Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold378
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: 305097
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 3
Found at i:221921 original size:11 final size:11
Alignment explanation
Indices: 221886--221947 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
221876 AAATAGCACC
221886 ATATAAAAA-A
1 ATATAAAAATA
*
221896 AT-TAAAATTTA
1 ATATAAAA-ATA
221907 ATATAAAAATA
1 ATATAAAAATA
*
221918 ATATAAATAA-G
1 ATATAAA-AATA
*
221929 ATGTAAAAAT-
1 ATATAAAAATA
221939 ATATAAAAA
1 ATATAAAAA
221948 ATTAGATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
9 5 0.12
10 12 0.29
11 18 0.43
12 7 0.17
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:226677 original size:3 final size:3
Alignment explanation
Indices: 226669--226703 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
226659 CTTTTTTCTG
226669 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
226704 TTGGTTTCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:227636 original size:14 final size:14
Alignment explanation
Indices: 227617--227643 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
227607 ATATAAAAAA
227617 TATGTGTGTGTGTG
1 TATGTGTGTGTGTG
227631 TATGTGTGTGTGT
1 TATGTGTGTGTGT
227644 ACACACACTT
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:0.07, C:0.00, G:0.41, T:0.52
Consensus pattern (14 bp):
TATGTGTGTGTGTG
Found at i:228210 original size:44 final size:44
Alignment explanation
Indices: 228161--228252 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
228151 GACCGAAATA
*
228161 AGTACCCACAACCACAAGAACAGGTGATAGGTGAGTGCAACAAT
1 AGTACCCACAACCACAAGAACAGGTGATAGGTGACTGCAACAAT
228205 AGTACCCACAACCACAAGAACAGGTGATAGGTGACTGCAACAAT
1 AGTACCCACAACCACAAGAACAGGTGATAGGTGACTGCAACAAT
228249 AGTA
1 AGTA
228253 AGGACAAGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.14
Consensus pattern (44 bp):
AGTACCCACAACCACAAGAACAGGTGATAGGTGACTGCAACAAT
Found at i:231128 original size:64 final size:57
Alignment explanation
Indices: 231049--231166 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 57
231039 TCAAAAATTT
231049 AAATTTTATAATATTTTATTTTACTAAATTAAATTATTATTATTATGATTATTTTATTTTATTC
1 AAATTTTATAATA-TTTA---TACTAAA-TAAATT-TTATTATTAT-ATTATTTTATTTTATTC
** * *
231113 AAATTTTATTTTATTTATACTAAATAAATTTTTTTATTATTTTATTTTATTTTA
1 AAATTTTATAATATTTATACTAAATAAATTTTATTATTATATTATTTTATTTTA
231167 ATAAATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
57 13 0.26
58 9 0.18
59 6 0.12
60 7 0.14
63 4 0.08
64 11 0.22
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (57 bp):
AAATTTTATAATATTTATACTAAATAAATTTTATTATTATATTATTTTATTTTATTC
Found at i:231137 original size:21 final size:21
Alignment explanation
Indices: 231097--231137 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
231087 ATTATTATGA
*
231097 TTATTTTATTTTATTCAAATT
1 TTATTTTATTTTACTCAAATT
231118 TTATTTTATTTATACT-AAAT
1 TTATTTTATTT-TACTCAAAT
231138 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTTTATTTTACTCAAATT
Found at i:231144 original size:36 final size:36
Alignment explanation
Indices: 231104--231177 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
231094 TGATTATTTT
*
231104 ATTTTATTCA-AATTTTATTTTATTTATACTAAA-TAA
1 ATTTT-TTCATAATTTTATTTTATTT-TAATAAATTAA
* *
231140 ATTTTTTTATTATTTTATTTTATTTTAATAAATTAA
1 ATTTTTTCATAATTTTATTTTATTTTAATAAATTAA
231176 AT
1 AT
231178 ATAAAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 9 0.27
36 24 0.73
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (36 bp):
ATTTTTTCATAATTTTATTTTATTTTAATAAATTAA
Found at i:232433 original size:20 final size:20
Alignment explanation
Indices: 232369--232439 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
232359 TATATCAATT
*
232369 TAATTTTAAATTAT-TT--A
1 TAATTTTATATTATATTAAA
232386 TAATTTTATAGTTATATTAAA
1 TAATTTTATA-TTATATTAAA
* *
232407 TATTTTTAT-TTATTATTAAT
1 TAATTTTATATTA-TATTAAA
*
232427 TAATTTTAAATTA
1 TAATTTTATATTA
232440 AATACTTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 9 0.21
18 4 0.09
19 5 0.12
20 13 0.30
21 12 0.28
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (20 bp):
TAATTTTATATTATATTAAA
Found at i:243447 original size:15 final size:16
Alignment explanation
Indices: 243427--243457 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
243417 AAATAGTAAT
243427 TCTGA-CCGAATTAAA
1 TCTGACCCGAATTAAA
243442 TCTGACCCGAATTAAA
1 TCTGACCCGAATTAAA
243458 AAGATTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (16 bp):
TCTGACCCGAATTAAA
Found at i:247169 original size:23 final size:23
Alignment explanation
Indices: 247143--247193 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
247133 ATCCGTATTT
247143 TTTAAATTAATTAAATT-TAATAA
1 TTTAAA-TAATTAAATTATAATAA
* * *
247166 TTTATATATTTATATTATAATAA
1 TTTAAATAATTAAATTATAATAA
247189 TTTAA
1 TTTAA
247194 TATATATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAATAATTAAATTATAATAA
Found at i:247199 original size:20 final size:22
Alignment explanation
Indices: 247152--247201 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
247142 TTTTAAATTA
*
247152 ATTAAATT-TAATAATTTATAT
1 ATTATATTATAATAATTTATAT
247173 ATTTATATTATAATAATTTA-AT
1 A-TTATATTATAATAATTTATAT
247195 A-TATATT
1 ATTATATT
247202 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 1 0.04
22 9 0.35
23 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTATATTATAATAATTTATAT
Found at i:247293 original size:18 final size:20
Alignment explanation
Indices: 247253--247293 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
247243 TTAAATAATT
*
247253 TAAAATATTATTTATTTATA
1 TAAAATATTATATATTTATA
*
247273 TAAAATTTTATAT-TTTA-A
1 TAAAATATTATATATTTATA
247291 TAA
1 TAA
247294 TTAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAAATATTATATATTTATA
Found at i:247328 original size:21 final size:20
Alignment explanation
Indices: 247295--247346 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
247285 TTTTAATAAT
*
