Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 126 of 325
Found at i:39342124 original size:29 final size:29
Alignment explanation
Indices: 39342091--39342150 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
39342081 CACATTCATA
39342091 AAGCAGCAATAACATTATGTATATATATG
1 AAGCAGCAATAACATTATGTATATATATG
39342120 AAGCAGCAATAACATTATGTATATATATG
1 AAGCAGCAATAACATTATGTATATATATG
39342149 AA
1 AA
39342151 CAATTCTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (29 bp):
AAGCAGCAATAACATTATGTATATATATG
Found at i:39342424 original size:9 final size:9
Alignment explanation
Indices: 39342410--39342436 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
39342400 CCAAAACTTG
39342410 CAATTTAAC
1 CAATTTAAC
39342419 CAATTTAAC
1 CAATTTAAC
39342428 CAATTTAAC
1 CAATTTAAC
39342437 TAAAATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (9 bp):
CAATTTAAC
Found at i:39348412 original size:57 final size:58
Alignment explanation
Indices: 39348317--39348452 Score: 143
Period size: 57 Copynumber: 2.4 Consensus size: 58
39348307 TTTTCGTATG
* * *
39348317 CTTAAATCTAATATTACTTATTTTATTTATTCATTTATTGT-TTTA-TATTTTAAAATA
1 CTTAAATTTAATATTACTTATTTTATCTATTCACTTATT-TATTTATTATTTTAAAATA
* * * *
39348374 CTTAAATTTAATATTATTTATTTT-TCCTATTTACTTATTTATTTATTATTTTTATATA
1 CTTAAATTTAATATTACTTATTTTAT-CTATTCACTTATTTATTTATTATTTTAAAATA
* * *
39348432 TTTAAATTTGATGTTACTTAT
1 CTTAAATTTAATATTACTTAT
39348453 ATTTCTCTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
56 2 0.03
57 36 0.55
58 27 0.42
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (58 bp):
CTTAAATTTAATATTACTTATTTTATCTATTCACTTATTTATTTATTATTTTAAAATA
Found at i:39355014 original size:3 final size:3
Alignment explanation
Indices: 39355006--39355049 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
39354996 GAGCTTTTAG
39355006 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
39355050 GATCACTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39359468 original size:42 final size:41
Alignment explanation
Indices: 39359405--39359508 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 41
39359395 CCAACTTTCT
* * *
39359405 AGACGAGGTTTTACATGTAATCAAATATCGATGCCAGTGTCCT
1 AGAC-AGGTCTTACATGTAATCAAATA-CGATGCCAATGTCCC
* * * *
39359448 AGATAGGTCTTACACGTAATCATATACGATGTCAATGTCCC
1 AGACAGGTCTTACATGTAATCAAATACGATGCCAATGTCCC
39359489 AGACATGGTCTTACATGTAA
1 AGACA-GGTCTTACATGTAA
39359509 ATCTCAAATC
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 16 0.31
42 32 0.63
43 3 0.06
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (41 bp):
AGACAGGTCTTACATGTAATCAAATACGATGCCAATGTCCC
Found at i:39362529 original size:28 final size:28
Alignment explanation
Indices: 39362468--39362532 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
39362458 TCAGTGTACG
* **
39362468 AAATATTGAGAATGGCACTTAATGTGTG
1 AAATATTGAGAATGACACTTAATGTGAA
* *
39362496 AGATATTGAGAATGACACTTAGTGTGAA
1 AAATATTGAGAATGACACTTAATGTGAA
39362524 AAATATTGA
1 AAATATTGA
39362533 ATGATTAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (28 bp):
AAATATTGAGAATGACACTTAATGTGAA
Found at i:39362649 original size:39 final size:39
Alignment explanation
Indices: 39362605--39362865 Score: 305
Period size: 39 Copynumber: 6.7 Consensus size: 39
39362595 GACTTTATAA
*
39362605 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGT
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
** *
39362644 TGGTGTTATATCCGGGCTAAGTCGTGAAGGCATTCATGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* * *
39362683 TGGTGTTATATCCGAGCTAAGTCCCAAAGGCATTCATGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* * * *
39362722 TGGTGTTATATCCGGACGAAGTCTCAAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
*
39362761 TGGTGTTATATCCGGGCT-A-TCCCCGAAGGCATTCGTGT
1 TGGTGTTATATCCGGGCTAAGT-CCCGAAGGCATTCGTGC
* *
39362799 TGGTGTTATATCCAGGCTAAAGTCCC-ACAGGC-TTTGTGC
1 TGGTGTTATATCCGGGCT-AAGTCCCGA-AGGCATTCGTGC
* *
39362838 TGGTATTATATCCGAGCTTAAAGTCCCG
1 TGGTGTTATATCCGGGC-T-AAGTCCCG
39362866 CATGCTTTGT
Statistics
Matches: 191, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
37 1 0.01
38 32 0.17
39 140 0.73
40 17 0.09
41 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (39 bp):
TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
Found at i:39369007 original size:28 final size:28
Alignment explanation
Indices: 39368966--39369045 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 28
39368956 GCAATCAAAT
* * *
39368966 ATGGTACTCAATGTACGAAATATTAAGA
1 ATGGCACTTAATGTGCGAAATATTAAGA
* *
39368994 ATGGCACTTAATGTGCGAGATATTGAGA
1 ATGGCACTTAATGTGCGAAATATTAAGA
* * *
39369022 ATGTCACTTAGTGTGCAAAATATT
1 ATGGCACTTAATGTGCGAAATATT
39369046 GAATGATTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (28 bp):
ATGGCACTTAATGTGCGAAATATTAAGA
Found at i:39369353 original size:40 final size:39
Alignment explanation
Indices: 39369120--39369342 Score: 331
Period size: 39 Copynumber: 5.7 Consensus size: 39
39369110 GACTTTATAA
*
39369120 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGT
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* * *
39369159 TGGTGTTATATCTGGGCTAAGTCCTGAAGGCATTCATGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
*
39369198 TGGTGTTAAATCCGGGCTAAGTCCCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
*
39369237 TGGTGTTATATCCGGGCTAAGCCCCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* *
39369276 TGGTGTTATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGC
1 TGGTGTTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGC
*
39369315 TGGTATTATATCCGGGCTTAAAGTCCCG
1 TGGTGTTATATCCGGGC-T-AAGTCCCG
39369343 CATGCTTTGT
Statistics
Matches: 168, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
39 147 0.88
40 21 0.12
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.30
Consensus pattern (39 bp):
TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
Found at i:39377285 original size:27 final size:27
Alignment explanation
Indices: 39377247--39377302 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
39377237 AACCCGAGCA
39377247 CTAACCCCACTAAATAACTTTATTTTT
1 CTAACCCCACTAAATAACTTTATTTTT
*
39377274 CTAACTCCACTAAATAACTTTATTTTT
1 CTAACCCCACTAAATAACTTTATTTTT
39377301 CT
1 CT
39377303 TTCATTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (27 bp):
CTAACCCCACTAAATAACTTTATTTTT
Found at i:39378444 original size:9 final size:9
Alignment explanation
Indices: 39378432--39378488 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
39378422 TTAATCATTT
39378432 TATTATTAC
1 TATTATTAC
**
39378441 TATTATTTT
1 TATTATTAC
39378450 TATTATTAC
1 TATTATTAC
39378459 TATTATTAC
1 TATTATTAC
** *
39378468 TCCTATTTC
1 TATTATTAC
39378477 T-TTATTAC
1 TATTATTAC
39378485 TATT
1 TATT
39378489 CTATCTTATT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
8 6 0.16
9 32 0.84
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.61
Consensus pattern (9 bp):
TATTATTAC
Found at i:39378452 original size:18 final size:18
Alignment explanation
Indices: 39378429--39378465 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39378419 ATTTTAATCA
39378429 TTTTATTATTACTATTAT
1 TTTTATTATTACTATTAT
39378447 TTTTATTATTACTATTAT
1 TTTTATTATTACTATTAT
39378465 T
1 T
39378466 ACTCCTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATTATTACTATTAT
Found at i:39380072 original size:6 final size:6
Alignment explanation
Indices: 39380063--39380112 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
39380053 TTGCTTTCCC
* * *
39380063 TTTTGT TTTTAT TTTTAT TTTTAC TTTTAA TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
39380111 TT
1 TT
39380113 ACACATTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:39384422 original size:31 final size:31
Alignment explanation
Indices: 39384384--39384446 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
39384374 GTTTATTGAC
39384384 AATATACTAATCTATTCAAAGACAGAATTCG
1 AATATACTAATCTATTCAAAGACAGAATTCG
39384415 AATATACTAATCTATTCAAAGACAGAATTCG
1 AATATACTAATCTATTCAAAGACAGAATTCG
39384446 A
1 A
39384447 GCATGCACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.29
Consensus pattern (31 bp):
AATATACTAATCTATTCAAAGACAGAATTCG
Found at i:39388172 original size:21 final size:21
Alignment explanation
Indices: 39388146--39388322 Score: 126
Period size: 21 Copynumber: 8.4 Consensus size: 21
39388136 AATTCTTGTG
* *
39388146 TGTTCAGCTATTACGAGCTTT
1 TGTTCAACTCTTACGAGCTTT
*
39388167 TGTTCAACTCTT-CTAAG-TTT
1 TGTTCAACTCTTAC-GAGCTTT
* * * *
39388187 CTGTTTAGCTCTTACGAACTTC
1 -TGTTCAACTCTTACGAGCTTT
* *
39388209 TGTTCAACTCTTATGAGTTTT
1 TGTTCAACTCTTACGAGCTTT
* *
39388230 TGTTTAGCTCTTACGAG-TTT
1 TGTTCAACTCTTACGAGCTTT
* *
39388250 CTGTTCAACTCTTACCAGCTTC
1 -TGTTCAACTCTTACGAGCTTT
* * *
39388272 AGTTCAACTCTTATGAGTTTT
1 TGTTCAACTCTTACGAGCTTT
* * *
39388293 TGTTCAGCTCTTACCAGCTTC
1 TGTTCAACTCTTACGAGCTTT
*
39388314 TATTCAACT
1 TGTTCAACT
39388323 TTGAAGCTTC
Statistics
Matches: 116, Mismatches: 34, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
20 7 0.06
21 104 0.90
22 5 0.04
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.45
Consensus pattern (21 bp):
TGTTCAACTCTTACGAGCTTT
Found at i:39388203 original size:42 final size:42
Alignment explanation
Indices: 39388146--39388305 Score: 160
Period size: 42 Copynumber: 3.8 Consensus size: 42
39388136 AATTCTTGTG
* * *
39388146 TGTTCAGCTATTACGAGCTTTTGTTCAACTCTTCTAAGTTTC
1 TGTTTAGCTCTTACGAGCTTTTGTTCAACTCTTATAAGTTTC
* * * *
39388188 TGTTTAGCTCTTACGAACTTCTGTTCAACTCTTATGAGTTTT
1 TGTTTAGCTCTTACGAGCTTTTGTTCAACTCTTATAAGTTTC
** *
39388230 TGTTTAGCTCTTACGAG-TTTCTGTTCAACTCTTACCAGCTTC
1 TGTTTAGCTCTTACGAGCTTT-TGTTCAACTCTTATAAGTTTC
* * * * * *
39388272 AGTTCAACTCTTATGAGTTTTTGTTCAGCTCTTA
1 TGTTTAGCTCTTACGAGCTTTTGTTCAACTCTTA
39388306 CCAGCTTCTA
Statistics
Matches: 98, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.02
42 93 0.95
43 3 0.03
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46
Consensus pattern (42 bp):
TGTTTAGCTCTTACGAGCTTTTGTTCAACTCTTATAAGTTTC
