Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008275.1 Hibiscus syriacus cultivar Beakdansim tig00110933_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: 1991061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:768507 original size:5 final size:5
Alignment explanation
Indices: 768497--768522 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
768487 GAAGTTTTGA
768497 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
768523 ACTGTGAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:771423 original size:31 final size:31
Alignment explanation
Indices: 771380--771438 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
771370 AAATTACACA
*
771380 TTTGCTCCTAATTACTTACATTTTCTATTAT
1 TTTGCTCCTAATTACTTACATATTCTATTAT
* * *
771411 TTTGGTCCTAATTATTTATATATTCTAT
1 TTTGCTCCTAATTACTTACATATTCTAT
771439 CAAATTGATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (31 bp):
TTTGCTCCTAATTACTTACATATTCTATTAT
Found at i:774507 original size:13 final size:14
Alignment explanation
Indices: 774489--774519 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
774479 TATTATATGT
774489 TTTAGA-TTTAAAA
1 TTTAGAGTTTAAAA
774502 TTTAGAGTTTAAAA
1 TTTAGAGTTTAAAA
774516 TTTA
1 TTTA
774520 AAATCATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTAGAGTTTAAAA
Found at i:775540 original size:24 final size:24
Alignment explanation
Indices: 775509--775591 Score: 130
Period size: 24 Copynumber: 3.5 Consensus size: 24
775499 TTGTTTGTGT
775509 TGTTCGTTTATGTTCGTTCGTTTG
1 TGTTCGTTTATGTTCGTTCGTTTG
*
775533 TTTTCGTTTATGTTCGTTCGTTTG
1 TGTTCGTTTATGTTCGTTCGTTTG
* * *
775557 TGTTCGTTCATGTTCGTTTGTTTA
1 TGTTCGTTTATGTTCGTTCGTTTG
775581 TGTTCGTTTAT
1 TGTTCGTTTAT
775592 TTATTAAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.06, C:0.12, G:0.22, T:0.60
Consensus pattern (24 bp):
TGTTCGTTTATGTTCGTTCGTTTG
Found at i:775589 original size:14 final size:14
Alignment explanation
Indices: 775501--775588 Score: 86
Period size: 14 Copynumber: 6.9 Consensus size: 14
775491 GTTTTTTTTT
*
775501 GTTTGTGTT-GTTC
1 GTTTATGTTCGTTC
775514 GTTTATGTTCGTTC
1 GTTTATGTTCGTTC
775528 G-TT-TGTT--TTC
1 GTTTATGTTCGTTC
775538 GTTTATGTTCGTTC
1 GTTTATGTTCGTTC
775552 G-TT-TG-T-GTTC
1 GTTTATGTTCGTTC
* *
775562 GTTCATGTTCGTTT
1 GTTTATGTTCGTTC
775576 GTTTATGTTCGTT
1 GTTTATGTTCGTT
775589 TATTTATTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
10 9 0.15
11 4 0.06
12 12 0.19
13 13 0.21
14 24 0.39
ACGTcount: A:0.05, C:0.11, G:0.24, T:0.60
Consensus pattern (14 bp):
GTTTATGTTCGTTC
Found at i:775594 original size:14 final size:14
Alignment explanation
Indices: 775566--775595 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
775556 GTGTTCGTTC
*
775566 ATGTTCGTTTGTTT
1 ATGTTCGTTTATTT
775580 ATGTTCGTTTATTT
1 ATGTTCGTTTATTT
775594 AT
1 AT
775596 TAAATGAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.17, T:0.63
Consensus pattern (14 bp):
ATGTTCGTTTATTT
Found at i:779257 original size:30 final size:29
Alignment explanation
Indices: 779223--779294 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
779213 TCATAGAATT
*
779223 ACAATCAGCTCACTCAATTAATTGATTATA
1 ACAATCAG-TCACTCAATTAATTAATTATA
* ** *
779253 ACAATTAAGTCACTGGATTCATTAATTATA
1 ACAA-TCAGTCACTCAATTAATTAATTATA
779283 ACAATCAAGTCA
1 ACAATC-AGTCA
779295 TGTGTCATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 1 0.03
30 30 0.88
31 3 0.09
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (29 bp):
ACAATCAGTCACTCAATTAATTAATTATA
Found at i:779639 original size:31 final size:31
Alignment explanation
Indices: 779604--779675 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
779594 GACTTTTTAA
* * *
779604 AATTGAATGA-TCCGTTTATAATCTTATTAGT
1 AATTGAATGACT-CATTTATAATCTTACTAAT
* *
779635 AATTGAGTGACTCATTTGTAATCTTACTAAT
1 AATTGAATGACTCATTTATAATCTTACTAAT
*
779666 AATTGGATGA
1 AATTGAATGA
779676 ATTATAATGC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (31 bp):
AATTGAATGACTCATTTATAATCTTACTAAT
Found at i:782459 original size:35 final size:35
Alignment explanation
Indices: 782413--782495 Score: 130
Period size: 35 Copynumber: 2.4 Consensus size: 35
782403 TGGCGAATCT
*
782413 AGAAAAATTTTATAAATCGAACTAATATAAACTTA
1 AGAAAATTTTTATAAATCGAACTAATATAAACTTA
* * *
782448 AGAAATTTTTTATAAATCTAGCTAATATAAACTTA
1 AGAAAATTTTTATAAATCGAACTAATATAAACTTA
782483 AGAAAATTTTTAT
1 AGAAAATTTTTAT
782496 TTAAAATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.37
Consensus pattern (35 bp):
AGAAAATTTTTATAAATCGAACTAATATAAACTTA
Found at i:783837 original size:17 final size:18
Alignment explanation
Indices: 783803--783843 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
783793 TAACAATGAG
*
783803 TTATTATAAAATATATTT
1 TTATTATAAAACATATTT
783821 TTATTAT-AAACATATTT
1 TTATTATAAAACATATTT
783838 TTATTA
1 TTATTA
783844 GTAATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATTATAAAACATATTT
Found at i:784106 original size:24 final size:25
Alignment explanation
Indices: 784075--784133 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
784065 AAAATAAAAC
* *
784075 TAAAAATATAATGTTCAAAA-TATT
1 TAAAAATATAATATTAAAAACTATT
*
784099 TAAAAATAAAATATTAAAAACTATT
1 TAAAAATATAATATTAAAAACTATT
* *
784124 TGAAACTATA
1 TAAAAATATA
784134 TTGAATCATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (25 bp):
TAAAAATATAATATTAAAAACTATT
Found at i:784442 original size:11 final size:10
Alignment explanation
Indices: 784356--784475 Score: 64
Period size: 11 Copynumber: 11.4 Consensus size: 10
784346 CTGGATTTTT
784356 ATATTATTAAA
1 ATATTATT-AA
*
784367 ATAGTCATTAA
1 ATA-TTATTAA
*
784378 AT-TTATAAA
1 ATATTATTAA
784387 ATGATTATTAA
1 AT-ATTATTAA
**
784398 ATGAGCATTAA
1 AT-ATTATTAA
* *
784409 ATTTTATCAA
1 ATATTATTAA
**
784419 ATTATTAGAAA
1 A-TATTATTAA
784430 ATAGTTATTAA
1 ATA-TTATTAA
784441 AT-TTATTAA
1 ATATTATTAA
*
784450 GATATTATAAA
1 -ATATTATTAA
*
784461 ATAATAATTAA
1 AT-ATTATTAA
784472 ATAT
1 ATAT
784476 GTCATTCTTT
Statistics
Matches: 83, Mismatches: 18, Indels: 17
0.70 0.15 0.14
Matches are distributed among these distances:
9 14 0.17
10 13 0.16
11 52 0.63
12 4 0.05
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (10 bp):
ATATTATTAA
Found at i:784456 original size:31 final size:30
Alignment explanation
Indices: 784356--784473 Score: 112
Period size: 31 Copynumber: 3.8 Consensus size: 30
784346 CTGGATTTTT
*
784356 ATATTATTAAAATAGTCATTAAATTTATAAA
1 ATATTA-TAAAATAGTCATTAAATTTATTAA
* *
784387 ATGATTATTAAATGAG-CATTAAATTTTATCAA
1 AT-ATTATAAAAT-AGTCATTAAA-TTTATTAA
* *
784419 ATTATTAGAAAATAGTTATTAAATTTATTAA
1 A-TATTATAAAATAGTCATTAAATTTATTAA
* *
784450 GATATTATAAAATAATAATTAAAT
1 -ATATTATAAAATAGTCATTAAAT
784474 ATGTCATTCT
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
31 42 0.58
32 29 0.40
33 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (30 bp):
ATATTATAAAATAGTCATTAAATTTATTAA
Found at i:795494 original size:234 final size:226
Alignment explanation
Indices: 795174--795643 Score: 627
Period size: 234 Copynumber: 2.0 Consensus size: 226
795164 TAAACATTTT
795174 TTAGGATTATTAACTTATAAAAGATATATATATTTTTGATAAAAAACAATTATTTATACAATCAT
1 TTAGGATTATTAACTTATAAAAGATATATATATTTTTGATAAAAAACAATTATTTATACAATCAT
* * * *
795239 AAACTATACATTTTTTAATTAATTTGGAGTAATTACAATGCAATATCTGCTTAAAAATAATTATT
66 AAACTAAACATTTTTTAATTAATTTGGAGTAAGTACAATGCAATATCTGCTCAAAAATAACTATT
* * *
795304 AATCATTTGATATTGGACGCTCAAACCCATGATATTCATGGTGCTCAAA-CTCGAGACCCTAAAG
131 AATCATTTGACATTAGACGCTCAAACCCATGATATTCATAGTGCTCAAACCT-GAGACCCTAAAG
* *
795368 AATAACAACAAATCATTTACTATTGAGGTTGC
195 AATAACAACAAATCATTTACCATTGAGGTTGA
*
795400 TTAGGATTATTTACTTATTAAAAGATAATATATTATTTTTTGATAAAATAATACAATTATTTATA
1 TTAGGATTATTAACTTA-TAAAAGAT-ATATA-TA-TTTTTGAT-AAA-AA-ACAATTATTTATA
* * * * *
795465 CTATCATAAATTAGAACATTTTTTAATTAATTTGGGGTAAGTACAATGCAGTATTTGCTCAAAAA
59 CAATCATAAACTA-AACATTTTTTAATTAATTTGGAGTAAGTACAATGCAATATCTGCTCAAAAA
* * * * * *
795530 TAACTCTTAATTATTTGACATTAGACGCTCACACTCATGATATTTATAGTGCTCGAACCTGAGAC
123 TAACTATTAATCATTTGACATTAGACGCTCAAACCCATGATATTCATAGTGCTCAAACCTGAGAC
* * *
795595 CTTAAAGAATAACAACAATTTATTTACCATTGAGGTTGA
188 CCTAAAGAATAACAACAAATCATTTACCATTGAGGTTGA
795634 TTAAGGATTA
1 TT-AGGATTA
795644 ATTTTATTAA
Statistics
Matches: 210, Mismatches: 24, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
226 16 0.08
227 8 0.04
228 5 0.02
229 2 0.01
230 8 0.04
231 3 0.01
232 2 0.01
233 24 0.11
234 133 0.63
235 9 0.04
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.37
Consensus pattern (226 bp):
TTAGGATTATTAACTTATAAAAGATATATATATTTTTGATAAAAAACAATTATTTATACAATCAT
AAACTAAACATTTTTTAATTAATTTGGAGTAAGTACAATGCAATATCTGCTCAAAAATAACTATT
AATCATTTGACATTAGACGCTCAAACCCATGATATTCATAGTGCTCAAACCTGAGACCCTAAAGA
ATAACAACAAATCATTTACCATTGAGGTTGA
Found at i:797022 original size:84 final size:81
Alignment explanation
Indices: 796836--797070 Score: 283
Period size: 81 Copynumber: 3.0 Consensus size: 81
796826 AAAAACGTTA
* *
796836 GATCATATGAA-TATACCTAAGATATTGAAGAACATGCAGAATAAAGCAATTATTAAAGGAAGAA
1 GATCATATGAATTATACCTAGGATATCGAAGAACATGCAGAATAAAGCAATTATTAAAGGAAGAA
*
796900 GAAGAAGAAGATGATG
66 GAAGAAGAAGAAGATG
*
796916 GATCATATGAATTATACCTAGGATATCGAATAACATGCAGAATAAAGCAATTATTAAAGGTGGAA
1 GATCATATGAATTATACCTAGGATATCGAAGAACATGCAGAATAAAGCAATTATTAAA---GGAA
*
796981 GCAGAAGAAGAAGAAGAAT-
63 GAAGAAGAAGAAGAAG-ATG
* * *
797000 GATCATATGAATTAAACCTAGGATAT--------ATGCAGACTAAAGCAATTATTAAAAGAAGAA
1 GATCATATGAATTATACCTAGGATATCGAAGAACATGCAGAATAAAGCAATTATTAAAGGAAGAA
*
797057 GACGAAGAAGAAGA
66 GAAGAAGAAGAAGA
797071 AGCTTACAGT
Statistics
Matches: 140, Mismatches: 10, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
72 1 0.01
73 17 0.12
76 23 0.16
80 11 0.08
81 43 0.31
84 43 0.31
85 2 0.01
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (81 bp):
