Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000885.1 Hibiscus syriacus cultivar Beakdansim tig00001728_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1639497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:524011 original size:41 final size:41
Alignment explanation
Indices: 523936--524016 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
523926 CGATATTGTC
*
523936 TGGTATCGATACCTTTACCATGGTATCGATACTACCATACTA
1 TGGTATCGATACCCTTACCA-GGTATCGATACTACCATACTA
523978 TGGTATCGATACCCCTTACCA-GTATCGATACTACCATAC
1 TGGTATCGATA-CCCTTACCAGGTATCGATACTACCATAC
524017 CGATACCCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
41 18 0.49
42 11 0.30
43 8 0.22
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (41 bp):
TGGTATCGATACCCTTACCAGGTATCGATACTACCATACTA
Found at i:528632 original size:59 final size:59
Alignment explanation
Indices: 528540--529485 Score: 1368
Period size: 59 Copynumber: 16.1 Consensus size: 59
528530 ATTTTCCATA
* *
528540 TGGAAATTCATACACTTAATATGATTTCCTT-CTCATTTTAGCACACTTAA-TGCTCTAAC
1 TGGAAATTCATACACTTAATATGATTTCCTTAC-CATTTTAGCACAC-AAAGTGCTCTATC
** * * **
528599 TGGAAAACCATACACTTAGTATGATTT-CTTTCTCATTTTAGCACACTTAGTGCTCTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTAC-CATTTTAGCACACAAAGTGCTCTATC
* * * * *
528658 TGGAAATTCATACACTTAGTATGATTTCATTATCATTTTAGCACCCGAAGTGC-CATATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTC-TATC
* ** *
528717 TGGAAATTCATACATTTAATATGATTTCCTTACCA-TTTAGCACACTTAGTGCTCTATT
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
* * ** * * *
528775 TGGAAATCCATACACTTAGTATGATTTCCTTATTATTTTAGCACACGAAGTAC-CATCTC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTC-TATC
* **
528834 TGGAAATTCATACATTTAATATGATTTTGTTACCATTTTAGCACA-AGAAGTG-TCGTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACA-AAGTGCTC-TATC
* * *
528893 TGGAAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACAAAAAGTGCTTTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
* * * *
528952 TGGAAATTCATACATTTAATATGATTTCCATACCATTTTAGCAGACAAAGTTCTCTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
*
529011 TGGAAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
*
529070 TGGAAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
*
529129 TGGAAATTCATACACTTAATATGATTTCCTTATCATTTTAGCACACAAAGTGCTCTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
*
529188 TGGAAATTCATACACTTAATATGGTTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
* *
529247 TAGAAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
* *
529306 TGGAAATTCATACACTTAATATGATTTCCTTATCATTTTAGCACACAAAATGCTCTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
* *
529365 TGGAAATTCATACATTTAATATGATTTCCTTACCATTTTAGCACACAATGTGCTCTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
*
529424 TGGAAATTCATACACTTAATATGATTTCCTTATCATTTTAGCACACAAAGTGCTCTATC
1 TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
529483 TGG
1 TGG
529486 TAATCACCAT
Statistics
Matches: 805, Mismatches: 71, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
58 54 0.07
59 747 0.93
60 4 0.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (59 bp):
TGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
Found at i:529994 original size:95 final size:95
Alignment explanation
Indices: 529798--529999 Score: 244
Period size: 95 Copynumber: 2.1 Consensus size: 95
529788 TTATGCTCAA
* ** * * ***
529798 TAGTATTGATACCACTACCATGGTACCGATACTTCTATACTATGGTACCGATACCCCTTTTTGGT
1 TAGTATCGATACCTTTACCATGGTACCGATACTACCATACTATGGTACCGATACCCCTTAAGGGT
*** * *
529863 ATCGATACCAATTTTAGGTTTGATATTGTC
66 ATCGATACCAAAAATAGATTCGATATTGTC
*
529893 TAGTATCGATACCTTTACCATGGTATCGATACTACCATACTATGGTACCGATACCCCTTAAGGGT
1 TAGTATCGATACCTTTACCATGGTACCGATACTACCATACTATGGTACCGATACCCCTTAAGGGT
*
529958 ATCGATACCAAAAATAGATTCGATGTT-TC
66 ATCGATACCAAAAATAGATTCGATATTGTC
*
529987 TTGGTATCGATAC
1 -TAGTATCGATAC
530000 TACCTCATCG
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
94 2 0.02
95 88 0.98
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (95 bp):
TAGTATCGATACCTTTACCATGGTACCGATACTACCATACTATGGTACCGATACCCCTTAAGGGT
ATCGATACCAAAAATAGATTCGATATTGTC
Found at i:531146 original size:2 final size:2
Alignment explanation
Indices: 531139--531170 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
531129 ACATTCTTCA
531139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
531171 TAAACACGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:531851 original size:54 final size:54
Alignment explanation
Indices: 531780--532969 Score: 1454
Period size: 54 Copynumber: 22.3 Consensus size: 54
531770 ATAAGTTATT
* * *
531780 TGGGGTGCACACCTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCTG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* * * *
531834 TGGGTTACACACTTAGTGCCGATACGGTCGTACATAAACATATTATGAATTTTG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* * *
531888 TGGGTTGTACAC--A-T-T-G-T-C---C-TTCATAAACAAATTATGAATTATG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* ** *
531931 TGGGTTGCACACTTATTACCGATACGGTCGTTCATAAACTTATTATGAATTCTG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* *
531985 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATT-TCA
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCT-G
* * * *
532039 TGGGTTGTACACTTACTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* * * *
532093 TGGGTTGCACACTTAGT-TCTGATATGATCGTTCATGAACA-ATTATGAATTCCG
1 TGGGTTGCACACTTAGTGTC-GATACGGTCGTTCATAAACATATTATGAATTCTG
* * * * *
532146 TGGGTTGCACACTTAGTGTCAATATGGTCATTCATAAACTTATTATGAATT-TCA
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCT-G
* * * * * **
532200 TGGGTTGCACACTTAGTGTCAATACGATCCTTCATAAACTTATTAAGAATTCCA
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* * * * *
532254 TGGGTTGCACAGTTAGTATCGATACGGTCGTTTATAAACTTATTATGAATTATG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* ** * * *
532308 TGAGTTGCACACTTAGTCCCGACACGGTCATTCATAAACATATTATGAATTATG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* *
532362 TGGGTTGCACACTTAGTGCCGATACGGTTGTTCATAAACATATTATGAATT-TCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCT-G
*
532416 TGGGTTGCACACTTAGTGTCGATACGGTTGTTCATAAACATATTATGAATTC-G
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* *
532469 TGGGTTGCACACTTAGTG-CCATACGGTCGTTCATAAACATATTATGAATTCCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* *
532522 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTTG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
*
532576 TGGGTTGCACACTTAGTG-CTGATACGGTCGTTCATAAACATATTATGAATTCCG
1 TGGGTTGCACACTTAGTGTC-GATACGGTCGTTCATAAACATATTATGAATTCTG
* * * * * **
532630 TGGGTTGCACACTTAGTG-CTAATACGGTTGTTCATAAACTTGTTATAAATTCCC
1 TGGGTTGCACACTTAGTGTC-GATACGGTCGTTCATAAACATATTATGAATTCTG
* *
532684 TGGGTTGCACACTTAGT-TCCATACGGTCGTTCATAAACATATTATGAATT-TCA
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCT-G
** *
532737 TGGGTTGCACACTTAGTGTCGATACGACCGTTCATAAACATATTATG-ATTTTCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCT-G
* *
532791 TGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAACTTATTATGAATTCTG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* *
532845 TGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAACATATTATGAATTATG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
* * * * *
532899 TGGGTTGAACACTTAGTGTCGATATGGTCGTTAATAAACATATTACGAATTCCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
*
532953 TGGGTTGCACAGTTAGT
1 TGGGTTGCACACTTAGT
532970 ATTGATAGTA
Statistics
Matches: 1000, Mismatches: 108, Indels: 56
0.86 0.09 0.05
Matches are distributed among these distances:
43 32 0.03
44 1 0.00
45 1 0.00
46 1 0.00
47 1 0.00
48 2 0.00
49 2 0.00
50 1 0.00
51 1 0.00
52 32 0.03
53 134 0.13
54 788 0.79
55 4 0.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCTG
Found at i:532797 original size:537 final size:531
Alignment explanation
Indices: 531785--532969 Score: 1709
Period size: 537 Copynumber: 2.2 Consensus size: 531
531775 TTATTTGGGG
* * * *
531785 TGCACACCTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTACACACTTAG
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAG
* * *
531850 TGCCGATACGGTCGTACATAAACATATTATGAATTTTGTGGGTTGTACAC--A-TTGTCCTTCAT
66 TGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTGCACACTTAGTTGTCCTTCAT
* * *
531912 AAACAAATTATGAATTATGTGGGTTGCACACTTATTACCGATACGGTCGTTCATAAACTTATTAT
131 AAACAAATTATGAATTACGTGGGTTGCACACTTAGTACCGATACGGTCGTTCATAAACATATTAT
*
531977 GAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCATGG
196 GAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCATGG
*
532042 GTTGTACACTTACTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTGCACACTT
261 GTTGCACACTTACTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTGCACACTT
* * * * * * *
532107 AGTTCTGATATGATCGTTCATGAACAATTATGAATTCCGTGGGTTGCACACTTAGTGTCAATATG
326 AGTGCTAATACGATCGTTCATAAACAATTATAAATTCCCTGGGTTGCACACTTAGTGTCAATACG
*
532172 GTCATTCATAAACTTATTATGAATTTCATGGGTTGCACACTTAGTGTCAATACGATCCTTCATAA
391 GTCATTCATAAACATATTATGAATTTCATGGGTTGCACACTTAGTGTCAATACGATCCTTCATAA
* * * *
532237 ACTTATTAAGAATTCCATGGGTTGCACAGTTAGTATCGATACGGTCGTTTATAAACTTATTATGA
456 ACATATTAAGAATTCCATGGGTTGCACACTTAGTATCAATACGGTCGTTCATAAACTTATTATGA
532302 ATTATGTGAGT
521 ATTATGTGAGT
** * *
532313 TGCACACTTAGTCCCGACACGGTCATTCATAAACATATTATGAATTATGTGGGTTGCACACTTAG
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAG
*
532378 TGCCGATACGGTTGTTCATAAACATATTATGAATTTCGTGGGTTGCACACTTAGTGTCGATACGG
66 TGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTGCACACTTAGT-T-G-T-C--
* * *
532443 TTGTTCATAAACATATTATGAATT-CGTGGGTTGCACACTTAGTGCC-ATACGGTCGTTCATAAA
125 --CTTCATAAACAAATTATGAATTACGTGGGTTGCACACTTAGTACCGATACGGTCGTTCATAAA
532506 CATATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAA
188 CATATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAA
** * *
532571 TTTTGTGGGTTGCACACTTAGTGCTGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTT
253 TTTCATGGGTTGCACACTTACTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTT
* * **
532636 GCACACTTAGTGCTAATACGGTTGTTCATAAACTTGTTATAAATTCCCTGGGTTGCACACTTAGT
318 GCACACTTAGTGCTAATACGATCGTTCATAAAC-AATTATAAATTCCCTGGGTTGCACACTTAGT
* * *
532701 -TCCATACGGTCGTTCATAAACATATTATGAATTTCATGGGTTGCACACTTAGTGTCGATACGA-
382 GTCAATACGGTCATTCATAAACATATTATGAATTTCATGGGTTGCACACTTAGTGTCAATACGAT
* * * * *
532764 CCGTTCATAAACATATTATGATTTTCGTGGGTTGCACACTTAGTGTCAATACGGTCGTTCATAAA
447 CC-TTCATAAACATATTAAGAATTCCATGGGTTGCACACTTAGTATCAATACGGTCGTTCATAAA
* *
532829 CTTATTATGAATTCTGTGGGT
511 CTTATTATGAATTATGTGAGT
* *
532850 TGCACACTTAGTGTCAATACGGTCGTTCATAAACATATTATGAATTATGTGGGTTGAACACTTAG
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAG
* * * * * *
532915 TGTCGATATGGTCGTTAATAAACATATTACGAATTCCGTGGGTTGCACAGTTAGT
66 TGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTGCACACTTAGT
532970 ATTGATAGTA
Statistics
Matches: 581, Mismatches: 63, Indels: 17
0.88 0.10 0.03
Matches are distributed among these distances:
528 103 0.18
530 1 0.00
531 1 0.00
532 1 0.00
533 1 0.00
534 1 0.00
535 1 0.00
536 2 0.00
537 404 0.70
538 46 0.08
539 20 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (531 bp):
TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAG
TGCCGATACGGTCGTTCATAAACATATTATGAATTTCGTGGGTTGCACACTTAGTTGTCCTTCAT
AAACAAATTATGAATTACGTGGGTTGCACACTTAGTACCGATACGGTCGTTCATAAACATATTAT
GAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCATGG
GTTGCACACTTACTGCCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGTTGCACACTT
AGTGCTAATACGATCGTTCATAAACAATTATAAATTCCCTGGGTTGCACACTTAGTGTCAATACG
GTCATTCATAAACATATTATGAATTTCATGGGTTGCACACTTAGTGTCAATACGATCCTTCATAA
ACATATTAAGAATTCCATGGGTTGCACACTTAGTATCAATACGGTCGTTCATAAACTTATTATGA
ATTATGTGAGT
Found at i:534047 original size:20 final size:21
Alignment explanation
