Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 17 of 27
Found at i:2227394 original size:14 final size:13
Alignment explanation
Indices: 2227365--2227398 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2227355 AATTATTATG
*
2227365 ATTATAAATTAAA
1 ATTATAAAATAAA
2227378 ATTATAAAATAATA
1 ATTATAAAATAA-A
2227392 ATTATAA
1 ATTATAA
2227399 TAACGATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTATAAAATAAA
Found at i:2233669 original size:18 final size:18
Alignment explanation
Indices: 2233621--2233681 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
2233611 ATTTATATCA
2233621 TAATTAAAATAATTTTAAAT
1 TAATT-AAATAATTTT-AAT
*
2233641 T-TTTAAATAATTTT-AT
1 TAATTAAATAATTTTAAT
2233657 TAATTAAATTAATATTTAAT
1 TAATTAAA-TAAT-TTTAAT
2233677 TAATT
1 TAATT
2233682 TATGATAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 3 0.09
17 5 0.14
18 14 0.40
19 5 0.14
20 8 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAAATAATTTTAAT
Found at i:2233934 original size:14 final size:14
Alignment explanation
Indices: 2233903--2233935 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2233893 TATTTAATAT
*
2233903 TTAAAAATTTTAAA
1 TTAAAAATATTAAA
2233917 -TAAAAATATTAAA
1 TTAAAAATATTAAA
2233930 TTAAAA
1 TTAAAA
2233936 GCTAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAAAAATATTAAA
Found at i:2235087 original size:26 final size:26
Alignment explanation
Indices: 2235029--2235081 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2235019 CAAATATAAA
2235029 TCATTTTATTTGAAGTTGTAACTTTT
1 TCATTTTATTTGAAGTTGTAACTTTT
2235055 TCATTTTATTTGAAGTTGTAACTTTT
1 TCATTTTATTTGAAGTTGTAACTTTT
2235081 T
1 T
2235082 AGTTTTCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.08, G:0.11, T:0.58
Consensus pattern (26 bp):
TCATTTTATTTGAAGTTGTAACTTTT
Found at i:2235213 original size:24 final size:24
Alignment explanation
Indices: 2235179--2235227 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2235169 TTTATATTTG
2235179 ATATATATTTAA-ATATAAATAAAT
1 ATATATATTTAAGATATAAA-AAAT
*
2235203 ATATATTTTTAAGTATATAAAAAAT
1 ATATATATTTAAG-ATATAAAAAAT
2235228 TAAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 4 0.18
26 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATATATTTAAGATATAAAAAAT
Found at i:2236385 original size:24 final size:24
Alignment explanation
Indices: 2236337--2236385 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
2236327 ACTTTTTTAA
*
2236337 TATTTAATTTTTTTAAACATAATT
1 TATTTAATTTTTTCAAACATAATT
2236361 TATTT-ATTCTTTTCAAA-ATATATT
1 TATTTAATT-TTTTCAAACATA-ATT
2236385 T
1 T
2236386 CACTGATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTAATTTTTTCAAACATAATT
Found at i:2242009 original size:37 final size:37
Alignment explanation
Indices: 2241939--2242009 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
2241929 ATAATTTAAA
* * *
2241939 TATTATAATTATATTTAAATTTTTTTATTTTTTATTG
1 TATTATAATTATATTTAAATTATATTATATTTTATTG
*
2241976 TATTATTAATT-TATTTATATTATATTATATTTTA
1 TATTA-TAATTATATTTAAATTATATTATATTTTA
2242010 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 24 0.83
38 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (37 bp):
TATTATAATTATATTTAAATTATATTATATTTTATTG
Found at i:2245306 original size:22 final size:21
Alignment explanation
Indices: 2245281--2245322 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
2245271 AAAATATAAT
*
2245281 TATTTTTTTAATATTTAAAAAA
1 TATTTATTTAAT-TTTAAAAAA
2245303 TATTTATTTAATTTTAAAAA
1 TATTTATTTAATTTTAAAAA
2245323 TGTGATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTATTTAATTTTAAAAAA
Found at i:2245352 original size:29 final size:28
Alignment explanation
Indices: 2245270--2245353 Score: 69
Period size: 29 Copynumber: 2.9 Consensus size: 28
2245260 AATTTTTATG
* *
2245270 AAAAATATAATTATTTTTTTAATATTTAA
1 AAAAATATATTTATTTTTTTAA-ATTGAA
* * ** *
2245299 AAAATATTTATTTAATTTTAAAAATGTGAT
1 AAAA-ATATATTTATTTTTTTAAAT-TGAA
*
2245329 AAAAATGTATTTATTTTTTTAAATT
1 AAAAATATATTTATTTTTTTAAATT
2245354 ATTATTTTTA
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
28 1 0.02
29 22 0.52
30 19 0.45
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
AAAAATATATTTATTTTTTTAAATTGAA
Found at i:2245878 original size:26 final size:25
Alignment explanation
Indices: 2245824--2245883 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
2245814 TTTTTTATCT
* *
2245824 TTAATTT-TTTTAAAATAATAGTAA
1 TTAATTTATTTTAAAATAAAAATAA
*
2245848 TTAATTTATTTTTAAATAAAAATAA
1 TTAATTTATTTTAAAATAAAAATAA
*
2245873 TGTAATATATT
1 T-TAATTTATT
2245884 ATTATCAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 7 0.23
25 15 0.50
26 8 0.27
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
TTAATTTATTTTAAAATAAAAATAA
Found at i:2257978 original size:3 final size:3
Alignment explanation
Indices: 2257972--2257996 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2257962 AAAATAAATA
2257972 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2257997 TAAGGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2258290 original size:2 final size:2
Alignment explanation
Indices: 2258283--2258318 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2258273 CTGCCAAACA
2258283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2258319 GTGAGAAAGA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2259395 original size:2 final size:2
Alignment explanation
Indices: 2259384--2259412 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2259374 ATAACAAATA
2259384 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2259413 GAATCAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2259766 original size:45 final size:45
Alignment explanation
Indices: 2259702--2259793 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
2259692 ATGCCTCTTA
2259702 ATTGAACCTTCCTAACAGGCAAATAAAGAAACAAAAAGTAATTTG
1 ATTGAACCTTCCTAACAGGCAAATAAAGAAACAAAAAGTAATTTG
2259747 ATTGAACCTTCCTAACAGGCAAATAAAGAAACAAAAAGTAATTTG
1 ATTGAACCTTCCTAACAGGCAAATAAAGAAACAAAAAGTAATTTG
2259792 AT
1 AT
2259794 GTTTAGGTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (45 bp):
ATTGAACCTTCCTAACAGGCAAATAAAGAAACAAAAAGTAATTTG
Found at i:2260012 original size:13 final size:13
Alignment explanation
Indices: 2259994--2260019 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2259984 AATATAATCT
2259994 TTCAAATGATTAG
1 TTCAAATGATTAG
2260007 TTCAAATGATTAG
1 TTCAAATGATTAG
2260020 AAACAATAGG
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:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
TTCAAATGATTAG
Found at i:2267731 original size:24 final size:24
Alignment explanation
Indices: 2267703--2267748 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2267693 GTGGTTATTT
2267703 TTGTTTGTAAAAAATGATGGCTTG
1 TTGTTTGTAAAAAATGATGGCTTG
* *
2267727 TTGTTTGTCAAAATTGATGGCT
1 TTGTTTGTAAAAAATGATGGCT
2267749 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGATGGCTTG
Found at i:2270205 original size:20 final size:19
Alignment explanation
Indices: 2270180--2270221 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2270170 ATAATTACAC
*
2270180 AATTAAGATATGTATAAAAT
1 AATTAAAATATG-ATAAAAT
*
2270200 AATTAAAATATGATATAAT
1 AATTAAAATATGATAAAAT
2270219 AAT
1 AAT
2270222 ATACATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (19 bp):
AATTAAAATATGATAAAAT
Found at i:2270288 original size:20 final size:20
Alignment explanation
Indices: 2270251--2270290 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2270241 TGTAGTATAA
