Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 156 of 185
Found at i:48065307 original size:2 final size:2
Alignment explanation
Indices: 48065302--48065365 Score: 51
Period size: 2 Copynumber: 33.0 Consensus size: 2
48065292 TGTAAGTATG
* * * * *
48065302 TA TA TA TA CA TA TA TA TG TA TA TA AA T- TA -A AA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
48065342 TA TA TA TG TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
48065366 AAAATTATGA
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:48065324 original size:10 final size:10
Alignment explanation
Indices: 48065298--48065365 Score: 63
Period size: 10 Copynumber: 7.0 Consensus size: 10
48065288 TATATGTAAG
48065298 TATGTATATA
1 TATGTATATA
*
48065308 TA--CATATA
1 TATGTATATA
48065316 TATGTATATA
1 TATGTATATA
* *
48065326 AAT-TA-AAA
1 TATGTATATA
48065334 TATGTATATATA
1 TATG--TATATA
48065346 TATGTATATA
1 TATGTATATA
48065356 TATGTATATA
1 TATGTATATA
48065366 AAAATTATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
8 11 0.24
9 2 0.04
10 25 0.54
11 2 0.04
12 6 0.13
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (10 bp):
TATGTATATA
Found at i:48065336 original size:18 final size:20
Alignment explanation
Indices: 48065315--48065367 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
48065305 ATATACATAT
48065315 ATATGTATATAAAT-TA-AA
1 ATATGTATATAAATGTATAA
*
48065333 ATATGTATATATATATGTATAT
1 ATATGTATATA-A-ATGTATAA
48065355 ATATGTATATAAA
1 ATATGTATATAAA
48065368 AATTATGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 11 0.37
19 1 0.03
20 3 0.10
21 3 0.10
22 12 0.40
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (20 bp):
ATATGTATATAAATGTATAA
Found at i:48065365 original size:12 final size:12
Alignment explanation
Indices: 48065287--48065358 Score: 57
Period size: 12 Copynumber: 6.3 Consensus size: 12
48065277 AAATATAAAA
48065287 ATATATGTAAGTAT
1 ATATATGT-A-TAT
* * *
48065301 GTATATATACAT
1 ATATATGTATAT
48065313 ATATATGTATAT
1 ATATATGTATAT
48065325 A-A-AT-TA-A-
1 ATATATGTATAT
48065332 A-ATATGTATAT
1 ATATATGTATAT
48065343 ATATATGTATAT
1 ATATATGTATAT
48065355 ATAT
1 ATAT
48065359 GTATATAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
7 2 0.04
8 3 0.06
9 4 0.09
10 3 0.06
11 2 0.04
12 26 0.55
13 1 0.02
14 6 0.13
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.44
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:48067367 original size:60 final size:60
Alignment explanation
Indices: 48067265--48067396 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 60
48067255 TACACTAGTA
* ** *
48067265 GTCAGCCAACTATTAATAAATTTATCTTTTGGTCATTTAACTATGAAAAGTTATAAAATG
1 GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
* * * * *
48067325 GTTATCCAACTATTAGTAAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
1 GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
48067385 GTCACCCAACTA
1 GTCACCCAACTA
48067397 CTCAATTTTG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (60 bp):
GTCACCCAACTATTAATAAATTTATCTTTTGGTCATCAAACTATGAAAAGTTACAAAATG
Found at i:48067411 original size:60 final size:59
Alignment explanation
Indices: 48067282--48067419 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 59
48067272 AACTATTAAT
* * ** * * * *
48067282 AAATTTATCTTTTGGTCATTTAACTATGAAAAGTTATAAAATGGTTATCCAACTATTAG
1 AAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTATCAG
48067341 TAAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTACTCA-
1 -AAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTA-TCAG
**
48067401 ATTTTGTCTTTTTTGGTCA
1 AAATT-TCTTTTTTGGTCA
48067420 CTAACTGGCT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 3 0.05
60 61 0.92
61 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (59 bp):
AAATTTCTTTTTTGGTCATCAAACTATGAAAAGTTACAAAATGGTCACCCAACTATCAG
Found at i:48068996 original size:28 final size:29
Alignment explanation
Indices: 48068959--48069018 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
48068949 TAATAGTGTT
48068959 TAAATTTATTATTATAATTTAAATTGTAA
1 TAAATTTATTATTATAATTTAAATTGTAA
* * *
48068988 TAAA-TTATTATTTTCATTTATATTGTAA
1 TAAATTTATTATTATAATTTAAATTGTAA
48069016 TAA
1 TAA
48069019 CAGATTTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (29 bp):
TAAATTTATTATTATAATTTAAATTGTAA
Found at i:48070678 original size:26 final size:25
Alignment explanation
Indices: 48070623--48070671 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
48070613 ATTACCTTTT
* *
48070623 TTATTTTTTTATTCATTTACTTATA
1 TTATTTTTTGATGCATTTACTTATA
48070648 TTATTTTTATGATGCATTTA-TTAT
1 TTATTTTT-TGATGCATTTACTTAT
48070672 TGTTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (25 bp):
TTATTTTTTGATGCATTTACTTATA
Found at i:48071088 original size:98 final size:98
Alignment explanation
Indices: 48070967--48071161 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
48070957 TTAAAAAAAA
* *
48070967 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
48071032 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
48071065 TAAAGGAAATATTCTGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGTGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
48071130 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
48071162 AGTTTTATTG
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:48073315 original size:31 final size:31
Alignment explanation
Indices: 48073272--48073336 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
48073262 AGCCAGCTGG
*
48073272 TGACAAAAAAAGATAA-A-ATTGAATAGTTGGA
1 TGACAAAAAAAGA-AATATACT-AATAGTTGGA
*
48073303 TGACCAAAAAAGAAATATACTAATAGTTGGA
1 TGACAAAAAAAGAAATATACTAATAGTTGGA
48073334 TGA
1 TGA
48073337 TAACTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 2 0.07
31 26 0.87
32 2 0.07
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.23
Consensus pattern (31 bp):
TGACAAAAAAAGAAATATACTAATAGTTGGA
Found at i:48076297 original size:12 final size:12
Alignment explanation
Indices: 48076250--48076308 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
48076240 ACTTAATTAC
48076250 TTTAATATTAAA
1 TTTAATATTAAA
*
48076262 TTAAAT-TTAAAA
1 TTTAATATT-AAA
*
48076274 TTT-ATCTATAAA
1 TTTAATAT-TAAA
48076286 TATTAA-ATTAAA
1 T-TTAATATTAAA
48076298 TTTAATATTAA
1 TTTAATATTAA
48076309 GATAATCACT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
11 8 0.21
12 25 0.66
13 4 0.11
14 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:48076647 original size:19 final size:19
Alignment explanation
Indices: 48076620--48076659 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
48076610 TTAGACCATC
*
48076620 AGTCTGATTTCACATAACA
1 AGTCCGATTTCACATAACA
*
48076639 AGTCCGATTTCACATAGCA
1 AGTCCGATTTCACATAACA
48076658 AG
1 AG
48076660 CCTGGTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (19 bp):
AGTCCGATTTCACATAACA
Found at i:48081532 original size:42 final size:42
Alignment explanation
Indices: 48081473--48081559 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
48081463 TGTGGATGGT
* * *
48081473 TTTGTTTCCCATTTGGGATTTTTTGGGTATCTCAAGATTGCC
1 TTTGTTTCCCATTTGGGATATTTTGAGTATCCCAAGATTGCC
* *
48081515 TTTGTTTCCCGTTTGGGATATTTTGAGTATCCCAGGATTGCC
1 TTTGTTTCCCATTTGGGATATTTTGAGTATCCCAAGATTGCC
48081557 TTT
1 TTT
48081560 CTTGCTTGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.47
Consensus pattern (42 bp):
TTTGTTTCCCATTTGGGATATTTTGAGTATCCCAAGATTGCC
Found at i:48083474 original size:40 final size:40
Alignment explanation
Indices: 48083399--48083541 Score: 141
Period size: 40 Copynumber: 3.6 Consensus size: 40
48083389 AGCACACCAG
* * *
48083399 TTTGGCACCCAGTGTCTCATCAGA-TAATTCTAAGTAATAA
1 TTTGACACCCAGTGTCTCATC-GACTAATCCAAAGTAATAA
* * *
48083439 TTTGACACCTAGTGTCTCATCGACTAAACCGAAGT-A-AA
1 TTTGACACCCAGTGTCTCATCGACTAATCCAAAGTAATAA
* * * *
48083477 -TTGGCACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAA
1 TTTGACACCCAGTGTCTCATCG-ACTAATCCAAAGTAATAA
*
48083517 ATTGACACCCAGTGTCTCATCGACT
1 TTTGACACCCAGTGTCTCATCGACT
48083542 CGAAGTCGAA
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
37 18 0.22
38 12 0.14
39 3 0.04
40 31 0.37
41 19 0.23
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (40 bp):
TTTGACACCCAGTGTCTCATCGACTAATCCAAAGTAATAA
Found at i:48090279 original size:13 final size:13
Alignment explanation
Indices: 48090261--48090287 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48090251 TTTCGGTTTA
48090261 ATTTAAACAATAT
1 ATTTAAACAATAT
48090274 ATTTAAACAATAT
1 ATTTAAACAATAT
48090287 A
1 A
48090288 GTTGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAACAATAT
Found at i:48091854 original size:23 final size:23
Alignment explanation
Indices: 48091819--48091863 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
48091809 CCTTATTTAA
**
48091819 TTCAAATTGATTAT-AATATTATC
1 TTCAAATAAATTATCAA-ATTATC
48091842 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
48091864 AAAATGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATC
Found at i:48095131 original size:91 final size:92
Alignment explanation
Indices: 48095008--48095203 Score: 265
Period size: 92 Copynumber: 2.1 Consensus size: 92
48094998 TTGATTTTAG
* * *
48095008 TAAATTCATATAAAAACATTTTATTATTAAGAATTTTATGAAA-TT-ATATATCACTATTAAATT
1 TAAATTCATA-AAAAACAATTTATTATCAAGAATTTTATGAAATTTAATAT-TAACTATTAAATT
* *
48095071 ATATTTAAT-ATTAATTATTTTAAATTGTA
64 ATATGTAATAATT-ATTATTTTAAATTATA
*
48095100 TAAATTCATAAAAGAA-AATTTATTATCAAGAATTTTATGAAATTTAATATTAATTATTAAATTA
1 TAAATTCATAAAA-AACAATTTATTATCAAGAATTTTATGAAATTTAATATTAACTATTAAATTA
48095164 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
48095192 CAAATTCATAAA
1 TAAATTCATAAA
48095204 TATAATTTAT
Statistics
Matches: 93, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
91 27 0.29
92 59 0.63
93 7 0.08
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TAAATTCATAAAAAACAATTTATTATCAAGAATTTTATGAAATTTAATATTAACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:48095179 original size:24 final size:25
Alignment explanation
Indices: 48095144--48095191 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
48095134 TTATGAAATT
