Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007861.1 Hibiscus syriacus cultivar Beakdansim tig00110226_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: 673920
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:488332 original size:22 final size:22
Alignment explanation
Indices: 488306--488348 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
488296 TAATAAATTA
*
488306 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAAGCAATCCATAT
*
488328 TTTAAAATAAAGCAATTCATA
1 TTTAAAATAAAGCAATCCATA
488349 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAAGCAATCCATAT
Found at i:488348 original size:133 final size:133
Alignment explanation
Indices: 488195--488567 Score: 449
Period size: 133 Copynumber: 2.8 Consensus size: 133
488185 TAATAAATTA
*
488195 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-A
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATA-AACTAAAATAA
*
488259 ATAAATCAAT-C-CAT-A-T-TTTAAAAT-AATCAATCCATACTAA-TAAATTATTTAAAATAAA
65 ATAAATCAATACTAATAATTATTTAAAATAAATCAATCCATAC-AACTAAA--A--T--AATAAA
488317 TCAATCCATAT
123 TCAATCCATAT
* ***
488328 TTTAAAATAAAGCAATTCATACTAATAAATTATTT-AAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAAACTAAAATAAA
* * * *
488392 TCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCG
66 TAAATCAATACTAAT-AATTATTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCC
488457 ATAT
130 ATAT
* ***
488461 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAAACTAAAATAAA
* *
488526 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
66 TAAATCAATACTAAT-AATTATTTAAAATAAATCAATCCATA
488568 TTTAAAAATA
Statistics
Matches: 217, Mismatches: 13, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
131 5 0.02
132 26 0.12
133 84 0.39
134 72 0.33
135 1 0.00
136 1 0.00
137 2 0.01
138 10 0.05
139 16 0.07
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (133 bp):
TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATAAACTAAAATAAA
TAAATCAATACTAATAATTATTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCA
TAT
Found at i:488410 original size:22 final size:21
Alignment explanation
Indices: 488362--488410 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
488352 ATAAATTATT
**
488362 TAAATAAATCAATCCATATTT
1 TAAATAAATCAATCCATATAA
*
488383 TAAAATAAATCAATCTATACTAA
1 T-AAATAAATCAATCCATA-TAA
488406 TAAAT
1 TAAAT
488411 TATTTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 20 0.87
23 2 0.09
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATAAATCAATCCATATAA
Found at i:488461 original size:80 final size:80
Alignment explanation
Indices: 488364--488513 Score: 282
Period size: 80 Copynumber: 1.9 Consensus size: 80
488354 AAATTATTTA
*
488364 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
488429 CCATACAACTACAAT
66 CCATACAACTACAAT
*
488444 AATAAATCAATCGATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
488509 CCATA
66 CCATA
488514 TTTTAAAATA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:488490 original size:22 final size:23
Alignment explanation
Indices: 488415--488489 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
488405 ATAAATTATT
488415 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
* **
488437 CTACAATAATAAATCAATCGATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
488463 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
488486 TAAA
1 TAAA
488490 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:488500 original size:32 final size:32
Alignment explanation
Indices: 488461--488612 Score: 155
Period size: 32 Copynumber: 5.4 Consensus size: 32
488451 CAATCGATAT
488461 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
488493 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
488515 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
488547 TTTAAAATAAATCAATCC--A-T-AT---TTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
488572 ---AAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
488601 TTTAAAATAAAT
1 TTTAAAATAAAT
488613 TATTTTAAAA
Statistics
Matches: 99, Mismatches: 1, Indels: 40
0.71 0.01 0.29
Matches are distributed among these distances:
22 30 0.30
23 2 0.02
24 2 0.02
25 4 0.04
26 5 0.05
28 5 0.05
29 4 0.04
30 2 0.02
31 2 0.02
32 43 0.43
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:488509 original size:54 final size:54
Alignment explanation
Indices: 488444--488612 Score: 311
Period size: 54 Copynumber: 3.1 Consensus size: 54
488434 CAACTACAAT
*
488444 AATAAATCAATCGATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
488498 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
488552 AATAAATCAATCCATATTTAAAAATAAATCAATACATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
488606 AATAAAT
1 AATAAAT
488613 TATTTTAAAA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 112 1.00
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:488519 original size:22 final size:22
Alignment explanation
Indices: 488493--488535 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
488483 TAATAAATTA
488493 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
488515 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
488536 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:488544 original size:22 final size:22
Alignment explanation
Indices: 488495--488543 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
488485 ATAAATTATT
**
488495 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
488517 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
488540 TAAA
1 TAAA
488544 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:488571 original size:21 final size:22
Alignment explanation
Indices: 488545--488589 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
488535 ACTAATAAAT
*
488545 TATTT-AAAATAAATCAATCCA
1 TATTTAAAAATAAATCAATACA
488566 TATTTAAAAATAAATCAATACA
1 TATTTAAAAATAAATCAATACA
488588 TA
1 TA
488590 CTAATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (22 bp):
TATTTAAAAATAAATCAATACA
Found at i:488598 original size:22 final size:22
Alignment explanation
Indices: 488550--488598 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
488540 TAAATTATTT
* *
488550 AAAATAAATCAATCCATATTTA
1 AAAATAAATCAATACATATCTA
488572 AAAATAAATCAATACATA-CTA
1 AAAATAAATCAATACATATCTA
488593 ATAAAT
1 A-AAAT
488599 TATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATAAATCAATACATATCTA
Found at i:488621 original size:15 final size:15
Alignment explanation
Indices: 488592--488724 Score: 151
Period size: 15 Copynumber: 8.5 Consensus size: 15
488582 AATACATACT
488592 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
488606 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
488621 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
488643 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
488658 AATAATTTATTTTAT
1 AATAAATTATTTTAA
*
488673 AATAAATTATTTTAT
1 AATAAATTATTTTAA
488688 AATAAATTATTTTAA
1 AATAAATTATTTTAA
488703 AATAAATTATTTTAA
1 AATAAATTATTTTAA
488718 AATAAAT
1 AATAAAT
488725 AACCTTATTA
Statistics
Matches: 105, Mismatches: 6, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
14 9 0.09
15 79 0.75
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:488686 original size:45 final size:45
Alignment explanation
Indices: 488591--488724 Score: 171
Period size: 45 Copynumber: 2.8 Consensus size: 45
488581 CAATACATAC
488591 TAATAAATTA-TTTAAAATAAATTATTTTAAAATAAATCAATCCATATTTTA
1 TAATAAATTATTTTAAAATAAATTATTTTAAAAT--A--AAT---TATTTTA
* * *
488642 TAATAATTTATTTTAAAATAATTTATTTTATAATAAATTATTTTA
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATTATTTTA
488687 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT
1 TAATAAATTATTTTAAAATAAATTATTTTAAAATAAAT
488725 AACCTTATTA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
45 42 0.55
48 3 0.04
50 1 0.01
51 9 0.12
52 21 0.28
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (45 bp):
TAATAAATTATTTTAAAATAAATTATTTTAAAATAAATTATTTTA
Found at i:492090 original size:26 final size:26
Alignment explanation
Indices: 492059--492124 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
492049 TGCATGGTTT
492059 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
492085 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
492111 GTGCATCGATGCAT
1 GTGCATCGATGCAT
492125 GGTATATGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (26 bp):
GTGCATCGATGCATCAAATGCACTGA
Found at i:494840 original size:23 final size:22
Alignment explanation
Indices: 494812--494891 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
494802 GCATGGCCTT
*
494812 GTGCATAGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
494834 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
494856 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
494878 ATGCATCGATGCAC
1 GTGCATCGATGCAC
494892 TGTTAGATGT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 15 0.33
22 16 0.35
23 15 0.33
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:494868 original size:21 final size:22
Alignment explanation
Indices: 494813--494891 Score: 88
Period size: 21 Copynumber: 3.6 Consensus size: 22
494803 CATGGCCTTG
* *
494813 TGCATAGATGCACATTCAAGGCG
1 TGCATCGATGCACATTCAAGG-A
* * *
494836 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
494857 TGTATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
494879 TGCATCGATGCAC
1 TGCATCGATGCAC