* **
2270251 AATATTAATATATTAAAATT
1 AATATAAATATAAAAAAATT
2270271 AATATAAATATAAAAAAATT
1 AATATAAATATAAAAAAATT
2270291 TAAATATGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAATATAAAAAAATT
Found at i:2270291 original size:52 final size:53
Alignment explanation
Indices: 2270191--2270292 Score: 118
Period size: 52 Copynumber: 1.9 Consensus size: 53
2270181 ATTAAGATAT
* * ** *
2270191 GTATAAAATAATTAAAATATGATATAATAATATACATATTTAAGAATTTATGTA
1 GTATAAAATAATTAAAATAT-ATAAAATAATATAAATATAAAAAAATTTATGTA
*
2270245 GTATAAAAT-ATTAATATAT-TAAAATTAATATAAATATAAAAAAATTTA
1 GTATAAAATAATTAAAATATATAAAA-TAATATAAATATAAAAAAATTTA
2270293 AATATGATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
51 4 0.10
52 19 0.46
53 9 0.22
54 9 0.22
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (53 bp):
GTATAAAATAATTAAAATATATAAAATAATATAAATATAAAAAAATTTATGTA
Found at i:2272370 original size:21 final size:20
Alignment explanation
Indices: 2272328--2272384 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2272318 AATTTAATAC
* **
2272328 ATAATAAATATAAAAATAAT
1 ATAATAAATATATATTTAAT
2272348 ATAATAAATATTATATTTAAT
1 ATAATAAATA-TATATTTAAT
* *
2272369 ATATTTAATATATATT
1 ATAATAAATATATATT
2272385 ATATTTATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATAAATATATATTTAAT
Found at i:2272371 original size:9 final size:9
Alignment explanation
Indices: 2272359--2272441 Score: 64
Period size: 9 Copynumber: 8.9 Consensus size: 9
2272349 TAATAAATAT
2272359 TATATTTAA
1 TATATTTAA
2272368 TATATTTAA
1 TATATTTAA
2272377 TATATATTATA
1 TATAT-TTA-A
2272388 TTTATATTTAA
1 --TATATTTAA
*
2272399 -A-ATTTTA
1 TATATTTAA
2272406 TCATATTTAA
1 T-ATATTTAA
* *
2272416 TAATATATAT
1 T-ATATTTAA
2272426 TATATTTAA
1 TATATTTAA
2272435 T-TATTTA
1 TATATTTA
2272442 TCACAAATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
7 5 0.08
8 7 0.12
9 22 0.37
10 16 0.27
11 2 0.03
12 3 0.05
13 5 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (9 bp):
TATATTTAA
Found at i:2272413 original size:17 final size:19
Alignment explanation
Indices: 2272369--2272435 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
2272359 TATATTTAAT
*
2272369 ATATTTAATATATATTATATTT
1 ATATTTAATA-ATA-TATA-TC
*
2272391 ATATTTAA-AAT-TTTATC
1 ATATTTAATAATATATATC
*
2272408 ATATTTAATAATATATATT
1 ATATTTAATAATATATATC
2272427 ATATTTAAT
1 ATATTTAAT
2272436 TATTTATCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 9 0.23
18 6 0.15
19 13 0.33
20 2 0.05
21 1 0.03
22 8 0.21
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTTAATAATATATATC
Found at i:2272442 original size:36 final size:38
Alignment explanation
Indices: 2272360--2272444 Score: 106
Period size: 36 Copynumber: 2.3 Consensus size: 38
2272350 AATAAATATT
2272360 ATATTTAAT-ATATTTAATATATATTATATTTATATTTA
1 ATATTT-ATCATATTTAATATATATTATATTTATATTTA
*
2272398 AAATTTTATCATATTTAATA-ATA-TATA-TTATATTTA
1 ATA-TTTATCATATTTAATATATATTATATTTATATTTA
2272434 ATTATTTATCA
1 A-TATTTATCA
2272445 CAAATAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
36 17 0.40
37 5 0.12
38 7 0.17
39 13 0.31
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (38 bp):
ATATTTATCATATTTAATATATATTATATTTATATTTA
Found at i:2272453 original size:36 final size:34
Alignment explanation
Indices: 2272348--2272453 Score: 94
Period size: 36 Copynumber: 3.1 Consensus size: 34
2272338 TAAAAATAAT
*
2272348 ATAATAAATATTATATTTAATATATT-T-AATAT-
1 ATAATATATATTATATTTAATAT-TTATCAATATA
* * *
2272380 ATATTATAT-TTATATTTAAAATTTTATCATATTTA
1 ATAATATATATTATATTTAATA-TTTATCA-ATATA
*
2272415 ATAATATATATTATATTTAATTATTTATCACAAATA
1 ATAATATATATTATATTTAA-TATTTATCA-ATATA
2272451 ATA
1 ATA
2272454 TTAAAGCACC
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
31 13 0.22
32 9 0.16
33 1 0.02
34 3 0.05
35 8 0.14
36 23 0.40
37 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (34 bp):
ATAATATATATTATATTTAATATTTATCAATATA
Found at i:2274353 original size:13 final size:14
Alignment explanation
Indices: 2274327--2274369 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2274317 TTCATATTTG
*
2274327 AATATAATATATTA
1 AATATAATAAATTA
2274341 AATATAA-AAATTA
1 AATATAATAAATTA
*
2274354 AATATCAATAATTTA
1 AATAT-AATAAATTA
2274369 A
1 A
2274370 TAAAATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.40
14 9 0.36
15 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATAATAAATTA
Found at i:2274366 original size:14 final size:13
Alignment explanation
Indices: 2274327--2274371 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
2274317 TTCATATTTG
2274327 AATATAATATATTA
1 AATATAATA-ATTA
*
2274341 AATATAAAAATTA
1 AATATAATAATTA
*
2274354 AATATCAATAATTT
1 AATAT-AATAATTA
2274368 AATA
1 AATA
2274372 AAATTTGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATAATAATTA
Found at i:2279269 original size:26 final size:25
Alignment explanation
Indices: 2279240--2279296 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 25
2279230 ATTAAATTAT
*
2279240 TTAAATTTTAAAATTTAATAAAAATA
1 TTAAATATTAAAATTTAA-AAAAATA
* * *
2279266 TTAAAAATTAAATTTTAAAATAATA
1 TTAAATATTAAAATTTAAAAAAATA
2279291 -TAAATA
1 TTAAATA
2279297 AATCTAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 5 0.19
25 6 0.23
26 15 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAAATATTAAAATTTAAAAAAATA
Found at i:2279299 original size:26 final size:26
Alignment explanation
Indices: 2279247--2279305 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
2279237 TATTTAAATT
* *
2279247 TTAAAATTTAATAAAAATATTAAAAA
1 TTAAATTTTAATAAAAATATAAAAAA
*
2279273 TTAAATTTTAA-AATAATATAAATAAA
1 TTAAATTTTAATAAAAATATAAA-AAA
2279299 TCTAAAT
1 T-TAAAT
2279306 GAATTTTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.32
26 14 0.50
27 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TTAAATTTTAATAAAAATATAAAAAA
Found at i:2279541 original size:46 final size:44
Alignment explanation
Indices: 2279468--2279553 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 44
2279458 TAAGATCAAG
2279468 TTATATTGGTCAAAAAAATT-AATTTTTTATAGTTAATTTTATAATT
1 TTATATTGGTCAAAAAAATTAAATTTTTTA-A--TAATTTTATAATT
*
2279514 TTATATTGG-CAAGAAAATTTAAATTTTTTAATAATTTTAT
1 TTATATTGGTCAA-AAAAATTAAATTTTTTAATAATTTTAT
2279554 GTATAATATT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
44 9 0.24
45 3 0.08
46 16 0.43
47 9 0.24
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (44 bp):
TTATATTGGTCAAAAAAATTAAATTTTTTAATAATTTTATAATT
Found at i:2280329 original size:3 final size:3
Alignment explanation
Indices: 2280321--2280356 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2280311 CATGCAACAC
2280321 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2280357 TGAAATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2281498 original size:20 final size:21
Alignment explanation
Indices: 2281461--2281499 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2281451 TTACTTAAAT
*
2281461 ATTTTTTATACTTAATATTTA
1 ATTTTTTATAATTAATATTTA
*
2281482 ATTTTTTTTAATT-ATATT
1 ATTTTTTATAATTAATATT
2281500 ATTTGTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTTTATAATTAATATTTA
Found at i:2282367 original size:17 final size:16
Alignment explanation
Indices: 2282347--2282389 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
2282337 TATAATATAT
2282347 AAATAATAATTA-ATTGA
1 AAATAATAATTACA-T-A
2282364 AAATAAATAATTACATA
1 AAAT-AATAATTACATA
2282381 AAATAATAA
1 AAATAATAA