48095144 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
48095168 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
48095192 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:48095344 original size:66 final size:63
Alignment explanation
Indices: 48095269--48095479 Score: 183
Period size: 66 Copynumber: 3.4 Consensus size: 63
48095259 AAATATATTT
48095269 AATATTAATTATTTCAAATTTTCATTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTTT-ATTTACAGTATCATATATTATGATTTGAGTAAATT-ATATAA
48095334 G
63 G
* * * * **
48095335 AATATTAATTATTAAGAATTTTA-TTA-A--ATTATATATT-TTAATT-A-T-AA-TATAT-TT
1 AATATTAATTATTTA-AATTTTATTTACAGTATCATATATTATGATTTGAGTAAATTATATAAG
* *
48095389 AATAATAATTATGTT-AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTTGTATA
1 AATATTAATTAT-TTAAATTT-TA-TTTACAGTATCATATATTATGATTTGAGTAAA-TTATATA
48095453 AG
62 AG
*
48095455 AATATTAATTATTAAGAATTTTATT
1 AATATTAATTATTTA-AATTTTATT
48095480 AAATTATATA
Statistics
Matches: 112, Mismatches: 16, Indels: 35
0.69 0.10 0.21
Matches are distributed among these distances:
53 5 0.04
54 13 0.12
55 5 0.04
56 4 0.04
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 3 0.03
64 3 0.03
65 9 0.08
66 32 0.29
67 5 0.04
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (63 bp):
AATATTAATTATTTAAATTTTATTTACAGTATCATATATTATGATTTGAGTAAATTATATAAG
Found at i:48095369 original size:120 final size:120
Alignment explanation
Indices: 48095238--48095523 Score: 479
Period size: 120 Copynumber: 2.4 Consensus size: 120
48095228 TTAAATTATT
* * *
48095238 TTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA-TTTACAG
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTAT-ATTTTACAG
48095300 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
63 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
48095358 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
**
48095423 CATATATTATGATTTGAGTAAATTTGTATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
48095478 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
48095524 TAAATATGAT
Statistics
Matches: 158, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
119 6 0.04
120 150 0.95
121 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTA
Found at i:48095391 original size:15 final size:15
Alignment explanation
Indices: 48095356--48095407 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
48095346 TTAAGAATTT
*
48095356 TATTAAATTAT-ATA
1 TATTTAATTATAATA
48095370 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
48095384 TATTTAATAATAAT-
1 TATTTAATTATAATA
48095398 TATGTTAATT
1 TAT-TTAATT
48095408 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:48095506 original size:16 final size:16
Alignment explanation
Indices: 48095485--48095526 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
48095475 TTATTAAATT
*
48095485 ATATATTTTAATTATA
1 ATATATTTTAATAATA
48095501 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
48095516 AT-TATGTTTAA
1 ATATAT-TTTAA
48095527 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:48095511 original size:15 final size:15
Alignment explanation
Indices: 48095476--48095517 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48095466 TTAAGAATTT
*
48095476 TATTAAATTAT-ATA
1 TATTTAATTATAATA
48095490 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
48095504 TATTTAATAATAAT
1 TATTTAATTATAAT
48095518 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:48095637 original size:156 final size:157
Alignment explanation
Indices: 48095460--48095775 Score: 589
Period size: 156 Copynumber: 2.0 Consensus size: 157
48095450 ATAAGAATAT
*
48095460 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
48095525 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
48095590 TAATAATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
48095617 TAATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
48095681 AAATATGATTAAATTATTTATTATTGATAATAATCATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
48095746 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
48095773 TAA
1 TAA
48095776 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
156 149 0.96
157 6 0.04
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:48095656 original size:18 final size:17
Alignment explanation
Indices: 48095628--48095662 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48095618 AATTATAAGA
*
48095628 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
48095645 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
48095663 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:48095906 original size:45 final size:41
Alignment explanation
Indices: 48095808--48095917 Score: 107
Period size: 45 Copynumber: 2.6 Consensus size: 41
48095798 TTTTCCATTA
48095808 TGCTATTACACCTCTATTCCATT-C-AACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACAAACCAAACACAAGAT
* * ***
48095847 TACTATTACGCCTCTATTCCATTACATTTAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACA---AACCAAACACAAGA-T
* *
48095892 TGCTATTACACCTCTAATCCAATACA
1 TGCTATTACACCTCTATTCCATTACA
48095918 CCTCTAATCC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
39 21 0.38
40 1 0.02
44 11 0.20
45 23 0.41
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (41 bp):
TGCTATTACACCTCTATTCCATTACAAACCAAACACAAGAT
Found at i:48095919 original size:16 final size:16
Alignment explanation
Indices: 48095898--48095933 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
48095888 GATTTGCTAT
48095898 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
48095914 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
48095930 TACA
1 TACA
48095934 GCAACCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:48097931 original size:35 final size:35
Alignment explanation
Indices: 48097903--48097978 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
48097893 TGTCTCACTG
*
48097903 AAGGGCCTATAAACCGTTTACACAGTGTCGCCTCA
1 AAGGACCTATAAACCGTTTACACAGTGTCGCCTCA
* ** *
48097938 AAGGACCTATAAATCGTTTACATGGTGTCGCCTTA
1 AAGGACCTATAAACCGTTTACACAGTGTCGCCTCA
48097973 AAGGAC
1 AAGGAC
48097979 AAGTCAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (35 bp):
AAGGACCTATAAACCGTTTACACAGTGTCGCCTCA
Found at i:48109282 original size:3 final size:3
Alignment explanation
Indices: 48109268--48109315 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
48109258 AAGGGCCCAA
* * * *
48109268 ATT ATC ATT ATT ATT ATT ACT ATT AAT ATT ATT ATT AAAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
48109314 AT
1 AT
48109316 CTTTTTTTAC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:48109310 original size:13 final size:12
Alignment explanation
Indices: 48109274--48109315 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
48109264 CCAAATTATC
*
48109274 ATTATTATTATT
1 ATTATTAATATT
*
48109286 ACTATTAATATT
1 ATTATTAATATT
48109298 ATTATTAAATATT
1 ATTATT-AATATT
48109311 ATTAT
1 ATTAT
48109316 CTTTTTTTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTATTAATATT
Found at i:48109905 original size:153 final size:151
Alignment explanation
Indices: 48109661--48110127 Score: 656
Period size: 153 Copynumber: 3.0 Consensus size: 151
48109651 GATTTTTATT
*
48109661 AAAAAGAGAAAATTTAGATTTTAAAAATAAAAATATGTTTTTTAAGTCATTTTAAAGGAAAATTT
1 AAAAAGAGAAAATTTAGATTTTAAAAATAAAAATATGTTTTTT-AGTCATTTTAAAGGAAAGTTT
* *
48109726 AAAAATTTAAAACAAAATTTTGATTTTTTTCAACTATTTCAATATAAAAGCTTTGATCTTTAAGA
65 -AAAATTTAAAACAAATTTTTTATTTTTTTCAACTATTTCAA-ATAAAAGCTTTGATCTTTAAGA
48109791 AAAGTAGTGATTTTTTT-AAGAAA
128 AAAGTAGTGATTTTTTTAAAGAAA
* *
48109814 AAAAAGGAGAAAATTTAAATTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAGGAAAGTTT
1 AAAAA-GAGAAAATTTAGATTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAGTTT
* *
48109879 AAAATTTTAAAACAAATTTTTTATTTTTTTCAACTATTTCAAAATAAAAGTTTTTATCTTTAAGA
65 AAAA-TTTAAAACAAATTTTTTATTTTTTTCAACTATTTC-AAATAAAAGCTTTGATCTTTAAGA
48109944 AAAGTAGTGATTATTTTTAAAAGAAAA
128 AAAGTAGTGATT-TTTTT-AAAG-AAA
* * *
48109971 AAAAAGAGGAAGTTTAGATTTTAAAAATAAAAATATGTTTTTTTAGTCCTTTTAAAGGAAAGTTT
1 AAAAAGAGAAAATTTAGATTTTAAAAATAAAAATATG-TTTTTTAGTCATTTTAAAGGAAAGTTT
*
48110036 AAAATTTAAAACAAAGTTTTGATT-TTTTTTTGAACTATTTCGAAAT-AAAGCTTTGATCTTTAA
65 AAAATTTAAAACAAA-TTTT--TTATTTTTTTCAACTATTTC-AAATAAAAGCTTTGATCTTTAA
* *
48110099 GAAAAGTATTGA--TTTTTAAAAAAA
126 GAAAAGTAGTGATTTTTTTAAAGAAA
48110123 AAAAA
1 AAAAA
48110128 CTTTGACTTT
Statistics
Matches: 285, Mismatches: 18, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
152 12 0.04
153 92 0.32
154 49 0.17
156 43 0.15
157 67 0.24
158 20 0.07
159 2 0.01
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (151 bp):
AAAAAGAGAAAATTTAGATTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAGTTTA
AAATTTAAAACAAATTTTTTATTTTTTTCAACTATTTCAAATAAAAGCTTTGATCTTTAAGAAAA
GTAGTGATTTTTTTAAAGAAA
Found at i:48110133 original size:23 final size:24
Alignment explanation
Indices: 48110107--48110151 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
48110097 AAGAAAAGTA
* *
48110107 TTGATTTTTAAAAAA-AAAAAACT
1 TTGACTTTGAAAAAATAAAAAACT
48110130 TTGACTTTGAAAAAATAAAAAA
1 TTGACTTTGAAAAAATAAAAAA
48110152 ATAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (24 bp):
TTGACTTTGAAAAAATAAAAAACT
Found at i:48113967 original size:33 final size:33
Alignment explanation
Indices: 48113892--48113994 Score: 120
Period size: 33 Copynumber: 3.1 Consensus size: 33
48113882 CAATGAACTT
* * * *
48113892 GAGCCGGGAGGAGTGGAGTACAGCGGTGGATAC
1 GAGCCGGAAGGAGCGGAGTACTGAGGTGGATAC
*
48113925 -AGGCTGGAAGGAGCGGAGTACTGAGGTGGATAC
1 GA-GCCGGAAGGAGCGGAGTACTGAGGTGGATAC
*
48113958 GAGCCGGAAGGTA-CGGACTACTGAGGTGGATAC
1 GAGCCGGAAGG-AGCGGAGTACTGAGGTGGATAC
48113991 GAGC
1 GAGC
48113995 TACGATGACT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
32 1 0.02
33 57 0.95
34 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.45, T:0.14
Consensus pattern (33 bp):
GAGCCGGAAGGAGCGGAGTACTGAGGTGGATAC
Found at i:48117017 original size:60 final size:60
Alignment explanation
Indices: 48116933--48117047 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
48116923 ATACTAAACT
