Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold423
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: 617052
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 4 of 6
Found at i:388572 original size:18 final size:18
Alignment explanation
Indices: 388549--388584 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
388539 TTGAAGCGAG
388549 GGGTCCAATGCCACCTAT
1 GGGTCCAATGCCACCTAT
388567 GGGTCCAATGCCACCTAT
1 GGGTCCAATGCCACCTAT
388585 AGGCCTTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (18 bp):
GGGTCCAATGCCACCTAT
Found at i:389175 original size:21 final size:21
Alignment explanation
Indices: 389149--389189 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
389139 TCAAGAGCAT
* *
389149 GAATCATAAACAGATAAACAC
1 GAATCACAAACAAATAAACAC
389170 GAATCACAAACAAATAAACA
1 GAATCACAAACAAATAAACA
389190 AATATAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.20, G:0.07, T:0.12
Consensus pattern (21 bp):
GAATCACAAACAAATAAACAC
Found at i:389478 original size:21 final size:21
Alignment explanation
Indices: 389449--389501 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
389439 ATAATAGTGA
* * * *
389449 TAATGAAATTAATTATTATAG
1 TAATAAAATTAAGTATAAGAG
389470 TAATAAAATTAAGTATAAGAG
1 TAATAAAATTAAGTATAAGAG
*
389491 TAATAAGATTA
1 TAATAAAATTA
389502 GAGCTTACGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (21 bp):
TAATAAAATTAAGTATAAGAG
Found at i:390671 original size:15 final size:16
Alignment explanation
Indices: 390634--390673 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
390624 TACCTCGTAA
390634 AATTTTTTTTTTCTTT
1 AATTTTTTTTTTCTTT
390650 AATTTTTTTTTAT-TTT
1 AATTTTTTTTT-TCTTT
*
390666 TATTTTTT
1 AATTTTTT
390674 AAAAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (16 bp):
AATTTTTTTTTTCTTT
Found at i:391838 original size:2 final size:2
Alignment explanation
Indices: 391831--391859 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
391821 TATGACATTA
391831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
391860 AGAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:396874 original size:11 final size:11
Alignment explanation
Indices: 396858--396895 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
396848 AGATATAATT
396858 ATATAAATATA
1 ATATAAATATA
396869 ATATAAATA-A
1 ATATAAATATA
396879 A-ATAAGATATA
1 ATATAA-ATATA
396890 ATATAA
1 ATATAA
396896 TATGATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.17
10 5 0.21
11 11 0.46
12 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
ATATAAATATA
Found at i:396922 original size:18 final size:18
Alignment explanation
Indices: 396901--396955 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 18
396891 TATAATATGA
396901 TTATATATATATTAAATT
1 TTATATATATATTAAATT
*
396919 TTATATA-ATA-AAAATT
1 TTATATATATATTAAATT
* *
396935 AT-TA-ATATATTAAAAT
1 TTATATATATATTAAATT
396951 TTATA
1 TTATA
396956 AAAAATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
14 1 0.03
15 5 0.17
16 11 0.38
17 5 0.17
18 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATATATATATTAAATT
Found at i:396951 original size:17 final size:15
Alignment explanation
Indices: 396906--396952 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
396896 TATGATTATA
396906 TATATATT-AAATTT
1 TATATATTAAAATTT
*
396920 TATATAATAAAAATTAT
1 TATAT-ATTAAAATT-T
396937 TAATATATTAAAATTT
1 T-ATATATTAAAATTT
396953 ATAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 5 0.19
15 2 0.07
16 6 0.22
17 10 0.37
18 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATTAAAATTT
Found at i:397334 original size:19 final size:20
Alignment explanation
Indices: 397310--397350 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
397300 TATATTTTTC
397310 AATTAAATATT-AAAATATA
1 AATTAAATATTCAAAATATA
* *
397329 AATTAAATTTTCACAATATA
1 AATTAAATATTCAAAATATA
397349 AA
1 AA
397351 AATTTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTAAATATTCAAAATATA
Found at i:398907 original size:29 final size:28
Alignment explanation
Indices: 398868--398923 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
398858 TATTATATTT
*
398868 TAATTATTTTATTAATATCATATTTATA
1 TAATTATTTTAATAATATCATATTTATA
*
398896 TAATTATGTTTAATATTATCATATTTAT
1 TAATTAT-TTTAATAATATCATATTTAT
398924 CTACACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (28 bp):
TAATTATTTTAATAATATCATATTTATA
Found at i:399441 original size:44 final size:44
Alignment explanation
Indices: 399345--399443 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
399335 TCAACTCATG
*
399345 AACAAATTTATTTTATATTACATGAAATCAAGAATAATGTCAAA
1 AACAAATATATTTTATATTACATGAAATCAAGAATAATGTCAAA
* * * *
399389 TATAAATATATTTTATATTAC-TTAGAATCAAGGATAATGTCAAA
1 AACAAATATATTTTATATTACATGA-AATCAAGAATAATGTCAAA
*
399433 AACGAATATAT
1 AACAAATATAT
399444 ATCCGAGATA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 2 0.04
44 44 0.96
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (44 bp):
AACAAATATATTTTATATTACATGAAATCAAGAATAATGTCAAA
Found at i:401368 original size:17 final size:17
Alignment explanation
Indices: 401325--401359 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
401315 TAAAAAAATT
*
401325 AAATATATTTATATTTA
1 AAATATATTTATATTCA
401342 AAATATATTTATATTCA
1 AAATATATTTATATTCA
401359 A
1 A
401360 TATTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATATATTTATATTCA
Found at i:401783 original size:21 final size:21
Alignment explanation
Indices: 401757--401797 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
401747 TTTATGTTTG
*
401757 AATATATATATCAAACATATA
1 AATATATATATCAAAAATATA
*
401778 AATATATATATTAAAAATAT
1 AATATATATATCAAAAATAT
401798 TTATGAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
AATATATATATCAAAAATATA
Found at i:401899 original size:2 final size:2
Alignment explanation
Indices: 401892--401924 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
401882 CATTATGCCC
401892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
401925 AAAGCAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:401997 original size:14 final size:15
Alignment explanation
Indices: 401974--402028 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 15
401964 ATGTAATTAT
401974 ATAAATATAATAAAA
1 ATAAATATAATAAAA
*
401989 ATAAA-ATAATTAAA
1 ATAAATATAATAAAA
* *
402003 ATACGATATAATATAAT
1 ATA-AATATAATA-AAA
402020 ATAAATATA
1 ATAAATATA
402029 TTTAAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 11 0.34
15 6 0.19
16 10 0.31
17 5 0.16
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAATATAATAAAA
Found at i:402069 original size:17 final size:16
Alignment explanation
Indices: 402023--402070 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
402013 ATATAATATA
*
402023 AATATATTTAAATTTT
1 AATATATTAAAATTTT
*
402039 -ATATCATAAAAATTATT
1 AATAT-ATTAAAATT-TT
402056 AATATATTAAAATTT
1 AATATATTAAAATTT
402071 ATAAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
15 4 0.15
16 8 0.31
17 10 0.38
18 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATATTAAAATTTT
Found at i:402459 original size:19 final size:20
Alignment explanation
Indices: 402435--402475 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
402425 TATATTTTTC
402435 AATTAAATATT-AAAATATA
1 AATTAAATATTCAAAATATA
* *
402454 AATTAAATTTTCATAATATA
1 AATTAAATATTCAAAATATA
402474 AA
1 AA
402476 ATTTTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTAAATATTCAAAATATA
Found at i:402543 original size:27 final size:27
Alignment explanation
Indices: 402513--402585 Score: 67
Period size: 27 Copynumber: 2.6 Consensus size: 27
402503 ATTATTTTAA
*
402513 AAATAAAAAATCATTTTTAAAAATT-TT
1 AAATAAAAAATCA-TATTAAAAATTATT
* *
402540 AAATATTAAAAATTATATTAAATATTATT
1 AAATA--AAAAATCATATTAAAAATTATT
* *
402569 AAATTAAAAATAATATT
1 AAATAAAAAATCATATT
402586 TATTTTCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 16 0.42
28 9 0.24
29 13 0.34
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
AAATAAAAAATCATATTAAAAATTATT
Found at i:402696 original size:14 final size:15
Alignment explanation
Indices: 402679--402707 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
402669 GTATTAATTT
402679 TTAAAT-TTAAAAAA
1 TTAAATCTTAAAAAA
402693 TTAAATCTTAAAAAA
1 TTAAATCTTAAAAAA
