Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 91 of 318
Found at i:30503248 original size:33 final size:33
Alignment explanation
Indices: 30503192--30503276 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
30503182 AAACTTGGGA
*
30503192 GGACAGACA--AACAACCTAGGACAAAG-AAAT
1 GGACAGACATTAACAACCTAAGACAAAGAAAAT
30503222 GGACAGACATTAAGCAACCTAAGACAAAGAAAAT
1 GGACAGACATTAA-CAACCTAAGACAAAGAAAAT
*
30503256 -GACAGACATTAATCCACCTAA
1 GGACAGACATTAA-CAACCTAA
30503277 ATAATAATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
30 9 0.19
32 2 0.04
33 33 0.69
34 4 0.08
ACGTcount: A:0.51, C:0.21, G:0.16, T:0.12
Consensus pattern (33 bp):
GGACAGACATTAACAACCTAAGACAAAGAAAAT
Found at i:30503629 original size:14 final size:14
Alignment explanation
Indices: 30503583--30503623 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
30503573 ATTTTATTCT
30503583 TAATAAATATTTGAA
1 TAATAAATATTT-AA
30503598 T--TAAATATTTAA
1 TAATAAATATTTAA
30503610 TAATAAA-ATTTAA
1 TAATAAATATTTAA
30503623 T
1 T
30503624 TGATAATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.12
13 16 0.67
14 4 0.17
15 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
TAATAAATATTTAA
Found at i:30505342 original size:19 final size:19
Alignment explanation
Indices: 30505318--30505357 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
30505308 TCAAGTATGT
*
30505318 AAATAATTTA-AAATTAAAA
1 AAATAAATTATAAA-TAAAA
30505337 AAATAAATTATAAATAAAA
1 AAATAAATTATAAATAAAA
30505356 AA
1 AA
30505358 TAAGTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATAAATTATAAATAAAA
Found at i:30508326 original size:30 final size:30
Alignment explanation
Indices: 30508292--30508348 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
30508282 ATAACTTGTT
30508292 AATA-TTTTAATATATAAAATATAAATTTTA
1 AATATTTTTAATATAT-AAATATAAATTTTA
* *
30508322 AATATTTTTAATCTATAAATATTAATT
1 AATATTTTTAATATATAAATATAAATT
30508349 ATTTATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
AATATTTTTAATATATAAATATAAATTTTA
Found at i:30508395 original size:33 final size:33
Alignment explanation
Indices: 30508300--30508396 Score: 85
Period size: 33 Copynumber: 2.8 Consensus size: 33
30508290 TTAATATTTT
*
30508300 AATATATAAAATATAAATTTTAAATATTTTTAATCTAT
1 AATATAT-AAATAT--ATTTTAAATA--TTTAATCTAG
*
30508338 AA-ATATTAAT-TATTTATAAA-ATTTAAT-TAG
1 AATATATAAATATATTT-TAAATATTTAATCTAG
30508368 AATATATAAACTATATTTTAAATATTTAA
1 AATATATAAA-TATATTTTAAATATTTAA
30508397 ATATAACCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
30 4 0.08
31 12 0.24
32 5 0.10
33 16 0.31
34 4 0.08
35 1 0.02
36 3 0.06
37 4 0.08
38 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (33 bp):
AATATATAAATATATTTTAAATATTTAATCTAG
Found at i:30510433 original size:24 final size:25
Alignment explanation
Indices: 30510386--30510436 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
30510376 ACACATGTTC
*
30510386 ATAATATATAAAACATACATATAAT
1 ATAATATATAAAACATACACATAAT
**
30510411 ATAATAT-TAAAACATTTACATAAT
1 ATAATATATAAAACATACACATAAT
30510435 AT
1 AT
30510437 GTACACACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAATATATAAAACATACACATAAT
Found at i:30510543 original size:21 final size:21
Alignment explanation
Indices: 30510509--30510548 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
30510499 AAGATATACT
*
30510509 TATATAAACATATATTAAAGA
1 TATATAAACATATAATAAAGA
* *
30510530 TATATACATATATAATAAA
1 TATATAAACATATAATAAA
30510549 ATACATGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (21 bp):
TATATAAACATATAATAAAGA
Found at i:30512639 original size:4 final size:4
Alignment explanation
Indices: 30512630--30512656 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
30512620 ATAATAATAA
30512630 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
30512657 GCCCTCCACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:30513249 original size:31 final size:31
Alignment explanation
Indices: 30513188--30513249 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
30513178 TATTTACATA
* *
30513188 AAATTTTAATTATAGTTCAAATGTAGATATT
1 AAATTTTAATTATAATTCAAATATAGATATT
* *
30513219 AAATTTTAATTATAATTCAATTATATATATT
1 AAATTTTAATTATAATTCAAATATAGATATT
30513250 TAAAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (31 bp):
AAATTTTAATTATAATTCAAATATAGATATT
Found at i:30515570 original size:31 final size:31
Alignment explanation
Indices: 30515535--30515596 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
30515525 TTAACGGATA
30515535 CAAAATTTTCTACAATTTATTCAATTTAATT
1 CAAAATTTTCTACAATTTATTCAATTTAATT
*
30515566 CAAAATTTTCTATAATTTATTCAATTTAATT
1 CAAAATTTTCTACAATTTATTCAATTTAATT
30515597 TGATGTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (31 bp):
CAAAATTTTCTACAATTTATTCAATTTAATT
Found at i:30517375 original size:19 final size:19
Alignment explanation
Indices: 30517333--30517377 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
30517323 GGTACTAAAA
30517333 AAATTAATTTTAAATTAATT
1 AAATT-ATTTTAAATTAATT
*
30517353 -AATTATTTTAAATTTATT
1 AAATTATTTTAAATTAATT
30517371 AAATTAT
1 AAATTAT
30517378 GAATTGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTATTTTAAATTAATT
Found at i:30524534 original size:44 final size:44
Alignment explanation
Indices: 30524485--30524701 Score: 265
Period size: 44 Copynumber: 4.9 Consensus size: 44
30524475 CCTTTGAAAT
* * *
30524485 AGATTGAGGCCACAAATATTATCTCCCTGAAGTTGCAGTGGAAC
1 AGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
* *
30524529 AGATTGAAGTCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGT
1 AGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
* * * *
30524573 AGATTGAAGCCACTAACCTTATCTCCCTAAAGTTGTAGTGGAGC
1 AGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
* ** * *
30524617 AGGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGCA-TGGAGC
1 AGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
* **
30524660 AAATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGG
1 AGATTGAAGCCA-CAAATCTTATCTCCCTGAAGTTGCAGTGG
30524702 GGTATATTGA
Statistics
Matches: 148, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
43 15 0.10
44 130 0.88
45 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
AGATTGAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
Found at i:30526183 original size:42 final size:45
Alignment explanation
Indices: 30526120--30526296 Score: 191
Period size: 49 Copynumber: 3.8 Consensus size: 45
30526110 CTTCGTTTTC
** *
30526120 TCGATGCCATAGTTCAACTATGGTCTTACAC-ATC-T-TCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACAATCATATCACAT-A
30526163 T-GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC--AAT--CATATCACATA
*
30526211 TCGATGCCATAGCTCAGCTATGGTCTTACACGTAATCAAATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC--AATC--ATATCACATA
*
30526260 TCGATGCCATAGCCCAGCTATGATCTTACACGAATCA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-AATCA
30526297 CATATCTCAC
Statistics
Matches: 117, Mismatches: 7, Indels: 17
0.83 0.05 0.12
Matches are distributed among these distances:
42 26 0.22
43 1 0.01
45 2 0.02
46 1 0.01
47 2 0.02
48 7 0.06
49 78 0.67
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (45 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACAATCATATCACATA
Found at i:30526221 original size:49 final size:49
Alignment explanation
Indices: 30526155--30526380 Score: 252
Period size: 49 Copynumber: 4.7 Consensus size: 49
30526145 TTACACATCT
30526155 TCACATAAT-GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA
1 TCACAT-ATCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA
* *
30526204 TCACATATCGATGCCATAGCTCAGCTATGGTCTTACACGTAATCAAATA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA
*
30526253 TCACATATCGATGCCATAGCCCAGCTATGATCTTACACG-AATCACATA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA
* * * * * *
30526301 TCTCACTA---ATGCCATATCCCAGATATGGTCTTATACAGT-AGCATATA
1 TCACA-TATCGATGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATA
* * * *
30526348 TCAC--ACCGATGCCATATCCCAGATATAGTCTTA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTA
30526381 TACGGAAATC
Statistics
Matches: 156, Mismatches: 14, Indels: 16
0.84 0.08 0.09
Matches are distributed among these distances:
44 1 0.01
46 24 0.15
47 34 0.22
48 14 0.09
49 83 0.53
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (49 bp):
TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATA
Found at i:30526392 original size:95 final size:93
Alignment explanation
Indices: 30526164--30526380 Score: 242
Period size: 95 Copynumber: 2.3 Consensus size: 93
30526154 TTCACATAAT
* *
30526164 GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATATCGATGCCATAGCTCAGC
1 GATGCCATAGCCCAGCTAT-GTCTTACACG-AATCACATATCACATA-C-ATGCCATAGCCCAGA
* *
30526229 TATGGTCTTACACGTAATCAAATATCACATATC
62 TATGGTCTTACACGTAAGCAAATATCACA-ACC
* *
30526262 GATGCCATAGCCCAGCTATGATCTTACACGAATCACATATCTCACTA-ATGCCATATCCCAGATA
1 GATGCCATAGCCCAGCTATG-TCTTACACGAATCACATATCACA-TACATGCCATAGCCCAGATA
* *
30526326 TGGTCTTATACAGT-AGCATATATCAC-ACC
64 TGGTCTTACAC-GTAAGCAAATATCACAACC
* *
30526355 GATGCCATATCCCAGATATAGTCTTA
1 GATGCCATAGCCCAGCTAT-GTCTTA
30526381 TACGGAAATC
Statistics
Matches: 105, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
93 24 0.23
94 1 0.01
95 34 0.32
96 2 0.02
97 14 0.13
98 30 0.29
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.28
Consensus pattern (93 bp):
GATGCCATAGCCCAGCTATGTCTTACACGAATCACATATCACATACATGCCATAGCCCAGATATG