** * *
48116933 AAACACACCAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATATTTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATATTTAC
* *
48116993 AAACACAAAAATTTGTAACATAATCCTAAATTACTAACGAATTAATTTTAAAATA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATA
48117048 ATTATAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATATTTAC
Found at i:48117126 original size:7 final size:7
Alignment explanation
Indices: 48117116--48117141 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48117106 ACTAAACATA
48117116 AATAATT
1 AATAATT
48117123 AATAATT
1 AATAATT
48117130 AATAATT
1 AATAATT
48117137 AATAA
1 AATAA
48117142 CAAAAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATAATT
Found at i:48117238 original size:3 final size:3
Alignment explanation
Indices: 48117230--48117285 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
48117220 CTTTCTTTCT
* *
48117230 TTC TTC TTC TTC TTC TTC TTC -TC TTC TTT TTT TTC TTC -TC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
48117275 TCTC TT- TTC TT
1 T-TC TTC TTC TT
48117286 TCTCTCTTCC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
2 8 0.17
3 35 0.76
4 3 0.07
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:48117254 original size:20 final size:18
Alignment explanation
Indices: 48117225--48117294 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 18
48117215 TTTTTCTTTC
48117225 TTTCTTTCTTCTTCTTCT
1 TTTCTTTCTTCTTCTTCT
48117243 TCTTCTTCTCTTCTT-TT-T
1 T-TTCTT-TCTTCTTCTTCT
48117261 TTTCTTCTCTT-TTCTCTCT
1 TTTCTT-TCTTCTTCT-TCT
48117280 TTTCTTTCTCTCTTC
1 TTTCTTTCT-TCTTC
48117295 CGGTGGATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.04
17 11 0.24
18 7 0.16
19 15 0.33
20 10 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTCTTTCTTCTTCTTCT
Found at i:48124050 original size:33 final size:33
Alignment explanation
Indices: 48123999--48124067 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
48123989 TATCGAATCT
* * *
48123999 ACTTCCTCTAAAGCATACCTGTTAGTTTACTTC
1 ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
48124032 ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
1 ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
48124065 ACT
1 ACT
48124068 ATTTGCTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.36
Consensus pattern (33 bp):
ACTTCCCCCAAAGAATACCTGTTAGTTTACTTC
Found at i:48124981 original size:14 final size:14
Alignment explanation
Indices: 48124962--48125001 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
48124952 TTGATTGGCT
48124962 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
48124976 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
48124990 GGAAAATGTTTT
1 GTAAAATGTTTT
48125002 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:48125014 original size:34 final size:35
Alignment explanation
Indices: 48124970--48125036 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
48124960 CTGTAAAATG
* *
48124970 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
48125004 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
48125037 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:48125023 original size:20 final size:20
Alignment explanation
Indices: 48124985--48125024 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
48124975 CGTAAAATGA
**
48124985 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
48125005 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
48125025 GGAAAATATT
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:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:48132629 original size:25 final size:23
Alignment explanation
Indices: 48132598--48132653 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 23
48132588 AATTAACATG
48132598 AATTATTTTAAATATATAATATAT
1 AATTATTTTAAATATATAA-ATAT
*
48132622 AATATATTTTAAATATTTAAATAT
1 AAT-TATTTTAAATATATAAATAT
48132646 AATTATTT
1 AATTATTT
48132654 GTAATTAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 5 0.17
24 10 0.33
25 15 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTATTTTAAATATATAAATAT
Found at i:48136556 original size:30 final size:30
Alignment explanation
Indices: 48136520--48136577 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
48136510 GACCATGCCA
48136520 GTCATAGCAAATTGGTACTTATGGTCTTAT
1 GTCATAGCAAATTGGTACTTATGGTCTTAT
48136550 GTCATAGCAAATTGGTACTTATGGTCTT
1 GTCATAGCAAATTGGTACTTATGGTCTT
48136578 GTACAAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (30 bp):
GTCATAGCAAATTGGTACTTATGGTCTTAT
Found at i:48138036 original size:18 final size:18
Alignment explanation
Indices: 48137998--48138041 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
48137988 GCTTCGAAAC
* **
48137998 GGGAAAGGGAAGGGGTGG
1 GGGAAAGGGAAGGAGAAG
48138016 GGGAAAGGGAAGGAGAAG
1 GGGAAAGGGAAGGAGAAG
48138034 GGGAAAGG
1 GGGAAAGG
48138042 AGAGAAGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.61, T:0.02
Consensus pattern (18 bp):
GGGAAAGGGAAGGAGAAG
Found at i:48138645 original size:15 final size:15
Alignment explanation
Indices: 48138625--48138656 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
48138615 TCAAATCAAG
48138625 ATGTGAGAGCCTGAT
1 ATGTGAGAGCCTGAT
48138640 ATGTGAGAGCCTGAT
1 ATGTGAGAGCCTGAT
48138655 AT
1 AT
48138657 TCTCAAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.28
Consensus pattern (15 bp):
ATGTGAGAGCCTGAT
Found at i:48149287 original size:22 final size:21
Alignment explanation
Indices: 48149262--48149310 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
48149252 AAGAATGCCC
48149262 AACAACTAATCCTTACCAAAGG
1 AACAAC-AATCCTTACCAAAGG
* * *
48149284 AACAACCATGCTTACCTAAGG
1 AACAACAATCCTTACCAAAGG
48149305 AACAAC
1 AACAAC
48149311 CACGAAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.45, C:0.29, G:0.10, T:0.16
Consensus pattern (21 bp):
AACAACAATCCTTACCAAAGG
Found at i:48149299 original size:21 final size:21
Alignment explanation
Indices: 48149273--48149312 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
48149263 ACAACTAATC
48149273 CTTACCAAAGGAACAACCATG
1 CTTACCAAAGGAACAACCATG
*
48149294 CTTACCTAAGGAACAACCA
1 CTTACCAAAGGAACAACCA
48149313 CGAAACATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.30, G:0.12, T:0.15
Consensus pattern (21 bp):
CTTACCAAAGGAACAACCATG
Found at i:48149763 original size:20 final size:22
Alignment explanation
Indices: 48149729--48149768 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
48149719 CAAAATTAAA
*
48149729 AAAAAAATATTAATT-AAAACT
1 AAAAAAATATAAATTGAAAACT
48149750 AAAAAAATA-AAATTGAAAA
1 AAAAAAATATAAATTGAAAA
48149769 GAAAATGCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (22 bp):
AAAAAAATATAAATTGAAAACT
Found at i:48150399 original size:12 final size:11
Alignment explanation
Indices: 48150372--48150405 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
48150362 TATATATATT
48150372 TAAAAATAATA
1 TAAAAATAATA
48150383 TAAAAATAATA
1 TAAAAATAATA
48150394 TAAAAATTAATA
1 TAAAAA-TAATA
48150406 CGGGTGGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:48153004 original size:30 final size:30
Alignment explanation
Indices: 48152969--48153095 Score: 148
Period size: 30 Copynumber: 4.3 Consensus size: 30
48152959 CAAAAAATAA
*
48152969 AAAATTGCATTTTGACCCCTAAATTTTTTT
1 AAAATTACATTTTGACCCCTAAATTTTTTT
* * *
48152999 AAAATTATATTTTGACCCCTAAACTTGTTT
1 AAAATTACATTTTGACCCCTAAATTTTTTT
* * *
48153029 AAAATTACATTTTAACCCATAAA-ATTTTT
1 AAAATTACATTTTGACCCCTAAATTTTTTT
* * * *
48153058 AAAATTACGTTTTGACCCCAAAATTTTCTC
1 AAAATTACATTTTGACCCCTAAATTTTTTT
48153088 AAAATTAC
1 AAAATTAC
48153096 GTTTAGATAC
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
29 23 0.29
30 57 0.71
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAAATTTTTTT
Found at i:48153092 original size:59 final size:60
Alignment explanation
Indices: 48152969--48153095 Score: 152
Period size: 59 Copynumber: 2.1 Consensus size: 60
48152959 CAAAAAATAA
* * * * * *
48152969 AAAATTGCATTTTGACCCCTAAATTTTTTTAAAATTATATTTTGACCCCTAAACTTGTTT
1 AAAATTACATTTTAACCCATAAATATTTTTAAAATTACATTTTGACCCCTAAAATTGTTT
*
48153029 AAAATTACATTTTAACCCATAAA-ATTTTTAAAATTACGTTTTGACCCC-AAAATT-TTCT
1 AAAATTACATTTTAACCCATAAATATTTTTAAAATTACATTTTGACCCCTAAAATTGTT-T
48153087 CAAAATTAC
1 -AAAATTAC
48153096 GTTTAGATAC
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
57 2 0.03
58 6 0.10
59 30 0.52
60 20 0.34
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (60 bp):
AAAATTACATTTTAACCCATAAATATTTTTAAAATTACATTTTGACCCCTAAAATTGTTT
Found at i:48153376 original size:30 final size:30
Alignment explanation
Indices: 48153341--48153496 Score: 161
Period size: 30 Copynumber: 5.2 Consensus size: 30
48153331 CAAAAAATAA
*
48153341 AAAATTGCATTTTGACCCCTAAATTTTTTT
1 AAAATTACATTTTGACCCCTAAATTTTTTT
* * *
48153371 AAAATTATATTTTGACCCCTAAACTTGTTT
1 AAAATTACATTTTGACCCCTAAATTTTTTT
* * *
48153401 AAAATTACATTTTAACCCATAAA-ATTTTT
1 AAAATTACATTTTGACCCCTAAATTTTTTT
* * * *
48153430 AAAATTACGTTTTGACCCCAAAATTTTCTC
1 AAAATTACATTTTGACCCCTAAATTTTTTT
* * **
48153460 AAAATTACGTTTAGACCCCATAAATTTTACT
1 AAAATTACATTTTGACCCC-TAAATTTTTTT
48153491 AAAATT
1 AAAATT
48153497 GCAATTTAGT
Statistics
Matches: 103, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
29 23 0.22
30 67 0.65
31 13 0.13
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAAATTTTTTT
Found at i:48153464 original size:59 final size:60
Alignment explanation
Indices: 48153341--48153484 Score: 152
Period size: 59 Copynumber: 2.4 Consensus size: 60
48153331 CAAAAAATAA
* * * * * *
48153341 AAAATTGCATTTTGACCCCTAAATTTTTTTAAAATTATATTTTGACCCCTAAACTTGTTT
1 AAAATTACATTTTAACCCATAAATATTTTTAAAATTACATTTTGACCCCTAAAATTGTTT
*
48153401 AAAATTACATTTTAACCCATAAA-ATTTTTAAAATTACGTTTTGACCCC-AAAATT-TTCT
1 AAAATTACATTTTAACCCATAAATATTTTTAAAATTACATTTTGACCCCTAAAATTGTT-T
*
48153459 CAAAATTAC-GTTTAGACCCCATAAAT
1 -AAAATTACATTTTA-A-CCCATAAAT
48153485 TTTACTAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
57 2 0.03
58 10 0.14
59 31 0.44
60 28 0.39
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.40
Consensus pattern (60 bp):
AAAATTACATTTTAACCCATAAATATTTTTAAAATTACATTTTGACCCCTAAAATTGTTT
