Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 20 of 378
Found at i:5425387 original size:15 final size:15
Alignment explanation
Indices: 5425369--5425402 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5425359 TTTCTTGAAA
5425369 TAAAAGTAAGAAAAT
1 TAAAAGTAAGAAAAT
**
5425384 TAAATTTAAGAAAAT
1 TAAAAGTAAGAAAAT
5425399 TAAA
1 TAAA
5425403 TTTTATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (15 bp):
TAAAAGTAAGAAAAT
Found at i:5425398 original size:29 final size:29
Alignment explanation
Indices: 5425337--5425396 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
5425327 TTTGCATTTT
**
5425337 AAATAAAAATAAAAAAATTAAATTTCTTG
1 AAATAAAAATAAAAAAATTAAATTTCAAG
* *
5425366 AAATAAAAGTAAGAAAATTAAATTT-AAG
1 AAATAAAAATAAAAAAATTAAATTTCAAG
5425394 AAA
1 AAA
5425397 ATTAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.27
Consensus pattern (29 bp):
AAATAAAAATAAAAAAATTAAATTTCAAG
Found at i:5425403 original size:15 final size:15
Alignment explanation
Indices: 5425375--5425405 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5425365 GAAATAAAAG
5425375 TAAGAAAATTAAATT
1 TAAGAAAATTAAATT
5425390 TAAGAAAATTAAATT
1 TAAGAAAATTAAATT
5425405 T
1 T
5425406 TATATATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
TAAGAAAATTAAATT
Found at i:5435248 original size:4 final size:4
Alignment explanation
Indices: 5435239--5435265 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5435229 CCCAAACACA
5435239 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
5435266 AACCTTGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5435472 original size:22 final size:22
Alignment explanation
Indices: 5435444--5435520 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
5435434 TTGTTCTTTG
5435444 TTTTGGAAGAGGTTTTTTTATT
1 TTTTGGAAGAGGTTTTTTTATT
*
5435466 TTTTGG-AG-GTGTTTTTTTGTTT
1 TTTTGGAAGAG-GTTTTTTT-ATT
*
5435488 TTTTGGAAAGAAGGTTGTTTTTGTT
1 TTTTGG-AAG-AGGTT-TTTTTATT
*
5435513 TCTTGGAA
1 TTTTGGAA
5435521 AGGCTAGTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
20 1 0.02
21 10 0.22
22 14 0.31
24 4 0.09
25 10 0.22
26 6 0.13
ACGTcount: A:0.16, C:0.01, G:0.26, T:0.57
Consensus pattern (22 bp):
TTTTGGAAGAGGTTTTTTTATT
Found at i:5435837 original size:3 final size:3
Alignment explanation
Indices: 5435823--5435908 Score: 65
Period size: 3 Copynumber: 28.3 Consensus size: 3
5435813 GAGCTTTGTT
* *
5435823 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
5435867 TT- TCTCA TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T
5435909 ATATGCCCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 7 0.10
3 52 0.76
4 7 0.10
5 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5435861 original size:27 final size:27
Alignment explanation
Indices: 5435822--5435908 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
5435812 AGAGCTTTGT
5435822 TTTATTATT-TTATTATTTTTACTATTA
1 TTTA-TATTATTATTATTTTTACTATTA
*
5435849 TTTATATTATTATTATTATTT-C--TCA
1 TTTATATTATTATTATT-TTTACTATTA
* * *
5435874 TGTATA-TATTATTATTTATATTATTA
1 TTTATATTATTATTATTTTTACTATTA
5435900 -TTATATTAT
1 TTTATATTAT
5435909 ATATGCCCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
23 2 0.04
24 10 0.21
25 11 0.23
26 9 0.19
27 13 0.27
28 3 0.06
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (27 bp):
TTTATATTATTATTATTTTTACTATTA
Found at i:5435883 original size:21 final size:18
Alignment explanation
Indices: 5435823--5435912 Score: 92
Period size: 18 Copynumber: 4.7 Consensus size: 18
5435813 GAGCTTTGTT
*
5435823 TTATTATTTTATTATTTTTA
1 TTATTA-TTTA-TATTATTA
*
5435843 CTATTATTTATATTATTA
1 TTATTATTTATATTATTA
*
5435861 TTATTATTTCTCATGTATATA
1 TTATTATTTAT-AT-TAT-TA
5435882 TTATTATTTATATTATTA
1 TTATTATTTATATTATTA
5435900 TTA-TATTATATAT
1 TTATTATT-TATAT
5435913 GCCCTCTCCA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.07
18 26 0.43
19 9 0.15
20 10 0.16
21 12 0.20
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (18 bp):
TTATTATTTATATTATTA
Found at i:5437751 original size:22 final size:24
Alignment explanation
Indices: 5437701--5437755 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 24
5437691 TATTGTATTT
* *
5437701 ATTTATTTTTAATTATTATAATTA
1 ATTTATTTTTAATAAATATAATTA
5437725 A--TATTTTTAA-AAATA-AATTA
1 ATTTATTTTTAATAAATATAATTA
5437745 ATTTATTTTTA
1 ATTTATTTTTA
5437756 TTTTTAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 6 0.22
21 3 0.11
22 17 0.63
24 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTATTTTTAATAAATATAATTA
Found at i:5437894 original size:18 final size:18
Alignment explanation
Indices: 5437871--5437922 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
5437861 ATGAAATATG
5437871 TATTTTAACAAGTTTTCAT
1 TATTTTAA-AAGTTTTCAT
**
5437890 T-TTTTAAATTTTTTTCAT
1 TATTTTAAA-AGTTTTCAT
5437908 TATTTTAAAAGTTTT
1 TATTTTAAAAGTTTT
5437923 TGTCAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 1 0.04
18 18 0.67
19 8 0.30
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.62
Consensus pattern (18 bp):
TATTTTAAAAGTTTTCAT
Found at i:5442388 original size:3 final size:3
Alignment explanation
Indices: 5442380--5442404 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5442370 TTTTGATGCT
5442380 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
5442405 AAATGATAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5444893 original size:6 final size:6
Alignment explanation
Indices: 5444882--5444912 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5444872 TAAGAAAGAG
*
5444882 TTTGAC TTTGAC TTTGAC TTTGCC TTTGAC T
1 TTTGAC TTTGAC TTTGAC TTTGAC TTTGAC T
5444913 ATATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (6 bp):
TTTGAC
Found at i:5444919 original size:2 final size:2
Alignment explanation
Indices: 5444912--5444936 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5444902 TGCCTTTGAC
5444912 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5444937 TTTTGCATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5445469 original size:30 final size:30
Alignment explanation
Indices: 5445433--5445493 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
5445423 TATTAATGTT
5445433 AATTAAATAAGGGTACTTGGATAAATCGAA
1 AATTAAATAAGGGTACTTGGATAAATCGAA
5445463 AATTAAATAAGGGTACTTGGATAAATCGAA
1 AATTAAATAAGGGTACTTGGATAAATCGAA
5445493 A
1 A
5445494 CGAATGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (30 bp):
AATTAAATAAGGGTACTTGGATAAATCGAA
Found at i:5448320 original size:43 final size:44
Alignment explanation
Indices: 5448259--5448351 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 44
5448249 TCCTAATTGG
*
5448259 GAAAATAGTTCCCTTATTCTAATAAACTAGTAAAACATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
5448302 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
5448346 -AAAATA
1 GAAAATA
5448352 TTTCTAGAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 45 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.28
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:5448468 original size:21 final size:21
Alignment explanation
Indices: 5448420--5448468 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5448410 TTAAAATATA
*
5448420 TACATATTTCAACACAACTAAG
1 TACAT-TTTCAACACAACTAAC
*
5448442 TTCATTTTCAAC-CAAACTAAC
1 TACATTTTCAACAC-AACTAAC
5448463 TACATT
1 TACATT
5448469 GTAACTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.33
Consensus pattern (21 bp):
TACATTTTCAACACAACTAAC
Found at i:5448677 original size:15 final size:15
Alignment explanation
Indices: 5448665--5448709 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
5448655 TTTCAAGCTG
5448665 ACCCTGCTCAAGCAC
1 ACCCTGCTCAAGCAC
5448680 ACCCTGCTCAAGCAC
1 ACCCTGCTCAAGCAC
*
5448695 ACCTTGCTCAAGCAC
1 ACCCTGCTCAAGCAC
5448710 CCCATTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.27, C:0.44, G:0.13, T:0.16
Consensus pattern (15 bp):
ACCCTGCTCAAGCAC
Found at i:5451633 original size:18 final size:17
Alignment explanation
Indices: 5451607--5451648 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
5451597 GTAAGACATT
5451607 TTCCATCCTTCCTCCTCC
1 TTCCATCCTT-CTCCTCC
* *
5451625 TTCCGTCCTTCTCCTTC
1 TTCCATCCTTCTCCTCC
5451642 TT-CATCC
1 TTCCATCC
5451649 AATTGGACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 4 0.19
17 8 0.38
18 9 0.43
ACGTcount: A:0.05, C:0.50, G:0.02, T:0.43
Consensus pattern (17 bp):
TTCCATCCTTCTCCTCC
Found at i:5451801 original size:17 final size:17
Alignment explanation
Indices: 5451776--5451808 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5451766 TTGTTGAAGA
5451776 ATCTATTTGGATTTTGC
1 ATCTATTTGGATTTTGC
*
5451793 ATCTGTTTGGATTTTG
1 ATCTATTTGGATTTTG
5451809 TATCAGTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.21, T:0.55
Consensus pattern (17 bp):
ATCTATTTGGATTTTGC
Found at i:5453756 original size:14 final size:14
Alignment explanation
Indices: 5453737--5453764 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5453727 GTTTCTTTGA
5453737 TTTCTCATGTTCAT
1 TTTCTCATGTTCAT
5453751 TTTCTCATGTTCAT
1 TTTCTCATGTTCAT
5453765 ATAGTAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTCTCATGTTCAT
Found at i:5455221 original size:32 final size:29
Alignment explanation
Indices: 5455195--5455250 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
5455185 AATGTGGTGA
5455195 AATATCAATTATGCACTTGGACAATGTGT
1 AATATCAATTATGCACTTGGACAATGTGT
* *
5455224 AATATTAGTTATGCACTTGGACAATGT
1 AATATCAATTATGCACTTGGACAATGT
5455251 TGTTATTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (29 bp):
AATATCAATTATGCACTTGGACAATGTGT
Found at i:5456365 original size:33 final size:34
Alignment explanation
Indices: 5456326--5456393 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
5456316 TGTAATAATG
* * *
5456326 ATATATACACAATATGGTA-TTAAGAATATATAT
1 ATATATACACAATATAGTATTTAAAAAAATATAT
*
5456359 ATATATATACAATATAGTATTTAAAAAAATATAT
1 ATATATACACAATATAGTATTTAAAAAAATATAT
5456393 A
1 A
5456394 CATAAGATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (34 bp):
ATATATACACAATATAGTATTTAAAAAAATATAT
Found at i:5456591 original size:3 final size:3
Alignment explanation
Indices: 5456585--5456616 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5456575 ATAAGAGTAT
5456585 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5456617 CTACAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5456730 original size:37 final size:37