GTCTTACACGTAAGCAAATATCACAACC
Found at i:30526445 original size:31 final size:31
Alignment explanation
Indices: 30526402--30526519 Score: 177
Period size: 31 Copynumber: 3.8 Consensus size: 31
30526392 CTTGTCACTT
30526402 GTAGCCGAAGCTACCACTATTT-ACTGATCAG
1 GTAGCCGAAGCTACCACT-TTTCACTGATCAG
30526433 GTAGCC-AGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
30526464 GTAGCCGAAGCTGCCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
**
30526495 GTAGTAGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
30526520 TGTCATTTGT
Statistics
Matches: 80, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
30 4 0.05
31 75 0.94
32 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:30526589 original size:50 final size:51
Alignment explanation
Indices: 30526501--30526623 Score: 221
Period size: 50 Copynumber: 2.4 Consensus size: 51
30526491 TCAGGTAGTA
* *
30526501 GAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCC
30526552 GAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCC
30526602 GAAGCTATCACTTATCACTTGT
1 GAAGCTATCACTTATCACTTGT
30526624 TGCCATGGTC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
50 50 0.72
51 19 0.28
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (51 bp):
GAAGCTATCACTTATCACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCC
Found at i:30532459 original size:44 final size:44
Alignment explanation
Indices: 30532396--30532479 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
30532386 TATAATGGCG
30532396 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCACT
* *
30532440 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT
30532480 TGTAATGGCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCACT
Found at i:30532587 original size:44 final size:44
Alignment explanation
Indices: 30532498--30532681 Score: 188
Period size: 44 Copynumber: 4.2 Consensus size: 44
30532488 CGAATCTTAA
* * ** *
30532498 CCACAAATCTTATCTCCCTAAAGCTGCAGTGGAACATATTGAAG
1 CCACAAATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAG
* * * *
30532542 CCATAAATCTTATCTCCCTGAAGTTACAGTAGAGTAGATTTAAG
1 CCACAAATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAG
* * *
30532586 CCACTAATCTTATCTCCCTAAAGTTGTAGTAGAGTAGGTTGAAG
1 CCACAAATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAG
** * * * * *
30532630 TTACAAGTCTTATCTCCCTGAAGTTGCAGTAGGGTATATTGAAA
1 CCACAAATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAG
*
30532674 CAACAAAT
1 CCACAAAT
30532682 TCTATACCTC
Statistics
Matches: 111, Mismatches: 29, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 111 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (44 bp):
CCACAAATCTTATCTCCCTAAAGTTGCAGTAGAGTAGATTGAAG
Found at i:30533667 original size:16 final size:17
Alignment explanation
Indices: 30533636--30533668 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30533626 TTCATAAGTA
30533636 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
30533653 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
30533669 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:30534014 original size:46 final size:46
Alignment explanation
Indices: 30533949--30534358 Score: 493
Period size: 46 Copynumber: 9.0 Consensus size: 46
30533939 TTATCTTTGA
* * * *
30533949 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
* **
30533995 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* ** * **
30534041 TACATTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * **
30534086 CATGTTACCATGGTATCTTTCAACTATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* ** * **
30534132 TACATTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
30534177 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
30534223 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
30534269 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
30534315 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
30534359 TTCAGAAAGT
Statistics
Matches: 319, Mismatches: 42, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
45 79 0.25
46 240 0.75
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:30534116 original size:91 final size:92
Alignment explanation
Indices: 30533954--30534356 Score: 506
Period size: 91 Copynumber: 4.4 Consensus size: 92
30533944 TTTGACATGA
* * * * * *
30533954 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
***
30534019 CATGGTCTTGTTCATTTCATGTTACAT
66 CATGGTCTTACACATTTCATGTTACAT
* *
30534046 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGTCATGTTACCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
* ***
30534110 TATGGTCTTGTTCATTTCATGTTACAT
66 CATGGTCTTACACATTTCATGTTACAT
*
30534137 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
* * * *
30534201 CATGGTCTTACACATTTTAT-ATCCTGT
66 CATGGTCTTACACATTTCATGTTAC-AT
* ***
30534228 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
* * **
30534293 CATGGTCTTACACATTTCATATCATGT
66 CATGGTCTTACACATTTCATGTTACAT
* *
30534320 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTC
30534357 ATTTCAGAAA
Statistics
Matches: 279, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
90 2 0.01
91 163 0.58
92 114 0.41
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATGTTACAT
Found at i:30534234 original size:137 final size:138
Alignment explanation
Indices: 30533949--30534357 Score: 518
Period size: 137 Copynumber: 3.0 Consensus size: 138
30533939 TTATCTTTGA
* * * *
30533949 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCAGGTTGCCATGGTATCT
1 CATGTTGCCATGGTATCTTTCAACTATGGTCTTACTCA-TTTCATGTCACGTTGCCATGGTATCT
* * ** **
30534013 TTCAACCATGGTCTTGTTCATTTCATGTTACATTGCCATGGTATCTTTCAACCATGGTCTTATTC
65 TTCAACCATGGTCTTATTCATTTCATGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
* *
30534078 A-TTCCCGT
130 ATTTCACAT
* ** * *
30534086 CATGTTACCATGGTATCTTTCAACTATGGTCTTGTTCATTTCATGTTACATTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACTATGGTCTTACTCATTTCATGTCACGTTGCCATGGTATCTT
**
30534151 TCAACCATGGTCTTATTCA-TTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
66 TCAACCATGGTCTTATTCATTTCATGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
* *
30534215 TTTTATAT
131 TTTCACAT
* * * * *
30534223 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACTATGGTCTTACTCATTTCATGTCACGTTGCCATGGTATCTT
** * *
30534288 TCAACCATGGTCTTACACATTTCATATCATGTTGTCATGGTATCTTTCAACCATGGTCTTACACA
66 TCAACCATGGTCTTATTCATTTCATGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
30534353 TTTCA
131 TTTCA
30534358 TTTCAGAAAG
Statistics
Matches: 231, Mismatches: 38, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
136 42 0.18
137 144 0.62
138 45 0.19
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (138 bp):
CATGTTGCCATGGTATCTTTCAACTATGGTCTTACTCATTTCATGTCACGTTGCCATGGTATCTT
TCAACCATGGTCTTATTCATTTCATGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
TTTCACAT
Found at i:30534310 original size:21 final size:21
Alignment explanation
Indices: 30534286--30534357 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
30534276 CCATGGTATC
30534286 TTTCAACCATGGTCTTACACA
1 TTTCAACCATGGTCTTACACA
* *
30534307 TTTCATATCATGTTGTCATGGTA-TC-
1 TTTCA-ACCATG--GTC-T--TACACA
30534332 TTTCAACCATGGTCTTACACA
1 TTTCAACCATGGTCTTACACA
30534353 TTTCA
1 TTTCA
30534358 TTTCAGAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.40
Consensus pattern (21 bp):
TTTCAACCATGGTCTTACACA
Found at i:30537626 original size:3 final size:3
Alignment explanation
Indices: 30537620--30537670 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
30537610 GTGTTGTTTC
30537620 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
30537669 TT
1 TT
30537671 CATGCATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30537770 original size:4 final size:4
Alignment explanation
Indices: 30537761--30537797 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
30537751 TTTTCTTCTA
* *
30537761 TATT TATT TATT TATG TATT TATG TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT T
30537798 CCTCGTCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:30541048 original size:30 final size:30
Alignment explanation
Indices: 30541014--30541072 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
30541004 CAATAATTCG
*
30541014 TCAATCAACTCATCATCATAATCGATATCA
1 TCAATCAACTCATCATCATAATCAATATCA
*
30541044 TCAATCAACTCATTATCATAATCAATATC
1 TCAATCAACTCATCATCATAATCAATATC
30541073 GTCATCCTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.25, G:0.02, T:0.32
Consensus pattern (30 bp):
TCAATCAACTCATCATCATAATCAATATCA
Found at i:30541578 original size:41 final size:41
Alignment explanation
Indices: 30541521--30541603 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
30541511 ACATTTATAG
30541521 ATAGATGTCTTTTAATTATACTCTAATTAGGAATCCAATAC
1 ATAGATGTCTTTTAATTATACTCTAATTAGGAATCCAATAC
* *
30541562 ATAGATGTGTTTTAATTATACTCTATTTAGGAATCCAATAC
1 ATAGATGTCTTTTAATTATACTCTAATTAGGAATCCAATAC
30541603 A
1 A
30541604 GAAGTGGAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (41 bp):
ATAGATGTCTTTTAATTATACTCTAATTAGGAATCCAATAC
Found at i:30556227 original size:129 final size:128
Alignment explanation
Indices: 30556073--30556394 Score: 434
Period size: 107 Copynumber: 2.7 Consensus size: 128
30556063 ATAATTAATA
30556073 TTGTTAATTACTCTGATAAAATTTTTGACGTGTTTTTTTAAACAAAATATTAGTTTAACAAAATA
1 TTGTTAATTACTCTGATAAAATTTTTGACGTGTTTTTTTAAACAAAATATTAGTTTAACAAAA-A
*
