Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold163
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: 1788591
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.32
Warning! 179834 characters in sequence are not A, C, G, or T
File 4 of 13
Found at i:327707 original size:2 final size:2
Alignment explanation
Indices: 327702--327731 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
327692 TTTTTCCTTT
327702 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
327732 CACACTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:327995 original size:21 final size:19
Alignment explanation
Indices: 327965--328007 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
327955 ATAATAAAAT
327965 AATATAAAAATA-ATATTTTA
1 AATATAAAAA-AGAT-TTTTA
327985 AATAGTAAAAAAGATTTTTA
1 AATA-TAAAAAAGATTTTTA
328005 AAT
1 AAT
328008 TAACTTAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (19 bp):
AATATAAAAAAGATTTTTA
Found at i:328265 original size:34 final size:33
Alignment explanation
Indices: 328197--328267 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 33
328187 TATAATATGA
*
328197 AAAACCTCGAATTAACTCTTTTTTTTTGCATAT
1 AAAACCTCGAATTAACTCTTTTTTATTGCATAT
*
328230 AAAACCTGGAATTAACT-TTTTTTAAATTGCATAT
1 AAAACCTCGAATTAACTCTTTTTT--ATTGCATAT
328264 AAAA
1 AAAA
328268 TTAAGTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 6 0.18
33 16 0.47
34 12 0.35
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (33 bp):
AAAACCTCGAATTAACTCTTTTTTATTGCATAT
Found at i:328469 original size:13 final size:13
Alignment explanation
Indices: 328446--328472 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
328436 ATATTTTTTA
328446 TAAAAAATTTAAT
1 TAAAAAATTTAAT
328459 TAAAAAATTTAAT
1 TAAAAAATTTAAT
328472 T
1 T
328473 TCTTGACCAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAAAAATTTAAT
Found at i:328531 original size:22 final size:22
Alignment explanation
Indices: 328487--328532 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
328477 GACCAAACTA
* *
328487 AATAATCTATAATAATAATAAT
1 AATAATATATAATAAGAATAAT
328509 AATAATATATAATTAAGAA-AAT
1 AATAATATATAA-TAAGAATAAT
328531 AA
1 AA
328533 AGCAAGGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AATAATATATAATAAGAATAAT
Found at i:330088 original size:20 final size:22
Alignment explanation
Indices: 330059--330101 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
330049 AATAAAAATT
*
330059 TTTTATAAT-ATT-AAATATAA
1 TTTTACAATAATTAAAATATAA
330079 TTTTACAATAATTAAAATATAA
1 TTTTACAATAATTAAAATATAA
330101 T
1 T
330102 CTTATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 3 0.15
22 9 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTACAATAATTAAAATATAA
Found at i:332159 original size:15 final size:15
Alignment explanation
Indices: 332135--332164 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
332125 TATGTAACTA
332135 AATATGTATAAATAT
1 AATATGTATAAATAT
*
332150 AATATTTATAAATAT
1 AATATGTATAAATAT
332165 TTTATAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
AATATGTATAAATAT
Found at i:332990 original size:40 final size:39
Alignment explanation
Indices: 332908--333003 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 39
332898 TAGGATATAA
*
332908 ACATAACATAAAAATAATTAAAATAAAACACAAAACACGAT
1 ACAT-ACA-AAAAATAATTAAAAGAAAACACAAAACACGAT
* * * *
332949 ACATCACAAAAAATAATTAAAAGAAGACATAAAATATGAT
1 ACAT-ACAAAAAATAATTAAAAGAAAACACAAAACACGAT
*
332989 ACGATAAAAAAAATA
1 AC-ATACAAAAAATA
333004 TGAACACGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
40 38 0.81
41 9 0.19
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (39 bp):
ACATACAAAAAATAATTAAAAGAAAACACAAAACACGAT
Found at i:333061 original size:32 final size:32
Alignment explanation
Indices: 333016--333088 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
333006 AACACGATAC
*
333016 AAATATATAAATATCTCAAAATTTATATAATAT
1 AAATATATAAATATATCAAAATTTATAT-ATAT
* *
333049 AAAT-TATTAATATATTAAAATTTATATATAT
1 AAATATATAAATATATCAAAATTTATATATAT
*
333080 AAAAATATA
1 AAATATATA
333089 CCAATGTTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 7 0.21
32 23 0.68
33 4 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (32 bp):
AAATATATAAATATATCAAAATTTATATATAT
Found at i:333077 original size:16 final size:16
Alignment explanation
Indices: 333033--333085 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
333023 TAAATATCTC
333033 AAAATTTATATA-ATAT
1 AAAATTTATATATAT-T
*
333049 AAATTATTA-ATATATT
1 AAAAT-TTATATATATT
*
333065 AAAATTTATATATATA
1 AAAATTTATATATATT
333081 AAAAT
1 AAAAT
333086 ATACCAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 3 0.10
16 23 0.74
17 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTTATATATATT
Found at i:333528 original size:20 final size:21
Alignment explanation
Indices: 333503--333541 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
333493 TGGTTTAATT
333503 AAAATAA-ATATTTATTTATG
1 AAAATAATATATTTATTTATG
*
333523 AAAATAATATTTTTATTTA
1 AAAATAATATATTTATTTA
333542 ATTAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
AAAATAATATATTTATTTATG
Found at i:333949 original size:35 final size:36
Alignment explanation
Indices: 333910--333994 Score: 104
Period size: 35 Copynumber: 2.4 Consensus size: 36
333900 TAAGTATTTA
*
333910 ATTTAATATTATAAATTTTA-AAATAAAATTAAAAT
1 ATTTAATATTATAAATTTTATAAATAAAAATAAAAT
*
333945 ATTTAATATT-TAAATTTTATTAATTAAAAATAAAAT
1 ATTTAATATTATAAATTTTA-TAAATAAAAATAAAAT
*
333981 -TTTAAAATATATAA
1 ATTTAATAT-TATAA
333995 TATAAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
34 9 0.21
35 17 0.40
36 14 0.33
37 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
ATTTAATATTATAAATTTTATAAATAAAAATAAAAT
Found at i:334240 original size:8 final size:8
Alignment explanation
Indices: 334213--334360 Score: 58
Period size: 8 Copynumber: 17.9 Consensus size: 8
334203 GCTACGTGTT
334213 TTTATCATA
1 TTTAT-ATA
* *
334222 TTTAAAAA
1 TTTATATA
334230 TTTATATA
1 TTTATATA
334238 TTTATTTGATA
1 TTTA--T-ATA
*
334249 ATTATATA
1 TTTATATA
334257 TTT-TATAA
1 TTTATAT-A
334265 TATTATA-A
1 T-TTATATA
334273 -TTATAT-
1 TTTATATA
*
334279 TTTAAATA
1 TTTATATA
334287 -TTATATA
1 TTTATATA
*
334294 TTAATATAA
1 TTTATAT-A
*
334303 TTTTTAATA
1 TTTAT-ATA
334312 TATTA-ATAA
1 T-TTATAT-A
334321 TTTATAT-
1 TTTATATA
* *
334328 TATATAAA
1 TTTATATA
*
334336 TTTTAAAATA
1 -TTT-ATATA
334346 TTTATATA
1 TTTATATA
334354 TTTATAT
1 TTTATAT
334361 TATATAATTT
Statistics
Matches: 103, Mismatches: 18, Indels: 37
0.65 0.11 0.23
Matches are distributed among these distances:
6 5 0.05
7 19 0.18
8 41 0.40
9 22 0.21
10 10 0.10
11 6 0.06
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (8 bp):
TTTATATA
Found at i:334277 original size:21 final size:21
Alignment explanation
Indices: 334253--334361 Score: 72
Period size: 20 Copynumber: 5.3 Consensus size: 21
334243 TTGATAATTA
334253 TATATTTTATAATATTATA-AT
1 TATATTTTA-AATATTATATAT
334274 TATATTTTAAATATTATATAT
1 TATATTTTAAATATTATATAT
* * *
334295 TA-A-TATAATTTTTAATATAT
1 TATATTTTAAATATT-ATATAT
*
334315 TAATAATTT--ATATTATATA-
1 T-ATATTTTAAATATTATATAT
334334 -A-ATTTTAAAATATTTATATATT
1 TATATTTT-AAATA-TTATATA-T
334356 TATATT
1 TATATT
334362 ATATAATTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 23
0.69 0.07 0.23
Matches are distributed among these distances:
16 4 0.06
17 1 0.01
19 10 0.15
20 29 0.43
21 17 0.25
22 1 0.01
23 3 0.04
24 3 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATTTTAAATATTATATAT
Found at i:334298 original size:25 final size:23
Alignment explanation