Found at i:39388249 original size:63 final size:63
Alignment explanation
Indices: 39388164--39388322 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 63
39388154 TATTACGAGC
* * * * * *
39388164 TTTTGTTCAACTCTT-CTAAGTTTCTGTTTAGCTCTTACGAACTTCTGTTCAACTCTTATGAGT
1 TTTTGTTCAGCTCTTAC-GAGTTTCTGTTCAACTCTTACCAACTTCAGTTCAACTCTTATGAGT
* *
39388227 TTTTGTTTAGCTCTTACGAGTTTCTGTTCAACTCTTACCAGCTTCAGTTCAACTCTTATGAGT
1 TTTTGTTCAGCTCTTACGAGTTTCTGTTCAACTCTTACCAACTTCAGTTCAACTCTTATGAGT
* * *
39388290 TTTTGTTCAGCTCTTACCAGCTTCTATTCAACT
1 TTTTGTTCAGCTCTTACGAGTTTCTGTTCAACT
39388323 TTGAAGCTTC
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 82 0.99
64 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.46
Consensus pattern (63 bp):
TTTTGTTCAGCTCTTACGAGTTTCTGTTCAACTCTTACCAACTTCAGTTCAACTCTTATGAGT
Found at i:39398778 original size:24 final size:24
Alignment explanation
Indices: 39398746--39398794 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
39398736 GTTTATTAAG
*
39398746 GAAAATTGGAAGATTTACTAAGGT
1 GAAAATTGGAAGATTCACTAAGGT
39398770 GAAAATTGGAAGATTCACTAAGGT
1 GAAAATTGGAAGATTCACTAAGGT
39398794 G
1 G
39398795 TTGCGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.27
Consensus pattern (24 bp):
GAAAATTGGAAGATTCACTAAGGT
Found at i:39403191 original size:17 final size:18
Alignment explanation
Indices: 39403169--39403203 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39403159 GATATGATAC
*
39403169 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
39403186 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
39403204 CAGGGAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:39403500 original size:23 final size:22
Alignment explanation
Indices: 39403457--39403514 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
39403447 AAAAGGTATC
* *
39403457 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
39403478 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
39403501 TGCATATCATATCT
1 TACAAATCATATCT
39403515 AAGATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:39403528 original size:22 final size:19
Alignment explanation
Indices: 39403484--39403531 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
39403474 AGATTACAAA
39403484 ATCATATCTTCTAAGATTG
1 ATCATATCTTCTAAGATTG
39403503 --CATATCATATCTAAGATTG
1 ATCATATC-T-TCTAAGATTG
39403522 TATCATATCT
1 -ATCATATCT
39403532 AAGATTGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
17 6 0.25
18 1 0.04
19 10 0.42
21 1 0.04
22 6 0.25
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (19 bp):
ATCATATCTTCTAAGATTG
Found at i:39403572 original size:36 final size:36
Alignment explanation
Indices: 39403496--39403573 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
39403486 CATATCTTCT
*
39403496 AAGATTGCATATCATATCTAAGATTGTATCATATCT
1 AAGATTGCATATCATATCTAAGATTGTATCATATCG
39403532 AAGATTGCATATCATATCTAAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCTAAGATTG--TATCATATCG
39403568 AAGATT
1 AAGATT
39403574 ATATTTCCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 32 0.82
37 1 0.03
38 6 0.15
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (36 bp):
AAGATTGCATATCATATCTAAGATTGTATCATATCG
Found at i:39403573 original size:17 final size:19
Alignment explanation
Indices: 39403493--39403565 Score: 132
Period size: 19 Copynumber: 3.9 Consensus size: 19
39403483 AATCATATCT
39403493 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39403512 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
39403529 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39403548 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
39403566 TGAAGATTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.33
19 35 0.67
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:39404022 original size:44 final size:45
Alignment explanation
Indices: 39403900--39404038 Score: 208
Period size: 45 Copynumber: 3.1 Consensus size: 45
39403890 GGAAGGCGAT
* *
39403900 ATCTGCTATCTTTGATCAGCTCCCCATCTAATACAAAGACGCCAA
1 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAAAGACGCCAA
* *
39403945 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAAAGACGCCAA
1 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAAAGACGCCAA
* * *
39403990 ATCTGCT-TCTTTAATCTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAAAGACGCCAA
39404034 ATCTG
1 ATCTG
39404039 TCATATTGGA
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
44 38 0.45
45 47 0.55
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.29
Consensus pattern (45 bp):
ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAAAGACGCCAA
Found at i:39404120 original size:92 final size:83
Alignment explanation
Indices: 39404003--39404284 Score: 323
Period size: 78 Copynumber: 3.4 Consensus size: 83
39403993 TGCTTCTTTA
*
39404003 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATATTGGATCTGCTTCAATGTAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGATGCCAAA----TCATCTTGGATCTGCTTCAAT-T---CA-
39404068 ATGAAGGTCAGATCTGCTATGTCTTCG
57 ATGAAGGTCAGATCTGCTATGTCTTCG
39404095 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAA-T--A--AAGGTC
1 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATTCAATGAAGGTC
* *
39404155 AGATCTACTGTGTCTTCG
66 AGATCTGCTATGTCTTCG
* * *
39404173 ATCTGCTCCACGTCTAATATAGAGATGCCAAATCATCTTGGATCTG---C--TTCAATGAAGGTT
1 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATTCAATGAAGGTC
39404233 AGATCTGCTATGTCTTCG
66 AGATCTGCTATGTCTTCG
* * **
39404251 ATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 ATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
39404285 TGTTTCTTCG
Statistics
Matches: 173, Mismatches: 12, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
74 1 0.01
75 1 0.01
76 1 0.01
78 117 0.68
80 1 0.01
86 1 0.01
88 19 0.11
92 32 0.18
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (83 bp):
ATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATTCAATGAAGGTC
AGATCTGCTATGTCTTCG
Found at i:39404200 original size:78 final size:77
Alignment explanation
Indices: 39404071--39404284 Score: 338
Period size: 78 Copynumber: 2.7 Consensus size: 77
39404061 TAAACACATG
*
39404071 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCT-CCCGTCTAATATAGAGATGCCAAATCATCTTGG
39404136 ATCTGCTTCAATA
65 ATCTGCTTCAATA
* *
39404149 AAGGTCAGATCTACTGTGTCTTCGATCTGCTCCACGTCTAATATAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCC-CGTCTAATATAGAGATGCCAAATCATCTTGG
*
39404214 ATCTGCTTCAATG
65 ATCTGCTTCAATA
* * *
39404227 AAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTC-CCGTCTAATATAGAGATGCCAAATC
39404285 TGTTTCTTCG
Statistics
Matches: 125, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
77 2 0.02
78 122 0.98
79 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (77 bp):
AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCGTCTAATATAGAGATGCCAAATCATCTTGGA
TCTGCTTCAATA
Found at i:39412839 original size:17 final size:17
Alignment explanation
Indices: 39412817--39412850 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
39412807 GATATGATAC
39412817 TAAAAT-TATTAAAAAAT
1 TAAAATATA-TAAAAAAT
39412834 TAAAATATATAAAAAAT
1 TAAAATATATAAAAAAT
39412851 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATATATAAAAAAT
Found at i:39413147 original size:23 final size:22
Alignment explanation
Indices: 39413104--39413161 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
39413094 AAAAGGTATC
* *
39413104 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
39413125 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
39413148 TGCATATCATATCT
1 TACAAATCATATCT
39413162 AAGATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:39413164 original size:19 final size:19
Alignment explanation
Indices: 39413140--39413176 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39413130 AATCATATCT
39413140 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
39413159 TCTAAGATTGTATATCAT
1 TCTAAGATTGCATATCAT
39413177 TGAAGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:39413184 original size:17 final size:19
Alignment explanation
Indices: 39413143--39413184 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39413133 CATATCTTCT
*
39413143 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
*
39413162 AAGATTGTATATCAT-T-G
1 AAGATTGCATATCATATCG
39413179 AAGATT
1 AAGATT
39413185 ATATTTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 1 0.05
19 14 0.67
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:39421109 original size:44 final size:43
Alignment explanation
Indices: 39421019--39421133 Score: 101
Period size: 44 Copynumber: 2.6 Consensus size: 43
39421009 CAAAGCCAAC
* * *
39421019 GTCCCAGACGTGGTCTTACATGAAATTCAGTATCGATGCTGAT
1 GTCCCAGACATGGTCTTACACGAAATTCAGAATCGATGCTGAT
* *
39421062 GTCCCAGACATGGTCTTACCCGTAAATTTCA-AATTGATGCCTG-T
1 GTCCCAGACATGGTCTTACACG-AAA-TTCAGAATCGATG-CTGAT
* *
39421106 GTCCCTA-ACACGTTCTTACACGATAATT
1 GTCCC-AGACATGGTCTTACACGA-AATT
39421134 TAGATCAAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
43 22 0.37
44 29 0.49
45 8 0.14
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGAAATTCAGAATCGATGCTGAT
Found at i:39428331 original size:44 final size:42
Alignment explanation
Indices: 39428200--39428358 Score: 133
Period size: 44 Copynumber: 3.7 Consensus size: 42
39428190 CAATGCCAAC
* * * *
39428200 GTCCCAGACGTGGTCTTACATGAAATTCAGTATCGATGCCTCT
1 GTCCCAGACATGGTCTTACACGAAATTCA-AATCGATGCCTAT
* * * * * *
39428243 GTCCTAGACAGGGTCTTATAC-AAGAAT-AGATACGATGCCGAT
1 GTCCCAGACATGGTCTTACACGAA-ATTCAAAT-CGATGCCTAT
39428285 GTCCCAGACATGGTCTTACACGTAAATTTCAAATCGATGCCTAT
1 GTCCCAGACATGGTCTTACACG-AAA-TTCAAATCGATGCCTAT
* * *
39428329 GTCCCTGACACGTTCTTACACGATAATTCA
1 GTCCCAGACATGGTCTTACACGA-AATTCA
39428359 GATCAATACC
Statistics
Matches: 91, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
41 2 0.02
42 29 0.32
43 24 0.26
44 33 0.36
45 3 0.03
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGAAATTCAAATCGATGCCTAT
Found at i:39429840 original size:68 final size:67