30556138 ATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
65 ATGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
* **
30556202 TTGTTAATTACTCT-ATAAAATTTTT----TATTAGTTT-AAC-----A--A----AAC----AA
1 TTGTTAATTACTCTGATAAAATTTTTGACGTGTTTTTTTAAACAAAATATTAGTTTAACAAAAAA
*
30556246 TGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAATTTT
66 TGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
30556309 TTGTTAATTACTCTGATAAAATTTTTGACGTGTTTTTTTAAACAAAATATTAGTTTAACAAAACA
1 TTGTTAATTACTCTGATAAAATTTTTGACGTGTTTTTTTAAACAAAATATTAGTTTAACAAAA-A
30556374 ATGATATGTTAAGTTGGAATA
65 ATGATATGTTAAGTTGGAATA
30556395 CATTTTTGTT
Statistics
Matches: 163, Mismatches: 8, Indels: 44
0.76 0.04 0.20
Matches are distributed among these distances:
107 77 0.47
108 11 0.07
112 9 0.06
113 3 0.02
116 1 0.01
118 2 0.01
120 1 0.01
123 3 0.02
124 9 0.06
128 11 0.07
129 36 0.22
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (128 bp):
TTGTTAATTACTCTGATAAAATTTTTGACGTGTTTTTTTAAACAAAATATTAGTTTAACAAAAAA
TGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
Found at i:30558779 original size:65 final size:64
Alignment explanation
Indices: 30558663--30558843 Score: 310
Period size: 65 Copynumber: 2.8 Consensus size: 64
30558653 CCATATGTTC
*
30558663 TCGAGTTAACTTATGAAACTAACTT-ATCGACAACATTATTAATATATACAATCTTGAGTTGGTG
1 TCGAGTTAACTTATGAAAC-AACTTAATCAACAACATTATTAATATATACAATCTTGAGTTGGTG
*
30558727 TCGAGTTAACTTGTGAAATCAACTTAATCAACAACATTATTAATATATACAATCTTGAGTTGGTG
1 TCGAGTTAACTTATGAAA-CAACTTAATCAACAACATTATTAATATATACAATCTTGAGTTGGTG
30558792 TCGAGTTAACTTATGAAACCAACTTAATCAACAACATTATTAATATATACAA
1 TCGAGTTAACTTATGAAA-CAACTTAATCAACAACATTATTAATATATACAA
30558844 CTGATGAAGG
Statistics
Matches: 111, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
64 22 0.20
65 89 0.80
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (64 bp):
TCGAGTTAACTTATGAAACAACTTAATCAACAACATTATTAATATATACAATCTTGAGTTGGTG
Found at i:30561838 original size:17 final size:19
Alignment explanation
Indices: 30561805--30561841 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
30561795 ATAAATTACA
30561805 ATAATAACAATAATAAAAG
1 ATAATAACAATAATAAAAG
30561824 ATAA-AACAA-AATAAAAG
1 ATAATAACAATAATAAAAG
30561841 A
1 A
30561842 ATATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 5 0.28
19 4 0.22
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (19 bp):
ATAATAACAATAATAAAAG
Found at i:30568513 original size:16 final size:15
Alignment explanation
Indices: 30568492--30568539 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
30568482 TTTTAAAGAA
*
30568492 AATATATACGTAAAAT
1 AATATATACAT-AAAT
*
30568508 AATATA-ACATCAAT
1 AATATATACATAAAT
30568522 AATATATACATAGAAT
1 AATATATACATA-AAT
30568538 AA
1 AA
30568540 GAAAATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 9 0.33
15 7 0.26
16 11 0.41
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.29
Consensus pattern (15 bp):
AATATATACATAAAT
Found at i:30569276 original size:7 final size:8
Alignment explanation
Indices: 30569259--30569283 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
30569249 TTAAAAGCAG
30569259 AAATAAAA
1 AAATAAAA
30569267 AAATAAAA
1 AAATAAAA
30569275 AAATAAAA
1 AAATAAAA
30569283 A
1 A
30569284 CTAAACACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:30569687 original size:4 final size:4
Alignment explanation
Indices: 30569666--30569699 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
30569656 TAATTTAATA
30569666 AAAT AAAAT AAA- AAAT AAAT AAAT AAAT AAAT AA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
30569700 TATCTTCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
3 3 0.11
4 21 0.75
5 4 0.14
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:30571290 original size:20 final size:20
Alignment explanation
Indices: 30571267--30571309 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
30571257 TTTAAATTCT
30571267 AAAATCTGAAAAGTAAGACC
1 AAAATCTGAAAAGTAAGACC
* *
30571287 AAAATTTGAAAAGTAATACC
1 AAAATCTGAAAAGTAAGACC
30571307 AAA
1 AAA
30571310 TTCTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (20 bp):
AAAATCTGAAAAGTAAGACC
Found at i:30576471 original size:31 final size:30
Alignment explanation
Indices: 30576417--30576504 Score: 140
Period size: 31 Copynumber: 2.9 Consensus size: 30
30576407 GTCATTAAGG
*
30576417 TATTTGAAAGTTTTTATTAAGTCACTAAAC
1 TATTTGAAAGTTTTTTTTAAGTCACTAAAC
30576447 TATTTGAAAGTTTTTCTTTAAGTCACTAAAC
1 TATTTGAAAGTTTTT-TTTAAGTCACTAAAC
* *
30576478 TATTCGAAAGTTTTTTTAAAGTCACTA
1 TATTTGAAAGTTTTTTTTAAGTCACTA
30576505 GACGATTAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 26 0.48
31 28 0.52
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (30 bp):
TATTTGAAAGTTTTTTTTAAGTCACTAAAC
Found at i:30576634 original size:65 final size:65
Alignment explanation
Indices: 30576538--30576669 Score: 167
Period size: 65 Copynumber: 2.0 Consensus size: 65
30576528 TTCGATTAAT
* * * *
30576538 TAGCTCTAAGCGACTATTCAACAATCGGTACAGTAGATCAGCATTCATC-AATAAGTAGAAGAAC
1 TAGCTCCAAGCGACTAGTCAACAATCAGTACAGTAGATCAGCATTCATCGAA-AAGAAGAAGAAC
30576602 A
65 A
* * * **
30576603 TAGCTCCAAGTGACTAGTCGACAATTAGTACAGTAGATCAGTTTTCATCGAAAAGAAGAAGAACA
1 TAGCTCCAAGCGACTAGTCAACAATCAGTACAGTAGATCAGCATTCATCGAAAAGAAGAAGAACA
30576668 TA
1 TA
30576670 CTTTAGATTC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 55 0.96
66 2 0.04
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (65 bp):
TAGCTCCAAGCGACTAGTCAACAATCAGTACAGTAGATCAGCATTCATCGAAAAGAAGAAGAACA
Found at i:30577991 original size:42 final size:42
Alignment explanation
Indices: 30577931--30578011 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
30577921 CATGAATTTA
* *
30577931 ATGTAATTATATGCATTAAATTTGAATT-TTGATTTATATGCG
1 ATGTAATTATATACATTAAATTTAAATTATT-ATTTATATGCG
* *
30577973 ATGTAATTATGTATATTAAATTTAAATTATTATTTATAT
1 ATGTAATTATATACATTAAATTTAAATTATTATTTATAT
30578012 ATATGCATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (42 bp):
ATGTAATTATATACATTAAATTTAAATTATTATTTATATGCG
Found at i:30578332 original size:13 final size:13
Alignment explanation
Indices: 30578314--30578343 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30578304 TTCATTTCGT
30578314 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
30578327 AAAAAAGAAAAAG
1 AAAAAAAAAAAAG
30578340 AAAA
1 AAAA
30578344 GGTTCAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:30583479 original size:23 final size:23
Alignment explanation
Indices: 30583453--30583500 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
30583443 TAGTGTTCTT
30583453 TTGGCCTCATATCAAAGTCACTA
1 TTGGCCTCATATCAAAGTCACTA
30583476 TTGGCCTCATATCAAAGTCACTA
1 TTGGCCTCATATCAAAGTCACTA
30583499 TT
1 TT
30583501 AAGGTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (23 bp):
TTGGCCTCATATCAAAGTCACTA
Found at i:30591554 original size:23 final size:23
Alignment explanation
Indices: 30591528--30591581 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
30591518 ATATTTGTTA
*
30591528 TATATTTATTTTGTTATGCAAGG
1 TATATATATTTTGTTATGCAAGG
30591551 TATATATATTTTGTTATGCAAGG
1 TATATATATTTTGTTATGCAAGG
30591574 TATGATAT
1 TAT-ATAT
30591582 TGTGGAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.50
Consensus pattern (23 bp):
TATATATATTTTGTTATGCAAGG
Found at i:30594501 original size:53 final size:53
Alignment explanation
Indices: 30594353--30594518 Score: 212
Period size: 53 Copynumber: 3.1 Consensus size: 53
30594343 GACGAAAAAT
* * **
30594353 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGAATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
30594405 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
30594458 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
30594512 TATGTGA
1 -ATGTGA
30594519 ACCGTGTAAG
Statistics
Matches: 102, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 80 0.78
54 1 0.01
55 6 0.06
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:30597869 original size:23 final size:23
Alignment explanation
Indices: 30597841--30597887 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
30597831 AAAAGGAATA
30597841 TTCTATTTTCCTAGTAATAAAAT
1 TTCTATTTTCCTAGTAATAAAAT
30597864 TTCTATTTTCCTAGTAATAAAAT
1 TTCTATTTTCCTAGTAATAAAAT
30597887 T
1 T
30597888 CAAAGTATGG
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:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (23 bp):
TTCTATTTTCCTAGTAATAAAAT
Found at i:30598043 original size:104 final size:105
Alignment explanation
Indices: 30597888--30598078 Score: 285
Period size: 104 Copynumber: 1.8 Consensus size: 105
30597878 TAATAAAATT
* * * * *
30597888 CAAAGTATGGAACAAAGAACAATAAAAGAAAAGTATGAATTAATTTATAGCTGGATAAACAATGG
1 CAAAATATGGAACAAAAAACAATAAAAGAAAAGTATAAATTAATTTATAGCTCGATAAAAAATGG
*
30597953 TGTAACCATTTTCTAAAAAAAAGGCTACTTTGTTTTCTTC
66 TCTAACCATTTTCTAAAAAAAAGGCTACTTTGTTTTCTTC
** * *
30597993 CAAAATATGGAA-AAAAAACAATAAAAGGGAAGTATAAATTAGTTTCTAGCTCGATAAAAAATGG
1 CAAAATATGGAACAAAAAACAATAAAAGAAAAGTATAAATTAATTTATAGCTCGATAAAAAATGG
30598057 TCTAACCATTTTCTAAAAAAAA
66 TCTAACCATTTTCTAAAAAAAA
30598079 TTTATTTTCC
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
104 65 0.86
105 11 0.14
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (105 bp):
CAAAATATGGAACAAAAAACAATAAAAGAAAAGTATAAATTAATTTATAGCTCGATAAAAAATGG
TCTAACCATTTTCTAAAAAAAAGGCTACTTTGTTTTCTTC
Found at i:30605983 original size:21 final size:21
Alignment explanation
