Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 88 of 128
Found at i:28915512 original size:30 final size:30
Alignment explanation
Indices: 28915468--28915530 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
28915458 ACTTAACAAG
28915468 CAAATGCCTATAAAATAATAACAAAATTAA
1 CAAATGCCTATAAAATAATAACAAAATTAA
* *
28915498 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTATAAAATAATAACAAAATTAA
28915528 CAA
1 CAA
28915531 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTATAAAATAATAACAAAATTAA
Found at i:28920009 original size:20 final size:20
Alignment explanation
Indices: 28919984--28920023 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28919974 TTGAAAAAGT
28919984 ATTGTTGATAAGTGTCAAAA
1 ATTGTTGATAAGTGTCAAAA
28920004 ATTGTTGATAAGTGTCAAAA
1 ATTGTTGATAAGTGTCAAAA
28920024 GTAACATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (20 bp):
ATTGTTGATAAGTGTCAAAA
Found at i:28921372 original size:13 final size:14
Alignment explanation
Indices: 28921355--28921386 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28921345 TAATATTTTT
28921355 ATTTTTA-ATT-TA
1 ATTTTTACATTCTA
28921367 ATTTTTACATTCTA
1 ATTTTTACATTCTA
28921381 ATTTTT
1 ATTTTT
28921387 TGTTTGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTTTACATTCTA
Found at i:28922637 original size:55 final size:56
Alignment explanation
Indices: 28922553--28922663 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 56
28922543 GAACAAAGAA
28922553 AATATAAAAGCAAGAGAGAATGTACTTTATTAATCAAATGGATGA-TACAATGCTT
1 AATATAAAAGCAAGAGAGAATGTACTTTATTAATCAAATGGATGATTACAATGCTT
28922608 AATATAAAAGCAAGAGAGAATGTACTTTATTAATCAAATGGATGATTACAATGCTT
1 AATATAAAAGCAAGAGAGAATGTACTTTATTAATCAAATGGATGATTACAATGCTT
28922664 CATCAGAGTC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 45 0.82
56 10 0.18
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (56 bp):
AATATAAAAGCAAGAGAGAATGTACTTTATTAATCAAATGGATGATTACAATGCTT
Found at i:28925829 original size:14 final size:14
Alignment explanation
Indices: 28925807--28925841 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
28925797 GAGAATGGGT
*
28925807 AAAACAAAGAATAA
1 AAAATAAAGAATAA
28925821 AAAATAAAGAATAA
1 AAAATAAAGAATAA
28925835 AGAAATA
1 A-AAATA
28925842 TGAAAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.77, C:0.03, G:0.09, T:0.11
Consensus pattern (14 bp):
AAAATAAAGAATAA
Found at i:28926059 original size:19 final size:19
Alignment explanation
Indices: 28926033--28926106 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
28926023 CATAACAAAA
*
28926033 TTAT-ATTTTTATAAAGTT
1 TTATGATTTTTATAAAATT
28926051 TTATGATTTTT-TAATTAATT
1 TTATGATTTTTATAA--AATT
*
28926071 TCTAATAATTTTTATAAAATT
1 T-T-ATGATTTTTATAAAATT
*
28926092 TTATGTTTTTTATAA
1 TTATGATTTTTATAA
28926107 TTCTAGAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
18 7 0.15
19 17 0.37
20 5 0.11
21 6 0.13
22 8 0.17
23 3 0.07
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (19 bp):
TTATGATTTTTATAAAATT
Found at i:28929425 original size:47 final size:47
Alignment explanation
Indices: 28929369--28929616 Score: 163
Period size: 47 Copynumber: 5.3 Consensus size: 47
28929359 GGACAACAGT
28929369 AACAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTA
1 AACAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTA
* * * * * ** *
28929416 AACAACATTCGAATAGCATT--TA-ACCAACATTTGGGCAGCATTAGTA
1 AACAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATT--TA
** * * ** * *
28929462 TGCTAAAAAAT-GGACAGCATT--TAAAC--AACATTCGGACAGCA-TTA
1 AAC--AACATTCGGACAGCATTAGTATGCTAAAAAAT-GGACAGCATTTA
* * *
28929506 ACCAACATTCGGATATCATTAGTATGCTAAAAAATGGACAGCATTTA
1 AACAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTA
* * ** *
28929553 AGCAAAATTTAGATAGCATTAGTATGCTCAAAAAATGGACAGCATTTA
1 AACAACATTCGGACAGCATTAGTATGCT-AAAAAATGGACAGCATTTA
28929601 AACAACATTCGGACAG
1 AACAACATTCGGACAG
28929617 TATTTAACCA
Statistics
Matches: 150, Mismatches: 38, Indels: 25
0.70 0.18 0.12
Matches are distributed among these distances:
42 4 0.03
43 8 0.05
44 17 0.11
45 5 0.03
46 15 0.10
47 65 0.43
48 36 0.24
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (47 bp):
AACAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTA
Found at i:28929511 original size:21 final size:22
Alignment explanation
Indices: 28929404--28929518 Score: 90
Period size: 22 Copynumber: 5.1 Consensus size: 22
28929394 GCTAAAAAAT
28929404 GGACAGCATTTAAACAACATTC
1 GGACAGCATTTAAACAACATTC
* * * *
28929426 GAATAGCATTTAACCAACATTT
1 GGACAGCATTTAAACAACATTC
* ** * *
28929448 GGGCAGCATTAGTATGCTAAAAAAT-
1 GGACAGCATT--TAAAC--AACATTC
28929473 GGACAGCATTTAAACAACATTC
1 GGACAGCATTTAAACAACATTC
*
28929495 GGACAGCA-TTAACCAACATTC
1 GGACAGCATTTAAACAACATTC
28929516 GGA
1 GGA
28929519 TATCATTAGT
Statistics
Matches: 71, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
21 19 0.27
22 33 0.46
23 3 0.04
24 3 0.04
25 9 0.13
26 4 0.06
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (22 bp):
GGACAGCATTTAAACAACATTC
Found at i:28929526 original size:21 final size:21
Alignment explanation
Indices: 28929473--28929518 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
28929463 GCTAAAAAAT
28929473 GGACAGCATTTAAACAACATTC
1 GGACAGCA-TTAAACAACATTC
*
28929495 GGACAGCATTAACCAACATTC
1 GGACAGCATTAAACAACATTC
28929516 GGA
1 GGA
28929519 TATCATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (21 bp):
GGACAGCATTAAACAACATTC
Found at i:28929527 original size:68 final size:68
Alignment explanation
Indices: 28929355--28929553 Score: 310
Period size: 69 Copynumber: 2.9 Consensus size: 68
28929345 ATTCACAATA
* *
28929355 ATTCGGACAACAGTAA-CAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAAAC
1 ATTCGGACAGCATTAACCAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAAAC
28929419 AAC
66 AAC
* * * *
28929422 ATTCGAATAGCATTTAACCAACATTTGGGCAGCATTAGTATGCTAAAAAATGGACAGCATTTAAA
1 ATTCGGACAGCA-TTAACCAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAAA
28929487 CAAC
65 CAAC
* *
28929491 ATTCGGACAGCATTAACCAACATTCGGATATCATTAGTATGCTAAAAAATGGACAGCATTTAA
1 ATTCGGACAGCATTAACCAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAA
28929554 GCAAAATTTA
Statistics
Matches: 118, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
67 9 0.08
68 50 0.42
69 59 0.50
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (68 bp):
ATTCGGACAGCATTAACCAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAAAC
AAC
Found at i:28929571 original size:68 final size:68
Alignment explanation
Indices: 28929371--28929573 Score: 291
Period size: 68 Copynumber: 3.0 Consensus size: 68
28929361 ACAACAGTAA
*
28929371 CAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAAACAACA-TTCGAATAGCAT
1 CAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAAACAACATTTAG-ATAGCA-
28929435 TTAAC
64 TTAAC
* * ** *
28929440 CAACATTTGGGCAGCATTAGTATGCTAAAAAATGGACAGCATTTAAACAACATTCGGACAGCATT
1 CAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAAACAACATTTAGATAGCATT
28929505 AAC
66 AAC
* * * *
28929508 CAACATTCGGATATCATTAGTATGCTAAAAAATGGACAGCATTTAAGCAAAATTTAGATAGCATT
1 CAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAAACAACATTTAGATAGCATT
28929573 A
66 A
28929574 GTATGCTCAA
Statistics
Matches: 119, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
68 62 0.52
69 55 0.46
70 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (68 bp):
CAACATTCGGACAGCATTAGTATGCTAAAAAATGGACAGCATTTAAACAACATTTAGATAGCATT
AAC
Found at i:28929596 original size:26 final size:26
Alignment explanation
Indices: 28929522--28929598 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 26
28929512 ATTCGGATAT
28929522 CATTAGTATGCT-AAAAAATGGACAG
1 CATTAGTATGCTCAAAAAATGGACAG
* ** * *
28929547 CATT--TAAG--CAAAATTTAGATAG
1 CATTAGTATGCTCAAAAAATGGACAG
28929569 CATTAGTATGCTCAAAAAATGGACAG
1 CATTAGTATGCTCAAAAAATGGACAG
28929595 CATT
1 CATT
28929599 TAAACAACAT
Statistics
Matches: 37, Mismatches: 10, Indels: 9
0.66 0.18 0.16
Matches are distributed among these distances:
22 13 0.35
23 3 0.08
24 3 0.08
25 4 0.11
26 14 0.38
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (26 bp):
CATTAGTATGCTCAAAAAATGGACAG
Found at i:28929621 original size:22 final size:22
Alignment explanation
Indices: 28929589--28929642 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
28929579 CTCAAAAAAT
28929589 GGACAGCATTTAAACAACATTC
1 GGACAGCATTTAAACAACATTC
* * * *
28929611 GGACAGTATTTAACCATCTTTC
1 GGACAGCATTTAAACAACATTC
*
28929633 GGACAACATT
1 GGACAGCATT
28929643 ATTATGCTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (22 bp):
GGACAGCATTTAAACAACATTC
Found at i:28929657 original size:117 final size:115
Alignment explanation
Indices: 28929430--28929688 Score: 367
Period size: 117 Copynumber: 2.2 Consensus size: 115
28929420 ACATTCGAAT
* * **
28929430 AGCATTTAACCAACATTTGGGCAGCATTAGTATGCTAAAAAATGGACAGCATTTAAACAACATTC
1 AGCATTTAACCAAAATTAGGATAGCATTAGTATGCTAAAAAATGGACAGCATTTAAACAACATTC
* *
28929495 GGACAGCATTAACCAACATTCGGATATCATTAGTATGCTAAAAAATGGAC
66 GGACAGCATTAACCAACATTCGGACAACATTAGTATGCTAAAAAATGGAC
*
28929545 AGCATTTAAGCAAAATTTA-GATAGCATTAGTATGCTCAAAAAATGGACAGCATTTAAACAACAT
1 AGCATTTAACCAAAA-TTAGGATAGCATTAGTATGCT-AAAAAATGGACAGCATTTAAACAACAT
* * * * *
28929609 TCGGACAGTATTTAACCATCTTTCGGACAACATTATTATGCTTAAAAATGGAC
64 TCGGACAGCA-TTAACCAACATTCGGACAACATTAGTATGCTAAAAAATGGAC
*
28929662 AGCATTTAACCAACATTAGGATAGCAT
1 AGCATTTAACCAAAATTAGGATAGCAT
28929689 CTTGTCATCA
Statistics
Matches: 126, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
115 28 0.22
116 41 0.33
117 57 0.45
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (115 bp):
AGCATTTAACCAAAATTAGGATAGCATTAGTATGCTAAAAAATGGACAGCATTTAAACAACATTC
GGACAGCATTAACCAACATTCGGACAACATTAGTATGCTAAAAAATGGAC
Found at i:28930399 original size:42 final size:43
Alignment explanation
Indices: 28930307--28930399 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 43
28930297 TATCCCAAAT
** *
28930307 ATGGTCTTACATGTTATAATATATCGATGCCACTGTCCCAGAC
1 ATGGTCTTACATGAAATAATATATCGATGCCAATGTCCCAGAC
* * ** *
28930350 AGGGTCTTACATGAAATCATATA-CGATTTCAATGTCCTAGAC
1 ATGGTCTTACATGAAATAATATATCGATGCCAATGTCCCAGAC
28930392 ATGGTCTT
1 ATGGTCTT
28930400 CCACAAAATC
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
42 22 0.54
43 19 0.46
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (43 bp):
ATGGTCTTACATGAAATAATATATCGATGCCAATGTCCCAGAC
Found at i:28938273 original size:20 final size:21
Alignment explanation
Indices: 28938234--28938275 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
28938224 NNNNGATATT
* *
28938234 TATAAATATTAATTAATTAAA
1 TATAAATATAAATAAATTAAA
28938255 TATAAA-ATAAATAAATTAAA
