Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 5 of 117
Found at i:455858 original size:15 final size:15
Alignment explanation
Indices: 455838--455866 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
455828 GAACACACAA
455838 AAAGAGGAAACATAC
1 AAAGAGGAAACATAC
455853 AAAGAGGAAACATA
1 AAAGAGGAAACATA
455867 AGCTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.10, G:0.21, T:0.07
Consensus pattern (15 bp):
AAAGAGGAAACATAC
Found at i:456369 original size:3 final size:3
Alignment explanation
Indices: 456363--456460 Score: 115
Period size: 3 Copynumber: 32.0 Consensus size: 3
456353 TTTTTCTTAT
* *
456363 TTA TTA TTA TTA TTA TTTC TTT TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
456409 TTA TTA TTA TTA TCA TCA TCA TCA TTA TCA TTA TTA TTA TTA TTA CTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
456458 TTA
1 TTA
456461 ATTACATTAG
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
3 81 0.94
4 5 0.06
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:456385 original size:31 final size:31
Alignment explanation
Indices: 456347--456410 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
456337 AAGGTTTTTT
*
456347 TTTCTTTTT-TTCTTATTTATTATTATTATTA
1 TTTCTTTTTATTATTA-TTATTATTATTATTA
456378 TTTCTTTTTATTATTATTATTATTATTATTA
1 TTTCTTTTTATTATTATTATTATTATTATTA
456409 TT
1 TT
456411 ATTATTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (31 bp):
TTTCTTTTTATTATTATTATTATTATTATTA
Found at i:456522 original size:16 final size:16
Alignment explanation
Indices: 456491--456520 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
456481 TATTCCTTAT
456491 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
456507 TTTA-TTTTATTTTT
1 TTTATTTTTATTTTT
456521 TAAAATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:456662 original size:17 final size:17
Alignment explanation
Indices: 456640--456673 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
456630 TGAAAATATC
*
456640 AATTTTTTTTAAAAATA
1 AATTTTTTTAAAAAATA
456657 AATTTTTTTAAAAAATA
1 AATTTTTTTAAAAAATA
456674 TTTTTGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTTTTTAAAAAATA
Found at i:456678 original size:16 final size:16
Alignment explanation
Indices: 456640--456670 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
456630 TGAAAATATC
456640 AATTTTTTTTAAAAAT
1 AATTTTTTTTAAAAAT
*
456656 AAATTTTTTTAAAAA
1 AATTTTTTTTAAAAA
456671 ATATTTTTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTTTTTTAAAAAT
Found at i:456729 original size:59 final size:58
Alignment explanation
Indices: 456529--456761 Score: 253
Period size: 57 Copynumber: 4.1 Consensus size: 58
456519 TTTAAAATGA
* * *
456529 TTTTCTT-AAAATAAAATTAT-AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAAT-AAATTTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAAT
* * * *
456586 TTTCCTTGAAAAT-AATTTTCTAAAAAATATTTTCGAGGAAAAGTTGAAAATATCAAT
1 TTTTCTTGAAAATAAATTTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAAT
* * *
456643 TTTTTTTAAAAATAAATTTTTTTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAATAAA-TTTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAAT
* * * * *
456702 TTTTCTCGAAATTAAAGTTTC-AGAAAAATA-TTTTG-GTAAAAAGTTGGAAGTACCAAT
1 TTTTCTTGAAAATAAATTTTCTA-AAAAATATTTTTGAG-AAAAAGTTGAAAGTATCAAT
456759 TTT
1 TTT
456762 CCTAAAAGAA
Statistics
Matches: 150, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
56 6 0.04
57 77 0.51
58 17 0.11
59 50 0.33
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (58 bp):
TTTTCTTGAAAATAAATTTTCTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAAT
Found at i:456744 original size:116 final size:116
Alignment explanation
Indices: 456550--456761 Score: 295
Period size: 116 Copynumber: 1.8 Consensus size: 116
456540 TAAAATTATA
* * *
456550 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAATTTTCTAAAAAATA
1 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAGTTTCTAAAAAATA
* *
456615 TTTTCGAGGAAAAGTTGAAAATATCAATTTTTTTTAAAAATAAATTTTTTT
66 TTTTCGAGAAAAAGTTGAAAATACCAATTTTTTTTAAAAATAAATTTTTTT
* *
456666 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTC-AGAAAAA
1 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAAT-AAGTTTCTA-AAAAA
* *
456730 TATTTT-G-GTAAAAAGTTGGAAGTACCAATTTT
64 TATTTTCGAG-AAAAAGTTGAAAATACCAATTTT
456762 CCTAAAAGAA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
115 1 0.01
116 66 0.79
117 17 0.20
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (116 bp):
AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAGTTTCTAAAAAATA
TTTTCGAGAAAAAGTTGAAAATACCAATTTTTTTTAAAAATAAATTTTTTT
Found at i:459210 original size:3 final size:3
Alignment explanation
Indices: 459202--459237 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
459192 TTTAATTTTA
459202 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
459238 TAATTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:459269 original size:14 final size:13
Alignment explanation
Indices: 459242--459279 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
459232 ATTATTTAAT
459242 TTTTTTTCTT-TC
1 TTTTTTTCTTCTC
459254 TTTTTCTTCTTCTC
1 TTTTT-TTCTTCTC
459268 TTTCTTTTCTTC
1 TTT-TTTTCTTC
459280 CCATTTCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 11 0.48
15 2 0.09
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTCTTCTC
Found at i:459473 original size:21 final size:22
Alignment explanation
Indices: 459449--459493 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
459439 TTTTCAGTTG
*
459449 AAAAA-TGGGATTCGAATCCCA
1 AAAAACTGAGATTCGAATCCCA
*
459470 AAAAATCTGAGATTTGAATCCCA
1 AAAAA-CTGAGATTCGAATCCCA
459493 A
1 A
459494 CAAGCTCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
23 15 0.75
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (22 bp):
AAAAACTGAGATTCGAATCCCA
Found at i:460686 original size:18 final size:18
Alignment explanation
Indices: 460647--460689 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
460637 TTTTTTTTAA
**
460647 TAATAAATAAAAATTGGT
1 TAATAAATAAAAATAAGT
460665 TAATAAATTAAAAATAAG-
1 TAATAAA-TAAAAATAAGT
460683 TAATAAA
1 TAATAAA
460690 AATAGGAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (18 bp):
TAATAAATAAAAATAAGT
Found at i:461275 original size:189 final size:188
Alignment explanation
Indices: 460955--461321 Score: 682
Period size: 189 Copynumber: 1.9 Consensus size: 188
460945 GACATAATTT
* *
460955 TTACGAAAAGTAAATTTAGACCTCCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTT
1 TTACGAAAAATAAATTGAGACCTCCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTT
461020 AAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGAACATTTTAAGAATT
66 AAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGAACATTTTAAGAATT
461085 ATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTTTAACATTTTC
131 ATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAAT-AATTTTTTTTAACATTTTC
461144 TTACGAAAAATAAATTCGAG-CCTCCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTT
1 TTACGAAAAATAAATT-GAGACCTCCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTT
461208 TAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGAACATTTTAAGAAT
65 TAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGAACATTTTAAGAAT
*
461273 TATTTCAATAAAAAGGTTTTGATTTATTTTTCTCGAGAATAATTTTTTT
130 TATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATTTTTTT
461322 AATAAATAAA
Statistics
Matches: 174, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
188 9 0.05
189 163 0.94
190 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (188 bp):
TTACGAAAAATAAATTGAGACCTCCAAAGATGAGATTCTAAAAGTATTCCGAGTAGAGATGCTTT
AAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGAACATTTTAAGAATT
ATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATTTTTTTTAACATTTTC
Found at i:461818 original size:23 final size:22
Alignment explanation
Indices: 461786--461829 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