Alignment explanation
Indices: 39429761--39429968 Score: 189
Period size: 67 Copynumber: 3.1 Consensus size: 67
39429751 CATCACGTGT
*
39429761 ACAAGAAAGCTACGAGATATTATAATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTACGAGATA-TATAATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
39429826 TAG
65 TAG
* ** * * * * *
39429829 ACAAGAGAGCTACG-G-GATAT-ATGTAGCTAGGTCGCATGCATGGTTCCAAGTGAAGGACACCA
1 ACAAGAGAGCTACGAGATATATAATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCA
39429891 TGTAG
63 TGTAG
* * * * *
39429896 ACAAGAGAGCTACGAGATA-A-ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT
1 ACAAGAGAGCTACGAGATATATAATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGT
39429957 -G
66 AG
39429958 TACAAGAGAGC
1 -ACAAGAGAGC
39429969 CGAACTATAT
Statistics
Matches: 112, Mismatches: 21, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
62 1 0.01
63 19 0.17
64 20 0.18
65 11 0.10
66 16 0.14
67 27 0.24
68 17 0.15
69 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23
Consensus pattern (67 bp):
ACAAGAGAGCTACGAGATATATAATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGT
AG
Found at i:39430303 original size:28 final size:27
Alignment explanation
Indices: 39430265--39430417 Score: 123
Period size: 28 Copynumber: 5.6 Consensus size: 27
39430255 AAACGAACGG
*
39430265 CACTTAGTGTGCGAAGTATTGAGGATGG
1 CACTTAGTGTGCGAAGTATTGA-GATGA
* * *
39430293 CACTTAGTGTGC-AAGACATCCGAAATGA
1 CACTTAGTGTGCGAAG-TAT-TGAGATGA
**
39430321 CAC--AGTGTATGAAGTATTGATGATGA
1 CACTTAGTGTGCGAAGTATTGA-GATGA
* ** *
39430347 CACTTAGTGTGCAAAACATCTGAAATGA
1 CACTTAGTGTGCGAAGTAT-TGAGATGA
* *
39430375 CACTTAGTGTGCGAAGTATCGAGGATGG
1 CACTTAGTGTGCGAAGTATTGA-GATGA
39430403 CACTTAGTGTGCGAA
1 CACTTAGTGTGCGAA
39430418 ACATCCGATA
Statistics
Matches: 96, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
25 2 0.02
26 14 0.15
27 8 0.08
28 67 0.70
29 5 0.05
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (27 bp):
CACTTAGTGTGCGAAGTATTGAGATGA
Found at i:39430335 original size:54 final size:54
Alignment explanation
Indices: 39430269--39430425 Score: 208
Period size: 54 Copynumber: 2.9 Consensus size: 54
39430259 GAACGGCACT
*
39430269 TAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGCAAGACATCCGAAATGACAC
1 TAGTGTACGAAGTATTGAGGATGGCACTTAGTGTGCAA-ACATCCGAAATGACAC
* * * *
39430324 -AGTGTATGAAGTATTGATGATGACACTTAGTGTGCAAAACATCTGAAATGACAC
1 TAGTGTACGAAGTATTGAGGATGGCACTTAGTGTGC-AAACATCCGAAATGACAC
* *
39430378 TTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTGCGAAACATCCGA
1 -TAGTGTACGAAGTATTGAGGATGGCACTTAGTGTGC-AAACATCCGA
39430426 TATAGCACTT
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
54 46 0.53
55 2 0.02
56 39 0.45
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.25
Consensus pattern (54 bp):
TAGTGTACGAAGTATTGAGGATGGCACTTAGTGTGCAAACATCCGAAATGACAC
Found at i:39430433 original size:28 final size:27
Alignment explanation
Indices: 39430347--39430450 Score: 86
Period size: 28 Copynumber: 3.7 Consensus size: 27
39430337 TTGATGATGA
* *
39430347 CACTTAGTGTGCAAAACATCTGAAATG
1 CACTTAGTGTGCGAAACATCCGAAATG
** *
39430374 ACACTTAGTGTGCGAAGTAT-CGAGGATGG
1 -CACTTAGTGTGCGAAACATCCGA-AAT-G
*
39430403 CACTTAGTGTGCGAAACATCCGATATAG
1 CACTTAGTGTGCGAAACATCCGAAAT-G
*
39430431 CACTTAGCGTGC-AAGACATC
1 CACTTAGTGTGCGAA-ACATC
39430451 GATTGTGCAG
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
27 4 0.06
28 54 0.87
29 4 0.06
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (27 bp):
CACTTAGTGTGCGAAACATCCGAAATG
Found at i:39430435 original size:56 final size:55
Alignment explanation
Indices: 39430265--39430442 Score: 227
Period size: 56 Copynumber: 3.2 Consensus size: 55
39430255 AAACGAACGG
39430265 CACTTAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGCAAGACATCCGAAATGA
1 CACTTAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGCAA-ACATCCGAAATGA
** * * *
39430321 CAC--AGTGTATGAAGTATTGATGATGACACTTAGTGTGCAAAACATCTGAAATGA
1 CACTTAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGC-AAACATCCGAAATGA
* *
39430375 CACTTAGTGTGCGAAGTATCGAGGATGGCACTTAGTGTGCGAAACATCCGATAT-A
1 CACTTAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGC-AAACATCCGAAATGA
*
39430430 GCACTTAGCGTGC
1 -CACTTAGTGTGC
39430443 AAGACATCGA
Statistics
Matches: 104, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
54 46 0.44
55 3 0.03
56 55 0.53
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (55 bp):
CACTTAGTGTGCGAAGTATTGAGGATGGCACTTAGTGTGCAAACATCCGAAATGA
Found at i:39432547 original size:44 final size:43
Alignment explanation
Indices: 39432457--39432571 Score: 101
Period size: 44 Copynumber: 2.6 Consensus size: 43
39432447 CTCGATCTAA
* * *
39432457 GTCCCAGACGTGGTCTTACATGAAATTCAGTATCGATGCCGAT
1 GTCCCAGACATGGTCTTACACGAAATTCAGAATCGATGCCGAT
* *
39432500 GTCCCAGACATGGTCTTACCCGTAAATTTCA-AATTGATGCCTG-T
1 GTCCCAGACATGGTCTTACACG-AAA-TTCAGAATCGATGCC-GAT
* *
39432544 GTCCCTA-ACACGTTCTTACACGATAATT
1 GTCCC-AGACATGGTCTTACACGA-AATT
39432572 TAGATCAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
43 22 0.37
44 31 0.53
45 6 0.10
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGAAATTCAGAATCGATGCCGAT
Found at i:39438554 original size:13 final size:13
Alignment explanation
Indices: 39438536--39438562 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39438526 TGAACACGGG
39438536 CGTGGGGCTTGCA
1 CGTGGGGCTTGCA
39438549 CGTGGGGCTTGCA
1 CGTGGGGCTTGCA
39438562 C
1 C
39438563 ACACGGGCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.26, G:0.44, T:0.22
Consensus pattern (13 bp):
CGTGGGGCTTGCA
Found at i:39441635 original size:55 final size:55
Alignment explanation
Indices: 39441516--39441642 Score: 132
Period size: 55 Copynumber: 2.3 Consensus size: 55
39441506 GATATGGCCG
* ** * *
39441516 TGGTCGAGCCTGCCAAAACACCACGGGCGTGCGACACGCCCGTGTGGAAGAACCG
1 TGGTCGAACCTGTTAAAACACCACGGGCGTGCGACACGCCCGTGTCGAAGAACCA
* * * *
39441571 TGGAT-GAACCTGTTAAAACAGCACGGGCGTGCGACACGTCCGTGTCTAA-CACTCA
1 TGG-TCGAACCTGTTAAAACACCACGGGCGTGCGACACGCCCGTGTCGAAGAAC-CA
*
39441626 TGGTCGAACCTATTAAA
1 TGGTCGAACCTGTTAAA
39441643 TGAACACGAG
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
54 3 0.05
55 55 0.93
56 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (55 bp):
TGGTCGAACCTGTTAAAACACCACGGGCGTGCGACACGCCCGTGTCGAAGAACCA
Found at i:39449158 original size:195 final size:193
Alignment explanation
Indices: 39448825--39449213 Score: 688
Period size: 195 Copynumber: 2.0 Consensus size: 193
39448815 CCTTATAATA
39448825 GCCTACGATGCCTTAAACATGCTTTAGAAGTGGTTCGGGACTAAACCGATAACATATGAAAATTT
1 GCCTACGATGCCTTAAACATGCTTTAGAAGTGGTTCGGGACTAAACCGATAACATATGAAAATTT
* * *
39448890 TGAAAACTTAGGAAAATTTCAAACATACAGGTACCCCACGCTCGAGTGAACAGGCCGTATGCCTC
66 TGAAAACTTAGGAAAATTTCAAACATACAGGGACCCCACGCCCGAGTGAACAGGCCGTATACCTC
* *
39448955 ACACGGCTCCAAACACGCCCGTGTCTTAGGTTGTATAAAAAAACAGAGCATACATACTGACTTGG
131 AAACGGCTCCAAACACGCCCGTGTCTTAGGTCGTAT--AAAAACAGAGCATACATACTGACTTGG
* *
39449020 GCCTACGATGCCTTAAACATGCTTTAGAAGTGGTTCGGGACTAAACCGATAACATGTGAAAGTTT
1 GCCTACGATGCCTTAAACATGCTTTAGAAGTGGTTCGGGACTAAACCGATAACATATGAAAATTT
39449085 TGAAAACTTAGGAAAATTTCAAACATACAGGGACCCCACGCCCGAGTGAACAGGCCGTATACCTC
66 TGAAAACTTAGGAAAATTTCAAACATACAGGGACCCCACGCCCGAGTGAACAGGCCGTATACCTC
*
39449150 AAACGGCTCCAAACACGCCCGTGTCTTAGGTCGTGTAAAAACAGAGCATACATACTGACTTGG
131 AAACGGCTCCAAACACGCCCGTGTCTTAGGTCGTATAAAAACAGAGCATACATACTGACTTGG
39449213 G
1 G
39449214 TCACACGACC
Statistics
Matches: 186, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
193 28 0.15
195 158 0.85
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (193 bp):
GCCTACGATGCCTTAAACATGCTTTAGAAGTGGTTCGGGACTAAACCGATAACATATGAAAATTT
TGAAAACTTAGGAAAATTTCAAACATACAGGGACCCCACGCCCGAGTGAACAGGCCGTATACCTC
AAACGGCTCCAAACACGCCCGTGTCTTAGGTCGTATAAAAACAGAGCATACATACTGACTTGG
Found at i:39450473 original size:25 final size:24
Alignment explanation
Indices: 39450414--39450514 Score: 82
Period size: 23 Copynumber: 4.2 Consensus size: 24
39450404 TTCATTTCTA
* *
39450414 CTCTTTTGAGCT-ATGATCAGTAAG
1 CTCTATTGAGCTGA-GAACAGTAAG
** *
39450438 CTCCTCCTGAGCTAATGAACAGTAAG
1 CT-CTATTGAGCTGA-GAACAGTAAG
*
39450464 CTCTATTGAGCTGA-AACGGTAAG
1 CTCTATTGAGCTGAGAACAGTAAG
*
39450487 CTCTGA-CGAGCTGAGAACAGTAAG
1 CTCT-ATTGAGCTGAGAACAGTAAG
39450511 CTCT
1 CTCT
39450515 TACAAGCTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
23 19 0.30
24 15 0.23
25 17 0.27
26 13 0.20
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
CTCTATTGAGCTGAGAACAGTAAG
Found at i:39450508 original size:47 final size:46
Alignment explanation
Indices: 39450454--39450559 Score: 124
Period size: 47 Copynumber: 2.3 Consensus size: 46
39450444 CTGAGCTAAT
** * *
39450454 GAACAGTAAGCTC-TATTGAGCTGAAACGGTAAGCTCTGACGAGCTGA
1 GAACAGTAAGCTCTTA-CAAGCTAAAACGGTAAGCTCTGACAAGCT-A
*
39450501 GAACAGTAAGCTCTTACAAGCTAAAACGGTAAGCTCTTACAAGCTA
1 GAACAGTAAGCTCTTACAAGCTAAAACGGTAAGCTCTGACAAGCTA
* *
39450547 AAACGGTAAGCTC
1 GAACAGTAAGCTC
39450560 CAACGACTGA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
46 12 0.24
47 37 0.73
48 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21
Consensus pattern (46 bp):
GAACAGTAAGCTCTTACAAGCTAAAACGGTAAGCTCTGACAAGCTA
Found at i:39450573 original size:23 final size:23
Alignment explanation
Indices: 39450472--39450559 Score: 122
Period size: 23 Copynumber: 3.8 Consensus size: 23
39450462 AGCTCTATTG
* * *
39450472 AGCTGAAACGGTAAGCTCTGACG
1 AGCTAAAACGGTAAGCTCTTACA
* *
39450495 AGCTGAGAACAGTAAGCTCTTACA
1 AGCT-AAAACGGTAAGCTCTTACA
39450519 AGCTAAAACGGTAAGCTCTTACA
1 AGCTAAAACGGTAAGCTCTTACA
39450542 AGCTAAAACGGTAAGCTC
1 AGCTAAAACGGTAAGCTC
39450560 CAACGACTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 39 0.68
24 18 0.32
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (23 bp):
AGCTAAAACGGTAAGCTCTTACA
Found at i:39450573 original size:46 final size:47
Alignment explanation
Indices: 39450472--39450585 Score: 115
Period size: 46 Copynumber: 2.4 Consensus size: 47
39450462 AGCTCTATTG
* * * * **
