Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008164.1 Hibiscus syriacus cultivar Beakdansim tig00110744_pilon, whole genome shotgun sequence
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: 2577652
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1353333 original size:5 final size:5
Alignment explanation
Indices: 1353325--1353674 Score: 63
Period size: 5 Copynumber: 67.8 Consensus size: 5
1353315 AAACTAAAGA
* * *
1353325 AAAAT AAAAT -AAAG AAAAT AAAAAT AAATGAA AAAAT GAAAAT AAGAT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAA--AT AAAAT -AAAAT AAAAT
* * *
1353373 AAAGA- AAAGAC ATAA- AAAAT AAAAT AAAGAT AAAAA ACTAAAT AAAAT
1 AAA-AT AAA-AT AAAAT AAAAT AAAAT AAA-AT AAAAT A--AAAT AAAAT
* * * *
1353421 -AAAG AACAT AAAA- AACAAA AGAAAT -AAA- AAAAT GAAGA- AAAAT
1 AAAAT AAAAT AAAAT AA-AAT A-AAAT AAAAT AAAAT -AAAAT AAAAT
**
1353464 -AAAT AAAAT --AAT CAAAAT AAAGAT AACGAGC AAAAT AAAAT AAAAAT
1 AAAAT AAAAT AAAAT -AAAAT AAA-AT AA--AAT AAAAT AAAAT -AAAAT
** * * * *
1353511 AAAAAT AAAAT AAAGG AAAAT ACTAAT -AATT GTATAT ACATAAT -AAAT
1 -AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT -AAAAT A-A-AAT AAAAT
* * *
1353559 -AAAT -AAAT -AAAC AAGAG AAAAAT ACAAAT GAAAAT AAATAT ATAAAT
1 AAAAT AAAAT AAAAT AAAAT AAA-AT A-AAAT -AAAAT AAA-AT A-AAAT
* * * *
1353606 AAAACT AATAT AAAAG AATAA- AAGAAT AAAA- AAAAT AAAAG AAAAA
1 AAAA-T AAAAT AAAAT AA-AAT AA-AAT AAAAT AAAAT AAAAT AAAAT
*
1353652 AAAAT AAAAT AAGA- AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAA
1353675 GGTAAATATA
Statistics
Matches: 256, Mismatches: 46, Indels: 86
0.66 0.12 0.22
Matches are distributed among these distances:
3 3 0.01
4 47 0.18
5 117 0.46
6 70 0.27
7 18 0.07
8 1 0.00
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1353344 original size:9 final size:9
Alignment explanation
Indices: 1353330--1353486 Score: 67
Period size: 9 Copynumber: 17.1 Consensus size: 9
1353320 AAAGAAAAAT
1353330 AAAATAAAG
1 AAAATAAAG
*
1353339 AAAATAAAA
1 AAAATAAAG
*
1353348 ATAAATGAA-
1 A-AAATAAAG
1353357 AAAATGAAA-
1 AAAAT-AAAG
1353366 ATAAGATAAAG
1 A-AA-ATAAAG
* *
1353377 AAAAGACATAA
1 AAAATA-A-AG
*
1353388 AAAATAAAAT
1 AAAAT-AAAG
1353398 AAAGATAAA-
1 AAA-ATAAAG
* *
1353407 AAACTAAAT
1 AAAATAAAG
1353416 AAAATAAAG
1 AAAATAAAG
*
1353425 AACATAAA-
1 AAAATAAAG
1353433 AAACA-AAAG
1 AAA-ATAAAG
1353442 -AAATAAA-
1 AAAATAAAG
*
1353449 AAAATGAAG
1 AAAATAAAG
*
1353458 AAAAATAAAT
1 -AAAATAAAG
**
1353468 AAAATAATC
1 AAAATAAAG
1353477 AAAATAAAG
1 AAAATAAAG
1353486 A
1 A
1353487 TAACGAGCAA
Statistics
Matches: 113, Mismatches: 19, Indels: 32
0.69 0.12 0.20
Matches are distributed among these distances:
7 1 0.01
8 24 0.21
9 48 0.42
10 28 0.25
11 11 0.10
12 1 0.01
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.14
Consensus pattern (9 bp):
AAAATAAAG
Found at i:1353405 original size:18 final size:18
Alignment explanation
Indices: 1353384--1353525 Score: 81
Period size: 18 Copynumber: 8.0 Consensus size: 18
1353374 AAGAAAAGAC
1353384 ATAAAAAATAAAATAAAG
1 ATAAAAAATAAAATAAAG
1353402 ATAAAAAACT-AAATAAA-
1 ATAAAAAA-TAAAATAAAG
1353419 ATAAAGAACATAAAA-AACA-
1 ATAAA-AA-ATAAAATAA-AG
*
1353438 A-AAGAAATAAAA-AAATG
1 ATAAAAAATAAAATAAA-G
1353455 A-AGAAAAAT-AAATAAA-
1 ATA-AAAAATAAAATAAAG
*
1353471 ATAATCAAAATAAAGATAACG
1 ATAA--AAAATAAA-ATAAAG
** *
1353492 A-GCAAAATAAAATAAAA
1 ATAAAAAATAAAATAAAG
1353509 AT-AAAAATAAAATAAAG
1 ATAAAAAATAAAATAAAG
1353526 GAAAATACTA
Statistics
Matches: 99, Mismatches: 9, Indels: 33
0.70 0.06 0.23
Matches are distributed among these distances:
15 1 0.01
16 10 0.10
17 31 0.31
18 43 0.43
19 9 0.09
20 4 0.04
21 1 0.01
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (18 bp):
ATAAAAAATAAAATAAAG
Found at i:1353418 original size:43 final size:41
Alignment explanation
Indices: 1353363--1353489 Score: 116
Period size: 44 Copynumber: 3.0 Consensus size: 41
1353353 TGAAAAAATG
1353363 AAAATAAGATAAAGAAAAGACATAAAAAATAAAATAAAGATAA
1 AAAATAA-ATAAA-AAAAGACATAAAAAATAAAATAAAGATAA
* * *
1353406 AAAACTAAATAAAATAAAGAACATAAAAAACAAAAGAAATA-AA
1 AAAA-TAAATAAAA-AAAG-ACATAAAAAATAAAATAAAGATAA
* * *
1353449 AAAATGAAGAAAAATA-A-ATAAAATAATCAAAATAAAGATAA
1 AAAATAAATAAAAAAAGACATAAAA-AAT-AAAATAAAGATAA
1353490 CGAGCAAAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
38 6 0.09
39 3 0.04
40 8 0.12
41 4 0.06
42 8 0.12
43 19 0.28
44 21 0.30
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (41 bp):
AAAATAAATAAAAAAAGACATAAAAAATAAAATAAAGATAA
Found at i:1353628 original size:8 final size:8
Alignment explanation
Indices: 1353615--1353660 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
1353605 TAAAACTAAT
1353615 ATAAAAGA
1 ATAAAAGA
1353623 ATAAAAGA
1 ATAAAAGA
*
1353631 ATAAAAAAA
1 AT-AAAAGA
1353640 ATAAAAGA
1 ATAAAAGA
*
1353648 A-AAAAAA
1 ATAAAAGA
1353655 ATAAAA
1 ATAAAA
1353661 TAAGAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 6 0.18
8 20 0.61
9 7 0.21
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.11
Consensus pattern (8 bp):
ATAAAAGA
Found at i:1353642 original size:9 final size:9
Alignment explanation
Indices: 1353602--1353674 Score: 58
Period size: 9 Copynumber: 7.9 Consensus size: 9
1353592 ATAAATATAT
*
1353602 AAATAAAAC
1 AAATAAAAA
*
1353611 TAATATAAAA
1 AAATA-AAAA
*
1353621 GAAT-AAAA
1 AAATAAAAA
*
1353629 GAATAAAAA
1 AAATAAAAA
1353638 AAATAAAAGA
1 AAATAAAA-A
*
1353648 AAAAAAAATA
1 AAATAAAA-A
*
1353658 AAATAAGAA
1 AAATAAAAA
1353667 AAATAAAA
1 AAATAAAA
1353675 GGTAAATATA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
8 8 0.15
9 23 0.44
10 21 0.40
ACGTcount: A:0.79, C:0.01, G:0.05, T:0.14
Consensus pattern (9 bp):
AAATAAAAA
Found at i:1355444 original size:46 final size:46
Alignment explanation
Indices: 1355358--1355454 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
1355348 GAGTCGAGGA
* * * *
1355358 TTCTACGCGGTCCTTCGGGAAAATTCTACGTGATCTTTCGGGACAT
1 TTCTACGCGATCCTTCAGGAAAATACTACGTGATCCTTCGGGACAT
* * * *
1355404 TTCTACGTGATCCTTCAGGACAATACTATGTGGTCCTTCGGGACAT
1 TTCTACGCGATCCTTCAGGAAAATACTACGTGATCCTTCGGGACAT
1355450 TTCTA
1 TTCTA
1355455 TGTGGCAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.34
Consensus pattern (46 bp):
TTCTACGCGATCCTTCAGGAAAATACTACGTGATCCTTCGGGACAT
Found at i:1355455 original size:23 final size:23
Alignment explanation
Indices: 1355357--1355459 Score: 107
Period size: 23 Copynumber: 4.5 Consensus size: 23
1355347 AGAGTCGAGG
* *
1355357 ATTCTACGCGGTCCTTCGGGAAA
1 ATTCTACGTGGTCCTTCGGGACA
* *
1355380 ATTCTACGTGATCTTTCGGGACA
1 ATTCTACGTGGTCCTTCGGGACA
* * *
1355403 TTTCTACGTGATCCTTCAGGACA
1 ATTCTACGTGGTCCTTCGGGACA
* *
1355426 ATACTATGTGGTCCTTCGGGACA
1 ATTCTACGTGGTCCTTCGGGACA
* *
1355449 TTTCTATGTGG
1 ATTCTACGTGG
1355460 CAATTTATAC
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.34
Consensus pattern (23 bp):
ATTCTACGTGGTCCTTCGGGACA
Found at i:1355589 original size:6 final size:6
Alignment explanation
Indices: 1355578--1355708 Score: 163
Period size: 6 Copynumber: 21.8 Consensus size: 6
1355568 TGAACAATAA
*
1355578 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGACG ATGATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
* * * * * * *
1355626 ATCATG ATCATG ATCATG ATCATG ATCATG ATGATG ATGATT ATCATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
* * *
1355674 ATCATG ATCATG ATGATG ACGATG ATGATG ATGAT
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGAT
1355709 ATGTATATAT
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 115 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.33
Consensus pattern (6 bp):
ATGATG
Found at i:1356790 original size:233 final size:233
Alignment explanation
Indices: 1356381--1357558 Score: 1534
Period size: 233 Copynumber: 5.1 Consensus size: 233
1356371 GTTATAAGTT
** *
1356381 AAAAAATGAGAAATATTTCTCATTT-AAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTT
1 AAAAAATGAGAAAGGTTTCTCATTTAAAAT-TGAAAATTGAAATTTTTAAAAAGTAAGAAAAGTT
* * * *
1356445 TCTTACCTAATAAATTATTTCCAAAGTTGGTAAGTCCTTCGGGCTATCAGTAAGTCTTTTGAGCA
65 TCTTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
* * *
1356510 TGATGCTTAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGAAAGATGATAAGTCTTTCATACCAT
130 TGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCAGACCAT
* * * * *
1356575 CAATAAGACCTTCAGGCAGGGTGTTTTCACATGTCTCTC
195 CCATAAGACCTTCGGGCAAGATGTTTTCACATATCTCTC
* *
1356614 GAAAAATGAGAAAGGTTTCTCATTTAAAATTGAAATTTGAAATTTTTAAAAAGTAAGAAAAGTTT
1 AAAAAATGAGAAAGGTTTCTCATTTAAAATTGAAAATTGAAATTTTTAAAAAGTAAGAAAAGTTT
*
1356679 CTTACATAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
66 CTTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * *
1356744 GATGCTTAAATCCTTCGGGTCAACTATAAGTCTTTCGAGCAAGATGATAAGCCTTTCAGACCATC
131 GATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCAGACCATC
* * *
1356809 TATAAGACCTTCGGGTAAGTTGTTTTCACATATCTCTC
196 CATAAGACCTTCGGGCAAGATGTTTTCACATATCTCTC
* *
1356847 --GAAATGAGAAAGGTTTCTCATTT-AAATCTGAAAATTGAAATTTTTTAAAAGTAAGAAAAGTT
1 AAAAAATGAGAAAGGTTTCTCATTTAAAAT-TGAAAATTGAAATTTTTAAAAAGTAAGAAAAGTT
*
1356909 TCTTACCTAGTAAACTATTTCCAAAGTTGGTAAGT--TT-GGGCCATTAGTAAGTCTTTCGAGCA
65 TCTTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
* * **
1356971 TGATACTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTC-TTCGGGTCAT
130 TGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCAGACCAT
1357035 CCATAAGACCTTCGGGCAAGATGTTTTCACATATCTCTC
195 CCATAAGACCTTCGGGCAAGATGTTTTCACATATCTCTC
* * * *
1357074 AAAAAATGAGAAAGGTTTCTCATTTAAATTTGACAATTGAAATTTTTTAATAGTAAGAAAAGTTT
1 AAAAAATGAGAAAGGTTTCTCATTTAAAATTGAAAATTGAAATTTTTAAAAAGTAAGAAAAGTTT
* * * *
1357139 CTTACCTAGTAAATTATTTCCAAAATTGGTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGAAT
66 CTTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * * * * * *
1357204 GATGATTAAA-CTCTTCGGGTCATTTGTAAGTCTTTTGAGAAAGATGATAAGTCCTTCGGGCCAT
131 GATGCTTAAATC-CTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCAGACCAT
** * * *
1357268 CCATAAGACCTTCGGGTGAGATGTTTTCACATTTGTTTTC
195 CCATAAGACCTTCGGGCAAGATGTTTTCACATAT-CTCTC
** * * **
1357308 AAAAAAAATGAGAAAATTTTCTCATTTAAATTTCAAAATTGATTTTTTTGGAAAAAGTAAGAAAA
1 --AAAAAATGAGAAAGGTTTCTCATTTAAAATTGAAAATTGAAATTTTT--AAAAAGTAAGAAAA
* * *
1357373 GTTTCTTACCTAGTAAACTA-TTCTCAAATTTGGTAAATCATTCGGGCCATCAGTAAGTCTTTCG
62 GTTTCTTACCTAGTAAACTATTTC-CAAAGTTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCG
* * * * * *
1357437 AGTATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTCTCGAGCAAGATGATAAGTCATTCGGA
126 AGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCAGA
* * * *
1357502 TCATCCATAAGTCCTTCGGG-AAGGATATTTTCACATGAT-TTTC
191 CCATCCATAAGACCTTCGGGCAA-GATGTTTTCACAT-ATCTCTC
1357545 TAAAAAATGAGAAA
1 -AAAAAATGAGAAA
1357559 ACAATTTCCA
Statistics
Matches: 842, Mismatches: 84, Indels: 35
0.88 0.09 0.04
Matches are distributed among these distances:
227 43 0.05
228 74 0.09
229 89 0.11
230 7 0.01