494892 TGTTAGATGT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 17 0.37
22 12 0.26
23 17 0.37
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:500678 original size:18 final size:19
Alignment explanation
Indices: 500632--500678 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
500622 GGACCCTTAG
*
500632 TGCATCGATGCACTAAGAG
1 TGCATCGATGCACTAAGAA
500651 TGCATCGATGCA-TAA-AA
1 TGCATCGATGCACTAAGAA
500668 TGCATTCGATG
1 TGCA-TCGATG
500679 TTTCAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 9 0.35
19 12 0.46
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCACTAAGAA
Found at i:500742 original size:45 final size:45
Alignment explanation
Indices: 500693--500778 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
500683 AAAATAGCCA
* *
500693 GAGTGCATCGATGCATGGTTTGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCACT
500738 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATG
1 GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATG
500779 TATTTGATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (45 bp):
GAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCACT
Found at i:500779 original size:19 final size:19
Alignment explanation
Indices: 500740--500779 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
500730 AATGCACTGA
***
500740 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAAT
500759 GTGCATCGATGCATAAAAT
1 GTGCATCGATGCATAAAAT
500778 GT
1 GT
500780 ATTTGATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATAAAAT
Found at i:504458 original size:22 final size:22
Alignment explanation
Indices: 504430--504473 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
504420 CACTCTCTCA
504430 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
504452 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
504474 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:504790 original size:20 final size:20
Alignment explanation
Indices: 504741--504799 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
504731 TTTATTCTCT
* **
504741 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
504761 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
504781 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
504800 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:506132 original size:18 final size:18
Alignment explanation
Indices: 506111--506158 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
506101 TCCACTTCGG
506111 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
506129 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
506147 GAGCCATCACCT
1 GAGCCATCACCT
506159 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:506627 original size:16 final size:17
Alignment explanation
Indices: 506594--506636 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
506584 ACTGCTAAAC
506594 TGTTTTT-GTTAGTATT
1 TGTTTTTGGTTAGTATT
*
506610 TGTTTTTGGTTTGT-TT
1 TGTTTTTGGTTAGTATT
*
506626 TGTCTTTGGTT
1 TGTTTTTGGTT
506637 GAAGTAATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.05, C:0.02, G:0.23, T:0.70
Consensus pattern (17 bp):
TGTTTTTGGTTAGTATT
Found at i:506743 original size:19 final size:19
Alignment explanation
Indices: 506693--506755 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
506683 TTTACTTTCA
*
506693 CAACACGAAATGACTATCG
1 CAACGCGAAATGACTATCG
*
506712 CAACGCGGAAATGGCTATCG
1 CAACGC-GAAATGACTATCG
* **
506732 CAATGCGAAATGAAAATCG
1 CAACGCGAAATGACTATCG
506751 CAACG
1 CAACG
506756 ACAAAATCGC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 19 0.53
20 17 0.47
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (19 bp):
CAACGCGAAATGACTATCG
Found at i:506763 original size:14 final size:14
Alignment explanation
Indices: 506744--506802 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
506734 ATGCGAAATG
506744 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
506758 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
506777 AAAATCGCAACGAC
1 AAAATCGCAACGAC
506791 AAAATCGCAACG
1 AAAATCGCAACG
506803 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:506770 original size:33 final size:33
Alignment explanation
Indices: 506728--506818 Score: 173
Period size: 33 Copynumber: 2.8 Consensus size: 33
506718 GGAAATGGCT
506728 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
506761 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
506794 ATCGCAACGCGAAATGAAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCA
506819 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:506782 original size:19 final size:19
Alignment explanation
Indices: 506728--506824 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
506718 GGAAATGGCT
506728 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
506747 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
506761 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
506780 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
506794 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
506813 ATCGCATTGCGA
1 ATCGCAATGCGA
506825 TTTTGTCGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 30 0.48
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:506838 original size:14 final size:14
Alignment explanation
Indices: 506819--506875 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
506809 GAAAATCGCA
506819 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
506833 TTGCGATTTTCATTTCGCG
1 TTGCGA-TTT--TGT--CG
506852 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
506866 TTGCGATTTT
1 TTGCGATTTT
506876 CATTTCCGCG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 8 0.22
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:506861 original size:33 final size:33
Alignment explanation
Indices: 506814--506892 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
506804 GAAATGAAAA
*
506814 TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
506847 TCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
506880 TCCGCGTTGCGAT
1 T-CGCGTTGCGAT
506893 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 33 0.75
34 11 0.25
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (33 bp):
TCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
Found at i:506887 original size:20 final size:20
Alignment explanation
Indices: 506831--506932 Score: 101
Period size: 20 Copynumber: 5.5 Consensus size: 20
506821 GCGATTTTGT
506831 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATTTTCATTTCCG
*
506850 CGTTGCGA-TTT--TGT---
1 CGTTGCGATTTTCATTTCCG
506864 CGTTGCGATTTTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
***
506884 CGTTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTTCCG
**
506904 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
506924 CGTTGCGAT
1 CGTTGCGAT
506933 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
14 8 0.11
15 3 0.04
16 2 0.03
17 2 0.03
18 3 0.04
19 8 0.11
20 45 0.63
ACGTcount: A:0.12, C:0.24, G:0.25, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:506933 original size:20 final size:20
Alignment explanation
Indices: 506864--506940 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
506854 GCGATTTTGT
**
506864 CGTTGCGATTTTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
506884 CGTTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCCG
506904 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
506924 CGTTGCGATAGTCATTT
1 CGTTGCGATAGTCATTT
506941 TTCGCGTTAC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.14, C:0.25, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:508808 original size:14 final size:14
Alignment explanation
Indices: 508774--508812 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
508764 TTGATTGTTT
508774 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
508788 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
508802 TGTTGATTTGT
1 AATTGATTTGT
508813 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:508973 original size:19 final size:19
Alignment explanation
Indices: 508949--509016 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
508939 ATCGCAACGA
508949 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
508968 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
508987 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
509001 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
509017 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:509068 original size:20 final size:20
Alignment explanation
Indices: 509045--509130 Score: 120
Period size: 20 Copynumber: 4.3 Consensus size: 20
509035 ATTTTCTAGC
509045 TGCGATAGCCATTTTCGCGT
1 TGCGATAGCCATTTTCGCGT
*** *
509065 TGCGATTTTTCA-TTTCGCAT
1 TGCGA-TAGCCATTTTCGCGT
509085 TGCGATAGCCATTTTCGCGT
1 TGCGATAGCCATTTTCGCGT
509105 TGCGATAGCCATTTTCGCGT
1 TGCGATAGCCATTTTCGCGT
509125 TGCGAT
1 TGCGAT
509131 TTCCCCGTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.05
20 50 0.89
21 3 0.05
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
TGCGATAGCCATTTTCGCGT
Found at i:509068 original size:34 final size:36
Alignment explanation
Indices: 509023--509110 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 36
509013 GCGATTTTCA
*
509023 TTTCGCATTGCGATTTTC-TAGC-TGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTAGCATGCGATAGCCAT
*
509057 TTTCGCGTTGCGATTTTTCATTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC--TTAGCA-TGCGATAGCCAT
509097 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