Found at i:48154474 original size:37 final size:37
Alignment explanation
Indices: 48154433--48154522 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 37
48154423 TTCAAAAAAA
*
48154433 TTCGTATTTTCAAAAAAAAACCTCGGGTTTCGAAATT
1 TTCGTATTTTCAAAAAAAAACCTCGGGTTTCAAAATT
* * ***** *
48154470 TTCGTGTCTTCAAAAATTTTTCTCGTGTTTCAAAATT
1 TTCGTATTTTCAAAAAAAAACCTCGGGTTTCAAAATT
*
48154507 CTCGTATTTTCAAAAA
1 TTCGTATTTTCAAAAA
48154523 TAAGGCAACG
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (37 bp):
TTCGTATTTTCAAAAAAAAACCTCGGGTTTCAAAATT
Found at i:48154510 original size:16 final size:17
Alignment explanation
Indices: 48154489--48154521 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
48154479 TCAAAAATTT
48154489 TTCTCGT-GTTTCAAAA
1 TTCTCGTAGTTTCAAAA
*
48154505 TTCTCGTATTTTCAAAA
1 TTCTCGTAGTTTCAAAA
48154522 ATAAGGCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (17 bp):
TTCTCGTAGTTTCAAAA
Found at i:48154720 original size:17 final size:17
Alignment explanation
Indices: 48154678--48154947 Score: 231
Period size: 17 Copynumber: 15.4 Consensus size: 17
48154668 TTCCATTTTC
* *
48154678 CAAAATTTTTCGTGTCTT
1 CAAAAATTTCCGTGT-TT
48154696 CTAAAAATTTCCGTGTTT
1 C-AAAAATTTCCGTGTTT
* *
48154714 CAAAAATTTTCTTGTTTT
1 CAAAAATTTCCGTG-TTT
*
48154732 CAAAAATTTCTGTGTTT
1 CAAAAATTTCCGTGTTT
*
48154749 CAAAAATTTTCGTGTTTT
1 CAAAAATTTCCGTG-TTT
* *
48154767 CAAAATTTTGCGTGTTT
1 CAAAAATTTCCGTGTTT
**
48154784 CAAAAATTTTGGTGTTTT
1 CAAAAATTTCCGTG-TTT
48154802 CAAAAA-TTCCGGTGTTT
1 CAAAAATTTCC-GTGTTT
*
48154819 CAAAAAATTCCCGTGTTT
1 C-AAAAATTTCCGTGTTT
*
48154837 TAAAAATTTCCGTGTTTT
1 CAAAAATTTCCGTG-TTT
*
48154855 C-AAAATTTTCGTGTTTT
1 CAAAAATTTCCGTG-TTT
* * *
48154872 CAAAATTTTTCGTATTT
1 CAAAAATTTCCGTGTTT
*
48154889 CAAAAA-TCCTCGTGTTTT
1 CAAAAATTTC-CGTG-TTT
*
48154907 CAAAAATTTCGGTGTTT
1 CAAAAATTTCCGTGTTT
* *
48154924 TAAAAATTTTCGTGTTTT
1 CAAAAATTTCCGTG-TTT
48154942 CAAAAA
1 CAAAAA
48154948 AAAAATCTAG
Statistics
Matches: 206, Mismatches: 33, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
16 1 0.00
17 99 0.48
18 89 0.43
19 17 0.08
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (17 bp):
CAAAAATTTCCGTGTTT
Found at i:48154747 original size:35 final size:35
Alignment explanation
Indices: 48154678--48154947 Score: 339
Period size: 35 Copynumber: 7.7 Consensus size: 35
48154668 TTCCATTTTC
* *
48154678 CAAAATTTTTCGTGTCTTCTAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAATTTCCGTGTTT
* *
48154714 CAAAAATTTTCTTGTTTTCAAAAATTTCTGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
* *
48154749 CAAAAATTTTCGTGTTTTCAAAATTTTGCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
*
48154784 CAAAAATTTTGGTGTTTTCAAAAA-TTCCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCC-GTGTTT
**
48154819 CAAAAAATTCCCGTGTTTT-AAAAATTTCCGTGTTTT
1 C-AAAAATTTTCGTGTTTTCAAAAATTTCCGTG-TTT
* * *
48154855 C-AAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
** *
48154889 CAAAAATCCTCGTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
*
48154924 TAAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
48154948 AAAAATCTAG
Statistics
Matches: 200, Mismatches: 28, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
34 21 0.10
35 141 0.70
36 38 0.19
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (35 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTT
Found at i:48155883 original size:17 final size:17
Alignment explanation
Indices: 48155844--48155887 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
48155834 TTTATTGCTC
*
48155844 TATTAACTAT-TAAAAT
1 TATTAAATATATAAAAT
48155860 T-TTAAATATATAAAAT
1 TATTAAATATATAAAAT
48155876 TATTAAATATAT
1 TATTAAATATAT
48155888 TTAAAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 8 0.32
17 10 0.40
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTAAATATATAAAAT
Found at i:48155892 original size:19 final size:17
Alignment explanation
Indices: 48155851--48155894 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
48155841 CTCTATTAAC
48155851 TATTAAAATTTTAAATA
1 TATTAAAATTTTAAATA
48155868 TA-TAAAATTATTAAATA
1 TATTAAAATT-TTAAATA
48155885 TATTTAAAAT
1 TA-TTAAAAT
48155895 GAAAGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.29
17 11 0.46
19 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATTAAAATTTTAAATA
Found at i:48158438 original size:122 final size:125
Alignment explanation
Indices: 48158128--48158510 Score: 515
Period size: 122 Copynumber: 3.0 Consensus size: 125
48158118 TTGGGTTAGT
* *
48158128 ACGAATAACATATAAGTTGTTCAAAGTACTAATGGAAAGAAGTCCATCAAATAAATAAGGTCTTG
1 ACGAATAACATATAAG-TGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTG
* * *
48158193 CAAAAGGAATTGCAAATAAGTTGCAATTATGGAATCC-TAGTAGTATTGCAAAAGTTTTCCTTTG
65 C-AAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTA-T-GCA-T-C-AAAG----CC-ATG
* *
48158257 TGTTA-GT
119 T-TCATGA
48158264 ACGAATAACATATAAGTTGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTG
1 ACGAATAACATATAAG-TGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTG
48158329 CAAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTATGCATCAAAGCCATGTTCATGA
65 CAAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTATGCATCAAAGCCATGTTCATGA
* * *
48158390 AC-AAT-GCTTTTAA-TGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTGC
1 ACGAATAACATATAAGTGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTGC
48158452 AAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTATGCATCAAAGCCATGTTCATG
66 AAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTATGCATCAAAGCCATGTTCATG
48158511 TTCAATCCGT
Statistics
Matches: 235, Mismatches: 10, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
122 108 0.46
124 5 0.02
125 5 0.02
126 6 0.03
127 2 0.01
131 4 0.02
132 1 0.00
133 1 0.00
134 2 0.01
135 35 0.15
136 66 0.28
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (125 bp):
ACGAATAACATATAAGTGTTCAAAGTACTAATAGAAAGAAGTCCATCAAATAAATAAGGCCTTGC
AAAGGAATTGCAAATAAATTGCAATTATGGAATCCTTATGCATCAAAGCCATGTTCATGA
Found at i:48169379 original size:25 final size:25
Alignment explanation
Indices: 48169345--48169397 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
48169335 CAAGTGAACA
*
48169345 GTCTGTTCTGACTAGGATAAAATGT
1 GTCTGTTCTGACTAAGATAAAATGT
48169370 GTCTGTTCTGACTAAGATAAAATGT
1 GTCTGTTCTGACTAAGATAAAATGT
48169395 GTC
1 GTC
48169398 GACTTAGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (25 bp):
GTCTGTTCTGACTAAGATAAAATGT
Found at i:48186849 original size:7 final size:7
Alignment explanation
Indices: 48186837--48186863 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
48186827 ATATTTTTTT
48186837 ATTTGAC
1 ATTTGAC
48186844 ATTTGAC
1 ATTTGAC
48186851 ATTTGAC
1 ATTTGAC
48186858 ATTTGA
1 ATTTGA
48186864 ATTATCCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (7 bp):
ATTTGAC
Found at i:48192394 original size:10 final size:10
Alignment explanation
Indices: 48192271--48192399 Score: 71
Period size: 10 Copynumber: 13.4 Consensus size: 10
48192261 CGAAAAAATG
48192271 ATAAAAAT-T
1 ATAAAAATAT
*
48192280 ATTAAAATCA-
1 ATAAAAAT-AT
48192290 ATAAAAATAT
1 ATAAAAATAT
48192300 -TAAAAAT-T
1 ATAAAAATAT
*
48192308 ATAGAATTATAT
1 ATA-AA-AATAT
*
48192320 ATAGAAATAT
1 ATAAAAATAT
48192330 ATAAAAATAT
1 ATAAAAATAT
** *
48192340 AT-TCAATTT
1 ATAAAAATAT
48192349 ATGAAAAAT-T
1 AT-AAAAATAT
*
48192359 ATTAAAAT-T
1 ATAAAAATAT
*
48192368 -TGAAAAT-T
1 ATAAAAATAT
48192376 ACT-AAAATAT
1 A-TAAAAATAT
48192386 ATAAAAATAT
1 ATAAAAATAT
48192396 ATAA
1 ATAA
48192400 TTTTTTTAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 25
0.71 0.10 0.19
Matches are distributed among these distances:
8 8 0.09
9 35 0.37
10 41 0.44
11 6 0.06
12 4 0.04
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:48194400 original size:37 final size:37
Alignment explanation
Indices: 48194359--48194437 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
48194349 TCTCAAGATC
48194359 ATTTAAAACTTGAGTTTGAAAAGATTCGTGCATTTAG
1 ATTTAAAACTTGAGTTTGAAAAGATTCGTGCATTTAG
48194396 ATTTAAAACTTGAGTTTGAAAAGATTCGTGCATTTAG
1 ATTTAAAACTTGAGTTTGAAAAGATTCGTGCATTTAG
48194433 ATTTA
1 ATTTA
48194438 TTGTGAAGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (37 bp):
ATTTAAAACTTGAGTTTGAAAAGATTCGTGCATTTAG
Found at i:48195312 original size:16 final size:17
Alignment explanation
Indices: 48195286--48195318 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
48195276 GAAAATAAAA
48195286 GTAATAAATATATATAT
1 GTAATAAATATATATAT
*
48195303 GTAA-AAATATGTATAT
1 GTAATAAATATATATAT
48195319 ATATATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
GTAATAAATATATATAT
Found at i:48195497 original size:3 final size:3
Alignment explanation
Indices: 48195489--48195533 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
48195479 ATAAGAAATT
* *
48195489 ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48195534 TGAAATTTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:48201923 original size:20 final size:20
Alignment explanation
Indices: 48201906--48201943 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48201896 TTGTAAAATT
48201906 TTATAAAAAT-CATAAAAAAA
1 TTAT-AAAATGCATAAAAAAA
48201926 TTATAAAATGCATAAAAA
1 TTATAAAATGCATAAAAA
48201944 GACCATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
TTATAAAATGCATAAAAAAA
Found at i:48201940 original size:29 final size:28
Alignment explanation
Indices: 48201882--48201943 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
48201872 AAAATATTTA
* **
48201882 AAAAATATAAAAAATTGTAAAATTTTAT
1 AAAAATATAAAAAATTATAAAATTGCAT
48201910 AAAAATCATAAAAAAATTATAAAA-TGCAT
1 AAAAAT-AT-AAAAAATTATAAAATTGCAT
48201939 AAAAA
1 AAAAA
48201944 GACCATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 10 0.34
30 13 0.45
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (28 bp):
AAAAATATAAAAAATTATAAAATTGCAT
Found at i:48202271 original size:29 final size:29
Alignment explanation
Indices: 48202199--48202272 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
48202189 TTATAATTTT
* *
48202199 TTTTTCTAATTTTTAATAAATATTAAGTA
1 TTTTTATAATTTTTATTAAATATTAAGTA