231 91 0.11
232 71 0.08
233 246 0.29
234 7 0.01
236 54 0.06
237 8 0.01
238 150 0.18
239 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (233 bp):
AAAAAATGAGAAAGGTTTCTCATTTAAAATTGAAAATTGAAATTTTTAAAAAGTAAGAAAAGTTT
CTTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
GATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCTTTCAGACCATC
CATAAGACCTTCGGGCAAGATGTTTTCACATATCTCTC
Found at i:1357221 original size:42 final size:41
Alignment explanation
Indices: 1357172--1357267 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
1357162 AATTGGTAAG
*
1357172 TCCTTCGGGCCATTAGTAAGTCTTTCGAGAATGATGATTAAAC
1 TCCTTCGGGCCATTAGTAAGTCTTTCGAGAAAGATGA-T-AAC
* * * *
1357215 T-CTTCGGGTCATTTGTAAGTCTTTTGAGAAAGATGATAAG
1 TCCTTCGGGCCATTAGTAAGTCTTTCGAGAAAGATGATAAC
1357255 TCCTTCGGGCCAT
1 TCCTTCGGGCCAT
1357268 CCATAAGACC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 3 0.07
41 11 0.24
42 31 0.67
43 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (41 bp):
TCCTTCGGGCCATTAGTAAGTCTTTCGAGAAAGATGATAAC
Found at i:1357224 original size:460 final size:465
Alignment explanation
Indices: 1356382--1357558 Score: 1604
Period size: 460 Copynumber: 2.5 Consensus size: 465
1356372 TTATAAGTTA
* *
1356382 AAAAATGAGAAATATTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAGTTTC
1 AAAAATGAGAAAAATTTCTCATTTAAATCTGAAAATTGAAATTTTTTAAAAGTAAGAAAAGTTTC
* * * *
1356447 TTACCTAATAAATTATTTCCAAAGTTGGTAAGTCCTTCGGGCTATCAGTAAGTCTTTTGAGCATG
66 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGT-CTTCGGGCCATCAGTAAGTCTTTCGAGCATG
* * * ** * *
1356512 ATGCTTAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGAAAGATGATAAGTCTTTCATACCATCA
130 ATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGATCATCC
* * * * *
1356577 ATAAGACCTTCAGGCAGGGTGTTTTCACATGTCTCTCGAAAAATGAGAAAGGTTTCTCATTTAAA
195 ATAAGACCTTCGGGCAAGATGTTTTCACATATCTCTCAAAAAATGAGAAAGGTTTCTCATTTAAA
*
1356642 ATTGAAATTTGAAATTTTTAAAAAGTAAGAAAAGTTTCTTACATAGTAAACTATTTCCAAAGTTG
260 ATTGAAATTTGAAATTTTTAAAAAGTAAGAAAAGTTTCTTACATAGTAAACTATTTCCAAAATTG
* *
1356707 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCAACTATA
325 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGAATGATGATTAAATCCTTCGGGTCAACTATA
* * *
1356772 AGTCTTTCGAGCAAGATGATAAG-CCTTTCAGACCATCTATAAGACCTTCGGGTAAGTTGTTTTC
390 AGTCTTTCGAGAAAGATGATAAGTCC-TTCAGACCATCCATAAGACCTTCGGGTAAGATGTTTTC
1356836 ACATAT-CTCTC
454 ACATATGCTCTC
* **
1356847 -GAAATGAGAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTTAAAAGTAAGAAAAGTTTC
1 AAAAATGAGAAAAATTTCTCATTTAAATCTGAAAATTGAAATTTTTTAAAAGTAAGAAAAGTTTC
*
1356911 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGT-TT-GGGCCATTAGTAAGTCTTTCGAGCATGA
66 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
* *
1356974 TACTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTC-TTCGGGTCATCCA
131 TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGATCATCCA
*
1357038 TAAGACCTTCGGGCAAGATGTTTTCACATATCTCTCAAAAAATGAGAAAGGTTTCTCATTTAAAT
196 TAAGACCTTCGGGCAAGATGTTTTCACATATCTCTCAAAAAATGAGAAAGGTTTCTCATTTAAAA
* * * *
1357103 TTGACAA-TTGAAATTTTTTAATAGTAAGAAAAGTTTCTTACCTAGTAAATTATTTCCAAAATTG
261 TTGA-AATTTGAAATTTTTAAAAAGTAAGAAAAGTTTCTTACATAGTAAACTATTTCCAAAATTG
* ** *
1357167 GTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGAATGATGATTAAA-CTCTTCGGGTCATTTGT
325 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGAATGATGATTAAATC-CTTCGGGTCAACTAT
* * * *
1357231 AAGTCTTTTGAGAAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTGAGATGTTTTC
389 AAGTCTTTCGAGAAAGATGATAAGTCCTTCAGACCATCCATAAGACCTTCGGGTAAGATGTTTTC
* * *
1357296 ACATTTGTTTTC
454 ACATATGCTCTC
* * * *
1357308 AAAAAAAATGAGAAAATTTTCTCATTTAAATTTCAAAATTG-ATTTTTTTGGAAAAAGTAAGAAA
1 ---AAAAATGAGAAAAATTTCTCATTTAAATCTGAAAATTGAAATTTTTT---AAAAGTAAGAAA
* *
1357372 AGTTTCTTACCTAGTAAACTA-TTCTCAAATTTGGTAAATCATTCGGGCCATCAGTAAGTCTTTC
60 AGTTTCTTACCTAGTAAACTATTTC-CAAAGTTGGTAAGTC-TTCGGGCCATCAGTAAGTCTTTC
* * * *
1357436 GAGTATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTCTCGAGCAAGATGATAAGTCATTCGG
123 GAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGG
* * *
1357501 ATCATCCATAAGTCCTTCGGG-AAGGATATTTTCACATGAT-TTTCTAAAAAATGAGAAA
188 ATCATCCATAAGACCTTCGGGCAA-GATGTTTTCACAT-ATCTCTC-AAAAAATGAGAAA
1357559 ACAATTTCCA
Statistics
Matches: 631, Mismatches: 62, Indels: 31
0.87 0.09 0.04
Matches are distributed among these distances:
459 1 0.00
460 239 0.38
461 80 0.13
462 2 0.00
464 98 0.16
465 32 0.05
466 3 0.00
467 45 0.07
469 2 0.00
470 75 0.12
471 39 0.06
472 15 0.02
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (465 bp):
AAAAATGAGAAAAATTTCTCATTTAAATCTGAAAATTGAAATTTTTTAAAAGTAAGAAAAGTTTC
TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
TGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGATCATCCA
TAAGACCTTCGGGCAAGATGTTTTCACATATCTCTCAAAAAATGAGAAAGGTTTCTCATTTAAAA
TTGAAATTTGAAATTTTTAAAAAGTAAGAAAAGTTTCTTACATAGTAAACTATTTCCAAAATTGG
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGAATGATGATTAAATCCTTCGGGTCAACTATAA
GTCTTTCGAGAAAGATGATAAGTCCTTCAGACCATCCATAAGACCTTCGGGTAAGATGTTTTCAC
ATATGCTCTC
Found at i:1357986 original size:134 final size:134
Alignment explanation
Indices: 1357795--1358726 Score: 1045
Period size: 133 Copynumber: 7.0 Consensus size: 134
1357785 GTGAATTGAA
* * *
1357795 CTCGATTCAATCTTCCCTGAGTAATAGTAGAATGAATCAAATTCCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCCCTCA
* * *
1357860 AGAAGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGC
66 AGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
*
1357925 CTTC
131 CTAC
* * *** *
1357929 CTCGATTCAATCTTCCCAGAGTGACAGTGGAATGAATCAACTTCCTTGGATCTGATTTCCCCTCA
1 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCCCTCA
** * * * * *
1357994 AGAAGAAGCATAACAAATCCATATCTTTCAAGATTTGATATTCCATGAGTAACAGGGGAACAGGT
66 AGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
*
1358059 CTGC
131 CTAC
** * * * * * *
1358063 CTTAATTCATTCTTCCCTAAGCAACAGTGGAATGAATCAACATCCCCATATCTAATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCCCTCA
* * * * * *
1358128 GGAAGAAGTGGAACAAA-CCTCTTTCGTTC-AGATTTGATATTCTCTGAGTAACAATGGAACAAG
66 AGAAGAAGCGGAACAAATCC-CTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
*
1358191 TATAC
130 TCTAC
* * * *
1358196 CTCGATTCAATCTTTCTTGAGTGACAGTCGAATGAATCAACTTCCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCCCTCA
** * * * * * *
1358261 AGAAGAAGCTAAATAGATCCATCTCTTTC-AGATTTTATATTCCCTAAGTAACAGTGAAACAAGT
66 AGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
1358325 CTAC
131 CTAC
* * * *
1358329 CTCTATTCAATCTTCCCTAAAG-AACAGTGGAATGAATCAACGTCCCCAGATATGATTTTCCCTC
1 CTCGATTCAATCTTCCCT-GAGTAACAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCCCTC
* * * * *
1358393 AAGAAGAAGCGAAACAGATCCCTCTCTTTC-AGATTTGGTATTCCTTGAGTAACAATGGAACAAG
65 AAGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
*
1358457 TCTTC
130 TCTAC
* * * * * *
1358462 TTCGATTCAATATTCCCTGAAG-AACACTGGAATGAATCAAC-ACCTCCAGATATTATTTTCCCT
1 CTCGATTCAATCTTCCCTG-AGTAACAGTGGAATGAATCAACTTCC-CCAGATCTGATTTTCCCT
*
1358525 CAAGAAGAAGAGGAACAAATCCCTC-CTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
64 CAAGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
*
1358589 GTCTGC
129 GTCTAC
* * ** * * * * * *
1358595 CTCTATTCAATCATCCCTGAAAAACAGTAGAATGAATCAA-TATCCCTAAATTTGACTTTACCTC
1 CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACT-TCCCCAGATCTGATTTTCCCTC
* * *
1358659 AAGAAGAATCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAATGGAACAAG
65 AAGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
1358724 TCT
130 TCT
1358727 GTCTCGATCT
Statistics
Matches: 663, Mismatches: 125, Indels: 20
0.82 0.15 0.02
Matches are distributed among these distances:
132 8 0.01
133 423 0.64
134 232 0.35
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACTTCCCCAGATCTGATTTTCCCTCA
AGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTAC
Found at i:1358883 original size:3 final size:3
Alignment explanation
Indices: 1358875--1358993 Score: 224
Period size: 3 Copynumber: 40.3 Consensus size: 3
1358865 GCAGCTGTCG
1358875 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1358923 A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1358970 ATT ATT ATT A-T ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1358994 CAGGCCCAAT
Statistics
Matches: 114, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
2 4 0.04
3 110 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1362061 original size:19 final size:19
Alignment explanation
Indices: 1362037--1362100 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
1362027 GATTATACAT
1362037 AAATATATTTGAGATTAAA
1 AAATATATTTGAGATTAAA
*
1362056 AAATATATAAAT-AGATTATACA
1 AAATATAT--TTGAGATTA-A-A
1362078 TAAATATATTTGAGATTAAA
1 -AAATATATTTGAGATTAAA
1362098 AAA
1 AAA
1362101 AATGAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
19 11 0.30
20 7 0.19
21 4 0.11
22 7 0.19
23 8 0.22
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (19 bp):
AAATATATTTGAGATTAAA
Found at i:1362067 original size:42 final size:41
Alignment explanation
Indices: 1362009--1362101 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 41
1361999 GGATTTTAAT
1362009 ATTAAAAAAATATAAATAGATTATACATAAATATATTTGAG
1 ATTAAAAAAATATAAATAGATTATACATAAATATATTTGAG
1362050 ATTAAAAAATATATAAATAGATTATACATAAATATATTTGAG
1 ATTAAAAAA-ATATAAATAGATTATACATAAATATATTTGAG
1362092 ATTAAAAAAA
1 ATTAAAAAAA
1362102 ATGAAAAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (41 bp):
ATTAAAAAAATATAAATAGATTATACATAAATATATTTGAG
Found at i:1362085 original size:23 final size:23
Alignment explanation
Indices: 1362018--1362086 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1362008 TATTAAAAAA
1362018 ATATAAATAGATTATACATAAAT
1 ATATAAATAGATTATACATAAAT
*
1362041 ATAT--TTGAGATTA-A-A-AAAT
1 ATATAAAT-AGATTATACATAAAT
1362060 ATATAAATAGATTATACATAAAT
1 ATATAAATAGATTATACATAAAT
1362083 ATAT
1 ATAT
1362087 TTGAGATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
19 8 0.21
20 7 0.18
21 4 0.11
22 7 0.18
23 12 0.32
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (23 bp):
ATATAAATAGATTATACATAAAT
Found at i:1368356 original size:20 final size:21
Alignment explanation
Indices: 1368316--1368366 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
1368306 TGGATTTATG
1368316 GTTTCGATACCAAACCCCTCA
1 GTTTCGATACCAAACCCCTCA
* *
1368337 GTTTCGATGCCGAA-CCCTCA
1 GTTTCGATACCAAACCCCTCA
* *
1368357 ATATCGATAC
1 GTTTCGATAC
1368367 TCCTTTAAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.25
Consensus pattern (21 bp):
GTTTCGATACCAAACCCCTCA
Found at i:1379571 original size:15 final size:17
Alignment explanation
Indices: 1379542--1379575 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1379532 CAAACTCCAA
1379542 TTATTATTTTATTCTAT
1 TTATTATTTTATTCTAT
1379559 TTATT-TTTT-TTCTAT
1 TTATTATTTTATTCTAT
1379574 TT
1 TT
