Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 4 of 33
Found at i:390012 original size:27 final size:26
Alignment explanation
Indices: 389970--390047 Score: 95
Period size: 27 Copynumber: 3.0 Consensus size: 26
389960 TCAGTTATTA
*
389970 AATT-TAAAATTCAAAATTTATATAAT
1 AATTATAAAATT-AAAATTTAAATAAT
* *
389996 AATTATAAATTTTAAAATTTAGATAAT
1 AATTATAAA-ATTAAAATTTAAATAAT
*
390023 AATTTTAAAATTAAAATTTAAATAA
1 AATTATAAAATTAAAATTTAAATAA
390048 AAATATCTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
26 18 0.40
27 25 0.56
28 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (26 bp):
AATTATAAAATTAAAATTTAAATAAT
Found at i:390967 original size:26 final size:28
Alignment explanation
Indices: 390938--390999 Score: 65
Period size: 30 Copynumber: 2.2 Consensus size: 28
390928 ATTTATATTT
*
390938 TTTAATT-AAAAATTA-TATTTTTTATA
1 TTTAATTAAAAAATTATTATTATTTATA
* *
390964 TTTATTTTAAAAAATTATTTATTATTTATT
1 TTTA-ATTAAAAAATTA-TTATTATTTATA
390994 TTTAAT
1 TTTAAT
391000 AATATTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
26 4 0.14
27 2 0.07
28 8 0.29
29 1 0.04
30 13 0.46
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTAATTAAAAAATTATTATTATTTATA
Found at i:391166 original size:17 final size:16
Alignment explanation
Indices: 391119--391166 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
391109 GAGTTAAGAG
* *
391119 TGATCTGAATCTAAAA
1 TGATCTAAATTTAAAA
* *
391135 TGTTTTAAATTTAAAA
1 TGATCTAAATTTAAAA
391151 TGATCTAAACTTTAAA
1 TGATCTAAA-TTTAAA
391167 TAATTATAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (16 bp):
TGATCTAAATTTAAAA
Found at i:391605 original size:3 final size:3
Alignment explanation
Indices: 391592--391629 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
391582 TCCCATTTTC
391592 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
391630 AGAGGAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:394437 original size:30 final size:31
Alignment explanation
Indices: 394403--394481 Score: 142
Period size: 32 Copynumber: 2.5 Consensus size: 31
394393 TAAGAAAAAG
394403 GTAATCTCATCCATTTATCC-AAAAAAAACA
1 GTAATCTCATCCATTTATCCAAAAAAAAACA
394433 GTAATCTCATCCATTTATCCAAAAAAAAAACA
1 GTAATCTCATCCATTTATCC-AAAAAAAAACA
394465 GTAATCTCATCCATTTA
1 GTAATCTCATCCATTTA
394482 AAAAACAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
30 20 0.43
32 27 0.57
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.29
Consensus pattern (31 bp):
GTAATCTCATCCATTTATCCAAAAAAAAACA
Found at i:396577 original size:2 final size:2
Alignment explanation
Indices: 396570--396604 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
396560 TTGAACGTCC
396570 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
396605 AGAATAGAAC
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:400151 original size:9 final size:9
Alignment explanation
Indices: 400137--400172 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
400127 AATTTGTGAG
400137 TAGTAATAA
1 TAGTAATAA
400146 TAGTAATAA
1 TAGTAATAA
*
400155 TAGCAATAA
1 TAGTAATAA
*
400164 TAATAATAA
1 TAGTAATAA
400173 GATATCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (9 bp):
TAGTAATAA
Found at i:401535 original size:2 final size:2
Alignment explanation
Indices: 401528--401558 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
401518 AGACTTACTT
401528 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
401559 TTCCATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:403545 original size:2 final size:2
Alignment explanation
Indices: 403538--403566 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
403528 TAATCATTCT
403538 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
403567 GTGAGTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:404279 original size:17 final size:18
Alignment explanation
Indices: 404238--404271 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
404228 GATAAATTTT
404238 TTTATT-AAATATTTAAA
1 TTTATTAAAATATTTAAA
404255 TTTATTAAAATATTTAA
1 TTTATTAAAATATTTAA
404272 TTATTTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTATTAAAATATTTAAA
Found at i:408524 original size:16 final size:15
Alignment explanation
Indices: 408499--408529 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
408489 CAAAGGAAGT
408499 AAAAAGATTTGTTTA
1 AAAAAGATTTGTTTA
408514 AAAATAGATTTGTTTA
1 AAAA-AGATTTGTTTA
408530 TAATTGAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (15 bp):
AAAAAGATTTGTTTA
Found at i:408646 original size:25 final size:25
Alignment explanation
Indices: 408618--408665 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
408608 GTTATTTATA
* * *
408618 TAATAATTAATATTTTATTTAAATT
1 TAATAATAAATATTATAATTAAATT
*
408643 TAATTATAAATATTATAATTAAA
1 TAATAATAAATATTATAATTAAA
408666 ATAAAATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TAATAATAAATATTATAATTAAATT
Found at i:409209 original size:25 final size:25
Alignment explanation
Indices: 409165--409228 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
409155 TGTAAAATCG
* *
409165 TGTCGTTTTTATATTTTTTTTATT-A
1 TGTCGTGTTTATA-TTATTTTATTCA
409190 TGTCGTAGTTTA-ATTATTTTATTCA
1 TGTCGT-GTTTATATTATTTTATTCA
*
409215 TGTTGTGTTTATAT
1 TGTCGTGTTTATAT
409229 CGTCTAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 14 0.42
25 15 0.45
26 4 0.12
ACGTcount: A:0.19, C:0.05, G:0.12, T:0.64
Consensus pattern (25 bp):
TGTCGTGTTTATATTATTTTATTCA
Found at i:410954 original size:29 final size:30
Alignment explanation
Indices: 410891--410973 Score: 100
Period size: 29 Copynumber: 2.8 Consensus size: 30
410881 AAATTTTAAA
410891 AAATTATAATTTAAATGATTAAT-TTGATTT
1 AAATTATAATTTAAAT-ATTAATATTGATTT
* * *
410921 GAATTATTATTTAAATAATAATATT-ATTT
1 AAATTATAATTTAAATATTAATATTGATTT
410950 AAATT-TAATTATAAATATTAATAT
1 AAATTATAATT-TAAATATTAATAT
410974 AAAAATATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.09
29 25 0.56
30 16 0.36
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (30 bp):
AAATTATAATTTAAATATTAATATTGATTT
Found at i:410958 original size:45 final size:42
Alignment explanation
Indices: 410861--410959 Score: 101
Period size: 45 Copynumber: 2.2 Consensus size: 42
410851 GGATAGAACA
*
410861 AAATTTAATTTATATGAATTAAATTTTAAAAAATTATAATTT
1 AAATTTAATTTATATGAATTAAATTTTAAAAAAATATAATTT
* * *
410903 AAATGATTAATTTGATTTGAATT-ATTATTTAAATAATAATATTATTT
1 AAAT--TTAATTT-ATATGAATTAAAT-TTTAAA-AA-AATATAATTT
410950 AAATTTAATT
1 AAATTTAATT
410960 ATAAATATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
42 4 0.09
44 9 0.19
45 20 0.43
46 2 0.04
47 12 0.26
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (42 bp):
AAATTTAATTTATATGAATTAAATTTTAAAAAAATATAATTT
Found at i:413025 original size:31 final size:33
Alignment explanation
Indices: 412990--413053 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 33
412980 TCCATAAAGC
412990 AAATCCTAAACTGAAATCACAC-A-GCAAACAA
1 AAATCCTAAACTGAAATCACACAATGCAAACAA
* *
413021 AAATCCTGAACTGAAATCATACAATGCAAACAA
1 AAATCCTAAACTGAAATCACACAATGCAAACAA