247295 TAAATTATTTTTTAATATTTTA
1 TAAATT-TTTTTTAA-AATTTA
247317 TAAATTTTTTTTAAAATTTA
1 TAAATTTTTTTTAAAATTTA
247337 TATAATTTTT
1 TA-AATTTTT
247347 ATATTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 7 0.25
21 15 0.54
22 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TAAATTTTTTTTAAAATTTA
Found at i:247354 original size:36 final size:36
Alignment explanation
Indices: 247303--247388 Score: 104
Period size: 36 Copynumber: 2.3 Consensus size: 36
247293 ATTAAATTAT
247303 TTTTTAATATTTTATAAATT-TTTTTTAAAATTTATATAA
1 TTTTTAATA--TTAT-AATTATTTTTTAAAATTTATA-AA
**
247342 TTTTT-ATATTATAATTATTTTTTATCATTTATAAA
1 TTTTTAATATTATAATTATTTTTTAAAATTTATAAA
247377 TTTTTAATATTA
1 TTTTTAATATTA
247389 ATTTTTGAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
35 11 0.26
36 24 0.56
38 3 0.07
39 5 0.12
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (36 bp):
TTTTTAATATTATAATTATTTTTTAAAATTTATAAA
Found at i:247359 original size:22 final size:21
Alignment explanation
Indices: 247290--247359 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 21
247280 TTATATTTTA
* * *
247290 ATAATTAAATTATTTTTTAAT
1 ATAATTATATAATTTTTTATT
*
247311 AT-TTTATA-AATTTTTT-TT
1 ATAATTATATAATTTTTTATT
*
247329 AAAATTTATATAATTTTTATATT
1 ATAA-TTATATAATTTTT-TATT
247352 ATAATTAT
1 ATAATTAT
247360 TTTTTATCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
18 2 0.05
19 7 0.19
20 9 0.24
21 9 0.24
22 5 0.14
23 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATAATTATATAATTTTTTATT
Found at i:247375 original size:20 final size:19
Alignment explanation
Indices: 247297--247387 Score: 68
Period size: 18 Copynumber: 4.8 Consensus size: 19
247287 TTAATAATTA
247297 AATTATTTTTTAATATTTTAT
1 AATTATTTTTT-ATA-TTTAT
*
247318 AAATT-TTTTTTAAAATTTAT
1 -AATTATTTTTT-ATATTTAT
*
247338 -A-TAATTTTTATA-TTAT
1 AATTATTTTTTATATTTAT
247354 AATTATTTTTTATCATTTAT
1 AATTATTTTTTAT-ATTTAT
*
247374 AA--ATTTTTAATATT
1 AATTATTTTTTATATT
247388 AATTTTTGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
16 4 0.07
17 7 0.12
18 23 0.39
19 1 0.02
20 11 0.19
21 9 0.15
22 4 0.07
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTATTTTTTATATTTAT
Found at i:247380 original size:17 final size:16
Alignment explanation
Indices: 247332--247387 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
247322 TTTTTTTAAA
247332 ATTTATATAATTTTTAT
1 ATTTATA-AATTTTTAT
247349 A-TTATAATTATTTTTTAT
1 ATTTATAA--A-TTTTTAT
247367 CATTTATAAATTTTTAAT
1 -ATTTATAAATTTTT-AT
247385 ATT
1 ATT
247388 AATTTTTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
15 1 0.03
16 5 0.15
17 10 0.30
18 10 0.30
19 1 0.03
20 6 0.18
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTATAAATTTTTAT
Found at i:247380 original size:56 final size:55
Alignment explanation
Indices: 247273--247381 Score: 152
Period size: 56 Copynumber: 2.0 Consensus size: 55
247263 TTTATTTATA
247273 TAAAATTTTATATTTTAATAATTAAATTATTTTTTAATATTTTATAAATTTTTTT
1 TAAAATTTTATATTTTAATAATTAAATTATTTTTTAATATTTTATAAATTTTTTT
*
247328 TAAAATTTATATAATTTTTAT-ATTATAATTATTTTTT-ATCA-TTTATAAATTTTT
1 TAAAATTT-TAT-ATTTTAATAATTA-AATTATTTTTTAAT-ATTTTATAAATTTTT
247382 AATATTAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
55 8 0.16
56 22 0.45
57 19 0.39
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (55 bp):
TAAAATTTTATATTTTAATAATTAAATTATTTTTTAATATTTTATAAATTTTTTT
Found at i:247793 original size:15 final size:16
Alignment explanation
Indices: 247773--247802 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
247763 TTAATTAAAT
247773 ATTTAAA-AAATATTA
1 ATTTAAATAAATATTA
247788 ATTTAAATAAATATT
1 ATTTAAATAAATATT
247803 TATATTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTAAATAAATATTA
Found at i:247848 original size:31 final size:32
Alignment explanation
Indices: 247791--247859 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 32
247781 AATATTAATT
247791 TAAATAAATATTTATATTATAATTTTATTAAA
1 TAAATAAATATTTATATTATAATTTTATTAAA
247823 TAAATAAATATTT-TA-TATTAATTTTATTAAA
1 TAAATAAATATTTATATTA-TAATTTTATTAAA
247854 TAAATA
1 TAAATA
247860 TTAATATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 2 0.06
31 21 0.58
32 13 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TAAATAAATATTTATATTATAATTTTATTAAA
Found at i:247872 original size:31 final size:31
Alignment explanation
Indices: 247790--247872 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
247780 AAATATTAAT
*
247790 TTAAATAAATATT--TATATTA-TAATTTTA
1 TTAAATAAATATTAATATAATATTAATTTTA
*
247818 TTAAATAAATA--AATATTTTATATTAATTTTA
1 TTAAATAAATATTAATA--TAATATTAATTTTA
247849 TTAAATAAATATTAATATAATATT
1 TTAAATAAATATTAATATAATATT
247873 TAACATTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
28 13 0.29
30 3 0.07
31 25 0.56
33 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTAAATAAATATTAATATAATATTAATTTTA
Found at i:250303 original size:12 final size:12
Alignment explanation
Indices: 250286--250312 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
250276 TCTGACATGA
250286 AATATTGATTTG
1 AATATTGATTTG
250298 AATATTGATTTG
1 AATATTGATTTG
250310 AAT
1 AAT
250313 TTTGCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (12 bp):
AATATTGATTTG
Found at i:251198 original size:19 final size:19
Alignment explanation
Indices: 251170--251244 Score: 60
Period size: 21 Copynumber: 3.7 Consensus size: 19
251160 TCAAATTATC
*
251170 TTTTAATTAATAAAAATAT
1 TTTTATTTAATAAAAATAT
*
251189 TTTTATTTAAATTAAAACTAT
1 TTTTATTT-AA-TAAAAATAT
*** *
251210 AAATATTTTATAAAAATAT
1 TTTTATTTAATAAAAATAT
251229 TTTTACTATTAATAAA
1 TTTTA-T-TTAATAAA
251245 TCATAAAAAT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 17 0.41
20 4 0.10
21 20 0.49
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTTATTTAATAAAAATAT
Found at i:252221 original size:23 final size:21
Alignment explanation
Indices: 252195--252236 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
252185 TAAATTATAG
252195 ATATAAAATATATATTTTTAATT
1 ATATAAAATA-A-ATTTTTAATT