2282390 ATGCTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 9 0.38
18 9 0.38
19 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
AAATAATAATTACATA
Found at i:2285602 original size:21 final size:21
Alignment explanation
Indices: 2285567--2285619 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
2285557 ATAATTTATA
* * *
2285567 TTATATAAAATTTAAAATATT
1 TTATATCATATTTTAAATATT
* *
2285588 TT-TATTATATTTTAATTATT
1 TTATATCATATTTTAAATATT
2285608 TTATATCATATT
1 TTATATCATATT
2285620 CATATAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATATCATATTTTAAATATT
Found at i:2286520 original size:15 final size:15
Alignment explanation
Indices: 2286500--2286529 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2286490 AAATAATAAT
*
2286500 TCAAATTTAATTTAA
1 TCAAATTGAATTTAA
2286515 TCAAATTGAATTTAA
1 TCAAATTGAATTTAA
2286530 ATTTTTTTTT
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:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (15 bp):
TCAAATTGAATTTAA
Found at i:2287010 original size:12 final size:12
Alignment explanation
Indices: 2286993--2287038 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
2286983 AATAATTCAG
2286993 ATATTTATATTA
1 ATATTTATATTA
*
2287005 ATATTTATGTTA
1 ATATTTATATTA
*
2287017 ATTTTTATA-TA
1 ATATTTATATTA
2287028 AT-TATTATATT
1 ATAT-TTATATT
2287039 TAAAAAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 1 0.03
11 9 0.31
12 19 0.66
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (12 bp):
ATATTTATATTA
Found at i:2287033 original size:24 final size:24
Alignment explanation
Indices: 2286996--2287041 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
2286986 AATTCAGATA
2286996 TTTATATTAATATT-TATGTTAATT
1 TTTATATTAATATTATAT-TTAATT
2287020 TTTATA-TAATTATTATATTTAA
1 TTTATATTAA-TATTATATTTAA
2287042 AAAGTTATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.15
24 14 0.70
25 3 0.15
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTATATTAATATTATATTTAATT
Found at i:2287499 original size:35 final size:35
Alignment explanation
Indices: 2287459--2287527 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 35
2287449 TATTTAATAA
2287459 ATTTTAA-A-ATATTTATATATTTATAATTTATTTAT
1 ATTTTAATACATA-TTATAT-TTTATAATTTATTTAT
*
2287494 ATTTTAATACCATATTATATTTTATATTTTATTT
1 ATTTTAATA-CATATTATATTTTATAATTTATTT
2287528 TTCTCGTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
35 7 0.23
36 14 0.47
37 6 0.20
38 3 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (35 bp):
ATTTTAATACATATTATATTTTATAATTTATTTAT
Found at i:2287727 original size:19 final size:19
Alignment explanation
Indices: 2287691--2287733 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2287681 CCGAGAATAA
2287691 ATAA-TTTTGTATTGTATTT
1 ATAATTTTTGTATTGTA-TT
*
2287710 ATAATTTTTTTATT-TATT
1 ATAATTTTTGTATTGTATT
2287728 ATAATT
1 ATAATT
2287734 ATATTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 8 0.36
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
ATAATTTTTGTATTGTATT
Found at i:2287757 original size:8 final size:8
Alignment explanation
Indices: 2287746--2287799 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
2287736 ATTTATATAA
2287746 ATTTTAAT
1 ATTTTAAT
2287754 ATTTTAAT
1 ATTTTAAT
2287762 ATTTT-AT
1 ATTTTAAT
2287769 ATTATATAA-
1 ATT-T-TAAT
2287778 ATTTTAAT
1 ATTTTAAT
2287786 ATATTTATAT
1 AT-TTTA-AT
2287796 ATTT
1 ATTT
2287800 ATATTATGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
7 8 0.20
8 17 0.43
9 10 0.25
10 5 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTTTAAT
Found at i:2287757 original size:18 final size:18
Alignment explanation
Indices: 2287734--2287787 Score: 71
Period size: 16 Copynumber: 3.2 Consensus size: 18
2287724 TATTATAATT
2287734 ATATTTATATAAATTTTA
1 ATATTTATATAAATTTTA
*
2287752 ATATTT-TA-ATATTTT-
1 ATATTTATATAAATTTTA
2287767 ATA-TTATATAAATTTTA
1 ATATTTATATAAATTTTA
2287784 ATAT
1 ATAT
2287788 ATTTATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 2 0.07
15 5 0.17
16 12 0.40
17 5 0.17
18 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTTATATAAATTTTA
Found at i:2287800 original size:8 final size:8
Alignment explanation
Indices: 2287705--2287803 Score: 55
Period size: 8 Copynumber: 12.1 Consensus size: 8
2287695 TTTTGTATTG
2287705 TATTTATA
1 TATTTATA
* *
2287713 -ATTTTTT
1 TATTTATA
2287720 TATTTATTA
1 TATTTA-TA
*
2287729 TAATTATA
1 TATTTATA
2287737 T-TTATATA
1 TATT-TATA
*
2287745 AATTT-TAA
1 TATTTAT-A
2287753 TATTT-TAA
1 TATTTAT-A
2287761 TATTT-TA
1 TATTTATA
2287768 TATTATATA
1 TATT-TATA
*
2287777 AATTTTAATA
1 TA-TTT-ATA
2287787 TATTTATA
1 TATTTATA
2287795 TATTTATA
1 TATTTATA
2287803 T
1 T
2287804 TATGTTTGTA
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
7 12 0.17
8 39 0.54
9 15 0.21
10 6 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTATA
Found at i:2287806 original size:33 final size:33
Alignment explanation
Indices: 2287720--2287806 Score: 124
Period size: 32 Copynumber: 2.6 Consensus size: 33
2287710 ATAATTTTTT
*
2287720 TATTTATTATAATTATATTTATATAAATTTTAATA
1 TATTTA-TATATTTATA-TTATATAAATTTTAATA
2287755 T-TTTA-ATATTTTATATTATATAAATTTTAATA
1 TATTTATATA-TTTATATTATATAAATTTTAATA
2287787 TATTTATATATTTATATTAT
1 TATTTATATATTTATATTAT
2287807 GTTTGTAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
32 21 0.44
33 19 0.40
34 7 0.15
35 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TATTTATATATTTATATTATATAAATTTTAATA
Found at i:2293572 original size:15 final size:15
Alignment explanation
Indices: 2293529--2293579 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2293519 TAACTTAATT
*
2293529 TATTT-ATACATTTA
1 TATTTAATAAATTTA
* *
2293543 T-TTTAAAAAAATTA
1 TATTTAATAAATTTA
2293557 TATTTAATAAATTTA
1 TATTTAATAAATTTA
2293572 TAGTTTAA
1 TA-TTTAA
2293580 ATCTTAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 3 0.10
14 8 0.28
15 13 0.45
16 5 0.17
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TATTTAATAAATTTA
Found at i:2295644 original size:24 final size:24
Alignment explanation
Indices: 2295602--2295674 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 24
2295592 ATATTGTTAA
*
2295602 AATTAAAATTAAAACCAAAAT-ATAT
1 AATTAAAA-TAAAATCAAAATCAT-T
*
2295627 AATTACAATAAAATCAAAATCATT
1 AATTAAAATAAAATCAAAATCATT
*
2295651 AATTAGAAATAAAATACTAAATCA
1 AATTA-AAATAAAAT-CAAAATCA
2295675 ATTAGAGCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 17 0.41
25 17 0.41
26 7 0.17
ACGTcount: A:0.62, C:0.10, G:0.01, T:0.27
Consensus pattern (24 bp):
AATTAAAATAAAATCAAAATCATT
Found at i:2297174 original size:23 final size:21
Alignment explanation
Indices: 2297127--2297176 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2297117 TATTGGTATT
*
2297127 ATTTAATAACTATTTTAATAT
1 ATTTAATAACTATTTTAATAA
* *
2297148 ATTTAATATATTATTTTTATCAA
1 ATTTAATA-ACTATTTTAAT-AA
2297171 ATTTAA
1 ATTTAA
2297177 AAATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTAATAACTATTTTAATAA
Found at i:2298604 original size:37 final size:36
Alignment explanation
Indices: 2298563--2298636 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 36
2298553 AGTTAAATCA
2298563 AATCATA-TATAATTTAAATTTAATAATTCA-TATATTT
1 AATCATATTATAA-TTAAATTTAA-AATT-ATTATATTT
*
2298600 AATCATATTATAATTATATTTAAAATTATTATATTT
1 AATCATATTATAATTAAATTTAAAATTATTATATTT
2298636 A
1 A
2298637 TATAAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
35 1 0.03
36 12 0.35
37 16 0.47
38 5 0.15