39450472 AGCTGAAACGGTAAGCTCTGACGAGCTGAGAACAGTAAGCTCTTACA
1 AGCTAAAACGGTAAGCTCTTACAAGCTGAAAACAGTAAGCTCCAACA
* *
39450519 AGCTAAAACGGTAAGCTCTTACAAGCT-AAAACGGTAAGCTCCAACG
1 AGCTAAAACGGTAAGCTCTTACAAGCTGAAAACAGTAAGCTCCAACA
**
39450565 A-CTGAAAACAATAAGCTCTTA
1 AGCT-AAAACGGTAAGCTCTTA
39450586 TGAACTGATA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
45 2 0.04
46 30 0.54
47 24 0.43
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (47 bp):
AGCTAAAACGGTAAGCTCTTACAAGCTGAAAACAGTAAGCTCCAACA
Found at i:39457628 original size:27 final size:23
Alignment explanation
Indices: 39457601--39457647 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
39457591 ACGTTTAATG
39457601 TATGTATAGAAAATAATTTTCAT
1 TATGTATAGAAAATAATTTTCAT
39457624 TATGTATAGAAAATAATTTTCAT
1 TATGTATAGAAAATAATTTTCAT
39457647 T
1 T
39457648 GCAAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (23 bp):
TATGTATAGAAAATAATTTTCAT
Found at i:39458715 original size:14 final size:14
Alignment explanation
Indices: 39458696--39458730 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
39458686 ATGTTACTAT
39458696 TAATGTAAAATTTA
1 TAATGTAAAATTTA
39458710 TAATGTAAAATTTA
1 TAATGTAAAATTTA
39458724 TAATGTA
1 TAATGTA
39458731 TGTTACTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (14 bp):
TAATGTAAAATTTA
Found at i:39460901 original size:24 final size:25
Alignment explanation
Indices: 39460855--39460902 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39460845 ATTTATGAGT
* *
39460855 ATAATATATTTAGCATTTTATTAGC
1 ATAATATATTTAGAATTTGATTAGC
39460880 ATAATATATTT-GAATTTGATTAG
1 ATAATATATTTAGAATTTGATTAG
39460903 AATTAGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (25 bp):
ATAATATATTTAGAATTTGATTAGC
Found at i:39482399 original size:24 final size:24
Alignment explanation
Indices: 39482365--39482416 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39482355 TTTCTAGAAG
* *
39482365 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
39482389 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
39482413 ATTT
1 ATTT
39482417 GACTTTAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:39482580 original size:5 final size:5
Alignment explanation
Indices: 39482566--39482602 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
39482556 CTGTGTGTTC
39482566 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
39482603 CACATGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:39490773 original size:30 final size:30
Alignment explanation
Indices: 39490739--39490799 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39490729 TCCTTAACTC
39490739 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
39490769 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
39490799 A
1 A
39490800 GGCTGGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:39497979 original size:27 final size:26
Alignment explanation
Indices: 39497935--39497986 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
39497925 CTCGCTGCAA
*
39497935 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
39497962 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
39497987 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:39498051 original size:33 final size:32
Alignment explanation
Indices: 39498002--39498065 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
39497992 CTCGCTGCAA
* *
39498002 TCTGGTGGCTTTGCCACATATATATATATCTGT
1 TCTGGTGGCCTAGCCACA-ATATATATATCTGT
* *
39498035 TCTGGTGGCCTAGCCACAATATCTGTATCTG
1 TCTGGTGGCCTAGCCACAATATATATATCTG
39498066 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGT
Found at i:39498079 original size:27 final size:26
Alignment explanation
Indices: 39498027--39498086 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
39498017 ACATATATAT
*
39498027 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
39498053 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
39498080 ATATCTG
1 ATATCTG
39498087 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:39505526 original size:27 final size:26
Alignment explanation
Indices: 39505488--39505547 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
39505478 CCACATATAT
* *
39505488 ATATTTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
39505514 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
39505541 ATATCTG
1 ATATCTG
39505548 GCAGCCTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:39506362 original size:46 final size:46
Alignment explanation
Indices: 39506292--39506412 Score: 206
Period size: 46 Copynumber: 2.6 Consensus size: 46
39506282 TACATTTCAC
* *
39506292 GAACTCAGACTCAACTCAATGAGTTCAGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGT
* *
39506338 GAACTCGGACTCAACTCAACGAGTTCGGACATTCTCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGT
39506384 GAACTCGGACTCAACTCAACGAGTTCAGA
1 GAACTCGGACTCAACTCAACGAGTTCAGA
39506413 TGCCCAAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGT
Found at i:39518543 original size:28 final size:26
Alignment explanation
Indices: 39518485--39518545 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
39518475 TAATATATAT
*
39518485 AATAATATTTCACGCAAATATAACAAC
1 AATAA-ATTTCACGCAAATATAAAAAC
39518512 -ATAAATTTCCACGCAAATATATAAAAC
1 AATAAATTT-CACGCAAATATA-AAAAC
39518539 AATAAAT
1 AATAAAT
39518546 AACATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 4 0.13
26 16 0.53
27 4 0.13
28 6 0.20
ACGTcount: A:0.54, C:0.16, G:0.03, T:0.26
Consensus pattern (26 bp):
AATAAATTTCACGCAAATATAAAAAC
Found at i:39519546 original size:22 final size:21
Alignment explanation
Indices: 39519511--39519586 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
39519501 AAAAGGTATC
* *
39519511 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
39519532 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
39519555 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
39519574 TGC-AATCATATCT
1 TACAAATCATATCT
39519587 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:39519603 original size:35 final size:37
Alignment explanation
Indices: 39519540--39519637 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
39519530 ATTACAAAAT
39519540 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGATTG
39519576 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGATATCATATCTAAGATTG
39519611 CATATCATATCTAAGATTGCATATCAT
1 CATATCATATCTAAGATTG-ATATCAT
39519638 TGAAGATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATTG
Found at i:39519645 original size:17 final size:19
Alignment explanation
Indices: 39519547--39519637 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
39519537 AATCATATCT
39519547 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39519566 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
39519584 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
39519601 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39519620 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
39519638 TGAAGATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:39521306 original size:15 final size:16
Alignment explanation
Indices: 39521282--39521324 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
39521272 CATATTTATT
39521282 ATATAATTCAATCAAA
1 ATATAATTCAATCAAA
*
39521298 ATA-AATTCAATCAAT
1 ATATAATTCAATCAAA
39521313 ATATAATTCAAT
1 ATATAATTCAAT
39521325 ATTAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAATTCAATCAAA
Found at i:39521470 original size:17 final size:18
Alignment explanation
Indices: 39521426--39521472 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
39521416 AGCTTCCAAA
*
39521426 TCCTCATTCTCCCTTTTCT
1 TCCTCTTTC-CCCTTTTCT
**
39521445 TTTTCTTTCCCCTTTTCT
1 TCCTCTTTCCCCTTTTCT
39521463 TCCT-TTTCCC
1 TCCTCTTTCCC
39521473 GTTTGCTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 6 0.26
18 11 0.48
19 6 0.26
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (18 bp):
TCCTCTTTCCCCTTTTCT
Found at i:39521536 original size:2 final size:2
Alignment explanation
Indices: 39521529--39521560 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39521519 TTTCATTTAC
39521529 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39521561 ATAACTTATT
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):
TA
Found at i:39521728 original size:20 final size:21
Alignment explanation
Indices: 39521705--39521752 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
39521695 TATAATTATT
* *
39521705 TAATTTATAAATATCT-TTTA
1 TAATTAATAAATATCTATTAA
39521725 TAATTAATAAATATCTATTAA
1 TAATTAATAAATATCTATTAA
39521746 TAATTAA
1 TAATTAA
39521753 ATACATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTAATAAATATCTATTAA
Found at i:39522150 original size:14 final size:14
Alignment explanation
Indices: 39522133--39522175 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
39522123 TCTTATAATA
39522133 TAATTATAATAAAT
1 TAATTATAATAAAT
39522147 TAATT-TAATATAAT
1 TAATTATAATA-AAT
*
39522161 TTATTACTAATAAAT
1 TAATTA-TAATAAAT
39522176 ATATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.20
14 12 0.48
15 3 0.12
16 5 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTATAATAAAT
Found at i:39527162 original size:15 final size:16
Alignment explanation
Indices: 39527138--39527180 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
39527128 CATATTTATT
39527138 ATATAATTCAATCAAA
1 ATATAATTCAATCAAA
*
39527154 ATA-AATTCAATCAAT
1 ATATAATTCAATCAAA
39527169 ATATAATTCAAT
1 ATATAATTCAAT
39527181 ATTAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAATTCAATCAAA
Found at i:39527463 original size:17 final size:18
Alignment explanation
Indices: 39527419--39527465 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
39527409 AGCTTCCAAA
*
39527419 TCCTCATTCTCCCTTTTCT
1 TCCTCTTTC-CCCTTTTCT
**
39527438 TTTTCTTTCCCCTTTTCT
1 TCCTCTTTCCCCTTTTCT
39527456 TCCT-TTTCCC
1 TCCTCTTTCCC
39527466 GTTTGCTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 6 0.26
18 11 0.48
19 6 0.26
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (18 bp):