252218 ATATAAAATAAATTTTTAA
1 ATATAAAATAAATTTTTAA
252237 AAAATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATAAAATAAATTTTTAATT
Found at i:253359 original size:18 final size:18
Alignment explanation
Indices: 253318--253369 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
253308 ATAAATTTTA
* *
253318 AAAAATTAAAAATTATTT
1 AAAAATTAAAATTTAATT
* *
253336 ATAAATTAATATTTAATT
1 AAAAATTAAAATTTAATT
253354 AAAAATATAAAATTTA
1 AAAAAT-TAAAATTTA
253370 TATTTTTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 19 0.70
19 8 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAATTAAAATTTAATT
Found at i:256460 original size:15 final size:16
Alignment explanation
Indices: 256440--256473 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
256430 AAATTAATAA
*
256440 AAATTTTATTT-ATTT
1 AAATTTAATTTAATTT
256455 AAATTTAATTTAATTT
1 AAATTTAATTTAATTT
256471 AAA
1 AAA
256474 ATATAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATTTAATTTAATTT
Found at i:256702 original size:17 final size:15
Alignment explanation
Indices: 256656--256723 Score: 73
Period size: 17 Copynumber: 4.1 Consensus size: 15
256646 CAGATTTAAA
256656 TAAAAAATATTATTTT
1 TAAAAAAT-TTATTTT
256672 TAAGACATAATTTATTTT
1 TAA-A-A-AATTTATTTT
256690 TAAATAAATTTTATTTT
1 TAAA-AAA-TTTATTTT
256707 TACAAAAATTTATTTT
1 TA-AAAAATTTATTTT
256723 T
1 T
256724 TAAATTTAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
16 14 0.30
17 16 0.35
18 13 0.28
19 3 0.07
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (15 bp):
TAAAAAATTTATTTT
Found at i:256724 original size:17 final size:17
Alignment explanation
Indices: 256680--256728 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
256670 TTTAAGACAT
256680 AATTTA-TTTTTAAATA
1 AATTTATTTTTTAAATA
256696 AATTT-TATTTTTACAA-A
1 AATTTAT-TTTTTA-AATA
256713 AATTTATTTTTTAAAT
1 AATTTATTTTTTAAAT
256729 TTAATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 7 0.25
17 18 0.64
18 3 0.11
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTATTTTTTAAATA
Found at i:256894 original size:3 final size:3
Alignment explanation
Indices: 256886--256926 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
256876 TGGGAAAAAT
256886 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
256927 TTTAAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:256936 original size:15 final size:15
Alignment explanation
Indices: 256880--256925 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
256870 ACATAGTGGG
256880 AAAAAT-ATAATAAT
1 AAAAATAATAATAAT
*
256894 AATAATAATAATAAT
1 AAAAATAATAATAAT
*
256909 AATAATAATAATAAT
1 AAAAATAATAATAAT
256924 AA
1 AA
256926 TTTTAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 5 0.17
15 25 0.83
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAATAATAATAAT
Found at i:257964 original size:21 final size:23
Alignment explanation
Indices: 257917--257961 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
257907 ATATAAATTA
*
257917 TTATTAAATATAATTTTATATTG
1 TTATAAAATATAATTTTATATTG
257940 TTATAAAATA-AATTTTAATATT
1 TTATAAAATATAATTTT-ATATT
257962 TATTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATAAAATATAATTTTATATTG
Found at i:257990 original size:27 final size:27
Alignment explanation
Indices: 257960--258020 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
257950 AATTTTAATA
*
257960 TTTATTATTATTATTATAT-TTAAAAAT
1 TTTATAATT-TTATTATATCTTAAAAAT
257987 TTTATAATTTTATTATATCTTAAAAAT
1 TTTATAATTTTATTATATCTTAAAAAT
*
258014 ATTATAA
1 TTTATAA
258021 AATCTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 9 0.29
27 22 0.71
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTATAATTTTATTATATCTTAAAAAT
Found at i:266616 original size:2 final size:2
Alignment explanation
Indices: 266611--266652 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
266601 TGTGTGTGTC
* * *
266611 TA TA TA TA CA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
266653 AAGGAATAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:267338 original size:46 final size:49
Alignment explanation
Indices: 267249--267340 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 49
267239 AATTAGGAAG
*
267249 ATAAATAAAAAAAGATTTAAAGTTTTTCCATTAAATATATTTATTTGGTC
1 ATAAATAAAAAAAGATTTAAAG-TTTTCAATTAAATATATTTATTTGGTC
267299 ATAAAT-AAAAAAGATTTAAA-TTTT-AATTAAAT-TATTTTATTT
1 ATAAATAAAAAAAGATTTAAAGTTTTCAATTAAATATA-TTTATTT
267341 TTAGATTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
45 2 0.05
46 14 0.35
47 4 0.10
49 14 0.35
50 6 0.15
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (49 bp):
ATAAATAAAAAAAGATTTAAAGTTTTCAATTAAATATATTTATTTGGTC
Found at i:267514 original size:17 final size:17
Alignment explanation
Indices: 267485--267520 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
267475 ATTCTACTTA
267485 TTAATTCATTTATTAAAT
1 TTAATTCATTTA-TAAAT
267503 TTAATT-ATTTATAAAT
1 TTAATTCATTTATAAAT
267519 TT
1 TT
267521 GTAACTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 5 0.28
18 6 0.33
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAATTCATTTATAAAT
Found at i:279519 original size:13 final size:13
Alignment explanation
Indices: 279497--279554 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
279487 GGTAGTAGCT
*
279497 TTGTAGCGATACA
1 TTGTATCGATACA
279510 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
279526 CTTATGTATCGATACA
1 --T-TGTATCGATACA
279542 TTGTATCGATACA
1 TTGTATCGATACA
279555 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:279535 original size:19 final size:19
Alignment explanation
Indices: 279511--279571 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
279501 AGCGATACAT
279511 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
279530 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
279543 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
279562 TGTATCGATA
1 TGTATCGATA
279572 TATTTACTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 9 0.25
14 1 0.03
16 6 0.17