1 TATAAATATAAATAAATTAAA
28938275 T
1 T
28938276 GGTGCCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TATAAATATAAATAAATTAAA
Found at i:28938381 original size:19 final size:19
Alignment explanation
Indices: 28938341--28938395 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
28938331 CTTGTGTTAT
* * *
28938341 AATTAAAAGA-TATTTATT
1 AATTAAATGATTATTAATA
28938359 AATTAAATGATTATTAATA
1 AATTAAATGATTATTAATA
* *
28938378 AATTATATTATTA-TAATA
1 AATTAAATGATTATTAATA
28938396 TAAAGTAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
AATTAAATGATTATTAATA
Found at i:28940640 original size:15 final size:17
Alignment explanation
Indices: 28940589--28940660 Score: 53
Period size: 16 Copynumber: 4.3 Consensus size: 17
28940579 AAAACAAATA
*
28940589 AAAAAAAGAAAGAAAAG
1 AAAAAGAGAAAGAAAAG
** *
28940606 --AAAGCCAAACGAAAAC
1 AAAAAGAGAAA-GAAAAG
28940622 AAAAAG-GAAA-AAAAG
1 AAAAAGAGAAAGAAAAG
28940637 AAAAAAGAGAAAGAGAAAG
1 -AAAAAGAGAAAGA-AAAG
28940656 AAAAA
1 AAAAA
28940661 CGCAAGGCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
15 10 0.24
16 11 0.26
17 7 0.17
18 10 0.24
19 4 0.10
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAAAGAAAAG
Found at i:28941633 original size:40 final size:40
Alignment explanation
Indices: 28941525--28941651 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
28941515 TGAGACATTG
* * **
28941525 GGTGTCAATTTACTACTTCGGATTAATTTGATGAGGCACTA
1 GGTGTCAAATTATTACTTCGGATT-ATCCGATGAGGCACTA
* * * *
28941566 GGTG-CCAA-T-TTACTTCGGTTTAGCCGATGAGGCACTG
1 GGTGTCAAATTATTACTTCGGATTATCCGATGAGGCACTA
*
28941603 GGTGTCAAATTATTACTTCGAATTATCCGATGAGGCACTA
1 GGTGTCAAATTATTACTTCGGATTATCCGATGAGGCACTA
28941643 GGTGTCAAA
1 GGTGTCAAA
28941652 CTGGTGTGTT
Statistics
Matches: 70, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
37 16 0.23
38 13 0.19
39 2 0.03
40 35 0.50
41 4 0.06
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (40 bp):
GGTGTCAAATTATTACTTCGGATTATCCGATGAGGCACTA
Found at i:28945395 original size:87 final size:87
Alignment explanation
Indices: 28945304--28945746 Score: 210
Period size: 87 Copynumber: 5.1 Consensus size: 87
28945294 CATTAGTAAC
28945304 TAAATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAAAAAAGTAAGTTTTTTTTA
1 TAAATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAAAAAAGTAAGTTTTTTTTA
28945369 AATCGTTAAATTATATTCTATG
66 AATCGTTAAATTATATTCTATG
* * * ***** * *
28945391 TAAATTAAGT-TATTAAACAAAAGATTACATAAAGAAAAG--TTG-TC-T-AAAAAA-TATG-CT
1 TAAATTAA-TAAATTAATC-TAA-ATT--AT-AATTTTGGCCTTGCTCTTAAAAAAAGTAAGTTT
** ** * * **
28945448 CATCCAAA--G-AAAATATATACCATTAGTAAC
60 TTTTTAAATCGTTAAAT-TAT---ATT-CTATG
28945478 TAAATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAAAAAAGTAAGTTTTTTTTA
1 TAAATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAAAAAAGTAAGTTTTTTTTA
28945543 AATCGTTAAATTATATTCTATG
66 AATCGTTAAATTATATTCTATG
* * * ***** * *
28945565 TAAATTAAGT-TATTAAACAAAAGATTACATAAAGAAAAG--TTG-TC-T-AAAAAA-TATG-CT
1 TAAATTAA-TAAATTAATC-TAA-ATT--AT-AATTTTGGCCTTGCTCTTAAAAAAAGTAAGTTT
** ** * * **
28945622 CATCCAAA--G-AAAATATATACCATTAGTAAC
60 TTTTTAAATCGTTAAAT-TAT---ATT-CTATG
28945652 TAAATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAAAAAAGTAAGTTTTTTTTA
1 TAAATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAAAAAAGTAAGTTTTTTTTA
28945717 AATCGTTAAATTATATTCTATG
66 AATCGTTAAATTATATTCTATG
28945739 TAAATTAA
1 TAAATTAA
28945747 GTTATTAAAC
Statistics
Matches: 240, Mismatches: 72, Indels: 88
0.60 0.18 0.22
Matches are distributed among these distances:
82 14 0.06
83 12 0.05
84 6 0.03
85 20 0.08
86 20 0.08
87 96 0.40
88 20 0.08
89 20 0.08
90 6 0.03
91 12 0.05
92 14 0.06
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.38
Consensus pattern (87 bp):
TAAATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAAAAAAGTAAGTTTTTTTTA
AATCGTTAAATTATATTCTATG
Found at i:28945467 original size:174 final size:174
Alignment explanation
Indices: 28945177--28945845 Score: 1338
Period size: 174 Copynumber: 3.8 Consensus size: 174
28945167 ATAATATACT
28945177 AAAAGTAAGTTTTTTTTAAATCGTTAAATTATATTCTATGTAAATTAAGTTATTAAACAAAAGAT
1 AAAAGTAAGTTTTTTTTAAATCGTTAAATTATATTCTATGTAAATTAAGTTATTAAACAAAAGAT
28945242 TACATAAAGAAAAGTTGTCTAAAAAATATGCTCATCCAAAGAAAATATATACCATTAGTAACTAA
66 TACATAAAGAAAAGTTGTCTAAAAAATATGCTCATCCAAAGAAAATATATACCATTAGTAACTAA
28945307 ATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAA
131 ATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAA
28945351 AAAAGTAAGTTTTTTTTAAATCGTTAAATTATATTCTATGTAAATTAAGTTATTAAACAAAAGAT
1 AAAAGTAAGTTTTTTTTAAATCGTTAAATTATATTCTATGTAAATTAAGTTATTAAACAAAAGAT
28945416 TACATAAAGAAAAGTTGTCTAAAAAATATGCTCATCCAAAGAAAATATATACCATTAGTAACTAA
66 TACATAAAGAAAAGTTGTCTAAAAAATATGCTCATCCAAAGAAAATATATACCATTAGTAACTAA
28945481 ATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAA
131 ATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAA
28945525 AAAAGTAAGTTTTTTTTAAATCGTTAAATTATATTCTATGTAAATTAAGTTATTAAACAAAAGAT
1 AAAAGTAAGTTTTTTTTAAATCGTTAAATTATATTCTATGTAAATTAAGTTATTAAACAAAAGAT
28945590 TACATAAAGAAAAGTTGTCTAAAAAATATGCTCATCCAAAGAAAATATATACCATTAGTAACTAA
66 TACATAAAGAAAAGTTGTCTAAAAAATATGCTCATCCAAAGAAAATATATACCATTAGTAACTAA
28945655 ATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAA
131 ATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAA
28945699 AAAAGTAAGTTTTTTTTAAATCGTTAAATTATATTCTATGTAAATTAAGTTATTAAACAAAAGAT
1 AAAAGTAAGTTTTTTTTAAATCGTTAAATTATATTCTATGTAAATTAAGTTATTAAACAAAAGAT
28945764 TACATAAAGAAAAGTTGTCTAAAAAATATGCTCATCCAAAGAAAATATATACCATTAGTAACTAA
66 TACATAAAGAAAAGTTGTCTAAAAAATATGCTCATCCAAAGAAAATATATACCATTAGTAACTAA
28945829 ATTAATAAATTAATCTA
131 ATTAATAAATTAATCTA
28945846 TATGATTTTA
Statistics
Matches: 495, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 495 1.00
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.36
Consensus pattern (174 bp):
AAAAGTAAGTTTTTTTTAAATCGTTAAATTATATTCTATGTAAATTAAGTTATTAAACAAAAGAT
TACATAAAGAAAAGTTGTCTAAAAAATATGCTCATCCAAAGAAAATATATACCATTAGTAACTAA
ATTAATAAATTAATCTAAATTATAATTTTGGCCTTGCTCTTAAA
Found at i:28946758 original size:111 final size:112
Alignment explanation
Indices: 28946615--28946844 Score: 437
Period size: 111 Copynumber: 2.1 Consensus size: 112
28946605 ATATTAATAT
28946615 ATAATTAGTATAATGATTCTGTTTTAATTAAATAAATTTAGATTTAAAATTAAATTACTATGATA
1 ATAATTAGTATAATGATTCTGTTTTAATTAAATAAATTTAGATTTAAAATTAAATTACTATGATA
28946680 AATTTATATAAATTATGAATTTAATTGAAATATGAT-AAAAAAATTA
66 AATTTATATAAATTATGAATTTAATTGAAATATGATAAAAAAAATTA
28946726 ATAATTAGTATAATGATTCTGTTTTTAA-TAAATAAATTTAGATTTAAAATTAAATTACTATGAT
1 ATAATTAGTATAATGATTCTG-TTTTAATTAAATAAATTTAGATTTAAAATTAAATTACTATGAT
28946790 AAATTTATATAAATTATGAATTTAATTGAAATATGATAAAAAAAATTA
65 AAATTTATATAAATTATGAATTTAATTGAAATATGATAAAAAAAATTA
28946838 ATAATTA
1 ATAATTA
28946845 AGATATATCA
Statistics
Matches: 117, Mismatches: 0, Indels: 3
0.98 0.00 0.03
Matches are distributed among these distances:
111 94 0.80
112 23 0.20
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (112 bp):
ATAATTAGTATAATGATTCTGTTTTAATTAAATAAATTTAGATTTAAAATTAAATTACTATGATA
AATTTATATAAATTATGAATTTAATTGAAATATGATAAAAAAAATTA
Found at i:28951859 original size:21 final size:21
Alignment explanation
Indices: 28951835--28951895 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
28951825 TATATTATAT
28951835 AAAATGCGTATGTTCATGAAA
1 AAAATGCGTATGTTCATGAAA
** * *
28951856 AAAATAAGTAT-AT-AT--AT
1 AAAATGCGTATGTTCATGAAA
28951873 AAAATGCGTATGTTCATGAAA
1 AAAATGCGTATGTTCATGAAA
28951894 AA
1 AA
28951896 TAATAAGTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
17 10 0.36
18 1 0.04
19 4 0.14
20 1 0.04
21 12 0.43
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
AAAATGCGTATGTTCATGAAA
Found at i:28951877 original size:38 final size:40
Alignment explanation
Indices: 28951825--28951906 Score: 150
Period size: 38 Copynumber: 2.1 Consensus size: 40
28951815 AATTAGAATA
28951825 TATATTATATAAAATGCGTATGTTCATGAAAAA-AATAAG
1 TATATTATATAAAATGCGTATGTTCATGAAAAATAATAAG
28951864 TATA-TATATAAAATGCGTATGTTCATGAAAAATAATAAG
1 TATATTATATAAAATGCGTATGTTCATGAAAAATAATAAG
28951903 TATA
1 TATA
28951907 GTAATAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 28 0.67
39 14 0.33
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (40 bp):
TATATTATATAAAATGCGTATGTTCATGAAAAATAATAAG
Found at i:28954221 original size:24 final size:24
Alignment explanation
Indices: 28954194--28954256 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
28954184 AATCAGACTG
*
28954194 CCGCTTTTTTGGCGTCGACTATAA
1 CCGCTTTATTGGCGTCGACTATAA
28954218 CCGCTTTATTGGCGTCGACTATAA
1 CCGCTTTATTGGCGTCGACTATAA
28954242 CCGCTTTATTGGCGT
1 CCGCTTTATTGGCGT
28954257 ACTTCGCAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (24 bp):
CCGCTTTATTGGCGTCGACTATAA
Found at i:28959029 original size:12 final size:12
Alignment explanation
Indices: 28959012--28959036 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28959002 TCATGAGGAC
28959012 CAATCTCAACCT
1 CAATCTCAACCT
28959024 CAATCTCAACCT
1 CAATCTCAACCT
28959036 C
1 C
28959037 GTCAAGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (12 bp):
CAATCTCAACCT
Found at i:28961018 original size:3 final size:3
Alignment explanation
Indices: 28961010--28961042 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
28961000 ACTGTTAAGG
28961010 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28961043 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28965896 original size:35 final size:32
Alignment explanation
Indices: 28965857--28965937 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 32
28965847 TAAGCCAATA
* * *
28965857 AAGATATAGTCGTAGGTTTTTTCTTTGAGGGCGAC
1 AAGATATAGTCATAGG-CTTTT-TTT-AGGACGAC
*
28965892 AAGATGTAGTCATAGGCTTTTTTTAGGACGAC
1 AAGATATAGTCATAGGCTTTTTTTAGGACGAC
*
28965924 AAGATATTGTCATA
1 AAGATATAGTCATA
28965938 TATGAGTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
32 19 0.47
33 3 0.08
34 4 0.10
35 14 0.35
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (32 bp):
AAGATATAGTCATAGGCTTTTTTTAGGACGAC
Found at i:28976893 original size:14 final size:14
Alignment explanation
Indices: 28976849--28976894 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
28976839 TCTAGGTCAA
*
28976849 TTTAGGATTAAGGG
1 TTTAGGGTTAAGGG
* * *
28976863 TTAAGGGTTTAGTG
1 TTTAGGGTTAAGGG
28976877 TTTAGGGTTAAGGG
1 TTTAGGGTTAAGGG
28976891 TTTA
1 TTTA
28976895 AGGTACCCTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (14 bp):
TTTAGGGTTAAGGG
Found at i:28979700 original size:19 final size:19
Alignment explanation
Indices: 28979678--28979718 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
28979668 TTTATTAGTA
28979678 AACAATTTTTAAATTACAT
