Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 65 of 206
Found at i:18299613 original size:5 final size:4
Alignment explanation
Indices: 18299597--18299658 Score: 61
Period size: 4 Copynumber: 14.0 Consensus size: 4
18299587 AATATTTAAT
*
18299597 TAAA TAAA TATAA TATAA TAAA GTAAA TATAA TAAAA TAAA TAAG TAAA
1 TAAA TAAA TA-AA TA-AA TAAA -TAAA TA-AA T-AAA TAAA TAAA TAAA
18299646 TGAAA TAAA TAAA
1 T-AAA TAAA TAAA
18299659 GAAACGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
4 27 0.53
5 23 0.45
6 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:18299623 original size:19 final size:18
Alignment explanation
Indices: 18299597--18299658 Score: 81
Period size: 19 Copynumber: 3.4 Consensus size: 18
18299587 AATATTTAAT
*
18299597 TAAATAAATATAATATAA
1 TAAATAAATATAATAAAA
18299615 TAAAGTAAATATAATAAAA
1 TAAA-TAAATATAATAAAA
* *
18299634 TAAATAAGTA-AATGAAA
1 TAAATAAATATAATAAAA
18299651 TAAATAAA
1 TAAATAAA
18299659 GAAACGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
17 13 0.33
18 9 0.23
19 17 0.44
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
TAAATAAATATAATAAAA
Found at i:18299636 original size:22 final size:22
Alignment explanation
Indices: 18299597--18299656 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 22
18299587 AATATTTAAT
18299597 TAAATAAATATAATAT-AATAAAG
1 TAAATAAATA-AATATAAAT-AAG
18299620 TAAATATAATAAA-ATAAATAAG
1 TAAATA-AATAAATATAAATAAG
18299642 TAAATGAAATAAATA
1 TAAAT-AAATAAATA
18299657 AAGAAACGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
22 16 0.48
23 13 0.39
24 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (22 bp):
TAAATAAATAAATATAAATAAG
Found at i:18300446 original size:24 final size:26
Alignment explanation
Indices: 18300392--18300446 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 26
18300382 GTGTTTTACA
18300392 ATTGAAATAGATTGATTTGATATATG
1 ATTGAAATAGATTGATTTGATATATG
*
18300418 A-TGAAAT-TATTGAATTT-ATAT-TG
1 ATTGAAATAGATTG-ATTTGATATATG
18300441 ATTGAA
1 ATTGAA
18300447 TTGAATTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.12
24 12 0.46
25 10 0.38
26 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (26 bp):
ATTGAAATAGATTGATTTGATATATG
Found at i:18300927 original size:21 final size:20
Alignment explanation
Indices: 18300879--18300927 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
18300869 GAAAAGCTAT
*
18300879 TTGAATAGAAAGTATGAGAT
1 TTGAATAGAAAGTATGAGAA
18300899 TTGAAATAGCAATAG-ATGAGAA
1 TTG-AATAG-AA-AGTATGAGAA
18300921 TTGAATA
1 TTGAATA
18300928 TGTTATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 9 0.36
22 11 0.44
23 2 0.08
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (20 bp):
TTGAATAGAAAGTATGAGAA
Found at i:18305681 original size:23 final size:24
Alignment explanation
Indices: 18305653--18305697 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
18305643 AGAAAAGATC
18305653 TTTCTTTCCA-GTGTTTGTTCCCT
1 TTTCTTTCCAGGTGTTTGTTCCCT
* *
18305676 TTTCTTTGCAGGTTTTTGTTCC
1 TTTCTTTCCAGGTGTTTGTTCC
18305698 TTGATTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.04, C:0.22, G:0.16, T:0.58
Consensus pattern (24 bp):
TTTCTTTCCAGGTGTTTGTTCCCT
Found at i:18317069 original size:2 final size:2
Alignment explanation
Indices: 18317062--18317114 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
18317052 AGCAAACTCG
*
18317062 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18317104 TA TA TA TA TA T
1 TA TA TA TA TA T
18317115 GGATCACATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18319003 original size:28 final size:28
Alignment explanation
Indices: 18318935--18319032 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
18318925 TTAATAAGTA
* * * *
18318935 CGCACACTTAGTGCTTAATAATCACACT
1 CGCACACTTAGTGCTTTACAATTAAACT
* *
18318963 -GCACACTTAGTGCTTTACCATTATACT
1 CGCACACTTAGTGCTTTACAATTAAACT
18318990 CGCACACTTAGTGCATTT-CAATTAAACT
1 CGCACACTTAGTGC-TTTACAATTAAACT
18319018 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
18319033 AATCTCATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 23 0.38
28 35 0.57
29 3 0.05
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (28 bp):
CGCACACTTAGTGCTTTACAATTAAACT
Found at i:18320709 original size:18 final size:17
Alignment explanation
Indices: 18320676--18320709 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18320666 AAGTTAGTAT
18320676 AATAAAAAAAATAAAGA
1 AATAAAAAAAATAAAGA
*
18320693 AATAAAGAAAGATAAAG
1 AATAAA-AAAAATAAAG
18320710 CCATACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
AATAAAAAAAATAAAGA
Found at i:18321185 original size:7 final size:7
Alignment explanation
Indices: 18321173--18321205 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
18321163 TAAAAATTGA
18321173 AATATTC
1 AATATTC
18321180 AATATTC
1 AATATTC
18321187 AATATTC
1 AATATTC
18321194 AATATTC
1 AATATTC
18321201 AATAT
1 AATAT
18321206 GAAATTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:18330510 original size:30 final size:30
Alignment explanation
Indices: 18330474--18330535 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
18330464 TATTCTTAAA
18330474 GACATTGGAGTTGGAAAGTTAAGTTTTTGT
1 GACATTGGAGTTGGAAAGTTAAGTTTTTGT
18330504 GACATTGGAGTTGGAAAGTTAAGTTTTTGT
1 GACATTGGAGTTGGAAAGTTAAGTTTTTGT
18330534 GA
1 GA
18330536 GCACTGCACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.39
Consensus pattern (30 bp):
GACATTGGAGTTGGAAAGTTAAGTTTTTGT
Found at i:18333449 original size:20 final size:20
Alignment explanation
Indices: 18333411--18333449 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18333401 TTGTACTGGA
* *
18333411 TTTGCACTTCGGTGTCTCTG
1 TTTGCACTTCAGTGCCTCTG
18333431 TTTGCACTTCAGTGCCTCT
1 TTTGCACTTCAGTGCCTCT
18333450 ATTATGCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.28, G:0.21, T:0.44
Consensus pattern (20 bp):
TTTGCACTTCAGTGCCTCTG
Found at i:18334427 original size:24 final size:24
Alignment explanation
Indices: 18334391--18334444 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
18334381 AAAAATGATG
* *
18334391 CACACAGCTTGGGACACGAG-TTGT
1 CACACGGCCTGGGACACG-GCTTGT
18334415 CACACGGCCTGGGACACGGCTTGT
1 CACACGGCCTGGGACACGGCTTGT
18334439 CACACG
1 CACACG
18334445 ATCGTGTACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.22, C:0.31, G:0.30, T:0.17
Consensus pattern (24 bp):
CACACGGCCTGGGACACGGCTTGT
Found at i:18335188 original size:33 final size:33
Alignment explanation
Indices: 18335087--18335190 Score: 81
Period size: 33 Copynumber: 3.2 Consensus size: 33
18335077 TGAACTAAGT
* *
18335087 ATGATAGTTGTGTGTATTTACAATGTTTAGATG
1 ATGATAGTTGTATGTATTTAGAATGTTTAGATG
* * * *
18335120 ATGATTCA-TT-CATATATTT-G-CTGCTTTATGTTG
1 ATGA-T-AGTTGTATGTATTTAGAATG-TTTA-GATG
*
18335153 ATGATAGTTGTTTGTATTTAGAATGTTTAGATG
1 ATGATAGTTGTATGTATTTAGAATGTTTAGATG
18335186 ATGAT
1 ATGAT
18335191 TCGTCTCAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 16
0.66 0.14 0.20
Matches are distributed among these distances:
31 3 0.06
32 7 0.13
33 31 0.60
34 8 0.15
35 3 0.06
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.48
Consensus pattern (33 bp):
ATGATAGTTGTATGTATTTAGAATGTTTAGATG
Found at i:18375671 original size:559 final size:553
Alignment explanation
Indices: 18374331--18376424 Score: 3208
Period size: 555 Copynumber: 3.8 Consensus size: 553
18374321 ATAAACCTTT
* * *
18374331 ATTGTTGTTGTCGCCTAAACCTTCTATTTTACCATCTCTTTCTTCTTCTTTTTGTATCAAGATTG
1 ATTGTTGTTGTCGCCTACACCTCCCATTTTACCATCTCTTTCTTCTTCTTTTTGTATCAAGATTG
* * *
18374396 TGCACCATCTTCTTTAATCTATTGCTTCCATTTATCCTCATTTAAATCAACACCAAATCTGAAAT
66 TGCACCATCTCCTTTAATCTATTGCTTCCATTTATCCTCATCTAAATCAGCACCAAATCTGAAAT
* * * *
18374461 CTTGAACTCCAAGATCGATTCTGAACATTGCCAAGAAAGTCCCATTATCATTTCTCTCAACTAGC
131 CTTAAACTCCAAGATCGATCCTGAACATTGCCAAGAAAGTGCCATTATCATTTCTTTCAACTAGC
* * *
18374526 TTGGGTAAGAACTATTATTTCTTCAAGTTTTTGATTAATCTTGCAAATTAAAAACCTAAATTTCC
196 TTGGGTAAGAACTCTTATTTCTTCAATTTTTTGATTAATCTTGCCAATTAAAAACCTAAATTTCC
18374591 AGATTTGGAATTTGGGAGAATTTTGATGATTTTTAATATATTTTTTTCAGTTTTTTAATGGGT-T
261 AGATTTGGAATTTGGGAGAATTTTGATGATTTTTAATATA-TTTTTTCAGTTTTTTAATGGGTCT
* * * *
18374655 TTAAATCGTATTTAAATTAGTCCCAAGTTCAAATCCATTCACTTTCAAATAATTTAATTTTTCGA
325 TTAAATCGTATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAATAATTTAATTTTT-GA
*
18374720 CAAAAACCCCTTATTTTAATGTGTGTGTCATCCAA-CCTTAGTAAACCTAGGTATAAGTATTATT
389 CAAAAACCCCTTATTTTAATGTGTGTGTCGTCCAAGCC-TAGTAAACCTAGGTATAAGTATTATT
*
18374784 TTTTCACAAATAATAAGCCTTTAATCCTCCTCCTCATTGCCCTAGTCATTCCTCTCCTTCTCTCA
453 TTTT-ACAAATAATAAGCCTTTAATCCTCCTCCTCATTGCCCTAGTCATTCCTCTCCTCCTCTCA
*
18374849 TTCTCTTTGATTTTAATGTTTTTTTTTCCTTTTCTCC
517 TTCTCTTTGATTTTAATGTTTTTTTTTCCTTTCCTCC
* *
18374886 ATTGTTGTTGTCGCCTACACCTCCCATTTTACTATCTCTTTCTTCCTCTTTTTGTATCAAGATTG
1 ATTGTTGTTGTCGCCTACACCTCCCATTTTACCATCTCTTTCTTCTTCTTTTTGTATCAAGATTG
* *
18374951 TGCACCATCTCCTTTAATCTATTGCTTCCATTTATCCTCATTTAAATCAGCACCAAATCTGAAGT
66 TGCACCATCTCCTTTAATCTATTGCTTCCATTTATCCTCATCTAAATCAGCACCAAATCTGAAAT
* * *
18375016 TTTAAACTCCAAGATCGATTCTGAACATTGCCAAGAATGTGCCATTATCATTTCTTTCAACTAGC
131 CTTAAACTCCAAGATCGATCCTGAACATTGCCAAGAAAGTGCCATTATCATTTCTTTCAACTAGC
* *
18375081 TTGGGTAAGAACTCTTCTTTCTTCAATTTTTTGATTAATCTTGCCAACTAAAAACCTAAATTTCC
196 TTGGGTAAGAACTCTTATTTCTTCAATTTTTTGATTAATCTTGCCAATTAAAAACCTAAATTTCC
18375146 AGATTTGGAATTTGGGAGAATTTTGATGATTTTTAATATATTTTTTTCAGTTTTTTAATGGGTCT
261 AGATTTGGAATTTGGGAGAATTTTGATGATTTTTAATATA-TTTTTTCAGTTTTTTAATGGGTCT
* * *
18375211 TTAAATCGTATTTAAATTAG-CCCTAACTTCAAATCCTTTCTCTTGCAAATAATTTAATGTTTTG
325 TTAAATCGTATTTAAATCAGTCCC-AAGTTCAAATCCCTTCTCTTGCAAATAATTTAAT-TTTTG
* * * *
18375275 AC-AAAACCTCCTTGTTTTAATGTATGTGTTGTCCAAGCCTAGTAAACTTAGGTATAAGTATTAT
388 ACAAAAACC-CCTTATTTTAATGTGTGTGTCGTCCAAGCCTAGTAAACCTAGGTATAAGTATTAT
*
18375339 TTTTTACAAATAATCAGCCTTTAATCCTCCTCCTCATTGCCCTAGTCATTCCTCTCCTCCTCTCA
452 TTTTTACAAATAATAAGCCTTTAATCCTCCTCCTCATTGCCCTAGTCATTCCTCTCCTCCTCTCA
18375404 TTCTCTTTGATTTTAATGTTTTTTTTTTCCTTTCCTCC
517 TTCTCTTTGATTTTAATG-TTTTTTTTTCCTTTCCTCC
* * *
18375442 ATTGTTGTTGTTGTTGCCTACACCTCTCATTTTACCATCTCTTTCGTCTTCTTTTTGTATCAAGA
1 A---TTGTTGTTGTCGCCTACACCTCCCATTTTACCATCTCTTTCTTCTTCTTTTTGTATCAAGA
* * * *
18375507 TTGCGCATCATCTCCTTTAATCTATTTCTTCCATTTATCCTCATCTAAATCAGCACCAAATCTAA
63 TTGTGCACCATCTCCTTTAATCTATTGCTTCCATTTATCCTCATCTAAATCAGCACCAAATCTGA
* * * *
18375572 AATCTTGAACTCCAAAATCGATCCTGAACATTGCCAAGAAAGTGCCATAATCGTTTCTTTCAACT
128 AATCTTAAACTCCAAGATCGATCCTGAACATTGCCAAGAAAGTGCCATTATCATTTCTTTCAACT
* *
18375637 AGCTTGGGTAAGAGCTCTTATTTCTTCAATTTTTTGATTAATCTTGCCAATGAAAAACCTAAATA
193 AGCTTGGGTAAGAACTCTTATTTCTTCAATTTTTTGATTAATCTTGCCAATTAAAAACCTAAAT-
* *
18375702 TT-CAGCTTTGGAATTTTGGGAGAATTTTGATGATTTTTAATATATTTTTT-ATTTTTTTAATGG
257 TTCCAGATTTGGAA-TTTGGGAGAATTTTGATGATTTTTAATATATTTTTTCAGTTTTTTAATGG
* *
18375765 GTCTTTAAATCGCATTTAAATCAGTCCCAAGTTCAAATCCCTTCTATTGCAAATAATTTAATTTT
321 GTCTTTAAATCGTATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAATAATTTAA-TTT
* *
18375830 TTGACAAAAATCCCTTATTTTAATGTGTGTGTCGTCCAAGCCTAGTAAACCAAGGTATAAGTATT
385 TTGACAAAAACCCCTTATTTTAATGTGTGTGTCGTCCAAGCCTAGTAAACCTAGGTATAAGTATT
* *
18375895 ATTTTTTTACAAATAATAAGCCTTTAATCCTCCTCCTCATTGCACTAGTCATTCCTCTCCTCCCC
450 A-TTTTTTACAAATAATAAGCCTTTAATCCTCCTCCTCATTGCCCTAGTCATTCCTCTCCTCCTC
18375960 TCATTCTCTTTGATTTTAATG-TTTTTTTTCCTTTCCTCC
514 TCATTCTCTTTGATTTTAATGTTTTTTTTTCCTTTCCTCC
*
18375999 ATTGTTGTTGTTGCCTACACCTCCCATTTTACCATCTCTTTCTTCTTCTTTTTGTATCAAGATTG
1 ATTGTTGTTGTCGCCTACACCTCCCATTTTACCATCTCTTTCTTCTTCTTTTTGTATCAAGATTG
* * * *
18376064 TGCACCATTTCCTTTAATCTATTGCTTTC-TTT-T-GTCATCT-AA--AGCATCAAATCTGAAAT
66 TGCACCATCTCCTTTAATCTATTGCTTCCATTTATCCTCATCTAAATCAGCACCAAATCTGAAAT
* * *
18376123 CTTAAACTCCAAGATTGATCCTGAACATTGCCAAGAAAGTGCCATTATCGTTTCTATCAACTAGC
131 CTTAAACTCCAAGATCGATCCTGAACATTGCCAAGAAAGTGCCATTATCATTTCTTTCAACTAGC
** * * * *
18376188 TTGGGTAAGAGTTCTTCTTTCTTAAATTTTTTGATTAATCTTGCCAATTAATAACCTAAATTTCT
196 TTGGGTAAGAACTCTTATTTCTTCAATTTTTTGATTAATCTTGCCAATTAAAAACCTAAATTTCC
* * * * * *
18376253 AGATTCGGAATTTGAGAGAAGTTTGATGATTTTAAATATATTTTTTCAATTTTTTACTGGGTCTT
261 AGATTTGGAATTTGGGAGAATTTTGATGATTTTTAATATATTTTTTCAGTTTTTTAATGGGTCTT
*