Alignment explanation
Indices: 5456659--5456730 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
5456649 AAAAATATAT
* *
5456659 ATATAAAATATTTACAATAATGATGTAAATAAACAAC
1 ATATAAAATATTTACAATAATCATATAAATAAACAAC
5456696 ATATAAAATATTTGA-AATAA-CATATAAATGAAACA
1 ATATAAAATATTT-ACAATAATCATATAAAT-AAACA
5456731 TAAAAAAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.74
38 1 0.03
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (37 bp):
ATATAAAATATTTACAATAATCATATAAATAAACAAC
Found at i:5457326 original size:21 final size:20
Alignment explanation
Indices: 5457272--5457326 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
5457262 TAGAAAGAAG
**
5457272 AAGAAAAAAAACAAAGAAAAA
1 AAGAAAAAAAA-ATCGAAAAA
5457293 AAGAAAAAAAAATCGAAAAA
1 AAGAAAAAAAAATCGAAAAA
*
5457313 AGAGAGAAAAAAAT
1 A-AGAAAAAAAAAT
5457327 GCAAACCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.04
Consensus pattern (20 bp):
AAGAAAAAAAAATCGAAAAA
Found at i:5458513 original size:54 final size:54
Alignment explanation
Indices: 5458431--5458681 Score: 450
Period size: 54 Copynumber: 4.6 Consensus size: 54
5458421 TGACCCGAGA
5458431 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGG
5458485 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTAAAAGG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGG
*
5458538 TTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGG
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGG
*
5458592 CTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAGG
1 CTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTAAAAGG
*
5458648 CTCAACTCACCTATCGCAATATGAGTTGATTTTT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5458682 TTTTTTTTGA
Statistics
Matches: 189, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
53 52 0.28
54 85 0.45
56 52 0.28
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (54 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGG
Found at i:5458618 original size:107 final size:109
Alignment explanation
Indices: 5458431--5458681 Score: 452
Period size: 107 Copynumber: 2.3 Consensus size: 109
5458421 TGACCCGAGA
5458431 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACC
5458496 TCTCGCAATATGAGTTGA-TTTTTG-AAAACAGAAATTAAAAGG
66 TCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAGG
* *
5458538 TTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTTAACTCACC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACC
5458603 TCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAGG
66 TCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTAAAAGG
*
5458648 CTCAACTCACCTATCGCAATATGAGTTGATTTTT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5458682 TTTTTTTTGA
Statistics
Matches: 137, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
107 81 0.59
109 6 0.04
110 50 0.36
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (109 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACTCACC
TCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAAGG
Found at i:5458836 original size:75 final size:76
Alignment explanation
Indices: 5458711--5458851 Score: 221
Period size: 75 Copynumber: 1.9 Consensus size: 76
5458701 TTGAAAAACG
* *
5458711 GAAATTGAAAATACCTCGGCGTGTGACCTGAGACTCAACTCACTTCTCGCAATATGAGTTAATTT
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGACTCAACTCACCTCTCGCAATATGAGTTAATTT
5458776 TTTTGATGAACA
65 TTTTGATGAACA
* * *
5458788 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGACTCAACTCACCTCTCGCAATATGAGTTAATTTT
5458852 GACGAACATA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 37 0.63
77 22 0.37
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (76 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGACTCAACTCACCTCTCGCAATATGAGTTAATTTT
TTTGATGAACA
Found at i:5458894 original size:86 final size:86
Alignment explanation
Indices: 5458784--5459534 Score: 344
Period size: 90 Copynumber: 9.0 Consensus size: 86
5458774 TTTTTTGATG
*
5458784 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* *
5458849 TTTGACGA-ACATAAATTGAAA
66 TTTGA-AACACAGAAATTGAAA
* * *
5458870 AATAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
5458935 TTTTTTGAAACACAGAAATTGAAG
65 --TTTTGAAACACAGAAATTGAAA
* * ** * * *
5458959 AACAGAAATGGAAAACACCTCAGAATATGACCCGAGGCTCAACTCACCTCTCGCAATATTAGTTG
1 AACAGAAATTGAAAATACCTCAG--CGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* *
5459024 ATTTTTTTAAACACAAAAATTGAAA
64 A--TTTTGAAACACAGAAATTGAAA
** ** * * *
5459049 AAC---------ACCT-CAGC-GTGTGACCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGAA
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-A
*
5459103 TTTTGAAAAACAGAAATTG--A
65 TTTTGAAACACAGAAATTGAAA
** * * * * *
5459123 AA-AG-ACCT---CA-ACAT--GTGAG-CC-GAGGCTCAACTCACCTCTCGCTATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
* *
5459178 TTTTGACAA-ACAAAAATTAGAATT
65 TTTTGA-AACACAGAAATT-GAA-A
* ** *** * * * * * * *
5459202 ACCTCAGCGTG----T-CCT--GAG-G--CTCA-ACTCACCTCTCGCAATAT-G-AGT-TGA-TT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCAC-C--TCTCGCAATATGAGTT
* *
5459252 -TTTTTGAAGA-GCAGAAA-T----
63 GATTTTGAA-ACACAGAAATTGAAA
* * * *
5459270 ---AGAAATCGAGAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
5459332 TTTTTTGAAA-AGCAGAAATTGAAA
65 --TTTTGAAACA-CAGAAATTGAAA
* * **
5459356 AGCAGAAATTAAAAATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
* *
5459421 TTTTGGAAAAACATAAATTGAAGAA
65 TTTT-GAAACACAGAAATTG-A-AA
* *
5459446 AACAGAAATTGAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
* *
5459511 TTTTTGAAAAACATAAATTGAAA
65 -TTTTGAAACACAGAAATTGAAA
5459534 A
1 A
5459535 GACCTCAACA
Statistics
Matches: 520, Mismatches: 83, Indels: 122
0.72 0.11 0.17
Matches are distributed among these distances:
65 2 0.00
69 1 0.00
70 3 0.01
72 2 0.00
73 3 0.01
74 7 0.01
75 62 0.12
76 32 0.06
77 44 0.08
78 16 0.03
79 6 0.01
80 8 0.02
81 18 0.03
82 1 0.00
86 60 0.12
87 5 0.01
88 16 0.03
89 96 0.18
90 99 0.19
91 39 0.08
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (86 bp):
AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTGAAACACAGAAATTGAAA
Found at i:5459027 original size:91 final size:89
Alignment explanation
Indices: 5458784--5459052 Score: 296
Period size: 86 Copynumber: 3.0 Consensus size: 89
5458774 TTTTTTGATG
* ** * * *
5458784 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
1 AACAGAAATGGAAAACACCTCAGCATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* *
5458848 --TTTTGACGA-ACATAAATTGAAA
66 TTTTTTGA-AACACAAAAATTGAAA
* * * * * ** *
5458870 AATAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGAT
1 AACAGAAATGGAAAACACCTCAGCATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* *
5458935 TTTTTTGAAACACAGAAATTGAAG
66 TTTTTTGAAACACAAAAATTGAAA
* *
5458959 AACAGAAATGGAAAACACCTCAGAATATGACCCGAGGCTCAACTCACCTCTCGCAATATTAGTTG
1 AACAGAAATGGAAAACACCTCAG--CATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
5459024 ATTTTTTT-AAACACAAAAATTGAAA
64 ATTTTTTTGAAACACAAAAATTGAAA
5459049 AACA
1 AACA
5459053 CCTCAGCGTG
Statistics
Matches: 158, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
86 60 0.38
88 1 0.01
89 37 0.23
90 19 0.12
91 41 0.26
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (89 bp):
AACAGAAATGGAAAACACCTCAGCATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTTGAAACACAAAAATTGAAA
Found at i:5459170 original size:75 final size:76
Alignment explanation
Indices: 5458953--5459841 Score: 637
Period size: 75 Copynumber: 11.3 Consensus size: 76
5458943 AACACAGAAA
* * * * *
5458953 TTGAAGAACAGAAATGGAAAACACCTCAGAATATGACCC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAAGACCTCAG-CTGTGACCCTGAGGCTCAACTCACCTCTCGCAATA
*
5459017 TTAGTTGATTTT
65 TGAGTTGATTTT
* * * * *
5459029 TTTAAACACAAAAATTGAAAAACACCTCAGCGTGTGA-CCTGAGGCTCAACTCACCTTTCGCAAT
1 TTGAAAAACAGAAATTG-AAAAGACCTCAGC-TGTGACCCTGAGGCTCAACTCACCTCTCGCAAT
*
5459093 ATGAGTTGA-ATT
64 ATGAGTTGATTTT
* * *
5459105 TTGAAAAACAGAAATTGAAAAGACCTCAACATGTGAGCC-GAGGCTCAACTCACCTCTCGCTATA
1 TTGAAAAACAGAAATTGAAAAGACCTCAGC-TGTGACCCTGAGGCTCAACTCACCTCTCGCAATA
5459169 TGAGTTGA-TTT
65 TGAGTTGATTTT
* * ** *
5459180 TTGACAAACAAAAATT-AGAATTACCTCAGC-GTG-TCCTGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGA-AAAGACCTCAGCTGTGACCCTGAGGCTCAACTCACCTCTCGCAATA
5459242 TGAGTTGATTTTT
65 TGAGTTGA-TTTT
* * *
5459255 TTGAAGAGCAGAAATAGAAATCGAGAATACCTCAGC-GTG-CCCTGAGGCTCAACTCACCTCTCG
1 TTGAAAAACAGAAATTGAAA---AG---ACCTCAGCTGTGACCCTGAGGCTCAACTCACCTCTCG
*
5459318 TAATATGAGTTGATTTTT
60 CAATATGAGTTGA-TTTT
* ** * * *
5459336 TTGAAAAGCAGAAATTGAAAAGCAGAAATTAAAAATACCTCAGCGTACCCTGAGGCTCAACTCAC
1 TTGAAAAACAGAAATTG-AAA--AG-ACCT-----CAGCT--GTG-ACCCTGAGGCTCAACTCAC
5459401 CTCTCGCAATATGAGTTGATTTT
54 CTCTCGCAATATGAGTTGATTTT
* * * *** ** * * * * *
5459424 TGGAAAAACATAAATTGAAGAAAACAGAAATTGAAATTACCTCAGCATGTCCTGAGGCTCAACTC
1 TTGAAAAACAGAAATTGAA-AAGACCTCAGCTG---TGACC-CTG-A-G-GCTCA---AC---TC
5459489 ACCTCTCGCAATATGAGTTGATTTT
52 ACCTCTCGCAATATGAGTTGATTTT
* * * *
5459514 TTGAAAAACATAAATTGAAAAGACCTCAACATGTGAGCC-GAGGCTCAACTCACCTCTCGCTATA
1 TTGAAAAACAGAAATTGAAAAGACCTCAGC-TGTGACCCTGAGGCTCAACTCACCTCTCGCAATA
*
5459578 TGAGTT-AATTT
65 TGAGTTGATTTT
* * * *
5459589 TTGACAAACAAAAATT-AAAATTACCTCAGC-GTG-TCCTGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAA-GACCTCAGCTGTGACCCTGAGGCTCAACTCACCTCTCGCAATA
5459651 TGAGTTGATTTTT
65 TGAGTTGA-TTTT
* * * *
5459664 TTGAAGAGCAGAAATAGAGATCGACAATACCTCAGC-GTG-CCCTGAGGCTCAACTCACCTCTCG
1 TTGAAAAACAGAAAT-----T-GAAAAGACCTCAGCTGTGACCCTGAGGCTCAACTCACCTCTCG
5459727 CAATATGAGTTGATTTTT
60 CAATATGAGTTGA-TTTT
* * ** *
5459745 TTGACAAACATAAATTGAAATTACCTCAGC-GTG-TCCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCTGTGACCCTGAGGCTCAACTCACCTCTCGCAATAT
5459808 GAGTTGATTTTT
66 GAGTTGA-TTTT
*
5459820 TTGAAAAGCAGAAATTGAAAAG
1 TTGAAAAACAGAAATTGAAAAG
5459842 CAGAAATTGA
Statistics
Matches: 661, Mismatches: 100, Indels: 105
0.76 0.12 0.12
Matches are distributed among these distances:
72 4 0.01
73 68 0.10
74 6 0.01
75 200 0.30
76 54 0.08
77 47 0.07
78 1 0.00
79 3 0.00
80 6 0.01
81 134 0.20
82 10 0.02
83 2 0.00
84 6 0.01
85 2 0.00
86 2 0.00
87 8 0.01
88 19 0.03
89 42 0.06
90 47 0.07
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (76 bp):