Indices: 534004--534047 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
533994 AAACTAACTT
** *
534004 ACATCCATAAATCTCCTTATA
1 ACATCCATAAATCTCCAAAGA
534025 ACATCCAT-AATCTCCAAAGA
1 ACATCCATAAATCTCCAAAGA
534045 ACA
1 ACA
534048 CTAAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.25
Consensus pattern (21 bp):
ACATCCATAAATCTCCAAAGA
Found at i:539022 original size:54 final size:54
Alignment explanation
Indices: 538959--539407 Score: 677
Period size: 54 Copynumber: 8.3 Consensus size: 54
538949 ATAAGTTCTT
* * * * *
538959 TGGGGTGCACACGTAGTGTCGATACAGTTGTTCATAAACTTATTATGAATTTCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTTCG
539013 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTTCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTTCG
* * * *
539067 TGGGTTGTACACTTAGTGTCGATAAGGTCGTTCATAAACTTGTTATGAATTTCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTTCG
* *
539121 TGGGTTGTACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTTCG
*
539175 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTTTG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTTCG
* *
539229 TAGGTTGCACACTTAGTGTCGATACGGTCGTTCATGAACATATTATGAATTTCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTTCG
* * *
539283 TAGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTTCG
* * *
539337 TGGGTTGTACACTTAGTG-CTGATATGGTTGTTCATAAACATATTATGAA-TTCTG
1 TGGGTTGCACACTTAGTGTC-GATACGGTCGTTCATAAACATATTATGAATTTC-G
*
539391 TGGGTTGCACACCTAGT
1 TGGGTTGCACACTTAGT
539408 TCCGATAGTA
Statistics
Matches: 363, Mismatches: 30, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
53 3 0.01
54 360 0.99
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTTCG
Found at i:542145 original size:22 final size:20
Alignment explanation
Indices: 542088--542136 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
542078 ATTAATTAAT
*
542088 AAATATAAATATATATAATAA
1 AAATATAAATAT-TTTAATAA
*
542109 ATATATAAATATTTTAATAA
1 AAATATAAATATTTTAATAA
542129 AAATATAA
1 AAATATAA
542137 CATTATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATAAATATTTTAATAA
Found at i:547325 original size:20 final size:21
Alignment explanation
Indices: 547281--547336 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
547271 TTCTGGGTAC
*
547281 GTAGTATCGATACTATTATTA
1 GTAGTATCGATACTACTATTA
547302 -TAGTATCGATACT-CT-TTA
1 GTAGTATCGATACTACTATTA
*
547320 GGTAGTATCAATACTAC
1 -GTAGTATCGATACTAC
547337 CAGATGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 3 0.10
19 1 0.03
20 25 0.83
21 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (21 bp):
GTAGTATCGATACTACTATTA
Found at i:548521 original size:20 final size:20
Alignment explanation
Indices: 548498--548548 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
548488 GCAAAAGTTG
548498 ATTTTGAAAAACAAAATAAA
1 ATTTTGAAAAACAAAATAAA
548518 ATTTTGAAAAACAAAATAAA
1 ATTTTGAAAAACAAAATAAA
548538 ATTTTGAAAAA
1 ATTTTGAAAAA
548549 TGATTTAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (20 bp):
ATTTTGAAAAACAAAATAAA
Found at i:550056 original size:21 final size:21
Alignment explanation
Indices: 550030--550075 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
550020 AGTGGTATCG
550030 ATACCATGAAGCATAGCATCA
1 ATACCATGAAGCATAGCATCA
* *
550051 ATACCATGAAGCATAGTATCG
1 ATACCATGAAGCATAGCATCA
550072 ATAC
1 ATAC
550076 TTGTCAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (21 bp):
ATACCATGAAGCATAGCATCA
Found at i:557246 original size:30 final size:30
Alignment explanation
Indices: 557210--557267 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
557200 AGGACCACTA
*
557210 TCCATATGTTCCAAAGAACATAGGTAACTG
1 TCCATATGTCCCAAAGAACATAGGTAACTG
*
557240 TCCATATGTCCCAAAGGACATAGGTAAC
1 TCCATATGTCCCAAAGAACATAGGTAAC
557268 CATCGACTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (30 bp):
TCCATATGTCCCAAAGAACATAGGTAACTG
Found at i:563214 original size:17 final size:17
Alignment explanation
Indices: 563194--563226 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
563184 TTGGGAGGAA
563194 GAATCGGTTGGTAGCAG
1 GAATCGGTTGGTAGCAG
563211 GAATCGGTTGGTAGCA
1 GAATCGGTTGGTAGCA
563227 AGTTCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.39, T:0.24
Consensus pattern (17 bp):
GAATCGGTTGGTAGCAG
Found at i:565606 original size:3 final size:3
Alignment explanation
Indices: 565600--565669 Score: 65
Period size: 3 Copynumber: 23.0 Consensus size: 3
565590 TATAATAATA
* *
565600 TAT TAT TA- TAT TAT TA- TAT TAT TA- TAT TAT TAT AAT GCTAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT --TAT TAT
565644 TAGGT TAT TAT TAT TAT TAT TAT TAT
1 TA--T TAT TAT TAT TAT TAT TAT TAT
565670 AAATAATACA
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
2 6 0.11
3 46 0.82
5 4 0.07
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:565609 original size:8 final size:8
Alignment explanation
Indices: 565598--565633 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
565588 TTTATAATAA
565598 TATATTAT
1 TATATTAT
565606 TATATTAT
1 TATATTAT
565614 TATATTAT
1 TATATTAT
565622 TATATTAT
1 TATATTAT
565630 TATA
1 TATA
565634 ATGCTATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATATTAT
Found at i:565616 original size:11 final size:11
Alignment explanation
Indices: 565603--565670 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
565593 AATAATATAT
565603 TATTA-TATTA
1 TATTATTATTA
565613 T-TATATTATTA
1 TAT-TATTATTA
*
565624 TATTATTATAA
1 TATTATTATTA
** *
565635 TGCTATTAGTA
1 TATTATTATTA
**
565646 GGTTATTATTA
1 TATTATTATTA
565657 TTATTATTATTA
1 -TATTATTATTA
565669 TA
1 TA
565671 AATAATACAA
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
9 1 0.02
10 3 0.07
11 30 0.68
12 10 0.23
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.57
Consensus pattern (11 bp):
TATTATTATTA
Found at i:574212 original size:22 final size:22
Alignment explanation
Indices: 574148--574212 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
574138 CTCACGAATT
*
574148 TGTAAATCCTTCAGGTCATA--
1 TGTAAATCCTTCGGGTCATATG
* *
574168 TGTAAGTCCTTCGAG-CATGATG
1 TGTAAATCCTTCGGGTCAT-ATG
*
574190 TGTAAATCCTTCGGGTTATATG
1 TGTAAATCCTTCGGGTCATATG
574212 T
1 T
574213 CAGTCTTTCG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 3 0.09
20 13 0.37
22 17 0.49
23 2 0.06
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.37
Consensus pattern (22 bp):
TGTAAATCCTTCGGGTCATATG
Found at i:574491 original size:22 final size:22
Alignment explanation
Indices: 574424--574491 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
574414 CATCTGTAAG
574424 TCTTTCGAGCATGATGTTTAAA
1 TCTTTCGAGCATGATGTTTAAA
* * * * *
574446 TCCTTCGGGTCAT-CTG--TCAG
1 TCTTTCGAG-CATGATGTTTAAA
574466 TCTTTCGAGCATGATGTTTAAA
1 TCTTTCGAGCATGATGTTTAAA
574488 TCTT
1 TCTT
574492 CGGGTCATCT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
22 15 0.47
23 3 0.09
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (22 bp):
TCTTTCGAGCATGATGTTTAAA
Found at i:574505 original size:41 final size:42
Alignment explanation
Indices: 574401--574516 Score: 216
Period size: 42 Copynumber: 2.8 Consensus size: 42
574391 ACGAATTTGA
*
574401 AAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGTTT
1 AAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATGTTT
574443 AAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATGTTT
1 AAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATGTTT
574485 AAAT-CTTCGGGTCATCTGTCAGTCTTTCGAGC
1 AAATCCTTCGGGTCATCTGTCAGTCTTTCGAGC
574517 TAGATGATAA
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
41 28 0.38
42 45 0.62
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (42 bp):
AAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATGTTT
Found at i:574723 original size:290 final size:292
Alignment explanation
Indices: 574150--574771 Score: 944
Period size: 290 Copynumber: 2.1 Consensus size: 292
574140 CACGAATTTG
* * * * *
574150 TAAATCCTTCAGGTCATATGTAAGTCCTTCGAGCATGATGTGTAAATCCTTCGGGTTATATGTCA
1 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATGTGTAAATCCTTCGGGTCATATGTCA
** * *
574215 GTCTTTCGAGCCAGATGATATTTCCTTAGGGCCATCCGTGAAACCTTTGGGTAGGATATTCACAT
66 GTCTTTCGAGCCAGATGATAAGTCCTTAAGGCCATCCGTCAAACCTTTGGGTAGGATATTCACAT
* *
574280 ATGATTTTCGCATGAAAATGAGATAGTGATTTTCAAAAGTTTCTCATTTAATGTTCTAGAAAATC
131 ATGATTTTCGCATGAAAATGAGATAGAGATTTTCAAAAGTTTCTCATTTAATGTTATAGAAAATC
* * *
574345 AAATATTTGAAAAGTAAGAAGTCTCTTACTCAGTAAATTATTTCTCACGAATTTGAAAATCCTTC
196 AAATATTTGAAAAGTAAGAAGTCTCTTACTCAGTAAATTATTTATAACAAATTTGAAAATCCTTC
*
574410 GGGTCATCTGTAAGTCTTTCGAGCATGATGTT
261 GGGTCATCTGTAAGTCCTTCGAGCATGATGTT
* *
574442 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATGTTTAAAT-CTTCGGGTCATCTGTCA
1 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATGTGTAAATCCTTCGGGTCATATGTCA
* * * * *
574506 GTCTTTCGAGCTAGATGATAAGTCCTTAAGGCTATCCGTCAAACCTTTGGGTGGGATGTTTACAT
66 GTCTTTCGAGCCAGATGATAAGTCCTTAAGGCCATCCGTCAAACCTTTGGGTAGGATATTCACAT
* * *
574571 ATGATTTTCGTATGAAAATGAGATAGAGATTTT-TAAAGTTTCTCATTTAATGTTATAGGAAATC
131 ATGATTTTCGCATGAAAATGAGATAGAGATTTTCAAAAGTTTCTCATTTAATGTTATAGAAAATC
* * *
574635 AAAT-TTATGAAAAGTAAGAAGTCTTTTACTCAGTAAATTATTTATAATAAATTTGTAAATCCTT
196 AAATATT-TGAAAAGTAAGAAGTCTCTTACTCAGTAAATTATTTATAACAAATTTGAAAATCCTT
574699 CGGGTCATCTGTAAGTCCTTCGAGCATGATGTT
260 CGGGTCATCTGTAAGTCCTTCGAGCATGATGTT
* *
574732 TAAATCCTTCGGGTTATCTGTCAGTCTTTCGAGCAAGATG
1 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATG
574772 ATAAGTCCTA
Statistics
Matches: 299, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
289 2 0.01
290 153 0.51
291 102 0.34
292 42 0.14
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (292 bp):
TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCATGATGTGTAAATCCTTCGGGTCATATGTCA
GTCTTTCGAGCCAGATGATAAGTCCTTAAGGCCATCCGTCAAACCTTTGGGTAGGATATTCACAT
ATGATTTTCGCATGAAAATGAGATAGAGATTTTCAAAAGTTTCTCATTTAATGTTATAGAAAATC
AAATATTTGAAAAGTAAGAAGTCTCTTACTCAGTAAATTATTTATAACAAATTTGAAAATCCTTC
GGGTCATCTGTAAGTCCTTCGAGCATGATGTT
Found at i:574751 original size:42 final size:42
Alignment explanation
Indices: 574690--574771 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
574680 AATAAATTTG
*
574690 TAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCATGATGTT
1 TAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCAAGATGTT
* * *
574732 TAAATCCTTCGGGTTATCTGTCAGTCTTTCGAGCAAGATG
1 TAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCAAGATG
574772 ATAAGTCCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCAAGATGTT
Found at i:574993 original size:3 final size:3
Alignment explanation
Indices: 574987--575035 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
574977 TATAATAATA
574987 TAT TAT TA- TAT TAT TA- TAT ATAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
575030 TAT TAT
1 TAT TAT
575036 AAATAATACA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.14
3 33 0.79
4 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:575009 original size:20 final size:20
Alignment explanation
Indices: 574984--575036 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
574974 TTTTATAATA
574984 ATATATTATTATATTATTAT
1 ATATATTATTATATTATTAT
575004 ATATATTA-TATTATTATTAT
1 ATATATTATTA-TATTATTAT
575024 -TATTATTATTATA
1 ATA-TATTATTATA
575037 AATAATACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.13
20 24 0.80
21 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATATTATTATATTATTAT
Found at i:576679 original size:17 final size:17
Alignment explanation
Indices: 576623--576683 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
576613 ATAAAGAGAT
* **
576623 AAAAATGAAATAGGATA
1 AAAAATGAAAAAAAATA
* *
576640 AAAAGTGAAAAAAAATG
1 AAAAATGAAAAAAAATA
576657 AAAAATGAAAAAAAA-A
1 AAAAATGAAAAAAAATA
576673 AAGAAAT-AAAA
1 AA-AAATGAAAA
576684 TTGGACATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
16 6 0.17
17 30 0.83