48202228 TTTTTAT-ATTTTTATTAAA-ATTTAA-TAA
1 TTTTTATAATTTTTATTAAATA-TTAAGT-A
48202256 TTTTTATAATTTTTATT
1 TTTTTATAATTTTTATT
48202273 GGTTTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 2 0.05
28 23 0.57
29 15 0.38
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (29 bp):
TTTTTATAATTTTTATTAAATATTAAGTA
Found at i:48205439 original size:54 final size:54
Alignment explanation
Indices: 48205375--48205480 Score: 203
Period size: 54 Copynumber: 2.0 Consensus size: 54
48205365 ACAAAGAGCA
48205375 ATTAATCAAGTCCGACAATGAGTTTTCCAACAAGTTTTACAAGGAGCTCTAGCG
1 ATTAATCAAGTCCGACAATGAGTTTTCCAACAAGTTTTACAAGGAGCTCTAGCG
*
48205429 ATTAATCAAGTTCGACAATGAGTTTTCCAACAAGTTTTACAAGGAGCTCTAG
1 ATTAATCAAGTCCGACAATGAGTTTTCCAACAAGTTTTACAAGGAGCTCTAG
48205481 GAACTTTGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (54 bp):
ATTAATCAAGTCCGACAATGAGTTTTCCAACAAGTTTTACAAGGAGCTCTAGCG
Found at i:48209696 original size:7 final size:7
Alignment explanation
Indices: 48209686--48209717 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
48209676 AATTATAATA
48209686 TATATTT
1 TATATTT
48209693 TATATTT
1 TATATTT
48209700 TATATTT
1 TATATTT
48209707 TATATTAT
1 TATATT-T
48209715 TAT
1 TAT
48209718 TAAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATATTT
Found at i:48210453 original size:43 final size:43
Alignment explanation
Indices: 48210405--48210607 Score: 157
Period size: 43 Copynumber: 4.7 Consensus size: 43
48210395 AAATAAACGT
48210405 CGCTATAGACCATA-ACCTTTAGCGGCGCTTCTACAACAAAAGC
1 CGCTATAGACCA-AGACCTTTAGCGGCGCTTCTACAACAAAAGC
* * * * *
48210448 CGCTATAG-CTCAAGACCTTTAGCGGCGGTTTTCCCACAAACGC
1 CGCTATAGAC-CAAGACCTTTAGCGGCGCTTCTACAACAAAAGC
* * * * ***
48210491 CACTGTAGATCAAGACCTTTAGCGGCGCTTTTTTTACAAACA-C
1 CGCTATAGACCAAGACCTTTAGCGGCGCTTCTACAACAAA-AGC
* * * *
48210534 CGCTATCGA-TAAGACCTTTTAGCGGCGCTTATATAA-AAAACGC
1 CGCTATAGACCAAGACC-TTTAGCGGCGCTTCTACAACAAAA-GC
* *
48210577 CGCTATAGAACAA-ACCTTTAGCGACGCTTCT
1 CGCTATAGACCAAGACCTTTAGCGGCGCTTCT
48210608 TGCAAAAACG
Statistics
Matches: 128, Mismatches: 24, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
41 1 0.01
42 24 0.19
43 101 0.79
44 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
CGCTATAGACCAAGACCTTTAGCGGCGCTTCTACAACAAAAGC
Found at i:48211496 original size:45 final size:45
Alignment explanation
Indices: 48211438--48211539 Score: 186
Period size: 45 Copynumber: 2.3 Consensus size: 45
48211428 CCCACTATCA
48211438 CCACATAAAGGTAATTAACTCAATAAGACATACTCAAACAATTAG
1 CCACATAAAGGTAATTAACTCAATAAGACATACTCAAACAATTAG
* *
48211483 CCACATAATGGTAATTAACTCAATAAGGCATACTCAAACAATTAG
1 CCACATAAAGGTAATTAACTCAATAAGACATACTCAAACAATTAG
48211528 CCACATAAAGGT
1 CCACATAAAGGT
48211540 TTAACATTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.23
Consensus pattern (45 bp):
CCACATAAAGGTAATTAACTCAATAAGACATACTCAAACAATTAG
Found at i:48220026 original size:45 final size:45
Alignment explanation
Indices: 48219962--48220459 Score: 687
Period size: 45 Copynumber: 11.1 Consensus size: 45
48219952 TTCAGAGAAC
48219962 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
48220007 AGATCGAGGATAGCAGATCTTGTCTTCCTGTATTAGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
48220052 AGATCGAGGATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
48220097 AGATCGAGGATAGCAGATTTTGTCTTCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
48220142 AGATCGAAGATAGCAGATTTTGT-ATCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * *
48220186 AGATCGAGGATAGCAAATCTTGTCTTCCAGTATTGGCAGCGAAAT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
*
48220231 AGATCGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
*
48220276 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGTAGCGAAGT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
** *
48220321 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAAGC
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * * * ** * * *
48220366 AGATCGAAGACACCAG-CCTTGCCTTTCTGTGCTGACAACGAAGC
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * *
48220410 AGA-CTGAAGATAGCAGATCATGCCTTCCTGTACTGGCAGCGAAGC
1 AGATC-GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
48220455 AGATC
1 AGATC
48220460 AAAAAACAAC
Statistics
Matches: 407, Mismatches: 42, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
43 1 0.00
44 71 0.17
45 334 0.82
46 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (45 bp):
AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
Found at i:48220263 original size:179 final size:180
Alignment explanation
Indices: 48219962--48220359 Score: 681
Period size: 179 Copynumber: 2.2 Consensus size: 180
48219952 TTCAGAGAAC
*
48219962 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAGATCT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAAATCT
* * * * *
48220027 TGTCTTCCTGTATTAGCAGCGAAGTAGATCGAGGATAGTAGATCTTGTCTTCCTGTATTGGCAGC
66 TGTCTTCCAGTATTAGCAGCGAAATAGATCGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGC
* *
48220092 GAAGTAGATCGAGGATAGCAGATTTTGTCTTCCTGTATTGGCAGCGAAGT
131 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* *
48220142 AGATCGAAGATAGCAGATTTTGT-ATCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAAATCT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAAATCT
*
48220206 TGTCTTCCAGTATTGGCAGCGAAATAGATCGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGC
66 TGTCTTCCAGTATTAGCAGCGAAATAGATCGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGC
*
48220271 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGTAGCGAAGT
131 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
48220321 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAG
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAG
48220360 TAAAGCAGAT
Statistics
Matches: 203, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
179 167 0.82
180 36 0.18
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (180 bp):
AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAAATCT
TGTCTTCCAGTATTAGCAGCGAAATAGATCGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGC
GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
Found at i:48220352 original size:224 final size:224
Alignment explanation
Indices: 48219962--48220375 Score: 693
Period size: 224 Copynumber: 1.8 Consensus size: 224
48219952 TTCAGAGAAC
* * * * *
48219962 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAGATCT
1 AGATCGAAGATAGCAAATCTTGTCTTCCAGTATTGGCAGCGAAATAGATCGAAGATAGCAAATCT
* *
48220027 TGTCTTCCTGTATTAGCAGCGAAGTAGATCGAGGATAGTAGATCTTGTCTTCCTGTATTGGCAGC
66 TGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGC
* * * *
48220092 GAAGTAGATCGAGGATAGCAGATTTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCA
131 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGATAGCA
48220157 GATTTTGTATCCTGTATTGGCAGCGAAGT
196 GATTTTGTATCCTGTATTGGCAGCGAAGT
*
48220186 AGATCGAGGATAGCAAATCTTGTCTTCCAGTATTGGCAGCGAAATAGATCGAAGATAGCAAATCT
1 AGATCGAAGATAGCAAATCTTGTCTTCCAGTATTGGCAGCGAAATAGATCGAAGATAGCAAATCT
* *
48220251 TGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGTAGC
66 TGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGC
*
48220316 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAAGCAGATCGAAGA
131 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGA
48220376 CACCAGCCTT
Statistics
Matches: 175, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
224 175 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (224 bp):
AGATCGAAGATAGCAAATCTTGTCTTCCAGTATTGGCAGCGAAATAGATCGAAGATAGCAAATCT
TGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGC
GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGATAGCA
GATTTTGTATCCTGTATTGGCAGCGAAGT
Found at i:48220421 original size:134 final size:134
Alignment explanation
Indices: 48219962--48220459 Score: 651
Period size: 134 Copynumber: 3.7 Consensus size: 134
48219952 TTCAGAGAAC
* *
48219962 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAGATCT
1 AGATCGAAGATACCAG-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCT
* *
48220027 TGTCTTCCTGTATTAGCAGCGAAGTAGATCGAGGATAGTAGATCTTGTCTTCCTGTATTGGCAGC
65 TGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAGATCTTGTCTTCCTGTATTGGCAGC
*
48220092 GAAGT
130 AAAGT
* * * *
48220097 AGATCGAGGATAGCAGATTTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATTT
1 AGATCGAAGATACCAG-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCT
* * *
48220162 TGT-ATCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAAATCTTGTCTTCCAGTATTGGCAGC
65 TGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAGATCTTGTCTTCCTGTATTGGCAGC
48220226 GAAA-T
130 -AAAGT
* *
48220231 AGATCGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCT
1 AGATCGAAGATA-CCAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCT
* * *
48220296 TGTCTTCCTGTATTGGTAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGT
65 TGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAGATCTTGTCTTCCTGTATTGGCAGC
*
48220361 AAAGC
130 AAAGT
* * * * ** * * * *
48220366 AGATCGAAGACACCAGCCTTGCCTTTCTGTGCTGACAACGAAGCAGA-CTGAAGATAGCAGATCA
1 AGATCGAAGATACCAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGCAGATCT
* * *
48220430 TGCCTTCCTGTACTGGCAGCGAAGCAGATC
65 TGTCTTCCTGTATTGGCAGCGAAGTAGATC
48220460 AAAAAACAAC
Statistics
Matches: 319, Mismatches: 39, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
133 1 0.00
134 185 0.58
135 133 0.42
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (134 bp):
AGATCGAAGATACCAGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTT
GTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAGATCTTGTCTTCCTGTATTGGCAGCA
AAGT
Found at i:48220421 original size:179 final size:178
Alignment explanation
Indices: 48219962--48220459 Score: 658
Period size: 179 Copynumber: 2.8 Consensus size: 178
48219952 TTCAGAGAAC
*
48219962 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAGATCT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATACCAG-TCT
* * *
48220027 TGTCTTCCTGTATTAGCAGCGAAGTAGATCGAGGATAGTAGATCTTGTCTTCCTGTATTGGCAGC
65 TGTCTTCCTGTATGA-CAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGC
* *
48220092 GAAGTAGATCGAGGATAGCAGATTTTGTCTTCCTGTATTGGCAGCGAAGT
129 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
* * * *
48220142 AGATCGAAGATAGCAGATTTTGT-ATCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAAATCT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATA-CCAGTCT
* * * *
48220206 TGTCTTCCAGTATTGGCAGCGAAATAGATCGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGC
65 TGTCTTCCTGTA-TGACAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGC
*
48220271 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGTAGCGAAGT
129 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
** * * * *
48220321 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAAGCAGATCGAAGACACCAGCCTT
1 AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATACCAGTCTT
* * * * * * * *
48220386 GCCTTTCTGTGCTGACAACGAAGCAGA-CTGAAGATAGCAGATCATGCCTTCCTGTACTGGCAGC
66 GTCTTCCTGT-ATGACAGCGAAGTAGATC-GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGC
*
48220450 GAAGCAGATC
129 GAAGTAGATC
48220460 AAAAAACAAC
Statistics
Matches: 275, Mismatches: 38, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
178 1 0.00
179 223 0.81
180 51 0.19
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (178 bp):
AGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATACCAGTCTT
GTCTTCCTGTATGACAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
AGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGT
Found at i:48220424 original size:224 final size:224
Alignment explanation
Indices: 48219961--48220452 Score: 684
Period size: 224 Copynumber: 2.2 Consensus size: 224
48219951 CTTCAGAGAA
* * *
48219961 CAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAGGATAGCAGATC
1 CAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAATAGATCGAAGATAGCAAATC
* *
48220026 TTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAGGATAGTAGATCTTGTCTTCCTGTATTGGCAG
66 TTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAG
* * * * * *
48220091 CGAAGTAGATCGAGGATAGCAGATTTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGC
131 CGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACC
** * * *
48220156 AGATTTTGTATCCTGTATTGGCAGCGAAG
196 AGACCTTGTATCCTGTACTGACAACGAAG
* * * *
48220185 TAGATCGAGGATAGCAAATCTTGTCTTCCAGTATTGGCAGCGAAATAGATCGAAGATAGCAAATC
1 CAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAATAGATCGAAGATAGCAAATC
* *
48220250 TTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGTAG
66 TTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAG
*
48220315 CGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTAAAGCAGATCGAAGACACC
131 CGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACC
* *
48220380 AG-CCTTGCCT-TTCTGTGCTGACAACGAAG
196 AGACCTTG--TATCCTGTACTGACAACGAAG
* * *
48220409 CAGA-CTGAAGATAGCAGATCATGCCTTCCTGTACTGGCAGCGAA
1 CAGATC-GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAA
48220453 GCAGATCAAA
Statistics
Matches: 233, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
223 4 0.02
224 228 0.98
225 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (224 bp):
CAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAATAGATCGAAGATAGCAAATC
TTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAG
CGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACC
AGACCTTGTATCCTGTACTGACAACGAAG
Found at i:48228779 original size:13 final size:13
Alignment explanation
Indices: 48228763--48228812 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
48228753 TTTAAACTAA
*
48228763 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
48228776 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* * *
48228789 ATTTTTCTACAGC
1 ACTTTTCAAAAGC
48228802 ACTTTTCAAAA
1 ACTTTTCAAAA
48228813 ACATTGCGAA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:48228935 original size:3 final size:3
Alignment explanation
Indices: 48228927--48228981 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
48228917 TAAAAGCCTT
48228927 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48228975 ATA ATA A
1 ATA ATA A
48228982 CAGGTTGTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:48230059 original size:23 final size:22
Alignment explanation
Indices: 48230025--48230068 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
48230015 AATTTTTTTT
* *
48230025 AAAAAATCAAAAGCAAAATTTC
1 AAAAAATAAAAAGAAAAATTTC
*
48230047 AAAAAATTAAAAATAAAAATTT
1 AAAAAA-TAAAAAGAAAAATTT
48230069 TCAAGGTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAAAATAAAAAGAAAAATTTC
Found at i:48232696 original size:26 final size:27
Alignment explanation
Indices: 48232667--48232735 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
48232657 CGATATATGA
48232667 CTCTTCGTGAGCTTCCCGATTAA-AGG
1 CTCTTCGTGAGCTTCCCGATTAATAGG
** * * *
48232693 CTCTTTATGAGCATCCTGATTAATTGG
1 CTCTTCGTGAGCTTCCCGATTAATAGG
*
48232720 CT-TGCGTGAGCTTCCC
1 CTCTTCGTGAGCTTCCC
48232736 TATATGGCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (27 bp):
CTCTTCGTGAGCTTCCCGATTAATAGG
Found at i:48232763 original size:23 final size:23
Alignment explanation
Indices: 48232717--48232763 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
48232707 CCTGATTAAT
* *
48232717 TGGCTTGCGTGAGCTTCCCTATA
1 TGGCTTGCGTGAACTTCCCGATA
* *
48232740 TGGCTTGCTTGAACTTCTCGATA
1 TGGCTTGCGTGAACTTCCCGATA
48232763 T
1 T
48232764 ATGGCTATCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (23 bp):
TGGCTTGCGTGAACTTCCCGATA
Found at i:48232831 original size:74 final size:73
Alignment explanation
Indices: 48232702--48232842 Score: 162
Period size: 74 Copynumber: 1.9 Consensus size: 73
48232692 GCTCTTTATG
* * * *
48232702 AGCATCCTGATTAATTGGCTTGCGTGAGCTTCCCTATATGGCTTGCTTGAACTTCTCGATATATG
1 AGCATCCTGATTAATTGGCTTGCGAGAGCTTCCCTATATGGCTCGCATGAACTTCTCAAT-TATG
48232767 GCTATCCAA
65 GCTATCCAA
* * *
48232776 AGCATCCTGATTAA-TGGCTCTTC-AGAGCTGTCCGT-TACTGGCTCGCATGAGCTTCTCAATTA
1 AGCATCCTGATTAATTGGCT-TGCGAGAGCT-TCCCTATA-TGGCTCGCATGAACTTCTCAATTA
48232838 TGGCT
63 TGGCT
48232843 CGCATGAGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
73 19 0.33
74 38 0.67
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (73 bp):
AGCATCCTGATTAATTGGCTTGCGAGAGCTTCCCTATATGGCTCGCATGAACTTCTCAATTATGG
CTATCCAA
Found at i:48240751 original size:23 final size:25
Alignment explanation
Indices: 48240711--48240763 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
48240701 TCTGATTAAT
*
48240711 TGGCTCGCATAAGCTTCCC-A-ATA
1 TGGCTCGCATAAACTTCCCGATATA
* *
48240734 TGGCTCGCTTAAATTTCCCGATATA
1 TGGCTCGCATAAACTTCCCGATATA
48240759 TGGCT
1 TGGCT
48240764 ATCCGAAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.64
24 1 0.04
25 8 0.32
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (25 bp):
TGGCTCGCATAAACTTCCCGATATA
Found at i:48242031 original size:42 final size:42
Alignment explanation
Indices: 48241958--48242108 Score: 259
Period size: 42 Copynumber: 3.6 Consensus size: 42
48241948 ACGGGAAGAG
*
48241958 ACACGGGCGTGTGT-TCAGCTGTGTGTGACACACGGCCTAGC
1 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
48241999 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
1 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
*
48242041 ACACGAGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
1 ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
**
48242083 ACACGGGCGTGTGTCTTGGCCGTGTG
1 ACACGGGCGTGTGTCTCAGCCGTGTG
48242109 ACTCCTGTAC
Statistics
Matches: 104, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
41 14 0.13
42 90 0.87
ACGTcount: A:0.16, C:0.28, G:0.34, T:0.21
Consensus pattern (42 bp):
ACACGGGCGTGTGTCTCAGCCGTGTGTGACACACGGCCTAGC
Found at i:48242308 original size:13 final size:13
Alignment explanation
Indices: 48242290--48242320 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
48242280 TGGCCATGTG
48242290 AGCCACACGGCCT
1 AGCCACACGGCCT
48242303 AGCCACACGGCCT
1 AGCCACACGGCCT
48242316 AGCCA
1 AGCCA
48242321 TACGAGCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.45, G:0.23, T:0.06
Consensus pattern (13 bp):
AGCCACACGGCCT
Found at i:48248745 original size:14 final size:15
Alignment explanation
Indices: 48248728--48248758 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
48248718 CCTAGTATTG
48248728 TATAAAAAATATTTTA
1 TATAAAAAATA-TTTA
48248744 TATAAAAAATATTTA
1 TATAAAAAATATTTA
48248759 ATACCGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TATAAAAAATATTTA
Found at i:48255208 original size:96 final size:97
Alignment explanation
Indices: 48255043--48255232 Score: 310
Period size: 96 Copynumber: 2.0 Consensus size: 97
48255033 TCTGCCCAAT
* * *
48255043 TTGTAGCAAATCGATGGGAGATATGGCGGTAAGAAAATTATTTTTAAAAGCATATTACTGTTTTA
1 TTGTAGAAAATCGATGGGAGATATGGCAGTAAGAAAATTATTTTTAAAAGCATACTACTGTTTTA
* *
48255108 AGTTATGATTACATATAAAATTGTTTTAGCAG
66 AGTTATGACTACATACAAAATTGTTTTAGCAG
*
48255140 TTGTAGAAAATCGATGGGAGATATGGCAGTAAG-AAATTCTTTTTAAAAGCATACTACTGTTTTA
1 TTGTAGAAAATCGATGGGAGATATGGCAGTAAGAAAATTATTTTTAAAAGCATACTACTGTTTTA
*
48255204 AGTTATGACTACATACAAGATTGTTTTAG
66 AGTTATGACTACATACAAAATTGTTTTAG
48255233 GGTATAGGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
96 55 0.64
97 31 0.36
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (97 bp):
TTGTAGAAAATCGATGGGAGATATGGCAGTAAGAAAATTATTTTTAAAAGCATACTACTGTTTTA
AGTTATGACTACATACAAAATTGTTTTAGCAG
Found at i:48257620 original size:17 final size:18
Alignment explanation
Indices: 48257598--48257631 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48257588 ATAATTGTAA
48257598 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
48257615 TTTAAATGTGTAATTAT
1 TTTAAATGTCTAATTAT
48257632 CATAACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Found at i:48257649 original size:44 final size:44
Alignment explanation
Indices: 48257599--48257688 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
48257589 TAATTGTAAT
* * *
48257599 TTAAATTCTAATTATTTTTAAATGTGTAATTATCATAACTTCTA
1 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
* *
48257643 TTAAATTATAATTGTTTTTAAATGTATAATTATCACGACTTCTA
1 TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