402708 AATTTATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAATCTTAAAAAA
Found at i:404039 original size:29 final size:28
Alignment explanation
Indices: 404000--404055 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
403990 TATTATATTT
*
404000 TAATTATTTTATTAATATCATATTTATA
1 TAATTATTTTAATAATATCATATTTATA
*
404028 TAATTATGTTTAATATTATCATATTTAT
1 TAATTAT-TTTAATAATATCATATTTAT
404056 CTACACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (28 bp):
TAATTATTTTAATAATATCATATTTATA
Found at i:404573 original size:44 final size:44
Alignment explanation
Indices: 404477--404575 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
404467 TCAACTCATG
* *
404477 AACAAATTTATTTTATATTACATGGAAACAAGAATAATGTCAAA
1 AACAAATATATTTTATATTACATAGAAACAAGAATAATGTCAAA
* * * * *
404521 TATAAATATATTTTATATTACTTAGAATCAAGGATAATGTCAAA
1 AACAAATATATTTTATATTACATAGAAACAAGAATAATGTCAAA
*
404565 AACGAATATAT
1 AACAAATATAT
404576 ATCCGAGATA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.34
Consensus pattern (44 bp):
AACAAATATATTTTATATTACATAGAAACAAGAATAATGTCAAA
Found at i:406766 original size:57 final size:57
Alignment explanation
Indices: 406678--406788 Score: 195
Period size: 57 Copynumber: 1.9 Consensus size: 57
406668 TGCCGTGCAT
* *
406678 TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATCGAAAATGGATTTGATCAC
1 TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGATCAC
*
406735 TAGCTCCTTCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGAT
1 TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGAT
406789 TATGATATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (57 bp):
TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGATCAC
Found at i:407070 original size:2 final size:2
Alignment explanation
Indices: 407063--407107 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
407053 CATTATGCCC
407063 AT AT AT 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 AT AT AT
407105 AT A
1 AT A
407108 AAAGTAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:407176 original size:31 final size:31
Alignment explanation
Indices: 407140--407236 Score: 101
Period size: 31 Copynumber: 3.1 Consensus size: 31
407130 GAACTTAATT
407140 ATATGAATATAATAAAAATAAA-ATAATTAAA
1 ATATG-ATATAATAAAAATAAATATAATTAAA
* *
407171 ATATGATATAATATAATATAAATATATTTAAA
1 ATATGATATAATA-AAAATAAATATAATTAAA
*
407203 AT-TTATATAATAAAAATTATTAATAT-ATTAAA
1 ATATGATATAATAAAAA-TA--AATATAATTAAA
407235 AT
1 AT
407237 TTATAAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
30 11 0.20
31 23 0.41
32 17 0.30
33 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
ATATGATATAATAAAAATAAATATAATTAAA
Found at i:407181 original size:21 final size:20
Alignment explanation
Indices: 407157--407301 Score: 56
Period size: 20 Copynumber: 7.2 Consensus size: 20
407147 TATAATAAAA
407157 ATAAAATAAT-TAAAATATGAT
1 ATAAAATAATAT-AAATAT-AT
*
407178 ATAATATAATATAAATATAT
1 ATAAAATAATATAAATATAT
* *
407198 TTAAAATTTATATAATAAAAAT-T
1 ATAAAA--TA-AT-ATAAATATAT
* *
407221 AT-TAAT-ATATTAAA-ATTT
1 ATAAAATAATA-TAAATATAT
*
407239 ATAAAA-AATTTAAAATATAT
1 ATAAAATAATAT-AAATATAT
* * *
407259 TTAATATAAT-TATAATA-AA
1 ATAAAATAATATA-AATATAT
407278 ATAAAAT-ATATAAATATGAT
1 ATAAAATAATATAAATAT-AT
407298 ATAA
1 ATAA
407302 TTATATAGAG
Statistics
Matches: 93, Mismatches: 15, Indels: 33
0.66 0.11 0.23
Matches are distributed among these distances:
17 3 0.03
18 16 0.17
19 16 0.17
20 24 0.26
21 18 0.19
22 5 0.05
23 4 0.04
24 7 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (20 bp):
ATAAAATAATATAAATATAT
Found at i:407211 original size:61 final size:61
Alignment explanation
Indices: 407145--407302 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
407135 TAATTATATG
*
407145 AATATAATAAAAATAAAATAATTAAAATATGATATAATATAATAT-AAATATATTTAAAATT
1 AATATAATAAAAATAAAATAATTAAAATATGATATAATAAAATATAAAATATATTTAAAA-T
* * * *
407206 TATATAATAAAAATTATTAATATATTAAAAT-T--TATAA-AAAATTTAAAATATATTTAATAT
1 AATATAATAAAAA-TA-AAATA-ATTAAAATATGATATAATAAAATATAAAATATATTTAAAAT
407266 AATTATAAT-AAAATAAAAT-A-TATAAATATGATATAAT
1 AA-TATAATAAAAATAAAATAATTA-AAATATGATATAAT
407303 TATATAGAGA
Statistics
Matches: 80, Mismatches: 7, Indels: 21
0.74 0.06 0.19
Matches are distributed among these distances:
55 2 0.03
56 5 0.06
57 1 0.01
58 3 0.04
59 7 0.09
60 11 0.14
61 36 0.45
62 2 0.03
63 5 0.06
64 8 0.10
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (61 bp):
AATATAATAAAAATAAAATAATTAAAATATGATATAATAAAATATAAAATATATTTAAAAT
Found at i:407234 original size:18 final size:18
Alignment explanation
Indices: 407191--407240 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
407181 ATATAATATA
*
407191 AATATATTTAAAA-T-TT
1 AATATATTAAAAATTATT
*
407207 -ATATAATAAAAATTATT
1 AATATATTAAAAATTATT
*
407224 AATATATTAAAATTTAT
1 AATATATTAAAAATTAT
407241 AAAAAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 10 0.37
16 1 0.04
17 2 0.07
18 14 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATATTAAAAATTATT
Found at i:407234 original size:32 final size:31
Alignment explanation
Indices: 407146--407241 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 31
407136 AATTATATGA
*
407146 ATATAATAAAAATA-AAATA-ATTAAAATATG
1 ATATAATAAAAATATAAATATATTAAAAT-TT
*
407176 ATATAAT-ATAATATAAATATATTTAAAATTT
1 ATATAATAAAAATATAAATATA-TTAAAATTT
*
407207 ATATAATAAAAATTATTAATATATTAAAATTT
1 ATATAATAAAAA-TATAAATATATTAAAATTT
407239 ATA
1 ATA
407242 AAAAATTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
29 5 0.09
30 12 0.21
31 9 0.16
32 22 0.39
33 9 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
ATATAATAAAAATATAAATATATTAAAATTT
Found at i:407742 original size:29 final size:26
Alignment explanation
Indices: 407685--407756 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 26
407675 TTGTTTTTAA
* *
407685 AAATTAAAAATTATCTTTAAAAATTTT
1 AAATTAAAAATTAT-ATCAAAAATTTT
*
407712 AACCATTAAAAATTATATCAAATATTATT
1 AA--ATTAAAAATTATATCAAAAATT-TT
*
407741 AAATTAAAAATAATAT
1 AAATTAAAAATTATAT
407757 TTATTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
27 15 0.39
28 7 0.18
29 16 0.42
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (26 bp):
AAATTAAAAATTATATCAAAAATTTT
Found at i:407863 original size:32 final size:31
Alignment explanation
Indices: 407789--407864 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
407779 CAAAATAGAG
* *
407789 TAAATTTTTTTATCATTTTATTATTTTATTTT
1 TAAATTTATTT-TCATTTTATAATTTTATTTT
**
407821 TAAAAATATTTT-ATTTTATAATTTTAATTTTT
1 TAAATTTATTTTCATTTTATAATTTT-A-TTTT
407853 TAAATTTATTTT
1 TAAATTTATTTT
407865 TGAATTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 12 0.33
31 2 0.06
32 22 0.61
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (31 bp):
TAAATTTATTTTCATTTTATAATTTTATTTT
Found at i:409205 original size:29 final size:28
Alignment explanation
Indices: 409166--409221 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
409156 TATTATATTT
*
409166 TAATTATTTTATTAATATCATATTTATA
1 TAATTATTTTAATAATATCATATTTATA
*
409194 TAATTATGTTTAATATTATCATATTTAT
1 TAATTAT-TTTAATAATATCATATTTAT
409222 CTACACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (28 bp):
TAATTATTTTAATAATATCATATTTATA
Found at i:409739 original size:44 final size:44
Alignment explanation
Indices: 409643--409741 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
409633 TCAACTCATG
* *
409643 AACAAATTTATTTTATATTACATGGAAGCAAGAATAATGTCAAA
1 AACAAATATATTTTATATTACATAGAAGCAAGAATAATGTCAAA
* * * * *
409687 TATAAATATATTTTATATTACTTAGAATCAAGGATAATGTCAAA
1 AACAAATATATTTTATATTACATAGAAGCAAGAATAATGTCAAA
*
409731 AACGAATATAT
1 AACAAATATAT
409742 ATCCGAGATA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.34
Consensus pattern (44 bp):
AACAAATATATTTTATATTACATAGAAGCAAGAATAATGTCAAA
Found at i:411928 original size:57 final size:57
Alignment explanation
Indices: 411840--411950 Score: 195
Period size: 57 Copynumber: 1.9 Consensus size: 57
411830 TGCCGTGCAT
* *
411840 TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATCGAAAATGGATTTGATCAC
1 TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGATCAC
*
411897 TAGCTCCTTCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGAT
1 TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGAT
411951 TATGATATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (57 bp):
TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGATCAC
Found at i:412231 original size:2 final size:2
Alignment explanation
Indices: 412224--412248 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
412214 CATTATGCCC
412224 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
412249 AAAGTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:412317 original size:31 final size:31
Alignment explanation
Indices: 412281--412377 Score: 101
Period size: 31 Copynumber: 3.1 Consensus size: 31
412271 GAACTTAATT
412281 ATATGAATATAATAAAAATAAA-ATAATTAAA
1 ATATG-ATATAATAAAAATAAATATAATTAAA
* *
412312 ATATGATATAATATAATATAAATATATTTAAA
1 ATATGATATAATA-AAAATAAATATAATTAAA
*
412344 AT-TTATATAATAAAAATTATTAATAT-ATTAAA
1 ATATGATATAATAAAAA-TA--AATATAATTAAA
412376 AT
1 AT
412378 TTATAAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
30 11 0.20
31 23 0.41
32 17 0.30
33 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
ATATGATATAATAAAAATAAATATAATTAAA
Found at i:412322 original size:21 final size:20
Alignment explanation
Indices: 412298--412442 Score: 56
Period size: 20 Copynumber: 7.2 Consensus size: 20
412288 TATAATAAAA
412298 ATAAAATAAT-TAAAATATGAT
1 ATAAAATAATAT-AAATAT-AT
*
412319 ATAATATAATATAAATATAT
1 ATAAAATAATATAAATATAT
* *
412339 TTAAAATTTATATAATAAAAAT-T
1 ATAAAA--TA-AT-ATAAATATAT
* *
412362 AT-TAAT-ATATTAAA-ATTT
1 ATAAAATAATA-TAAATATAT
*
412380 ATAAAA-AATTTAAAATATAT
1 ATAAAATAATAT-AAATATAT
* * *
412400 TTAATATAAT-TATAATA-AA
1 ATAAAATAATATA-AATATAT
412419 ATAAAAT-ATATAAATATGAT
1 ATAAAATAATATAAATAT-AT
412439 ATAA
1 ATAA
412443 TTATATAGAG
Statistics
Matches: 93, Mismatches: 15, Indels: 33
0.66 0.11 0.23
Matches are distributed among these distances:
17 3 0.03
18 16 0.17
19 16 0.17
20 24 0.26
21 18 0.19
22 5 0.05
23 4 0.04
24 7 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (20 bp):
ATAAAATAATATAAATATAT
Found at i:412360 original size:61 final size:61
Alignment explanation
Indices: 412286--412443 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
412276 TAATTATATG
*
412286 AATATAATAAAAATAAAATAATTAAAATATGATATAATATAATAT-AAATATATTTAAAATT
1 AATATAATAAAAATAAAATAATTAAAATATGATATAATAAAATATAAAATATATTTAAAA-T
* * * *
412347 TATATAATAAAAATTATTAATATATTAAAAT-T--TATAA-AAAATTTAAAATATATTTAATAT
1 AATATAATAAAAA-TA-AAATA-ATTAAAATATGATATAATAAAATATAAAATATATTTAAAAT
412407 AATTATAAT-AAAATAAAAT-A-TATAAATATGATATAAT
1 AA-TATAATAAAAATAAAATAATTA-AAATATGATATAAT
412444 TATATAGAGA
Statistics
Matches: 80, Mismatches: 7, Indels: 21
0.74 0.06 0.19
Matches are distributed among these distances:
55 2 0.03
56 5 0.06
57 1 0.01
58 3 0.04
59 7 0.09
60 11 0.14
61 36 0.45
62 2 0.03
63 5 0.06
64 8 0.10
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (61 bp):
AATATAATAAAAATAAAATAATTAAAATATGATATAATAAAATATAAAATATATTTAAAAT
Found at i:412375 original size:18 final size:18
Alignment explanation
Indices: 412332--412381 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
412322 ATATAATATA
*
412332 AATATATTTAAAA-T-TT
1 AATATATTAAAAATTATT
*
412348 -ATATAATAAAAATTATT
1 AATATATTAAAAATTATT
*
412365 AATATATTAAAATTTAT
1 AATATATTAAAAATTAT
412382 AAAAAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 10 0.37
16 1 0.04
17 2 0.07
18 14 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATATTAAAAATTATT
Found at i:412375 original size:32 final size:31
Alignment explanation
Indices: 412287--412382 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 31
412277 AATTATATGA
*
412287 ATATAATAAAAATA-AAATA-ATTAAAATATG
1 ATATAATAAAAATATAAATATATTAAAAT-TT
*
412317 ATATAAT-ATAATATAAATATATTTAAAATTT
1 ATATAATAAAAATATAAATATA-TTAAAATTT
*
412348 ATATAATAAAAATTATTAATATATTAAAATTT
1 ATATAATAAAAA-TATAAATATATTAAAATTT
412380 ATA
1 ATA
412383 AAAAATTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
29 5 0.09
30 12 0.21
31 9 0.16
32 22 0.39
33 9 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
ATATAATAAAAATATAAATATATTAAAATTT
Found at i:412883 original size:29 final size:26
Alignment explanation
Indices: 412826--412897 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 26
412816 TTGTTTTTAA
* *
412826 AAATTAAAAATTATCTTTAAAAATTTT
1 AAATTAAAAATTAT-ATCAAAAATTTT
*
412853 AACCATTAAAAATTATATCAAATATTATT
1 AA--ATTAAAAATTATATCAAAAATT-TT
*
412882 AAATTAAAAATAATAT
1 AAATTAAAAATTATAT
412898 TTATTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
27 15 0.39
28 7 0.18
29 16 0.42
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (26 bp):
AAATTAAAAATTATATCAAAAATTTT
Found at i:413004 original size:32 final size:31
Alignment explanation
Indices: 412930--413005 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
412920 CAAAATAGAG
* *
412930 TAAATTTTTTTATCATTTTATTATTTTATTTT
1 TAAATTTATTT-TCATTTTATAATTTTATTTT
**
412962 TAAAAATATTTT-ATTTTATAATTTTAATTTTT
1 TAAATTTATTTTCATTTTATAATTTT-A-TTTT
412994 TAAATTTATTTT
1 TAAATTTATTTT
413006 TGAATTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 12 0.33
31 2 0.06
32 22 0.61
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (31 bp):
TAAATTTATTTTCATTTTATAATTTTATTTT
Found at i:414346 original size:29 final size:28
Alignment explanation
Indices: 414307--414362 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
414297 TATTATATTT
*
414307 TAATTATTTTATTAATATCATATTTATA
1 TAATTATTTTAATAATATCATATTTATA
*
414335 TAATTATGTTTAATATTATCATATTTAT
1 TAATTAT-TTTAATAATATCATATTTAT
414363 CTACACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (28 bp):
TAATTATTTTAATAATATCATATTTATA
Found at i:414880 original size:44 final size:44
Alignment explanation
Indices: 414784--414882 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
414774 TCAACTCATG
* *
414784 AACAAATTTATTTTATATTACATGGAAGCAAGAATAATGTCAAA
1 AACAAATATATTTTATATTACATAGAAGCAAGAATAATGTCAAA
* * * * *
414828 TATAAATATATTTTATATTACTTAGAATCAAGGATAATGTCAAA
1 AACAAATATATTTTATATTACATAGAAGCAAGAATAATGTCAAA
*
414872 AACGAATATAT
1 AACAAATATAT
414883 ATCCGAGATA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.34
Consensus pattern (44 bp):
AACAAATATATTTTATATTACATAGAAGCAAGAATAATGTCAAA
Found at i:417069 original size:57 final size:57
Alignment explanation
Indices: 416981--417091 Score: 195
Period size: 57 Copynumber: 1.9 Consensus size: 57
416971 TGCCGTGCAT
* *
416981 TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATCGAAAATGGATTTGATCAC
1 TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGATCAC
*
417038 TAGCTCCTTCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGAT
1 TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGAT
417092 TATGATATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (57 bp):
TAGCTCCATCTAAGTTCAAAGTCAATTTTCAATTAAATAGAAAATAGATTTGATCAC
Found at i:417373 original size:2 final size:2
Alignment explanation
Indices: 417366--417390 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
417356 CATTATGCCC
417366 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
417391 AAAGTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:417459 original size:31 final size:31
Alignment explanation
Indices: 417423--417519 Score: 101
Period size: 31 Copynumber: 3.1 Consensus size: 31
417413 GAACTTAATT
417423 ATATGAATATAATAAAAATAAA-ATAATTAAA
1 ATATG-ATATAATAAAAATAAATATAATTAAA
* *
417454 ATATGATATAATATAATATAAATATATTTAAA
1 ATATGATATAATA-AAAATAAATATAATTAAA
*
417486 AT-TTATATAATAAAAATTATTAATAT-ATTAAA
1 ATATGATATAATAAAAA-TA--AATATAATTAAA
417518 AT
1 AT
417520 TTATAAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
30 11 0.20
31 23 0.41
32 17 0.30
33 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
ATATGATATAATAAAAATAAATATAATTAAA
Found at i:417464 original size:21 final size:20
Alignment explanation
Indices: 417440--417584 Score: 56
Period size: 20 Copynumber: 7.2 Consensus size: 20
417430 TATAATAAAA
417440 ATAAAATAAT-TAAAATATGAT
1 ATAAAATAATAT-AAATAT-AT
*
417461 ATAATATAATATAAATATAT
1 ATAAAATAATATAAATATAT
* *
417481 TTAAAATTTATATAATAAAAAT-T
1 ATAAAA--TA-AT-ATAAATATAT
* *
417504 AT-TAAT-ATATTAAA-ATTT
1 ATAAAATAATA-TAAATATAT
*
417522 ATAAAA-AATTTAAAATATAT
1 ATAAAATAATAT-AAATATAT
* * *
417542 TTAATATAAT-TATAATA-AA
1 ATAAAATAATATA-AATATAT
417561 ATAAAAT-ATATAAATATGAT