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (36 bp):
AATCATATTATAATTAAATTTAAAATTATTATATTT
Found at i:2302947 original size:13 final size:14
Alignment explanation
Indices: 2302929--2302957 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2302919 AAATTATATC
2302929 TTTTATC-TTTTTA
1 TTTTATCGTTTTTA
2302942 TTTTATCGTTTTTA
1 TTTTATCGTTTTTA
2302956 TT
1 TT
2302958 CACTGATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTATCGTTTTTA
Found at i:2303135 original size:15 final size:14
Alignment explanation
Indices: 2303104--2303132 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2303094 AACTCTTAAA
2303104 ATTTTATAATATTT
1 ATTTTATAATATTT
2303118 ATTTT-TAATATTT
1 ATTTTATAATATTT
2303131 AT
1 AT
2303133 ATTCGATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTTATAATATTT
Found at i:2303532 original size:61 final size:61
Alignment explanation
Indices: 2303437--2303559 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 61
2303427 ATTCATCTTC
* *
2303437 TTTCCTGCCTATTCCAACACACACATAGCTCATGTAAATGAAATCCCTCCTATATGGGATT
1 TTTCCTGCCAATTCCAACACACACATAGCTCATGTAAATGAAATCCCTCCTACATGGGATT
* * * *
2303498 TTTCCTGCCAATTCCAACATACATATAGCTCATGTAAATGAAATCTCTCTTACATGGGATT
1 TTTCCTGCCAATTCCAACACACACATAGCTCATGTAAATGAAATCCCTCCTACATGGGATT
2303559 T
1 T
2303560 GGAGTATTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (61 bp):
TTTCCTGCCAATTCCAACACACACATAGCTCATGTAAATGAAATCCCTCCTACATGGGATT
Found at i:2304124 original size:18 final size:17
Alignment explanation
Indices: 2304103--2304171 Score: 51
Period size: 16 Copynumber: 4.2 Consensus size: 17
2304093 AATTATTTAT
2304103 TAATAAAATATTATAATA
1 TAAT-AAATATTATAATA
*
2304121 TAAT--TTATTAATAATA
1 TAATAAATATT-ATAATA
2304137 T-ATAAAT-TTAT-ATA
1 TAATAAATATTATAATA
2304151 TCAATAATATATTA-AATA
1 T-AATAA-ATATTATAATA
2304169 TAA
1 TAA
2304172 ATTTAATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 17
0.68 0.03 0.28
Matches are distributed among these distances:
14 4 0.10
15 8 0.20
16 13 0.32
17 5 0.12
18 11 0.27
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATAAATATTATAATA
Found at i:2304131 original size:26 final size:24
Alignment explanation
Indices: 2304085--2304186 Score: 77
Period size: 26 Copynumber: 4.2 Consensus size: 24
2304075 TATTATCTGT
2304085 TAAAATA-T-AATT-ATTTATTAA
1 TAAAATATTAAATTAATTTATTAA
2304106 TAAAATATTATAATATAATTTATTAA
1 TAAAATATTA-AAT-TAATTTATTAA
* * * *
2304132 TAATATA-TAAATTTATATATCAA
1 TAAAATATTAAATTAATTTATTAA
* *
2304155 TAATATATTAAATATAAATTTAATAA
1 TAAAATATTAAAT-T-AATTTATTAA
*
2304181 AAAAAT
1 TAAAAT
2304187 TTCTTAGTTC
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
21 7 0.11
22 1 0.02
23 15 0.24
24 11 0.17
25 4 0.06
26 25 0.40
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAAATATTAAATTAATTTATTAA
Found at i:2304132 original size:13 final size:13
Alignment explanation
Indices: 2304097--2304134 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2304087 AAATATAATT
2304097 ATTTATTAATAAA
1 ATTTATTAATAAA
*
2304110 ATATTA-TAATATA
1 AT-TTATTAATAAA
2304123 ATTTATTAATAA
1 ATTTATTAATAA
2304135 TATATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 3 0.14
13 15 0.71
14 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTATTAATAAA
Found at i:2304179 original size:23 final size:23
Alignment explanation
Indices: 2304102--2304180 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 23
2304092 TAATTATTTA
*
2304102 TTAATAAAATATTATAATAT-AAT
1 TTAATAATATATTA-AATATAAAT
* * *
2304125 TTATTAATAATATATAAATTTATAT
1 TTAATAAT-ATAT-TAAATATAAAT
*
2304150 ATCAATAATATATTAAATATAAAT
1 -TTAATAATATATTAAATATAAAT
2304174 TTAATAA
1 TTAATAA
2304181 AAAAATTTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
23 12 0.28
24 17 0.40
25 8 0.19
26 6 0.14
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAATAATATATTAAATATAAAT
Found at i:2304840 original size:28 final size:27
Alignment explanation
Indices: 2304802--2304872 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 27
2304792 AATTAATTAT
2304802 TATATTTAATACTTTTTTATCAAAACTA
1 TATATTTAATACTTTTTTATCAAAAC-A
* *
2304830 TATATTTAATATTTATTTTTTATCAAATCA
1 TATATTTAATA---CTTTTTTATCAAAACA
2304860 TATATTTAATACT
1 TATATTTAATACT
2304873 GTAATTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 1 0.03
28 11 0.30
30 12 0.32
31 13 0.35
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (27 bp):
TATATTTAATACTTTTTTATCAAAACA
Found at i:2313009 original size:21 final size:22
Alignment explanation
Indices: 2312983--2313024 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2312973 CTTATTAATA
2312983 TTATTAAATAAA-AATAATTTT
1 TTATTAAATAAATAATAATTTT
*
2313004 TTATTATATAAATAATAATTT
1 TTATTAAATAAATAATAATTT
2313025 AAATTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATTAAATAAATAATAATTTT
Found at i:2313051 original size:14 final size:15
Alignment explanation
Indices: 2313015--2313052 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
2313005 TATTATATAA
*
2313015 ATAATAATTTAAATT
1 ATAATAATTTAAAAT
2313030 A-AATAATTTAAAAT
1 ATAATAATTTAAAAT
2313044 ATAA-AATTT
1 ATAATAATTT
2313053 TTATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 18 0.86
15 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATAATTTAAAAT
Found at i:2319201 original size:30 final size:30
Alignment explanation
Indices: 2319128--2319203 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
2319118 TTAACATTAT
*
2319128 TTTATATTAAA-ATAAGTTTTTAAATTTTTA
1 TTTATATTAAATA-AAGTTTTTAAATTTTAA
* * *
2319158 TTTGTATAAAAATAAATTTTTTAAA-TTTAA
1 TTTATAT-TAAATAAAGTTTTTAAATTTTAA
2319188 TTTATATCTAAATAAA
1 TTTATAT-TAAATAAA
2319204 AATAAAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 23 0.62
31 13 0.35
32 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
TTTATATTAAATAAAGTTTTTAAATTTTAA
Found at i:2319213 original size:29 final size:28
Alignment explanation
Indices: 2319180--2319270 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 28
2319170 TAAATTTTTT
2319180 AAATTTAATTTATATCTAAATAAAAATAA
1 AAATTTAATTTAT-TCTAAATAAAAATAA
*
2319209 AAATTTTAATTTATGCTTAAATAAAATATAA
1 AAA-TTTAATTTATTC-TAAATAAAA-ATAA
* *
2319240 ATTAATTT--TTTATTTTAAATAAAAATTA
1 A--AATTTAATTTATTCTAAATAAAAATAA
2319268 AAA
1 AAA
2319271 CATAAATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
26 2 0.04
28 4 0.08
29 13 0.25
30 24 0.45
31 5 0.09
32 3 0.06
33 2 0.04
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (28 bp):
AAATTTAATTTATTCTAAATAAAAATAA
Found at i:2319283 original size:19 final size:18
Alignment explanation
Indices: 2319255--2319295 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2319245 TTTTTTATTT
*
2319255 TAAATAAAAATTAAAACA
1 TAAATAAAAATAAAAACA
*
2319273 TAAATTAAAAATAAAAATA
1 TAAA-TAAAAATAAAAACA
2319292 TAAA
1 TAAA
2319296 ATAATTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAATAAAAATAAAAACA
Found at i:2321024 original size:24 final size:24
Alignment explanation
Indices: 2320987--2321056 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
2320977 AAAAATATAA
* *
2320987 AATATTATATAATTTATATAAATT
1 AATATAATAAAATTTATATAAATT
2321011 AATATAATAAAA-TTATA-AATTATT
1 AATATAATAAAATTTATATAA--ATT
* *
2321035 TATATATTAAAATTTATATAAA
1 AATATAATAAAATTTATATAAA
2321057 AAATATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.05
23 5 0.13
24 24 0.63
25 5 0.13
26 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATATAATAAAATTTATATAAATT
Found at i:2322257 original size:19 final size:20