509111 AGCCATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
34 12 0.26
35 5 0.11
38 3 0.07
39 1 0.02
40 25 0.54
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.41
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTAGCATGCGATAGCCAT
Found at i:509369 original size:20 final size:20
Alignment explanation
Indices: 509344--509393 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
509334 TTGAAGATGA
509344 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
509364 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
509384 TTGCGATTTT
1 TTGCGATTTT
509394 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:510283 original size:24 final size:24
Alignment explanation
Indices: 510256--510309 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
510246 GTATTCGAAA
*
510256 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
510280 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
510304 TTTGAT
1 TTTGAT
510310 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:511490 original size:42 final size:42
Alignment explanation
Indices: 511423--511502 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
511413 CGATGACAGT
* * *
511423 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
511465 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
511503 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:511901 original size:91 final size:90
Alignment explanation
Indices: 511724--511908 Score: 293
Period size: 91 Copynumber: 2.0 Consensus size: 90
511714 ATTTCAAACT
511724 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAAT--A-AGTTTAGC
511789 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
511817 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT-AGTTTAGC
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAA-AGAATAAGTTTAGC
*
511880 AGTATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
511908 T
1 T
511909 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
91 36 0.41
93 19 0.22
95 32 0.36
96 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:513055 original size:62 final size:62
Alignment explanation
Indices: 512958--513083 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
512948 GTCTGGCCTC
512958 TCTGCCTAAAAAGCCGGCATACAAAAGTAGTAGAAGGCATACTCGGACAACATCGACGTCAT
1 TCTGCCTAAAAAGCCGGCATACAAAAGTAGTAGAAGGCATACTCGGACAACATCGACGTCAT
513020 TCTGCCTAAAAAGCCGGCATACAAAAGTAGTAGAAGGCATACTCGGACAACATCGACGTCAT
1 TCTGCCTAAAAAGCCGGCATACAAAAGTAGTAGAAGGCATACTCGGACAACATCGACGTCAT
513082 TC
1 TC
513084 ATCGAGTAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.18
Consensus pattern (62 bp):
TCTGCCTAAAAAGCCGGCATACAAAAGTAGTAGAAGGCATACTCGGACAACATCGACGTCAT
Found at i:513715 original size:19 final size:19
Alignment explanation
Indices: 513651--513762 Score: 101
Period size: 20 Copynumber: 6.1 Consensus size: 19
513641 TCTTTTGGTT
* *
513651 GAAATGAAAATCGCAACGA
1 GAAATGAATATCGCAACGC
*
513670 GATAATGAAAATCGCAACGC
1 GA-AATGAATATCGCAACGC
*
513690 GGAAATGACTATCGCAACGC
1 -GAAATGAATATCGCAACGC
*
513710 GAAATGACTATCGCAA--C
1 GAAATGAATATCGCAACGC
513727 G--A-G-ATATCGCAACGC
1 GAAATGAATATCGCAACGC
* *
513742 GAAATGAAAATCGCAATGC
1 GAAATGAATATCGCAACGC
513761 GA
1 GA
513763 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
13 8 0.10
14 1 0.01
15 3 0.04
17 3 0.04
18 1 0.01
19 30 0.38
20 31 0.39
21 2 0.03
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAATATCGCAACGC
Found at i:513780 original size:19 final size:19
Alignment explanation
Indices: 513758--513799 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
513748 AAAATCGCAA
**
513758 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
513777 TGCGGTTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
513796 TGCG
1 TGCG
513800 GTAGTCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.19, G:0.31, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:513807 original size:19 final size:19
Alignment explanation
Indices: 513769--513810 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
513759 GCGATTTTGG
**
513769 TTTCGCGTTGCGGTTTTCA
1 TTTCGCGTTGCGGTAGTCA
513788 TTTCGCGTTGCGGTAGTCA
1 TTTCGCGTTGCGGTAGTCA
513807 TTTC
1 TTTC
513811 CACGATGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.21, G:0.26, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGGTAGTCA
Found at i:514389 original size:20 final size:20
Alignment explanation
Indices: 514362--514455 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
514352 CGATAGTAAG
514362 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
514382 ATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
514402 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
514423 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
514443 ATTCGCATTGCGA
1 ATTCGCATTGCGA
514456 ATTATGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 45 0.73
21 17 0.27
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:514412 original size:41 final size:40
Alignment explanation
Indices: 514362--514455 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
514352 CGATAGTAAG
* * *
514362 ATTCGCATTGCGATTTACGTATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
514402 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
514443 ATTCGCATTGCGA
1 ATTCGCATTGCGA
514456 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:514468 original size:41 final size:42
Alignment explanation
Indices: 514386--514518 Score: 130
Period size: 41 Copynumber: 3.2 Consensus size: 42
514376 TTACGTATTT
* * * *
514386 GCATTGCGATTTTCCTAATTCGCATTGCGATTTACT--TAATC
1 GCATTGCGATTTACGTAATTCGCATTGCGAATTA-TGAAAATC
*
514427 GCGTTGCGATTTACGT-ATTCGCATTGCGAATTATGAAAATC
1 GCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAATC
** * * * *
514468 GCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAAAATC
1 GCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAATC
514509 GCATTGCGAT
1 GCATTGCGAT
514519 AGTCATAATC
Statistics
Matches: 74, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
39 1 0.01
40 21 0.28
41 52 0.70
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (42 bp):
GCATTGCGATTTACGTAATTCGCATTGCGAATTATGAAAATC
Found at i:514476 original size:21 final size:21
Alignment explanation
Indices: 514452--514511 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
514442 TATTCGCATT
*
514452 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
514473 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
514493 GCGAATTAGGAAAATCGCA
1 GCGAATTACGAAAATCGCA
514512 TTGCGATAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:514516 original size:21 final size:21
Alignment explanation
Indices: 514445--514517 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
514435 ATTTACGTAT
* *
514445 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
514466 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
514486 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
514507 TCGCATTGCGA
1 TCGCAATGCGA
514518 TAGTCATAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:518071 original size:13 final size:13
Alignment explanation
Indices: 518053--518145 Score: 98
Period size: 13 Copynumber: 7.2 Consensus size: 13
518043 TCACTATTAG
*
518053 AAAGAAGACAACA
1 AAAGAAGACAAGA
*
518066 AAAGAAGATAAGA
1 AAAGAAGACAAGA
*
518079 AAA-AAAACAAGA
1 AAAGAAGACAAGA
* *
518091 TAAGAAGACAACA
1 AAAGAAGACAAGA
*
518104 AAAGAAGATAAGA
1 AAAGAAGACAAGA
*
518117 AAAAAAGACAAGA
1 AAAGAAGACAAGA
* *
518130 TAAGAAGACAACA
1 AAAGAAGACAAGA
518143 AAA
1 AAA
518146 TATTACCCTA
Statistics
Matches: 63, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
12 9 0.14
13 54 0.86
ACGTcount: A:0.71, C:0.09, G:0.16, T:0.04
Consensus pattern (13 bp):
AAAGAAGACAAGA
Found at i:518088 original size:25 final size:25
Alignment explanation
Indices: 518051--518098 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
518041 AATCACTATT
* *
518051 AGAAAGAAGACAACAAAAGAAGATA
1 AGAAAAAAAACAACAAAAGAAGATA
* *
518076 AGAAAAAAAACAAGATAAGAAGA
1 AGAAAAAAAACAACAAAAGAAGA
518099 CAACAAAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.71, C:0.06, G:0.19, T:0.04
Consensus pattern (25 bp):
AGAAAAAAAACAACAAAAGAAGATA
Found at i:518105 original size:38 final size:39
Alignment explanation
Indices: 518054--518145 Score: 177
Period size: 38 Copynumber: 2.4 Consensus size: 39
518044 CACTATTAGA
518054 AAGAAGACAACAAAAGAAGATAAGAAAAAAA-ACAAGAT
1 AAGAAGACAACAAAAGAAGATAAGAAAAAAAGACAAGAT
518092 AAGAAGACAACAAAAGAAGATAAGAAAAAAAGACAAGAT
1 AAGAAGACAACAAAAGAAGATAAGAAAAAAAGACAAGAT
518131 AAGAAGACAACAAAA
1 AAGAAGACAACAAAA
518146 TATTACCCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 31 0.58
39 22 0.42
ACGTcount: A:0.71, C:0.09, G:0.16, T:0.04
Consensus pattern (39 bp):
AAGAAGACAACAAAAGAAGATAAGAAAAAAAGACAAGAT
Found at i:524926 original size:15 final size:15
Alignment explanation
Indices: 524869--524949 Score: 78
Period size: 15 Copynumber: 5.3 Consensus size: 15
524859 TTGAATTATA
*
524869 AAATATAAAATTATT
1 AAATATAAAAATATT
*
524884 CAAATATTCAAAATATT
1 -AAATA-TAAAAATATT
*
524901 AAATATAAAAATACT
1 AAATATAAAAATATT
524916 AAATATAAAAA-A-T
1 AAATATAAAAATATT
524929 AAATTATTAAAAAT-TT
1 AAA-TA-TAAAAATATT
524945 AAATA
1 AAATA
524950 CACATATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
13 4 0.07
14 3 0.05
15 27 0.48
16 14 0.25
17 8 0.14
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATAAAAATATT
Found at i:525396 original size:2 final size:2