461776 AGTAGTAAAA
461786 AAAAAAAAAAAACAAAACAAATC
1 AAAAAAAAAAAACAAAA-AAATC
* *
461809 AAAAATAAAAAGCAAAAAAAT
1 AAAAAAAAAAAACAAAAAAAT
461830 TCACACACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.82, C:0.09, G:0.02, T:0.07
Consensus pattern (22 bp):
AAAAAAAAAAAACAAAAAAATC
Found at i:472994 original size:45 final size:45
Alignment explanation
Indices: 472932--473693 Score: 1067
Period size: 45 Copynumber: 17.3 Consensus size: 45
472922 TGCTGAGAGA
*
472932 AGCCTCT--TGAGAGGAGCTTTTCAAGAGAATTTTAAAGTCGTTG
1 AGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTG
* *
472975 AGCCTCTGCTGAGAGGAGCTTTTCCAATAAAATTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAGCTTTT-CAAGAGAATTTTAAAGTTGTTG
*
473021 AGCCTCTGTTGAGAGGAG-----C-------TTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTG
473054 AGCCTCTGCTGAGAGGAGCTTTTCAAGATGAATTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAGCTTTTCAAGA-GAATTTTAAAGTTGTTG
473100 AGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTG
473145 AGCCTCTGCTGAGAGGAGCTTTTCCAAGA-AATTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAGCTTTT-CAAGAGAATTTTAAAGTTGTTG
473190 AGCCTCTGCTGAGAGGAGCTTTTTCAAGAGAATTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAGC-TTTTCAAGAGAATTTTAAAGTTGTTG
*
473236 AGCCTCTGCTGAGAGGAGCTTTTCCAAGATAAAATTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAGCTTTT-CAAG--AGAATTTTAAAGTTGTTG
*
473284 AGCCTCTGCTGAGAGGACCTTTTCAAGAGAATTTTAAA---GTTG
1 AGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTG
* *
473326 AGCCT-TGCTGAGAGGAGCTTTTCAAGATAAATTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTG
473370 AGCCTCTGCTGAGAGGAGCTTTTCAAGAG-ATTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTG
*
473414 AGCCTCTGCTAAGAGGAGCCTTTTCAAGAGAATTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAG-CTTTTCAAGAGAATTTTAAAGTTGTTG
*
473460 AGCCT-TGCTGAGAGGAGCTTTT--ATAG-ATTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTG
473501 AGCCTCTGCTGAGAGGAGCCTTTTCAAGAG-ATTTTAAAG-TGTTG
1 AGCCTCTGCTGAGAGGAG-CTTTTCAAGAGAATTTTAAAGTTGTTG
* *
473545 AGCTTCTGCTGAGAGGAGCTTTTTCCAAGATAATTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAGC-TTTT-CAAGAGAATTTTAAAGTTGTTG
* *
473592 A-CCTCTGCTGAGAGAAGGCTTTTCAAGAGAATTTTAAAGTCGTTG
1 AGCCTCTGCTGAGAGGA-GCTTTTCAAGAGAATTTTAAAGTTGTTG
**
473637 AGCCTCTGCTGAGAGGAGCCTTTTCATTAG-ATTTTAAAGTTGTTG
1 AGCCTCTGCTGAGAGGAG-CTTTTCAAGAGAATTTTAAAGTTGTTG
473682 AGCCTCTGCTGA
1 AGCCTCTGCTGA
473694 ATGGAGCCTT
Statistics
Matches: 653, Mismatches: 27, Indels: 76
0.86 0.04 0.10
Matches are distributed among these distances:
33 31 0.05
38 1 0.00
40 1 0.00
41 49 0.08
42 24 0.04
43 13 0.02
44 71 0.11
45 217 0.33
46 195 0.30
47 12 0.02
48 39 0.06
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.34
Consensus pattern (45 bp):
AGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTG
Found at i:473049 original size:33 final size:33
Alignment explanation
Indices: 473007--473076 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
472997 TCCAATAAAA
*
473007 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC
473040 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC
473073 TTTT
1 TTTT
473077 CAAGATGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.20, C:0.13, G:0.29, T:0.39
Consensus pattern (33 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC
Found at i:473214 original size:91 final size:90
Alignment explanation
Indices: 473040--473693 Score: 994
Period size: 91 Copynumber: 7.3 Consensus size: 90
473030 TGAGAGGAGC
473040 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGATGAATTTTAAAGTTGTTGAGCCT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGA-GAATTTTAAAGTTGTTGAGCCT
473105 CTGCTGAGAGGAGCTTTTCAAGAGAA
65 CTGCTGAGAGGAGCTTTTCAAGAGAA
473131 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGA-AATTTTAAAGTTGTTGAGCCT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT-CAAGAGAATTTTAAAGTTGTTGAGCCT
473195 CTGCTGAGAGGAGCTTTTTCAAGAGAA
65 CTGCTGAGAGGAGC-TTTTCAAGAGAA
*
473222 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATAAAATTTTAAAGTTGTTGAGC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTT-CAAG--AGAATTTTAAAGTTGTTGAGC
*
473287 CTCTGCTGAGAGGACCTTTTCAAGAGAA
63 CTCTGCTGAGAGGAGCTTTTCAAGAGAA
* *
473315 TTTTAAA---GTTGAGCCT-TGCTGAGAGGAGCTTTTCAAGATAAATTTAAAGTTGTTGAGCCTC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTGAGCCTC
473376 TGCTGAGAGGAGCTTTTCAAGAG-A
66 TGCTGAGAGGAGCTTTTCAAGAGAA
*
473400 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGCCTTTTCAAGAGAATTTTAAAGTTGTTGAGCCT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCAAGAGAATTTTAAAGTTGTTGAGCCT
*
473465 -TGCTGAGAGGAGCTTTT--ATAG-A
65 CTGCTGAGAGGAGCTTTTCAAGAGAA
*
473487 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTCAAGAG-ATTTTAAAG-TGTTGAGCTT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCAAGAGAATTTTAAAGTTGTTGAGCCT
*
473550 CTGCTGAGAGGAGCTTTTTCCAAGATAA
65 CTGCTGAGAGGAGC-TTTT-CAAGAGAA
* *
473578 TTTTAAAGTTGTTGA-CCTCTGCTGAGAGAAGGCTTTTCAAGAGAATTTTAAAGTCGTTGAGCCT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGA-GCTTTTCAAGAGAATTTTAAAGTTGTTGAGCCT
**
473642 CTGCTGAGAGGAGCCTTTTCATTAG-A
65 CTGCTGAGAGGAG-CTTTTCAAGAGAA
473668 TTTTAAAGTTGTTGAGCCTCTGCTGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGA
473694 ATGGAGCCTT
Statistics
Matches: 524, Mismatches: 18, Indels: 42
0.90 0.03 0.07
Matches are distributed among these distances:
85 17 0.03
86 66 0.13
87 51 0.10
88 13 0.02
89 45 0.09
90 117 0.22
91 130 0.25
92 30 0.06
93 21 0.04
94 34 0.06
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (90 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCAAGAGAATTTTAAAGTTGTTGAGCCTC
TGCTGAGAGGAGCTTTTCAAGAGAA
Found at i:474946 original size:19 final size:19
Alignment explanation
Indices: 474922--474958 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
474912 TCAGGTAAAA
*
474922 AAATTTTTTTTATTTTTTT
1 AAATTTTTCTTATTTTTTT
474941 AAATTTTTCTTATTTTTT
1 AAATTTTTCTTATTTTTT
474959 ATATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (19 bp):
AAATTTTTCTTATTTTTTT
Found at i:474972 original size:19 final size:18
Alignment explanation
Indices: 474929--474973 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
474919 AAAAAATTTT
*
474929 TTTTATTTTTTTAAATTT
1 TTTTATTTTTTTAAATTA
*
474947 TTCTTATTTTTTATATATTA
1 TT-TTATTTTTT-TAAATTA
474967 TTTTATT
1 TTTTATT
474974 AATATTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 14 0.61
20 7 0.30
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTTTTTTAAATTA
Found at i:475317 original size:20 final size:18
Alignment explanation
Indices: 475275--475321 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
475265 AAAAATTTTT
475275 TTAATATAAA-TAAAAAGA
1 TTAATA-AAATTAAAAAGA
*
475293 TTAATTAAAATTAAAAATA
1 TTAA-TAAAATTAAAAAGA
475312 TGTAATAAAA
1 T-TAATAAAA
475322 AATAGGAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 15 0.60
20 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (18 bp):
TTAATAAAATTAAAAAGA
Found at i:475819 original size:192 final size:194
Alignment explanation
Indices: 475569--475953 Score: 695
Period size: 192 Copynumber: 2.0 Consensus size: 194
475559 GCATGGCATG
* *
475569 CATGACATAATTTCTTACGAAAAGTAAATTTAGACCTCCCAAAGATGAGATTCTAAAAGTATTCC
1 CATGACAT-ATTTCTTACGAAAAATAAATTGAGACCT-CCAAAGATGAGATTCTAAAAGTATTCC
475634 GAGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGG
64 GAGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGG
*
475699 AACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAATTTTTTTTA
129 AACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTTA
475764 A
194 A
475765 CATGACAT-TTTCTTACGAAAAATAAATTCGAG-CCT-CAAAGATGAGATTCTAAAAGTATTCCG
1 CATGACATATTTCTTACGAAAAATAAATT-GAGACCTCCAAAGATGAGATTCTAAAAGTATTCCG
475827 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGA
65 AGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGA
475892 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTT
130 ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTT
475954 AATAAATAAA
Statistics
Matches: 185, Mismatches: 3, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
192 153 0.83
194 22 0.12
195 2 0.01
196 8 0.04
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (194 bp):
CATGACATATTTCTTACGAAAAATAAATTGAGACCTCCAAAGATGAGATTCTAAAAGTATTCCGA
GTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGAA
CATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTTAA
Found at i:480332 original size:8 final size:8
Alignment explanation
Indices: 480321--480345 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
480311 CTTCATTTAT
480321 TTATTTTC
1 TTATTTTC
480329 TTATTTTC
1 TTATTTTC
480337 TTATTTTC
1 TTATTTTC
480345 T
1 T
480346 CTTTTCCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTTTC
Found at i:480337 original size:25 final size:24
Alignment explanation
Indices: 480291--480342 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
480281 TTTTTATTTG
480291 TTTATTTATTTTCATTTCTTCTTCA
1 TTTATTTATTTTCATTTCTTCTT-A
*
480316 TTTATTTATTTTC-TTATTTTCTTA
1 TTTATTTATTTTCATT-TCTTCTTA
480340 TTT
1 TTT
480343 TCTCTTTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTATTTATTTTCATTTCTTCTTA
Found at i:486446 original size:19 final size:20
Alignment explanation
Indices: 486406--486452 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
486396 TGAAATCGTT
486406 AAAAATAATGGAAAGAAAGA
1 AAAAATAATGGAAAGAAAGA
*
486426 AAAAATAA-GAGAAA-AATGA
1 AAAAATAATG-GAAAGAAAGA
486445 AAAAATAA
1 AAAAATAA
486453 AGCTTTAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (20 bp):
AAAAATAATGGAAAGAAAGA
Found at i:487383 original size:35 final size:36
Alignment explanation
Indices: 487344--487431 Score: 115
Period size: 38 Copynumber: 2.4 Consensus size: 36
487334 ATATTTTTGA
*
487344 AAAAGACATTTGCATTTCATGTG-CATCATTTTAAG
1 AAAAGACATTTGCATTGCATGTGACATCATTTTAAG
* *
487379 AAAAGACATTTGAATTGCATTTGCATCATCATTTTAAG
1 AAAAGACATTTGCATTGCATGTG-A-CATCATTTTAAG
*
487417 AGAAGACATTTGCAT
1 AAAAGACATTTGCAT
487432 CATAATGGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 20 0.44
38 25 0.56
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (36 bp):
AAAAGACATTTGCATTGCATGTGACATCATTTTAAG
Found at i:487726 original size:42 final size:42
Alignment explanation
Indices: 487666--487757 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
487656 ATTCGAAGTC
487666 ATTTGCATATTCTCGGTGGTGATATCCAAGTGTTAAAGCTTG
1 ATTTGCATATTCTCGGTGGTGATATCCAAGTGTTAAAGCTTG
* * *
487708 ATTTGTATTTTCTTGGTGGTGATATCCAAGTGTTAAAGCTTG
1 ATTTGCATATTCTCGGTGGTGATATCCAAGTGTTAAAGCTTG
487750 ATTTGCAT
1 ATTTGCAT
487758 TCTCTCAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (42 bp):
ATTTGCATATTCTCGGTGGTGATATCCAAGTGTTAAAGCTTG
Found at i:487770 original size:42 final size:42
Alignment explanation
Indices: 487682--487772 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
487672 ATATTCTCGG
* * ***
487682 TGGTGATATCCAAGTGTTAAAGCTTGATTTGTATTTTCTTGG
1 TGGTGATATCCAAGTGTTAAAGCTTGATTTGCATTCTCTCAA
487724 TGGTGATATCCAAGTGTTAAAGCTTGATTTGCATTCTCTCAA
1 TGGTGATATCCAAGTGTTAAAGCTTGATTTGCATTCTCTCAA
487766 TGGTGAT
1 TGGTGAT
487773 GTTCGAGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (42 bp):
TGGTGATATCCAAGTGTTAAAGCTTGATTTGCATTCTCTCAA
Found at i:487879 original size:99 final size:104
Alignment explanation
Indices: 487750--487982 Score: 278
Period size: 108 Copynumber: 2.2 Consensus size: 104
487740 TTAAAGCTTG
* * *
487750 ATTTGCATTCTCTCAATGGTGATGTTCGAGTTTCCTTCGGTGATGATAT-C-TG-AA-G-TCATT
1 ATTTGCATTTTCTCAATGGTGATATTCGAGTTTCCTTCAGTGATGATATCCATGTAAGGTTCATT
* * *
487810 TGCATTTTATCGGTGGTAATATCTTAGCATTAAAAAATT
66 TGCATTTTATCAGTGGTAATATCTGAGCATTAAAAAATC
*
487849 ATTTGCATTTTCTCAATGGTGATATTCGAGTTTCCTTCAGTGGTGATATCCAAGTGTTAAGGTTT
1 ATTTGCATTTTCTCAATGGTGATATTCGAGTTTCCTTCAGTGATGATATCC-A-TG-TAAGG-TT
* * **
487914 GATTTGCATTTTCTCAGTGGTAATATCTGAGTGTTAAAAAATC
62 CATTTGCATTTTATCAGTGGTAATATCTGAGCATTAAAAAATC
*
487957 ATTTGCATTTTCTTCGATGGTGATAT
1 ATTTGCATTTTC-TCAATGGTGATAT
487983 CCAAAGTTAT
Statistics
Matches: 112, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
99 45 0.40
100 1 0.01
103 2 0.02
105 2 0.02
106 1 0.01
108 49 0.44
109 12 0.11
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.42
Consensus pattern (104 bp):
ATTTGCATTTTCTCAATGGTGATATTCGAGTTTCCTTCAGTGATGATATCCATGTAAGGTTCATT
TGCATTTTATCAGTGGTAATATCTGAGCATTAAAAAATC
Found at i:488056 original size:30 final size:32
Alignment explanation
Indices: 487967--488057 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 32
487957 ATTTGCATTT
* *
487967 TCTTCGATGGTGATATCCAAAGTTATTTACATC
1 TCTTCGATGGTGATATTCGAAGTTATTTA-ATC
* *
488000 TTTTCGGTGGTGATA-TCTG-AGATTATTT-ATC
1 TCTTCGATGGTGATATTC-GAAG-TTATTTAATC
488031 -CTTCGATGGTGATATTCGAAGTTATTT
1 TCTTCGATGGTGATATTCGAAGTTATTT
488058 TTTAGTGGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
30 19 0.40
31 7 0.15
32 3 0.06
33 19 0.40
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (32 bp):
TCTTCGATGGTGATATTCGAAGTTATTTAATC
Found at i:488227 original size:48 final size:49
Alignment explanation
Indices: 488157--488276 Score: 145
Period size: 49 Copynumber: 2.4 Consensus size: 49
488147 TGAGCTTCTT
* * * *
488157 TAAATTTTCAAAATTTGTTGAGCCTCTTC-TGATAGGAGCTTTTT-CAAGA
1 TAAATTTT-TAAATTTGTTGAGCCTCTACTTG-GAGAAGCTTTTTCCAAGA
*
488206 TAAATTTTTAAATTTATTGAGCCTCTACTTGGAGAAGCTTTTTCCAAGA
1 TAAATTTTTAAATTTGTTGAGCCTCTACTTGGAGAAGCTTTTTCCAAGA
* *
488255 TGAATTTTTAAAGTTGTTGAGC
1 TAAATTTTTAAATTTGTTGAGC
488277 TTTTGATTAG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
48 27 0.44
49 34 0.56
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (49 bp):
TAAATTTTTAAATTTGTTGAGCCTCTACTTGGAGAAGCTTTTTCCAAGA
Found at i:488294 original size:49 final size:48
Alignment explanation
Indices: 488081--488297 Score: 133
Period size: 49 Copynumber: 4.6 Consensus size: 48
488071 TTTATTTTTG
* * * *
488081 TTGAACCTCTACCTAGAGGAGCCTTTTTCAAAATGAGA-TTTTAAAGTTA
1 TTGAGCCTCTACTTAGAGGAG-CTTTTTCAAGAT-AAATTTTTAAAGTTA
** * * * ** * *
488130 CAGAGCCTCTGCTAAGATGAGCTTCTTT-AA-AT---TTTCAAAATTTG
1 TTGAGCCTCTACTTAGAGGAGCTT-TTTCAAGATAAATTTTTAAAGTTA
* * * *
488174 TTGAGCCTCTTCTGATAGGAGCTTTTTCAAGATAAATTTTTAAATTTA
1 TTGAGCCTCTACTTAGAGGAGCTTTTTCAAGATAAATTTTTAAAGTTA
* * * *
488222 TTGAGCCTCTACTTGGAGAAGCTTTTTCCAAGATGAATTTTTAAAGTTG
1 TTGAGCCTCTACTTAGAGGAGCTTTTT-CAAGATAAATTTTTAAAGTTA
* *
488271 TTGAGCTTTTGA-TTAGAGGAGCTTTTT
1 TTGAGCCTCT-ACTTAGAGGAGCTTTTT
488298 AAATTCCAAA
Statistics
Matches: 127, Mismatches: 32, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
43 3 0.02
44 27 0.21
45 2 0.02
47 2 0.02
48 36 0.28
49 56 0.44
50 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (48 bp):
TTGAGCCTCTACTTAGAGGAGCTTTTTCAAGATAAATTTTTAAAGTTA
Found at i:488454 original size:25 final size:25
Alignment explanation
Indices: 488426--488478 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
488416 ATAGACACCA
*
488426 TTTTATTATTT-ATTTATTTCTTTTC
1 TTTTATT-TTTCATTTATTTATTTTC
*
488451 TTTTCTTTTTCATTTATTTATTTTC
1 TTTTATTTTTCATTTATTTATTTTC
488476 TTT
1 TTT
488479 CTTTCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTATTTTTCATTTATTTATTTTC
Found at i:488473 original size:33 final size:33
Alignment explanation
Indices: 488431--488493 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
488421 CACCATTTTA
488431 TTATTTA-TTTATTTCTTTTCTTTTCTTTTTCAT
1 TTATTTATTTTATTTC-TTTCTTTTCTTTTTCAT
* *
488464 TTATTTATTTTCTTTCTTTCTTTTTTTTTT
1 TTATTTATTTTATTTCTTTCTTTTCTTTTT
488494 TTTTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (33 bp):
TTATTTATTTTATTTCTTTCTTTTCTTTTTCAT
Found at i:488489 original size:29 final size:29
Alignment explanation
Indices: 488433--488488 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
488423 CCATTTTATT
488433 ATTTATTTATTTCTTTTCTTTTCTTTTTC
1 ATTTATTTATTTCTTTTCTTTTCTTTTTC