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.11
Consensus pattern (17 bp):
AAAAATGAAAAAAAATA
Found at i:577881 original size:37 final size:35
Alignment explanation
Indices: 577839--578276 Score: 309
Period size: 37 Copynumber: 11.9 Consensus size: 35
577829 ACAATATATA
*
577839 AAAATATTTTCAAAAATTATATAATATATATTTTCCC
1 AAAATATTTTCAAAAACTATATAATATATATTTT--C
* ***
577876 CAAATATTTTTTTAAACTATATAATATATATAATTTC
1 AAAATATTTTCAAAAACTATATAATATATAT--TTTC
* * * *
577913 AAAA-ATGTTTTAAAAGATTATATATTATATACTTTC
1 AAAATAT-TTTCAAAA-ACTATATAATATATATTTTC
*
577949 AGAATAATTTT-AAAAACTATAT-AT-TATATTTTC
1 AAAAT-ATTTTCAAAAACTATATAATATATATTTTC
* *
577982 AAAATGTTTTTCAAAAACCATATATTATATATATTTTTC
1 AAAAT-ATTTTCAAAAA-C-TATATAATATATA-TTTTC
*
578021 AAAATATTTT-AAAAACTATATATTATATATATATTTA
1 AAAATATTTTCAAAAACTATATA--ATATATAT-TTTC
* * * *
578058 AAAAAAATTTCAAAAACCATATAATATATATATTTTT
1 AAAATATTTTCAAAAACTATAT-A-ATATATATTTTC
*
578095 AAAATGTTTCTCAAAAAACTATATAATATATATTTTC
1 AAAATATTT-TC-AAAAACTATATAATATATATTTTC
578132 AAAACGT-TTTTCAAAAACTATATATTATATATATTTTTC
1 AAAA--TATTTTCAAAAACTATATA--ATATATA-TTTTC
*
578171 AAAATATTTT-AAAAACCATATATTATATATAAGTTTTC
1 AAAATATTTTCAAAAA-C-TATATAATATAT-A-TTTTC
* * * *
578209 GAAAAATATTTTTAAAAACCATATATTATATAATTTCC
1 --AAAATATTTTCAAAAACTATATAATATAT-ATTTTC
*
578247 AAAATGA-TTTCAAACTA-TATATAATATATA
1 AAAAT-ATTTTCAAA-AACTATATAATATATA
578277 CTAAAAAATC
Statistics
Matches: 328, Mismatches: 40, Indels: 68
0.75 0.09 0.16
Matches are distributed among these distances:
33 16 0.05
34 6 0.02
35 13 0.04
36 53 0.16
37 104 0.32
38 70 0.21
39 50 0.15
40 11 0.03
41 5 0.02
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (35 bp):
AAAATATTTTCAAAAACTATATAATATATATTTTC
Found at i:577972 original size:75 final size:72
Alignment explanation
Indices: 577838--578276 Score: 314
Period size: 75 Copynumber: 5.9 Consensus size: 72
577828 AACAATATAT
* ** * **
577838 AAAAATATTTTCAAAAATTATATA-ATATATATTTTCCCCAAATATTTTTTTAAAC-TATATAAT
1 AAAAATGTTTT-AAAAACCATATATATATATATTTT--CAAAATA-TTTTAAAAACATATATAAT
577901 ATATATAATTTC
62 ATATAT-ATTTC
** * *
577913 AAAAATGTTTTAAAAGATTATATAT-TATATACTTTCAGAATAATTTTAAAAAC-TATAT-AT-T
1 AAAAATGTTTTAAAA-ACCATATATATATATATTTTCAAAAT-ATTTTAAAAACATATATAATAT
577974 ATAT-TTTC
64 ATATATTTC
*
577982 -AAAATGTTTTTCAAAAACCATATATTATATATATTTTTCAAAATATTTTAAAAACTATATATTA
1 AAAAATG-TTTT-AAAAACCATATA-TATATATA-TTTTCAAAATATTTTAAAAAC-ATATATAA
*
578046 TATATATATTTA
61 TATATATATTTC
** * * *
578058 AAAAAAATTTCAAAAACCATATAATATATATATTTTTAAAATGTTTCTCAAAAA-ACTATATAAT
1 AAAAATGTTTTAAAAACCATAT-ATATATATATTTTCAAAATATTT-T-AAAAACA-TATATAAT
578122 ATATAT-TTTC
62 ATATATATTTC
* * *
578132 -AAAACGTTTTTCAAAAACTATATATTATATATATTTTTCAAAATATTTTAAAAACCATATATTA
1 AAAAATG-TTTT-AAAAACCATATA-TATATATA-TTTTCAAAATATTTTAAAAA-CATATATAA
578196 TATATA-AGTTTTC
61 TATATATA--TTTC
* * *
578209 GAAAAATATTTTTAAAAACCATATAT-TATATAATTTCCAAAATGA-TTT-CAAACTATATATAA
1 -AAAAAT-GTTTTAAAAACCATATATATATAT-ATTTTCAAAAT-ATTTTAAAAAC-ATATATAA
578271 TATATA
61 TATATA
578277 CTAAAAAATC
Statistics
Matches: 300, Mismatches: 31, Indels: 66
0.76 0.08 0.17
Matches are distributed among these distances:
68 6 0.02
69 14 0.05
70 5 0.02
71 22 0.07
72 10 0.03
73 26 0.09
74 33 0.11
75 112 0.37
76 42 0.14
77 11 0.04
78 11 0.04
79 8 0.03
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (72 bp):
AAAAATGTTTTAAAAACCATATATATATATATTTTCAAAATATTTTAAAAACATATATAATATAT
ATATTTC
Found at i:578159 original size:150 final size:149
Alignment explanation
Indices: 577856--578276 Score: 446
Period size: 150 Copynumber: 2.8 Consensus size: 149
577846 TTTCAAAAAT
* * * ** * * *
577856 TATATAATATATATTTTCCCCAAATATTTTTTTAAACTATATAATATATATAA-TTTC-AAAAAT
1 TATATTATATATATTTT-TCAAAATA-TTTTAAAAACCATATATTATATATAAGTTTCAAAAAAA
* * ** * * * * *
577919 GTTTTAAAAGATTATATATTATATACTTT-CAGAATAATTT-TAAAAACTATAT-AT-TATATTT
64 ATTTCAAAA-ACCATATAATATATAATTTCCAAAATGATTTCAAAAAACTATATAATATATATTT
*
577980 TCAAAATGTTTTTCAAAAACCA
128 TCAAAACGTTTTTCAAAAACCA
*
578002 TATATTATATATATTTTTCAAAATATTTTAAAAACTATATATTATATATATA-TTT-AAAAAAAA
1 TATATTATATATATTTTTCAAAATATTTTAAAAACCATATATTATATATA-AGTTTCAAAAAAAA
** *
578065 TTTCAAAAACCATATAATATATATATTTTTAAAATGTTTCTCAAAAAACTATATAATATATATTT
65 TTTCAAAAACCATATAATATATA-ATTTCCAAAATGATT-TCAAAAAACTATATAATATATATTT
*
578130 TCAAAACGTTTTTCAAAAACTA
128 TCAAAACGTTTTTCAAAAACCA
*
578152 TATATTATATATATTTTTCAAAATATTTTAAAAACCATATATTATATATAAGTTTTCGAAAAATA
1 TATATTATATATATTTTTCAAAATATTTTAAAAACCATATATTATATATAAG-TTTC-AAAAAAA
* * * **
578217 TTTTTAAAAACCATATATTATATAATTTCCAAAATGATTTCAAACTA-TATATAATATATA
64 ATTTCAAAAACCATATAATATATAATTTCCAAAATGATTTCAAAAAACTATATAATATATA
578277 CTAAAAAATC
Statistics
Matches: 233, Mismatches: 30, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
144 34 0.15
145 25 0.11
146 22 0.09
147 1 0.00
148 11 0.05
149 3 0.01
150 89 0.38
151 9 0.04
152 12 0.05
153 27 0.12
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.43
Consensus pattern (149 bp):
TATATTATATATATTTTTCAAAATATTTTAAAAACCATATATTATATATAAGTTTCAAAAAAAAT
TTCAAAAACCATATAATATATAATTTCCAAAATGATTTCAAAAAACTATATAATATATATTTTCA
AAACGTTTTTCAAAAACCA
Found at i:579115 original size:73 final size:72
Alignment explanation
Indices: 578979--579121 Score: 164
Period size: 73 Copynumber: 2.0 Consensus size: 72
578969 GGTGTACGCA
* * * * * *
578979 TACCTATCATAAAATTTGATTTTTTTCAATTAGTTATTTATTTTATTGATGGTATCCATCCTAAA
1 TACCTATCATAAAATCTGATTTTTTTCAACTAATTACTTATTTTATTGATGGTATACACCCT-AA
579044 ATTTTTCG
65 ATTTTTCG
* * *
579052 TACCTATCCTAAAATCTGAGTTTTCTTT-AACTAATTACTTA-TTTATTGATGGTGTATACCCTA
1 TACCTATCATAAAATCTGA-TTTT-TTTCAACTAATTACTTATTTTATTGATGGTATACACCCTA
579115 AATTTTT
64 AATTTTT
579122 ATTTGTACAC
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
72 8 0.14
73 34 0.58
74 14 0.24
75 3 0.05
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (72 bp):
TACCTATCATAAAATCTGATTTTTTTCAACTAATTACTTATTTTATTGATGGTATACACCCTAAA
TTTTTCG
Found at i:581965 original size:14 final size:14
Alignment explanation
Indices: 581943--582018 Score: 53
Period size: 16 Copynumber: 4.9 Consensus size: 14
581933 TTTTTTTTTC
581943 ATTTATATTATATT
1 ATTTATATTATATT
*
581957 ATTTTTATTATATAT
1 ATTTATATTATAT-T
*
581972 ATCTTATATCATTATAT
1 AT-TTATATTA-TAT-T
*
581989 ATATATATATATATAT
1 ATTTATAT-TATAT-T
*
582005 ATATATATATATAT
1 ATTTATAT-TATAT
582019 ATATATGTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
14 12 0.23
15 3 0.06
16 30 0.57
17 8 0.15
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTATATTATATT
Found at i:581972 original size:2 final size:2
Alignment explanation
Indices: 581965--582024 Score: 88
Period size: 2 Copynumber: 30.5 Consensus size: 2
581955 TTATTTTTAT
*
581965 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
582006 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
582025 GTATGTATAG
Statistics
Matches: 54, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
1 2 0.04
2 50 0.93
3 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:582168 original size:31 final size:31
Alignment explanation
Indices: 582113--582255 Score: 82
Period size: 31 Copynumber: 4.5 Consensus size: 31
582103 TATTTTCTTA
**
582113 ATATTATATTTTTGTTTTCA-TTTATTTATAT
1 ATATTATATTTTTACTTT-ATTTTATTTATAT
*
582144 ATATTATATTTTTACTTTATTTTATTT-TTT
1 ATATTATATTTTTACTTTATTTTATTTATAT
* * * * *
582174 CTATTATTATTTTT-CTTAATATCATGTATAT
1 ATATTA-TATTTTTACTTTATTTTATTTATAT
* *
582205 CT-TTAT-TTTTTA-TTTGTTTTACTTAGTATTAT
1 ATATTATATTTTTACTTTATTTTA-TT--TA-TAT
582237 ATATTTATTATTTTTACTT
1 ATA-TTA-TATTTTTACTT
582256 GTTTTAGTAA
Statistics
Matches: 84, Mismatches: 15, Indels: 20
0.71 0.13 0.17
Matches are distributed among these distances:
28 10 0.12
29 2 0.02
30 20 0.24
31 36 0.43
32 4 0.05
34 3 0.04
35 1 0.01
36 6 0.07
37 2 0.02
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (31 bp):
ATATTATATTTTTACTTTATTTTATTTATAT
Found at i:582187 original size:16 final size:16
Alignment explanation
Indices: 582062--582187 Score: 62
Period size: 16 Copynumber: 7.5 Consensus size: 16
582052 ATTTACTATG
*
582062 TATATTTTTTCTTAATAT
1 TATATTTTTACTT--TAT
*
582080 TATATTTTATACGTTTTTT
1 TATATTTT-TAC--TTTAT
582099 TATATATTTT-CTTAATAT
1 TATAT-TTTTACTT--TAT
**
582117 TATATTTTTGTTTTCAT
1 TATATTTTTACTTT-AT
* *
582134 T-TATTTATA-TATAT
1 TATATTTTTACTTTAT
582148 TATATTTTTACTTTAT
1 TATATTTTTACTTTAT
* *
582164 TTTATTTTTTCTATTAT
1 TATATTTTTACT-TTAT
582181 TAT-TTTT
1 TATATTTT
582188 CTTAATATCA
Statistics
Matches: 85, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
14 3 0.04
15 9 0.11
16 27 0.32
17 13 0.15
18 18 0.21
19 10 0.12
20 3 0.04
21 2 0.02
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.69
Consensus pattern (16 bp):
TATATTTTTACTTTAT
Found at i:582331 original size:17 final size:18
Alignment explanation
Indices: 582300--582333 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
582290 TTTTTAATCA
582300 TTTTTAATTTCTTTTACC
1 TTTTTAATTTCTTTTACC
*
582318 TTTTTTATTT-TTTTAC
1 TTTTTAATTTCTTTTAC
582334 TCCATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTAATTTCTTTTACC
Found at i:582397 original size:18 final size:18
Alignment explanation
Indices: 582376--582416 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
582366 GTTTTTTAAC
582376 ATTTTATTCATTTTGTTT
1 ATTTTATTCATTTTGTTT
* * *
582394 ATTTTGTTTATTTTTTTT
1 ATTTTATTCATTTTGTTT
582412 ATTTT
1 ATTTT
582417 TTACGTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (18 bp):
ATTTTATTCATTTTGTTT
Found at i:582418 original size:9 final size:9
Alignment explanation
Indices: 582385--582416 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
582375 CATTTTATTC
582385 ATTTTGTTT
1 ATTTTGTTT
582394 ATTTTGTTT
1 ATTTTGTTT
*
582403 ATTTTTTTT
1 ATTTTGTTT
582412 ATTTT
1 ATTTT
582417 TTACGTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:585515 original size:7 final size:7
Alignment explanation
Indices: 585503--585549 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
585493 CAATCAGAAT
585503 AAAAAGA
1 AAAAAGA
585510 AAAAAGA
1 AAAAAGA
585517 GAAAAA-A
1 -AAAAAGA
*
585524 GAAAAGA
1 AAAAAGA
* *
585531 GAAAATA
1 AAAAAGA
585538 AAAAAGA
1 AAAAAGA
585545 AAAAA
1 AAAAA
585550 ATGAAAATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
6 4 0.12
7 25 0.74
8 5 0.15
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:585528 original size:14 final size:14
Alignment explanation
Indices: 585511--585556 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
585501 ATAAAAAGAA
585511 AAAAGAGAAAAAAG
1 AAAAGAGAAAAAAG
585525 AAAAGAGAAAATAA-
1 AAAAGAGAAAA-AAG
585539 AAAAGA-AAAAAATG
1 AAAAGAGAAAAAA-G
585553 AAAA
1 AAAA
585557 TTGAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.07
13 4 0.14
14 21 0.72
15 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (14 bp):
AAAAGAGAAAAAAG
Found at i:585747 original size:69 final size:69
Alignment explanation
Indices: 585628--585766 Score: 210
Period size: 69 Copynumber: 2.0 Consensus size: 69
585618 GATTTAAACT
585628 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTTCACTCGAAGATCAT-AGAGC
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTTCACTCGAAGATCATGA-AGC
585692 ATCAA
65 ATCAA
* * * *
585697 ATGAGATTGATCAAGCATAATCATTTCTGAATTACTGCATCAC-TCTACTCGAAGATCATGAAGC
1 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTTC-ACTCGAAGATCATGAAGC
585761 ATCAA
65 ATCAA
585766 A
1 A
585767 GAGGGACACA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
68 2 0.03
69 61 0.95
70 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTTCACTCGAAGATCATGAAGCA
TCAA
Found at i:587347 original size:36 final size:36
Alignment explanation
Indices: 587300--587489 Score: 135
Period size: 36 Copynumber: 5.4 Consensus size: 36
587290 ATTGAAAACA
* *
587300 TTTCCCTTGAAACAAACTTCGTATCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
