Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold266
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: 372371
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
File 2 of 3
Found at i:150895 original size:2 final size:2
Alignment explanation
Indices: 150888--150937 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
150878 CTTAAACAGA
*
150888 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
150930 TC TC TC TC
1 TC TC TC TC
150938 GCTGACTCCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
TC
Found at i:152949 original size:2 final size:2
Alignment explanation
Indices: 152942--152977 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
152932 TTGTGGGTAA
152942 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
152978 TTGAGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:155387 original size:2 final size:2
Alignment explanation
Indices: 155380--155415 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
155370 GAGATCAAGC
*
155380 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
155416 TCTAAAGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:157658 original size:33 final size:32
Alignment explanation
Indices: 157605--157692 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 32
157595 ATATAAAAAA
*
157605 ATTAAAATATAATATAATATAAATAAATAA-AT
1 ATTAAAAT-TTATATAATATAAATAAATAACAT
*
157637 ATTTTAAAATTTATATAATAT-AATAATTAACAT
1 A--TTAAAATTTATATAATATAAATAAATAACAT
* *
157670 ATCAAATTTTATATAAATATAAA
1 ATTAAAATTTATAT-AATATAAA
157693 ATATTTTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
31 11 0.23
32 14 0.30
33 15 0.32
34 7 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (32 bp):
ATTAAAATTTATATAATATAAATAAATAACAT
Found at i:163311 original size:30 final size:32
Alignment explanation
Indices: 163256--163314 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
163246 ATTCAATTCA
163256 ATTAAAAACAATGTAAATCTTTATAAATTACT
1 ATTAAAAACAATGTAAATCTTTATAAATTACT
* *
163288 ATTAAAAATAAT-T-AATTTTTATAAATT
1 ATTAAAAACAATGTAAATCTTTATAAATT
163315 TAATGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 13 0.52
31 1 0.04
32 11 0.44
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (32 bp):
ATTAAAAACAATGTAAATCTTTATAAATTACT
Found at i:164353 original size:2 final size:2
Alignment explanation
Indices: 164346--164372 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
164336 ATAATTGATG
164346 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
164373 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:164377 original size:2 final size:2
Alignment explanation
Indices: 164372--164411 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
164362 TATATATATA
164372 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
164412 GGTTGTTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:164771 original size:16 final size:16
Alignment explanation
Indices: 164750--164790 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
164740 ATGGATTAAA
164750 TTTTATTAAATTTGAT
1 TTTTATTAAATTTGAT
* *
164766 TTTTATTTAGTTTGAT
1 TTTTATTAAATTTGAT
*
164782 TTTAATTAA
1 TTTTATTAA
164791 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
TTTTATTAAATTTGAT
Found at i:167050 original size:14 final size:15
Alignment explanation
Indices: 167024--167053 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
167014 ACTATTTTTT
167024 TAAGCAGTTTAAATA
1 TAAGCAGTTTAAATA
167039 TAAGCA-TTTAAATA
1 TAAGCAGTTTAAATA
167053 T
1 T
167054 TATATGCGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37
Consensus pattern (15 bp):
TAAGCAGTTTAAATA
Found at i:167264 original size:17 final size:16
Alignment explanation
Indices: 167207--167271 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
167197 AAGCAAAACA
167207 GAAAGAAAAAGAAAGC
1 GAAAGAAAAAGAAAGC
* **
167223 CAAAGCCAAAGCCAAAGC
1 GAAAGAAAAAG--AAAGC
*
167241 GAAAGAAAGAGAAAGC
1 GAAAGAAAAAGAAAGC
167257 GAAAAGAAAAAGAAA
1 G-AAAGAAAAAGAAA
167272 ATGAAAAAGG
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
16 14 0.37
17 12 0.32
18 12 0.32
ACGTcount: A:0.65, C:0.12, G:0.23, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAAGAAAGC
Found at i:167277 original size:12 final size:11
Alignment explanation
Indices: 167242--167306 Score: 51
Period size: 12 Copynumber: 5.7 Consensus size: 11
167232 AGCCAAAGCG
167242 AAAGAAAGAGAA
1 AAAGAAA-AGAA
**
167254 AGCGAAAAGAA
1 AAAGAAAAGAA
167265 AAAGAAAATGAA
1 AAAGAAAA-GAA
*
167277 AAAGGAAAAGGA
1 AAA-GAAAAGAA
*
167289 AAAGGAAA-AA
1 AAAGAAAAGAA
*
167299 AGAGAAAA
1 AAAGAAAA
167307 AGAATAATAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
10 7 0.17
11 14 0.33
12 16 0.38
13 5 0.12
ACGTcount: A:0.72, C:0.02, G:0.25, T:0.02
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:167284 original size:19 final size:20
Alignment explanation
Indices: 167258--167310 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
167248 AGAGAAAGCG
*
167258 AAAA-GAAAAAGAAAATG-A
1 AAAAGGAAAAAGAAAAGGAA
*
167276 AAAAGGAAAAGGAAAAGGAA
1 AAAAGGAAAAAGAAAAGGAA
167296 AAAAGAGAAAAAGAA
1 AAAAG-GAAAAAGAA
167311 TAATAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 11 0.38
20 6 0.21
21 8 0.28
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (20 bp):
AAAAGGAAAAAGAAAAGGAA
Found at i:167298 original size:13 final size:12
Alignment explanation
Indices: 167246--167297 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
167236 AAAGCGAAAG
*
167246 AAAGAGAAAGCGA
1 AAAGAAAAAG-GA
167259 AAAGAAAAA-GA
1 AAAGAAAAAGGA
167270 AAATGAAAAAGGA
1 AAA-GAAAAAGGA
*
167283 AAAGGAAAAGGA
1 AAAGAAAAAGGA
167295 AAA
1 AAA
167298 AAGAGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 5 0.14
12 17 0.49
13 13 0.37
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (12 bp):
AAAGAAAAAGGA
Found at i:168753 original size:9 final size:9
Alignment explanation
Indices: 168736--168768 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
168726 CTCTGGTTTC
168736 TTCTTTTTT
1 TTCTTTTTT
168745 TT-TTTTTT
1 TTCTTTTTT
*
168753 TTCATTTTT
1 TTCTTTTTT
168762 TTCTTTT
1 TTCTTTT
168769 AAAATGTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:174372 original size:24 final size:22
Alignment explanation
Indices: 174345--174390 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
174335 ATAATAAAAA
174345 TATAAATACCAAAATAAAAATTAT
1 TATAAA-ACC-AAATAAAAATTAT
* *
174369 TATAAAATCAAATATAAATTAT
1 TATAAAACCAAATAAAAATTAT
174391 AAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 2 0.10
24 6 0.30
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TATAAAACCAAATAAAAATTAT
Found at i:174401 original size:18 final size:19
Alignment explanation
Indices: 174367--174402 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
174357 AATAAAAATT
174367 ATTATAAAATCAAATATAA
1 ATTATAAAATCAAATATAA
174386 ATTATAAAAT-AAATATA
1 ATTATAAAATCAAATATA
174403 TAATAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTATAAAATCAAATATAA
Found at i:174413 original size:20 final size:19
Alignment explanation
Indices: 174370--174414 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
174360 AAAAATTATT
*
174370 ATAAAATCAAATATAAATT
1 ATAAAATCAAATATAAATA
174389 ATAAAAT-AAATATATAATA
1 ATAAAATCAAATATA-AATA
*
174408 ATTAAAT
1 ATAAAAT
174415 ACATCTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAATCAAATATAAATA
Found at i:174414 original size:19 final size:18
Alignment explanation
Indices: 174325--174415 Score: 64
