 Score: 147
Period size: 58 Copynumber: 2.0 Consensus size: 57
16609000 CATACATGTA
* * **
16609010 TATGGCCCACTAGGCCCAATCTTATTCAAATGGCCCATCTTGCCCAGTTCATATTCT
1 TATGGCCCACTAGGCCCAATCTCATTCAAATGGCCCATCTGGCCCAAATCATATTCT
* *
16609067 TATGGCCCACTAGGCCTAATTCTCATTCATATGGCCCAT-TAGGCCCAAATCATATT
1 TATGGCCCACTAGGCCCAA-TCTCATTCAAATGGCCCATCT-GGCCCAAATCATATT
16609123 ATATTCATGC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 19 0.40
58 29 0.60
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (57 bp):
TATGGCCCACTAGGCCCAATCTCATTCAAATGGCCCATCTGGCCCAAATCATATTCT
Found at i:16609371 original size:16 final size:16
Alignment explanation
Indices: 16609330--16609373 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
16609320 GTAGCCCAAG
*
16609330 TTTCGGCTTTTCAGCA
1 TTTCGGCTTTTTAGCA
* *
16609346 TTTTGACTTTTTAGCA
1 TTTCGGCTTTTTAGCA
16609362 TTTCGGCTTTTT
1 TTTCGGCTTTTT
16609374 CCGGTTCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (16 bp):
TTTCGGCTTTTTAGCA
Found at i:16613072 original size:65 final size:65
Alignment explanation
Indices: 16612968--16613097 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
16612958 CAAAAGTATG
* *
16612968 AAAATGATAGCTTGATAGTGTGATGAAGTCTCCGACTATCTCCGAATTCGAGCTAGCTTTGAAAT
1 AAAATGATAGCTTGATAGTGTGATGAAGTCTCCGACTATCTCCGAATCCAAGCTAGCTTTGAAAT
* *
16613033 AAAATGATAGCTTGATAGTGTGATGAAGTTTCTGACTATCTCCGAATCCAAGCTAGCTTTGAAAT
1 AAAATGATAGCTTGATAGTGTGATGAAGTCTCCGACTATCTCCGAATCCAAGCTAGCTTTGAAAT
16613098 CACTATAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (65 bp):
AAAATGATAGCTTGATAGTGTGATGAAGTCTCCGACTATCTCCGAATCCAAGCTAGCTTTGAAAT
Found at i:16613643 original size:14 final size:14
Alignment explanation
Indices: 16613624--16613655 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16613614 AGGTCATTTA
16613624 GCCCAACCAAACAG
1 GCCCAACCAAACAG
*
16613638 GCCCAACCAAACTG
1 GCCCAACCAAACAG
16613652 GCCC
1 GCCC
16613656 GGTGATTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.47, G:0.16, T:0.03
Consensus pattern (14 bp):
GCCCAACCAAACAG
Found at i:16617191 original size:42 final size:42
Alignment explanation
Indices: 16617132--16617211 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
16617122 AGGAAGTGCC
16617132 AACAATGTTGCTGATGCACTTAGTCGAAAGATGGAATTTGCA
1 AACAATGTTGCTGATGCACTTAGTCGAAAGATGGAATTTGCA
16617174 AACAATGTTGCTGATGCACTTAGTCGAAAGATGGAATT
1 AACAATGTTGCTGATGCACTTAGTCGAAAGATGGAATT
16617212 CGCAGCAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (42 bp):
AACAATGTTGCTGATGCACTTAGTCGAAAGATGGAATTTGCA
Found at i:16619459 original size:27 final size:27
Alignment explanation
Indices: 16619429--16619605 Score: 203
Period size: 27 Copynumber: 6.5 Consensus size: 27
16619419 TATTGAGTCT
* * * *
16619429 GCACACTCAGTGCTATATAATCAACTC
1 GCACACTTAGTGCTACATAGTCAAATC
* *
16619456 GCACACTTAGTGCTACGTAATCAAATC
1 GCACACTTAGTGCTACATAGTCAAATC
16619483 GCACACTTAGTGCTACATAGTCAAACTC
1 GCACACTTAGTGCTACATAGTCAAA-TC
** * *
16619511 GCACACTTAGTGCCGCATGGTCAATTC
1 GCACACTTAGTGCTACATAGTCAAATC
* **
16619538 GCACACTTAGTGC-ATCATATTCATTTC
1 GCACACTTAGTGCTA-CATAGTCAAATC
*
16619565 GCACACTTAGTGCAACATAGTCAAATC
1 GCACACTTAGTGCTACATAGTCAAATC
16619592 GCACACTTAGTGCT
1 GCACACTTAGTGCT
16619606 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
GCACACTTAGTGCTACATAGTCAAATC
Found at i:16619567 original size:82 final size:81
Alignment explanation
Indices: 16619449--16619604 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16619439 TGCTATATAA
* *
16619449 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16619514 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
16619531 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16619595 CACTTAGTGC