TCCTCTTTCCCCTTTTCT
Found at i:39527494 original size:15 final size:16
Alignment explanation
Indices: 39527474--39527505 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
39527464 CCGTTTGCTA
39527474 TTCTGTTT-CTTTCTT
1 TTCTGTTTCCTTTCTT
39527489 TTCTGTTTCCTTTCTT
1 TTCTGTTTCCTTTCTT
39527505 T
1 T
39527506 CTTTTATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.00, C:0.22, G:0.06, T:0.72
Consensus pattern (16 bp):
TTCTGTTTCCTTTCTT
Found at i:39527711 original size:20 final size:21
Alignment explanation
Indices: 39527688--39527735 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
39527678 TATAATTATT
* *
39527688 TAATTTATAAATATCT-TTTA
1 TAATTAATAAATATCTATTAA
39527708 TAATTAATAAATATCTATTAA
1 TAATTAATAAATATCTATTAA
39527729 TAATTAA
1 TAATTAA
39527736 ATACATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTAATAAATATCTATTAA
Found at i:39527966 original size:9 final size:9
Alignment explanation
Indices: 39527952--39527976 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39527942 TACACTTGTC
39527952 TTTATTTTA
1 TTTATTTTA
39527961 TTTATTTTA
1 TTTATTTTA
39527970 TTTATTT
1 TTTATTT
39527977 CATATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTTA
Found at i:39528134 original size:14 final size:14
Alignment explanation
Indices: 39528117--39528159 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
39528107 TCTTATAATA
39528117 TAATTATAATAAAT
1 TAATTATAATAAAT
39528131 TAATT-TAATATAAT
1 TAATTATAATA-AAT
*
39528145 TTATTACTAATAAAT
1 TAATTA-TAATAAAT
39528160 ATATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.20
14 12 0.48
15 3 0.12
16 5 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTATAATAAAT
Found at i:39528605 original size:3 final size:3
Alignment explanation
Indices: 39528597--39528675 Score: 76
Period size: 3 Copynumber: 26.0 Consensus size: 3
39528587 AAAATTGTAC
39528597 ATA ATA ATAA ATA ATAA ATA ATA A-A ATA ATA A-A ATA AT- ATA ATA
1 ATA ATA AT-A ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
39528641 TATA ATAA ATA ATA AAA ATA AT- ATA ATGA ATA ATA
1 -ATA AT-A ATA ATA ATA ATA ATA ATA AT-A ATA ATA
39528676 TATTATAAAG
Statistics
Matches: 65, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
2 8 0.12
3 42 0.65
4 15 0.23
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:39528609 original size:7 final size:7
Alignment explanation
Indices: 39528599--39528675 Score: 88
Period size: 7 Copynumber: 11.0 Consensus size: 7
39528589 AATTGTACAT
39528599 AATAATA
1 AATAATA
39528606 AATAATA
1 AATAATA
39528613 AATAATAA
1 AATAAT-A
39528621 AATAAT-
1 AATAATA
39528627 AA-AATA
1 AATAATA
39528633 ATATAATA
1 A-ATAATA
*
39528641 TATAATA
1 AATAATA
39528648 AATAATA
1 AATAATA
39528655 AA-AATA
1 AATAATA
*
39528661 ATATAATG
1 A-ATAATA
39528669 AATAATA
1 AATAATA
39528676 TATTATAAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
5 3 0.05
6 8 0.13
7 34 0.57
8 15 0.25
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (7 bp):
AATAATA
Found at i:39528639 original size:28 final size:28
Alignment explanation
Indices: 39528597--39528675 Score: 108
Period size: 28 Copynumber: 2.8 Consensus size: 28
39528587 AAAATTGTAC
39528597 ATAATAATAA-ATAATAAATAATAAAATA
1 ATAA-AATAATATAATAAATAATAAAATA
*
39528625 ATAAAATAATATAATATATAAT-AAATA
1 ATAAAATAATATAATAAATAATAAAATA
*
39528652 ATAAAAATAATATAATGAATAATA
1 AT-AAAATAATATAATAAATAATA
39528676 TATTATAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.27
28 33 0.73
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (28 bp):
ATAAAATAATATAATAAATAATAAAATA
Found at i:39528646 original size:35 final size:35
Alignment explanation
Indices: 39528599--39528684 Score: 120
Period size: 35 Copynumber: 2.5 Consensus size: 35
39528589 AATTGTACAT
*
39528599 AATAATAAATAATAAATAAT-AAAATAATAAAATA
1 AATAATATATAATAAATAATAAAAATAATAAAATA
* *
39528633 ATATAATATATAATAAATAATAAAAATAATATAATG
1 A-ATAATATATAATAAATAATAAAAATAATAAAATA
*
39528669 AATAATATATTATAAA
1 AATAATATATAATAAA
39528685 GCATATAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
34 1 0.02
35 32 0.70
36 13 0.28
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (35 bp):
AATAATATATAATAAATAATAAAAATAATAAAATA
Found at i:39528683 original size:28 final size:27
Alignment explanation
Indices: 39528597--39528684 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 27
39528587 AAAATTGTAC
* *
39528597 ATAATAATAA-ATAATAAATAATAAAAT
1 ATAAAAATAATATAAT-AATAATAAATT
*
39528624 A-ATAAAATAATATAATATATAATAAATA
1 ATA-AAAATAATATAATA-ATAATAAATT
*
39528652 ATAAAAATAATATAATGAATAATATATT
1 ATAAAAATAATATAAT-AATAATAAATT
39528680 ATAAA
1 ATAAA
39528685 GCATATAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.02
27 8 0.16
28 40 0.78
29 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (27 bp):
ATAAAAATAATATAATAATAATAAATT
Found at i:39528695 original size:35 final size:36
Alignment explanation
Indices: 39528600--39528696 Score: 108
Period size: 35 Copynumber: 2.8 Consensus size: 36
39528590 ATTGTACATA
* *
39528600 ATAATAAATAATAAATAAT-AAAATAATAAAATAAT
1 ATAATATATAATAAAGAATAAAAATAATAAAATAAT
* * *
39528635 ATAATATATAATAAATAATAAAAATAATATAATGA-
1 ATAATATATAATAAAGAATAAAAATAATAAAATAAT
* * *
39528670 ATAATATATTATAAAGCATATAAATAA
1 ATAATATATAATAAAGAATAAAAATAA
39528697 AATGTATAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
35 41 0.76
36 13 0.24
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (36 bp):
ATAATATATAATAAAGAATAAAAATAATAAAATAAT
Found at i:39528802 original size:29 final size:27
Alignment explanation
Indices: 39528765--39528820 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
39528755 GTTTATAGTA
*
39528765 AAAATAAAT-AA-TATATAAAATATTT
1 AAAATAAATAAATTATATAAAAAATTT
*
39528790 AAAATAAATAAATTGTATAAAAAATTT
1 AAAATAAATAAATTATATAAAAAATTT
39528817 AAAA
1 AAAA
39528821 AGGACGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 9 0.33
26 2 0.07
27 16 0.59
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAATAAATAAATTATATAAAAAATTT
Found at i:39533971 original size:47 final size:46
Alignment explanation
Indices: 39533908--39534691 Score: 1066
Period size: 47 Copynumber: 16.6 Consensus size: 46
39533898 CCCTTCGGGA
* * *
39533908 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACA-TTTCACATTCATCACATTGGCCATTCGGC
*
39533955 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCAGC
1 CTTATCACATATATACA-TTTCACATTCATCACATTGGCCATTCGGC
* *
39534002 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGC
* *
39534049 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGC
* *
39534096 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGC
* *
39534143 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGC
* *
39534190 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGC
* *
39534237 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGC
* *
39534284 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGC
* *
39534331 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACAT-TTCACATTCATCACATTGGCCATTCGGC
*
39534378 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCAC--ATATATACA-TTTCACATTCATCACATTGGCCATTCGGC
** *
39534427 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACA-TTTCACATTCATCACATTGGCCATTCGGC
* *
39534474 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACA-TTTCACATTCATCACATTGGCCATTCGGC
* *
39534521 CTTATCACATATGTATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATA--TATACA-TTTCACATTCATCACATTGGCCATTCGGC
* *
39534570 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACA-TTTCACATTCATCACATTGGCCATTCGGC
* *
39534617 CTTATCACATATATATACATTTTCACATT-ATCACATTGGCAATTAGGC
1 CTTATCAC--ATATATACA-TTTCACATTCATCACATTGGCCATTCGGC
39534665 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACA-TTTCACATT
39534692 TATTCAAATA
Statistics
Matches: 692, Mismatches: 37, Indels: 17
0.93 0.05 0.02
Matches are distributed among these distances:
46 19 0.03
47 540 0.78
48 25 0.04
49 107 0.15
50 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (46 bp):
CTTATCACATATATACATTTCACATTCATCACATTGGCCATTCGGC
Found at i:39536206 original size:56 final size:55
Alignment explanation
Indices: 39536139--39536257 Score: 220
Period size: 56 Copynumber: 2.1 Consensus size: 55
39536129 TATTAGTTTA
39536139 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTT-ATGACATGTT
*
39536195 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTATGACATGTT
39536250 TTGCCCAT
1 TTGCCCAT
39536258 CATCCCTTGT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 18 0.29
56 44 0.71
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (55 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTATGACATGTT
Found at i:39537547 original size:40 final size:40
Alignment explanation
Indices: 39537502--39537818 Score: 481
Period size: 40 Copynumber: 7.9 Consensus size: 40
39537492 CGAATACACG
* * * * *
39537502 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
* * * *** * *
39537542 ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
*
39537582 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
39537622 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
39537662 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
39537702 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
39537742 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
* * *
39537782 TCACTAGCATGAATGCTCTTTGGGACTTAACCCGGAT
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGAT
39537819 TTAGTAACTC
Statistics
Matches: 259, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 259 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:39537843 original size:120 final size:120
Alignment explanation
Indices: 39537502--39537856 Score: 498
Period size: 120 Copynumber: 3.0 Consensus size: 120
39537492 CGAATACACG
* * * * * * * * *
39537502 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGG
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
* *
39537567 TTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
66 CTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