Alignment explanation
Indices: 525389--525434 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
525379 TATTTACATG
*
525389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
525430 TA TA T
1 TA TA T
525435 TTTAAGTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:525499 original size:16 final size:16
Alignment explanation
Indices: 525474--525510 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
525464 TTTCTTAGTA
525474 ATTTATTTTTTAATAAT
1 ATTTATTTTTTAA-AAT
525491 ATTTATTTTTTAAAAT
1 ATTTATTTTTTAAAAT
525507 ATTT
1 ATTT
525511 GAATAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATTTTTTAAAAT
Found at i:535883 original size:21 final size:21
Alignment explanation
Indices: 535845--535885 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
535835 ATTATATTTT
*
535845 TTATTTTTAATAATAAAAATA
1 TTATTTTTAACAATAAAAATA
*
535866 TTATTTTTAACCAAAAAAAA
1 TTATTTTTAA-CAATAAAAA
535886 AAAGAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
TTATTTTTAACAATAAAAATA
Found at i:536792 original size:30 final size:30
Alignment explanation
Indices: 536756--536826 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
536746 TTTCGCTTCC
536756 AGTAAAAATTATTCATTTTTATATTAAAAA
1 AGTAAAAATTATTCATTTTTATATTAAAAA
*
536786 AGTAAAAATTATTCATTTTTTTATTAAAAA
1 AGTAAAAATTATTCATTTTTATATTAAAAA
536816 AGTAAAAATTA
1 AGTAAAAATTA
536827 CTTCTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (30 bp):
AGTAAAAATTATTCATTTTTATATTAAAAA
Found at i:537903 original size:22 final size:22
Alignment explanation
Indices: 537878--537924 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
537868 TATATTATTT
537878 AAATTATTTACGTTTATGTGTA
1 AAATTATTTACGTTTATGTGTA
*
537900 AAATTATTTATGTTTATGTGTA
1 AAATTATTTACGTTTATGTGTA
537922 AAA
1 AAA
537925 ATTTTATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (22 bp):
AAATTATTTACGTTTATGTGTA
Found at i:543598 original size:17 final size:18
Alignment explanation
Indices: 543566--543599 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
543556 TAGTTAAATA
543566 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
543584 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
543600 ACCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:544665 original size:20 final size:20
Alignment explanation
Indices: 544640--544915 Score: 150
Period size: 20 Copynumber: 13.7 Consensus size: 20
544630 GATTTTCCAG
*
544640 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
544660 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
544680 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
544700 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
544721 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
544741 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * * *
544762 AATCACAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
544782 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
544802 AATCACAATGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
544822 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * *
544842 AATCGCAATGCGTAT-CCATA
1 AATCGCAACGCGAATACGA-A
544862 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
544883 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
544903 AATCGCAACGCGA
1 AATCGCAACGCGA
544916 TTGATAATTC
Statistics
Matches: 199, Mismatches: 42, Indels: 30
0.73 0.15 0.11
Matches are distributed among these distances:
19 4 0.02
20 140 0.70
21 54 0.27
22 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:544816 original size:40 final size:41
Alignment explanation
Indices: 544701--544912 Score: 311
Period size: 41 Copynumber: 5.2 Consensus size: 41
544691 GATTCTGACT
* *
544701 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
544742 ATCGCAACGACAATACGTAAAATCACAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * * *
544783 ATCACAACGAGAATACGT-AAATCACAATGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
544823 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
544863 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
544904 ATCGCAACG
1 ATCGCAACG
544913 CGATTGATAA
Statistics
Matches: 155, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 73 0.47
41 82 0.53
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:545261 original size:20 final size:20
Alignment explanation
Indices: 545233--545281 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
545223 CAACGCGGAA
545233 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
545253 ATCGTAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
545273 ATCGCAACG
1 ATCGCAACG
545282 AAAGAATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:545314 original size:33 final size:34
Alignment explanation
Indices: 545273--545348 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
545263 GGAAATGACT
*
545273 ATCGCAACGAAAGAATCGCATTGCG-AAATGAAA
1 ATCGCAACGAAAGAATCGCAATGCGAAAATGAAA
* **
545306 ATCTCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAAAGAATCGCAATGCGAAAATGAAA
545340 ATCGCAACG
1 ATCGCAACG
545349 CGAAATTAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (34 bp):
ATCGCAACGAAAGAATCGCAATGCGAAAATGAAA
Found at i:545341 original size:34 final size:33
Alignment explanation
Indices: 545264--545348 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
545254 TCGTAACGCG
** ** *
545264 GAAATGACTATCGCAACGAAAGAATCGCATTGC
1 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
*
545297 GAAATGAAAATCTCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
545330 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
545349 CGAAATTAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 28 0.64
34 16 0.36
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGTGAATCGCAATGC
Found at i:545383 original size:20 final size:19
Alignment explanation
Indices: 545358--545512 Score: 97
Period size: 20 Copynumber: 8.8 Consensus size: 19
545348 GCGAAATTAG
545358 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
545377 TTTTCGCATTGCGA--TTCA
1 -TTTCGCGTTGCGATTTTCA
*
545395 ---CTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
545411 TTTCGCATTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
545427 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
545444 TTTTCGCGTTTCGATTTTCA
1 -TTTCGCGTTGCGATTTTCA
*
545464 TTTTCGCATTGCGA--TTCA
1 -TTTCGCGTTGCGATTTTCA
* *
545482 ---CTCGTTGCGATTTTTA
1 TTTCGCGTTGCGATTTTCA
*
545498 TTTCGCATTGCGATT
1 TTTCGCGTTGCGATT
545513 CTCTCGTTGC
Statistics
Matches: 103, Mismatches: 16, Indels: 33
0.68 0.11 0.22
Matches are distributed among these distances:
14 25 0.24
16 10 0.10
17 3 0.03
18 8 0.08
19 18 0.17
20 39 0.38
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:545406 original size:34 final size:34
Alignment explanation
Indices: 545363--545459 Score: 160
Period size: 33 Copynumber: 2.9 Consensus size: 34
545353 ATTAGTTTCG
545363 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
545397 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* *
545430 CGTTGCGATTTTCATTTTCGCGTTTCGATT
1 CGTTGCGATTTTCATTTTCGCATTGCGATT
545460 TTCATTTTCG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.54
34 27 0.46
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:545466 original size:87 final size:87
Alignment explanation
Indices: 545358--545545 Score: 331
Period size: 87 Copynumber: 2.2 Consensus size: 87
545348 GCGAAATTAG
545358 TTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGCG
1 TTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGCG
**
545423 ATTCTCTCGTTGCGATTTTCAT
66 ATTCTCTCGTTGCGATAGTCAT
* *
545445 TTTCGCGTTTCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTTATTTCGCATTGCG
1 TTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGCG
545510 ATTCTCTCGTTGCGATAGTCAT
66 ATTCTCTCGTTGCGATAGTCAT
*
545532 TTCCGCGTTGCGAT
1 TTTCGCGTTGCGAT
545546 AGTCTGTTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 95 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (87 bp):
TTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATAGTCAT
Found at i:545486 original size:54 final size:53
Alignment explanation
Indices: 545397--545512 Score: 180
Period size: 54 Copynumber: 2.2 Consensus size: 53
545387 GCGATTCACT
*
545397 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTTCG
* *
545450 CGTTTCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTTA-TTTCG
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTTCG
*
545503 CATTGCGATT
1 CGTTGCGATT
545513 CTCTCGTTGC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
53 26 0.46
54 31 0.54
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (53 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTTCG
Found at i:545504 original size:33 final size:34
Alignment explanation
Indices: 545450--545545 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 34
545440 TTCATTTTCG
*
545450 CGTTTCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* *
545484 CGTTGCGATTTTTA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
545517 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
545546 AGTCTGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 29 0.55
34 24 0.45
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:545668 original size:14 final size:14
Alignment explanation
Indices: 545649--545683 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
545639 TCAATTAAAA
545649 AAATCAACATTTAC
1 AAATCAACATTTAC
* *
545663 AAATCATCTTTTAC