1 AACAATTTTTAAATTACAT
*
28979697 AACAATTTTTAAATTATAT
1 AACAATTTTTAAATTACAT
28979716 AAC
1 AAC
28979719 TTACATAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
AACAATTTTTAAATTACAT
Found at i:28979774 original size:17 final size:18
Alignment explanation
Indices: 28979754--28979787 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28979744 ACATTTTTAA
28979754 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
28979771 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
28979788 TTATCAATCA
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:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:28979812 original size:25 final size:25
Alignment explanation
Indices: 28979784--28979834 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
28979774 ATTTTTTTCA
28979784 AAATTTATCAATCATAGCATAACTT
1 AAATTTATCAATCATAGCATAACTT
*
28979809 AAATTTATCAATCATATCATAACTT
1 AAATTTATCAATCATAGCATAACTT
28979834 A
1 A
28979835 TATATAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.37
Consensus pattern (25 bp):
AAATTTATCAATCATAGCATAACTT
Found at i:28979941 original size:19 final size:19
Alignment explanation
Indices: 28979899--28979942 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
28979889 TATAAACTTG
*
28979899 CATAACAATTTTTAAATTA
1 CATAACAATTTTTAAAGTA
28979918 CATAACAATTTTTAAAGTA
1 CATAACAATTTTTAAAGTA
*
28979937 TATAAC
1 CATAAC
28979943 TTACATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (19 bp):
CATAACAATTTTTAAAGTA
Found at i:28982911 original size:21 final size:21
Alignment explanation
Indices: 28982886--28982946 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
28982876 AACTTAAAAC
* *
28982886 AGAGGCAGCAGTGAGGGAAGA
1 AGAGGCAGCAGCGAGAGAAGA
*
28982907 AGAGGCTA-CAGCGAGAGAAGC
1 AGAGGC-AGCAGCGAGAGAAGA
*
28982928 AGAGGCCGCAGCGAGAGAA
1 AGAGGCAGCAGCGAGAGAA
28982947 CCAGCGATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.43, T:0.03
Consensus pattern (21 bp):
AGAGGCAGCAGCGAGAGAAGA
Found at i:28983464 original size:42 final size:42
Alignment explanation
Indices: 28983403--28983543 Score: 203
Period size: 42 Copynumber: 3.4 Consensus size: 42
28983393 TGAAATAAGA
* **
28983403 GCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTGACCAAGC
1 GCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTCCCAAGC
* *
28983445 GCCGCTATAGAACATTACTTTTAGTGGCGTTTTTTCCCAAGC
1 GCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTCCCAAGC
*
28983487 GCCGCTAAAGAACATGAAC-TTTAGCGGCGTTTTTTCCCAAGC
1 GCCGCTAAAGAACAT-TACTTTTAGCGGCGTTTTTTCCCAAGC
*
28983529 GCAGCTAAAGAACAT
1 GCCGCTAAAGAACAT
28983544 GATCGTTCGC
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 87 0.98
43 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (42 bp):
GCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTTCCCAAGC
Found at i:28983696 original size:43 final size:42
Alignment explanation
Indices: 28983567--28983735 Score: 248
Period size: 42 Copynumber: 4.0 Consensus size: 42
28983557 ATTTTCTTCC
*
28983567 CATGTTCTTTAGCGGCGTTTTTTCCTAAGCCCCGCTAAAGAA
1 CATGTTCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAA
*
28983609 CATGATCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAA
1 CATGTTCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAA
* *
28983651 CATGTTCTTTAGCGGCGTTTATTTTCTTAGCGCCGCTAAAGAA
1 CATGTTCTTTAGCGGCGTTT-TTTCCTAAGCGCCGCTAAAGAA
* * *
28983694 CATGTTCTTTAACGGCGTTTTTTTCTGTAAGCGCCGCAAAAG
1 CATGTTCTTTAGCGGCG-TTTTTTC-CTAAGCGCCGCTAAAG
28983736 TTAGCGACGT
Statistics
Matches: 114, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
42 59 0.52
43 39 0.34
44 16 0.14
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (42 bp):
CATGTTCTTTAGCGGCGTTTTTTCCTAAGCGCCGCTAAAGAA
Found at i:28983710 original size:85 final size:86
Alignment explanation
Indices: 28983567--28983735 Score: 252
Period size: 85 Copynumber: 2.0 Consensus size: 86
28983557 ATTTTCTTCC
*
28983567 CATGTTCTTTAGCGGCGTTTTTTCCTAAGCCCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTT
1 CATGTTCTTTAGCGGCGTTTTTTCCTAAGCCCCGCTAAAGAACATGATCTTTAACGGCGTTTTTT
*
28983631 TC-CTAAGCGCCGCTAAAGAA
66 TCTCTAAGCGCCGCAAAAGAA
* * * *
28983651 CATGTTCTTTAGCGGCGTTTATTTTCTTAGCGCCGCTAAAGAACATGTTCTTTAACGGCGTTTTT
1 CATGTTCTTTAGCGGCGTTT-TTTCCTAAGCCCCGCTAAAGAACATGATCTTTAACGGCGTTTTT
*
28983716 TTCTGTAAGCGCCGCAAAAG
65 TTCTCTAAGCGCCGCAAAAG
28983736 TTAGCGACGT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
84 20 0.27
85 34 0.45
86 7 0.09
87 14 0.19
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (86 bp):
CATGTTCTTTAGCGGCGTTTTTTCCTAAGCCCCGCTAAAGAACATGATCTTTAACGGCGTTTTTT
TCTCTAAGCGCCGCAAAAGAA
Found at i:28984204 original size:12 final size:12
Alignment explanation
Indices: 28984183--28984213 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28984173 TTTTTCCGCA
28984183 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
28984195 AAAAAGAAAAAG
1 AAAAAAAAAAAG
28984207 AAAAAAA
1 AAAAAAA
28984214 GAAGATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:28988854 original size:7 final size:7
Alignment explanation
Indices: 28988842--28988866 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28988832 TTTCACCCAT
28988842 GCTTAAA
1 GCTTAAA
28988849 GCTTAAA
1 GCTTAAA
28988856 GCTTAAA
1 GCTTAAA
28988863 GCTT
1 GCTT
28988867 GGCAAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (7 bp):
GCTTAAA
Found at i:28988948 original size:5 final size:6
Alignment explanation
Indices: 28988933--28988966 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
28988923 AGTTTCACAA
28988933 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
28988967 AACCCTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:28988967 original size:18 final size:18
Alignment explanation
Indices: 28988933--28988966 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
28988923 AGTTTCACAA
28988933 AAAAAGAAAAAGAAAAAG
1 AAAAAGAAAAAGAAAAAG
28988951 AAAAAG-AAAAGAAAAA
1 AAAAAGAAAAAGAAAAA
28988967 AACCCTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAAAG
Found at i:28991755 original size:18 final size:18
Alignment explanation
Indices: 28991732--28991767 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
28991722 GAAATTTATA
28991732 TTAAAAT-CCTAGAAGGAT
1 TTAAAATCCCTA-AAGGAT
28991750 TTAAAATCCCTAAAGGAT
1 TTAAAATCCCTAAAGGAT
28991768 ATAGAGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (18 bp):
TTAAAATCCCTAAAGGAT
Found at i:29000349 original size:23 final size:24
Alignment explanation
Indices: 29000312--29000358 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
29000302 GTAAAAAGGG
29000312 AGGGAAAGTAAAAAAAAAATTGAAA
1 AGGGAAAGT-AAAAAAAAATTGAAA
29000337 AGGGAAAGT-AAAAAAAATTGAA
1 AGGGAAAGTAAAAAAAAATTGAA
29000359 TAGAAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 13 0.59
25 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.13
Consensus pattern (24 bp):
AGGGAAAGTAAAAAAAAATTGAAA
Found at i:29001544 original size:8 final size:8
Alignment explanation
Indices: 29001533--29001605 Score: 71
Period size: 8 Copynumber: 9.2 Consensus size: 8
29001523 TCATATAAAC
*
29001533 ATAAAAAT
1 ATAATAAT
29001541 ATAATAAT
1 ATAATAAT
29001549 ATAATAAT
1 ATAATAAT
* *
29001557 ATGAACAAC
1 AT-AATAAT
29001566 ATAATAATT
1 ATAATAA-T
*
29001575 ATATTAAT
1 ATAATAAT
29001583 -TAA-AAT
1 ATAATAAT
29001589 A-AATAAT
1 ATAATAAT
29001596 ATAATAAT
1 ATAATAAT
29001604 AT
1 AT
29001606 TTTCTTACCA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
6 5 0.09
7 6 0.11
8 30 0.57
9 12 0.23
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (8 bp):
ATAATAAT
Found at i:29001971 original size:22 final size:22
Alignment explanation
Indices: 29001926--29001974 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
29001916 TTAGGATAGA
* **
29001926 AAATTAAGAGAAAAAGAGTTTG
1 AAATTAAGAGAAAAAAAGGATG
*
29001948 AAATTGAGAGAAAAAAAGGATG
1 AAATTAAGAGAAAAAAAGGATG
29001970 AAATT
1 AAATT
29001975 TAATAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.20
Consensus pattern (22 bp):
AAATTAAGAGAAAAAAAGGATG
Found at i:29003593 original size:12 final size:10
Alignment explanation
Indices: 29003564--29003603 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
29003554 TCGAAAATAG
29003564 TTAAAATTAA
1 TTAAAATTAA
*
29003574 TCAAAATTAA
1 TTAAAATTAA
29003584 CTATAAAATTAA
1 -T-TAAAATTAA
29003596 TTAAAATT
1 TTAAAATT
29003604 CATCATGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 16 0.62
11 2 0.08
12 8 0.31
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAAATTAA
Found at i:29008919 original size:44 final size:44
Alignment explanation
Indices: 29008871--29009667 Score: 1533
Period size: 44 Copynumber: 18.1 Consensus size: 44
29008861 ATTTTAATCC
*
29008871 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29008915 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29008959 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009003 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009047 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009091 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009135 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009179 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009223 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009267 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009311 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009355 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009399 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009443 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009487 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009531 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
29009575 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
* * * *
29009619 GCTCCGCTGTAATCTCAAGGAGATAAGATTTCTGGCTTC-GATCT
1 GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAG-TCT
29009663 GCTCC
1 GCTCC
29009668 ACTATTGTTT
Statistics
Matches: 747, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
43 1 0.00
44 746 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (44 bp):
GCTCCGCTGTAATCTCAGGGAGATAGGATTACTAGCTTCAGTCT
Found at i:29019054 original size:20 final size:20
Alignment explanation
Indices: 29019037--29019075 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
29019027 TCTTTCAACC
29019037 GCTCT-ATTT-TCTTTTCAA
1 GCTCTAATTTCTCTTTTCAA
29019055 GCTCTAAATTTCTCTTTTCAA
1 GCTCT-AATTTCTCTTTTCAA
29019076 AATCTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (20 bp):
GCTCTAATTTCTCTTTTCAA
Found at i:29021097 original size:27 final size:26
Alignment explanation
Indices: 29021067--29021117 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