65 CACTTAGTGC
16619605 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:16627643 original size:27 final size:27
Alignment explanation
Indices: 16627613--16627791 Score: 207
Period size: 27 Copynumber: 6.6 Consensus size: 27
16627603 GCATATTGAG
* * * *
16627613 TCGCACACTCAGTGCTATATAATCAAC
1 TCGCACACTTAGTGCTACATAGTCAAA
* *
16627640 TCGCACACTTAGTGCTACGTAATCAAA
1 TCGCACACTTAGTGCTACATAGTCAAA
16627667 TCGCACACTTAGTGCTACATAGTCAAA
1 TCGCACACTTAGTGCTACATAGTCAAA
** * *
16627694 CTCGCACACTTAGTGCCGCATGGTCAAT
1 -TCGCACACTTAGTGCTACATAGTCAAA
* **
16627722 TCGCACACTTAGTGC-ATCATATTCATT
1 TCGCACACTTAGTGCTA-CATAGTCAAA
*
16627749 TCGCACACTTAGTGCAACATAGTCAAA
1 TCGCACACTTAGTGCTACATAGTCAAA
16627776 TCGCACACTTAGTGCT
1 TCGCACACTTAGTGCT
16627792 GTACAATTTA
Statistics
Matches: 131, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
27 107 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
TCGCACACTTAGTGCTACATAGTCAAA
Found at i:16627753 original size:82 final size:81
Alignment explanation
Indices: 16627635--16627790 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16627625 TGCTATATAA
* *
16627635 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16627700 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
16627717 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16627781 CACTTAGTGC
65 CACTTAGTGC
16627791 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:16630275 original size:14 final size:14
Alignment explanation
Indices: 16630256--16630287 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16630246 AGGTCATTTA
16630256 GCCCAACCAAACAG
1 GCCCAACCAAACAG
*
16630270 GCCCAACCAAACTG
1 GCCCAACCAAACAG
16630284 GCCC
1 GCCC
16630288 GGTGATTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.47, G:0.16, T:0.03
Consensus pattern (14 bp):
GCCCAACCAAACAG
Found at i:16632500 original size:48 final size:46
Alignment explanation
Indices: 16632280--16632591 Score: 228
Period size: 44 Copynumber: 6.7 Consensus size: 46
16632270 TTACCAATGC
* * *
16632280 CATGTCCCAGACATGGTCTTACACTGGCTCACATATATGCGTGCTGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCACATCTCT--GTGCCGATG
* * * *
16632329 CATGTCCCAGACATGTCTTACACTAG--CACAACTCT-TAACCAATG
1 CATGTCCCAGACATGTCTTACACTGGCTCACATCTCTGT-GCCGATG
** * * *
16632373 TGTGTCCAAGACACGTCTTACACTGGCT---ATCTCTGTTGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTGGCTCACATCTCTG-T---GCCGATG
* * *
16632420 CATGTCCCAGACATGTCTTACTCTGGCACTCATCTCTGTGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCACATCTCTGTGCCGATG
* * * *
16632466 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATTTATGTTTGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCACATCTCTG--TGCCGATG
* *
16632516 CATGTCCCAGACATGTCTTACACTAG--CACAACTCT-TAGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCACATCTCTGT-GCCGATG
* * *
16632560 CGTGTCCCAAACATGTCTTACACTGGCGCACA
1 CATGTCCCAGACATGTCTTACACTGGCTCACA
16632592 AATTACCCAA
Statistics
Matches: 210, Mismatches: 36, Indels: 37
0.74 0.13 0.13
Matches are distributed among these distances:
43 7 0.03
44 54 0.26
45 1 0.00
46 21 0.10
47 42 0.20
48 42 0.20
49 29 0.14
50 14 0.07
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTCACATCTCTGTGCCGATG
Found at i:16637349 original size:28 final size:28
Alignment explanation
Indices: 16637309--16637404 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 28
16637299 ATATTAAGTC
* *
16637309 CGCACACTCAGTGCTATGTAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
16637337 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
16637365 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
16637394 CGCACACTTAG
1 CGCACACTTAG