48257687 TT
1 TT
48257689 TTATTTCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.50
Consensus pattern (44 bp):
TTAAATTATAATTATTTTTAAATGTATAATTATCACAACTTCTA
Found at i:48265744 original size:12 final size:12
Alignment explanation
Indices: 48265719--48265871 Score: 54
Period size: 12 Copynumber: 12.8 Consensus size: 12
48265709 TTTATCAAGA
48265719 TAAATATTAAAT
1 TAAATATTAAAT
48265731 TAAAT-TTAATAT
1 TAAATATTAA-AT
*
48265743 TAAATCTT--AT
1 TAAATATTAAAT
*
48265753 TAAAATAATGTAGA-
1 T-AAAT-AT-TAAAT
*
48265767 TAAACATTAAAT
1 TAAATATTAAAT
48265779 TAAAT-TTAATAT
1 TAAATATTAA-AT
* * *
48265791 TAATATAATCATT
1 TAA-ATATTAAAT
*
48265804 TTAATATTAAAT
1 TAAATATTAAAT
* * *
48265816 TAATAAAATACTAT
1 TAA-ATATTA-AAT
*
48265830 TAAGATA-AAAAT
1 TAA-ATATTAAAT
48265842 T-AA-ATTAAAT
1 TAAATATTAAAT
*
48265852 TAAATATTAAAA
1 TAAATATTAAAT
48265864 T-AATATTA
1 TAAATATTA
48265872 TTTTTAGAAT
Statistics
Matches: 104, Mismatches: 21, Indels: 33
0.66 0.13 0.21
Matches are distributed among these distances:
9 1 0.01
10 9 0.09
11 25 0.24
12 42 0.40
13 16 0.15
14 10 0.10
15 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:48265819 original size:20 final size:18
Alignment explanation
Indices: 48265671--48265820 Score: 60
Period size: 17 Copynumber: 8.7 Consensus size: 18
48265661 TTCAACTATG
48265671 ATTAAACTTAATCACTTTAAT
1 ATTAAA-TTAAT-A-TTTAAT
48265692 ATTAAATTAATA--TAAT
1 ATTAAATTAATATTTAAT
* * * *
48265708 ATT-TATCAAGA-TAAAT
1 ATTAAATTAATATTTAAT
48265724 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
48265741 ATTAAATCT--TA-TTAA-
1 ATTAAAT-TAATATTTAAT
* *
48265756 AAT-AATGTAGATA---AAC
1 ATTAAAT-TA-ATATTTAAT
48265772 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
48265789 ATT-AATATAATCATTTTAAT
1 ATTAAAT-TAAT-A-TTTAAT
48265809 ATTAAATTAATA
1 ATTAAATTAATA
48265821 AAATACTATT
Statistics
Matches: 100, Mismatches: 11, Indels: 38
0.67 0.07 0.26
Matches are distributed among these distances:
14 5 0.05
15 10 0.10
16 25 0.25
17 29 0.29
18 1 0.01
19 3 0.03
20 18 0.18
21 9 0.09
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:48267365 original size:20 final size:21
Alignment explanation
Indices: 48267340--48267388 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
48267330 TATTGATCCA
*
48267340 GTATCGATACT-TTTCTTAAG
1 GTATCGATACTATTTCCTAAG
*
48267360 GTATCGAT-GTATTTCCTAAG
1 GTATCGATACTATTTCCTAAG
48267380 GTATCGATA
1 GTATCGATA
48267389 TTCCTGCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (21 bp):
GTATCGATACTATTTCCTAAG
Found at i:48267912 original size:19 final size:19
Alignment explanation
Indices: 48267888--48267925 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
48267878 TAGGGAAATC
48267888 TTTAATTGTGGTAAGCTAA
1 TTTAATTGTGGTAAGCTAA
48267907 TTTAATTGTGGTAAGCTAA
1 TTTAATTGTGGTAAGCTAA
48267926 GTAGTTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (19 bp):
TTTAATTGTGGTAAGCTAA
Found at i:48275239 original size:101 final size:101
Alignment explanation
Indices: 48275067--48275262 Score: 347
Period size: 101 Copynumber: 1.9 Consensus size: 101
48275057 ACAACTATGC
*
48275067 TATTTGCTAAGCAATAAGGAAGATGATAATGGTTGTTATCATATGTTAGAATCGAGTAACTCGAA
1 TATTTGCTAAGCAATAAGGAAGATGATAATGGTTGATATCATATGTTAGAATCGAGTAACTCGAA
* * *
48275132 TTATTATTTAAGTAAAATATAGTGGTAAAACTATAT
66 TCATTATTTAAATAAAATACAGTGGTAAAACTATAT
*
48275168 TATTTGCTAAGCAATAAGGAAGATGATAATGGTTGATATCATCTGTTAGAATCGAGTAACTCGAA
1 TATTTGCTAAGCAATAAGGAAGATGATAATGGTTGATATCATATGTTAGAATCGAGTAACTCGAA
48275233 TCATTATTTAAATAAAATACAGTGGTAAAA
66 TCATTATTTAAATAAAATACAGTGGTAAAA
48275263 TAAAATAAAA
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 90 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (101 bp):
TATTTGCTAAGCAATAAGGAAGATGATAATGGTTGATATCATATGTTAGAATCGAGTAACTCGAA
TCATTATTTAAATAAAATACAGTGGTAAAACTATAT
Found at i:48286064 original size:22 final size:22
Alignment explanation
Indices: 48286039--48286170 Score: 56
Period size: 22 Copynumber: 6.0 Consensus size: 22
48286029 GCTTGTATGA
48286039 GTTTAGCACTTCTGTGCTCTCT
1 GTTTAGCACTTCTGTGCTCTCT
** * * *
48286061 GTTTAGTGCTTCGGTACTCTTT
1 GTTTAGCACTTCTGTGCTCTCT
* *
48286083 GTTCAGTC-CTT-TGGTAG-TATCT
1 GTTTAG-CACTTCT-GT-GCTCTCT
* * * *
48286105 GATCAGCAC-TCCGATGCTCTTT
1 GTTTAGCACTTCTG-TGCTCTCT
* * *
48286127 GGTTAGCACTTTTGTGCTATCT
1 GTTTAGCACTTCTGTGCTCTCT
* *
48286149 GTTTAGCACTACGGTGCTCTCT
1 GTTTAGCACTTCTGTGCTCTCT
48286171 AGTGTGGTGT
Statistics
Matches: 76, Mismatches: 26, Indels: 16
0.64 0.22 0.14
Matches are distributed among these distances:
21 4 0.05
22 70 0.92
23 2 0.03
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.42
Consensus pattern (22 bp):
GTTTAGCACTTCTGTGCTCTCT
Found at i:48289356 original size:39 final size:39
Alignment explanation
Indices: 48289313--48289426 Score: 149
Period size: 39 Copynumber: 2.9 Consensus size: 39
48289303 AGTACACCAG
* * * * *
48289313 CACACAGCTTGCTAGGCAAAAAGCCCAAATAATCA-TCGT
1 CACACAACTTGCTAGGCACATAGCCCGAATAATCACT-GA
*
48289352 CACACAACCTGCTAGGCACATAGCCCGAATAATCACTGA
1 CACACAACTTGCTAGGCACATAGCCCGAATAATCACTGA
*
48289391 CACACAACTTACTAGGCACATAGCCCGAATAATCAC
1 CACACAACTTGCTAGGCACATAGCCCGAATAATCAC
48289427 CGTATTTCTA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
39 65 0.98
40 1 0.02
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.17
Consensus pattern (39 bp):
CACACAACTTGCTAGGCACATAGCCCGAATAATCACTGA
Found at i:48294393 original size:45 final size:45
Alignment explanation
Indices: 48294343--48294577 Score: 230
Period size: 45 Copynumber: 5.3 Consensus size: 45
48294333 GTGGCTTTGT
* * *
48294343 CCACAACCTACACGTCAGCTTGTCTAC-AGATATTGGTGGTTTCAG
1 CCACAACCTACACGGCAGCTTGTTTGCGA-ATATTGGTGGTTTCAG
* * * * *
48294388 CCACAACCTACATGGAAACTTGTCTGCGAATATTGGTGGCTTC-G
1 CCACAACCTACACGGCAGCTTGTTTGCGAATATTGGTGGTTTCAG
*
48294432 TCCACAA-CTAGCACGGCAGCTTGTTTGCGAATATTGGTGGTTTCAC
1 -CCACAACCTA-CACGGCAGCTTGTTTGCGAATATTGGTGGTTTCAG
* * * *
48294478 CCACAACCTACATGGCAACTTGTTTTCGAATATTGGTGGCTTC-G
1 CCACAACCTACACGGCAGCTTGTTTGCGAATATTGGTGGTTTCAG
* * * *
48294522 TCCACAACCTACATGGTAGCTTGTTTGCAAAT-TTGGTGGTTT-AT
1 -CCACAACCTACACGGCAGCTTGTTTGCGAATATTGGTGGTTTCAG
*
48294566 CCGCAACCTACA
1 CCACAACCTACA
48294578 TGGAAGCTAT
Statistics
Matches: 159, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
43 11 0.07
44 13 0.08
45 131 0.82
46 4 0.03
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (45 bp):
CCACAACCTACACGGCAGCTTGTTTGCGAATATTGGTGGTTTCAG
Found at i:48294482 original size:90 final size:89
Alignment explanation
Indices: 48294329--48294614 Score: 355
Period size: 90 Copynumber: 3.2 Consensus size: 89
48294319 AGGAGGAAGA
* * * * *
48294329 ATTGGTGGCTTTGTCCACAACCTACACGTCAGCTTGTCTACAGATATTGGTGGTTTCAGCCACAA
1 ATTGGTGGCTTCGTCCACAACCTACACGGCAGCTTGTTTGCA-ATATTGGTGGTTTCACCCACAA
48294394 CCTACATGGAAACTTGTCTGCGAAT
65 CCTACATGGAAACTTGTCTGCGAAT
48294419 ATTGGTGGCTTCGTCCACAA-CTAGCACGGCAGCTTGTTTGCGAATATTGGTGGTTTCACCCACA
1 ATTGGTGGCTTCGTCCACAACCTA-CACGGCAGCTTGTTTGC-AATATTGGTGGTTTCACCCACA
* * *
48294483 ACCTACATGGCAACTTGTTTTCGAAT
64 ACCTACATGGAAACTTGTCTGCGAAT
* * * *
48294509 ATTGGTGGCTTCGTCCACAACCTACATGGTAGCTTGTTTGCAA-ATTTGGTGGTTT-ATCCGCAA
1 ATTGGTGGCTTCGTCCACAACCTACACGGCAGCTTGTTTGCAATA-TTGGTGGTTTCACCCACAA
* * **
48294572 CCTACATGGAAGC-TATCTGTAAAT
65 CCTACATGGAAACTTGTCTGCGAAT
*
48294596 ATTGGTGGCTTCGACCACA
1 ATTGGTGGCTTCGTCCACA
48294615 TCTTTTGTAG
Statistics
Matches: 172, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
87 24 0.14
88 18 0.10
89 15 0.09
90 111 0.65
91 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.31
Consensus pattern (89 bp):
ATTGGTGGCTTCGTCCACAACCTACACGGCAGCTTGTTTGCAATATTGGTGGTTTCACCCACAAC
CTACATGGAAACTTGTCTGCGAAT
Found at i:48294601 original size:43 final size:45
Alignment explanation
Indices: 48294329--48294607 Score: 217
Period size: 45 Copynumber: 6.3 Consensus size: 45
48294319 AGGAGGAAGA
** * ** * * *
48294329 ATTGGTGGCTTTGTCCACAACCTACACGTCAGCTTGTCTACAGAT
1 ATTGGTGGCTTCATCCACAACCTACATGGAAGCTTATCTGCAAAT
* * * * *
48294374 ATTGGTGGTTTCAGCCACAACCTACATGGAAACTTGTCTGCGAAT
1 ATTGGTGGCTTCATCCACAACCTACATGGAAGCTTATCTGCAAAT
* * * * * *
48294419 ATTGGTGGCTTCGTCCACAA-CTAGCACGGCAGCTTGTTTGCGAAT
1 ATTGGTGGCTTCATCCACAACCTA-CATGGAAGCTTATCTGCAAAT
* * * * * *
48294464 ATTGGTGGTTTCACCCACAACCTACATGGCAA-CTTGTTTTCGAAT
1 ATTGGTGGCTTCATCCACAACCTACATGG-AAGCTTATCTGCAAAT
* * * *
48294509 ATTGGTGGCTTCGTCCACAACCTACATGGTAGCTTGTTTGCAAAT
1 ATTGGTGGCTTCATCCACAACCTACATGGAAGCTTATCTGCAAAT
* * *
48294554 -TTGGTGG-TTTATCCGCAACCTACATGGAAGC-TATCTGTAAAT
1 ATTGGTGGCTTCATCCACAACCTACATGGAAGCTTATCTGCAAAT
48294596 ATTGGTGGCTTC
1 ATTGGTGGCTTC
48294608 GACCACATCT
Statistics
Matches: 190, Mismatches: 38, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
42 8 0.04
43 27 0.14
44 13 0.07
45 138 0.73
46 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (45 bp):
ATTGGTGGCTTCATCCACAACCTACATGGAAGCTTATCTGCAAAT
Found at i:48295897 original size:30 final size:30
Alignment explanation
Indices: 48295851--48295929 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
48295841 AGCAAATTTG
*
48295851 ACTTGTTTGAAAATCATTTAAAATGATTTTA
1 ACTTGATTG-AAATCATTTAAAATGATTTTA
48295882 ACTTGATTGAAATCATTTAAAATGATTTTA
1 ACTTGATTGAAATCATTTAAAATGATTTTA
* *
48295912 ATTTGATTGAAATTATTT
1 ACTTGATTGAAATCATTT
48295930 GACTTGGTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 37 0.82
31 8 0.18
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (30 bp):
ACTTGATTGAAATCATTTAAAATGATTTTA
Found at i:48296240 original size:18 final size:18
Alignment explanation
Indices: 48296217--48296251 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48296207 ATGAGTTTAC
48296217 AAATATTTTAAACTATTG
1 AAATATTTTAAACTATTG
*
48296235 AAATATTTTAAATTATT
1 AAATATTTTAAACTATT
48296252 TATGATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
AAATATTTTAAACTATTG
Found at i:48297662 original size:24 final size:27
Alignment explanation
Indices: 48297606--48297665 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 27
48297596 GAGAAAATAT
* *
48297606 ATTTAATTTTCCTGTATTCAACAGTTC
1 ATTTAATTTTCATGTATTCAACACTTC