*
39537622 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGAA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
* *
39537687 CTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
66 CTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
*
39537742 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTTGGGA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
* * * * * *
39537807 CTTAACCCGGATTTAGTAACTCGCACCAATGC-CTTCGG-GCTTAGCCCGGA
66 CTTAGCCCGGATATA-TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGA
39537857 ATTAGTAACT
Statistics
Matches: 210, Mismatches: 24, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
119 11 0.05
120 187 0.89
121 12 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (120 bp):
TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
CTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:39537862 original size:39 final size:40
Alignment explanation
Indices: 39537793--39537883 Score: 130
Period size: 39 Copynumber: 2.3 Consensus size: 40
39537783 CACTAGCATG
* * *
39537793 AATGCTCTTTGGGACTTAACCCGGATTTAGTAACTCGCACC
1 AATGC-CTTCGGGACTTAACCCGGAATTAGTAACTCGCACA
*
39537834 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACA
39537873 AATGCCTTCGG
1 AATGCCTTCGG
39537884 ATCATAGTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 35 0.76
40 6 0.13
41 5 0.11
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACA
Found at i:39537877 original size:120 final size:120
Alignment explanation
Indices: 39537515--39537898 Score: 398
Period size: 120 Copynumber: 3.2 Consensus size: 120
39537505 CCAGCATGAT
* * * * * * *** * *
39537515 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTTAACCCGGATA
* * * * **
39537580 TATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
66 CATAACTAGCACCAATGCTCTTCGGAACTTAGCCCGGATACATAACTAGCACAAA
*
39537635 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATA
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTTAACCCGGATA
* ** * **
39537700 CATCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
66 CATAACTAGCACCAATGCTCTTCGGAACTTAGCCCGGATACATAACTAGCACAAA
* * *
39537755 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTTGGGACTTAACCCGGATT
1 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTTAACCCGGATA
* * * * *
39537820 TAGTAACTCGCACCAATGC-CTTCGG-GCTTAGCCCGGAATTA-GTAACTCGCACAAA
66 CA-TAACTAGCACCAATGCTCTTCGGAACTTAGCCCGG-A-TACATAACTAGCACAAA
* * *
39537875 TGC-CTTCGGATCATAGTCCGGATA
1 TGCTCTTCGGAACTTAGCCCGGATA
39537899 TGGTCACTTA
Statistics
Matches: 231, Mismatches: 30, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
119 28 0.12
120 189 0.82
121 14 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (120 bp):
TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGAACTTAACCCGGATA
CATAACTAGCACCAATGCTCTTCGGAACTTAGCCCGGATACATAACTAGCACAAA
Found at i:39540279 original size:47 final size:47
Alignment explanation
Indices: 39540216--39540937 Score: 1062
Period size: 47 Copynumber: 15.6 Consensus size: 47
39540206 CCCTTCGGGA
* * *
39540216 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39540263 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39540310 CTTATCTC--ATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
39540355 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
39540402 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
39540449 CTTATCACATATAT----GTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39540492 CTTATCAC----ATACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
39540535 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
39540582 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39540628 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39540675 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39540722 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39540769 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39540816 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39540863 CTTATCACATATATATACATTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACAC-TTTCACATTCATCACATTGGCCATTCGGC
39540911 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
39540938 TATTCAAATA
Statistics
Matches: 641, Mismatches: 20, Indels: 28
0.93 0.03 0.04
Matches are distributed among these distances:
39 2 0.00
43 72 0.11
44 1 0.00
45 41 0.06
46 46 0.07
47 433 0.68
48 46 0.07
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:39540937 original size:367 final size:361
Alignment explanation
Indices: 39540216--39540937 Score: 994
Period size: 367 Copynumber: 2.0 Consensus size: 361
39540206 CCCTTCGGGA
*
39540216 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
* * * * *
39540281 TTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATGCATGTTCACATTCATCACATTGG
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATGTTCACATTCATCACATCGG
* * *
39540346 CCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACA
131 CCATTAGGCCTTATCACACATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
* *
39540411 CATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGTTCACATTCATC
196 CATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGTTCACATTCATC
* * *
39540476 ACATTGGCCATTCGGCCTTATCACATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATC
261 ACATCGGCCATTAGGCCTTATCACATACATGTTCACATTCATCACATTGGCCATTAGGCCTTAT-
* *
39540541 ACACATACACATGTTCACATTCATCACATTGGCCATTCGGC
325 ACACAT--A-ATATACACATT-ATCACATTGGCCATTCGGC
* *
39540582 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
39540646 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT-TTCACATTCATCACAT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATACA-TGTTCACATTCATCACAT
* *
39540710 CGGCCATTAGGCCTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTAGGCCTTAT
128 CGGCCATTAGGCCTTATCACACATACACA-TGTTCACATTCATCACATCGGCCATTAGGCCTTAT
* * *
39540774 CACATATATACACT-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
192 CACACATACACA-TGTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT----GTTC
39540838 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAT-TTCACATTCATCACATTGG
252 ACATTCATCACATCGGCCATTAGGCCTTATCAC------ATACATGTTCACATTCATCACATTGG
39540902 CCATTAGGCCTTAT-CACAT-ATATACAC-TT-TCACATT
311 CCATTAGGCCTTATACACATAATATACACATTATCACATT
39540938 TATTCAAATA
Statistics
Matches: 318, Mismatches: 23, Indels: 29
0.86 0.06 0.08
Matches are distributed among these distances:
365 64 0.20
366 31 0.10
367 135 0.42
368 3 0.01
369 2 0.01
370 6 0.02
371 34 0.11
374 5 0.02
376 32 0.10
377 6 0.02
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (361 bp):
CTTATCACATATATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATGTTCACATTCATCACATCGG
CCATTAGGCCTTATCACACATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
CATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGTTCACATTCATC
ACATCGGCCATTAGGCCTTATCACATACATGTTCACATTCATCACATTGGCCATTAGGCCTTATA
CACATAATATACACATTATCACATTGGCCATTCGGC
Found at i:39542450 original size:56 final size:56
Alignment explanation
Indices: 39542383--39542502 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
39542373 TATTAGTTTA
39542383 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
39542439 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
39542495 TTGCCCAT
1 TTGCCCAT
39542503 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:39546643 original size:21 final size:21
Alignment explanation
Indices: 39546618--39546756 Score: 145
Period size: 21 Copynumber: 6.6 Consensus size: 21
39546608 AGTGTTTTAC
39546618 TTTCTGTTCAGCTCTTACGA-
1 TTTCTGTTCAGCTCTTACGAG
* * **
39546638 TCTTCTATTCAACTCTTATAAG
1 T-TTCTGTTCAGCTCTTACGAG
* * *
39546660 TTTTTGTTCAGATTTTACGAG
1 TTTCTGTTCAGCTCTTACGAG
* * *
39546681 CTTCTGTTCAACTCTTATGAG
1 TTTCTGTTCAGCTCTTACGAG
* *
39546702 TTTTTGTTTAGCTCTTACGAG
1 TTTCTGTTCAGCTCTTACGAG
39546723 TTTCTGTTCAGCTCTTACGAG
1 TTTCTGTTCAGCTCTTACGAG
*
39546744 CTTCTGTTCAGCT
1 TTTCTGTTCAGCT
39546757 TTCAAGCTTT
Statistics
Matches: 92, Mismatches: 25, Indels: 3
0.77 0.21 0.03
Matches are distributed among these distances:
20 1 0.01
21 90 0.98
22 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.15, T:0.47
Consensus pattern (21 bp):
TTTCTGTTCAGCTCTTACGAG
Found at i:39546685 original size:42 final size:42
Alignment explanation
Indices: 39546622--39546739 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
39546612 TTTTACTTTC
* *
39546622 TGTTCAGCTCTTACGATCTTCTATTCAACTCTTATAAGTTTT
1 TGTTCAGCTCTTACGAGCTTCTGTTCAACTCTTATAAGTTTT
* * *
39546664 TGTTCAGATTTTACGAGCTTCTGTTCAACTCTTATGAGTTTT
1 TGTTCAGCTCTTACGAGCTTCTGTTCAACTCTTATAAGTTTT
* * *
39546706 TGTTTAGCTCTTACGAGTTTCTGTTCAGCTCTTA
1 TGTTCAGCTCTTACGAGCTTCTGTTCAACTCTTA
39546740 CGAGCTTCTG
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (42 bp):
TGTTCAGCTCTTACGAGCTTCTGTTCAACTCTTATAAGTTTT
Found at i:39552598 original size:71 final size:71
Alignment explanation
Indices: 39552506--39552712 Score: 387
Period size: 71 Copynumber: 2.9 Consensus size: 71
39552496 TCTGAGTAAA
* *
39552506 AGTATAATCAAGGCCTTTCATAATACGCTCGGTAGCCTCGAGCCCATATTCAGCAACAGTAGGAG
1 AGTATAATCAAGGTCTGTCATAATACGCTCGGTAGCCTCGAGCCCATATTCAGCAACAGTAGGAG
39552571 CAAAAG
66 CAAAAG
*
39552577 ATTATAATCAAGGTCTGTCATAATACGCTCGGTAGCCTCGAGCCCATATTCAGCAACAGTAGGAG
1 AGTATAATCAAGGTCTGTCATAATACGCTCGGTAGCCTCGAGCCCATATTCAGCAACAGTAGGAG
39552642 CAAAAG
66 CAAAAG
39552648 AGTATAATCAAGGTCTGTCATAATACGCTCGGTAGCCTCGAGCCCATATTCAGCAACAGTAGGAG
1 AGTATAATCAAGGTCTGTCATAATACGCTCGGTAGCCTCGAGCCCATATTCAGCAACAGTAGGAG
39552713 AAACTCCTAT
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 132 1.00
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (71 bp):
AGTATAATCAAGGTCTGTCATAATACGCTCGGTAGCCTCGAGCCCATATTCAGCAACAGTAGGAG
CAAAAG
Found at i:39557247 original size:34 final size:34
Alignment explanation
Indices: 39557194--39557261 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
39557184 GCACAGTTGA
* *