Indices: 334253--334328 Score: 68
Period size: 25 Copynumber: 3.3 Consensus size: 23
334243 TTGATAATTA
*
334253 TATATTTTATA-ATATT-ATAAT
1 TATATTTTAAATATATTAATAAT
*
334274 TATATTTTAAATATTATATATTAA-
1 TATATTTTAAATA-TAT-TAATAAT
*
334298 TATAATTTTTAATATATTAATAATT
1 TAT-ATTTTAAATATATTAATAA-T
334323 TATATT
1 TATATT
334329 ATATAAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
21 10 0.23
22 1 0.02
23 8 0.18
24 10 0.23
25 15 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATATTTTAAATATATTAATAAT
Found at i:334327 original size:33 final size:33
Alignment explanation
Indices: 334280--334372 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
334270 TAATTATATT
*
334280 TTAA-ATATTATATATTAATATAATTTTTAATATA
1 TTAATATATT-TATATT-ATATAATTTTTAAAATA
*
334314 TTAATA-ATTTATATTATATAAATTTTAAAATA
1 TTAATATATTTATATTATATAATTTTTAAAATA
*
334346 TTTATATATTTATATTATATAATTTTT
1 TTAATATATTTATATTATATAATTTTT
334373 TTATAATATC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
32 20 0.38
33 25 0.47
34 7 0.13
35 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTAATATATTTATATTATATAATTTTTAAAATA
Found at i:334331 original size:18 final size:17
Alignment explanation
Indices: 334246--334365 Score: 63
Period size: 18 Copynumber: 6.9 Consensus size: 17
334236 TATTTATTTG
*
334246 ATAA-TTAT-ATATTTT
1 ATAATTTATAATATATT
334261 ATAATATTATAATTATATT
1 ATAAT-TTATAA-TATATT
* *
334280 TTAAATATTAT-ATATTAAT
1 AT-AAT-TTATAATA-TATT
*
334299 ATAATTTTTAATATATT
1 ATAATTTATAATATATT
*
334316 AATAATTTATATTATA-T
1 -ATAATTTATAATATATT
*
334333 A-AATTT-TAAAATATTT
1 ATAATTTATAATATA-TT
*
334349 ATATATTTATATTATAT
1 ATA-ATTTATAATATAT
334366 AATTTTTTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
14 5 0.06
15 9 0.11
16 3 0.04
17 12 0.15
18 27 0.34
19 16 0.20
20 8 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAATTTATAATATATT
Found at i:335129 original size:11 final size:11
Alignment explanation
Indices: 335072--335133 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
335062 ATAATATAAT
335072 TATTATAATTA
1 TATTATAATTA
*
335083 AATTTAATAATTTA
1 TA-TT-ATAA-TTA
**
335097 TATTATTTTTA
1 TATTATAATTA
* *
335108 TATTTTTATTA
1 TATTATAATTA
335119 TATTATAATTA
1 TATTATAATTA
335130 TATT
1 TATT
335134 TAAAATATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
11 26 0.65
12 4 0.10
13 6 0.15
14 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTATAATTA
Found at i:335178 original size:32 final size:31
Alignment explanation
Indices: 335137--335245 Score: 105
Period size: 32 Copynumber: 3.4 Consensus size: 31
335127 TTATATTTAA
335137 AATATTTTATATTAATATAAATATAATATATT
1 AATATTTTATATT-ATATAAATATAATATATT
* * *
335169 AATAATTTATATTATATTAACTTTAATATATT
1 AATATTTTATATTATA-TAAATATAATATATT
* * *
335201 TATATTTT-TATGTCTCATATATATATATATATT
1 AATATTTTATAT-TAT-ATAAATATA-ATATATT
335234 AAT-TTTTATATT
1 AATATTTTATATT
335246 TTATCATATT
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
31 6 0.10
32 43 0.69
33 13 0.21
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (31 bp):
AATATTTTATATTATATAAATATAATATATT
Found at i:335258 original size:64 final size:66
Alignment explanation
Indices: 335095--335259 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 66
335085 TTTAATAATT
335095 TATATT-ATTTTTATATTTTTATTATATTATAATTATATTTAAAATATTTTATATTAATATAAAT
1 TATATTAATTTTTATA-TTTTATTATATT-TAA-TATATTTAAAATATTTTATATTAATATAAAT
335159 ATAA
63 ATAA
* * * * * *
335163 TATATTAATAATTTATATTATATTA-ACTTTAATATATTT-ATAT-TTTTATGTCTCATATATAT
1 TATATTAAT-TTTTATATTTTATTATA-TTTAATATATTTAAAATATTTTATAT-TAATATAAAT
335225 AT-A
63 ATAA
*
335228 TATATTAATTTTTATATTTTATCATATTTAAT
1 TATATTAATTTTTATATTTTATTATATTTAAT
335260 GTTATTAAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 14
0.78 0.08 0.13
Matches are distributed among these distances:
64 18 0.22
65 18 0.22
66 13 0.16
67 7 0.08
68 10 0.12
69 11 0.13
70 6 0.07
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (66 bp):
TATATTAATTTTTATATTTTATTATATTTAATATATTTAAAATATTTTATATTAATATAAATATA
A
Found at i:335287 original size:17 final size:18
Alignment explanation
Indices: 335267--335300 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
335257 AATGTTATTA
335267 AATATAATT-ATAATTTT
1 AATATAATTAATAATTTT
*
335284 AATATATTTAATAATTT
1 AATATAATTAATAATTT
335301 ATATTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATAATTAATAATTTT
Found at i:335321 original size:24 final size:25
Alignment explanation
Indices: 335268--335321 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
335258 ATGTTATTAA
* *
335268 ATATAATTATAATTTTAATATATTT
1 ATATAATTATAATTTAAATATATTG
335293 A-ATAATT-TATATTTAAAT-TATTG
1 ATATAATTATA-ATTTAAATATATTG
335316 ATATAA
1 ATATAA
335322 AAATAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 17 0.68
25 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
ATATAATTATAATTTAAATATATTG
Found at i:336307 original size:19 final size:19
Alignment explanation
Indices: 336285--336334 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
336275 TTGAATTCAA
336285 AAAATTTATTTTATTATTT
1 AAAATTTATTTTATTATTT
* * *
336304 AAAATATATTATATTTTTT
1 AAAATTTATTTTATTATTT
*
336323 ATAATTATATTT
1 AAAATT-TATTT
336335 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AAAATTTATTTTATTATTT
Found at i:336369 original size:21 final size:21
Alignment explanation
Indices: 336323--336369 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
336313 TATATTTTTT
336323 ATAATTATATTTAAATAAAAA
1 ATAATTATATTTAAATAAAAA
* * *
336344 TTAATTTTATTT-ATTAAATAA
1 ATAATTATATTTAAATAAA-AA
336365 ATAAT
1 ATAAT
336370 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAATTATATTTAAATAAAAA
Found at i:336848 original size:12 final size:13
Alignment explanation
Indices: 336831--336860 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
336821 TAAATTATAC
336831 TAAATTT-AAATT
1 TAAATTTAAAATT
336843 TAAATTTAAAATT
1 TAAATTTAAAATT
336856 TAAAT
1 TAAAT
336861 CTTTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:336856 original size:7 final size:6
Alignment explanation
Indices: 336831--336860 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
336821 TAAATTATAC
336831 TAAATT TAAATT TAAATT TAAAATT TAAAT
1 TAAATT TAAATT TAAATT T-AAATT TAAAT
336861 CTTTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:338339 original size:21 final size:20
Alignment explanation
Indices: 338309--338347 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
338299 CACATTTTTG
338309 TCCAAATGTATCGATACATT
1 TCCAAATGTATCGATACATT
338329 TCCAGAATGTATCGATACA
1 TCCA-AATGTATCGATACA
338348 AGGTCCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (20 bp):
TCCAAATGTATCGATACATT
Found at i:338358 original size:21 final size:20
Alignment explanation
Indices: 338308--338358 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
338298 TCACATTTTT
*
338308 GTCCAAATGTATCGATACAT
1 GTCCAAATGTATCGATACAG
*
338328 TTCCAGAATGTATCGATACAAG
1 GTCCA-AATGTATCGATAC-AG
*
338350 GTCCCAATG
1 GTCCAAATG
338359 GTCAAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 4 0.16
21 17 0.68
22 4 0.16
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (20 bp):
GTCCAAATGTATCGATACAG
Found at i:341870 original size:22 final size:22
Alignment explanation
Indices: 341845--341896 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
341835 AAGTTCACCT
341845 AACACACCTAATATGTTTACCC
1 AACACACCTAATATGTTTACCC
*
341867 AACACACCTAATATGTTTACCT
1 AACACACCTAATATGTTTACCC
341889 AACACACC
1 AACACACC
341897 ATCTAACACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.33, G:0.04, T:0.25