GATCATATGAATTATACCTAGGATATCGAAGAACATGCAGAATAAAGCAATTATTAAAGGAAGAA
GAAGAAGAAGAAGATG
Found at i:797650 original size:25 final size:26
Alignment explanation
Indices: 797598--797654 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
797588 CCGACATGTG
797598 ATTTGACTCGAGTTTAGAAAAATTTT
1 ATTTGACTCGAGTTTAGAAAAATTTT
797624 ATTTGACTCGAGTTTAGAAAAA-TTT
1 ATTTGACTCGAGTTTAGAAAAATTTT
797649 ATTTGA
1 ATTTGA
797655 TTTGAAATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 9 0.29
26 22 0.71
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (26 bp):
ATTTGACTCGAGTTTAGAAAAATTTT
Found at i:798270 original size:99 final size:99
Alignment explanation
Indices: 798140--798337 Score: 380
Period size: 99 Copynumber: 2.0 Consensus size: 99
798130 TAAAGATCAT
798140 GTTTAACTTAATTTTAATCTCAAATCAAAATAAAAATGTGTAATGTTTTTTAAATGAAATTAACT
1 GTTTAACTTAATTTTAATCTCAAATCAAAATAAAAATGTGTAATGTTTTTTAAATGAAATTAACT
798205 TGTTTAAGGGTTGAGCTAAT-AATTCGGATATAA
66 TGTTTAAGGGTTGAGCTAATAAATTCGGATATAA
798238 GTTTAACTTAATTTTAAATCTCAAATCAAAATAAAAATGTGTAATGTTTTTTAAATGAAATTAAC
1 GTTTAACTTAATTTT-AATCTCAAATCAAAATAAAAATGTGTAATGTTTTTTAAATGAAATTAAC
798303 TTGTTTAAGGGTTGAGCTAATAAATTCGGATATAA
65 TTGTTTAAGGGTTGAGCTAATAAATTCGGATATAA
798338 AAAAACTATA
Statistics
Matches: 98, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
98 15 0.15
99 70 0.71
100 13 0.13
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (99 bp):
GTTTAACTTAATTTTAATCTCAAATCAAAATAAAAATGTGTAATGTTTTTTAAATGAAATTAACT
TGTTTAAGGGTTGAGCTAATAAATTCGGATATAA
Found at i:798575 original size:4 final size:4
Alignment explanation
Indices: 798568--800565 Score: 2845
Period size: 4 Copynumber: 511.5 Consensus size: 4
798558 ACACACACAA
* * * *
798568 ATGT ATGT ATGT ATGT ACGT ACGT ACGT ATGT ATGT ATGT A-GT ACGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * *
798615 ACGT ATGT ACGT ATGT ACGT ATGT ACGT ATGT ACGT ATGT ACGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
798663 ACGT ATGT ACGT ATGT ACGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
798711 ATGTT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATG-T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
798760 AT-T TTGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
798806 ATGT ATGT ATGGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT
1 ATGT ATGT AT-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
798852 ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
798898 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
798946 ATGT ATGT ATGT ATGT ATGT ACGT ATGT ACGT ATGT ACGT ATGT ACGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
798994 ATGT ACGT ATGT ACG- ATGT ATGT A-GT ATGT ACGT ATGT ACGT A-GT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * *
799039 ACGT ATGT ACGT ATGT ACGT A-GT ATGT ACGT ATGT ACGT ATGT ACGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * *
799086 ATGT ACGT ATGT ACGT ATGT -CGT ATGT ACGT ATGT ACGT ATGT ACGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * *
799133 ATGT ACGT ATGT ACGT ATGT ACG- ATGT ACGT ACGT ACGT ACGT ACGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
799180 ACGT ACGT ACGT ACGT ATGT -TGT A-GT ATGT ATGT ATGT ATG- GTGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
799225 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATTT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799271 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799317 A-GT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799363 ATGT ATGT ATGT ATGT ATGT A-GT ATGT A-GT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799409 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799457 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799503 ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799549 ATGT ATGT ATGT ATGT ATGT -TGT ATGT ATGT ATGT AT-T ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799595 ATG- ATGT ATGT ATGT ATGT ATGT ATGT -TGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
799641 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT-T GTGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799688 ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799734 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799782 ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799828 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799876 ATGT ATGT ATGT ATGT ATGT A-GT A-GT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799922 ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
799969 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
800017 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
800065 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
800112 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
800159 AGGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
800207 ACGT ATGT ATGT ATGT A-GT ATGT ACGT ATGT ACGT ATGT ACGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
800254 A-GT ATGT ACGT A-GT ACGT ATGT ACGT ATGT ACGT ATGT ACGT A-GT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
800299 A-GT ATGT AAGT ATGT ACGT ATGT ACGT ATGT ACGT ATGT ACGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * *
800346 ACGT ATGT ACGT ATGT ACGT ATGT ACGT ATGT ACGT ATGT ACGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * *
800394 ACGT ATGT ACGT ATGT ACGT ATGT ACGT ACGT ACGT ATGT ACGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
800442 ATGT ACGT ACGT ATGT ACGT ATGT ACGT ACGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
800490 ATGT ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT A--T ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
800536 ACGT ACGT ATGT ACGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
800566 TTGAGATTTA
Statistics
Matches: 1810, Mismatches: 134, Indels: 100
0.89 0.07 0.05
Matches are distributed among these distances:
2 18 0.01
3 90 0.05
4 1694 0.94
5 8 0.00
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (4 bp):
ATGT
Found at i:801204 original size:22 final size:22
Alignment explanation
Indices: 801174--801231 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
801164 CCTACATTAA
801174 TAACC-CTAAACCATAGCCATG
1 TAACCTCTAAACCATAGCCATG
*
801195 TAACCTCTAAACCATAGCCTTG
1 TAACCTCTAAACCATAGCCATG
801217 TAACCTCTAAACCAT
1 TAACCTCTAAACCAT
801232 GAAACCTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 5 0.14
22 30 0.86
ACGTcount: A:0.36, C:0.33, G:0.07, T:0.24
Consensus pattern (22 bp):
TAACCTCTAAACCATAGCCATG
Found at i:809556 original size:2 final size:2
Alignment explanation
Indices: 809549--809579 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
809539 TTAAACGAGT
809549 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
809580 GGATATAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:813161 original size:20 final size:20
Alignment explanation
Indices: 813087--813164 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 20
813077 GATTCTGACT
* *
813087 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTACCTA
* *
813107 ATTCGCGTTGCGATTTTCCTA
1 A-TCGCATTGCGATTTACCTA
*
813128 ATTCGCACTT-CGATTTACGTA
1 A-TCGCA-TTGCGATTTACCTA
813149 ATCGCATTGCGATTTA
1 ATCGCATTGCGATTTA
813165 GTAAATCGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.04
20 13 0.27
21 32 0.65
22 2 0.04
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATTTACCTA
Found at i:813171 original size:20 final size:20
Alignment explanation
Indices: 813087--813174 Score: 72
Period size: 20 Copynumber: 4.3 Consensus size: 20
813077 GATTCTGACT
* *
813087 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTACTAA
* *
813107 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTTACTAA
*
813129 TTCGCACTT-CGATTTACGT-A
1 ATCGCA-TTGCGATTTAC-TAA
*
813149 ATCGCATTGCGATTTAGTAA
1 ATCGCATTGCGATTTACTAA
813169 ATCGCA
1 ATCGCA
813175 ACGAGATTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
19 3 0.05
20 25 0.45
21 18 0.33
22 9 0.16
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATTTACTAA
Found at i:814064 original size:24 final size:24
Alignment explanation
Indices: 814037--814090 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
814027 GTATTCAAAA
*
814037 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
814061 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
814085 TTTGAT
1 TTTGAT
814091 GATTTTTCAG
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:814482 original size:20 final size:20
Alignment explanation
Indices: 814455--814532 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
814445 CGATAGTCAA
*
814455 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACCT
* *
814475 ATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACCT
*
814495 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACCT
*
814516 AATCGCATTGCGATTTA
1 ATTCGCATTGCGATTTA
814533 GTTGGTCATT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 33 0.66
21 17 0.34
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACCT
Found at i:814504 original size:41 final size:41
Alignment explanation
Indices: 814435--814531 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
814425 GCGCTATGTA
** *
814435 AATCGCATTGCGATAGT-CAAATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
* * *
814475 ATTTGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTT
1 AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
814516 AATCGCATTGCGATTT
1 AATCGCATTGCGATTT
814532 AGTTGGTCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (41 bp):
AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
Found at i:816416 original size:22 final size:21
Alignment explanation