16637405 CGCCAATCTC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 45 0.74
29 16 0.26
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:16645335 original size:28 final size:28
Alignment explanation
Indices: 16645292--16645387 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 28
16645282 ATATTAAGTC
* * *
16645292 CGCACACTCAGTGCTATGTAATCAAACT
1 CGCACACTTAGGGCTATATAATCAAACT
16645320 CGCACACTTAGGGCTATATAATCAAACT
1 CGCACACTTAGGGCTATATAATCAAACT
* * * * *
16645348 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGGGCTATATAA-TCAAACT
16645377 CGCACACTTAG
1 CGCACACTTAG
16645388 CGCCAATCTC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 43 0.73
29 16 0.27
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGGGCTATATAATCAAACT
Found at i:16649579 original size:12 final size:12
Alignment explanation
Indices: 16649552--16649590 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
16649542 TAAAAGGGTA
16649552 TAAAATGTAAAG-
1 TAAAATGT-AAGC
*
16649564 TAAATTGTAAGC
1 TAAAATGTAAGC
16649576 TAAAATGTAAGC
1 TAAAATGTAAGC
16649588 TAA
1 TAA
16649591 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.28
Consensus pattern (12 bp):
TAAAATGTAAGC
Found at i:16654639 original size:22 final size:22
Alignment explanation
Indices: 16654622--16654719 Score: 135
Period size: 22 Copynumber: 4.4 Consensus size: 22
16654612 AGCTCATTGC
16654622 AGCTTATCGTTCAGCTCAATAG
1 AGCTTATCGTTCAGCTCAATAG
*
16654644 AGCTTATTGTTCAGCTCAATAG
1 AGCTTATCGTTCAGCTCAATAG
*
16654666 AGCTTACCGTTTCAGCTCAATAG
1 AGCTTATCG-TTCAGCTCAATAG
* *
16654689 AGTTTATTGTTCAGCTCAA-AGG
1 AGCTTATCGTTCAGCTCAATA-G
16654711 AGCTTATCG
1 AGCTTATCG
16654720 ACCATGACTC
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.02
22 46 0.70
23 19 0.29
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (22 bp):
AGCTTATCGTTCAGCTCAATAG
Found at i:16654680 original size:45 final size:44
Alignment explanation
Indices: 16654622--16654716 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 44
16654612 AGCTCATTGC
*
16654622 AGCTTATCGTTCAGCTCAATAGAGCTTATTGTTCAGCTCAATA-G
1 AGCTTACCGTTCAGCTCAATAGAGCTTATTGTTCAGCTCAA-AGG
*
16654666 AGCTTACCGTTTCAGCTCAATAGAGTTTATTGTTCAGCTCAAAGG
1 AGCTTACCG-TTCAGCTCAATAGAGCTTATTGTTCAGCTCAAAGG
16654711 AGCTTA
1 AGCTTA
16654717 TCGACCATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
44 9 0.19
45 38 0.81
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (44 bp):
AGCTTACCGTTCAGCTCAATAGAGCTTATTGTTCAGCTCAAAGG
Found at i:16659929 original size:26 final size:26
Alignment explanation
Indices: 16659900--16659960 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
16659890 ATAAGAGCCA
* * *
16659900 TAATCAGGAAGTTCACAAAGAACTTT
1 TAATCAAGAAGCTCACAAAGAACCTT
* *
16659926 TAATCAAGAAGCTCACGAAGAGCCTT
1 TAATCAAGAAGCTCACAAAGAACCTT
16659952 TAATCAAGA
1 TAATCAAGA
16659961 GTGTAACATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (26 bp):
TAATCAAGAAGCTCACAAAGAACCTT
Found at i:16660217 original size:13 final size:13
Alignment explanation
Indices: 16660199--16660223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16660189 GGTTTGTTTA
16660199 TTAAACTAATTAT
1 TTAAACTAATTAT
16660212 TTAAACTAATTA
1 TTAAACTAATTA
16660224 ACTGGTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:16663164 original size:6 final size:6
Alignment explanation
Indices: 16663132--16663223 Score: 107
Period size: 6 Copynumber: 15.5 Consensus size: 6
16663122 TATGTCTTTC
* * * * *
16663132 AAAAT- AAAATA ATAAT- AAAATT GAAATA AAAATA AAAATT AAAAGA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
16663178 AAAATA AAAATA AAAATA AAAATA AGAATA AATAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA-AATA AAAATA AAA
16663224 GGAATCAATG