1379576 TTTCTTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTATTTTATTCTAT
Found at i:1381069 original size:21 final size:21
Alignment explanation
Indices: 1381045--1381094 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1381035 AGCAATTTCA
1381045 CAAGAAAAGATGGTTACATCC
1 CAAGAAAAGATGGTTACATCC
* *
1381066 CAAGAAAAGCTGGTTGCATCC
1 CAAGAAAAGATGGTTACATCC
*
1381087 CAGGAAAA
1 CAAGAAAA
1381095 ATTCCAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGAAAAGATGGTTACATCC
Found at i:1386639 original size:24 final size:24
Alignment explanation
Indices: 1386622--1386757 Score: 154
Period size: 24 Copynumber: 5.7 Consensus size: 24
1386612 TTGATTTGAT
1386622 TTCTGATCTGATACTTGA-TATGGA
1 TTCTGATCTGATACTTGACT-TGGA
*
1386646 TTCTGATTTGATA-TCTGA-TATGGA
1 TTCTGATCTGATACT-TGACT-TGGA
* *
1386670 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACTTGGA
1386694 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACTTGGA
*
1386718 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACTTGGA
* *
1386742 TTTTGATATGATACTT
1 TTCTGATCTGATACTT
1386758 AACATGAATT
Statistics
Matches: 101, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
23 1 0.01
24 99 0.98
25 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACTTGGA
Found at i:1386693 original size:48 final size:48
Alignment explanation
Indices: 1386622--1386757 Score: 170
Period size: 48 Copynumber: 2.8 Consensus size: 48
1386612 TTGATTTGAT
* *
1386622 TTCTGATCTGATACTTGATATGGATTCTGATTTGATA-TCTGA-TATGGA
1 TTCTGATCTGATACTTGACATGGATTCTGATATGATACT-TGACT-TGGA
* *
1386670 TTCTGATATGATA-TCTGACATGGATTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACT-TGACATGGATTCTGATATGATACTTGACTTGGA
* *
1386718 TTCTGATCTGATACTTGACCTGGATTTTGATATGATACTT
1 TTCTGATCTGATACTTGACATGGATTCTGATATGATACTT
1386758 AACATGAATT
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
47 1 0.01
48 73 0.95
49 3 0.04
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (48 bp):
TTCTGATCTGATACTTGACATGGATTCTGATATGATACTTGACTTGGA
Found at i:1386763 original size:72 final size:72
Alignment explanation
Indices: 1386622--1386763 Score: 191
Period size: 72 Copynumber: 2.0 Consensus size: 72
1386612 TTGATTTGAT
* * *
1386622 TTCTGATCTGATACTTGATATGGATTCTGATTTGATATCTGATATGGATTCTGATATGATATCTG
1 TTCTGATCTGATACTTGATATGGATTCTGATCTGATATCTGACATGGATTCTGATATGATATCTA
1386687 ACATGGA
66 ACATGGA
* *
1386694 TTCTGATCTGATACTTGACT-TGGATTCTGATCTGATA-CTTGACCTGGATTTTGATATGATA-C
1 TTCTGATCTGATACTTGA-TATGGATTCTGATCTGATATC-TGACATGGATTCTGATATGATATC
1386756 TTAACATG
64 -TAACATG
1386764 AATTATGGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
71 2 0.03
72 59 0.95
73 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (72 bp):
TTCTGATCTGATACTTGATATGGATTCTGATCTGATATCTGACATGGATTCTGATATGATATCTA
ACATGGA
Found at i:1391495 original size:24 final size:24
Alignment explanation
Indices: 1391468--1391609 Score: 180
Period size: 24 Copynumber: 5.9 Consensus size: 24
1391458 TCTATTTGAT
* *
1391468 TTCTGATCTGATACTTGATATGGA
1 TTCTGATATGATACTTGACATGGA
*
1391492 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
1391516 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
*
1391540 TTCTGATATGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* *
1391564 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
* *
1391588 TTTTGATATGATACTTAACATG
1 TTCTGATATGATACTTGACATG
1391610 AATTATGGTT
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
23 1 0.01
24 105 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:1391520 original size:12 final size:12
Alignment explanation
Indices: 1391487--1391569 Score: 66
Period size: 12 Copynumber: 6.9 Consensus size: 12
1391477 GATACTTGAT
1391487 ATGGATTCTGATC
1 ATGGATTCTGA-C
1391500 -T-GATATCTGAC
1 ATGGAT-TCTGAC
*
1391511 ATGGATTCTGAT
1 ATGGATTCTGAC
1391523 AT-GATATCTGAC
1 ATGGAT-TCTGAC
*
1391535 ATGGATTCTGAT
1 ATGGATTCTGAC
*
1391547 AT-GATACTTGAC
1 ATGGATTC-TGAC
*
1391559 TTGGATTCTGA
1 ATGGATTCTGA
1391570 TCTGATACTT
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
11 11 0.20
12 35 0.62
13 10 0.18
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.39
Consensus pattern (12 bp):
ATGGATTCTGAC
Found at i:1391609 original size:72 final size:72
Alignment explanation
Indices: 1391468--1391609 Score: 200
Period size: 72 Copynumber: 2.0 Consensus size: 72
1391458 TCTATTTGAT
* *
1391468 TTCTGATCTGATACTTGATATGGATTCTGATCTGATATCTGACATGGATTCTGATATGATATCTG
1 TTCTGATATGATACTTGATATGGATTCTGATCTGATATCTGACATGGATTCTGATATGATATCTA
1391533 ACATGGA
66 ACATGGA
* *
1391540 TTCTGATATGATACTTGACT-TGGATTCTGATCTGATA-CTTGACCTGGATTTTGATATGATA-C
1 TTCTGATATGATACTTGA-TATGGATTCTGATCTGATATC-TGACATGGATTCTGATATGATATC
1391602 TTAACATG
64 -TAACATG
1391610 AATTATGGTT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
71 2 0.03
72 60 0.95
73 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (72 bp):
TTCTGATATGATACTTGATATGGATTCTGATCTGATATCTGACATGGATTCTGATATGATATCTA
ACATGGA
Found at i:1393386 original size:24 final size:24
Alignment explanation
Indices: 1393359--1393476 Score: 166
Period size: 24 Copynumber: 4.9 Consensus size: 24
1393349 TCGATTTGAT
1393359 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
1393383 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
1393407 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
*
1393431 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* * *
1393455 TTTTGATATGATACTTAACATG
1 TTCTGATCTGATACTTGACATG
1393477 AATTATGGTT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 82 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:1393411 original size:12 final size:12
Alignment explanation
Indices: 1393374--1393412 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1393364 ATCTGATACT
1393374 TGACATGGATTC
1 TGACATGGATTC
*
1393386 TGATAT-GATATC
1 TGACATGGAT-TC
1393398 TGACATGGATTC
1 TGACATGGATTC
1393410 TGA
1 TGA
1393413 TCTGATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:1398565 original size:20 final size:20
Alignment explanation
Indices: 1398540--1398578 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1398530 ACGTGGCATG
1398540 AATTTTTCCTTAACATGTTA
1 AATTTTTCCTTAACATGTTA
1398560 AATTTTTCCTTAACATGTT
1 AATTTTTCCTTAACATGTT
1398579 TGATTGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.05, T:0.51
Consensus pattern (20 bp):
AATTTTTCCTTAACATGTTA
Found at i:1401957 original size:19 final size:20
Alignment explanation
Indices: 1401933--1401980 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
1401923 AATGATTTTC
* *
1401933 TTTTGAAAACTAAAATG-GA
1 TTTTGAAAACCAAAATGAAA
1401952 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACCAAAATGAAA
1401972 TTTTGAAAA
1 TTTTGAAAA
1401981 AGGATTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACCAAAATGAAA
Found at i:1403522 original size:20 final size:21
Alignment explanation
Indices: 1403497--1403536 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1403487 CTCTATATAG
1403497 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
1403517 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
1403537 CCCAACGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:1408612 original size:12 final size:13
Alignment explanation
Indices: 1408594--1408624 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1408584 AACCGGACCC
1408594 GACCCGACCCGTT
1 GACCCGACCCGTT
1408607 -ACCCGACCCGTT
1 GACCCGACCCGTT
1408619 GACCCG
1 GACCCG
1408625 TTGATCGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.16, C:0.48, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1408624 original size:8 final size:8
Alignment explanation
Indices: 1408611--1408645 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
1408601 CCCGTTACCC
1408611 GACCCGTT
1 GACCCGTT
1408619 GACCCGTT
1 GACCCGTT
*
1408627 GA-TCGTT
1 GACCCGTT
1408634 GACCCGTT
1 GACCCGTT
1408642 GACC
1 GACC
1408646 GGTGTTGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.26
Consensus pattern (8 bp):
GACCCGTT
Found at i:1408635 original size:15 final size:15
Alignment explanation
Indices: 1408615--1408643 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1408605 TTACCCGACC
1408615 CGTTGACCCGTTGAT
1 CGTTGACCCGTTGAT
1408630 CGTTGACCCGTTGA
1 CGTTGACCCGTTGA
1408644 CCGGTGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.28, G:0.28, T:0.31
Consensus pattern (15 bp):
CGTTGACCCGTTGAT
Found at i:1411166 original size:24 final size:24
Alignment explanation
Indices: 1411139--1411253 Score: 135
Period size: 24 Copynumber: 4.8 Consensus size: 24
1411129 TTCGATTTGA
1411139 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
1411163 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
* *
1411187 ATTCTGATCTGATACTTAACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
1411211 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
* * *
1411234 ATTCCGATATGTTACTTGAC
1 ATTCTGATCTGATACTTGAC
1411254 CTGATTTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
23 20 0.25
24 59 0.74
25 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1411246 original size:23 final size:23
Alignment explanation
Indices: 1411210--1411259 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1411200 ACTTAACTTG
* *
1411210 GATTCTGATCTGTTACTTGACCT
1 GATTCCGATATGTTACTTGACCT
1411233 GATTCCGATATGTTACTTGACCT
1 GATTCCGATATGTTACTTGACCT
1411256 GATT
1 GATT
1411260 TATGTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (23 bp):
GATTCCGATATGTTACTTGACCT
Found at i:1411265 original size:19 final size:20
Alignment explanation
Indices: 1411220--1411265 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 20
1411210 GATTCTGATC
1411220 TGTTACTTGACCTGATTCCGATA
1 TGTTACTTGACCTGATT-C--TA
1411243 TGTTACTTGACCTGATT-TA
1 TGTTACTTGACCTGATTCTA
1411262 TGTT
1 TGTT
1411266 TTGATTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.26
23 17 0.74
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (20 bp):
TGTTACTTGACCTGATTCTA
Found at i:1413367 original size:13 final size:13
Alignment explanation
Indices: 1413346--1413383 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1413336 TCATAACCCG
1413346 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
1413359 ACCCAACCCGTTT
1 ACCCGACCCGTTT
1413372 ACCCGACCCGTT
1 ACCCGACCCGTT
1413384 GACCGTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.18, C:0.47, G:0.13, T:0.21
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:1413410 original size:10 final size:8
Alignment explanation
Indices: 1413376--1413422 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
1413366 CCGTTTACCC
1413376 GACCCGTT
1 GACCCGTT
1413384 GA-CCGTT
1 GACCCGTT
1413391 GACCCGTT
1 GACCCGTT
1413399 GACCGGCGTT
1 GACC--CGTT
1413409 GACCACTGTT
1 GACC-C-GTT
1413419 GACC
1 GACC
1413423 AAAACTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 1 0.03
10 15 0.44
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:1415947 original size:24 final size:24