Period size: 18 Copynumber: 5.1 Consensus size: 18
174315 TTTAATTATT
174325 TAAAT-TAAA-AATAATAA
1 TAAATATAAATAATAA-AA
**
174342 -AAATATAAATACCAAAA
1 TAAATATAAATAATAAAA
* * *
174359 TAAAAAT-TATTATAAAA
1 TAAATATAAATAATAAAA
*
174376 TCAAATATAAATTATAAAA
1 T-AAATATAAATAATAAAA
*
174395 TAAATATATAATAATTAAA
1 TAAATATA-AATAATAAAA
174414 TA
1 TA
174416 CATCTTAATT
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
16 4 0.07
17 13 0.23
18 20 0.35
19 20 0.35
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAATATAAATAATAAAA
Found at i:174569 original size:23 final size:24
Alignment explanation
Indices: 174526--174606 Score: 121
Period size: 25 Copynumber: 3.4 Consensus size: 24
174516 ACCTATCACT
174526 ATTATTTATAAAAAAATTAATAAA
1 ATTATTTATAAAAAAATTAATAAA
174550 ATTATTTATAAAAAAA-TAATAAA
1 ATTATTTATAAAAAAATTAATAAA
174573 ATTTTATTTATAAAAAAATTAA-AAA
1 A--TTATTTATAAAAAAATTAATAAA
*
174598 TTTATTTAT
1 ATTATTTAT
174607 TCATCCCAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
23 16 0.30
24 16 0.30
25 18 0.34
26 3 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTATTTATAAAAAAATTAATAAA
Found at i:177260 original size:28 final size:26
Alignment explanation
Indices: 177229--177281 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 26
177219 TTAAGAGATA
177229 AAAAAGTTATCTATAATAATTATTTTTT
1 AAAAAGTTATCTATAA-AA-TATTTTTT
** *
177257 AAAATTTTATCTTTAAAATATTTTT
1 AAAAAGTTATCTATAAAATATTTTT
177282 GATATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 7 0.32
27 2 0.09
28 13 0.59
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
AAAAAGTTATCTATAAAATATTTTTT
Found at i:178319 original size:17 final size:17
Alignment explanation
Indices: 178262--178320 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
178252 TTAATATTTT
*
178262 TTAAAATTATATTTATA
1 TTAAAATTATATTTAAA
*
178279 TTAATTAA-TAAATTATAAA
1 TTAA--AATTATATT-TAAA
*
178298 TTAAAATTATATTTACA
1 TTAAAATTATATTTAAA
178315 TTAAAA
1 TTAAAA
178321 ATAAAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 15 0.44
18 10 0.29
19 9 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAAATTATATTTAAA
Found at i:178333 original size:36 final size:36
Alignment explanation
Indices: 178262--178338 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
178252 TTAATATTTT
* * *
178262 TTAAAATTATATTTATATTAATTAATAAATTATAAA
1 TTAAAATTATATTTACATTAATAAATAAATAATAAA
178298 TTAAAATTATATTTACATTAA-AAATAAAATAATAAA
1 TTAAAATTATATTTACATTAATAAAT-AAATAATAAA
*
178334 ATAAA
1 TTAAA
178339 TATAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 3 0.08
36 33 0.92
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (36 bp):
TTAAAATTATATTTACATTAATAAATAAATAATAAA
Found at i:178442 original size:7 final size:7
Alignment explanation
Indices: 178430--178456 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
178420 CACTTTTTTT
178430 AAAAATA
1 AAAAATA
178437 AAAAATA
1 AAAAATA
178444 AAAAATA
1 AAAAATA
178451 AAAAAT
1 AAAAAT
178457 GCATCTAGTG
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:178814 original size:13 final size:13
Alignment explanation
Indices: 178773--178852 Score: 78
Period size: 13 Copynumber: 6.2 Consensus size: 13
178763 ATATTATGTT
*
178773 TTTATAT-TATAA
1 TTTATATATAAAA
178785 TTTA-AT-TAAAA
1 TTTATATATAAAA
178796 -TTATATATAAAA
1 TTTATATATAAAA
*
178808 TTTATATATAAAT
1 TTTATATATAAAA
178821 TTTAATATATTAATAA
1 TTT-ATATA-TAA-AA
*
178837 TTTATATATATAA
1 TTTATATATAAAA
178850 TTT
1 TTT
178853 TTTTATATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
10 3 0.05
11 8 0.14
12 9 0.16
13 19 0.33
14 7 0.12
15 8 0.14
16 4 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTATATATAAAA
Found at i:178817 original size:17 final size:17
Alignment explanation
Indices: 178797--178850 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 17
178787 TAATTAAAAT
178797 TATATATAA-AATTT-A
1 TATATATAATAATTTAA
178812 TATATA-AAT--TTTAA
1 TATATATAATAATTTAA
178826 TATAT-TAATAATTT-A
1 TATATATAATAATTTAA
178841 TATATATAAT
1 TATATATAAT
178851 TTTTTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.09
14 11 0.33
15 12 0.36
16 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATATAATAATTTAA
Found at i:178848 original size:31 final size:31
Alignment explanation
Indices: 178805--178872 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
178795 ATTATATATA
178805 AAATTTATATATA-AATTTTAATATATTAAT
1 AAATTTATATATATAATTTTAATATATTAAT
** *
178835 -AATTTATATATATAATTTTTTTATATTTAT
1 AAATTTATATATATAATTTTAATATATTAAT
178865 AAATTTAT
1 AAATTTAT
178873 GTTTTATGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 12 0.36
30 14 0.42
31 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
AAATTTATATATATAATTTTAATATATTAAT
Found at i:178860 original size:13 final size:13
Alignment explanation
Indices: 178756--178852 Score: 71
Period size: 13 Copynumber: 7.5 Consensus size: 13
178746 TAATAATTTA
178756 ATAATTTATAT-T
1 ATAATTTATATAT
* *
178768 AT-GTTTTTATATT
1 ATAATTTATATA-T
178781 ATAATTTA-AT-T
1 ATAATTTATATAT
*
178792 A-AAATTATATAT
1 ATAATTTATATAT
*
178804 AAAATTTATATAT
1 ATAATTTATATAT
178817 A-AATTTTAATATATT
1 ATAA-TTT-ATATA-T
178832 AATAATTTATATAT
1 -ATAATTTATATAT
178846 ATAATTT
1 ATAATTT
178853 TTTTATATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
10 5 0.07
11 10 0.15
12 6 0.09
13 26 0.38
14 9 0.13
15 6 0.09
16 4 0.06
17 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (13 bp):
ATAATTTATATAT
Found at i:185899 original size:20 final size:20
Alignment explanation
Indices: 185874--185927 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
185864 AAAAACCCTG
185874 AATGTATCGATACAAT-GAA
1 AATGTATCGATACAATAGAA
* *
185893 TAATGTATCGATAAAATAGCA
1 -AATGTATCGATACAATAGAA
185914 AATGTATCGATACA
1 AATGTATCGATACA
185928 TTTATTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATAGAA
Found at i:187667 original size:13 final size:13
Alignment explanation
Indices: 187649--187674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
187639 CAATTTTTTG
187649 TGTATCGATACAT
1 TGTATCGATACAT
187662 TGTATCGATACAT
1 TGTATCGATACAT
187675 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:188373 original size:21 final size:21
Alignment explanation
Indices: 188332--188375 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
188322 CTCCCCTTTA
* *
188332 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
188353 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
188374 TC
1 TC
188376 ATATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:190190 original size:13 final size:13
Alignment explanation
Indices: 190172--190197 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
190162 ATAATCACCC
190172 TGTATCGATACAA
1 TGTATCGATACAA
190185 TGTATCGATACAA
1 TGTATCGATACAA
190198 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:192296 original size:15 final size:15
Alignment explanation
Indices: 192276--192306 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
192266 ATTTCGTTTG
*
192276 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
192291 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
192306 G
1 G
192307 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:194139 original size:21 final size:21
Alignment explanation
Indices: 194110--194154 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
194100 AAGTTTTCAT
*
194110 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
194130 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