29021057 ATGAAATTCT
*
29021067 TACAAA-CAATATGATTGATTAACAATA
1 TACAAAGCAA-ATGA-TGAATAACAATA
29021094 TACAAAGCAAATGATGAATAACAA
1 TACAAAGCAAATGATGAATAACAA
29021118 ATTAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 10 0.45
28 3 0.14
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.24
Consensus pattern (26 bp):
TACAAAGCAAATGATGAATAACAATA
Found at i:29026641 original size:8 final size:8
Alignment explanation
Indices: 29026627--29026660 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
29026617 GACTGAATTG
29026627 AATGATTA
1 AATGATTA
*
29026635 TATGATTA
1 AATGATTA
29026643 AATGATTA
1 AATGATTA
29026651 AATGAGTTA
1 AATGA-TTA
29026660 A
1 A
29026661 TTTTGAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (8 bp):
AATGATTA
Found at i:29031323 original size:40 final size:39
Alignment explanation
Indices: 29031279--29031389 Score: 170
Period size: 40 Copynumber: 2.8 Consensus size: 39
29031269 TTTGGACAAA
*
29031279 AAAACGCCGCTAAAAATCCAGCATTAGCGGCGCTTTACAT
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTAC-T
*
29031319 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTACT
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTACT
*
29031358 AATAGCGCCGCTAAAAAT-GAGCATTAGCGGCG
1 AA-AACGCCGCTAAAAATCGAGCATTAGCGGCG
29031390 TTTTTTGTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
39 17 0.26
40 49 0.74
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTACT
Found at i:29031508 original size:41 final size:41
Alignment explanation
Indices: 29031449--29031904 Score: 702
Period size: 41 Copynumber: 11.1 Consensus size: 41
29031439 TGACCTTTTG
* *
29031449 GGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
* ** *
29031490 GGGCTTTAACGGTTTTTTTGAAGAAGCGCCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
29031531 GGGCTTTAGCGGCGTTTTT-AATGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAA-GAAGCGCCGCTAATGCTCA
*
29031572 GGGCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
* *
29031613 AGGCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
*
29031654 GGGCTTTACCGGCGTTTTTGAAGAAGCGCCGCTAATGC-CA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
*
29031694 GGGCTTTAGCGGTGTTTTTGAAGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
29031735 GGGCTTTAGCGGCGTTTTTGATA-AAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGA-AGAAGCGCCGCTAATGCTCA
* *
29031776 GGGTTTTAGCGGCGTTTTTGAAGAAGCGCCGCGAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
* * *
29031817 GGGATTTAACGGCGCTTTTGAAGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
* * *
29031858 AGGTTTTAGCGGTGTTTTTGAAGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
29031899 GGGCTT
1 GGGCTT
29031905 CAAATATTTT
Statistics
Matches: 381, Mismatches: 29, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
40 41 0.11
41 337 0.88
42 3 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
Found at i:29031721 original size:245 final size:245
Alignment explanation
Indices: 29031449--29031904 Score: 736
Period size: 245 Copynumber: 1.9 Consensus size: 245
29031439 TGACCTTTTG
* **
29031449 GGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGCTTAGGGCTTTAACGGTTTTTTTGA-AG
1 GGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGGGCTTTAACGGCGTTTTTGATA-
* * *
29031513 AAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTT-AATGAAGCGCCGCTAATGCTCAGGGCT
65 AAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAA-GAAGCGCCGCGAATGCTCAGGGAT
* * * *
29031577 TTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTTGAATAAGCGC
129 TTAACGGCGCTTTTGAAGAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTTGAAGAAGCGC
29031642 CGCTAATGCTCAGGGCTTTACCGGCGTTTTTGAAGAAGCGCCGCTAATGCCA
194 CGCTAATGCTCAGGGCTTTACCGGCGTTTTTGAAGAAGCGCCGCTAATGCCA
* * *
29031694 GGGCTTTAGCGGTGTTTTTGAAGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGATAA
1 GGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGGGCTTTAACGGCGTTTTTGATAA
*
29031759 AGCGCCGCTAATGCTCAGGGTTTTAGCGGCGTTTTTGAAGAAGCGCCGCGAATGCTCAGGGATTT
66 AGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCGAATGCTCAGGGATTT
* *
29031824 AACGGCGCTTTTGAAGAAGCGCCGCTAATGCTCAAGGTTTTAGCGGTGTTTTTGAAGAAGCGCCG
131 AACGGCGCTTTTGAAGAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTTGAAGAAGCGCCG
29031889 CTAATGCTCAGGGCTT
196 CTAATGCTCAGGGCTT
29031905 CAAATATTTT
Statistics
Matches: 193, Mismatches: 16, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
245 190 0.98
246 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (245 bp):
GGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGGGCTTTAACGGCGTTTTTGATAA
AGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCGAATGCTCAGGGATTT
AACGGCGCTTTTGAAGAAGCGCCGCTAATGCTCAAGGCTTTAGCGGCGTTTTTGAAGAAGCGCCG
CTAATGCTCAGGGCTTTACCGGCGTTTTTGAAGAAGCGCCGCTAATGCCA
Found at i:29032582 original size:21 final size:20
Alignment explanation
Indices: 29032536--29032582 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
29032526 TGTAAAAGAG
29032536 GGGTTAGCGGTTAGCGGTTA
1 GGGTTAGCGGTTAGCGGTTA
*
29032556 GAGGTTAG-GAGTTAGGGGTTTA
1 G-GGTTAGCG-GTTAGCGG-TTA
29032578 GGGTT
1 GGGTT
29032583 TAGGGTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 2 0.09
21 17 0.74
22 4 0.17
ACGTcount: A:0.17, C:0.04, G:0.47, T:0.32
Consensus pattern (20 bp):
GGGTTAGCGGTTAGCGGTTA
Found at i:29037018 original size:42 final size:42
Alignment explanation
Indices: 29036807--29037160 Score: 429
Period size: 43 Copynumber: 8.3 Consensus size: 42
29036797 NNNNNNNNNN
** *
29036807 TAGCGGCGTTTGTGTCAAAAGCGCCGCTAAAGGTCGTGGTCTA
1 TAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGTCCTGGTCTA
* ** *
29036850 TAGTGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCGTGGTCTA
1 TAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGTCCTGGTCTA
* ** *
29036893 TAGTGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCGTGGTCTA
1 TAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGTCCTGGTCTA
* * *
29036936 TAGCGGTGTTTGTTGGTAAAGCGCCGCTAAAGGTCGTGGTCTA
1 TAGCGGCGTTTG-TGGGAAAGCGCCGCTAAAGGTCCTGGTCTA
* *
29036979 TAGCGGCGTTTGTGGGGAAGCGCCGCTAAAGGTCCTGGTCTT
1 TAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCCTGGTCTA
* * * * *
29037021 TAGTGGCGTTTGTGGGGAAGCGCCGTTAAAGGTCCTGTTCTT
1 TAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCCTGGTCTA
* * *
29037063 TCGCGGCGTTTGTAGGAAAGCGCCGCTAAAGGTCCTGGTCTT
1 TAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCCTGGTCTA
* *
29037105 TAGCGGCGTTTGTGGGTAAAGCGCCGCTAAAGGTCCTAGTCTT
1 TAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCCTGGTCTA
29037148 TAGCGGCGTTTGT
1 TAGCGGCGTTTGT
29037161 CGGTAAAAAC
Statistics
Matches: 286, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
42 115 0.40
43 169 0.59
44 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.28
Consensus pattern (42 bp):
TAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCCTGGTCTA
Found at i:29037280 original size:22 final size:22
Alignment explanation
Indices: 29037252--29037294 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
29037242 TAGTAGTGCT
*
29037252 AAAAAGCGCCTCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAGGCCTA
29037274 AAAAAGCGCCGCTAAAGGCCT
1 AAAAAGCGCCGCTAAAGGCCT
29037295 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.28, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAGGCCTA
Found at i:29047021 original size:15 final size:15
Alignment explanation
Indices: 29047001--29047040 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
29046991 AACCGATGAC
29047001 GCAAATCGACAGAGA
1 GCAAATCGACAGAGA
29047016 GCAAATCGACAGAGA
1 GCAAATCGACAGAGA
29047031 GCAAATCGAC
1 GCAAATCGAC
29047041 CGAAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.45, C:0.23, G:0.25, T:0.07
Consensus pattern (15 bp):
GCAAATCGACAGAGA
Found at i:29048427 original size:43 final size:43
Alignment explanation
Indices: 29048374--29048491 Score: 168
Period size: 43 Copynumber: 2.7 Consensus size: 43
29048364 TTATCTTTAA
* * *
29048374 AAACACCGCTAAAGGTCATGTTCTTTAGCGGTGCTTTA-T-ACAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC--TACTCACAC
*
29048417 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTACTCCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTACTCACAC
29048460 AAACGCCGCTAAAGATCATGTTCTTTAGCGGC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGC
29048492 AATTTTTCAC
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
41 2 0.03
42 1 0.01
43 66 0.96
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTACTCACAC
Found at i:29048968 original size:66 final size:66
Alignment explanation
Indices: 29048857--29048994 Score: 233
Period size: 66 Copynumber: 2.1 Consensus size: 66
29048847 CTCTCGCTGC
* *
29048857 AACCTCTGCTTCTCTGGATGCCGCATTAGCTTTAAGTTGTCGCTGGAGTTCTTCATATTTCTTTT
1 AACCTCTGCTTCTCTCGATGCCGCATTAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTT
29048922 G
66 G
*
29048923 AACCTCTGCTTCTCTCGCTGCCGCATCT-GCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTT
1 AACCTCTGCTTCTCTCGATGCCGCAT-TAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTT
29048987 TG
65 TG
29048989 AACCTC
1 AACCTC
29048995 AACTGTGGTC
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
66 67 0.99
67 1 0.01
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.41
Consensus pattern (66 bp):
AACCTCTGCTTCTCTCGATGCCGCATTAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTT
G
Found at i:29061776 original size:41 final size:41
Alignment explanation
Indices: 29061725--29061947 Score: 304
Period size: 41 Copynumber: 5.4 Consensus size: 41
29061715 GCGTTTTTTA
* * * *
29061725 AAAAAGCGCCGCTAAAGGCCTGAGA-ATTAGCGGCGCATCCAT
1 AAAAA-CGCCGCTAAAGCCCAGA-ACATTAGCGGCGCTTACAT
* * * *
29061767 AAAAACGCCGCTAAATCCCAGAATATTAGCGGCGCATAAAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
*
29061808 AAAAACGCCGCTAAAGCCCAGAACATTAGAGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
* *
29061849 AAAAACGCCGCTAAAGCACATAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
*
29061890 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTCCAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
*
29061931 AAAATCGCCGCTAAAGC
1 AAAAACGCCGCTAAAGC
29061948 TCCCGAAAAG
Statistics
Matches: 163, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
40 1 0.01
41 157 0.96
42 5 0.03
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.15
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
Found at i:29067345 original size:11 final size:10
Alignment explanation
Indices: 29067316--29067387 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
29067306 ATACCTTATT
* *
29067316 TTTCTATTTT