587336 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * * *
587365 TTTTATTTGAAACAAATTTCATCTCCCTTGAGACAA
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *** * * *
587401 ATTATTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
587438 TTTCTCTTGAAACAAATTTCGTCTCTATTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
587474 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
587490 ATCTTTGAAT
Statistics
Matches: 118, Mismatches: 26, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
28 2 0.02
29 18 0.15
30 2 0.02
31 1 0.01
34 1 0.01
35 1 0.01
36 64 0.54
37 29 0.25
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:587542 original size:65 final size:67
Alignment explanation
Indices: 587438--587599 Score: 183
Period size: 65 Copynumber: 2.5 Consensus size: 67
587428 CTTGAGACAG
* * * ** * **
587438 TTTCTCTTGAAACAAATTTCGTCTCTATTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATT
1 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGAAAGTTTCCCTTGAAACACAAAATCTTCAAATT
587501 TA
66 TA
*
587503 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGAAAGTTTCTCTTGAAACACAAAATCTTCAAATT
1 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGAAAGTTTCCCTTGAAACACAAAATCTTCAAATT
587568 TA
66 TA
*
587570 TTTC-CCTTAAAA-AAA-TTTGT-TTCCTTGAGA
1 TTTCTCC-TAAAACAAATTTTGTCTCCCTTGAGA
587600 CCGTTTTTCA
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
64 9 0.11
65 43 0.51
66 7 0.08
67 25 0.30
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (67 bp):
TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGAAAGTTTCCCTTGAAACACAAAATCTTCAAATT
TA
Found at i:588597 original size:106 final size:106
Alignment explanation
Indices: 588325--588685 Score: 386
Period size: 106 Copynumber: 3.3 Consensus size: 106
588315 ACGAAGGGGC
* *
588325 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGAGATATTGGACTTAAGACAACACAAGCT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCT
* * * *
588390 CAAATTCATAACGAAGGGGAACTGATTATCAACAAACAACT
66 CAACTTCACAACGAAGGGGGACTGATTGTCAACAAACAACT
* * * * *
588431 TT-TCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGACGGATATTGAACTCGAGACAACACA
1 TTCCCAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACA
** * ** *
588495 AGCTCAACTTCACAGTGAAGGGGCGGCTGGCTGTCAACAAATAA-T
62 AGCTCAACTTCACAACGAAGGGG-GACTGATTGTCAACAAACAACT
* * * * * *
588540 TTCCCAGTTTCAGAGCCAATTTTAAGTTCGCAGTGAGGGATATTGGACTCAACACAACGCAAGCT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCT
588605 CAACTTCACAACGAAGGGGAGACTGATTGTCAACAAACAACT
66 CAACTTCACAACGAAGGGG-GACTGATTGTCAACAAACAACT
* *
588647 TT-TCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGA
1 TTCCCAG--T--TTCAGAGCCAATTTCAACTTCACAGCGA
588686 AGGGGCGACT
Statistics
Matches: 203, Mismatches: 41, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
105 3 0.01
106 85 0.42
107 4 0.02
108 2 0.01
109 69 0.34
110 40 0.20
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (106 bp):
TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCT
CAACTTCACAACGAAGGGGGACTGATTGTCAACAAACAACT
Found at i:588740 original size:63 final size:65
Alignment explanation
Indices: 588604--588743 Score: 180
Period size: 67 Copynumber: 2.2 Consensus size: 65
588594 CAACGCAAGC
*
588604 TCAACTTCACAACGAAGGGGAGACTGATTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAA
1 TCAACTTCACAACGAAGGGGAGACTGACTGTCAACAAACAACTTTTCAGTTTC--TCAGAGTCAA
588669 TT
64 TT
* * *
588671 TCAACTTCACAGCGAAGGGGCGACTGGCTGTCAACAAACAA-TTTTCCAG-TTC-CAGAG-CTAA
1 TCAACTTCACAACGAAGGGGAGACTGACTGTCAACAAACAACTTTT-CAGTTTCTCAGAGTC-AA
588732 TT
64 TT
588734 TCAACTTCAC
1 TCAACTTCAC
588744 GACGGAGGAT
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.28
66 7 0.10
67 40 0.60
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (65 bp):
TCAACTTCACAACGAAGGGGAGACTGACTGTCAACAAACAACTTTTCAGTTTCTCAGAGTCAATT
Found at i:590152 original size:14 final size:15
Alignment explanation
Indices: 590136--590214 Score: 81
Period size: 16 Copynumber: 5.2 Consensus size: 15
590126 CCTCTTTTTT
590136 TATTTATATTATAT-
1 TATTTATATTATATA
*
590150 TATTTTTATTATATA
1 TATTTATATTATATA
*
590165 TATCTTATATCAT-TA
1 TAT-TTATATTATATA
*
590180 TATATATATATATATA
1 TATTTATAT-TATATA
*
590196 TATATATATATATATA
1 TATTTATAT-TATATA
590212 TAT
1 TAT
590215 AGATGTATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
14 18 0.32
15 10 0.18
16 28 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATATTATATA
Found at i:590156 original size:23 final size:23
Alignment explanation
Indices: 590098--590167 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 23
590088 TATATTTTTA
* *
590098 ATTATATTTTTTATTTATTTACTAT
1 ATTATTTTTTTTATTTA--TATTAT
*
590123 ATTCCTCTTTTTTTATTTATATTAT
1 ATT-AT-TTTTTTTATTTATATTAT
* *
590148 ATTATTTTTATTATATATAT
1 ATTATTTTTTTTATTTATAT
590168 CTTATATCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 13 0.35
24 1 0.03
25 11 0.30
26 1 0.03
27 11 0.30
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTATTTTTTTTATTTATATTAT
Found at i:590166 original size:2 final size:2
Alignment explanation
Indices: 590159--590215 Score: 82
Period size: 2 Copynumber: 29.0 Consensus size: 2
590149 TTATTTTTAT
*
590159 TA TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
590200 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
590216 GATGTATTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.92
3 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:590286 original size:37 final size:34
Alignment explanation
Indices: 590245--590324 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 34
590235 ATTTACTATG
590245 TATATATTTTTTCATAATATTATATTTTATACGTTTT
1 TATATATTTTTTCATAATATTATATTTT-TA--TTTT
* * *
590282 TATATATATTTTCTTAATATTCTATTTTTATTTT
1 TATATATTTTTTCATAATATTATATTTTTATTTT
*
590316 TATTTATTT
1 TATATATTT
590325 ATATATACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
34 11 0.29
36 2 0.05
37 25 0.66
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (34 bp):
TATATATTTTTTCATAATATTATATTTTTATTTT
Found at i:593130 original size:21 final size:21
Alignment explanation
Indices: 593106--593152 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
593096 AATATGTAAA
593106 TCGCATTACGATTTTCCAAAT
1 TCGCATTACGATTTTCCAAAT
* *
593127 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTACGATTTTCCAAAT
593148 TCGCA
1 TCGCA
593153 ACGCGAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (21 bp):
TCGCATTACGATTTTCCAAAT
Found at i:593201 original size:20 final size:20
Alignment explanation
Indices: 593143--593212 Score: 90
Period size: 19 Copynumber: 3.6 Consensus size: 20
593133 TGCGATTTTC
**
593143 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAATTT
*
593163 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
593182 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
593202 -AATTTCGCAAC
1 CAAATTCGCAAC
593213 AGGTTTTAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
19 26 0.59
20 18 0.41
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:596432 original size:18 final size:18
Alignment explanation
Indices: 596411--596456 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
596401 AGGAAATCAA
*
596411 AATCAAAATCAAAATCTC
1 AATCAAAATCAAAATCCC
* *
596429 AATCAAAACCAAATTCCC
1 AATCAAAATCAAAATCCC
*
596447 AATCACAATC
1 AATCAAAATC
596457 GCTTCACCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:596450 original size:24 final size:24
Alignment explanation
Indices: 596405--596456 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
596395 AGCAAAAGGA
* *
596405 AATCAAAATCAAAATCAAAATCTC
1 AATCAAAACCAAAATCAAAATCAC
* **
596429 AATCAAAACCAAATTCCCAATCAC
1 AATCAAAACCAAAATCAAAATCAC
596453 AATC
1 AATC
596457 GCTTCACCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (24 bp):
AATCAAAACCAAAATCAAAATCAC
Found at i:596784 original size:20 final size:20
Alignment explanation
Indices: 596743--596785 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
596733 GATCAATGTA
*
596743 AAAGTCAAATTCGTAACGCG
1 AAAGTCAAATTCGAAACGCG
* *
596763 AAAGTCAAATTTGAAACTCG
1 AAAGTCAAATTCGAAACGCG
596783 AAA
1 AAA
596786 TAAGCGTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (20 bp):
AAAGTCAAATTCGAAACGCG
Found at i:596991 original size:25 final size:25
Alignment explanation
Indices: 596953--597010 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
596943 AAATCAATTA
*
596953 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
596978 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
597003 AACATTGT
1 AACATTGT
597011 ATGTATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.43
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:597299 original size:39 final size:39
Alignment explanation
Indices: 597252--597338 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
597242 TCTGATGCTC
597252 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
* *
597291 ATCCAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
597330 ATCAAAATC
1 ATCAAAATC
597339 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:597707 original size:31 final size:30
Alignment explanation
Indices: 597669--597747 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 30
597659 ATTAAACAAG
597669 CAAAAAATAATTCTTATTGACAAATCAAATT-A
1 CAAAAAATAA-TCTTATT-ACAAATC-AATTAA
597701 -AAAAAATCAA-CTT-TTACAAATCAATTAA
1 CAAAAAAT-AATCTTATTACAAATCAATTAA
597729 TCAAAAAATAAATCTTATT
1 -CAAAAAAT-AATCTTATT
597748 TCCTCATCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
27 4 0.10
28 8 0.20
29 2 0.05
30 12 0.30
31 10 0.25
32 4 0.10
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (30 bp):
CAAAAAATAATCTTATTACAAATCAATTAA
Found at i:597736 original size:32 final size:32
Alignment explanation
Indices: 597639--597736 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 32
597629 TAGAAACAAC
*
597639 AAATCAACTTTTACAAATCAATTAAACAAGCAAA
1 AAATCAACTTTTACAAATCAATTAATCAA--AAA
*
597673 AAAT-AATTCTTATTGACAAATC-A--AAT-TAAAA
1 AAATCAA--CTT-TT-ACAAATCAATTAATCAAAAA
597704 AAATCAACTTTTACAAATCAATTAATCAAAAA
1 AAATCAACTTTTACAAATCAATTAATCAAAAA
597736 A
1 A
597737 TAAATCTTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 20
0.69 0.04 0.27
Matches are distributed among these distances:
28 7 0.13
29 3 0.06
30 3 0.06
31 10 0.19
32 7 0.13
33 3 0.06
34 6 0.12
35 3 0.06
36 3 0.06
37 7 0.13
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (32 bp):
AAATCAACTTTTACAAATCAATTAATCAAAAA
Found at i:599189 original size:20 final size:20
Alignment explanation
Indices: 599127--599191 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
599117 CATATGAATC
* *
599127 GGGCTCTTGAACGGCGG-CG
1 GGGCTCTTGAACGGTGGAAG
* * *
599146 GGACCTCTTGAACGAT-GATGG
1 GG-GCTCTTGAACGGTGGA-AG
599167 GGGCTCTTGAACGGTGGAAG
1 GGGCTCTTGAACGGTGGAAG
599187 GGGCT
1 GGGCT
599192 TCTTCGATGA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
19 3 0.09
20 27 0.77
21 5 0.14
ACGTcount: A:0.17, C:0.20, G:0.43, T:0.20
Consensus pattern (20 bp):
GGGCTCTTGAACGGTGGAAG
Found at i:599244 original size:21 final size:21
Alignment explanation
Indices: 599205--599244 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
599195 TCGATGACGA
*
599205 GAGGGGCCTCTTGAATGATAG
1 GAGGCGCCTCTTGAATGATAG
599226 GAGGCGCCTCTTGAATGAT
1 GAGGCGCCTCTTGAATGAT
599245 GATAGGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (21 bp):
GAGGCGCCTCTTGAATGATAG
Found at i:601751 original size:22 final size:22
Alignment explanation
Indices: 601726--601776 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
601716 GATGGAGATA
*
601726 GACGGATTTCATTGGAAATGGG
1 GACGGATTTCATCGGAAATGGG
* *
601748 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCATCGGAAATGGG
*
601770 AACGGAT
1 GACGGAT
601777 GTTGCCGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.39, T:0.24
Consensus pattern (22 bp):
GACGGATTTCATCGGAAATGGG