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
5 9 0.12
6 58 0.79
7 6 0.08
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:16673655 original size:21 final size:20
Alignment explanation
Indices: 16673617--16673656 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16673607 CCCTTAAAAC
*
16673617 AGGGCACACGCCCGTGTGGA
1 AGGGCACACGCCCATGTGGA
*
16673637 AGGGCAACACGCCTATGTGG
1 AGGGC-ACACGCCCATGTGG
16673657 TCATTTTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.12
Consensus pattern (20 bp):
AGGGCACACGCCCATGTGGA
Found at i:16676811 original size:8 final size:8
Alignment explanation
Indices: 16676794--16676838 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
16676784 ATTATATACT
*
16676794 TTATTTTA
1 TTATTATA
16676802 TTATTATA
1 TTATTATA
16676810 TTATATTATA
1 -T-TATTATA
*
16676820 TTAATATA
1 TTATTATA
16676828 TTATTATA
1 TTATTATA
16676836 TTA
1 TTA
16676839 ATTTCTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 23 0.72
9 2 0.06
10 7 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATTATA
Found at i:16676816 original size:18 final size:17
Alignment explanation
Indices: 16676775--16676831 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 17
16676765 TTTGTTTCTT
16676775 TTATATTTTATTATATA
1 TTATATTTTATTATATA
16676792 CTT-TATTTTATTATTATA
1 -TTATATTTTATTA-TATA
*
16676810 TTATATTATATTAATATA
1 TTATATTTTATT-ATATA
16676828 TTAT
1 TTAT
16676832 TATATTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
17 12 0.34
18 22 0.63
19 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATATTTTATTATATA
Found at i:16676819 original size:5 final size:5
Alignment explanation
Indices: 16676775--16676838 Score: 53
Period size: 5 Copynumber: 12.6 Consensus size: 5
16676765 TTTGTTTCTT
* *
16676775 TTATA TTTTA TTATA -TACT- TTATT TTATTA TTATA TTATA TTATA TTA-A
1 TTATA TTATA TTATA TTA-TA TTATA TTA-TA TTATA TTATA TTATA TTATA
16676824 TATATTA TTATA TTA
1 T-TA-TA TTATA TTA
16676839 ATTTCTTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
4 5 0.10
5 36 0.73
6 6 0.12
7 2 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:16676839 original size:16 final size:17
Alignment explanation
Indices: 16676778--16676840 Score: 67
Period size: 18 Copynumber: 3.7 Consensus size: 17
16676768 GTTTCTTTTA
*
16676778 TATTTTATT-ATATACTT
1 TATTATATTAATATA-TT
* *
16676795 TATTTTATTATTATATT
1 TATTATATTAATATATT
16676812 ATATTATATTAATATA-T
1 -TATTATATTAATATATT
16676829 TATTATATTAAT
1 TATTATATTAAT
16676841 TTCTTAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
16 12 0.29
17 12 0.29
18 17 0.41
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATATTAATATATT
Found at i:16684128 original size:47 final size:49
Alignment explanation
Indices: 16684055--16684281 Score: 172
Period size: 47 Copynumber: 4.8 Consensus size: 49
16684045 GGTAAGGTGC
* * *
16684055 TGATGCCATGTCCTAGACACGATCTTACACTGGCTCAT-ATCTC-AAGT
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGT
* * * *
16684102 TGATGCCATGTCCCAAACATGGTCTTACATTGACT-ATCATCTCGTA-T
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGT
* * * * * * *
16684149 CTGATG-CATGTCCCAGACAT-ATTTTGCACTCGCTTAT-GTCTCGAGGT
1 -TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGT
* * * * *
16684196 TGATG-CATGTCCCAAACAT-GTCTTACACTAGC-CCTCGTCTC-AATGC
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAA-GT
*
16684242 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCAT
1 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAT
16684282 AATGTGACTG
Statistics
Matches: 140, Mismatches: 30, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
45 2 0.01
46 52 0.37
47 64 0.46
48 21 0.15
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.31