Indices: 816390--816433 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
816380 AATAATAAAA
816390 TTTT-AGATTATTTTATTTTATT
1 TTTTAAGATTA-TTTA-TTTATT
*
816412 TTTTAATATTATTTATTTATT
1 TTTTAAGATTATTTATTTATT
816433 T
1 T
816434 GATGTAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 8 0.40
23 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTAAGATTATTTATTTATT
Found at i:820864 original size:20 final size:21
Alignment explanation
Indices: 820815--820865 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
820805 ATTTATTGAA
820815 ATAAAAT-TTAAAAAAAAAATT
1 ATAAAATATT-AAAAAAAAATT
820836 ATAAAATATTAAAAAAAAATT
1 ATAAAATATTAAAAAAAAATT
*
820857 A-AATATATT
1 ATAAAATATT
820866 TTCAGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 7 0.25
21 19 0.68
22 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAAATATTAAAAAAAAATT
Found at i:820985 original size:17 final size:17
Alignment explanation
Indices: 820963--820996 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
820953 TCCAATGGAT
*
820963 TTAATTATTATTATTTA
1 TTAATTATTAGTATTTA
820980 TTAATTATTAGTATTTA
1 TTAATTATTAGTATTTA
820997 ATTCATCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTAATTATTAGTATTTA
Found at i:826261 original size:43 final size:41
Alignment explanation
Indices: 826212--826305 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 41
826202 GTGGCGAGAA
* *
826212 GTTCGTTTATTTAATAAATAAACGAACATGAACAAGATTTTGT
1 GTTCGTTTATTTAATAAATAAACAAACATGAACAA-ATGTT-T
*
826255 GTTCGTTTA---ATTAAATAAACAAACATGAACAAATGTTT
1 GTTCGTTTATTTAATAAATAAACAAACATGAACAAATGTTT
*
826293 GTTCGTTCATTTA
1 GTTCGTTTATTTA
826306 CGTTCGTGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
38 9 0.20
39 4 0.09
40 21 0.48
41 1 0.02
43 9 0.20
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (41 bp):
GTTCGTTTATTTAATAAATAAACAAACATGAACAAATGTTT
Found at i:826627 original size:13 final size:14
Alignment explanation
Indices: 826606--826646 Score: 59
Period size: 13 Copynumber: 3.0 Consensus size: 14
826596 TTTGTTTTTG
826606 TGTTGTTCGTTTAT
1 TGTTGTTCGTTTAT
826620 TG-TGTTCGTTTA-
1 TGTTGTTCGTTTAT
826632 TGTTCGTTCGTTTAT
1 TGTT-GTTCGTTTAT
826647 AAAATGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 11 0.46
14 11 0.46
ACGTcount: A:0.07, C:0.10, G:0.22, T:0.61
Consensus pattern (14 bp):
TGTTGTTCGTTTAT
Found at i:826670 original size:17 final size:18
Alignment explanation
Indices: 826643--826678 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
826633 GTTCGTTCGT
826643 TTATAAAATGAACGAACA
1 TTATAAAATGAACGAACA
826661 TTAT-AAATGAACGAACA
1 TTATAAAATGAACGAACA
826678 T
1 T
826679 GAACAAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (18 bp):
TTATAAAATGAACGAACA
Found at i:832311 original size:31 final size:30
Alignment explanation
Indices: 832224--832311 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
832214 TAGAAGTTTG
* * *
832224 ATAAATTTAATGAACATTTTATAATAATTTG
1 ATAAATTTAATGAATATTTTATAA-CATTTA
**
832255 ATAAAATTTAATGGCTATTTTATAACATTTCA
1 AT-AAATTTAATGAATATTTTATAACATTT-A
*
832287 ATAAATTTAATGATTATTTTATAAC
1 ATAAATTTAATGAATATTTTATAAC
832312 TTTTGAAAGT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 27 0.56
32 21 0.44
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (30 bp):
ATAAATTTAATGAATATTTTATAACATTTA
Found at i:832759 original size:21 final size:21
Alignment explanation
Indices: 832733--832794 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
832723 CGCAACTCAG
832733 TTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
* *
832754 TTTCC-ATTTCACGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
** *
832774 AGTCCAAATTCGCATTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
832795 ATCGCAACGC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (21 bp):
TTTCCAAATTCGCGTTGCGAT
Found at i:832795 original size:21 final size:21
Alignment explanation
Indices: 832735--832795 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
832725 CAACTCAGTT
**
832735 TCCAAATTCGCGTTGCGATTT
1 TCCAAATTCGCGTTGCGATAG
* *
832756 TCC-ATTTCACGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
*
832776 TCCAAATTCGCATTGCGATA
1 TCCAAATTCGCGTTGCGATA
832796 TCGCAACGCG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (21 bp):
TCCAAATTCGCGTTGCGATAG
Found at i:832854 original size:21 final size:21
Alignment explanation
Indices: 832828--832867 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
832818 CAACTCCGTT
* *
832828 TCCAAATTCGCGTTGCGATAG
1 TCCAAAATCGCATTGCGATAG
832849 TCCAAAATCGCATTGCGAT
1 TCCAAAATCGCATTGCGAT
832868 TTATTAACCA
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:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (21 bp):
TCCAAAATCGCATTGCGATAG
Found at i:834698 original size:26 final size:24
Alignment explanation
Indices: 834669--834744 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 24
834659 TTCATATTTC
*
834669 TAAAAAATAATTACAATTTTATGAAT
1 TAAAAAATAATTATAATTTTA--AAT
* * *
834695 TAAAAGATTAATTATAAATTTAATT
1 TAAAA-AATAATTATAATTTTAAAT
834720 TAAAAAATACATTTATAATTTTAAA
1 TAAAAAATA-A-TTATAATTTTAAA
834745 AATGAATCAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
24 3 0.08
25 8 0.20
26 16 0.40
27 13 0.32
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (24 bp):
TAAAAAATAATTATAATTTTAAAT
Found at i:835189 original size:9 final size:10
Alignment explanation
Indices: 835175--835207 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
835165 TTTTATGAGG
835175 TTATTA-TTA
1 TTATTATTTA
835184 TTATTATTTA
1 TTATTATTTA
835194 TTA-TATTTA
1 TTATTATTTA
835203 TTATT
1 TTATT
835208 TATCAGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATTATTTA
Found at i:835196 original size:16 final size:16
Alignment explanation
Indices: 835175--835210 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
835165 TTTTATGAGG
835175 TTATTAT-TATTATTAT
1 TTATTATAT-TTATTAT
835191 TTATTATATTTATTAT
1 TTATTATATTTATTAT
835207 TTAT
1 TTAT
835211 CAGGTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTATATTTATTAT
Found at i:836166 original size:20 final size:19
Alignment explanation
Indices: 836123--836170 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
836113 GTTAAATACC
836123 TAATTTT-AATAAAAAAAT
1 TAATTTTAAATAAAAAAAT
*
836141 T-A-TTTAAATACCAAAAAT
1 TAATTTTAAATA-AAAAAAT
836159 TAATTTTAAATA
1 TAATTTTAAATA
836171 TAGTTTTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.12
17 5 0.20
18 8 0.32
19 1 0.04
20 8 0.32
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATTTTAAATAAAAAAAT
Found at i:836609 original size:27 final size:28
Alignment explanation
Indices: 836560--836619 Score: 113
Period size: 27 Copynumber: 2.2 Consensus size: 28
836550 TTTCCCACAG
836560 TTTCTCCAAATTTACCAATGAAATGAAA
1 TTTCTCCAAATTTACCAATGAAATGAAA
836588 TTTCTCCAAA-TTACCAATGAAATGAAA
1 TTTCTCCAAATTTACCAATGAAATGAAA
836615 TTTCT
1 TTTCT
836620 AGGGTTAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 22 0.69
28 10 0.31
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (28 bp):
TTTCTCCAAATTTACCAATGAAATGAAA
Found at i:840355 original size:13 final size:13
Alignment explanation
Indices: 840337--840362 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
840327 TTTTTAAAAA
840337 AAAATTATTGATT
1 AAAATTATTGATT
840350 AAAATTATTGATT
1 AAAATTATTGATT
840363 TTGAATCGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
AAAATTATTGATT
Found at i:843148 original size:3 final size:3
Alignment explanation
Indices: 843140--843183 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
843130 CCCCCTCCCC
**
843140 CTT CTT CTT CTT CTT CTT CTT CGTT -TT CTT CTT CAA CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CT
843184 CCCGTTCACT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.05, C:0.32, G:0.02, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:843658 original size:12 final size:12
Alignment explanation
Indices: 843620--843714 Score: 86
Period size: 12 Copynumber: 7.9 Consensus size: 12
843610 ATTTATAAAA
*
843620 AGAAGAAGGCGG
1 AGAAGAAGGAGG
843632 ATGAAG-AGGAGG
1 A-GAAGAAGGAGG
*
843644 AGAAGAAGGAAG
1 AGAAGAAGGAGG
*
843656 AGAAGAAGGTGG
1 AGAAGAAGGAGG
*
843668 AGAATG-AGAAGG
1 AGAA-GAAGGAGG
*
843680 AGAAGAAGGAGA
1 AGAAGAAGGAGG
* *
843692 AGGAGAAGGAGA
1 AGAAGAAGGAGG
*
843704 AGGAGAAGGAG
1 AGAAGAAGGAG
843715 AAGGGGGTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
11 5 0.07
12 60 0.86
13 5 0.07
ACGTcount: A:0.48, C:0.01, G:0.47, T:0.03
Consensus pattern (12 bp):
AGAAGAAGGAGG
Found at i:843677 original size:15 final size:15
Alignment explanation
Indices: 843641--843717 Score: 66
Period size: 15 Copynumber: 4.9 Consensus size: 15
843631 GATGAAGAGG
*
843641 AGGAGAAGAAGGAAG-
1 AGGAGAAGGA-GAAGA
* * *
843656 AGAAGAAGGTGGAGA
1 AGGAGAAGGAGAAGA
*
843671 ATGAGAAGGAGAAGA
1 AGGAGAAGGAGAAGA
843686 AGGAGAAGGAGAAGGAGA
1 AGGAGAAGGAG-A--AGA
843704 AGGAGAAGGAGAAG
1 AGGAGAAGGAGAAG
843718 GGGGTTAACG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
14 3 0.06
15 30 0.61
16 1 0.02
17 1 0.02
18 14 0.29
ACGTcount: A:0.51, C:0.00, G:0.47, T:0.03
Consensus pattern (15 bp):
AGGAGAAGGAGAAGA
Found at i:843682 original size:6 final size:6
Alignment explanation
Indices: 843666--843718 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
843656 AGAAGAAGGT
*
843666 GGAGAA TGAGAA GGAG-A --AGAA GGAGAA GGAGAA GGAGAA GGAGAA
1 GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA
843711 GGAGAA GG
1 GGAGAA GG
843719 GGGTTAACGA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 2 0.05
4 1 0.02
5 1 0.02
6 38 0.90
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (6 bp):
GGAGAA
Found at i:843683 original size:21 final size:21
Alignment explanation
Indices: 843638--843708 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 21