18376318 TAAATCATATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTT-CTAAATAATTTAAATTTTTGA
326 TAAATCGTATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGC-AAATAATTT-AATTTTTGA
18376382 CAAAAACCCCTTTATTTTAATGTGTGTGTCGTCCAAGCCTAGT
389 CAAAAACCCC-TTATTTTAATGTGTGTGTCGTCCAAGCCTAGT
18376425 GATGGCCACT
Statistics
Matches: 1419, Mismatches: 100, Indels: 46
0.91 0.06 0.03
Matches are distributed among these distances:
547 36 0.03
548 220 0.16
549 34 0.02
550 2 0.00
551 6 0.00
552 1 0.00
553 3 0.00
554 86 0.06
555 390 0.27
556 125 0.09
557 25 0.02
558 120 0.08
559 339 0.24
560 32 0.02
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.43
Consensus pattern (553 bp):
ATTGTTGTTGTCGCCTACACCTCCCATTTTACCATCTCTTTCTTCTTCTTTTTGTATCAAGATTG
TGCACCATCTCCTTTAATCTATTGCTTCCATTTATCCTCATCTAAATCAGCACCAAATCTGAAAT
CTTAAACTCCAAGATCGATCCTGAACATTGCCAAGAAAGTGCCATTATCATTTCTTTCAACTAGC
TTGGGTAAGAACTCTTATTTCTTCAATTTTTTGATTAATCTTGCCAATTAAAAACCTAAATTTCC
AGATTTGGAATTTGGGAGAATTTTGATGATTTTTAATATATTTTTTCAGTTTTTTAATGGGTCTT
TAAATCGTATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAATAATTTAATTTTTGACA
AAAACCCCTTATTTTAATGTGTGTGTCGTCCAAGCCTAGTAAACCTAGGTATAAGTATTATTTTT
TACAAATAATAAGCCTTTAATCCTCCTCCTCATTGCCCTAGTCATTCCTCTCCTCCTCTCATTCT
CTTTGATTTTAATGTTTTTTTTTCCTTTCCTCC
Found at i:18380896 original size:538 final size:544
Alignment explanation
Indices: 18378794--18381170 Score: 2964
Period size: 538 Copynumber: 4.4 Consensus size: 544
18378784 GTAACAACTA
* * * *
18378794 TTCTTTTTTCAATTTTTTGATTAATCTTGCTAATTAAAAACCTAAATTT-CATGATTTTGAATTT
1 TTCTTTCTTCAATTTTTTAATTAATCTTGCCAATTAAAAACCTAAATTTCCA-GATTTGGAATTT
* * *
18378858 GGGAGAATTGTGATGATTTTACATATATTTTTTCAATTTTTTAATAGGTCTTTAAATCGTATTTA
65 GGGAGAATTTTGATGATTTTAAATATATTTTTTCAGTTTTTTAATAGGTCTTTAAATCGTATTTA
* * *
18378923 AATCAATCCCAACTTTAAATCCCTTCTCTTGCAAATAAGTTAATTTTTTGACAAAAACCCCTTGT
130 AATCAGTCCCAAGTTTAAATCCCTTCTCTTGCAAATAATTTAATTTTTTGA-AAAAACCCCTTGT
* * * *
18378988 TTTAATGTATGTATTGTCCAAGCCTAGTAAAGCTAGGTATAAGTATTAATTTGTCACAAATAATC
194 TTTAATGTATGTGTCGTCCAAGCCTAGTAAACCTAGGTATAAGTATTATTTTGTCACAAATAA-C
* * * *
18379053 AGTCTTTAACCCTCCTCTTCATTTCTCTAATCATTCCTCTCCTCCTCTCATTTTCTTTAATTTTA
258 A--C-TTAA--CTCCTCTT-ATATC-CTAGTCATTCCTCTCCTCCTCTCATTCTCTTTGATTTTA
* * * *
18379118 ATGTTTTTTTCCTTTCCACCATTGTTGTTGTCGCCTACACCTCCCCTTTTGCCATCTCTTTCTTT
316 ATGTTTTTTTCCTTTCCTCCATTGTTGTTGTCGCCTACACCTCCCCTTTTACCATCTATTTCTTC
* * * *
18379183 TTCTTTTTGTATCAAGATTGTGCACTATTTGCTTTAATCTATTCCTTCCATTTGTCCTCATCTAA
381 TTCTTTTTGTATCAAGATTGTGCACTATCTCCTTTAATCTATTGCTTCCATTTATCCTCATCTAA
* *** * * * * *
18379248 ATCTGTTTCAAATCTAAAATATTAAACTCC---A-AGATCCTGAACATTACCAAAAAAGTGTCAT
446 ATCAGCACCAAATTTAAAATCTTAAACTCCAAGATAGATCCTGAACATTGCCAAGAAAGTGCCAT
* * *
18379309 TATTGTTTCTCTCATCTAGCTTGAGTAAAAGCTC
511 TATCGTTTCTCTCAACTAGCTTGAGTAAGAGCTC
* * * *
18379343 TTATTTCTTCAATTTTTTAATTAATCTTGCCAATTCAAAATCTAAATTTCCAGATTTGGAATCTG
1 TTCTTTCTTCAATTTTTTAATTAATCTTGCCAATTAAAAACCTAAATTTCCAGATTTGGAATTTG
* * * *
18379408 GAAGGATTTTGATGATTTTAAATATATTTTTTTAGTTTTTTAATGGGTCTTTAAATCGTATTTAA
66 GGAGAATTTTGATGATTTTAAATATATTTTTTCAGTTTTTTAATAGGTCTTTAAATCGTATTTAA
* * *
18379473 ATCAGTCCCAAGTTAAAATCCCTTCTCTTGCAAATAATTTAATTTTTTCATAAAAACCCCTTATT
131 ATCAGTCCCAAGTTTAAATCCCTTCTCTTGCAAATAATTTAATTTTTTGA-AAAAACCCCTTGTT
* * *
18379538 TTAATGTGTGCGTCGTCCAACCCTAGTAAACCTAGGTATAAGTATTATTTTGTCACAAA-AA-A-
195 TTAATGTATGTGTCGTCCAAGCCTAGTAAACCTAGGTATAAGTATTATTTTGTCACAAATAACAC
* * * *
18379600 ATCAGT-CT-TTA-ATCCTAGTCATTCCTCTCCTCCTCTTATTCTCTTTGATTTTAATGTTTTTT
260 TTAACTCCTCTTATATCCTAGTCATTCCTCTCCTCCTCTCATTCTCTTTGATTTTAATGTTTTTT
* * *
18379662 TCCTTTCCTCCATTGTTGTTGTCACCTACACCTCCCCTTTTACCATCTCTTTCTTCTTCTATTTG
325 TCCTTTCCTCCATTGTTGTTGTCGCCTACACCTCCCCTTTTACCATCTATTTCTTCTTCTTTTTG
* * *
18379727 TATCAAGATTGTGCACCATCTCCTTTAATCTATGGCTTCCATTTATCCTCATCTAAGTCAGCACC
390 TATCAAGATTGTGCACTATCTCCTTTAATCTATTGCTTCCATTTATCCTCATCTAAATCAGCACC
* * * * * *
18379792 AAATTTGAAATCTTGAACTCCACGATCGATCTTGAACATTGCCAAGAAAGTGCCATTATCATTTC
455 AAATTTAAAATCTTAAACTCCAAGATAGATCCTGAACATTGCCAAGAAAGTGCCATTATCGTTTC
*
18379857 TCTTAACTAGCTTGAGTAAGAGCTC
520 TCTCAACTAGCTTGAGTAAGAGCTC
* * * *
18379882 TTCTTTCTTCAATTTTTTAATTAATCTTGCCAAGTAAAAACCTAAATTTCCAAATTTTGAAGTTG
1 TTCTTTCTTCAATTTTTTAATTAATCTTGCCAATTAAAAACCTAAATTTCCAGATTTGGAATTTG
* * * * * **
18379947 GGATAATTTTGATGATGTTATATATATTTTTTAAGTTTTTTCATTTGTCTTTAAATCGTATTTAA
66 GGAGAATTTTGATGATTTTAAATATATTTTTTCAGTTTTTTAATAGGTCTTTAAATCGTATTTAA
* * * * *
18380012 ATCAATCCCAAGTTCAAATCCCTTCTCTTGCAAATAATTTAATTTTTTGAGAAAGCCCTTTGTTT
131 ATCAGTCCCAAGTTTAAATCCCTTCTCTTGCAAATAATTTAATTTTTTGAAAAAACCCCTTGTTT
* *
18380077 TAATGTGTGTGTCGTCCAAGCCTAGTAAACCTAGGTATAAGTATTATTTTTTCACAAATAATCAG
196 TAATGTATGTGTCGTCCAAGCCTAGTAAACCTAGGTATAAGTATTATTTTGTCACAAATAA-CA-
* * *
18380142 CCTTTCATCCTCCTCCTTATTGTCATAGTCATTCCTCTCCTCCTCTCATTCT-TTTGATTTTAAT
259 -C-TT-A-ACTCCT-CTTA-TATCCTAGTCATTCCTCTCCTCCTCTCATTCTCTTTGATTTTAAT
* *
18380206 GTTTTTTTTTTCCTTTCCTCCATTGTTGTTGTCGCCTACACCTACCCTTTTACCATC-ACATTCT
318 G---TTTTTTTCCTTTCCTCCATTGTTGTTGTCGCCTACACCTCCCCTTTTACCATCTA-TTTCT
* *
18380270 TCTTCTTTTTG-ATCAAGATTGTGCA-TCATATCCTTTAATCTATTGCTTCCATTTATCCTCGTC
379 TCTTCTTTTTGTATCAAGATTGTGCACT-ATCTCCTTTAATCTATTGCTTCCATTTATCCTCATC
* * *
18380333 TAAATCAACACCAAATTTGAAATCTTAAAATCCAAGATAGATCCTGAACATTGCCAAGAAAGTGC
443 TAAATCAGCACCAAATTTAAAATCTTAAACTCCAAGATAGATCCTGAACATTGCCAAGAAAGTGC
* * *
18380398 CCTTATCGTTTCTCTCAACTAGCTTGGGTTAGAGCTC
508 CATTATCGTTTCTCTCAACTAGCTTGAGTAAGAGCTC
* * * *
18380435 TTCTCTCTTTAATTTTTTTTATTAATCTTGCCAATTAAAAACCTAAATTTCTAGATTTGGAATTT
1 TTCTTTCTTCAA-TTTTTTAATTAATCTTGCCAATTAAAAACCTAAATTTCCAGATTTGGAATTT
* * * *
18380500 GGGAGAATTTTGATGATTTGAAATATATTTTTTTAGTTTCTGAATAGGT-TTGTAAATCGTATTT
65 GGGAGAATTTTGATGATTTTAAATATATTTTTTCAGTTTTTTAATAGGTCTT-TAAATCGTATTT
* *
18380564 AAATCAGTCCCAAGTTTAAAACCCTTCTCTTGCAAACAATTTAATTTTTTGACAAAAACCCCTTG
129 AAATCAGTCCCAAGTTTAAATCCCTTCTCTTGCAAATAATTTAATTTTTTGA-AAAAACCCCTTG
* *
18380629 TTTTAATGTATGTGTCATCCAAGGCTAGTAAACCTAGGTATAAGTATTATTTTGTCACAAAT-A-
193 TTTTAATGTATGTGTCGTCCAAGCCTAGTAAACCTAGGTATAAGTATTATTTTGTCACAAATAAC
* * ** *
18380692 A-TT-A-TCCT-TTA-ATCCTAGTCATTCCTCTCTTTCTCAAATTCTCTTTGATTTTATTGTTTT
258 ACTTAACTCCTCTTATATCCTAGTCATTCCTCTCCTCCTCTCATTCTCTTTGATTTTAATGTTTT
* * * *
18380752 TTTTCTTTCCTCCATTGTTGTTGTCGCCCACACCCCCCCTTTTACCATGTATTTCTTCTTCTTTT
323 TTTCCTTTCCTCCATTGTTGTTGTCGCCTACACCTCCCCTTTTACCATCTATTTCTTCTTCTTTT
* * *
18380817 TGT-T-ACAGATTGTGCACTATCTCCTTTAATCTATTGGTTCCATTTTTCCTCATCTAAATTAGC
388 TGTATCA-AGATTGTGCACTATCTCCTTTAATCTATTGCTTCCATTTATCCTCATCTAAATCAGC
* * * * * *
18380880 ACCAAATATAAAATCTTGAATTTCAAGATCGATCCTGAACATTGCCAAGAAAGTTCCATTATCGT
452 ACCAAATTTAAAATCTTAAACTCCAAGATAGATCCTGAACATTGCCAAGAAAGTGCCATTATCGT
* *
18380945 TTCTCTCAACTAGCTT-AGGTCAGAGTTC
517 TTCTCTCAACTAGCTTGA-GTAAGAGCTC
18380973 TTCTTT-TTCAAATTTTTT-ATTAATCTTG-CAAGTTAAAAACCTAAATTTCCAGATTTGGAATT
1 TTCTTTCTTC-AATTTTTTAATTAATCTTGCCAA-TTAAAAACCTAAATTTCCAGATTTGGAATT
* * * *
18381035 TGGGAGAATTGTGAAGATTTTAAATATA-TTTTTCAG-TTTTAAATGGGTCTTTAAATCGTATTT
64 TGGGAGAATTTTGATGATTTTAAATATATTTTTTCAGTTTTTTAATAGGTCTTTAAATCGTATTT
* * * * *
18381098 AAATTAGTCCCAAGTTCAAATCCCTTCTCTTGTAAACAATTTAATTTTTTG-AAAAACACCATTG
129 AAATCAGTCCCAAGTTTAAATCCCTTCTCTTGCAAATAATTTAATTTTTTGAAAAAAC-CCCTTG
*
18381162 TATTAATGT
193 TTTTAATGT
18381171 GCGCTTTCAA
Statistics
Matches: 1593, Mismatches: 198, Indels: 90
0.85 0.11 0.05
Matches are distributed among these distances:
532 6 0.00
533 13 0.01
534 68 0.04
535 187 0.12
536 66 0.04
537 10 0.01
538 270 0.17
539 220 0.14
540 26 0.02
541 13 0.01
542 5 0.00
544 4 0.00
545 1 0.00
546 1 0.00
547 1 0.00
548 6 0.00
549 222 0.14
550 5 0.00
551 13 0.01
552 29 0.02
553 149 0.09
554 211 0.13
555 67 0.04
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.43
Consensus pattern (544 bp):
TTCTTTCTTCAATTTTTTAATTAATCTTGCCAATTAAAAACCTAAATTTCCAGATTTGGAATTTG
GGAGAATTTTGATGATTTTAAATATATTTTTTCAGTTTTTTAATAGGTCTTTAAATCGTATTTAA
ATCAGTCCCAAGTTTAAATCCCTTCTCTTGCAAATAATTTAATTTTTTGAAAAAACCCCTTGTTT
TAATGTATGTGTCGTCCAAGCCTAGTAAACCTAGGTATAAGTATTATTTTGTCACAAATAACACT
TAACTCCTCTTATATCCTAGTCATTCCTCTCCTCCTCTCATTCTCTTTGATTTTAATGTTTTTTT
CCTTTCCTCCATTGTTGTTGTCGCCTACACCTCCCCTTTTACCATCTATTTCTTCTTCTTTTTGT
ATCAAGATTGTGCACTATCTCCTTTAATCTATTGCTTCCATTTATCCTCATCTAAATCAGCACCA
AATTTAAAATCTTAAACTCCAAGATAGATCCTGAACATTGCCAAGAAAGTGCCATTATCGTTTCT
CTCAACTAGCTTGAGTAAGAGCTC
Found at i:18381265 original size:226 final size:230
Alignment explanation
Indices: 18380950--18381382 Score: 725
Period size: 227 Copynumber: 1.9 Consensus size: 230
18380940 ATCGTTTCTC
* *
18380950 TCAACTAGCTTAGGTCAGAGTTCTTCTTTTTCAAATTTTTTATTAATCTTGCAAGTTAAAAACCT
1 TCAACTAGCTTAGGTAAGAGCTCTTCTTTTTCAAATTTTTTATTAATCTTGCAAGTTAAAAACCT
18381015 AAATTTCCAGATTTGGAATTTGGGAGAATTGTGAAGATTTTAAATATA-TTTTTCAGTTTTAAAT
66 AAATTTCCAGATTTGGAATTTGGGAGAATTGTGAAGATTTTAAATATATTTTTTCAGTTTTAAAT
* *
18381079 GGGTCTTTAAATCGTATTTAAATTAGTCCCAAGTTCAAATCCCTTCTCTTGTAAACAATTTAATT
131 GGGTCTTTAAATCGTATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAACAATTTAATT
18381144 -TTTTGA-AAAACACCATTGTATTAATGTGCGCTT
196 ATTTTGACAAAACACCATTGTATTAATGTGCGCTT
*
18381177 TCAACTAGCTTGGGTAAGAGCTCTTCTTTCTTC-AA-TTTTTATTAATCTTGGCAA-TTAAAAAC
1 TCAACTAGCTTAGGTAAGAGCTCTTCTTT-TTCAAATTTTTTATTAATCTT-GCAAGTTAAAAAC
* *
18381239 CTAAATTTCCATATTTGGAATTTGGGAGAATTGTGAAGATTTTAAATATATTTTTTCAGTTTTTA
64 CTAAATTTCCAGATTTGGAATTTGGGAGAATTGTGAAGATTTTAAATATATTTTTTCAGTTTTAA
* *
18381304 ATGGGTCTTTAAATCGTATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAATAATTTAT
129 ATGGGTCTTTAAATCGTATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAACAATTTAA
18381369 TTATTTTGACAAAA
194 TTATTTTGACAAAA
18381383 ACCCCAAGTT
Statistics
Matches: 192, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
226 71 0.37
227 108 0.56
228 9 0.05
229 4 0.02
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (230 bp):
TCAACTAGCTTAGGTAAGAGCTCTTCTTTTTCAAATTTTTTATTAATCTTGCAAGTTAAAAACCT
AAATTTCCAGATTTGGAATTTGGGAGAATTGTGAAGATTTTAAATATATTTTTTCAGTTTTAAAT
GGGTCTTTAAATCGTATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAACAATTTAATT
ATTTTGACAAAACACCATTGTATTAATGTGCGCTT
Found at i:18381282 original size:538 final size:528
Alignment explanation
Indices: 18378798--18381254 Score: 1870
Period size: 539 Copynumber: 4.5 Consensus size: 528
18378788 CAACTATTCT
* *
18378798 TTTTTC-AATTTTTTGATTAATCTTGCTAA-TTAAAAACCTAAATTT-CATGATTTTGAATTTGG
1 TTTTTCAAATTTTTT-ATTAATCTTGCCAAGTTAAAAACCTAAATTTCCA-GATTTGGAATTTGG
* * * *
18378860 GAGAATTGTGATGATTTTACATATATTTTTTCAATTTTTTAATAGGTCTTTAAATCGTATTTAAA
64 GAGAATTTTGATGATTTTAAATATATTTTTT-AAGTTTTAAATAGGTCTTTAAATCGTATTTAAA
* * * * * *
18378925 TCAATCCCAACTTTAAATCCCTTCTCTTGCAAATAAGTTAATTTTTTGACAAAA-ACCCCTTGTT
128 TCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAACAATTTAATTTTTTGACAAAACA-CCATTGTT
* * * * * *
18378989 TTAATGTATGTATTGTCCAAGCCTAGTAAAGCTAGGTATAAG-TATTAATTTGTCACAAATAATC
192 TTAATG--TGTGTT-T-CAA--C---T--AGCT-GGTA-AAGCTCTT-ATTTTTCA-ATATTATT
* ****** * * * * ** * *
18379053 AGTCTT-TAACCCTCCTCTTCATTTCTCTAATCATTCCTCTCCTCCTCTCATTTTCTTTAATTTT
242 A-TCTTACAATTAAAATCCTAATTTC-C--AT-ATTTCTCT-TTCC-CAAATTCT-TTTGATTTT
* * * * *
18379117 AATGTTTTTTTCCTTTCCACCATTGTTGTTGTCGCCTACACCTCCCCTTTTGCCATCTCTTTCTT
299 ATTGTTTTTTTTCTTTCCTCCATTGTTGTTGTCGCCTACACCTCCCCTTTTACCAT-TATTTCTT
* * * ** *
18379182 TTTCTTTTTGTATCAAGATTGTGCACTATTTGCTTTAATCTATTCCTTCCATTTGTCCTCATCTA
363 CTTCTTTTTGTA-CAAGATTGTGCACTATCTCCTTTAATCTATTGGTTCCATTTATCCTCATCTA
* *** * * * * * *
18379247 AATCTGTTTCAAATCTAAAATATT-AAACTCC-A-A--GATCCTGAACATTACCAAAAAAGTGTC
427 AATCAGCACCAAATTTGAAATCTTGAAA-TCCAAGATCGATCCTGAACATTGCCAAGAAAGTGCC
* * * *
18379307 ATTATTGTTTCTCTCATCTAGCTTGAGTAAAAGCTCTTA
491 ATTATCGTTTCTCTCAACTAGCTTG-GTAAGAGCTCTTC
* * *
18379346 TTTCTTC-AATTTTTTAATTAATCTTGCCAA-TTCAAAATCTAAATTTCCAGATTTGGAATCTGG
1 TTT-TTCAAATTTTTT-ATTAATCTTGCCAAGTTAAAAACCTAAATTTCCAGATTTGGAATTTGG
* * * * *
18379409 AAGGATTTTGATGATTTTAAATATATTTTTTTAGTTTTTTAATGGGTCTTTAAATCGTATTTAAA
64 GAGAATTTTGATGATTTTAAATATATTTTTTAAG-TTTTAAATAGGTCTTTAAATCGTATTTAAA
* * * * * *
18379474 TCAGTCCCAAGTTAAAATCCCTTCTCTTGCAAATAATTTAATTTTTTCATAAAA-ACCCCTTATT