Consensus pattern (49 bp):
TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAAGT
Found at i:16684236 original size:46 final size:46
Alignment explanation
Indices: 16684186--16684319 Score: 126
Period size: 47 Copynumber: 2.9 Consensus size: 46
16684176 ACTCGCTTAT
*
16684186 GTCTCGAGGTTGATGCATGTCCCAAACATGTCTTACACTAGCCCTC
1 GTCTCGAGGCTGATGCATGTCCCAAACATGTCTTACACTAGCCCTC
* * * * * *
16684232 GTCTCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC
1 GTCTCGAGGCTGATG-CATGTCCCAAACAT-GTCTTACACTAGCCCTC
* * * * *
16684280 ATAAT-GTGACTGATGCATGTCCCATACATGTCTTACACTA
1 GT-CTCGAGGCTGATGCATGTCCCAAACATGTCTTACACTA
16684320 TCTCACACAC
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
46 21 0.30
47 26 0.38
48 21 0.30
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
GTCTCGAGGCTGATGCATGTCCCAAACATGTCTTACACTAGCCCTC
Found at i:16698701 original size:34 final size:33
Alignment explanation
Indices: 16698638--16698703 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
16698628 GTATTCATTT
* *
16698638 TTGATACTGTACTGAATTGGTCTATGGCCCATA
1 TTGATACTGTACTGAATTGGGCTAAGGCCCATA
16698671 TTGATACTGCTACTGTAA-TGGGCTAAGGCCCAT
1 TTGATACTG-TACTG-AATTGGGCTAAGGCCCAT
16698704 GCTAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 9 0.31
34 18 0.62
35 2 0.07
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (33 bp):
TTGATACTGTACTGAATTGGGCTAAGGCCCATA
Found at i:16705278 original size:25 final size:25
Alignment explanation
Indices: 16705244--16705292 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
16705234 CATGGTACTT
16705244 AACTTACCATTCATTCTATTTTGAA
1 AACTTACCATTCATTCTATTTTGAA
16705269 AACTTACCATTCATTCTATTTTGA
1 AACTTACCATTCATTCTATTTTGA
16705293 GGTAACTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (25 bp):
AACTTACCATTCATTCTATTTTGAA
Found at i:16707332 original size:5 final size:5
Alignment explanation
Indices: 16707322--16707348 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
16707312 TGGACCATAT
16707322 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
16707349 ATTTTCAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:16712238 original size:26 final size:26
Alignment explanation
Indices: 16712209--16712357 Score: 107
Period size: 26 Copynumber: 6.0 Consensus size: 26
16712199 TATATAATAA
16712209 GAAGCTCACAAAGAGCCATTAATCAG
1 GAAGCTCACAAAGAGCCATTAATCAG
*
16712235 GAAGCTCACAAAAAGCC--T-ATCAG
1 GAAGCTCACAAAGAGCCATTAATCAG
* * **
16712258 GAAGCTTATC-CAG-GTTATATAA-CAG
1 GAAGCTCA-CAAAGAGCCAT-TAATCAG
*
16712283 GAAGCTCA-TAAGAGCCA-TAATCAG
1 GAAGCTCACAAAGAGCCATTAATCAG
* * **
16712307 GAAGTTCACAAAGAACTTTTAATCAG
1 GAAGCTCACAAAGAGCCATTAATCAG
* * *
16712333 GATGCTCACAAAGGGCCTTTAATCA
1 GAAGCTCACAAAGAGCCATTAATCA
16712358 AGAGCTCCGG
Statistics
Matches: 93, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
22 1 0.01
23 16 0.17
24 14 0.15
25 18 0.19
26 44 0.47
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (26 bp):
GAAGCTCACAAAGAGCCATTAATCAG
Found at i:16712491 original size:65 final size:65
Alignment explanation
Indices: 16712410--16712550 Score: 192
Period size: 65 Copynumber: 2.2 Consensus size: 65
16712400 TATCAAGACG
* * * * *
16712410 CTCACAAAGAGTTGCGTTTGTGTCTGCAACATATGCAGGATCACAACCAATCATAAAACAGGACA
1 CTCACAAAGAGCTGCGTTTATGTCCGCAACATATACAAGATCACAACCAATCATAAAACAGGACA
* * * * *
16712475 CTCACAAAGAGCTGCGTTTATGTCCGTAATATATATAAGATCACAACCGATCATATAACAGGACA
1 CTCACAAAGAGCTGCGTTTATGTCCGCAACATATACAAGATCACAACCAATCATAAAACAGGACA
16712540 CTCACAAAGAG
1 CTCACAAAGAG
16712551 ATGCAGTAGT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (65 bp):
CTCACAAAGAGCTGCGTTTATGTCCGCAACATATACAAGATCACAACCAATCATAAAACAGGACA
Done.