Consensus pattern (22 bp):
AACACACCTAATATGTTTACCC
Found at i:341907 original size:34 final size:34
Alignment explanation
Indices: 341867--341966 Score: 137
Period size: 37 Copynumber: 2.9 Consensus size: 34
341857 ATGTTTACCC
*
341867 AACACACCTAATATGTTTACCTAACACACCATCT
1 AACACACCTAATATGTTTACCTAACACACCATAT
* * *
341901 AACACACTTAATATATTACTCACCTAACATACCATAT
1 AACACACCTAATATGTT--T-ACCTAACACACCATAT
341938 AACACACCTAATATGTTTACCTAACACAC
1 AACACACCTAATATGTTTACCTAACACAC
341967 TTAATAAAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
34 25 0.45
35 1 0.02
36 1 0.02
37 29 0.52
ACGTcount: A:0.41, C:0.30, G:0.02, T:0.27
Consensus pattern (34 bp):
AACACACCTAATATGTTTACCTAACACACCATAT
Found at i:347156 original size:66 final size:66
Alignment explanation
Indices: 347043--347169 Score: 227
Period size: 66 Copynumber: 1.9 Consensus size: 66
347033 ATAAAAAACT
* *
347043 AACTCATAAAAGAATTTATGGCCAAAATATTTTCAACATTCTATTTTCTTTAGTGTCAACGAAAT
1 AACTCATAAAAGAATTTATGGCCAAAATATTTTCAACATTCTATTTTCTTAAATGTCAACGAAAT
347108 G
66 G
*
347109 AACTCATAAAAGAATTTATGGCCAAAATATTTTCAACATTTTATTTTCTTAAATGTCAACG
1 AACTCATAAAAGAATTTATGGCCAAAATATTTTCAACATTCTATTTTCTTAAATGTCAACG
347170 TTTTATCATC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (66 bp):
AACTCATAAAAGAATTTATGGCCAAAATATTTTCAACATTCTATTTTCTTAAATGTCAACGAAAT
G
Found at i:347303 original size:3 final size:3
Alignment explanation
Indices: 347236--347288 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
347226 TTTTTGCTCT
347236 TTA TTA TTA 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 TTA TTA TTA
347284 TTA TT
1 TTA TT
347289 TAAAAATAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:347446 original size:16 final size:16
Alignment explanation
Indices: 347425--347456 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
347415 GTATCATATT
347425 TATATTTAAAATTTTA
1 TATATTTAAAATTTTA
*
347441 TATATTTAATATTTTA
1 TATATTTAAAATTTTA
347457 CATTGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTTAAAATTTTA
Found at i:349494 original size:2 final size:2
Alignment explanation
Indices: 349489--349517 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
349479 TCTCTATGTG
349489 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
349518 TATCATTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:350070 original size:2 final size:2
Alignment explanation
Indices: 350063--350088 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
350053 TTTTTATCAT
350063 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
350089 AGACTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:350135 original size:24 final size:24
Alignment explanation
Indices: 350108--350157 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
350098 AATTGATTGT
350108 GAAAATCATACATGTAATGGAGGG
1 GAAAATCATACATGTAATGGAGGG
*
350132 GAAAATCATATATGTAATGGAGGG
1 GAAAATCATACATGTAATGGAGGG
350156 GA
1 GA
350158 CCTAAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.06, G:0.30, T:0.22
Consensus pattern (24 bp):
GAAAATCATACATGTAATGGAGGG
Found at i:352395 original size:171 final size:168
Alignment explanation
Indices: 352108--352437 Score: 498
Period size: 171 Copynumber: 1.9 Consensus size: 168
352098 AGAAGCACAT
* * *
352108 ATTAAAAAAAAAAAAAAAACTTTTCTTACAAACTGTAATTGCAAATTATTTAAACTTGATCGGTT
1 ATTAAAAAAAAAAAAAAAACCTTTCTTACAAACTGTAATTGCAAACTATTTAAACTTGATCAGTT
** * *
352173 AATGTTGCATCAGAAACTCGAGTTTGCATCAACCATGAAGTCTAGAAGGGGAATCCGAGTAGAGT
66 AAAATTGCATCAGAAACTCGAGATTGCATCAACCATGAAGTCTAGAAGGGGAATCCGACTAGAGT
* * *
352238 TCATCATATGCATATGATAGATTAAGCTGTTTTAGTAG
131 TCATCATACGCAGATGATAGATAAAGCTGTTTTAGTAG
* *
352276 ATTAAAAAAAAAACAAGAAAACCTTTCTTACAAACTGTATTTGCAAACTATTTATAAGTTGATCA
1 ATTAAAAAAAAAA-AA-AAAACCTTTCTTACAAACTGTAATTGCAAACTATTTA-AACTTGATCA
* *
352341 GTTAAAATTGCATCAGAAACTCGAGATTGCATCACCCATGAAGTCTTGAAGGGGAATCCGACTAG
63 GTTAAAATTGCATCAGAAACTCGAGATTGCATCAACCATGAAGTCTAGAAGGGGAATCCGACTAG
*
352406 AGTTCATCATACGTAGATGATAGATAAAGCTG
128 AGTTCATCATACGCAGATGATAGATAAAGCTG
352438 CCTTACAGAT
Statistics
Matches: 144, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
168 13 0.09
169 2 0.01
170 34 0.24
171 95 0.66
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (168 bp):
ATTAAAAAAAAAAAAAAAACCTTTCTTACAAACTGTAATTGCAAACTATTTAAACTTGATCAGTT
AAAATTGCATCAGAAACTCGAGATTGCATCAACCATGAAGTCTAGAAGGGGAATCCGACTAGAGT
TCATCATACGCAGATGATAGATAAAGCTGTTTTAGTAG
Found at i:354555 original size:2 final size:2
Alignment explanation
Indices: 354481--354541 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
354471 TGAGTATGCA
*
354481 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
354522 AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
354542 TTGATTATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:354915 original size:14 final size:14
Alignment explanation
Indices: 354896--354952 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
354886 ATTTACTTTT
354896 ATTATAAATTTATA
1 ATTATAAATTTATA
* *
354910 ATTATAATTTTTTA
1 ATTATAAATTTATA
*
354924 A-TATATATTTAATA
1 ATTATAAATTT-ATA
354938 ATTATTTAAATTTAT
1 ATTA--TAAATTTAT
354953 TTTAAATCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 7 0.21
14 16 0.48
15 2 0.06
16 2 0.06
17 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATAAATTTATA
Found at i:354956 original size:22 final size:23
Alignment explanation
Indices: 354894--354957 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
354884 GAATTTACTT
*
354894 TTATTATAAATTTATAATT-ATAA
1 TTATT-TAAATTTATATTTAATAA
* *
354917 TT-TTTTAATATATATTTAATAA
1 TTATTTAAATTTATATTTAATAA
354939 TTATTTAAATTTAT-TTTAA
1 TTATTTAAATTTATATTTAA
354958 ATCAATAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 10 0.29
22 13 0.38
23 11 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATTTAAATTTATATTTAATAA
Found at i:356213 original size:3 final size:3
Alignment explanation
Indices: 356205--356237 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
356195 TCTCAAGGCC
356205 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
356238 TAATAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:356498 original size:30 final size:30
Alignment explanation
Indices: 356458--356517 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
356448 TAATCTCTTG
*
356458 AAATTCATATTTATTATTTAATAATTATAT
1 AAATTAATATTTATTATTTAATAATTATAT
356488 AAATTAATATTTATTATTTAATAATTATAT
1 AAATTAATATTTATTATTTAATAATTATAT
356518 GTGTTGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
AAATTAATATTTATTATTTAATAATTATAT
Found at i:356510 original size:14 final size:14
Alignment explanation
Indices: 356464--356515 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
356454 CTTGAAATTC
356464 ATATTTATTATTTA
1 ATATTTATTATTTA
* *
356478 ATAATTATATAAATTA
1 AT-ATT-TATTATTTA
356494 ATATTTATTATTTA
1 ATATTTATTATTTA
*
356508 ATAATTAT
1 ATATTTAT
356516 ATGTGTTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 16 0.52
15 6 0.19
16 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATTTATTATTTA
Found at i:357273 original size:21 final size:21
Alignment explanation
Indices: 357239--357279 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
357229 ACCTCACATT
*
357239 ATTATATTAAATTTAAATATA
1 ATTATATCAAATTTAAATATA
* *
357260 ATTATATCATATTTATATAT
1 ATTATATCAAATTTAAATAT
357280 TTTTATTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTATATCAAATTTAAATATA
Found at i:357329 original size:56 final size:55
Alignment explanation
Indices: 357238--357358 Score: 142