Alignment explanation
Indices: 1415920--1416030 Score: 136
Period size: 24 Copynumber: 4.7 Consensus size: 24
1415910 ATTTGAATTA
1415920 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
*
1415944 TGATCTGATA-TCTGACATAGATTC
1 TGATCTGATACT-TGACATGGATTC
* *
1415968 TGATCTGATACTTAACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* *
1415992 TGATCTGTTACTTGACCT-GATTC
1 TGATCTGATACTTGACATGGATTC
* *
1416015 CGATCTGTTACTTGAC
1 TGATCTGATACTTGAC
1416031 CTGATTTATG
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
23 21 0.27
24 55 0.71
25 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:1424081 original size:21 final size:21
Alignment explanation
Indices: 1424055--1424101 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1424045 AATAGGCAGG
1424055 GGTTTAGAAACCTAATGTAGA
1 GGTTTAGAAACCTAATGTAGA
1424076 GGTTTAGAAACCTAATGTAGA
1 GGTTTAGAAACCTAATGTAGA
1424097 GGTTT
1 GGTTT
1424102 GGGTAGGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.32
Consensus pattern (21 bp):
GGTTTAGAAACCTAATGTAGA
Found at i:1434446 original size:21 final size:21
Alignment explanation
Indices: 1434416--1434483 Score: 118
Period size: 21 Copynumber: 3.2 Consensus size: 21
1434406 ATAAGAAGGG
*
1434416 GGTTTCGAAACCTACTGTAGA
1 GGTTTAGAAACCTACTGTAGA
*
1434437 GGTTTAGAAACCTATTGTAGA
1 GGTTTAGAAACCTACTGTAGA
1434458 GGTTTAGAAACCTACTGTAGA
1 GGTTTAGAAACCTACTGTAGA
1434479 GGTTT
1 GGTTT
1434484 GGGTTGGGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (21 bp):
GGTTTAGAAACCTACTGTAGA
Found at i:1436151 original size:39 final size:39
Alignment explanation
Indices: 1436108--1436225 Score: 114
Period size: 39 Copynumber: 3.0 Consensus size: 39
1436098 AAAATATTTT
* * *
1436108 AAATAATAATTTAGAATTTTAATGTGAAATGATTTGAGA
1 AAATAAGAATTTAGAATATTAATGTGAAATAATTTGAGA
* *
1436147 AAATAAGAATTTAAAATATT-ATGGTGACAA-AATTTAAGA
1 AAATAAGAATTTAGAATATTAAT-GTGA-AATAATTTGAGA
* * * * *
1436186 AACTAAGAATTTCGAGTCTTAAAGTGAAATAATTTGAGA
1 AAATAAGAATTTAGAATATTAATGTGAAATAATTTGAGA
1436225 A
1 A
1436226 TTATAAATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
38 4 0.06
39 56 0.89
40 3 0.05
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.33
Consensus pattern (39 bp):
AAATAAGAATTTAGAATATTAATGTGAAATAATTTGAGA
Found at i:1436249 original size:3 final size:3
Alignment explanation
Indices: 1436241--1436271 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1436231 AATAAAAATT
1436241 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1436272 TAATCGTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1441183 original size:12 final size:12
Alignment explanation
Indices: 1441166--1441241 Score: 60
Period size: 12 Copynumber: 6.8 Consensus size: 12
1441156 TTTTTCATTT
1441166 ATTATTATTAAA
1 ATTATTATTAAA
1441178 ATTATTATT---
1 ATTATTATTAAA
1441187 ATTATTA-TAAA
1 ATTATTATTAAA
1441198 TATTATTATT---
1 -ATTATTATTAAA
**
1441208 ATTATTATTATT
1 ATTATTATTAAA
1441220 ATTATTATT-AA
1 ATTATTATTAAA
1441231 ATATATTATTA
1 AT-TATTATTA
1441242 CAAGCCCAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 19
0.71 0.03 0.26
Matches are distributed among these distances:
8 1 0.02
9 16 0.31
11 2 0.04
12 32 0.62
13 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATTATTAAA
Found at i:1441187 original size:18 final size:18
Alignment explanation
Indices: 1441164--1441241 Score: 106
Period size: 18 Copynumber: 4.3 Consensus size: 18
1441154 AATTTTTCAT
1441164 TTATTATTATTAAAATTA
1 TTATTATTATTAAAATTA
1441182 TTATTATTATTATAAA-TA
1 TTATTATTATTA-AAATTA
**
1441200 TTATTATTATTATTATTA
1 TTATTATTATTAAAATTA
1441218 TTATTATTATT-AAATATA
1 TTATTATTATTAAAAT-TA
1441236 TTATTA
1 TTATTA
1441242 CAAGCCCAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
17 3 0.06
18 47 0.89
19 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTATTATTAAAATTA
Found at i:1441241 original size:3 final size:3
Alignment explanation
Indices: 1441164--1441229 Score: 96
Period size: 3 Copynumber: 22.0 Consensus size: 3
1441154 AATTTTTCAT
** * *
1441164 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1441212 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
1441230 AATATATTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1441668 original size:25 final size:23
Alignment explanation
Indices: 1441640--1441704 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 23
1441630 CACAAAAGAA
*
1441640 AAGACAGAGAGCAACAAAAAAAAAC
1 AAGAAAGAGAG-AA-AAAAAAAAAC
*
1441665 AAGAAAGGGAG-AAAAAAAAAAC
1 AAGAAAGAGAGAAAAAAAAAAAC
*
1441687 -AGAAAGATA-AAAAAAAAA
1 AAGAAAGAGAGAAAAAAAAA
1441705 GAGGAGACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 15 0.43
22 10 0.29
23 1 0.03
25 9 0.26
ACGTcount: A:0.74, C:0.08, G:0.17, T:0.02
Consensus pattern (23 bp):
AAGAAAGAGAGAAAAAAAAAAAC
Found at i:1441680 original size:22 final size:19
Alignment explanation
Indices: 1441655--1441704 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
1441645 AGAGAGCAAC
1441655 AAAAAAAAACAAGAAAGGGAGA
1 AAAAAAAAAC-AGAAA--GAGA
*
1441677 AAAAAAAAACAGAAAGATA
1 AAAAAAAAACAGAAAGAGA
1441696 AAAAAAAAA
1 AAAAAAAAA
1441705 GAGGAGACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.44
21 5 0.19
22 10 0.37
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAAAAACAGAAAGAGA
Found at i:1441700 original size:21 final size:22
Alignment explanation
Indices: 1441655--1441704 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1441645 AGAGAGCAAC
* *
1441655 AAAAAAAAACAAGAAAGGGAGA
1 AAAAAAAAACAAGAAAGAGAAA
*
1441677 AAAAAAAAAC-AGAAAGATAAA
1 AAAAAAAAACAAGAAAGAGAAA
1441698 AAAAAAA
1 AAAAAAA
1441705 GAGGAGACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAAAAAACAAGAAAGAGAAA
Found at i:1442750 original size:20 final size:19
Alignment explanation
Indices: 1442717--1442766 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
1442707 TAAATATCCT
1442717 ATTTTTTAAATTATATATTA
1 ATTTTTT-AATTATATATTA
* *
1442737 ATTATTTTAATTATTTATTT
1 ATT-TTTTAATTATATATTA
1442757 ATTTTTTAAT
1 ATTTTTTAAT
1442767 ATCGAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 16 0.59
21 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTTTAATTATATATTA
Found at i:1442844 original size:22 final size:22
Alignment explanation
Indices: 1442813--1442861 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1442803 CTTTTTCTGA
*
1442813 TATTTCTAAATAAATAAAAATT
1 TATTTATAAATAAATAAAAATT
* *
1442835 TATTTATAAATATATATAAATT
1 TATTTATAAATAAATAAAAATT
*
1442857 AATTT
1 TATTT
1442862 TTTTTCATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTTATAAATAAATAAAAATT
Found at i:1443392 original size:28 final size:26
Alignment explanation
Indices: 1443351--1443430 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 26
1443341 TAATTCTTTC
*
1443351 TTTTCA-AATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATA--TATTA
*
1443378 TTTTCATAATATTTATATGTATATTA
1 TTTTCATAATATTTATATATATATTA
*
1443404 TTTT-TTAATATTT-T-TAT-T-TTA
1 TTTTCATAATATTTATATATATATTA
1443425 TTTTCA
1 TTTTCA
1443431 AGTATTTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 7 0.15
22 1 0.02
23 2 0.04
24 1 0.02
25 8 0.17
26 9 0.20
27 6 0.13
28 12 0.26
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (26 bp):
TTTTCATAATATTTATATATATATTA
Found at i:1443402 original size:26 final size:27
Alignment explanation
Indices: 1443351--1443416 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
1443341 TAATTCTTTC
*
1443351 TTTTCA-AATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATAC-TATTA
*
1443378 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCATAATATTTATATATACTATTA
*
1443404 TTTT-TTAATATTT
1 TTTTCATAATATTT
1443417 TTATTTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.23
26 9 0.26
27 6 0.17
28 12 0.34
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTCATAATATTTATATATACTATTA
Found at i:1445024 original size:12 final size:12
Alignment explanation
Indices: 1445007--1445065 Score: 79
Period size: 12 Copynumber: 5.2 Consensus size: 12
1444997 ACATTCACAT
1445007 ATTTACATTTGC
1 ATTTACATTTGC
1445019 ATTTACATTTGC
1 ATTTACATTTGC
*
1445031 ATTTGCATTT--
1 ATTTACATTTGC
*
1445041 -TTTACGTTTGC
1 ATTTACATTTGC
1445052 ATTTACATTTGC
1 ATTTACATTTGC
1445064 AT
1 AT
1445066 ATTTCCATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 7 0.17
12 33 0.82
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.53
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:1445050 original size:21 final size:21
Alignment explanation
Indices: 1445020--1445061 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1445010 TACATTTGCA
*
1445020 TTTACATTTGCATTTGCATTT
1 TTTACATTTGCATTTACATTT
*
1445041 TTTACGTTTGCATTTACATTT
1 TTTACATTTGCATTTACATTT
1445062 GCATATTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (21 bp):
TTTACATTTGCATTTACATTT
Found at i:1449459 original size:30 final size:30
Alignment explanation
Indices: 1449425--1449482 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
1449415 CTACAATTGA
1449425 TGAATCCGGACCACATCTCTTCATGGCTAT
1 TGAATCCGGACCACATCTCTTCATGGCTAT
1449455 TGAATCCGGACCACATCTCTTCATGGCT
1 TGAATCCGGACCACATCTCTTCATGGCT
1449483 TCATAATCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.29
Consensus pattern (30 bp):
TGAATCCGGACCACATCTCTTCATGGCTAT
Found at i:1451527 original size:20 final size:19
Alignment explanation
Indices: 1451488--1451529 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1451478 TTTCTTTGAT
1451488 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1451507 ATTAAAATAATTAATATATA
1 ATTAAAA-AATAAATAAATA
1451527 ATT
1 ATT
1451530 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1451640 original size:120 final size:120
Alignment explanation
Indices: 1451396--1451633 Score: 288
Period size: 120 Copynumber: 2.0 Consensus size: 120
1451386 GAAAAAATAT
* * * *
1451396 TAATTTATATAT-ATTTAT-AAATAAAATATCTATTTATTTAGAAATATCAGAAAAGGACTTCTA
1 TAATTAATATATAATTTATAAAATAAAATATCTATTTATTTAAAAATATCAGAAAAGGACATCCA
* * *
1451459 GGTGCCTTAAGACAACTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAA
66 GGTACCTTAAGACAACTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAA
** *
1451514 TAATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCC
1 TAATTAATATATAATTTATAAAATAAAATATCTATTTATTTAAAAATATCAGAAAA-GGACATCC
* ** ** *
1451579 AGTTATTTTAAGACTGC-CCTTTC-TTAATATTGAAAAATAAATAAAT-ATTAAAA
65 AGGTACCTTAAGACAACTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAA
1451632 TA
1 TA
1451634 GGATTAAAAT
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 20 0.20
119 27 0.27
120 37 0.37
121 17 0.17
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (120 bp):
TAATTAATATATAATTTATAAAATAAAATATCTATTTATTTAAAAATATCAGAAAAGGACATCCA
GGTACCTTAAGACAACTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAA
Found at i:1451730 original size:3 final size:3
Alignment explanation
Indices: 1451722--1451751 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1451712 TTTATGGCTA