Found at i:601928 original size:20 final size:20
Alignment explanation
Indices: 601903--602008 Score: 101
Period size: 20 Copynumber: 5.3 Consensus size: 20
601893 TCGTAAAAAC
601903 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
601923 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
601943 ATTTGACTTAT-GTGTTGCG-
1 ATTTGACTT-TCGCGTTGCGA
* *** *
601962 ATTT-ACAAATTCGCACCGTGA
1 ATTTGAC--TTTCGCGTTGCGA
601983 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
602003 ATTTGA
1 ATTTGA
602009 AAAATCGCAA
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
18 2 0.03
19 5 0.08
20 52 0.79
21 5 0.08
22 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:602000 original size:40 final size:41
Alignment explanation
Indices: 601903--602029 Score: 111
Period size: 40 Copynumber: 3.1 Consensus size: 41
601893 TCGTAAAAAC
** ***
601903 ATTTGACTT-TCGCGTTGCGAATTTG-ACTATCGCGTTGCGA
1 ATTTGACTTAT-GCGTTGCGAATTTGAAAAATCGCAACGCGA
* * * *
601943 ATTTGACTTATGTGTTGCG-ATTT-ACAAATTCGCACCGTGA
1 ATTTGACTTATGCGTTGCGAATTTGA-AAAATCGCAACGCGA
601983 ATTTGACTT-TCGCGTTGCGAATTTGAAAAATCGCAACGCGA
1 ATTTGACTTAT-GCGTTGCGAATTTGAAAAATCGCAACGCGA
602024 ATTTGA
1 ATTTGA
602030 AAATCGCAAC
Statistics
Matches: 69, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
39 5 0.07
40 40 0.58
41 23 0.33
42 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (41 bp):
ATTTGACTTATGCGTTGCGAATTTGAAAAATCGCAACGCGA
Found at i:602029 original size:41 final size:41
Alignment explanation
Indices: 601903--602093 Score: 133
Period size: 41 Copynumber: 4.7 Consensus size: 41
601893 TCGTAAAAAC
** ***
601903 ATTTGACTTTCGCGTTGCGAATTTG-ACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGAATTTGAAAAATCGCAACGCGA
* * * *
601943 ATTTGACTTAT-GTGTTGCG-ATTT-ACAAATTCGCACCGTGA
1 ATTTGACTT-TCGCGTTGCGAATTTGA-AAAATCGCAACGCGA
601983 ATTTGACTTTCGCGTTGCGAATTTGAAAAATCGCAACGCGA
1 ATTTGACTTTCGCGTTGCGAATTTGAAAAATCGCAACGCGA
*** *** * * *
602024 ATTTGAAAATCGCAACGCGAATTTGGAAAATTGCAATGCG-
1 ATTTGACTTTCGCGTTGCGAATTTGAAAAATCGCAACGCGA
*
602064 ATTT-ACATATTCGCGTTGCGAAATTGAAAA
1 ATTTGAC-T-TTCGCGTTGCGAATTTGAAAA
602094 CTGGGTTGCG
Statistics
Matches: 114, Mismatches: 29, Indels: 15
0.72 0.18 0.09
Matches are distributed among these distances:
39 6 0.05
40 44 0.39
41 63 0.55
42 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (41 bp):
ATTTGACTTTCGCGTTGCGAATTTGAAAAATCGCAACGCGA
Found at i:602067 original size:20 final size:21
Alignment explanation
Indices: 601999--602064 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
601989 CTTTCGCGTT
*
601999 GCGAATTTGAAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
602020 GCGAATTT-GAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
* *
602040 GCGAATTTGGAAAATTGCAAT
1 GCGAATTTGGAAAATCGCAAC
602061 GCGA
1 GCGA
602065 TTTACATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 19 0.46
21 22 0.54
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:609521 original size:17 final size:18
Alignment explanation
Indices: 609494--609532 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
609484 TTTCTTTGTA
609494 ATTTCCATGCAAAAATTT
1 ATTTCCATGCAAAAATTT
**
609512 ATTT-CATGCAATTATTT
1 ATTTCCATGCAAAAATTT
609529 ATTT
1 ATTT
609533 ACTTTGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTTCCATGCAAAAATTT
Found at i:609568 original size:6 final size:6
Alignment explanation
Indices: 609557--609591 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
609547 AAAATAATAA
*
609557 TTTTAT TTTTAT TTTTAT TTTTAT TTTAAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
609592 AAATTTTACC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:611080 original size:19 final size:20
Alignment explanation
Indices: 611010--611063 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
611000 AAATAGATTG
611010 AAAGTATCGATACTATCC--CA
1 AAAGTATCGATAC--TCCAGCA
*
611030 AGAGTATCGATACTCCAGCA
1 AAAGTATCGATACTCCAGCA
*
611050 AAAGTTTCGATACT
1 AAAGTATCGATACT
611064 TCATATAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 3 0.10
20 26 0.90
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAGTATCGATACTCCAGCA
Found at i:616122 original size:13 final size:13
Alignment explanation
Indices: 616100--616138 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
616090 TTTTTTTCAA
616100 AAAAACAAAAAAAC
1 AAAAA-AAAAAAAC
**
616114 AAAAAAAAAAGGC
1 AAAAAAAAAAAAC
616127 AAAAAAAAAAAA
1 AAAAAAAAAAAA
616139 GCCAAAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:616129 original size:21 final size:18
Alignment explanation
Indices: 616098--616138 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
616088 ATTTTTTTTC
616098 AAAAAAACAAAAAAACAAA
1 AAAAAAACAAAAAAA-AAA
616117 AAAAAAAGGCAAAAAAAAAA
1 AAAAAAA--CAAAAAAAAAA
616137 AA
1 AA
616139 GCCAAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 5 0.25
21 8 0.40
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAAAAAA
Found at i:616132 original size:15 final size:15
Alignment explanation
Indices: 616114--616147 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
616104 ACAAAAAAAC
*
616114 AAAAAAAAAAGGCAA
1 AAAAAAAAAAGCCAA
616129 AAAAAAAAAAGCCAA
1 AAAAAAAAAAGCCAA
616144 AAAA
1 AAAA
616148 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGCCAA
Found at i:622373 original size:16 final size:16
Alignment explanation
Indices: 622348--622418 Score: 62
Period size: 16 Copynumber: 4.8 Consensus size: 16
622338 GCAACCATTT
622348 ATGATATCACTTATTG
1 ATGATATCACTTATTG
*
622364 ATGATTTCAC---TTG
1 ATGATATCACTTATTG
*
622377 TTGATATCACTT-TT-
1 ATGATATCACTTATTG
* *
622391 CTGATATCATTTATTG
1 ATGATATCACTTATTG
*
622407 ATGATTTCACTT
1 ATGATATCACTT
622419 TTTCAACAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
13 11 0.26
14 10 0.23
15 4 0.09
16 18 0.42
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (16 bp):
ATGATATCACTTATTG
Found at i:624463 original size:47 final size:45
Alignment explanation
Indices: 624387--624511 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
624377 TATAAAATCT
* * *
624387 CTTACCATTTATCCCATATGCTCTTAAGCTTATTTTAACAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
* *
624432 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
*
624479 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
624512 GCATACTTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 21 0.29
44 3 0.04
45 10 0.14
46 2 0.03
47 36 0.50
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAACAAAATA
Found at i:624519 original size:38 final size:41
Alignment explanation
Indices: 624387--624525 Score: 113
Period size: 47 Copynumber: 3.2 Consensus size: 41
624377 TATAAAATCT
* * * *
624387 CTTACCATTTATCCCATATGCTCTTAAGCTTATTTTAACAAAATA
1 CTTACCA-TTAT-TCATAAGCTCGTAAGCTTATTTTAGC--AATA
*
624432 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCA-TT--ATT-CATAAGCTCGTAAGCTTATTTTAGC-A-ATA
*
624479 CTTGCCATTATTCATAAGCTCGTAAGCTTA-TTT-GC-ATA
1 CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
624517 CTTACCATT
1 CTTACCATT
624526 TATTAACCAA
Statistics
Matches: 83, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
38 11 0.13
41 1 0.01
42 3 0.04
43 18 0.22
44 3 0.04
45 10 0.12
46 4 0.05
47 33 0.40
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (41 bp):
CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
Found at i:636497 original size:33 final size:34
Alignment explanation
Indices: 636455--636520 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
636445 AAACTAATTT
*
636455 GATGTCATTGCTTACATC-AATTTGTTAGGTGAA
1 GATGTCATTGCTTACATCAAATTAGTTAGGTGAA
636488 GATGTCATTGCTTACATCAAATTAGTTAGGTGA
1 GATGTCATTGCTTACATCAAATTAGTTAGGTGA
636521 GAGTTAGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (34 bp):
GATGTCATTGCTTACATCAAATTAGTTAGGTGAA
Found at i:638508 original size:2 final size:2
Alignment explanation
Indices: 638501--638540 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
638491 TGAAATCTGC
*
638501 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
638541 CGTTTAGGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:653820 original size:82 final size:83
Alignment explanation
Indices: 653661--653897 Score: 300
Period size: 83 Copynumber: 2.9 Consensus size: 83
653651 AGTAGTATAA
* * * *
653661 AAACGCCGCAACATATTAGTACTTTAGCAGTGTTTTTTTTACAAACGCCGCAATAATTTGGTATG
1 AAACGCCGCAACATACTAGTACTTTAGCAGCG-ATTTTTTACAAACGCCACAATAATTTGGTATG
*
653726 TTTGT-GC-CTTTTTCAAC
65 TTTGTGGCATTTTTTCAAC
* * * * * * *
653743 AAACGCAGCAACAAAGTAGTACTTTAGCAGCGGTTTTTTACAAACGCCACAATAGTTTAGTATGA
1 AAACGCCGCAACATACTAGTACTTTAGCAGCGATTTTTTACAAACGCCACAATAATTTGGTATGT
653808 TTGTGGCATTTTTTCAAC
66 TTGTGGCATTTTTTCAAC
* * *
653826 AAACGCCGCAACATACTAGTACTTTAGCGGC-ATATTTTTACAAACACAACAATAATTTGGTATG
1 AAACGCCGCAACATACTAGTACTTTAGCAGCGAT-TTTTTACAAACGCCACAATAATTTGGTATG
653890 TTTGTGGC
65 TTTGTGGC
653898 GTTTGGGTTT
Statistics
Matches: 132, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
81 32 0.24
82 31 0.23
83 69 0.52
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (83 bp):
AAACGCCGCAACATACTAGTACTTTAGCAGCGATTTTTTACAAACGCCACAATAATTTGGTATGT
TTGTGGCATTTTTTCAAC
Found at i:653858 original size:42 final size:42
Alignment explanation
Indices: 653734--653864 Score: 101
Period size: 42 Copynumber: 3.1 Consensus size: 42
653724 TGTTTGTGCC
* * * * *
653734 TTTTTCAACAAACGCAGCAACAAAGTAGTACTTTAGCAGCGGT
1 TTTTTCAACAAACGCCGCAACATACTAGTACTTTAGCGGC-AT
* * * *
653777 TTTTT--ACAAACGCCACAATAGT-TTAGTA-TGATT-GTGGCAT
1 TTTTTCAACAAACGCCGCAACA-TACTAGTACT--TTAGCGGCAT
653817 TTTTTCAACAAACGCCGCAACATACTAGTACTTTAGCGGCAT
1 TTTTTCAACAAACGCCGCAACATACTAGTACTTTAGCGGCAT
653859 ATTTTT
1 -TTTTT
653865 ACAAACACAA
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
40 7 0.10
41 23 0.34
42 26 0.39
43 11 0.16
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (42 bp):
TTTTTCAACAAACGCCGCAACATACTAGTACTTTAGCGGCAT
Found at i:655561 original size:44 final size:43
Alignment explanation
Indices: 655449--655565 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
655439 GTTTTGTATT
* * * *
655449 AAAAACGCCACTAAAAACAAGAGAATTAGCTGCGTTTGTAGCA
1 AAAAAAGCCACTAAAGACAAGATAATTAGCAGCGTTTGTAGCA
* * *
655492 AAAAATGCCACTAAAGACAATATAATTAGCAGCGTTTGTGGCAA
1 AAAAAAGCCACTAAAGACAAGATAATTAGCAGCGTTTGTAGC-A
* *
655536 AAAAAAGCCACTAAAGATAGGATAATTAGC
1 AAAAAAGCCACTAAAGACAAGATAATTAGC
655566 GTCATTTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
43 36 0.57
44 27 0.43
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (43 bp):
AAAAAAGCCACTAAAGACAAGATAATTAGCAGCGTTTGTAGCA
Found at i:662108 original size:3 final size:3
Alignment explanation
Indices: 662089--662147 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
662079 AAATGAGTAA
* * * **
662089 AAT AGT AAT AGT AAT AAT AAT AAT AAT AAT ACT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
662137 AAT AATT AAT A
1 AAT AA-T AAT A
662148 GAAGTTTACA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:662443 original size:5 final size:5
Alignment explanation
Indices: 662428--662461 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
662418 AGTAAAATTG
*
662428 AAAAT AGAAT AAAAT -AAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
662462 GGGTTGCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:662452 original size:14 final size:14
Alignment explanation
Indices: 662429--662459 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
662419 GTAAAATTGA
*
662429 AAATAGAATAAAAT
1 AAATAAAATAAAAT
662443 AAATAAAATAAAAT
1 AAATAAAATAAAAT
662457 AAA
1 AAA
662460 ATGGGTTGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:671568 original size:28 final size:30
Alignment explanation
Indices: 671530--671585 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
671520 AAATTTTGAA
*
671530 AAGTGGCCAAAATATAAGTTTT-AAAAGTT
1 AAGTGGCCAAAATATAAATTTTGAAAAGTT
*
671559 AAGTGG-CAAAGTATAAATTTTGAAAAG