Period size: 56 Copynumber: 2.2 Consensus size: 55
357228 AACCTCACAT
* *
357238 TATTATA-TTAAATTTAAATATAATTATATCATA-TTTATATATTTTTATTTATTA
1 TATTATATTTAAATTTAAATATAATTATATAATATTTTATATATTTTTATAT-TTA
*
357292 TAATTATATTTAAATTTTAATAT-ATTA-ATAAATTATTTTATATATTTTTATATTTA
1 T-ATTATATTTAAATTTAAATATAATTATAT-AA-TATTTTATATATTTTTATATTTA
357348 TATATATATTT
1 TAT-TATATTT
357359 TTTATTATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
54 3 0.05
55 13 0.22
56 26 0.45
57 16 0.28
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (55 bp):
TATTATATTTAAATTTAAATATAATTATATAATATTTTATATATTTTTATATTTA
Found at i:358810 original size:7 final size:7
Alignment explanation
Indices: 358798--358824 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
358788 AATTAGGGGT
358798 AATTTAA
1 AATTTAA
358805 AATTTAA
1 AATTTAA
358812 AATTTAA
1 AATTTAA
358819 AATTTA
1 AATTTA
358825 TATTTTTTAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:358842 original size:6 final size:6
Alignment explanation
Indices: 358798--358869 Score: 53
Period size: 7 Copynumber: 12.0 Consensus size: 6
358788 AATTAGGGGT
* * *
358798 AATTTAA AATTTAA AATTTAA AATTTA TATTTTT TATTTA AATTTA AATTTA
1 AATTT-A AATTT-A AATTT-A AATTTA -AATTTA AATTTA AATTTA AATTTA
358850 AA-TTA AA-TT- AA-TTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA
358870 TTTTAAAGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
4 4 0.07
5 9 0.16
6 20 0.36
7 23 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:358889 original size:26 final size:26
Alignment explanation
Indices: 358811--358889 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 26
358801 TTAAAATTTA
*
358811 AAATTTAAAATTTATATT--TTTTATTT
1 AAATTT-AAATTTAAATTAATTTTA-TT
* *
358837 AAATTTAAATTTAAATTAAATTAATT
1 AAATTTAAATTTAAATTAATTTTATT
* *
358863 AAATTT-ATTTTAAAGTTTATTTTATT
1 AAATTTAAATTTAAA-TTAATTTTATT
358889 A
1 A
358890 TTAAAATACT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
25 17 0.40
26 23 0.53
27 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
AAATTTAAATTTAAATTAATTTTATT
Found at i:359345 original size:19 final size:17
Alignment explanation
Indices: 359296--359364 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 17
359286 TTATTATAAA
359296 ATATATTTATTATTTTTT
1 ATAT-TTTATTATTTTTT
*
359314 ATATCTTAGTTATATTTTT
1 ATATTTTA-TTAT-TTTTT
*
359333 ATATTTTATTTATTATATT
1 ATATTTTA-TTATT-TTTT
*
359352 ATATGTTA-TATTT
1 ATATTTTATTATTT
359365 ATTCTATAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.02
17 7 0.16
18 9 0.21
19 26 0.60
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (17 bp):
ATATTTTATTATTTTTT
Found at i:361147 original size:25 final size:23
Alignment explanation
Indices: 361119--361182 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
361109 TTATATTTAA
361119 AATATTTTATATTTATATAAAATTT
1 AATATTTTATATTTATAT--AATTT
*
361144 AATATATTAATAATTTATATAATTT
1 AATAT-TTTAT-ATTTATATAATTT
* *
361169 ATTATATTATATTT
1 AATATTTTATATTT
361183 TAATTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 4 0.12
24 3 0.09
25 14 0.42
26 4 0.12
27 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTTTATATTTATATAATTT
Found at i:361151 original size:27 final size:27
Alignment explanation
Indices: 361113--361165 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
361103 TTATAATTAT
*
361113 ATTTAAAATATT-TTATATTTATATAAA
1 ATTTAAAATATTAATA-ATTTATATAAA
*
361140 ATTTAATATATTAATAATTTATATAA
1 ATTTAAAATATTAATAATTTATATAA
361166 TTTATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTAAAATATTAATAATTTATATAAA
Found at i:361546 original size:17 final size:18
Alignment explanation
Indices: 361506--361548 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
361496 TTATTACATC
* *
361506 AATTATTATATTATATAT
1 AATTTTTATATTAGATAT
*
361524 ATTTTTTAT-TTAGATAT
1 AATTTTTATATTAGATAT
361541 AATTTTTA
1 AATTTTTA
361549 AAATTAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
AATTTTTATATTAGATAT
Found at i:361960 original size:2 final size:2
Alignment explanation
Indices: 361955--361987 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
361945 AAAAAAATAA
361955 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
361988 ATGGGAAAAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:362839 original size:38 final size:38
Alignment explanation
Indices: 362763--362840 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
362753 AGCCTCAAAC
*
362763 TTAAAAATAAGTAATATAAATATTTAAATTTAAATTTA
1 TTAAAAATAAGTAATATAAATAATTAAATTTAAATTTA
* * * *
362801 TTAAAAATAATTAA-ATAAATAAATTATATTTTATTTTA
1 TTAAAAATAAGTAATATAAAT-AATTAAATTTAAATTTA
362839 TT
1 TT
362841 TTTTTCATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 6 0.18
38 28 0.82
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (38 bp):
TTAAAAATAAGTAATATAAATAATTAAATTTAAATTTA
Found at i:363814 original size:18 final size:18
Alignment explanation
Indices: 363793--363841 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
363783 TTATTTTTAA
363793 AAAATTATTT-AATAAATT
1 AAAA-TATTTAAATAAATT
*
363811 AAAATATTTAAATAATTT
1 AAAATATTTAAATAAATT
*
363829 AAAA-ATTAAAATA
1 AAAATATTTAAATA
363842 TATTTTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATATTTAAATAAATT
Found at i:363840 original size:17 final size:18
Alignment explanation
Indices: 363803--363846 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
363793 AAAATTATTT
* *
363803 AATAAATTAAAATATTTA
1 AATAATTTAAAATATTAA
363821 AATAATTTAAAA-ATTAA
1 AATAATTTAAAATATTAA
363838 AATATATTT
1 AATA-ATTT
363847 TTATCTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATAATTTAAAATATTAA
Found at i:363840 original size:25 final size:26
Alignment explanation
Indices: 363794--363842 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
363784 TATTTTTAAA
*
363794 AAATTATTTAATAAATTAAAATATTT
1 AAATAATTTAATAAATTAAAATATTT
363820 AAATAATTTAA-AAATTAAAATAT
1 AAATAATTTAATAAATTAAAATAT
363843 ATTTTTATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATAATTTAATAAATTAAAATATTT
Found at i:365125 original size:19 final size:20
Alignment explanation
Indices: 365103--365140 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
365093 CATGCTGTAT
*
365103 ATTATTATTTTAT-TTTTTA
1 ATTAATATTTTATATTTTTA
365122 ATTAATATTTTATATTTTT
1 ATTAATATTTTATATTTTT
365141 TAAATTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTAATATTTTATATTTTTA
Found at i:369418 original size:15 final size:14
Alignment explanation
Indices: 369382--369419 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
369372 TTTAAATAAT
*
369382 AAAATATTTTTTTA
1 AAAATATTATTTTA
369396 AAAA-ATTATTTTA
1 AAAATATTATTTTA
369409 AATAATATTAT
1 AA-AATATTAT
369420 AAAATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 10 0.48
14 6 0.29
15 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAATATTATTTTA
Found at i:369428 original size:33 final size:34
Alignment explanation
Indices: 369363--369430 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
369353 TTAATTGATT
***
369363 AAAATTAATTTTAAATAATAAAATATTTTTTTAA
1 AAAATTAATTTTAAATAATAAAATAAAATTTTAA
**
369397 AAAATT-ATTTTAAATAATATTATAAAATTTTAA
1 AAAATTAATTTTAAATAATAAAATAAAATTTTAA
369430 A
1 A
369431 TTACTTTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 23 0.79
34 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
AAAATTAATTTTAAATAATAAAATAAAATTTTAA
Found at i:369571 original size:20 final size:21
Alignment explanation
Indices: 369542--369586 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
369532 GATATAAAAT
369542 TATAAAAAATATAAAAATAA-