194152 TTT
1 TTT
194155 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:196325 original size:20 final size:20
Alignment explanation
Indices: 196283--196321 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
196273 CGTGTAAATG
* *
196283 TATCGATACAATTTTTGATA
1 TATCGATACAATATTTGAAA
196303 TATCGATAC-ATATTTGAAA
1 TATCGATACAATATTTGAAA
196322 ATATAGCCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATACAATATTTGAAA
Found at i:196390 original size:13 final size:13
Alignment explanation
Indices: 196372--196397 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
196362 CAATTTTTTG
196372 TGTATCGATACAT
1 TGTATCGATACAT
196385 TGTATCGATACAT
1 TGTATCGATACAT
196398 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:200201 original size:13 final size:13
Alignment explanation
Indices: 200183--200207 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
200173 AAATTCATCA
200183 TGTATCGATACAT
1 TGTATCGATACAT
200196 TGTATCGATACA
1 TGTATCGATACA
200208 ATACAAACAG
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:200299 original size:13 final size:13
Alignment explanation
Indices: 200281--200306 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
200271 TACAATGAAC
200281 TTGTATCGATACA
1 TTGTATCGATACA
200294 TTGTATCGATACA
1 TTGTATCGATACA
200307 AAGCATGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:202652 original size:20 final size:21
Alignment explanation
Indices: 202627--202666 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
202617 TTTATTGGTG
*
202627 ATTTTGATG-AAAAATGAAGT
1 ATTTTGAAGTAAAAATGAAGT
202647 ATTTTGAAGTAAAAATGAAG
1 ATTTTGAAGTAAAAATGAAG
202667 AAATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (21 bp):
ATTTTGAAGTAAAAATGAAGT
Found at i:207697 original size:19 final size:21
Alignment explanation
Indices: 207649--207704 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
207639 AATTTCAACA
207649 ATTTGTATCGATACAAACAGT
1 ATTTGTATCGATACAAACAGT
** *
207670 AACTGTATCGATACATA-AGT
1 ATTTGTATCGATACAAACAGT
*
207690 -TTTGTATCAATACAA
1 ATTTGTATCGATACAA
207705 TGTATCGCTA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
19 11 0.39
20 3 0.11
21 14 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (21 bp):
ATTTGTATCGATACAAACAGT
Found at i:207774 original size:13 final size:13
Alignment explanation
Indices: 207756--207781 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
207746 ATTACTCAAA
207756 TGTATCGATACAT
1 TGTATCGATACAT
207769 TGTATCGATACAT
1 TGTATCGATACAT
207782 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:212130 original size:20 final size:20
Alignment explanation
Indices: 212107--212231 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
212097 AAGTACCCAG
*
212107 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
212127 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
212147 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
212167 ATGTATCGATACATTCTGTCTTTTTACTCA
1 ATGTATCGATACA--------TTTT--TCA
212197 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
212218 ATGTATCGATACAT
1 ATGTATCGATACAT
212232 CTAGTTAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
20 59 0.69
21 3 0.04
23 4 0.05
28 3 0.04
30 3 0.04
31 13 0.15
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:214034 original size:21 final size:21
Alignment explanation
Indices: 213993--214036 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
213983 CTCCCCTTTA
* *
213993 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
214014 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
214035 TC
1 TC
214037 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:215046 original size:13 final size:13
Alignment explanation
Indices: 215028--215052 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
215018 ACTGAAGTAA
215028 TGTATCGATACAT
1 TGTATCGATACAT
215041 TGTATCGATACA
1 TGTATCGATACA
215053 ATCTGGAAAA
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:218788 original size:13 final size:13
Alignment explanation
Indices: 218770--218795 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
218760 ACAATTTTTG
218770 TGTATCGATACAT
1 TGTATCGATACAT
218783 TGTATCGATACAT
1 TGTATCGATACAT
218796 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:218792 original size:32 final size:32
Alignment explanation
Indices: 218751--218813 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
218741 TACAAGCTAA
**
218751 TGTATCGATACAATTTTTG-TGTATCGATACAT
1 TGTATCGATAC-ATACTTGCTGTATCGATACAT
218783 TGTATCGATACATACTTGCTGTATCGATACA
1 TGTATCGATACATACTTGCTGTATCGATACA
218814 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATACTTGCTGTATCGATACAT
Found at i:224877 original size:20 final size:19
Alignment explanation
Indices: 224830--224880 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
224820 GCTTGAGTTT
*
224830 TTTTATGAAAT-ATGTTAC
1 TTTTATGATATGATGTTAC
*
224848 TTGT-TGATATGATGTTAAC
1 TTTTATGATATGATGTT-AC
224867 TTTTATGATATGAT
1 TTTTATGATATGAT
224881 TTTGATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 5 0.19
18 8 0.30
19 5 0.19
20 9 0.33
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (19 bp):
TTTTATGATATGATGTTAC
Found at i:228855 original size:12 final size:12
Alignment explanation
Indices: 228838--228866 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
228828 CAAACACAAG
228838 ATCAACATCAAA
1 ATCAACATCAAA
228850 ATCAACATCAAA
1 ATCAACATCAAA
228862 ATCAA
1 ATCAA
228867 TTTTCAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.17
Consensus pattern (12 bp):
ATCAACATCAAA
Found at i:235716 original size:17 final size:18
Alignment explanation
Indices: 235678--235717 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
235668 ATTATCATTG
235678 ATAA-AAATTTAATTAGA
1 ATAATAAATTTAATTAGA
*
235695 A-AATAAATTTTATTA-A
1 ATAATAAATTTAATTAGA
235711 ATAATAA
1 ATAATAA
235718 TTATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAATAAATTTAATTAGA
Found at i:235838 original size:16 final size:17
Alignment explanation
Indices: 235819--235851 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
235809 ATAATTAATG
235819 ATATTTTTAATT-TTTT
1 ATATTTTTAATTGTTTT
235835 ATATTTTTAATTGTTTT
1 ATATTTTTAATTGTTTT
235852 TAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
ATATTTTTAATTGTTTT
Found at i:236084 original size:22 final size:22
Alignment explanation
Indices: 236043--236100 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
236033 TGTACATTTA
* *
236043 AATATACAAAAAAATAAAAATAT
1 AATATA-AAAATAATAAAAACAT
* *
236066 GATATAAAAATAATTAAAACAT
1 AATATAAAAATAATAAAAACAT
236088 AATATAAAAATAA
1 AATATAAAAATAA
236101 ATGTAACACA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 25 0.83
23 5 0.17
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (22 bp):
AATATAAAAATAATAAAAACAT
Found at i:236100 original size:11 final size:11
Alignment explanation
Indices: 236043--236100 Score: 59
Period size: 11 Copynumber: 5.2 Consensus size: 11
236033 TGTACATTTA
236043 AATATACAAAA-
1 AATATA-AAAAT
236054 AA-ATAAAAAT
1 AATATAAAAAT
236064 ATGATATAAAAAT
1 A--ATATAAAAAT
236077 AAT-TAAAACAT
1 AATATAAAA-AT
236088 AATATAAAAAT
1 AATATAAAAAT
236099 AA
1 AA
236101 ATGTAACACA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 4 0.10
10 9 0.22
11 13 0.32
12 6 0.15
13 9 0.22
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:236108 original size:22 final size:23
Alignment explanation