843628 GCGGATGAAG
*
843638 AGGAGGAGAAGAAGGAAGAGAAGA
1 AGGAGGAGAAGGA-GAAG-G-AGA
* *
843662 AGGTGGAGAATGAGAAGGAGA
1 AGGAGGAGAAGGAGAAGGAGA
*
843683 AGAAGGAGAAGGAGAAGGAGA
1 AGGAGGAGAAGGAGAAGGAGA
843704 AGGAG
1 AGGAG
843709 AAGGAGAAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 25 0.62
22 1 0.03
23 4 0.10
24 10 0.25
ACGTcount: A:0.49, C:0.00, G:0.48, T:0.03
Consensus pattern (21 bp):
AGGAGGAGAAGGAGAAGGAGA
Found at i:844359 original size:24 final size:24
Alignment explanation
Indices: 844300--844348 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
844290 AATCATAAAG
844300 AACGTGTCACAAGAGTAGAGAAAA
1 AACGTGTCACAAGAGTAGAGAAAA
844324 AACGTGTCACAAGAGTAGAGAAAA
1 AACGTGTCACAAGAGTAGAGAAAA
844348 A
1 A
844349 CATTGTCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.24, T:0.12
Consensus pattern (24 bp):
AACGTGTCACAAGAGTAGAGAAAA
Found at i:844922 original size:21 final size:21
Alignment explanation
Indices: 844891--844951 Score: 106
Period size: 21 Copynumber: 2.9 Consensus size: 21
844881 TGTTGTATAT
844891 AGCCG-TTGGGGATGTTTTGG
1 AGCCGTTTGGGGATGTTTTGG
844911 AGCCGTTTGGGGATGTTTTGG
1 AGCCGTTTGGGGATGTTTTGG
844932 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATG-TTTT
844952 TCTACTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.13
21 30 0.77
22 4 0.10
ACGTcount: A:0.11, C:0.10, G:0.41, T:0.38
Consensus pattern (21 bp):
AGCCGTTTGGGGATGTTTTGG
Found at i:845112 original size:21 final size:21
Alignment explanation
Indices: 845086--845142 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
845076 CGGTGTTTGA
*
845086 GTGCATGGATGCACTGCCGGG
1 GTGCATGGATGCACTGCAGGG
845107 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
845128 GTGCATGGATGCACT
1 GTGCATGGATGCACT
845143 TTGACACCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.18, C:0.21, G:0.40, T:0.21
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:856475 original size:6 final size:6
Alignment explanation
Indices: 856464--856488 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
856454 CTTTGCTTGC
856464 TGCCAA TGCCAA TGCCAA TGCCAA T
1 TGCCAA TGCCAA TGCCAA TGCCAA T
856489 CGAAAGGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (6 bp):
TGCCAA
Found at i:862059 original size:26 final size:26
Alignment explanation
Indices: 862023--862076 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
862013 TTAAGTTACA
862023 TAGAGCAAATCGTCTATCCGTGCCAC
1 TAGAGCAAATCGTCTATCCGTGCCAC
862049 TAGAGCAAATCGTCTATCCGTGCCAC
1 TAGAGCAAATCGTCTATCCGTGCCAC
862075 TA
1 TA
862077 TGTTATATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (26 bp):
TAGAGCAAATCGTCTATCCGTGCCAC
Found at i:870246 original size:24 final size:24
Alignment explanation
Indices: 870217--870277 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
870207 TAATTTTATG
*
870217 TATGTTTGTTTATATT-TGTTCGTT
1 TATGTTCGTTTATATTCT-TTCGTT
*
870241 TGTGTTCGTTTATATTCTTTCGTT
1 TATGTTCGTTTATATTCTTTCGTT
*
870265 TATGTTCATTTAT
1 TATGTTCGTTTAT
870278 TATTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.15, T:0.64
Consensus pattern (24 bp):
TATGTTCGTTTATATTCTTTCGTT
Found at i:888151 original size:126 final size:124
Alignment explanation
Indices: 887924--888174 Score: 420
Period size: 126 Copynumber: 2.0 Consensus size: 124
887914 AAAAATTAAA
887924 ATATTTAAATATTAGTATATTATTTGTACTGAAAATGTTACTATATATATATAAAAGAAGAAAGG
1 ATATTTAAATATTAGTATATTATTTGTACTGAAAATGTTACTATATATATATAAAAGAAGAAAGG
887989 TGATTATGAAAATATATCATTTATCAGTTCCATCCACAAATTATAGCC-TGCA-TTCAT
66 TGATTATGAAAATATATCATTTATCAGTTCCATCCACAAATTATAGCCATGCATTTCAT
888046 ATATTT-AATATTAGTATATTATTTGTACTGAAAATGTTACTATATATATATATATATA-AAGAA
1 ATATTTAAATATTAGTATATTATTTGTACTGAAAATGTTACTATATATATATA-A-A-AGAAG--
888109 AGAAGGTGATTATGAAAATATATCATTTATCAGTTCCATCCACAAATTATAGCCATGCATTTCAT
61 A-AAGGTGATTATGAAAATATATCATTTATCAGTTCCATCCACAAATTATAGCCATGCATTTCAT
888174 A
1 A
888175 AAAACGGGCA
Statistics
Matches: 121, Mismatches: 0, Indels: 10
0.92 0.00 0.08
Matches are distributed among these distances:
121 46 0.38
122 7 0.06
123 4 0.03
124 1 0.01
125 1 0.01
126 52 0.43
127 4 0.03
128 6 0.05
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (124 bp):
ATATTTAAATATTAGTATATTATTTGTACTGAAAATGTTACTATATATATATAAAAGAAGAAAGG
TGATTATGAAAATATATCATTTATCAGTTCCATCCACAAATTATAGCCATGCATTTCAT
Found at i:890016 original size:12 final size:13
Alignment explanation
Indices: 889987--890020 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
889977 TGGATTTAAA
889987 AAAAATAAATTAT
1 AAAAATAAATTAT
890000 AAAAATAAATTAT
1 AAAAATAAATTAT
890013 -AAAATAAA
1 AAAAATAAA
890021 ATTTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAATAAATTAT
Found at i:890027 original size:12 final size:13
Alignment explanation
Indices: 889988--890027 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
889978 GGATTTAAAA
889988 AAAAT-AAATTAT
1 AAAATAAAATTAT
890000 AAAA-ATAAATTAT
1 AAAATA-AAATTAT
890013 AAAATAAAATT-T
1 AAAATAAAATTAT
890025 AAA
1 AAA
890028 TAACTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.32
13 16 0.64
14 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATAAAATTAT
Found at i:890098 original size:19 final size:18
Alignment explanation
Indices: 890074--890118 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
890064 TAAGTTTGAA
*
890074 TTAATTTACTCAACTTAAT
1 TTAATTTACTCAA-ATAAT
*
890093 TTAATTCACTCAAATAAT
1 TTAATTTACTCAAATAAT
890111 TTCAATTT
1 TT-AATTT
890119 TTTTAACTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTTACTCAAATAAT
Found at i:891042 original size:65 final size:64
Alignment explanation
Indices: 890953--891075 Score: 203
Period size: 65 Copynumber: 1.9 Consensus size: 64
890943 TAATTTGGGA
890953 TGATTATGAAAATATGACACTTATCAATTCCCATTCACAAATTACAGTCATA-ATTTCATGAAAG
1 TGATTATGAAAATATGACACTTATCAATT-CCATTC-CAAATTACAGTCATACATTTCATGAAAG
891017 G
64 G
* *
891018 TGATTATGAAAATATGACATTTATCAATTCCATTCCAAATTATAGTCATACATTTCAT
1 TGATTATGAAAATATGACACTTATCAATTCCATTCCAAATTACAGTCATACATTTCAT
891076 AATAACGGGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
63 14 0.25
64 13 0.24
65 28 0.51
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (64 bp):
TGATTATGAAAATATGACACTTATCAATTCCATTCCAAATTACAGTCATACATTTCATGAAAGG
Found at i:891528 original size:18 final size:19
Alignment explanation
Indices: 891505--891540 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
891495 AAAATTAGAT
*
891505 AGTAAAATTAATA-ATTTC
1 AGTAAAAATAATATATTTC
891523 AGTAAAAATAATATATTT
1 AGTAAAAATAATATATTT
891541 TACGTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (19 bp):
AGTAAAAATAATATATTTC
Found at i:894709 original size:2 final size:2
Alignment explanation
Indices: 894702--894737 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
894692 GAAACTTAAT
894702 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
894738 AATTTTATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:895958 original size:19 final size:19
Alignment explanation
Indices: 895934--896033 Score: 76
Period size: 19 Copynumber: 5.2 Consensus size: 19
895924 ATGTATATAT
895934 ATGTATAATTTATTAATGC
1 ATGTATAATTTATTAATGC
* * * *
895953 ATGTATGCATATATTTATGT
1 ATGTAT-AATTTATTAATGC
* *
895973 ATGTATAATCTATTTATGC
1 ATGTATAATTTATTAATGC
* ** * *
895992 ATGTATCATGCATGT-ACGT
1 ATGTATAATTTAT-TAATGC
896011 ATGTATAATTTATTAATGC
1 ATGTATAATTTATTAATGC
896030 ATGT
1 ATGT
896034 CACATAACCC
Statistics
Matches: 61, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
18 1 0.02
19 44 0.72
20 16 0.26
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (19 bp):
ATGTATAATTTATTAATGC
Found at i:895964 original size:29 final size:29
Alignment explanation
Indices: 895906--895964 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
895896 TATGTATGTT
* *
895906 TGTATAATTTATTAACGTATGTATATATA
1 TGTATAATTTATTAACGCATGTATACATA
* *
895935 TGTATAATTTATTAATGCATGTATGCATA
1 TGTATAATTTATTAACGCATGTATACATA
895964 T
1 T
895965 ATTTATGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (29 bp):
TGTATAATTTATTAACGCATGTATACATA
Found at i:896151 original size:27 final size:25
Alignment explanation
Indices: 896114--896168 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
896104 AGTGTATATA
*
896114 TATGTATGTAATATATTAATGTATG
1 TATGTATGTAATATATTAATGCATG
* *
896139 TATGTATAAGTAATTTTTTAATGCATG
1 TATGTAT--GTAATATATTAATGCATG
896166 TAT
1 TAT
896169 CATGTATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
27 18 0.72
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.49
Consensus pattern (25 bp):
TATGTATGTAATATATTAATGCATG
Found at i:897053 original size:15 final size:16
Alignment explanation
Indices: 897036--897071 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
897026 ATATTATCTG
*
897036 TTTGAACCTGAACTGT
1 TTTGAACCTGAACTGA
897052 TTTG-ACCTGAACTGA
1 TTTGAACCTGAACTGA
897067 TTTGA
1 TTTGA
897072 TCTGCCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (16 bp):
TTTGAACCTGAACTGA
Found at i:898903 original size:43 final size:43
Alignment explanation
Indices: 898838--898975 Score: 195
Period size: 43 Copynumber: 3.2 Consensus size: 43
898828 AATTCTTGTC
898838 TTAGTGGCTTTTTTTTACCACAAACGCCGCTAATGCTATTGTTT
1 TTAGTGGC-TTTTTTTACCACAAACGCCGCTAATGCTATTGTTT
* * * * *
898882 TTAGTGGGTTTTTTTACCACAAACGTCACTGATGCTATTGCTT
1 TTAGTGGCTTTTTTTACCACAAACGCCGCTAATGCTATTGTTT
* * *
898925 TTAGTGGCCTTTTTTGCCACAAACGCCGTTAATGCTATTGTTT
1 TTAGTGGCTTTTTTTACCACAAACGCCGCTAATGCTATTGTTT
898968 TTAGTGGC
1 TTAGTGGC
898976 ATTTGTAATA
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
43 74 0.91
44 7 0.09
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.42
Consensus pattern (43 bp):
TTAGTGGCTTTTTTTACCACAAACGCCGCTAATGCTATTGTTT
Found at i:899016 original size:86 final size:86
Alignment explanation