1 TATAAAAAATATAAAAATAAC
* *
369562 TATAATAAATATAATAATAAC
1 TATAAAAAATATAAAAATAAC
369583 TATA
1 TATA
369587 TATTTCCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
TATAAAAAATATAAAAATAAC
Found at i:369598 original size:29 final size:26
Alignment explanation
Indices: 369566--369632 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 26
369556 AAATAATATA
369566 ATAAATATAATA-ATAACTATATATTTCCT
1 ATAAATATAATACA-AA-TATAT-TTT-CT
*
369595 ATAAATATAAATACAAATATATTTTTT
1 ATAAATAT-AATACAAATATATTTTCT
369622 ATAAATATAAT
1 ATAAATATAAT
369633 TATGATAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
26 3 0.09
27 9 0.26
28 3 0.09
29 13 0.37
30 6 0.17
31 1 0.03
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (26 bp):
ATAAATATAATACAAATATATTTTCT
Found at i:373407 original size:41 final size:43
Alignment explanation
Indices: 373362--373453 Score: 102
Period size: 41 Copynumber: 2.2 Consensus size: 43
373352 TTTAATTTAA
*
373362 TTTATTTATATTA-TTTATAATT-AATAAAAATAACAAAT-ATT
1 TTTATTTATAATATTTTATAATTAAATAAAAATAA-AAATAATT
* **
373403 TTTATATA-AATATTTTATAATTAAATTTAAATAAAAATAATT
1 TTTATTTATAATATTTTATAATTAAATAAAAATAAAAATAATT
*
373445 TTTAATTAT
1 TTTATTTAT
373454 TAACTATCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
40 3 0.07
41 20 0.49
42 18 0.44
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (43 bp):
TTTATTTATAATATTTTATAATTAAATAAAAATAAAAATAATT
Found at i:374050 original size:21 final size:19
Alignment explanation
Indices: 374041--374080 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 19
374031 TTAAAATATT
374041 ATATAAAATAAAAAAATTG
1 ATATAAAATAAAAAAATTG
374060 ATATAAATATATAAATAAATT
1 ATATAAA-ATA-AAA-AAATT
374081 AAAATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 3 0.17
22 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
ATATAAAATAAAAAAATTG
Found at i:374067 original size:18 final size:19
Alignment explanation
Indices: 374023--374074 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 19
374013 TTAGACAAAA
374023 ATAAATAATTAAAATATTAT
1 ATAAATAA-TAAAATATTAT
374043 ATAAAATAA-AAAA-ATTGAT
1 AT-AAATAATAAAATATT-AT
374062 ATAAATATATAAA
1 ATAAATA-ATAAA
374075 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 8 0.29
19 9 0.32
20 5 0.18
21 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAAATAATAAAATATTAT
Found at i:374095 original size:27 final size:24
Alignment explanation
Indices: 374036--374100 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 24
374026 AATAATTAAA
*
374036 ATATTATATAAAATAAAAAAATTG
1 ATATAATATAAAATAAAAAAATTG
*
374060 ATATAAATATATAAATAAATTAAAATTT
1 ATAT-AATATA-AAATAAA--AAAATTG
374088 ATATAATA-AAAAT
1 ATATAATATAAAAT
374101 TATTAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
24 4 0.11
25 9 0.26
26 8 0.23
27 4 0.11
28 10 0.29
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
ATATAATATAAAATAAAAAAATTG
Found at i:374109 original size:18 final size:19
Alignment explanation
Indices: 374023--374126 Score: 63
Period size: 18 Copynumber: 5.3 Consensus size: 19
374013 TTAGACAAAA
374023 ATAA-ATAATTAAAATATTAT
1 ATAATATAA-TAAAA-ATTAT
*
374043 ATAAAATAA-AAAAATTGAT
1 ATAATATAATAAAAATT-AT
*
374062 ATAA-ATATATAAATAAATTAAA
1 ATAATATA-AT-AA-AAATT-AT
*
374084 ATTTATATAATAAAAATTAT
1 A-TAATATAATAAAAATTAT
* *
374104 -TAATATATTAAAATTTAT
1 ATAATATAATAAAAATTAT
374122 ATAAT
1 ATAAT
374127 TATTTATTAT
Statistics
Matches: 68, Mismatches: 7, Indels: 19
0.72 0.07 0.20
Matches are distributed among these distances:
18 21 0.31
19 15 0.22
20 5 0.07
21 11 0.16
22 9 0.13
23 4 0.06
24 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (19 bp):
ATAATATAATAAAAATTAT
Found at i:374115 original size:32 final size:33
Alignment explanation
Indices: 374064--374126 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
374054 AAATTGATAT
374064 AAATATATAAATAAATTAAAATTTATATAATAA
1 AAATATATAAATAAATTAAAATTTATATAATAA
* *
374097 AAAT-TATTAATATATTAAAATTTATATAAT
1 AAATATATAAATAAATTAAAATTTATATAAT
374127 TATTTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
AAATATATAAATAAATTAAAATTTATATAATAA
Found at i:375789 original size:2 final size:2
Alignment explanation
Indices: 375782--375825 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
375772 TTAGTGATAG
375782 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
375824 AT
1 AT
375826 GACATTCACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:379203 original size:12 final size:11
Alignment explanation
Indices: 379176--379209 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
379166 TGTTATTTTT
379176 TATTTTTAATA
1 TATTTTTAATA
*
379187 TATTTTTAATT
1 TATTTTTAATA
379198 TAATTTTTAATA
1 T-ATTTTTAATA
379210 ATAAACATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTTAATA
Found at i:379313 original size:20 final size:21
Alignment explanation
Indices: 379290--379333 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
379280 ATAAGTTAAA
379290 AAATAGTAAAATAAAAT-TAT
1 AAATAGTAAAATAAAATATAT
* **
379310 AAATATTATTATAAAATATAT
1 AAATAGTAAAATAAAATATAT
379331 AAA
1 AAA
379334 ATTATATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATAGTAAAATAAAATATAT
Found at i:379337 original size:20 final size:20
Alignment explanation
Indices: 379300--379338 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
379290 AAATAGTAAA
379300 ATAAAATTATAAATATTATT
1 ATAAAATTATAAATATTATT
379320 ATAAAATATATAAA-ATTAT
1 ATAAAAT-TATAAATATTAT
379339 ATTTTAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAAATTATAAATATTATT
Found at i:380290 original size:3 final size:3
Alignment explanation
Indices: 380284--380319 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
380274 TCATACATTA
380284 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
380320 TTATTCAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:380477 original size:14 final size:14
Alignment explanation
Indices: 380460--380486 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
380450 AATTTATTTT
380460 ATATAAATTTTAAA
1 ATATAAATTTTAAA
380474 ATATAAATTTTAA
1 ATATAAATTTTAA
380487 TTATATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATAAATTTTAAA
Found at i:380510 original size:27 final size:26
Alignment explanation
Indices: 380441--380538 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 26
380431 TAGATTATTA
*
380441 TATATTAATAATTTATTTTATATAAATTT
1 TATATT-AT-ATTTATTTTA-ATTAATTT
* **
380470 TA-A-AATATAAATTTTAATT-ATATT
1 TATATTATATTTATTTTAATTAAT-TT
380494 TATATTATATTATATTTTAATTAATTT
1 TATATTATATT-TATTTTAATTAATTT
*
380521 TATTTTATATTTATTTTA
1 TATATTATATTTATTTTA
380539 TGTAGTTATA
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
23 2 0.04
24 6 0.11
25 9 0.16
26 13 0.23
27 21 0.38
28 3 0.05
29 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TATATTATATTTATTTTAATTAATTT
Found at i:380537 original size:11 final size:11
Alignment explanation
Indices: 380487--380539 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 11
380477 TAAATTTTAA
*
380487 TTATATTTATA
1 TTATATTTATT
380498 TTATATTATATT
1 TTATATT-TATT
380510 TTAATTAATTTTATT
1 TT-A-T-A-TTTATT
380525 TTATATTTATT
1 TTATATTTATT
380536 TTAT
1 TTAT
380540 GTAGTTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
11 17 0.47
12 6 0.17
13 2 0.06
14 2 0.06
15 7 0.19
16 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATTTATT
Found at i:380538 original size:16 final size:16
Alignment explanation
Indices: 380487--380539 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
380477 TAAATTTTAA
380487 TTATATTTATATTATATT
1 TTAT-TTTATATT-TATT