Indices: 236042--236117 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 23
236032 TTGTACATTT
*
236042 AAATATACAAAA-AAATAAAA-AT
1 AAATATA-AAAATAAATAAAACAC
* *
236064 ATGATATAAAAATAATTAAAACA-
1 A-AATATAAAAATAAATAAAACAC
* **
236087 TAATATAAAAATAAATGTAACAC
1 AAATATAAAAATAAATAAAACAC
236110 AAATATAA
1 AAATATAA
236118 GAACATATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
22 22 0.52
23 19 0.45
24 1 0.02
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (23 bp):
AAATATAAAAATAAATAAAACAC
Found at i:236262 original size:15 final size:16
Alignment explanation
Indices: 236235--236266 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
236225 TTCTCCTTCC
236235 TTTTCTTTCTTTTCTT
1 TTTTCTTTCTTTTCTT
236251 TTTTCTTT-TTTTCTT
1 TTTTCTTTCTTTTCTT
236266 T
1 T
236267 GCATCTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTTCTTTTCTT
Found at i:237354 original size:35 final size:36
Alignment explanation
Indices: 237289--237363 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 36
237279 ATGAAATAAA
** *
237289 ATAAATTATTAATATATAAAAATTTTATATAAAATT
1 ATAAATTATTAATATATAAAAAAATAATATAAAATT
237325 ATAATATT-TTAA-ATATAAAAAAATAATAT-AAA-T
1 ATAA-ATTATTAATATATAAAAAAATAATATAAAATT
237358 ATAAAT
1 ATAAAT
237364 ATGTAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
32 2 0.06
33 5 0.14
34 3 0.09
35 14 0.40
36 8 0.23
37 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (36 bp):
ATAAATTATTAATATATAAAAAAATAATATAAAATT
Found at i:241161 original size:23 final size:23
Alignment explanation
Indices: 241135--241180 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
241125 AAACAGGCAT
241135 CTTTAAAATAAATAACACTCCAA
1 CTTTAAAATAAATAACACTCCAA
241158 CTTTAAAATAAATAACACTCCAA
1 CTTTAAAATAAATAACACTCCAA
241181 GACATAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (23 bp):
CTTTAAAATAAATAACACTCCAA
Found at i:243812 original size:14 final size:11
Alignment explanation
Indices: 243781--243807 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
243771 TATTAATTTT
243781 AAATATAATAA
1 AAATATAATAA
243792 AAATATAATAA
1 AAATATAATAA
243803 AAATA
1 AAATA
243808 ATATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATATAATAA
Found at i:243822 original size:21 final size:21
Alignment explanation
Indices: 243796--243837 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
243786 TAATAAAAAT
243796 ATAATAAAAAT-AATATATTTA
1 ATAATAAAAATAAAT-TATTTA
*
243817 ATAATAAATATAAATTATTTA
1 ATAATAAAAATAAATTATTTA
243838 TTTAAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATAAAAATAAATTATTTA
Found at i:243826 original size:25 final size:26
Alignment explanation
Indices: 243793--243842 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
243783 ATATAATAAA
243793 AATATAATAAAAATAATATATTTAAT
1 AATATAATAAAAATAATATATTTAAT
* * *
243819 AATA-AATATAAATTATTTATTTAA
1 AATATAATAAAAATAATATATTTAA
243843 ATACTATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATATAATAAAAATAATATATTTAAT
Found at i:246300 original size:20 final size:20
Alignment explanation
Indices: 246280--246318 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
246270 GATAAGTTTT
246280 ATTTAAAAATAAATTAATTTA
1 ATTT-AAAATAAATTAATTTA
*
246301 ATTTAAATTAAATTAATT
1 ATTTAAAATAAATTAATT
246319 GAGTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTAAAATAAATTAATTTA
Found at i:246309 original size:15 final size:15
Alignment explanation
Indices: 246289--246318 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
246279 TATTTAAAAA
*
246289 TAAATTAATTTAATT
1 TAAATTAAATTAATT
246304 TAAATTAAATTAATT
1 TAAATTAAATTAATT
246319 GAGTTTTAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATTAAATTAATT
Found at i:246490 original size:14 final size:15
Alignment explanation
Indices: 246473--246501 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
246463 TATTATATTA
246473 TTTTAAAT-ATAAAT
1 TTTTAAATAATAAAT
246487 TTTTAAATAATAAAT
1 TTTTAAATAATAAAT
246502 AATTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTAAATAATAAAT
Found at i:247145 original size:23 final size:24
Alignment explanation
Indices: 247085--247148 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
247075 AAATTATACG
247085 ATATAAAT-ATAATAT-AAAAATT
1 ATATAAATCATAATATAAAAAATT
* *
247107 ATATAAATTATGATATAAAAAATT
1 ATATAAATCATAATATAAAAAATT
**
247131 ATATTTA-CATAATATAAA
1 ATATAAATCATAATATAAA
247149 TATATAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 8 0.23
23 15 0.43
24 12 0.34
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATAAATCATAATATAAAAAATT
Found at i:247192 original size:22 final size:23
Alignment explanation
Indices: 247150--247201 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
247140 TAATATAAAT
*
247150 ATATAAATATTTTAAATTTATATA
1 ATATAAATATATTAAATTTAT-TA
247174 ATATAAAT-TATT-AATTTATTA
1 ATATAAATATATTAAATTTATTA
*
247195 AAATAAA
1 ATATAAA
247202 ATTTTCATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.31
22 7 0.27
23 3 0.12
24 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATAAATATATTAAATTTATTA
Found at i:247360 original size:24 final size:22
Alignment explanation
Indices: 247333--247388 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 22
247323 TATAAAGATA
*
247333 AAATATAATTATAATATATTTAAT
1 AAATATAATTAT-A-ACATTTAAT
*
247357 AAATATAAATATAACATTTAAT
1 AAATATAATTATAACATTTAAT
247379 ATAATATAAT
1 A-AATATAAT
247389 ATTATATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.32
23 8 0.29
24 11 0.39
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATATAATTATAACATTTAAT
Found at i:247385 original size:5 final size:5
Alignment explanation
Indices: 247334--247404 Score: 51
Period size: 5 Copynumber: 14.2 Consensus size: 5
247324 ATAAAGATAA
* *
247334 AATAT AATTAT AATAT -ATTT AATA- AATAT AAATAT AACATTT AATAT
1 AATAT AA-TAT AATAT AATAT AATAT AATAT -AATAT -A-ATAT AATAT
*
247381 AATAT AATAT --TAT ATTAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT A
247405 TATTTTATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
3 3 0.06
4 7 0.13
5 28 0.52
6 13 0.24
7 3 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (5 bp):
AATAT
Found at i:247423 original size:37 final size:37
Alignment explanation
Indices: 247382--247476 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
247372 ATTTAATATA
* *
247382 ATATAATATTATATTATAATATATATTT-TATATTTAT
1 ATATAATATAATAATATAATATAT-TTTATATATTTAT
* *
247419 ATATAAAATAATAATATAATTTATTTTATATATTTAT
1 ATATAATATAATAATATAATATATTTTATATATTTAT
*
247456 ATATAAT-TAAT-ATAAAATATA
1 ATATAATATAATAATATAATATA
247477 ATACTCATAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 8 0.16
36 7 0.14
37 35 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
ATATAATATAATAATATAATATATTTTATATATTTAT
Found at i:247871 original size:32 final size:32
Alignment explanation
Indices: 247820--247900 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
247810 TATATTTTTT
*
247820 TATTTATTA-TTATTATATATGTAA-TTTAATA
1 TATTTATTATTTATTATATAT-AAATTTTAATA
* *
247851 TATTAATTATTTATTTTATATAAATTTTAATA
1 TATTTATTATTTATTATATATAAATTTTAATA
*
247883 TATTTATT-TTTAATATAT
1 TATTTATTATTTATTATAT
247901 TTATATATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
31 18 0.43
32 24 0.57
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (32 bp):
TATTTATTATTTATTATATATAAATTTTAATA
Found at i:247888 original size:25 final size:25
Alignment explanation
Indices: 247853--247939 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 25