128 TCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAACAATTTAATTTTTTGACAAAACA-CCATTGTT
* * * ** * * * *
18379538 TTAATGTGTGCGTCGTCCAAC--CCTAGTAAA-C-C-TAGGTAT-AAGTATTATTTTGTCACAA-
192 TTAATGTGT--GT--TTCAACTAGCTGGTAAAGCTCTTATTTTTCAA-TATTATTATCTTACAAT
* * ** * * ** *
18379596 AAAAATCAGTCTTTAATCCTAGTCATTCCTCTCCTCCTCTTATTCTCTTTGATTTTAATGTTTTT
252 TAAAATC-CTAATT--TCC-A-T-ATTTCTCT-TTCC-CAAATTCT-TTTGATTTTATTGTTTTT
* * * *
18379661 TTCCTTTCCTCCATTGTTGTTGTCACCTACACCTCCCCTTTTACCATCTCTTTCTTCTTCTATTT
308 TTTCTTTCCTCCATTGTTGTTGTCGCCTACACCTCCCCTTTTACCAT-TATTTCTTCTTCTTTTT
* *
18379726 GTATCAAGATTGTGCACCATCTCCTTTAATCTA-TGGCTTCCATTTATCCTCATCTAAGTCAGCA
372 GTA-CAAGATTGTGCACTATCTCCTTTAATCTATTGG-TTCCATTTATCCTCATCTAAATCAGCA
* * * *
18379790 CCAAATTTGAAATCTTGAACTCCACGATCGATCTTGAACATTGCCAAGAAAGTGCCATTATCATT
435 CCAAATTTGAAATCTTGAAATCCAAGATCGATCCTGAACATTGCCAAGAAAGTGCCATTATCGTT
*
18379855 TCTCTTAACTAGCTTGAGTAAGAGCTCTTC
500 TCTCTCAACTAGCTTG-GTAAGAGCTCTTC
* * *
18379885 TTTCTTC-AATTTTTTAATTAATCTTGCCAAG-TAAAAACCTAAATTTCCAAATTTTGAAGTTGG
1 TTT-TTCAAATTTTTT-ATTAATCTTGCCAAGTTAAAAACCTAAATTTCCAGATTTGGAATTTGG
* * * ** **
18379948 GATAATTTTGATGATGTTATATATATTTTTTAAGTTTTTTCATTTGTCTTTAAATCGTATTTAAA
64 GAGAATTTTGATGATTTTAAATATATTTTTTAAG-TTTTAAATAGGTCTTTAAATCGTATTTAAA
* * * * *
18380013 TCAATCCCAAGTTCAAATCCCTTCTCTTGCAAATAATTTAATTTTTTGAGAAAGC-CCTTTGTTT
128 TCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAACAATTTAATTTTTTGACAAAACACCATTGTTT
* * * *
18380077 TAATGTGTGTGTCGTCCAAGCCTAGTAAACCTAGGTATAAG-TATTATTTTTTCACAAATAATCA
193 TAATGTGTGT-T--T-CAA--CTAG-----CT-GGTA-AAGCTCTTA-TTTTTCA-ATATTATTA
* * ***** * * **
18380141 GCCTTTC-ATCCTCCTCCTTATTGT-CATAGTCATTCCTCTCCTCCTCTCATTCTTTTGATTTTA
243 -TCTTACAATTAAAATCCTAATT-TCCATA-T--TT-CTCT-TTCC-CAAATTCTTTTGATTTT-
* * * *
18380204 ATGTTTTTTTTTTCCTTTCCTCCATTGTTGTTGTCGCCTACACCTACCCTTTTACCATCACATTC
299 AT-TGTTTTTTTT-CTTTCCTCCATTGTTGTTGTCGCCTACACCTCCCCTTTTACCATTA-TTTC
* * *
18380269 TTCTTCTTTTTG-ATCAAGATTGTGCA-TCATATCCTTTAATCTATTGCTTCCATTTATCCTCGT
361 TTCTTCTTTTTGTA-CAAGATTGTGCACT-ATCTCCTTTAATCTATTGGTTCCATTTATCCTCAT
* * *
18380332 CTAAATCAACACCAAATTTGAAATCTTAAAATCCAAGATAGATCCTGAACATTGCCAAGAAAGTG
424 CTAAATCAGCACCAAATTTGAAATCTTGAAATCCAAGATCGATCCTGAACATTGCCAAGAAAGTG
* *
18380397 CCCTTATCGTTTCTCTCAACTAGCTTGGGTTAGAGCTCTTC
489 CCATTATCGTTTCTCTCAACTAGCTT-GGTAAGAGCTCTTC
* *
18380438 TCTCTTT-AATTTTTTTTATTAATCTTGCCAA-TTAAAAACCTAAATTTCTAGATTTGGAATTTG
1 T-T-TTTCAA-ATTTTTTATTAATCTTGCCAAGTTAAAAACCTAAATTTCCAGATTTGGAATTTG
* * *
18380501 GGAGAATTTTGATGATTTGAAATATATTTTTTTAGTTTCTGAATAGGT-TTGTAAATCGTATTTA
63 GGAGAATTTTGATGATTTTAAATATATTTTTTAAGTTT-TAAATAGGTCTT-TAAATCGTATTTA
* * *
18380565 AATCAGTCCCAAGTTTAAAACCCTTCTCTTGCAAACAATTTAATTTTTTGACAAAA-ACCCCTTG
126 AATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAACAATTTAATTTTTTGACAAAACA-CCATTG
* * * * * ** * * * * *
18380629 TTTTAATGTATGTGTCATCCAAGGCTAGTAAA-C-C-TAGGTAT-AAGTATTATTTTGTCACAAA
190 TTTTAATGTGTGTTTCA-ACTA-GCTGGTAAAGCTCTTATTTTTCAA-TATTATTATCTTACAAT
* *
18380690 TAATTATCCT--TTAATCCTAGTCATTCCTCTCTTTCTCAAATTCTCTTTGATTTTATTGTTTTT
252 TAA-AATCCTAATT--TCC-A-T-ATT--TCTCTTTCCCAAATTCT-TTTGATTTTATTGTTTTT
* *
18380753 TTTCTTTCCTCCATTGTTGTTGTCGCCCACACCCCCCCTTTTACCATGTATTTCTTCTTCTTTTT
308 TTTCTTTCCTCCATTGTTGTTGTCGCCTACACCTCCCCTTTTACCAT-TATTTCTTCTTCTTTTT
* *
18380818 GTTAC-AGATTGTGCACTATCTCCTTTAATCTATTGGTTCCATTTTTCCTCATCTAAATTAGCAC
372 G-TACAAGATTGTGCACTATCTCCTTTAATCTATTGGTTCCATTTATCCTCATCTAAATCAGCAC
* * * * *
18380882 CAAATATAAAATCTTGAATTTCAAGATCGATCCTGAACATTGCCAAGAAAGTTCCATTATCGTTT
436 CAAATTTGAAATCTTGAAATCCAAGATCGATCCTGAACATTGCCAAGAAAGTGCCATTATCGTTT
* *
18380947 CTCTCAACTAGCTTAGGTCAGAGTTCTTC
501 CTCTCAACTAGCTT-GGTAAGAGCTCTTC
18380976 TTTTTCAAATTTTTTATTAATCTTG-CAAGTTAAAAACCTAAATTTCCAGATTTGGAATTTGGGA
1 TTTTTCAAATTTTTTATTAATCTTGCCAAGTTAAAAACCTAAATTTCCAGATTTGGAATTTGGGA
* * * * *
18381040 GAATTGTGAAGATTTTAAATATA-TTTTTCAGTTTTAAATGGGTCTTTAAATCGTATTTAAATTA
66 GAATTTTGATGATTTTAAATATATTTTTTAAGTTTTAAATAGGTCTTTAAATCGTATTTAAATCA
* *
18381104 GTCCCAAGTTCAAATCCCTTCTCTTGTAAACAATTTAATTTTTTGA-AAAACACCATTGTATTAA
131 GTCCCAAGTTCAAATCCCTTCTCTTGCAAACAATTTAATTTTTTGACAAAACACCATTGTTTTAA
* * * *
18381168 TGTGCGCTTTCAACTAGCTTGGGTAAGAGCTCTTCTTTCTTCAATTTTTATTAATCTTGGCAATT
196 TGTGTG-TTTCAACTAGC-T-GGTAA-AGCTCTTATTT-TTCAA-TATTATT-ATCTT-ACAATT
*
18381233 AAAAACCTAAATTTCCATATTT
253 AAAATCCT-AATTTCCATATTT
18381255 GGAATTTGGG
Statistics
Matches: 1555, Mismatches: 254, Indels: 211
0.77 0.13 0.10
Matches are distributed among these distances:
532 2 0.00
533 26 0.02
534 89 0.06
535 189 0.12
536 81 0.05
537 6 0.00
538 213 0.14
539 241 0.15
540 28 0.02
541 26 0.02
542 16 0.01
543 3 0.00
544 5 0.00
545 3 0.00
546 2 0.00
547 6 0.00
548 8 0.01
549 177 0.11
550 5 0.00
551 17 0.01
552 22 0.01
553 159 0.10
554 207 0.13
555 24 0.02
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.43
Consensus pattern (528 bp):
TTTTTCAAATTTTTTATTAATCTTGCCAAGTTAAAAACCTAAATTTCCAGATTTGGAATTTGGGA
GAATTTTGATGATTTTAAATATATTTTTTAAGTTTTAAATAGGTCTTTAAATCGTATTTAAATCA
GTCCCAAGTTCAAATCCCTTCTCTTGCAAACAATTTAATTTTTTGACAAAACACCATTGTTTTAA
TGTGTGTTTCAACTAGCTGGTAAAGCTCTTATTTTTCAATATTATTATCTTACAATTAAAATCCT
AATTTCCATATTTCTCTTTCCCAAATTCTTTTGATTTTATTGTTTTTTTTCTTTCCTCCATTGTT
GTTGTCGCCTACACCTCCCCTTTTACCATTATTTCTTCTTCTTTTTGTACAAGATTGTGCACTAT
CTCCTTTAATCTATTGGTTCCATTTATCCTCATCTAAATCAGCACCAAATTTGAAATCTTGAAAT
CCAAGATCGATCCTGAACATTGCCAAGAAAGTGCCATTATCGTTTCTCTCAACTAGCTTGGTAAG
AGCTCTTC
Found at i:18382213 original size:538 final size:538
Alignment explanation
Indices: 18381177--18383325 Score: 2708
Period size: 532 Copynumber: 4.0 Consensus size: 538
18381167 ATGTGCGCTT
* *
18381177 TCAACTAGCTTGGGTAAGAGCTCTTCTTTCTTCAA-TTTTTATTAATCTTGGCAATTAAAAACCT
1 TCAACTAGCTTGGGTAAGAGCTCTTCTTTCTTCAATTTTTTATTAATCATGCCAATTAAAAACCT
* * *
18381241 AAATTTCCATATTTGGAATTTGGGAGAATTGTGAAGATTTTAAATATATTTTTTCAG-TTTTTAA
66 AAATTTCCAGATTTGGAATTTGGGAGAATTGTGATGATTTTAAATATATTTTTTAAGTTTTTTAA
* *
18381305 TGGGTCTTTAAATCGTATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAATAATTTATT
131 TGGGTCTTTAAATCATATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAATAATTTAAT
** * * *
18381370 TATTTTGACAAAAACCC-CAAGTTTTAATGTCTG-AGTCACCCAAGCCTAGTAAACCTTGGTATA
196 T-TTTTGACAAAAACCCTTTA-TTTTAATGTGTGTA-TCATCCAAGCCTAGTAAACCTAGGTATA
* * *
18381433 AGCATTATTTTTTTACAAATAATCAACCTTTAATCCTCATCTTCATTGCCCTAGTCATTCCTCTC
258 AGTATTATTTTTTCACAAATAATCAGCCTTTAAT-C-C-T-TTCATT--CC---TC--T-C-CTC
* *
18381498 CTCCTCTCATTCTCTTTGATTTTAATGTTTTTTTTCCTTTCCTCCATTGTTGTTGTCGCCTACAC
310 CT--TCTCATTCTCTTTGATTTTAATGTTTTTTTTACTTTCCTCCATTGTTGTTGTCGCCCACAC
* * * * *
18381563 CTCCCATTTTACCATCTCTTTCTTCTGCTTTTTATATCAAGATTTTGCACCATCTCCTCTAATCT
373 CTCCCCTTTTACCATCTCTTTCTTCTTCTTTTTGTATCAAGATTGTGCACCATCTCCTTTAATCT
* * * *
18381628 ATTGCTTCCATTTATCCTCATATGAATCAGCACCAAATCTGAAATCTTGAACTCCAAGATCAATC
438 ATTGCTTCCATTTATCCTCATCTAAATCAGCACCAAATCTAAAATCTTGAACTCCAAGATCGATC
*
18381693 CTGAACATTGCCAAGAAA-TGGCCATTATCGTTTCTT
503 CTGAACATTGCCAAGAAAGT-GCCATTATCGTTTCTC
*
18381729 TGAACTAGCTTGGGTAAGAGCTCTTCTTTCTTCAATTTTTTTTATTAATCATGCCAATTAAAAA-
1 TCAACTAGCTTGGGTAAGAGCTCTTCTTTCTTCAA--TTTTTTATTAATCATGCCAATTAAAAAC
* ** *
18381793 CTGAAATTTCTAGATTTGGAATTTGAAAGAATTGTGATGATTTGAAATATA-TTTTTAAGTCTTT
64 CT-AAATTTCCAGATTTGGAATTTGGGAGAATTGTGATGATTTTAAATATATTTTTTAAGT-TTT
*
18381857 TT-ATGGGTCTTTAAATCATATTTAAATCAGTCCCAAGATCAAATCCCTTCTCTTGCAAATAATT
127 TTAATGGGTCTTTAAATCATATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAATAATT
* *
18381921 TAATTTTTTGACAAAAACCCTTTATTTTAATGTGTGCATCGTCCAAGCCTAGTAAACCTAGGTAT
192 TAATTTTTTGACAAAAACCCTTTATTTTAATGTGTGTATCATCCAAGCCTAGTAAACCTAGGTAT
18381986 AAGTATTATTTTTTCACAAATAATCAGCCTTTAATCCTATTCATTCCTCTCCTCCTT-TCATTCT
257 AAGTATTATTTTTTCACAAATAATCAGCCTTTAATCCT-TTCATTCCTCTCCTCCTTCTCATTCT
* * * *
18382050 CTTTGATTTTAATGTCTTTTTT-CTTTCCTCCATTGTTGTTATCCCCCACACCTCCCCTTTTAGC
321 CTTTGATTTTAATGTTTTTTTTACTTTCCTCCATTGTTGTTGTCGCCCACACCTCCCCTTTTACC
* *
18382114 ATCTCTTTCTTCTTCTTTTTGTATCAAGATTGTGTACCATCTCCTTTAATCTATGGCTTCCATTT
386 ATCTCTTTCTTCTTCTTTTTGTATCAAGATTGTGCACCATCTCCTTTAATCTATTGCTTCCATTT
* ** * * * * *
18382179 TTTTTTATCTAAATCAGCACCAACTCTAAAATCTTGAACTACAAGATCGATCCTTAACATTTCCA
451 ATCCTCATCTAAATCAGCACCAAATCTAAAATCTTGAACTCCAAGATCGATCCTGAACATTGCCA
* *
18382244 AGAAAGTTCCATTATTGTTTCTC
516 AGAAAGTGCCATTATCGTTTCTC
* * * * *
18382267 TCAACTAGCCTGAGTAAGAGCTCGTCTTTCTTCAATTTTTTATTAATCTTGCCAATTAAAACCCT
1 TCAACTAGCTTGGGTAAGAGCTCTTCTTTCTTCAATTTTTTATTAATCATGCCAATTAAAAACCT
*** ** * * * * * *
18382332 AAAATTT-TTTATTTATAATTTGTGAGAATTTTTATGACTTTAAATATATTTTATATGTTTTTTA
66 -AAATTTCCAGATTTGGAATTTGGGAGAATTGTGATGATTTTAAATATATTTTTTAAGTTTTTTA
*
18382396 ATGGGTCTTTAAATCGTATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAATAATTTAA
130 ATGGGTCTTTAAATCATATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAATAATTTAA
* * * * *
18382461 ATTTTTGATAAAAACCCCTTGTTTTAATGTGTGTGTCATCCAAGCCTAGTAAACCTAGGTATAAG
195 TTTTTTGACAAAAACCCTTTATTTTAATGTGTGTATCATCCAAGCCTAGTAAACCTAGGTATAAG
* ** ** *
18382526 TATTATTTTGTCACAAATAATCAGCCTTTAATCC--T--TTCCTCAACT-CTTCTCAGCCTTTTT
260 TATTATTTTTTCACAAATAATCAGCCTTTAATCCTTTCATTCCTCTCCTCCTTCTCATTCTCTTT
* * * *
18382586 GATTTTAATG-TTTTTTTATTTTCCTCTATTGTTGTTGTCACCTACA-CTGCCCCTTTTACCATC
325 GATTTTAATGTTTTTTTTACTTTCCTCCATTGTTGTTGTCGCCCACACCT-CCCCTTTTACCATC
* *
18382649 TCTTTCTTCTTCTTTTTGTATCAAGATTGTGAACTATCTCCTTTAATCTATTGCTTCCATTTATC
389 TCTTTCTTCTTCTTTTTGTATCAAGATTGTGCACCATCTCCTTTAATCTATTGCTTCCATTTATC
* * * * *
18382714 TTCATCTAAATCAGGATCAAATCTAACATCTTGTACTCCAAGATCGATCCTGAACATTGCCAAGA
454 CTCATCTAAATCAGCACCAAATCTAAAATCTTGAACTCCAAGATCGATCCTGAACATTGCCAAGA
18382779 AAGTGCCATTATCGTTTCTC
519 AAGTGCCATTATCGTTTCTC
*
18382799 TCAACTAGCTTGGGT-AGAGCTCTTCTTTCTTCAATATTTTTTATTAATTATGCCAATTAAAAAC
1 TCAACTAGCTTGGGTAAGAGCTCTTCTTTCTTC-A-ATTTTTTATTAATCATGCCAATTAAAAAC
*
18382863 CTAAATTTCCAGATTTGGAATTTGGGAGAATTTTGATGATTTTAAATATATTTTTTCAA-TTTTT
64 CTAAATTTCCAGATTTGGAATTTGGGAGAATTGTGATGATTTTAAATATATTTTTT-AAGTTTTT
* ** *
18382927 TAATAGGTCTTTAAATCATATTTAAATCAGTCCCAAGTTCAAATCTTATTCTC-TACTAAATAAT
128 TAATGGGTCTTTAAATCATATTTAAATCAGTCCCAAGTTCAAATC-CCTTCTCTTGC-AAATAAT
* ** * *
18382991 TTAATTTTTTGACAAAATTCCCTTGTA--TTAATGTGTGTGCCGTCCAACCCTAGTAAACCTAGG
191 TTAATTTTTTGACAAAA-ACCCTT-TATTTTAATGTGTGTATCATCCAAGCCTAGTAAACCTAGG
* * * * **
18383054 TATAATTATTATTTTTTCACAACTAATCAGCCTTTAATCCTTGCCATTCCTCTCTTCC-TCAAAT
254 TATAAGTATTATTTTTTCACAAATAATCAGCCTTTAATCCTT-TCATTCCTCTCCTCCTTCTCAT
* * * * * * *
18383118 TCTTTTTGATTTTATTACTTTTTTTTTCTTTCCTTCATTGTTATTGTCGTCCACACCTCCCCTTT
318 TCTCTTTGATTTTAAT-GTTTTTTTTACTTTCCTCCATTGTTGTTGTCGCCCACACCTCCCCTTT
* * * * *
18383183 TACCATCTTTTTCTTCTTATTTTTGTATAAAGATTGTGCACTATCTCCTTTAATCTACTGCTTCC
382 TACCATCTCTTTCTTCTTCTTTTTGTATCAAGATTGTGCACCATCTCCTTTAATCTATTGCTTCC
* * * *
18383248 ATTTGTCCTCATCTAAATCAGCACCAAATCTGACATCTTGAATTCCAAGATCGATCCTGAACATT
447 ATTTATCCTCATCTAAATCAGCACCAAATCTAAAATCTTGAACTCCAAGATCGATCCTGAACATT
18383313 GCCAAGAAAGTGC
512 GCCAAGAAAGTGC
18383326 TTGTAAAAAT
Statistics
Matches: 1396, Mismatches: 169, Indels: 75
0.85 0.10 0.05
Matches are distributed among these distances:
531 27 0.02
532 216 0.15
533 116 0.08
534 99 0.07
535 4 0.00
536 62 0.04
537 169 0.12
538 198 0.14
539 53 0.04
540 2 0.00
541 166 0.12
542 7 0.01
543 1 0.00
544 1 0.00
546 2 0.00
549 2 0.00
551 7 0.01
552 35 0.03
553 1 0.00
554 91 0.07
555 132 0.09
556 5 0.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (538 bp):
TCAACTAGCTTGGGTAAGAGCTCTTCTTTCTTCAATTTTTTATTAATCATGCCAATTAAAAACCT
AAATTTCCAGATTTGGAATTTGGGAGAATTGTGATGATTTTAAATATATTTTTTAAGTTTTTTAA
TGGGTCTTTAAATCATATTTAAATCAGTCCCAAGTTCAAATCCCTTCTCTTGCAAATAATTTAAT
TTTTTGACAAAAACCCTTTATTTTAATGTGTGTATCATCCAAGCCTAGTAAACCTAGGTATAAGT
ATTATTTTTTCACAAATAATCAGCCTTTAATCCTTTCATTCCTCTCCTCCTTCTCATTCTCTTTG
ATTTTAATGTTTTTTTTACTTTCCTCCATTGTTGTTGTCGCCCACACCTCCCCTTTTACCATCTC
TTTCTTCTTCTTTTTGTATCAAGATTGTGCACCATCTCCTTTAATCTATTGCTTCCATTTATCCT
CATCTAAATCAGCACCAAATCTAAAATCTTGAACTCCAAGATCGATCCTGAACATTGCCAAGAAA
GTGCCATTATCGTTTCTC
Found at i:18397768 original size:18 final size:18
Alignment explanation
Indices: 18397747--18397783 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