TTGAAAAACAGAAATTGAAAAGACCTCAGCTGTGACCCTGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTT
Found at i:5459336 original size:81 final size:82
Alignment explanation
Indices: 5459198--5459998 Score: 712
Period size: 81 Copynumber: 9.7 Consensus size: 82
5459188 CAAAAATTAG
*
5459198 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAG
1 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAG
*
5459263 CAGAAATAGAAATCGAG
66 CAGAAATAGAAATCGAA
* *
5459280 AA-TACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAG
1 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAG
* *
5459344 CAGAAATTGAAAAGCAGAAATTAA
66 CAGAAATAG-AAATC-G-----AA
* ** * *
5459368 AAATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGGAAAAA
1 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAG
* *
5459432 CATAAATTGAAGAAAACAGAAATTGA
66 CAGAAA-T--AGAAATC-G--A---A
*
5459458 AATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAA-
1 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAG
* *
5459520 -A-ACAT--AAATTGAA
66 CAGAAATAGAAATCGAA
* * * * *
5459533 AA-GACCTCAACATGTGAGCC-GAGGCTCAACTCACCTCTCGCTATATGAGTT-A-ATTTTTG--
1 AATTACCTCAGC--GTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
*
5459592 -A-CA-AACA-A-AAAT-TAA
63 AAGCAGAA-ATAGAAATCGAA
*
5459607 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAG
1 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAG
* *
5459672 CAGAAATAGAGATCGAC
66 CAGAAATAGAAATCGAA
*
5459689 AA-TACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG---A-
1 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAG
*
5459749 CA-AACAT--AAATTG-A
66 CAGAA-ATAGAAATCGAA
5459763 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAG
1 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAG
*
5459828 CAGAAATTGAAAAGCAGAAATTGAA
66 CAGAAA-T-------AGAAATCGAA
** * *
5459853 AA-TACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA-TTTTTTGAAAAA
1 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAG
* *
5459916 CATAAATTGAAGAAAACAGAAATTGA
66 CAGAAA-T--AGAAATC-G--A---A
* *
5459942 AATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT
1 AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5459999 GAAACAGAAA
Statistics
Matches: 605, Mismatches: 56, Indels: 107
0.79 0.07 0.14
Matches are distributed among these distances:
72 2 0.00
73 34 0.06
74 16 0.03
75 88 0.15
76 34 0.06
77 6 0.01
78 4 0.01
79 6 0.01
80 7 0.01
81 129 0.21
82 9 0.01
83 7 0.01
84 1 0.00
85 1 0.00
86 3 0.00
87 2 0.00
88 36 0.06
89 106 0.18
90 109 0.18
91 5 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (82 bp):
AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAG
CAGAAATAGAAATCGAA
Found at i:5459355 original size:14 final size:14
Alignment explanation
Indices: 5459336--5459369 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5459326 GTTGATTTTT
5459336 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
5459350 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
5459364 TT-AAAA
1 TTGAAAA
5459370 ATACCTCAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:5459449 original size:16 final size:16
Alignment explanation
Indices: 5459428--5459458 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5459418 GATTTTTGGA
*
5459428 AAAACATAAATTGAAG
1 AAAACAGAAATTGAAG
5459444 AAAACAGAAATTGAA
1 AAAACAGAAATTGAA
5459459 ATTACCTCAG
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:0.65, C:0.06, G:0.13, T:0.16
Consensus pattern (16 bp):
AAAACAGAAATTGAAG
Found at i:5459495 original size:90 final size:89
Alignment explanation
Indices: 5459280--5459534 Score: 395
Period size: 90 Copynumber: 2.9 Consensus size: 89
5459270 AGAAATCGAG
* *
5459280 AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAAAGC
1 AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAAC
* *
5459345 AGAAATTG-AAAAGCAGAAATTAAA
65 ATAAATTGAAAAAACAGAAATTAAA
* *
5459369 AATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGGAAAAACA
1 AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
*
5459434 TAAATTGAAGAAAACAGAAATTGAA
66 TAAATTGAA-AAAACAGAAATTAAA
* * *
5459459 ATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
1 AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
5459524 TAAATTGAAAA
66 TAAATTGAAAA
5459535 GACCTCAACA
Statistics
Matches: 152, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
88 18 0.12
89 52 0.34
90 82 0.54
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (89 bp):
AATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
TAAATTGAAAAAACAGAAATTAAA
Found at i:5459605 original size:409 final size:394
Alignment explanation
Indices: 5459040--5459926 Score: 1384
Period size: 409 Copynumber: 2.2 Consensus size: 394
5459030 TTAAACACAA
* * *
5459040 AAATTGAAAAACACCTCAGCGTGTGACCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGA-AT
1 AAATTG-AAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
*
5459104 TTTGAAAAACAGAAATTGAAAAGACCTCAACATGTGAGCCGAGGCTCAACTCACCTCTCGCTATA
63 TTTGAAAAACATAAATTGAAAAGACCTCAACATGTGAGCCGAGGCTCAACTCACCTCTCGCTATA
* *
5459169 TGAGTTGATTTTTGACAAACAAAAATTAGAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
128 TGAGTTAATTTTTGACAAACAAAAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
*
5459234 TCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATAGAAATCGAGAATACCTCAGCGTGCCCTG
193 TCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATAGAAATCGACAATACCTCAGCGTGCCCTG
*
5459299 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGA-AAAGCAGAAATTGAAAAGCAGAA
258 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAA-CAGAAATT--------GAA
5459363 ATTAAAAATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGG
314 A-T-----TACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGG
*
5459427 AAAAACATAAATTGAAGAAAACAG
373 AAAAACAGAAATTG-A-AAAACAG
* *
5459451 AAATTGAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
5459516 GAAAAACATAAATTGAAAAGACCTCAACATGTGAGCCGAGGCTCAACTCACCTCTCGCTATATGA
66 GAAAAACATAAATTGAAAAGACCTCAACATGTGAGCCGAGGCTCAACTCACCTCTCGCTATATGA
5459581 GTTAATTTTTGACAAACAAAAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG
131 GTTAATTTTTGACAAACAAAAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG
*
5459646 CAATATGAGTTGATTTTTTTGAAGAGCAGAAATAGAGATCGACAATACCTCAGCGTGCCCTGAGG
196 CAATATGAGTTGATTTTTTTGAAGAGCAGAAATAGAAATCGACAATACCTCAGCGTGCCCTGAGG
*
5459711 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACATAAATTGAAATTACCTCAGCG
261 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAATTACCTCAGCG
** * *
5459776 TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAA
326 TACCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAACAGAAATTGAAAA
*
5459841 GCAG
391 ACAG
** *
5459845 AAATTGAAAATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
5459910 GAAAAACATAAATTGAA
66 GAAAAACATAAATTGAA
5459927 GAAAACAGAA
Statistics
Matches: 450, Mismatches: 23, Indels: 23
0.91 0.05 0.05
Matches are distributed among these distances:
394 83 0.18
395 48 0.11
396 18 0.04
400 1 0.00
401 4 0.01
408 35 0.08
409 238 0.53
410 17 0.04
411 6 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (394 bp):
AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
GAAAAACATAAATTGAAAAGACCTCAACATGTGAGCCGAGGCTCAACTCACCTCTCGCTATATGA
GTTAATTTTTGACAAACAAAAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG
CAATATGAGTTGATTTTTTTGAAGAGCAGAAATAGAAATCGACAATACCTCAGCGTGCCCTGAGG
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAATTACCTCAGCG
TACCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGGAAAAACAGAAATTGAAAA
ACAG
Found at i:5459782 original size:156 final size:154
Alignment explanation
Indices: 5459445--5459926 Score: 647
Period size: 156 Copynumber: 3.1 Consensus size: 154
5459435 AAATTGAAGA
* *
5459445 AAACAGAAATTGAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* * * *
5459510 -TTTTTTGAAA--A-ACATA-A-ATTGAAAAGACCTCAACATGTGAGCC-GAGGCTCAACTCACC
66 TTTTTTTGAAAGCAGAAATAGAGATTGAAAATACCTCAGC--GTG-CCCTGAGGCTCAACTCACC
* *
5459568 TCTCGCTATATGAGTT-AATTTTTGAC
128 TCTCGCAATATGAGTTGATTTTTTGAC
* *
5459594 AAACAAAAATTAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* *
5459659 TTTTTTTGAAGAGCAGAAATAGAGATCGACAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTC
66 TTTTTTTGAA-AGCAGAAATAGAGATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTC
5459724 TCGCAATATGAGTTGATTTTTTTGAC
130 TCGCAATATGAGTTGA-TTTTTTGAC
5459750 AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
5459815 TTTTTTTGAAAAGCAGAAATTGAAAAGCAGAAATTGAAAATACCTCAGCGTACCCTGAGGCTCAA
66 TTTTTTTG-AAAGCAGAAA-T----AG-AG--ATTGAAAATACCTCAGCGTGCCCTGAGGCTCAA
* *
5459880 CTCACCTCTCGCAATATGAGCTGATTTTTTGAA
122 CTCACCTCTCGCAATATGAGTTGATTTTTTGAC
5459913 AAACATAAATTGAA
1 AAACATAAATTGAA
5459927 GAAAACAGAA
Statistics
Matches: 296, Mismatches: 18, Indels: 24
0.88 0.05 0.07
Matches are distributed among these distances:
149 62 0.21
150 9 0.03
151 1 0.00
153 3 0.01
154 37 0.12
155 2 0.01
156 100 0.34
157 3 0.01
161 2 0.01
162 2 0.01
163 22 0.07
164 53 0.18
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (154 bp):
AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTTTGAAAGCAGAAATAGAGATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATTTTTTGAC
Found at i:5459809 original size:484 final size:478
Alignment explanation
Indices: 5458737--5460002 Score: 1756
Period size: 484 Copynumber: 2.6 Consensus size: 478
5458727 CGGCGTGTGA
* * * ** *
5458737 CCTGAGACTCAACTCACTTCTCGCAATATGAGTTAATTTTTTTGATGAACAGAAATTGAAATTAC
1 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACATAAATTGAAATTAC
* *
5458802 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTGACGAA-CATAA
66 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA-AAAGCAGAA
** ** *
5458863 ATTGAAAAATAGAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATG
130 ATTGAAAAGCAGAAATTGAAAATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATG
* * * ** * *
5458928 AGCTGATTTTTTTGAAACACAGAAATTGAAG--AACAGAAATGGAAAACACCTCAGAATATGACC
195 AGCTGA-TTTTTTGAAAAACATAAATTGAAGAAAACAGAAATTGAAATTACCTCAG--CATGTCC
* * * *
5458991 CGAGGCTCAACTCACCTCTCGCAATATTAGTTGATTTTTTTAAACACAAAAATTGAAAAACACCT
257 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAAAAATTGAAAAACACCT
* * * *
5459056 CAGCGTGTGACCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGAATTTTGAAAAACAGAAATT
322 CAACATGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAAACAAAAATT
*
5459121 GAAAAGACCTCAACATGTGAGCCGAGGCTCAACTCACCTCTCGCTATATGAGTTGATTTTTGACA
387 GAAAAGACCTCAACA-GTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA
*
5459186 AACAAAAATTAGAATTACCTCAGCGTGT
451 AACAAAAATTAGAATTACCTCAGCGTGC
*
5459214 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAA-ATAGAAATCG
1 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT---GA-CA-AACAT--AAATTG
* *
5459278 AGAA-TACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGAAA
59 A-AATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
*
5459342 AGCAGAAATTGAAAAGCAGAAATTAAAAATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCG
123 AGCAGAAATTGAAAAGCAGAAATTGAAAATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCG
* *
5459407 CAATATGAGTTGATTTTTGGAAAAACATAAATTGAAGAAAACAGAAATTGAAATTACCTCAGCAT
188 CAATATGAGCTGATTTTTTGAAAAACATAAATTGAAGAAAACAGAAATTGAAATTACCTCAGCAT
* *
5459472 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAATTG-AAAAG
253 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAAAAATTGAAAAAC
* *
5459536 ACCTCAACATGTGAGCC-GAGGCTCAACTCACCTCTCGCTATATGAGTT-AATTTTTGACAAACA
318 ACCTCAACATGTGA-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA-TTTTGAAAAACA
* * *
5459599 AAAATT-AAAATTACCTCAGC-GTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
381 AAAATTGAAAA-GACCTCAACAGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--
* *
5459661 TTTTTGA-AGAGCAGAAA-TAGAGATCGACAATACCTCAGCGTGC
442 TTTTTGACA-AACAAAAATTAGA-AT------TACCTCAGCGTGC
5459704 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACATAAATTGAAATTAC
1 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACATAAATTGAAATTAC
5459769 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAA
66 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAA
5459834 TTGAAAAGCAGAAATTGAAAATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATGA
131 TTGAAAAGCAGAAATTGAAAATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATGA
5459899 GCTGATTTTTTGAAAAACATAAATTGAAGAAAACAGAAATTGAAATTACCTCAGCATGTCCTGAG
196 GCTGATTTTTTGAAAAACATAAATTGAAGAAAACAGAAATTGAAATTACCTCAGCATGTCCTGAG
*
5459964 GCTCAACTCACCTCTCGCAATATGAGTTGA-ATTTTGAAA
261 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAA
5460003 CAGAAATAAA
Statistics
Matches: 707, Mismatches: 52, Indels: 54
0.87 0.06 0.07
Matches are distributed among these distances:
477 40 0.06
480 2 0.00
481 3 0.00
482 37 0.05
483 74 0.10
484 314 0.44
485 82 0.12
486 78 0.11
487 22 0.03
490 55 0.08
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (478 bp):
CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACATAAATTGAAATTAC
CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAA
TTGAAAAGCAGAAATTGAAAATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATGA
GCTGATTTTTTGAAAAACATAAATTGAAGAAAACAGAAATTGAAATTACCTCAGCATGTCCTGAG
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAAAAATTGAAAAACACCTCAAC
ATGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAAACAAAAATTGAAA
AGACCTCAACAGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAA
AAATTAGAATTACCTCAGCGTGC
Found at i:5459839 original size:14 final size:14
Alignment explanation
Indices: 5459820--5459854 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
5459810 GTTGATTTTT
5459820 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
5459834 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
5459848 TTGAAAA
1 TTGAAAA
5459855 TACCTCAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:5459907 original size:89 final size:90
Alignment explanation
Indices: 5459750--5460009 Score: 386
Period size: 89 Copynumber: 2.9 Consensus size: 90
5459740 TTTTTTTGAC
*
5459750 AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
5459815 TTTTTTTGAAAAGCAGAAATTG-A-A
66 -TTTTTTGAAAAACAGAAATTGAAGA
* * ** *
5459839 AAGCAGAAATTGAAAATACCTCAGCGTACCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
5459904 TTTTTTGAAAAACATAAATTGAAGA
66 TTTTTTGAAAAACAGAAATTGAAGA
*
5459929 AAACAGAAATTGAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
5459994 -ATTTTG--AAACAGAAAT
66 TTTTTTGAAAAACAGAAAT
5460010 AAAAGCATCA
Statistics
Matches: 153, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
87 9 0.06
88 19 0.12
89 65 0.42
90 60 0.39
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (90 bp):
AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTTGAAAAACAGAAATTGAAGA
Found at i:5459933 original size:16 final size:16
Alignment explanation
Indices: 5459912--5459942 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5459902 GATTTTTTGA
*
5459912 AAAACATAAATTGAAG
1 AAAACAGAAATTGAAG
5459928 AAAACAGAAATTGAA
1 AAAACAGAAATTGAA
5459943 ATTACCTCAG
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:0.65, C:0.06, G:0.13, T:0.16
Consensus pattern (16 bp):
AAAACAGAAATTGAAG
Found at i:5462235 original size:21 final size:20
Alignment explanation
Indices: 5462209--5462264 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
5462199 ATTTGATCTC
5462209 TCTTTTTTGTTTTTTTCCTTG
1 TCTTTTTTGTTTTTTT-CTTG
*
5462230 TCTTTTATT-TTTTTATTTTTG
1 TCTTTT-TTGTTTTT-TTCTTG
5462251 T-TTTTTTGTTTTTT
1 TCTTTTTTGTTTTTT
5462265 CTTTTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 3 0.10
20 9 0.29
21 15 0.48
22 4 0.13
ACGTcount: A:0.04, C:0.07, G:0.07, T:0.82
Consensus pattern (20 bp):
TCTTTTTTGTTTTTTTCTTG
Found at i:5462269 original size:21 final size:20
Alignment explanation
Indices: 5462211--5462275 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
5462201 TTGATCTCTC
**
5462211 TTTTTTGTTTTTTTCCTTGT
1 TTTTTTGTTTTTTTTTTTGT
*
5462231 CTTTTATT-TTTTTATTTTTGT
1 -TTTT-TTGTTTTTTTTTTTGT
*
5462252 TTTTTTGTTTTTTCTTTTTCT
1 TTTTTTGTTTTTT-TTTTTGT
5462273 TTT
1 TTT
5462276 CATGACTGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 2 0.06
20 9 0.25
21 23 0.64
22 2 0.06
ACGTcount: A:0.03, C:0.08, G:0.06, T:0.83
Consensus pattern (20 bp):
TTTTTTGTTTTTTTTTTTGT
Found at i:5466650 original size:33 final size:31
Alignment explanation
Indices: 5466589--5466653 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
5466579 TGTAATAATG
* *
5466589 ATATATACACAATATGGTATTAAGAATATAT
1 ATATATACACAATATAGTATTAAAAATATAT
*
5466620 ATATATATACAATATAGTATTTAAAAA-ATAT
1 ATATATACACAATATAGTA-TTAAAAATATAT
5466651 ATA
1 ATA
5466654 CATAAGATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (31 bp):
ATATATACACAATATAGTATTAAAAATATAT
Found at i:5466851 original size:3 final size:3
Alignment explanation
Indices: 5466845--5466883 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5466835 ATAAGAGTAT
5466845 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5466884 TCTACAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5466991 original size:36 final size:39
Alignment explanation
Indices: 5466925--5466997 Score: 91
Period size: 37 Copynumber: 1.9 Consensus size: 39
5466915 CAAAAAATAT
* *
5466925 ATATATAAATATTTACAATAATGATGTAAAT-AAACAAC
1 ATATATAAATATTTACAATAATCATATAAATGAAACAAC
5466963 ATATA-AAATATTTGA-AATAA-CATATAAATGAAACA
1 ATATATAAATATTT-ACAATAATCATATAAATGAAACA
5466998 TAAAAAAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 7 0.23
37 18 0.58
38 6 0.19
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (39 bp):
ATATATAAATATTTACAATAATCATATAAATGAAACAAC
Found at i:5467559 original size:20 final size:22
Alignment explanation
Indices: 5467533--5467595 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
5467523 TATGTATATA
5467533 GAAAGAAGAAGAAAAAAAAA-C
1 GAAAGAAGAAGAAAAAAAAATC
*
5467554 -AAAGAAAAAAAGAAAAAAAAATC
1 GAAAG--AAGAAGAAAAAAAAATC
*
5467577 GAAAAAAGAGAGAAAAAAA
1 GAAAGAAGA-AGAAAAAAA
5467596 TGCAAACCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
20 4 0.12
22 17 0.50
23 10 0.29
24 3 0.09
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (22 bp):
GAAAGAAGAAGAAAAAAAAATC
Found at i:5467571 original size:21 final size:21
Alignment explanation
Indices: 5467541--5467595 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
5467531 TAGAAAGAAG
5467541 AAGA-AAAAAAAACAAAGAAAA
1 AAGAGAAAAAAAA-AAAGAAAA
**
5467562 AA-AGAAAAAAAAATCGAAAA
1 AAGAGAAAAAAAAAAAGAAAA
*
5467582 AAGAGAGAAAAAAA
1 AAGAGAAAAAAAAA
5467596 TGCAAACCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.02
Consensus pattern (21 bp):
AAGAGAAAAAAAAAAAGAAAA
Found at i:5467583 original size:22 final size:23
Alignment explanation
Indices: 5467541--5467595 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
5467531 TAGAAAGAAG
5467541 AAGAAAAAAAAACAAAGAAAA-A
1 AAGAAAAAAAAACAAAGAAAAGA
*
5467563 AAGAAAAAAAAATCGAA-AAAAGA
1 AAGAAAAAAAAA-CAAAGAAAAGA
*
5467586 GAGAAAAAAA
1 AAGAAAAAAA
5467596 TGCAAACCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.02
Consensus pattern (23 bp):
AAGAAAAAAAAACAAAGAAAAGA
Found at i:5467596 original size:21 final size:20
Alignment explanation
Indices: 5467557--5467596 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
5467547 AAAAAACAAA
5467557 GAAAAAAAGAAAAAAAAATC
1 GAAAAAAAGAAAAAAAAATC
*
5467577 GAAAAAAGAGAGAAAAAAAT
1 GAAAAAA-AGAAAAAAAAAT
5467597 GCAAACCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.05
Consensus pattern (20 bp):
GAAAAAAAGAAAAAAAAATC
Found at i:5470502 original size:3 final size:3
Alignment explanation
Indices: 5470494--5470561 Score: 79
Period size: 3 Copynumber: 23.3 Consensus size: 3
5470484 TGGCAATGAC
5470494 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT -AT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
5470539 CAT AGAA AAT AAT GAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT A
5470562 TATGAATTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
2 5 0.09
3 48 0.87
4 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5470576 original size:29 final size:28
Alignment explanation
Indices: 5470495--5470597 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 28
5470485 GGCAATGACA
5470495 ATAATAATAATA-ATA-ATAATAATAATAAT
1 ATAATAATAATATA-ACATAA-AA-AATAAT
*
5470524 ATAATAATAATATAACATAGAAAATAAT
1 ATAATAATAATATAACATAAAAAATAAT
** *
5470552 GATAATAAT-ATATGAATTTAAAAAATATT
1 -ATAATAATAATAT-AACATAAAAAATAAT
5470581 ATATATACATACATATA
1 ATA-ATA-ATA-ATATA
5470598 CCAAAGACAT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
28 13 0.21