488462 ATTTATTTATTT-TCTTTC-TTTCTTTTT
1 ATTTATTTATTTCT-TTTCTTTTCTTTTT
488489 TTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (29 bp):
ATTTATTTATTTCTTTTCTTTTCTTTTTC
Found at i:489272 original size:12 final size:13
Alignment explanation
Indices: 489250--489282 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
489240 ATTGGATCAG
489250 ATTGAACCAAACC
1 ATTGAACCAAACC
489263 ATTG-ACCAAACC
1 ATTGAACCAAACC
*
489275 ATCGAACC
1 ATTGAACC
489283 GTTGATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.42, C:0.33, G:0.09, T:0.15
Consensus pattern (13 bp):
ATTGAACCAAACC
Found at i:489393 original size:22 final size:20
Alignment explanation
Indices: 489346--489407 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
489336 GGTAAAAAAA
489346 ATATTTTTTTAAATTTTTTT
1 ATATTTTTTTAAATTTTTTT
* * *
489366 AGATTTTTTTATATATTATTT
1 ATATTTTTTTAAAT-TTTTTT
*
489387 -T-TTATTTTAAATTTTTATT
1 ATATTTTTTTAAATTTTT-TT
489406 AT
1 AT
489408 TAATATTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
18 3 0.09
19 11 0.34
20 13 0.41
21 5 0.16
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
ATATTTTTTTAAATTTTTTT
Found at i:489416 original size:13 final size:13
Alignment explanation
Indices: 489371--489417 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
489361 TTTTTAGATT
*
489371 TTTTTATATATTAT
1 TTTTTAT-TATTAA
489385 TTTTTATT-TTAAA
1 TTTTTATTATT-AA
489398 TTTTTATTATTAA
1 TTTTTATTATTAA
*
489411 TATTTAT
1 TTTTTAT
489418 GCATGTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 2 0.07
13 18 0.62
14 9 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTATTATTAA
Found at i:493902 original size:5 final size:5
Alignment explanation
Indices: 493883--493923 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
493873 ATCAAGCACT
* *
493883 TTTTG TTTTAT TTTTG TTTTG TTTTG TTTTG TTTTT TTTTG
1 TTTTG TTTT-G TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
493924 GAATTGGAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.02, C:0.00, G:0.15, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:493907 original size:21 final size:20
Alignment explanation
Indices: 493883--493923 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
493873 ATCAAGCACT
493883 TTTTGTTTTATTTTTGTTTTG
1 TTTTGTTTTATTTTT-TTTTG
*
493904 TTTTGTTTTGTTTTTTTTTG
1 TTTTGTTTTATTTTTTTTTG
493924 GAATTGGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.02, C:0.00, G:0.15, T:0.83
Consensus pattern (20 bp):
TTTTGTTTTATTTTTTTTTG
Found at i:494204 original size:25 final size:24
Alignment explanation
Indices: 494176--494227 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
494166 ATAAGGTTTA
*
494176 ATTAAATAAAAAATAATATTTTATG
1 ATTAAAT-AAAAATAATATTCTATG
*
494201 ATTACATAAAAATAATATTCTATG
1 ATTAAATAAAAATAATATTCTATG
494225 ATT
1 ATT
494228 TCATTTAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (24 bp):
ATTAAATAAAAATAATATTCTATG
Found at i:495430 original size:58 final size:58
Alignment explanation
Indices: 495335--495473 Score: 217
Period size: 58 Copynumber: 2.4 Consensus size: 58
495325 TTGTGCCGGA
* * *
495335 AAAATTGATACTTTCAACTTTT-TCCTAAAATATTTTTTAAAAATTTTAATCTCGAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAAAAACTTTAATCTCGAGG
* *
495392 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAAAAACTTTAATCTCGAGG
*
495450 AAAATTGATACTTTCAATTTTTCC
1 AAAATTGATACTTTCAACTTTTCC
495474 TAAAAAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
57 22 0.29
58 53 0.71
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.42
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAAAAACTTTAATCTCGAGG
Found at i:495480 original size:58 final size:58
Alignment explanation
Indices: 495335--495615 Score: 253
Period size: 63 Copynumber: 4.7 Consensus size: 58
495325 TTGTGCCGGA
* * * *
495335 AAAATTGATACTTTCAACTTTTTCCT--AAAATATTTTTTAAAAATTTTAATCTCGAGG
1 AAAATTGATACTTTCAA-TTTTTCCTAAAAAATATTTTTTGAAAACTTTAATTTCAAGG
* ** *
495392 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAATTTTTCCTAAAAAATATTTTTTGAAAACTTTAATTTCAAGG
* * *
495450 AAAATTGATACTTTCAATTTTTCCTAAAAAAAAAAAACCTTTTTTGAAAA-TTTATTTTTAAGG
1 AAAATTGATACTTTCAATTTTTCCT----AAAAAATA--TTTTTTGAAAACTTTAATTTCAAGG
* * * *
495513 AAAATTGATACTTTCAACTTTTCCTCAAAAAAAATCATTTTTTTGAAAACTTTATTTTTAAGT
1 AAAATTGATACTTTCAATTTTTCCT---AAAAAAT-A-TTTTTTGAAAACTTTAATTTCAAGG
* ** *
495576 AAAATTGATACTTTTAACTTTTTCCTCGAGAATATTTTTT
1 AAAATTGATACTTTCAA-TTTTTCCTAAAAAATATTTTTT
495616 TTTTGAAATT
Statistics
Matches: 191, Mismatches: 22, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
56 6 0.03
57 17 0.09
58 51 0.27
59 6 0.03
60 1 0.01
61 4 0.02
62 25 0.13
63 63 0.33
64 18 0.09
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.43
Consensus pattern (58 bp):
AAAATTGATACTTTCAATTTTTCCTAAAAAATATTTTTTGAAAACTTTAATTTCAAGG
Found at i:495635 original size:63 final size:62
Alignment explanation
Indices: 495389--495602 Score: 258
Period size: 63 Copynumber: 3.5 Consensus size: 62
495379 TTTAATCTCG
* * **
495389 AGGAAAATTGATACTTTCAACTTTTCC-C--CAAAAAT-A-TTTTTTGAAAACTTTAATTTCG
1 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAATCATTTTTTTGAAAA-TTTATTTTTA
* * ** *
495447 AGGAAAATTGATACTTTCAATTTTTCCTAAAAAAAAAAAACCTTTTTTGAAAATTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAATCA-TTTTTTTGAAAATTTATTTTTA
495510 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAATCATTTTTTTGAAAACTTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAATCATTTTTTTGAAAA-TTTATTTTTA
* *
495573 AGTAAAATTGATACTTTTAACTTTTTCCTC
1 AGGAAAATTGATACTTTCAAC-TTTTCCTC
495603 GAGAATATTT
Statistics
Matches: 134, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
58 26 0.19
61 5 0.04
62 12 0.09
63 72 0.54
64 19 0.14
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (62 bp):
AGGAAAATTGATACTTTCAACTTTTCCTCAAAAAAAATCATTTTTTTGAAAATTTATTTTTA
Found at i:498096 original size:13 final size:13
Alignment explanation
Indices: 498075--498105 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
498065 AAAAAATGAT
498075 AAATATGAAATAA
1 AAATATGAAATAA
*
498088 AAATCTGAAATAA
1 AAATATGAAATAA
498101 AAATA
1 AAATA
498106 AAAAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (13 bp):
AAATATGAAATAA
Found at i:498110 original size:21 final size:21
Alignment explanation
Indices: 498058--498133 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
498048 ACCATAAGAT
*
498058 AAAAATTAAAAAATGATAAATA
1 AAAAATAAAAAAAT-ATAAATA
** *
498080 TGAAAT--AAAAATCTGAAAT-
1 AAAAATAAAAAAATAT-AAATA
498099 AAAAATAAAAAAA-ATAAATAA
1 AAAAATAAAAAAATATAAAT-A
498120 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
498134 TTACAATCGA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 9 0.21
20 11 0.26
21 18 0.43
22 4 0.10
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAAATAAAAAAATATAAATA
Found at i:498117 original size:13 final size:13
Alignment explanation
Indices: 498101--498132 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
498091 TCTGAAATAA
498101 AAATAAAAAAAAT
1 AAATAAAAAAAAT
498114 AAAT-AAAAAAAT
1 AAATAAAAAAAAT
498126 AAA-AAAA
1 AAATAAAA
498133 TTTACAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAATAAAAAAAAT
Found at i:498117 original size:19 final size:20
Alignment explanation
Indices: 498095--498133 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
498085 TAAAAATCTG
*
498095 AAATAAAAATA-AAAAAAAT
1 AAATAAAAAAATAAAAAAAT
498114 AAATAAAAAAATAAAAAAAT
1 AAATAAAAAAATAAAAAAAT
498134 TTACAATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (20 bp):
AAATAAAAAAATAAAAAAAT
Found at i:498132 original size:9 final size:10
Alignment explanation
Indices: 498095--498130 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
498085 TAAAAATCTG
498095 AAATAAAAAT
1 AAATAAAAAT
498105 AAA-AAAAAT
1 AAATAAAAAT
498114 AAAT-AAAA-
1 AAATAAAAAT
498122 AAATAAAAA
1 AAATAAAAA
498131 AATTTACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 4 0.17