247843 ATTTAATATA
247853 TTAAT-TATTTATTTTATATAAATT
1 TTAATATATTTATTTTATATAAATT
*
247877 TTAATATATTTATTTT-TA-ATATAT
1 TTAATATATTTATTTTATATAAAT-T
* *
247901 TT-ATATATTTTATTTTATGTAATTT
1 TTAATATA-TTTATTTTATATAAATT
247926 TTATATTATATTTA
1 TTA-A-TATATTTA
247940 AAGTTATTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
23 8 0.16
24 18 0.35
25 14 0.27
26 2 0.04
27 5 0.10
28 4 0.08
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (25 bp):
TTAATATATTTATTTTATATAAATT
Found at i:247893 original size:15 final size:15
Alignment explanation
Indices: 247875--247904 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
247865 TTTATATAAA
247875 TTTTAATATATTTAT
1 TTTTAATATATTTAT
247890 TTTTAATATATTTAT
1 TTTTAATATATTTAT
247905 ATATTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAATATATTTAT
Found at i:247925 original size:23 final size:22
Alignment explanation
Indices: 247860--247938 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 22
247850 ATATTAATTA
247860 TTTATTTTATATAAATTTTAATAT
1 TTTATTTTATAT-AATTTT-ATAT
247884 ATTTATTTT-TAATATATTTATATAT
1 -TTTATTTTAT-ATA-ATTT-TATAT
*
247909 TTTATTTTATGTAATTTTTATAT
1 TTTATTTTATATAA-TTTTATAT
*
247932 TATATTT
1 TTTATTT
247939 AAAGTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
23 12 0.26
24 15 0.32
25 19 0.40
26 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (22 bp):
TTTATTTTATATAATTTTATAT
Found at i:247938 original size:47 final size:45
Alignment explanation
Indices: 247802--247938 Score: 129
Period size: 47 Copynumber: 2.9 Consensus size: 45
247792 ATAATTATAT
* *
247802 TATATTTATATATTT-TTTTATTTATTATTAT-TATATATGTAATTTAA
1 TATATTTATATATTTATTTTATTAATTTTTATAT-TATAT-T--TTTAA
*
247849 TATATTAAT-TATTTATTTTATATAAATTTTAATATATT-TATTTTTAA
1 TATATTTATATATTTATTTTAT-T-AATTTT--TATATTATATTTTTAA
247896 TATATTTATATATTTTATTTTATGTAATTTTTATATTATATTT
1 TATATTTATATA-TTTATTTTAT-TAATTTTTATATTATATTT
247939 AAAGTTATTA
Statistics
Matches: 76, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
46 11 0.14
47 32 0.42
48 9 0.12
49 16 0.21
50 3 0.04
51 4 0.05
52 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (45 bp):
TATATTTATATATTTATTTTATTAATTTTTATATTATATTTTTAA
Found at i:247956 original size:51 final size:49
Alignment explanation
Indices: 247860--247958 Score: 117
Period size: 51 Copynumber: 2.0 Consensus size: 49
247850 ATATTAATTA
*** *
247860 TTTATTTTATATAAATTTTAATATATTTATTTTTAATATATTTATATAT
1 TTTATTTTATATAAATTTTAATATATTTAAAGTTAATAAATTTATATAT
* * *
247909 TTTATTTTATGTAATTTTTATATTATATTTAAAGTTATTAAATTTATATA
1 TTTATTTTATATAAATTTTA-A-TATATTTAAAGTTAATAAATTTATATA
247959 GTAACTTCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 18 0.44
50 1 0.02
51 22 0.54
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (49 bp):
TTTATTTTATATAAATTTTAATATATTTAAAGTTAATAAATTTATATAT
Found at i:248243 original size:2 final size:2
Alignment explanation
Indices: 248226--248264 Score: 51
Period size: 2 Copynumber: 18.5 Consensus size: 2
248216 TATTATTAAT
*
248226 TA TA TA TG TA TGA TA TA TA TA TA TA TA TA TA TGA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA T-A TA TA T
248265 TTGTATTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 29 0.88
3 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (2 bp):
TA
Found at i:249028 original size:34 final size:33
Alignment explanation
Indices: 248982--249166 Score: 187
Period size: 34 Copynumber: 5.5 Consensus size: 33
248972 GTAAAAACCA
248982 CCATTTAATCAACAATGACAACCTACCAAATCTC
1 CCATTTAATCAACAATGA-AACCTACCAAATCTC
* *
249016 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAAT-G-AAACCTACCAAATCTC
* * *
249050 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAAT-GAAACCTACCAAATCTC
* * * *
249084 CCATTTAATCAACAATGGTAAGCTACCAAATTTT
1 CCATTTAATCAACAAT-GAAACCTACCAAATCTC
* *
249118 CCATTTAGTCAACAATAGTAAA-CTACCAAATC-A
1 CCATTTAATCAACAAT-G-AAACCTACCAAATCTC
249151 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
249167 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
33 18 0.14
34 105 0.80
35 7 0.05
36 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.06, T:0.26
Consensus pattern (33 bp):
CCATTTAATCAACAATGAAACCTACCAAATCTC
Found at i:249096 original size:68 final size:68
Alignment explanation
Indices: 248982--249166 Score: 237
Period size: 68 Copynumber: 2.7 Consensus size: 68
248972 GTAAAAACCA
** * *
248982 CCATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
249047 CAC
66 CAC
* * * *
249050 CCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
***
249115 TTT
66 CAC
* * *
249118 CCATTTAGTCAACAATAGTAAACTACCAAATC-ACCATTTAATCAACAAT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAAT
249167 TCTCCCACTT
Statistics
Matches: 102, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
67 16 0.16
68 86 0.84
ACGTcount: A:0.41, C:0.26, G:0.06, T:0.26
Consensus pattern (68 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
CAC
Found at i:253727 original size:33 final size:34
Alignment explanation
Indices: 253580--253763 Score: 228
Period size: 34 Copynumber: 5.5 Consensus size: 34
253570 GTAAAAACCA
** *
253580 CCATTTAATCAACAATGACAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* * *
253614 CCATTTAGTCAACAATGGTAAACCACCAAATCAC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
253648 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
253682 CCATTTAATCAACAATGGTAAGCTACCAAAT-TT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* * * *
253715 TCATTTAGTCAACAATAGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
253748 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
253764 TTTTCTTCTA
Statistics
Matches: 129, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
33 42 0.33
34 87 0.67
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTC
Found at i:257422 original size:25 final size:24
Alignment explanation
Indices: 257392--257449 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
257382 AATGTTAATG
*
257392 TAACACATG-ACGAGAAAATATGACA
1 TAACACATGTA-G-GAAAATATAACA
257417 TAACACATTGTAGGAAAATATAACA
1 TAACACA-TGTAGGAAAATATAACA
*
257442 GAACACAT
1 TAACACAT
257450 AGCAGGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 1 0.03
25 24 0.83
26 3 0.10
27 1 0.03
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.19
Consensus pattern (24 bp):
TAACACATGTAGGAAAATATAACA
Found at i:257456 original size:25 final size:25
Alignment explanation
Indices: 257405--257457 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
257395 CACATGACGA
* * * *
257405 GAAAATATGACATAACACATTGTAG
1 GAAAATATAACAGAACACATAGCAG
257430 GAAAATATAACAGAACACATAGCAG
1 GAAAATATAACAGAACACATAGCAG
257455 GAA
1 GAA
257458 TTGAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.53, C:0.13, G:0.17, T:0.17
Consensus pattern (25 bp):
GAAAATATAACAGAACACATAGCAG
Found at i:261585 original size:2 final size:2
Alignment explanation
Indices: 261541--261571 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
261531 TATTTAACAC
*
261541 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
261572 GTATCGGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:263464 original size:19 final size:20
Alignment explanation
Indices: 263426--263464 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
263416 CCTTAAATCA
* *
263426 AGATAATATTTTTTAAATTT
1 AGATAATATATTTAAAATTT
263446 AGATAATA-ATTTAAAATTT
1 AGATAATATATTTAAAATTT