1 TTTCTCTTTC
29067326 TTTCTCTTTC
1 TTTCTCTTTC
29067336 TTTCTCCTTTC
1 TTTCT-CTTTC
*
29067347 --TCTATTCTC
1 TTTCTCTT-TC
29067356 TTTCTCTTTC
1 TTTCTCTTTC
* *
29067366 TCTCTTTTTC
1 TTTCTCTTTC
29067376 TTT-TCTTT-
1 TTTCTCTTTC
29067384 TTTC
1 TTTC
29067388 GGCACCGCCC
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
8 5 0.10
9 9 0.18
10 25 0.51
11 10 0.20
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTCTCTTTC
Found at i:29067362 original size:6 final size:6
Alignment explanation
Indices: 29067326--29067368 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
29067316 TTTCTATTTT
29067326 TTTCTC -TT-TC TTTCTCC TTTCTC TATTCTC TTTCTC TTTCTC T
1 TTTCTC TTTCTC TTTCT-C TTTCTC T-TTCTC TTTCTC TTTCTC T
29067369 CTTTTTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 2 0.06
5 4 0.12
6 15 0.45
7 12 0.36
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTCTC
Found at i:29067369 original size:14 final size:14
Alignment explanation
Indices: 29067334--29067378 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
29067324 TTTTTCTCTT
29067334 TCTTTCTC-CTTTC
1 TCTTTCTCTCTTTC
*
29067347 TCTAT-TCTCTTTC
1 TCTTTCTCTCTTTC
*
29067360 TCTTTCTCTCTTTT
1 TCTTTCTCTCTTTC
29067374 TCTTT
1 TCTTT
29067379 TCTTTTTTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 2 0.07
13 13 0.48
14 12 0.44
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTTCTCTCTTTC
Found at i:29067382 original size:19 final size:19
Alignment explanation
Indices: 29067332--29067383 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
29067322 TTTTTTTCTC
29067332 TTTCTTTCTCCTTTCTCTAT
1 TTTCTTTCT-CTTTCTCTAT
* *
29067352 TCTCTTTCTCTTTCTCTCTT
1 TTTCTTTCTCTTTCTCT-AT
29067372 TTTCTTT-TCTTT
1 TTTCTTTCTCTTT
29067384 TTTCGGCACC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTCTTTCTCTTTCTCTAT
Found at i:29073096 original size:11 final size:11
Alignment explanation
Indices: 29073080--29073122 Score: 68
Period size: 11 Copynumber: 3.7 Consensus size: 11
29073070 AATAACTTCG
29073080 TAAATATTTAA
1 TAAATATTTAA
29073091 TAAATATTTAA
1 TAAATATTTAA
29073102 TGTAAATATTTAA
1 --TAAATATTTAA
29073115 TAAATATT
1 TAAATATT
29073123 ACTGGTCCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.63
13 11 0.37
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
TAAATATTTAA
Found at i:29073109 original size:13 final size:13
Alignment explanation
Indices: 29073079--29073115 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
29073069 TAATAACTTC
29073079 GTAAATATTTAA-
1 GTAAATATTTAAT
29073091 -TAAATATTTAAT
1 GTAAATATTTAAT
29073103 GTAAATATTTAAT
1 GTAAATATTTAAT
29073116 AAATATTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
13 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (13 bp):
GTAAATATTTAAT
Found at i:29074716 original size:15 final size:15
Alignment explanation
Indices: 29074696--29074725 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29074686 GGGTTACAAG
29074696 GCATTACCTAGCACA
1 GCATTACCTAGCACA
29074711 GCATTACCTAGCACA
1 GCATTACCTAGCACA
29074726 ACACAGTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (15 bp):
GCATTACCTAGCACA
Found at i:29075795 original size:30 final size:30
Alignment explanation
Indices: 29075761--29075936 Score: 185
Period size: 30 Copynumber: 5.7 Consensus size: 30
29075751 ATCCAATGCT
29075761 CAAAT-AATTTCAGCAATATATATCCATATA
1 CAAATCAA-TTCAGCAATATATATCCATATA
* * *
29075791 CAAATCAAGTCAGCAATGTATATCGATATA
1 CAAATCAATTCAGCAATATATATCCATATA
* *
29075821 CAAATCAATTTAGCAATGTATATCCATATA
1 CAAATCAATTCAGCAATATATATCCATATA
* *
29075851 CAAATCAATTCGGCTATATATATATATCTATATA
1 CAAATCAATTCAGC---A-ATATATATCCATATA
* *
29075885 TAAATTAATTC-GACAATATATATCCATATA
1 CAAATCAATTCAG-CAATATATATCCATATA
* *
29075915 CAAATCAATTCGGAAATATATA
1 CAAATCAATTCAGCAATATATA
29075937 AAACATATAC
Statistics
Matches: 123, Mismatches: 16, Indels: 14
0.80 0.10 0.09
Matches are distributed among these distances:
30 94 0.76
31 4 0.03
33 2 0.02
34 23 0.19
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (30 bp):
CAAATCAATTCAGCAATATATATCCATATA
Found at i:29075912 original size:64 final size:63
Alignment explanation
Indices: 29075772--29075936 Score: 196
Period size: 64 Copynumber: 2.7 Consensus size: 63
29075762 AAATAATTTC
* * * *
29075772 AGCAATATATATCCATATACAAATCAAGTCAGC--A-ATGTATATCGATATACAAATCAATTT
1 AGCAATATATATCCATATACAAATCAATTCGGCATATATATATATCGATATACAAATCAATTG
* * * *
29075832 AGCAATGTATATCCATATACAAATCAATTCGGCTATATATATATATCTATATATAAATTAATTCG
1 AGCAATATATATCCATATACAAATCAATTCGGC-ATATATATATATCGATATACAAATCAATT-G
*
29075897 A-CAATATATATCCATATACAAATCAATTCGG-AAATATATA
1 AGCAATATATATCCATATACAAATCAATTCGGCATATATATA
29075937 AAACATATAC
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
60 30 0.33
62 8 0.09
63 1 0.01
64 50 0.56
65 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (63 bp):
AGCAATATATATCCATATACAAATCAATTCGGCATATATATATATCGATATACAAATCAATTG
Found at i:29083023 original size:62 final size:60
Alignment explanation
Indices: 29082872--29083016 Score: 182
Period size: 60 Copynumber: 2.4 Consensus size: 60
29082862 ATCCAATGCT
* *
29082872 CAAATAAATTCGGCAATATATATCCATATACAAATCAATTCAGCAATGTATATCCATATA
1 CAAATTAATTCGGCAATATATATCCATATACAAATCAATTCAGCAATATATATCCATATA
** * * * * *
29082932 CAAATTAATTTAGCAATGTATATCCATATACAAATCAATTCGGTTATTTATATATCTATATA
1 CAAATTAATTCGGCAATATATATCCATATACAAATCAATTCAG-CA-ATATATATCCATATA
*
29082994 TAAATTAATTCGGCAATATATAT
1 CAAATTAATTCGGCAATATATAT
29083017 ATATATATAT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
60 38 0.54
61 1 0.01
62 31 0.44
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (60 bp):
CAAATTAATTCGGCAATATATATCCATATACAAATCAATTCAGCAATATATATCCATATA
Found at i:29083025 original size:30 final size:30
Alignment explanation
Indices: 29082872--29083016 Score: 164
Period size: 30 Copynumber: 4.8 Consensus size: 30
29082862 ATCCAATGCT
*
29082872 CAAATAAATTCGGCAATATATATCCATATA
1 CAAATCAATTCGGCAATATATATCCATATA
* *
29082902 CAAATCAATTCAGCAATGTATATCCATATA
1 CAAATCAATTCGGCAATATATATCCATATA
* ** *
29082932 CAAATTAATTTAGCAATGTATATCCATATA
1 CAAATCAATTCGGCAATATATATCCATATA
* * *
29082962 CAAATCAATTCGGTTATTTATATATCTATATA
1 CAAATCAATTCGG-CA-ATATATATCCATATA
* *
29082994 TAAATTAATTCGGCAATATATAT
1 CAAATCAATTCGGCAATATATAT
29083017 ATATATATAT
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
30 72 0.74
31 2 0.02
32 23 0.24
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (30 bp):
CAAATCAATTCGGCAATATATATCCATATA
Found at i:29083026 original size:32 final size:32
Alignment explanation
Indices: 29082957--29083027 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
29082947 ATGTATATCC
* ** * *
29082957 ATATACAAATCAATTCGGTTATTTATATATCT
1 ATATATAAATCAATTCGGCAATATATATATAT
*
29082989 ATATATAAATTAATTCGGCAATATATATATAT
1 ATATATAAATCAATTCGGCAATATATATATAT
29083021 ATATATA
1 ATATATA
29083028 TCTATATACA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (32 bp):
ATATATAAATCAATTCGGCAATATATATATAT
Found at i:29086018 original size:16 final size:16
Alignment explanation
Indices: 29085997--29086027 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29085987 CTATGCATGC
*
29085997 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
29086013 AAAATACAAAAGACA
1 AAAATACAAAAGACA
29086028 TAATAATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:29092701 original size:34 final size:34
Alignment explanation
Indices: 29092655--29092735 Score: 126
Period size: 34 Copynumber: 2.4 Consensus size: 34
29092645 TACTTCATCA
*
29092655 AAATTAAATTTTCTTAAAATCACTTAGATTTTCC
1 AAATTAAATTTTCTTAAAATCACTTAGATTTACC
* *
29092689 AAATTAATTTTTCTTAAAATCATTTAGATTTACC
1 AAATTAAATTTTCTTAAAATCACTTAGATTTACC
*
29092723 AAAATAAATTTTC
1 AAATTAAATTTTC
29092736 AAGAAAATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.44
Consensus pattern (34 bp):
AAATTAAATTTTCTTAAAATCACTTAGATTTACC
Found at i:29093828 original size:16 final size:16
Alignment explanation
Indices: 29093807--29093837 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29093797 CTATGCATGC
29093807 AAAATAAAAAAGACAG
1 AAAATAAAAAAGACAG
29093823 AAAATAAAAAAGACA
1 AAAATAAAAAAGACA
29093838 TAATAGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.06, G:0.10, T:0.06
Consensus pattern (16 bp):
AAAATAAAAAAGACAG
Found at i:29115569 original size:24 final size:24
Alignment explanation
Indices: 29115535--29115581 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
29115525 CTTTAAAAAA
29115535 TTAAAAATTTCTAGAATTTTTTTC
1 TTAAAAATTTCTAGAATTTTTTTC
*
29115559 TTAAAATTTTCTAGAATTTTTTT
1 TTAAAAATTTCTAGAATTTTTTT
29115582 TGACTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TTAAAAATTTCTAGAATTTTTTTC
Found at i:29118959 original size:61 final size:58
Alignment explanation
Indices: 29118871--29119003 Score: 169
Period size: 61 Copynumber: 2.2 Consensus size: 58
29118861 TCCAAAAAAA
* ** *
29118871 ATATTATTTTAATAGTTTTAATATT-AAATTATATTTAATATTTATCTTATGGATAAATATT
1 ATATTAATTTAATAAATTTAATATTAAAATTA-ATCTAATATTTATC-T-T-GATAAATATT
* *
29118932 ATATTAATTTAATAAATTTAATATTAAAATTAATCTACTATTTATCTTGATAAGTATT
1 ATATTAATTTAATAAATTTAATATTAAAATTAATCTAATATTTATCTTGATAAATATT
29118990 ATATTAATTTAATA
1 ATATTAATTTAATA
29119004 TTAAAATGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
58 23 0.35
59 1 0.02
60 1 0.02
61 34 0.52
62 6 0.09
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (58 bp):
ATATTAATTTAATAAATTTAATATTAAAATTAATCTAATATTTATCTTGATAAATATT
Found at i:29119427 original size:16 final size:16
Alignment explanation
Indices: 29119406--29119436 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29119396 AAATTCTAGT
29119406 TTTTCCGCTAAACTTA
1 TTTTCCGCTAAACTTA
*
29119422 TTTTCCGCTACACTT
1 TTTTCCGCTAAACTT
29119437 TTCAAACCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.45
Consensus pattern (16 bp):
TTTTCCGCTAAACTTA
Found at i:29120137 original size:347 final size:347
Alignment explanation
Indices: 29119502--29120522 Score: 1413
Period size: 347 Copynumber: 3.0 Consensus size: 347
29119492 AGTATAAACA
29119502 AATAATCAAAATAGATTTCTCTTCTTCTTGAATGATTCGATTATATAGAAAGTGACATTATTTAG
1 AATAATCAAAATAGATTTCTCTTCTTCTTGAATGATTCGATTATATAGAAAGTGACATTATTTAG
29119567 ATTTTATGCATCTTTTGAGTTATATATGCGATTAGGTTATAATAGAAAGTGACATTCGATTATAT
66 ATTTTATGCATCTTTTGAGTTATATATGCGATTAGGTTATAATAGAAAGTGACATTCGATTATAT
29119632 ATTTTGTTATATAATTGTTATTTTATTACCAAGATTTTGGTTCTTAGGAAATAGACTGTGGACTA
131 ATTTTGTTATATAATTGTTATTTTATTACCAAGATTTTGGTTCTTAGGAAATAGACTGTGGACTA
29119697 TCATCTCCATGTAGGACTTTTTTTTTTAAAATTCATATAATTCTTGTGAAGTCGAAAACGAATAA
196 TCATCTCCATGTAGGACTTTTTTTTTTAAAATTCATATAATTCTTGTGAAGTCGAAAACGAATAA
29119762 AGGACTTAAAATGGAACGATGGTGGTTGAAGACCCAAGGAATGCCTTGTGGTGAAAAAAATTGTA