Indices: 30605957--30605997 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30605947 AGACGAGCAA
*
30605957 TACTCCACAGCAGGTGGAGTG
1 TACTCCACAACAGGTGGAGTG
*
30605978 TACTCCAGAACAGGTGGAGT
1 TACTCCACAACAGGTGGAGT
30605998 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.32, T:0.20
Consensus pattern (21 bp):
TACTCCACAACAGGTGGAGTG
Found at i:30608864 original size:22 final size:21
Alignment explanation
Indices: 30608839--30608883 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
30608829 TAAGCAATAG
30608839 AATTAAATATCAAG-AAAAGAAA
1 AATTAAA-A-CAAGAAAAAGAAA
30608861 AATTAAAACAAGAAAAAGAAA
1 AATTAAAACAAGAAAAAGAAA
30608882 AA
1 AA
30608884 CATGAACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.18
21 11 0.50
22 7 0.32
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.13
Consensus pattern (21 bp):
AATTAAAACAAGAAAAAGAAA
Found at i:30613572 original size:38 final size:38
Alignment explanation
Indices: 30613530--30613604 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
30613520 TAGTCCGATG
*
30613530 TTTACTTGCAAGTGTTAATTTCATTTTCATGTTTATTT
1 TTTACTTGCAAGTGCTAATTTCATTTTCATGTTTATTT
*
30613568 TTTACTTGCAAGTGCTATTTTCATTTTCATGTTTATT
1 TTTACTTGCAAGTGCTAATTTCATTTTCATGTTTATT
30613605 GCATCAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.20, C:0.12, G:0.11, T:0.57
Consensus pattern (38 bp):
TTTACTTGCAAGTGCTAATTTCATTTTCATGTTTATTT
Found at i:30613723 original size:14 final size:14
Alignment explanation
Indices: 30613704--30613732 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
30613694 ACTTTTGTTG
30613704 GGTTGTTTTAATTT
1 GGTTGTTTTAATTT
30613718 GGTTGTTTTAATTT
1 GGTTGTTTTAATTT
30613732 G
1 G
30613733 AAGAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.24, T:0.62
Consensus pattern (14 bp):
GGTTGTTTTAATTT
Found at i:30615085 original size:13 final size:15
Alignment explanation
Indices: 30615067--30615100 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
30615057 TCTCGATATG
30615067 TATCAAACAT-G-AA
1 TATCAAACATGGAAA
30615080 TATCAAACATGGAAA
1 TATCAAACATGGAAA
30615095 TATCAA
1 TATCAA
30615101 GAAAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 1 0.05
15 8 0.42
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.24
Consensus pattern (15 bp):
TATCAAACATGGAAA
Found at i:30620884 original size:25 final size:23
Alignment explanation
Indices: 30620844--30620891 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
30620834 ATTTTTTATA
* *
30620844 TTTAAATTTAATCTTTATATATTTT
1 TTTAAATTAAACCTTT-TAT-TTTT
30620869 TTTAAATTAAACCTTTTATTTTT
1 TTTAAATTAAACCTTTTATTTTT
30620892 AGAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 3 0.14
25 14 0.67
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTAAATTAAACCTTTTATTTTT
Found at i:30621865 original size:14 final size:14
Alignment explanation
Indices: 30621830--30621868 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
30621820 CTACTGATAT
30621830 AATATTTATATTTTAA
1 AATA-TTAT-TTTTAA
30621846 AA-ATTATTTTTAA
1 AATATTATTTTTAA
30621859 AATATTATTT
1 AATATTATTT
30621869 ATTTAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 11 0.50
15 1 0.05
16 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATTATTTTTAA
Found at i:30623831 original size:105 final size:105
Alignment explanation
Indices: 30623699--30623904 Score: 324
Period size: 105 Copynumber: 2.0 Consensus size: 105
30623689 TGCTAGTTAC
* * * *
30623699 CCTACCGTACTCATTCCAAATTCAACTTTTACGAGGTCAATAAATTCTTAAAAAGCTTTTGAA-G
1 CCTACCATACTCATTCCAAATTCAACTTTCACGAGATCAACAAATTCTTAAAAAGCTTTTGAATG
30623763 AAGTGAAATAAAAGAAAAATGTCATCCACATAGATTTTTCA
66 -AGTGAAATAAAAGAAAAATGTCATCCACATAGATTTTTCA
* * * *
30623804 CCTACCATACTCATTTCAAATTCAACTTTCACGAGATCTACAAATTCTTAAGAAGTTTTTGAATG
1 CCTACCATACTCATTCCAAATTCAACTTTCACGAGATCAACAAATTCTTAAAAAGCTTTTGAATG
30623869 AGTGAAATAAAAGAAAAATGTCATCCACATAGATTT
66 AGTGAAATAAAAGAAAAATGTCATCCACATAGATTT
30623905 GTCCTAAATT
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
105 91 0.99
106 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (105 bp):
CCTACCATACTCATTCCAAATTCAACTTTCACGAGATCAACAAATTCTTAAAAAGCTTTTGAATG
AGTGAAATAAAAGAAAAATGTCATCCACATAGATTTTTCA
Found at i:30625150 original size:5 final size:5
Alignment explanation
Indices: 30625126--30625165 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
30625116 TTTTGAAATC
* *
30625126 TTTTA ATTTA TCTTA GTTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTT
30625166 TCTCTCACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:30625166 original size:16 final size:15
Alignment explanation
Indices: 30625126--30625165 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
30625116 TTTTGAAATC
*
30625126 TTTTAATTTATCTTA
1 TTTTATTTTATCTTA
*
30625141 GTTTTATTTTATTTTA
1 -TTTTATTTTATCTTA
30625157 TTTTATTTT
1 TTTTATTTT
30625166 TCTCTCACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTATTTTATCTTA
Found at i:30625640 original size:22 final size:22
Alignment explanation
Indices: 30625610--30625654 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
30625600 TGGGAGTGTT
*
30625610 TTTGTATCAAAACGATACCAGG
1 TTTGCATCAAAACGATACCAGG
30625632 TTTGCATCAAAACGATACCAGG
1 TTTGCATCAAAACGATACCAGG
30625654 T
1 T
30625655 GTGTACTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (22 bp):
TTTGCATCAAAACGATACCAGG
Found at i:30627622 original size:18 final size:18
Alignment explanation
Indices: 30627599--30627635 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30627589 TAGTGAAATG
30627599 ATGTTAGAGGTTAACCCA
1 ATGTTAGAGGTTAACCCA
30627617 ATGTTAGAGGTTAACCCA
1 ATGTTAGAGGTTAACCCA
30627635 A
1 A
30627636 CTCTTTAACA
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:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (18 bp):
ATGTTAGAGGTTAACCCA
Found at i:30650491 original size:15 final size:15
Alignment explanation
Indices: 30650473--30650504 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30650463 AATACTAAAA
*
30650473 TTATATTTTAACATT
1 TTATATTTTAAAATT
30650488 TTATATTTTAAAATT
1 TTATATTTTAAAATT
30650503 TT
1 TT
30650505 TTTCTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATATTTTAAAATT
Found at i:30652869 original size:11 final size:11
Alignment explanation
Indices: 30652855--30652910 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
30652845 AGATAAATAT
30652855 TATTTTATTAA
1 TATTTTATTAA
*
30652866 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
30652879 TATTTTATTAT
1 TATTTTATTAA
*
30652890 TATTTTATTAT
1 TATTTTATTAA
30652901 TATTTTATTA
1 TATTTTATTA
30652911 GTATATAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
11 27 0.68
12 6 0.15
13 7 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:30655117 original size:45 final size:46
Alignment explanation
Indices: 30655050--30655225 Score: 230
Period size: 46 Copynumber: 3.8 Consensus size: 46
30655040 GCTCTCTGAT
** *
30655050 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
*
30655096 ATGAAATG-ATAAGAACATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* *
30655141 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * * * *
30655187 A-GAAAATGAGTAAGACCGTAGTTGAAAGACACTATGGCA
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
30655226 TCATGTCAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
45 42 0.36
46 74 0.64
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
Found at i:30655248 original size:91 final size:90
Alignment explanation
Indices: 30655060--30655230 Score: 227
Period size: 91 Copynumber: 1.9 Consensus size: 90
30655050 ATGAAATGTG
* * * *
30655060 TAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGATAAGAACATGGTTGAAAGAT
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGATAAGAACATAGTTGAAAGAC
*
30655125 ACCATGGCAACGTGACATGAAAAGAA
66 ACCATGGCAACATGACA-GAAAAGAA
* *
30655151 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCGTAGTTGAAAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGA-TAAGAACATAGTTGAAAG
* *
30655215 ACACTATGGCATCATG
64 ACACCATGGCAACATG
30655231 TCAAAGATAA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
90 1 0.01
91 41 0.59
92 27 0.39
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.20
Consensus pattern (90 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGATAAGAACATAGTTGAAAGAC
ACCATGGCAACATGACAGAAAAGAA
Found at i:30656629 original size:15 final size:15
Alignment explanation
Indices: 30656609--30656639 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30656599 TCAAATTAGT
30656609 TATTTACTATTATTA
1 TATTTACTATTATTA
*
30656624 TATTTATTATTATTA
1 TATTTACTATTATTA
30656639 T
1 T
30656640 TGTTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTACTATTATTA
Found at i:30656657 original size:18 final size:18
Alignment explanation
Indices: 30656612--30656658 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
30656602 AATTAGTTAT
30656612 TTACTATTATTATATTTA
1 TTACTATTATTATATTTA
* * *
30656630 TTATTATTATTGTTTTTA
1 TTACTATTATTATATTTA
*
30656648 TTACTGTTATT
1 TTACTATTATT
30656659 TTTATTATCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (18 bp):
TTACTATTATTATATTTA
Found at i:30656748 original size:25 final size:23
Alignment explanation
Indices: 30656709--30656770 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
30656699 TTATTACTTT
* *
30656709 CTATTATTGTAATTATTAACATATA
1 CTATTATTATTATTATT-A-ATATA
30656734 CTATTATTATTATTATTAATATA
1 CTATTATTATTATTATTAATATA
* *
30656757 TTATTATTACTATT
1 CTATTATTATTATT