1 AAGTGGCCAAAATATAAATTTTGAAAAG
671586 CTTAGGGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (30 bp):
AAGTGGCCAAAATATAAATTTTGAAAAGTT
Found at i:674551 original size:30 final size:30
Alignment explanation
Indices: 674515--674571 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
674505 ATGAAAGTCA
*
674515 ATGTGAAAGTTATGACAAGTATATGAAATT
1 ATGTGAAAGTTATGACAAATATATGAAATT
*
674545 ATGTGAAATTTATGACAAATATATGAA
1 ATGTGAAAGTTATGACAAATATATGAA
674572 TATTGAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.33
Consensus pattern (30 bp):
ATGTGAAAGTTATGACAAATATATGAAATT
Found at i:677389 original size:26 final size:24
Alignment explanation
Indices: 677351--677552 Score: 157
Period size: 26 Copynumber: 8.8 Consensus size: 24
677341 TCATTCCCTA
*
677351 ATGCATCCTTTCATGCATATTAATT
1 ATGCATCCTTTCATGCATCTT-ATT
677376 ATGGCATCCTTTCATGC--CTTA--
1 AT-GCATCCTTTCATGCATCTTATT
* *
677397 ATGCATCATTTCATGCATTTTAATT
1 ATGCATCCTTTCATGCATCTT-ATT
*
677422 ATTACATCCTTTCATGC--CTTA--
1 A-TGCATCCTTTCATGCATCTTATT
*
677443 ATGCATCCTTTCATGCATTTTAATT
1 ATGCATCCTTTCATGCATCTT-ATT
677468 ATGTCATCCTTTCATGC--CTTA--
1 ATG-CATCCTTTCATGCATCTTATT
*
677489 ATGCATCCTTTCATGCATTTTCATT
1 ATGCATCCTTTCATGCATCTT-ATT
677514 ATGGCATCCTTTCATGC--CTTA--
1 AT-GCATCCTTTCATGCATCTTATT
*
677535 ATGCATCATTTCATGCAT
1 ATGCATCCTTTCATGCAT
677553 TTTACATACT
Statistics
Matches: 144, Mismatches: 12, Indels: 45
0.72 0.06 0.22
Matches are distributed among these distances:
20 53 0.37
21 8 0.06
22 6 0.04
23 7 0.05
24 8 0.06
25 8 0.06
26 54 0.38
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (24 bp):
ATGCATCCTTTCATGCATCTTATT
Found at i:677408 original size:20 final size:20
Alignment explanation
Indices: 677379--677550 Score: 128
Period size: 20 Copynumber: 7.7 Consensus size: 20
677369 ATTAATTATG
677379 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
677399 GCATCATTTCATGCATTTTAATTATT
1 GCATCCTTTCATGC--CTT-A--A-T
*
677425 ACATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
677445 GCATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
677470 GTCATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
677491 GCATCCTTTCATGCATTTTCATTAT
1 GCATCCTTTCATGC--CTT-A--AT
677516 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
677537 GCATCATTTCATGC
1 GCATCCTTTCATGC
677551 ATTTTACATA
Statistics
Matches: 123, Mismatches: 11, Indels: 36
0.72 0.06 0.21
Matches are distributed among these distances:
20 53 0.43
21 6 0.05
22 6 0.05
23 6 0.05
24 6 0.05
25 6 0.05
26 40 0.33
ACGTcount: A:0.22, C:0.25, G:0.09, T:0.44
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:677409 original size:46 final size:46
Alignment explanation
Indices: 677335--677556 Score: 354
Period size: 46 Copynumber: 4.8 Consensus size: 46
677325 TTTTACGTTT
* * * *
677335 ATCCATTCATTCCCTAATGCATCCTTTCATGCATATTAATTATGGC
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGC
* **
677381 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATTAC
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGC
*
677427 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGTC
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGC
*
677473 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTCATTATGGC
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGC
*
677519 ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTA
1 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
677557 CATACTTTAA
Statistics
Matches: 162, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 162 1.00
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (46 bp):
ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGC
Found at i:678042 original size:20 final size:20
Alignment explanation
Indices: 678017--678074 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 20
678007 TTCGATGTTT
*
678017 CATGGTATCGATACCCTTAC
1 CATGGTATCGATACCCATAC
678037 CATGGTATCGATACTACCATAC
1 CATGGTATCGATAC--CCATAC
* *
678059 TATGGTACCGATACCC
1 CATGGTATCGATACCC
678075 CCTTACGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 16 0.48
22 17 0.52
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (20 bp):
CATGGTATCGATACCCATAC
Found at i:678089 original size:95 final size:95
Alignment explanation
Indices: 677950--678125 Score: 237
Period size: 95 Copynumber: 1.9 Consensus size: 95
677940 AACCTTGTAC
* * * * *
677950 CGATACTTCTATACTATAGTACTGATACCCCGTTCTGATATCGATACCAATGTTAGATTCGATGT
1 CGATACTACCATACTATAGTACCGATACCCCCTTCTGACATCGATACCAATGTTAGATTCGATGT
* *
678015 TTCATGGTATCGATACCCTTACCATGGTAT
66 TGCATGGTATCCATACCCTTACCATGGTAT
* * *
678045 CGATACTACCATACTATGGTACCGATACCCCCTTAC-GACATCGATACCGATTTTAGATTCGATG
1 CGATACTACCATACTATAGTACCGATACCCCCTT-CTGACATCGATACCAATGTTAGATTCGATG
*
678109 TTGCCTGGTATCCATAC
65 TTGCATGGTATCCATAC
678126 TACCTCGTCG
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
95 68 0.99
96 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (95 bp):
CGATACTACCATACTATAGTACCGATACCCCCTTCTGACATCGATACCAATGTTAGATTCGATGT
TGCATGGTATCCATACCCTTACCATGGTAT
Found at i:682111 original size:20 final size:21
Alignment explanation
Indices: 682077--682131 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
682067 GATCCATCGA
**
682077 AGGATCAACTAAAACAAATAC
1 AGGATCATTTAAAACAAATAC
682098 AGGATCA-TTAAAACAAATAC
1 AGGATCATTTAAAACAAATAC
*
682118 AGGCTCATTTAAAA
1 AGGATCATTTAAAA
682132 GATGAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.20
Consensus pattern (21 bp):
AGGATCATTTAAAACAAATAC
Found at i:684211 original size:46 final size:46
Alignment explanation
Indices: 684122--684312 Score: 240
Period size: 46 Copynumber: 4.2 Consensus size: 46
684112 TCCATTTATA
* * * *
684122 CATTTAAATTATGGCATCCATTCATGACC-TAATTCATCCTTTCATG
1 CATTTTAATTATGACATCCTTTCATG-CCTTAATGCATCCTTTCATG
* * * *
684168 CCTTTTAATTATGGCATCCTTTTATGCCTTAATGCATCATTTCATG
1 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
* * * *
684214 CATTTTTACTATGACATCCTTTTATTCCTTAATGCATCCTTTCATG
1 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
* *
684260 CATTTTCATTATGACATCCTTTCATGTCTTAATGCATCCTTTCATG
1 CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
684306 CATTTTA
1 CATTTTA
684313 CATACTCTAA
Statistics
Matches: 126, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
45 2 0.02
46 124 0.98
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.45
Consensus pattern (46 bp):
CATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATG
Found at i:684277 original size:26 final size:24
Alignment explanation
Indices: 684156--684312 Score: 95
Period size: 20 Copynumber: 6.8 Consensus size: 24
684146 TGACCTAATT
*
684156 CATCCTTTCATGCCTTTTAATTATGG
1 CATCCTTTCATGCATTTT-ATTAT-G
* *
684182 CATCCTTTTATGC--CTTA--ATG
1 CATCCTTTCATGCATTTTATTATG
* *
684202 CATCATTTCATGCATTTTTACTATG
1 CATCCTTTCATGCA-TTTTATTATG
* * *
684227 ACATCCTTTTATTC--CTTA--ATG
1 -CATCCTTTCATGCATTTTATTATG
684248 CATCCTTTCATGCATTTTCATTATG
1 CATCCTTTCATGCATTTT-ATTATG
*
684273 ACATCCTTTCATG--TCTTA--ATG
1 -CATCCTTTCATGCATTTTATTATG
684294 CATCCTTTCATGCATTTTA
1 CATCCTTTCATGCATTTTA
684313 CATACTCTAA
Statistics
Matches: 103, Mismatches: 14, Indels: 32
0.69 0.09 0.21
Matches are distributed among these distances:
20 35 0.34
21 8 0.08
22 6 0.06
23 9 0.09
24 5 0.05
25 6 0.06
26 34 0.33
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.46
Consensus pattern (24 bp):
CATCCTTTCATGCATTTTATTATG
Found at i:684854 original size:95 final size:95
Alignment explanation
Indices: 684717--684905 Score: 261
Period size: 95 Copynumber: 2.0 Consensus size: 95
684707 GATACTTCTA
* * *
684717 TACTATAGTACCGATACCCCCTTTCGGTATAGATACCAATTTTAGATTCAATGTTTCCTGGTAAC
1 TACTATAGTACCAATACCCCCTTACGGTATAGATACCAATTTTAGATTCAATGTTGCCTGGTAAC
* *
684782 GATACCCTTACCATGGTATCGGTACTACCC
66 GATACCCTTACAATGGTATCGATACTACCC
* * * * ** *
684812 TACTATGGTACCAATACCCCCTTACGGTATCGATATCGATTTTAGATTTGATGTTGCCTGGTATC
1 TACTATAGTACCAATACCCCCTTACGGTATAGATACCAATTTTAGATTCAATGTTGCCTGGTAAC
*
684877 GATACCCTTACAATGGTATTGATACTACC
66 GATACCCTTACAATGGTATCGATACTACC
684906 TCGTCATTAT
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
95 81 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (95 bp):
TACTATAGTACCAATACCCCCTTACGGTATAGATACCAATTTTAGATTCAATGTTGCCTGGTAAC
GATACCCTTACAATGGTATCGATACTACCC
Found at i:690729 original size:46 final size:46
Alignment explanation
Indices: 690668--690807 Score: 167
Period size: 46 Copynumber: 3.0 Consensus size: 46
690658 ATCGTCATGT
* * * **
690668 ATTTTCTTTTGTGGCATCATTTCATGTTAATTATGCTCCGTTATTC
1 ATTTTCATTTATGGCATCCTTTCATGCAAATTATGCTCCGTTATTC
* *
690714 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCAT-CATTATGT-
1 ATTTTCATTTATGGCATCCTTTCATGCAAATTATGC-TCCGTTAT-TC
* *
690760 ATTTTCATTTATGGCATCCTTTCATGCAAATTATGCACCGTTTTTC
1 ATTTTCATTTATGGCATCCTTTCATGCAAATTATGCTCCGTTATTC
690806 AT
1 AT
690808 ATAACTTGCA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
45 1 0.01
46 77 0.96
47 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.11, T:0.48
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCCTTTCATGCAAATTATGCTCCGTTATTC
Found at i:690748 original size:22 final size:22
Alignment explanation
Indices: 690722--690794 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
690712 TCATTTTCAT
690722 TTATGGCATCCTTTCATGCCAA
1 TTATGGCATCCTTTCATGCCAA
* * ** *
690744 TTAT-GCATCATTATGTATTTTCAT
1 TTATGGCATCCTT-T-CA-TGCCAA
*
690768 TTATGGCATCCTTTCATGCAAA
1 TTATGGCATCCTTTCATGCCAA
690790 TTATG
1 TTATG
690795 CACCGTTTTT
Statistics
Matches: 36, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
21 7 0.19
22 12 0.33
23 2 0.06
24 8 0.22
25 7 0.19
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (22 bp):
TTATGGCATCCTTTCATGCCAA
Found at i:690946 original size:81 final size:81
Alignment explanation
Indices: 690838--691672 Score: 975
Period size: 81 Copynumber: 10.4 Consensus size: 81
690828 CTTTGTACCA
* ** * * * * *
690838 AAATGCACAGTTACACATTTAGTCTTTTATCCCAAAGGGATTTAACCTTTCATCTAACTTGCATT
1 AAATGCACAGCTAGGCATTTAATCTTTTA-CTCAAAGGTATTTAACCTTTCATCTAACTGGCATG
* *
690903 ATTGGCACCTTTCTCT-
65 ATTGACACCTTTCTGTC
* *
690919 AAATGCACAGTTAGACATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
*
690984 TTGACACCTTTC--TA
66 TTGACACCTTTCTGTC
* *
690998 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAAATGGCATTA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
691063 TTGACACCTTTCTGTC
66 TTGACACCTTTCTGTC
* * * * **
691079 AAATGCACAACTAGGCATTTAGTCTTTTACTCAAAGGTATTTAGCCTTTCATCTAACCGATATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
*
691144 TTGACAGCTTTCTGTC
66 TTGACACCTTTCTGTC
* * * * * * * * **
691160 AAATGCACAACTAGGAATTTAGTCCTCTAGTCGAAGGTATTTAACGTTTCATCTAACTGTAAAT-
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTG-GCATG
* *
691224 ATTGATACCTTTCTATC
65 ATTGACACCTTTCTGTC
* * *
691241 AAACGCGCAGCTAGGCATTTAATCTTTTACACAAAGGTATTTAACCTTTCATCTAACTGGCATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
*
691306 TTGACACCTTTCAGTC
66 TTGACACCTTTCTGTC
* * * * * *
691322 AACTGCACAGTTAGTCATTTAATCTTTTACTGAAAGGTATTTAACCTTTCAACTAATTGGCATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
*
691387 TTGACACCTTTATGT-
66 TTGACACCTTTCTGTC
* * ** *
691402 AAATACACAACTAGGTGTTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
*
691467 -TAACACCTTTCTGTC
66 TTGACACCTTTCTGTC
* * ** * *
691482 AAATGCTCAGCTTGGCATTTAATCTTTTACTCAAAAATATTTAACTTTTCATCTAACTAGCATGA
1 AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
* *
691547 TTGACACATTTTTGTC
66 TTGACACCTTTCTGTC
* * * *
691563 AAATGCACAACTTA-GCATTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAAGTAGCATG
1 AAATGCACAGC-TAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATG
*
691627 ATTGACACCTTTCTATC
65 ATTGACACCTTTCTGTC
* * *
691644 AAATGCATAACTAGG-AATTAATTCTTTTA
1 AAATGCACAGCTAGGCATTTAA-TCTTTTA
691673 TTTTAACACT
Statistics