261 AGGACTTAAAATGGAACGATGGTGGTTGAAGACCCAAGGAATGCCTTGTGGTGAAAAAAATTGTA
29119827 ATTTTTGCTTTTCATTTATTTT
326 ATTTTTGCTTTTCATTTATTTT
29119849 AATAATCAAAATAGATTTCTCTTCTTCTTGAATGATTCGATTATATAGAAAGTGACATTATTTAG
1 AATAATCAAAATAGATTTCTCTTCTTCTTGAATGATTCGATTATATAGAAAGTGACATTATTTAG
29119914 ATTTTATGCATCTTTTGAGTTATATATGCGATTAGGTTATAATAGAAAGTGACATTCGATTATAT
66 ATTTTATGCATCTTTTGAGTTATATATGCGATTAGGTTATAATAGAAAGTGACATTCGATTATAT
29119979 ATTTTGTTATATAATTGTTATTTTATTACCAAGATTTTGGTTCTTAGGAAATAGACTGTGGACTA
131 ATTTTGTTATATAATTGTTATTTTATTACCAAGATTTTGGTTCTTAGGAAATAGACTGTGGACTA
29120044 TCATCTCCATGTAGGACTTTTTTTTTTAAAATTCATATAATTCTTGTGAAGTCGAAAACGAATAA
196 TCATCTCCATGTAGGACTTTTTTTTTTAAAATTCATATAATTCTTGTGAAGTCGAAAACGAATAA
29120109 AGGACTTAAAATGGAACGATGGTGGTTGAAGACCCAAGGAATGCCTTGTGGTGAAAAAAATTGTA
261 AGGACTTAAAATGGAACGATGGTGGTTGAAGACCCAAGGAATGCCTTGTGGTGAAAAAAATTGTA
29120174 ATTTTTGCTTTTCATTTATTTT
326 ATTTTTGCTTTTCATTTATTTT
* ** ****** ** * * *** * **
29120196 -AT-A--GAAATAGA-ACCATGGAAACCTTGGTTGA--CAATTTTATTTTAA-TTACCCATCTCC
1 AATAATCAAAATAGATTTC-TCTTCTTCTTGAATGATTCGATTATATAGAAAGTGA--CAT-TAT
* * * * * * * *
29120253 TTATATATT-T-C-T-TTTAT-AATTGTTTAT---AATA-TTTATATTATG---GT---A-T--A
62 TTAGATTTTATGCATCTTT-TGAGTTATATATGCGATTAGGTTATAATA-GAAAGTGACATTCGA
* * * ** * *
29120300 TTATA-AGTTTGATATAT-ATGTGTAAGATGA-T-CCACA-ACTGATTGGTTCTTAGGAAATAGA
125 TTATATATTTTGTTATATAAT-TGTTATTTTATTACCA-AGA-T-TTTGGTTCTTAGGAAATAGA
29120360 CTGTGGACTATCATCTCCATGTAGGACTTTTTTTTTTAAAATTCATATAATTCTTGTGAAGTCGA
186 CTGTGGACTATCATCTCCATGTAGGACTTTTTTTTTTAAAATTCATATAATTCTTGTGAAGTCGA
29120425 AAACGAATAAAGGACTTAAAATGGAACGATGGTGGTTGAAGACCCAAGGAATG-CTTGTGGTGAA
251 AAACGAATAAAGGACTTAAAATGGAACGATGGTGGTTGAAGACCCAAGGAATGCCTTGTGGTG-A
29120489 AAAAAATTGTAATTTTTGCTTTTCATTTATTTT
315 AAAAAATTGTAATTTTTGCTTTTCATTTATTTT
29120522 A
1 A
29120523 TAGAAATAGA
Statistics
Matches: 628, Mismatches: 34, Indels: 44
0.89 0.05 0.06
Matches are distributed among these distances:
324 4 0.01
325 14 0.02
326 187 0.30
327 6 0.01
329 1 0.00
330 1 0.00
333 2 0.00
335 7 0.01
336 4 0.01
339 10 0.02
340 4 0.01
341 10 0.02
342 5 0.01
343 23 0.04
345 1 0.00
346 2 0.00
347 347 0.55
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (347 bp):
AATAATCAAAATAGATTTCTCTTCTTCTTGAATGATTCGATTATATAGAAAGTGACATTATTTAG
ATTTTATGCATCTTTTGAGTTATATATGCGATTAGGTTATAATAGAAAGTGACATTCGATTATAT
ATTTTGTTATATAATTGTTATTTTATTACCAAGATTTTGGTTCTTAGGAAATAGACTGTGGACTA
TCATCTCCATGTAGGACTTTTTTTTTTAAAATTCATATAATTCTTGTGAAGTCGAAAACGAATAA
AGGACTTAAAATGGAACGATGGTGGTTGAAGACCCAAGGAATGCCTTGTGGTGAAAAAAATTGTA
ATTTTTGCTTTTCATTTATTTT
Found at i:29120543 original size:326 final size:326
Alignment explanation
Indices: 29119668--29120669 Score: 1333
Period size: 326 Copynumber: 3.0 Consensus size: 326
29119658 TACCAAGATT
29119668 TTGGTTCTTAGGAAATAGACTGTGGACTATCATCTCCATGTAGGACTTTTTTTTTTAAAATTCAT
1 TTGGTTCTTAGGAAATAGACTGTGGACTATCATCTCCATGTAGGACTTTTTTTTTTAAAATTCAT
29119733 ATAATTCTTGTGAAGTCGAAAACGAATAAAGGACTTAAAATGGAACGATGGTGGTTGAAGACCCA
66 ATAATTCTTGTGAAGTCGAAAACGAATAAAGGACTTAAAATGGAACGATGGTGGTTGAAGACCCA
*
29119798 AGGAATGCCTTGTGGTGAAAAAAATTGTAATTTTTGCTTTTCATTTATTTTAATAATCAAAATAG
131 AGGAATGCCTTGTGGTGAAAAAAATTGTAATTTTTGCTTTTCATTTATTTT-AT-A--GAAATAG
** ****** ** * * *** * ** * *
29119863 ATTTC-TCTTCTTCTTGAATGATTCGATTATATAGAAAGTGA--CAT-TATTTAGATTTTATGCA
192 A-ACCATGGAAACCTTGGTTGA--CAATTTTATTTTAA-TTACCCATCTCCTTATATATT-T-C-
* * * * * * * *
29119924 TCTTT-TGAGTTATATATGCGATTAGGTTATAATA-GAAAGTGACATTCGATTATATATTTTGTT
250 T-TTTAT-AATTGTTTAT---AATA-TTTATATTATG---GT---A-T--ATTATA-AGTTTGAT
* ** * *
29119987 ATATAAT-TGTTATTTTATTACCA-AGA-T-T
299 ATAT-ATGTGTAAGATGA-T-CCACA-ACTGA
29120015 TTGGTTCTTAGGAAATAGACTGTGGACTATCATCTCCATGTAGGACTTTTTTTTTTAAAATTCAT
1 TTGGTTCTTAGGAAATAGACTGTGGACTATCATCTCCATGTAGGACTTTTTTTTTTAAAATTCAT
29120080 ATAATTCTTGTGAAGTCGAAAACGAATAAAGGACTTAAAATGGAACGATGGTGGTTGAAGACCCA
66 ATAATTCTTGTGAAGTCGAAAACGAATAAAGGACTTAAAATGGAACGATGGTGGTTGAAGACCCA
29120145 AGGAATGCCTTGTGGTGAAAAAAATTGTAATTTTTGCTTTTCATTTATTTTATAGAAATAGAACC
131 AGGAATGCCTTGTGGTGAAAAAAATTGTAATTTTTGCTTTTCATTTATTTTATAGAAATAGAACC
29120210 ATGGAAACCTTGGTTGACAATTTTATTTTAATTACCCATCTCCTTATATATTTCTTTTATAATTG
196 ATGGAAACCTTGGTTGACAATTTTATTTTAATTACCCATCTCCTTATATATTTCTTTTATAATTG
29120275 TTTATAATATTTATATTATGGTATATTATAAGTTTGATATATATGTGTAAGATGATCCACAACTG
261 TTTATAATATTTATATTATGGTATATTATAAGTTTGATATATATGTGTAAGATGATCCACAACTG
29120340 A
326 A
29120341 TTGGTTCTTAGGAAATAGACTGTGGACTATCATCTCCATGTAGGACTTTTTTTTTTAAAATTCAT
1 TTGGTTCTTAGGAAATAGACTGTGGACTATCATCTCCATGTAGGACTTTTTTTTTTAAAATTCAT
29120406 ATAATTCTTGTGAAGTCGAAAACGAATAAAGGACTTAAAATGGAACGATGGTGGTTGAAGACCCA
66 ATAATTCTTGTGAAGTCGAAAACGAATAAAGGACTTAAAATGGAACGATGGTGGTTGAAGACCCA
29120471 AGGAATG-CTTGTGGTGAAAAAAAATTGTAATTTTTGCTTTTCATTTATTTTATAGAAATAGAAC
131 AGGAATGCCTTGTGGTG-AAAAAAATTGTAATTTTTGCTTTTCATTTATTTTATAGAAATAGAAC
29120535 CATGGAAACCTTGGTTGACAATTTTATTTTAATTACCCATCTCCTTATATATTTCTTTTATAATT
195 CATGGAAACCTTGGTTGACAATTTTATTTTAATTACCCATCTCCTTATATATTTCTTTTATAATT
29120600 GTTTATAATATTTATATTATGGTATATTATAAGTTTGATATATATGTGTAAGATGATCCACAACT
260 GTTTATAATATTTATATTATGGTATATTATAAGTTTGATATATATGTGTAAGATGATCCACAACT
29120665 GA
325 GA
29120667 TTG
1 TTG
29120670 ATTAAAAAAA
Statistics
Matches: 610, Mismatches: 34, Indels: 43
0.89 0.05 0.06
Matches are distributed among these distances:
324 4 0.01
325 14 0.02
326 335 0.55
327 6 0.01
329 1 0.00
330 1 0.00
333 2 0.00
335 7 0.01
336 4 0.01
339 10 0.02
340 4 0.01
341 10 0.02
342 5 0.01
343 23 0.04
345 1 0.00
346 2 0.00
347 181 0.30
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (326 bp):
TTGGTTCTTAGGAAATAGACTGTGGACTATCATCTCCATGTAGGACTTTTTTTTTTAAAATTCAT
ATAATTCTTGTGAAGTCGAAAACGAATAAAGGACTTAAAATGGAACGATGGTGGTTGAAGACCCA
AGGAATGCCTTGTGGTGAAAAAAATTGTAATTTTTGCTTTTCATTTATTTTATAGAAATAGAACC
ATGGAAACCTTGGTTGACAATTTTATTTTAATTACCCATCTCCTTATATATTTCTTTTATAATTG
TTTATAATATTTATATTATGGTATATTATAAGTTTGATATATATGTGTAAGATGATCCACAACTG
A
Found at i:29121258 original size:22 final size:22
Alignment explanation
Indices: 29121230--29121275 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
29121220 AATATATATA
*
29121230 CAGAACAAATCAGATACAGATG
1 CAGAACAAATCAGATACAAATG
*
29121252 CAGAACATATCAGATACAAATG
1 CAGAACAAATCAGATACAAATG
29121274 CA
1 CA
29121276 AATTCCTACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.20, G:0.15, T:0.15
Consensus pattern (22 bp):
CAGAACAAATCAGATACAAATG
Found at i:29122057 original size:63 final size:63
Alignment explanation
Indices: 29121979--29122115 Score: 168
Period size: 63 Copynumber: 2.2 Consensus size: 63
29121969 AAATATTCTC
* * * *
29121979 CTACATGACTTGGACA-AACGCCTGTGTCTTTGGCTCGTGTGACTCTAATTCCAAAACAGTGAG
1 CTACATGACCTGGACACAA-GCCTGTGTCTCTGACTCGTATGACTCTAATTCCAAAACAGTGAG
* * * * *
29122042 CTACACGACCTGGACACAAGCTTGTGTCTCTGACTCGTATGACTTTAATTCTAAAATAGTGAG
1 CTACATGACCTGGACACAAGCCTGTGTCTCTGACTCGTATGACTCTAATTCCAAAACAGTGAG
*
29122105 TTACATGACCT
1 CTACATGACCT
29122116 ACCACATGGC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
63 60 0.97
64 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (63 bp):
CTACATGACCTGGACACAAGCCTGTGTCTCTGACTCGTATGACTCTAATTCCAAAACAGTGAG
Found at i:29131013 original size:28 final size:27
Alignment explanation
Indices: 29130958--29131019 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 27
29130948 CATGTATCCC
29130958 TTTTATAAATATACATACACGTACATAT
1 TTTTATAAATATACATACAC-TACATAT
*
29130986 TTTTATAAATATATATACA-TACTTATAT
1 TTTTATAAATATACATACACTAC--ATAT
29131014 TTTTAT
1 TTTTAT
29131020 TTTATAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 3 0.10
28 28 0.90
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (27 bp):
TTTTATAAATATACATACACTACATAT
Found at i:29131334 original size:15 final size:15
Alignment explanation
Indices: 29131306--29131351 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
29131296 ATATACTTGA
29131306 TTTGT-TTTTT-TTT
1 TTTGTATTTTTATTT
29131319 TTATGTA-TTTTATTT
1 TT-TGTATTTTTATTT
*
29131334 TTTTTATTTTTATTT
1 TTTGTATTTTTATTT
29131349 TTT
1 TTT
29131352 TTATGGTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 2 0.07
14 10 0.36
15 16 0.57
ACGTcount: A:0.11, C:0.00, G:0.04, T:0.85
Consensus pattern (15 bp):
TTTGTATTTTTATTT
Found at i:29131352 original size:15 final size:15
Alignment explanation
Indices: 29131326--29131355 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29131316 TTTTTATGTA
29131326 TTTTATTTTTTTTAT
1 TTTTATTTTTTTTAT
29131341 TTTTATTTTTTTTAT
1 TTTTATTTTTTTTAT
29131356 GGTTGCTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTATTTTTTTTAT
Found at i:29142274 original size:42 final size:43
Alignment explanation
Indices: 29142201--29142282 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
29142191 CCAGGAATGG
*
29142201 GCAGTTCAAATTTTGGATCAAAATGGGGCATGAGGTGATCAAA
1 GCAGCTCAAATTTTGGATCAAAATGGGGCATGAGGTGATCAAA
* * * *
29142244 GCAGCTCAAATTTT-TATCAGATTGGGGCATGTGGTGATC
1 GCAGCTCAAATTTTGGATCAAAATGGGGCATGAGGTGATC
29142283 TTGTCATACC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
42 21 0.62
43 13 0.38
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.29
Consensus pattern (43 bp):
GCAGCTCAAATTTTGGATCAAAATGGGGCATGAGGTGATCAAA
Found at i:29143254 original size:49 final size:49
Alignment explanation
Indices: 29143185--29143313 Score: 213
Period size: 49 Copynumber: 2.6 Consensus size: 49
29143175 GCCATAAGTT
*
29143185 TTATCTTCCTGAAGTTGCAGTGGAGCAAATTGAAGACCAGCTACAAATC
1 TTATTTTCCTGAAGTTGCAGTGGAGCAAATTGAAGACCAGCTACAAATC
*
29143234 TTATTTTCCTGAAGTTGCAGTGGAGCAAATTGAAGACCGGCTACAAATC
1 TTATTTTCCTGAAGTTGCAGTGGAGCAAATTGAAGACCAGCTACAAATC
* * *
29143283 TTATTTCCCTGAAGTTACAGTGGAACAAATT
1 TTATTTTCCTGAAGTTGCAGTGGAGCAAATT
29143314 AAAGCTAAAT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 75 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (49 bp):
TTATTTTCCTGAAGTTGCAGTGGAGCAAATTGAAGACCAGCTACAAATC
Found at i:29144104 original size:5 final size:5
Alignment explanation
Indices: 29144089--29144138 Score: 82
Period size: 5 Copynumber: 9.8 Consensus size: 5
29144079 ATCTGTGTTT
*
29144089 TTTTA TCTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT
29144139 TTGAACCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 37 0.88
6 5 0.12
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:29145544 original size:19 final size:19
Alignment explanation
Indices: 29145522--29145560 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29145512 GCTTGATTTG
29145522 TTTTTTTATGTATTTTATT
1 TTTTTTTATGTATTTTATT
* *
29145541 TTTTTTTATTTTTTTTATT
1 TTTTTTTATGTATTTTATT
29145560 T
1 T