30656771 TACATGTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 17 0.52
24 1 0.03
25 15 0.45
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (23 bp):
CTATTATTATTATTATTAATATA
Found at i:30656780 original size:20 final size:20
Alignment explanation
Indices: 30656735--30656780 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
30656725 TAACATATAC
* *
30656735 TATTATTATTATTATTAATA
1 TATTATTATTACTATTAACA
*
30656755 TATTATTATTACTATTTACA
1 TATTATTATTACTATTAACA
*
30656775 TGTTAT
1 TATTAT
30656781 CATTTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTATTATTACTATTAACA
Found at i:30656815 original size:3 final size:3
Alignment explanation
Indices: 30656807--30657037 Score: 105
Period size: 3 Copynumber: 76.7 Consensus size: 3
30656797 TATTACGGTT
* * * *
30656807 TTA TTA TTA TTA CTA TTA TTA CTA TTT TTA TT- TTCA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
* * * * * *
30656852 TTA TCA TCCTA TT- TTA TTA CTA TTA TCA CTT- TTG TAA TTA CTA TTA
1 TTA TTA T--TA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* ** *
30656898 TTA TTG TT- TTA TTA TTA TTA TTA TTTA GCA -TA TTA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* ** * * * * *
30656942 TTG CCA TCA TTA TTA TTA TTA TTA TTA CTTT TTA CTA TTA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * * * * *
30656988 TTA ATA TCA TTA GTA TTA TTA TTA TTA CTG TT- TTCA TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
30657033 TTA TT
1 TTA TT
30657038 TTTTTGTAAT
Statistics
Matches: 167, Mismatches: 48, Indels: 26
0.69 0.20 0.11
Matches are distributed among these distances:
2 11 0.07
3 145 0.87
4 9 0.05
5 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:30658257 original size:46 final size:46
Alignment explanation
Indices: 30658197--30658431 Score: 283
Period size: 46 Copynumber: 4.9 Consensus size: 46
30658187 TTTGATATGA
* * * * * *
30658197 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
30658243 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
30658289 TGCCATGGTATCTTTCAACCATTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATC--T------TTCAACCATGGTCTTACACATTTCATATCAGGT
*
30658343 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
30658389 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
30658432 AAGAGCACAC
Statistics
Matches: 168, Mismatches: 12, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
45 4 0.02
46 121 0.72
48 1 0.01
52 1 0.01
54 41 0.24
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:30658383 original size:100 final size:100
Alignment explanation
Indices: 30658210--30658410 Score: 305
Period size: 100 Copynumber: 2.0 Consensus size: 100
30658200 CATAGTGTCT
* * * * ***
30658210 TTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTC
1 TTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
*
30658275 ATTTCATATCACGTTGCCATGGTATCTTTCAACCA
66 ATTTCATATCACGCTGCCATGGTATCTTTCAACCA
30658310 TTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
1 TTCAACCATGGTCTTACACATTTTC-TATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
*
30658374 CATTTCATATCAGGCTGCCATGGTATCTTTCAACCA
65 CATTTCATATCACGCTGCCATGGTATCTTTCAACCA
30658410 T
1 T
30658411 GGTCTTACAC
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 4 0.04
100 87 0.96
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (100 bp):
TTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
ATTTCATATCACGCTGCCATGGTATCTTTCAACCA
Found at i:30661226 original size:51 final size:51
Alignment explanation
Indices: 30661171--30661279 Score: 200
Period size: 51 Copynumber: 2.1 Consensus size: 51
30661161 ATTTCTATAG
30661171 TTCTATAGTTTCTTTCTGTACATATTTACCCAATTTATCATTTATATCCAT
1 TTCTATAGTTTCTTTCTGTACATATTTACCCAATTTATCATTTATATCCAT
*
30661222 TTCTATAGTTTCTTTCTGTACATATTTACCCAATTTATCATTTGTATCCAT
1 TTCTATAGTTTCTTTCTGTACATATTTACCCAATTTATCATTTATATCCAT
30661273 TCTCTAT
1 T-TCTAT
30661280 CTTTTCATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
51 51 0.91
52 5 0.09
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51
Consensus pattern (51 bp):
TTCTATAGTTTCTTTCTGTACATATTTACCCAATTTATCATTTATATCCAT
Found at i:30661267 original size:26 final size:26
Alignment explanation
Indices: 30661187--30661267 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
30661177 AGTTTCTTTC
30661187 TGTACATATTTACCCAATTTATCATT
1 TGTACATATTTACCCAATTTATCATT
* * * * *
30661213 TATATC-CATTT--CTATAGTT-TCTTT
1 TGTA-CATATTTACCCA-ATTTATCATT
30661237 CTGTACATATTTACCCAATTTATCATT
1 -TGTACATATTTACCCAATTTATCATT
30661264 TGTA
1 TGTA
30661268 TCCATTCTCT
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
24 7 0.18
25 10 0.26
26 14 0.37
27 7 0.18
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (26 bp):
TGTACATATTTACCCAATTTATCATT
Found at i:30663562 original size:46 final size:46
Alignment explanation
Indices: 30663502--30663782 Score: 366
Period size: 46 Copynumber: 5.9 Consensus size: 46
30663492 TTTGACATGA
* * * * * *
30663502 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCACGT
***
30663548 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
*
30663594 TGCCATGGTATCTTTCAACCATTCAACCATGGTCTTACACATTTCATATTACGT
1 TGCCATGGTATC--T------TTCAACCATGGTCTTACACATTTCATATCACGT
*
30663648 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
*
30663694 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
30663740 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
30663783 GAGAGCACAC
Statistics
Matches: 213, Mismatches: 13, Indels: 18
0.87 0.05 0.07
Matches are distributed among these distances:
45 4 0.02
46 166 0.78
48 1 0.00
52 1 0.00
54 41 0.19
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
Found at i:30666601 original size:19 final size:19
Alignment explanation
Indices: 30666577--30666625 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
30666567 TTTTACACTA
30666577 AGGTACTAATTAATCAACT
1 AGGTACTAATTAATCAACT
30666596 AGGTACTAATTAATCAACT
1 AGGTACTAATTAATCAACT
*
30666615 AGGTACCAATT
1 AGGTACTAATT
30666626 TTTGGGCGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (19 bp):
AGGTACTAATTAATCAACT
Found at i:30669223 original size:23 final size:21
Alignment explanation
Indices: 30669171--30669266 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
30669161 CCTGATCAGT
** * *
30669171 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
30669192 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
30669213 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
30669234 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
30669255 AAATACGACACA
1 --ATACGACACA
30669267 TAAAGTGCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 57 0.85
23 10 0.15
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:30669231 original size:42 final size:43
Alignment explanation
Indices: 30669171--30669276 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 43
30669161 CCTGATCAGT
*
30669171 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG-
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
* * * *
30669213 ATACGACACACGAGGTGCCTGATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTG-A
*
30669257 ATACGACACATAAAGTGCCT
1 ATACGACACACAAAGTGCCT
30669277 GATCGATAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 37 0.69
44 17 0.31
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (43 bp):
ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
Found at i:30670744 original size:16 final size:17
Alignment explanation
Indices: 30670709--30670744 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
30670699 CCTAATTCTC
30670709 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
30670725 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
30670740 CCTTC
1 CCTTC
30670745 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:30677054 original size:21 final size:21
Alignment explanation
Indices: 30677026--30677163 Score: 204
Period size: 21 Copynumber: 6.5 Consensus size: 21
30677016 CCTGATCAGT
** * *
30677026 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
30677047 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
30677068 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
*
30677089 ATACGACACACGAGGTGCTTG
1 ATACGACACACGAGGTGCCTG
30677110 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
30677131 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
30677152 AAATACGACACA
1 --ATACGACACA
30677164 TAAAGTGCCT
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
21 97 0.91
23 10 0.09
ACGTcount: A:0.34, C:0.27, G:0.25, T:0.14
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:30678643 original size:16 final size:17
Alignment explanation
Indices: 30678608--30678643 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
30678598 CCTAATTCTC
30678608 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
30678624 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
30678639 CCTTC
1 CCTTC
30678644 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:30679894 original size:139 final size:139
Alignment explanation
Indices: 30679644--30679922 Score: 522
Period size: 139 Copynumber: 2.0 Consensus size: 139
30679634 ATGCCACATT
* *
30679644 ACCAAAAGAAAATATACATCACCAAAAGTTTGTTAAAGTCGGGTCTGGCTTTGGATGCTGGTTCA
1 ACCAAAAGAAAATATACATCACCAAAAGTTTGCTAAAGTCGGGTCTGGCTTTAGATGCTGGTTCA
*
30679709 GTACTTGACTTCTACAACCTGCGCACGGAAACAACCGTACGCTGAGTATGCATATACTCAGTGGT