Alignment explanation
Indices: 2322233--2322271 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2322223 AAAACTTATA
*
2322233 TTCATAT-AAAATTTAAAAT
1 TTCATATCAAAAATTAAAAT
2322252 TTCATATCAAAAATTAAAAT
1 TTCATATCAAAAATTAAAAT
2322272 ATTTCCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (20 bp):
TTCATATCAAAAATTAAAAT
Found at i:2322282 original size:21 final size:21
Alignment explanation
Indices: 2322233--2322276 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2322223 AAAACTTATA
*
2322233 TTCATAT--AAAATTTAAAAT
1 TTCATATCAAAAATTAAAAAT
2322252 TTCATATCAAAAATTAAAATAT
1 TTCATATCAAAAATTAAAA-AT
2322274 TTC
1 TTC
2322277 CTTCAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (21 bp):
TTCATATCAAAAATTAAAAAT
Found at i:2322456 original size:22 final size:22
Alignment explanation
Indices: 2322438--2322483 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2322428 GACTATACAT
*
2322438 TAAAAATAATAATAATATAATA
1 TAAAAATAAAAATAATATAATA
* *
2322460 TAATATTAAAAATAATATAA-A
1 TAAAAATAAAAATAATATAATA
2322481 TAA
1 TAA
2322484 TATATAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAATAAAAATAATATAATA
Found at i:2322490 original size:28 final size:28
Alignment explanation
Indices: 2322436--2322487 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
2322426 ACGACTATAC
2322436 ATTAAAAATAATAATAATATAATATAAT
1 ATTAAAAATAATAATAATATAATATAAT
2322464 ATTAAAAATAAT-ATAA-ATAATATA
1 ATTAAAAATAATAATAATATAATATA
2322488 TAAATAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 8 0.33
27 4 0.17
28 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
ATTAAAAATAATAATAATATAATATAAT
Found at i:2322491 original size:11 final size:12
Alignment explanation
Indices: 2322445--2322493 Score: 61
Period size: 11 Copynumber: 4.3 Consensus size: 12
2322435 CATTAAAAAT
2322445 AATAATAATAT-
1 AATAATAATATA
2322456 AAT-ATAATATTA
1 AATAATAATA-TA
2322468 AA-AATAATATA
1 AATAATAATATA
2322479 AATAAT-ATATA
1 AATAATAATATA
2322490 AATA
1 AATA
2322494 GTTGGATCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.18
11 17 0.50
12 11 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AATAATAATATA
Found at i:2322491 original size:22 final size:23
Alignment explanation
Indices: 2322443--2322491 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
2322433 TACATTAAAA
*
2322443 ATAATAATAATATAATATAATAT
1 ATAAAAATAATATAATATAATAT
2322466 -TAAAAATAATATAA-ATAATAT
1 ATAAAAATAATATAATATAATAT
2322487 ATAAA
1 ATAAA
2322492 TAGTTGGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
ATAAAAATAATATAATATAATAT
Found at i:2322978 original size:17 final size:18
Alignment explanation
Indices: 2322956--2323004 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
2322946 ATGTTATCAT
2322956 ATTTTATATTTATATA-A
1 ATTTTATATTTATATATA
2322973 ATTTTAATATTT-TA-ATA
1 ATTTT-ATATTTATATATA
2322990 A-TTTATA-TTATATAT
1 ATTTTATATTTATATAT
2323005 TTTAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 2 0.07
15 5 0.18
16 6 0.21
17 9 0.32
18 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTATATTTATATATA
Found at i:2323007 original size:22 final size:22
Alignment explanation
Indices: 2322979--2323043 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 22
2322969 ATAAATTTTA
2322979 ATATTTTAATAATTTATATTAT
1 ATATTTTAATAATTTATATTAT
* *
2323001 ATATTTTAAATATTTTTGTATTAT
1 ATATTTT-AATA-ATTTATATTAT
*
2323025 AT-TTATAA-AA-TTATATTAT
1 ATATTTTAATAATTTATATTAT
2323044 TTTTATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
19 8 0.22
21 1 0.03
22 9 0.25
23 7 0.19
24 11 0.31
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATATTTTAATAATTTATATTAT
Found at i:2323031 original size:30 final size:31
Alignment explanation
Indices: 2322959--2323062 Score: 88
Period size: 31 Copynumber: 3.3 Consensus size: 31
2322949 TTATCATATT
2322959 TTATATTTATATAAATTTTAATATTTTAATAA
1 TTATATTTATAT-AATTTTAATATTTTAATAA
**
2322991 TT-TATATTATAT-ATTTTAAATATTTTTGT-A
1 TTATAT-TTATATAATTTT-AATATTTTAATAA
* * * * *
2323021 TTATATTTATAAAATTATATTATTTTTATTAT
1 TTATATTTATATAATTTTAATA-TTTTAATAA
2323053 TTATATTTAT
1 TTATATTTAT
2323063 TTACGCGGAC
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
30 16 0.28
31 24 0.41
32 18 0.31
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.62
Consensus pattern (31 bp):
TTATATTTATATAATTTTAATATTTTAATAA
Found at i:2323044 original size:22 final size:21
Alignment explanation
Indices: 2322979--2323044 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
2322969 ATAAATTTTA
2322979 ATATTTTAATAATTTATATTA-T
1 ATATTTTAA-AA-TTATATTATT
*
2323001 ATATTTTAAATATT-TTTGTATT
1 ATATTTTAAA-ATTATAT-TATT
2323023 ATATTTATAAAATTATATTATT
1 ATATTT-TAAAATTATATTATT
2323045 TTTATTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 2 0.05
21 5 0.14
22 24 0.65
23 6 0.16
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATATTTTAAAATTATATTATT
Found at i:2323860 original size:14 final size:13
Alignment explanation
Indices: 2323843--2323898 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
2323833 TTTAATATAT
*
2323843 TATTTTTTTATAAA
1 TATTTTATTA-AAA
2323857 TATTTTATTAAAA
1 TATTTTATTAAAA
* *
2323870 TATTATAAT-AAA
1 TATTTTATTAAAA
2323882 TATTTTA-TAAATA
1 TATTTTATTAAA-A
2323895 TATT
1 TATT
2323899 ATTGATATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 1 0.03
12 11 0.31
13 15 0.42
14 9 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTTATTAAAA
Found at i:2323864 original size:11 final size:11
Alignment explanation
Indices: 2323848--2323900 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
2323838 TATATTATTT
2323848 TTTTATAAATA
1 TTTTATAAATA
2323859 TTTTATTAAAATA
1 TTTTA-T-AAATA
*
2323872 TTATAATAAATA
1 TT-TTATAAATA
2323884 TTTTATAAATA
1 TTTTATAAATA
*
2323895 TATTAT
1 TTTTAT
2323901 TGATATAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 18 0.50
12 8 0.22
13 8 0.22
14 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTATAAATA
Found at i:2323886 original size:25 final size:25
Alignment explanation
Indices: 2323852--2323900 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2323842 TTATTTTTTT
2323852 ATAAATATTTTATTAAA-ATATTATA
1 ATAAATATTTTA-TAAATATATTATA
2323877 ATAAATATTTTATAAATATATTAT
1 ATAAATATTTTATAAATATATTAT
2323901 TGATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATAAATATTTTATAAATATATTATA
Found at i:2323916 original size:36 final size:36
Alignment explanation
Indices: 2323848--2323916 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 36
2323838 TATATTATTT
* ** *
2323848 TTTTATAAATATTTTATTAAAATATTATAATAAATA
1 TTTTATAAATATATTATTAAAATAAAAAAATAAATA
* *
2323884 TTTTATAAATATATTATTGATATAAAAAAATAA
1 TTTTATAAATATATTATTAAAATAAAAAAATAA
2323917 TTAAAATTAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (36 bp):
TTTTATAAATATATTATTAAAATAAAAAAATAAATA
Found at i:2325611 original size:20 final size:22
Alignment explanation
Indices: 2325561--2325611 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 22
2325551 ATATTTTATT
*
2325561 AAAATATT-ATTATTTATTTAA
1 AAAATATTAATTATTTATTAAA
* *
2325582 TAAATTTTAATT-TTT-TTAAA
1 AAAATATTAATTATTTATTAAA
2325602 AAAATATTAA
1 AAAATATTAA
2325612 ATAAAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 12 0.50
21 9 0.38
22 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATATTAATTATTTATTAAA
Found at i:2325640 original size:21 final size:20
Alignment explanation
Indices: 2325600--2325657 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