1 ATAAAATAATATAAATAT-AT
417581 ATAA
1 ATAA
417585 TTATATAGAG
Statistics
Matches: 93, Mismatches: 15, Indels: 33
0.66 0.11 0.23
Matches are distributed among these distances:
17 3 0.03
18 16 0.17
19 16 0.17
20 24 0.26
21 18 0.19
22 5 0.05
23 4 0.04
24 7 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (20 bp):
ATAAAATAATATAAATATAT
Found at i:417502 original size:61 final size:61
Alignment explanation
Indices: 417428--417585 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
417418 TAATTATATG
*
417428 AATATAATAAAAATAAAATAATTAAAATATGATATAATATAATAT-AAATATATTTAAAATT
1 AATATAATAAAAATAAAATAATTAAAATATGATATAATAAAATATAAAATATATTTAAAA-T
* * * *
417489 TATATAATAAAAATTATTAATATATTAAAAT-T--TATAA-AAAATTTAAAATATATTTAATAT
1 AATATAATAAAAA-TA-AAATA-ATTAAAATATGATATAATAAAATATAAAATATATTTAAAAT
417549 AATTATAAT-AAAATAAAAT-A-TATAAATATGATATAAT
1 AA-TATAATAAAAATAAAATAATTA-AAATATGATATAAT
417586 TATATAGAGA
Statistics
Matches: 80, Mismatches: 7, Indels: 21
0.74 0.06 0.19
Matches are distributed among these distances:
55 2 0.03
56 5 0.06
57 1 0.01
58 3 0.04
59 7 0.09
60 11 0.14
61 36 0.45
62 2 0.03
63 5 0.06
64 8 0.10
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (61 bp):
AATATAATAAAAATAAAATAATTAAAATATGATATAATAAAATATAAAATATATTTAAAAT
Found at i:417517 original size:18 final size:18
Alignment explanation
Indices: 417474--417523 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
417464 ATATAATATA
*
417474 AATATATTTAAAA-T-TT
1 AATATATTAAAAATTATT
*
417490 -ATATAATAAAAATTATT
1 AATATATTAAAAATTATT
*
417507 AATATATTAAAATTTAT
1 AATATATTAAAAATTAT
417524 AAAAAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 10 0.37
16 1 0.04
17 2 0.07
18 14 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATATTAAAAATTATT
Found at i:417517 original size:32 final size:31
Alignment explanation
Indices: 417429--417524 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 31
417419 AATTATATGA
*
417429 ATATAATAAAAATA-AAATA-ATTAAAATATG
1 ATATAATAAAAATATAAATATATTAAAAT-TT
*
417459 ATATAAT-ATAATATAAATATATTTAAAATTT
1 ATATAATAAAAATATAAATATA-TTAAAATTT
*
417490 ATATAATAAAAATTATTAATATATTAAAATTT
1 ATATAATAAAAA-TATAAATATATTAAAATTT
417522 ATA
1 ATA
417525 AAAAATTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
29 5 0.09
30 12 0.21
31 9 0.16
32 22 0.39
33 9 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
ATATAATAAAAATATAAATATATTAAAATTT
Found at i:417979 original size:20 final size:20
Alignment explanation
Indices: 417945--417992 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
417935 TAAAAATTAA
* *
417945 AAAAGATTAATAATTATTTTT
1 AAAA-ATTAAAAATTATCTTT
417966 AAAAATTAAAAATTATCTTT
1 AAAAATTAAAAATTATCTTT
417986 AAAAATT
1 AAAAATT
417993 TTAATCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAAATTAAAAATTATCTTT
Found at i:419293 original size:6 final size:6
Alignment explanation
Indices: 419282--419354 Score: 59
Period size: 6 Copynumber: 12.8 Consensus size: 6
419272 CGTTAATGCA
* *
419282 TATATT TATA-T TATAGTT ATATATT T-TA-T TATA-T AATAAT TATATT
1 TATATT TATATT TATA-TT -TATATT TATATT TATATT TATATT TATATT
*
419328 TA-ATA TAT-TT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATAT
419355 AAATTTTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
4 2 0.04
5 21 0.38
6 25 0.45
7 3 0.05
8 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (6 bp):
TATATT
Found at i:419340 original size:16 final size:16
Alignment explanation
Indices: 419300--419345 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
419290 TATTATAGTT
*
419300 ATATATTTTATTATATA
1 ATATATTTTA-TATTTA
419317 ATA-A--TTATATTTA
1 ATATATTTTATATTTA
419330 ATATATTTTATATTTA
1 ATATATTTTATATTTA
419346 TATTTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 8 0.32
14 4 0.16
16 10 0.40
17 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATATTTTATATTTA
Found at i:419347 original size:13 final size:12
Alignment explanation
Indices: 419282--419354 Score: 59
Period size: 11 Copynumber: 6.4 Consensus size: 12
419272 CGTTAATGCA
419282 TATATTTATA-T
1 TATATTTATATT
419293 TATAGTTATATATT
1 TATA-TT-TATATT
419307 T-TA-TTATA-T
1 TATATTTATATT
* *
419316 AATAATTATATT
1 TATATTTATATT
*
419328 TA-ATATAT-TT
1 TATATTTATATT
419338 TATATTTATATT
1 TATATTTATATT
419350 TATAT
1 TATAT
419355 AAATTTTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
9 1 0.02
10 10 0.20
11 19 0.39
12 11 0.22
13 6 0.12
14 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (12 bp):
TATATTTATATT
Found at i:421815 original size:38 final size:38
Alignment explanation
Indices: 421756--421926 Score: 236
Period size: 38 Copynumber: 4.5 Consensus size: 38
421746 GAGTTCAATT
* ** * *
421756 TTGAATTCTCTAGCCACCAGCCACCGGCCAA-TTCTAAA
1 TTGAATTCTCTAACCGTCAGCCGCCAGCCAATTTC-AAA
** * *
421794 TTGAATTCTCTAGTCGTCAGCCGCCGGTCAATTTCAAA
1 TTGAATTCTCTAACCGTCAGCCGCCAGCCAATTTCAAA
*
421832 TTGAATTCTCTAACCGTCAGCCGCCAGCTAATTTCAAA
1 TTGAATTCTCTAACCGTCAGCCGCCAGCCAATTTCAAA
421870 TTGAATTCTCTAACCGTCAGCCGCCAGCCAATTTCAAA
1 TTGAATTCTCTAACCGTCAGCCGCCAGCCAATTTCAAA
421908 TTGAATTCTCTAACCGTCA
1 TTGAATTCTCTAACCGTCA
421927 ACTAATTTAA
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
38 118 0.98
39 3 0.02
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (38 bp):
TTGAATTCTCTAACCGTCAGCCGCCAGCCAATTTCAAA
Found at i:423039 original size:2 final size:2
Alignment explanation
Indices: 423034--423076 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
423024 GAGATGGAGA
*
423034 AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
423075 AT
1 AT
423077 TACTCTAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:423990 original size:2 final size:2
Alignment explanation
Indices: 423985--424035 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
423975 GTGTGTGTGT
*
423985 GA GA GA GA GA GA GA GA GA GA GA GA GA CA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
424027 GA GA AA GA G
1 GA GA GA GA G
424036 TACATACACG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.02, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:428186 original size:18 final size:20
Alignment explanation
Indices: 428141--428187 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
428131 AATTTATTTT
*
428141 TATTTGATTATACGAGTTTA
1 TATTTTATTATACGAGTTTA
*
428161 TATTTTATTATATGA-TTTA
1 TATTTTATTATACGAGTTTA
428180 T-TTTTATT
1 TATTTTATT
428188 TGTAAAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.28
19 5 0.20
20 13 0.52
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.62
Consensus pattern (20 bp):
TATTTTATTATACGAGTTTA
Found at i:428267 original size:73 final size:71
Alignment explanation
Indices: 428062--428267 Score: 247
Period size: 69 Copynumber: 2.9 Consensus size: 71
428052 TTTATAAAAA
* * * *
428062 TATTTTTAGATGTGATTATATACGTTTAAATTTTTAAAGATATGATTTATTTTTATTCATAAAAA
1 TATTTTTAAAT-TGATTATAGAAGTTTAAATTTTT-AAGATATGATTTATTTTTATTTATAAAAA
428127 TTTAAATT
64 TTTAAATT
* * ** * *
428135 TATTTTT-ATTTGATTATACG-AGTTTATA-TTTTATTATATGATTTATTTTTATTTGTAAAAGT
1 TATTTTTAAATTGATTATA-GAAGTTTAAATTTTTAAGATATGATTTATTTTTATTTATAAAAAT
428197 TTAAATT
65 TTAAATT
*
428204 TATTTTTTAAATTGATTATAGAAGTTTAAATTATTTAAGATCTGATTTATTTTTATTTATAAAA
1 TA-TTTTTAAATTGATTATAGAAGTTTAAATT-TTTAAGATATGATTTATTTTTATTTATAAAA
428268 TTAATTTAAT
Statistics
Matches: 111, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
69 34 0.31
70 10 0.09
71 31 0.28
72 2 0.02
73 34 0.31
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (71 bp):
TATTTTTAAATTGATTATAGAAGTTTAAATTTTTAAGATATGATTTATTTTTATTTATAAAAATT
TAAATT
Found at i:428281 original size:71 final size:71
Alignment explanation
Indices: 428064--428281 Score: 241
Period size: 71 Copynumber: 3.1 Consensus size: 71
428054 TATAAAAATA
* * * *
428064 TTTTTAGATGTGATTATATACGTTTAAATTTTTAAAGATATGATTTATTTTTATTCATAAAAATT
1 TTTTTAAAT-TGATTATAGAAGTTTAAATTTTT-AAGATATGATTTATTTTTATTTAT-AAAATT
428129 TAAATTTA-
63 TAAATTTAT
* * ** *
428137 TTTTT-ATTTGATTATACG-AGTTTATA-TTTTATTATATGATTTATTTTTATTTGTAAAAGTTT
1 TTTTTAAATTGATTATA-GAAGTTTAAATTTTTAAGATATGATTTATTTTTATTTATAAAA-TTT
428199 AAATTTAT
64 AAATTTAT
*
428207 TTTTTAAATTGATTATAGAAGTTTAAATTATTTAAGATCTGATTTATTTTTATTTATAAAA-TT-
1 TTTTTAAATTGATTATAGAAGTTTAAATT-TTTAAGATATGATTTATTTTTATTTATAAAATTTA