66 GTACTTGACTTCTACAACCTGCGCACGGAAACAACCGTACACTGAGTATGCATATACTCAGTGGT
30679774 ATCACTATA
131 ATCACTATA
*
30679783 ACCAAAAGAAAATATACATCACCAAAAGTTTGCTGAAGTCGGGTCTGGCTTTAGATGCTGGTTCA
1 ACCAAAAGAAAATATACATCACCAAAAGTTTGCTAAAGTCGGGTCTGGCTTTAGATGCTGGTTCA
30679848 GTACTTGACTTCTACAACCTGCGCACGGAAACAACCGTACACTGAGTATGCATATACTCAGTGGT
66 GTACTTGACTTCTACAACCTGCGCACGGAAACAACCGTACACTGAGTATGCATATACTCAGTGGT
30679913 ATCACTATA
131 ATCACTATA
30679922 A
1 A
30679923 TTTAGTTTAT
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (139 bp):
ACCAAAAGAAAATATACATCACCAAAAGTTTGCTAAAGTCGGGTCTGGCTTTAGATGCTGGTTCA
GTACTTGACTTCTACAACCTGCGCACGGAAACAACCGTACACTGAGTATGCATATACTCAGTGGT
ATCACTATA
Found at i:30680240 original size:18 final size:18
Alignment explanation
Indices: 30680219--30680253 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30680209 AATCAGTAAT
*
30680219 CAGTAACGGTAGCAGTAG
1 CAGTAACGGTAACAGTAG
30680237 CAGTAACGGTAACAGTA
1 CAGTAACGGTAACAGTA
30680254 TTTGACACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.29, T:0.17
Consensus pattern (18 bp):
CAGTAACGGTAACAGTAG
Found at i:30681603 original size:33 final size:32
Alignment explanation
Indices: 30681545--30681607 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
30681535 ATTATTTAAT
30681545 TAATAAATATCTCTTAATTATAATAATAATAAA
1 TAATAAATATCTCTTAATTATAATAA-AATAAA
30681578 TAATAAATATCTAC-TAACTTA-AATAAAATA
1 TAATAAATATCT-CTTAA-TTATAATAAAATA
30681608 TTATAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 4 0.14
33 20 0.71
34 4 0.14
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.37
Consensus pattern (32 bp):
TAATAAATATCTCTTAATTATAATAAAATAAA
Found at i:30682629 original size:28 final size:28
Alignment explanation
Indices: 30682589--30682645 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
30682579 ATAAGGAGCC
30682589 GTCGGGTATGATCCTCTGCTCATGTTAA
1 GTCGGGTATGATCCTCTGCTCATGTTAA
30682617 GTCGGGTATGATCCTCTGCTCATGTTAA
1 GTCGGGTATGATCCTCTGCTCATGTTAA
30682645 G
1 G
30682646 ATAGTATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (28 bp):
GTCGGGTATGATCCTCTGCTCATGTTAA
Found at i:30691304 original size:38 final size:38
Alignment explanation
Indices: 30691261--30691417 Score: 260
Period size: 38 Copynumber: 4.1 Consensus size: 38
30691251 AAAGGCTCGA
* *
30691261 ATATAATACCAGCACTAGGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
30691299 ATATAATACCAGCAAGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
30691337 ATATATTACCAGCACGAAGCCTGCGGAATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
30691375 ATATAATACCAGCACGAAACCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
30691413 ATATA
1 ATATA
30691418 CATTAAATAT
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 110 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:30697012 original size:38 final size:38
Alignment explanation
Indices: 30696969--30697276 Score: 501
Period size: 38 Copynumber: 8.1 Consensus size: 38
30696959 AAAGGCTCGA
* *
30696969 ATATAATACCAGCACTAGGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
30697007 ATATAATACCAGCACCAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
30697045 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
30697083 ATACAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
30697121 ATATAATACCAGCACGAAGCCTGTGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * **
30697159 ACATATTACCAGCACGAAGCCTGCGGGATTT-ACCTAG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
30697196 ATATAATACCAGCACGAAGCCTGCGGGATTTAACTCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
30697234 ATATAATACCAGTACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
30697272 ATATA
1 ATATA
30697277 CATCAAATAT
Statistics
Matches: 249, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
37 33 0.13
38 216 0.87
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:30701785 original size:44 final size:42
Alignment explanation
Indices: 30701737--30702054 Score: 133
Period size: 44 Copynumber: 7.2 Consensus size: 42
30701727 CTTATCTCCT
30701737 TAAGCAGTAGTGGAGTAGATCGAAGGCAGTAAGCCTTAACCCCC
1 TAAGCAGTAGTGGAGTAGATCGAA-G-AGTAAGCCTTAACCCCC
** * * * * * *
30701781 TAAGCAGTAG-GGTAACAGGCTGGAA-ATTACAGATCTTATCTCCC
1 TAAGCAGTAGTGG-AGTA-GATCGAAGAGTA-AG-CCTTAACCCCC
30701825 TAAGCAGTAGTGGAGTAGATCGAAGATAGTAAGCCTTAACCCCC
1 TAAGCAGTAGTGGAGTAGATCGAAG--AGTAAGCCTTAACCCCC
* * ** * * * ** * *
30701869 TAAGCAGTAGAGAAACAGGCTAGAA-ATTACAGATGTTATCTCCC
1 TAAGCAGTAGTGGAGTA-GATCGAAGAGTA-AG-CCTTAACCCCC
* * *
30701913 TAAGCAATAGTGGAGCAGATTGAAGACGGTAAGCCTTAACCCCC
1 TAAGCAGTAGTGGAGTAGATCGAAGA--GTAAGCCTTAACCCCC
* ** * * * * * *
30701957 TAAGGAGTAG-GGTAACAGGCTGGAA-ATTACAGATCTTATCTCCC
1 TAAGCAGTAGTGG-AGTA-GATCGAAGAGTA-AG-CCTTAACCCCC
* *
30702001 TAAGCAGTAGTGGAGCAGATTGAAGACAGTAAGCCTTAACCCCC
1 TAAGCAGTAGTGGAGTAGATCGAAG--AGTAAGCCTTAACCCCC
30702045 TAAGCAGTAG
1 TAAGCAGTAG
30702055 GGTAACAGGC
Statistics
Matches: 197, Mismatches: 55, Indels: 44
0.67 0.19 0.15
Matches are distributed among these distances:
42 8 0.04
43 25 0.13
44 131 0.66
45 25 0.13
46 8 0.04
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (42 bp):
TAAGCAGTAGTGGAGTAGATCGAAGAGTAAGCCTTAACCCCC
Found at i:30701829 original size:88 final size:88
Alignment explanation
Indices: 30701670--30702154 Score: 718
Period size: 88 Copynumber: 5.5 Consensus size: 88
30701660 CATGTCCCTA
* * * * * *
30701670 GAAGACGGTGAGCCTTAACTCCCTAAGCAGTAGGGTAATAGGCTGGAAACTAAAGATCTTATCTC
1 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
* *
30701735 CTTAAGCAGTAGTGGAGTAGATC
66 CCTAAGCAGTAGTGGAGCAGATC
*
30701758 GAAGGCAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
1 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
*
30701823 CCTAAGCAGTAGTGGAGTAGATC
66 CCTAAGCAGTAGTGGAGCAGATC
* * * * *
30701846 GAAGATAGTAAGCCTTAACCCCCTAAGCAGTAGAGAAACAGGCTAGAAATTACAGATGTTATCTC
1 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
* *
30701911 CCTAAGCAATAGTGGAGCAGATT
66 CCTAAGCAGTAGTGGAGCAGATC
* *
30701934 GAAGACGGTAAGCCTTAACCCCCTAAGGAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
1 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
*
30701999 CCTAAGCAGTAGTGGAGCAGATT
66 CCTAAGCAGTAGTGGAGCAGATC
* * *
30702022 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTATAGATCTTATCAC
1 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
*
30702087 CCTAAGCAGTAGGGGAGCAGATC
66 CCTAAGCAGTAGTGGAGCAGATC
* * * *
30702110 AAAGACGGTGAGCCTTAACCCCCTCAGCAGTAGGGTAACAGGCTG
1 GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTG
30702155 AAGATCAAAA
Statistics
Matches: 361, Mismatches: 36, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 361 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (88 bp):
GAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGATCTTATCTC
CCTAAGCAGTAGTGGAGCAGATC
Found at i:30702090 original size:44 final size:43
Alignment explanation
Indices: 30701771--30702100 Score: 190
Period size: 44 Copynumber: 7.5 Consensus size: 43
30701761 GGCAGTAAGC
* *
30701771 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGGAAATTACAGAT
1 CTTATCCCCCTAAGCAGTAGGG-AACAGGCTGAAAATTACAGAT
* ** * * *
30701815 CTTATCTCCCTAAGCAGTAGTGGAGTA-GATCGAAGATAGTA-AG-C
1 CTTATCCCCCTAAGCAGTAG-GGAACAGGCT-GAA-A-ATTACAGAT
* *
30701859 CTTAACCCCCTAAGCAGTAGAGAAACAGGCT-AGAAATTACAGAT
1 CTTATCCCCCTAAGCAGTAG-GGAACAGGCTGA-AAATTACAGAT
* * * * ** ** *
30701903 GTTATCTCCCTAAGCAATAGTGGAGCAGATTGAAGACGGTA-AG-C
1 CTTATCCCCCTAAGCAGTAG-GGAACAGGCTGAA-A-ATTACAGAT
* * *
30701947 CTTAACCCCCTAAGGAGTAGGGTAACAGGCTGGAAATTACAGAT
1 CTTATCCCCCTAAGCAGTAGGG-AACAGGCTGAAAATTACAGAT
* * ** * *
30701991 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGTA-AG-C
1 CTTATCCCCCTAAGCAGTAG-GGAACAGGCTGAA-A-ATTACAGAT
* *
30702035 CTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAAATTATAGAT
1 CTTATCCCCCTAAGCAGTAGGG-AACAGGCTGAAAATTACAGAT
*
30702079 CTTATCACCCTAAGCAGTAGGG
1 CTTATCCCCCTAAGCAGTAGGG
30702101 GAGCAGATCA
Statistics
Matches: 207, Mismatches: 59, Indels: 40
0.68 0.19 0.13
Matches are distributed among these distances:
42 8 0.04
43 16 0.08
44 159 0.77
45 16 0.08
46 8 0.04
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (43 bp):
CTTATCCCCCTAAGCAGTAGGGAACAGGCTGAAAATTACAGAT
Found at i:30702416 original size:45 final size:42
Alignment explanation
Indices: 30702303--30702425 Score: 140
Period size: 41 Copynumber: 2.9 Consensus size: 42
30702293 AGCTATGAAT
*
30702303 AAACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA-GATCA
1 AAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGATCA
* * *
30702344 AAACAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGA
1 AAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGATCA
* * * *
30702386 AGTCACCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 A---AACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
30702426 ACTAAAACAC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 34 0.49
42 4 0.06
45 31 0.45
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (42 bp):
AAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGATCA
Found at i:30702779 original size:19 final size:19
Alignment explanation
Indices: 30702726--30702779 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
30702716 AAGCCCAAAT
30702726 CAAA-CCAAAACCCAGATTA
1 CAAACCCAAAACCCA-ATTA
* ** *
30702745 AAAACCCATCAGCCAATTA
1 CAAACCCAAAACCCAATTA
30702764 CAAACCCAAAACCCAA
1 CAAACCCAAAACCCAA