413054 GAAGCCATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 20 0.69
32 1 0.03
33 8 0.28
ACGTcount: A:0.53, C:0.23, G:0.08, T:0.16
Consensus pattern (33 bp):
AAATCCTAAACTGAAATCACACAATGCAAACAA
Found at i:413127 original size:6 final size:6
Alignment explanation
Indices: 413112--413145 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
413102 GTTAGAGCTT
413112 ATTT-A ATTTGA ATTTGA ATTTGA ATTTGA ATTTG
1 ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTG
413146 TGGCTGAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (6 bp):
ATTTGA
Found at i:417833 original size:3 final size:3
Alignment explanation
Indices: 417825--417850 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
417815 TCTCCAAATT
417825 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
417851 TAGTAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:419003 original size:24 final size:23
Alignment explanation
Indices: 418959--419003 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
418949 TTATTAAATA
*
418959 TTAAATATTATATTAATATATAT
1 TTAAATATTATATTAAAATATAT
418982 TTAAGATATTA-ATATAAAATAT
1 TTAA-ATATTATAT-TAAAATAT
419004 TATGTATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAATATTATATTAAAATATAT
Found at i:419050 original size:13 final size:12
Alignment explanation
Indices: 419029--419069 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
419019 AATTATAATA
419029 TAAATATTTATT
1 TAAATATTTATT
*
419041 TAAATAATTTTTT
1 TAAAT-ATTTATT
*
419054 TAAATATTTAAT
1 TAAATATTTATT
419066 TAAA
1 TAAA
419070 AAAATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TAAATATTTATT
Found at i:426261 original size:22 final size:21
Alignment explanation
Indices: 426236--426277 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
426226 AAAATAAAAA
426236 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
426256 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
426277 A
1 A
426278 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:433766 original size:23 final size:23
Alignment explanation
Indices: 433740--433785 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
433730 TCATCAAGAT
*
433740 ATTACATTGATAATATTAAAAAA
1 ATTACATTGACAATATTAAAAAA
*
433763 ATTATATTGACAATATTAAAAAA
1 ATTACATTGACAATATTAAAAAA
433786 TTAATACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
ATTACATTGACAATATTAAAAAA
Found at i:435214 original size:32 final size:31
Alignment explanation
Indices: 435143--435216 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
435133 TTACATGTTG
**
435143 AATAAATTTACTTTAAAATTAAAAGGATTAAT
1 AATAAATTTACTCAAAAATTAAAA-GATTAAT
*
435175 GATAAATTTACTCAAAAATTAAAA-ATATAAT
1 AATAAATTTACTCAAAAATTAAAAGAT-TAAT
*
435206 AATAAAATTAC
1 AATAAATTTAC
435217 ACGAGATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 2 0.06
31 13 0.36
32 21 0.58
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (31 bp):
AATAAATTTACTCAAAAATTAAAAGATTAAT
Found at i:435877 original size:27 final size:28
Alignment explanation
Indices: 435846--435959 Score: 85
Period size: 28 Copynumber: 4.1 Consensus size: 28
435836 TTTATTTTAC
435846 ATATTTAATA-ATTTAATAATTTATATT
1 ATATTTAATACATTTAATAATTTATATT
* * *
435873 ATATTTATATA-TTTTATTAAATTATAATT
1 ATATTTA-ATACATTTAATAATTTAT-ATT
* * * *
435902 ATATTTAAAATATTTTAT-ATTAATA-T
1 ATATTTAATACATTTAATAATTTATATT
* *
435928 AAACTTTAATACA-TCAATAATTTATATT
1 ATA-TTTAATACATTTAATAATTTATATT
435956 ATAT
1 ATAT
435960 AAATTTTAAA
Statistics
Matches: 65, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
26 6 0.09
27 22 0.34
28 23 0.35
29 14 0.22
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (28 bp):
ATATTTAATACATTTAATAATTTATATT
Found at i:435895 original size:29 final size:27
Alignment explanation
Indices: 435846--435919 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 27
435836 TTTATTTTAC
* *
435846 ATATTTAATAATTTAATAATT-TATATT
1 ATATTTAATATTTTATTAATTATA-ATT
435873 ATATTTATATATTTTATTAAATTATAATT
1 ATATTTA-ATATTTTATT-AATTATAATT
435902 ATATTTAAAATATTTTAT
1 ATATTT--AATATTTTAT
435920 ATTAATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
27 7 0.17
28 8 0.20
29 13 0.32
30 11 0.28
31 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATATTTAATATTTTATTAATTATAATT
Found at i:435929 original size:30 final size:29
Alignment explanation
Indices: 435846--435919 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
435836 TTTATTTTAC
* * *
435846 ATATTT-AATAATTTAATAATTTAT-ATT
1 ATATTTAAATATTTTATTAAATTATAATT
*
435873 ATATTTATATATTTTATTAAATTATAATT
1 ATATTTAAATATTTTATTAAATTATAATT
435902 ATATTTAAAATATTTTAT
1 ATATTT-AAATATTTTAT
435920 ATTAATATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 6 0.15
28 14 0.36
29 9 0.23
30 10 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
ATATTTAAATATTTTATTAAATTATAATT
Found at i:435998 original size:24 final size:23
Alignment explanation
Indices: 435962--436026 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
435952 TATTATATAA
* * *
435962 ATTTTAAAATATATTTTTATGTAT
1 ATTTTATATTATATTTGTAT-TAT
**
435986 ATTTTATATTATATACGTATTAT
1 ATTTTATATTATATTTGTATTAT
436009 ATTTATATAATTATATTT
1 ATTT-TAT-ATTATATTT
436027 AAAATTATCA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 7 0.22
24 18 0.56
25 7 0.22
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (23 bp):
ATTTTATATTATATTTGTATTAT
Found at i:437271 original size:18 final size:19
Alignment explanation
Indices: 437241--437281 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
437231 ATAATTTTTT
*
437241 AAAA-AAATTATAATT-TA
1 AAAATAAATAATAATTATA
437258 AAAATAAATAATAATTATA
1 AAAATAAATAATAATTATA
437277 AAAAT
1 AAAAT
437282 TGAAATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATAAATAATAATTATA
Found at i:437405 original size:28 final size:30
Alignment explanation
Indices: 437340--437414 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
437330 AAAAATAAAG
**
437340 TAATAAATTATA-AAAAATTATAATTTTAA
1 TAATAAATTATATAAATTTTATAATTTTAA
*
437369 TTATAAATT-TATTAAATTTTAT-ATTTTAA
1 TAATAAATTATA-TAAATTTTATAATTTTAA
437398 TAAT-AATTATATAAATT
1 TAATAAATTATATAAATT
437415 AATCAATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 12 0.31
29 20 0.51
30 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAATAAATTATATAAATTTTATAATTTTAA
Found at i:437587 original size:2 final size:2
Alignment explanation
Indices: 437580--437616 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
437570 CCACTGGAAT
437580 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
437617 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:437621 original size:2 final size:2
Alignment explanation
Indices: 437616--437652 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
437606 TATATATATA
437616 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
437653 CTTGGTGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:438208 original size:20 final size:19
Alignment explanation