39557194 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGAGCCTAAGCCCATTTCAGTA-CAGTG
*
39557229 ACAGT-TTGAGCCTTAGCCCATTTCAGTACAGTG
1 ACAGTCTTGAGCCTAAGCCCATTTCAGTACAGTG
39557262 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (34 bp):
ACAGTCTTGAGCCTAAGCCCATTTCAGTACAGTG
Found at i:39563773 original size:21 final size:21
Alignment explanation
Indices: 39563743--39563930 Score: 153
Period size: 21 Copynumber: 9.0 Consensus size: 21
39563733 AGCTTCTGTT
*
39563743 CTCTTATGAGCTTCTATTCAA
1 CTCTTATGAGTTTCTATTCAA
* * * *
39563764 CTCTTTTGAGTTTCTGTTTAG
1 CTCTTATGAGTTTCTATTCAA
* *
39563785 CTCTTATGAGCTTCTATGT-AG
1 CTCTTATGAGTTTCTAT-TCAA
* * *
39563806 CTCTTATGAGTTTCTGTTTAG
1 CTCTTATGAGTTTCTATTCAA
* * *
39563827 GTCTTATGAGTTTTTATTTAA
1 CTCTTATGAGTTTCTATTCAA
*
39563848 CTCTTATGAGTTTCTGTTCAA
1 CTCTTATGAGTTTCTATTCAA
** * *
39563869 CTCTTACCAGCTGCTATTCAA
1 CTCTTATGAGTTTCTATTCAA
* *
39563890 CTCTTATGAGTTTCTGTTCAG
1 CTCTTATGAGTTTCTATTCAA
** *
39563911 CTCTTACCAGCTTCTATTCA
1 CTCTTATGAGTTTCTATTCA
39563931 GCTTTGAAGC
Statistics
Matches: 132, Mismatches: 33, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
20 1 0.01
21 130 0.98
22 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.47
Consensus pattern (21 bp):
CTCTTATGAGTTTCTATTCAA
Found at i:39563796 original size:42 final size:42
Alignment explanation
Indices: 39563743--39563930 Score: 234
Period size: 42 Copynumber: 4.5 Consensus size: 42
39563733 AGCTTCTGTT
* *
39563743 CTCTTATGAGCTTCTATTCAACTCTTTTGAGTTTCTGTTTAG
1 CTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAG
* *
39563785 CTCTTATGAGCTTCTATGT-AGCTCTTATGAGTTTCTGTTTAG
1 CTCTTATGAGCTTCTAT-TCAACTCTTATGAGTTTCTGTTCAG
* * * * *
39563827 GTCTTATGAGTTTTTATTTAACTCTTATGAGTTTCTGTTCAA
1 CTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAG
** *
39563869 CTCTTACCAGCTGCTATTCAACTCTTATGAGTTTCTGTTCAG
1 CTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAG
**
39563911 CTCTTACCAGCTTCTATTCA
1 CTCTTATGAGCTTCTATTCA
39563931 GCTTTGAAGC
Statistics
Matches: 127, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.01
42 125 0.98
43 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.14, T:0.47
Consensus pattern (42 bp):
CTCTTATGAGCTTCTATTCAACTCTTATGAGTTTCTGTTCAG
Found at i:39566543 original size:40 final size:40
Alignment explanation
Indices: 39566308--39566529 Score: 281
Period size: 40 Copynumber: 5.6 Consensus size: 40
39566298 AATGATGTCT
* * ***
39566308 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCGTATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCC
* * *
39566348 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
39566388 GGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
39566427 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
39566467 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCC
*
39566507 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
39566530 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.21
40 117 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:39574641 original size:40 final size:40
Alignment explanation
Indices: 39574412--39574634 Score: 283
Period size: 40 Copynumber: 5.6 Consensus size: 40
39574402 TGAATGATGT
* * * *
39574412 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATC
* * *
39574452 CGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTC
1 CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATC
* *
39574492 CGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATC
*
39574531 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATC
*
39574571 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-C
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATC
*
39574611 CGGGCTATGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTG
39574635 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 33 0.20
40 118 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATC
Found at i:39574656 original size:119 final size:119
Alignment explanation
Indices: 39574417--39574667 Score: 278
Period size: 119 Copynumber: 2.1 Consensus size: 119
39574407 GATGTCGGGC
*
39574417 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
* ** *
39574482 ATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATTCGGGT
66 ATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATTCCGGT
* * * **
39574536 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
* * * *
39574599 AGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA-TCCGGT
64 AGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAATTCCGGT
* *
39574655 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
39574668 TACGTGATTT
Statistics
Matches: 111, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 80 0.72
120 28 0.25
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
ATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATTCCGGT
Found at i:39584725 original size:24 final size:24
Alignment explanation
Indices: 39584668--39584785 Score: 132
Period size: 23 Copynumber: 5.0 Consensus size: 24
39584658 CTAAGTTGAT
*
39584668 AAACAGTAAGCTCTATTGAGCTG-
1 AAACAGTAAGCTCTAATGAGCTGA
* * *
39584691 ATACAGTAAGCTCTGACGAGCTGA
1 AAACAGTAAGCTCTAATGAGCTGA
*
39584715 GAACAGTAAGCTCTAATGAGCT-A
1 AAACAGTAAGCTCTAATGAGCTGA
* * *
39584738 AAACTGTAAGCTCCAACGAGCTGA
1 AAACAGTAAGCTCTAATGAGCTGA
* *
39584762 AAACAGTAAACTCTTATGAGCTGA
1 AAACAGTAAGCTCTAATGAGCTGA
39584786 TATATCGATA
Statistics
Matches: 76, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
23 38 0.50
24 38 0.50
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (24 bp):
AAACAGTAAGCTCTAATGAGCTGA
Found at i:39584727 original size:47 final size:47
Alignment explanation
Indices: 39584668--39584787 Score: 152
Period size: 47 Copynumber: 2.6 Consensus size: 47
39584658 CTAAGTTGAT
**
39584668 AAACAGTAAGCTCTATTGAGCTGATACAGTAAGCTCTGACGAGCTGA
1 AAACAGTAAGCTCTATTGAGCTGATACAGTAAGCTCCAACGAGCTGA
* * * * *
39584715 GAACAGTAAGCTCTAATGAGCTAAAACTGTAAGCTCCAACGAGCTGA
1 AAACAGTAAGCTCTATTGAGCTGATACAGTAAGCTCCAACGAGCTGA
*
39584762 AAACAGTAAACTCT-TATGAGCTGATA
1 AAACAGTAAGCTCTAT-TGAGCTGATA
39584788 TATCGATAAG
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (47 bp):
AAACAGTAAGCTCTATTGAGCTGATACAGTAAGCTCCAACGAGCTGA
Found at i:39595259 original size:14 final size:14
Alignment explanation
Indices: 39595240--39595269 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39595230 AAGATATTCT
39595240 TTTTCTAAATAAAG
1 TTTTCTAAATAAAG
*
39595254 TTTTCTAAATGAAG
1 TTTTCTAAATAAAG
39595268 TT
1 TT
39595270 AAACCAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (14 bp):
TTTTCTAAATAAAG
Found at i:39595309 original size:14 final size:16
Alignment explanation
Indices: 39595290--39595326 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
39595280 CGATATCCTT
39595290 TTTGCAT-TCAT-GCA
1 TTTGCATCTCATAGCA
39595304 TTTGCATCTCATAGCA
1 TTTGCATCTCATAGCA
39595320 TTT-CATC
1 TTTGCATC
39595327 ACATCGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (16 bp):
TTTGCATCTCATAGCA
Found at i:39595326 original size:15 final size:15
Alignment explanation
Indices: 39595290--39595339 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
39595280 CGATATCCTT
39595290 TTTGCAT-TCATGCA
1 TTTGCATCTCATGCA
39595304 TTTGCATCTCATAGCA
1 TTTGCATCTCAT-GCA
* *
39595320 TTT-CATCACAT-CG
1 TTTGCATCTCATGCA
39595333 TTTGCAT
1 TTTGCAT
39595340 TCAAGGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 4 0.13
14 10 0.32
15 11 0.35
16 6 0.19
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (15 bp):
TTTGCATCTCATGCA
Found at i:39603736 original size:205 final size:205
Alignment explanation
Indices: 39603378--39603857 Score: 687
Period size: 205 Copynumber: 2.3 Consensus size: 205
39603368 AGATCTAGCG
* * * *
39603378 GAAGCAAGATCCAAGATGGTTTGGCATCCTTGTACTTACAAGGAAAAAACTGAAGACATAGCTGA
1 GAAGC-AGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGACAAATC-GAAGACATAGTTGA
39603443 TTTGGATTTCACGTGTTGACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
64 TTTGGATTTCACGTGTTGACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
* * * *
39603508 AACAAATCAAAGTCTGGCATCTCCA-CTTCGACGG-GGAGCAGATACATAGTAGATCTCACCTTC
129 AACAAATCAAAGTCTGGCATCTCCATATTCGACGGAGG-GCAGACACATAGCAGATCTAACCTTC
39603571 AGATGTTTATACT
193 AGATGTTTATACT
*
39603584 GAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAAACATAGTTGAT
1 GAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGA-CAAATCGAAGACATAGTTGAT
*
39603649 TTGGCTTTCACGTGCTT-ACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
65 TTGGATTTCACGTG-TTGACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAG
* * *
39603713 AACAAATCGAAGTTTGGCATCTCCATATTCGATGGAGGGCAGACACATAGCAGATCTAACCTTCA
129 AACAAATCAAAGTCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTCA
39603778 GATGTTTATACT
194 GATGTTTATACT
* * * * * * * * *
39603790 GAAGTAGATCCAAGATGATTTAGCATTCTTGTGTTTACAAGAAACAAATTGAGGACATAGTAGAT
1 GAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAG-GACAAATCGAAGACATAGTTGAT
39603855 TTG
65 TTG
39603858 ACTCTTAGAT
Statistics
Matches: 246, Mismatches: 23, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
205 133 0.54
206 110 0.45
207 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (205 bp):
GAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGACAAATCGAAGACATAGTTGATT
TGGATTTCACGTGTTGACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAA
CAAATCAAAGTCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAGATCTAACCTTCAGA
TGTTTATACT
Found at i:39606197 original size:24 final size:26
Alignment explanation
Indices: 39606151--39606201 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
39606141 ATACTAATTC
*
39606151 TTTTATCATTTACGTATTAAATGTTA
1 TTTTATCAATTACGTATTAAATGTTA
*
39606177 TTTTAT-AATTAC-TATTTAATGTTA
1 TTTTATCAATTACGTATTAAATGTTA
39606201 T
1 T
39606202 ATTTTATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 12 0.52
25 5 0.22
26 6 0.26
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (26 bp):
TTTTATCAATTACGTATTAAATGTTA
Found at i:39609586 original size:22 final size:22