263465 GAAATTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AGATAATATATTTAAAATTT
Found at i:263677 original size:2 final size:2
Alignment explanation
Indices: 263670--263704 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
263660 AACATAGTTG
263670 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 A
263705 CCACAAAACT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:264748 original size:11 final size:11
Alignment explanation
Indices: 264732--264756 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
264722 TAGACAACTT
264732 AAATAATCTAA
1 AAATAATCTAA
264743 AAATAATCTAA
1 AAATAATCTAA
264754 AAA
1 AAA
264757 GTATATTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAATCTAA
Found at i:265830 original size:32 final size:32
Alignment explanation
Indices: 265762--265831 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
265752 AATTTTCAAG
* * *
265762 TCATTTCAAGTTTAAATCATTCCAGTTTTAGG
1 TCATTTCAAGTTTAAATCATTCCAATTTCAGA
* *
265794 TCATTTGAAGTTTAAATCACTT-TAATTTCAGA
1 TCATTTCAAGTTTAAATCA-TTCCAATTTCAGA
265826 TCATTT
1 TCATTT
265832 TAGATTCGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (32 bp):
TCATTTCAAGTTTAAATCATTCCAATTTCAGA
Found at i:265848 original size:32 final size:32
Alignment explanation
Indices: 265812--265872 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
265802 AGTTTAAATC
*
265812 ACTTTAA-TTTCAGATCATTTTAGATTCGAATT
1 ACTTTAAGTTT-AGATCATTTTAAATTCGAATT
265844 ACTTTAAGTTTAGATCATTTTAAATTCGA
1 ACTTTAAGTTTAGATCATTTTAAATTCGA
265873 GTCAATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (32 bp):
ACTTTAAGTTTAGATCATTTTAAATTCGAATT
Found at i:265865 original size:16 final size:16
Alignment explanation
Indices: 265788--265866 Score: 54
Period size: 16 Copynumber: 4.9 Consensus size: 16
265778 TCATTCCAGT
* *
265788 TTTAGGTCATTTGAAG
1 TTTAGATCATTTTAAG
* *
265804 TTTAAATCACTTTAA-
1 TTTAGATCATTTTAAG
265819 TTTCAGATCATTTT-AG
1 TTT-AGATCATTTTAAG
* * * *
265835 ATTCGAATTACTTTAAG
1 TTTAG-ATCATTTTAAG
265852 TTTAGATCATTTTAA
1 TTTAGATCATTTTAA
265867 ATTCGAGTCA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
15 5 0.11
16 35 0.78
17 5 0.11
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.47
Consensus pattern (16 bp):
TTTAGATCATTTTAAG
Found at i:268639 original size:3 final size:3
Alignment explanation
Indices: 268631--268673 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
268621 ATTTGGATCT
268631 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
268674 GTTAGTAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:268809 original size:17 final size:18
Alignment explanation
Indices: 268773--268811 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
268763 TTATAAATTT
*
268773 TTATTTAAATTTTAAAAA
1 TTATTTAAATATTAAAAA
*
268791 TTATTT-AATATTAATAA
1 TTATTTAAATATTAAAAA
268808 TTAT
1 TTAT
268812 ATATTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTTAAATATTAAAAA
Found at i:269171 original size:6 final size:6
Alignment explanation
Indices: 269160--269188 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
269150 TGAGGGTACC
269160 TTTCAA TTTCAA TTTCAA TTTCAA TTTCA
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCA
269189 TTTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTCAA
Found at i:269799 original size:26 final size:25
Alignment explanation
Indices: 269765--269815 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
269755 TTTTGCATTC
* *
269765 ATATGTAATTTTATTTGTTATTTTTA
1 ATATGTAATTTCATTT-CTATTTTTA
*
269791 ATATTTAATTTCATTTCTATTTTTA
1 ATATGTAATTTCATTTCTATTTTTA
269816 CTAAATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (25 bp):
ATATGTAATTTCATTTCTATTTTTA
Found at i:270115 original size:22 final size:24
Alignment explanation
Indices: 270090--270134 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
270080 TTTAGATTTA
270090 AATTAATTAAGTTT-GAT-ACTTC
1 AATTAATTAAGTTTAGATCACTTC
* *
270112 AATTATTTGAGTTTAGATCACTT
1 AATTAATTAAGTTTAGATCACTT
270135 TAGTTTTGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 3 0.16
24 4 0.21
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (24 bp):
AATTAATTAAGTTTAGATCACTTC
Found at i:271462 original size:3 final size:3
Alignment explanation
Indices: 271454--271485 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
271444 AAAATATTCA
271454 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
271486 AAAAGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:271529 original size:6 final size:6
Alignment explanation
Indices: 271520--271558 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
271510 AAAGGATATT
* * *
271520 GATGTG GATGTG GATATG GATGTA GATGTG GATATG GAT
1 GATGTG GATGTG GATGTG GATGTG GATGTG GATGTG GAT
271559 ATAAGTTGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.41, T:0.33
Consensus pattern (6 bp):
GATGTG
Found at i:271536 original size:18 final size:18
Alignment explanation
Indices: 271513--271558 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
271503 GAAAAAGAAA
* *
271513 GGATATTGATGTGGATGT
1 GGATATGGATGTAGATGT
271531 GGATATGGATGTAGATGT
1 GGATATGGATGTAGATGT
271549 GGATATGGAT
1 GGATATGGAT
271559 ATAAGTTGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.39, T:0.35
Consensus pattern (18 bp):
GGATATGGATGTAGATGT
Found at i:271745 original size:26 final size:27
Alignment explanation
Indices: 271701--271751 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
271691 TTTAAAGGTT
*
271701 TAAAAGATAGATTTTAAATTAATTTTG
1 TAAAAGATAGATTTCAAATTAATTTTG
*
271728 TAAAA-ATAGATTTCAAATTGATTT
1 TAAAAGATAGATTTCAAATTAATTT
271752 AAAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (27 bp):
TAAAAGATAGATTTCAAATTAATTTTG
Found at i:271758 original size:26 final size:26
Alignment explanation
Indices: 271702--271760 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
271692 TTAAAGGTTT
* * **
271702 AAAAGATAGATTTTAAATTAATTTTG
1 AAAAAATAGATTTCAAATTAATTTAA
* *
271728 TAAAAATAGATTTCAAATTGATTTAA
1 AAAAAATAGATTTCAAATTAATTTAA
271754 AAAAAAT
1 AAAAAAT
271761 TATCTTATAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (26 bp):
AAAAAATAGATTTCAAATTAATTTAA
Found at i:275219 original size:52 final size:52
Alignment explanation
Indices: 275155--275291 Score: 229
Period size: 52 Copynumber: 2.6 Consensus size: 52
275145 ACTAGAAAGA
* *
275155 AAATGTATCGATACATTTTTCATTGTATCTATACATTTTAGGTTTTTGACCC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTTTAGGTTTTTGACCC
275207 AAATGTATCGATACATTATTCATTGTATCGATACATTTTAGGTTTTTGACCC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTTTAGGTTTTTGACCC
* * *
275259 AAATGTATTGATACATTCTTCAATGTATCGATA
1 AAATGTATCGATACATTATTCATTGTATCGATA
275292 TATGCAGGCA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 80 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (52 bp):
AAATGTATCGATACATTATTCATTGTATCGATACATTTTAGGTTTTTGACCC
Found at i:280043 original size:59 final size:59
Alignment explanation
Indices: 279982--280236 Score: 185
Period size: 59 Copynumber: 4.2 Consensus size: 59
279972 AATTATGCAA
* * * *
279982 TTTCTATGCATTGT-AGGTTTATTTAAGTTATTTTTCGTAATCTAGGGACAATTTTATAAT
1 TTTC-ATGCATTGTAAGG-TCATTTAAGTTATTTTCCATAATCTAGAGACAATTTTATAAT
* * * * *
280042 TTTCATGCATTTTATGGTCATTTAGGTTATTTTCCATAATCTAAAAACCATTATACCTTTATGTA
1 TTTCATGCATTGTAAGGTCATTTAAGTTATTTTCCATAATCTAGAGA-CA--AT---TTTA--TA
280107 AT
58 AT
* * * ** * *
280109 TTTTATGCATT-TGAGGTTATACAAGTTATTTTCCATAATTTAGAGACAATTTTGTAAT
1 TTTCATGCATTGTAAGGTCATTTAAGTTATTTTCCATAATCTAGAGACAATTTTATAAT