Indices: 438161--438209 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
438151 ATGTTTAAAG
*
438161 TATTTTATATTTATAAAAA
1 TATTATATATTTATAAAAA
* *
438180 TTTTAATATATTTATAATACA
1 TATT-ATATATTTATAA-AAA
438201 TATTATATA
1 TATTATATA
438210 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.12
20 16 0.67
21 5 0.21
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTATATATTTATAAAAA
Found at i:439440 original size:2 final size:2
Alignment explanation
Indices: 439433--439464 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
439423 ATTTAATTTG
439433 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
439465 CAATCTTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:439739 original size:25 final size:23
Alignment explanation
Indices: 439687--439731 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
439677 TTTACAAAAG
439687 ATCTTCTTTTCTTATGTCATTTA
1 ATCTTCTTTTCTTATGTCATTTA
*
439710 ATCTTCTTTTTTTATGTCATTT
1 ATCTTCTTTTCTTATGTCATTT
439732 TCAGTCTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.04, T:0.64
Consensus pattern (23 bp):
ATCTTCTTTTCTTATGTCATTTA
Found at i:441724 original size:25 final size:23
Alignment explanation
Indices: 441683--441740 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
441673 TATCAGATTA
*
441683 ATATTATAT-AAAAAATAATTAAG
1 ATATAATATAAAAAAAT-ATTAAG
*
441706 ATATAATATAAAAATAATATTAAT
1 ATATAATATAAAAA-AATATTAAG
441730 ATATAAATATA
1 ATAT-AATATA
441741 TTAAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 8 0.27
24 13 0.43
25 9 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATAATATAAAAAAATATTAAG
Found at i:441731 original size:17 final size:16
Alignment explanation
Indices: 441709--441744 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
441699 AATTAAGATA
441709 TAATATAAAAATAATAT
1 TAATATAAAAAT-ATAT
*
441726 TAATATATAAATATAT
1 TAATATAAAAATATAT
441742 TAA
1 TAA
441745 AATTTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATAAAAATATAT
Found at i:441731 original size:22 final size:23
Alignment explanation
Indices: 441679--441732 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
441669 TGGGTATCAG
*
441679 ATTAATATTATATAAAAAATAAT
1 ATTAATATAATATAAAAAATAAT
*
441702 -TAAGATATAATAT-AAAAATAAT
1 ATTA-ATATAATATAAAAAATAAT
441724 ATTAATATA
1 ATTAATATA
441733 TAAATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTAATATAATATAAAAAATAAT
Found at i:442769 original size:27 final size:26
Alignment explanation
Indices: 442707--442778 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 26
442697 TTGAATTACT
* * *
442707 ATTTAATAATAAAAATATTTTTATTTAA
1 ATTTAAT-AT-AAAATATATATATATAA
442735 ATTT-ATATAAAATATATATATATAA
1 ATTTAATATAAAATATATATATATAA
*
442760 ATATTAATATAAAAAATAT
1 AT-TTAATATAAAATATAT
442779 GTTAATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
25 16 0.42
26 4 0.11
27 14 0.37
28 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTAATATAAAATATATATATATAA
Found at i:447524 original size:18 final size:19
Alignment explanation
Indices: 447479--447565 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 19
447469 TAGATTAATA
*
447479 ATTTATATTATATAAATTTT
1 ATTTAT-TTATATATATTTT
**
447499 AAAATATTTATATAT-TTTT
1 -ATTTATTTATATATATTTT
*
447518 ATTTATTTATAT-TATTTC
1 ATTTATTTATATATATTTT
447536 ATTATATTTTATATTATATTTT
1 ATT-TA-TTTATA-TATATTTT
*
447558 AATTATTT
1 ATTTATTT
447566 TTCATATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
17 1 0.02
18 16 0.30
19 6 0.11
20 16 0.30
21 7 0.13
22 7 0.13
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTATTTATATATATTTT
Found at i:447562 original size:23 final size:23
Alignment explanation
Indices: 447509--447572 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
447499 AAAATATTTA
*
447509 TATATTTTTATT-TA-TTTATA-
1 TATATTTTAATTATATTTTATAT
*
447529 T-TA-TTTCATTATATTTTATAT
1 TATATTTTAATTATATTTTATAT
447550 TATATTTTAATTAT-TTTTCATAT
1 TATATTTTAATTATATTTT-ATAT
447573 AAAATAATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 6 0.17
19 4 0.11
20 7 0.19
21 1 0.03
22 6 0.17
23 12 0.33
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (23 bp):
TATATTTTAATTATATTTTATAT
Found at i:448923 original size:22 final size:24
Alignment explanation
Indices: 448860--448923 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 24
448850 AAATTGATTT
448860 AAATTATATTATTATTTAATAATAATA
1 AAATTAT-TT-TTATTTAAT-ATAATA
* **
448887 AATTTATTTAAATTTAAT-T-ATA
1 AAATTATTTTTATTTAATATAATA
448909 AAATTATTTTTATTT
1 AAATTATTTTTATTT
448924 TTTTTATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 15 0.48
23 1 0.03
25 7 0.23
26 2 0.06
27 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AAATTATTTTTATTTAATATAATA
Found at i:448970 original size:10 final size:10
Alignment explanation
Indices: 448945--448999 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
448935 ATTTAAATTT
448945 TTTAATTAAA
1 TTTAATTAAA
448955 -TTAATTAAA
1 TTTAATTAAA
448964 TTTAATTTAAA
1 TTTAA-TTAAA
**
448975 TTTAAAAAAA
1 TTTAATTAAA
**
448985 TTTAAAAAAA
1 TTTAATTAAA
448995 TTTAA
1 TTTAA
449000 AAATATTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
9 9 0.22
10 22 0.54
11 10 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAATTAAA
Found at i:449000 original size:10 final size:10
Alignment explanation
Indices: 448972--449002 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
448962 AATTTAATTT
448972 AAATTTAAAA
1 AAATTTAAAA
448982 AAATTTAAAA
1 AAATTTAAAA
448992 AAATTTAAAA
1 AAATTTAAAA
449002 A
1 A
449003 TATTAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATTTAAAA
Found at i:454564 original size:2 final size:2
Alignment explanation
Indices: 454557--454605 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
454547 TTTCTCTGCT
454557 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 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
454599 TC TC TC T
1 TC TC TC T
454606 TTATCTTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:456934 original size:6 final size:6
Alignment explanation
Indices: 456925--456953 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
456915 CTTCATCTTC
456925 GCCTCA GCCTCA GCCTCA GCCTCA GCCTC
1 GCCTCA GCCTCA GCCTCA GCCTCA GCCTC
456954 CCAGCGGTAC
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:0.14, C:0.52, G:0.17, T:0.17
Consensus pattern (6 bp):
GCCTCA
Found at i:458743 original size:18 final size:18
Alignment explanation
Indices: 458709--458755 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
458699 AATCATAAAT
458709 TTAA-ATTTAAT--TTAA
1 TTAATATTTAATAATTAA
458724 TTAAT-TTTATATAATTAA
1 TTAATATTTA-ATAATTAA
458742 TTAATATTTAATAA
1 TTAATATTTAATAA
458756 ATTTAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.30
16 2 0.07
18 13 0.48
19 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATATTTAATAATTAA
Found at i:459898 original size:2 final size:2
Alignment explanation
Indices: 459891--459925 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
459881 TTTATGTTGT