18397737 TGAATTTTCG
*
18397747 AATTCGAATAACTCAAAT
1 AATTCGAATAAATCAAAT
18397765 AATTCGAATAAATCAAAT
1 AATTCGAATAAATCAAAT
18397783 A
1 A
18397784 TCAAACTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:18397858 original size:17 final size:19
Alignment explanation
Indices: 18397832--18397876 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
18397822 ACTTTTTTCT
* *
18397832 TTTTATTTCCCC-C-AAAG
1 TTTTACTTCCCCTCAAAAA
18397849 TTTTACTTCCCCTCAAAAA
1 TTTTACTTCCCCTCAAAAA
18397868 TTTTACTTC
1 TTTTACTTC
18397877 TCTTCAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.46
18 1 0.04
19 12 0.50
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.44
Consensus pattern (19 bp):
TTTTACTTCCCCTCAAAAA
Found at i:18402874 original size:39 final size:39
Alignment explanation
Indices: 18402820--18402996 Score: 121
Period size: 39 Copynumber: 4.5 Consensus size: 39
18402810 CTCTGGGGTT
18402820 AACTGAGATTTTTCTTCAGTGCA-TTTTATCGGTGCCAGC
1 AACTGAGATTTTTCTTCAGTGCACTTTTAT-GGTGCCAGC
* * * *
18402859 AACTGAGATTTTTCTTCA--GCAAGTTCTATAGGCGTCAGC
1 AACTGAGATTTTTCTTCAGTGC-ACTTTTAT-GGTGCCAGC
* * * * *
18402898 GAGTGAGATTTTTCTTCTGTGTACTCTTT-TAGTGCCAGC
1 AACTGAGATTTTTCTTCAGTGCACT-TTTATGGTGCCAGC
* * * * *
18402937 AACTGGGATTTTTCTTCAATGTACTCTTT-TGGTGTCATC
1 AACTGAGATTTTTCTTCAGTGCACT-TTTATGGTGCCAGC
* * *
18402976 AGCTGAGGTTTCTCTTCAGTG
1 AACTGAGATTTTTCTTCAGTG
18402997 TACTGAACAG
Statistics
Matches: 107, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
37 2 0.02
38 1 0.01
39 98 0.92
40 3 0.03
41 3 0.03
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (39 bp):
AACTGAGATTTTTCTTCAGTGCACTTTTATGGTGCCAGC
Found at i:18403257 original size:20 final size:21
Alignment explanation
Indices: 18403220--18403258 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18403210 TTCAGTTCAA
*
18403220 AGGGAGACCAAGAAAAGAAAG
1 AGGGAGAACAAGAAAAGAAAG
18403241 AGGGAGAACAA-AAAAGAA
1 AGGGAGAACAAGAAAAGAA
18403259 CAATTGCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.62, C:0.08, G:0.31, T:0.00
Consensus pattern (21 bp):
AGGGAGAACAAGAAAAGAAAG
Found at i:18419811 original size:22 final size:21
Alignment explanation
Indices: 18419786--18419826 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
18419776 ATTTATTTTA
* *
18419786 TCTTTTTATTTTTCTATTCTTT
1 TCTTTCTAATTTTCT-TTCTTT
18419808 TCTTTCTAATTTTCTTTCT
1 TCTTTCTAATTTTCTTTCT
18419827 ACTCTACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (21 bp):
TCTTTCTAATTTTCTTTCTTT
Found at i:18420364 original size:21 final size:21
Alignment explanation
Indices: 18420338--18420392 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
18420328 GCAAGTCTCG
*
18420338 ATACTTGGCCTGTAAGCCTCA
1 ATACTTGGCCTATAAGCCTCA
**
18420359 ATACTTAGG-CTATAAGTTTCA
1 ATACTT-GGCCTATAAGCCTCA
*
18420380 AGACTTGGCCTAT
1 ATACTTGGCCTAT
18420393 TTATTGTAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (21 bp):
ATACTTGGCCTATAAGCCTCA
Found at i:18423097 original size:29 final size:29
Alignment explanation
Indices: 18423034--18423103 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
18423024 TCATCAACAA
*
18423034 ATGAAAAGGGATAGCTTTGACAATCGAAT
1 ATGAAAAGGGATAGCTTCGACAATCGAAT
* *
18423063 AAGAAAGGGGATAGCTTCGACAATC-AATT
1 ATGAAAAGGGATAGCTTCGACAATCGAA-T
18423092 ATGAAAAGGGAT
1 ATGAAAAGGGAT
18423104 GGTGATGACC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 2 0.06
29 33 0.94
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.21
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGACAATCGAAT
Found at i:18423129 original size:30 final size:30
Alignment explanation
Indices: 18423092--18423227 Score: 125
Period size: 30 Copynumber: 4.6 Consensus size: 30
18423082 ACAATCAATT
18423092 ATGAAAAGGGATGGTGATGACCATC-AACA
1 ATGAAAAGGGATGGTGATGACCATCGAACA
* * *
18423121 ATGAAAAAGGACGGTGATGACCATCGAACT
1 ATGAAAAGGGATGGTGATGACCATCGAACA
* * * **
18423151 ATGAAAAGGGATGGCT--TCGGCTATCCAATT
1 ATGAAAAGGGATGG-TGAT-GACCATCGAACA
* **
18423181 ATGAAAAGGGATGGTGACGACCATTAAACA
1 ATGAAAAGGGATGGTGATGACCATCGAACA
*
18423211 ATGAAAAGGGATAGTGA
1 ATGAAAAGGGATGGTGA
18423228 CTACTATCAA
Statistics
Matches: 85, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
29 25 0.29
30 59 0.69
31 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (30 bp):
ATGAAAAGGGATGGTGATGACCATCGAACA
Found at i:18423245 original size:30 final size:30
Alignment explanation
Indices: 18423080--18423254 Score: 106
Period size: 30 Copynumber: 5.9 Consensus size: 30
18423070 GGGATAGCTT
* *
18423080 CGACAATC-AATTATGAAAAGGGATGGTGA
1 CGACTATCAAATTATGAAAAGGGATAGTGA
* * * **
18423109 TGACCATCAACA--ATGAAAAAGGACGGTGA
1 CGACTATCAA-ATTATGAAAAGGGATAGTGA
* * * * * *
18423138 TGACCATCGAACTATGAAAAGGGATGGCT-T
1 CGACTATCAAATTATGAAAAGGGATAG-TGA
* * *
18423168 CGGCTATCCAATTATGAAAAGGGATGGTGA
1 CGACTATCAAATTATGAAAAGGGATAGTGA
* * **
18423198 CGACCATTAAACAATGAAAAGGGATAGTGA
1 CGACTATCAAATTATGAAAAGGGATAGTGA
* *
18423228 CTACTATCAAATTATGAAAAAGGATAG
1 CGACTATCAAATTATGAAAAGGGATAG
18423255 CTTCGACTGT
Statistics
Matches: 113, Mismatches: 27, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
28 1 0.01
29 31 0.27
30 79 0.70
31 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.21
Consensus pattern (30 bp):
CGACTATCAAATTATGAAAAGGGATAGTGA
Found at i:18423281 original size:90 final size:88
Alignment explanation
Indices: 18423071--18423282 Score: 246
Period size: 90 Copynumber: 2.4 Consensus size: 88
18423061 ATAAGAAAGG
* * * *
18423071 GGATAGCTTCGACAATCAATTATGAAAAGGGATGGTGATGACCATCAACAATGAAAAAGGACGGT
1 GGATAGCTTCGACTATCAATTATGAAAAGGGATGGTGACGACCATAAACAATGAAAAAGGACAGT
* *
18423136 GATGACCATCGAACTATGAAAAG
66 GATGACCATCAAACTATGAAAAA
* * * *
18423159 GGATGGCTTCGGCTATCCAATTATGAAAAGGGATGGTGACGACCATTAAACAATGAAAAGGGATA
1 GGATAGCTTCGACTAT-CAATTATGAAAAGGGATGGTGACGACCA-TAAACAATGAAAAAGGACA
* *
18423224 GTGACT-ACTATCAAATTATGAAAAA
64 GTGA-TGACCATCAAACTATGAAAAA
* * *
18423249 GGATAGCTTCGACTGTCGAACTATGAATAGGGAT
1 GGATAGCTTCGACTATC-AATTATGAAAAGGGAT
18423283 AATTTCAATT
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
88 13 0.13
89 28 0.27
90 61 0.59
91 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (88 bp):
GGATAGCTTCGACTATCAATTATGAAAAGGGATGGTGACGACCATAAACAATGAAAAAGGACAGT
GATGACCATCAAACTATGAAAAA
Found at i:18429023 original size:12 final size:12
Alignment explanation
Indices: 18429003--18429033 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
18428993 CGCCACATGA
*
18429003 CCGTATGGTAGG
1 CCGTGTGGTAGG
18429015 CCGTGTGGTAGG
1 CCGTGTGGTAGG
18429027 CCGTGTG
1 CCGTGTG
18429034 AGCCACACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.45, T:0.26
Consensus pattern (12 bp):
CCGTGTGGTAGG
Found at i:18449611 original size:34 final size:34
Alignment explanation
Indices: 18449573--18449683 Score: 125
Period size: 34 Copynumber: 3.3 Consensus size: 34
18449563 TTACAGTGTT
*
18449573 ATTTGGTGTAATGGATGGATTTTG-TCATACGAGC
1 ATTTGGTGTAATGGATGGA-TTGGCTCATACGAGC
* *
18449607 ATTTGGTGTACTGGATGGATTGGCTCATATGAGC
1 ATTTGGTGTAATGGATGGATTGGCTCATACGAGC
* ** ** *
18449641 ATTTGGTATGCTGGATGGGCTGGCTCATATGAGC
1 ATTTGGTGTAATGGATGGATTGGCTCATACGAGC
18449675 ATTTGGTGT
1 ATTTGGTGT
18449684 GCTGGCTGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 3 0.04
34 65 0.96
ACGTcount: A:0.20, C:0.11, G:0.32, T:0.37
Consensus pattern (34 bp):
ATTTGGTGTAATGGATGGATTGGCTCATACGAGC
Found at i:18449687 original size:34 final size:34
Alignment explanation
Indices: 18449597--18449688 Score: 139
Period size: 34 Copynumber: 2.7 Consensus size: 34
18449587 ATGGATTTTG
* * *
18449597 TCATACGAGCATTTGGTGTACTGGATGGATTGGC
1 TCATATGAGCATTTGGTGTGCTGGATGGACTGGC
* *
18449631 TCATATGAGCATTTGGTATGCTGGATGGGCTGGC
1 TCATATGAGCATTTGGTGTGCTGGATGGACTGGC
18449665 TCATATGAGCATTTGGTGTGCTGG
1 TCATATGAGCATTTGGTGTGCTGG
18449689 CTGGTTAACC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.18, C:0.14, G:0.34, T:0.34
Consensus pattern (34 bp):
TCATATGAGCATTTGGTGTGCTGGATGGACTGGC
Found at i:18457804 original size:13 final size:13
Alignment explanation
Indices: 18457786--18457810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18457776 TAAAGATAAA
18457786 TAAAATTAAATCC
1 TAAAATTAAATCC
18457799 TAAAATTAAATC
1 TAAAATTAAATC
18457811 ATCTTTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAATTAAATCC
Found at i:18458160 original size:70 final size:70
Alignment explanation
Indices: 18458073--18458210 Score: 276
Period size: 70 Copynumber: 2.0 Consensus size: 70
18458063 TACTCAAAAT
18458073 AAATACATAATTAATACATAAAAATACGTTATTCTAAAGTATTATCAAATTTCCCCTACTTAGTC
1 AAATACATAATTAATACATAAAAATACGTTATTCTAAAGTATTATCAAATTTCCCCTACTTAGTC
18458138 CATAA
66 CATAA
18458143 AAATACATAATTAATACATAAAAATACGTTATTCTAAAGTATTATCAAATTTCCCCTACTTAGTC
1 AAATACATAATTAATACATAAAAATACGTTATTCTAAAGTATTATCAAATTTCCCCTACTTAGTC
18458208 CAT
66 CAT
18458211 GCTTGCCCTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.35
Consensus pattern (70 bp):
AAATACATAATTAATACATAAAAATACGTTATTCTAAAGTATTATCAAATTTCCCCTACTTAGTC
CATAA
Found at i:18458520 original size:16 final size:16
Alignment explanation
Indices: 18458499--18458530 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18458489 CTTTTTTTTC
18458499 ATTTATTTTGATTTAT
1 ATTTATTTTGATTTAT
*
18458515 ATTTATTTTTATTTAT
1 ATTTATTTTGATTTAT
18458531 TTATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
ATTTATTTTGATTTAT
Found at i:18459587 original size:5 final size:5
Alignment explanation
Indices: 18459577--18459639 Score: 51
Period size: 5 Copynumber: 12.2 Consensus size: 5
18459567 AGCAATAAAT
*
18459577 AATAA AATAA AATAA AGTAATA AATAA AAT-A AAT-A AATAA AATAA TAA-ATA
1 AATAA AATAA AATAA AAT-A-A AATAA AATAA AATAA AATAA AATAA -AATA-A
18459628 AATAAA AATAA A
1 AAT-AA AATAA A
18459640 TTAGGTTGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
4 8 0.16
5 28 0.57
6 9 0.18
7 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:18459591 original size:13 final size:12
Alignment explanation
Indices: 18459570--18459639 Score: 83
Period size: 13 Copynumber: 5.8 Consensus size: 12
18459560 CCAAATAAGC
18459570 AATAAATAATAA-
1 AATAAATAA-AAT
*
18459582 AATAAAATAAAGT
1 AAT-AAATAAAAT
18459595 AATAAATAAAAT
1 AATAAATAAAAT
18459607 AAATAAATAAAAT
1 -AATAAATAAAAT
18459620 AATAAAT-AAAT
1 AATAAATAAAAT
18459631 AA-AAATAAA
1 AATAAATAAA
18459640 TTAGGTTGCC
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
10 4 0.08
11 8 0.15
12 19 0.37
13 21 0.40
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.23
Consensus pattern (12 bp):
AATAAATAAAAT
Found at i:18459600 original size:25 final size:25
Alignment explanation
Indices: 18459562--18459639 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
18459552 ATTAATATCC
*
18459562 AAAT-AAGCAATAAATAATAAAATA
1 AAATAAAGTAATAAATAATAAAATA
*
18459586 AAATAAAGTAATAAATAAAATAAAT-
1 AAATAAAGTAATAAATAATA-AAATA
*
18459611 AAATAAAATAATAAATAAATAAAAATA
1 AAATAAAGTAATAAAT-AAT-AAAATA
18459638 AA
1 AA
18459640 TTAGGTTGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
24 4 0.09
25 28 0.62
26 10 0.22
27 3 0.07
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (25 bp):
AAATAAAGTAATAAATAATAAAATA
Found at i:18459615 original size:30 final size:31
Alignment explanation
Indices: 18459573--18459640 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
18459563 AATAAGCAAT
18459573 AAAT-AATAAAATAAAATAA-AGTAATAAAT-A
1 AAATAAATAAAATAAAATAATA--AATAAATAA
18459603 AAATAAAT-AAATAAAATAATAAATAAATAA
1 AAATAAATAAAATAAAATAATAAATAAATAA
18459633 AAATAAAT
1 AAATAAAT
18459641 TAGGTTGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 7 0.20
30 24 0.69
31 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (31 bp):
AAATAAATAAAATAAAATAATAAATAAATAA
Found at i:18459635 original size:17 final size:16
Alignment explanation
Indices: 18459570--18459638 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 16
18459560 CCAAATAAGC
*
18459570 AATAAATAATAAAATAA
1 AATAAATAATAAAA-AT
18459587 AATAAAGTAATAAATAA-
1 AATAAA-TAATAAA-AAT
18459604 AATAAATAA-ATAAAAT
1 AATAAATAATA-AAAAT
18459620 AATAAATAAATAAAAAT
1 AATAAAT-AATAAAAAT
18459637 AA
1 AA
18459639 ATTAGGTTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.07