* *
380505 ATATTTTA-ATTAATT
1 TTATTTTATATTTATT
380520 TTATTTTATATTTATT
1 TTATTTTATATTTATT
380536 TTAT
1 TTAT
380540 GTAGTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 10 0.33
16 13 0.43
17 4 0.13
18 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTATATTTATT
Found at i:389372 original size:52 final size:52
Alignment explanation
Indices: 389290--389393 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
389280 AATATATCAA
* * *
389290 GGTCTTGGCGTGCCTAAGTTGCTGGTTTGTAGTTGGAACATTAGTACCCGCC
1 GGTCTTGGCATGCCTAAGTTGCCGGGTTGTAGTTGGAACATTAGTACCCGCC
389342 GGTCTTGGCATGCCTAAGTTGCCGGGTTGTAGTTGGAACATTAGTACCCGCC
1 GGTCTTGGCATGCCTAAGTTGCCGGGTTGTAGTTGGAACATTAGTACCCGCC
389394 TGCAGTAGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (52 bp):
GGTCTTGGCATGCCTAAGTTGCCGGGTTGTAGTTGGAACATTAGTACCCGCC
Found at i:392474 original size:6 final size:6
Alignment explanation
Indices: 392463--392523 Score: 50
Period size: 7 Copynumber: 8.8 Consensus size: 6
392453 AATATTTAAT
392463 AATTTA AATTTA AATTTTA AATTTTA ATATTTTAA AATTTA AATTTTA
1 AATTTA AATTTA AA-TTTA AA-TTTA A-A-TTT-A AATTTA AA-TTTA
392511 ATATTTA TAATTT
1 A-ATTTA -AATTT
392524 TTTTTTTATC
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
6 11 0.22
7 28 0.57
8 8 0.16
9 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
AATTTA
Found at i:392475 original size:14 final size:14
Alignment explanation
Indices: 392456--392517 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
392446 AAAAAATAAT
*
392456 ATTTAATAATTTAA
1 ATTTAATATTTTAA
392470 ATTTAA-ATTTTAA
1 ATTTAATATTTTAA
392483 ATTTTAATATTTTAAA
1 A-TTTAATATTTT-AA
392499 ATTTAA-ATTTTAA
1 ATTTAATATTTTAA
392512 TATTTA
1 -ATTTA
392518 TAATTTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
13 9 0.21
14 21 0.49
15 10 0.23
16 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTAATATTTTAA
Found at i:392503 original size:22 final size:22
Alignment explanation
Indices: 392471--392516 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
392461 ATAATTTAAA
*
392471 TTTAAATTTTAAATTTTAATAT
1 TTTAAAATTTAAATTTTAATAT
392493 TTTAAAATTTAAATTTTAATAT
1 TTTAAAATTTAAATTTTAATAT
392515 TT
1 TT
392517 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTAAAATTTAAATTTTAATAT
Found at i:392509 original size:29 final size:29
Alignment explanation
Indices: 392452--392526 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
392442 CAATAAAAAA
*
392452 TAATA-TTTAATAATTTAAATTTAAATTT
1 TAATATTTTAATATTTTAAATTTAAATTT
392480 TAA-ATTTTAATATTTTAAAATTTAAATTT
1 TAATATTTTAATATTTT-AAATTTAAATTT
*
392509 TAATATTTATAATTTTTT
1 TAATATTT-TAATATTTT
392527 TTTTATCCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
27 1 0.02
28 13 0.32
29 15 0.37
30 4 0.10
31 8 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TAATATTTTAATATTTTAAATTTAAATTT
Found at i:396444 original size:21 final size:22
Alignment explanation
Indices: 396420--396468 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
396410 ATGCATTATT
396420 ATTAAT-AAATATTTAAA-AAAA
1 ATTAATAAAAT-TTTAAATAAAA
* *
396441 ATTATTAAAATTTTAAATAATA
1 ATTAATAAAATTTTAAATAAAA
396463 ATTAAT
1 ATTAAT
396469 TATTTAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATAAAATTTTAAATAAAA
Found at i:396802 original size:14 final size:14
Alignment explanation
Indices: 396756--396803 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
396746 ATCAAAATTT
396756 ATTTATATTTTT--A
1 ATTTA-ATTTTTAAA
396769 ATTT-ATTTTTAAAA
1 ATTTAATTTTT-AAA
396783 ATTTAATTTTTAAA
1 ATTTAATTTTTAAA
396797 ATTTAAT
1 ATTTAAT
396804 AATTTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.19
13 4 0.13
14 15 0.48
15 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTAATTTTTAAA
Found at i:396807 original size:22 final size:22
Alignment explanation
Indices: 396776--396826 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
396766 TTAATTTATT
396776 TTTAAAAATTTAATTTT-TAAAA
1 TTTAAAAATTT-ATTTTATAAAA
* *
396798 TTTAATAATTTATTTTATTAAA
1 TTTAAAAATTTATTTTATAAAA
396820 TTTAAAA
1 TTTAAAA
396827 TATAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAAAAATTTATTTTATAAAA
Found at i:396916 original size:24 final size:24
Alignment explanation
Indices: 396858--396928 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
396848 TTTAATATTT
* * *
396858 TTAATATAATA-CTACATGTAAAA
1 TTAATATAATATATAAATATAAAA
396881 -TAATATAATATATAAATATAAAA
1 TTAATATAATATATAAATATAAAA
* *
396904 TTAATATATTATATAATTATAAAA
1 TTAATATAATATATAAATATAAAA
396928 T
1 T
396929 GAATTGACCT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 10 0.24
23 9 0.22
24 22 0.54
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (24 bp):
TTAATATAATATATAAATATAAAA
Found at i:397533 original size:33 final size:33
Alignment explanation
Indices: 397476--397544 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 33
397466 TTTAATTTTT
* *
397476 TTTTGATATATTTATATTTATATTTATA-AAAA
1 TTTTAATATATTAATATTTATATTTATATAAAA
397508 TTTTAATATATTAATAATTTATATTTATATAAAA
1 TTTTAATATATTAAT-ATTTATATTTATATAAAA
397542 TTT
1 TTT
397545 AAAATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 13 0.39
33 13 0.39
34 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (33 bp):
TTTTAATATATTAATATTTATATTTATATAAAA
Found at i:397543 original size:17 final size:17
Alignment explanation
Indices: 397491--397545 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
397481 ATATATTTAT
397491 ATTTATATTTATA-AAA
1 ATTTATATTTATATAAA
*
397507 ATTT-TA-ATATATTAATA
1 ATTTATATTTATA-TAA-A
397524 ATTTATATTTATATAAA
1 ATTTATATTTATATAAA
397541 ATTTA
1 ATTTA
397546 AAATTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.12
15 2 0.06
16 6 0.19
17 11 0.34
18 5 0.16
19 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATATTTATATAAA
Found at i:397860 original size:13 final size:14
Alignment explanation
Indices: 397829--397859 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
397819 AGGTATGAAA
*
397829 AAAATTTAAAAATT
1 AAAATTAAAAAATT
397843 AAAATTAAAAAATT
1 AAAATTAAAAAATT
397857 AAA
1 AAA
397860 TATGATAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTAAAAAATT
Found at i:399163 original size:19 final size:20
Alignment explanation
Indices: 399139--399176 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
399129 AATTTTTAAA
399139 AAATTTTAATTA-AATTATT
1 AAATTTTAATTATAATTATT
399158 AAATTTTAATTATAATTAT
1 AAATTTTAATTATAATTAT
399177 AAAGTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTTAATTATAATTATT
Found at i:399214 original size:14 final size:14
Alignment explanation
Indices: 399195--399221 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
399185 TTTTTTTTCC
399195 ATTTAACATTATGA
1 ATTTAACATTATGA
399209 ATTTAACATTATG
1 ATTTAACATTATG
399222 GTTCGACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (14 bp):
ATTTAACATTATGA
Found at i:400288 original size:18 final size:17
Alignment explanation
Indices: 400253--400300 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
400243 CATCCATCTT
400253 TGCTCCTTTG-CT-TTC
1 TGCTCCTTTGCCTATTC
400268 TGCTCCTTCTGCCTATTC
1 TGCTCCTT-TGCCTATTC
400286 TGCTCCTTTTGCCTA
1 TGCTCC-TTTGCCTA
400301 AGCTTTCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.28
16 2 0.07
17 2 0.07
18 15 0.52
19 2 0.07
ACGTcount: A:0.04, C:0.35, G:0.12, T:0.48
Consensus pattern (17 bp):
TGCTCCTTTGCCTATTC
Found at i:401999 original size:10 final size:10
Alignment explanation
Indices: 401983--402022 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
401973 TAATGTTTTA
401983 TTAATATATT