29 37 0.61
30 6 0.10
31 1 0.02
32 4 0.07
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (28 bp):
ATAATAATAATATAACATAAAAAATAAT
Found at i:5471134 original size:28 final size:27
Alignment explanation
Indices: 5471085--5471174 Score: 85
Period size: 30 Copynumber: 3.1 Consensus size: 27
5471075 GTGTACATGA
5471085 AAAATAATAATGATATGATAAAAAAAGAT
1 AAAATAATAAT-ATATGATAAAAAAA-AT
*
5471114 ACAATATAATAATA-ATG-TAAAGAAAAT
1 A-AA-ATAATAATATATGATAAAAAAAAT
*
5471141 AAAATAATAATATTTATAATAAAAGAAAAT
1 AAAATAATAATA--TATGATAAAA-AAAAT
5471171 AAAA
1 AAAA
5471175 GAGTGTATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
25 9 0.18
26 2 0.04
27 3 0.06
28 9 0.18
29 8 0.16
30 12 0.24
31 8 0.16
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.26
Consensus pattern (27 bp):
AAAATAATAATATATGATAAAAAAAAT
Found at i:5471164 original size:25 final size:25
Alignment explanation
Indices: 5471119--5471172 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
5471109 AAGATACAAT
*
5471119 ATAATAATAATGTAAAGAAAATAAA
1 ATAATAATAATGTAAAGAAAAGAAA
* *
5471144 ATAATAAT-ATTTATAATAAAAGAAA
1 ATAATAATAATGTA-AAGAAAAGAAA
5471169 ATAA
1 ATAA
5471173 AAGAGTGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (25 bp):
ATAATAATAATGTAAAGAAAAGAAA
Found at i:5471784 original size:13 final size:13
Alignment explanation
Indices: 5471758--5471800 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
5471748 CCGGCTCCGT
**
5471758 CCGCCGCCATCCA
1 CCGCCGCCGGCCA
5471771 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
* *
5471784 CCGTCGTCGGCCA
1 CCGCCGCCGGCCA
5471797 CCGC
1 CCGC
5471801 GCACGGTGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.09, C:0.58, G:0.26, T:0.07
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:5472620 original size:44 final size:44
Alignment explanation
Indices: 5472571--5473265 Score: 991
Period size: 44 Copynumber: 16.3 Consensus size: 44
5472561 AGGAACACCG
* *
5472571 ATCTGTTATTTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
5472615 ATCTGTTATCTTCGATCTGCTCTCCG-CGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* ** *
5472658 ATCTGTTATCTTCGATCTGTTCTCTACCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
*
5472702 A----TTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
*
5472742 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTAAAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * *
5472786 ATCTGTTATCTTCGATCTGCTCTCTGCTGCTACAGAGGCGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
5472830 ATCTGTTATCTTCGATCTGTTCTCCGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * *
5472874 ATC----ATCTTCGATCTGCTTTCCGTCGTTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * *
5472914 ATCTGTTATCTTCGATCTGTTCTCCGCCGCTACAGAGATGCTAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
5472958 ATC----ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * *
5472998 ATCTGTTATCTTCGATCTGCTCTCTGCCGCTATAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
5473042 ATATGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
*
5473086 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
*
5473130 ATC----ATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
5473170 ATC----ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
5473210 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGCGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
5473254 ATCTGTTATCTT
1 ATCTGTTATCTT
5473266 TTTCAAGGAA
Statistics
Matches: 588, Mismatches: 46, Indels: 34
0.88 0.07 0.05
Matches are distributed among these distances:
40 188 0.32
43 40 0.07
44 360 0.61
ACGTcount: A:0.21, C:0.31, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
Found at i:5473001 original size:212 final size:211
Alignment explanation
Indices: 5472571--5473265 Score: 1017
Period size: 212 Copynumber: 3.3 Consensus size: 211
5472561 AGGAACACCG
*
5472571 ATCTGTTATTTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
1 ATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
**
5472636 CTCCG-CGCTACAGAGACGCCAAATCTGTTATCTTCGATCTG-TTCTCTACCGCTACAGAGATGC
66 CTCCGCCGCTACAGAGACGCCAAATC---TATCTTCGATCTGCTT-TCCGCCGCTACAGAGATGC
* *
5472699 CAAA--TTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGC
127 CAAATCTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATC----ATCTTCGATCTGC
*
5472762 TCTCCGCCGCTAAAGAGACGCCAA
188 TCTCCGCCGCTACAGAGACGCCAA
* * *
5472786 ATCTGTTATCTTCGATCTGCTCTCTGCTGCTACAGAGGCGCCAAATCTGTTATCTTCGATCTGTT
1 ATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
* * * *
5472851 CTCCGCCGCTACAGAGATGCCAAATC-ATCTTCGATCTGCTTTCCGTCGTTACAGAGACGCCAAA
66 CTCCGCCGCTACAGAGACGCCAAATCTATCTTCGATCTGCTTTCCGCCGCTACAGAGATGCCAAA
* *
5472915 TCTGTTATCTTCGATCTGTTCTCCGCCGCTACAGAGATGCTAAATCATCTTCGATCTGCTCTCCG
131 TC--TTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCCG
5472980 CCGCTACAGAGACGCCAA
194 CCGCTACAGAGACGCCAA
* * *
5472998 ATCTGTTATCTTCGATCTGCTCTCTGCCGCTATAGAGATGCCAAATATGTTATCTTCGATCTGCT
1 ATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
* *
5473063 CTCTGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCC
66 CTCCGCCGCTACAGAGACGCCAAATC---TATCTTCGATCTGCTTTCCGCCGCTACAGAGATGCC
5473128 AAATC--ATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCC
128 AAATCTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCC
5473191 GCCGCTACAGAGACGCCAA
193 GCCGCTACAGAGACGCCAA
* * *
5473210 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGCGATGCCAAATCTGTTATCTT
1 ATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCTT
5473266 TTTCAAGGAA
Statistics
Matches: 437, Mismatches: 33, Indels: 23
0.89 0.07 0.05
Matches are distributed among these distances:
212 276 0.63
213 2 0.00
215 66 0.15
216 93 0.21
ACGTcount: A:0.21, C:0.31, G:0.18, T:0.30
Consensus pattern (211 bp):
ATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
CTCCGCCGCTACAGAGACGCCAAATCTATCTTCGATCTGCTTTCCGCCGCTACAGAGATGCCAAA
TCTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCCGCC
GCTACAGAGACGCCAA
Found at i:5473029 original size:256 final size:255
Alignment explanation
Indices: 5472571--5473265 Score: 1074
Period size: 256 Copynumber: 2.7 Consensus size: 255
5472561 AGGAACACCG
* * *
5472571 ATCTGTTATTTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATC----ATCTTCGATCTGCT
**
5472636 CTCCGCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGTTCTCTACCGCTACAGAGATGCCA
62 CTCCGCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGTTCTCCGCCGCTACAGAGATGCCA
* *
5472701 AATTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTC
127 AATCATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTC
* * *
5472766 CGCCGCTAAAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGCTGCTACAGAGGCGCCAA
192 CGCCGCTAAAGAGACGCCAAATATGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAA
* *
5472830 ATCTGTTATCTTCGATCTGTTCTCCGCCGCTACAGAGATGCCAAATCATCTTCGATCTGCTTTCC
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCC
* *
5472895 GTCGTTACAGAGACGCCAAATCTGTTATCTTCGATCTGTTCTCCGCCGCTACAGAGATGCTAAAT
66 G-CGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGTTCTCCGCCGCTACAGAGATGCCAAAT
*
5472960 CATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGC
130 CATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGC
* *
5473025 CGCTATAGAGATGCCAAATATGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAA
195 CGCTAAAGAGACGCCAAATATGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAA
5473086 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCC
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCC
* * *
5473151 GCCGCTACAGAGATGCCAAATC----ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAAT
66 G-CGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGTTCTCCGCCGCTACAGAGATGCCAAAT
* *
5473212 CTGTTATCTTCGATCTGCTCTCCGCCGCTACAGCGATGCCAAATCTGTTATCTT
130 C----ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTT
5473266 TTTCAAGGAA
Statistics
Matches: 404, Mismatches: 27, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
252 37 0.09
255 18 0.04
256 306 0.76
259 43 0.11
ACGTcount: A:0.21, C:0.31, G:0.18, T:0.30
Consensus pattern (255 bp):
ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATCATCTTCGATCTGCTCTCC
GCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGTTCTCCGCCGCTACAGAGATGCCAAATC
ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCCGCC
GCTAAAGAGACGCCAAATATGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAA
Found at i:5484951 original size:80 final size:77
Alignment explanation
Indices: 5484816--5484974 Score: 275
Period size: 80 Copynumber: 2.0 Consensus size: 77
5484806 CGGAGAGATA
5484816 TTTGATTATTTCGGTCAGAACGGGAGATTGCAACCCAGATAGGGCACTATTCCCCGAACTGCCCA
1 TTTGATTATTTCGGTCAGAACGGGAGATTGCAACCCAGATAGGGCACTATTCCCCGAACTGCCCA
5484881 AACATCAAACAC
66 AACATCAAACAC
5484893 TTTGATTATTTCGGTCAG-ACGGGAGATTGCAACCCAGCACGATAGGGCACTATTCCCCGAACTG
1 TTTGATTATTTCGGTCAGAACGGGAGATTGCAA-CC--CA-GATAGGGCACTATTCCCCGAACTG
5484957 CCCAAACATCAAACAC
62 CCCAAACATCAAACAC
5484973 TT
1 TT
5484975 CTTTCGTTTT
Statistics
Matches: 78, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
76 14 0.18
77 20 0.26
79 2 0.03
80 42 0.54
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (77 bp):
TTTGATTATTTCGGTCAGAACGGGAGATTGCAACCCAGATAGGGCACTATTCCCCGAACTGCCCA
AACATCAAACAC
Found at i:5485735 original size:3 final size:3
Alignment explanation
Indices: 5485727--5485754 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5485717 AATGACAATG
5485727 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5485755 ATAGAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5485975 original size:23 final size:23
Alignment explanation
Indices: 5485948--5486025 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
5485938 TGATATTAAA
5485948 AATATATACATAAAAATATA-AT
1 AATATATACATAAAAATATACAT
* *
5485970 AGATATATATAT-ATAATATACAT
1 A-ATATATACATAAAAATATACAT
* *
5485993 AATATAGTA-TTAAAAATATATAT
1 AATATA-TACATAAAAATATACAT
*
5486016 AATACATACA
1 AATATATACA
5486026 CATTAGAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
22 16 0.36
23 28 0.64
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.35
Consensus pattern (23 bp):
AATATATACATAAAAATATACAT
Found at i:5486374 original size:25 final size:25
Alignment explanation