Indices: 898838--899035 Score: 206
Period size: 86 Copynumber: 2.3 Consensus size: 86
898828 AATTCTTGTC
* ** * *
898838 TTAGTGGCTTTTTTTTACCACAAACGCCGCTAATGCTATTGTTTTTAGTGGGTTTTTTTACCACA
1 TTAGTGGC-CTTTTTTACCACAAACGCCGCTAATGCTATTGTTTTTAGTGGGCATTTGTAACACA
* * * *
898903 AACGTCACTGATGCTATTGCTT
65 AACGCCACTCATACTATTGATT
* * *
898925 TTAGTGGCCTTTTTTGCCACAAACGCCGTTAATGCTATTGTTTTTAGT-GGCATTTGTAATACAA
1 TTAGTGGCCTTTTTTACCACAAACGCCGCTAATGCTATTGTTTTTAGTGGGCATTTGTAACACAA
* *
898989 ACGCCATTACATATTA-TGATT
66 ACGCCACT-CATACTATTGATT
*
899010 TATAGT-GACTTTTTTACCAC-AACGCC
1 T-TAGTGGCCTTTTTTACCACAAACGCC
899036 ACTATTTGCA
Statistics
Matches: 93, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
84 6 0.06
85 34 0.37
86 45 0.48
87 8 0.09
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (86 bp):
TTAGTGGCCTTTTTTACCACAAACGCCGCTAATGCTATTGTTTTTAGTGGGCATTTGTAACACAA
ACGCCACTCATACTATTGATT
Found at i:899511 original size:28 final size:28
Alignment explanation
Indices: 899471--899526 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
899461 TTGTCATCCG
*
899471 AGGCTGAATGTTGGTGCAACCCTACATA
1 AGGCTGAATGTTGATGCAACCCTACATA
*
899499 AGGCTGAGTGTTGATGCAACCCTACATA
1 AGGCTGAATGTTGATGCAACCCTACATA
899527 CAAAGTTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (28 bp):
AGGCTGAATGTTGATGCAACCCTACATA
Found at i:901935 original size:41 final size:40
Alignment explanation
Indices: 901817--901935 Score: 100
Period size: 41 Copynumber: 3.0 Consensus size: 40
901807 TAAAAAAAGT
* * *
901817 CACTATAAATGAATCCTATTACGATATTTGTATAAAAATG
1 CACTATAAATGAACCCTATTACGACATTTGTATAAAAATC
* ** * * *
901857 CAATA-AAAT-ACTACGTTATTGCAACATTTGCT-GAAAAATAC
1 CACTATAAATGA--ACCCTATTACGACATTTG-TATAAAAAT-C
901898 CACTATAAATGAACCCTATTACGACATTTGTATAAAAA
1 CACTATAAATGAACCCTATTACGACATTTGTATAAAAA
901936 CGCTGCTAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 13
0.67 0.18 0.15
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 23 0.40
41 24 0.42
42 4 0.07
43 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (40 bp):
CACTATAAATGAACCCTATTACGACATTTGTATAAAAATC
Found at i:902003 original size:85 final size:81
Alignment explanation
Indices: 901808--902034 Score: 222
Period size: 85 Copynumber: 2.7 Consensus size: 81
901798 GGCGTTTGTT
* * * * ** * *
901808 AAAAAAAGTCACTATAAATGAATCCTATTACGATATTTGTATAAAAATGCAATAAAATACTACGT
1 AAAAAAA-CCACTATAAATGAACCCTATTACGACATTTGTATAAAAACGCGCTAAAGTACAACGT
901873 TATTGCAACATTTGCTG
65 TATTGCAACATTTGCTG
* *
901890 AAAAATACCACTATAAATGAACCCTATTACGACATTTGTATAAAAACGCTGCTAAAGTACAACTT
1 AAAAAAACCACTATAAATGAACCCTATTACGACATTTGTATAAAAACGC-GCTAAAGTACAACGT
* **
901955 TGTTGCAACATTTTTTTG
65 TATTGCAACA-TTTGCTG
* * ** *
901973 AAAAAAAGGCCACTATAGAA-GTACCTTATTATAACATTTATATAAAAACGCCGCTAAAGTAC
1 AAAAAAA--CCACTATA-AATGAACCCTATTACGACATTTGTATAAAAACG-CGCTAAAGTAC
902035 TATGCTAGTG
Statistics
Matches: 120, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
81 38 0.32
82 25 0.21
83 11 0.09
85 43 0.36
86 3 0.03
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (81 bp):
AAAAAAACCACTATAAATGAACCCTATTACGACATTTGTATAAAAACGCGCTAAAGTACAACGTT
ATTGCAACATTTGCTG
Found at i:902649 original size:3 final size:3
Alignment explanation
Indices: 902641--902718 Score: 129
Period size: 3 Copynumber: 25.7 Consensus size: 3
902631 TTTTTACCCA
* *
902641 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
902689 TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
902719 AATACATATA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
3 67 0.96
4 3 0.04
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:902837 original size:25 final size:25
Alignment explanation
Indices: 902790--902838 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
902780 GCCCAATTAC
*
902790 AACTAGACCGGCCCAGTTACAAACA
1 AACTAGACCGGCCCAGATACAAACA
*
902815 AACTAGAACCGGTCCAGAT-CAAAC
1 AACTAG-ACCGGCCCAGATACAAAC
902839 CAGAAACCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.41, C:0.31, G:0.16, T:0.12
Consensus pattern (25 bp):
AACTAGACCGGCCCAGATACAAACA
Found at i:910735 original size:299 final size:294
Alignment explanation
Indices: 910203--910799 Score: 1026
Period size: 299 Copynumber: 2.0 Consensus size: 294
910193 TCCTCTACCA
910203 TTTCATACAAAGATACCCGCAGGGTACCTTGGATTATACTACCAATGTTTCAATGTAGGAGATCT
1 TTTCATACAAAGATACCCGCAGGGTACCTTGGATTATACTACCAATGTTTCAATGTAGGAGATCT
910268 GTTTCTCTAGAAAAATAAGAGAAAATACAAGTTTGGGTACAACATCGACGTCTGAAGCAGTGAGC
66 GTTTCTCTAGAAAAATAAGAGAAAATACAAGTTTGGGTACAACATCGACGTCTGAAGCAGTGAGC
910333 GAAGTCGGTTTCTTTACGAAGTGGGAGATGTTACTCTCCCGAAACATCCAATGCTTCAGAACAAG
131 GAAGTCGGTTTCTTTACGAAGTGGGAGATGTTACTCTCCCGAAACATCCAATGCTTCAGAACAAG
910398 TGAAATCAAAAGGAAAAGCCATGGCAATACCTCAGAAGGTATTTTGAGATGAATCCCTTCC-CA-
196 TGAAATCAAAAGGAAAAGCCATGGCAATACCTCAGAAGGTA-TTTGAG-TG-ATCCCTTCCACAT
910461 TTAATGAG-CTGTGACAG-AAAACAAGCCCAAGAAAT
258 TTAATGAGCCTGTGACAGAAAAACAAGCCCAAGAAAT
910496 TTTCATACAAAGATACCCGCAGGGTACCTTGGAATTATACTACCAA-GTTTCAATGGTAGGAGGA
1 TTTCATACAAAGATACCCGCAGGGTACCTTGG-ATTATACTACCAATGTTTCAAT-GTAGGA-GA
910560 TCTGTTTCTCTAGAAAAATAGAAGAGAAAATACAGAGTTTGGGTAC-ACATCGACGTCTGAAGCA
63 TCTGTTTCTCTAGAAAAAT--AAGAGAAAATACA-AGTTTGGGTACAACATCGACGTCTGAAGCA
910624 GTGAGCGAAGTCGGTTTCTTTACGAGAAGTGGGAGATGTTACTCTCCCGAAACATCCAATGCTTC
125 GTGAGCGAAGTCGGTTTCTTTAC--GAAGTGGGAGATGTTACTCTCCCGAAACATCCAATGCTTC
910689 AGAACAAGTGAAATCAAAAGGAAAAGCCATGGCAATACCTCAGAAGGTATTTGAGTGATCCCTTC
188 AGAACAAGTGAAATCAAAAGGAAAAGCCATGGCAATACCTCAGAAGGTATTTGAGTGATCCCTTC
* *
910754 CAGATTTAATGAGCCTGTGACAGAAAAAACAAGCCCAAGAATT
253 CACATTTAATGAGCCTGTGACAG-AAAAACAAGCCCAAGAAAT
910797 TTT
1 TTT
910800 GAAATTCTTG
Statistics
Matches: 289, Mismatches: 2, Indels: 18
0.94 0.01 0.06
Matches are distributed among these distances:
293 40 0.14
294 19 0.07
295 21 0.07
296 9 0.03
297 57 0.20
298 25 0.09
299 98 0.34
301 20 0.07
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (294 bp):
TTTCATACAAAGATACCCGCAGGGTACCTTGGATTATACTACCAATGTTTCAATGTAGGAGATCT
GTTTCTCTAGAAAAATAAGAGAAAATACAAGTTTGGGTACAACATCGACGTCTGAAGCAGTGAGC
GAAGTCGGTTTCTTTACGAAGTGGGAGATGTTACTCTCCCGAAACATCCAATGCTTCAGAACAAG
TGAAATCAAAAGGAAAAGCCATGGCAATACCTCAGAAGGTATTTGAGTGATCCCTTCCACATTTA
ATGAGCCTGTGACAGAAAAACAAGCCCAAGAAAT
Found at i:913667 original size:62 final size:63
Alignment explanation
Indices: 913570--913694 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 63
913560 AGGCAGAATG
913570 GCTAGATGGCAGATGTTATTATCTGAGTTTGATATTGTATATGTCAACC-AAAAAGCGATAAA
1 GCTAGATGGCAGATGTTATTATCTGAGTTTGATATTGTATATGTCAACCAAAAAAGCGATAAA
913632 GCTAGATGGCAGATGTTATTATCTGAGTTTGATATTGTATATGTCAACCAAAAAAGCGATAAA
1 GCTAGATGGCAGATGTTATTATCTGAGTTTGATATTGTATATGTCAACCAAAAAAGCGATAAA
913695 AGGAAGTATA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 49 0.79
63 13 0.21
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (63 bp):
GCTAGATGGCAGATGTTATTATCTGAGTTTGATATTGTATATGTCAACCAAAAAAGCGATAAA
Found at i:915551 original size:7 final size:7
Alignment explanation
Indices: 915539--915611 Score: 62
Period size: 7 Copynumber: 10.3 Consensus size: 7
915529 ATGCTTGAAG
915539 AAAAAGA
1 AAAAAGA
915546 AAAAAGGAA
1 AAAAA-G-A
915555 AGAAAAGA
1 A-AAAAGA
915563 AAAAA-A
1 AAAAAGA
*
915569 AATAAAAA
1 AA-AAAGA
915577 AAAAAGA
1 AAAAAGA
915584 AAAAAG-
1 AAAAAGA
*
915590 AGAAA-A
1 AAAAAGA
*
915596 AAGAAGA
1 AAAAAGA
915603 AAAAAGA
1 AAAAAGA
915610 AA
1 AA
915612 GGAGGTCAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
6 10 0.19
7 31 0.57
8 6 0.11
9 3 0.06
10 4 0.07
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (7 bp):
AAAAAGA
Found at i:915570 original size:10 final size:10
Alignment explanation
Indices: 915545--915612 Score: 66
Period size: 10 Copynumber: 6.7 Consensus size: 10
915535 GAAGAAAAAG
*
915545 AAAAAAGGAA
1 AAAAAAGAAA
*
915555 AGAAAAGAAA
1 AAAAAAGAAA
*
915565 AAAAAATAAA
1 AAAAAAGAAA
915575 AAAAAA-AGAA
1 AAAAAAGA-AA
*
915585 AAAAGAGAAA
1 AAAAAAGAAA
*
915595 AAAGAAGAAA
1 AAAAAAGAAA
915605 AAAGAAAG
1 AAA-AAAG
915613 GAGGTCAAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
9 1 0.02
10 42 0.89
11 4 0.09
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:915576 original size:11 final size:11
Alignment explanation
Indices: 915539--915612 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
915529 ATGCTTGAAG
915539 AAAAAGAAAAA
1 AAAAAGAAAAA
*
915550 AGGAAAGAAAAGA
1 A-AAAAGAAAA-A
915563 AAAAA-AAATAA
1 AAAAAGAAA-AA
*
915574 AAAAA-AAAGA
1 AAAAAGAAAAA
915584 AAAAAGAGAAAA
1 AAAAAGA-AAAA
*
915596 AAGAAGAAAAA
1 AAAAAGAAAAA
*
915607 AGAAAG
1 AAAAAG
915613 GAGGTCAAGG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
10 6 0.12
11 22 0.43
12 21 0.41
13 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:915594 original size:30 final size:30
Alignment explanation
Indices: 915540--915612 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
915530 TGCTTGAAGA
*
915540 AAAAGAAAAAAGGAAAGAAAAGAAAAAAAAAT
1 AAAA-AAAAAA-GAAAGAAAAGAAAAAAAAAG
*
915572 AAAAAAAAAAGAAA-AAAGAGAAAAAAGAAG
1 AAAAAAAAAAGAAAGAAA-AGAAAAAAAAAG
*
915602 AAAAAAGAAAG
1 AAAAAAAAAAG
915613 GAGGTCAAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 24 0.65
31 6 0.16
32 4 0.11
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (30 bp):
AAAAAAAAAAGAAAGAAAAGAAAAAAAAAG
Found at i:915595 original size:26 final size:25
Alignment explanation
Indices: 915536--915611 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 25
915526 ATTATGCTTG
*
915536 AAGAAAAAGAAAAAAGGAAAGAAAAGA
1 AAGAAAAA-AAAAAA-AAAAGAAAAGA
*
915563 AAAAAAAATAAAAAAAAAAGAAAA-A
1 AAGAAAAA-AAAAAAAAAAGAAAAGA
*
915588 AGAGAAAAAAGAAGAAAAAAGAAA
1 A-AGAAAAAA-AAAAAAAAAGAAA
915612 GGAGGTCAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
25 3 0.07
26 26 0.62
27 13 0.31