*
1451722 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1451752 TAAAAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1453112 original size:3 final size:3
Alignment explanation
Indices: 1453106--1453158 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
1453096 ATTATTTATT
* *
1453106 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1453150 TAA TAA TAA
1 TAA TAA TAA
1453159 ATAAAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1453128 original size:19 final size:18
Alignment explanation
Indices: 1453106--1453161 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
1453096 ATTATTTATT
1453106 TAATAATAATAATATAATA
1 TAATAATAATAATA-AATA
* *
1453125 TAATAATAATATTAAAACA
1 TAATAATAATAAT-AAATA
*
1453144 AAATAATAATAATAAATA
1 TAATAATAATAATAAATA
1453162 AAACAAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 26 0.84
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATAAATA
Found at i:1453131 original size:22 final size:21
Alignment explanation
Indices: 1453084--1453162 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
1453074 ATTGGGCCTG
* * *
1453084 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
1453106 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
*
1453128 TAATAATATTAAA-ACA-A-AA
1 TAATAATAATAAATA-ATATAA
1453147 TAATAATAATAAATAA
1 TAATAATAATAAATAA
1453163 AACAAATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.31
20 3 0.06
21 2 0.04
22 23 0.47
23 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:1453169 original size:22 final size:22
Alignment explanation
Indices: 1453106--1453169 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
1453096 ATTATTTATT
* *
1453106 TAATAAT-AATAATATAATATAA
1 TAATAATAAATAAAACAA-ATAA
*
1453128 TAATAATA-TTAAAACAAAATAA
1 TAATAATAAATAAAAC-AAATAA
1453150 TAATAATAAATAAAACAAAT
1 TAATAATAAATAAAACAAAT
1453170 GAAAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAATAAATAAAACAAATAA
Found at i:1453663 original size:3 final size:3
Alignment explanation
Indices: 1453657--1453709 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
1453647 ATTATTTATT
* *
1453657 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1453701 TAA TAA TAA
1 TAA TAA TAA
1453710 ATAAAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1453679 original size:19 final size:19
Alignment explanation
Indices: 1453633--1453712 Score: 72
Period size: 19 Copynumber: 4.1 Consensus size: 19
1453623 TAATTGGGCC
*
1453633 TATAATAATAATAAATTATTTA
1 TATAATAATAAT-AA-TA-TAA
*
1453655 TTTAATAATAATAATATAA
1 TATAATAATAATAATATAA
* *
1453674 TATAATAATAATATTAAAA
1 TATAATAATAATAATATAA
* *
1453693 CAAAATAATAATAATA-AA
1 TATAATAATAATAATATAA
1453711 TA
1 TA
1453713 AAACAAATGA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
18 3 0.06
19 31 0.63
20 2 0.04
21 2 0.04
22 11 0.22
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (19 bp):
TATAATAATAATAATATAA
Found at i:1453682 original size:22 final size:21
Alignment explanation
Indices: 1453634--1453713 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 21
1453624 AATTGGGCCT
* *
1453634 ATAATAATAATAAATTATTTA
1 ATAATAATAATAAATAATATA
*
1453655 TTTAATAATAATAATATAATATA
1 -ATAATAATAATAA-ATAATATA
*
1453678 ATAATAATATTAAA-ACA-A-A
1 ATAATAATAATAAATA-ATATA
1453697 ATAATAATAATAAATAA
1 ATAATAATAATAAATAA
1453714 AACAAATGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 15 0.31
20 3 0.06
21 2 0.04
22 23 0.47
23 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAATAATAATAAATAATATA
Found at i:1453720 original size:22 final size:22
Alignment explanation
Indices: 1453657--1453720 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
1453647 ATTATTTATT
* *
1453657 TAATAAT-AATAATATAATATAA
1 TAATAATAAATAAAACAA-ATAA
*
1453679 TAATAATA-TTAAAACAAAATAA
1 TAATAATAAATAAAAC-AAATAA
1453701 TAATAATAAATAAAACAAAT
1 TAATAATAAATAAAACAAAT
1453721 GAAAAAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAATAAATAAAACAAATAA
Found at i:1454162 original size:553 final size:550
Alignment explanation
Indices: 1453067--1454167 Score: 1988
Period size: 553 Copynumber: 2.0 Consensus size: 550
1453057 GGCTGAGTTG
* *
1453067 ATTTGTAATTGGGCCTGTAATAATAATAAATTATTTATTTAATAATAATAATATAATATAATAAT
1 ATTTATAATTGGGCCTATAATAATAATAAATTATTTATTTAATAATAATAATATAATATAATAAT
1453132 AATATTAAAACAAAATAATAATAATAAATAAAACAAATGAAAAAAAAAACTAGTGTCTTCAGCAG
66 AATATTAAAACAAAATAATAATAATAAATAAAACAAATG-AAAAAAAAACTAGTGTCTTCAGCAG
* * *
1453197 TCGCTCTTTGTTCATTCTTGTGTTAACGAGAATAGGGCAAAGACGAAAAGACAATAAATGTTTTT
130 CCCCTCTTTGTTCATTCTTGTGTTAACGAGAATAGGGCAAAGACGAAAAGACAATAAATATTTTT
1453262 TTTTTCATTTGACGTCACTTGATTATGATGGAAATGTTGAACAAGTTCTTCTTCTTTGGGATTAG
195 TTTTTCATTTGACGTCACTTGATTATGATGGAAATGTTGAACAAGTTCTTCTTCTTTGGGATTAG
* *
1453327 TTCTTCTCAATATGAAGTTTTCCACTGGGGATGACAATTCATCTCCTTCTGTGAAGTAATCTAGC
260 TTCTTCTCAATATGAACTTTTCCACTGGCGATGACAATTCATCTCCTTCTGTGAAGTAATCTAGC
*
1453392 AAAAACAACTGAACAAATTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTCGAAATAC
325 AAAAAAAACTGAACAAATTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTCGAAATAC
*
1453457 TGATGATGATATATCTCCTTCTGTGATGGAGTCATGAAAAAGGTTGAACAAATTCTTCTCATTAT
390 TGATGATGATATATATCCTTCTGTGATGGAGTCATGAAAAAGGTTGAACAAATTCTTCTCATTAT
*
1453522 GAATTTCTTCTTCCTCTTCATATAAGTTCTTCTCATTCTGAACTTTCTCTGGAAATGTTGATCCA
455 GAATTTCTTCTTCCTCTTCATATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCA
1453587 TCAAGTGATGAATTTGAACAAAAGGTTATTT
520 TCAAGTGATGAATTTGAACAAAAGGTTATTT
1453618 ATTTATAATTGGGCCTATAATAATAATAAATTATTTATTTAATAATAATAATATAATATAATAAT
1 ATTTATAATTGGGCCTATAATAATAATAAATTATTTATTTAATAATAATAATATAATATAATAAT
*
1453683 AATATTAAAACAAAATAATAATAATAAATAAAACAAATG-AAAAAAAACTAGTGTCTTCAGCTGC
66 AATATTAAAACAAAATAATAATAATAAATAAAACAAATGAAAAAAAAACTAGTGTCTTCAGCAGC
*
1453747 CCCTCTTTGTTCATTCTTGTGTTAACGAGAATAGGGCAAAGACGAAAAGACAATAAGTATTTTTT
131 CCCTCTTTGTTCATTCTTGTGTTAACGAGAATAGGGCAAAGACGAAAAGACAATAAATATTTTTT
*
1453812 TTTTCATTTGACTTCACTTGATTATGATGGAAATGTTGAACAAGTTCTTCTTCTTTGGGATTAGT
196 TTTTCATTTGACGTCACTTGATTATGATGGAAATGTTGAACAAGTTCTTCTTCTTTGGGATTAGT
* *
1453877 TCTTCTCATTATGAACTTTTCCACTGGCGATGACAATTCATTTCCTTCTGTGAAGTAATCTAGCA
261 TCTTCTCAATATGAACTTTTCCACTGGCGATGACAATTCATCTCCTTCTGTGAAGTAATCTAGC-
* *
1453942 AAAAAAAAAAATTGAACAAATTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAA
325 ---AAAAAAAACTGAACAAATTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTCGAAA
*
1454007 TACTGATGATGATATATATCCTTCTGTGATGGAGTCATGCAAAAGGTTGAACAAATTCTTCTCAT
387 TACTGATGATGATATATATCCTTCTGTGATGGAGTCATGAAAAAGGTTGAACAAATTCTTCTCAT
1454072 TATGAATTTCTTCTTCCTCTTCATATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGAT
452 TATGAATTTCTTCTTCCTCTTCATATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGAT
1454137 CCATCAAGTGATGAATTTGAACAAAAGGTTA
517 CCATCAAGTGATGAATTTGAACAAAAGGTTA
1454168 AACAAGTTCT
Statistics
Matches: 528, Mismatches: 18, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
549 209 0.40
551 102 0.19
553 217 0.41
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (550 bp):
ATTTATAATTGGGCCTATAATAATAATAAATTATTTATTTAATAATAATAATATAATATAATAAT
AATATTAAAACAAAATAATAATAATAAATAAAACAAATGAAAAAAAAACTAGTGTCTTCAGCAGC
CCCTCTTTGTTCATTCTTGTGTTAACGAGAATAGGGCAAAGACGAAAAGACAATAAATATTTTTT
TTTTCATTTGACGTCACTTGATTATGATGGAAATGTTGAACAAGTTCTTCTTCTTTGGGATTAGT
TCTTCTCAATATGAACTTTTCCACTGGCGATGACAATTCATCTCCTTCTGTGAAGTAATCTAGCA
AAAAAAACTGAACAAATTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTCGAAATACT
GATGATGATATATATCCTTCTGTGATGGAGTCATGAAAAAGGTTGAACAAATTCTTCTCATTATG
AATTTCTTCTTCCTCTTCATATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCAT
CAAGTGATGAATTTGAACAAAAGGTTATTT
Found at i:1454337 original size:225 final size:225
Alignment explanation
Indices: 1454045--1454487 Score: 710
Period size: 225 Copynumber: 2.0 Consensus size: 225
1454035 ATGGAGTCAT
* * *
1454045 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCATATAAGTTCTTCTCA
1 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
* *
1454110 TTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAG-
66 TTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAGC
*
1454174 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TCTG
131 TT-TTCTCATTATGAACTTCCTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTCTCTG
*
1454238 GAAATGCTGATCCATCGAATGATGAATTCAA
195 GAAAAGCTGATCCATCGAATGATGAATTCAA
* *
1454269 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
* * * *
1454334 ATTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACACG
65 ATTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAG
* *
1454399 CTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTG
130 CTTTTCTCATTATGAACTTCCTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTCTCTG
*
1454464 GAAAAGCTGATCCATCGAGTGATG
195 GAAAAGCTGATCCATCGAATGATG
1454488 GATTTGAATC
Statistics
Matches: 200, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
224 41 0.20
225 131 0.65
226 28 0.14
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (225 bp):
GCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
TTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAGC
TTTTCTCATTATGAACTTCCTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTCTCTGG
AAAAGCTGATCCATCGAATGATGAATTCAA
Found at i:1454417 original size:113 final size:113
Alignment explanation
Indices: 1454045--1454494 Score: 665
Period size: 113 Copynumber: 4.0 Consensus size: 113
1454035 ATGGAGTCAT
* * * *
1454045 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCATATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1454109 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
* * *
1454157 ACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * **
1454222 ATTATGAACTCT-TCTGGAAATGCTGATCCATCGAA-TGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATC-AAGTGATGAATTTGA
*
1454269 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1454334 ATTATGAACTTTCTCTAGAAAAGTTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
* *
1454382 GCAAAAGGTTGAACACGCTT-TTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCT
1 GCAAAAGGTTGAACAAG-TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
1454446 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGA
65 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
1454495 ATCTTTGCTA
Statistics
Matches: 305, Mismatches: 28, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
112 142 0.47
113 161 0.53
114 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTTGA
Found at i:1456043 original size:16 final size:16
Alignment explanation
Indices: 1456024--1456057 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1456014 CTTTTTTTTC
1456024 TTTTTT-TTCATTTCAT
1 TTTTTTCTTC-TTTCAT
1456040 TTTTTTCTTCTTTCAT
1 TTTTTTCTTCTTTCAT
1456056 TT
1 TT
1456058 CATTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTCTTCTTTCAT
Found at i:1456065 original size:20 final size:21