18 1 0.03
19 19 0.53
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:279544 original size:32 final size:32
Alignment explanation
Indices: 279498--279571 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
279488 GTAGTAGCTT
*
279498 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
279530 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
279562 TGTATCGATA
1 TGTATCGATA
279572 TATTTACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:280661 original size:29 final size:30
Alignment explanation
Indices: 280613--280697 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 30
280603 AGAAAAAGAT
280613 CCACCAACTTGTGTGGGCTTTTGAAAGGGTTG
1 CCACCAACTTGTGT--GCTTTTGAAAGGGTTG
280645 -CACCAACTTGTGTGCTTTTG-AA-GGTTG
1 CCACCAACTTGTGTGCTTTTGAAAGGGTTG
** *
280672 CCACTGACTTGTGGGCTTTTGGAAAG
1 CCACCAACTTGTGTGCTTTT-GAAAG
280698 ATACCACTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 5 0.11
28 18 0.39
29 8 0.17
30 2 0.04
31 13 0.28
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (30 bp):
CCACCAACTTGTGTGCTTTTGAAAGGGTTG
Found at i:280711 original size:57 final size:56
Alignment explanation
Indices: 280650--280948 Score: 372
Period size: 57 Copynumber: 5.2 Consensus size: 56
280640 GGTTGCACCA
* *
280650 ACTTGTGTGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGGAAAGATACCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC-TTTGGAAAGATGCCACTG
* * *
280707 ACTTGTGGGC--TTGAAAGGGGTGCCATTGACTTGTGGGCTTTTGGAAAGATACCACTG
1 ACTTGTGGGCTTTTG-AA-GGTTGCCACTGACTTGTGGGC-TTTGGAAAGATGCCACTG
* * * * *
280764 ACTTGTGGGCTTTTGGAAAGATACCACTGACTTGTGGGC-TT-GAAAGGGGTGCCATTG
1 ACTTGTGGGCTTTT-GAAGGTTGCCACTGACTTGTGGGCTTTGGAAA--GATGCCACTG
*
280821 ACTTGTGGGCTTTTTGAAGATTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
1 ACTTGTGGGC-TTTTGAAGGTTGCCACTGACTTGTGGGCTTTGG-AAAGATGCCACTG
280879 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGG-AAAGATGCCACTG
*
280936 ACTTGTAGGCTTT
1 ACTTGTGGGCTTT
280949 GAAAAGGTGA
Statistics
Matches: 213, Mismatches: 18, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
55 7 0.03
56 4 0.02
57 152 0.71
58 41 0.19
59 5 0.02
60 4 0.02
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.32
Consensus pattern (56 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGATGCCACTG
Found at i:280712 original size:29 final size:29
Alignment explanation
Indices: 280650--280948 Score: 332
Period size: 29 Copynumber: 10.4 Consensus size: 29
280640 GGTTGCACCA
* * *
280650 ACTTGTGTGCTTTT-GAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGGAAAGATGCCACTG
*
280678 ACTTGTGGGCTTTTGGAAAGATACCACTG
1 ACTTGTGGGCTTTTGGAAAGATGCCACTG
* *
280707 ACTTGTGGGC--TT-GAAAGGGGTGCCATTG
1 ACTTGTGGGCTTTTGGAAA--GATGCCACTG
*
280735 ACTTGTGGGCTTTTGGAAAGATACCACTG
1 ACTTGTGGGCTTTTGGAAAGATGCCACTG
*
280764 ACTTGTGGGCTTTTGGAAAGATACCACTG
1 ACTTGTGGGCTTTTGGAAAGATGCCACTG
* *
280793 ACTTGTGGGC--TT-GAAAGGGGTGCCATTG
1 ACTTGTGGGCTTTTGGAAA--GATGCCACTG
*
280821 ACTTGTGGGCTTTTTG-AAGATTGCCACTG
1 ACTTGTGGGCTTTTGGAAAGA-TGCCACTG
280850 ACTTGTGGGC-TTTGGAAAAGATGCCACTG
1 ACTTGTGGGCTTTTGG-AAAGATGCCACTG
* *
280879 ACTTGTGGGCTTTT-GAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGGAAAGATGCCACTG
280907 ACTTGTGGGC-TTTGGAAAAGATGCCACTG
1 ACTTGTGGGCTTTTGG-AAAGATGCCACTG
*
280936 ACTTGTAGGCTTT
1 ACTTGTGGGCTTT
280949 GAAAAGGTGA
Statistics
Matches: 232, Mismatches: 21, Indels: 34
0.81 0.07 0.12
Matches are distributed among these distances:
26 8 0.03
27 7 0.03
28 74 0.32
29 123 0.53
30 15 0.06
31 5 0.02
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.32
Consensus pattern (29 bp):
ACTTGTGGGCTTTTGGAAAGATGCCACTG
Found at i:280762 original size:86 final size:86
Alignment explanation
Indices: 280650--280948 Score: 430
Period size: 86 Copynumber: 3.5 Consensus size: 86
280640 GGTTGCACCA
* * *
280650 ACTTGTGTGCTTTT-GAAGGTTGCCACTGACTTGTGGGCTTTTGGAAAGATACCACTGACTTGTG
1 ACTTGTGGGCTTTTGGAAAGATGCCACTGACTTGTGGGCTTTTGGAAAGATACCACTGACTTGTG
280714 GGCTTGAAAGGGGTGCCATTG
66 GGCTTGAAAGGGGTGCCATTG
*
280735 ACTTGTGGGCTTTTGGAAAGATACCACTGACTTGTGGGCTTTTGGAAAGATACCACTGACTTGTG
1 ACTTGTGGGCTTTTGGAAAGATGCCACTGACTTGTGGGCTTTTGGAAAGATACCACTGACTTGTG
280800 GGCTTGAAAGGGGTGCCATTG
66 GGCTTGAAAGGGGTGCCATTG
* *
280821 ACTTGTGGGCTTTTTG-AAGATTGCCACTGACTTGTGGGC-TTTGGAAAAGATGCCACTGACTTG
1 ACTTGTGGGCTTTTGGAAAGA-TGCCACTGACTTGTGGGCTTTTGG-AAAGATACCACTGACTTG
* *
280884 TGGGCTTTTG-AA-GGTTGCCACTG
64 TGGGC--TTGAAAGGGGTGCCATTG
*
280907 ACTTGTGGGC-TTTGGAAAAGATGCCACTGACTTGTAGGCTTT
1 ACTTGTGGGCTTTTGG-AAAGATGCCACTGACTTGTGGGCTTT
280949 GAAAAGGTGA
Statistics
Matches: 195, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
85 26 0.13
86 158 0.81
87 8 0.04
88 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.32
Consensus pattern (86 bp):
ACTTGTGGGCTTTTGGAAAGATGCCACTGACTTGTGGGCTTTTGGAAAGATACCACTGACTTGTG
GGCTTGAAAGGGGTGCCATTG
Found at i:282340 original size:4 final size:4
Alignment explanation
Indices: 282331--282392 Score: 65
Period size: 4 Copynumber: 15.8 Consensus size: 4
282321 TTTTGTTGTT
* * *
282331 TTTG TTTG TTTG TTTG TTTG TTTTG TTT- TTTT TTTG TTT- TTTC TTTC
1 TTTG TTTG TTTG TTTG TTTG -TTTG TTTG TTTG TTTG TTTG TTTG TTTG
*
282378 TTTT TTTG TTTG TTT
1 TTTG TTTG TTTG TTT
282393 TTTTTTTTGC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
3 6 0.12
4 42 0.81
5 4 0.08
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (4 bp):
TTTG
Found at i:282348 original size:12 final size:11
Alignment explanation
Indices: 282321--282395 Score: 71
Period size: 11 Copynumber: 6.5 Consensus size: 11
282311 TCCGGACCCT
282321 TTTTGTTGTTT-
1 TTTT-TTGTTTG
*
282332 TTGTTTGTTTG
1 TTTTTTGTTTG
282343 TTTGTTTGTTTTG
1 TTT-TTTG-TTTG
*
282356 TTTTTTTTTTG
1 TTTTTTGTTTG
* *
282367 TTTTTTCTTTCT
1 TTTTTTGTTT-G
282379 TTTTTTGTTTG
1 TTTTTTGTTTG
282390 TTTTTT
1 TTTTTT
282396 TTTTTGCGGA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
10 6 0.11
11 24 0.45
12 16 0.30
13 7 0.13
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.83