*
428270 AATTTAA
65 AATTTAT
428277 TTTTT
1 TTTTT
428282 GAGATATTTA
Statistics
Matches: 122, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
68 4 0.03
69 30 0.25
70 21 0.17
71 33 0.27
72 2 0.02
73 32 0.26
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (71 bp):
TTTTTAAATTGATTATAGAAGTTTAAATTTTTAAGATATGATTTATTTTTATTTATAAAATTTAA
ATTTAT
Found at i:428462 original size:26 final size:26
Alignment explanation
Indices: 428400--428470 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 26
428390 TATTTTTGGG
*
428400 TATAATTATATGATTTTAAATTTTTTAAAA
1 TATAATT-TAT-ATTTT--ATTTTTAAAAA
428430 TATAATTTAT-TTTTATTTTTAAAAA
1 TATAATTTATATTTTATTTTTAAAAA
*
428455 TTTAAATTTATATTTT
1 TAT-AATTTATATTTT
428471 GATATGATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 12 0.32
26 7 0.19
27 8 0.22
29 3 0.08
30 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (26 bp):
TATAATTTATATTTTATTTTTAAAAA
Found at i:429005 original size:73 final size:73
Alignment explanation
Indices: 428833--429035 Score: 191
Period size: 73 Copynumber: 2.8 Consensus size: 73
428823 TAAGTTTTTT
* * * * * *
428833 TTTTTTTGATATGATTATATAAATTTAAAT-TATTTAAAATATAATTTA-TTTTATTTGTAAAAA
1 TTTTTTAGAT-TGATTAT-TAAAGTTAAATATTTTTAAAGTATAATTAATTTTTATTTATAAAAA
428896 TTTAAATTTA
64 TTTAAATTTA
* * * *
428906 -GTTTTAGTTTGATTA-TACCAGTTTAAATATTTTTAAAGTATTATTAATTTTTATTTATAAAAA
1 TTTTTTAGATTGATTATTA-AAG-TTAAATATTTTTAAAGTATAATTAATTTTTATTTATAAAAA
428969 TTTAAATTTA
64 TTTAAATTTA
* * * *
428979 TTTTTTAGATTGATTATTAGAGTTAAA-ATTTTTTAAGATATGATTTATTTTTTATTT
1 TTTTTTAGATTGATTATTAAAGTTAAATATTTTTAAAG-TAT-AATTAATTTTTATTT
429036 GTAAGATTAG
Statistics
Matches: 105, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
69 2 0.02
70 1 0.01
71 12 0.11
72 29 0.28
73 32 0.30
74 27 0.26
75 2 0.02
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (73 bp):
TTTTTTAGATTGATTATTAAAGTTAAATATTTTTAAAGTATAATTAATTTTTATTTATAAAAATT
TAAATTTA
Found at i:429028 original size:67 final size:72
Alignment explanation
Indices: 428856--428995 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 72
428846 ATTATATAAA
* * * * * *
428856 TTTAAAT-TATTTAAAATATAATTTATTTTATTTGTAAAAATTTAAATTTAGTTTTAGTTTGATT
1 TTTAAATATTTTTAAAGTATTATTAATTTTATTTATAAAAATTTAAATTTAGTTTTAGATTGATT
428920 ATACCAG
66 ATACCAG
*
428927 TTTAAATATTTTTAAAGTATTATTAATTTTTATTTATAAAAATTTAAATTTATTTTTTAGATTGA
1 TTTAAATATTTTTAAAGTATTATTAA-TTTTATTTATAAAAATTTAAATTTA-GTTTTAGATTGA
428992 TTAT
64 TTAT
428996 TAGAGTTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
71 7 0.12
72 14 0.24
73 24 0.41
74 14 0.24
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (72 bp):
TTTAAATATTTTTAAAGTATTATTAATTTTATTTATAAAAATTTAAATTTAGTTTTAGATTGATT
ATACCAG
Found at i:435940 original size:19 final size:19
Alignment explanation
Indices: 435918--435954 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
435908 TTTTTCATGT
435918 TTTATGTCATATTTTATAA
1 TTTATGTCATATTTTATAA
* *
435937 TTTATTTTATATTTTATA
1 TTTATGTCATATTTTATA
435955 TAATTTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTATGTCATATTTTATAA
Found at i:435942 original size:12 final size:12
Alignment explanation
Indices: 435927--435980 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
435917 TTTTATGTCA
435927 TATTTTATAATT
1 TATTTTATAATT
435939 TATTTTAT-A-T
1 TATTTTATAATT
*
435949 T-TTATATAATT
1 TATTTTATAATT
*
435960 TATTATAATAATT
1 TATT-TTATAATT
435973 TAATTTTA
1 T-ATTTTA
435981 ACTTTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
9 5 0.15
10 3 0.09
11 3 0.09
12 10 0.30
13 9 0.27
14 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTTTATAATT
Found at i:436386 original size:17 final size:17
Alignment explanation
Indices: 436340--436387 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
436330 TATTTATATA
436340 TAAAATATAAATTATTTT
1 TAAAATATAAATT-TTTT
* * *
436358 T-TAATTTTAATTTTTT
1 TAAAATATAAATTTTTT
436374 TAAAATATAAATTT
1 TAAAATATAAATTT
436388 AAAAAGATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
16 5 0.22
17 17 0.74
18 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAAATATAAATTTTTT
Found at i:437215 original size:17 final size:15
Alignment explanation
Indices: 437185--437218 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
437175 AATTTATCTC
437185 AATTTTAATAAAATT
1 AATTTTAATAAAATT
437200 AATTTTATATTAAAATT
1 AATTTTA-A-TAAAATT
437217 AA
1 AA
437219 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTTAATAAAATT
Found at i:437990 original size:19 final size:18
Alignment explanation
Indices: 437968--438004 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
437958 TATTAATTAC
437968 ATTTAATTTTTATATTTAA
1 ATTTAATTTTTAT-TTTAA
*
437987 ATTTTATTTTTATTTTAA
1 ATTTAATTTTTATTTTAA
438005 TTACAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTAATTTTTATTTTAA
Found at i:438111 original size:20 final size:20
Alignment explanation
Indices: 438088--438127 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
438078 CATAAAAGTT
*
438088 TTAAAATTTTATTTTATTAA
1 TTAAAATTTTATTTCATTAA
**
438108 TTAATTTTTTATTTCATTAA
1 TTAAAATTTTATTTCATTAA
438128 ATTATGCATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAAAATTTTATTTCATTAA
Found at i:440973 original size:50 final size:50
Alignment explanation
Indices: 440898--441000 Score: 197
Period size: 50 Copynumber: 2.1 Consensus size: 50
440888 ATTTATAACT
440898 TATTCCCTTATATGGCACATGCATATCTTGATAGTCATCACACAATTAAG
1 TATTCCCTTATATGGCACATGCATATCTTGATAGTCATCACACAATTAAG
*
440948 TATTCCCTTATATGGCACATGCATATCTTGATATTCATCACACAATTAAG
1 TATTCCCTTATATGGCACATGCATATCTTGATAGTCATCACACAATTAAG
440998 TAT
1 TAT
441001 GTGTTACCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (50 bp):
TATTCCCTTATATGGCACATGCATATCTTGATAGTCATCACACAATTAAG
Found at i:442794 original size:23 final size:23
Alignment explanation
Indices: 442744--442810 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
442734 TTGCACTAAT
* * *
442744 TTAAAAATAAAATATTTATTTTATA
1 TTAAAAAT-AAA-ATTAATTTAAAA
442769 TTAAAAATAAAATTAATTTAAAA
1 TTAAAAATAAAATTAATTTAAAA
*
442792 TTAAATA-AAAATATAATTT
1 TTAAAAATAAAAT-TAATTT
442811 TTTTATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.14
23 21 0.57
24 3 0.08
25 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAAAAATAAAATTAATTTAAAA
Found at i:443221 original size:17 final size:19
Alignment explanation
Indices: 443195--443236 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
443185 TATAAAACTT
443195 AAAAAA-TAAA-AT-TTTA
1 AAAAAATTAAACATGTTTA
*
443211 AAAAAATTAAACTTGTTTA
1 AAAAAATTAAACATGTTTA
443230 AAAAAAT
1 AAAAAAT
443237 ATCGAGCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 4 0.18
18 1 0.05
19 11 0.50
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAAATTAAACATGTTTA
Found at i:443415 original size:38 final size:35
Alignment explanation
Indices: 443345--443460 Score: 100
Period size: 38 Copynumber: 3.3 Consensus size: 35
443335 TTTATCATAT
*
443345 AAAAATATATATAATATTA-T-AAT-GTAAA-TAATA
1 AAAAATATAT-TAA-ATTACTAAATATTAAATTAATA
* *
443378 AAAAATATATTAAATTATTTAAATTTTTAAACTTAAT-
1 AAAAATATATTAAATTA-CTAAA-TATTAAA-TTAATA
*
443415 AAAAATAATATTAAATTACTAAATATTAAATT-TTA
1 AAAAAT-ATATTAAATTACTAAATATTAAATTAATA
443450 AAAAATATATT
1 AAAAATATATT
443461 TTAAAAATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
31 4 0.06
32 3 0.04
33 11 0.16
34 8 0.11
35 9 0.13
36 10 0.14
37 10 0.14
38 15 0.21
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (35 bp):
AAAAATATATTAAATTACTAAATATTAAATTAATA
Found at i:444033 original size:7 final size:8
Alignment explanation
Indices: 444016--444071 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
444006 TTAAATTTGA
444016 TTTTTATT
1 TTTTTATT
444024 TTTTTATT
1 TTTTTATT
*
444032 TTTTATGTT
1 TTTT-TATT
**
444041 TTTTTAGA
1 TTTTTATT
444049 TTTTTATT
1 TTTTTATT
444057 TTTTATAATT
1 TTTT-T-ATT
444067 TTTTT
1 TTTTT
444072 GAAAAAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 23 0.59
9 9 0.23
10 7 0.18
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (8 bp):
TTTTTATT
Found at i:444044 original size:17 final size:16
Alignment explanation
Indices: 444016--444070 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
444006 TTAAATTTGA
444016 TTTTTA-TTTTTTTAT