2325590 AATTTTTTTA
**
2325600 AAAAAATATTAAATAAAAAATT
1 AAAAAA-ATTAAATTTAAAA-T
2325622 AAAAAAATTAAATTTAAAAT
1 AAAAAAATTAAATTTAAAAT
**
2325642 AATCAAATT-AATTTAA
1 AAAAAAATTAAATTTAA
2325658 TTTTAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 7 0.22
20 8 0.25
21 11 0.34
22 6 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAAATTAAATTTAAAAT
Found at i:2328594 original size:85 final size:85
Alignment explanation
Indices: 2328448--2328607 Score: 275
Period size: 85 Copynumber: 1.9 Consensus size: 85
2328438 TACACACGGG
* *
2328448 TTAGATTGCTGGTATATGCAACTCAAGATACTCGTACTTCTTTGCATGTATCAAGGCGGGTGCAA
1 TTAGATTGCTGGTATATGCAACTCAAGATACTCATACTTCTTTACATGTATCAAGGCGGGTGCAA
*
2328513 ATATGTGTTATACATATGGA
66 ATATCTGTTATACATATGGA
* *
2328533 TTAGATTGCTGGTATATGCAACTTAAGATACTCATACTTCTTTACATGTATCAAGGTGGGTGCAA
1 TTAGATTGCTGGTATATGCAACTCAAGATACTCATACTTCTTTACATGTATCAAGGCGGGTGCAA
2328598 ATATCTGTTA
66 ATATCTGTTA
2328608 GTCGTGGTTC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (85 bp):
TTAGATTGCTGGTATATGCAACTCAAGATACTCATACTTCTTTACATGTATCAAGGCGGGTGCAA
ATATCTGTTATACATATGGA
Found at i:2331564 original size:18 final size:18
Alignment explanation
Indices: 2331533--2331583 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
2331523 GCAAATATTG
*
2331533 ATTTCAAATTTTTAATTT-
1 ATTT-AAATATTTAATTTA
2331551 ATTATAAATATTT-ATTTA
1 ATT-TAAATATTTAATTTA
2331569 ATTTAAATATATTAA
1 ATTTAAATAT-TTAA
2331584 AATTTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 11 0.39
18 15 0.54
19 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTAAATATTTAATTTA
Found at i:2331573 original size:27 final size:26
Alignment explanation
Indices: 2331543--2331601 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
2331533 ATTTCAAATT
*
2331543 TTTAATTTATTATAAATATTTATT-TAA
1 TTTAATATATTA-AAATATTTATTAT-A
*
2331570 TTTAAATATATTAAAATTTTTATTATA
1 TTT-AATATATTAAAATATTTATTATA
2331597 TTTAA
1 TTTAA
2331602 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 2 0.07
27 17 0.61
28 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTAATATATTAAAATATTTATTATA
Found at i:2331602 original size:27 final size:28
Alignment explanation
Indices: 2331550--2331602 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
2331540 ATTTTTAATT
2331550 TATTATAAATATTTATTTAATTTAAATA
1 TATTATAAATATTTATTTAATTTAAATA
*
2331578 TATTA-AAATTTTTA-TTATATTTAAA
1 TATTATAAATATTTATTTA-ATTTAAA
2331603 AAAATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 15 0.65
28 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TATTATAAATATTTATTTAATTTAAATA
Found at i:2338643 original size:17 final size:18
Alignment explanation
Indices: 2338608--2338679 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 18
2338598 AATAATTACT
2338608 AAAAATTTATTATTTTTA
1 AAAAATTTATTATTTTTA
* *
2338626 ATAAATTTTTTA-TTTTA
1 AAAAATTTATTATTTTTA
*
2338643 AAAAA-TAATT-TTTTT-
1 AAAAATTTATTATTTTTA
2338658 ---AATTTATTATATTTTA
1 AAAAATTTATTAT-TTTTA
2338674 AAAAAT
1 AAAAAT
2338680 AAAAAATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 15
0.66 0.10 0.25
Matches are distributed among these distances:
12 2 0.05
13 4 0.10
14 1 0.03
15 4 0.10
16 7 0.17
17 9 0.22
18 10 0.25
19 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAAAATTTATTATTTTTA
Found at i:2340603 original size:56 final size:59
Alignment explanation
Indices: 2340537--2340685 Score: 169
Period size: 65 Copynumber: 2.5 Consensus size: 59
2340527 CAAATACAAG
2340537 TTTATATCAAATGTTCATCTCAAATTCAT-ATC-CCAAATTCAAATAACATAACCAGCA
1 TTTATATCAAATGTTCATCTCAAATTCATAATCACCAAATTCAAATAACATAACCAGCA
* * * *
2340594 -TTATATCAAATGTTCATCCCAAATTTGAATTACATAATCAGCAAATTCGAATAACATAATCAGC
1 TTTATATCAAATGTTCATCTC--A----AATT-CATAATCACCAAATTCAAATAACATAACCAGC
2340658 A
59 A
*
2340659 TTTATATCAAATATTCATCTCAAATTC
1 TTTATATCAAATGTTCATCTCAAATTC
2340686 GAATAACATA
Statistics
Matches: 76, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
56 19 0.25
58 1 0.01
59 1 0.01
60 4 0.05
62 4 0.05
63 3 0.04
64 4 0.05
65 22 0.29
66 18 0.24
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.34
Consensus pattern (59 bp):
TTTATATCAAATGTTCATCTCAAATTCATAATCACCAAATTCAAATAACATAACCAGCA
Found at i:2340645 original size:22 final size:22
Alignment explanation
Indices: 2340613--2340658 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2340603 ATGTTCATCC
* *
2340613 CAAATTTGAATTACATAATCAG
1 CAAATTCGAATAACATAATCAG
2340635 CAAATTCGAATAACATAATCAG
1 CAAATTCGAATAACATAATCAG
2340657 CA
1 CA
2340659 TTTATATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (22 bp):
CAAATTCGAATAACATAATCAG
Found at i:2340652 original size:65 final size:66
Alignment explanation
Indices: 2340570--2340702 Score: 205
Period size: 66 Copynumber: 2.0 Consensus size: 66
2340560 ATTCATATCC
* * *
2340570 CAAATTCAAATAACATAACCAGCA-TTATATCAAATGTTCATCCCAAATTTGAATTACATAATCA
1 CAAATTCAAATAACATAACCAGCATTTATATCAAATATTCATCCCAAATTCGAATAACATAATCA
2340634 G
66 G
* * *
2340635 CAAATTCGAATAACATAATCAGCATTTATATCAAATATTCATCTCAAATTCGAATAACATAATCA
1 CAAATTCAAATAACATAACCAGCATTTATATCAAATATTCATCCCAAATTCGAATAACATAATCA
2340700 G
66 G
2340701 CA
1 CA
2340703 TTATATCCCA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
65 22 0.36
66 39 0.64
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (66 bp):
CAAATTCAAATAACATAACCAGCATTTATATCAAATATTCATCCCAAATTCGAATAACATAATCA
G
Found at i:2346825 original size:27 final size:27
Alignment explanation
Indices: 2346733--2346825 Score: 86
Period size: 27 Copynumber: 3.4 Consensus size: 27
2346723 TGAAGAATAC
* * *
2346733 ATAAATATATTATAATTT-ATATATGAT
1 ATAAATATATAATATTTTAAAATAT-AT
*
2346760 ATAAAT-TATTAATATTTTAAAATTTAT
1 ATAAATATA-TAATATTTTAAAATATAT
2346787 ATAAATATATAATATTTT-AAATATA-
1 ATAAATATATAATATTTTAAAATATAT
2346812 ATTATAATATATAA
1 A-TA-AATATATAA
2346826 ATTACTGAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.02
26 10 0.18
27 39 0.70
28 6 0.11
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
ATAAATATATAATATTTTAAAATATAT
Found at i:2347290 original size:19 final size:19
Alignment explanation
Indices: 2347266--2347302 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2347256 AATTCGTATA
2347266 TTTATATTATTAT-ATTATT
1 TTTATA-TATTATAATTATT
2347285 TTTATATATTATAATTAT
1 TTTATATATTATAATTAT
2347303 AATTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTATAATTATT
Found at i:2347338 original size:20 final size:21
Alignment explanation
Indices: 2347315--2347353 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2347305 TTAAAAAATT
2347315 ATATATTTATA-TAAATTTTA
1 ATATATTTATATTAAATTTTA
*
2347335 ATATATTTTTATTAAATTT
1 ATATATTTATATTAAATTT
2347354 ATTTTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATATTTATATTAAATTTTA
Found at i:2347361 original size:22 final size:21
Alignment explanation
Indices: 2347312--2347370 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
2347302 TAATTAAAAA
*
2347312 ATTATATATTTATATAAATTTT
1 ATTATATTTTTAT-TAAATTTT
*
2347334 AATATATTTTTATTAAATTTAT
1 ATTATATTTTTATTAAATTT-T
* *
2347356 TTTATATTTTAATTA
1 ATTATATTTTTATTA
2347371 TTAAGACAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTATATTTTTATTAAATTTT
Found at i:2348146 original size:20 final size:20
Alignment explanation
Indices: 2348096--2348147 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
2348086 ATATAAATAA
2348096 ATTTAAATTTTAAAATAATTT
1 ATTTAAA-TTTAAAATAATTT
*