1 TTAATATATT
*
401993 TTTATATATT
1 TTAATATATT
402003 TTAAT-TATAT
1 TTAATATAT-T
402013 TTAATATATT
1 TTAATATATT
402023 ATACATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 3 0.12
10 20 0.77
11 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTAATATATT
Found at i:402019 original size:20 final size:20
Alignment explanation
Indices: 401983--402036 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
401973 TAATGTTTTA
*
401983 TTAA-TATATTTTTATATATT
1 TTAATTATA-TTTAATATATT
402003 TTAATTATATTTAATATATT
1 TTAATTATATTTAATATATT
*
402023 ATACATT-TATTTAA
1 TTA-ATTATATTTAA
402037 ATTTTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATTATATTTAATATATT
Found at i:402332 original size:14 final size:15
Alignment explanation
Indices: 402290--402329 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
402280 TAATAATTTT
*
402290 AAATATATATAATAA
1 AAATATAAATAATAA
402305 AAA-ATAAATAATAA
1 AAATATAAATAATAA
402319 AAATATAAATA
1 AAATATAAATA
402330 TAATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATATAAATAATAA
Found at i:402383 original size:14 final size:14
Alignment explanation
Indices: 402333--402385 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
402323 ATAAATATAA
*
402333 TATATATCAAAATT
1 TATATATTAAAATT
*
402347 TATTTATTATAAATTAT
1 TATATATTA-AAA-T-T
402364 TAATATATTAAAATT
1 T-ATATATTAAAATT
402379 TATATAT
1 TATATAT
402386 AATATCATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 13 0.41
15 5 0.16
16 2 0.06
17 5 0.16
18 7 0.22
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATATTAAAATT
Found at i:402402 original size:32 final size:31
Alignment explanation
Indices: 402323--402403 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 31
402313 TAATAAAAAT
* *
402323 ATAAATATAATATATATCAAAATTTATTTATT
1 ATAAATA-AATATATATCAAAATTTATATATA
* * *
402355 ATAAATTATTAATATATTAAAATTTATATATA
1 ATAAATAAAT-ATATATCAAAATTTATATATA
*
402387 ATATCATAAATATATAT
1 ATA-AATAAATATATAT
402404 AATATTAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
31 2 0.05
32 33 0.85
33 4 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (31 bp):
ATAAATAAATATATATCAAAATTTATATATA
Found at i:402412 original size:16 final size:17
Alignment explanation
Indices: 402289--402412 Score: 66
Period size: 16 Copynumber: 7.2 Consensus size: 17
402279 TTAATAATTT
402289 TAAATATATATAATA-A
1 TAAATATATATAATATA
* * *
402305 AAAATAAATAATAAAAATA
1 TAAATATAT-AT-AATATA
402324 TAAATATA-AT-ATATA
1 TAAATATATATAATATA
* *
402339 TCAAA-ATTTAT-TTATTA
1 T-AAATATATATAATA-TA
402356 TAAAT-TAT-TAATATA
1 TAAATATATATAATATA
402371 TTAAAATTTATATATAATATCA
1 -T-AAA--TATATATAATAT-A
402393 TAAATATATATAATAT-
1 TAAATATATATAATATA
402409 TAAA
1 TAAA
402413 AAAAAGTAAC
Statistics
Matches: 83, Mismatches: 10, Indels: 30
0.67 0.08 0.24
Matches are distributed among these distances:
15 10 0.12
16 26 0.31
17 10 0.12
18 15 0.18
19 8 0.10
20 6 0.07
21 7 0.08
22 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATATATATAATATA
Found at i:402719 original size:16 final size:16
Alignment explanation
Indices: 402684--402717 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
402674 TTTTAAAGTA
402684 TTTATATATATGATAT
1 TTTATATATATGATAT
*
402700 TTTATATAT-TTATAT
1 TTTATATATATGATAT
402715 TTT
1 TTT
402718 TAAAAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTATATATATGATAT
Found at i:405472 original size:28 final size:26
Alignment explanation
Indices: 405420--405474 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
405410 TATATTTAAT
*
405420 TTTTTATATTTATATTTAAAATATTA
1 TTTTTATATTCATATTTAAAATATTA
*
405446 TTTTTATATTCATATTTCAAATA-TA
1 TTTTTATATTCATATTTAAAATATTA
405471 TTTT
1 TTTT
405475 AAATACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTTATATTCATATTTAAAATATTA
Found at i:408320 original size:2 final size:2
Alignment explanation
Indices: 408313--408350 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
408303 ACCAAATGTA
408313 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
408351 TAAACTGACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:410273 original size:14 final size:15
Alignment explanation
Indices: 410250--410317 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
410240 AAATTAACTC
410250 AAATTAATTAATTTT
1 AAATTAATTAATTTT
410265 AAATT-ATTAATTTT
1 AAATTAATTAATTTT
* *
410279 ---TT-ATCAA-CTT
1 AAATTAATTAATTTT
*
410289 AAATTAATTTAAATTT
1 AAATTAA-TTAATTTT
410305 AAATTAATTAATT
1 AAATTAATTAATT
410318 AACTTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 2 0.05
11 6 0.14
13 2 0.05
14 10 0.24
15 13 0.31
16 9 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATTAATTAATTTT
Found at i:411074 original size:14 final size:15
Alignment explanation
Indices: 411057--411101 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
411047 ATTATAAAAA
*
411057 TATTTTTATTAT-TT
1 TATTTATATTATATT
411071 TATTTATATTATATT
1 TATTTATATTATATT
*
411086 TATATA-ATTATATT
1 TATTTATATTATATT
411100 TA
1 TA
411102 AAATTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTATATTATATT
Found at i:413827 original size:159 final size:159
Alignment explanation
Indices: 413538--413855 Score: 636
Period size: 159 Copynumber: 2.0 Consensus size: 159
413528 GCATCTCTTG
413538 CATTGCGATAATGCTGTTTAGTTAATGCCTTAATAATATGTTACTAATTTGGCAAGATTGATTTT
1 CATTGCGATAATGCTGTTTAGTTAATGCCTTAATAATATGTTACTAATTTGGCAAGATTGATTTT
413603 AATTTGCACATGCTATGAAGATTAAACATGATTAAAATATAATGAGCACTTTGGGATGCGTACAC
66 AATTTGCACATGCTATGAAGATTAAACATGATTAAAATATAATGAGCACTTTGGGATGCGTACAC
413668 TCTTTATTTAGCTAATAACAAGAAGATTA
131 TCTTTATTTAGCTAATAACAAGAAGATTA
413697 CATTGCGATAATGCTGTTTAGTTAATGCCTTAATAATATGTTACTAATTTGGCAAGATTGATTTT
1 CATTGCGATAATGCTGTTTAGTTAATGCCTTAATAATATGTTACTAATTTGGCAAGATTGATTTT
413762 AATTTGCACATGCTATGAAGATTAAACATGATTAAAATATAATGAGCACTTTGGGATGCGTACAC
66 AATTTGCACATGCTATGAAGATTAAACATGATTAAAATATAATGAGCACTTTGGGATGCGTACAC
413827 TCTTTATTTAGCTAATAACAAGAAGATTA
131 TCTTTATTTAGCTAATAACAAGAAGATTA
413856 TATGCTTTCT
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 159 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (159 bp):
CATTGCGATAATGCTGTTTAGTTAATGCCTTAATAATATGTTACTAATTTGGCAAGATTGATTTT
AATTTGCACATGCTATGAAGATTAAACATGATTAAAATATAATGAGCACTTTGGGATGCGTACAC
TCTTTATTTAGCTAATAACAAGAAGATTA
Found at i:421984 original size:2 final size:2
Alignment explanation
Indices: 421977--422044 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
421967 TACTGATCTC
*
421977 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT AT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
422019 GT GT GT GT GT GT GT GT GC GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
422045 TTCCTGAGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.01, C:0.01, G:0.49, T:0.49
Consensus pattern (2 bp):
GT
Found at i:423267 original size:2 final size:2
Alignment explanation
Indices: 423262--423296 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
423252 AGTATATATA
423262 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
423297 CTTTTATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:424284 original size:4 final size:4
Alignment explanation
Indices: 424275--424306 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
424265 CAACCAAATA
424275 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
424307 TTCACTAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:426272 original size:13 final size:13
Alignment explanation
Indices: 426254--426280 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
426244 ACTCGAATTC