Alignment explanation
Indices: 1456011--1456069 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1456001 GACCCTCCTT
* *
1456011 TTTCTTTTTTTTCTTTTTTTTCA
1 TTTCATTTTTTTC--TTCTTTCA
1456034 TTTCATTTTTTTCTTCTTTCA
1 TTTCATTTTTTTCTTCTTTCA
1456055 TTTCA-TTTTTTCTTC
1 TTTCATTTTTTTCTTC
1456070 AAGCATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 10 0.29
21 12 0.35
23 12 0.35
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTCATTTTTTTCTTCTTTCA
Found at i:1463396 original size:11 final size:11
Alignment explanation
Indices: 1463382--1463413 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1463372 ATGAATAATG
1463382 AATGCATGCAA
1 AATGCATGCAA
1463393 AATGCATGCAA
1 AATGCATGCAA
1463404 AATGCATGCA
1 AATGCATGCA
1463414 TGCAAAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (11 bp):
AATGCATGCAA
Found at i:1466769 original size:28 final size:27
Alignment explanation
Indices: 1466718--1466771 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
1466708 ATATTAATAA
* *
1466718 AATAATATATATAAATACTATGAAAAT
1 AATAATATATATAAAAAATATGAAAAT
*
1466745 AATAAGTATATATAAAAAATTTGAAAA
1 AATAA-TATATATAAAAAATATGAAAA
1466772 GAAAGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (27 bp):
AATAATATATATAAAAAATATGAAAAT
Found at i:1467399 original size:20 final size:19
Alignment explanation
Indices: 1467360--1467401 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1467350 TTTCTTCGAT
1467360 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1467379 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
1467399 ATT
1 ATT
1467402 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1467512 original size:120 final size:120
Alignment explanation
Indices: 1467269--1467505 Score: 295
Period size: 120 Copynumber: 2.0 Consensus size: 120
1467259 AAAAAATATT
* * * * *
1467269 AATTTATATAT-ATTTAT-AAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAG
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAA
* * *
1467332 GTGCCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAAC
66 GTACCTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAAC
**
1467387 AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCA
* ** * *
1467452 ATTATTTTAAGACTGC-CCTTTCTT-AATATTGAAAAATAAATAAAT-ATTAAAAC
65 AGTACCTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAAC
1467505 A
1 A
1467506 GGATTAAAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 19 0.19
119 25 0.25
120 40 0.40
121 17 0.17
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (120 bp):
AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAA
GTACCTTAAGACAGCTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:1467602 original size:3 final size:3
Alignment explanation
Indices: 1467594--1467623 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1467584 TTTATGGCTA
*
1467594 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1467624 TAAAAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1468981 original size:3 final size:3
Alignment explanation
Indices: 1468975--1469036 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
1468965 ATTATTTATT
* *
1468975 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1469019 TAA TAA TAAA TAA -AA TAA
1 TAA TAA T-AA TAA TAA TAA
1469037 ATAAAAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
2 10 0.20
3 38 0.75
4 3 0.06
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1469000 original size:22 final size:22
Alignment explanation
Indices: 1468953--1469040 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 22
1468943 ATTGGGCTTG
* * *
1468953 TAATAATAAT-AAATTATTTATT
1 TAATAATAATAAAATAATATA-A
*
1468975 TAATAATAATAATATAATATAA
1 TAATAATAATAAAATAATATAA
* * *
1468997 TAATAATATTAAAACAAAATAA
1 TAATAATAATAAAATAATATAA
1469019 TAATAATAAATAAAATAA-ATAA
1 TAATAAT-AATAAAATAATATAA
1469041 AAAAAAAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
22 39 0.72
23 15 0.28
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (22 bp):
TAATAATAATAAAATAATATAA
Found at i:1469040 original size:19 final size:18
Alignment explanation
Indices: 1468976--1469036 Score: 77
Period size: 19 Copynumber: 3.3 Consensus size: 18
1468966 TTATTTATTT
*
1468976 AATAATAATAATATAATAT
1 AATAATAATAATA-AATAA
* *
1468995 AATAATAATATTAAAACAA
1 AATAATAATAAT-AAATAA
1469014 AATAATAATAATAAATAA
1 AATAATAATAATAAATAA
1469032 AATAA
1 AATAA
1469037 ATAAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 10 0.28
19 25 0.69
20 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAATAATAATAAATAA
Found at i:1469784 original size:22 final size:22
Alignment explanation
Indices: 1469752--1469816 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
1469742 ACATCTACAC
*
1469752 TCTTTTCAAAGATGATAGATTA
1 TCTTTTTAAAGATGATAGATTA
1469774 TCTTTTTAAAGATGATAGATTA
1 TCTTTTTAAAGATGATAGATTA
*
1469796 T-TTTTTCAAAGATGAAAGATT
1 TCTTTTT-AAAGATGATAGATT
1469817 TATTGGATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.12
22 35 0.88
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (22 bp):
TCTTTTTAAAGATGATAGATTA
Found at i:1471395 original size:455 final size:454
Alignment explanation
Indices: 1470487--1471806 Score: 2399
Period size: 455 Copynumber: 2.9 Consensus size: 454
1470477 CTATTTCCCA
1470487 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1470552 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1470617 GATGTTTTCAAAGCCTTAGGGTCATATGTAAGTCCTAGAGTGCATGATGTTTCCAAAAAGCCTTT
131 GATGTTTTCAAAGCCTTAGGGTCATATGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCC-TT
*
1470682 CGGGAGCTTTTTGATG-TTTCAAAGCCTTAGGATCATCTGTAAGTCCTTCAGTGCATGATGTTTT
195 CGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTT
1470746 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTG
260 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTG
*
1470811 CATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
325 CATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAA
*
1470876 ATCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCGTTTTGATGTTTTCAAAGCTTAGGG
390 GT-CTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCGTTTTGATGTTTTCAAAGCTTAGGG
1470941 T
454 T
1470942 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471007 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1471072 GATGTTTTCAAAGCCTTAGGGTCATATATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTAGGGTCATATGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
1471137 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC
*
1471202 AAGAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGC
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGC
1471267 ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAG
326 ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAG
* *
1471332 TCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTTAGGGT
391 TCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCGTTTTGATGTTTTCAAAG-CTTAGGGT
1471397 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
1471462 AGCCTTAGGGTCATCTGTAAGTCCTACAGCGCATGATGTTTCCAAAAAGCCTTCGAGAGTTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * *
1471527 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTAGGGTCATATGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
* * *
1471592 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCCTCTGTAAGTCCTACAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC
* *
1471657 AAAAAGCCTTCGGGAGCTTTTTGTTGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGC
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGC
*
1471722 ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAGGTTTTCAAAGCCTTAGGGTCATCTGTAAG
326 ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAG
* *
1471787 CCCTTCAGTGCATGATGTTT
391 -TCTACAGTGCATGATGTTT
1471807 TTAAGACCTC
Statistics
Matches: 838, Mismatches: 24, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
454 71 0.08
455 750 0.89
456 17 0.02
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (454 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGGGTCATATGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC
AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGC
ATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAG
TCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCGTTTTGATGTTTTCAAAGCTTAGGGT
Found at i:1471840 original size:76 final size:76
Alignment explanation
Indices: 1470487--1471806 Score: 2385
Period size: 76 Copynumber: 17.4 Consensus size: 76
1470477 CTATTTCCCA
1470487 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1470552 AGCCTTAGGGT
66 AGCCTTAGGGT
1470563 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1470628 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1470639 CATATGTAAGTCCTAGAGTGCATGATGTTTCCAAAAAGCCTTTCGGGAGCTTTTTGATG-TTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCC-TTCGGGAGCTTTTTGATGTTTTCA
*
1470703 AAGCCTTAGGAT
65 AAGCCTTAGGGT
* *
1470715 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1470780 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1470791 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1470856 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1470867 CATCTGTAAATCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCGTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1470932 AG-CTTAGGGT
66 AGCCTTAGGGT
1470942 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471007 AGCCTTAGGGT
66 AGCCTTAGGGT
1471018 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471083 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1471094 CATATATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471159 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
1471170 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAGAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471235 AGCCTTAGGGT
66 AGCCTTAGGGT
1471246 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471311 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1471322 CATCTGTAAGT-CTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471386 AGCCTTAGGGT
66 AGCCTTAGGGT
1471397 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471462 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
1471473 CATCTGTAAGTCCTACAGCGCATGATGTTTCCAAAAAGCCTTCGAGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471538 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1471549 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471614 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1471625 CCTCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGTTGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471690 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1471701 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAGGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1471766 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1471777 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