* * * * *
280167 TTTCATGCA-TGTTAAGGTCATTTAGGTTACTTTT-CGTAATCTAGGGACCATTTTGTAAT
1 TTTCATGCATTG-TAAGGTCATTTAAGTTA-TTTTCCATAATCTAGAGACAATTTTATAAT
280226 TTTCATGCATT
1 TTTCATGCATT
280237 TTTTTAGTCT
Statistics
Matches: 152, Mismatches: 30, Indels: 26
0.73 0.14 0.12
Matches are distributed among these distances:
57 1 0.01
58 12 0.08
59 73 0.48
60 16 0.11
62 2 0.01
63 2 0.01
65 6 0.04
66 26 0.17
67 14 0.09
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (59 bp):
TTTCATGCATTGTAAGGTCATTTAAGTTATTTTCCATAATCTAGAGACAATTTTATAAT
Found at i:280218 original size:125 final size:126
Alignment explanation
Indices: 279974--280209 Score: 325
Period size: 125 Copynumber: 1.9 Consensus size: 126
279964 CTAAGATTAA
** * * *
279974 TTATGCAATTTCTATGCATTGTAGGTTTATTTAAGTTATTTTTCGTAATCTAGGGACAATTTTAT
1 TTATGCAATTTCTATGCATTGTAGGTTTATACAAGTTATTTTCCATAATCTAGAGACAATTTTAT
* *
280039 AATTTTCATGCATTTTATGGTCATTTAGGTTATTTTCCATAATCTAAAAACCATTATACCT
66 AATTTTCATGCATGTTAAGGTCATTTAGGTTATTTTCCATAATCTAAAAACCATTATACCT
* * * *
280100 TTATGTAATTTTTATGCATT-TGAGG-TTATACAAGTTATTTTCCATAATTTAGAGACAATTTTG
1 TTATGCAATTTCTATGCATTGT-AGGTTTATACAAGTTATTTTCCATAATCTAGAGACAATTTTA
*
280163 TAATTTTCATGCATGTTAAGGTCATTTAGGTTACTTTT-CGTAATCTA
65 TAATTTTCATGCATGTTAAGGTCATTTAGGTTA-TTTTCCATAATCTA
280210 GGGACCATTT
Statistics
Matches: 96, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
125 71 0.74
126 25 0.26
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.47
Consensus pattern (126 bp):
TTATGCAATTTCTATGCATTGTAGGTTTATACAAGTTATTTTCCATAATCTAGAGACAATTTTAT
AATTTTCATGCATGTTAAGGTCATTTAGGTTATTTTCCATAATCTAAAAACCATTATACCT
Found at i:280318 original size:49 final size:49
Alignment explanation
Indices: 280242--280360 Score: 148
Period size: 49 Copynumber: 2.4 Consensus size: 49
280232 GCATTTTTTT
* * ** *
280242 AGTCTTTTAGGGTTAGTTTTGAACCTACGATCGAAATTAACCAAAATCG
1 AGTCTTTTAAGGTTAGTTTTGAACCTACGATCAAAACCAACCAAAATCA
* * * *
280291 AGTCTTTTAAGGTTAGTTTTGAGCCTACTATTAAAACCGACCAAAATCA
1 AGTCTTTTAAGGTTAGTTTTGAACCTACGATCAAAACCAACCAAAATCA
*
280340 AGTCTTTTAATGTTAGTTTTG
1 AGTCTTTTAAGGTTAGTTTTG
280361 TATTTTCTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (49 bp):
AGTCTTTTAAGGTTAGTTTTGAACCTACGATCAAAACCAACCAAAATCA
Found at i:280385 original size:49 final size:49
Alignment explanation
Indices: 280242--280409 Score: 144
Period size: 49 Copynumber: 3.4 Consensus size: 49
280232 GCATTTTTTT
* * * * *
280242 AGTCTTTTAGGGTTAGTTTTGAACCTACGATCGAAATT-AACCAAAATCG
1 AGTCTTTTAAGGTTAGTTTTGAGCCTACTATCAAAATTGAA-CAAAATCA
* ** *
280291 AGTCTTTTAAGGTTAGTTTTGAGCCTACTATTAAAACCGACCAAAATCA
1 AGTCTTTTAAGGTTAGTTTTGAGCCTACTATCAAAATTGAACAAAATCA
* ** * *
280340 AGTCTTTTAATGTTAGTTTTGTA-TTTTCTATCAAAATTGAACAAAATCT
1 AGTCTTTTAAGGTTAGTTTTG-AGCCTACTATCAAAATTGAACAAAATCA
* *
280389 AGCCCTTT-AGGATTAGTTTTG
1 AGTCTTTTAAGG-TTAGTTTTG
280410 TACTTCCATC
Statistics
Matches: 95, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
48 2 0.02
49 91 0.96
50 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (49 bp):
AGTCTTTTAAGGTTAGTTTTGAGCCTACTATCAAAATTGAACAAAATCA
Found at i:283495 original size:6 final size:6
Alignment explanation
Indices: 283486--283522 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
283476 AACTAGAACG
*
283486 AGAAAA AGAAAA A-AGAA AGAAAA A-AAAA AGAAAA AGA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGA
283523 TAAATGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:283506 original size:11 final size:11
Alignment explanation
Indices: 283488--283520 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
283478 CTAGAACGAG
283488 AAAAAGAAAAA
1 AAAAAGAAAAA
*
283499 AGAAAGAAAAA
1 AAAAAGAAAAA
283510 AAAAAGAAAAA
1 AAAAAGAAAAA
283521 GATAAATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:283514 original size:15 final size:16
Alignment explanation
Indices: 283489--283518 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
283479 TAGAACGAGA
283489 AAAAGAAAAAAGAAAG
1 AAAAGAAAAAAGAAAG
283505 AAAA-AAAAAAGAAA
1 AAAAGAAAAAAGAAA
283519 AAGATAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAG
Found at i:284586 original size:77 final size:77
Alignment explanation
Indices: 284505--284945 Score: 295
Period size: 78 Copynumber: 5.7 Consensus size: 77
284495 TTTCAAGCTA
** * *
284505 ATACATGTTTATTAGGGTTATTAAGGTAATATTACATTAATACCAAGTCTTTAGTGT-ATGTGGG
1 ATACATGTCCATTAGGGTCATTAAGGTAATATTACATTAATACCAAGT-TTTAGTGTCATGTGAG
* *
284569 AACTTTTATGTTG
65 AACTTTCATGTCG
* * * * * * * *
284582 ATACATATCCAATAGGGTTATTTAGGTAATATTACATTAGTACTAAGTTTATAGAGTCATGTTGC
1 ATACATGTCCATTAGGGTCATTAAGGTAATATTACATTAATACCAAGTTT-TAGTGTCATG-TGA
*
284647 GAACTTTCATGCCG
64 GAACTTTCATGTCG
* * * * * * **
284661 ATTCATGTCCATTAGGATTA-TATAGGTAATATTATTACATTAATGCCGAGTTTAAG-GTCACAT
1 ATACATGTCCATTAGGGTCATTA-AGGT-A-A-TATTACATTAATACCAAGTTTTAGTGTCATGT
* * * *
284724 AAGAACTTTCGTGGCA
62 GAGAACTTTCATGTCG
*** * * *
284740 ATA-ATGTCCA-TAGAGGTCATTAAGG-AATATTACATTAATATTGAGTCCTTAGGGTCATG-CA
1 ATACATGTCCATTAG-GGTCATTAAGGTAATATTACATTAATACCAAGT-TTTAGTGTCATGTGA
* *
284801 GGAATTTTCATGTTG
64 -GAACTTTCATGTCG
* * * *
284816 ATACATGTCCATTAGGGTCATTTAA-GTAATATTGCATTAGTACCGAGTCTTTAATGTCATGTGA
1 ATACATGTCCATTAGGGTCA-TTAAGGTAATATTACATTAATACCAAGT-TTTAGTGTCATGTGA
284880 GAACTTTCATGTCG
64 GAACTTTCATGTCG
* ** * * * * *
284894 ATACATATTTATGAGGGTCATTTAGGTAATAGTACACTAATACAAAGTTTTA
1 ATACATGTCCATTAGGGTCATTAAGGTAATATTACATTAATACCAAGTTTTA
284946 ATAAAATCTA
Statistics
Matches: 280, Mismatches: 66, Indels: 36
0.73 0.17 0.09
Matches are distributed among these distances:
74 16 0.06
75 5 0.02
76 19 0.07
77 69 0.25
78 96 0.34
79 50 0.18
80 5 0.02
81 3 0.01
82 17 0.06
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (77 bp):
ATACATGTCCATTAGGGTCATTAAGGTAATATTACATTAATACCAAGTTTTAGTGTCATGTGAGA
ACTTTCATGTCG
Found at i:285807 original size:2 final size:2
Alignment explanation
Indices: 285800--285830 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
285790 TTGCTCATTT
*
285800 TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
285831 ATATTTGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:288706 original size:27 final size:27
Alignment explanation
Indices: 288669--288746 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
288659 AAAAGCCACC
* * *
288669 CTTTGTGTTTGTCAACAATGGTGGTTA
1 CTTTGTTTTTGTCAAAAATGATGGTTA
*
288696 CTTTGTTTTTGTCAAAAATGATGGTTC
1 CTTTGTTTTTGTCAAAAATGATGGTTA
*
288723 CTTT-TTGTTTGTCAAAAATTATGG
1 CTTTGTT-TTTGTCAAAAATGATGG
288747 CTTATTGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 2 0.04
27 43 0.96
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.47
Consensus pattern (27 bp):
CTTTGTTTTTGTCAAAAATGATGGTTA
Found at i:288759 original size:24 final size:25
Alignment explanation
Indices: 288703--288763 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
288693 TTACTTTGTT
*
288703 TTTGTCAAAAATGATGGTTCCTTTTTG
1 TTTGTCAAAAATGATGG-T-CTTATTG
*
288730 TTTGTCAAAAATTATGG-CTTATTG
1 TTTGTCAAAAATGATGGTCTTATTG
288754 TTTGTCAAAA
1 TTTGTCAAAA
288764 TTGGTGGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 16 0.50
27 16 0.50
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (25 bp):
TTTGTCAAAAATGATGGTCTTATTG
Found at i:288842 original size:13 final size:13
Alignment explanation
Indices: 288824--288872 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
288814 GAGGCTCTCT
288824 CATCCCTCTCAAG
1 CATCCCTCTCAAG
*