Indices: 5486329--5486382 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
5486319 ACGATACAAT
*
5486329 ATAATAATAATGTAAAGAAAATAAA
1 ATAATAATAATGTAAAGAAAAGAAA
* *
5486354 ATAATAAT-ATTTATAATAAAAGAAA
1 ATAATAATAATGTA-AAGAAAAGAAA
5486379 ATAA
1 ATAA
5486383 AAGAGTGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (25 bp):
ATAATAATAATGTAAAGAAAAGAAA
Found at i:5487001 original size:13 final size:13
Alignment explanation
Indices: 5486985--5487009 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5486975 CATCCGCCGC
5486985 CGCCGGCCACCGT
1 CGCCGGCCACCGT
5486998 CGCCGGCCACCG
1 CGCCGGCCACCG
5487010 CGCACGGTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.56, G:0.32, T:0.04
Consensus pattern (13 bp):
CGCCGGCCACCGT
Found at i:5487192 original size:24 final size:24
Alignment explanation
Indices: 5487160--5487217 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
5487150 TTGCACTTCT
*
5487160 TTTTTTTTTTTG-ATGGCTTTGTTA
1 TTTTTTTTTTTGTATGGC-TTGCTA
* *
5487184 TTTTTTTTTTTGTATTGCTTGCTG
1 TTTTTTTTTTTGTATGGCTTGCTA
5487208 TTTTTTTTTT
1 TTTTTTTTTT
5487218 AAGAAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.05, C:0.05, G:0.14, T:0.76
Consensus pattern (24 bp):
TTTTTTTTTTTGTATGGCTTGCTA
Found at i:5495727 original size:59 final size:59
Alignment explanation
Indices: 5495587--5495727 Score: 146
Period size: 59 Copynumber: 2.4 Consensus size: 59
5495577 GATTTCATTT
* * * * * * *
5495587 TATTATTATA-TTACTACTATTTTGTTATTATTATTTGGGTATTGTATAATTTTTATTT
1 TATTATTAAATTTACTACTATTTTGTTATTATTATTTAGATATAGTATAACTCTTATTA
* *
5495645 TATTATTAATATCGTTAC--C-ATTTTGTTGTTATTATTTAGATATAGTATAACTCTTGTTA
1 TATTATTAA-AT--TTACTACTATTTTGTTATTATTATTTAGATATAGTATAACTCTTATTA
5495704 TATTATTAAATTTACTACTATTTT
1 TATTATTAAATTTACTACTATTTT
5495728 ATAAGCATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
56 4 0.06
58 11 0.16
59 47 0.70
60 1 0.01
62 4 0.06
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.57
Consensus pattern (59 bp):
TATTATTAAATTTACTACTATTTTGTTATTATTATTTAGATATAGTATAACTCTTATTA
Found at i:5499570 original size:30 final size:31
Alignment explanation
Indices: 5499515--5499572 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5499505 AAATTTTAAA
*
5499515 ATTCGAAAAGAATAGGGACTAAAATTGACCG
1 ATTCGAAAAGAACAGGGACTAAAATTGACCG
* *
5499546 ATTCGAAAAGTACATGGA-TAAAATTGA
1 ATTCGAAAAGAACAGGGACTAAAATTGA
5499573 TCAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (31 bp):
ATTCGAAAAGAACAGGGACTAAAATTGACCG
Found at i:5501154 original size:9 final size:9
Alignment explanation
Indices: 5501140--5501170 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5501130 GTTTAATTTT
*
5501140 ATAATTTGA
1 ATAATTTAA
5501149 ATAATTTAA
1 ATAATTTAA
5501158 ATAATTTAA
1 ATAATTTAA
5501167 ATAA
1 ATAA
5501171 CAAATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (9 bp):
ATAATTTAA
Found at i:5501279 original size:20 final size:19
Alignment explanation
Indices: 5501233--5501284 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
5501223 TTTTTCTCTC
5501233 AAAAAA-TTTAAAATAATT
1 AAAAAATTTTAAAATAATT
*
5501251 AAAATAATTTTAAAATATTT
1 AAAA-AATTTTAAAATAATT
*
5501271 ATAAAAATTCTAAA
1 A-AAAAATTTTAAA
5501285 TTTTATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 20 0.69
21 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAAATTTTAAAATAATT
Found at i:5503698 original size:21 final size:21
Alignment explanation
Indices: 5503672--5503711 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5503662 TAAATTAAAT
*
5503672 AAAATTGA-TTATTTTTATTAA
1 AAAATT-ATTTATTTGTATTAA
5503693 AAAATTATTTATTTGTATT
1 AAAATTATTTATTTGTATT
5503712 GTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
AAAATTATTTATTTGTATTAA
Found at i:5506031 original size:32 final size:33
Alignment explanation
Indices: 5505979--5506055 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 33
5505969 AAATCTAATA
*
5505979 AATTCAATTAATCAATGAGTTA-TCAAATTAAATT
1 AATT-AATTAATCAATGAGTTACT-AAATTAAAGT
* *
5506013 AATTAATTTATC-ATGAGTTACTAAATTCAAGT
1 AATTAATTAATCAATGAGTTACTAAATTAAAGT
5506045 AATTAATTAAT
1 AATTAATTAAT
5506056 ATGTTTATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 26 0.68
33 8 0.21
34 4 0.11
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.40
Consensus pattern (33 bp):
AATTAATTAATCAATGAGTTACTAAATTAAAGT
Found at i:5506847 original size:11 final size:10
Alignment explanation
Indices: 5506827--5506894 Score: 59
Period size: 9 Copynumber: 6.4 Consensus size: 10
5506817 TAACCCTTTT
5506827 AAATT-TTAA
1 AAATTATTAA
5506836 AAATTATTTAA
1 AAATTA-TTAA
5506847 AAATTA-TAA
1 AAATTATTAA
*
5506856 AAATTATAAA
1 AAATTATTAA
5506866 CAAGATTTATTTAAA
1 -AA-A-TTA-TT-AA
5506881 AAATTATTAA
1 AAATTATTAA
5506891 AAAT
1 AAAT
5506895 AAAAATACCA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
9 14 0.29
10 8 0.16
11 14 0.29
12 4 0.08
13 4 0.08
14 3 0.06
15 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (10 bp):
AAATTATTAA
Found at i:5507829 original size:13 final size:13
Alignment explanation
Indices: 5507811--5507846 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
5507801 TAAAATTGTG
5507811 AAAAAATAACAAC
1 AAAAAATAACAAC
*
5507824 AAAAAATAATAAC
1 AAAAAATAACAAC
5507837 AAAACAATAA
1 AAAA-AATAA
5507847 ATAAAATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAAAATAACAAC
Found at i:5507865 original size:23 final size:22
Alignment explanation
Indices: 5507813--5507868 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
5507803 AAATTGTGAA
* *
5507813 AAAATAACAA-CAAAAAATAAT
1 AAAATAACAATAAAAAAATAAG
5507834 AACAA-AACAATAAATAAAATAAG
1 AA-AATAACAATAAA-AAAATAAG
5507857 AAAATAACAATA
1 AAAATAACAATA
5507869 TCCAACCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 7 0.24
22 6 0.21
23 16 0.55
ACGTcount: A:0.75, C:0.09, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAATAACAATAAAAAAATAAG
Found at i:5511313 original size:21 final size:21
Alignment explanation
Indices: 5511289--5511329 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5511279 TTTTTAATCC
5511289 ATTTATAC-TCGTAATTATTTA
1 ATTT-TACTTCGTAATTATTTA
*
5511310 ATTTTACTTTGTAATTATTT
1 ATTTTACTTCGTAATTATTT
5511330 GAAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTTACTTCGTAATTATTTA
Found at i:5522203 original size:14 final size:15
Alignment explanation
Indices: 5522184--5522212 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5522174 GAATATAGTA
5522184 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
5522198 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
5522213 GAGATACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:5523438 original size:16 final size:15
Alignment explanation
Indices: 5523408--5523470 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 15
5523398 TAGTGGAATG
5523408 GAATAGGACTT-TAAT
1 GAATAGGA-TTGTAAT
5523423 AGAATAGGATTGTAAT
1 -GAATAGGATTGTAAT
*
5523439 GCAATAGGGTTGTAAT
1 G-AATAGGATTGTAAT
5523455 GAAATA-GAGTTGTAAT
1 G-AATAGGA-TTGTAAT
5523471 TAGTAATTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.10
16 37 0.90
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (15 bp):
GAATAGGATTGTAAT
Found at i:5529289 original size:30 final size:31
Alignment explanation
Indices: 5529229--5529292 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
5529219 TCTTCATTGT
*
5529229 TAATTATATTACTAAATTAACATTAGAATAA
1 TAATTATATTACTAAATTAACATGAGAATAA
* *
5529260 TAATT-TATTACTATTATT-ACATGATAATAA
1 TAATTATATTACTA-AATTAACATGAGAATAA
5529290 TAA
1 TAA
5529293 AAGAACGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (31 bp):
TAATTATATTACTAAATTAACATGAGAATAA
Found at i:5537319 original size:92 final size:92
Alignment explanation
Indices: 5537174--5537342 Score: 250
Period size: 92 Copynumber: 1.8 Consensus size: 92
5537164 CCATAGTGTC
* * * * * ***
5537174 TTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTGTT
1 TTTCAACCATAGTCTTACTCATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
5537239 CATTTCATATCACGTTGCCACGGTATT
66 CATTTCATATCACGTTGCCACGGTATT
5537266 TTTCAACCATAGTCTTA-TACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTAC
1 TTTCAACCATAGTCTTACT-CATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTAC
5537330 ACATTTCATATCA
65 ACATTTCATATCA
5537343 GAGAGCACGC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
91 1 0.01
92 67 0.99
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (92 bp):
TTTCAACCATAGTCTTACTCATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACA
CATTTCATATCACGTTGCCACGGTATT
Found at i:5537341 original size:46 final size:46
Alignment explanation
Indices: 5537162--5537343 Score: 213
Period size: 46 Copynumber: 4.0 Consensus size: 46
5537152 TTTGACATGA
* * * * * *
5537162 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
5537208 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* * * * *
5537254 TGCCACGGTATTTTTCAACCATAGTCTTATACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5537300 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5537344 AGAGCACGCT
Statistics
Matches: 116, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
45 4 0.03
46 112 0.97
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:5539515 original size:20 final size:21
Alignment explanation
Indices: 5539478--5539537 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
5539468 CCTTTTATGA
*
5539478 TAAAATAATAAAATATCTCAT
1 TAAAATAATAAAATATCTAAT
*
5539499 TAAAATAAT-ATATATCTAAT
1 TAAAATAATAAAATATCTAAT
*
5539519 TAAATAATCATAAAATATC
1 T-AA-AATAATAAAATATC
5539538 ATCAACATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.31
21 11 0.34
22 5 0.16
23 6 0.19
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATAATAAAATATCTAAT
Found at i:5544042 original size:18 final size:16
Alignment explanation
Indices: 5544008--5544050 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
5543998 TAATCTTTTT
5544008 ATTTTTATAAAAATTG
1 ATTTTTATAAAAATTG
**
5544024 AAATTTTTATAAATCTTG
1 --ATTTTTATAAAAATTG
5544042 ATTTTTATA
1 ATTTTTATA
5544051 TATTTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTTTTATAAAAATTG
Found at i:5552817 original size:2 final size:2
Alignment explanation
Indices: 5552810--5552848 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5552800 AATCCTTTGC