459891 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
459926 TTCATTTTCT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:460985 original size:2 final size:2
Alignment explanation
Indices: 460980--461011 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
460970 TTCTAAAAAA
460980 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
461012 GTTCTCTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:462793 original size:22 final size:22
Alignment explanation
Indices: 462765--462835 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
462755 TAAATATAAG
462765 TTTTATATAATATTTAATAAAT
1 TTTTATATAATATTTAATAAAT
*
462787 TTTTATATAATTTTTTAATATAAT
1 TTTTATATAA-TATTTAATA-AAT
*
462811 TTGATAATTATAATATTATAATAAA
1 TT--TTA-TATAATATT-TAATAAA
462836 AAAATACAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 10 0.25
23 8 0.20
24 5 0.12
26 7 0.17
27 10 0.25
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (22 bp):
TTTTATATAATATTTAATAAAT
Found at i:462801 original size:11 final size:11
Alignment explanation
Indices: 462758--462812 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
462748 TCACTTATAA
*
462758 ATATAAGTTTT
1 ATATAATTTTT
*
462769 ATATAATATTT
1 ATATAATTTTT
462780 A-ATAAATTTTT
1 ATAT-AATTTTT
462791 ATATAATTTTTT
1 ATATAA-TTTTT
462803 AATATAATTT
1 -ATATAATTT
462813 GATAATTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.05
11 19 0.51
12 10 0.27
13 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
ATATAATTTTT
Found at i:463446 original size:39 final size:39
Alignment explanation
Indices: 463373--463449 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
463363 ATTAGTATGA
* * *
463373 AATTATTATTTAAAAAATTATTTATTTATTTATATTTAC
1 AATTATAATTTAAAAAATTATTTAATAATTTATATTTAC
463412 AATTATAATTT-AAAAA-TATATTAATAATTATATATTTA
1 AATTATAATTTAAAAAATTAT-TTAATAATT-TATATTTA
463450 GATAAATTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 3 0.09
38 12 0.36
39 18 0.55
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (39 bp):
AATTATAATTTAAAAAATTATTTAATAATTTATATTTAC
Found at i:463691 original size:81 final size:81
Alignment explanation
Indices: 463535--463692 Score: 178
Period size: 81 Copynumber: 2.0 Consensus size: 81
463525 CCGTAGCTGG
** * ** **
463535 AAATTTAAAAGATTTGAATTTTAACTTAATAAAAAAATTTGCATGTTATCTTTTTTTTTAAAGTT
1 AAATTTAAAAGATTCAAATTTTAACTTAATAAAAAAATTTACACATTATCTTTTTTTTTAAAGCC
*
463600 GAAATTATATATTTAA
66 GAAATCATATATTTAA
* *
463616 AAATTTTAAAGATTCAAATTTTAA-TATCAT-AAAAAATTTACACATTATCTTTTTTTTTCAAA-
1 AAATTTAAAAGATTCAAATTTTAACT-TAATAAAAAAATTTACACATTATCTTTTTTTTT-AAAG
463678 CCGAAATGCATATAT
64 CCGAAAT-CATATAT
463693 ATGAAGCTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
80 31 0.48
81 33 0.52
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (81 bp):
AAATTTAAAAGATTCAAATTTTAACTTAATAAAAAAATTTACACATTATCTTTTTTTTTAAAGCC
GAAATCATATATTTAA
Found at i:464167 original size:23 final size:22
Alignment explanation
Indices: 464124--464209 Score: 72
Period size: 23 Copynumber: 4.0 Consensus size: 22
464114 CATTTCAATC
*
464124 TAAATTAAAAATTTATCTAAATT
1 TAAATTAAAAATTAAT-TAAATT
*
464147 TAAATTAAAAATTCAATTAAA-A
1 TAAATTAAAAATT-AATTAAATT
*
464169 TAAA--AAAAA-TAATAAAATT
1 TAAATTAAAAATTAATTAAATT
* *
464188 TAAGTAAAAAATTAAATTAAAT
1 TAAATTAAAAATT-AATTAAAT
464210 AAAATAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
18 6 0.12
19 4 0.08
20 5 0.10
21 5 0.10
22 5 0.10
23 24 0.47
24 2 0.04
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (22 bp):
TAAATTAAAAATTAATTAAATT
Found at i:466108 original size:31 final size:30
Alignment explanation
Indices: 466049--466110 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
466039 CTGGGTTTAG
* *
466049 TGAAAACCGAAAGAAAGAAAGGAAAAAAAA
1 TGAAAACAGAAAAAAAGAAAGGAAAAAAAA
466079 TGAAAGACAGAAAAAAAGGAAA-GAAAAAAAA
1 TGAAA-ACAGAAAAAAA-GAAAGGAAAAAAAA
466110 T
1 T
466111 TTATACATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.18
31 19 0.68
32 4 0.14
ACGTcount: A:0.71, C:0.05, G:0.19, T:0.05
Consensus pattern (30 bp):
TGAAAACAGAAAAAAAGAAAGGAAAAAAAA
Found at i:466167 original size:20 final size:19
Alignment explanation
Indices: 466129--466167 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
466119 ATTAGTATTT
* *
466129 ATATTATTTTTTATTTAAA
1 ATATTATTATTTATATAAA
466148 ATATTATATATTTATATAAA
1 ATATTAT-TATTTATATAAA
466168 TTTTTTACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTATTATTTATATAAA
Found at i:468249 original size:24 final size:24
Alignment explanation
Indices: 468222--468298 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 24
468212 CTTTTTTAAA
*
468222 TAAATTATTAAAATAATATTAATT
1 TAAATTATTAAAATATTATTAATT
*
468246 TAAAAAATTATTAAAATATTATTATTT
1 T---AAATTATTAAAATATTATTAATT
* * *
468273 TAACTTATGAAAA-ATTATTAAAT
1 TAAATTATTAAAATATTATTAATT
468296 TAA
1 TAA
468299 TTGATGTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
23 11 0.25
24 11 0.25
27 22 0.50
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (24 bp):
TAAATTATTAAAATATTATTAATT
Found at i:468253 original size:27 final size:28
Alignment explanation
Indices: 468216--468275 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
468206 GCTATTCTTT
468216 TTTAAATAAATTATTAAAATAATATTAA
1 TTTAAATAAATTATTAAAATAATATTAA
* *
468244 TTTAAA-AAATTATTAAAATATTATTAT
1 TTTAAATAAATTATTAAAATAATATTAA
468271 TTTAA
1 TTTAA
468276 CTTATGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 24 0.80
28 6 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTAAATAAATTATTAAAATAATATTAA
Found at i:468298 original size:23 final size:24
Alignment explanation
Indices: 468253--468298 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
468243 ATTTAAAAAA
* **
468253 TTATTAAAATATTATTATTTTAAC
1 TTATGAAAATATTATTAAATTAAC
468277 TTATGAAAA-ATTATTAAATTAA
1 TTATGAAAATATTATTAAATTAA
468299 TTGATGTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TTATGAAAATATTATTAAATTAAC
Found at i:468809 original size:18 final size:15
Alignment explanation
Indices: 468766--468803 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
468756 ACAATAATAA
468766 TATTTT-AA-TAATT
1 TATTTTAAATTAATT
468779 TATTTTAAATTAATAT
1 TATTTTAAATTAAT-T
468795 TATTTTAAA
1 TATTTTAAA
468804 AATTAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 2 0.09
15 4 0.18
16 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTTAAATTAATT
Found at i:474651 original size:2 final size:2
Alignment explanation
Indices: 474644--474676 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
474634 TTTATGTTGT
474644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
474677 TCATTTTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:475260 original size:11 final size:11
Alignment explanation
Indices: 475221--475269 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
475211 TTAAAGTTTT
*
475221 AATAAAAGAAAA
1 AATAAAA-AATA
* *
475233 AATATAAAATT
1 AATAAAAAATA
*
475244 ATTAAAAAATA
1 AATAAAAAATA
475255 AATAAAAAATA
1 AATAAAAAATA
475266 AATA
1 AATA