288837 CATCCCTCTTAAG
1 CATCCCTCTCAAG
*
288850 CATCTCTCTCAAG
1 CATCCCTCTCAAG
288863 CATCCCTCTC
1 CATCCCTCTC
288873 TTGTATCCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.20, C:0.45, G:0.06, T:0.29
Consensus pattern (13 bp):
CATCCCTCTCAAG
Found at i:290944 original size:28 final size:28
Alignment explanation
Indices: 290888--290965 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
290878 GGAATAAAGC
*** **
290888 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
290916 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
290944 CGAGGTTGGAGTATCCTCGATG
1 CGGGGTTGGAGTATCCCCGATG
290966 GTGAAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:291043 original size:52 final size:52
Alignment explanation
Indices: 290968--291174 Score: 231
Period size: 54 Copynumber: 3.9 Consensus size: 52
290958 CCTCGATGGT
* * *
290968 GAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTCGGAGTATCCCCGATTAAA
1 GAAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
* **
291021 GAAAAATTAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATT-GT
1 GAAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
* * * * *
291072 GAAAAATTGGTATTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCTGATTATA
1 GAAAAA-T--TAGTGTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
* *
291127 -AAAAATTAGTGTTTTGAAAATAAAATTGGAGTTGG-GATACCCCCGATT
1 GAAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAG-TATCCCCGATT
291175 GCGGAGAATT
Statistics
Matches: 130, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
50 1 0.01
51 40 0.31
52 35 0.27
53 12 0.09
54 42 0.32
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.32
Consensus pattern (52 bp):
GAAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
Found at i:291102 original size:54 final size:54
Alignment explanation
Indices: 290948--291174 Score: 211
Period size: 52 Copynumber: 4.3 Consensus size: 54
290938 AAATAACGAG
* ** *
290948 GTTGGAGTATCCTCGATGGTGAAAAATTGG--TGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTTTGGAAATAAAATCGGA
* * * * * *
291000 GTCGGAGTATCCCCGATTAAAGAAAAA-T--TAGTGTTTTGAAAATAAAATCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTTTTGGAAATAAAATCGGA
*
291052 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTTTGGAAATAAAATCGGA
* * * * * *
291106 GTTGGAGTATCCCTGATTAT-AAAAAAT--TAGTGTTTTGAAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTTTGGAAATAAAATCGGA
*
291157 GTTGG-GATACCCCCGATT
1 GTTGGAG-TATCCCCGATT
291175 GCGGAGAATT
Statistics
Matches: 142, Mismatches: 26, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
50 1 0.01
51 40 0.28
52 51 0.36
53 12 0.08
54 38 0.27
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.32
Consensus pattern (54 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTTTTGGAAATAAAATCGGA
Found at i:291117 original size:106 final size:103
Alignment explanation
Indices: 290947--291175 Score: 334
Period size: 105 Copynumber: 2.2 Consensus size: 103
290937 GAAATAACGA
* *
290947 GGTTGGAGTATCCTCGATGGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTCGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTCGGAGTATCC
291012 CCGATTAAAGAAAAATTAGTGTTTTGAAAATAAAATCGG
66 CCGATTAAA-AAAAATTAGTGTTTTGAAAATAAAATCGG
* *
291051 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTTTGGAAATAAAATCGGAGTTGGAGTAT
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGG--TGTTTTTGGAAATAAAATCGGAGTCGGAGTAT
* * *
291116 CCCTGATTATAAAAAATTAGTGTTTTGAAAATAAAATTGG
64 CCCCGATTAAAAAAAATTAGTGTTTTGAAAATAAAATCGG
* *
291156 AGTTGG-GATACCCCCGATTG
1 GGTTGGAG-TATCCCCGATTG
291176 CGGAGAATTG
Statistics
Matches: 113, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
104 30 0.27
105 44 0.39
106 39 0.35
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (103 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTCGGAGTATCC
CCGATTAAAAAAAATTAGTGTTTTGAAAATAAAATCGG
Found at i:293564 original size:34 final size:33
Alignment explanation
Indices: 293519--293585 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
293509 AACTTCCTAG
*
293519 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAA-AAATGTATCGATACA
* *
293553 ATGTATTGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
293586 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.47
34 16 0.53
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:293645 original size:19 final size:19
Alignment explanation
Indices: 293617--293680 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
293607 AGCGATACAT
*
293617 TGTATTGATACAACACTTA
1 TGTATCGATACAACACTTA
293636 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
293649 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
293668 TGTATCGATACAA
1 TGTATCGATACAA
293681 ATCGCTGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 21 0.55
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:293650 original size:32 final size:32
Alignment explanation
Indices: 293609--293679 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
293599 AGCTTCCTAG
*
293609 CGATACATTGTATTGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
293641 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
293673 CGATACA
1 CGATACA
293680 AATCGCTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:293654 original size:13 final size:13
Alignment explanation
Indices: 293636--293660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
293626 ACAACACTTA
293636 TGTATCGATACAT
1 TGTATCGATACAT
293649 TGTATCGATACA
1 TGTATCGATACA
293661 ACACTTATGT
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:293743 original size:21 final size:21
Alignment explanation
Indices: 293736--293793 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
293726 ACATTTGTAG
293736 AATGTATCGATACATTCCACA
1 AATGTATCGATACATTCCACA
293757 AATGTATCGATACATTCCACA
1 AATGTATCGATACATTCCACA
293778 AATGTATCGATACATT
1 AATGTATCGATACATT
293794 TGGATAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACATTCCACA
Found at i:297506 original size:27 final size:27
Alignment explanation
Indices: 297475--297552 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
297465 AAAAACCACC
* *
297475 CTTTGTGTTTGTCAACAAT-AGTGGTTA
1 CTTTGTGTTTGTAAAAAATGA-TGGTTA
* *
297502 CTTTGTATTTGTAAAAAATGATGGTTC
1 CTTTGTGTTTGTAAAAAATGATGGTTA
* * *
297529 CTTTTTGTTTGTGAAAAATTATGG
1 CTTTGTGTTTGTAAAAAATGATGG
297553 CTTATTGTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 41 0.98
28 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
CTTTGTGTTTGTAAAAAATGATGGTTA
Found at i:297649 original size:13 final size:13
Alignment explanation
Indices: 297631--297679 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
297621 AAGGTTCCCT
297631 CATCCCTCTCAAG
1 CATCCCTCTCAAG
*
297644 CATCCCTCTTAAG
1 CATCCCTCTCAAG
*
297657 CATCTCTCTCAAG
1 CATCCCTCTCAAG
297670 CATCCCTCTC
1 CATCCCTCTC
297680 TTGTATCCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.20, C:0.45, G:0.06, T:0.29
Consensus pattern (13 bp):
CATCCCTCTCAAG
Found at i:300185 original size:23 final size:21
Alignment explanation
Indices: 300147--300191 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
300137 TTTTTATTAT
*
300147 ATTATAAATTTTAAATACATA
1 ATTATAAATTTTAAATAAATA
*
300168 ATTATATATTTTAAAAATAAATA
1 ATTATAAATTTT--AAATAAATA
300191 A
1 A
300192 AACTAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
23 9 0.45
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTATAAATTTTAAATAAATA
Done.