30702780 ACCTAAATCA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.52, C:0.35, G:0.04, T:0.09
Consensus pattern (19 bp):
CAAACCCAAAACCCAATTA
Found at i:30703912 original size:28 final size:27
Alignment explanation
Indices: 30703852--30703913 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
30703842 ATCATTTTTC
*
30703852 ATTATTTTGCTATTTTATTTTTAAATT
1 ATTATTTTGCTATTTTATATTTAAATT
*
30703879 AGTTATTTT-CTATTATTATATTTATTATT
1 A-TTATTTTGCTATT-TTATATTTA-AATT
30703908 ATTATT
1 ATTATT
30703914 GTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.20
28 20 0.67
29 4 0.13
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.66
Consensus pattern (27 bp):
ATTATTTTGCTATTTTATATTTAAATT
Found at i:30703921 original size:15 final size:15
Alignment explanation
Indices: 30703882--30703923 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
30703872 TTAAATTAGT
*
30703882 TATTTTCTATTATTA
1 TATTTTTTATTATTA
*
30703897 TATTTATTATTATTA
1 TATTTTTTATTATTA
30703912 T-TGTTTTTATTA
1 TAT-TTTTTATTA
30703924 CTGTTATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (15 bp):
TATTTTTTATTATTA
Found at i:30704012 original size:22 final size:22
Alignment explanation
Indices: 30703987--30704028 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
30703977 TACTTTCGAT
30703987 TATTATCATTATTAACATATAC
1 TATTATCATTATTAACATATAC
* *
30704009 TATTATTATTATTAATATAT
1 TATTATCATTATTAACATAT
30704029 TATTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTATCATTATTAACATATAC
Found at i:30704032 original size:20 final size:20
Alignment explanation
Indices: 30703985--30704051 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
30703975 ATTACTTTCG
*
30703985 ATTATTATCATTATTAACATAT
1 ATTATTATTATTATT-A-ATAT
*
30704007 ACTATTATTATTATTAATAT
1 ATTATTATTATTATTAATAT
* *
30704027 ATTATTATTACTATTTATAT
1 ATTATTATTATTATTAATAT
*
30704047 GTTAT
1 ATTAT
30704052 CATTTCTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 25 0.64
21 1 0.03
22 13 0.33
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.55
Consensus pattern (20 bp):
ATTATTATTATTATTAATAT
Found at i:30704218 original size:41 final size:41
Alignment explanation
Indices: 30704137--30704218 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
30704127 TATCATCCTA
* * *
30704137 TTTTATTACTATTATCACTTTTGTAATTACTATTACTATTG
1 TTTTATTACTATTATCACTTTAGCAATTACTACTACTATTG
* * *
30704178 TTTTATTACTATTATTA-TTTAGCATATTATTACTATTATTG
1 TTTTATTACTATTATCACTTTAGCA-ATTACTACTACTATTG
30704219 CCATCATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 5 0.15
41 29 0.85
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (41 bp):
TTTTATTACTATTATCACTTTAGCAATTACTACTACTATTG
Found at i:30704316 original size:3 final size:3
Alignment explanation
Indices: 30704078--30704300 Score: 87
Period size: 3 Copynumber: 74.0 Consensus size: 3
30704068 TATTACGGTT
* * * * *
30704078 TTA TTA TTA TTA CTA TTA TTA CTA TTT TTA TT- TTCA TCA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
* * * * * *
30704123 TTA TTA TCA TCCTA TT- TTA TTA CTA TTA TCA CTT- TTG TAA TTA CTA
1 TTA TTA TTA T--TA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * ** *
30704169 TTA CTA TTG TT- TTA TTA CTA TTA TTA TTTA GCA -TA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* ** * * * *
30704213 TTA TTG CCA TCA TTA TTA TTA TTA TTA TTA CTTT TTA CTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * * * *
30704259 TTA CTA CTA TTA ATA TCA TTA GTA TTA GTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30704301 CTGTTTTCAT
Statistics
Matches: 158, Mismatches: 51, Indels: 22
0.68 0.22 0.10
Matches are distributed among these distances:
2 9 0.06
3 140 0.89
4 7 0.04
5 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:30705873 original size:23 final size:23
Alignment explanation
Indices: 30705842--30705890 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
30705832 AAATGAGATG
30705842 TTTAAAAAT-TAATTTTAA-ATATT
1 TTTAAAAATAT-ATTTTAATA-ATT
*
30705865 TTTATAAATATATTTTAATAATT
1 TTTAAAAATATATTTTAATAATT
30705888 TTT
1 TTT
30705891 CGATTCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTAAAAATATATTTTAATAATT
Found at i:30707073 original size:21 final size:21
Alignment explanation
Indices: 30707049--30707092 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
30707039 CTTGGTATGA
* *
30707049 TGCAAGGTGAGCTTACTCAGT
1 TGCAAGCTGAACTTACTCAGT
*
30707070 TGCAAGCTGAATTTACTCAGT
1 TGCAAGCTGAACTTACTCAGT
30707091 TG
1 TG
30707093 GATGCTAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (21 bp):
TGCAAGCTGAACTTACTCAGT
Found at i:30711075 original size:15 final size:15
Alignment explanation
Indices: 30711055--30711084 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30711045 TATTTTATTT
*
30711055 ATATTAGGATAATTA
1 ATATTAAGATAATTA
30711070 ATATTAAGATAATTA
1 ATATTAAGATAATTA
30711085 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:30714848 original size:18 final size:18
Alignment explanation
Indices: 30714823--30714892 Score: 90
Period size: 18 Copynumber: 3.9 Consensus size: 18
30714813 GCAACCCAAT
30714823 TTTTATTTTTT-TTATTA
1 TTTTATTTTTTATTATTA
*
30714840 TTCTTATTTTTTATTTTTA
1 TT-TTATTTTTTATTATTA
*
30714859 -TTTATTTTTTCTTATTA
1 TTTTATTTTTTATTATTA
*
30714876 TTTTATTATTTATTATT
1 TTTTATTTTTTATTATT
30714893 TTCAGATATT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
17 16 0.36
18 24 0.53
19 5 0.11
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTATTTTTTATTATTA
Found at i:30714851 original size:17 final size:15
Alignment explanation
Indices: 30714830--30714894 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 15
30714820 AATTTTTATT
30714830 TTTTTTATTATTCTTA
1 TTTTTTATTATT-TTA
*
30714846 TTTTTTATTTTTATTTATT
1 TTTTTTA---TTATTT-TA
30714865 TTTTCTTATTATTTTA
1 TTTT-TTATTATTTTA
*
30714881 TTATTTATTATTTT
1 TTTTTTATTATTTT
30714895 CAGATATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
15 10 0.24
16 11 0.27
17 6 0.15
18 1 0.02
19 10 0.24
20 3 0.07
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTATTATTTTA
Found at i:30714854 original size:25 final size:25
Alignment explanation
Indices: 30714822--30714892 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 25
30714812 GGCAACCCAA
30714822 TTTTTATTTTTTTTATTATTCTTAT
1 TTTTTATTTTTTTTATTATTCTTAT
*
30714847 TTTTTATTTTTATTTATTTTTTCTTAT
1 TTTTTATTTTT-TTTA-TTATTCTTAT
*
30714874 TATTTTATTATTTATTATT
1 T-TTTTATT-TTTTTTATT
30714893 TTCAGATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 11 0.28
26 4 0.10
27 12 0.30
28 10 0.25
29 3 0.08
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTTATTTTTTTTATTATTCTTAT
Found at i:30714855 original size:7 final size:7
Alignment explanation
Indices: 30714830--30714894 Score: 53
Period size: 7 Copynumber: 8.9 Consensus size: 7
30714820 AATTTTTATT
30714830 TTTTTTA
1 TTTTTTA
30714837 TTATTCTTA
1 TT-TT-TTA
30714846 TTTTTTA
1 TTTTTTA
30714853 -TTTTTA
1 TTTTTTA
30714859 TTTATTT-
1 TTT-TTTA
*
30714866 TTTCTTA
1 TTTTTTA
30714873 TTATTTTA
1 TT-TTTTA
*
30714881 TTATTTA
1 TTTTTTA
30714888 TTATTTT
1 TT-TTTT
30714895 CAGATATTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
6 8 0.17
7 18 0.38
8 16 0.34
9 5 0.11
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:30715843 original size:7 final size:7
Alignment explanation
Indices: 30715832--30715864 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
30715822 AAAATAAAAT
30715832 AAAAAGTA
1 AAAAAG-A
30715840 AAAAA-A
1 AAAAAGA
30715846 AAAAAGA
1 AAAAAGA
30715853 AAAAAGA
1 AAAAAGA
30715860 AAAAA
1 AAAAA
30715865 AAGAGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 13 0.54
8 5 0.21
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (7 bp):
AAAAAGA
Found at i:30715862 original size:16 final size:16
Alignment explanation
Indices: 30715839--30715873 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
30715829 AATAAAAAGT
30715839 AAAAAAAAAAAAGA-A
1 AAAAAAAAAAAAGAGA
30715854 AAAAGAAAAAAAAGAGA
1 AAAA-AAAAAAAAGAGA
30715871 AAA
1 AAA
30715874 TATATGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 10 0.56
17 4 0.22
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAGAGA
Found at i:30716465 original size:15 final size:15
Alignment explanation
Indices: 30716445--30716474 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30716435 TATTTTATTT
*
30716445 ATATTAGGATAATTA
1 ATATTAAGATAATTA
30716460 ATATTAAGATAATTA
1 ATATTAAGATAATTA
30716475 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:30716518 original size:10 final size:10
Alignment explanation
Indices: 30716499--30716530 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
30716489 ATTTAGGATT
30716499 TTAT-TTTAA
1 TTATCTTTAA
30716508 TTATCTTTAA
1 TTATCTTTAA
30716518 TTATCTTTAA
1 TTATCTTTAA
30716528 TTA
1 TTA
30716531 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:30717339 original size:6 final size:7
Alignment explanation
Indices: 30717324--30717348 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30717314 AGATTCTTAA
30717324 TTTTATT
1 TTTTATT
30717331 TTTTATT
1 TTTTATT
30717338 TTTTATT
1 TTTTATT
30717345 TTTT
1 TTTT
30717349 CAGGAACGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:30718273 original size:44 final size:44
Alignment explanation
Indices: 30718210--30718298 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
30718200 TAAACGAGTC
30718210 GTTTTGGCTGGAACACTGCTTAAATTCTACTGCTGCTGTTAGAA
1 GTTTTGGCTGGAACACTGCTTAAATTCTACTGCTGCTGTTAGAA