2348117 -TTATATATTTAAAA-AATTAT
1 ATT-TAAATTTAAAATAATT-T
2348137 ATTTAAATTTA
1 ATTTAAATTTA
2348148 TATCTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 4 0.15
20 17 0.65
21 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTAAATTTAAAATAATTT
Found at i:2353407 original size:20 final size:21
Alignment explanation
Indices: 2353382--2353430 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2353372 TTGTGAAATT
*
2353382 ATTATTTATTTAA-AATTAAA
1 ATTATTTAGTTAATAATTAAA
*
2353402 ATTATTTAGTTAATATTTAAA
1 ATTATTTAGTTAATAATTAAA
*
2353423 ATTTTTTA
1 ATTATTTA
2353431 ATTCGCATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTATTTAGTTAATAATTAAA
Found at i:2354071 original size:21 final size:21
Alignment explanation
Indices: 2353999--2354075 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 21
2353989 TTATATATTA
2353999 AAAATAAAATTTTTAATTTTACCTT
1 AAAATAAAATTTTT-ATTTT---TT
* *
2354024 -AAATAAACTTATT-TTTTTT
1 AAAATAAAATTTTTATTTTTT
**
2354043 AAGTTAAAATTTTTATTTTTT
1 AAAATAAAATTTTTATTTTTT
2354064 AAAAT-AAATTTT
1 AAAATAAAATTTT
2354076 AAATGATATA
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
19 2 0.05
20 16 0.38
21 9 0.21
22 4 0.10
24 11 0.26
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (21 bp):
AAAATAAAATTTTTATTTTTT
Found at i:2354691 original size:7 final size:6
Alignment explanation
Indices: 2354662--2354693 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
2354652 AATAAGTTTG
2354662 AATTTA AATTTA AATTTA AATTTAA AATTTA A
1 AATTTA AATTTA AATTTA AATTT-A AATTTA A
2354694 TTAGATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AATTTA
Found at i:2354891 original size:20 final size:20
Alignment explanation
Indices: 2354866--2354904 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2354856 ATAATAATTT
*
2354866 AAAATAAAATATATATATTA
1 AAAATAAAAAATATATATTA
*
2354886 AAAATAAAAAATTTATATT
1 AAAATAAAAAATATATATT
2354905 TAAATATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATAAAAAATATATATTA
Found at i:2355071 original size:22 final size:23
Alignment explanation
Indices: 2355032--2355081 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
2355022 TGTTTAAAGC
* *
2355032 ATAAAAATATAAACAAAACCTTA
1 ATAAAAATAAAAAAAAAACCTTA
* *
2355055 ATAAAAA-AAAAAAAAAACTTTT
1 ATAAAAATAAAAAAAAAACCTTA
2355077 ATAAA
1 ATAAA
2355082 TAGACTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (23 bp):
ATAAAAATAAAAAAAAAACCTTA
Found at i:2355813 original size:31 final size:27
Alignment explanation
Indices: 2355789--2355840 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
2355779 TAAAATATAC
2355789 AAATATT-TTTATAATTAAATTTAAATAA
1 AAATATTATTT-TAA-TAAATTTAAATAA
2355817 AAATATTATTTTAATAAA-TTAAAT
1 AAATATTATTTTAATAAATTTAAAT
2355841 TAAATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 6 0.26
27 4 0.17
28 10 0.43
29 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATATTATTTTAATAAATTTAAATAA
Found at i:2355841 original size:5 final size:5
Alignment explanation
Indices: 2355831--2355855 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2355821 ATTATTTTAA
2355831 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
2355856 GACAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:2356131 original size:18 final size:18
Alignment explanation
Indices: 2356100--2356169 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 18
2356090 TTACGATCAA
2356100 AATA-AAATTATATAATAT
1 AATATAAATT-TATAATAT
2356118 AATATAAATTTATAA-A-
1 AATATAAATTTATAATAT
*
2356134 AATATTAAAATT-TAAT-T
1 AATA-TAAATTTATAATAT
2356151 AATATAAA-TTATTAATAT
1 AATATAAATTTA-TAATAT
2356169 A
1 A
2356170 TTAAAAAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
15 2 0.05
16 11 0.25
17 15 0.34
18 11 0.25
19 5 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATAAATTTATAATAT
Found at i:2356158 original size:33 final size:33
Alignment explanation
Indices: 2356112--2356203 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 33
2356102 TAAAATTATA
2356112 TAATATAATATAAATTTATAAAAATATTAAAATT
1 TAATATAATATAAA-TTATAAAAATATTAAAATT
* *
2356146 TAAT-TAATATAAATTATTAATATATTAAAA--
1 TAATATAATATAAATTATAAAAATATTAAAATT
2356176 -AATATATATATAAATTCAATAAAAATAT
1 TAATATA-ATATAAATT--ATAAAAATAT
2356204 CTATTATCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
29 3 0.06
30 2 0.04
31 9 0.18
32 15 0.30
33 17 0.34
34 4 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (33 bp):
TAATATAATATAAATTATAAAAATATTAAAATT
Found at i:2357696 original size:18 final size:18
Alignment explanation
Indices: 2357642--2357698 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 18
2357632 ATTATTTATT
*
2357642 TTTAAAAATTTAATAAA-A
1 TTTAAAAA-TTAAAAAATA
*
2357660 TTTATTAAATTATTAAAAATA
1 TTTA-AAAATTA--AAAAATA
2357681 TTTAAAAATTAAAAAATA
1 TTTAAAAATTAAAAAATA
2357699 AAATATGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 14 0.44
19 3 0.09
20 10 0.31
21 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAAAATTAAAAAATA
Found at i:2357704 original size:23 final size:25
Alignment explanation
Indices: 2357675--2357722 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
2357665 TAAATTATTA
**
2357675 AAAATATTTAAAAA-TTAAA-AAAT
1 AAAATATGAAAAAATTTAAATAAAT
2357698 AAAATATGAAAAAATTTAAATAAAT
1 AAAATATGAAAAAATTTAAATAAAT
2357723 TTTAATTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 5 0.24
25 4 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAATATGAAAAAATTTAAATAAAT
Found at i:2357798 original size:11 final size:11
Alignment explanation
Indices: 2357777--2357839 Score: 53
Period size: 10 Copynumber: 5.9 Consensus size: 11
2357767 AAATTTTATT
2357777 TTAAA-TTAAA
1 TTAAATTTAAA
2357787 TTAAATTTAAA
1 TTAAATTTAAA
*
2357798 -TAAATATAAA
1 TTAAATTTAAA
2357808 -T-AATATTAATA
1 TTAAAT-TTAA-A
*
2357819 TTATATTTAAA
1 TTAAATTTAAA
*
2357830 TTCAATTTAA
1 TTAAATTTAA
2357840 TTTTACCCGT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 3 0.07
10 18 0.42
11 15 0.35
12 5 0.12
13 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:2361719 original size:2 final size:2
Alignment explanation
Indices: 2361707--2361752 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
2361697 AATAGAATTA
* *
2361707 AT AT A- AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2361747 A- AT AT A
1 AT AT AT A
2361753 AAAATCTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2362360 original size:14 final size:14
Alignment explanation
Indices: 2362343--2362396 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
2362333 TATTAAATAT
2362343 ATAAATTTAATTAA
1 ATAAATTTAATTAA
*
2362357 ATAAATTTAAATAA
1 ATAAATTTAATTAA
* * *
2362371 TTTAATTTATCTTAA
1 ATAAATTTA-ATTAA
2362386 ATCAAATTTAA
1 AT-AAATTTAA
2362397 ATTTTAAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
14 20 0.67
15 4 0.13
16 6 0.20
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAAATTTAATTAA
Found at i:2363072 original size:16 final size:17
Alignment explanation
Indices: 2363053--2363085 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2363043 ATTATAATTT
2363053 TATTTA-AAAAATTTTA
1 TATTTATAAAAATTTTA
*
2363069 TATTTATATAAATTTTA
1 TATTTATAAAAATTTTA
2363086 ACTATATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTATAAAAATTTTA
Found at i:2364907 original size:20 final size:20
Alignment explanation
Indices: 2364882--2364933 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
2364872 AAATGTAAAG
2364882 GATAATTTTTAGAAAAAAAA
1 GATAATTTTTAGAAAAAAAA
*