1471807 TTAAGACCTC
Statistics
Matches: 1194, Mismatches: 46, Indels: 8
0.96 0.04 0.01
Matches are distributed among these distances:
75 165 0.14
76 1011 0.85
77 18 0.02
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1471974 original size:12 final size:11
Alignment explanation
Indices: 1471957--1472020 Score: 64
Period size: 12 Copynumber: 5.9 Consensus size: 11
1471947 TTTTTCATTT
1471957 ATTATTATTAAA
1 ATTATTATT-AA
1471969 ATTATTATT--
1 ATTATTATTAA
1471978 ATTATTA-TAA
1 ATTATTATTAA
*
1471988 A-TATTATTATT
1 ATTATTATTA-A
1471999 ATTATTATTAA
1 ATTATTATTAA
1472010 ATATATTATTA
1 AT-TATTATTA
1472021 CAAGCCCAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
8 1 0.02
9 12 0.27
10 3 0.07
11 3 0.07
12 25 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATTATTAA
Found at i:1471978 original size:18 final size:18
Alignment explanation
Indices: 1471955--1472003 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
1471945 AATTTTTCAT
1471955 TTATTATTATTA-AAATTA
1 TTATTATTATTATAAA-TA
1471973 TTATTATTATTATAAATA
1 TTATTATTATTATAAATA
1471991 TTATTATTATTAT
1 TTATTATTATTAT
1472004 TATTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 27 0.90
19 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTATTATTATAAATA
Found at i:1471981 original size:21 final size:21
Alignment explanation
Indices: 1471955--1472020 Score: 100
Period size: 21 Copynumber: 3.1 Consensus size: 21
1471945 AATTTTTCAT
1471955 TTATTATTATTAAAATTATTA
1 TTATTATTATTAAAATTATTA
1471976 TTATTATTA-TAAATATTATTA
1 TTATTATTATTAAA-ATTATTA
1471997 TTATTATTATT-AAATATATTA
1 TTATTATTATTAAAAT-TATTA
1472018 TTA
1 TTA
1472021 CAAGCCCAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.14
21 35 0.83
22 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATTATTATTAAAATTATTA
Found at i:1472020 original size:3 final size:3
Alignment explanation
Indices: 1471955--1472008 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
1471945 AATTTTTCAT
** * *
1471955 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1472003 TTA TTA
1 TTA TTA
1472009 AATATATTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1473035 original size:29 final size:28
Alignment explanation
Indices: 1473003--1473067 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
1472993 ATTTTTTACA
*
1473003 AATTTTATTTATT-TTAAATATATAGTGTT
1 AATTTTATTCATTGTTAAAT-TATA-TGTT
* *
1473032 AATTTTATTCATTGTTTAGTTATATGTT
1 AATTTTATTCATTGTTAAATTATATGTT
1473060 AATTTTAT
1 AATTTTAT
1473068 ATGTTTACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 12 0.38
29 16 0.50
30 4 0.12
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.60
Consensus pattern (28 bp):
AATTTTATTCATTGTTAAATTATATGTT
Found at i:1473325 original size:20 final size:20
Alignment explanation
Indices: 1473295--1473342 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1473285 GTATCCTATT
1473295 TTTTAAATTATATATTAATTG
1 TTTT-AATTATATATTAATTG
* * *
1473316 TTTTAATTATTTATTTATTT
1 TTTTAATTATATATTAATTG
1473336 TTTTAAT
1 TTTTAAT
1473343 ATCGAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTAATTATATATTAATTG
Found at i:1473416 original size:121 final size:116
Alignment explanation
Indices: 1473196--1473433 Score: 271
Period size: 121 Copynumber: 2.0 Consensus size: 116
1473186 ATTTTAATCC
* * * * *
1473196 TGTTTTAATATTTATTTATTTTTTCATATTAAGAAATGGCAGTCTTAAAACAACTGGATGTTCAT
1 TGTTTTAATATTTATTTATTTTTTAATATGAAGAAAAGGCAGTCTTAAAACAACTAGAAGTTCAT
* * * *
1473261 TTTCTGATATTTTTAAATAAATAAGTATCCTATTTTTTAAATTATATATTAAT
66 TTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAA-TATATATAAAT
* ** *
1473314 TGTTTTAATTATTTATTTATTTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAG-
1 TGTTTTAA-TATTTATTTA-TTTTTTAATAT-GAAGAAAAG-GCAGTCTTAAAACAACTAGAAGT
* **
1473378 TCCTTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAAT
62 TCATTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
1473433 T
1 T
1473434 AATTTTTTTC
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
118 8 0.08
119 21 0.21
120 17 0.17
121 38 0.38
122 16 0.16
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (116 bp):
TGTTTTAATATTTATTTATTTTTTAATATGAAGAAAAGGCAGTCTTAAAACAACTAGAAGTTCAT
TTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAAT
Found at i:1473447 original size:27 final size:29
Alignment explanation
Indices: 1473398--1473452 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
1473388 ATATTTCTAA
*
1473398 ATAAATAAATATTTTATTTATAAATATAT
1 ATAAATAAATATTTTATTCATAAATATAT
* *
1473427 ATAAATTAAT-TTTT-TTCATAATTATA
1 ATAAATAAATATTTTATTCATAAATATA
1473453 ATTTTGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.43
28 4 0.17
29 9 0.39
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAATAAATATTTTATTCATAAATATAT
Found at i:1476435 original size:17 final size:16
Alignment explanation
Indices: 1476413--1476457 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
1476403 TTATGAGATG
*
1476413 AAAATATTATTATTGTA
1 AAAATATAATTATT-TA
1476430 AAAATATAATTATTT-
1 AAAATATAATTATTTA
1476445 AAAATAATAATTA
1 AAAAT-ATAATTA
1476458 ATTTCGAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 5 0.19
16 8 0.31
17 13 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
AAAATATAATTATTTA
Found at i:1478259 original size:20 final size:21
Alignment explanation
Indices: 1478230--1478269 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1478220 CTCTGTATAG
*
1478230 TAGTATCGATACCAT-AGGCA
1 TAGTAACGATACCATCAGGCA
1478250 TAGTAACGATACCATCAGGC
1 TAGTAACGATACCATCAGGC
1478270 CCCAACAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (21 bp):
TAGTAACGATACCATCAGGCA
Found at i:1481719 original size:20 final size:21
Alignment explanation
Indices: 1481694--1481733 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1481684 CTCTGTATAG
1481694 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
1481714 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
1481734 CCCAACGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:1493479 original size:10 final size:10
Alignment explanation
Indices: 1493464--1493490 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1493454 AAACGACTTT
1493464 TTCATCCTTA
1 TTCATCCTTA
1493474 TTCATCCTTA
1 TTCATCCTTA
1493484 TTCATCC
1 TTCATCC
1493491 ATTGTCGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (10 bp):
TTCATCCTTA
Found at i:1494790 original size:23 final size:23
Alignment explanation
Indices: 1494751--1494800 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1494741 CATATTTTTA
*
1494751 CATTCTATGTTGTACTACATATG
1 CATTCTATGTTGCACTACATATG
* *
1494774 CATTCTATG-TGACACTATATGTG
1 CATTCTATGTTG-CACTACATATG
1494797 CATT
1 CATT
1494801 ATGGGGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (23 bp):
CATTCTATGTTGCACTACATATG
Found at i:1505035 original size:17 final size:17
Alignment explanation
Indices: 1505013--1505070 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
1505003 AGTGTATGAA
1505013 GGTGCACGGGGTTTTAC
1 GGTGCACGGGGTTTTAC
*
1505030 GGTGCAC-AGGTTTCTAC
1 GGTGCACGGGGTTT-TAC
*
1505047 GGTGCACGGGGTTCTAC
1 GGTGCACGGGGTTTTAC
*
1505064 CGTGCAC
1 GGTGCAC
1505071 CTAAAGAGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 5 0.14
17 26 0.74
18 4 0.11
ACGTcount: A:0.14, C:0.24, G:0.36, T:0.26
Consensus pattern (17 bp):
GGTGCACGGGGTTTTAC
Found at i:1510481 original size:23 final size:23
Alignment explanation
Indices: 1510455--1510498 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1510445 GAAGGTATAT
*
1510455 GAAAAATGTACCATAAAGGCAAA
1 GAAAAATCTACCATAAAGGCAAA
1510478 GAAAAATCTACCATAAAGGCA
1 GAAAAATCTACCATAAAGGCA
1510499 GAGTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.14
Consensus pattern (23 bp):
GAAAAATCTACCATAAAGGCAAA
Found at i:1515298 original size:32 final size:33
Alignment explanation
Indices: 1515221--1515298 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 33
1515211 AATATTATTA
1515221 TTAAAACTAT-TTTAGATATGATTATATAAATT
1 TTAAAACTATATTTAGATATGATTATATAAATT
1515253 TTAAAA-TAAATATTTAGATAAT-ATT-T-TAAATT
1 TTAAAACT--ATATTTAGAT-ATGATTATATAAATT
1515285 TTAAACACTATATT
1 TTAAA-ACTATATT
1515299 ATATAAAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
31 1 0.03
32 22 0.55
33 4 0.10
34 11 0.28
35 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (33 bp):
TTAAAACTATATTTAGATATGATTATATAAATT
Found at i:1517028 original size:17 final size:17
Alignment explanation
Indices: 1517002--1517035 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1516992 AATAAGTCCG
1517002 TATATAAACCCCTAAGA
1 TATATAAACCCCTAAGA
*
1517019 TATATGAACCCCTAAGA
1 TATATAAACCCCTAAGA
1517036 GGGGATCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.24
Consensus pattern (17 bp):
TATATAAACCCCTAAGA
Found at i:1518258 original size:16 final size:16
Alignment explanation
Indices: 1518239--1518269 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1518229 TTTTTTCCCA
*
1518239 TTACACTTTTAAGTAT
1 TTACACTTCTAAGTAT
1518255 TTACACTTCTAAGTA
1 TTACACTTCTAAGTA
1518270 ACTACATTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (16 bp):
TTACACTTCTAAGTAT
Found at i:1518548 original size:15 final size:17
Alignment explanation
Indices: 1518516--1518549 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1518506 CAAGGATTTT
1518516 TTTTCTCTCCTCTTATA
1 TTTTCTCTCCTCTTATA
1518533 TTTTCT-TCCT-TTATA
1 TTTTCTCTCCTCTTATA
1518548 TT
1 TT
1518550 AGTGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 4 0.24
17 6 0.35
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTCTCTCCTCTTATA
Found at i:1518985 original size:56 final size:56
Alignment explanation
Indices: 1518918--1519040 Score: 201
Period size: 56 Copynumber: 2.2 Consensus size: 56
1518908 TACACAAATT
*
1518918 TATTTTGCCTTTGGTTGGGTGCAGATAAGCGACCTTATCGTCACTTTTTGAATCTC
1 TATTTTGCCTTTGGTTGGATGCAGATAAGCGACCTTATCGTCACTTTTTGAATCTC
* * * *
1518974 TATTTTGCCTTTGGTTGGATGCTGATGAGCGACCTTATCGTCCCTTTTTGAATCTT
1 TATTTTGCCTTTGGTTGGATGCAGATAAGCGACCTTATCGTCACTTTTTGAATCTC
1519030 TATTTTGCCTT
1 TATTTTGCCTT
1519041 GCAATTATCA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (56 bp):
TATTTTGCCTTTGGTTGGATGCAGATAAGCGACCTTATCGTCACTTTTTGAATCTC
Found at i:1525696 original size:2 final size:2
Alignment explanation
Indices: 1525689--1525713 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1525679 TTGATAGGAA
1525689 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1525714 AGGGAAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1528935 original size:20 final size:20
Alignment explanation
Indices: 1528899--1528936 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1528889 ATCCTATTCC
**
1528899 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1528919 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1528937 GTAAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1540623 original size:29 final size:30
Alignment explanation