475270 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
11 24 0.80
12 6 0.20
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (11 bp):
AATAAAAAATA
Found at i:478143 original size:2 final size:2
Alignment explanation
Indices: 478138--478166 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
478128 TAAATATATA
478138 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
478167 ACTTGAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:478763 original size:25 final size:24
Alignment explanation
Indices: 478733--478806 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
478723 GAAATTAAAA
478733 TTTAATGATTATAATTTATTATATT
1 TTTAAT-ATTATAATTTATTATATT
*
478758 TTTAATAATT-TATATTTA-TATAAAT
1 TTTAAT-ATTATA-ATTTATTAT-ATT
* *
478783 TTTAATATAATAATTAATTTATAT
1 TTTAATATTATAATTTA-TTATAT
478807 AAATTTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
24 11 0.28
25 25 0.64
26 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (24 bp):
TTTAATATTATAATTTATTATATT
Found at i:478807 original size:28 final size:30
Alignment explanation
Indices: 478760--478843 Score: 104
Period size: 29 Copynumber: 2.9 Consensus size: 30
478750 ATTATATTTT
*
478760 TAATAATTTATATTTATATAAA-TTTTAATA
1 TAATAA-TTATATTTATATAAATTTTTAAAA
478790 TAATAATTA-ATTTATATAAATTTTTAAAA
1 TAATAATTATATTTATATAAATTTTTAAAA
* *
478819 TATTAA-TATATTTATAT-TATTTTTA
1 TAATAATTATATTTATATAAATTTTTA
478844 TTTTTTTAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
28 20 0.41
29 23 0.47
30 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TAATAATTATATTTATATAAATTTTTAAAA
Found at i:478825 original size:29 final size:28
Alignment explanation
Indices: 478743--478843 Score: 97
Period size: 28 Copynumber: 3.7 Consensus size: 28
478733 TTTAATGATT
*
478743 ATAATTTAT-TATATTTTTAATAAT-TT-
1 ATAATTTATATAAATTTTTAA-AATATTA
* *
478769 AT-ATTTATATAAA-TTTTAATATAATA
1 ATAATTTATATAAATTTTTAAAATATTA
478795 ATTAATTTATATAAATTTTTAAAATATTA
1 A-TAATTTATATAAATTTTTAAAATATTA
*
478824 ATATATTTATAT-TATTTTTA
1 ATA-ATTTATATAAATTTTTA
478844 TTTTTTTAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
24 2 0.03
25 13 0.21
26 6 0.10
27 1 0.02
28 20 0.32
29 20 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
ATAATTTATATAAATTTTTAAAATATTA
Found at i:478859 original size:23 final size:24
Alignment explanation
Indices: 478833--478877 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
478823 AATATATTTA
* *
478833 TATTATTTTTAT-TTTTTTAATCT
1 TATTATGTTTATATTATTTAATCT
478856 TATTATGTTTATATTATTTAAT
1 TATTATGTTTATATTATTTAAT
478878 TATACTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (24 bp):
TATTATGTTTATATTATTTAATCT
Found at i:479315 original size:16 final size:17
Alignment explanation
Indices: 479279--479316 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
479269 AAAATTTTTT
* *
479279 AATTTTTTGTAAATTAT
1 AATTTTTTGTAAATAAA
479296 AATTTTTTG-AAATAAA
1 AATTTTTTGTAAATAAA
479312 AATTT
1 AATTT
479317 GTTAAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
AATTTTTTGTAAATAAA
Found at i:479637 original size:20 final size:20
Alignment explanation
Indices: 479601--479638 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
479591 TAATGATATT
*
479601 AAATAATTATTTTTTTAATA
1 AAATAATTATTTATTTAATA
479621 AAATAATT-TTATATTTAA
1 AAATAATTATT-TATTTAA
479639 ATTTTAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATAATTATTTATTTAATA
Found at i:479836 original size:2 final size:2
Alignment explanation
Indices: 479829--479855 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
479819 CCTGAGCCAA
479829 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 A
479856 AAATTAGCTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:480099 original size:2 final size:2
Alignment explanation
Indices: 480092--480129 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
480082 TGAAGGTATC
480092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
480130 CGACAACCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:480343 original size:22 final size:22
Alignment explanation
Indices: 480266--480344 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 22
480256 TATATATCGG
*
480266 CAACCAATTAAAATAAGTGAAC
1 CAACCAATTAAAATAAATGAAC
*
480288 CAACCAAAGTCTAAAAGTATATAT-AGC
1 CAACC-AA-T-TAAAA-TA-A-ATGAAC
*
480315 CAAACCAATTAAAATAAATGATC
1 C-AACCAATTAAAATAAATGAAC
480338 CAACCAA
1 CAACCAA
480345 AGTTGACAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
22 13 0.28
23 6 0.13
24 3 0.07
25 10 0.22
26 3 0.07
27 6 0.13
28 5 0.11
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.19
Consensus pattern (22 bp):
CAACCAATTAAAATAAATGAAC
Found at i:480489 original size:15 final size:15
Alignment explanation
Indices: 480469--480502 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
480459 TTTTTGAACT
*
480469 TTGTGAACTGAAAGA
1 TTGTGAACTGAAAAA
480484 TTGTGAACTGAAAAA
1 TTGTGAACTGAAAAA
480499 TTGT
1 TTGT
480503 AAAGATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (15 bp):
TTGTGAACTGAAAAA
Found at i:480589 original size:39 final size:40
Alignment explanation
Indices: 480540--480621 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 40
480530 TTTTTTTAAC
480540 TTTGTGAACTGAAAAATTGTAAGGTTATGGGGTCT-TTTT
1 TTTGTGAACTGAAAAATTGTAAGGTTATGGGGTCTATTTT
480579 TTTGTGAACTGAAAAATTGTAAGGTTATGGGGTCTATTTT
1 TTTGTGAACTGAAAAATTGTAAGGTTATGGGGTCTATTTT
480619 TTT
1 TTT
480622 AAGTACGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 35 0.83
40 7 0.17
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (40 bp):
TTTGTGAACTGAAAAATTGTAAGGTTATGGGGTCTATTTT
Found at i:480697 original size:27 final size:26
Alignment explanation
Indices: 480658--480710 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
480648 ATTATTTATA
* *
480658 ATTTTTTTAATTTTAATTTTAAATAT
1 ATTTTTATAATTTTAATTATAAATAT
*
480684 ATTTTTATATATTTTTATTATAAATAT
1 ATTTTTATA-ATTTTAATTATAAATAT
480711 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
ATTTTTATAATTTTAATTATAAATAT
Found at i:481453 original size:16 final size:16
Alignment explanation
Indices: 481414--481454 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
481404 TAAAAAATAA
481414 ATAATTTATTTTATTTG
1 ATAATTTA-TTTATTTG
*
481431 -TATTTTATTTATTTG
1 ATAATTTATTTATTTG
481446 ATAATTTAT
1 ATAATTTAT
481455 ATGTGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (16 bp):
ATAATTTATTTATTTG
Found at i:482204 original size:17 final size:18
Alignment explanation
Indices: 482155--482204 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
482145 AATTAGTCAC
*
482155 TAAAATAACA-TAAAAAT
1 TAAAATAACATTAATAAT
* *
482172 TAAATTAATATT-ATAAT
1 TAAAATAACATTAATAAT
482189 TAAAATAA-ATTAATAA
1 TAAAATAACATTAATAA
482205 ATATATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 3 0.11
17 23 0.85
18 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAATAACATTAATAAT
Found at i:483702 original size:118 final size:118
Alignment explanation
Indices: 483566--483783 Score: 316