1 TTTTTATTTTTTTTAT
*
444031 TTTTTATGTTTTTTTAGA
1 TTTTTAT-TTTTTTTA-T
*
444049 TTTTTATTTTTTATAAT
1 TTTTTATTTTTT-TTAT
444066 TTTTT
1 TTTTT
444071 TGAAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.18
17 18 0.55
18 9 0.27
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTTTATTTTTTTTAT
Found at i:444122 original size:7 final size:7
Alignment explanation
Indices: 444110--444134 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
444100 TAAATAACCA
444110 AAAAAAG
1 AAAAAAG
444117 AAAAAAG
1 AAAAAAG
444124 AAAAAAG
1 AAAAAAG
444131 AAAA
1 AAAA
444135 GACCCCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:444559 original size:19 final size:19
Alignment explanation
Indices: 444523--444560 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
444513 ATTTTTAATT
*
444523 TAAATTTAATTATGAAATA
1 TAAATTTAATTATAAAATA
444542 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
444561 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:444852 original size:16 final size:17
Alignment explanation
Indices: 444824--444857 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
444814 AACATAAATA
444824 AATAATATTTTTTTATT
1 AATAATATTTTTTTATT
444841 AATAAT-TTTTTTTATT
1 AATAATATTTTTTTATT
444857 A
1 A
444858 TTCGTATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATAATATTTTTTTATT
Found at i:445648 original size:22 final size:22
Alignment explanation
Indices: 445617--445660 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
445607 TCCTAAGGGT
445617 TAATAAAAAA-ATAATTATAATA
1 TAATAAAAAATATAA-TATAATA
*
445639 TAATATAAAATATAATATAATA
1 TAATAAAAAATATAATATAATA
445661 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAATAAAAAATATAATATAATA
Found at i:445652 original size:12 final size:12
Alignment explanation
Indices: 445617--445658 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
445607 TCCTAAGGGT
*
445617 TAATA-AAAAAA
1 TAATATAAAATA
*
445628 TAAT-TATAATA
1 TAATATAAAATA
445639 TAATATAAAATA
1 TAATATAAAATA
445651 TAATATAA
1 TAATATAA
445659 TAAAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 12 0.46
12 14 0.54
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATATAAAATA
Found at i:445702 original size:17 final size:17
Alignment explanation
Indices: 445634--445702 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 17
445624 AAAATAATTA
445634 TAATATAATAT-AAAAT
1 TAATATAATATAAAAAT
*
445650 ATAATATAATAAAAAAAT
1 -TAATATAATATAAAAAT
*
445668 TAATTTAAACTATGTAAAAAT
1 TAATAT-AA-TA--TAAAAAT
*
445689 TTATATAATATAAA
1 TAATATAATATAAA
445703 TTATTAGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
17 19 0.45
18 7 0.17
19 4 0.10
20 2 0.05
21 10 0.24
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (17 bp):
TAATATAATATAAAAAT
Found at i:445968 original size:11 final size:10
Alignment explanation
Indices: 445948--446011 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
445938 AGATCGATAA
445948 TTTATATATT
1 TTTATATATT
*
445958 TTTAT-TATA
1 TTTATATATT
445967 TTTATATA-T
1 TTTATATATT
445976 TTTATCATATT
1 TTTAT-ATATT
* *
445987 ATAATA-ATAT
1 TTTATATAT-T
*
445997 TTAATATATT
1 TTTATATATT
446007 TTTAT
1 TTTAT
446012 TTATATAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 15 0.35
10 22 0.51
11 6 0.14
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTATATATT
Found at i:445974 original size:8 final size:8
Alignment explanation
Indices: 445947--446075 Score: 52
Period size: 9 Copynumber: 15.0 Consensus size: 8
445937 GAGATCGATA
445947 ATTTATAT
1 ATTTATAT
445955 ATTTTTATTAT
1 A--TTTA-TAT
445966 ATTTATAT
1 ATTTATAT
445974 ATTTTATCAT
1 A-TTTAT-AT
445984 ATTATAATAAT
1 ATT-T-AT-AT
445995 ATTTAATAT
1 ATTT-ATAT
446004 ATTT-T-T
1 ATTTATAT
446010 ATTTATAT
1 ATTTATAT
446018 AAAATTTGATAT
1 ---ATTT-ATAT
*
446030 ATTAATA-
1 ATTTATAT
446037 ATTTATAT
1 ATTTATAT
**
446045 -TAAATAT
1 ATTTATAT
*
446052 -TTTAAAAT
1 ATTT-ATAT
446060 ATTTATAT
1 ATTTATAT
*
446068 ATTCATAT
1 ATTTATAT
446076 CGTATTTATA
Statistics
Matches: 95, Mismatches: 10, Indels: 32
0.69 0.07 0.23
Matches are distributed among these distances:
6 5 0.05
7 14 0.15
8 22 0.23
9 23 0.24
10 12 0.13
11 15 0.16
12 4 0.04
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.57
Consensus pattern (8 bp):
ATTTATAT
Found at i:445987 original size:23 final size:22
Alignment explanation
Indices: 445947--446018 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 22
445937 GAGATCGATA
445947 ATTTATATATTT--T-TATTAT
1 ATTTATATATTTAATATATTAT
*
445966 ATTTATATATTTTATCATATTAT
1 ATTTATATATTTAAT-ATATTAT
* *
445989 A-ATA-ATATTTAATATATTTTT
1 ATTTATATATTTAATATA-TTAT
446010 ATTTATATA
1 ATTTATATA
446019 AAATTTGATA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 12 0.29
20 3 0.07
21 13 0.31
22 4 0.10
23 10 0.24
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTATATATTTAATATATTAT
Found at i:446006 original size:30 final size:28
Alignment explanation
Indices: 445948--446112 Score: 92
Period size: 30 Copynumber: 5.8 Consensus size: 28
445938 AGATCGATAA
* * *
445948 TTTATATATTTTTATTATATTTATATAT
1 TTTATATATTATAATAATATTTATATAT
445976 TTTATCATATTATAATAATATTTAATATAT
1 TTTAT-ATATTATAATAATATTT-ATATAT
*
446006 TTT-TAT-TTAT-ATAAAATTTGATATA-
1 TTTATATATTATAATAATATTT-ATATAT
* * *
446031 TTAATA-ATTTATATTAAATATTT-TAAAAT
1 TTTATATA-TTATAAT-AATATTTAT-ATAT
**
446060 ATTTATATATTCAT-ATCGTATTTATATTATT
1 -TTTATATATT-ATAATAATATTTATA-TA-T
* *
446091 TTTTTATATTATAATTATATTT
1 TTTATATATTATAATAATATTT
446113 TATGATTATT
Statistics
Matches: 104, Mismatches: 17, Indels: 30
0.69 0.11 0.20
Matches are distributed among these distances:
25 2 0.02
26 15 0.14
27 9 0.09
28 10 0.10
29 29 0.28
30 35 0.34
31 4 0.04
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (28 bp):
TTTATATATTATAATAATATTTATATAT
Found at i:446012 original size:26 final size:26
Alignment explanation
Indices: 445966--446032 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
445956 TTTTTATTAT
*
445966 ATTT-ATATATTTTATCATATTATAATAAT
1 ATTTAATATATTTT-T-AT-TTAT-ATAAA
445995 ATTTAATATATTTTTATTTATATAAA
1 ATTTAATATATTTTTATTTATATAAA
*
446021 ATTTGATATATT
1 ATTTAATATATT
446033 AATAATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 15 0.43
27 4 0.11
28 2 0.06
29 5 0.14
30 9 0.26
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (26 bp):
ATTTAATATATTTTTATTTATATAAA
Found at i:446036 original size:44 final size:48
Alignment explanation
Indices: 445947--446038 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 48
445937 GAGATCGATA
* * *
445947 ATTTATATATTTTTATTATATTTATATATTTTATCATATTATAATAAT
1 ATTTATATATTTTTATTATATATATAAATTTGATCATATTATAATAAT
445995 ATTTAATATATTTTTATT-TATATA-AAATTTGAT-ATATTAATAAT
1 ATTT-ATATATTTTTATTATATATATAAATTTGATCATATT-ATAAT
446039 TTATATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
46 5 0.13
47 12 0.31
48 9 0.23
49 13 0.33
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (48 bp):
ATTTATATATTTTTATTATATATATAAATTTGATCATATTATAATAAT
Found at i:446054 original size:46 final size:49
Alignment explanation
Indices: 445947--446054 Score: 120
Period size: 47 Copynumber: 2.3 Consensus size: 49
445937 GAGATCGATA
* * *
445947 ATTT-ATATATTTTTATTATATTTATATATTTTATCATATTATAATAAT
1 ATTTAATATATTTTTATTATATATATAAATTTGATCATATTATAATAAT
*
445995 ATTTAATATATTTTTATT-TATATA-AAATTTGAT-ATATTAATAAT-TT
1 ATTTAATATATTTTTATTATATATATAAATTTGATCATATT-ATAATAAT
446041 ATATTAA-ATATTTT
1 AT-TTAATATATTTT
446055 AAAATATTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
46 15 0.28
47 16 0.30
48 9 0.17
49 13 0.25
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (49 bp):
ATTTAATATATTTTTATTATATATATAAATTTGATCATATTATAATAAT
Found at i:446113 original size:21 final size:21
Alignment explanation
Indices: 446097--446137 Score: 73
Period size: 21 Copynumber: 1.9 Consensus size: 21
446087 TATTTTTTTA
446097 TATTATAATTATATTTTATGAT
1 TATT-TAATTATATTTTATGAT
446119 TATTTAATTATATTTTATG
1 TATTTAATTATATTTTATG
446138 TCGTGTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
TATTTAATTATATTTTATGAT
Found at i:446659 original size:2 final size:2
Alignment explanation
Indices: 446652--446721 Score: 63
Period size: 2 Copynumber: 35.0 Consensus size: 2
446642 AAGTTAGTGT
* * *