9 17 0.71
10 3 0.12
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:498294 original size:13 final size:12
Alignment explanation
Indices: 498276--498306 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
498266 AACTGGATTA
498276 TTTTTTTTGCCTT
1 TTTTTTTTG-CTT
498289 TTTTTTTTGCTT
1 TTTTTTTTGCTT
498301 TTTTTT
1 TTTTTT
498307 CTTTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTTTTTGCTT
Found at i:498546 original size:12 final size:12
Alignment explanation
Indices: 498516--498546 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
498506 ACAGAGGCAA
498516 TTTTTTTGTTTT
1 TTTTTTTGTTTT
*
498528 TTGTTTTGTTTT
1 TTTTTTTGTTTT
498540 TTTTTTT
1 TTTTTTT
498547 CAAAGGTCCT
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:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:498546 original size:124 final size:123
Alignment explanation
Indices: 498318--498545 Score: 329
Period size: 124 Copynumber: 1.9 Consensus size: 123
498308 TTTTTAAATT
* * *
498318 TTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGGAAAACATAAATAAAGCTCATTTAAA
1 TTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGGAAAACATAAACAAAGCTCACTTAAA
498383 CAGAGGCTCAACTTTTTTTTTTGTTTTCTTGCTTTTTTTTTGTTTTTTTTTTGAAAAAA
66 CAGAGGC-CAACTTTTTTTTTTGTTTTCTTGCTTTTTTTTTGTTTTTTTTTTGAAAAAA
* *
498442 TTGATCAAAGCTCCTCTAAACAGAGGCTCAACGA-TTTTGAGAAACATAAACAAAGCTCCCTTAA
1 TTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGGA-AAACATAAACAAAGCTCACTTAA
* *
498506 ACAGAGG-CAA-TTTTTTTGTTT-TTTGTTTTGTTTTTTTTTT
65 ACAGAGGCCAACTTTTTTT-TTTGTTT-TCTTGCTTTTTTTTT
498546 TCAAAGGTCC
Statistics
Matches: 94, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
121 10 0.11
122 19 0.20
123 5 0.05
124 60 0.64
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (123 bp):
TTGATCAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGGAAAACATAAACAAAGCTCACTTAAA
CAGAGGCCAACTTTTTTTTTTGTTTTCTTGCTTTTTTTTTGTTTTTTTTTTGAAAAAA
Found at i:498681 original size:41 final size:41
Alignment explanation
Indices: 498553--498761 Score: 325
Period size: 42 Copynumber: 5.1 Consensus size: 41
498543 TTTTCAAAGG
498553 TCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATTGC
*
498595 TCCTCTAAACAGAGGCACCATGACTTTGAAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTGC
*
498637 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTAC
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
* * *
498678 TCCTCT--ACAGAGGTACCACAACTTTGAAAAATAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
498717 TCCTCTAAACAGAGGCACCACGACTTTTG-AAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGC
498758 TCCT
1 TCCT
498762 TGACAATCAT
Statistics
Matches: 153, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
39 35 0.23
41 47 0.31
42 70 0.46
43 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (41 bp):
TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
Found at i:498737 original size:80 final size:82
Alignment explanation
Indices: 498553--498761 Score: 334
Period size: 80 Copynumber: 2.5 Consensus size: 82
498543 TTTTCAAAGG
**
498553 TCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCATGA
1 TCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATTGCTCCTCT-AACAGAGGCACCACAA
498618 CTTTGAAAAAGTAAATTGC
64 CTTTGAAAAAGTAAATTGC
* *
498637 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTACTCCTCT-ACAGAGGTACCACAACT
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAACAGAGGCACCACAACT
498701 TTGAAAAA-TAAATTGC
66 TTGAAAAAGTAAATTGC
498717 TCCTCTAAACAGAGGCACCACGACTTTTG-AAAGTAAATTGCTCCT
1 TCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATTGCTCCT
498762 TGACAATCAT
Statistics
Matches: 119, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
80 47 0.39
81 26 0.22
83 17 0.14
84 29 0.24
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (82 bp):
TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAACAGAGGCACCACAACT
TTGAAAAAGTAAATTGC
Found at i:500226 original size:14 final size:13
Alignment explanation
Indices: 500208--500252 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 13
500198 CATTTTCTCA
500208 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
*
500221 TCTTTTTTTTTCTT
1 T-TTTTTTCTTCTT
*
500235 TTTTTTT-TTATT
1 TTTTTTTCTTCTT
500247 TTTTTT
1 TTTTTT
500253 CATCATCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.34
13 7 0.24
14 12 0.41
ACGTcount: A:0.02, C:0.09, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:500232 original size:10 final size:10
Alignment explanation
Indices: 500219--500253 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
500209 TTTTTTCTTC
500219 TTTCTTTTTT
1 TTTCTTTTTT
500229 TTTCTTTTTT
1 TTTCTTTTTT
*
500239 TTTTTATTTTT
1 TTTCT-TTTTT
500250 TTTC
1 TTTC
500254 ATCATCTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:500243 original size:17 final size:17
Alignment explanation
Indices: 500208--500243 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
500198 CATTTTCTCA
500208 TTTTTTTCTTCTTTCTT
1 TTTTTTTCTTCTTTCTT
500225 TTTTTTTCTT-TTT-TT
1 TTTTTTTCTTCTTTCTT
500240 TTTT
1 TTTT
500244 ATTTTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 3 0.16
17 10 0.53
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTTTTCTTCTTTCTT
Found at i:500283 original size:30 final size:30
Alignment explanation
Indices: 500230--500286 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
500220 TTCTTTTTTT
* **
500230 TTCTTTTTTTTTTTATTTTTTTTCATCATC
1 TTCTTTTCTTTTTTATCATTTTTCATCATC
*
500260 TTCTTTTCTTTTTTCTCATTTTTCATC
1 TTCTTTTCTTTTTTATCATTTTTCATC
500287 CATTGTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (30 bp):
TTCTTTTCTTTTTTATCATTTTTCATCATC
Found at i:503611 original size:58 final size:58
Alignment explanation
Indices: 503481--503687 Score: 229
Period size: 65 Copynumber: 3.4 Consensus size: 58
503471 TTGTGCCGAA
* * *
503481 AAAATTAATACTTTCAACTTTTTCCCAAAATATTTTTTTGTGGAAAGC-TT-ATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAA-ATATTTTT-TGGAAA-CTTTAATTTT-AAGG
*
503541 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTAATTTTGAGG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTAATTTTAAGG
** * *
503599 AAAATTGATACTTTCAACTTTTCTTCAAAAAAAAAATCATTTTTTTGAAAACTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTC--C---CCAAAAAT-A-TTTTTTGGAAACTTTAATTTTAAGG
503664 AAAATTGATACTTTCAACTTTTCC
1 AAAATTGATACTTTCAACTTTTCC
503688 TCGAGAATTT
Statistics
Matches: 129, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
57 1 0.01
58 34 0.26
59 12 0.09
60 29 0.22
63 7 0.05
64 1 0.01
65 45 0.35
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.43
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTAATTTTAAGG
Found at i:507063 original size:39 final size:38
Alignment explanation
Indices: 507020--507121 Score: 98
Period size: 41 Copynumber: 2.6 Consensus size: 38
507010 AAGTTATTTT
*
507020 TTTTAATA-TAGACTATGATTTTTTAAAAATTCGTAGTCC
1 TTTTAATACTAAACTAT-ATTTTTTAAAAATT-GTAGTCC
* * * * * *
507059 TTTTATATATTATATTATAATTTTTTGAAAATTGTATTCT
1 TTTTA-ATACTAAACTAT-ATTTTTTAAAAATTGTAGTCC
507099 TTTTAATACTAAACTATATTTTT
1 TTTTAATACTAAACTATATTTTT
507122 CATACTAAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
38 6 0.12
39 14 0.27
40 13 0.25
41 19 0.37
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (38 bp):
TTTTAATACTAAACTATATTTTTTAAAAATTGTAGTCC
Found at i:507139 original size:22 final size:19
Alignment explanation
Indices: 507098--507134 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
507088 AATTGTATTC
507098 TTTTTAATACTAAACTATA
1 TTTTTAATACTAAACTATA
*
507117 TTTTTCATACTAAACTAT
1 TTTTTAATACTAAACTAT
507135 TATATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTTAATACTAAACTATA
Found at i:507292 original size:22 final size:21
Alignment explanation
Indices: 507258--507315 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
507248 ATTAAATGAA
*
507258 TTAAATAATAAAACTTAATTATT
1 TTAAATAATAAAA--TAATAATT