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (25 bp):
AAGAAAAAAAAAAAAAAAGAAAAGA
Found at i:915608 original size:19 final size:19
Alignment explanation
Indices: 915542--915609 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
915532 CTTGAAGAAA
915542 AAGAAAAAAG-GAAAGAAAAG
1 AAGAAAAAAGAG-AA-AAAAG
* * *
915562 AAAAAAAAATA-AAAAAAA
1 AAGAAAAAAGAGAAAAAAG
915580 AAGAAAAAAGAGAAAAAAG
1 AAGAAAAAAGAGAAAAAAG
915599 AAGAAAAAAGA
1 AAGAAAAAAGA
915610 AAGGAGGTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 13 0.32
19 19 0.47
20 8 0.20
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (19 bp):
AAGAAAAAAGAGAAAAAAG
Found at i:915981 original size:18 final size:17
Alignment explanation
Indices: 915940--915985 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
915930 CTATTTCAAG
*
915940 TTCAATTTATTTGAAAT
1 TTCAATTTATTTGAAAA
* *
915957 TTAAATTATTTTTGAAAA
1 TTCAATT-TATTTGAAAA
915975 TTCAATTTATT
1 TTCAATTTATT
915986 CTTTTCTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (17 bp):
TTCAATTTATTTGAAAA
Found at i:915984 original size:19 final size:18
Alignment explanation
Indices: 915940--915985 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
915930 CTATTTCAAG
915940 TTCAATTTA--TTTGAAA
1 TTCAATTTATTTTTGAAA
* *
915956 TTTAAATTATTTTTGAAAA
1 TTCAATTTATTTTTG-AAA
915975 TTCAATTTATT
1 TTCAATTTATT
915986 CTTTTCTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 7 0.30
18 4 0.17
19 12 0.52
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (18 bp):
TTCAATTTATTTTTGAAA
Found at i:917168 original size:80 final size:83
Alignment explanation
Indices: 916756--917206 Score: 842
Period size: 83 Copynumber: 5.5 Consensus size: 83
916746 AATGTATGCT
916756 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
916821 TTTAGAAGATAAATTTGC
66 TTTAGAAGATAAATTTGC
916839 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
916904 TTTAGAAGATAAATTTGC
66 TTTAGAAGATAAATTTGC
916922 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
*
916987 TTTAGAAGATGAATTTGC
66 TTTAGAAGATAAATTTGC
917005 CAATAGCATCTTCTGGAA--GTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
*
917068 -TTAGAAGATGAATTTGC
66 TTTAGAAGATAAATTTGC
917085 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGCAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
917149 -TTAGAAGATAAATTT-C
66 TTTAGAAGATAAATTTGC
917165 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
917207 ATTCGGTAGG
Statistics
Matches: 364, Mismatches: 2, Indels: 7
0.98 0.01 0.02
Matches are distributed among these distances:
80 78 0.21
81 80 0.22
82 23 0.06
83 183 0.50
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (83 bp):
CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
TTTAGAAGATAAATTTGC
Found at i:918228 original size:112 final size:114
Alignment explanation
Indices: 917940--918354 Score: 556
Period size: 113 Copynumber: 3.6 Consensus size: 114
917930 ATTCAAATCT
* *
917940 ATCATTTGATGGATCATCATTTCCAGAAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 ATCATTTGATGGATCAACATTGCCAG--GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
* *
918005 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTT-TCTG-ATTC
64 AGGAAGAAGAAGTTCATAAT-AG-AGAATTTGTTCAA-CTTTTTGTTTGAATTC
* * * *** *
918057 ATCACTGGATGGATTATTTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 ATCATTTGATGGATCAACATTGCC--AGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
*
918122 A-GAAGAATAAGTTCATAAT-GAGAATTTGTTCAACTTTTTGTTTGAATTC
64 AGGAAGAAGAAGTTCATAATAGAGAATTTGTTCAACTTTTTGTTTGAATTC
*
918171 ATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAATTCGTCATCTGAAGAAG
1 ATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
*
918236 GAAGAAGAAG-TCATAATGAGAGAACTTGTTCAAC-TTTTGTTTGAATTC
66 GAAGAAGAAGTTCATAAT-AGAGAATTTGTTCAACTTTTTGTTTGAATTC
* * *
918284 ATCATTTGATGGACCAACATTGTCAGGAAGAGTTCATAATGAGAAG-ACTCATCATCTGAAGAAG
1 ATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
918348 GAAGAAG
66 GAAGAAG
918355 TTTATAATAA
Statistics
Matches: 269, Mismatches: 22, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
112 75 0.28
113 83 0.31
114 36 0.13
116 16 0.06
117 57 0.21
119 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (114 bp):
ATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
GAAGAAGAAGTTCATAATAGAGAATTTGTTCAACTTTTTGTTTGAATTC
Found at i:918695 original size:3 final size:3
Alignment explanation
Indices: 918687--918782 Score: 126
Period size: 3 Copynumber: 32.7 Consensus size: 3
918677 TTTTTACCCA
*
918687 TAT TAT TAT TAT TAT CAT T-T TAT TAT TA- TAT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * *
918731 TAT TAT CAT TAT TA- TAT TAT TAT TAT TAT TAT TAT CAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
918778 TAT TA
1 TAT TA
918783 AATATATTAA
Statistics
Matches: 83, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
2 6 0.07
3 74 0.89
4 3 0.04
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:918733 original size:35 final size:35
Alignment explanation
Indices: 918687--918782 Score: 137
Period size: 35 Copynumber: 2.8 Consensus size: 35
918677 TTTTTACCCA
918687 TATTATTATTATTATCATTTTATTATTA-TATTATT
1 TATTATTATTATTATCATTTTATTATTATTATTA-T
918722 TATTATTATTATTATCA--TTATTA-TATTATTAT
1 TATTATTATTATTATCATTTTATTATTATTATTAT
*
918754 TATTATTATTATCATCATTATTATTATTA
1 TATTATTATTATTATCATT-TTATTATTA
918783 AATATATTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
32 19 0.35
33 11 0.20
35 23 0.42
36 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (35 bp):
TATTATTATTATTATCATTTTATTATTATTATTAT
Found at i:920156 original size:17 final size:19
Alignment explanation
Indices: 920123--920159 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
920113 TAATTTAGTC
920123 ATTTATTTTATATGTTTTT
1 ATTTATTTTATATGTTTTT
920142 ATTTA-TTTA-ATGTTTTT
1 ATTTATTTTATATGTTTTT
920159 A
1 A
920160 AAATATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 4 0.22
19 5 0.28
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTT
Found at i:921528 original size:35 final size:37
Alignment explanation
Indices: 921482--921554 Score: 132
Period size: 35 Copynumber: 2.0 Consensus size: 37
921472 ACATAATAGA
921482 TGTCATTGTGGGTATCGCGGTC-TGAAC-TTTTAATG
1 TGTCATTGTGGGTATCGCGGTCGTGAACTTTTTAATG
921517 TGTCATTGTGGGTATCGCGGTCGTGAACTTTTTAATG
1 TGTCATTGTGGGTATCGCGGTCGTGAACTTTTTAATG
921554 T
1 T
921555 TGCACAACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 22 0.61
36 5 0.14
37 9 0.25
ACGTcount: A:0.16, C:0.14, G:0.29, T:0.41
Consensus pattern (37 bp):
TGTCATTGTGGGTATCGCGGTCGTGAACTTTTTAATG
Found at i:921684 original size:23 final size:24
Alignment explanation
Indices: 921649--921700 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
921639 TAAGACTAAA
* *
921649 TTAAATAAAATTAAGTT-TACATT
1 TTAAATAAAATTAAATTATAAATT
**
921672 TTAAATAGGATTAAATTATAAATT
1 TTAAATAAAATTAAATTATAAATT
921696 TTAAA
1 TTAAA
921701 AATGGAGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (24 bp):
TTAAATAAAATTAAATTATAAATT
Found at i:921807 original size:23 final size:23
Alignment explanation
Indices: 921779--921830 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
921769 ACTCCTCTCT
921779 CCTTCCCCAACCTTTCTGCCTCC
1 CCTTCCCCAACCTTTCTGCCTCC
* * *
921802 TCTTCCCCGACTTTTCTGCCTCC
1 CCTTCCCCAACCTTTCTGCCTCC
921825 CCTTCC
1 CCTTCC
921831 TCCTTCCCCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.06, C:0.54, G:0.06, T:0.35
Consensus pattern (23 bp):
CCTTCCCCAACCTTTCTGCCTCC
Found at i:924270 original size:15 final size:15
Alignment explanation
Indices: 924250--924282 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
924240 ATATTTAGTT
924250 GGGTGGGCGGATGCG
1 GGGTGGGCGGATGCG
924265 GGGTGGGCGGATGCG
1 GGGTGGGCGGATGCG
924280 GGG
1 GGG
924283 CGGATAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.70, T:0.12
Consensus pattern (15 bp):
GGGTGGGCGGATGCG
Found at i:930392 original size:2 final size:2
Alignment explanation
Indices: 930387--930411 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
930377 TCATATATGC
930387 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
930412 TCCTATTCTA
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:934678 original size:2 final size:2
Alignment explanation
Indices: 934671--934706 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
934661 CACTAGTTTG
934671 AT AT 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 AT AT
934707 GTTGGGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:937443 original size:2 final size:2
Alignment explanation
Indices: 937410--937435 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
937400 CTCAATTTAC
937410 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
937436 CAATATATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:941604 original size:29 final size:30
Alignment explanation
Indices: 941523--941605 Score: 71
Period size: 31 Copynumber: 2.8 Consensus size: 30
941513 TAGTTGAGTG
*
941523 ACCATTTTGTAACTTTTAATAGTCGAGAAT
1 ACCATTATGTAACTTTTAATAGTCGAGAAT
* ** * **
941553 ATCAACAAAGTAACTCCCT-ATAGTCG-GAAT
1 A-CCATTATGTAACT-TTTAATAGTCGAGAAT
941583 ACCATTATGTAACTTTTAATAGT
1 ACCATTATGTAACTTTTAATAGT
941606 TGAGGGACTC
Statistics
Matches: 37, Mismatches: 13, Indels: 7
0.65 0.23 0.12
Matches are distributed among these distances:
28 1 0.03
29 14 0.38
30 6 0.16
31 15 0.41
32 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (30 bp):
ACCATTATGTAACTTTTAATAGTCGAGAAT
Found at i:942988 original size:32 final size:32
Alignment explanation
Indices: 942942--943050 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 32
942932 TTTTTACAAG
* * **
942942 TTTAAGGACTATTTTGTAATGGTTTGATAAGT
1 TTTAATGACCATTTTGTAATAATTTGATAAGT
*
942974 TTTAATGACCATTTTGTAACAATTTGATAAG-