446652 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA AA AA GT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
446694 GTG T- TA TA TA TA TA CA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
446722 AGACATCCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
1 2 0.04
2 54 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:446997 original size:123 final size:123
Alignment explanation
Indices: 446778--447023 Score: 483
Period size: 123 Copynumber: 2.0 Consensus size: 123
446768 TTTTAAGCTG
446778 CTGATTTTCATATAAGTGTTAGTGATTTAACATTAAGCTCATCAAATCTTGGTAATGAAAAATGT
1 CTGATTTTCATATAAGTGTTAGTGATTTAACATTAAGCTCATCAAATCTTGGTAATGAAAAATGT
*
446843 AAAAATCAAAAATGAAAATCCCAATTTTGAAGCTATAAAAAGAATCAATCCTTATTCT
66 AAAAATCAAAAATAAAAATCCCAATTTTGAAGCTATAAAAAGAATCAATCCTTATTCT
446901 CTGATTTTCATATAAGTGTTAGTGATTTAACATTAAGCTCATCAAATCTTGGTAATGAAAAATGT
1 CTGATTTTCATATAAGTGTTAGTGATTTAACATTAAGCTCATCAAATCTTGGTAATGAAAAATGT
446966 AAAAATCAAAAATAAAAATCCCAATTTTGAAGCTATAAAAAGAATCAATCCTTATTCT
66 AAAAATCAAAAATAAAAATCCCAATTTTGAAGCTATAAAAAGAATCAATCCTTATTCT
447024 TCTTCTTCTT
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 122 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (123 bp):
CTGATTTTCATATAAGTGTTAGTGATTTAACATTAAGCTCATCAAATCTTGGTAATGAAAAATGT
AAAAATCAAAAATAAAAATCCCAATTTTGAAGCTATAAAAAGAATCAATCCTTATTCT
Found at i:447028 original size:3 final size:3
Alignment explanation
Indices: 447020--447047 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
447010 TCAATCCTTA
447020 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
447048 CTGCAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:447175 original size:3 final size:3
Alignment explanation
Indices: 447167--447205 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
447157 TACGTCATTT
447167 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
447206 AATAATATTT
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:448087 original size:19 final size:17
Alignment explanation
Indices: 448046--448081 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
448036 TATAGACCCC
448046 AAAGGGCAAGAGAGAGG
1 AAAGGGCAAGAGAGAGG
448063 AAAGGGCAAGAGAGAGG
1 AAAGGGCAAGAGAGAGG
448080 AA
1 AA
448082 TTAGGGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.44, T:0.00
Consensus pattern (17 bp):
AAAGGGCAAGAGAGAGG
Found at i:448151 original size:9 final size:9
Alignment explanation
Indices: 448139--448309 Score: 50
Period size: 9 Copynumber: 17.9 Consensus size: 9
448129 AATTTAATAA
*
448139 TTTATTTAT
1 TTTATATAT
*
448148 TTTATCGTAT
1 TTTAT-ATAT
448158 TTTATATAT
1 TTTATATAT
*
448167 TATA-ATTAT
1 TTTATA-TAT
*
448176 GTTTA-AAAT
1 -TTTATATAT
* *
448185 ATTATAAAAT
1 TTTAT-ATAT
*
448195 TATATATAT
1 TTTATATAT
448204 TTTAATATAT
1 TTT-ATATAT
* *
448214 TAATAATTTAT
1 T--TTATATAT
448225 TTTATATAAAT
1 TTTATAT--AT
*
448236 TTTA-ACAT
1 TTTATATAT
448244 ATTTATATAT
1 -TTTATATAT
448254 TTATATTATATT
1 TT-TA-TATA-T
448266 TTTATTATTAT
1 TTTA-TA-TAT
448277 TTTATCATA-
1 TTTAT-ATAT
448286 TTTAT-T-T
1 TTTATATAT
448293 TTTAT-TAT
1 TTTATATAT
448301 ATTTATATA
1 -TTTATATA
448310 ATCATATTAT
Statistics
Matches: 125, Mismatches: 16, Indels: 41
0.69 0.09 0.23
Matches are distributed among these distances:
7 7 0.06
8 7 0.06
9 41 0.33
10 37 0.30
11 27 0.22
12 6 0.05
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (9 bp):
TTTATATAT
Found at i:448238 original size:32 final size:33
Alignment explanation
Indices: 448193--448264 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
448183 ATATTATAAA
* *
448193 ATTATATATATTTTAATATATTAATA-ATTTAT
1 ATTATATAAATTTTAACATATTAATATATTTAT
* *
448225 TTTATATAAATTTTAACATATTTATATATTTAT
1 ATTATATAAATTTTAACATATTAATATATTTAT
448258 ATTATAT
1 ATTATAT
448265 TTTTATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 22 0.65
33 12 0.35
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
ATTATATAAATTTTAACATATTAATATATTTAT
Found at i:448265 original size:11 final size:11
Alignment explanation
Indices: 448249--448324 Score: 57
Period size: 11 Copynumber: 6.7 Consensus size: 11
448239 AACATATTTA
448249 TATATTTATAT
1 TATATTTATAT
*
448260 TATATTTTTAT
1 TATATTTATAT
448271 TATTATTT-TAT
1 TA-TATTTATAT
* *
448282 CATATTTATTT
1 TATATTTATAT
*
448293 TTTA-TTATATT
1 TATATTTATA-T
*
448304 TATATAATCATAT
1 TATAT--TTATAT
448317 TATATTTA
1 TATATTTA
448325 AAATTATTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
10 9 0.18
11 26 0.52
12 5 0.10
13 6 0.12
14 4 0.08
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:448266 original size:19 final size:18
Alignment explanation
Indices: 448138--448324 Score: 84
Period size: 19 Copynumber: 10.3 Consensus size: 18
448128 AAATTTAATA
*
448138 ATTTATTTATTTTATCGTAT
1 ATTTATATATTTTAT--TAT
*
448158 -TTTATATATTATAATTAT
1 ATTTATATATT-TTATTAT
* * * * *
448176 GTTTA-AAATATTATAAA
1 ATTTATATATTTTATTAT
*
448193 ATTATATATATTTTAATAT
1 ATT-TATATATTTTATTAT
*
448212 A-TTA-ATAATTTATT-T
1 ATTTATATATTTTATTAT
* * **
448227 -TATATAAATTTTAACAT
1 ATTTATATATTTTATTAT
448244 ATTTATATATTTATATTAT
1 ATTTATATATTT-TATTAT
*
448263 ATTTTTATTATTATTTTATCAT
1 A--TTTA-TA-TATTTTATTAT
448285 ATTTAT-T-TTTTATTAT
1 ATTTATATATTTTATTAT
**
448301 ATTTATATAATCATATTAT
1 ATTTATAT-ATTTTATTAT
448320 ATTTA
1 ATTTA
448325 AAATTATTAA
Statistics
Matches: 123, Mismatches: 28, Indels: 33
0.67 0.15 0.18
Matches are distributed among these distances:
15 3 0.02
16 28 0.23
17 11 0.09
18 18 0.15
19 39 0.32
20 7 0.06
21 4 0.03
22 8 0.07
23 5 0.04
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.59
Consensus pattern (18 bp):
ATTTATATATTTTATTAT
Found at i:448280 original size:24 final size:25
Alignment explanation
Indices: 448246--448309 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
448236 TTTAACATAT
448246 TTATATATTTATAT-TATA-TTTTTA
1 TTATAT-TTTATATATATATTTTTTA
*
448270 TTATTATTTTATCATATTTATTTTTTA
1 TTA-TATTTTAT-ATATATATTTTTTA
448297 TTATA-TTTATATA
1 TTATATTTTATATA
448310 ATCATATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
24 11 0.31
25 10 0.29
26 5 0.14
27 9 0.26
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
TTATATTTTATATATATATTTTTTA
Found at i:448796 original size:25 final size:25
Alignment explanation
Indices: 448767--448816 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
448757 TACATACATG
448767 TAATTT-ATAAA-ATTTTACTTTTTTT
1 TAATTTAATAAACA-TTTA-TTTTTTT
448792 TAATTTAATAAACATTTATTTTTTT
1 TAATTTAATAAACATTTATTTTTTT
448817 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 13 0.57
26 9 0.39
27 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
TAATTTAATAAACATTTATTTTTTT
Found at i:450905 original size:2 final size:2
Alignment explanation
Indices: 450898--450924 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
450888 CGTTTACTAT
450898 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 T
450925 TTAATGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:458625 original size:21 final size:22
Alignment explanation
Indices: 458551--458625 Score: 68
Period size: 26 Copynumber: 3.4 Consensus size: 22
458541 AATAATTTTT
*
458551 TTATTAAATAAATAATAATTTAAA
1 TTATTAAA-AAATAAT-ATATAAA
458575 TTAATTTAAAAATATAA-ATATAAA
1 TT-A-TTAAAAA-ATAATATATAAA
458599 -TA-TAAAAAA-AATATATAAA
1 TTATTAAAAAATAATATATAAA
458618 TTATTAAA
1 TTATTAAA
458626 TTTAAATAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
18 2 0.05
19 8 0.18
20 8 0.18
21 4 0.09
22 1 0.02
23 1 0.02
24 8 0.18
25 3 0.07
26 9 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTATTAAAAAATAATATATAAA
Found at i:459137 original size:5 final size:5
Alignment explanation
Indices: 459127--459169 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
459117 CTTTTGTCAA
* *
459127 ATTAT ATTAT ATTTT A-TAT ATTTT ATTAT ATTAT AATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT -ATTAT ATT
459170 TAAAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.09
5 24 0.75
6 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
ATTAT
Found at i:459168 original size:30 final size:28
Alignment explanation
Indices: 459127--459205 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 28
459117 CTTTTGTCAA
459127 ATTATATTATATTTTATATATTTTATTAT
1 ATTATATTATATTTTATATATTTTA-TAT
* *
459156 ATTATAATTATATTTAAAATATTTTATAT