5552810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5552849 ACCTTAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5553210 original size:22 final size:22
Alignment explanation
Indices: 5553185--5553263 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
5553175 TGGCCCCTTT
**
5553185 ATATTAAACTCCAAAACCCTTC
1 ATATTAAACTCCAAAACCCAAC
*
5553207 ATATTAAACCCCAAAACCCAAC
1 ATATTAAACTCCAAAACCCAAC
*
5553229 ACATTAAACT--AAAACCCAAC
1 ATATTAAACTCCAAAACCCAAC
*
5553249 AAATTAAAC-CCAAAA
1 ATATTAAACTCCAAAA
5553264 ATACCCATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 18 0.37
21 4 0.08
22 27 0.55
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (22 bp):
ATATTAAACTCCAAAACCCAAC
Found at i:5553244 original size:20 final size:20
Alignment explanation
Indices: 5553219--5553257 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5553209 ATTAAACCCC
*
5553219 AAAACCCAACACATTAAACT
1 AAAACCCAACAAATTAAACT
5553239 AAAACCCAACAAATTAAAC
1 AAAACCCAACAAATTAAAC
5553258 CCAAAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAACCCAACAAATTAAACT
Found at i:5555952 original size:26 final size:26
Alignment explanation
Indices: 5555921--5556028 Score: 164
Period size: 26 Copynumber: 4.2 Consensus size: 26
5555911 TGAAATGGCC
5555921 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
5555947 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
* *
5555973 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
5555999 ATCATAGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
5556025 ATCA
1 ATCA
5556029 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
25 4 0.05
26 68 0.91
27 3 0.04
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:5557331 original size:20 final size:17
Alignment explanation
Indices: 5557306--5557358 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 17
5557296 TTCTTTATTA
5557306 AATATTGTTATTATTATTC
1 AATATT-TTATTATTA-TC
*
5557325 TAATATTATTAATATTATC
1 -AATATT-TTATTATTATC
5557344 AATATATTTATTATT
1 AATAT-TTTATTATT
5557359 TTTAGTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 12 0.41
19 3 0.10
20 14 0.48
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (17 bp):
AATATTTTATTATTATC
Found at i:5557521 original size:22 final size:22
Alignment explanation
Indices: 5557479--5557560 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 22
5557469 AATACTAGTG
*
5557479 TATATTTTATTATGTATGTATA
1 TATATTTTATTATATATGTATA
*
5557501 TATATTCTTTTTATATA-GTAT-
1 TATATT-TTATTATATATGTATA
* *
5557522 TATCGTTTCTATTATTATATCTATA
1 TAT-ATTT-TATTA-TATATGTATA
*
5557547 TTTATGTTTATTAT
1 TATAT-TTTATTAT
5557561 TTTCACTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
21 4 0.09
22 16 0.35
23 13 0.28
24 9 0.20
25 4 0.09
ACGTcount: A:0.28, C:0.05, G:0.06, T:0.61
Consensus pattern (22 bp):
TATATTTTATTATATATGTATA
Found at i:5557767 original size:21 final size:21
Alignment explanation
Indices: 5557736--5557791 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
5557726 TAAATATTAT
*
5557736 ATTTTCTATATATTATGTATAC
1 ATTTT-TATATATTACGTATAC
*
5557758 ATTTTTATATATTACGTATAT
1 ATTTTTATATATTACGTATAC
5557779 ATCTTTTA-ATATT
1 AT-TTTTATATATT
5557792 GTACTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTTTTATATATTACGTATAC
Found at i:5557815 original size:59 final size:62
Alignment explanation
Indices: 5557703--5557821 Score: 147
Period size: 59 Copynumber: 2.0 Consensus size: 62
5557693 TAAATACTCT
* * * *
5557703 TATATTATGTATATTATTCTTTTTAAATATTATATTTTCTATATATTATGTATACATTTTTA
1 TATATTACGTATATTATTCTTTTTAAATATTATATTTTATACATATCATGTATACATTTTTA
* *
5557765 TATATTACGTATA-TA-TC-TTTT-AATATTGTACTTTTATACATATCATGTATATATTTT
1 TATATTACGTATATTATTCTTTTTAAATATTATA-TTTTATACATATCATGTATACATTTT
5557822 GAATACTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
58 8 0.16
59 26 0.52
60 2 0.04
61 2 0.04
62 12 0.24
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (62 bp):
TATATTACGTATATTATTCTTTTTAAATATTATATTTTATACATATCATGTATACATTTTTA
Found at i:5557890 original size:16 final size:16
Alignment explanation
Indices: 5557869--5557899 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5557859 TATATTATGC
*
5557869 TTTTTAATACTATATT
1 TTTTTAATACCATATT
5557885 TTTTTAATACCATAT
1 TTTTTAATACCATAT
5557900 ATATTGTGTT
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:0.10, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTTAATACCATATT
Found at i:5558259 original size:25 final size:23
Alignment explanation
Indices: 5558198--5558281 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 23
5558188 TTTCTAATAC
5558198 TATATTATGTTTTCATATATATTATG
1 TATA-TAT-TTTTCATATATA-TATG
5558224 TATATACATTTTTCAATATTATATATG
1 TATAT--ATTTTTC-ATA-TATATATG
**
5558251 TATATA-TTTTCATATATATGCG
1 TATATATTTTTCATATATATATG
5558273 TATATATTT
1 TATATATTT
5558282 ATGTAGTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
22 12 0.24
23 5 0.10
24 5 0.10
25 2 0.04
26 9 0.18
27 14 0.27
28 4 0.08
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (23 bp):
TATATATTTTTCATATATATATG
Found at i:5558269 original size:27 final size:26
Alignment explanation
Indices: 5558207--5558269 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 26
5558197 CTATATTATG
*
5558207 TTTTCATATATATTATGTATATACAT
1 TTTTCATATATATTATATATATACAT
* *
5558233 TTTTC--A-ATATTATATATGTATAT
1 TTTTCATATATATTATATATATACAT
5558256 ATTTTCATATATAT
1 -TTTTCATATATAT
5558270 GCGTATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 14 0.47
24 6 0.20
26 6 0.20
27 4 0.13
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (26 bp):
TTTTCATATATATTATATATATACAT
Found at i:5558601 original size:22 final size:21
Alignment explanation
Indices: 5558569--5558631 Score: 51
Period size: 22 Copynumber: 3.0 Consensus size: 21
5558559 CTAATATAGG
5558569 TATATA-T-TGTATATATTTT
1 TATATATTATGTATATATTTT
5558588 ATATATATTATGTACT-TATTTT
1 -TATATATTATGTA-TATATTTT
* *
5558610 TAATGTTTTAATGTATATATTT
1 T-ATATATT-ATGTATATATTT
5558632 CTTAAACTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 6 0.17
21 2 0.06
22 16 0.46
23 11 0.31
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
TATATATTATGTATATATTTT
Found at i:5570858 original size:73 final size:73
Alignment explanation
Indices: 5570753--5570889 Score: 231
Period size: 73 Copynumber: 1.9 Consensus size: 73
5570743 TTGGTTTCAA
*
5570753 AAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTC-AATTT
1 AAAAATCAACTCACATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGAGGT-ATTTCTAATTT
5570817 CTGCTTGCC
65 CTGCTTGCC
* *
5570826 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTATTTCTAATTT
1 AAAAATCAACTCACATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGAGGTATTTCTAATTT
5570890 TCGTTTTTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 5 0.08
73 55 0.92
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (73 bp):
AAAAATCAACTCACATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGAGGTATTTCTAATTTC
TGCTTGCC
Found at i:5570954 original size:87 final size:87
Alignment explanation
Indices: 5570808--5570987 Score: 292
Period size: 87 Copynumber: 2.1 Consensus size: 87
5570798 GCTGAGGTAA
*
5570808 TTTCAATTTCTGCTTGCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGC
1 TTTCAATTTATGCTTGCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGC
5570873 TGAGGTA-TTTCTAATTT-TCGTT
66 TGAGGTATTTTC-AATTTCT-GTT
** *
5570895 TTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTTCAATTTATGCTTGCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGC
5570960 TGAGGTATTTTCAATTTCTGTT
66 TGAGGTATTTTCAATTTCTGTT
5570982 TTTCAA
1 TTTCAA
5570988 AAATCAACTC
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
87 82 0.94
88 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (87 bp):
TTTCAATTTATGCTTGCCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGC
TGAGGTATTTTCAATTTCTGTT
Found at i:5571054 original size:54 final size:55
Alignment explanation
Indices: 5570967--5571074 Score: 175
Period size: 54 Copynumber: 2.0 Consensus size: 55
5570957 CGCTGAGGTA
* *
5570967 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGA-AAGGTGAGTTGAGCC
1 TTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAA-ATGAGTTGAGCC
5571022 TTTT-AATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGC
1 TTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGC
5571075 TCAGGATCAC
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
54 44 0.88
55 6 0.12
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (55 bp):
TTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCC
Found at i:5571529 original size:22 final size:22
Alignment explanation
Indices: 5571494--5571540 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5571484 CAATTTTGGC
* * *
5571494 CCCTTTATATTAAACTCCAAAA
1 CCCTTCATACTAAACCCCAAAA
5571516 CCCTTCATACTAAACCCCAAAA
1 CCCTTCATACTAAACCCCAAAA
5571538 CCC
1 CCC
5571541 AACACATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (22 bp):
CCCTTCATACTAAACCCCAAAA
Found at i:5571551 original size:22 final size:21
Alignment explanation
Indices: 5571502--5571564 Score: 56
Period size: 22 Copynumber: 3.0 Consensus size: 21
5571492 GCCCCTTTAT
** *
5571502 ATTAAACTCCAAAACCCTTCAT
1 ATTAAAC-CCAAAACCCAACAC
*
5571524 ACTAAACCCCAAAACCCAACAC
1 ATTAAA-CCCAAAACCCAACAC
*
5571546 ATTAAA-CTAAAACCCAACA
1 ATTAAACCCAAAACCCAACA
5571565 AATAGATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 12 0.35
22 21 0.62
23 1 0.03
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (21 bp):
ATTAAACCCAAAACCCAACAC
Found at i:5571783 original size:22 final size:22
Alignment explanation
Indices: 5571758--5571808 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
5571748 ATTATATTTC
* *
5571758 TATATATTATGTATACATTTTT
1 TATATATTACGTATACATCTTT
*
5571780 TATATATTACGTATATATCTTT
1 TATATATTACGTATACATCTTT
5571802 TA-ATATT
1 TATATATT
5571809 GTACTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (22 bp):
TATATATTACGTATACATCTTT
Found at i:5571907 original size:16 final size:16
Alignment explanation
Indices: 5571886--5571916 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5571876 TATATTTTGC
*
5571886 TTTTTAATACTATATT
1 TTTTTAATACCATATT
5571902 TTTTTAATACCATAT
1 TTTTTAATACCATAT
5571917 ATATTGTGTT
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:0.10, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTTAATACCATATT
Found at i:5572384 original size:19 final size:18
Alignment explanation
Indices: 5572350--5572385 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5572340 ATTATGTATG
5572350 TATATATATATACATTTA
1 TATATATATATACATTTA
*
5572368 TATATATTATGTACATTT
1 TATATA-TATATACATTT
5572386 TAAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (18 bp):
TATATATATATACATTTA
Found at i:5572588 original size:24 final size:24
Alignment explanation
Indices: 5572567--5572631 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
5572557 CTAATATAGG
5572567 TATATA-T-TGTATATATTTTATA
1 TATATATTATGTATATATTTTATA
*
5572589 TATATATTATGTATTTATTTTA-A
1 TATATATTATGTATATATTTTATA
* *
5572612 -ATGTTTTCATGTATATATTT
1 TATATATT-ATGTATATATTT
5572632 CTTAAACTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 11 0.31
23 13 0.36
24 12 0.33
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (24 bp):
TATATATTATGTATATATTTTATA
Found at i:5581268 original size:22 final size:22
Alignment explanation
Indices: 5581240--5581283 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5581230 GCTAGCATAT
5581240 ATCCATTGGCTAAAACAATGTA
1 ATCCATTGGCTAAAACAATGTA
5581262 ATCCATTGGCTAAAACAATGTA
1 ATCCATTGGCTAAAACAATGTA
5581284 TTTCTACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (22 bp):
ATCCATTGGCTAAAACAATGTA
Found at i:5583677 original size:16 final size:18
Alignment explanation
Indices: 5583645--5583680 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5583635 TATAATACTT
5583645 TATATTATGTTATATTTA
1 TATATTATGTTATATTTA
5583663 TATATTATG-TA-ATTTA
1 TATATTATGTTATATTTA
5583679 TA
1 TA
5583681 ACATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
TATATTATGTTATATTTA
Found at i:5590796 original size:3 final size:3
Alignment explanation
Indices: 5590790--5590826 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5590780 GACACTATAT
5590790 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5590827 ACTATTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5591650 original size:26 final size:26
Alignment explanation
Indices: 5591614--5591723 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
5591604 TGATACAAAT
5591614 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
5591640 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5591666 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5591692 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
5591718 TGATAA
1 TGATAA
5591724 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:5593431 original size:27 final size:26
Alignment explanation
Indices: 5593327--5593441 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
5593317 TGGAGGAAGC
* *
5593327 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
5593354 GATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
5593381 GTTCTGGTGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* **
5593408 GTATCTGGTGACTCTATCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
5593435 GTTCTGG
1 GTTCTGG
5593442 CAGCCATGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.08
27 56 0.72
28 16 0.21
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:5593434 original size:54 final size:54
Alignment explanation
Indices: 5593327--5593441 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
5593317 TGGAGGAAGC
* *
5593327 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTACCACATATATCT
* * * *
5593381 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTATCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTACCACATATATCT
5593435 GTTCTGG
1 GTTCTGG
5593442 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTACCACATATATCT
Found at i:5596070 original size:3 final size:3
Alignment explanation
Indices: 5596064--5596111 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
5596054 TTTTATATAC
5596064 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5596112 GTTATGTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5596241 original size:12 final size:12
Alignment explanation
Indices: 5596224--5596253 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5596214 TTTCAATATT
5596224 ATTATTATTATC
1 ATTATTATTATC
5596236 ATTATTATTATC
1 ATTATTATTATC
*
5596248 AATATT
1 ATTATT
5596254 TATATATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:5596828 original size:25 final size:25
Alignment explanation
Indices: 5596768--5596838 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
5596758 AATACTATAT
*
5596768 TACATTTTTACATATTATATCATGTATA
1 TACA-TTTT-CATA-TATATCATGTACA
* *
5596796 TATATTTTCATATATATTATGTACA
1 TACATTTTCATATATATCATGTACA
*
5596821 TACGTTTTCA-ATAT-TCAT
1 TACATTTTCATATATATCAT
5596839 TTTATACATA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
23 3 0.08
24 4 0.11
25 19 0.51
26 4 0.11
27 4 0.11
28 3 0.08
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (25 bp):
TACATTTTCATATATATCATGTACA
Found at i:5598394 original size:26 final size:26
Alignment explanation
Indices: 5598358--5598467 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
5598348 TGATACAAAT
5598358 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5598384 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5598410 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5598436 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5598462 TGATAA
1 TGATAA
5598468 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:5600122 original size:27 final size:27
Alignment explanation
Indices: 5600081--5600219 Score: 174
Period size: 27 Copynumber: 5.2 Consensus size: 27
5600071 GAGGAAGCGT
*
5600081 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
5600108 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5600135 TCTGGT-GCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5600161 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
5600189 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
5600215 TCTGG
1 TCTGG
5600220 CAGCCATGCT
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
26 29 0.29
27 56 0.56
28 15 0.15
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:5600165 original size:53 final size:54
Alignment explanation
Indices: 5600081--5600219 Score: 192
Period size: 53 Copynumber: 2.6 Consensus size: 54
5600071 GAGGAAGCGT
* * *
5600081 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGT-GCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
5600135 TCTGGTGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
*
5600189 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TCTGGTG-CTCTGCCACATATATCTGTTCTGG
5600220 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
53 41 0.53
54 26 0.34
55 10 0.13
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.35
Consensus pattern (54 bp):
TCTGGTGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
Found at i:5609941 original size:72 final size:72
Alignment explanation
Indices: 5609846--5610083 Score: 374
Period size: 72 Copynumber: 3.3 Consensus size: 72
5609836 AAATGCTAAA
*
5609846 CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
5609911 GTGTAAT
66 GTGTAAT
* * *
5609918 CTAGTTTTACCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATATAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
5609983 GTGTAAT
66 GTGTAAT
* *
5609990 CTAGTTTTATTAATAGTTGTTTATGTTTGGTATTTGGATATTG-ATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
* *
5610054 ACT-AAAT
66 -GTGTAAT
5610061 -TAGTTTTATCAATAGTTGTTTAT
1 CTAGTTTTATCAATAGTTGTTTAT
5610084 ATATGATTTT
Statistics
Matches: 153, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
70 22 0.14
71 23 0.15
72 108 0.71
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.55
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTGTAAT
Found at i:5611308 original size:35 final size:35
Alignment explanation
Indices: 5611262--5611331 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
5611252 TTGAACGAAC
*
5611262 TTTTGGTGTTTTGAAAAAAAAATGGGCCATTTTAA
1 TTTTGGTGTTTTGAAAAAAAAAGGGGCCATTTTAA
5611297 TTTTGGTGTTTTGAAAAAAAAAGGGGCCATTTTAA
1 TTTTGGTGTTTTGAAAAAAAAAGGGGCCATTTTAA
5611332 GGGATATGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (35 bp):
TTTTGGTGTTTTGAAAAAAAAAGGGGCCATTTTAA
Found at i:5611550 original size:12 final size:12
Alignment explanation
Indices: 5611513--5611551 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5611503 GAGAAAGTGA
*
5611513 TGATGATGACGA
1 TGATGATGACGG
* *
5611525 CGATGATGATGG
1 TGATGATGACGG
5611537 TGATGATGACGG
1 TGATGATGACGG
5611549 TGA
1 TGA
5611552 ATCAAGCAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.28, C:0.08, G:0.38, T:0.26
Consensus pattern (12 bp):
TGATGATGACGG
Found at i:5612006 original size:19 final size:19
Alignment explanation
Indices: 5611938--5611996 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
5611928 TTACTTAGAA
*
5611938 ATATTTAAA-ATTAATATTAT
1 ATATTAAAATATTAATA--AT
5611958 ATATTAAAATATTAATAAT
1 ATATTAAAATATTAATAAT
5611977 ATATTAAAATATTAATAAT
1 ATATTAAAATATTAATAAT
5611996 A
1 A
5611997 AGTTATAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
19 22 0.59
20 8 0.22
21 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTAAAATATTAATAAT
Found at i:5612197 original size:26 final size:26
Alignment explanation
Indices: 5612168--5612241 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
5612158 TTTCAAAAAT
*
5612168 ACTTCTCAAAAGCACTTCTCAAAAGC
1 ACTTTTCAAAAGCACTTCTCAAAAGC
* *
5612194 ACTTTTTC-ACAGCACTTTTCAAAAGC
1 AC-TTTTCAAAAGCACTTCTCAAAAGC
*
5612220 ACTTTTCAAAAGCA-TTGTCAAA
1 ACTTTTCAAAAGCACTTCTCAAA
5612242 CTGCCCTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 12 0.29
26 25 0.61
27 4 0.10
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTCTCAAAAGC
Found at i:5612207 original size:13 final size:14
Alignment explanation
Indices: 5612173--5612233 Score: 76
Period size: 13 Copynumber: 4.6 Consensus size: 14
5612163 AAAATACTTC
*
5612173 TCAAAAGCAC-TTC
1 TCAAAAGCACTTTT
5612186 TCAAAAGCACTTTT
1 TCAAAAGCACTTTT
*
5612200 TC-ACAGCAC-TTT
1 TCAAAAGCACTTTT
5612212 TCAAAAGCAC-TTT
1 TCAAAAGCACTTTT
5612225 TCAAAAGCA
1 TCAAAAGCA
5612234 TTGTCAAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
12 5 0.12
13 34 0.79
14 4 0.09
ACGTcount: A:0.38, C:0.26, G:0.08, T:0.28
Consensus pattern (14 bp):
TCAAAAGCACTTTT
Done.