16 12 0.26
17 21 0.46
18 9 0.20
19 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.23
Consensus pattern (16 bp):
AATAAATAATAAAAAT
Found at i:18459640 original size:4 final size:4
Alignment explanation
Indices: 18459570--18459633 Score: 62
Period size: 4 Copynumber: 15.5 Consensus size: 4
18459560 CCAAATAAGC
18459570 AATA AAT- AATAA AATAA AATA AAGT- AATA AATAA AATA AATA AATA
1 AATA AATA AAT-A AAT-A AATA AA-TA AATA AAT-A AATA AATA AATA
18459616 AA-A TAATA AATA AATA AA
1 AATA -AATA AATA AATA AA
18459634 AATAAATTAG
Statistics
Matches: 53, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
3 5 0.09
4 34 0.64
5 14 0.26
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:18465929 original size:3 final size:3
Alignment explanation
Indices: 18465921--18465983 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
18465911 CTAAAACTCT
* * *
18465921 GAA GAA GAA GAA AAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GAG
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
18465969 GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA
18465984 ATTTCCCAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:18467070 original size:2 final size:2
Alignment explanation
Indices: 18467007--18467050 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
18466997 ACAAAATGGA
*
18467007 GT GT GT TT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
18467049 GT
1 GT
18467051 TGCAACACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
GT
Found at i:18467902 original size:18 final size:18
Alignment explanation
Indices: 18467879--18467925 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
18467869 TTCTATTAGG
18467879 TTTATTTAGA-TTAATTAA
1 TTTATTTA-ATTTAATTAA
18467897 TTTATTTAATTTAATTAA
1 TTTATTTAATTTAATTAA
*
18467915 TAT-TTTAATTT
1 TTTATTTAATTT
18467926 TGAATCAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTATTTAATTTAATTAA
Found at i:18470164 original size:14 final size:14
Alignment explanation
Indices: 18470137--18470177 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
18470127 TGAGAAAATT
18470137 ATTTAATTAGAATTTA
1 ATTTAATT--AATTTA
*
18470153 ATTTAGTTAATTTA
1 ATTTAATTAATTTA
18470167 ATTTAATTAAT
1 ATTTAATTAAT
18470178 AAAACAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 16 0.70
16 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
ATTTAATTAATTTA
Found at i:18480823 original size:80 final size:80
Alignment explanation
Indices: 18480660--18480868 Score: 264
Period size: 80 Copynumber: 2.6 Consensus size: 80
18480650 AAATGACAGT
* *
18480660 AATACCCTCTATGGGTAAAATGATCGAAATACCCTCAATGGGTAAAATGACCGAAATACCCTCGA
1 AATACCCTCGATGGGTAAAATTATCGAAATA-CCTCAATGGGTAAAATGACCGAAATACCCTCGA
* *
18480725 TGGGTAAAATGATTGA
65 AGGGTAAAATGATCGA
* * *
18480741 AATACCCTCGATGGGTAAAATTATCGAAATACCTCGATGGGTAAAATTATCGAAATACCCTCGAA
1 AATACCCTCGATGGGTAAAATTATCGAAATACCTCAATGGGTAAAATGACCGAAATACCCTCGAA
*
18480806 GGGTAAAATTATCGA
66 GGGTAAAATGATCGA
18480821 AATACCC-CTGAAT-GGTAAAATTA-CTGAAATACCTCCATAT-GGTAAAAT
1 AATACCCTC-G-ATGGGTAAAATTATC-GAAATACCT-CA-ATGGGTAAAAT
18480869 AACTGTTATA
Statistics
Matches: 114, Mismatches: 9, Indels: 10
0.86 0.07 0.08
Matches are distributed among these distances:
79 2 0.02
80 70 0.61
81 40 0.35
82 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (80 bp):
AATACCCTCGATGGGTAAAATTATCGAAATACCTCAATGGGTAAAATGACCGAAATACCCTCGAA
GGGTAAAATGATCGA
Found at i:18480837 original size:27 final size:27
Alignment explanation
Indices: 18480660--18480853 Score: 261
Period size: 27 Copynumber: 7.2 Consensus size: 27
18480650 AAATGACAGT
* *
18480660 AATACCCTCTATGGGTAAAATGATCGA
1 AATACCCTCGATGGGTAAAATTATCGA
* * *
18480687 AATACCCTCAATGGGTAAAATGACCGA
1 AATACCCTCGATGGGTAAAATTATCGA
* *
18480714 AATACCCTCGATGGGTAAAATGATTGA
1 AATACCCTCGATGGGTAAAATTATCGA
18480741 AATACCCTCGATGGGTAAAATTATCGA
1 AATACCCTCGATGGGTAAAATTATCGA
18480768 AATA-CCTCGATGGGTAAAATTATCGA
1 AATACCCTCGATGGGTAAAATTATCGA
*
18480794 AATACCCTCGAAGGGTAAAATTATCGA
1 AATACCCTCGATGGGTAAAATTATCGA
18480821 AATACCC-CTGAAT-GGTAAAATTA-CTGA
1 AATACCCTC-G-ATGGGTAAAATTATC-GA
18480848 AATACC
1 AATACC
18480854 TCCATATGGT
Statistics
Matches: 154, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
26 28 0.18
27 125 0.81
28 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (27 bp):
AATACCCTCGATGGGTAAAATTATCGA
Found at i:18480880 original size:107 final size:107
Alignment explanation
Indices: 18480660--18480870 Score: 268
Period size: 107 Copynumber: 2.0 Consensus size: 107
18480650 AAATGACAGT
*
18480660 AATACCCTCTATGGGTAAAATGATCGAAATACCCTCAATGGGTAAAATGACCGAAATACCCTCGA
1 AATA-CCTCGATGGGTAAAATGATCGAAATACCCTCAATGGGTAAAATGACCGAAATACCCTCGA
* * *
18480725 TGGGTAAAATGATTGAAATACCCTCGATGGGTAAAATTATCGA
65 TGGGTAAAATGACTGAAATACCCTCCATGGGTAAAATAATCGA
* * *
18480768 AATACCTCGATGGGTAAAATTATCGAAATACCCTCGAA-GGGTAAAATTATCGAAATACCC-CTG
1 AATACCTCGATGGGTAAAATGATCGAAATACCCTC-AATGGGTAAAATGACCGAAATACCCTC-G
* *
18480831 AAT-GGTAAAATTACTGAAATA-CCTCCATATGGTAAAATAA
64 -ATGGGTAAAATGACTGAAATACCCTCCAT-GGGTAAAATAA
18480871 CTGTTATACC
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
106 7 0.08
107 75 0.83
108 8 0.09
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (107 bp):
AATACCTCGATGGGTAAAATGATCGAAATACCCTCAATGGGTAAAATGACCGAAATACCCTCGAT
GGGTAAAATGACTGAAATACCCTCCATGGGTAAAATAATCGA
Found at i:18482162 original size:18 final size:17
Alignment explanation
Indices: 18482135--18482169 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
18482125 AAAAAATTGT
18482135 TTATTGGGTTAGTTAAA
1 TTATTGGGTTAGTTAAA
18482152 TTATATGGGTTAGTTAAA
1 TTAT-TGGGTTAGTTAAA
18482170 AGTCTAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (17 bp):
TTATTGGGTTAGTTAAA
Found at i:18483881 original size:16 final size:17
Alignment explanation
Indices: 18483851--18483896 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
18483841 AAAGTGAATA
*
18483851 TATAAGAAATATAAAATT
1 TATAA-AAATATAAAAAT
*
18483869 TA-AAAAATTTAAAAAT
1 TATAAAAATATAAAAAT
18483885 TATAAAAATATA
1 TATAAAAATATA
18483897 TTAATATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 12 0.50
17 10 0.42
18 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
TATAAAAATATAAAAAT
Found at i:18483956 original size:24 final size:25
Alignment explanation
Indices: 18483929--18483979 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
18483919 AAATATAATT
18483929 TTAA-AATTTTCAAAAAAAT-TAAAA
1 TTAATAATTTT-AAAAAAATCTAAAA
*
18483953 TTAATTATTTTAAAAAAATCTAAAA
1 TTAATAATTTTAAAAAAATCTAAAA
18483978 TT
1 TT
18483980 TTCAATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (25 bp):
TTAATAATTTTAAAAAAATCTAAAA
Found at i:18484191 original size:17 final size:18
Alignment explanation
Indices: 18484171--18484207 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
18484161 AAAATTTAGG
18484171 TAAAA-TAAAAAATATTT
1 TAAAATTAAAAAATATTT
*
18484188 TAAAATTAGAAAATATTT
1 TAAAATTAAAAAATATTT
18484206 TA
1 TA
18484208 TATAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAATTAAAAAATATTT
Found at i:18492589 original size:22 final size:22
Alignment explanation
Indices: 18492524--18492595 Score: 108
Period size: 22 Copynumber: 3.3 Consensus size: 22
18492514 TTTATTGTTC
*
18492524 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
18492546 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
18492568 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
18492590 TAACAT
1 AAACAT
18492596 AACATCCCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:18496135 original size:57 final size:58
Alignment explanation
Indices: 18496072--18496185 Score: 153
Period size: 57 Copynumber: 2.0 Consensus size: 58
18496062 TTCCAGGTCA
* *
18496072 TTTTTCATTTTCATTTTGGA-AAAGACCACA-TTCATTTCCAAATGTTTC-CATTTCTCC
1 TTTTTCATTTTCATATTGGAGAAA-ACCACATTTCATTTCC-AATATTTCTCATTTCTCC
* *
18496129 TTTTTCATTTTCATATTGGAGAAATCCATATTTCATTTCCAATATTTCTCATTTCTC
1 TTTTTCATTTTCATATTGGAGAAAACCACATTTCATTTCCAATATTTCTCATTTCTC
18496186 TACCATTTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
57 30 0.60
58 20 0.40
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48
Consensus pattern (58 bp):
TTTTTCATTTTCATATTGGAGAAAACCACATTTCATTTCCAATATTTCTCATTTCTCC
Found at i:18497579 original size:19 final size:19
Alignment explanation
Indices: 18497555--18497595 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
18497545 AATTTAATAA
*
18497555 TAAGGTTTATTAAGTAAAT
1 TAAGGTTAATTAAGTAAAT
* *
18497574 TAAGGTTAATTATGTTAAT
1 TAAGGTTAATTAAGTAAAT
18497593 TAA
1 TAA
18497596 CCATTTAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (19 bp):
TAAGGTTAATTAAGTAAAT
Found at i:18500031 original size:16 final size:17
Alignment explanation
Indices: 18500010--18500043 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18500000 TGGAAATGAC
18500010 TATCTATCATATT-ATA
1 TATCTATCATATTCATA
*
18500026 TATCTATGATATTCATA
1 TATCTATCATATTCATA
18500043 T
1 T
18500044 TTGTATGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (17 bp):
TATCTATCATATTCATA
Found at i:18502364 original size:8 final size:8
Alignment explanation
Indices: 18502351--18502401 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
18502341 TGGATGAGAT
18502351 ATTTTAAA
1 ATTTTAAA
18502359 ATTTTAAA
1 ATTTTAAA
***
18502367 AAACTAAA
1 ATTTTAAA
* *
18502375 ATTCTAAC
1 ATTTTAAA
18502383 ATTTTAAA
1 ATTTTAAA
18502391 ATTTTAAA
1 ATTTTAAA
18502399 ATT
1 ATT
18502402 CAAAATTTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (8 bp):
ATTTTAAA
Found at i:18507078 original size:28 final size:29
Alignment explanation
Indices: 18507014--18507094 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
18507004 AATACTTTTT
* *
18507014 TCTAAATTGGTATTTAAATCTATTTTGAG
1 TCTAATTTGGTATTTAAATTTATTTTGAG
*
18507043 TCTAATTTGGTATTTAAATTTTTTTTG-G
1 TCTAATTTGGTATTTAAATTTATTTTGAG
*
18507071 T-TCAATTTGGTATCTAAATTTATT
1 TCT-AATTTGGTATTTAAATTTATT
18507095 AAATGTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.02
28 21 0.46
29 24 0.52
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.54
Consensus pattern (29 bp):
TCTAATTTGGTATTTAAATTTATTTTGAG
Found at i:18519121 original size:24 final size:24
Alignment explanation
Indices: 18519093--18519156 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
18519083 TTGTTCTATG
18519093 GCAAAGGATGAATTGACAGTAAAT
1 GCAAAGGATGAATTGACAGTAAAT
* *
18519117 GCAAAGGATGAATTGACGGTATAT
1 GCAAAGGATGAATTGACAGTAAAT
*
18519141 GTAAAGGATGAATTGA
1 GCAAAGGATGAATTGA
18519157 TGGCAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.42, C:0.06, G:0.28, T:0.23
Consensus pattern (24 bp):
GCAAAGGATGAATTGACAGTAAAT
Found at i:18519274 original size:21 final size:21
Alignment explanation
Indices: 18519236--18519279 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
18519226 TCTCACGAGC
*
18519236 TTTTGTTTAACTCATATGAGT
1 TTTTGTTTAACCCATATGAGT
* *
18519257 TTTTGTTTAACCCTTATGGGT
1 TTTTGTTTAACCCATATGAGT
18519278 TT
1 TT
18519280 CCGTTTAGCT
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:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (21 bp):
TTTTGTTTAACCCATATGAGT
Found at i:18519387 original size:42 final size:42
Alignment explanation
Indices: 18519239--18519388 Score: 149
Period size: 42 Copynumber: 3.6 Consensus size: 42
18519229 CACGAGCTTT
* * * * *
18519239 TGTTTAACTCATATGAGTTTTTGTTTAACCCTTATGGGTTTC
1 TGTTTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTC
* * *
18519281 CGTTTAGCTC-TATTGAGCTTCTATTCAACCCTTATGGGTTTT
1 TGTTTAGCTCTTA-TGAGCTTCTGTTCAACCCTTATGGGTTTC
* * * **
18519323 TGTTAAGTTCTTGTGAGCTTCTGTTCAACCCTTACAGGTTTC
1 TGTTTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTC
* *
18519365 TGTTTAGCACTTATGTGCTTCTGT
1 TGTTTAGCTCTTATGAGCTTCTGT
18519389 GCAGCCTTCG
Statistics
Matches: 86, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
41 2 0.02
42 83 0.97
43 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.18, T:0.47
Consensus pattern (42 bp):
TGTTTAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGTTTC
Found at i:18525821 original size:20 final size:20
Alignment explanation
Indices: 18525793--18525844 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