1 TTTAATGACCATTTTGTAATAATTTGATAAGT
** * *
943005 TTTAATGATTATTTTATAATAATCTGATAA-T
1 TTTAATGACCATTTTGTAATAATTTGATAAGT
*
943036 TGTAATGACCATTTT
1 TTTAATGACCATTTT
943051 ATAACTTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
31 37 0.59
32 26 0.41
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (32 bp):
TTTAATGACCATTTTGTAATAATTTGATAAGT
Found at i:943012 original size:31 final size:31
Alignment explanation
Indices: 942964--943075 Score: 115
Period size: 31 Copynumber: 3.6 Consensus size: 31
942954 TTTGTAATGG
*
942964 TTTGATAAGTTTTAATGACCATTTTGTAACAA
1 TTTGATAAG-TTTAATGACCATTTTATAACAA
** *
942996 TTTGATAAGTTTAATGATTATTTTATAATAA
1 TTTGATAAGTTTAATGACCATTTTATAACAA
*
943027 TCTGATAA-TTGTAATGACCATTTTATAAC--
1 TTTGATAAGTT-TAATGACCATTTTATAACAA
*
943056 TTCTGA-AACTTTAATGACCA
1 TT-TGATAAGTTTAATGACCA
943076 ATAAATTATT
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
29 12 0.18
30 7 0.10
31 40 0.59
32 9 0.13
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.44
Consensus pattern (31 bp):
TTTGATAAGTTTAATGACCATTTTATAACAA
Found at i:951291 original size:31 final size:28
Alignment explanation
Indices: 951248--951423 Score: 214
Period size: 27 Copynumber: 6.1 Consensus size: 28
951238 TTTTCACCCT
951248 AAACCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGAATATCACACTTAAAA
951276 AAACCGACAGACCCGAATATCACACTTAAAA
1 AAACC--C-GACCCGAATATCACACTTAAAA
* *
951307 AAA-CCGACCTGAATATTACACTTAAAA
1 AAACCCGACCCGAATATCACACTTAAAA
*
951334 AAACCCGACCAACCCGAATATCAAACTT-AAA
1 AAACCCG----ACCCGAATATCACACTTAAAA
*
951365 AAACCCGACCCGAATATCACAATTAAAA
1 AAACCCGACCCGAATATCACACTTAAAA
*
951393 AAACCCGACCCGAATAGTGA-ACTTAAAA
1 AAACCCGACCCGAATA-TCACACTTAAAA
951421 AAA
1 AAA
951424 TGACCCAACC
Statistics
Matches: 129, Mismatches: 9, Indels: 20
0.82 0.06 0.13
Matches are distributed among these distances:
27 38 0.29
28 38 0.29
29 2 0.02
30 2 0.02
31 35 0.27
32 14 0.11
ACGTcount: A:0.49, C:0.28, G:0.09, T:0.15
Consensus pattern (28 bp):
AAACCCGACCCGAATATCACACTTAAAA
Found at i:951349 original size:59 final size:60
Alignment explanation
Indices: 951252--951402 Score: 236
Period size: 59 Copynumber: 2.6 Consensus size: 60
951242 CACCCTAAAC
*
951252 CCGACCCGAATATCACACTTAAAAAAA-CCGA-CAGACCCGAATATCACACTTAAAAAAA
1 CCGACCCGAATATCACACTTAAAAAAACCCGACCAGACCCGAATATCAAACTTAAAAAAA
* * *
951310 CCGACCTGAATATTACACTTAAAAAAACCCGACCA-ACCCGAATATCAAACTTAAAAAAC
1 CCGACCCGAATATCACACTTAAAAAAACCCGACCAGACCCGAATATCAAACTTAAAAAAA
*
951369 CCGACCCGAATATCACAATTAAAAAAACCCGACC
1 CCGACCCGAATATCACACTTAAAAAAACCCGACC
951403 CGAATAGTGA
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
58 25 0.30
59 57 0.68
60 2 0.02
ACGTcount: A:0.47, C:0.30, G:0.08, T:0.15
Consensus pattern (60 bp):
CCGACCCGAATATCACACTTAAAAAAACCCGACCAGACCCGAATATCAAACTTAAAAAAA
Found at i:951436 original size:59 final size:55
Alignment explanation
Indices: 951248--951423 Score: 203
Period size: 59 Copynumber: 3.1 Consensus size: 55
951238 TTTTCACCCT
*
951248 AAACCCGACCCGAATATCACACTTAAAAAAACCGACAGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGAATATCACACTTAAAAAAACC--C-GACCCGAATAT-AAACTTAAAA
* *
951307 AAA-CCGACCTGAATATTACACTTAAAAAAACCCGACCAACCCGAATATCAAACTT-AAA
1 AAACCCGACCCGAATATCACACTTAAAAAAACCCG----ACCCGAATAT-AAACTTAAAA
* *
951365 AAACCCGACCCGAATATCACAATTAAAAAAACCCGACCCGAATAGTGAACTTAAAA
1 AAACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAATA-TAAACTTAAAA
951421 AAA
1 AAA
951424 TGACCCAACC
Statistics
Matches: 103, Mismatches: 7, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
55 15 0.15
56 8 0.08
58 33 0.32
59 47 0.46
ACGTcount: A:0.49, C:0.28, G:0.09, T:0.15
Consensus pattern (55 bp):
AAACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAATATAAACTTAAAA
Found at i:952363 original size:79 final size:79
Alignment explanation
Indices: 952241--952786 Score: 763
Period size: 79 Copynumber: 6.9 Consensus size: 79
952231 AATCTCAATG
* * * * *
952241 TTATTGATG-ATGTTTACGTCT-GTACGACTATCAAATCTAGATACATTGATGATCCAGGGAGAT
1 TTATTGATGTATGTTTATGT-TGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGAT
*
952304 GTCTGAATCCCGGTA
65 GTCTGAATCCCGATA
* * * *
952319 TTATTGATGTATGTTTATGTCGATGCGACTGTCGAATCTCGATACATTGATGTTCCAGGGAGAAG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
*
952384 TCTGAATCCCCATA
66 TCTGAATCCCGATA
* *
952398 TTATTGATGTATGTTTATGTTGGTGCGACAATCGAATCTCGATACATTGATGTTTCAGGGAGATG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
*
952463 TCTGAATCCCGGTA
66 TCTGAATCCCGATA
* * * *
952477 TTATTGATGTATGTTTATGTTGGTTCTACTATCGAATCTCGATACATTGACGTTCCTGGGAGATG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
* *
952542 TCTGGATCCCGGTA
66 TCTGAATCCCGATA
* * * * * * *
952556 TTATTGATGTATGTTTATGTCGATGCAAATGTCGAATTTCGATACATTGATGTTCCATGGAGATG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
*
952621 TCTGAATCCCCATA
66 TCTGAATCCCGATA
* * *
952635 TCATTGATGTATGTTTATGTTGGTGCGACTATTGAATCTCGATGCATTGATGTTCCAGGGAGATG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
952700 TCTGAATCCCGATA
66 TCTGAATCCCGATA
* * *
952714 TTATTGATGTATGTTTATGTTGGTGCAACTATCGAATCTCGATACGTTGATGTTCCATGGAGATG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
952779 TCTGAATC
66 TCTGAATC
952787 ACAGATCTTA
Statistics
Matches: 410, Mismatches: 56, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
78 9 0.02
79 401 0.98
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (79 bp):
TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
TCTGAATCCCGATA
Found at i:952674 original size:237 final size:237
Alignment explanation
Indices: 952241--952786 Score: 846
Period size: 237 Copynumber: 2.3 Consensus size: 237
952231 AATCTCAATG
* * * * * *
952241 TTATTGATG-ATGTTTACGTCT-GTACGACTATCAAATCTAGATACATTGATGATCCAGGGAGAT
1 TTATTGATGTATGTTTATGT-TGGTACAACTATCGAATCTCGATACATTGATGTTCCTGGGAGAT
* *
952304 GTCTGAATCCCGGTATTATTGATGTATGTTTATGTCGATGCGACTGTCGAATCTCGATACATTGA
65 GTCTGAATCCCGGTATTATTGATGTATGTTTATGTCGATGCAAATGTCGAATCTCGATACATTGA
*
952369 TGTTCCAGGGAGAAGTCTGAATCCCCATATTATTGATGTATGTTTATGTTGGTGCGACAATCGAA
130 TGTTCCAGGGAGAAGTCTGAATCCCCATATCATTGATGTATGTTTATGTTGGTGCGACAATCGAA
* *
952434 TCTCGATACATTGATGTTTCAGGGAGATGTCTGAATCCCGGTA
195 TCTCGATACATTGATGTTCCAGGGAGATGTCTGAATCCCGATA
* * *
952477 TTATTGATGTATGTTTATGTTGGTTCTACTATCGAATCTCGATACATTGACGTTCCTGGGAGATG
1 TTATTGATGTATGTTTATGTTGGTACAACTATCGAATCTCGATACATTGATGTTCCTGGGAGATG
* *
952542 TCTGGATCCCGGTATTATTGATGTATGTTTATGTCGATGCAAATGTCGAATTTCGATACATTGAT
66 TCTGAATCCCGGTATTATTGATGTATGTTTATGTCGATGCAAATGTCGAATCTCGATACATTGAT
* * * *
952607 GTTCCATGGAGATGTCTGAATCCCCATATCATTGATGTATGTTTATGTTGGTGCGACTATTGAAT
131 GTTCCAGGGAGAAGTCTGAATCCCCATATCATTGATGTATGTTTATGTTGGTGCGACAATCGAAT
*
952672 CTCGATGCATTGATGTTCCAGGGAGATGTCTGAATCCCGATA
196 CTCGATACATTGATGTTCCAGGGAGATGTCTGAATCCCGATA
* *
952714 TTATTGATGTATGTTTATGTTGGTGCAACTATCGAATCTCGATACGTTGATGTTCCAT-GGAGAT
1 TTATTGATGTATGTTTATGTTGGTACAACTATCGAATCTCGATACATTGATGTTCC-TGGGAGAT
952778 GTCTGAATC
65 GTCTGAATC
952787 ACAGATCTTA
Statistics
Matches: 282, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
236 10 0.04
237 271 0.96
238 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (237 bp):
TTATTGATGTATGTTTATGTTGGTACAACTATCGAATCTCGATACATTGATGTTCCTGGGAGATG
TCTGAATCCCGGTATTATTGATGTATGTTTATGTCGATGCAAATGTCGAATCTCGATACATTGAT
GTTCCAGGGAGAAGTCTGAATCCCCATATCATTGATGTATGTTTATGTTGGTGCGACAATCGAAT
CTCGATACATTGATGTTCCAGGGAGATGTCTGAATCCCGATA
Found at i:955354 original size:29 final size:30
Alignment explanation
Indices: 955319--955384 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
955309 ATGGAATCCA
955319 CATTCCC-CGTTTGAGTTGGTCGGGAATGT
1 CATTCCCGCGTTTGAGTTGGTCGGGAATGT
955348 CATTCCCGCGTTTGAGTTGGTCGGGAATGT
1 CATTCCCGCGTTTGAGTTGGTCGGGAATGT
955378 CATTCCC
1 CATTCCC
955385 AATAATCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 7 0.19
30 29 0.81
ACGTcount: A:0.14, C:0.24, G:0.29, T:0.33
Consensus pattern (30 bp):
CATTCCCGCGTTTGAGTTGGTCGGGAATGT
Found at i:957900 original size:229 final size:230
Alignment explanation
Indices: 957520--958243 Score: 1062
Period size: 229 Copynumber: 3.2 Consensus size: 230
957510 GGAGTACTTG
*
957520 TTGTCATGTTTGAAACATGTTTGAGATAATGTTGGATTTTGTGGTTTTCTATTGGCATGAAGGAT
1 TTGTCATGTTTGAAACATGTTTGAGATAATGTTGGATTTTGTGGTTTTCTATTGGTATGAAGGAT
* **
957585 TCACTATTTTAGGATATTGGAAAAGATAGAGTAAAGCACACCGACATATCGAAATGGAACTGAAT
66 GCACTATTTTAGGATACCGGAAAAGATAGAGTAAAGCACACCGACATATCGAAATGGAACTGAAT
** *
957650 CTTATCGACATAGAGCCTAAACAGTACATACGGTCCGTATTTATATGGTATCGATAATCATGGTT
131 CTTATCGATTTAGAGCCTAAACAGTACATACGGTCCGTATTGATATGGTATCGATAATCATGGTT
**
957715 TTTTATTTCAAGGTGATGATATATGGGATTGCTCA
196 TTTGGTTTCAAGGTGATGATATATGGGATTGCTCA
*
957750 TTGTCATGTTTGAAACAT-TTTGAGATAATGTTGGATTTTGTGGTTTTATATTGGTAT-AAGGGA
1 TTGTCATGTTTGAAACATGTTTGAGATAATGTTGGATTTTGTGGTTTTCTATTGGTATGAA-GGA
957813 TGCACTATTTTAGGATACCGGAAAAGATAGAGTAAAGCACACCGACATATCGAAATGGAACTGAA
65 TGCACTATTTTAGGATACCGGAAAAGATAGAGTAAAGCACACCGACATATCGAAATGGAACTGAA
*
957878 TCTTATTGATTTAGAGCCTAAACAGTACATACGGTCCGTATTGATATGGTATCGATAATCATGGT
130 TCTTATCGATTTAGAGCCTAAACAGTACATACGGTCCGTATTGATATGGTATCGATAATCATGGT
*
957943 TTTTGGTTTCAAGGTGATGATATTTGGGATTGCTCA
195 TTTTGGTTTCAAGGTGATGATATATGGGATTGCTCA
957979 TTGTCATGTTTG----A----T---ATAATGTTGGATTTTGTGGTTTTCTATTGGTATGAAGGAT
1 TTGTCATGTTTGAAACATGTTTGAGATAATGTTGGATTTTGTGGTTTTCTATTGGTATGAAGGAT
* * * * *
958033 GCACTATTTTAGGATACCGGAAGAGATAGACTAAAGCACACTGATATATCGAAATGGAACTTAAT
66 GCACTATTTTAGGATACCGGAAAAGATAGAGTAAAGCACACCGACATATCGAAATGGAACTGAAT
* * * * * *
958098 CTTATCGATTTAGAACCTAAACAGTACATACAGTCCGTACTGATATGG-AGCCGATGATCTTGGT
131 CTTATCGATTTAGAGCCTAAACAGTACATACGGTCCGTATTGATATGGTA-TCGATAATCATGGT
* * *
958162 TTTTGGTTTGAAGGTGGAGGGGGATATATGGGATTGTTCA