507281 TTAAA-AATAAAATAATAATT
1 TTAAATAATAAAATAATAATT
507301 TTAAATAATTAAAAT
1 TTAAATAA-TAAAAT
507316 TTGTTTAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 12 0.38
21 2 0.06
22 13 0.41
23 5 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAATAATAAAATAATAATT
Found at i:508081 original size:19 final size:19
Alignment explanation
Indices: 508059--508095 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
508049 AGTTGTAATC
*
508059 TTTTTAATATTAAACTATA
1 TTTTTAATACTAAACTATA
*
508078 TTTTTCATACTAAACTAT
1 TTTTTAATACTAAACTAT
508096 TATATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTTAATACTAAACTATA
Found at i:508234 original size:21 final size:22
Alignment explanation
Indices: 508178--508263 Score: 88
Period size: 21 Copynumber: 4.0 Consensus size: 22
508168 AATTTATCAC
* *
508178 ATTATTTTAAAAAATAAGAATAAA
1 ATTATTTTAAATAATAA-AA-ATA
*
508202 ATTA-ATTAAATAATAAAAATA
1 ATTATTTTAAATAATAAAAATA
*
508223 ATTATTTT-AATAAT-AAAATC
1 ATTATTTTAAATAATAAAAATA
*
508243 ATTATTTTAAATAATTAAAAT
1 ATTATTTTAAATAATAAAAAT
508264 TTCTTTAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 13 0.24
21 18 0.33
22 9 0.17
23 10 0.19
24 4 0.07
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (22 bp):
ATTATTTTAAATAATAAAAATA
Found at i:510063 original size:19 final size:19
Alignment explanation
Indices: 510019--510067 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
510009 ATTTGACATA
510019 AAATAATTTAATAATAATT
1 AAATAATTTAATAATAATT
* * *
510038 TATTAATTTGATAA-ATATT
1 AAATAATTTAATAATA-ATT
510057 AAATAATTTAA
1 AAATAATTTAA
510068 AATTTTTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AAATAATTTAATAATAATT
Found at i:510639 original size:41 final size:40
Alignment explanation
Indices: 510574--510679 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 40
510564 TAAACTACAA
* * *
510574 TTTTATCTATATAAACTATGATTTTTTTAAAAATCGTAGTCC
1 TTTTATATAT-TAAACTAT-ATTTTTTTAAAAATCATAATCC
* * * *
510616 TTTTATATATTAGACTATAATTTTTTGAAAATCATAATCT
1 TTTTATATATTAAACTATATTTTTTTAAAAATCATAATCC
510656 TTTTA-ATATTAAACTATATTTTTT
1 TTTTATATATTAAACTATATTTTTT
510680 ATACTAAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
39 17 0.31
40 22 0.40
41 7 0.13
42 9 0.16
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (40 bp):
TTTTATATATTAAACTATATTTTTTTAAAAATCATAATCC
Found at i:510796 original size:22 final size:22
Alignment explanation
Indices: 510772--510842 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
510762 AAATTTATCA
510772 AATTATTTAAAAATAAGAATAA-
1 AATTATTTAAAAATAA-AATAAT
*
510794 AATTAATTAAATAATAAAA-AAT
1 AATTATTTAAA-AATAAAATAAT
510816 AATTATTTTAAAAATAAAATAAT
1 AATTA-TTTAAAAATAAAATAAT
510839 AATT
1 AATT
510843 TTAAATAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.05
22 24 0.56
23 17 0.40
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (22 bp):
AATTATTTAAAAATAAAATAAT
Found at i:510807 original size:20 final size:18
Alignment explanation
Indices: 510782--510820 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
510772 AATTATTTAA
510782 AAATAAGAATAAAATTAATT
1 AAATAAGAA-AAAA-TAATT
*
510802 AAATAATAAAAAATAATT
1 AAATAAGAAAAAATAATT
510820 A
1 A
510821 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATAAGAAAAAATAATT
Found at i:510836 original size:20 final size:21
Alignment explanation
Indices: 510772--510857 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 21
510762 AAATTTATCA
*
510772 AATTATTTAAA-AATAAGAATAA
1 AATTATTTAAATAATAA-AA-AT
*
510794 AATTAATTAAATAATAAAAAAT
1 AATTATTTAAATAAT-AAAAAT
510816 AATTATTTTAAA-AAT-AAAAT
1 AATTA-TTTAAATAATAAAAAT
* *
510836 AATAATTTTAAATAATCAAAAT
1 AATTA-TTTAAATAATAAAAAT
510858 TTGTTTAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
20 16 0.29
21 3 0.05
22 24 0.44
23 10 0.18
24 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (21 bp):
AATTATTTAAATAATAAAAAT
Found at i:511893 original size:21 final size:20
Alignment explanation
Indices: 511864--511903 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
511854 TAAAATATAT
*
511864 TTATTAAATTAAAAAATTAA
1 TTATTAAATGAAAAAATTAA
511884 TTATTAAAATGAAATAAATT
1 TTATT-AAATGAAA-AAATT
511904 CGTGCCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
TTATTAAATGAAAAAATTAA
Found at i:511975 original size:49 final size:49
Alignment explanation
Indices: 511922--512018 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
511912 CTCCCTTATC
*
511922 TCATTTTTAAATTTTAAAAATTTCATTATCAATATATAAAATTATAGCA
1 TCATTTTTAAATTATAAAAATTTCATTATCAATATATAAAATTATAGCA
* *
511971 TCATTTTTAAATTATAAAATTTTTATTATCAATATATAAAATTATAGC
1 TCATTTTTAAATTATAAAAATTTCATTATCAATATATAAAATTATAGC
512019 TGATGCATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (49 bp):
TCATTTTTAAATTATAAAAATTTCATTATCAATATATAAAATTATAGCA
Found at i:512170 original size:14 final size:14
Alignment explanation
Indices: 512147--512179 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
512137 AGGTAACATA
*
512147 TAAA-TAAAGTTTT
1 TAAAGTAAAGTTTG
512160 TAAAGTAAAGTTTG
1 TAAAGTAAAGTTTG
512174 TAAAGT
1 TAAAGT
512180 TTTTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (14 bp):
TAAAGTAAAGTTTG
Found at i:514795 original size:13 final size:13
Alignment explanation
Indices: 514777--514805 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
514767 AACAAGTTAT
514777 AAATGAGAGGCCA
1 AAATGAGAGGCCA
514790 AAATGAGAGGCCA
1 AAATGAGAGGCCA
514803 AAA
1 AAA
514806 GAATTGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.14, G:0.28, T:0.07
Consensus pattern (13 bp):
AAATGAGAGGCCA
Found at i:515009 original size:18 final size:18
Alignment explanation
Indices: 514986--515020 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
514976 TATGATAGAG
*
514986 TTTTTACAAATTTATTAA
1 TTTTTACAAATATATTAA
*
515004 TTTTTATAAATATATTA
1 TTTTTACAAATATATTA
515021 TTATAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTACAAATATATTAA
Found at i:523102 original size:28 final size:27
Alignment explanation
Indices: 523070--523150 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 27
523060 ATTTATGCTC
523070 TTTTTTTAGTTAATAAATTATGAAATAA
1 TTTTTTTA-TTAATAAATTATGAAATAA
* *
523098 TTTTTTAATT--TAATATAATGAAA-AA
1 TTTTTTTATTAATAA-ATTATGAAATAA
*
523123 TTTTATTATATAATAAACTTAT-AAATAA
1 TTTTTTTAT-TAATAAA-TTATGAAATAA
523151 ATAAAATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
25 12 0.29
26 9 0.21
27 6 0.14
28 15 0.36
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (27 bp):
TTTTTTTATTAATAAATTATGAAATAA
Found at i:523136 original size:25 final size:26
Alignment explanation
Indices: 523073--523137 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
523063 TATGCTCTTT
*
523073 TTTTAGTTA-ATAA-ATTATGAAATAA
1 TTTTA-TTATATAATATAATGAAATAA
*
523098 TTTT-TTAATTTAATATAATGAAA-AA
1 TTTTATT-ATATAATATAATGAAATAA
523123 TTTTATTATATAATA
1 TTTTATTATATAATA
523138 AACTTATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
23 2 0.06
24 1 0.03
25 20 0.61
26 10 0.30
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (26 bp):
TTTTATTATATAATATAATGAAATAA
Found at i:523196 original size:17 final size:17
Alignment explanation
Indices: 523118--523219 Score: 53
Period size: 17 Copynumber: 5.5 Consensus size: 17
523108 TAATATAATG
523118 AAAAATT-TTATTATAT
1 AAAAATTATTATTATAT
* * *
523134 AATAAACTTATAAATAAAT
1 AA-AAA-TTATTATTATAT
523153 AAAATTATTATTATATTATGAATT
1 AAAA--ATTA-T-TATTAT--A-T
*
523177 AAAAATTATTATTTTAT
1 AAAAATTATTATTATAT
**
523194 AAATTTTATTATTATAT
1 AAAAATTATTATTATAT
523211 AAATAATTA
1 AAA-AATTA
523220 ATAACCAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 20
0.66 0.13 0.21
Matches are distributed among these distances:
16 2 0.03
17 21 0.33
18 8 0.13
19 11 0.17
20 7 0.11
21 4 0.06
22 4 0.06
23 1 0.02
24 5 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (17 bp):
AAAAATTATTATTATAT
Found at i:523399 original size:19 final size:20
Alignment explanation