Matches: 643, Mismatches: 101, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
78 1 0.00
79 85 0.13
80 159 0.25
81 394 0.61
82 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (81 bp):
AAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGA
TTGACACCTTTCTGTC
Found at i:691479 original size:322 final size:321
Alignment explanation
Indices: 690870--691672 Score: 997
Period size: 322 Copynumber: 2.5 Consensus size: 321
690860 TCTTTTATCC
* * * * * * *
690870 CAAAGGGATTTAACCTTTCATCTAACTTGCATTATTGGCACCTTTCTCT-AAATGCACAGTTAGA
1 CAAAGGTATTTAACCTTTCATCTAACTT-AAATATTGACACCTTTCTATCAAATGCACAGCTAGG
690934 CATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTAA
65 CATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTAA
* *
690999 AATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAAATGGCATTAT
130 AATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCAACTAAATGGCATGAT
* * *
691064 TGACACCTTTCTGTCAAATGCACAACTAGGCATTTAGTCTTTTACTCAAAGGTATTTAGCCTTTC
195 TGACACCTTTATGTCAAATACACAACTAGGCATTTAGTCTTTTACTCAAAGGTATTTAACCTTTC
* * * * *
691129 ATCTAACCGATATGATTGACAGCTTTCTGTCAAATGCACAACTAGGAATTTAGTCCTCTAGT
260 ATCTAACCGACATGATTAACACCTTTCTGTCAAATGCACAACTAGGAATTTAATCCTCTACT
* * * * *
691191 CGAAGGTATTTAACGTTTCATCTAACTGTAAATATTGATACCTTTCTATCAAACGCGCAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACT-TAAATATTGACACCTTTCTATCAAATGCACAGCTAGG
*
691256 CATTTAATCTTTTACACAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCAGT
65 CATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTC--T
* * * * * *
691321 CAACTGCACAGTTAGTCATTTAATCTTTTACTGAAAGGTATTTAACCTTTCAACTAATTGGCATG
128 AAAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCAACTAAATGGCATG
**
691386 ATTGACACCTTTATGT-AAATACACAACTAGGTGTTTAGTCTTTTACTCAAAGGTATTTAACCTT
193 ATTGACACCTTTATGTCAAATACACAACTAGGCATTTAGTCTTTTACTCAAAGGTATTTAACCTT
* * * * * * * *
691450 TCATCTAACTGGCATGA-TAACACCTTTCTGTCAAATGCTCAGCTTGGCATTTAATCTTTTACT
258 TCATCTAACCGACATGATTAACACCTTTCTGTCAAATGCACAACTAGGAATTTAATCCTCTACT
** * * * * * *
691513 CAAAAATATTTAACTTTTCATCTAAC-TAGCATGATTGACACATTTTTGTCAAATGCACAACTTA
1 CAAAGGTATTTAACCTTTCATCTAACTTA-AAT-ATTGACACCTTTCTATCAAATGCACAGC-TA
* * *
691577 -GCATTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAAGTAGCATGATTGACACCTTTCT
63 GGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCT
* * *
691641 ATCAAATGCATAACTAGG-AATTAATTCTTTTA
128 A--AAATGCACAGCTAGGCATTTAA-TCTTTTA
691673 TTTTAACACT
Statistics
Matches: 410, Mismatches: 62, Indels: 19
0.84 0.13 0.04
Matches are distributed among these distances:
320 3 0.01
321 46 0.11
322 228 0.56
323 60 0.15
324 73 0.18
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (321 bp):
CAAAGGTATTTAACCTTTCATCTAACTTAAATATTGACACCTTTCTATCAAATGCACAGCTAGGC
ATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTAAA
ATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCAACTAAATGGCATGATT
GACACCTTTATGTCAAATACACAACTAGGCATTTAGTCTTTTACTCAAAGGTATTTAACCTTTCA
TCTAACCGACATGATTAACACCTTTCTGTCAAATGCACAACTAGGAATTTAATCCTCTACT
Found at i:691607 original size:403 final size:403
Alignment explanation
Indices: 690853--691646 Score: 1100
Period size: 403 Copynumber: 2.0 Consensus size: 403
690843 CACAGTTACA
* * * * *
690853 CATTTAGTCTTTTATCCCAAAGGGATTTAACCTTTCATCTAACTTGCATTATTGGCACCTTTCTC
1 CATTTAATCTTTTATCACAAAGGGATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTC
*
690918 TAAATGCACAGTTAGACATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATG
66 TAAATGCACAGTTAGACATTTAATCTTTTACTCAAAGGTATTTAACCTTTCAACTAACTGGCATG
* * *
690983 ATTGACACCTTTCTAAAATGCACAGCTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTC
131 ATTGACACCTTTATAAAATACACAACTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTC
* * *
691048 ATCTAAATGGCATTATTGACACCTTTCTGTCAAATGCACAACTAGGCATTTAGTCTTTTACTCAA
196 ATCTAAATGGCATGATTAACACCTTTCTGTCAAATGCACAACTAGGCATTTAATCTTTTACTCAA
** * * *
691113 AGGTATTTAGCCTTTCATCTAACCGATATGATTGACAGCTTTCTGTCAAATGCACAACTAGGAAT
261 AAATATTTAACCTTTCATCTAACAGACATGATTGACAGCTTTCTGTCAAATGCACAACTAGGAAT
* * * *
691178 TTAGTCCTCTAGTCGAAGGTATTTAACGTTTCATCTAACTGTA-AAT-ATTGATACCTTTCTATC
326 TTAGTCCTCTACTCAAAGGTATTTAACCTTTCATCTAA--GTAGAATGATTGACACCTTTCTATC
691241 AAACGCGCAGCTAGG
389 AAACGCGCAGCTAGG
*
691256 CATTTAATCTTTTA-CACAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCAG
1 CATTTAATCTTTTATCACAAAGGGATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTC--
* * * *
691320 TC-AACTGCACAGTTAGTCATTTAATCTTTTACTGAAAGGTATTTAACCTTTCAACTAATTGGCA
64 TCTAAATGCACAGTTAGACATTTAATCTTTTACTCAAAGGTATTTAACCTTTCAACTAACTGGCA
* ** *
691384 TGATTGACACCTTTATGTAAATACACAACTAGGTGTTTAGTCTTTTACTCAAAGGTATTTAACCT
129 TGATTGACACCTTTAT-AAAATACACAACTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCT
* * * *
691449 TTCATCTAACTGGCATGA-TAACACCTTTCTGTCAAATGCTCAGCTTGGCATTTAATCTTTTACT
193 TTCATCTAAATGGCATGATTAACACCTTTCTGTCAAATGCACAACTAGGCATTTAATCTTTTACT
* *
691513 CAAAAATATTTAACTTTTCATCTAACTAG-CATGATTGACA-CATTTTTGTCAAATGCACAACTT
258 CAAAAATATTTAACCTTTCATCTAAC-AGACATGATTGACAGC-TTTCTGTCAAATGCACAAC-T
* * * *
691576 A-GCATTTAGTCTTTTACTCAAAGGTATTTAACCTTTCATCTAAGTAGCATGATTGACACCTTTC
320 AGGAATTTAGTCCTCTACTCAAAGGTATTTAACCTTTCATCTAAGTAGAATGATTGACACCTTTC
691640 TATCAAA
385 TATCAAA
691647 TGCATAACTA
Statistics
Matches: 343, Mismatches: 40, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
401 3 0.01
402 46 0.13
403 231 0.67
404 63 0.18
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (403 bp):
CATTTAATCTTTTATCACAAAGGGATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTC
TAAATGCACAGTTAGACATTTAATCTTTTACTCAAAGGTATTTAACCTTTCAACTAACTGGCATG
ATTGACACCTTTATAAAATACACAACTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTC
ATCTAAATGGCATGATTAACACCTTTCTGTCAAATGCACAACTAGGCATTTAATCTTTTACTCAA
AAATATTTAACCTTTCATCTAACAGACATGATTGACAGCTTTCTGTCAAATGCACAACTAGGAAT
TTAGTCCTCTACTCAAAGGTATTTAACCTTTCATCTAAGTAGAATGATTGACACCTTTCTATCAA
ACGCGCAGCTAGG
Found at i:696173 original size:130 final size:130
Alignment explanation
Indices: 695940--696200 Score: 522
Period size: 130 Copynumber: 2.0 Consensus size: 130
695930 GTGTTTGTTT
695940 TTTAGCATTTGCATCATAACAAGAGGCTATTGATCTTTAAAAAGCGTTTATTATACACAAAATAA
1 TTTAGCATTTGCATCATAACAAGAGGCTATTGATCTTTAAAAAGCGTTTATTATACACAAAATAA
696005 TCTAAATTAATGGACAAAGGTGTTGTAATACACAAAGCTATATGTCAGAGTTGGTTAGCTATGCC
66 TCTAAATTAATGGACAAAGGTGTTGTAATACACAAAGCTATATGTCAGAGTTGGTTAGCTATGCC
696070 TTTAGCATTTGCATCATAACAAGAGGCTATTGATCTTTAAAAAGCGTTTATTATACACAAAATAA
1 TTTAGCATTTGCATCATAACAAGAGGCTATTGATCTTTAAAAAGCGTTTATTATACACAAAATAA
696135 TCTAAATTAATGGACAAAGGTGTTGTAATACACAAAGCTATATGTCAGAGTTGGTTAGCTATGCC
66 TCTAAATTAATGGACAAAGGTGTTGTAATACACAAAGCTATATGTCAGAGTTGGTTAGCTATGCC
696200 T
1 T
696201 CTATCAGCCT
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 131 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (130 bp):
TTTAGCATTTGCATCATAACAAGAGGCTATTGATCTTTAAAAAGCGTTTATTATACACAAAATAA
TCTAAATTAATGGACAAAGGTGTTGTAATACACAAAGCTATATGTCAGAGTTGGTTAGCTATGCC
Found at i:701556 original size:106 final size:106
Alignment explanation
Indices: 701363--701626 Score: 456
Period size: 106 Copynumber: 2.5 Consensus size: 106
701353 ACGAAGGGGC
*
701363 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAATACAAGTT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
* * *
701428 CAACTTCACAGCGGAGGTACGGCTGGTTGTCAACAAACAAT
66 CAACTTCACACCGAAGGGACGGCTGGTTGTCAACAAACAAT
*
701469 TTCCCAGATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
701534 CAACTTCACACCGAAGGGACGGCTGGTTGTCAACAAACAAT
66 CAACTTCACACCGAAGGGACGGCTGGTTGTCAACAAACAAT
* *
701575 TTCCCCAGTTTCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCG
1 TT-CCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
701627 GAACAGTACA
Statistics
Matches: 149, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
106 103 0.69
107 46 0.31
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (106 bp):
TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
CAACTTCACACCGAAGGGACGGCTGGTTGTCAACAAACAAT
Found at i:705935 original size:2 final size:2
Alignment explanation
Indices: 705928--705952 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
705918 CAAGAAAAGC
705928 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
705953 CTTTCTGACA
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:707840 original size:79 final size:81
Alignment explanation
Indices: 707737--707908 Score: 206
Period size: 81 Copynumber: 2.1 Consensus size: 81
707727 ATGCGTCATT
* * *
707737 TTTCATCTAACTTGCATCAGTGGCA-CCTTATGCC-AATGCACAGTGAGGCATTTAGTCTTTAT-
1 TTTCATCTAACTTCCATCAGTGGCATCCTTATGCCAAATGCACAGTCAGGCATTTAATCTTT-TG
707799 CCCAAAGGCATTTAACC
65 CCCAAAGGCATTTAACC
* * ** * *
707816 TTTCATCTAACTTCCATTATTGGCATTTTTCTTCCAAATGCACAGTCAGGCATTTAATCTTTTGC
1 TTTCATCTAACTTCCATCAGTGGCATCCTTATGCCAAATGCACAGTCAGGCATTTAATCTTTTGC
* * *
707881 TCAAAGGTATTTATCC
66 CCAAAGGCATTTAACC
707897 TTTCATCTAACT
1 TTTCATCTAACT
707909 GGCATGATTG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
79 22 0.28
80 6 0.08
81 50 0.64
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.38
Consensus pattern (81 bp):
TTTCATCTAACTTCCATCAGTGGCATCCTTATGCCAAATGCACAGTCAGGCATTTAATCTTTTGC
CCAAAGGCATTTAACC
Found at i:707928 original size:81 final size:80
Alignment explanation
Indices: 707771--707986 Score: 224
Period size: 81 Copynumber: 2.7 Consensus size: 80
707761 ACCTTATGCC
* * * * * * *
707771 AATGCACAGTGAGGCATTTAGTCTTTATCCCAAAGGCATTTAACCTTTCATCTAACTTCCATTAT
1 AATGCACAGTCAGGCATTTAATCTTT-TCTCAAAGGTATTTATCCTTTCATCTAACTGCCATGAT
* **
707836 TGGCATTTTTCT-TCCA
65 TGACACATTTCTGT-CA
*
707852 AATGCACAGTCAGGCATTTAATCTTTTGCTCAAAGGTATTTATCCTTTCATCTAACTGGCATGAT
1 AATGCACAGTCAGGCATTTAATCTTTT-CTCAAAGGTATTTATCCTTTCATCTAACTGCCATGAT
707917 TGACACATTTCTGTCA
65 TGACACATTTCTGTCA
* * *
707933 AATGCACA-ACTAGG-AGTTTAATCTTTACTCAAAGGTACTTAAT-CTTTCATCTAA
1 AATGCACAGTC-AGGCA-TTTAATCTTTTCTCAAAGGTA-TTTATCCTTTCATCTAA
707987 GTTCTGTCAA
Statistics
Matches: 116, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
80 24 0.21
81 91 0.78
82 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (80 bp):
AATGCACAGTCAGGCATTTAATCTTTTCTCAAAGGTATTTATCCTTTCATCTAACTGCCATGATT
GACACATTTCTGTCA
Found at i:708031 original size:63 final size:62
Alignment explanation
Indices: 707925--708048 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 62
707915 ATTGACACAT
*
707925 TTCTGTCAAATGCACAACTAGGAGTTTAATCTTTACTCAAAGGTACTTAATCTTTCATCTAAG
1 TTCTGTCAAATGCACAACTAGGAGTTTAATCTTTACTCAAAGGTACTTAA-CCTTCATCTAAG
*
707988 TTCTGTCAAATGCACAACTAGGCA-TTTAATCTTTTACTC-AAGGTATTTAACCTTCATCTAA
1 TTCTGTCAAATGCACAACTAGG-AGTTTAATC-TTTACTCAAAGGTACTTAACCTTCATCTAA
708049 CTGGCATGAT
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
62 10 0.18
63 39 0.68
64 8 0.14
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (62 bp):
TTCTGTCAAATGCACAACTAGGAGTTTAATCTTTACTCAAAGGTACTTAACCTTCATCTAAG
Found at i:710581 original size:267 final size:266
Alignment explanation
Indices: 710106--710637 Score: 1005
Period size: 267 Copynumber: 2.0 Consensus size: 266
710096 AAAATTAGAT
710106 GGATAAATGGCTAATGATCAAAATAGTCGATTGTAGAGAATGATTCTTAGCGACACTGACAATCC
1 GGATAAATGGCTAATGATCAAAATAGTCGATTGTAGAGAATGATTCTTAGCGACACTGACAATCC
710171 CAAGCAAAATGGTAAAAAGCATTGCAAAGCCATTACCACAAAAAAAAAAAGGATTCATGTTGGGA
66 CAAGCAAAATGGTAAAAAGCATTGCAAAGCCATTACCAC--AAAAAAAAAGGATTCATGTTGGGA
710236 ACCAGTGAGGAACTAAGGAGAAATAATGAAGAAGCTCATAAGCATGGTAAAGGGAAGATGAAAGA
129 ACCAGTGAGGAACTAAGGAGAAATAATGAAGAAGCTCATAAGCATGGTAAAGGGAAGATGAAAGA
710301 AGTTGAGACCAAATCGCATGAGAGTCAATTCACA-CACCAGACATAATGTAGAGTAGCAATTTAG
194 AGTTGAGACCAAATCGCATGAGAGTCAATTCACAGCACCAGACATAATGTAGAGTAGCAATTTAG
710365 AATCAATG
259 AATCAATG
710373 GGATAAATGGCTAATGATCAAAATAGTCGATTGTAGAGAATGATTCTTAGCGACACTGACAATCC
1 GGATAAATGGCTAATGATCAAAATAGTCGATTGTAGAGAATGATTCTTAGCGACACTGACAATCC