30718254 GTTTTGGCTGGAACACTGCTTAAATTCTACTGCTGCTGTTAGAA
1 GTTTTGGCTGGAACACTGCTTAAATTCTACTGCTGCTGTTAGAA
30718298 G
1 G
30718299 AATCCGTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (44 bp):
GTTTTGGCTGGAACACTGCTTAAATTCTACTGCTGCTGTTAGAA
Found at i:30723455 original size:19 final size:19
Alignment explanation
Indices: 30723433--30723469 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
30723423 TTTAGTTAGT
30723433 TTATATTTACCTTTTGGAC
1 TTATATTTACCTTTTGGAC
30723452 TTATATTTACCTTTTGGA
1 TTATATTTACCTTTTGGA
30723470 GTAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.14, G:0.11, T:0.54
Consensus pattern (19 bp):
TTATATTTACCTTTTGGAC
Found at i:30732983 original size:43 final size:43
Alignment explanation
Indices: 30732889--30733047 Score: 117
Period size: 43 Copynumber: 3.7 Consensus size: 43
30732879 GGTTACCGAG
* *
30732889 ATGAGATTACATGTAAAACCATGTCTGGGAAATTGGAATTGTA
1 ATGAGATTACATGTAAGACCATGTCTGGGAAATTGGAATCGTA
* * *
30732932 TTGAGATTACATGTAAGACCATGTTTGGGACATT-GATATCGTTA
1 ATGAGATTACATGTAAGACCATGTCTGGGAAATTGGA-ATCG-TA
* * * * * * * * *
30732976 AT-CGATTACGTGTACGACCCTGCCTAGGACAGTGGCATCG-A
1 ATGAGATTACATGTAAGACCATGTCTGGGAAATTGGAATCGTA
* * *
30733017 TATGTGATAACATGTAAGACCATATCTGGGA
1 -ATGAGATTACATGTAAGACCATGTCTGGGA
30733048 TATGGCATTG
Statistics
Matches: 88, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
41 1 0.01
42 4 0.05
43 79 0.90
44 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (43 bp):
ATGAGATTACATGTAAGACCATGTCTGGGAAATTGGAATCGTA
Found at i:30733525 original size:36 final size:36
Alignment explanation
Indices: 30733478--30733551 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
30733468 AGATTAAAGT
30733478 GAATGGAAGCTGTGCACCAGGTAGAAAGCCAGAAAA
1 GAATGGAAGCTGTGCACCAGGTAGAAAGCCAGAAAA
30733514 GAATGGAAGCTGTGCACCAGGTAGAAAGCCAGAAAA
1 GAATGGAAGCTGTGCACCAGGTAGAAAGCCAGAAAA
30733550 GA
1 GA
30733552 GGAGGTGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.42, C:0.16, G:0.31, T:0.11
Consensus pattern (36 bp):
GAATGGAAGCTGTGCACCAGGTAGAAAGCCAGAAAA
Found at i:30734205 original size:60 final size:59
Alignment explanation
Indices: 30734085--30734221 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 59
30734075 CAGTGTTAAC
* *
30734085 TGGGCCTTAGCCCATATCAATATTAATCTAGGCCATAGCCCCTTACAGTATCAGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTAGGCCATAGCCCATTACAG-ATCAGAGTATAT
* * * *
30734146 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCTTATTACA-AGTC-GAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTAGGCCATAGCC-CATTACAGA-TCAGAG-TATAT
* *
30734206 TGGGTCTTGCCCATAT
1 TGGGCCTAGCCCATAT
30734222 TAACATAGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 4 0.06
60 50 0.77
61 11 0.17
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAATATCAATCTAGGCCATAGCCCATTACAGATCAGAGTATAT
Found at i:30736667 original size:18 final size:18
Alignment explanation
Indices: 30736630--30736664 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
30736620 TTTCCCTATC
30736630 TAATAATAATTATTATAA
1 TAATAATAATTATTATAA
30736648 TAATAATAATT-TTATAA
1 TAATAATAATTATTATAA
30736665 ATATATCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATAATAATTATTATAA
Found at i:30738837 original size:28 final size:28
Alignment explanation
Indices: 30738787--30738841 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
30738777 GTCCACTTCT
** * *
30738787 CCCAAATTGGTACTTATAGTTTTTTTTC
1 CCCAAATTGGTACCCAAACTTTTTTTTC
30738815 CCCAAATTGGTACCCAAACTTTTTTTT
1 CCCAAATTGGTACCCAAACTTTTTTTT
30738842 GTTAACAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (28 bp):
CCCAAATTGGTACCCAAACTTTTTTTTC
Found at i:30740026 original size:21 final size:21
Alignment explanation
Indices: 30739972--30740043 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
30739962 AAAGAGGCCA
*
30739972 GCCCGTGTGGCTACCCCACAC
1 GCCCGTGTGGATACCCCACAC
* * * * *
30739993 GCTCGTATAGATATCCCACAT
1 GCCCGTGTGGATACCCCACAC
30740014 GCCCGTGTGGATACCCCACAC
1 GCCCGTGTGGATACCCCACAC
30740035 AG-CCGTGTG
1 -GCCCGTGTG
30740044 CTCAAATCGT
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
21 38 0.97
22 1 0.03
ACGTcount: A:0.19, C:0.38, G:0.24, T:0.19
Consensus pattern (21 bp):
GCCCGTGTGGATACCCCACAC
Found at i:30740243 original size:21 final size:20
Alignment explanation
Indices: 30740210--30740259 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
30740200 ATCAAAATCA
30740210 ACCCCACACGCCCGTATGGAT
1 ACCCCACACGCCCGTAT-GAT
* * *
30740231 ACCCTACATGCCCGTGTGAT
1 ACCCCACACGCCCGTATGAT
30740251 ACCCCACAC
1 ACCCCACAC
30740260 AGCCGTGTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.24, C:0.44, G:0.16, T:0.16
Consensus pattern (20 bp):
ACCCCACACGCCCGTATGAT
Found at i:30741267 original size:46 final size:46
Alignment explanation
Indices: 30741191--30741688 Score: 683
Period size: 46 Copynumber: 10.8 Consensus size: 46
30741181 TGATGTCATA
* * * * *
30741191 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCACGTTGCCATG
* * *** *
30741237 GTATCTTTCAACCATGATCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGTTGCCATG
* * *
30741284 ATATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
*
30741330 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* *** *
30741376 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGTTGCCATG
* *
30741423 ATATCTTTCAACCATGGTCTTACTCATTTCATATCAAGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
*
30741469 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
*
30741515 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
*
30741561 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* * * *
30741607 GTATCTTTCAACCATAGTCTTACACATTTCATATCAGGTTGTCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
* *
30741653 GTATCTTTCAACCATGGTCTTACACATTCCATATCA
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCA
30741689 GAGAGCACAC
Statistics
Matches: 413, Mismatches: 36, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
46 336 0.81
47 77 0.19
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATG
Found at i:30741441 original size:139 final size:139
Alignment explanation
Indices: 30741191--30741674 Score: 738
Period size: 139 Copynumber: 3.5 Consensus size: 139
30741181 TGATGTCATA
* * * * * *
30741191 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATGGTATCTTTCAACCATGAT
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGT
*
30741255 CTTATTCATTTTCCCGTCATGTTGCCATGATATCTTTCAACCATGGTCTTACTCATTTCATGTCA
65 CTTATTCATTTTCCCGTCATGTTGCCATGATATCTTTCAACCATGGTCTTACTCATTTCATATCA
*
30741320 GGTTGCCATG
130 AGTTGCCATG
*
30741330 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
30741395 TTATTCATTTTCCCGTCATGTTGCCATGATATCTTTCAACCATGGTCTTACTCATTTCATATCAA
66 TTATTCATTTTCCCGTCATGTTGCCATGATATCTTTCAACCATGGTCTTACTCATTTCATATCAA
30741460 GTTGCCATG
131 GTTGCCATG
*
30741469 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
** *** * * * *
30741534 TTACACA-TTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAC
66 TTATTCATTTTCCCGTCATGTTGCCATGATATCTTTCAACCATGGTCTTACTCATTTCATATCAA
30741598 GTTGCCATG
131 GTTGCCATG
* * * *
30741607 GTATCTTTCAACCATAGTCTTACACATTTCATATCAGGTTGTCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
30741672 TTA
66 TTA
30741675 CACATTCCAT
Statistics
Matches: 321, Mismatches: 23, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
138 126 0.39
139 195 0.61
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (139 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC
TTATTCATTTTCCCGTCATGTTGCCATGATATCTTTCAACCATGGTCTTACTCATTTCATATCAA
GTTGCCATG
Found at i:30744603 original size:22 final size:23
Alignment explanation
Indices: 30744569--30744612 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
30744559 TGAAATGGCT
*
30744569 TATTTTCCATAATAACC-AATTC
1 TATTTTACATAATAACCTAATTC
* *
30744591 TATTTTACTTAATCACCTAATT
1 TATTTTACATAATAACCTAATT
30744613 GGCACTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTTTACATAATAACCTAATTC
Found at i:30757288 original size:30 final size:30
Alignment explanation
Indices: 30757252--30757321 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
30757242 ACGAAATTAT
30757252 CATTTTTCATCACAGACTTAACGGAGCTAC
1 CATTTTTCATCACAGACTTAACGGAGCTAC
* * * * * * *
30757282 CGTTTTTCGTTATATACTTAACGGAGTTTC
1 CATTTTTCATCACAGACTTAACGGAGCTAC
30757312 CATTTTTCAT
1 CATTTTTCAT
30757322 TCCCTTATCA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.41
Consensus pattern (30 bp):
CATTTTTCATCACAGACTTAACGGAGCTAC
Found at i:30767462 original size:19 final size:20
Alignment explanation
Indices: 30767438--30767476 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
30767428 TGGTCACCAC
30767438 AATATAA-ATTAA-ATATAAT
1 AATATAAGA-TAAGATATAAT
30767457 AATATAAGATAAGATATAAT
1 AATATAAGATAAGATATAAT
30767477 TATGCCCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AATATAAGATAAGATATAAT
Found at i:30769364 original size:28 final size:28
Alignment explanation
Indices: 30769324--30769386 Score: 65
Period size: 30 Copynumber: 2.2 Consensus size: 28
30769314 AATTTCACAA
* *
30769324 TTTTAATAGATT-ATTATATATTTATAAT
1 TTTTAAAAGATTAATTAAATATTTAT-AT
* *
30769352 TTTTAAAATATTAAATTAAATTTTTATAT
1 TTTTAAAAGATT-AATTAAATATTTATAT
30769381 TTTTAA
1 TTTTAA
30769387 GAGGAGAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 10 0.34
29 8 0.28
30 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTAAAAGATTAATTAAATATTTATAT
Done.