1 AAATCAACATTTAC
545677 AAATCAA
1 AAATCAA
545684 TTAAACAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACATTTAC
Found at i:547134 original size:42 final size:42
Alignment explanation
Indices: 547055--547147 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
547045 CCTCTTCAAC
* * *
547055 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
547097 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
547139 GATGACAGG
1 GATGACAGG
547148 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:547650 original size:20 final size:20
Alignment explanation
Indices: 547627--547695 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
547617 GAAACTTAAA
547627 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
547647 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
547667 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
547687 ATCGCAACG
1 ATCGCAACG
547696 AGAGAATCGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:547682 original size:40 final size:37
Alignment explanation
Indices: 547626--547731 Score: 121
Period size: 40 Copynumber: 2.9 Consensus size: 37
547616 TGAAACTTAA
*
547626 AATCGCAACGCGAAAATGACTATCGCAATGCGAAAATG
1 AATCGCAATGCGAAAATGACTATCGCAATGCGAAAA-G
*
547664 ACTATCGCAATGCGAAAATGACTATCGCAA--CG-AGAG
1 A--ATCGCAATGCGAAAATGACTATCGCAATGCGAAAAG
**
547700 AATCGCAATGCG-AAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAAATGACTATCGCAATGCGA
547732 TTATAGTTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
33 13 0.22
34 11 0.19
35 2 0.03
36 2 0.03
37 2 0.03
38 3 0.05
40 26 0.44
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.16
Consensus pattern (37 bp):
AATCGCAATGCGAAAATGACTATCGCAATGCGAAAAG
Found at i:547762 original size:14 final size:14
Alignment explanation
Indices: 547743--547769 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
547733 TATAGTTTCG
547743 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
547757 CGTTGCGATTTTG
1 CGTTGCGATTTTG
547770 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:547774 original size:33 final size:33
Alignment explanation
Indices: 547727--547799 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
547717 AAAATCGCAA
* * *
547727 TGCGATTATAGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTATAGTTTCGCGTTGCAATTCTCTCGT
* *
547760 TGCGATTTTGGTTTCGCGTTGCAATTCTCTCGT
1 TGCGATTATAGTTTCGCGTTGCAATTCTCTCGT
547793 TGCGATT
1 TGCGATT
547800 CATTTCACGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.18, G:0.26, T:0.45
Consensus pattern (33 bp):
TGCGATTATAGTTTCGCGTTGCAATTCTCTCGT
Found at i:547781 original size:19 final size:18
Alignment explanation
Indices: 547727--547781 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
547717 AAAATCGCAA
*
547727 TGCGATTATAGTTTCGCGT
1 TGCGATT-TTGTTTCGCGT
547746 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
547760 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
547779 TGC
1 TGC
547782 AATTCTCTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
14 12 0.40
15 1 0.03
16 1 0.03
17 1 0.03
18 2 0.07
19 13 0.43
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.45
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:547812 original size:17 final size:18
Alignment explanation
Indices: 547790--547837 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 18
547780 GCAATTCTCT
547790 CGTTGCGATTCA-TTTCA
1 CGTTGCGATTCATTTTCA
547807 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGAT--TCA-TTTTCA
547828 CGTTGCGATT
1 CGTTGCGATT
547838 TTAAGTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.33
19 4 0.15
21 14 0.52
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.42
Consensus pattern (18 bp):
CGTTGCGATTCATTTTCA
Found at i:548049 original size:94 final size:94
Alignment explanation
Indices: 547903--548282 Score: 602
Period size: 94 Copynumber: 4.1 Consensus size: 94
547893 ATGGATTGTA
* *
547903 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
547967 TTAGTAGAATTGATAGCAACCGAACAAAT
66 TTAGCAGAATTGACAGCAACCGAACAAAT
*
547996 TTACTTTCAACCAAAAGAAAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
548061 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGACAGCAACCGAACAAAT
*
548090 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
548155 TTAGCAGAATTGACAGTAACCGAATAAAT
66 TTAGCAGAATTGACAGCAACCGAACAAAT
* *
548184 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCATAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * * *
548248 TTTAGTAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGACAGCAACCGAACAAAT
548278 TTACT
1 TTACT
548283 AAGCAATCTA
Statistics
Matches: 267, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
93 22 0.08
94 245 0.92
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGACAGCAACCGAACAAAT
Found at i:550003 original size:20 final size:20
Alignment explanation
Indices: 549980--550035 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
549970 TGAAATGAAA
549980 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
550000 ATCGCAATGCG-GA-AATGACT
1 ATCGCAA--CGAGAGAATGACT
550020 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
550036 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 24 0.75
21 2 0.06
22 2 0.06
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:550050 original size:33 final size:33
Alignment explanation
Indices: 549971--550094 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 33
549961 TCTTTTGGTT
*
549971 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAATGC
1 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAACGC
**
550010 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
550044 GAAATGAAAATTGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
550077 GAAATTAAAATCGCAACG
1 GAAATGAAAATCGCAACG
550095 CGAAATGAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
33 46 0.61
34 9 0.12
36 2 0.03
37 1 0.01
38 3 0.04
40 15 0.20
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:550061 original size:19 final size:19
Alignment explanation
Indices: 549971--550116 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
549961 TCTTTTGGTT
*
549971 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
** *
549990 GAGAATGACTATCGCAATGC
1 GA-AATGAAAATCGCAACGC
**
550010 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
550028 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
550044 GAAATGAAAATTGCAA--C
1 GAAATGAAAATCGCAACGC
*
550061 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
550077 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
550096 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
550115 GA
1 GA
550117 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 18 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 42 0.42
20 27 0.27
21 2 0.02
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:550134 original size:19 final size:19
Alignment explanation
Indices: 550112--550233 Score: 83
Period size: 20 Copynumber: 6.5 Consensus size: 19
550102 AAAATCGCAA
** *
550112 TGCGATTTTGGTTTCTCGT
1 TGCGATTTTCATTTCGCGT
550131 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
550150 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
550164 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGT
** *
550185 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
**
550205 TGCGATTTTCATTTTCATGT
1 TGCGATTTTCA-TTTCGCGT
550225 TGCGATTTT
1 TGCGATTTT
550234 AAGTTTAGAA
Statistics
Matches: 85, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 21 0.25
20 30 0.35
21 18 0.21
ACGTcount: A:0.11, C:0.19, G:0.20, T:0.50
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:550181 original size:21 final size:20
Alignment explanation
Indices: 550162--550233 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
550152 CGATTCTCTC
550162 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
550182 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
550203 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
550223 GTTGCGATTTT
1 GTTGCGATTTT
550234 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:550815 original size:20 final size:19
Alignment explanation
Indices: 550788--551027 Score: 167
Period size: 20 Copynumber: 11.8 Consensus size: 19
550778 CGCTTTAAAA
550788 ATCGCGTTGCGATTTACGG
1 ATCGCGTTGCGATTTACGG
*
550807 ATACGCGTTGCGATTTTACGT
1 AT-CGCGTTGCGA-TTTACGG
* *
550828 ATTGTCGTTGCGATTTTACGT
1 ATCG-CGTTGCGA-TTTACGG
*
550849 ATTGTCGTTGCGATTTACGG
1 ATCG-CGTTGCGATTTACGG
* * *
550869 ATGCGCATTGCAATTTACGT
1 AT-CGCGTTGCGATTTACGG
*
550889 ATTCTCGTTGCGATTTACGG
1 A-TCGCGTTGCGATTTACGG
*
550909 ATGCGCGTTGCGATTTACGT
1 AT-CGCGTTGCGATTTACGG
** *
550929 ATTTTCGTTGCGATTTATGG
1 A-TCGCGTTGCGATTTACGG
*
550949 ATACGCGTTGCGATTTTACGT
1 AT-CGCGTTGCGA-TTTACGG
* *
550970 ATTGTCATTGCGATTTTACGG
1 ATCG-CGTTGCGA-TTTACGG
* * *
550991 ATACTCGTTGCGATAGT-CAGA
1 AT-CGCGTTGCGAT-TTAC-GG
551012 ATCGCGTTGCGATTTA
1 ATCGCGTTGCGATTTA
551028 TATGTTCGCG
Statistics
Matches: 176, Mismatches: 31, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
19 5 0.03
20 97 0.55
21 74 0.42
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.39
Consensus pattern (19 bp):
ATCGCGTTGCGATTTACGG
Found at i:550897 original size:40 final size:40
Alignment explanation
Indices: 550790--551001 Score: 212
Period size: 40 Copynumber: 5.2 Consensus size: 40
550780 CTTTAAAAAT
* * * *
550790 CGCGTTGCGATTTACGGATACG-CGTTGCGATTTTACGTATTG
1 CGCGTTGCAATTTACGTAT-TGTCGTTGCGA-TTTACGGA-TG