710438 CAAGCAAAATGGTAAAAAGCATTGCAAAGCCATTACCAC-AAAAAAAAGGAATTCATGTTGGGGA
66 CAAGCAAAATGGTAAAAAGCATTGCAAAGCCATTACCACAAAAAAAAAGG-ATTCATGTT-GGGA
710502 ACCAGTTGAGGAACTAAGGAGAAATAATGAAGAAGCTCATAAGCATGGTAAAGGGAAGATGAAAG
129 ACCAG-TGAGGAACTAAGGAGAAATAATGAAGAAGCTCATAAGCATGGTAAAGGGAAGATGAAAG
710567 AAGTTGAGACCAAATCGCATGAGAGTCAATTCACAGCACCAGACATAATGTAGAGTAGCAATTTA
193 AAGTTGAGACCAAATCGCATGAGAGTCAATTCACAGCACCAGACATAATGTAGAGTAGCAATTTA
710632 GAATCA
258 GAATCA
710638 TTGTCGATAG
Statistics
Matches: 261, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
264 10 0.04
265 9 0.03
266 9 0.03
267 198 0.76
268 35 0.13
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (266 bp):
GGATAAATGGCTAATGATCAAAATAGTCGATTGTAGAGAATGATTCTTAGCGACACTGACAATCC
CAAGCAAAATGGTAAAAAGCATTGCAAAGCCATTACCACAAAAAAAAAGGATTCATGTTGGGAAC
CAGTGAGGAACTAAGGAGAAATAATGAAGAAGCTCATAAGCATGGTAAAGGGAAGATGAAAGAAG
TTGAGACCAAATCGCATGAGAGTCAATTCACAGCACCAGACATAATGTAGAGTAGCAATTTAGAA
TCAATG
Found at i:712363 original size:7 final size:7
Alignment explanation
Indices: 712351--712400 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
712341 CTTTTATAGT
712351 TAAACCC
1 TAAACCC
712358 TAAACCC
1 TAAACCC
712365 TAAACCC
1 TAAACCC
712372 TAAACCC
1 TAAACCC
712379 TAAACCC
1 TAAACCC
712386 TAAACCC
1 TAAACCC
712393 TAAACCC
1 TAAACCC
712400 T
1 T
712401 CGGTATTTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:720534 original size:188 final size:185
Alignment explanation
Indices: 720213--720585 Score: 623
Period size: 188 Copynumber: 2.0 Consensus size: 185
720203 TGACGATTGA
720213 AGGTATTTTCTAAAGTGATTCTATTTTCTATTCCGGTAAATTTCGAGGCCAGAATTTTATTTAAG
1 AGGTATTTTCTAAAGTGATTCTATTTTCTATTCCGGTAAATTTCGAGGCCAGAATTTTATTTAAG
720278 GAGAGAATTGTAACAAGAATTTCCCAAATCCAAAGTCCTAAAATTTGAGAATTTATTCTTCAAAT
66 GAGAGAATTGTAACAAGAATTTCCCAAATCCAAAGTCCTAAAATTTGAGAATTTATTCTTCAAAT
720343 CCCT-AATTGAGTGTAGGACTAAATT-AA-TTTGACAGAATTTTGGTGACCATTTT
131 CCCTAAATTGAGTGTAGGACTAAATTAAATTTTGACAGAA-TTTGGTGACCATTTT
720396 AGGTATTTTCTAAAGTGATTCTATTTTC-ATTCCGGT-AA-TTCGAGGCCAGAATTTTATTTAAG
1 AGGTATTTTCTAAAGTGATTCTATTTTCTATTCCGGTAAATTTCGAGGCCAGAATTTTATTT-A-
720458 GAGGAGAGAATTGTAACAAGCCGAATTTTCCCCAAATCCAAAGTCCTAAAATTTGAGAATTTATT
64 -AGGAGAGAATTGTAACAA---GAA-TTT-CCCAAATCCAAAGTCCTAAAATTTGAGAATTTATT
720523 CTTCAAATCCCTAAATTGAGTGTAGGACTAAATTAAATTTTGACAGAATTTGGTGACCATTTT
123 CTTCAAATCCCTAAATTGAGTGTAGGACTAAATTAAATTTTGACAGAATTTGGTGACCATTTT
720586 TGAAAGTACG
Statistics
Matches: 179, Mismatches: 0, Indels: 15
0.92 0.00 0.08
Matches are distributed among these distances:
180 21 0.12
181 3 0.02
182 8 0.04
183 46 0.26
186 3 0.02
187 3 0.02
188 47 0.26
189 21 0.12
190 17 0.09
191 10 0.06
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (185 bp):
AGGTATTTTCTAAAGTGATTCTATTTTCTATTCCGGTAAATTTCGAGGCCAGAATTTTATTTAAG
GAGAGAATTGTAACAAGAATTTCCCAAATCCAAAGTCCTAAAATTTGAGAATTTATTCTTCAAAT
CCCTAAATTGAGTGTAGGACTAAATTAAATTTTGACAGAATTTGGTGACCATTTT
Found at i:721585 original size:15 final size:15
Alignment explanation
Indices: 721544--721587 Score: 72
Period size: 16 Copynumber: 2.9 Consensus size: 15
721534 GATATTGAAT
721544 ATAT-TTATTCGGAC
1 ATATGTTATTCGGAC
721558 ATATGTTATTTCGGAC
1 ATATGTTA-TTCGGAC
721574 ATATGTTATTCGGA
1 ATATGTTATTCGGA
721588 TCGGATCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.14
15 9 0.32
16 15 0.54
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.43
Consensus pattern (15 bp):
ATATGTTATTCGGAC
Found at i:721738 original size:330 final size:335
Alignment explanation
Indices: 721296--721967 Score: 1209
Period size: 330 Copynumber: 2.0 Consensus size: 335
721286 AATTGATTGT
*
721296 TTGGGATTGGTTGCAAGCATGATTGTTATGTGTACTGCTACGTTGTTTATAAAATCAACATGCAT
1 TTGGGATTGGTTGCAAGCATGATTGTTATGTGTACTGCTACGTTGTTTATAAAATCAACAAGCAT
*
721361 ATCATTTGAAAGTTAGTTTCGAGTGGTGACGGTTTGTGATATTGATGTATCATCTAAAATCAGGA
66 ATCATTTGAAAGTTAGTTTCGAGTGGTGACGGTTTGTGATATTGATGTATCAGCTAAAATCAGGA
721426 AATTATGTAAAGCTACTTATGTTATTTATCGAATTCAGATCATGTTATGCATTCGGATTATTTGT
131 AATTATGTAAAGCTACTTATGTTATTTATCGAATTCAGATCATGTTATGCATTCGGATTATTTGT
721491 ATATGTAGCTATTACATTCAGATCATATC-AAAATCGGATATATGATA-TTGAATATAT-TTATT
196 ATATGTAGCTATTACATTCAGATCATATCAAAAATCGGATATATGATATTTGAATATATGTTATT
721553 CGGACATATGTTATTTCGGACATATGTTATTCGGATCGGATCAGATGCTGAATATATGTGCCATT
261 CGGACATATGTTA-TTCGGACATATGTTATTCGGATCGGATCAGATGCTGAATATATGTGCCATT
721618 TGCATGTCATA
325 TGCATGTCATA
721629 TTGGGATTGGTTGCAAGCATGATTG-T-TGTGTACTGCTACGTTGTTT-T-AAATCAGACAAGCA
1 TTGGGATTGGTTGCAAGCATGATTGTTATGTGTACTGCTACGTTGTTTATAAAATCA-ACAAGCA
721690 TATTC-TTTGAAAGTTAGTTTCGAGT-GTGACGGTTTTGTGATATTGATGTATCAGCTAAAATCA
65 TA-TCATTTGAAAGTTAGTTTCGAGTGGTGACGG-TTTGTGATATTGATGTATCAGCTAAAATCA
*
721753 GGAAATTATGTAAAGCTACTTGTGTTATTTATCGAATTCAGATCATGTTATGCATTCGGATTATT
128 GGAAATTATGTAAAGCTACTTATGTTATTTATCGAATTCAGATCATGTTATGCATTCGGATTATT
*
721818 TGTATATGTAGCTATTACATTCAGATCATATCAAAAATCGGATATATGATATTTGAGTATATGTT
193 TGTATATGTAGCTATTACATTCAGATCATATCAAAAATCGGATATATGATATTTGAATATATGTT
721883 ATTCGGACATATGTTATTCGGACATATGTTATTCGGATCGGATCAGATGCTGAATATATGTGCCA
258 ATTCGGACATATGTTATTCGGACATATGTTATTCGGATCGGATCAGATGCTGAATATATGTGCCA
721948 TTTGCATGTCATA
323 TTTGCATGTCATA
721961 TTGGGAT
1 TTGGGAT
721968 GAATTTTTAT
Statistics
Matches: 329, Mismatches: 4, Indels: 13
0.95 0.01 0.04
Matches are distributed among these distances:
329 13 0.04
330 154 0.47
331 40 0.12
332 79 0.24
333 43 0.13
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (335 bp):
TTGGGATTGGTTGCAAGCATGATTGTTATGTGTACTGCTACGTTGTTTATAAAATCAACAAGCAT
ATCATTTGAAAGTTAGTTTCGAGTGGTGACGGTTTGTGATATTGATGTATCAGCTAAAATCAGGA
AATTATGTAAAGCTACTTATGTTATTTATCGAATTCAGATCATGTTATGCATTCGGATTATTTGT
ATATGTAGCTATTACATTCAGATCATATCAAAAATCGGATATATGATATTTGAATATATGTTATT
CGGACATATGTTATTCGGACATATGTTATTCGGATCGGATCAGATGCTGAATATATGTGCCATTT
GCATGTCATA
Found at i:721894 original size:15 final size:15
Alignment explanation
Indices: 721876--721919 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
721866 ATATTTGAGT
721876 ATATGTTATTCGGAC
1 ATATGTTATTCGGAC
721891 ATATGTTATTCGGAC
1 ATATGTTATTCGGAC
721906 ATATGTTATTCGGA
1 ATATGTTATTCGGA
721920 TCGGATCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.41
Consensus pattern (15 bp):
ATATGTTATTCGGAC
Found at i:723703 original size:21 final size:21
Alignment explanation
Indices: 723677--723724 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
723667 GTGCCCATTG
723677 GACGCACAAATCAAACAATGT
1 GACGCACAAATCAAACAATGT
723698 GACGCACAAATCAAACAATGT
1 GACGCACAAATCAAACAATGT
723719 GACGCA
1 GACGCA
723725 AGGCATCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.46, C:0.25, G:0.17, T:0.12
Consensus pattern (21 bp):
GACGCACAAATCAAACAATGT
Found at i:727396 original size:35 final size:35
Alignment explanation
Indices: 727346--727435 Score: 144
Period size: 35 Copynumber: 2.5 Consensus size: 35
727336 TATAATCTTT
*
727346 GATCGAAATAAAACTTAAACCACATGATATTGAAAC
1 GATCG-AACAAAACTTAAACCACATGATATTGAAAC
*
727382 GATCGAACAAAACTTAAACCACGTGATATTGAAAC
1 GATCGAACAAAACTTAAACCACATGATATTGAAAC
*
727417 TATCGAACAAAACTTAAAC
1 GATCGAACAAAACTTAAAC
727436 TACTTGACAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 46 0.90
36 5 0.10
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.21
Consensus pattern (35 bp):
GATCGAACAAAACTTAAACCACATGATATTGAAAC
Found at i:731169 original size:16 final size:16
Alignment explanation
Indices: 731144--731202 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
731134 ATAAATAAAT
731144 GAACATAAACGAACAC
1 GAACATAAACGAACAC
* *
731160 TAAAATAAACGAACAC
1 GAACATAAACGAACAC
*
731176 GAACATAAATGAACAC
1 GAACATAAACGAACAC
731192 GAACATAAACG
1 GAACATAAACG
731203 TTGGAGACCC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:731193 original size:22 final size:22
Alignment explanation
Indices: 731138--731196 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
731128 CATTTAATAA
*
731138 ATAAATGAACA-TAA-ACGAAC
1 ATAAATGAACACGAACACGAAC
731158 ACTAAAAT-AA-ACGAACACGAAC
1 A-T-AAATGAACACGAACACGAAC
731180 ATAAATGAACACGAACA
1 ATAAATGAACACGAACA
731197 TAAACGTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
20 6 0.19
21 8 0.25
22 18 0.56
ACGTcount: A:0.59, C:0.19, G:0.10, T:0.12
Consensus pattern (22 bp):
ATAAATGAACACGAACACGAAC
Found at i:732887 original size:20 final size:23
Alignment explanation
Indices: 732841--732887 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 23
732831 GAAACCGGTT
*
732841 AACCGGTTTTCAACCGGGTTATG
1 AACCGGTTTTCAACCGGGTTACG
732864 -ACCGG-TTTCAA-CGGGTT-CG
1 AACCGGTTTTCAACCGGGTTACG
732883 AACCG
1 AACCG
732888 TTTGACCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 1 0.05
20 10 0.45
21 6 0.27
22 5 0.23
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
AACCGGTTTTCAACCGGGTTACG
Found at i:732950 original size:17 final size:17
Alignment explanation
Indices: 732928--732982 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
732918 CCGGTTGACC
*
732928 GACCCGACCCAACCGTT
1 GACCCGACCCGACCGTT
732945 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
732962 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
732979 GACC
1 GACC
732983 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.20, C:0.47, G:0.22, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:740083 original size:9 final size:9
Alignment explanation
Indices: 740028--740086 Score: 64
Period size: 9 Copynumber: 6.3 Consensus size: 9
740018 GCTGCTGGAA
*
740028 ACCGGTTTA
1 ACCGGTTTG
740037 ACCGGTTTG
1 ACCGGTTTG
*
740046 ACCGGTTTC
1 ACCGGTTTG
* *
740055 AGCTGGTTCG
1 A-CCGGTTTG
740065 AACCGGTTTG
1 -ACCGGTTTG
740075 ACCGGTTTG
1 ACCGGTTTG
740084 ACC
1 ACC
740087 CGACCCGACC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
9 29 0.71
10 11 0.27
11 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:740093 original size:5 final size:5
Alignment explanation
Indices: 740083--740135 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
740073 TGACCGGTTT
* *
740083 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
740132 GACC
1 GACC
740136 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:740103 original size:17 final size:17
Alignment explanation
Indices: 740081--740142 Score: 79
Period size: 17 Copynumber: 3.4 Consensus size: 17
740071 TTTGACCGGT
740081 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
740098 TTGACCCGACCCGACCCGACCG
1 TT-----GACCCGACCCGACCG
740120 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
740137 TTGACC
1 TTGACC
740143 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 23 0.57
22 17 0.43
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.13
Consensus pattern (17 bp):
TTGACCCGACCCGACCG
Found at i:740109 original size:22 final size:22
Alignment explanation
Indices: 740083--740149 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
740073 TGACCGGTTT
740083 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
740105 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
740127 GACCCGACCGTTGACCGTTGACC
1 GACCCGACC--CGACCGTTGACC
740150 GTTGACCGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.18, C:0.46, G:0.24, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:740142 original size:7 final size:7
Alignment explanation
Indices: 740132--740162 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
740122 GACCCGACCC
740132 GACCGTT
1 GACCGTT
740139 GACCGTT
1 GACCGTT
740146 GACCGTT
1 GACCGTT
740153 GACCGTT
1 GACCGTT
740160 GAC
1 GAC
740163 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:742167 original size:14 final size:14
Alignment explanation
Indices: 742150--742180 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
742140 AGCGCACATA
*
742150 AACGAACATAATTG
1 AACGAACATAAATG
742164 AACGAACATAAATG
1 AACGAACATAAATG
742178 AAC
1 AAC
742181 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (14 bp):
AACGAACATAAATG
Done.