*
48297633 ACTTAATTTTCAT-T-TTCAA-ACTTC
1 ATTTAATTTTCATGTATTCAACACTTC
48297657 ATTTAATTT
1 ATTTAATTT
48297666 GAAAAAGCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 12 0.41
25 5 0.17
26 1 0.03
27 11 0.38
ACGTcount: A:0.28, C:0.17, G:0.03, T:0.52
Consensus pattern (27 bp):
ATTTAATTTTCATGTATTCAACACTTC
Found at i:48298174 original size:16 final size:16
Alignment explanation
Indices: 48298153--48298205 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
48298143 ATCGGGTTGA
*
48298153 GAAAATTATTTAATTG
1 GAAAATTAATTAATTG
48298169 GAAAATTAATTAATT-
1 GAAAATTAATTAATTG
48298184 ---AATTAATTAATT-
1 GAAAATTAATTAATTG
48298196 -AAAATTAATT
1 GAAAATTAATT
48298206 TATGATGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
12 12 0.35
14 8 0.24
16 14 0.41
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
GAAAATTAATTAATTG
Found at i:48298181 original size:4 final size:4
Alignment explanation
Indices: 48298172--48298205 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
48298162 TTAATTGGAA
48298172 AATT AATT AATT AATT AATT AATT AA-- AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT
48298206 TATGATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:48298532 original size:28 final size:26
Alignment explanation
Indices: 48298500--48298560 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
48298490 GGCTAAAAAT
*
48298500 AAAATATTGAGATATTATTATTATTCTA
1 AAAATAGTGAGA-ATT-TTATTATTCTA
* *
48298528 AAAATAGTGAGAATTTTTTTTTTCTA
1 AAAATAGTGAGAATTTTATTATTCTA
*
48298554 AATATAG
1 AAAATAG
48298561 ATTCTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 15 0.52
27 3 0.10
28 11 0.38
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (26 bp):
AAAATAGTGAGAATTTTATTATTCTA
Found at i:48306376 original size:23 final size:24
Alignment explanation
Indices: 48306332--48306389 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
48306322 AACATTCTAT
48306332 TATGTATGCATGTGCTGTAGCTGG
1 TATGTATGCATGTGCTGTAGCTGG
*
48306356 TATGTAT-CATGTG-TTTGAGCTGG
1 TATGTATGCATGTGCTGT-AGCTGG
48306379 TATGTATGCAT
1 TATGTATGCAT
48306390 CATTTTCGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 2 0.06
23 19 0.61
24 10 0.32
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.41
Consensus pattern (24 bp):
TATGTATGCATGTGCTGTAGCTGG
Found at i:48314632 original size:5 final size:5
Alignment explanation
Indices: 48314622--48314686 Score: 53
Period size: 5 Copynumber: 12.6 Consensus size: 5
48314612 TAAGAATAAT
* * *
48314622 AAATA AAATA AACTA AAA-A TTAGTA AAATA AAA-A GAAATA AAATAA
1 AAATA AAATA AAATA AAATA -AAATA AAATA AAATA -AAATA AAAT-A
48314668 TAAATA AAATA AAATA AAA
1 -AAATA AAATA AAATA AAA
48314687 AAGAAGGGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
4 2 0.04
5 38 0.79
6 4 0.08
7 4 0.08
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:48314653 original size:15 final size:15
Alignment explanation
Indices: 48314611--48314687 Score: 73
Period size: 15 Copynumber: 4.8 Consensus size: 15
48314601 AAATCTAAGT
48314611 ATAAGAATAATAAATAAA
1 ATAA-AATAA-AAAT-AA
* *
48314629 ATAAACTAAAAATTA
1 ATAAAATAAAAATAA
* *
48314644 GTAAAATAAAAAGAA
1 ATAAAATAAAAATAA
48314659 ATAAAATAATAAATAAA
1 ATAAAATAA-AAAT-AA
48314676 ATAAAATAAAAA
1 ATAAAATAAAAA
48314688 AGAAGGGGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
15 20 0.41
16 10 0.20
17 15 0.31
18 4 0.08
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (15 bp):
ATAAAATAAAAATAA
Found at i:48318976 original size:27 final size:27
Alignment explanation
Indices: 48318944--48319196 Score: 258
Period size: 27 Copynumber: 9.4 Consensus size: 27
48318934 GGCAATTTAT
48318944 CGAAATACCCTCGAAGGGTAAAATTAC
1 CGAAATACCCTCGAAGGGTAAAATTAC
* *
48318971 CGAAATACCCTTGAAGGGTAAAATTAT
1 CGAAATACCCTCGAAGGGTAAAATTAC
* * *
48318998 CGAAATACCCCCGAAAGGTAAAATTAT
1 CGAAATACCCTCGAAGGGTAAAATTAC
* * * *
48319025 CGAAATACCC-CCATAGTGTGAAATTAT
1 CGAAATACCCTCGA-AGGGTAAAATTAC
* **
48319052 TGAAATACCCTCGAACAGTAAAATTAC
1 CGAAATACCCTCGAAGGGTAAAATTAC
*
48319079 CGAAATACCCTTGAAGGGTAAAATTAC
1 CGAAATACCCTCGAAGGGTAAAATTAC
* * *
48319106 TGAAATACTCTTGAAGGGTAAAATTAC
1 CGAAATACCCTCGAAGGGTAAAATTAC
** * * *
48319133 TAAAATACCCTTGAAGGGTAAAAGTAT
1 CGAAATACCCTCGAAGGGTAAAATTAC
* *
48319160 CAAAATATCCCT-GAAAGGTAAAATTAC
1 CGAAATA-CCCTCGAAGGGTAAAATTAC
*
48319187 CAAAATACCC
1 CGAAATACCC
48319197 ACATAGTGTG
Statistics
Matches: 194, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
26 5 0.03
27 183 0.94
28 6 0.03
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (27 bp):
CGAAATACCCTCGAAGGGTAAAATTAC
Found at i:48319003 original size:54 final size:54
Alignment explanation
Indices: 48318940--48319196 Score: 306
Period size: 54 Copynumber: 4.8 Consensus size: 54
48318930 CATGGGCAAT
*
48318940 TTATCGAAATACCCTCGAAGGGTAAAATTACCGAAATACCCTTGAAGGGTAAAA
1 TTATCGAAATACCCTCGAAAGGTAAAATTACCGAAATACCCTTGAAGGGTAAAA
* * ** * *
48318994 TTATCGAAATACCCCCGAAAGGTAAAATTATCGAAATACCC-CCATAGTGTGAAA
1 TTATCGAAATACCCTCGAAAGGTAAAATTACCGAAATACCCTTGA-AGGGTAAAA
*
48319048 TTATTGAAATACCCTCGAACA-GTAAAATTACCGAAATACCCTTGAAGGGTAAAA
1 TTATCGAAATACCCTCGAA-AGGTAAAATTACCGAAATACCCTTGAAGGGTAAAA
* * * **
48319102 TTA-CTGAAATACTCTTGAAGGGTAAAATTACTAAAATACCCTTGAAGGGTAAAA
1 TTATC-GAAATACCCTCGAAAGGTAAAATTACCGAAATACCCTTGAAGGGTAAAA
* * *
48319156 GTATCAAAATATCCCT-GAAAGGTAAAATTACCAAAATACCC
1 TTATCGAAATA-CCCTCGAAAGGTAAAATTACCGAAATACCC
48319197 ACATAGTGTG
Statistics
Matches: 171, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
53 1 0.01
54 164 0.96
55 6 0.04
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (54 bp):
TTATCGAAATACCCTCGAAAGGTAAAATTACCGAAATACCCTTGAAGGGTAAAA
Found at i:48319222 original size:81 final size:78
Alignment explanation
Indices: 48318974--48319225 Score: 227
Period size: 81 Copynumber: 3.1 Consensus size: 78
48318964 AAATTACCGA
* * *
48318974 AATACCCTTGAAGGGTAAAATTATCGAAATACCCCCGAAAGGTAAAATTATCGAAATACCCCCAT
1 AATACCCTTGAAGGGTAAAATTATCGAAATA-CCCTGAAAGGTAAAATTACCGAAATACCCACAT
*
48319039 AGTGTGAAATTATT
65 AGTGTGAAATTCTT
* ** * * * **
48319053 GAAATACCCTCGAACAGTAAAATTACCGAAATACCCTTGAAGGGTAAAATTACTGAAATACTCTT
1 --AATACCCTTGAAGGGTAAAATTATCGAAATACCC-TGAAAGGTAAAATTACCGAAATAC-CCA
* * * *
48319118 GA-AGGGTAAAATTACTAA
62 CATAGTGTGAAATT-CT-T
* * *
48319136 AATACCCTTGAAGGGTAAAAGTATCAAAATATCCCTGAAAGGTAAAATTACCAAAATACCCACAT
1 AATACCCTTGAAGGGTAAAATTATCGAAATA-CCCTGAAAGGTAAAATTACCGAAATACCCACAT
48319201 AGTGTGAAATGGTCTT
65 AGTGTGAAAT--TCTT
*
48319217 TATACCCTT
1 AATACCCTT
48319226 AGGAGATGAA
Statistics
Matches: 132, Mismatches: 31, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
80 5 0.04
81 118 0.89
82 8 0.06
83 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.25
Consensus pattern (78 bp):
AATACCCTTGAAGGGTAAAATTATCGAAATACCCTGAAAGGTAAAATTACCGAAATACCCACATA
GTGTGAAATTCTT
Found at i:48319637 original size:28 final size:27
Alignment explanation
Indices: 48319570--48319637 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
48319560 TTGCATTTTA
* *
48319570 TGTACTATATTGGGTTAAGGCCCACAC
1 TGTACTGTATTGGGCTAAGGCCCACAC
* *
48319597 TGCTACTGAATTGGGCTAAGGCCCTCAC
1 TG-TACTGTATTGGGCTAAGGCCCACAC
48319625 TGTACTGTCATTG
1 TGTACTGT-ATTG
48319638 AATAGGGCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 7 0.21
28 27 0.79
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (27 bp):
TGTACTGTATTGGGCTAAGGCCCACAC
Found at i:48332050 original size:20 final size:21
Alignment explanation
Indices: 48332003--48332048 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
48331993 AGTTGACGAG
*
48332003 AAAAAA-TAAATATATATTAT
1 AAAAAATTAAATATAAATTAT
*
48332023 AAAAAATTAAATATAAATTTT
1 AAAAAATTAAATATAAATTAT
48332044 AAAAA
1 AAAAA
48332049 TTTTAAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAAATTAAATATAAATTAT
Found at i:48337511 original size:21 final size:20
Alignment explanation
Indices: 48337458--48337542 Score: 75
Period size: 21 Copynumber: 4.2 Consensus size: 20
48337448 TTATTAACTA
* *
48337458 TTAAAAATTTTAAA-AATAT
1 TTAATAATTTTAAATAATTT
*
48337477 TT-ATAATTTCAAATAATTT
1 TTAATAATTTTAAATAATTT
*
48337496 TTAATTACTTTTAAATAACTTT
1 TTAA-TAATTTTAAATAA-TTT
* *
48337518 TTTATAATTTTTAATAATTGT
1 TTAATAATTTTAAATAATT-T
48337539 TTAA
1 TTAA
48337543 GAAACCACTT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
18 9 0.17
19 8 0.15
20 3 0.06
21 26 0.50
22 6 0.12
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (20 bp):
TTAATAATTTTAAATAATTT
Found at i:48337524 original size:11 final size:10
Alignment explanation
Indices: 48337465--48337542 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
48337455 CTATTAAAAA
*
48337465 TTTTAAAAAT
1 TTTTAATAAT
*
48337475 ATTT-ATAAT
1 TTTTAATAAT
**
48337484 TTCAAATAAT
1 TTTTAATAAT
*
48337494 TTTTAATTACT
1 TTTTAA-TAAT
*
48337505 TTTAAATAACT
1 TTTTAATAA-T
*
48337516 TTTTTATAAT
1 TTTTAATAAT
48337526 TTTTAATAAT
1 TTTTAATAAT
48337536 TGTTTAA
1 T-TTTAA
48337543 GAAACCACTT
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
9 5 0.10
10 25 0.49
11 21 0.41
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:48342793 original size:27 final size:27
Alignment explanation
Indices: 48342758--48342839 Score: 112
Period size: 27 Copynumber: 3.0 Consensus size: 27
48342748 TACATAGTAT
48342758 TGGTGCCTATCTGGGAGGCGCCAATGG
1 TGGTGCCTATCTGGGAGGCGCCAATGG
* **
48342785 TGGTGCCTATCTGGGAGGCGCCATTAT
1 TGGTGCCTATCTGGGAGGCGCCAATGG
*
48342812 TGGTGCC-ATACTGAGAGGCGCCAATGG
1 TGGTGCCTAT-CTGGGAGGCGCCAATGG
48342839 T
1 T
48342840 CTGATTTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.04
27 45 0.96
ACGTcount: A:0.17, C:0.22, G:0.37, T:0.24
Consensus pattern (27 bp):
TGGTGCCTATCTGGGAGGCGCCAATGG
Found at i:48342927 original size:18 final size:18
Alignment explanation
Indices: 48342906--48342942 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
48342896 AAGAAATAAG
48342906 AAAGAAGGAAGCAAAAGA
1 AAAGAAGGAAGCAAAAGA
*
48342924 AAAGAAGGAAGGAAAAGA
1 AAAGAAGGAAGCAAAAGA
48342942 A
1 A
48342943 GAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.30, T:0.00
Consensus pattern (18 bp):
AAAGAAGGAAGCAAAAGA
Done.