Consensus pattern (11 bp):
TTTTTTGTTTG
Found at i:282386 original size:39 final size:37
Alignment explanation
Indices: 282320--282401 Score: 110
Period size: 39 Copynumber: 2.2 Consensus size: 37
282310 ATCCGGACCC
* *
282320 TTTTTGTTGTTTTTGTTTGTTTGTTTGTTTGTTTTGTT
1 TTTTTGTTGTTTTTCTTTCTTTGTTTGTTTGTTTT-TT
* *
282358 TTTTTTTTGTTTTTTCTTTCTTTTTTTGTTTGTTTTTT
1 TTTTTGTTG-TTTTTCTTTCTTTGTTTGTTTGTTTTTT
282396 TTTTTG
1 TTTTTG
282402 CGGAGGACAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 15 0.39
39 23 0.61
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (37 bp):
TTTTTGTTGTTTTTCTTTCTTTGTTTGTTTGTTTTTT
Found at i:282396 original size:12 final size:12
Alignment explanation
Indices: 282320--282401 Score: 80
Period size: 12 Copynumber: 6.8 Consensus size: 12
282310 ATCCGGACCC
282320 TTTTTG-TTGTTT
1 TTTTTGTTTG-TT
282332 TTGTTTGTTTGTT
1 TT-TTTGTTTGTT
*
282345 TGTTTGTTTTGTT
1 TTTTTG-TTTGTT
282358 TTTTT-TTTG-T
1 TTTTTGTTTGTT
* *
282368 TTTTTCTTTCTT
1 TTTTTGTTTGTT
282380 TTTTTGTTTGTT
1 TTTTTGTTTGTT
*
282392 TTTTTTTTTG
1 TTTTTGTTTG
282402 CGGAGGACAC
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
10 6 0.10
11 7 0.12
12 26 0.44
13 17 0.29
14 3 0.05
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (12 bp):
TTTTTGTTTGTT
Found at i:296276 original size:13 final size:13
Alignment explanation
Indices: 296258--296285 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
296248 ATACAAAGAT
296258 CAATGTATCGATA
1 CAATGTATCGATA
296271 CAATGTATCGATA
1 CAATGTATCGATA
296284 CA
1 CA
296286 TTGAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:296361 original size:19 final size:19
Alignment explanation
Indices: 296337--296397 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
296327 AGCGATACAT
296337 TGTATCGATATAACACTTA
1 TGTATCGATATAACACTTA
296356 TGTATCG--AT-ACA--T-
1 TGTATCGATATAACACTTA
*
296369 TGTATCGATACAACACTTA
1 TGTATCGATATAACACTTA
*
296388 TATATCGATA
1 TGTATCGATA
296398 CATTTACTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
13 7 0.21
14 1 0.03
15 1 0.03
16 6 0.18
17 2 0.06
18 1 0.03
19 16 0.47
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TGTATCGATATAACACTTA
Found at i:296370 original size:32 final size:32
Alignment explanation
Indices: 296324--296401 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
296314 GCAGTAGCTT
* *
296324 TATAGCGATACATTGTATCGATATAACACTTA
1 TATATCGATACATTGTATCGATACAACACTTA
*
296356 TGTATCGATACATTGTATCGATACAACACTTA
1 TATATCGATACATTGTATCGATACAACACTTA
296388 TATATCGATACATT
1 TATATCGATACATT
296402 TACTGTTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
TATATCGATACATTGTATCGATACAACACTTA
Found at i:296374 original size:13 final size:13
Alignment explanation
Indices: 296356--296380 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
296346 ATAACACTTA
296356 TGTATCGATACAT
1 TGTATCGATACAT
296369 TGTATCGATACA
1 TGTATCGATACA
296381 ACACTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:298186 original size:15 final size:16
Alignment explanation
Indices: 298162--298203 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
298152 ACTTATTTAA
298162 AAAAATACAAAAAAAT
1 AAAAATACAAAAAAAT
298178 AAAAA-ACAAAAAAAT
1 AAAAATACAAAAAAAT
298193 AAAAATA-AAAA
1 AAAAATACAAAA
298204 TGAATGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAATACAAAAAAAT
Found at i:299754 original size:23 final size:22
Alignment explanation
Indices: 299704--299755 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
299694 AAGCAAAAGC
299704 ACAAAAAATGAAAAGAAAACAA
1 ACAAAAAATGAAAAGAAAACAA
* *
299726 AGAAAAAAGTGCAAAAGAGAAC-A
1 ACAAAAAA-TG-AAAAGAAAACAA
299749 ACAAAAA
1 ACAAAAA
299756 TAAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 7 0.28
23 9 0.36
24 9 0.36
ACGTcount: A:0.73, C:0.10, G:0.13, T:0.04
Consensus pattern (22 bp):
ACAAAAAATGAAAAGAAAACAA
Found at i:299755 original size:24 final size:22
Alignment explanation
Indices: 299706--299749 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
299696 GCAAAAGCAC
299706 AAAAAATGAAAAGAAAACAAAG
1 AAAAAATGAAAAGAAAACAAAG
*
299728 AAAAAAGTGCAAAAGAGAACAA
1 AAAAAA-TG-AAAAGAAAACAA
299750 CAAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 2 0.11
24 11 0.58
ACGTcount: A:0.73, C:0.07, G:0.16, T:0.05
Consensus pattern (22 bp):
AAAAAATGAAAAGAAAACAAAG
Found at i:301812 original size:139 final size:137
Alignment explanation
Indices: 301088--302952 Score: 947
Period size: 139 Copynumber: 13.3 Consensus size: 137
301078 GGTAGCATCT
* * * * * * * *
301088 TTTTCAAAGCCTACGAGTCGGTGCCATCCTTTCGAAGCCCACGAGTCGGGTGGCATCC-TTTCGA
1 TTTTCAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCA--AGTC-AGTGGCA-CCTTTTCAA
* * * * * *
301152 AGCCCACGAGTCAGTGGCATCCTTTCAAAGGCCCACAAGTTAATGGCACATTTTTC---A--CA-
62 AGCCCACGAGTCAGTGGCACCCTTTCAAA-ACCTACAAGTCAGTGG--CATCTTTCAAAACCCAC
*
301211 -AGTTAGTGGCACC
124 GAGTCAGTGGCACC
* * * * * * *
301224 CTTTGAAAACCCACAAGTTAGTGGCACCCTTTCAAAGCCCATGAGTCACTGACATCC-TTTCAAA
1 TTTTCAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCA--AGTCAGTGGCA-CCTTTTCAAA
* * ** * * * * * * *
301288 GCCTACGAGTAAGTGGCACATTTTCAAAGCCCACGAGTCAGTAGTACCCTTTCAAAGCCCACGAG
63 GCCCACGAGTCAGTGGCACCCTTTCAAAACCTACAAGTCAGTGGCA-TCTTTCAAAACCCACGAG
* *
301353 TCAGTGACACTT
127 TCAGTGGCAC-C
* * * * *
301365 TTTTTAAAGCACCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCACTAGCACCCTTTCAAA
1 TTTTCAAAGC-CCACAAGTCAGTGGCAACCTTTCAAAG-CC-CAAGTCAGTGGCACCTTTTCAAA
* * ** * * * * *
301430 GCCCATGAGTCATTGGCACTTTTTCAAAGCCCACGAGCCAATGGCATCTTGTCAAAAGCCCACGA
63 GCCCACGAGTCAGTGGCACCCTTTCAAAACCTACAAGTCAGTGGCATCTT-TCAAAA-CCCACGA
*
301495 GTCGGTGGCATCC
126 GTCAGTGGCA-CC
* ** * *
301508 -TTTCAAAGCTCATGAGTCGGTGGCAATCCTTTCAAAG-CCATGAGTCAGTGGCATCTTTTCAAA
1 TTTTCAAAGCCCACAAGTCAGTGGCAA-CCTTTCAAAGCCCA--AGTCAGTGGCACCTTTTC-AA
* * * * * * *
301571 AGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACGAGTTAGTGGCATCCTTTCAAAGCCCACGA