Alignment explanation
Indices: 39609555--39609599 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39609545 ATTAGGATTA
39609555 CCCGTCCGGGCTAAATACAATC
1 CCCGTCCGGGCTAAATACAATC
* *
39609577 CCCGTTCGGGCTAAATCCAATC
1 CCCGTCCGGGCTAAATACAATC
39609599 C
1 C
39609600 ATAACATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.38, G:0.18, T:0.20
Consensus pattern (22 bp):
CCCGTCCGGGCTAAATACAATC
Found at i:39613446 original size:7 final size:6
Alignment explanation
Indices: 39613434--39613489 Score: 53
Period size: 7 Copynumber: 9.0 Consensus size: 6
39613424 ATAAATTTTA
*
39613434 TTATAT GTTATAT TTTTAT TATATAT ATTATAT TTATAT TT-TA- TTATAT
1 TTATAT -TTATAT TTATAT T-TATAT -TTATAT TTATAT TTATAT TTATAT
39613483 GTTATAT
1 -TTATAT
39613490 ATTTTTTACT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
4 2 0.05
5 4 0.10
6 14 0.33
7 21 0.50
8 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (6 bp):
TTATAT
Found at i:39613451 original size:27 final size:26
Alignment explanation
Indices: 39613397--39613475 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 26
39613387 TATATGAAAA
* * *
39613397 ATAATATATATTATTATATACATCTTT
1 ATAATATATATTA-TATTTATATTTTT
*
39613424 ATAA-ATTTTATTATATGTTATATTTTT
1 ATAATA-TATATTATAT-TTATATTTTT
*
39613451 ATTATATATATTATATTTATATTTT
1 ATAATATATATTATATTTATATTTT
39613476 ATTATATGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
26 13 0.30
27 29 0.67
28 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (26 bp):
ATAATATATATTATATTTATATTTTT
Found at i:39613469 original size:18 final size:17
Alignment explanation
Indices: 39613430--39613491 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 17
39613420 CTTTATAAAT
*
39613430 TTTAT-TATATGTTATA
1 TTTATATATATATTATA
39613446 TTTTTATTATATATATTATA
1 --TTTA-TATATATATTATA
*
39613466 TTTATAT-TTTATTATA
1 TTTATATATATATTATA
39613482 TGTTATATAT
1 T-TTATATAT
39613492 TTTTTACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 9 0.24
17 9 0.24
18 9 0.24
19 1 0.03
20 10 0.26
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTATATATATATTATA
Found at i:39613480 original size:25 final size:27
Alignment explanation
Indices: 39613432--39613482 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 27
39613422 TTATAAATTT
39613432 TATTATATGTTATATTTTTATTATATA
1 TATTATATGTTATATTTTTATTATATA
39613459 TATTATAT-TTATA-TTTTATTATAT
1 TATTATATGTTATATTTTTATTATAT
39613483 GTTATATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 11 0.46
26 5 0.21
27 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
TATTATATGTTATATTTTTATTATATA
Found at i:39613496 original size:21 final size:21
Alignment explanation
Indices: 39613429--39613636 Score: 100
Period size: 21 Copynumber: 10.1 Consensus size: 21
39613419 TCTTTATAAA
39613429 TTTTATTATATGTTATAT-TT
1 TTTTATTATATGTTATATATT
* *
39613449 TTATTATATATAT-TATATTTATA
1 TT-TTAT-TATATGT-TATATATT
39613472 TTTTATTATATGTTATATATT
1 TTTTATTATATGTTATATATT
* *
39613493 TTTTACTATAT-AT-TAT-TT
1 TTTTATTATATGTTATATATT
* * *
39613511 TTTTACTATAT-TTTTATATG
1 TTTTATTATATGTTATATATT
***
39613531 TAAAATTACT-TGTTATATCA-T
1 TTTTATTA-TATGTTATAT-ATT
39613552 TTTTATTAT-T-TTATATATT
1 TTTTATTATATGTTATATATT
** *
39613571 ACTTATCATATTGTTCATATTATT
1 TTTTATTATA-TGTT-ATA-TATT
* * **
39613595 ATATATT-T-TGTT-TATAAA
1 TTTTATTATATGTTATATATT
39613613 TTTTATTATATGTTATATATT
1 TTTTATTATATGTTATATATT
39613634 TTT
1 TTT
39613637 CCACCTATTA
Statistics
Matches: 140, Mismatches: 29, Indels: 37
0.68 0.14 0.18
Matches are distributed among these distances:
18 22 0.16
19 22 0.16
20 15 0.11
21 49 0.35
22 17 0.12
23 7 0.05
24 8 0.06
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (21 bp):
TTTTATTATATGTTATATATT
Found at i:39613894 original size:16 final size:16
Alignment explanation
Indices: 39613875--39613909 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
39613865 AAACATCTTT
*
39613875 ATTTTTATTTTATTTG
1 ATTTTTATTTTATATG
39613891 ATTTTTATTTTATATG
1 ATTTTTATTTTATATG
39613907 ATT
1 ATT
39613910 ATAATTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
ATTTTTATTTTATATG
Found at i:39614074 original size:2 final size:2
Alignment explanation
Indices: 39614067--39614098 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
39614057 AAATATTATC
*
39614067 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39614099 TGCAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:39615937 original size:31 final size:31
Alignment explanation
Indices: 39615878--39615945 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
39615868 CCAAAGGCCC
* *
39615878 GCCCGAAAAATGGGAGGTTTGGGTAAAAATATAG
1 GCCCGAAAAAT-GGAGGCTTGGGCAAAAA-A-AG
39615912 GCCCGAAAAAT-G-GGCTTGGGCAAAAAAAG
1 GCCCGAAAAATGGAGGCTTGGGCAAAAAAAG
39615941 GCCCG
1 GCCCG
39615946 TTTAGAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 7 0.22
30 1 0.03
31 12 0.38
32 1 0.03
34 11 0.34
ACGTcount: A:0.37, C:0.16, G:0.32, T:0.15
Consensus pattern (31 bp):
GCCCGAAAAATGGAGGCTTGGGCAAAAAAAG
Found at i:39616189 original size:25 final size:26
Alignment explanation
Indices: 39616144--39616194 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
39616134 ATATTTGTTT
*
39616144 TTATGTTTTTAAATATATTTTATTTA
1 TTATATTTTTAAATATATTTTATTTA
*
39616170 TTATATTTTTAAA-ATTTTTTATTTA
1 TTATATTTTTAAATATATTTTATTTA
39616195 ATGAAATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
TTATATTTTTAAATATATTTTATTTA
Found at i:39632933 original size:28 final size:28
Alignment explanation
Indices: 39632868--39632994 Score: 164
Period size: 28 Copynumber: 4.5 Consensus size: 28
39632858 ATGAGATTGA
* * **
39632868 CACTAAGTGTGCGGGTTTAAATTGCATAG
1 CACTAAGTGTGCGAGTTT-GATTATATAG
*
39632897 CACTAAGTGTGCAAGTTTGATTATATAG
1 CACTAAGTGTGCGAGTTTGATTATATAG
*
39632925 CACTAAGTGTGCGAGTTTGATTATGTAAG
1 CACTAAGTGTGCGAGTTTGATTATAT-AG
* *
39632954 CACTAAGTGTGTGAGTTTGATTATATAA
1 CACTAAGTGTGCGAGTTTGATTATATAG
39632982 CACTAAGTGTGCG
1 CACTAAGTGTGCG
39632995 GACTTACTAT
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 44 0.51
29 42 0.49
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTGATTATATAG
Found at i:39632956 original size:57 final size:57
Alignment explanation
Indices: 39632867--39632994 Score: 177
Period size: 57 Copynumber: 2.2 Consensus size: 57
39632857 CATGAGATTG
*
39632867 ACACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
1 ACACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
* * * * **
39632924 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGTGAGTTTGATTATATA
1 ACACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATA
39632981 ACACTAAGTGTGCG
1 ACACTAAGTGTGCG
39632995 GACTTACTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 59 0.95
58 3 0.05
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.34
Consensus pattern (57 bp):
ACACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
Found at i:39639385 original size:27 final size:27
Alignment explanation
Indices: 39639355--39639505 Score: 171
Period size: 27 Copynumber: 5.6 Consensus size: 27
39639345 ATATTGAGTC
* * *
39639355 CGCACACTCAGTGCTATATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39639382 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39639410 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
**
39639437 CGCACACTTAGTGCATCACAT--TCATTT
1 CGCACACTTAGTGC-T-ACATAGTCAAAT
*
39639464 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39639491 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39639506 GTACAATTTA
Statistics
Matches: 105, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.04
27 75 0.71
28 23 0.22
29 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39648166 original size:27 final size:27
Alignment explanation
Indices: 39648075--39648223 Score: 151
Period size: 27 Copynumber: 5.5 Consensus size: 27
39648065 ATATTGAGTC
* * * *
39648075 CGCACACTCAGTGCTATATAATCAA-T
1 CGCACACTTAGTGCCACATAGTCAATT
* *
39648101 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCCACATAGTC-AATT
* *
39648129 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCCACATAGTCAATT
*
39648156 CGCACACTTAGTGCATCACAT--TCATTT
1 CGCACACTTAGTGC--CACATAGTCAATT
* *
39648183 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCCACATAGTCAATT
39648210 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39648224 TGTACAATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.04
26 20 0.19
27 56 0.53
28 21 0.20
29 4 0.04
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCCACATAGTCAATT
Found at i:39663673 original size:21 final size:21
Alignment explanation
Indices: 39663649--39663701 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
39663639 CCTAATATTG
39663649 AAATCCTAAATCCTAAACATA
1 AAATCCTAAATCCTAAACATA
* * *
39663670 AAATCCTAAACCCTAAACTTT
1 AAATCCTAAATCCTAAACATA
*
39663691 AAACCCTAAAT
1 AAATCCTAAAT
39663702 TAATTAGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (21 bp):
AAATCCTAAATCCTAAACATA
Found at i:39666962 original size:33 final size:33
Alignment explanation
Indices: 39666922--39666988 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
39666912 CGTGTTTGGA
39666922 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
1 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
39666955 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
1 TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
39666988 T
1 T
39666989 TTAGCCTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (33 bp):
TAGAGCGCAAGAAACCATGGGTGTATGGACTCC
Found at i:39679516 original size:26 final size:26
Alignment explanation
Indices: 39679480--39679533 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
39679470 CGAGAAGTAA
39679480 AAAAAAACACTATCACCCAAATTCAC
1 AAAAAAACACTATCACCCAAATTCAC
39679506 AAAAAAACACTATCACCCAAATTCAC
1 AAAAAAACACTATCACCCAAATTCAC
39679532 AA
1 AA
39679534 TAGAAGCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.56, C:0.30, G:0.00, T:0.15
Consensus pattern (26 bp):
AAAAAAACACTATCACCCAAATTCAC
Done.