* *
550832 -TCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATG
1 CGCGTTGC-AATTTACGTATTGTCGTTGCGATTTACGGATG
* *
550872 CGCATTGCAATTTACGTATTCTCGTTGCGATTTACGGATG
1 CGCGTTGCAATTTACGTATTGTCGTTGCGATTTACGGATG
* * * *
550912 CGCGTTGCGATTTACGTATTTTCGTTGCGATTTATGGATA
1 CGCGTTGCAATTTACGTATTGTCGTTGCGATTTACGGATG
* * *
550952 CGCGTTGCGATTTTACGTATTGTCATTGCGATTTTACGGATA
1 CGCGTTGC-AATTTACGTATTGTCGTTGCGA-TTTACGGATG
*
550994 CTCGTTGC
1 CGCGTTGC
551002 GATAGTCAGA
Statistics
Matches: 144, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
40 75 0.52
41 37 0.26
42 32 0.22
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.40
Consensus pattern (40 bp):
CGCGTTGCAATTTACGTATTGTCGTTGCGATTTACGGATG
Found at i:550945 original size:60 final size:61
Alignment explanation
Indices: 550790--551004 Score: 211
Period size: 60 Copynumber: 3.5 Consensus size: 61
550780 CTTTAAAAAT
* *
550790 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTTACGTATTG
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGA-TTTACGGATTG
* * * *
550853 -TCGTTGCGATTTACGGATGCGCATTGCAATTTACGTATTCTCGTTGCGATTTACGGA-TG
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATTG
* *** * * * * *
550912 CGCGTTGCGATTTACGTATTTTCGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTG
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGA-TTTACGGATTG
* * *
550974 -TCATTGCGATTTTACGGATACTCGTTGCGAT
1 CGCGTTGCGA-TTTACGGATACGCGTTGCGAT
551005 AGTCAGAATC
Statistics
Matches: 125, Mismatches: 23, Indels: 9
0.80 0.15 0.06
Matches are distributed among these distances:
59 2 0.02
60 45 0.36
61 33 0.26
62 45 0.36
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.40
Consensus pattern (61 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATTG
Found at i:551056 original size:41 final size:39
Alignment explanation
Indices: 551011--551126 Score: 115
Period size: 41 Copynumber: 2.9 Consensus size: 39
551001 CGATAGTCAG
*
551011 AATCGCGTTGCGATTTATATGTTCGCGTTGCGATTCTGAAA
1 AATCGCGTTGCGATTTATAT-TTCGCATTGCGATTCTG-AA
** * * * *
551052 AATCGCAATGCGAATTTGTACTATCGTATTGCGATTCTGGA
1 AATCGCGTTGCG-ATTTATA-TTTCGCATTGCGATTCTGAA
* *
551093 GATCGCGTTGCGATTTTTATTTCGCATTGCGATT
1 AATCGCGTTGCGATTTATATTTCGCATTGCGATT
551127 TTATTGGTCA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
39 13 0.22
40 6 0.10
41 20 0.33
42 20 0.33
43 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (39 bp):
AATCGCGTTGCGATTTATATTTCGCATTGCGATTCTGAA
Found at i:551383 original size:75 final size:74
Alignment explanation
Indices: 551239--551383 Score: 173
Period size: 75 Copynumber: 1.9 Consensus size: 74
551229 GACAGATACA
* * * * ** *
551239 AATAAAATTTCAGGGTGACACTTTTAGTAAAATGAACAACTGATATAAAAAAATTTGAATTCCAT
1 AATAAAATTTCAGGATGACACATTTAATAAAATGAACAACTAATATAAAAAAATTCAAATTCCAG
551304 GGTGGGCAC
66 GGTGGGCAC
* ** * *
551313 AATAAAATTTTAGGATGGACACATTTAATAAAATGAACGGCTAATATAAATAAATTCAAATTTCA
1 AATAAAATTTCAGGAT-GACACATTTAATAAAATGAACAACTAATATAAAAAAATTCAAATTCCA
551378 GGGTGG
65 GGGTGG
551384 ACAGATGCCT
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
74 14 0.24
75 44 0.76
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.29
Consensus pattern (74 bp):
AATAAAATTTCAGGATGACACATTTAATAAAATGAACAACTAATATAAAAAAATTCAAATTCCAG
GGTGGGCAC
Found at i:562222 original size:31 final size:28
Alignment explanation
Indices: 562161--562262 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 28
562151 AAAATTTTGG
*
562161 TTAGTGACCAAA-ATGTAAATTTTAAAAGT
1 TTAGTGACCAAAGA--TAAATTTAAAAAGT
*
562190 TTAGTGACCAATGTATAAAGTTTGAAAAAGT
1 TTAGTGACCAAAG-ATAAA-TTT-AAAAAGT
* *
562221 TTAGAGACCAAAAAGATAAATTTTAAAAGT
1 TTAGTGACC--AAAGATAAATTTAAAAAGT
562251 TTAGTGACCAAA
1 TTAGTGACCAAA
562263 ATTATACTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
28 3 0.05
29 15 0.25
30 17 0.28
31 18 0.30
32 5 0.08
33 3 0.05
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (28 bp):
TTAGTGACCAAAGATAAATTTAAAAAGT
Found at i:562251 original size:30 final size:30
Alignment explanation
Indices: 562161--562264 Score: 133
Period size: 30 Copynumber: 3.5 Consensus size: 30
562151 AAAATTTTGG
562161 TTAGTGACCAAAATG-TAAATTTTAAAAGT
1 TTAGTGACCAAAATGATAAATTTTAAAAGT
*
562190 TTAGTGACC--AATGTATAAAGTTTGAAAAAGT
1 TTAGTGACCAAAATG-ATAAA-TTT-TAAAAGT
* *
562221 TTAGAGACCAAAAAGATAAATTTTAAAAGT
1 TTAGTGACCAAAATGATAAATTTTAAAAGT
562251 TTAGTGACCAAAAT
1 TTAGTGACCAAAAT
562265 TATACTTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
27 4 0.06
29 13 0.21
30 21 0.33
31 17 0.27
32 5 0.08
33 3 0.05
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (30 bp):
TTAGTGACCAAAATGATAAATTTTAAAAGT
Found at i:563470 original size:20 final size:20
Alignment explanation
Indices: 563445--563485 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
563435 CTGGAAATTA
*
563445 ATGTTAGAGTGATG-AATTTG
1 ATGTTAGAATG-TGAAATTTG
563465 ATGTTAGAATGTGAAATTTG
1 ATGTTAGAATGTGAAATTTG
563485 A
1 A
563486 CTATTTTGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (20 bp):
ATGTTAGAATGTGAAATTTG
Found at i:565162 original size:19 final size:18
Alignment explanation
Indices: 565138--565199 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
565128 TATGCATTTG
565138 GCTATGAACTTGAAAATAA
1 GCTATGAA-TTGAAAATAA
*
565157 GCTATGAATTTGAAACTAA
1 GCTATGAA-TTGAAAATAA
*
565176 GTTATGAATCTG-AAATAA
1 GCTATGAAT-TGAAAATAA
565194 G-TATGA
1 GCTATGA
565200 GTCTTTAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 5 0.13
18 7 0.18
19 26 0.68
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.31
Consensus pattern (18 bp):
GCTATGAATTGAAAATAA
Found at i:565214 original size:36 final size:37
Alignment explanation
Indices: 565151--565222 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
565141 ATGAACTTGA
565151 AAATAAGCTATGAATTTGAAACTAAGTTATGAATCTG
1 AAATAAGCTATGAATTTGAAACTAAGTTATGAATCTG
* * *
565188 AAATAAG-TATGAGTCTTTAAAC-AAGTTCTGAATCT
1 AAATAAGCTATGAAT-TTGAAACTAAGTTATGAATCT
565223 AAGAATGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 18 0.58
37 13 0.42
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (37 bp):
AAATAAGCTATGAATTTGAAACTAAGTTATGAATCTG
Found at i:565290 original size:25 final size:24
Alignment explanation
Indices: 565255--565319 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
565245 AAGTACGGAT
*
565255 TATGAAAATGAAATGTGAAAG-TGAA
1 TATGAATATGAAA-GT-AAAGATGAA
565280 TATGAATATGAAAGTAAAGATGAA
1 TATGAATATGAAAGTAAAGATGAA
* *
565304 AATGAGATACGAAAGT
1 TATGA-ATATGAAAGT
565320 TTTGTATTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.11
24 10 0.29
25 21 0.60
ACGTcount: A:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (24 bp):
TATGAATATGAAAGTAAAGATGAA
Found at i:565293 original size:18 final size:18
Alignment explanation
Indices: 565270--565308 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
565260 AAATGAAATG
* * *
565270 TGAAAGTGAATATGAATA
1 TGAAAGTAAAGATGAAAA
565288 TGAAAGTAAAGATGAAAA
1 TGAAAGTAAAGATGAAAA
565306 TGA
1 TGA
565309 GATACGAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (18 bp):
TGAAAGTAAAGATGAAAA
Found at i:566069 original size:182 final size:182
Alignment explanation
Indices: 565649--566122 Score: 671
Period size: 182 Copynumber: 2.6 Consensus size: 182
565639 GATCCAAATT
* * * * * **
565649 AAAAATGTATCGATCCACAACGATATAACAGGTAAAACTATGACAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * * *
565714 AAACCTGTAAAGCGGTACCGAATATATTTAAAGTTTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * * *
565779 GTTAATTTAAAAGAGAAGCAGTTTTAGCACCTATAAAGTGTCGATACTTTCA
131 GTGAATTTAAAAGAGAAGCAATTTTAGCACCTATAAAGTGCCGATACTTTAA
* * * *
565831 AAAAATATATCGATCAACAACGATATAACATGTAAAAATATGATAAAACTGGTATCAAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
565896 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
565960 GTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAGTGCCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAATTTTAGCACCTATAAAGTGCCGATACTTTAA
*
566012 AAAAATGTATCGATCAAATAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGAT
*
566077 AAAACCGGTAAAATGATACCGGATATATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
566123 CGTAAGTACG
Statistics
Matches: 258, Mismatches: 33, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
181 79 0.31
182 179 0.69
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCAACAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAATTTTAGCACCTATAAAGTGCCGATACTTTAA
Found at i:566091 original size:17 final size:19
Alignment explanation
Indices: 566052--566094 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
566042 AAGTAAAAAT
566052 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
566072 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
566089 ATGATA
1 ATGATA
566095 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:568465 original size:33 final size:33
Alignment explanation
Indices: 568423--568488 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
568413 AAATAGATGG
*
568423 AGTGGTGAAAGAAGTAGAGGTATTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTATTAAGGGGTGA
* *
568456 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTATTAAGGGGTGA
568489 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTATTAAGGGGTGA
Found at i:569432 original size:182 final size:182
Alignment explanation
Indices: 569119--570835 Score: 3017
Period size: 182 Copynumber: 9.5 Consensus size: 182
569109 AAGCCTACGG
*