62 AGCCCACGAGTCAGTGGCACCCTTTCAAAACCTACAAGTCAGTGGCAT-CTTTCAAAACCCACGA
*
301636 GTCAGTGGCGTCC
126 GTCAGTGGC-ACC
* * * * * *
301649 -TTTCAAAACCCACGAGTAAATGGCAACAATTTCAAAGCCCAAGTCAGTGGCACCTTTTCAAACC
1 TTTTCAAAGCCCACAAGTCAGTGGCAAC-CTTTCAAAGCCCAAGTCAGTGGCACCTTTTCAAAGC
* * *
301713 CCACAAGTCAGTGGCACCCTTTGAAAACCTACAAGTCAGCGGCACTCTTTCAAAACCCACGAGTC
65 CCACGAGTCAGTGGCACCCTTTCAAAACCTACAAGTCAGTGGCA-TCTTTCAAAACCCACGAGTC
*
301778 AGTGACACC
129 AGTGGCACC
* * * * * *
301787 TTTTCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAAGCCATAATTCAGTGGCA-CTTTTAAAAG
1 TTTTCAAAGCCCACAAGTCAGTGGCAACCTTTC-AAAGCC-CAAGTCAGTGGCACCTTTTCAAAG
* * * * * * * * * * * *
301851 CCCACGAGTTAGTGGCAACCTTCCAAAGCCCATAAGTTAGTGGCATCCCTCCAAAGCCCACAAAT
64 CCCACGAGTCAGTGGCACCCTTTCAAAACCTACAAGTCAGTGGCAT-CTTTCAAAACCCACGAGT
*
301916 TAGTGGCACC
128 CAGTGGCACC
* * * * * * * * *
301926 CTTTCAAAGCCCACAAATC-GTGACATCCTGTCAAAGCACACGAGT-TGATGGCATCTTTTTAAA
1 TTTTCAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGC-C-CAAGTCAG-TGGCACCTTTTCAAA
* *
301989 GCCCACGAGTCAGTGGCATCCTTTCAAAAGCC-ACGAGTCAGTGGCATCCTTTTCAAAAGCCCAC
63 GCCCACGAGTCAGTGGCACCCTTTCAAAA-CCTACAAGTCAGTGGCAT-C-TTTCAAAA-CCCAC
*
302053 AAGTCAGTGGCACC
124 GAGTCAGTGGCACC
* * * * **
302067 TTTTCAAAGCCCACGAGTTAGTGGCATCCTTTCAAAGCCCACGAGTAAGTGATACCTTTTCAAAG
1 TTTTCAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCA--AGTCAGTGGCACCTTTTCAAAG
* * *** * *
302132 GCCATGAGTCCAGTGGCACCCTTTCAAAGGTTCACAAGTCAATGGCATCTTTTCAAAAGCCCACA
64 CCCACGAGT-CAGTGGCACCCTTTCAAAACCT-ACAAGTCAGTGGCATC-TTTCAAAA-CCCACG
**
302197 AGTCAGTGATACCC
125 AGTCAGTGGCA-CC
* * * * * *
302211 TTTT-AAAGCTCACAAGTTA-TTGCAAATCCTTTCAAAACGCATGAGTTAGTGGCACCTTTTCAA
1 TTTTCAAAGCCCACAAGTCAGTGGC-AA-CCTTTCAAAGCCCA--AGTCAGTGGCACCTTTTCAA
* * * * * * * * * *
302274 AGCTCACGAGTCAGTGGAATCCTTTCAAAAACTCACAAGTTAATGGGACCTTTTAAACCCCACGA
62 AGCCCACGAGTCAGTGGCACCCTTTCAAAACCT-ACAAGTCAGTGGCATCTTTCAAAACCCACGA
302339 GTCAGTGGCAACC
126 GTCAGTGGC-ACC
* * * *
302352 TTCT-AAAGCCCATAAGTCAGT-GCATCC-CTCTAAAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 TTTTCAAAGCCCACAAGTCAGTGGCAACCTTTC-AAAG-CC-CAAGTCAGTGGCA-CCTTTTCAA
* ** * * * *
302414 AACCCATAAGTCCA-TGGCACCTTTTTCAAAA-CTCACAAGTTAGTGGCACCTTGT-AAAGCCCA
62 AGCCCACGAGT-CAGTGGCACC-CTTTCAAAACCT-ACAAGTCAGTGGCATCTT-TCAAAACCCA
*
302476 TGAGTCAGTGGCACC
123 CGAGTCAGTGGCACC
* * * * * *
302491 TTGT-AAAGCCTATAAGTCAGTGGC-ACCTTTTAAAGCCCACGAGTCAATGGCACCCTTTCAAAG
1 TTTTCAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCA--AGTCAGTGGCACCTTTTCAAAG
* * * * * * **
302554 CCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAATGGCAATCCTTCCAAAGCCCATAA
64 CCCACGAGTCAGTGGCACCC-TTTCAAAACCTACAAGTCAGTGGC-AT-CTTTCAAAACCCACGA
* *
302619 GTTACTGGCACCC
126 GTCAGTGGCA-CC
* * * * * * * * *
302632 TTTTTAAAGCCCAGAATTCAGTGGCATTCTTTTTAAAGCCAATGAGTCAGTGGCACCCTTTAAAA
1 TTTTCAAAGCCCACAAGTCAGTGGCA-ACCTTTCAAAGCCCA--AGTCAGTGGCACCTTTTCAAA
* * * * * * * *
302697 GCCCACCAGTCAGTAGCATCCTTT-AAAAGCCTACAAGCCAGTGGCAACCCTTTAAAAATCCACA
63 GCCCACGAGTCAGTGGCACCCTTTCAAAA-CCTACAAGTCAGTGGC-A-TCTTTCAAAACCCACG
302761 AGTCAAGTGGCA-C
125 AGTC-AGTGGCACC
* * * * *
302774 TTTGT-AAAGCCTATAAGT-AGT-GC-A-CTTTGTAAAGCCCCACGAGTTAGTGGTACCTTTT-A
1 TTT-TCAAAGCCCACAAGTCAGTGGCAACCTTT-CAAAG-CCCA--AGTCAGTGGCACCTTTTCA
* * * * * * * * * * **
302833 AAGCCCACGAGTCAATAGCAAACCTTCCAAAGCCCACAAGTCAGTGGTAACCCTCCAAAGGCCAC
61 AAGCCCACGAGTCAGTGGC-ACCCTTTCAAAACCTACAAGTCAGTGG-CATCTTTCAAAACCCAC
* *
302898 AAGTGAGTGGCACCC
124 GAGTCAGTGGCA-CC
* * * * *
302913 TTTT-AAAGCTCACAAGTGAATGGCACCCTTTTAAAGCCCA
1 TTTTCAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCA
302953 CAGTTTAATG
Statistics
Matches: 1363, Mismatches: 283, Indels: 162
0.75 0.16 0.09
Matches are distributed among these distances:
132 1 0.00
133 4 0.00
134 12 0.01
135 36 0.03
136 36 0.03
137 20 0.01
138 121 0.09
139 320 0.23
140 144 0.11
141 174 0.13
142 238 0.17
143 141 0.10
144 116 0.09
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (137 bp):
TTTTCAAAGCCCACAAGTCAGTGGCAACCTTTCAAAGCCCAAGTCAGTGGCACCTTTTCAAAGCC
CACGAGTCAGTGGCACCCTTTCAAAACCTACAAGTCAGTGGCATCTTTCAAAACCCACGAGTCAG
TGGCACC
Found at i:302196 original size:29 final size:28
Alignment explanation
Indices: 301002--303201 Score: 1093
Period size: 28 Copynumber: 77.5 Consensus size: 28
300992 ATTTTCCTCC
* *
301002 TTTCAAAGCCCAACTAGTC-GATGGCATCT
1 TTTCAAAGCCC-ACAAGTCAG-TGGCACCT
* * *
301031 TGTCAAAGCCCACGAGTCGGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
** * * *
301059 TTTCAAAGCCCA-TGGTCGGGGTAGCATCTT
1 TTTCAAAGCCCACAAGTC--AGTGGCA-CCT
* * * *
301089 TTTCAAAGCCTACGAGTCGGTGCCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * *
301117 TTTCGAAGCCCACGAGTCGGGTGGCATCC-
1 TTTCAAAGCCCACAAGTC-AGTGGCA-CCT
* *
301146 TTTCGAAGCCCACGAGTCAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * *
301174 TTTCAAAGGCCCACAAGTTAATGGCACAT
1 TTTCAAA-GCCCACAAGTCAGTGGCACCT
* * *
301203 TTT------TCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * * *
301225 TTTGAAAACCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
** * *
301253 TTTCAAAGCCCATGAGTCACTGACATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * * *
301281 TTTCAAAGCCTACGAGTAAGTGGCACAT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * * *
301309 TTTCAAAGCCCACGAGTCAGTAGTACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * *
301337 TTTCAAAGCCCACGAGTCAGTGACACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CT
* *
301366 TTTTAAAGCACCACAAGTCAGTGGCACCC
1 TTTCAAAGC-CCACAAGTCAGTGGCACCT
* * *
301395 TTTCAAAGCCCACAAGTCACTAGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
** * *
301423 TTTCAAAGCCCATGAGTCATTGGCACTT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * * *
301451 TTTCAAAGCCCACGAGCCAATGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * *
301479 TGTCAAAAGCCCACGAGTCGGTGGCATCC-
1 TTTC-AAAGCCCACAAGTCAGTGGCA-CCT
* ** *
301508 TTTCAAAGCTCATGAGTCGGTGGCAATCC-
1 TTTCAAAGCCCACAAGTCAGTGGC-A-CCT