18525783 AACAAAAGAA
*
18525793 AAATT-AAAATGTAAAAATT
1 AAATTAAAAATGAAAAAATT
**
18525812 AAATTAAAAACAAAAAAATT
1 AAATTAAAAATGAAAAAATT
*
18525832 AAAATATAAAATG
1 AAATTA-AAAATG
18525845 GCTAAATTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 5 0.20
20 16 0.64
21 4 0.16
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (20 bp):
AAATTAAAAATGAAAAAATT
Found at i:18528924 original size:10 final size:10
Alignment explanation
Indices: 18528909--18528933 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18528899 GTTGATTGGC
18528909 TGATTGACTG
1 TGATTGACTG
18528919 TGATTGACTG
1 TGATTGACTG
18528929 TGATT
1 TGATT
18528934 CCTTTGCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.28, T:0.44
Consensus pattern (10 bp):
TGATTGACTG
Found at i:18529420 original size:9 final size:10
Alignment explanation
Indices: 18529391--18529436 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
18529381 TTTACATACA
18529391 TAATAAATA-
1 TAATAAATAT
*
18529400 TAA-ATATAT
1 TAATAAATAT
18529409 TAATAAAT-T
1 TAATAAATAT
18529418 TAATAAATAT
1 TAATAAATAT
18529428 ATAATAAAT
1 -TAATAAAT
18529437 CTTGCATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
8 4 0.13
9 15 0.48
10 4 0.13
11 8 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAATAAATAT
Found at i:18532166 original size:49 final size:49
Alignment explanation
Indices: 18532111--18532214 Score: 147
Period size: 49 Copynumber: 2.1 Consensus size: 49
18532101 TCATGTGTTA
* * ** *
18532111 TAATTTTATACAGTGTTGAGTTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
*
18532160 TAATTTTATAAAGTGTTCCCCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
18532209 T-ATTTT
1 TAATTTT
18532215 GTTTTTTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
48 5 0.10
49 44 0.90
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.52
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:18533878 original size:14 final size:14
Alignment explanation
Indices: 18533861--18533894 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18533851 TGTTTAAATT
* *
18533861 TTTTAGTTTTTTAA
1 TTTTAATTTTTGAA
18533875 TTTTAATTTTTGAA
1 TTTTAATTTTTGAA
18533889 TTTTAA
1 TTTTAA
18533895 GAATAAAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTAATTTTTGAA
Found at i:18534184 original size:121 final size:122
Alignment explanation
Indices: 18533991--18534224 Score: 425
Period size: 121 Copynumber: 1.9 Consensus size: 122
18533981 GTAAGTATTG
*
18533991 TAGTATTATATATTATGATTTTAGTAAATTCATATAAAGAATATTTAATATTAAGAATTTTATTA
1 TAGTATTATATATTATGATTTTAATAAATTCATATAAAGAATATTTAATATTAAGAATTTTATTA
*
18534056 AATTATATATTTTTATTAAATTATGTTTAAAAATAATTATGTTAAAATTATATTTTA
66 AATTATATATTTTTATTAAATTATATTTAAAAATAATTATGTTAAAATTATATTTTA
*
18534113 TAGTATTATATATTATGATTTTAATAAATTCATAT-AAGAATATTTAATATTAATAATTTTATTA
1 TAGTATTATATATTATGATTTTAATAAATTCATATAAAGAATATTTAATATTAAGAATTTTATTA
*
18534177 AATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAAT
66 AATTATATATTTTTATTAAATTATATTTAAAAATAATTATGTTAAAAT
18534225 ATGATTAAAT
Statistics
Matches: 108, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
121 74 0.69
122 34 0.31
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (122 bp):
TAGTATTATATATTATGATTTTAATAAATTCATATAAAGAATATTTAATATTAAGAATTTTATTA
AATTATATATTTTTATTAAATTATATTTAAAAATAATTATGTTAAAATTATATTTTA
Found at i:18534190 original size:18 final size:18
Alignment explanation
Indices: 18534156--18534202 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
18534146 ATAAGAATAT
18534156 TTAATATTA-ATAATTTTA
1 TTAA-ATTATATAATTTTA
*
18534174 TTAAATTATATATTTTTA
1 TTAAATTATATAATTTTA
18534192 TTAAATTATAT
1 TTAAATTATAT
18534203 TTAATAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATTATATAATTTTA
Found at i:18534266 original size:44 final size:40
Alignment explanation
Indices: 18534153--18534269 Score: 101
Period size: 41 Copynumber: 2.7 Consensus size: 40
18534143 CATATAAGAA
* *
18534153 TATTTAATATTAATAATTTTATT-AAATTATATATTTTTAT
1 TATTT-ATATTAATAATATTATTAAAATTATAAATTTTTAT
*
18534193 TAAATTATATTTAATAATAATTATGTTAAAATATGATTAAATTATTTAT
1 T-ATTTATA-TTAATAAT-ATTA--TTAAAAT-T-A-TAAATT-TTTAT
*
18534242 TATTTATATTAATAATCTTATTAAAATT
1 TATTTATATTAATAATATTATTAAAATT
18534270 TAATAACAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
40 4 0.06
41 11 0.18
42 3 0.05
43 1 0.02
44 9 0.15
45 4 0.06
46 4 0.06
47 9 0.15
48 11 0.18
49 6 0.10
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (40 bp):
TATTTATATTAATAATATTATTAAAATTATAAATTTTTAT
Found at i:18534448 original size:46 final size:44
Alignment explanation
Indices: 18534362--18534454 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 44
18534352 TTACCCATCT
* *
18534362 ATTCCATTCAACCAAACACAAGAAAACCATTACGCCTCTATTCC
1 ATTCAATTCAACCAAACAAAAGAAAACCATTACGCCTCTATTCC
**
18534406 ATTCAATTCAACCAAACAAAATGATTACCTATTACGCCTCTATTCC
1 ATTCAATTCAACCAAACAAAA-GAAAACC-ATTACGCCTCTATTCC
18534452 ATT
1 ATT
18534455 ACAGCGAACC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 19 0.44
45 5 0.12
46 19 0.44
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.28
Consensus pattern (44 bp):
ATTCAATTCAACCAAACAAAAGAAAACCATTACGCCTCTATTCC
Found at i:18538449 original size:22 final size:22
Alignment explanation
Indices: 18538418--18538468 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
18538408 CATAACCGAA
*
18538418 ACATGCTAGATATAAATAAAGC
1 ACATGATAGATATAAATAAAGC
*
18538440 ACGTGATAGATATAAATAAAGC
1 ACATGATAGATATAAATAAAGC
18538462 ACATGAT
1 ACATGAT
18538469 TTTATCTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.24
Consensus pattern (22 bp):
ACATGATAGATATAAATAAAGC
Found at i:18544190 original size:26 final size:26
Alignment explanation
Indices: 18544147--18544197 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
18544137 AAAAAATAGC
*
18544147 AATGTTCAAAATAGAAATAACATAAA
1 AATGTTCAAAATAGAAATAAAATAAA
*
18544173 AATGTCTCACAATA-AAATAAAATAA
1 AATGT-TCAAAATAGAAATAAAATAA
18544198 CTAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.24
Consensus pattern (26 bp):
AATGTTCAAAATAGAAATAAAATAAA
Found at i:18545922 original size:15 final size:15
Alignment explanation
Indices: 18545897--18545934 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
18545887 TACGAAAATA
*
18545897 AATACATAATACTAAC
1 AATA-ATAATAATAAC
18545913 AATAATAATAATAAC
1 AATAATAATAATAAC
18545928 AA-AATAA
1 AATAATAA
18545935 ATGGACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.24
15 12 0.57
16 4 0.19
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:18551883 original size:16 final size:17
Alignment explanation
Indices: 18551851--18551883 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18551841 TAAAAATCTC
18551851 ATTTATTGTTCTTGTTA
1 ATTTATTGTTCTTGTTA
*
18551868 ATTTATT-TTGTTGTTA
1 ATTTATTGTTCTTGTTA
18551884 GTTGCTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.18, C:0.03, G:0.12, T:0.67
Consensus pattern (17 bp):
ATTTATTGTTCTTGTTA
Found at i:18553423 original size:2 final size:2
Alignment explanation
Indices: 18553376--18553409 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18553366 GATACTTATA
18553376 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
18553410 GCAAACAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18553734 original size:18 final size:20
Alignment explanation
Indices: 18553695--18553737 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
18553685 TTAAAATTTT
*
18553695 AATATATGAGAGGGACCAAA
1 AATATATGAAAGGGACCAAA
*
18553715 AATATATGAAAGGGACAAAA
1 AATATATGAAAGGGACCAAA
18553735 AAT
1 AAT
18553738 GCAAATTTTC
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:0.56, C:0.07, G:0.21, T:0.16
Consensus pattern (20 bp):
AATATATGAAAGGGACCAAA
Found at i:18555684 original size:5 final size:5
Alignment explanation
Indices: 18555664--18555726 Score: 55
Period size: 5 Copynumber: 13.2 Consensus size: 5
18555654 ACTTTGATCC
*
18555664 ATATT ATATT -T-TT ATAATAT ATATT ATATT ATATT AT-TT TTA-T ATATT
1 ATATT ATATT ATATT AT-AT-T ATATT ATATT ATATT ATATT ATATT ATATT
*
18555712 ATATA AT-TT ATATT A
1 ATATT ATATT ATATT A
18555727 CATAAATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
3 2 0.04
4 11 0.23
5 28 0.60
6 3 0.06
7 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:18555700 original size:30 final size:32
Alignment explanation
Indices: 18555664--18555726 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 32
18555654 ACTTTGATCC
18555664 ATATTATATTTT-TATAATATAT-A-TTATATT
1 ATATTAT-TTTTATATAATATATAATTTATATT
*
18555694 ATATTATTTTTATATATTATATAATTTATATT
1 ATATTATTTTTATATAATATATAATTTATATT
18555726 A
1 A
18555727 CATAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 4 0.14
30 16 0.55
31 1 0.03
32 8 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
ATATTATTTTTATATAATATATAATTTATATT
Found at i:18555721 original size:16 final size:18
Alignment explanation
Indices: 18555675--18555724 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
18555665 TATTATATTT
* *
18555675 TTATAATATATAT-TATA
1 TTATATTATATTTATATA
*
18555692 TTATATTATTTTTATATA
1 TTATATTATATTTATATA
18555710 TTATA-TA-ATTTATAT
1 TTATATTATATTTATAT
18555725 TACATAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 7 0.25
17 12 0.43
18 9 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATTATATTTATATA
Found at i:18556930 original size:17 final size:18
Alignment explanation
Indices: 18556896--18556936 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
18556886 TTTCTGCTTC
18556896 TTCTTCTCGTACGCTTCTT
1 TTCTTCTCG-ACGCTTCTT
*
18556915 TTCTTCTC-ACGTTTCTT
1 TTCTTCTCGACGCTTCTT
18556932 TTCTT
1 TTCTT
18556937 TTCTCCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.62
19 8 0.38
ACGTcount: A:0.05, C:0.29, G:0.07, T:0.59
Consensus pattern (18 bp):
TTCTTCTCGACGCTTCTT
Found at i:18558312 original size:23 final size:23
Alignment explanation
Indices: 18558285--18558367 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
18558275 GTGTTATAAT
18558285 GTTCATGTTTTGGTTTCTGTTAA
1 GTTCATGTTTTGGTTTCTGTTAA
*
18558308 GTTCATGTTTTGGTTTATG-T-A
1 GTTCATGTTTTGGTTTCTGTTAA
* * * *
18558329 TTATAATGTTCAT-GCTTCTGTTAA
1 GT-TCATGTT-TTGGTTTCTGTTAA
18558353 GTTCATGTTTTGGTT
1 GTTCATGTTTTGGTT
18558368 CATGTTTTGG
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
21 2 0.04
22 13 0.29
23 28 0.62
24 2 0.04
ACGTcount: A:0.16, C:0.08, G:0.20, T:0.55
Consensus pattern (23 bp):
GTTCATGTTTTGGTTTCTGTTAA
Found at i:18558353 original size:45 final size:44
Alignment explanation
Indices: 18558297--18558454 Score: 208
Period size: 45 Copynumber: 3.8 Consensus size: 44
18558287 TCATGTTTTG
18558297 GTTTCTGTTAAGTTCATGTTTTGGTTTATGTATTATAATGTTCAT
1 GTTTCTGTTAAGTTCATGTTTTGGTTTATGT-TTATAATGTTCAT
* *
18558342 GCTTCTGTTAAGTTCATGTTTTGGTTCATG-TT-T--TG-----
1 GTTTCTGTTAAGTTCATGTTTTGGTTTATGTTTATAATGTTCAT
*
18558377 GTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTTATAATGTTCAT
1 GTTTCTGTTAAGTTCATGTTTTGGTTTATGT-TTATAATGTTCAT
18558422 GTTTCTGTTAAGTTCATGTTTTGGTTTATGTTT
1 GTTTCTGTTAAGTTCATGTTTTGGTTTATGTTT
18558455 TGGTTCATGT
Statistics
Matches: 97, Mismatches: 6, Indels: 21
0.78 0.05 0.17
Matches are distributed among these distances:
35 27 0.28
37 2 0.02
38 1 0.01
40 4 0.04
42 1 0.01
43 2 0.02
44 2 0.02
45 58 0.60
ACGTcount: A:0.16, C:0.08, G:0.20, T:0.56
Consensus pattern (44 bp):
GTTTCTGTTAAGTTCATGTTTTGGTTTATGTTTATAATGTTCAT
Found at i:18558368 original size:12 final size:12
Alignment explanation
Indices: 18558353--18558471 Score: 80
Period size: 12 Copynumber: 9.2 Consensus size: 12
18558343 CTTCTGTTAA
18558353 GTTCATGTTTTG
1 GTTCATGTTTTG
18558365 GTTCATGTTTTG
1 GTTCATGTTTTG
**
18558377 GTTTC-TG-TTAA
1 G-TTCATGTTTTG
*
18558388 GTTCATGTTTAG
1 GTTCATGTTTTG
* *
18558400 GTTTATGTGTTATAAT
1 GTTCATGT-TT-T--G
18558416 GTTCATGTTTCTG
1 GTTCATGTTT-TG
18558429 TTAAGTTCATGTTTTG
1 ----GTTCATGTTTTG
*
18558445 GTTTATGTTTTG
1 GTTCATGTTTTG
18558457 GTTCATGTTTTG
1 GTTCATGTTTTG
18558469 GTT
1 GTT
18558472 TCTGTTAAGT
Statistics
Matches: 85, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
10 3 0.04
11 5 0.06
12 50 0.59
13 5 0.06
15 3 0.04
16 9 0.11
17 10 0.12
ACGTcount: A:0.13, C:0.07, G:0.23, T:0.57