426254 ATATGTCAGTATA
1 ATATGTCAGTATA
426267 ATATGTCAGTATA
1 ATATGTCAGTATA
426280 A
1 A
426281 GAGACAAAGT
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:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATATGTCAGTATA
Found at i:429599 original size:50 final size:50
Alignment explanation
Indices: 429542--429795 Score: 324
Period size: 50 Copynumber: 5.2 Consensus size: 50
429532 AGTTGTTGTC
* * * *
429542 ATTGTTGACTATCCTTCACCAACCTTTGACAATAAAGAGAAGTGGCCATC
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAAAGAGAGGTGGCCATA
*
429592 ATTGTTGACGATTCTTCACCAACCTTTGACAAT--A-A-A-GTGGTCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAAAGAGAGGTGGCCATA
*
429637 ATTGTTGACGATTCTTCACCAACCTTTAACAATAGAA-AGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATA-AAGAGAGGTGGCCATA
* * *
429687 ATTGTTCATGATTCTTCACCAACCTTTGACAATAGAAG-GAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATA-AAGAGAGGTGGCCATA
* * * *
429737 ATTATTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGTCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAAAGAGAGGTGGCCATA
429787 ATTGTTGAC
1 ATTGTTGAC
429796 TCTAAGTATA
Statistics
Matches: 180, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
45 39 0.22
46 1 0.01
47 1 0.01
48 3 0.02
49 3 0.02
50 133 0.74
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAAAGAGAGGTGGCCATA
Found at i:429700 original size:95 final size:98
Alignment explanation
Indices: 429542--429792 Score: 339
Period size: 95 Copynumber: 2.6 Consensus size: 98
429532 AGTTGTTGTC
* * * * *
429542 ATTGTTGACTATCCTTCACCAACCTTTGACAATA-AAGAGAAGTGGCCATCATTGTTGACGATTC
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAA-AGAGGTGGCCATAATTGTTCACGATTC
*
429606 TTCACCAACCTTTGACAATA-AA-GTGGT-CATA
65 TTCACCAACCTTTGACAATAGAAGGAGGTACATA
* *
429637 ATTGTTGACGATTCTTCACCAACCTTTAACAATAGAAAGAGGTGGCCATAATTGTTCATGATTCT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAGAGGTGGCCATAATTGTTCACGATTCT
429702 TCACCAACCTTTGACAATAGAAGGAGGTGACCATA
66 TCACCAACCTTTGACAATAGAAGGAGGT-A-CATA
* ** *
429737 ATTATTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGTCATAATTGTT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAGAGGTGGCCATAATTGTT
429793 GACTCTAAGT
Statistics
Matches: 137, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
95 74 0.54
96 4 0.03
97 4 0.03
100 55 0.40
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (98 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAGAGGTGGCCATAATTGTTCACGATTCT
TCACCAACCTTTGACAATAGAAGGAGGTACATA
Found at i:434200 original size:50 final size:50
Alignment explanation
Indices: 434131--434339 Score: 312
Period size: 50 Copynumber: 4.2 Consensus size: 50
434121 AGTTGTTGCC
* * * *
434131 ATTGTTGACTATCCTTCACCAATCTTTGACAATAGAGAGAGGTGGCCATC
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
434181 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
434231 ATTGTTGACGATTCTTCACTAACCTTTGACAATAGA-ATGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGA-GAGGTGGCCATA
** * * *
434281 ATTGTTGATAATTTTTCACCAACCTTTGACAATAGAGGGAGGTGGTCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
434331 ATTGTTGAC
1 ATTGTTGAC
434340 TTTAAGTATA
Statistics
Matches: 145, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
49 1 0.01
50 144 0.99
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:440275 original size:32 final size:31
Alignment explanation
Indices: 440200--440275 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 31
440190 TTCAATCACT
*
440200 AATGTAGAAAAGTAAAAAATAAAAGTTTTAG
1 AATGTAGAAAATTAAAAAATAAAAGTTTTAG
** * *
440231 TGTGTATAAAAATTAAAAGAATATAA-TTTTAG
1 AATGTA-GAAAATTAAAA-AATAAAAGTTTTAG
440263 AATGTAGCAAAAT
1 AATGTAG-AAAAT
440276 AATAATGTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
31 4 0.12
32 24 0.71
33 6 0.18
ACGTcount: A:0.54, C:0.01, G:0.14, T:0.30
Consensus pattern (31 bp):
AATGTAGAAAATTAAAAAATAAAAGTTTTAG
Found at i:440775 original size:25 final size:25
Alignment explanation
Indices: 440718--440800 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
440708 TTTATATGCT
* * *
440718 TATATTATTTATATTTACTATTCATA
1 TATATTTTTTATA-TTAATATTTATA
440744 -ATAATTTTTTATATTAATATTTATA
1 TAT-ATTTTTTATATTAATATTTATA
* *
440769 TATATTTTATA-ATTAA-ATTTAAA
1 TATATTTTTTATATTAATATTTATA
440792 TA-ATTTTTT
1 TATATTTTTT
440801 TAATTATTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
22 6 0.12
23 8 0.16
24 5 0.10
25 19 0.39
26 11 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TATATTTTTTATATTAATATTTATA
Found at i:440788 original size:23 final size:22
Alignment explanation
Indices: 440750--440814 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
440740 CATAATAATT
*
440750 TTTTATATTAATATTTATATATA
1 TTTTATATTAATATTTAAATA-A
440773 TTTTATAATTAA-ATTTAAATAA
1 TTTTAT-ATTAATATTTAAATAA
440795 TTTT-T-TTAAT-TATTAAATAA
1 TTTTATATTAATAT-TTAAATAA
440815 AAATTCGAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 5 0.13
20 8 0.21
21 1 0.03
22 5 0.13
23 14 0.37
24 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTATATTAATATTTAAATAA
Found at i:440882 original size:26 final size:26
Alignment explanation
Indices: 440846--440905 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
440836 GATCCAAATT
* *
440846 TATAAAAAAACTTATCTA-AAACTCGA
1 TATAAATAAACTAATCTATAAACT-GA
440872 TATAAATAAACTAATCTATTAAACTGA
1 TATAAATAAACTAATCTA-TAAACTGA
440899 -ATAAATA
1 TATAAATA
440906 GTTCAACTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 23 0.77
27 2 0.07
28 5 0.17
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (26 bp):
TATAAATAAACTAATCTATAAACTGA
Found at i:440922 original size:2 final size:2
Alignment explanation
Indices: 440915--440951 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
440905 AGTTCAACTC
440915 AT AT 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 AT AT A
440952 GTCTATAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:441787 original size:21 final size:21
Alignment explanation
Indices: 441761--441800 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
441751 TATTAAAATA
441761 ATATTTT-TAATTAATATTTTT
1 ATATTTTATAATTAA-ATTTTT
441782 ATATTTTATAATTAAATTT
1 ATATTTTATAATTAAATTT
441801 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTTT
Found at i:443984 original size:30 final size:30
Alignment explanation
Indices: 443920--443985 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
443910 AAATTAAAAT
*
443920 TTATTTAGGTACAAATTAAAGATTAAGAGT
1 TTATTTAGGTACAAATTAAAGATTAAGAGC
* *
443950 TTATTTA-GTCACAAGTTAAA-AGTTAATAGC
1 TTATTTAGGT-ACAAATTAAAGA-TTAAGAGC
443980 TTATTT
1 TTATTT
443986 GAATGTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (30 bp):
TTATTTAGGTACAAATTAAAGATTAAGAGC
Found at i:444863 original size:22 final size:21
Alignment explanation
Indices: 444838--444879 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
444828 ACTTTAAAAA
444838 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
444858 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
444879 A
1 A
444880 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:445657 original size:12 final size:12
Alignment explanation
Indices: 445640--445679 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
445630 TTTTTACGTA
445640 TTATATTATATT
1 TTATATTATATT
445652 TTATATTATATT
1 TTATATTATATT
445664 TTA-ATTAT-TT
1 TTATATTATATT
445674 TTATAT
1 TTATAT
445680 ATTACTCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 5 0.19
11 7 0.26
12 15 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATATTATATT
Done.