Period size: 118 Copynumber: 1.8 Consensus size: 118
483556 TTTAAAATTC
* *
483566 TAATTTTTCATTAATCTTAAAAAGT-AAAAA-ATAAATATTAATCTAA-TTTAGATTTTAATGTA
1 TAATTTTTCATTAATCTTAAAAAGTGAAAAAGAT-AA-ATTAATCTAATTTTACATATTAAT-TA
*
483628 AATTTCGATTAACATACAGTTTATTAATTTTAATTATTTATATAATTTTAGAGTTT
63 AATTTCGATTAACATACACTTTATTAATTTTAATTATTTATATAATTTTAGAGTTT
* * * *
483684 TAATTTTTTATTATTCTTAAAAAGTGAAAAAGATAAATTACTGTAATTTTACATATTAATTAAAT
1 TAATTTTTCATTAATCTTAAAAAGTGAAAAAGATAAATTAATCTAATTTTACATATTAATTAAAT
*
483749 TTTGATTAACATACACTTTATTAATTTTAATTATT
66 TTCGATTAACATACACTTTATTAATTTTAATTATT
483784 CATAGAGTAA
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
118 69 0.78
119 18 0.20
120 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (118 bp):
TAATTTTTCATTAATCTTAAAAAGTGAAAAAGATAAATTAATCTAATTTTACATATTAATTAAAT
TTCGATTAACATACACTTTATTAATTTTAATTATTTATATAATTTTAGAGTTT
Found at i:483910 original size:12 final size:12
Alignment explanation
Indices: 483867--483918 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
483857 AATTTTAATA
483867 TTTTTATCAAAAT
1 TTTTTAT-AAAAT
*
483880 TTTTTAAAAAAT
1 TTTTTATAAAAT
* *
483892 TTATTATAATAT
1 TTTTTATAAAAT
*
483904 TTTTTATATAAT
1 TTTTTATAAAAT
483916 TTT
1 TTT
483919 AACAACTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 26 0.81
13 6 0.19
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTTATAAAAT
Found at i:487347 original size:24 final size:22
Alignment explanation
Indices: 487320--487397 Score: 79
Period size: 24 Copynumber: 3.5 Consensus size: 22
487310 ATCATTTGAT
*
487320 AAATTTAAAAATTTATATTTTTTA
1 AAATTTAAAAATTTATA--TATTA
** *
487344 AAATAAAAAAAATTATATATTA
1 AAATTTAAAAATTTATATATTA
*
487366 AAATTT-AAAATTTA-AAATTA
1 AAATTTAAAAATTTATATATTA
487386 AAATTTAAAAAT
1 AAATTTAAAAAT
487398 CTTAAAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
20 11 0.24
21 12 0.27
22 8 0.18
24 14 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATTTAAAAATTTATATATTA
Found at i:487373 original size:7 final size:7
Alignment explanation
Indices: 487363--487395 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
487353 AAATTATATA
487363 TTAAAAT
1 TTAAAAT
487370 TTAAAAT
1 TTAAAAT
487377 TTAAAA-
1 TTAAAAT
487383 TTAAAAT
1 TTAAAAT
487390 TTAAAA
1 TTAAAA
487396 ATCTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TTAAAAT
Found at i:487386 original size:13 final size:14
Alignment explanation
Indices: 487363--487395 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
487353 AAATTATATA
487363 TTAAAATTTAAAAT
1 TTAAAATTTAAAAT
487377 TTAAAA-TTAAAAT
1 TTAAAATTTAAAAT
487390 TTAAAA
1 TTAAAA
487396 ATCTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAAATTTAAAAT
Found at i:490912 original size:2 final size:2
Alignment explanation
Indices: 490905--490950 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
490895 ATTTTTCTGC
490905 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
490947 CT CT
1 CT CT
490951 TTTAGATCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:492770 original size:28 final size:28
Alignment explanation
Indices: 492716--492778 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
492706 TTAATAAAAG
*
492716 AAAAAAATATAAAATTATTAAAGATTAA
1 AAAAAAATATAAAATTATTAAAAATTAA
* *
492744 ATAAAAATA-AAAATTTTTAAAAAATTAA
1 AAAAAAATATAAAATTATT-AAAAATTAA
492772 AAAAAAA
1 AAAAAAA
492779 AATTGCGAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAAAAATATAAAATTATTAAAAATTAA
Found at i:494023 original size:27 final size:27
Alignment explanation
Indices: 493991--494045 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
493981 AGAATAAAGA
493991 GATTAATTTAATTTCAGAAGAATGAAT
1 GATTAATTTAATTTCAGAAGAATGAAT
*
494018 GATTAATTTAATTTCAGAATAATGAAT
1 GATTAATTTAATTTCAGAAGAATGAAT
494045 G
1 G
494046 TTCAGTGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.38
Consensus pattern (27 bp):
GATTAATTTAATTTCAGAAGAATGAAT
Found at i:494113 original size:6 final size:6
Alignment explanation
Indices: 494102--494128 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
494092 GTTCCGGAGT
494102 ACCATA ACCATA ACCATA ACCATA ACC
1 ACCATA ACCATA ACCATA ACCATA ACC
494129 TGAGTTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCATA
Found at i:496039 original size:17 final size:17
Alignment explanation
Indices: 496019--496072 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 17
496009 ATTTTTTAAT
496019 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
496036 ATTTTA-ATATA-ATTAA
1 ATTTTATATTTATA-TAA
*
496052 A-ATT-TATTTATATAA
1 ATTTTATATTTATATAA
496067 ATTTTA
1 ATTTTA
496073 AAATATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
15 11 0.39
16 11 0.39
17 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:496131 original size:28 final size:31
Alignment explanation
Indices: 496076--496142 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
496066 AATTTTAAAA
*
496076 TATTAATATATTCATATTACTTTTTTAT-CT
1 TATTAATATATTCATATTACTTTATTATACT
496106 TATTAATAT-TT-ATATTA-TTTAATTATACT
1 TATTAATATATTCATATTACTTT-ATTATACT
496135 TATCTAAT
1 TAT-TAAT
496143 GTTATCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 10 0.30
29 7 0.21
30 13 0.39
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.58
Consensus pattern (31 bp):
TATTAATATATTCATATTACTTTATTATACT
Found at i:496536 original size:16 final size:17
Alignment explanation
Indices: 496510--496552 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
496500 ATAAATTTAT
496510 ATAATTATTTTTAA-AAA
1 ATAA-TATTTTTAATAAA
496527 ATAATA-TTTTAATAAA
1 ATAATATTTTTAATAAA
*
496543 ATAAAATTTT
1 ATAATATTTT
496553 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 10 0.43
17 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAATATTTTTAATAAA
Found at i:496553 original size:16 final size:16
Alignment explanation
Indices: 496518--496555 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
496508 ATATAATTAT
*
496518 TTTTAA-AAAATAATA
1 TTTTAATAAAATAAAA
496533 TTTTAATAAAATAAAA
1 TTTTAATAAAATAAAA
496549 TTTTAAT
1 TTTTAAT
496556 TTTTTTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTTAATAAAATAAAA
Found at i:497463 original size:2 final size:2
Alignment explanation
Indices: 497456--497481 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
497446 TAAAAGTATC
497456 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
497482 TTTAATTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:498128 original size:57 final size:56
Alignment explanation
Indices: 498040--498154 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 56
498030 ATTCTTTTCT
* ** *
498040 TTCTTTTTCAATTCTCATTTCTACACTATTTTTATTTTATGTTTTTTTCCCACATCA
1 TTCTTTTTCAATTCACATTTCTACACTATTTTTATTCAATG-TTTCTTCCCACATCA
498097 TTCTTTTTCAATTCACATTTCTACACTATTTTTATTCAATGTTTCTTCCCACATCA
1 TTCTTTTTCAATTCACATTTCTACACTATTTTTATTCAATGTTTCTTCCCACATCA
498153 TT
1 TT
498155 GGGTGACGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
56 16 0.30
57 38 0.70
ACGTcount: A:0.21, C:0.23, G:0.02, T:0.55