2364902 GATAATTTTTTAGAAAAAATA
1 GATAA-TTTTTAGAAAAAAAA
2364923 -ATAGATTTTTA
1 GATA-ATTTTTA
2364934 AAATAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (20 bp):
GATAATTTTTAGAAAAAAAA
Found at i:2364932 original size:21 final size:21
Alignment explanation
Indices: 2364882--2364920 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2364872 AAATGTAAAG
2364882 GATAA-TTTTTAGAAAAAAAA
1 GATAATTTTTTAGAAAAAAAA
2364902 GATAATTTTTTAGAAAAAA
1 GATAATTTTTTAGAAAAAA
2364921 TAATAGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (21 bp):
GATAATTTTTTAGAAAAAAAA
Found at i:2366442 original size:15 final size:15
Alignment explanation
Indices: 2366419--2366449 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2366409 CATATATAAC
2366419 GTACATGATTTCTAT
1 GTACATGATTTCTAT
*
2366434 GTACGTGATTTCTAT
1 GTACATGATTTCTAT
2366449 G
1 G
2366450 ATATCTGCCT
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:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (15 bp):
GTACATGATTTCTAT
Found at i:2368879 original size:19 final size:19
Alignment explanation
Indices: 2368847--2368886 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2368837 AAAATTATTT
*
2368847 TTATATTAATATTTATATA
1 TTATATTAATATTTAAATA
2368866 TTATAATTAA-ATTTAAATA
1 TTAT-ATTAATATTTAAATA
2368885 TT
1 TT
2368887 TTTATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATATTAATATTTAAATA
Found at i:2372097 original size:7 final size:7
Alignment explanation
Indices: 2372066--2372095 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2372056 AAAATTATAT
2372066 ATATTAA
1 ATATTAA
2372073 ATATTAA
1 ATATTAA
2372080 ATATTAA
1 ATATTAA
*
2372087 ATTTTAA
1 ATATTAA
2372094 AT
1 AT
2372096 TTGATGAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
ATATTAA
Found at i:2375964 original size:25 final size:26
Alignment explanation
Indices: 2375936--2375995 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
2375926 TTTTAAATAA
* *
2375936 TAAAATTT-TTTATTTAT-ATTTTTAT
1 TAAAATTTATTAAATTATCATTTTT-T
2375961 T-AAATTTATTAAATTATCATTTTTT
1 TAAAATTTATTAAATTATCATTTTTT
*
2375986 TAAAAATTAT
1 TAAAATTTAT
2375996 ATTCTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 6 0.21
25 10 0.34
26 13 0.45
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TAAAATTTATTAAATTATCATTTTTT
Found at i:2375994 original size:18 final size:18
Alignment explanation
Indices: 2375971--2376005 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2375961 TAAATTTATT
2375971 AAATTATCATT-TTTTTAA
1 AAATTAT-ATTCTTTTTAA
2375989 AAATTATATTCTTTTTA
1 AAATTATATTCTTTTTA
2376006 TATATAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
AAATTATATTCTTTTTAA
Found at i:2376188 original size:11 final size:11
Alignment explanation
Indices: 2376164--2376212 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 11
2376154 AAACAACAAT
2376164 TATTATTATTAA
1 TATTATT-TTAA
2376176 TATTATTTTAA
1 TATTATTTTAA
*
2376187 TATTATATTCAACA
1 TATTAT-TT-TA-A
2376201 TATTATTTTAA
1 TATTATTTTAA
2376212 T
1 T
2376213 TTAAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 12 0.38
12 10 0.31
13 3 0.09
14 7 0.22
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTATTTTAA
Found at i:2379305 original size:21 final size:19
Alignment explanation
Indices: 2379281--2379334 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
2379271 AAATTAATTG
*
2379281 TTATAATAATAAAATTGAGTA
1 TTATAATAATAAAATT-A-AA
*
2379302 TTATATTAATAAAATTAAA
1 TTATAATAATAAAATTAAA
2379321 TT-TAATAATAAAAT
1 TTATAATAATAAAAT
2379335 ATATGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.37
19 3 0.10
20 1 0.03
21 15 0.50
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
TTATAATAATAAAATTAAA
Found at i:2379374 original size:18 final size:18
Alignment explanation
Indices: 2379348--2379400 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2379338 TGTTTGATTG
2379348 TAAAAATAATGAT-AATAA
1 TAAAAATAAT-ATAAATAA
*
2379366 TAAATATAATATAAATAA
1 TAAAAATAATATAAATAA
*
2379384 TTATAAAT-ATATAAATA
1 -TAAAAATAATATAAATA
2379401 TATATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 2 0.07
18 23 0.77
19 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
TAAAAATAATATAAATAA
Found at i:2382291 original size:25 final size:25
Alignment explanation
Indices: 2382263--2382312 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2382253 ATTTTTAATT
* * * *
2382263 AATTTTTATAAGTATCAATTAAATA
1 AATTTATATAAATATAAATAAAATA
2382288 AATTTATATAAATATAAATAAAATA
1 AATTTATATAAATATAAATAAAATA
2382313 TAAATTATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
AATTTATATAAATATAAATAAAATA
Found at i:2383412 original size:15 final size:15
Alignment explanation
Indices: 2383377--2383416 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
2383367 GGTAAGTATG
2383377 ATAATAT-TAAATAT
1 ATAATATATAAATAT
*
2383391 A-ATTATATAAATAT
1 ATAATATATAAATAT
2383405 ATAATATATAAA
1 ATAATATATAAA
2383417 ATAATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 4 0.18
14 9 0.41
15 9 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATATATAAATAT
Found at i:2383419 original size:16 final size:16
Alignment explanation
Indices: 2383387--2383416 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2383377 ATAATATTAA
2383387 ATATAATTATATAAAT
1 ATATAATTATATAAAT
2383403 ATATAA-TATATAAA
1 ATATAATTATATAAA
2383417 ATAATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTATATAAAT
Found at i:2383493 original size:19 final size:19
Alignment explanation
Indices: 2383458--2383542 Score: 63
Period size: 19 Copynumber: 4.5 Consensus size: 19
2383448 TTTAAAAATT
2383458 TATATAAATAAATTATAAA
1 TATATAAATAAATTATAAA
*
2383477 TATATTAAATAGA-TATAAA
1 TATA-TAAATAAATTATAAA
* *
2383496 TATA-AAA-ATATTTTAAA
1 TATATAAATAAATTATAAA
2383513 TATTATTAAAATATAA-TA-AAA
1 TA-TA-T-AAATA-AATTATAAA
2383534 TATATAAAT
1 TATATAAAT
2383543 TATTAAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 17
0.71 0.07 0.23
Matches are distributed among these distances:
16 2 0.04
17 10 0.19
18 6 0.11
19 15 0.28
20 9 0.17
21 8 0.15
22 2 0.04
23 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (19 bp):
TATATAAATAAATTATAAA
Found at i:2383495 original size:48 final size:46
Alignment explanation
Indices: 2383441--2383543 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 46
2383431 TATGATATTA
*
2383441 ATATAAATTTAAAAAT-TTATATAAATA-AATTATAAATATATTAAATAG
1 ATATAAATTTAAAAATATT-T-TAAATATAATTA-AAATATAATAAA-AG
* * *
2383489 ATATAAATATAAAAATATTTTAAATATTATTAAAATATAATAAAAT
1 ATATAAATTTAAAAATATTTTAAATATAATTAAAATATAATAAAAG
2383535 ATATAAATT
1 ATATAAATT
2383544 ATTAAATTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
46 9 0.19
47 17 0.35
48 20 0.42
49 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (46 bp):
ATATAAATTTAAAAATATTTTAAATATAATTAAAATATAATAAAAG
Found at i:2383500 original size:36 final size:37
Alignment explanation
Indices: 2383459--2383550 Score: 102
Period size: 36 Copynumber: 2.5 Consensus size: 37
2383449 TTAAAAATTT
2383459 ATATAAATAAATTATAAATA-TATTAAATAGAT-ATAA
1 ATATAAATAAATTATAAATATTATTAAA-AGATAATAA
* *
2383495 ATATAAA-AATATTTTAAATATTATTAAAATATAATAA
1 ATATAAATAA-ATTATAAATATTATTAAAAGATAATAA
*
2383532 A-ATATATAAATTATTAAAT
1 ATATAAATAAATTA-TAAAT
2383551 TTAATTTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
35 2 0.04
36 26 0.55
37 19 0.40
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (37 bp):
ATATAAATAAATTATAAATATTATTAAAAGATAATAA
Done.