Consensus pattern (12 bp):
GTTCATGTTTTG
Found at i:18558391 original size:23 final size:23
Alignment explanation
Indices: 18558365--18558490 Score: 123
Period size: 23 Copynumber: 5.5 Consensus size: 23
18558355 TCATGTTTTG
18558365 GTTCATGTTTTGGTTTCTGTTAA
1 GTTCATGTTTTGGTTTCTGTTAA
* * *
18558388 GTTCATGTTTAGGTTTATGTGTTA
1 GTTCATGTTTTGGTTTCTGT-TAA
* *
18558412 --TAATGTTCAT-GTTTCTGTTAA
1 GTTCATGTT-TTGGTTTCTGTTAA
* **
18558433 GTTCATGTTTTGGTTTATGTTTTG
1 GTTCATGTTTTGGTTTCTG-TTAA
18558457 GTTCATGTTTTGGTTTCTGTTAA
1 GTTCATGTTTTGGTTTCTGTTAA
*
18558480 GTTGATGTTTT
1 GTTCATGTTTT
18558491 TCTGTATTAA
Statistics
Matches: 80, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
21 2 0.03
22 14 0.17
23 42 0.52
24 22 0.28
ACGTcount: A:0.14, C:0.06, G:0.22, T:0.57
Consensus pattern (23 bp):
GTTCATGTTTTGGTTTCTGTTAA
Found at i:18558413 original size:80 final size:80
Alignment explanation
Indices: 18558285--18558459 Score: 314
Period size: 80 Copynumber: 2.2 Consensus size: 80
18558275 GTGTTATAAT
*
18558285 GTTCATGTTTTGGTTTCTGTTAAGTTCATGTTTTGGTTTATGTATTATAATGTTCATGCTTCTGT
1 GTTCATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTATTATAATGTTCATGCTTCTGT
18558350 TAAGTTCATGTTTTG
66 TAAGTTCATGTTTTG
* *
18558365 GTTCATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTTATAATGTTCATGTTTCTGT
1 GTTCATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTATTATAATGTTCATGCTTCTGT
18558430 TAAGTTCATGTTTTG
66 TAAGTTCATGTTTTG
*
18558445 GTTTATGTTTTGGTT
1 GTTCATGTTTTGGTT
18558460 CATGTTTTGG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 91 1.00
ACGTcount: A:0.15, C:0.07, G:0.21, T:0.56
Consensus pattern (80 bp):
GTTCATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTATTATAATGTTCATGCTTCTGT
TAAGTTCATGTTTTG
Found at i:18558477 original size:12 final size:12
Alignment explanation
Indices: 18558438--18558477 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
18558428 GTTAAGTTCA
*
18558438 TGTTTTGGTTTA
1 TGTTTTGGTTTC
18558450 TGTTTTGG-TTC
1 TGTTTTGGTTTC
18558461 ATGTTTTGGTTTC
1 -TGTTTTGGTTTC
18558474 TGTT
1 TGTT
18558478 AAGTTGATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 2 0.08
12 20 0.80
13 3 0.12
ACGTcount: A:0.05, C:0.05, G:0.25, T:0.65
Consensus pattern (12 bp):
TGTTTTGGTTTC
Found at i:18558494 original size:19 final size:20
Alignment explanation
Indices: 18558470--18558511 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
18558460 CATGTTTTGG
18558470 TTTCTG-TTAAGTTGATGTT
1 TTTCTGATTAAGTTGATGTT
18558489 TTTCTGTATTAAGTTGATGTT
1 TTTCTG-ATTAAGTTGATGTT
18558510 TT
1 TT
18558512 CCGTTTCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
21 15 0.71
ACGTcount: A:0.17, C:0.05, G:0.19, T:0.60
Consensus pattern (20 bp):
TTTCTGATTAAGTTGATGTT
Found at i:18558556 original size:12 final size:12
Alignment explanation
Indices: 18558539--18558572 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
18558529 TTATCTCTAT
*
18558539 TGTTTTGGTTCA
1 TGTTTTGGTTAA
18558551 TGTTTTGGTTAA
1 TGTTTTGGTTAA
18558563 TGTTTTGGTT
1 TGTTTTGGTT
18558573 TCTGTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.03, G:0.26, T:0.62
Consensus pattern (12 bp):
TGTTTTGGTTAA
Found at i:18558595 original size:19 final size:20
Alignment explanation
Indices: 18558571--18558612 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
18558561 AATGTTTTGG
18558571 TTTCTG-TTAAGTTGATGTT
1 TTTCTGATTAAGTTGATGTT
18558590 TTTCTGTATTAAGTTGATGTT
1 TTTCTG-ATTAAGTTGATGTT
18558611 TT
1 TT
18558613 CCCATACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
21 15 0.71
ACGTcount: A:0.17, C:0.05, G:0.19, T:0.60
Consensus pattern (20 bp):
TTTCTGATTAAGTTGATGTT
Found at i:18559502 original size:15 final size:15
Alignment explanation
Indices: 18559482--18559513 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
18559472 AAATTAACTT
18559482 TTTTTATTTTTAATA
1 TTTTTATTTTTAATA
18559497 TTTTTATTTTTAATA
1 TTTTTATTTTTAATA
18559512 TT
1 TT
18559514 CCAATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTATTTTTAATA
Found at i:18559511 original size:130 final size:127
Alignment explanation
Indices: 18559367--18559773 Score: 666
Period size: 130 Copynumber: 3.2 Consensus size: 127
18559357 TTTGGATATT
18559367 TTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAATTAAATGCA
1 TTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAATTAAATGCA
18559432 TAAAACTAATTAAATTATATATTTACAAATTAATTAAATTAAATTAACTTTTTTTATTTTTAATA
66 TAAAACTAATTAAATTATATATTTACAAATTAATTAAATT-AATTAA--TTTTTTATTTTTAATA
*
18559497 TTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAGTTAAATGCA
1 TTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAATTAAATGCA
* *
18559562 TAAAACTAATTAAATTATATATTTACAAATTAATTAAATT-A-T-ATTATAT-TTTTTAATA
66 TAAAACTAATTAAATTATATATTTACAAATTAATTAAATTAATTAATTTTTTATTTTTAATA
*
18559620 TTTTTATTTTTAATATTCCAATTTATTAAATAATGCATTTGTTAAAATAAAAATAATTAAATGCA
1 TTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAATTAAATGCA
* * * *
18559685 TAAAAATAATTAAATTATGTATTAACAAATT-ATTAAATTAATTAAATTTTTA-TTTTAATA
66 TAAAACTAATTAAATTATATATTTACAAATTAATTAAATTAATTAATTTTTTATTTTTAATA
18559745 TTTTTA-TTTTAATATTCCAATTTATTAAA
1 TTTTTATTTTTAATATTCCAATTTATTAAA
18559774 ATAAAAATAA
Statistics
Matches: 262, Mismatches: 11, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
122 8 0.03
123 101 0.39
124 28 0.11
125 18 0.07
126 1 0.00
127 1 0.00
128 1 0.00
130 104 0.40
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (127 bp):
TTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAATTAAATGCA
TAAAACTAATTAAATTATATATTTACAAATTAATTAAATTAATTAATTTTTTATTTTTAATA
Found at i:18559749 original size:14 final size:14
Alignment explanation
Indices: 18559726--18559760 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
18559716 ATTAAATTAA
18559726 TTAA-ATTTTTATT
1 TTAATATTTTTATT
18559739 TTAATATTTTTATT
1 TTAATATTTTTATT
18559753 TTAATATT
1 TTAATATT
18559761 CCAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTAATATTTTTATT
Found at i:18562177 original size:49 final size:49
Alignment explanation
Indices: 18562104--18562207 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
18562094 TCATGTGTTA
* * * *
18562104 TAATTTTATACAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
18562153 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
18562202 TAATTT
1 TAATTT
18562208 GTTTTTTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:18563820 original size:7 final size:8
Alignment explanation
Indices: 18563809--18563851 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
18563799 AAATTGTAAA
18563809 AAAAATAT
1 AAAAATAT
18563817 AAAAATAT
1 AAAAATAT
*
18563825 AAAATTTTAT
1 AAAA--ATAT
18563835 AAAAATCAT
1 AAAAAT-AT
18563844 AAAAATAT
1 AAAAATAT
18563852 TATAAAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 15 0.50
9 8 0.27
10 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (8 bp):
AAAAATAT
Found at i:18563821 original size:29 final size:27
Alignment explanation
Indices: 18563778--18563860 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
18563768 CACATGTGAC
*
18563778 AAAAAAATTATAAAAAATATAAAATTGT
1 AAAAAAAATATAAAAAATATAAAATT-T
18563806 AAAAAAAATAT-AAAAATATAAAATTT
1 AAAAAAAATATAAAAAATATAAAATTT
* *
18563832 TATAAAAATCATAAAAATATTATAAAATT
1 AAAAAAAAT-ATAAAAA-A-TATAAAATT
18563861 CATCAAAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 8 0.17
27 16 0.33
28 14 0.29
29 1 0.02
30 9 0.19
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (27 bp):
AAAAAAAATATAAAAAATATAAAATTT
Found at i:18563827 original size:19 final size:18
Alignment explanation
Indices: 18563780--18563828 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
18563770 CATGTGACAA
*
18563780 AAAAATTATAAAAAATAT
1 AAAAATTAAAAAAAATAT
*
18563798 AAAATTGTAAAAAAAATAT
1 AAAAAT-TAAAAAAAATAT
18563817 AAAAATATAAAA
1 AAAAAT-TAAAA
18563829 TTTTATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAAATTAAAAAAAATAT
Found at i:18564096 original size:19 final size:18
Alignment explanation
Indices: 18564042--18564098 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
18564032 TTGGTATGAT
18564042 CATTTTTATAATTATT-TTA
1 CATTTTTAT-ATT-TTCTTA
*
18564061 CGAATTTTATA-TTTCTTA
1 C-ATTTTTATATTTTCTTA
18564079 CATTTTTATCATTTTCTTA
1 CATTTTTAT-ATTTTCTTA
18564098 C
1 C
18564099 GGCTTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 9 0.28
18 6 0.19
19 10 0.31
20 7 0.22
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (18 bp):
CATTTTTATATTTTCTTA
Found at i:18564134 original size:29 final size:31
Alignment explanation
Indices: 18564102--18564173 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 31
18564092 TTCTTACGGC
* *
18564102 TTTATAAATTTTTCTA-TATTTCTAT-ACAT
1 TTTATAAATTTTTCTACGATTTCTATAAAAT
* *
18564131 TTTAT-AATTTTTTTACGATTTTTATAAAAT
1 TTTATAAATTTTTCTACGATTTCTATAAAAT
18564161 TTTATAAATTTTT
1 TTTATAAATTTTT
18564174 AAAAAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 9 0.25
29 12 0.33
30 8 0.22
31 7 0.19
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (31 bp):
TTTATAAATTTTTCTACGATTTCTATAAAAT
Found at i:18564143 original size:10 final size:10
Alignment explanation
Indices: 18564102--18564274 Score: 67
Period size: 10 Copynumber: 17.5 Consensus size: 10
18564092 TTCTTACGGC
18564102 TTTATAAATT
1 TTTATAAATT
* *
18564112 TTTCTATATT
1 TTTATAAATT
* *
18564122 TCTATACA-T
1 TTTATAAATT
18564131 TTTAT-AATT
1 TTTATAAATT
* *
18564140 TTTTTACGATT
1 TTTATA-AATT
*
18564151 TTTATAAAAT
1 TTTATAAATT
18564161 TTTATAAATT
1 TTTATAAATT
**
18564171 TTTA-AAAAA
1 TTTATAAATT
* *
18564180 ATTATAATCTT
1 TTTATAA-ATT
*
18564191 TTTCT-AATT
1 TTTATAAATT
*
18564200 TTTAATAAA-A
1 TTT-ATAAATT
*
18564210 ATTA-AATATT
1 TTTATAA-ATT
18564220 TTT-TAATATTT
1 TTTATAA-A-TT
*
18564231 TTTATTAAAAT
1 TTTA-TAAATT
*
18564242 TTAAT-AATT
1 TTTATAAATT
18564251 TTTAT-AATT
1 TTTATAAATT
*
18564260 TTTATTAATT
1 TTTATAAATT
18564270 TTTAT
1 TTTAT
18564275 TTTTTATCAT
Statistics
Matches: 118, Mismatches: 31, Indels: 28
0.67 0.18 0.16
Matches are distributed among these distances:
8 3 0.03
9 39 0.33
10 50 0.42
11 22 0.19
12 1 0.01
13 3 0.03
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (10 bp):
TTTATAAATT
Found at i:18564174 original size:29 final size:30
Alignment explanation
Indices: 18564102--18564174 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
18564092 TTCTTACGGC
* *
18564102 TTTATAAATTTTT-CTATATTTCTATACAT
1 TTTATAAATTTTTACGATATTTCTATAAAT
*
18564131 TTTATAATTTTTTTACGAT-TTT-TATAAAAT
1 TTTATAA-ATTTTTACGATATTTCTAT-AAAT
18564161 TTTATAAATTTTTA
1 TTTATAAATTTTTA
18564175 AAAAAATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 16 0.43
30 18 0.49
31 3 0.08
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.60
Consensus pattern (30 bp):
TTTATAAATTTTTACGATATTTCTATAAAT
Found at i:18564184 original size:19 final size:20
Alignment explanation
Indices: 18564148--18564186 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
18564138 TTTTTTTACG
**
18564148 ATTTTTATAAAATTTTATAA
1 ATTTTTATAAAAAATTATAA
18564168 ATTTTTA-AAAAAATTATAA
1 ATTTTTATAAAAAATTATAA
18564187 TCTTTTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTTATAAAAAATTATAA
Found at i:18564267 original size:29 final size:29
Alignment explanation
Indices: 18564160--18564264 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 29
18564150 TTTTATAAAA
* *
18564160 TTTTATAAATTTTTAAAAAAATTATAAT-CT
1 TTTTAT-AATTTTTATAAAAATT-TAATAAT
* * *
18564190 TTTTCTAATTTTTAATAAAAATTAAATATT
1 TTTTATAATTTTT-ATAAAAATTTAATAAT
* *
18564220 TTTTAATATTTTTTATTAAAATTTAATAAT
1 TTTT-ATAATTTTTATAAAAATTTAATAAT
18564250 TTTTATAATTTTTAT
1 TTTTATAATTTTTAT
18564265 TAATTTTTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
29 20 0.32
30 35 0.56
31 7 0.11
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTTATAATTTTTATAAAAATTTAATAAT
Found at i:18565373 original size:61 final size:61
Alignment explanation
Indices: 18565285--18565475 Score: 337
Period size: 61 Copynumber: 3.1 Consensus size: 61
18565275 AATTAATCAC
* * *
18565285 ATTAATATTAAATTAACAAAATACTATCTATCTAAATATTAAATTAAATTTAATATCGCAT
1 ATTAATATTAAATTAATAAAATACTATCTATCTGAATATTAAATTAAATTTAATATCACAT