569119 AATAACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
*
569184 AAAACCGGTCTCGAAATGATAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
*
569249 TATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCA
131 TATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
* *
569301 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAATAATATGAC
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
569366 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
* * *
569431 TATTATAAGTATCAACACTTTTTGAATTTAAAAGAGAAGAAGTTATAGTGCC
131 TATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
*
569483 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAC
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
* *
569548 AAAATCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
* *
569613 TATTATAAGTATCGAGACTTTTGGAATTTAAAAGAGAAGAAGTTATAGTGCC
131 TATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
*
569665 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAAAATATAACATGTAAAAATATGAC
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
**
569730 AAAATTGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
*
569795 TATTATAAGTATCG--ACTTTTGGAA-TTAATAAGAGACGAAGTTATAGCGCC
131 TATTATAAGTATCGACACTTTTGGAATTTAA-AAGAGAAGAAGTTATAGCGCC
*
569845 AATAACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
*
569910 AAAACCAGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
*
569975 TATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGTGCC
131 TATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
*
570027 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAATAATATGAC
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
570092 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
570157 TATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
131 TATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
570209 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
*
570274 AAAACCGGTCTCGAAATGACAAAACATGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
*
570339 TATTATAAGTATCG--ACTTTTGGAA-TT---A-ATAAGAAGTTATAGCGCC
131 TATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
*
570384 AATAACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
570449 AAAACCGGTCTCGAAATGAC-AAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
* *
570513 TATTATAAGTATCAAAACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
131 TATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
* *
570565 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAGAACAATATAACATGTAAAAATATGAA
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
* *
570630 AAAACCGGTCTCGAAATGACAAAATAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
*
570695 TATTATAAGTATCGACACTTTTGGAA-TTAATAAGAGAATAAGTTATAGCGCC
131 TATTATAAGTATCGACACTTTTGGAATTTAA-AAGAGAAGAAGTTATAGCGCC
* *
570747 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACATGTAAAAATATGAT
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
**
570812 AAAACCGGTCTATAAATGACAAAA
66 AAAACCGGTCTCGAAATGACAAAA
570836 GGTGAACGCA
Statistics
Matches: 1471, Mismatches: 51, Indels: 26
0.95 0.03 0.02
Matches are distributed among these distances:
174 56 0.04
175 101 0.07
176 11 0.01
177 2 0.00
179 6 0.00
180 179 0.12
181 103 0.07
182 1009 0.69
183 4 0.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
TATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
Found at i:570155 original size:544 final size:543
Alignment explanation
Indices: 569119--570835 Score: 3070
Period size: 544 Copynumber: 3.2 Consensus size: 543
569109 AAGCCTACGG
*
569119 AATAACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
*
569184 AAAACCGGTCTCGAAATGATAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
* *
569249 TATTATAAGTATCGACACTTTTGGAATTTAA-AAGAGAAGAAGTTATAGCGCAAATAAAGTGTCG
131 TATTATAAGTATCG--ACTTTTGGAA-TTAATAAGAG-AGAAGTTATAGCGCCAATAACGTGTCG
* *
569313 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAATAATATGACAAAACCGGTCTC
192 ATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTC
569378 GAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTAT
257 GAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTAT
*
569443 CAACACTTTTTGAATTTAAAAGAGAAGAAGTTATAGTGCCAATAAAGTGTCGATACTTTATAAAA
322 CAACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGTGCCAATAAAGTGTCGATACTTTATAAAA
* *
569508 ATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAAC
387 ATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAAC
*
569573 AGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGAGACTTTTGGA
452 AGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGA
*
569638 ATTTAAAAGAGAAGAAGTTATAGTGCC
517 ATTTAAAAGAGAAGAAGTTATAGCGCC
*
569665 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAAAATATAACATGTAAAAATATGAC
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
**
569730 AAAATTGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
569795 TATTATAAGTATCGACTTTTGGAATTAATAAGAGACGAAGTTATAGCGCCAATAACGTGTCGATA
131 TATTATAAGTATCGACTTTTGGAATTAATAAGAGA-GAAGTTATAGCGCCAATAACGTGTCGATA
*
569860 CTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCAGTCTCGAA
195 CTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAA
*
569925 ATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
260 ATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCAA
569990 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGTGCCAATAAAGTGTCGATACTTTATAAAAATG
325 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGTGCCAATAAAGTGTCGATACTTTATAAAAATG
*
570055 TATCGATCCATAACAATATAACATGTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGG
390 TATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGG
*
570120 TAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATT
455 TAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATT
570185 TAAAAGAGAAGAAGTTATAGCGCC
520 TAAAAGAGAAGAAGTTATAGCGCC
570209 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
*
570274 AAAACCGGTCTCGAAATGACAAAACATGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
66 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
570339 TATTATAAGTATCGACTTTTGGAATTAAT---A-AGAAGTTATAGCGCCAATAACGTGTCGATAC
131 TATTATAAGTATCGACTTTTGGAATTAATAAGAGAGAAGTTATAGCGCCAATAACGTGTCGATAC
570400 TTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAA
196 TTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAA
*
570465 TGAC-AAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCAAA
261 TGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCAAC
*
570529 ACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGT
326 ACTTTTGGAATTTAAAAGAGAAGAAGTTATAGTGCCAATAAAGTGTCGATACTTTATAAAAATGT
* * *
570594 ATCGATCCAGAACAATATAACATGTAAAAATATGAAAAAACCGGTCTCGAAATGACAAAATAGGT
391 ATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
570659 AAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA-TT
456 AAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
*
570723 AATAAGAGAATAAGTTATAGCGCC
521 AA-AAGAGAAGAAGTTATAGCGCC
* *
570747 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACATGTAAAAATATGAT
1 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
**
570812 AAAACCGGTCTATAAATGACAAAA
66 AAAACCGGTCTCGAAATGACAAAA
570836 GGTGAACGCA
Statistics
Matches: 1132, Mismatches: 36, Indels: 14
0.96 0.03 0.01
Matches are distributed among these distances:
537 4 0.00
538 349 0.31
539 98 0.09
540 1 0.00
541 1 0.00
543 5 0.00
544 535 0.47
546 139 0.12
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (543 bp):
AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
TATTATAAGTATCGACTTTTGGAATTAATAAGAGAGAAGTTATAGCGCCAATAACGTGTCGATAC
TTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAA
TGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCAAC
ACTTTTGGAATTTAAAAGAGAAGAAGTTATAGTGCCAATAAAGTGTCGATACTTTATAAAAATGT
ATCGATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGT
AAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTT
AAAAGAGAAGAAGTTATAGCGCC
Found at i:571076 original size:87 final size:87
Alignment explanation
Indices: 570971--571133 Score: 292
Period size: 87 Copynumber: 1.9 Consensus size: 87
570961 AAATAGGTCA
570971 ATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
571036 CCAGTTAAATACCTATTTTATT
66 CCAGTTAAATACCTATTTTATT
*
571058 ATATAAGCGCTATC-TATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATT
1 ATATAAGCGCTA-CATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATT
*
571122 TCCGGTTAAATA
65 TCCAGTTAAATA
571134 ATATAACATA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
87 72 0.99
88 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACATATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCAGTTAAATACCTATTTTATT
Found at i:571105 original size:23 final size:23
Alignment explanation
Indices: 571055--571099 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
571045 TACCTATTTT
* *
571055 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
571078 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
571100 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:572329 original size:18 final size:18
Alignment explanation
Indices: 572303--572356 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
572293 TTATTAATCT
*
572303 ACATTTGATAACTGTAAA
1 ACATCTGATAACTGTAAA
*
572321 ACATCTGATAATTG-AAA
1 ACATCTGATAACTGTAAA
*
572338 ATCATCTGATAACTATAAA
1 A-CATCTGATAACTGTAAA