** *
301537 TTTCAAAG-CCATGAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* *
301564 TTTCAAAAGCCCACAAGTTAGTGGCACCC
1 TTTC-AAAGCCCACAAGTCAGTGGCACCT
* *
301593 TTTCAAAGCCCACGAGTTAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* *
301621 TTTCAAAGCCCACGAGTCAGTGGCGTCC-
1 TTTCAAAGCCCACAAGTCAGTGGC-ACCT
* * * * **
301649 TTTCAAAACCCACGAGTAAATGGCAACAA
1 TTTCAAAGCCCACAAGTCAGTGGC-ACCT
301678 TTTCAAAG-CC-CAAGTCAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* *
301704 TTTCAAACCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * * *
301732 TTTGAAAACCTACAAGTCAGCGGCA-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * *
301759 CTTTCAAAACCCACGAGTCAGTGACACCT
1 -TTTCAAAGCCCACAAGTCAGTGGCACCT
*
301788 TTTCAAAGCCCACGAGTCAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * *
301816 TTCCAAAAG-CCATAATTCAGTGGCA-CT
1 TTTC-AAAGCCCACAAGTCAGTGGCACCT
* * *
301843 TTTAAAAGCCCACGAGTTAGTGGCAACC-
1 TTTCAAAGCCCACAAGTCAGTGGC-ACCT
* * *
301871 TTCCAAAGCCCATAAGTTAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * * * *
301899 CTCCAAAGCCCACAAATTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* *
301927 TTTCAAAGCCCACAAATC-GTGACATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * * * *
301954 TGTCAAAGCACACGAGT-TGATGGCATCT
1 TTTCAAAGCCCACAAGTCAG-TGGCACCT
* *
301982 TTTTAAAGCCCACGAGTCAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
*
302010 TTTCAAAAG-CCACGAGTCAGTGGCATCCT
1 TTTC-AAAGCCCACAAGTCAGTGGCA-CCT
302039 TTTCAAAAGCCCACAAGTCAGTGGCACCT
1 TTTC-AAAGCCCACAAGTCAGTGGCACCT
* *
302068 TTTCAAAGCCCACGAGTTAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * **
302096 TTTCAAAGCCCACGAGTAAGTGATACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* ** *
302124 TTTCAAAGGCCATGAGTCCAGTGGCACCC
1 TTTCAAAGCCCACAAGT-CAGTGGCACCT
** * *
302153 TTTCAAAGGTTCACAAGTCAATGGCATCT
1 TTTCAAA-GCCCACAAGTCAGTGGCACCT
**
302182 TTTCAAAAGCCCACAAGTCAGTGATACCCT
1 TTTC-AAAGCCCACAAGTCAGTGGCA-CCT
* * *
302212 TTT-AAAGCTCACAAGTTA-TTGCAAATCC-
1 TTTCAAAGCCCACAAGTCAGTGGC--A-CCT
* * ** *
302240 TTTCAAAACGCATGAGTTAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * *
302268 TTTCAAAGCTCACGAGTCAGTGGAATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * * * *
302296 TTTCAAAAACTCACAAGTTAATGGGACCT
1 TTTC-AAAGCCCACAAGTCAGTGGCACCT
* *
302325 TTT-AAACCCCACGAGTCAGTGGCAACCT
1 TTTCAAAGCCCACAAGTCAGTGGC-ACCT
* * *
302353 TCT-AAAGCCCATAAGTCAGT-GCATCCC
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
*
302380 TCT-AAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* *
302408 TTTCAAAACCCATAAGTCCA-TGGCACCTT
1 TTTCAAAGCCCACAAGT-CAGTGGCACC-T
* * *
302437 TTTCAAAACTCACAAGTTAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* **
302465 TGT-AAAGCCCATGAGTCAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * *
302492 TGT-AAAGCCTATAAGTCAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * *
302519 TTT-AAAGCCCACGAGTCAATGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
302546 TTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
*
302575 TTTCAAAGCCCACAAGTCAATGGCAATCC-
1 TTTCAAAGCCCACAAGTCAGTGGC-A-CCT
* * * *
302604 TTCCAAAGCCCATAAGTTACTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * * *
302633 TTTTAAAGCCCAGAATTCAGTGGCATTCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * ** *
302662 TTTTAAAGCCAATGAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * *
302690 TTTAAAAGCCCACCAGTCAGTAGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * * *
302718 TTTAAAAGCCTACAAGCCAGTGGCAACCC
1 TTTCAAAGCCCACAAGTCAGTGGC-ACCT
* **
302747 TTTAAAAATCCACAAGTCAAGTGGCA-CT
1 TTTCAAAGCCCACAAGTC-AGTGGCACCT
* *
302775 TTGT-AAAGCCTATAAGT-AGT-GCA-CT
1 TT-TCAAAGCCCACAAGTCAGTGGCACCT
* * *
302800 TTGT-AAAGCCCCACGAGTTAGTGGTACCT
1 TT-TCAAAG-CCCACAAGTCAGTGGCACCT
* * *
302829 TTT-AAAGCCCACGAGTCAATAGCAAACC-
1 TTTCAAAGCCCACAAGTCAGTGGC--ACCT
* *
302857 TTCCAAAGCCCACAAGTCAGTGGTAACC-
1 TTTCAAAGCCCACAAGTCAGTGG-CACCT
* * * *
302885 CTCCAAAGGCCACAAGTGAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* * *
302914 TTT-AAAGCTCACAAGTGAATGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* *
302942 TTT-AAAGCCCAC-AGTTTAATGGCACCCT
1 TTTCAAAGCCCACAAG-TCAGTGGCA-CCT
** * * * **
302970 TTT-AAAGTTCATAGGTTAACGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* ***
302998 TTTCAAAGCCCACAAGCCAGTATTAACCT
1 TTTCAAAGCCCACAAGTCAGT-GGCACCT
**
303027 TTTCAAAGCCCACACAAGTTGGTGGCACATCT
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC--CT
* * *
303059 TTTTAAAGTCCACACAAGT-TGATGGCATCGT
1 TTTCAAAG-CC-CACAAGTCAG-TGGCA-CCT
*
303090 TTTCCAAAAGTCCACACAAGTCGGTGGCACCTCTT
1 TTT-C-AAAG-CC-CACAAGTCAGTGGCA-C-C-T
*
303125 TTTCAAAGCCCACATATGTCGGTGGCAACCTT
1 TTTCAAAGCCCACA-A-GTCAGTGGC-ACC-T
* * *
303157 TTTCAAAACCCACATAAGTCGGTGGTAACCTT
1 TTTCAAAGCCCAC--AAGTCAGTGG-CACC-T
303189 TTTC-AAGCCCACA
1 TTTCAAAGCCCACA
303202 CAAGTTGGTG
Statistics
Matches: 1733, Mismatches: 328, Indels: 220
0.76 0.14 0.10
Matches are distributed among these distances:
22 18 0.01
25 13 0.01
26 25 0.01
27 185 0.11
28 838 0.48
29 448 0.26
30 75 0.04
31 27 0.02
32 59 0.03
33 37 0.02
34 4 0.00
35 4 0.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.24
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCT
Found at i:302395 original size:27 final size:27
Alignment explanation
Indices: 302327--302400 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
302317 TGGGACCTTT
* * *
302327 TAAACCCCACGAGTCAGTGGCAACCTTC
1 TAAAGCCCACAAGTCAGT-GCAACCCTC
* *
302355 TAAAGCCCATAAGTCAGTGCATCCCTC
1 TAAAGCCCACAAGTCAGTGCAACCCTC
302382 TAAAGCCCACAAGTCAGTG
1 TAAAGCCCACAAGTCAGTG
302401 GCACCCTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 25 0.62
28 15 0.38
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (27 bp):
TAAAGCCCACAAGTCAGTGCAACCCTC
Found at i:303072 original size:32 final size:32
Alignment explanation
Indices: 303025--303240 Score: 179
Period size: 32 Copynumber: 6.7 Consensus size: 32
303015 CAGTATTAAC
* *
303025 CTTTTCAAAGCCCACACAAGTTGGTGGCACAT