18565346 ATTAATATTAAATTAATAAAATACTATCTATCTGAATATTAAATTAAATTTAATATCACAT
1 ATTAATATTAAATTAATAAAATACTATCTATCTGAATATTAAATTAAATTTAATATCACAT
* *
18565407 ATTAATATTAAATTAATAAAATAATATCTATCTGAATATTAAATTAAATTTAATATCTCAT
1 ATTAATATTAAATTAATAAAATACTATCTATCTGAATATTAAATTAAATTTAATATCACAT
18565468 ATTAATAT
1 ATTAATAT
18565476 CTAGATAAAT
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 125 1.00
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (61 bp):
ATTAATATTAAATTAATAAAATACTATCTATCTGAATATTAAATTAAATTTAATATCACAT
Found at i:18566621 original size:17 final size:17
Alignment explanation
Indices: 18566599--18566633 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18566589 AACCTCTCAC
18566599 TCTAACGAGGTGTAACT
1 TCTAACGAGGTGTAACT
18566616 TCTAACGAGGTGTAACT
1 TCTAACGAGGTGTAACT
18566633 T
1 T
18566634 TGGCATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (17 bp):
TCTAACGAGGTGTAACT
Found at i:18570713 original size:368 final size:368
Alignment explanation
Indices: 18570036--18570760 Score: 1218
Period size: 368 Copynumber: 2.0 Consensus size: 368
18570026 GCTATATTTT
*
18570036 GAATGATGTGCCAACTAAGGGAGCATCGAAAACCCATATGAATTGTAGCATGACAGGAAGTCAAA
1 GAATGATGTGCCAACTAAGGGAGCATCGAAAACCCATACGAATTGTAGCATGACAGGAAGTCAAA
* * * **
18570101 TTTTAATCATTTTAATATTTGGGGATGCTCGACCAACATATTGGATAAATATGTGAGGAAGTTGA
66 TATTAATCATTTTAAGATTTGAGGATGCTCGACCAACATATTGGATAAATATGCAAGGAAGTTGA
* * *
18570166 ACTTATGAACAGAATTGTGCATGTTTGTACAATATCAAAATAGAACAAATGGTGGTTTATTTTTA
131 ACTTACGAACAGAATTGTGCATGTTTGTACAATATCAAAAGAGAACAAAGGGTGGTTTATTTTTA
*
18570231 ACCCGAAAGAGCAAACTGTTATGATCTCAGCTCATGCTACCTTTCTTGAAGAAAGTTACATGAAT
196 ACCCGAAAGAGCAAACTGTTATGATATCAGCTCATGCTACCTTTCTTGAAGAAAGTTACATGAAT
* **
18570296 AACTTCAAACCTCGGAGTAAAGAGGTACTTTATGAGCTTTCGAGAATTATACAAAACCCTAAAAA
261 AACTTCAAACATCGGAGTAAAGAGGTACTCGATGAGCTTTCGAGAATTATACAAAACCCTAAAAA
18570361 AATGGTTCTAGAACCAACTCTTAATAGTAGACCTGCATGACAG
326 AATGGTTCTAGAACCAACTCTTAATAGTAGACCTGCATGACAG
* * *
18570404 GAATGATGTGCCAATTAGGGGAGCATCGAAAACCCATACGAATTGTAGCATGACAGGAAGTCGAA
1 GAATGATGTGCCAACTAAGGGAGCATCGAAAACCCATACGAATTGTAGCATGACAGGAAGTCAAA
* **
18570469 TATTAATCATTTTAGGATTTGAGGATGCTCGACCAATGTATTGGATAAATATGCAAGGAAGTTGA
66 TATTAATCATTTTAAGATTTGAGGATGCTCGACCAACATATTGGATAAATATGCAAGGAAGTTGA
*
18570534 ACTTACGAACAGAATTGTGCATGTTTGTACAATATCTAAAGAGAACAAAGGGTGGTTTATTTTAT
131 ACTTACGAACAGAATTGTGCATGTTTGTACAATATCAAAAGAGAACAAAGGGTGGTTTATTTT-T
* *
18570599 AACCCGAAAGAGTAAACTGTTATGATATTAGCTCATGCTACC-TTCTTGAAGAAAGTTACATGAA
195 AACCCGAAAGAGCAAACTGTTATGATATCAGCTCATGCTACCTTTCTTGAAGAAAGTTACATGAA
* *
18570663 TGACTTCAAACATCGGAGTAAAGAGGTACTCGATGAGCTTTCGAGAATTATACAAAACCCTACAA
260 TAACTTCAAACATCGGAGTAAAGAGGTACTCGATGAGCTTTCGAGAATTATACAAAACCCTAAAA
18570728 AAATGGTTCTAGAACCAACTCTTAATAGTAGAC
325 AAATGGTTCTAGAACCAACTCTTAATAGTAGAC
18570761 GTGTAAATGA
Statistics
Matches: 332, Mismatches: 24, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
368 292 0.88
369 40 0.12
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (368 bp):
GAATGATGTGCCAACTAAGGGAGCATCGAAAACCCATACGAATTGTAGCATGACAGGAAGTCAAA
TATTAATCATTTTAAGATTTGAGGATGCTCGACCAACATATTGGATAAATATGCAAGGAAGTTGA
ACTTACGAACAGAATTGTGCATGTTTGTACAATATCAAAAGAGAACAAAGGGTGGTTTATTTTTA
ACCCGAAAGAGCAAACTGTTATGATATCAGCTCATGCTACCTTTCTTGAAGAAAGTTACATGAAT
AACTTCAAACATCGGAGTAAAGAGGTACTCGATGAGCTTTCGAGAATTATACAAAACCCTAAAAA
AATGGTTCTAGAACCAACTCTTAATAGTAGACCTGCATGACAG
Found at i:18576916 original size:1 final size:1
Alignment explanation
Indices: 18576910--18576936 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
18576900 TTTTGAAACC
18576910 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
18576937 TAGAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18580586 original size:23 final size:21
Alignment explanation
Indices: 18580544--18580596 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 21
18580534 TGAATTAAAA
*
18580544 AATA-TTTTTTTAAAGTAAGT
1 AATAGTTTTTTTAAAATAAGT
* *
18580564 TATATTTTTTTTAAAAATAAAGT
1 AATAGTTTTTTT-AAAAT-AAGT
18580587 AATAGTTTTT
1 AATAGTTTTT
18580597 AAGTAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 4 0.15
23 12 0.46
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.53
Consensus pattern (21 bp):
AATAGTTTTTTTAAAATAAGT
Found at i:18582322 original size:9 final size:9
Alignment explanation
Indices: 18582308--18582345 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
18582298 CCTTCTCTTA
18582308 AACTCTCTC
1 AACTCTCTC
18582317 AACTCTCTC
1 AACTCTCTC
18582326 AACTCTCTC
1 AACTCTCTC
18582335 AACTCTCTC
1 AACTCTCTC
18582344 AA
1 AA
18582346 GCTTTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.26, C:0.42, G:0.00, T:0.32
Consensus pattern (9 bp):
AACTCTCTC
Found at i:18592249 original size:16 final size:16
Alignment explanation
Indices: 18592228--18592292 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
18592218 TTCGCTGTAT
18592228 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
18592244 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
*
18592260 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
18592276 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
18592292 T
1 T
18592293 AGCAAATCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.38, C:0.05, G:0.35, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:18592332 original size:45 final size:44
Alignment explanation
Indices: 18592271--18592361 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 44
18592261 GGAATAGAGG
18592271 TGTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAA
* *
18592316 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
18592360 TG
1 TG
18592362 GAATAGAGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.42
45 24 0.56
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
Found at i:18592543 original size:16 final size:16
Alignment explanation
Indices: 18592506--18592547 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
18592496 TTAATCATAT
*
18592506 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
18592522 TT-AAATATATTATAA
1 TTAAAATATATTATAA
18592537 TTAAAATATAT
1 TTAAAATATAT
18592548 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:18592554 original size:14 final size:15
Alignment explanation
Indices: 18592515--18592556 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
18592505 TTTAAACATA
*
18592515 ATTATTATTAAATAT
1 ATTATAATTAAATAT
18592530 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
18592544 A-TATAATTTAATA
1 ATTATAATTAAATA
18592557 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:18594296 original size:401 final size:401
Alignment explanation
Indices: 18593553--18594358 Score: 1594
Period size: 401 Copynumber: 2.0 Consensus size: 401
18593543 ATTGAAGCTG
18593553 GTTCAAATGCACTGCTTGTGATTTCTGCTACTGATAGTTGCTCATGGTAAGCCTTTTCCGCTGAA
1 GTTCAAATGCACTGCTTGTGATTTCTGCTACTGATAGTTGCTCATGGTAAGCCTTTTCCGCTGAA
18593618 ATCACTGGTGCATATGAAGACAACATGAAATGGATTCAGGGTATGGGACTAAATTGGTCTGAAAC
66 ATCACTGGTGCATATGAAGACAACATGAAATGGATTCAGGGTATGGGACTAAATTGGTCTGAAAC
*
18593683 TCATTCACATCCACATTCAAAGCACCATCAAATCTCAAAGATGCAGTCAAGGAAGAAATAACCTG
131 TCATTCACATCCACATTCAAAGCACCATCAAATCTCAAAGATGCAGTCAAGAAAGAAATAACCTG
18593748 TAAACGATCCAAACATCATAAGTATACACATACAATGCAAACAATCAAATTAAAACAAACATCAT
196 TAAACGATCCAAACATCATAAGTATACACATACAATGCAAACAATCAAATTAAAACAAACATCAT
18593813 AAGGAAGAAATAACTTTATAACCTACAAGAAAACATAGAATGTACACAAGCAATGGTACAGCTTG
261 AAGGAAGAAATAACTTTATAACCTACAAGAAAACATAGAATGTACACAAGCAATGGTACAGCTTG
*
18593878 TAAAAAATAGTCCAGAATAAACTGCAGAAAAATGGAAGGAGATCAATAGCAACAATGCTGGAGAT
326 TAAAAAATAGTCCAGAATAAACTACAGAAAAATGGAAGGAGATCAATAGCAACAATGCTGGAGAT
18593943 CCTTAACAGTT
391 CCTTAACAGTT
18593954 GTTCAAATGCACTGCTTGTGATTTCTGCTACTGATAGTTGCTCATGGTAAGCCTTTTCCGCTGAA
1 GTTCAAATGCACTGCTTGTGATTTCTGCTACTGATAGTTGCTCATGGTAAGCCTTTTCCGCTGAA
18594019 ATCACTGGTGCATATGAAGACAACATGAAATGGATTCAGGGTATGGGACTAAATTGGTCTGAAAC
66 ATCACTGGTGCATATGAAGACAACATGAAATGGATTCAGGGTATGGGACTAAATTGGTCTGAAAC
18594084 TCATTCACATCCACATTCAAAGCACCATCAAATCTCAAAGATGCAGTCAAGAAAGAAATAACCTG
131 TCATTCACATCCACATTCAAAGCACCATCAAATCTCAAAGATGCAGTCAAGAAAGAAATAACCTG
18594149 TAAACGATCCAAACATCATAAGTATACACATACAATGCAAACAATCAAATTAAAACAAACATCAT
196 TAAACGATCCAAACATCATAAGTATACACATACAATGCAAACAATCAAATTAAAACAAACATCAT
18594214 AAGGAAGAAATAACTTTATAACCTACAAGAAAACATAGAATGTACACAAGCAATGGTACAGCTTG
261 AAGGAAGAAATAACTTTATAACCTACAAGAAAACATAGAATGTACACAAGCAATGGTACAGCTTG
18594279 TAAAAAATAGTCCAGAATAAACTACAGAAAAATGGAAGGAGATCAATAGCAACAATGCTGGAGAT
326 TAAAAAATAGTCCAGAATAAACTACAGAAAAATGGAAGGAGATCAATAGCAACAATGCTGGAGAT
18594344 CCTTAACAGTT
391 CCTTAACAGTT
18594355 GTTC
1 GTTC
18594359 TCTACTTAAA
Statistics
Matches: 403, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
401 403 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (401 bp):
GTTCAAATGCACTGCTTGTGATTTCTGCTACTGATAGTTGCTCATGGTAAGCCTTTTCCGCTGAA
ATCACTGGTGCATATGAAGACAACATGAAATGGATTCAGGGTATGGGACTAAATTGGTCTGAAAC
TCATTCACATCCACATTCAAAGCACCATCAAATCTCAAAGATGCAGTCAAGAAAGAAATAACCTG
TAAACGATCCAAACATCATAAGTATACACATACAATGCAAACAATCAAATTAAAACAAACATCAT
AAGGAAGAAATAACTTTATAACCTACAAGAAAACATAGAATGTACACAAGCAATGGTACAGCTTG
TAAAAAATAGTCCAGAATAAACTACAGAAAAATGGAAGGAGATCAATAGCAACAATGCTGGAGAT
CCTTAACAGTT
Found at i:18599901 original size:21 final size:21
Alignment explanation
Indices: 18599877--18599916 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18599867 CCGTGTGGTT
* *
18599877 AAGGGACACGGCTGTGTGACC
1 AAGGCACACGCCTGTGTGACC
18599898 AAGGCACACGCCTGTGTGA
1 AAGGCACACGCCTGTGTGA
18599917 AAATCGACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (21 bp):
AAGGCACACGCCTGTGTGACC
Found at i:18608857 original size:18 final size:19
Alignment explanation
Indices: 18608826--18608868 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
18608816 TTTATTTAGA
*
18608826 TATTATTTATATTTATTTT
1 TATTATTTAAATTTATTTT
*
18608845 TATT-TTTAAATTT-CTTT
1 TATTATTTAAATTTATTTT
18608862 TATTATT
1 TATTATT
18608869 ATTTTCTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 7 0.33
18 10 0.48
19 4 0.19
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
TATTATTTAAATTTATTTT
Found at i:18616795 original size:13 final size:13
Alignment explanation
Indices: 18616777--18616809 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
18616767 TAGATTTTTC
*
18616777 CTAAATATTACCA
1 CTAAATATTACAA
18616790 CTAAATATTACAA
1 CTAAATATTACAA
18616803 CTAAATA
1 CTAAATA
18616810 ATTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (13 bp):
CTAAATATTACAA
Found at i:18624612 original size:23 final size:23
Alignment explanation
Indices: 18624583--18624634 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
18624573 AATATTACCA
18624583 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
18624606 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
18624629 CAAAAT
1 CTAAAT
18624635 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:18624624 original size:13 final size:13
Alignment explanation
Indices: 18624570--18624625 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
18624560 TAAATTTTTC
*
18624570 CTAAATATTACCA
1 CTAAATATTATCA
18624583 CTAAATATTATCA
1 CTAAATATTATCA
*
18624596 CTAAATA--AT-T
1 CTAAATATTATCA
18624606 CTAAATATTATCA
1 CTAAATATTATCA
18624619 CTAAATA
1 CTAAATA
18624626 ATTCAAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 7 0.19
11 2 0.05
12 2 0.05
13 26 0.70
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:18628169 original size:4 final size:4
Alignment explanation
Indices: 18628160--18628193 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
18628150 ATTAATCTAA
18628160 AATT AATT AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AATT AA
18628194 GCCAATATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:18630346 original size:20 final size:19
Alignment explanation
Indices: 18630318--18630364 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
18630308 ATTTAAGTTC
*
18630318 AAAAATTATTAAAATATTAT
1 AAAAATTATTAAAA-ACTAT
*
18630338 AAGAATTATTAAAAACTAT
1 AAAAATTATTAAAAACTAT
18630357 AAAAATTA
1 AAAAATTA
18630365 GAAAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAATTATTAAAAACTAT
Done.