Indices: 1540597--1540655 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1540587 AAATCAATTT
*
1540597 GGCCACCGAACT-TTCAATTGATTCAATCA
1 GGCCACCCAACTATTCAATTGATTCAATCA
* *
1540626 GGCCACCCAACTATTTAATTGGTTCAATCA
1 GGCCACCCAACTATTCAATTGATTCAATCA
1540656 AACCACCGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.29
Consensus pattern (30 bp):
GGCCACCCAACTATTCAATTGATTCAATCA
Found at i:1540662 original size:30 final size:29
Alignment explanation
Indices: 1540599--1540662 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
1540589 ATCAATTTGG
* **
1540599 CCACCGAACTTTCAATTGATTCAATCAGG
1 CCACCCAACTTTCAATTGATTCAATCAAA
* *
1540628 CCACCCAACTATTTAATTGGTTCAATCAAA
1 CCACCCAACT-TTCAATTGATTCAATCAAA
1540658 CCACC
1 CCACC
1540663 GACCGTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.33, C:0.31, G:0.09, T:0.27
Consensus pattern (29 bp):
CCACCCAACTTTCAATTGATTCAATCAAA
Found at i:1544696 original size:200 final size:200
Alignment explanation
Indices: 1544363--1545105 Score: 988
Period size: 200 Copynumber: 3.7 Consensus size: 200
1544353 TCTTCTCGGT
** * * * **
1544363 TTAAAGACCTTGGTTTAAAAATTCAACCGAAAATTAGTTCCTCGATAT--TACCATATGGTTGAT
1 TTAAAGACCTCAGTTT-AAACTTCAACCGGAAAGTAGTTCCTC-AT-TGCTACCATGCGGTTGAT
* * * * **
1544426 ATGCCGTT-GAGCTAAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCACATTTT
63 ATGCC-TTCGAGCTGAATGGAATCGAACTCAAAAG-TTTTATTGACAGATAGCCCTTCACACCTT
1544490 GAGCTATGCTGTAAATTCGGCTGGGAGATAGTTCATTGTTGCTAAATCGTAGCCAACCTAGGTCT
126 GAGCTATGCTGTAAATTCGGCTGGGAGATAGTTCATTGTTGCTAAATCGTAGCCAACCTAGGTCT
1544555 TCTTCTTGAC
191 TCTTCTTGAC
* * * *
1544565 TTAAAGACCTCAGTTTAAACTTTAACTGGAAAGTAGTTCCTCATTGCTACTATACGGTTGATATG
1 TTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTCCTCATTGCTACCATGCGGTTGATATG
* ** * * * * * *
1544630 CCTTTGAGCTGAATATAATTGAACTCAAAAATTTTGTTGACATATATCCCTTCACGCCTTGAGCT
66 CCTTCGAGCTGAATGGAATCGAACTCAAAAGTTTTATTGACAGATAGCCCTTCACACCTTGAGCT
* *
1544695 ATGTTGTAAATTCGGCTGGGAGATTGTTCATTGTTGCTAAATCGTAGCCAACCTAGGTCTTCTTC
131 ATGCTGTAAATTCGGCTGGGAGATAGTTCATTGTTGCTAAATCGTAGCCAACCTAGGTCTTCTTC
1544760 TTGAC
196 TTGAC
* *
1544765 TTAAAGGCCTCAGTTTAAACTTCAACCGGAAAGTAGTTCCTCATTGCTACCATGCAGTTGATATG
1 TTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTCCTCATTGCTACCATGCGGTTGATATG
* * * * ** * *
1544830 CCTTCGAGCTTAATGGAATCGAACTCGAAAGTTTTATTGACAAATAACCCTTTTCGCCGTGAGCT
66 CCTTCGAGCTGAATGGAATCGAACTCAAAAGTTTTATTGACAGATAGCCCTTCACACCTTGAGCT
* * * * *
1544895 ATGCTGTAAATTTGGCTGGGAGTTAGTTTATTGTTGCTAAATCGCAGCCAACCTAGGTCTTCTTT
131 ATGCTGTAAATTCGGCTGGGAGATAGTTCATTGTTGCTAAATCGTAGCCAACCTAGGTCTTCTTC
1544960 TTGAC
196 TTGAC
* * *
1544965 TTAAAGACATCAGTTTAAACTTCAACCGGAAAGTAGTTTCTCGTTGCTACCATGCGGTTGATATG
1 TTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTCCTCATTGCTACCATGCGGTTGATATG
* *
1545030 CCTTCGAGCTGAATGGAATCGAACTCAAAAGTTTTATTGACAGATAGCCCTTCTCACTTTGAGCT
66 CCTTCGAGCTGAATGGAATCGAACTCAAAAGTTTTATTGACAGATAGCCCTTCACACCTTGAGCT
1545095 ATGCTGTAAAT
131 ATGCTGTAAAT
1545106 GGTTCTTCTA
Statistics
Matches: 476, Mismatches: 62, Indels: 8
0.87 0.11 0.01
Matches are distributed among these distances:
199 1 0.00
200 403 0.85
201 58 0.12
202 14 0.03
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (200 bp):
TTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTCCTCATTGCTACCATGCGGTTGATATG
CCTTCGAGCTGAATGGAATCGAACTCAAAAGTTTTATTGACAGATAGCCCTTCACACCTTGAGCT
ATGCTGTAAATTCGGCTGGGAGATAGTTCATTGTTGCTAAATCGTAGCCAACCTAGGTCTTCTTC
TTGAC
Found at i:1545306 original size:86 final size:86
Alignment explanation
Indices: 1545165--1545536 Score: 555
Period size: 86 Copynumber: 4.3 Consensus size: 86
1545155 ATTCTTTAGT
* * * * *
1545165 TGACTCCCTTTCACGGGAGAGCCAAGTGGTATATTCTTCAGGTGGTTTCCCTTCGCGGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
1545230 CCAGGTGAGATGATCTTTGGA
66 CCAGGTGAGATGATCTTTGGA
*
1545251 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCATTCGCGGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
* *
1545316 CCAGGAGAGATGATCTTTGAA
66 CCAGGTGAGATGATCTTTGGA
* * **
1545337 TGACTCCTCTTTACGGGAAAGTCATGTGGTATATTCTTCAGACGGTTCCCCTTCGCGGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
1545402 CCAGGTGAGATGATCTTTGGA
66 CCAGGTGAGATGATCTTTGGA
* * * *
1545423 TGGCTCCCTTTCATGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGAGGGTCTGAA
1 TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
* *
1545488 CCATGTGAGATTATCTTTGGA
66 CCAGGTGAGATGATCTTTGGA
* * *
1545509 GGACTCCTCTTCAAGGGAAAGTCATGTG
1 TGACTCCCCTTCACGGGAAAGTCATGTG
1545537 AGATGTTCTT
Statistics
Matches: 256, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 256 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (86 bp):
TGACTCCCCTTCACGGGAAAGTCATGTGGTATATTCTTCAGGTGGTTCCCCTTCGCGGGTCTGAA
CCAGGTGAGATGATCTTTGGA
Found at i:1548323 original size:15 final size:17
Alignment explanation
Indices: 1548303--1548335 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1548293 AACTAAAAGT
1548303 TCTA-CCCACATG-TTA
1 TCTACCCCACATGCTTA
1548318 TCTACCCCACATGCTTA
1 TCTACCCCACATGCTTA
1548335 T
1 T
1548336 TATTCCTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.24, C:0.36, G:0.06, T:0.33
Consensus pattern (17 bp):
TCTACCCCACATGCTTA
Found at i:1549524 original size:16 final size:16
Alignment explanation
Indices: 1549462--1549523 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
1549452 GTTAAAAGAG
*
1549462 AAAATAAAAATAAAAC
1 AAAATAAAGATAAAAC
* **
1549478 AAAATAAAGA-AGTAGG
1 AAAATAAAGATA-AAAC
1549494 AAAATAAAGATAAAAC
1 AAAATAAAGATAAAAC
1549510 AAAATAAA-ATAAAA
1 AAAATAAAGATAAAA
1549524 AAAGAAGTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 7 0.19
16 29 0.78
17 1 0.03
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (16 bp):
AAAATAAAGATAAAAC
Found at i:1549578 original size:11 final size:10
Alignment explanation
Indices: 1549564--1549617 Score: 62
Period size: 8 Copynumber: 5.7 Consensus size: 10
1549554 AGGAAAGAAA
*
1549564 AAAATAAAGGT
1 AAAATAAA-AT
1549575 AAAATAAAAT
1 AAAATAAAAT
1549585 AAAATAAAAT
1 AAAATAAAAT
1549595 --AATAAAAT
1 AAAATAAAAT
1549603 AAAAT--AAT
1 AAAATAAAAT
1549611 AAAATAA
1 AAAATAA
1549618 TAAATAATAG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
8 16 0.42
10 14 0.37
11 8 0.21
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:1549584 original size:5 final size:5
Alignment explanation
Indices: 1549564--1549617 Score: 62
Period size: 5 Copynumber: 11.4 Consensus size: 5
1549554 AGGAAAGAAA
*
1549564 AAAAT AAAGGT AAAAT AAAAT AAAAT AAAAT --AAT AAAAT AAAAT --AAT
1 AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1549611 AAAAT AA
1 AAAAT AA
1549618 TAAATAATAG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
3 6 0.14
5 32 0.76
6 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1549600 original size:13 final size:13
Alignment explanation
Indices: 1549582--1549617 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
1549572 GGTAAAATAA
1549582 AATAAAATAAAAT
1 AATAAAATAAAAT
1549595 AATAAAATAAAAT
1 AATAAAATAAAAT
1549608 AATAAAATAA
1 AATAAAATAA
1549618 TAAATAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:1549643 original size:21 final size:19
Alignment explanation
Indices: 1549574--1549643 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 19
1549564 AAAATAAAGG
1549574 TAAAAT-AAAATAAAATAA
1 TAAAATAAAAATAAAATAA
1549592 -AATAAT-AAAATAAAATAA
1 TAA-AATAAAAATAAAATAA
*
1549610 TAAAATAATAAATAATAGTAA
1 TAAAATAA-AAATAA-AATAA
1549631 TAAAGATAAAAAT
1 TAAA-ATAAAAAT
1549644 GGAATTTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
17 2 0.04
18 18 0.40
19 3 0.07
20 6 0.13
21 12 0.27
22 4 0.09
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
TAAAATAAAAATAAAATAA
Found at i:1552091 original size:173 final size:173
Alignment explanation
Indices: 1551802--1552143 Score: 639
Period size: 173 Copynumber: 2.0 Consensus size: 173
1551792 ATTTCTTGTT
1551802 ATCATATTATAACTTATCTAGGTGACCAAGACATGTATTTAAGCATAAATCATACTTTGGCCAAC
1 ATCATATTATAACTTATCTAGGTGACCAAGACATGTATTTAAGCATAAATCATACTTTGGCCAAC
1551867 TTAGGCATACTTAATAATGGTACATAACATGTAATCTAACATCAAAACACATCATTTCATTATTC
66 TTAGGCATACTTAATAATGGTACATAACATGTAATCTAACATCAAAACACATCATTTCATTATTC
*
1551932 ATTATAGGATCAAAGCATAATATAAGTCATTATAGGTCATGTA
131 ATTATAGAATCAAAGCATAATATAAGTCATTATAGGTCATGTA
1551975 ATCATATTATAACTTATCTAGGTGACCAAGACATGTATTTAAGCATAAATCATACTTTGGCCAAC
1 ATCATATTATAACTTATCTAGGTGACCAAGACATGTATTTAAGCATAAATCATACTTTGGCCAAC
* *
1552040 TTTGGCATACTTAATAATGTTACATAACATGTAATCTAACATCAAAACACATCATTTCATTATTC
66 TTAGGCATACTTAATAATGGTACATAACATGTAATCTAACATCAAAACACATCATTTCATTATTC
* *
1552105 ATTATAGAATCAATGCATAATATAAGTCATTATATGTCA
131 ATTATAGAATCAAAGCATAATATAAGTCATTATAGGTCA
1552144 CTTATGCACT
Statistics
Matches: 164, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
173 164 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (173 bp):
ATCATATTATAACTTATCTAGGTGACCAAGACATGTATTTAAGCATAAATCATACTTTGGCCAAC
TTAGGCATACTTAATAATGGTACATAACATGTAATCTAACATCAAAACACATCATTTCATTATTC
ATTATAGAATCAAAGCATAATATAAGTCATTATAGGTCATGTA
Found at i:1555176 original size:16 final size:16
Alignment explanation
Indices: 1555155--1555191 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1555145 AAAGATTTTA
1555155 TGAGTTCACGATAACG
1 TGAGTTCACGATAACG
*
1555171 TGAGTTCACGATAAGG
1 TGAGTTCACGATAACG
1555187 TGAGT
1 TGAGT
1555192 GGTTACCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (16 bp):
TGAGTTCACGATAACG
Found at i:1555532 original size:62 final size:62
Alignment explanation
Indices: 1555429--1555597 Score: 257
Period size: 62 Copynumber: 2.7 Consensus size: 62
1555419 TGATCATGAG
* * * *
1555429 TTATGGTGCATTGGAACTAAGTGATCTTTTGCAAGCATGTATATTGAAGGATGTTAATTATAAT
1 TTATGTTGCATT-GAAGTGAGTGAT-TATTGCAAGCATGTATATTGAAGGATGTTAATTATAAT
* *
1555493 TTATGTTGCATTGAAGTGAGTGATTATTGCAAGCATGTATTTTGAAGGATGTTATTTATAAT
1 TTATGTTGCATTGAAGTGAGTGATTATTGCAAGCATGTATATTGAAGGATGTTAATTATAAT
*
1555555 TTATGTTGCATTGATGTGAGTGATTATTGCAAGCATGTATATT
1 TTATGTTGCATTGAAGTGAGTGATTATTGCAAGCATGTATATT
1555598 TGAGTATGAA
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
62 76 0.78
63 10 0.10
64 11 0.11
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (62 bp):
TTATGTTGCATTGAAGTGAGTGATTATTGCAAGCATGTATATTGAAGGATGTTAATTATAAT
Found at i:1563878 original size:20 final size:20
Alignment explanation
Indices: 1563853--1563937 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 20
1563843 TTAATTTCAT
*
1563853 TTATGGTATCATTTCATGCC
1 TTATGGCATCATTTCATGCC
*
1563873 TTATGGCATCCTTTCATGCATTTC
1 TTATGGCATCATTTCATGC----C
*
1563897 ATTTATGGCATCCTTTCATGCC
1 --TTATGGCATCATTTCATGCC
1563919 TTAAT-GCATCATTTCATGC
1 TT-ATGGCATCATTTCATGC
1563938 ATTTTATTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
20 32 0.58
21 2 0.04
22 1 0.02
24 1 0.02
26 19 0.35
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.44
Consensus pattern (20 bp):
TTATGGCATCATTTCATGCC
Done.