Consensus pattern (56 bp):
TTCTTTTTCAATTCACATTTCTACACTATTTTTATTCAATGTTTCTTCCCACATCA
Found at i:499197 original size:33 final size:33
Alignment explanation
Indices: 499155--499220 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
499145 AGATAATTTT
499155 TTACATTATACTTTATAACTTAAGCATTTGAAA
1 TTACATTATACTTTATAACTTAAGCATTTGAAA
499188 TTACATTATACTTTATAACTTAAGCATTTGAAA
1 TTACATTATACTTTATAACTTAAGCATTTGAAA
499221 ATCAGAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (33 bp):
TTACATTATACTTTATAACTTAAGCATTTGAAA
Found at i:508768 original size:31 final size:29
Alignment explanation
Indices: 508733--508807 Score: 77
Period size: 31 Copynumber: 2.7 Consensus size: 29
508723 ATAACATGAA
508733 AATTATATAAAATATAATAATATATAAAAAT
1 AATTATATAAAATAT-A-AATATATAAAAAT
** *
508764 AATTATATGTAATATAAATATAT--TAA-
1 AATTATATAAAATATAAATATATAAAAAT
508790 AATT-TATAAAATATAAAT
1 AATTATATAAAATATAAAT
508808 TTATTAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 12 0.31
26 4 0.10
27 2 0.05
29 7 0.18
30 1 0.03
31 13 0.33
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (29 bp):
AATTATATAAAATATAAATATATAAAAAT
Found at i:508819 original size:16 final size:16
Alignment explanation
Indices: 508776--508836 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 16
508766 TTATATGTAA
508776 TATAAATATATTAAAATT
1 TATAAA-ATATT-AAATT
508794 TATAAAATA-TAAATT
1 TATAAAATATTAAATT
*
508809 TATTAATATATTAAATTT
1 TA-TAAAATATTAAA-TT
508827 TATATAAATA
1 TATA-AAATA
508837 ATATCATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 7 0.19
16 7 0.19
17 9 0.24
18 14 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAAAATATTAAATT
Found at i:508825 original size:17 final size:16
Alignment explanation
Indices: 508780--508826 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
508770 ATGTAATATA
508780 AATATATTAAAATTTAT
1 AATATATT-AAATTTAT
*
508797 AAAATA-TAAATTTATT
1 AATATATTAAATTTA-T
508813 AATATATTAAATTT
1 AATATATTAAATTT
508827 TATATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 7 0.27
16 7 0.27
17 12 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATATTAAATTTAT
Found at i:512589 original size:2 final size:2
Alignment explanation
Indices: 512582--512607 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
512572 TTATTATTTC
512582 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
512608 GTCATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:513153 original size:17 final size:17
Alignment explanation
Indices: 513131--513164 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
513121 GAAAACAAAA
513131 AAAATAATTTTAATTTT
1 AAAATAATTTTAATTTT
*
513148 AAAATAATTTTAGTTTT
1 AAAATAATTTTAATTTT
513165 TTATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AAAATAATTTTAATTTT
Found at i:518778 original size:12 final size:12
Alignment explanation
Indices: 518761--518789 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
518751 CTGAGTAATA
518761 AATAAGATTTTT
1 AATAAGATTTTT
518773 AATAAGATTTTT
1 AATAAGATTTTT
518785 AATAA
1 AATAA
518790 TTCAAATCAA
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:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (12 bp):
AATAAGATTTTT
Found at i:519801 original size:19 final size:19
Alignment explanation
Indices: 519753--519801 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
519743 TACAAAATAA
*
519753 AAATAATATAAATTTGATAT
1 AAATAA-ATTAATTTGATAT
*
519773 AAATATATTAATTT-ATAT
1 AAATAAATTAATTTGATAT
519791 AATATAAATTA
1 AA-ATAAATTA
519802 TAAACTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAATAAATTAATTTGATAT
Found at i:520984 original size:13 final size:12
Alignment explanation
Indices: 520957--521008 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
520947 GTTAAATTTA
*
520957 ATAATTTTAAAT
1 ATAATTATAAAT
520969 ATAATTATATAAT
1 ATAATTATA-AAT
520982 ATAA-TATAAAT
1 ATAATTATAAAT
* *
520993 AAAAATATTAAAT
1 ATAATTA-TAAAT
521006 ATA
1 ATA
521009 TAGCACAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 6 0.18
12 14 0.41
13 14 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATTATAAAT
Found at i:521035 original size:13 final size:13
Alignment explanation
Indices: 521018--521065 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
521008 ATAGCACAAA
521018 TATATATTAAAAT
1 TATATATTAAAAT
* *
521031 AATATAATAAATTAT
1 TATATATTAAA--AT
521046 TATCATATTAAAAT
1 TAT-ATATTAAAAT
521060 TATATA
1 TATATA
521066 AATTATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 12 0.43
14 5 0.18
15 4 0.14
16 7 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATATTAAAAT
Found at i:521042 original size:24 final size:24
Alignment explanation
Indices: 520964--521042 Score: 58
Period size: 24 Copynumber: 3.2 Consensus size: 24
520954 TTAATAATTT
*
520964 TAAATATAATTATATAATATAATATAAA
1 TAAATAT-A-TAT-TAAAATAATAT-AA
520992 TAAA-A-ATATT-AAAT-ATATAGCA
1 TAAATATATATTAAAATAATATA--A
*
521014 CAAATATATATTAAAATAATATAA
1 TAAATATATATTAAAATAATATAA
521038 TAAAT
1 TAAAT
521043 TATTATCATA
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
20 1 0.02
21 4 0.10
22 7 0.17
23 2 0.05
24 13 0.31
25 5 0.12
26 5 0.12
27 1 0.02
28 4 0.10
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (24 bp):
TAAATATATATTAAAATAATATAA
Found at i:522288 original size:25 final size:24
Alignment explanation
Indices: 522241--522325 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 24
522231 AGATTGAAAT
* *
522241 TAAAATTTAATGATTATAATTAT-
1 TAAATTTTAATAATTATAATTATA
* *
522264 TATATTTTTAATAATTTATATTTATA
1 TA-AATTTTAATAA-TTATAATTATA
*
522290 TAAATTTTAATATAATAATTAATTTATA
1 TAAATTTT-A-ATAATTA-TAA-TTATA
522318 TAAATTTT
1 TAAATTTT
522326 TTAAAATATT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
23 2 0.04
24 8 0.17
25 14 0.29
26 5 0.10
27 6 0.12
28 13 0.27
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (24 bp):
TAAATTTTAATAATTATAATTATA
Found at i:522291 original size:24 final size:25
Alignment explanation
Indices: 522241--522310 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
522231 AGATTGAAAT
* *
522241 TAAAATTTAATGATTATAATTATTA
1 TAAATTTTAATAATTATAATTATTA
* *
522266 T-ATTTTTAATAATTTATATTTA-TA
1 TAAATTTTAATAA-TTATAATTATTA
*
522290 TAAATTTTAAT-ATAATAATTA
1 TAAATTTTAATAATTATAATTA
522311 ATTTATATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
23 7 0.19
24 12 0.33
25 17 0.47
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (25 bp):
TAAATTTTAATAATTATAATTATTA
Found at i:522328 original size:30 final size:29
Alignment explanation
Indices: 522272--522344 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
522262 ATTATATTTT
*
522272 TAATAATTTATATTTATATAAATTTTAATA
1 TAATAA-TTATATTTATATAAATTTTAAAA
522302 TAATAATTA-ATTTATATAAATTTTTTAAAA
1 TAATAATTATATTTATATAAA--TTTTAAAA
*
522332 TATTAA-TATATTT
1 TAATAATTATATTT
522345 TTATTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 11 0.29
29 5 0.13
30 22 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TAATAATTATATTTATATAAATTTTAAAA