Indices: 523377--523419 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
523367 TTTGACATAA
*
523377 AAATAATTTACTGATTTT-T
1 AAATAATTTACTAATTTTAT
*
523396 AAATAATTTATTAATTTTAT
1 AAATAATTTACTAATTTTAT
523416 AAAT
1 AAAT
523420 GTTAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATAATTTACTAATTTTAT
Found at i:524027 original size:20 final size:20
Alignment explanation
Indices: 523999--524037 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
523989 GATGATAGAG
523999 TTTTTTAAAGAT-TTATTAA
1 TTTTTTAAAGATATTATTAA
*
524018 TTTTTATAAATATATTATTA
1 TTTTT-TAAAGATATTATTA
524038 TAAAATACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTTAAAGATATTATTAA
Found at i:526929 original size:144 final size:144
Alignment explanation
Indices: 526729--527135 Score: 636
Period size: 144 Copynumber: 2.8 Consensus size: 144
526719 ACCTCTATAG
* *
526729 AAATATGTTTTCTGGATCGATACCTCAAGAAATAGGGATGCTTAAATCTCTCACTGACTTTCAGT
1 AAATATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTCAGT
* * *
526794 TGAGTCATAATAATTTCTCTGGTTCAATCCCTGCTTTCATAAGAAACTTGACCAGTTTATCCATT
66 TGAGTCATAATAATTTCTCTGGTTCAATCCCTGCTTTCATAGGAAACTTGACCAGTCTATCCACT
526859 CTCTACCCTCACCA
131 CTCTACCCTCACCA
* * *
526873 TAATATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGT
1 AAATATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTCAGT
* * *
526938 TGAGTCATAATAATTTCTTTGGTTCAATCCCTGCTTCCATAGGAAACTTGACTAGTCTATCCACT
66 TGAGTCATAATAATTTCTCTGGTTCAATCCCTGCTTTCATAGGAAACTTGACCAGTCTATCCACT
* * *
527003 CTCTACCTTGATCA
131 CTCTACCCTCACCA
*
527017 AAATATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTAACTTTGC-G
1 AAATATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTT-CAG
* * *
527081 TTGAGTCAAAATAATTTCTCTGGTTCAATCCCCGCTTTCATAGGAAACTTAACCA
65 TTGAGTCATAATAATTTCTCTGGTTCAATCCCTGCTTTCATAGGAAACTTGACCA
527136 AATTGTCTAG
Statistics
Matches: 238, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
144 238 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (144 bp):
AAATATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTCAGT
TGAGTCATAATAATTTCTCTGGTTCAATCCCTGCTTTCATAGGAAACTTGACCAGTCTATCCACT
CTCTACCCTCACCA
Found at i:526947 original size:72 final size:71
Alignment explanation
Indices: 526874--527093 Score: 166
Period size: 72 Copynumber: 3.1 Consensus size: 71
526864 CCCTCACCAT
526874 AATATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTT
1 AATATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACT-ACTTTGAGTT
*
526939 GAGTCAT
65 GAGTCAA
* * **** ** * * *
526946 AATAAT-TTCTT-TGGTTCAATCCCTGC-TTCCATA-GGAAACTTGACTAGTCTATCCACT-CTC
1 AAT-ATGTT-TTCTGGGTCAATACCT-CAAGAGATAGGGATGCTT-A--AATCTCT-CACTACTT
*
527006 T-ACCTTGA-TCAA
59 TGA-GTTGAGTCAA
* *
527018 AATATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTAACTTTGCGTT
1 AATATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACT-ACTTTGAGTT
527083 GAGTCAA
65 GAGTCAA
527090 AATA
1 AATA
527094 ATTTCTCTGG
Statistics
Matches: 105, Mismatches: 27, Indels: 32
0.64 0.16 0.20
Matches are distributed among these distances:
69 4 0.04
70 5 0.05
71 18 0.17
72 51 0.49
73 18 0.17
74 5 0.05
75 4 0.04
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (71 bp):
AATATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTACTTTGAGTTG
AGTCAA
Found at i:527154 original size:144 final size:144
Alignment explanation
Indices: 526669--527203 Score: 628
Period size: 144 Copynumber: 3.7 Consensus size: 144
526659 ACTATCTACG
* * * * * *** *
526669 TGGTTCTATCCCCGCTTCCATAGGAAACTTGACCTACTTATCTGTTCTCCACC-TCTAT-AGAAA
1 TGGTTCAATCCCTGCTTTCATAGGAAACTTGACCAAATTATCCACTCTCTACCTTC-ATCA-AAA
* * *
526732 TATGTTTTCTGGATCGATACCTCAAGAAATAGGGATGCTTAAATCTCTCACTGACTTT-CAGTTG
64 TATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGC-GTTG
526796 AGTCATAATAATTTCTC
128 AGTCATAATAATTTCTC
* ** * * * *
526813 TGGTTCAATCCCTGCTTTCATAAGAAACTTGACCAGTTTATCCATTCTCTACCCTCACCATAATA
1 TGGTTCAATCCCTGCTTTCATAGGAAACTTGACCAAATTATCCACTCTCTACCTTCATCAAAATA
*
526878 TGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGT
66 TGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGCGTTGAGT
*
526943 CATAATAATTTCTT
131 CATAATAATTTCTC
* * * *
526957 TGGTTCAATCCCTGCTTCCATAGGAAACTTGA-CTAGTCTATCCACTCTCTACCTTGATCAAAAT
1 TGGTTCAATCCCTGCTTTCATAGGAAACTTGACCAAAT-TATCCACTCTCTACCTTCATCAAAAT
* *
527021 ATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTAACTTTGCGTTGAG
65 ATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGCGTTGAG
*
527086 TCAAAATAATTTCTC
130 TCATAATAATTTCTC
* * * * ** * ** *
527101 TGGTTCAATCCCCGCTTTCATAGGAAACTTAACCAAATTGTCTAGACTTTACCTTTTTGAAAATA
1 TGGTTCAATCCCTGCTTTCATAGGAAACTTGACCAAATTATCCACTCTCTACCTTCATCAAAATA
* * * *
527166 AGCTTTCCGGGTCAATACCTCAAGAGGTAGGGATGCTT
66 TGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTT
527204 GTACATCTTA
Statistics
Matches: 336, Mismatches: 50, Indels: 10
0.85 0.13 0.03
Matches are distributed among these distances:
143 2 0.01
144 328 0.98
145 6 0.02
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.35
Consensus pattern (144 bp):
TGGTTCAATCCCTGCTTTCATAGGAAACTTGACCAAATTATCCACTCTCTACCTTCATCAAAATA
TGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGCGTTGAGT
CATAATAATTTCTC
Found at i:527199 original size:288 final size:288
Alignment explanation
Indices: 526669--527203 Score: 727
Period size: 288 Copynumber: 1.9 Consensus size: 288
526659 ACTATCTACG
* ***
526669 TGGTTCTATCCCCGCTTCCATAGGAAACTTGACCTACTTATCTGTTCTCCACCTCTATAGAAATA
1 TGGTTCAATCCCCGCTTCCATAGGAAACTTGACCTACTTATCCACTCTCCACCTCTATAGAAATA
*
526734 TGTTTTCTGGATCGATACCTCAAGAAATAGGGATGCTTAAATCTCTCACTGACTTTCAGTTGAGT
66 TGTTTTCTGGATCGATACCTCAAGAAATAGGGATGCTTAAATCTCTCACTAACTTTCAGTTGAGT
* * * ** **
526799 CATAATAATTTCTCTGGTTCAATCCCTGCTTTCATAAGAAACTTGACCAGTTTATCCATTCTCTA
131 CAAAATAATTTCTCTGGTTCAATCCCCGCTTTCATAAGAAACTTAACCAAATTATCCAGACTCTA
* * * *
526864 CCCTCACCATAATATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTG
196 CCCTCACCAAAATAAGCTTTCCGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTG
526929 ACTTTGAGTTGAGTCATAATAATTTCTT
261 ACTTTGAGTTGAGTCATAATAATTTCTT
* * *
526957 TGGTTCAATCCCTGCTTCCATAGGAAACTTGA-CTAGTCTATCCACTCTCTACCT-TGATCA-AA
1 TGGTTCAATCCCCGCTTCCATAGGAAACTTGACCTACT-TATCCACTCTCCACCTCT-AT-AGAA
* *
527019 ATATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTAACTTTGC-GTT
63 ATATGTTTTCTGGATCGATACCTCAAGAAATAGGGATGCTTAAATCTCTCACTAACTTT-CAGTT
* * *
527083 GAGTCAAAATAATTTCTCTGGTTCAATCCCCGCTTTCATAGGAAACTTAACCAAATTGTCTAGAC
127 GAGTCAAAATAATTTCTCTGGTTCAATCCCCGCTTTCATAAGAAACTTAACCAAATTATCCAGAC
* * **** *
527148 TTTACCTTTTTGAAAATAAGCTTTCCGGGTCAATACCTCAAGAGGTAGGGATGCTT
192 TCTACCCTCACCAAAATAAGCTTTCCGGGTCAATACCTCAAGAGATAGGGATGCTT
527204 GTACATCTTA
Statistics
Matches: 212, Mismatches: 31, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
287 5 0.02
288 205 0.97
289 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.35
Consensus pattern (288 bp):
TGGTTCAATCCCCGCTTCCATAGGAAACTTGACCTACTTATCCACTCTCCACCTCTATAGAAATA
TGTTTTCTGGATCGATACCTCAAGAAATAGGGATGCTTAAATCTCTCACTAACTTTCAGTTGAGT
CAAAATAATTTCTCTGGTTCAATCCCCGCTTTCATAAGAAACTTAACCAAATTATCCAGACTCTA
CCCTCACCAAAATAAGCTTTCCGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTG
ACTTTGAGTTGAGTCATAATAATTTCTT
Found at i:530648 original size:55 final size:54
Alignment explanation
Indices: 530587--530693 Score: 153
Period size: 55 Copynumber: 2.0 Consensus size: 54
530577 ATGTCAACAA
* * *
530587 TAATAATTGTCTTTGTTAAATCAATGTGCAC-ATTGCAAAATATAAAAATTTAATG
1 TAATAATTCTCATTGTTAAATCAATGT-C-CGAATGCAAAATATAAAAATTTAATG
*
530642 TAATAATTCTCATTGTTAAATCAATGTCCGAATGCAAAATATAAAACTTTAA
1 TAATAATTCTCATTGTTAAATCAATGTCCGAATGCAAAATATAAAAATTTAA
530694 GTTGAGTTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
53 1 0.02
54 21 0.45
55 25 0.53
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (54 bp):
TAATAATTCTCATTGTTAAATCAATGTCCGAATGCAAAATATAAAAATTTAATG
Found at i:531794 original size:20 final size:22