195 TTTTGGTTTCAAGGT-GA---TGATATATGGGATTGCTCA
958202 TTGTCATGTTTGAAACATGTTTGAGATAATGTTGGATTTTGT
1 TTGTCATGTTTGAAACATGTTTGAGATAATGTTGGATTTTGT
958244 TTTTGTAACC
Statistics
Matches: 447, Mismatches: 29, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
218 1 0.00
219 165 0.37
220 4 0.01
222 1 0.00
223 28 0.06
225 1 0.00
227 1 0.00
228 2 0.00
229 208 0.47
230 18 0.04
231 1 0.00
234 17 0.04
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (230 bp):
TTGTCATGTTTGAAACATGTTTGAGATAATGTTGGATTTTGTGGTTTTCTATTGGTATGAAGGAT
GCACTATTTTAGGATACCGGAAAAGATAGAGTAAAGCACACCGACATATCGAAATGGAACTGAAT
CTTATCGATTTAGAGCCTAAACAGTACATACGGTCCGTATTGATATGGTATCGATAATCATGGTT
TTTGGTTTCAAGGTGATGATATATGGGATTGCTCA
Found at i:958893 original size:24 final size:24
Alignment explanation
Indices: 958855--958924 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
958845 CAAAACAGAG
* *
958855 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
958879 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
*
958903 TCCAGGTCAAAAATCATATAAA
1 TCCAGGTCAAATATCATATAAA
958925 CTATTTATAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:959659 original size:29 final size:29
Alignment explanation
Indices: 959621--959688 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
959611 CATTTTACAC
* *
959621 AAATATCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
* * * *
959650 ATATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
959679 AAATAGCACC
1 AAATAGCACC
959689 AAAACCAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.31
Consensus pattern (29 bp):
AAATAGCACCCTTTTCAAAATAATTACCA
Found at i:959752 original size:22 final size:23
Alignment explanation
Indices: 959724--959774 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
959714 CACCAGTCAA
959724 CGGGTCGAGTCAAC-GGTCGGGT
1 CGGGTCGAGTCAACGGGTCGGGT
*
959746 CGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGAGTCAACGGGTCGGGT
959769 CGGGTC
1 CGGGTC
959775 AACGGTCGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.10, C:0.24, G:0.49, T:0.18
Consensus pattern (23 bp):
CGGGTCGAGTCAACGGGTCGGGT
Found at i:959764 original size:18 final size:18
Alignment explanation
Indices: 959741--959785 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
959731 AGTCAACGGT
959741 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
959759 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
959777 C-GGTCGGGT
1 CGGGTCGGGT
959786 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.09, C:0.22, G:0.51, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCGGGTCAA
Found at i:959766 original size:13 final size:13
Alignment explanation
Indices: 959719--959769 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
959709 AATAACACCA
*
959719 GTCAACGGGTCGA
1 GTCAACGGGTCGG
959732 GTCAAC-GGTCGG
1 GTCAACGGGTCGG
959744 GT---CGGGTCGG
1 GTCAACGGGTCGG
959754 GTCAACGGGTCGG
1 GTCAACGGGTCGG
959767 GTC
1 GTC
959770 GGGTCAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 1 0.03
10 8 0.24
12 7 0.21
13 17 0.52
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.18
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:959804 original size:9 final size:9
Alignment explanation
Indices: 959790--959838 Score: 62
Period size: 9 Copynumber: 5.1 Consensus size: 9
959780 TCGGGTTGTG
959790 ACCGGTCAA
1 ACCGGTCAA
959799 ACCGGTCAAA
1 ACCGGTC-AA
959809 ACCGGGTCAAA
1 ACC-GGTC-AA
*
959820 ACCGGTTAA
1 ACCGGTCAA
959829 ACCGGTCAA
1 ACCGGTCAA
959838 A
1 A
959839 ATAGGTTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
9 18 0.50
10 8 0.22
11 10 0.28
ACGTcount: A:0.37, C:0.29, G:0.22, T:0.12
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:959818 original size:11 final size:11
Alignment explanation
Indices: 959793--959824 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
959783 GGTTGTGACC
959793 GGTC-AAACC-
1 GGTCAAAACCG
959802 GGTCAAAACCG
1 GGTCAAAACCG
959813 GGTCAAAACCG
1 GGTCAAAACCG
959824 G
1 G
959825 TTAAACCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 4 0.19
10 5 0.24
11 12 0.57
ACGTcount: A:0.34, C:0.28, G:0.28, T:0.09
Consensus pattern (11 bp):
GGTCAAAACCG
Found at i:959818 original size:20 final size:18
Alignment explanation
Indices: 959790--959838 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
959780 TCGGGTTGTG
959790 ACCGGTCAAACCGGTCAAA
1 ACCGGTCAAACCGGT-AAA
*
959809 ACCGGGTCAAAACCGGTTAA
1 ACC-GGTC-AAACCGGTAAA
959829 ACCGGTCAAA
1 ACCGGTCAAA
959839 ATAGGTTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 7 0.26
20 9 0.33
21 8 0.30
ACGTcount: A:0.37, C:0.29, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCGGTCAAACCGGTAAA
Found at i:959845 original size:19 final size:20
Alignment explanation
Indices: 959807--959845 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
959797 AAACCGGTCA
*
959807 AAACCGGGTCAAAACCGGTT
1 AAACCGGGTCAAAACAGGTT
*
959827 AAACC-GGTCAAAATAGGTT
1 AAACCGGGTCAAAACAGGTT
959846 TCCAGCGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (20 bp):
AAACCGGGTCAAAACAGGTT
Found at i:966052 original size:24 final size:24
Alignment explanation
Indices: 966025--966083 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
966015 TCCATGTCAG
*
966025 TATCATATAAAAATTCAGGTCAAA
1 TATCATATAAAAATCCAGGTCAAA
* *
966049 TATCATATCAGAATCCAGGTCAAA
1 TATCATATAAAAATCCAGGTCAAA
* *
966073 AATCAGATAAA
1 TATCATATAAA
966084 CTATTTATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.25
Consensus pattern (24 bp):
TATCATATAAAAATCCAGGTCAAA
Found at i:966832 original size:28 final size:28
Alignment explanation
Indices: 966774--966847 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
966764 GTCAAACATT
*
966774 TTACACAAATAGCACCATTTTTAAAATAA
1 TTAC-CAAATAGCACCATTTTCAAAATAA
* *
966803 TTACCAATATAGCACC-TTTTCGAATTAA
1 TTACCAA-ATAGCACCATTTTCAAAATAA
*
966831 TTCCCAAAATAGCACCA
1 TTACC-AAATAGCACCA
966848 AAACCAAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 24 0.63
29 14 0.37
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (28 bp):
TTACCAAATAGCACCATTTTCAAAATAA
Found at i:966894 original size:13 final size:13
Alignment explanation
Indices: 966876--966905 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
966866 GAATAACATC
*
966876 GGTCAACGGGTCG
1 GGTCAACAGGTCG
966889 GGTCAACAGGTCG
1 GGTCAACAGGTCG
966902 GGTC
1 GGTC
966906 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:966919 original size:17 final size:18
Alignment explanation
Indices: 966882--966923 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
966872 CATCGGTCAA
966882 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
966900 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACAGGT
966917 CGGGTCG
1 CGGGTCG
966924 TGACCGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:966939 original size:10 final size:10
Alignment explanation
Indices: 966926--966960 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
966916 TCGGGTCGTG
966926 ACCGGTCAAA
1 ACCGGTCAAA
*
966936 ACCGGT-TAA
1 ACCGGTCAAA
966945 ACCGGTCAAA
1 ACCGGTCAAA
966955 ACCGGT
1 ACCGGT
966961 TTCCAGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.34, C:0.29, G:0.23, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:968480 original size:83 final size:79
Alignment explanation
Indices: 968264--968535 Score: 227
Period size: 83 Copynumber: 3.3 Consensus size: 79
968254 TTAATTTTGA
* * * * *
968264 AATATTTTATGATTTAATATAATATTTTTTTTATGTATTTAGTTCTT-AAAATTAATTTGAACTC
1 AATATTTTATAATTTATTATAATA-TTTATAT-TGTATTT--TTCTTAAAAATTAATTTGAA-TG
* *
968328 AAATTGACATTAATTTTTATTT
61 AAATTGACTTTAA--TGT-TTT
* * *
968350 AATATTTTA-AA--TGTTATAATATCTATATTGGATTCATTATCTTAAAAATTAATTTGCAATGA
1 AATATTTTATAATTTATTATAATATTTATATTGTATT--TT-TCTTAAAAATTAATTTG-AATGA
968412 AATTGACCTTTAATGTTTT
62 AATTGA-CTTTAATGTTTT
* *
968431 CAATATTTTATAATTTATTATAATATTTGTATTGTATTTTTCTTGAAAAATTAATTTAAATCGAA
1 -AATATTTTATAATTTATTATAATATTTATATTGTATTTTTCTT-AAAAATTAATTTGAAT-GAA
*
968496 ATT-AATTT--TG-TTT
63 ATTGACTTTAATGTTTT
968509 AATATTTTATAATTTATTATAATATTT
1 AATATTTTATAATTTATTATAATATTT
968536 TTGTTATATT
Statistics
Matches: 158, Mismatches: 16, Indels: 33
0.76 0.08 0.16
Matches are distributed among these distances:
77 27 0.17
78 3 0.02
79 2 0.01
81 12 0.08
82 27 0.17
83 51 0.32
84 7 0.04
85 20 0.13
86 9 0.06
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (79 bp):
AATATTTTATAATTTATTATAATATTTATATTGTATTTTTCTTAAAAATTAATTTGAATGAAATT
GACTTTAATGTTTT
Found at i:970431 original size:15 final size:16
Alignment explanation
Indices: 970411--970445 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
970401 TTTAAATCGT
*
970411 AAAATCAAACTGAA-C
1 AAAATCAAACCGAATC
970426 AAAATCAAACCGAATC
1 AAAATCAAACCGAATC
970442 AAAA
1 AAAA
970446 ACCACAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.63, C:0.20, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAATCAAACCGAATC
Found at i:973501 original size:32 final size:32
Alignment explanation
Indices: 973454--973520 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
973444 CTTGCTTCCC
**
973454 CAAGAAGTAGTTGTGAAGTGGTCCAACATAAT
1 CAAGAAGTAAATGTGAAGTGGTCCAACATAAT
973486 CAAGAAGTAAATGTGAAGTGGTCCAACATAAT
1 CAAGAAGTAAATGTGAAGTGGTCCAACATAAT
973518 CAA
1 CAA
973521 TACGATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.22
Consensus pattern (32 bp):
CAAGAAGTAAATGTGAAGTGGTCCAACATAAT
Found at i:986323 original size:20 final size:21
Alignment explanation
Indices: 986300--986342 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
986290 CTATATTTTC
*
986300 AAATATTAT-TTATTATTA-AT
1 AAAT-TTATATTATCATTATAT
986320 AAATTTATATTATCATTATAT
1 AAATTTATATTATCATTATAT
986341 AA
1 AA
986343 TACTATAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTTATATTATCATTATAT
Done.