Found at i:522829 original size:18 final size:19
Alignment explanation
Indices: 522793--522830 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
522783 AAATTTTTAA
* *
522793 TTTTTTGTAAATTATAATT
1 TTTTTTGTAAATAAAAATT
522812 TTTTTTG-AAATAAAAATT
1 TTTTTTGTAAATAAAAATT
522830 T
1 T
522831 GTTAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTTTGTAAATAAAAATT
Found at i:522911 original size:2 final size:2
Alignment explanation
Indices: 522904--522929 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
522894 GTGGAACTCC
522904 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
522930 TAATAGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:523118 original size:20 final size:20
Alignment explanation
Indices: 523082--523119 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
523072 TAATGATATT
*
523082 AAATAATTATTTTTTTAATA
1 AAATAATTATTTATTTAATA
523102 AAATAATT-TTATATTTAA
1 AAATAATTATT-TATTTAA
523120 ATTTTAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATAATTATTTATTTAATA
Found at i:524139 original size:25 final size:27
Alignment explanation
Indices: 524111--524162 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
524101 ATTATTTATA
*
524111 ATTTTT-TA-ATTTTAATTTTAAATAT
1 ATTTTTATATATTTTAATTATAAATAT
*
524136 ATTTTTATATATTTTTATTATAAATAT
1 ATTTTTATATATTTTAATTATAAATAT
524163 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 2 0.09
27 15 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTTTATATATTTTAATTATAAATAT
Found at i:524434 original size:2 final size:2
Alignment explanation
Indices: 524427--524458 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
524417 ATAAAAATTA
524427 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
524459 TTTCAAACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:524932 original size:16 final size:17
Alignment explanation
Indices: 524893--524948 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 17
524883 TAAAAAATAA
*
524893 ATAAGTTATGTTATTTG
1 ATAATTTATGTTATTTG
*
524910 -TATTTTAT-TTATTTG
1 ATAATTTATGTTATTTG
524925 ATAATTTATATGTGTATTTG
1 ATAA-TT-TATGT-TATTTG
524945 ATAA
1 ATAA
524949 AAATTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 7 0.23
16 8 0.26
17 2 0.06
18 3 0.10
19 1 0.03
20 10 0.32
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (17 bp):
ATAATTTATGTTATTTG
Found at i:527170 original size:119 final size:118
Alignment explanation
Indices: 527033--527251 Score: 325
Period size: 119 Copynumber: 1.8 Consensus size: 118
527023 TTTAAAATTC
* *
527033 TAATTTTTCATTAATCTTAAAAAGT-AAAAA-ATAAATATTAATCTAATTTTAGATTTTAATGTA
1 TAATTTTTCATTAATCTTAAAAAGTGAAAAAGAT-AA-ATTAATCTAATTTTACATATTAAT-TA
*
527096 AATTTCGATTAACATACAGTTTATTAATTTTAATTATTTATATAATTTTAGAGTTT
63 AATTTCGATTAACATACACTTTATTAATTTTAATTATTTATATAATTTTAGAGTTT
* * * *
527152 TAATTTTTTATTATTCTTAAAAAGTGAAAAAGATAAATTACTGTAATTTTACATATTAATTAAAT
1 TAATTTTTCATTAATCTTAAAAAGTGAAAAAGATAAATTAATCTAATTTTACATATTAATTAAAT
*
527217 TTTGATTAACATACACTTTATTAATTTTAATTATT
66 TTCGATTAACATACACTTTATTAATTTTAATTATT
527252 CATAGAGTAA
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
118 38 0.42
119 43 0.48
120 7 0.08
121 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (118 bp):
TAATTTTTCATTAATCTTAAAAAGTGAAAAAGATAAATTAATCTAATTTTACATATTAATTAAAT
TTCGATTAACATACACTTTATTAATTTTAATTATTTATATAATTTTAGAGTTT
Found at i:527378 original size:12 final size:12
Alignment explanation
Indices: 527335--527386 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
527325 AATTTTAATA
527335 TTTTTATCAAAAT
1 TTTTTAT-AAAAT
*
527348 TTTTTAAAAAAT
1 TTTTTATAAAAT
* *
527360 TTATTATAATAT
1 TTTTTATAAAAT
*
527372 TTTTTATATAAT
1 TTTTTATAAAAT
527384 TTT
1 TTT
527387 AACAACTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 26 0.81
13 6 0.19
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTTATAAAAT
Found at i:530812 original size:24 final size:22
Alignment explanation
Indices: 530785--530862 Score: 79
Period size: 24 Copynumber: 3.5 Consensus size: 22
530775 ATTATTTGAT
*
530785 AAATTTAAAAATTTATATTTTTTA
1 AAATTTAAAAATTTATA--TATTA
** *
530809 AAATAAAAAAAATTATATATTA
1 AAATTTAAAAATTTATATATTA
*
530831 AAATTT-AAAATTTA-AAATTA
1 AAATTTAAAAATTTATATATTA
530851 AAATTTAAAAAT
1 AAATTTAAAAAT
530863 CTTAAAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
20 11 0.24
21 12 0.27
22 8 0.18
24 14 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATTTAAAAATTTATATATTA
Found at i:530838 original size:7 final size:7
Alignment explanation
Indices: 530828--530860 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
530818 AAATTATATA
530828 TTAAAAT
1 TTAAAAT
530835 TTAAAAT
1 TTAAAAT
530842 TTAAAA-
1 TTAAAAT
530848 TTAAAAT
1 TTAAAAT
530855 TTAAAA
1 TTAAAA
530861 ATCTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TTAAAAT
Found at i:530851 original size:13 final size:14
Alignment explanation
Indices: 530828--530860 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
530818 AAATTATATA
530828 TTAAAATTTAAAAT
1 TTAAAATTTAAAAT
530842 TTAAAA-TTAAAAT
1 TTAAAATTTAAAAT
530855 TTAAAA
1 TTAAAA
530861 ATCTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAAATTTAAAAT
Found at i:534382 original size:2 final size:2
Alignment explanation
Indices: 534375--534418 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
534365 ATTTTTCTGC
534375 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
534417 CT
1 CT
534419 TTTAGATCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:536233 original size:28 final size:27
Alignment explanation
Indices: 536177--536240 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
536167 AAAGTTTTAA
*
536177 TAAAAAAAATATAAAATTATTAAAGAT
1 TAAAAAAAATATAAAATTATTAAAAAT
*
536204 TAAATAAAAATA-AAAATTTTTAAAAAAT
1 TAAA-AAAAATATAAAATTATT-AAAAAT
536232 TAAAAAAAA
1 TAAAAAAAA
536241 ATTGCGAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 17 0.52
28 16 0.48
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (27 bp):
TAAAAAAAATATAAAATTATTAAAAAT
Found at i:536241 original size:28 final size:28
Alignment explanation
Indices: 536178--536242 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
536168 AAGTTTTAAT
*
536178 AAAAAAAATATAAAATTATTAAAGATTA
1 AAAAAAAATATAAAATTATTAAAAATTA
* *
536206 AATAAAAATA-AAAATTTTTAAAAAATTA
1 AAAAAAAATATAAAATTATT-AAAAATTA
536234 AAAAAAAAT
1 AAAAAAAAT
536243 TGCGAAGGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 8 0.25
28 24 0.75
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (28 bp):
AAAAAAAATATAAAATTATTAAAAATTA
Found at i:537475 original size:27 final size:27
Alignment explanation
Indices: 537443--537497 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
537433 AGAATAAAGA
537443 GATTAATTTAATTTCAGAAGAATGAAT
1 GATTAATTTAATTTCAGAAGAATGAAT
*
537470 GATTAATTTAATTTCAGAATAATGAAT
1 GATTAATTTAATTTCAGAAGAATGAAT
537497 G
1 G
537498 TTCAGTGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.38
Consensus pattern (27 bp):
GATTAATTTAATTTCAGAAGAATGAAT
Done.