29145561 ATTTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (19 bp):
TTTTTTTATGTATTTTATT
Found at i:29145570 original size:17 final size:16
Alignment explanation
Indices: 29145517--29145572 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
29145507 TATATGCTTG
* *
29145517 ATTTGTTTTTTTATGT
1 ATTTTTTTTTTTATTT
*
29145533 ATTTTATTTTTT-TTT
1 ATTTTTTTTTTTATTT
29145548 ATTTTTTTTATTTATTT
1 ATTTTTTTT-TTTATTT
29145565 ATTTTTTT
1 ATTTTTTT
29145573 GATGGTTGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 10 0.29
16 13 0.38
17 11 0.32
ACGTcount: A:0.14, C:0.00, G:0.04, T:0.82
Consensus pattern (16 bp):
ATTTTTTTTTTTATTT
Found at i:29147067 original size:30 final size:30
Alignment explanation
Indices: 29147028--29147087 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29147018 ATTCTTTATT
* *
29147028 TAATTAAATTTGACCTTCAATCCTTT-AAAA
1 TAATCAAATTTGACCATCAA-CCTTTCAAAA
*
29147058 TAATCAAATTTGATCATCAACCTTTCAAAA
1 TAATCAAATTTGACCATCAACCTTTCAAAA
29147088 AAAGAGGCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (30 bp):
TAATCAAATTTGACCATCAACCTTTCAAAA
Found at i:29149450 original size:30 final size:29
Alignment explanation
Indices: 29149389--29149481 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 29
29149379 AACATTTCAG
*
29149389 TCACTAAACTTTCAAAAGTGATAACTCAA
1 TCACTAAACTTTCAAAAGTGATAAATCAA
*
29149418 TCACTAAACTTTACGAAAA-TTATAAATCAA
1 TCACTAAACTTT-C-AAAAGTGATAAATCAA
** *
29149448 TCACTAATGTTTTCAAAAGTGACAAATCAA
1 TCACTAA-ACTTTCAAAAGTGATAAATCAA
29149478 TCAC
1 TCAC
29149482 CTTGAGCCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
29 16 0.30
30 31 0.57
31 7 0.13
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.29
Consensus pattern (29 bp):
TCACTAAACTTTCAAAAGTGATAAATCAA
Found at i:29149556 original size:21 final size:21
Alignment explanation
Indices: 29149515--29149561 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
29149505 CCCTAACAGG
* *
29149515 ATAGCTGATGTGGGCCGTTAA
1 ATAGCTGACGTGGGCCATTAA
29149536 ATAGCTGACGT-GGCCTATTAA
1 ATAGCTGACGTGGGCC-ATTAA
*
29149557 CTAGC
1 ATAGC
29149562 CATGTTGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (21 bp):
ATAGCTGACGTGGGCCATTAA
Found at i:29161150 original size:93 final size:93
Alignment explanation
Indices: 29160991--29161161 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
29160981 GATGGAAGTT
* * * *
29160991 TAAACTTAGGCAAATTCTTTTTTTTTTAATTTTCCTATTATTGCTACTAATATCTAAACTTAGGC
1 TAAACTTAGGCAAATTCTTTTTTTGTAAATTTTCATATTATTGCTACTAATAACTAAACTTAGGC
29161056 AGATAGCTACATTGACGCTATTGATTTC
66 AGATAGCTACATTGACGCTATTGATTTC
*
29161084 TAAACTTAGGCATATTCTTTTTTTGTAAATTTTCATATTATTGCTACTAATAACTAAACTTAGGC
1 TAAACTTAGGCAAATTCTTTTTTTGTAAATTTTCATATTATTGCTACTAATAACTAAACTTAGGC
*
29161149 AGATAGTTACATT
66 AGATAGCTACATT
29161162 CTTTTTTGTA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (93 bp):
TAAACTTAGGCAAATTCTTTTTTTGTAAATTTTCATATTATTGCTACTAATAACTAAACTTAGGC
AGATAGCTACATTGACGCTATTGATTTC
Found at i:29166083 original size:113 final size:115
Alignment explanation
Indices: 29165901--29166559 Score: 585
Period size: 113 Copynumber: 5.8 Consensus size: 115
29165891 AAATCTCAAG
* * * *
29165901 ACCAACACGCAGCGTTCTGGTCTTGATGTATATTAGAATTAGTGGCGC--ATACGAACAAACGCC
1 ACCAAAACGCAGAGTT-TGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAGGA-AAACGCC
* ** *
29165964 GGTAATGCATAGTATTAGCGGCGCTTAG-CAAAAGCG-CGCAAAAGATGTTA
64 GCTAATGCATAGTATTAGCGGCGCTTAGTGGAAAGCGCCGCAAAAGATCTTA
* * *
29166014 ACCAAAACGCAAAGTTTGGTCTTGATGTATATTACAATTAGTGGCGCTTATAAAGAAAACGCCGC
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAGGAAAACGCCGC
* * * * * * *
29166079 TAATGTATAGTATTAGCGGCACTGAGTGTTAAA-TGCCACAAAACATCTTA
66 TAATGCATAGTATTAGCGGCGCTTAGTG-GAAAGCGCCGCAAAAGATCTTA
* * *
29166129 ACCAAAACGCAGCGTTTTGGTCTTGATGTATATTATAATTAGTGGCG-TT-TAAGGAAAACGCCA
1 ACCAAAACGCAGAG-TTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAGGAAAACGCCG
* * * * * * * *
29166192 CTAAAGCATAGTAATAGCAGCGTTTGGTGGTAAGCGCCTCAAAATATCTTA
65 CTAATGCATAGTATTAGCGGCGCTTAGTGGAAAGCGCCGCAAAAGATCTTA
* * * * *
29166243 ACCAAAACGCGGAATTTAGTCTTGAGGTATATTAGAATTAGTGGCGCTTAT-TGGAAAACGCCGC
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAGGAAAACGCCGC
* * * *
29166307 TAAAGTATAGTAGTAGCGGCG-TTTGTGGAAAGCGCCGC-AAAGTATCTTA
66 TAATGCATAGTATTAGCGGCGCTTAGTGGAAAGCGCCGCAAAAG-ATCTTA
* * * * **
29166356 ACCAAAACGTAGAGTTTGGCCTTGACGTATATTAGAGTTAGTGGCGCTTACT--TCAAAACGCCG
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTA-TAAGGAAAACGCCG
** * ** * *
29166419 CTAATGTTTACTATTTA-CGGCGCTTTTTGGTAAGCGCCGCCAAAAGATATTA
65 CTAATGCATAGTA-TTAGCGGCGCTTAGTGGAAAGCGCCG-CAAAAGATCTTA
* * * * * * *
29166471 ACGAAAACACAGCGTTTAGTTCTTGATGTATATTGGAATTAGTGGCGC--ACACAGGAAAACACC
1 ACCAAAACGCAGAGTTT-GGTCTTGATGTATATTAGAATTAGTGGCGCTTATA-AGGAAAACGCC
29166534 GCTGAA-GCATAGTATTAGCGGCGCTT
64 GCT-AATGCATAGTATTAGCGGCGCTT
29166560 TTCCCGAAAC
Statistics
Matches: 443, Mismatches: 82, Indels: 39
0.79 0.15 0.07
Matches are distributed among these distances:
112 33 0.07
113 162 0.37
114 112 0.25
115 51 0.12
116 83 0.19
117 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (115 bp):
ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAGGAAAACGCCGC
TAATGCATAGTATTAGCGGCGCTTAGTGGAAAGCGCCGCAAAAGATCTTA
Found at i:29166302 original size:228 final size:228
Alignment explanation
Indices: 29165901--29166402 Score: 557
Period size: 228 Copynumber: 2.2 Consensus size: 228
29165891 AAATCTCAAG
* * **
29165901 ACCAACACGCAGCGTTCTGGTCTTGATGTATATTAGAATTAGTGGCGCATACGAACAAACGCCGG
1 ACCAAAACGCAGCGTTCTGGTCTTGATGTATATTAGAATTAGTGGCGCATAAGAACAAACGCCAC
* * * *
29165966 TAATGCATAGTATTAGCGGCGCTTAGCAAAAGCGCGCAAAAGATGTTAACCAAAACGCAAAGTTT
66 TAAAGCATAGTAATAGCAGCGCTTAGCAAAAGCGCGCAAAAGATCTTAACCAAAACGCAAAGTTT
* * * *
29166031 GGTCTTGATGTATATTACAATTAGTGGCGCTTATAAAGAAAACGCCGCTAATGTATAGTATTAGC
131 AGTCTTGAGGTATATTACAATTAGTGGCGCTTATAAAGAAAACGCCGCTAAAGTATAGTAGTAGC
29166096 GGCACTGAGTGTTAAATGCCACAAAACATCTTA
196 GGCACTGAGTGTTAAATGCCACAAAACATCTTA
* * ** *
29166129 ACCAAAACGCAGCGTTTTGGTCTTGATGTATATTATAATTAGTGGCGTTTAAGGA-AAACGCCAC
1 ACCAAAACGCAGCGTTCTGGTCTTGATGTATATTAGAATTAGTGGCGCATAAGAACAAACGCCAC
* * *** * * *
29166193 TAAAGCATAGTAATAGCAGCGTTTGGTGGTAAGCGCCTCAAAATATCTTAACCAAAACGCGGAA-
66 TAAAGCATAGTAATAGCAGCGCTTAG-CAAAAGCG-CGCAAAAGATCTTAACCAAAACGC-AAAG
* **
29166257 TTTAGTCTTGAGGTATATTAGAATTAGTGGCGCTTAT-TGGAAAACGCCGCTAAAGTATAGTAGT
128 TTTAGTCTTGAGGTATATTACAATTAGTGGCGCTTATAAAGAAAACGCCGCTAAAGTATAGTAGT
* ** * * * **
29166321 AGCGGC-GTTTGTG-GAAAGCGCCGCAAAGTATCTTA
193 AGCGGCACTGAGTGTTAAA-TGCCACAAAACATCTTA
* * * * *
29166356 ACCAAAACGTAGAGTT-TGGCCTTGACGTATATTAGAGTTAGTGGCGC
1 ACCAAAACGCAGCGTTCTGGTCTTGATGTATATTAGAATTAGTGGCGC
29166403 TTACTTCAAA
Statistics
Matches: 227, Mismatches: 43, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
226 29 0.13
227 59 0.26
228 82 0.36
229 55 0.24
230 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (228 bp):
ACCAAAACGCAGCGTTCTGGTCTTGATGTATATTAGAATTAGTGGCGCATAAGAACAAACGCCAC
TAAAGCATAGTAATAGCAGCGCTTAGCAAAAGCGCGCAAAAGATCTTAACCAAAACGCAAAGTTT
AGTCTTGAGGTATATTACAATTAGTGGCGCTTATAAAGAAAACGCCGCTAAAGTATAGTAGTAGC
GGCACTGAGTGTTAAATGCCACAAAACATCTTA
Found at i:29166516 original size:229 final size:227
Alignment explanation
Indices: 29165901--29166556 Score: 568
Period size: 229 Copynumber: 2.9 Consensus size: 227
29165891 AAATCTCAAG
* * * * * * * * **
29165901 ACCAACACGCAGCGTTCTGGTCTTGATGTATATTAGAATTAGTGGCGCATACGAACAAACGCCGG
1 ACCAAAACGCAGAGTTTTGGCCTTGACGTATATTAGAATTAGTGGCGCTTAAGCA-AAACGCCAC
* * * * * * *** * *
29165966 TAATGCATAGTATTAGCGGCGCTTAG-CAAAAGCG-CGCAAAAGATGTTAACCAAAACGCAAAGT
65 TAAAGCATACTAATAGCAGCGTTTGGTGGTAAGCGCCGCAAAAGATATTAACCAAAACGCAGAGT
* * * *
29166029 TTGGTCTTGATGTATATTACAATTAGTGGCGCTTATAAAGAAAACGCCGCTAATGTATAGTATTA
130 TTAGTCTTGATGTATATTAGAATTAGTGGCGCTTAT-AGGAAAACGCCGCTAAAGTATAGTATTA
* * *
29166094 GCGGCACTGAGTGTTAAATGCCACAAAACATCTTA
194 GCGGC-GTGAGTGTGAAACGCCACAAAACATCTTA
* * * * * *
29166129 ACCAAAACGCAGCGTTTTGGTCTTGATGTATATTATAATTAGTGGCGTTTAAGGAAAACGCCACT
1 ACCAAAACGCAGAGTTTTGGCCTTGACGTATATTAGAATTAGTGGCGCTTAAGCAAAACGCCACT
* * * * * *
29166194 AAAGCATAGTAATAGCAGCGTTTGGTGGTAAGCGCCTCAAAATATCTTAACCAAAACGCGGAATT
66 AAAGCATACTAATAGCAGCGTTTGGTGGTAAGCGCCGCAAAAGATATTAACCAAAACGCAGAGTT
* * *
29166259 TAGTCTTGAGGTATATTAGAATTAGTGGCGCTTATTGGAAAACGCCGCTAAAGTATAGTAGTAGC
131 TAGTCTTGATGTATATTAGAATTAGTGGCGCTTATAGGAAAACGCCGCTAAAGTATAGTATTAGC
** * **
29166324 GGCGTTTGTG-GAAAGCGCCGCAAAGTATCTTA
196 GGCGTGAGTGTGAAA-CGCCACAAAACATCTTA
* * ** *
29166356 ACCAAAACGTAGAG-TTTGGCCTTGACGTATATTAGAGTTAGTGGCGCTTACTTCAAAACGCCGC
1 ACCAAAACGCAGAGTTTTGGCCTTGACGTATATTAGAATTAGTGGCGCTTA-AGCAAAACGCCAC
* ** * * * * *
29166420 TAATGTTTACTATTTA-CGGCGCTTT-TTGGTAAGCGCCGCCAAAAGATATTAACGAAAACACAG
65 TAAAGCATACTA-ATAGCAGCG-TTTGGTGGTAAGCGCCG-CAAAAGATATTAACCAAAACGCAG
* * ** * * * *
29166483 CGTTTAGTTCTTGATGTATATTGGAATTAGTGGCGCACACAGGAAAACACCGCTGAAGCATAGTA
127 AGTTTAG-TCTTGATGTATATTAGAATTAGTGGCGCTTATAGGAAAACGCCGCTAAAGTATAGTA
29166548 TTAGCGGCG
191 TTAGCGGCG
29166557 CTTTTCCCGA
Statistics
Matches: 346, Mismatches: 74, Indels: 15
0.80 0.17 0.03
Matches are distributed among these distances:
226 34 0.10
227 89 0.26
228 111 0.32
229 112 0.32
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (227 bp):
ACCAAAACGCAGAGTTTTGGCCTTGACGTATATTAGAATTAGTGGCGCTTAAGCAAAACGCCACT
AAAGCATACTAATAGCAGCGTTTGGTGGTAAGCGCCGCAAAAGATATTAACCAAAACGCAGAGTT
TAGTCTTGATGTATATTAGAATTAGTGGCGCTTATAGGAAAACGCCGCTAAAGTATAGTATTAGC
GGCGTGAGTGTGAAACGCCACAAAACATCTTA
Found at i:29166684 original size:18 final size:18
Alignment explanation
Indices: 29166663--29166698 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
29166653 TCATTTTATA
29166663 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
29166681 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
29166699 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:29167092 original size:20 final size:20
Alignment explanation
Indices: 29167059--29167099 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29167049 TATGGTTTAA
*
29167059 GGGTTAGGGGTTAGGGATTT
1 GGGTTAGGAGTTAGGGATTT
* *
29167079 GGGTTAGGATTTAGGGTTTT
1 GGGTTAGGAGTTAGGGATTT
29167099 G
1 G
29167100 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.39
Consensus pattern (20 bp):
GGGTTAGGAGTTAGGGATTT
Found at i:29167092 original size:81 final size:81
Alignment explanation
Indices: 29166999--29167155 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 81
29166989 TTCGGTGTCA
* * ** *
29166999 GGTTAGGCTTTAGGGTTTAGATTAATTAGTGTGTTTTAATTT-T-TATAAAATATGGTTTAAGGG
1 GGTTAGGATTTAGGGTTTAGATTAATTAAT-AATTTTAATTTATGTATAAAATAAGGTTT-AGGG
*