572357 TATCTTACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 4 0.13
18 23 0.77
19 3 0.10
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (18 bp):
ACATCTGATAACTGTAAA
Found at i:573917 original size:22 final size:22
Alignment explanation
Indices: 573891--573936 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
573881 TCCAATCAAC
*
573891 TTTCTAA-CTTAAAATTCCAGCA
1 TTTCTAATATTAAAATT-CAGCA
573913 TTTCTAATATTAAAATTCAGCA
1 TTTCTAATATTAAAATTCAGCA
573935 TT
1 TT
573937 AACACTCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTCTAATATTAAAATTCAGCA
Found at i:575123 original size:30 final size:31
Alignment explanation
Indices: 575089--575170 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 31
575079 TAAAATATAT
*
575089 AACTTTTCAAAATTTCATTTTTTATCCC-TA
1 AACTTTTCAAAATTTCATTTTTTAGCCCTTA
* **
575119 AACTTTTACAAAGTTT-ATACTTTAGCCCTTA
1 AACTTTT-CAAAATTTCATTTTTTAGCCCTTA
*
575150 AAC-TTTCAAAACTTACATTTT
1 AACTTTTCAAAA-TTTCATTTT
575171 AGTCACTAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
29 4 0.10
30 21 0.52
31 15 0.38
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.45
Consensus pattern (31 bp):
AACTTTTCAAAATTTCATTTTTTAGCCCTTA
Found at i:576401 original size:22 final size:22
Alignment explanation
Indices: 576376--576420 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
576366 AATTTATTAG
576376 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
576398 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
576420 T
1 T
576421 TATCACTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:576483 original size:31 final size:31
Alignment explanation
Indices: 576446--576504 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
576436 AGTTGTATGG
* *
576446 ATTATTTAAATTTCAATATTGTAAAACTAAA
1 ATTATTTAAATCTCAATATTGCAAAACTAAA
*
576477 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAATATTGCAAAACT
576505 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAATATTGCAAAACTAAA
Found at i:577422 original size:95 final size:95
Alignment explanation
Indices: 577312--577513 Score: 334
Period size: 95 Copynumber: 2.1 Consensus size: 95
577302 GTTGTTGTGG
* * *
577312 GTATCGATACCAAGAGAAAGGTATCAATACCA-GAGATTCCAGAATGTAAAAATGGTATCGATAC
1 GTATCGATACTAAGAGAAAGGTATCAATACCATGA-ATTACAGAATGTAAAAATGATATCGATAC
*
577376 TGAAAGGGAGTATCGGTACCATAGTATAGAA
65 TGAAAAGGAGTATCGGTACCATAGTATAGAA
*
577407 GTATCGATACTAAGAGAAAGGTATCAATACCATGAATTACAGAATGTAGAAATGATATCGATACT
1 GTATCGATACTAAGAGAAAGGTATCAATACCATGAATTACAGAATGTAAAAATGATATCGATACT
577472 GAAAAGGAGTATCGGTACCATAGTATAGAA
66 GAAAAGGAGTATCGGTACCATAGTATAGAA
*
577502 GTATCCATACTA
1 GTATCGATACTA
577514 TAAGATAGGC
Statistics
Matches: 100, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
95 98 0.98
96 2 0.02
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (95 bp):
GTATCGATACTAAGAGAAAGGTATCAATACCATGAATTACAGAATGTAAAAATGATATCGATACT
GAAAAGGAGTATCGGTACCATAGTATAGAA
Found at i:577950 original size:45 final size:45
Alignment explanation
Indices: 577899--578135 Score: 318
Period size: 45 Copynumber: 5.2 Consensus size: 45
577889 AAATGAATGA
*
577899 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATCGACATGAAAGGATGCC
* * *
577944 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGAC
1 ATAAATGAAATGCATAATGGTGCATTATCGACATGAAAGGATGCC
*
577989 ATAAATGAAATGCATAATGGTGCA-TATTCGACATGAAAGGATGTC
1 ATAAATGAAATGCATAATGGTGCATTA-TCGACATGAAAGGATGCC
* *
578034 ATAAATGAAAATGCATAATGGTGCATTAT-AAGCATGAAAGGATGCT
1 ATAAATG-AAATGCATAATGGTGCATTATCGA-CATGAAAGGATGCC
* * *
578080 ATAAATGAAAATGCATAATGGTGCATTAT-AAGCATGAAAGGATACT
1 ATAAATG-AAATGCATAATGGTGCATTATCGA-CATGAAAGGATGCC
578126 ATAAATGAAA
1 ATAAATGAAA
578136 ATAAAGGATA
Statistics
Matches: 179, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
44 2 0.01
45 93 0.52
46 82 0.46
47 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (45 bp):
ATAAATGAAATGCATAATGGTGCATTATCGACATGAAAGGATGCC
Found at i:586166 original size:29 final size:28
Alignment explanation
Indices: 586120--586181 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
586110 AAGGACAATT
586120 TAAAACTATAAATATATC-ACCTTAAAACA
1 TAAAACTATAAATATATCTA-CTT-AAACA
*
586149 TAAAACTATAAATCTATCTACTTAAACA
1 TAAAACTATAAATATATCTACTTAAACA
586177 TAAAA
1 TAAAA
586182 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 10 0.32
29 20 0.65
30 1 0.03
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (28 bp):
TAAAACTATAAATATATCTACTTAAACA
Found at i:586857 original size:43 final size:45
Alignment explanation
Indices: 586764--586858 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 45
586754 AGTGAATGAA
* * *
586764 GAAAACTTAGGGTTTGTAGTGAAGAGAGAAGAGGGAAATCGTGAG
1 GAAAAATTAGGGTTTATAGTGAAGAGAGAAGAGAGAAATCGTGAG
* *
586809 AAAAAATTAGGGTTTATAGTGAAGAGA-AA-AGAGAAATCTTGAG
1 GAAAAATTAGGGTTTATAGTGAAGAGAGAAGAGAGAAATCGTGAG
586852 GAAAAAT
1 GAAAAAT
586859 ATGAGTTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
43 18 0.41
44 2 0.05
45 24 0.55
ACGTcount: A:0.45, C:0.03, G:0.31, T:0.21
Consensus pattern (45 bp):
GAAAAATTAGGGTTTATAGTGAAGAGAGAAGAGAGAAATCGTGAG
Found at i:591024 original size:26 final size:26
Alignment explanation
Indices: 590993--591084 Score: 184
Period size: 26 Copynumber: 3.5 Consensus size: 26
590983 GCATGGTATT
590993 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
591019 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
591045 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
591071 GTGCATCGATGCAT
1 GTGCATCGATGCAT
591085 GGTATGTGCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 66 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (26 bp):
GTGCATCGATGCATCAAATGCACTGA
Found at i:591605 original size:2 final size:2
Alignment explanation
Indices: 591598--591622 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
591588 AATTGAGTAA
591598 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
591623 GCTTAAGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:592283 original size:21 final size:21
Alignment explanation
Indices: 592259--592323 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
592249 GTGTCGGAGG
*
592259 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
592280 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* * *
592301 ACGG-GCATCTCGTGAAGAGCT
1 A-GGAGCAGCACGAGAAGAGCT
592322 AG
1 AG
592324 CTCCCGGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
20 1 0.03
21 36 0.92
22 2 0.05
ACGTcount: A:0.31, C:0.18, G:0.38, T:0.12
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:597802 original size:22 final size:21
Alignment explanation
Indices: 597760--597799 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
597750 GAGTTTATTT
*
597760 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
597781 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
597800 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:599753 original size:26 final size:26
Alignment explanation
Indices: 599722--599788 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
599712 TTGAAAAAGC
*
599722 CTGAGTACATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATCAAATGCA
599748 CTGAGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATCAAATGCA
599774 CTGAGTGCATCGATG
1 CTGAGTGCATCGATG
599789 TATGGTATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (26 bp):
CTGAGTGCATCGATGCATCAAATGCA
Found at i:602311 original size:12 final size:12
Alignment explanation
Indices: 602294--602326 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
602284 TTTTGTTGTA
602294 ATATGTATATAT
1 ATATGTATATAT
602306 ATATGTATATAT
1 ATATGTATATAT
*
602318 ATATATATA
1 ATATGTATA
602327 ATTGTTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:603465 original size:16 final size:16
Alignment explanation
Indices: 603444--603493 Score: 82
Period size: 16 Copynumber: 3.0 Consensus size: 16
603434 TTGAAATCAA
603444 GTTTTGAAATTACTCC
1 GTTTTGAAATTACTCC
603460 GTTTTGAAATTACTCCCC
1 GTTTTGAAATTACT--CC
603478 GTTTTGAAATTACTCC
1 GTTTTGAAATTACTCC
603494 CCCTTACTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.50
18 16 0.50
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (16 bp):
GTTTTGAAATTACTCC
Found at i:603481 original size:18 final size:18
Alignment explanation
Indices: 603444--603495 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
603434 TTGAAATCAA
603444 GTTTTGAAATTACT--CC
1 GTTTTGAAATTACTCCCC
603460 GTTTTGAAATTACTCCCC
1 GTTTTGAAATTACTCCCC
603478 GTTTTGAAATTACTCCCC
1 GTTTTGAAATTACTCCCC
603496 CTTACTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 14 0.41
18 20 0.59
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (18 bp):
GTTTTGAAATTACTCCCC
Found at i:605863 original size:20 final size:20
Alignment explanation
Indices: 605811--605871 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
605801 TTCCCCTGTA
* *
605811 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AT
605834 GGGGGAATCGATTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
605854 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
605872 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:613596 original size:21 final size:21
Alignment explanation
Indices: 613572--613611 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
613562 TTTTCAAAGG
613572 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
**
613593 CATGCATTGATGCATCAAT
1 CATGCACCGATGCATCAAT
613612 GAATAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Done.