1 CTTTTTAAAGCCCACACAAGTCGGTGGCACAT
* * *
303057 CTTTTTAAAGTCCACACAAGTTGATGG--CAT
1 CTTTTTAAAGCCCACACAAGTCGGTGGCACAT
* * *
303087 CGTTTTCCAAAAGTCCACACAAGTCGGTGGCACCT
1 C-TTTT--TAAAGCCCACACAAGTCGGTGGCACAT
* * *
303122 CTTTTTCAAAGCCCACATATGTCGGTGGCA-AC
1 CTTTTT-AAAGCCCACACAAGTCGGTGGCACAT
* * * *
303154 CTTTTTCAAAACCCACATAAGTCGGTGGTA-AC
1 CTTTTT-AAAGCCCACACAAGTCGGTGGCACAT
* * *
303186 CTTTTTCAAGCCCACACAAGTTGGTGGCACTT
1 CTTTTTAAAGCCCACACAAGTCGGTGGCACAT
*
303218 CTTTTTAAAGGACCACACAAGTC
1 CTTTTTAAA-GCCCACACAAGTC
303241 AATGGTAACC
Statistics
Matches: 150, Mismatches: 26, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
30 4 0.03
31 22 0.15
32 67 0.45
33 50 0.33
34 4 0.03
35 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (32 bp):
CTTTTTAAAGCCCACACAAGTCGGTGGCACAT
Found at i:303116 original size:65 final size:65
Alignment explanation
Indices: 303022--303214 Score: 214
Period size: 65 Copynumber: 3.0 Consensus size: 65
303012 AGCCAGTATT
* * *
303022 AACCTTTT-C-AAAGCCCACACAAGTTGGTGGCACATCTTTTTAAAGTCCACACAAGTTGATGGC
1 AACCTTTTCCAAAAGCCCACACAAGTCGGTGGCACATCTTTTTAAAGCCCACACAAGTTGGTGGC
* * * * * * *
303085 ATCGTTTTCCAAAAGTCCACACAAGTCGGTGGCACCTCTTTTTCAAAGCCCACATATGTCGGTGG
1 AACCTTTTCCAAAAGCCCACACAAGTCGGTGGCACATCTTTTT-AAAGCCCACACAAGTTGGTGG
303150 C
65 C
* * * * *
303151 AACCTTTTTCAAAA-CCCACATAAGTCGGTGGTA-ACCTTTTTCAAGCCCACACAAGTTGGTGGC
1 AACCTTTTCCAAAAGCCCACACAAGTCGGTGGCACATCTTTTTAAAGCCCACACAAGTTGGTGGC
303214 A
1 A
303215 CTTCTTTTTA
Statistics
Matches: 105, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
63 25 0.24
64 7 0.07
65 45 0.43
66 28 0.27
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (65 bp):
AACCTTTTCCAAAAGCCCACACAAGTCGGTGGCACATCTTTTTAAAGCCCACACAAGTTGGTGGC
Found at i:303118 original size:33 final size:32
Alignment explanation
Indices: 303026--303240 Score: 158
Period size: 33 Copynumber: 6.7 Consensus size: 32
303016 AGTATTAACC
*
303026 TTTTC-AAAGCCCACACAAGTTGGTGGCACATCT
1 TTTTCAAAAGCCCACACAAGTCGGTGG--CATCT
* * *
303059 TTTT--AAAGTCCACACAAGTTGATGGCATCGT
1 TTTTCAAAAGCCCACACAAGTCGGTGGCATC-T
* *
303090 TTTCCAAAAGTCCACACAAGTCGGTGGCACCTCT
1 TTTTCAAAAGCCCACACAAGTCGGTGGCA--TCT
* * *
303124 TTTTC-AAAGCCCACATATGTCGGTGGCAACCT
1 TTTTCAAAAGCCCACACAAGTCGGTGGC-ATCT
* * *
303156 TTTTCAAAA-CCCACATAAGTCGGTGGTAACCT
1 TTTTCAAAAGCCCACACAAGTCGGTGG-CATCT
*
303188 TTTTC--AAGCCCACACAAGTTGGTGGCACTTCT
1 TTTTCAAAAGCCCACACAAGTCGGTGGCA--TCT
* *
303220 TTTT-AAAGGACCACACAAGTC
1 TTTTCAAAAGCCCACACAAGTC
303241 AATGGTAACC
Statistics
Matches: 150, Mismatches: 19, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
30 7 0.05
31 19 0.13
32 57 0.38
33 59 0.39
34 6 0.04
35 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (32 bp):
TTTTCAAAAGCCCACACAAGTCGGTGGCATCT
Found at i:303453 original size:54 final size:52
Alignment explanation
Indices: 303395--303535 Score: 149
Period size: 52 Copynumber: 2.7 Consensus size: 52
303385 AATGTCGTCG
*
303395 GCCTTAAATCAACACATTGGCACTCATTCTCTTTCTTAAAGTCCAATATCA-CTA
1 GCCTTAAATCAACACATTGGCACTC-TTCTC-ATCTTAAAGTCCAATAT-AGCTA
* * * * * * *
303449 GCCTTGAATCAATACGTTGGCACTCTTCTCATCTTTAAGTTCAATGTAGCTG
1 GCCTTAAATCAACACATTGGCACTCTTCTCATCTTAAAGTCCAATATAGCTA
* * *
303501 GCCTTAAATCAACACAGTGGCACCCTTCTTATCTT
1 GCCTTAAATCAACACATTGGCACTCTTCTCATCTT
303536 TATGTCTAGG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
51 1 0.01
52 44 0.61
53 5 0.07
54 22 0.31
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (52 bp):
GCCTTAAATCAACACATTGGCACTCTTCTCATCTTAAAGTCCAATATAGCTA
Found at i:303863 original size:15 final size:16
Alignment explanation
Indices: 303827--303865 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
303817 TAGACTTATT
303827 TAAAAAAC-AAAAAAA
1 TAAAAAACAAAAAAAA
303842 TAAAAAACAAAAAAAA
1 TAAAAAACAAAAAAAA
303858 TTAAAAAA
1 -TAAAAAA
303866 AAGAGTGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.36
16 7 0.32
17 7 0.32
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (16 bp):
TAAAAAACAAAAAAAA
Found at i:304142 original size:19 final size:18
Alignment explanation
Indices: 304111--304146 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
304101 AAAAATGATG
*
304111 AAAAAATTAAAAAATAAA
1 AAAAAATAAAAAAATAAA
304129 AAAAAATAATAAAAATAA
1 AAAAAATAA-AAAAATAA
304147 GACAACTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAAATAAAAAAATAAA
Found at i:304691 original size:3 final size:3
Alignment explanation
Indices: 304678--304729 Score: 63
Period size: 3 Copynumber: 17.0 Consensus size: 3
304668 TATGGGTAAG
304678 GAA GAAA GAA GAA GAA GAA GAA TGAA GAA GAA GAA -AA GAA GAAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA G-AA GAA
304725 -AA GAA
1 GAA GAA
304730 AAAAAAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.09
3 31 0.70
4 9 0.20
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:304696 original size:13 final size:11
Alignment explanation
Indices: 304678--304746 Score: 61
Period size: 13 Copynumber: 6.0 Consensus size: 11
304668 TATGGGTAAG
304678 GAAGAAAGAAGAA
1 GAAG-AAGAA-AA
304691 GAAGAAGAATGAA
1 GAAGAAGAA--AA
304704 GAAGAAGAAAA
1 GAAGAAGAAAA
304715 GAAGAAAGAAAA
1 GAAG-AAGAAAA
304727 GAA-AA-AAAA
1 GAAGAAGAAAA
* *
304736 AAAAAAGAAAA
1 GAAGAAGAAAA
304747 ATATGACATG
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
9 6 0.12
10 4 0.08
11 10 0.20
12 15 0.29
13 16 0.31
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.01
Consensus pattern (11 bp):
GAAGAAGAAAA
Found at i:304699 original size:16 final size:16
Alignment explanation
Indices: 304678--304730 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
304668 TATGGGTAAG
304678 GAAGAAAGAAGAAGAA
1 GAAGAAAGAAGAAGAA
*
304694 GAAGAATGAAGAAGAA
1 GAAGAAAGAAGAAGAA
304710 G-A-AAAGAAGAAAGAA
1 GAAGAAAGAAG-AAGAA
304725 -AAGAAA
1 GAAGAAA
304731 AAAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 6 0.19
15 7 0.22
16 19 0.59
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (16 bp):
GAAGAAAGAAGAAGAA
Done.