29167062 TTAGGGGTTAGGGATTTG
64 TTAGGAGTTAGGGATTTG
* *
29167080 GGTTAGGATTTAGGGTTTTGATTAATTAATAATTTTAATTTATGTATTAAATAAGGTTTAGGGTT
1 GGTTAGGATTTAGGGTTTAGATTAATTAATAATTTTAATTTATGTATAAAATAAGGTTTAGGGTT
*
29167145 AGTAGTTAGGG
66 AGGAGTTAGGG
29167156 TCGGGGTTAG
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 9 0.14
81 43 0.66
82 13 0.20
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.45
Consensus pattern (81 bp):
GGTTAGGATTTAGGGTTTAGATTAATTAATAATTTTAATTTATGTATAAAATAAGGTTTAGGGTT
AGGAGTTAGGGATTTG
Found at i:29167580 original size:7 final size:7
Alignment explanation
Indices: 29167579--29167620 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
29167569 TGTTTGGGGT
29167579 TTTGGGA
1 TTTGGGA
29167586 TTTGGGA
1 TTTGGGA
*
29167593 TTTGGGGG
1 TTT-GGGA
29167601 TTTGGGA
1 TTTGGGA
29167608 TTTGGGA
1 TTTGGGA
29167615 TTTGGG
1 TTTGGG
29167621 GTTTAAGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.10, C:0.00, G:0.48, T:0.43
Consensus pattern (7 bp):
TTTGGGA
Found at i:29167589 original size:15 final size:15
Alignment explanation
Indices: 29167571--29167624 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
29167561 ACTTTTAGTG
29167571 TTTGGGGTTTTGGGA
1 TTTGGGGTTTTGGGA
* * *
29167586 TTTGGGATTTGGGGG
1 TTTGGGGTTTTGGGA
*
29167601 TTT-GGGATTTGGGA
1 TTTGGGGTTTTGGGA
29167615 TTTGGGGTTT
1 TTTGGGGTTT
29167625 AAGGTTTAGA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
14 10 0.33
15 20 0.67
ACGTcount: A:0.07, C:0.00, G:0.46, T:0.46
Consensus pattern (15 bp):
TTTGGGGTTTTGGGA
Found at i:29167596 original size:22 final size:22
Alignment explanation
Indices: 29167571--29167624 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
29167561 ACTTTTAGTG
29167571 TTTGGGGTTTTGGGATTTGGGA
1 TTTGGGGTTTTGGGATTTGGGA
*
29167593 TTTGGGGGTTTGGGATTTGGGA
1 TTTGGGGTTTTGGGATTTGGGA
29167615 TTTGGGGTTT
1 TTTGGGGTTT
29167625 AAGGTTTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.07, C:0.00, G:0.46, T:0.46
Consensus pattern (22 bp):
TTTGGGGTTTTGGGATTTGGGA
Found at i:29169363 original size:42 final size:43
Alignment explanation
Indices: 29169287--29169383 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 43
29169277 TCATATCAAA
* * * *
29169287 TAGTGGCGTTTGTGAAATAAGCGCCGCTAAAGAACACTAGTTT
1 TAGTGGCGTTTTTGAAACAAGCGACGCTAAAGAACACTACTTT
* * *
29169330 TAGTGGCGTTTTTG-ACCAAGCGACGCTATAGAACATTACTTT
1 TAGTGGCGTTTTTGAAACAAGCGACGCTAAAGAACACTACTTT
* *
29169372 TAGCGGTGTTTT
1 TAGTGGCGTTTT
29169384 CTTCCTAAGC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 32 0.71
43 13 0.29
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (43 bp):
TAGTGGCGTTTTTGAAACAAGCGACGCTAAAGAACACTACTTT
Found at i:29169446 original size:45 final size:46
Alignment explanation
Indices: 29169370--29169459 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 46
29169360 GAACATTACT
* *
29169370 TTTAGCGGTGTTTTCTTCCTAAGCGCCGCTAAAGAACATGATCTTC
1 TTTAGCGGCGTTTTCTTCATAAGCGCCGCTAAAGAACATGATCTTC
29169416 TTTAGCGGCGTTTT-TTCATAAGCGCCGCTAAAGAACATGATCTT
1 TTTAGCGGCGTTTTCTTCATAAGCGCCGCTAAAGAACATGATCTT
29169460 TAGCGGCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 29 0.69
46 13 0.31
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (46 bp):
TTTAGCGGCGTTTTCTTCATAAGCGCCGCTAAAGAACATGATCTTC
Found at i:29173596 original size:2 final size:2
Alignment explanation
Indices: 29173589--29173630 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
29173579 TCTAACCTGA
* *
29173589 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29173631 CCATTGATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29173809 original size:1 final size:1
Alignment explanation
Indices: 29173805--29173835 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
29173795 AGTTTTTCTC
29173805 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29173836 GGTTTGGGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29179934 original size:15 final size:16
Alignment explanation
Indices: 29179906--29179945 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
29179896 ATTTGTTTAT
29179906 ATTTTAAAATTTTAAA
1 ATTTTAAAATTTTAAA
29179922 ATTTTAAAA-TTTAAA
1 ATTTTAAAATTTTAAA
*
29179937 TTTTTAAAA
1 ATTTTAAAA
29179946 AAAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAAAATTTTAAA
Found at i:29179936 original size:7 final size:8
Alignment explanation
Indices: 29179906--29179945 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
29179896 ATTTGTTTAT
29179906 ATTTTAAA
1 ATTTTAAA
29179914 ATTTTAAA
1 ATTTTAAA
29179922 ATTTTAAA
1 ATTTTAAA
29179930 A-TTTAAA
1 ATTTTAAA
*
29179937 TTTTTAAA
1 ATTTTAAA
29179945 A
1 A
29179946 AAAAATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTTTAAA
Found at i:29192234 original size:23 final size:22
Alignment explanation
Indices: 29192191--29192234 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
29192181 TTCTAAGTCG
29192191 ATATTCAATTCAATTCCACACCA
1 ATATTCAATTCAATT-CACACCA
29192214 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
29192235 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCA
Found at i:29192339 original size:45 final size:45
Alignment explanation
Indices: 29192279--29192372 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
29192269 AACAGATGCT
* * *
29192279 CGGTGGATTCTGCACATAGAAACCACCTTATTAATCAATAATGTC
1 CGGTGGAATCAGCACATAGAAACCACCTTACTAATCAATAATGTC
* *
29192324 CGGTGGAATCAGCACATAGAAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGAAACCACCTTACTAATCAATAATGTC
29192369 CGGT
1 CGGT
29192373 TCACATAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGAAACCACCTTACTAATCAATAATGTC
Found at i:29192441 original size:51 final size:52
Alignment explanation
Indices: 29192378--29192513 Score: 188
Period size: 50 Copynumber: 2.7 Consensus size: 52
29192368 TCGGTTCACA
*
29192378 TAGTAGCGTGCACATAGTACTACACATGTGACCATTACCATCT-GATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTCGATACACG
* * * * *
29192429 TAGTAGCCTGCACATAGTACTACACATGCGACC--TATCGTTTCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTCGATACACG
*
29192479 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
29192514 CACTTTCACT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
49 5 0.07
50 38 0.51
51 31 0.42
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (52 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTCGATACACG
Found at i:29193068 original size:33 final size:33
Alignment explanation
Indices: 29193024--29193088 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
29193014 ATACGTGCAT
29193024 ATCATTCATGGGTAAATTTTTAAACACAAACCA
1 ATCATTCATGGGTAAATTTTTAAACACAAACCA
* *
29193057 ATCATTTATGGGTAAATTTTTAAGCACAAACC
1 ATCATTCATGGGTAAATTTTTAAACACAAACC
29193089 CTAGTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (33 bp):
ATCATTCATGGGTAAATTTTTAAACACAAACCA
Found at i:29193944 original size:17 final size:18
Alignment explanation
Indices: 29193922--29193970 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
29193912 GGGCCCATAA
29193922 TATTTGGATAGATTA-TT
1 TATTTGGATAGATTAGTT
*
29193939 TATTTGAGA-AAATTAGTT
1 TATTTG-GATAGATTAGTT
*
29193957 AATTT-GATAGATTA
1 TATTTGGATAGATTA
29193971 ACTAAGTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
16 2 0.08
17 16 0.62
18 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (18 bp):
TATTTGGATAGATTAGTT
Found at i:29194520 original size:21 final size:21
Alignment explanation
Indices: 29194476--29194520 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29194466 GGGTGGATCT
*
29194476 GCTCTCACGAGCTTCTGTTCA
1 GCTCTCACGAGCTTCTATTCA
* *
29194497 GCTCTTACGAGCTTCTATTTA
1 GCTCTCACGAGCTTCTATTCA
29194518 GCT
1 GCT
29194521 TTCAAGCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.38
Consensus pattern (21 bp):
GCTCTCACGAGCTTCTATTCA
Found at i:29195790 original size:18 final size:19
Alignment explanation
Indices: 29195763--29195801 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29195753 ATTTTGAAAT
29195763 AAAATAG-AAAACTTTGGA
1 AAAATAGAAAAACTTTGGA
* *
29195781 AAAATTGAAAAATTTTGGA
1 AAAATAGAAAAACTTTGGA
29195800 AA
1 AA
29195802 CAGGGGTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (19 bp):
AAAATAGAAAAACTTTGGA
Found at i:29197600 original size:87 final size:87
Alignment explanation
Indices: 29197488--29197766 Score: 353
Period size: 87 Copynumber: 3.2 Consensus size: 87
29197478 ATGTTGCAAT
* * * * * * * *
29197488 TTAAACTACCAGATCATATAATAGTACGCAGCAACGCTGACGTACATGCGGTATAGTACGGTAAA
1 TTAAACTGCCAGATTAGATAATAGTACGCAGCAAAGATGACGTACAAGCGGTACAGTGCGGTAAA
*
29197553 CCACTGTACCGATAAGTTACAG
66 CCACTATACCGATAAGTTACAG
** *
29197575 TTAAACTGTTAGATTAGATAATAGTACGCAGCAAAGATGATGTACAAGCGGTACAGTGCGGTAAA
1 TTAAACTGCCAGATTAGATAATAGTACGCAGCAAAGATGACGTACAAGCGGTACAGTGCGGTAAA
* * *
29197640 CCGCTATACTGATAAGTT-TAG
66 CCACTATACCGATAAGTTACAG
* * * * *
29197661 TTAAACTGCCATATTAGATAACAGTACACAACAAAGTTGACGTACAAGCGGTACAGTGCGGTAAA
1 TTAAACTGCCAGATTAGATAATAGTACGCAGCAAAGATGACGTACAAGCGGTACAGTGCGGTAAA
*
29197726 CCACTATACCGATAAGTTAGAG
66 CCACTATACCGATAAGTTACAG
*
29197748 TTAAACTGCCAGATCAGAT
1 TTAAACTGCCAGATTAGAT
29197767 CATAATCAGT
Statistics
Matches: 163, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
86 75 0.46
87 88 0.54
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (87 bp):
TTAAACTGCCAGATTAGATAATAGTACGCAGCAAAGATGACGTACAAGCGGTACAGTGCGGTAAA
CCACTATACCGATAAGTTACAG
Found at i:29203784 original size:25 final size:25
Alignment explanation
Indices: 29203727--29203791 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
29203717 TAACCCATAG
*
29203727 CTCGTGTGAGCATACTGATTCACAA
1 CTCGTGTGAGCATACCGATTCACAA
*
29203752 CTCATGTGAGCATACCGATTCACAGA
1 CTCGTGTGAGCATACCGATTCACA-A
*
29203778 -TTGTGTGAGCATAC
1 CTCGTGTGAGCATAC
29203792 ATGTACAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 34 0.97
26 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (25 bp):
CTCGTGTGAGCATACCGATTCACAA
Found at i:29207531 original size:17 final size:17
Alignment explanation
Indices: 29207498--29207530 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29207488 TTTTATTTCC
29207498 ATTTGTCTTTCCATTTT
1 ATTTGTCTTTCCATTTT
*
29207515 ATTT-TCTTTCCCTTTT
1 ATTTGTCTTTCCATTTT
29207531 TGGTTTCCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTGTCTTTCCATTTT
Found at i:29209066 original size:25 final size:25
Alignment explanation
Indices: 29209025--29209073 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
29209015 TTTATAGCTC
*
29209025 GTATGAGCTTCTCGATAAATGGCTT
1 GTATGAGATTCTCGATAAATGGCTT
29209050 GTATGAGATTC-CTGATAAATGGCT
1 GTATGAGATTCTC-GATAAATGGCT
29209074 CGCAAGAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (25 bp):
GTATGAGATTCTCGATAAATGGCTT
Done.