1 ATTAT-ATTATATTTTATATATTTTATAT
* *
459185 -TTATATAAAATTTTATATATT
1 ATTATATTATATTTTATATATT
459206 AATAATTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
27 13 0.30
28 4 0.09
29 8 0.19
30 18 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTATATTATATTTTATATATTTTATAT
Found at i:459177 original size:20 final size:21
Alignment explanation
Indices: 459154--459245 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 21
459144 ATATTTTATT
459154 ATATTATA-ATTATATTTAAA
1 ATATTATATATTATATTTAAA
* *
459174 ATATTTTATATT-TATATAAA
1 ATATTATATATTATATTTAAA
* *
459194 ATTTTATATATTAATAATTTATA
1 ATATTATATATT-AT-ATTTAAA
459217 ATA-TATA-A--AT-TTTAAA
1 ATATTATATATTATATTTAAA
459233 ATATTTATATATT
1 ATA-TTATATATT
459246 CAGATATATT
Statistics
Matches: 55, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
16 8 0.15
18 6 0.11
19 1 0.02
20 24 0.44
21 4 0.07
22 5 0.09
23 7 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTATATATTATATTTAAA
Found at i:459210 original size:18 final size:17
Alignment explanation
Indices: 459163--459210 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
459153 TATATTATAA
*
459163 TTATATTTAA-AATATT
1 TTATATTTAATAAAATT
459179 TTATATTTATATAAAATT
1 TTATATTTA-ATAAAATT
459197 TTATATATTAATAA
1 TTATAT-TTAATAA
459211 TTTATAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 9 0.32
17 1 0.04
18 15 0.54
19 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATATTTAATAAAATT
Found at i:459230 original size:16 final size:16
Alignment explanation
Indices: 459176--459236 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
459166 TATTTAAAAT
*
459176 ATTTTATATTTATATAAA
1 ATTTTATA-ATATAT-AA
459194 ATTTTAT-ATAT-TAA
1 ATTTTATAATATATAA
*
459208 TAATTTATAATATATAA
1 -ATTTTATAATATATAA
*
459225 ATTTTAAAATAT
1 ATTTTATAATAT
459237 TTATATATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 2 0.06
15 7 0.19
16 17 0.47
17 3 0.08
18 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTATAATATATAA
Found at i:459253 original size:32 final size:31
Alignment explanation
Indices: 459168--459254 Score: 76
Period size: 32 Copynumber: 2.9 Consensus size: 31
459158 TATAATTATA
*
459168 TTTAAAATATTT-TATATT-TATATA-AAAT
1 TTTAAAATATTTATATATTAAATATATAAAT
* *
459196 TTT-ATATATTAATA-ATTTATAATATATAAAT
1 TTTAAAATATTTATATA-TTA-AATATATAAAT
*
459227 TTTAAAATATTTATATATTCAGATATAT
1 TTTAAAATATTTATATATT-AAATATAT
459255 TTATATTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
27 7 0.16
28 7 0.16
30 5 0.11
31 7 0.16
32 17 0.38
33 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (31 bp):
TTTAAAATATTTATATATTAAATATATAAAT
Found at i:461520 original size:21 final size:21
Alignment explanation
Indices: 461494--461533 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
461484 ATTAAAAAAT
461494 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
461515 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
461534 AATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:461898 original size:39 final size:38
Alignment explanation
Indices: 461854--461942 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 38
461844 TAATCAATGA
*
461854 AAATATTAAATTTAATTAT-AAA-AATATAAATATACTATT
1 AAATATTAAATTT-ATT-TCAAATAATA-AAATAAACTATT
* *
461893 AAATATTTAAATATATTTCAAATAATAAAATAAACTTTT
1 AAATA-TTAAATTTATTTCAAATAATAAAATAAACTATT
461932 AAA-ATTAAATT
1 AAATATTAAATT
461943 AAATCTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
37 6 0.14
38 2 0.05
39 24 0.56
40 11 0.26
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (38 bp):
AAATATTAAATTTATTTCAAATAATAAAATAAACTATT
Found at i:462679 original size:20 final size:21
Alignment explanation
Indices: 462629--462687 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
462619 AATAAAAATG
* **
462629 ATAATAAGATTAGTTATTATA
1 ATAATGAGATTAAATATTATA
462650 ATAATGAGATTAAATATTATA
1 ATAATGAGATTAAATATTATA
*
462671 A-AGTGAGATTAAA-ATTA
1 ATAATGAGATTAAATATTA
462688 ATGATTGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.12
20 11 0.32
21 19 0.56
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (21 bp):
ATAATGAGATTAAATATTATA
Found at i:462808 original size:20 final size:19
Alignment explanation
Indices: 462780--462826 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
462770 TTTGAATATA
462780 TATAATAAATAATTAAAATT
1 TATAATAAATAA-TAAAATT
* *
462800 TATATTAAATAATAAAATG
1 TATAATAAATAATAAAATT
462819 TA-AATAAA
1 TATAATAAA
462827 ATATAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 5 0.21
19 8 0.33
20 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
TATAATAAATAATAAAATT
Found at i:462828 original size:19 final size:19
Alignment explanation
Indices: 462786--462833 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
462776 TATATATAAT
* * *
462786 AAATAATTAAAATTTATATT
1 AAATAA-TAAAATGTAAATA
462806 AAATAATAAAATGTAAATA
1 AAATAATAAAATGTAAATA
462825 AAAT-ATAAA
1 AAATAATAAA
462834 TAAAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 5 0.20
19 14 0.56
20 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AAATAATAAAATGTAAATA
Found at i:462841 original size:12 final size:11
Alignment explanation
Indices: 462810--462843 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
462800 TATATTAAAT
*
462810 AATAAAATGTA
1 AATAAAATATA
462821 AATAAAATATA
1 AATAAAATATA
462832 AATAAAAATATA
1 AAT-AAAATATA
462844 TTTATGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAAAATATA
Found at i:463174 original size:12 final size:13
Alignment explanation
Indices: 463142--463174 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
463132 GGCTCCCTCC
*
463142 TCCCTCTCAAGGA
1 TCCCTCTCAAGCA
463155 TCCCTCTCAAGCA
1 TCCCTCTCAAGCA
463168 T-CCTCTC
1 TCCCTCTC
463175 TTGTATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.18, C:0.45, G:0.09, T:0.27
Consensus pattern (13 bp):
TCCCTCTCAAGCA
Found at i:465663 original size:21 final size:22
Alignment explanation
Indices: 465634--465679 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
465624 TATTCAGACA
** *
465634 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
465656 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
465677 AGT
1 AGT
465680 TTTAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:467412 original size:24 final size:25
Alignment explanation
Indices: 467380--467474 Score: 95
Period size: 26 Copynumber: 3.7 Consensus size: 25
467370 AACAAAAACC
*
467380 ACTTATTGTTTGTCAAAATTGTGGTT
1 ACTT-TTGTTTGTCAAAATGGTGGTT
467406 ACTTTGTGTTTGTCAAAATGGTGGTT
1 ACTTT-TGTTTGTCAAAATGGTGGTT
* * *
467432 TCTTTTTATTTGTCAAAAATGGTGG-C
1 AC-TTTTGTTTGTC-AAAATGGTGGTT
*
467458 A-TGTTGTTTGTCAAAAT
1 ACTTTTGTTTGTCAAAAT
467475 TTGTGGCTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
23 5 0.08
24 9 0.15
25 1 0.02
26 31 0.53
27 13 0.22
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.47
Consensus pattern (25 bp):
ACTTTTGTTTGTCAAAATGGTGGTT
Found at i:467416 original size:26 final size:26
Alignment explanation
Indices: 467386--467456 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
467376 AACCACTTAT
*
467386 TGTTTGTCAAAATTGTGGTTACTTTG
1 TGTTTGTCAAAATGGTGGTTACTTTG
* *
467412 TGTTTGTCAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAATGGTGGTTACTTTG
*
467438 TATTTGTCAAAAATGGTGG
1 TGTTTGTC-AAAATGGTGG
467457 CATGTTGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 30 0.75
27 10 0.25
ACGTcount: A:0.21, C:0.07, G:0.24, T:0.48
Consensus pattern (26 bp):
TGTTTGTCAAAATGGTGGTTACTTTG
Found at i:469136 original size:29 final size:30
Alignment explanation
Indices: 469064--469136 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
469054 AATTTGTATG
469064 ATATCAAT-TTTGATA-TATTTTTAATATTT
1 ATAT-AATATTTGATATTATTTTTAATATTT
** *
469093 ATATCGTATTT-ATATTATTTTTTATA-TT
1 ATATAATATTTGATATTATTTTTAATATTT
469121 ATATAATATTTGATAT
1 ATATAATATTTGATAT
469137 AGTGATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (30 bp):
ATATAATATTTGATATTATTTTTAATATTT
Found at i:473250 original size:2 final size:2
Alignment explanation
Indices: 473243--473270 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
473233 TTCAACTGTG
473243 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
473271 CACACATAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.