Alignment explanation
Indices: 531771--531810 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
531761 TAAAATATAT
531771 TTATT-AAATTAAA-AAATTAA
1 TTATTAAAATTAAATAAATTAA
531791 TTATTAAAATTAAATAAATT
1 TTATTAAAATTAAATAAATT
531811 CGTGCCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTATTAAAATTAAATAAATTAA
Found at i:534389 original size:20 final size:19
Alignment explanation
Indices: 534360--534405 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
534350 CTTCTTACAC
* *
534360 TTTTTAATTATTTGGTGTTA
1 TTTTTTATTATTT-GTCTTA
*
534380 TTTTTTATTATTTTTCTTA
1 TTTTTTATTATTTGTCTTA
534399 TTTTTTA
1 TTTTTTA
534406 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (19 bp):
TTTTTTATTATTTGTCTTA
Found at i:535689 original size:15 final size:17
Alignment explanation
Indices: 535669--535717 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 17
535659 TTTATTTTTT
535669 TTATTT-TTTAAT-TAA
1 TTATTTATTTAATATAA
*
535684 TTATTTATTTATTATAA
1 TTATTTATTTAATATAA
535701 TTATTATTATTTAATAT
1 TTA-T-TTATTTAATAT
535718 TATTGTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 6 0.21
16 5 0.18
17 6 0.21
18 1 0.04
19 10 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTATTTAATATAA
Found at i:535692 original size:19 final size:18
Alignment explanation
Indices: 535668--535733 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 18
535658 CTTTATTTTT
535668 TTTATTTTTTAATTAATTA
1 TTTATTTTTTAA-TAATTA
*
535687 TTTATTTATT-ATAATTA
1 TTTATTTTTTAATAATTA
*
535704 -TTATTATTTAAT-ATTA
1 TTTATTTTTTAATAATTA
535720 TTGTA-TTTTTAATA
1 TT-TATTTTTTAATA
535734 TTTAAAAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 11 0.28
17 16 0.41
18 3 0.08
19 9 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTTTTAATAATTA
Found at i:536408 original size:84 final size:84
Alignment explanation
Indices: 536135--536409 Score: 304
Period size: 84 Copynumber: 3.3 Consensus size: 84
536125 ACAAGAAATC
* * * * *
536135 ATGCTCGGAGGTCTTACAAATTTTGAAAC-AAAGCAAATTCAACTTAAAAAACTTACGAATCCTA
1 ATGCTCAGAGGTCTTACAAATCTCGAAACTAAAACAAATTCAACTCAAAAAACTTACGAAT-CT-
536199 T-CC-AGAGGACTTAGAGATT
64 TGCCTAGAGGACTTAGAGATT
* * * * * *
536218 ATGCTCAGATGTCTTACAAATCTCAAAACTAAAATAGATTCAGCTCAAAAAAACTTATGAATCTT
1 ATGCTCAGAGGTCTTACAAATCTCGAAACTAAAACAAATTCAACTC-AAAAAACTTACGAATCTT
536283 GCCTAGAGGACTTAGAGATT
65 GCCTAGAGGACTTAGAGATT
* * ** * * * *
536303 ACGTTTGGGGGTCTTATAAATCTCGAAACTAAAACAAATTTAACTCAGAAAACTTACGAATCTTG
1 ATGCTCAGAGGTCTTACAAATCTCGAAACTAAAACAAATTCAACTCAAAAAACTTACGAATCTTG
*
536368 CCTAGAAGACTTAGAGATT
66 CCTAGAGGACTTAGAGATT
* *
536387 ATGCTCAAAGGTTTTACAAATCT
1 ATGCTCAGAGGTCTTACAAATCT
536410 TAACCTTTTT
Statistics
Matches: 154, Mismatches: 34, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
83 25 0.16
84 65 0.42
85 64 0.42
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (84 bp):
ATGCTCAGAGGTCTTACAAATCTCGAAACTAAAACAAATTCAACTCAAAAAACTTACGAATCTTG
CCTAGAGGACTTAGAGATT
Found at i:536676 original size:32 final size:33
Alignment explanation
Indices: 536612--536689 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 33
536602 GTGCCACCTT
536612 AACTAGGCTTAAAATCTCAACTATGTGCTAGCTA
1 AACTAGGCTTAAAATCTCAAC-ATGTGCTAGCTA
*
536646 AACTGGGCTTAAAATCTCAAC-TGTGCTAGCTA
1 AACTAGGCTTAAAATCTCAACATGTGCTAGCTA
*
536678 AACTTGGCTTAA
1 AACTAGGCTTAA
536690 TTATCATCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 22 0.52
34 20 0.48
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (33 bp):
AACTAGGCTTAAAATCTCAACATGTGCTAGCTA
Found at i:543207 original size:16 final size:16
Alignment explanation
Indices: 543186--543216 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
543176 TTAGGGTTTT
543186 GATTTTAGAGTTTGGA
1 GATTTTAGAGTTTGGA
*
543202 GATTTTAGGGTTTGG
1 GATTTTAGAGTTTGG
543217 GTTTTGTGGT
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:0.00, G:0.35, T:0.45
Consensus pattern (16 bp):
GATTTTAGAGTTTGGA
Found at i:543242 original size:21 final size:21
Alignment explanation
Indices: 543209--543251 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
543199 GGAGATTTTA
*
543209 GGGTTTGGGTTTT-GTGGTTTG
1 GGGTTTGGATTTTAG-GGTTTG
*
543230 GGGTTTTGATTTTAGGGTTTG
1 GGGTTTGGATTTTAGGGTTTG
543251 G
1 G
543252 ATTTTAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.05, C:0.00, G:0.44, T:0.51
Consensus pattern (21 bp):
GGGTTTGGATTTTAGGGTTTG
Found at i:543267 original size:51 final size:52
Alignment explanation
Indices: 543173--543282 Score: 127
Period size: 51 Copynumber: 2.1 Consensus size: 52
543163 GGATATGGAA
* * * *
543173 GGTTTAGGGTTTTGATTTTAGAGTTTGGAGATTTTAGGGTTTGGGTTTT-GT
1 GGTTTGGGGTTTTGATTTTAGAGTTTGGAGATTTTAGAGTTTGGATTTTGGG
* *
543224 GGTTTGGGGTTTTGATTTTAGGGTTT-G-GATTTTAAAGATTTTGGATTTTGGG
1 GGTTTGGGGTTTTGATTTTAGAGTTTGGAGATTTT--AGAGTTTGGATTTTGGG
543276 GGTTTGG
1 GGTTTGG
543283 ATTTTGTGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
49 6 0.12
50 1 0.02
51 35 0.70
52 8 0.16
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (52 bp):
GGTTTGGGGTTTTGATTTTAGAGTTTGGAGATTTTAGAGTTTGGATTTTGGG
Found at i:543309 original size:16 final size:15
Alignment explanation
Indices: 543229--543375 Score: 118
Period size: 15 Copynumber: 9.5 Consensus size: 15
543219 TTTGTGGTTT
*
543229 GGGGTTTTGATTTTA
1 GGGGTTTGGATTTTA
543244 -GGGTTTGGATTTTAA
1 GGGGTTTGGATTTT-A
* ** *
543259 AGATTTTGGATTTTG
1 GGGGTTTGGATTTTA
543274 GGGGTTTGGATTTT-
1 GGGGTTTGGATTTTA
*
543288 GTGGGTTTCGAATTTTA
1 G-GGGTTT-GGATTTTA
*
543305 GGGGTTTGGATTTAA
1 GGGGTTTGGATTTTA
* *
543320 GGGATTTTAGATTTTTA
1 GGG-GTTTGGA-TTTTA
543337 GGGGTTTGGATTTTA
1 GGGGTTTGGATTTTA
*
543352 TGAGGTTTTGGATTTTA
1 -G-GGGTTTGGATTTTA
*
543369 GGTGTTT
1 GGGGTTT
543376 TAGAAACCTA
Statistics
Matches: 105, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
14 13 0.12
15 36 0.34
16 35 0.33
17 21 0.20
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.50
Consensus pattern (15 bp):
GGGGTTTGGATTTTA
Found at i:543368 original size:32 final size:31
Alignment explanation
Indices: 543230--543375 Score: 154
Period size: 31 Copynumber: 4.7 Consensus size: 31
543220 TTGTGGTTTG
*
543230 GGGTTTT-GATTTTA-GGGTTTGGATTTTAA
1 GGGTTTTGGATTTTAGGGGTTTGGATTTTAT
* * * *
543259 AGATTTTGGATTTTGGGGGTTTGGATTTTGT
1 GGGTTTTGGATTTTAGGGGTTTGGATTTTAT
* * *
543290 GGGTTTCGAATTTTAGGGGTTTGGA-TTTAA
1 GGGTTTTGGATTTTAGGGGTTTGGATTTTAT
*
543320 GGGATTTTAGATTTTTAGGGGTTTGGATTTTAT
1 GGG-TTTTGGA-TTTTAGGGGTTTGGATTTTAT
*
543353 GAGGTTTTGGATTTTAGGTGTTT
1 G-GGTTTTGGATTTTAGGGGTTT
543376 TAGAAACCTA
Statistics
Matches: 93, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
29 5 0.05
30 12 0.13
31 37 0.40
32 26 0.28
33 11 0.12
34 2 0.02
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.50
Consensus pattern (31 bp):
GGGTTTTGGATTTTAGGGGTTTGGATTTTAT
Found at i:543376 original size:16 final size:15
Alignment explanation
Indices: 543230--543376 Score: 118
Period size: 16 Copynumber: 9.5 Consensus size: 15
543220 TTGTGGTTTG
543230 GGGTTTT-GATTTTA
1 GGGTTTTGGATTTTA
543244 GGG-TTTGGATTTTAA
1 GGGTTTTGGATTTT-A
* * *
543259 AGATTTTGGATTTTG
1 GGGTTTTGGATTTTA
* *
543274 GGGGTTTGGATTTTGT
1 GGGTTTTGGATTTT-A
* *
543290 GGGTTTCGAATTTTA
1 GGGTTTTGGATTTTA
* *
543305 GGGGTTTGGATTTAA
1 GGGTTTTGGATTTTA
*
543320 GGGATTTTAGATTTTTA
1 GGG-TTTTGGA-TTTTA
*
543337 GGGGTTTGGATTTTA
1 GGGTTTTGGATTTTA
543352 TGAGGTTTTGGATTTTA
1 -G-GGTTTTGGATTTTA
543369 GGTGTTTT
1 GG-GTTTT
543377 AGAAACCTAG
Statistics
Matches: 103, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
13 3 0.03
14 9 0.09
15 33 0.32
16 38 0.37
17 20 0.19
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.50
Consensus pattern (15 bp):
GGGTTTTGGATTTTA
Found at i:544678 original size:36 final size:36
Alignment explanation
Indices: 544631--544700 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
544621 CCCATGCCTC
*
544631 TTTATTTCTTCTGTATTTTCTGGTAGTAGGGTAGAA
1 TTTATTTCTTCTGTATTTTCTAGTAGTAGGGTAGAA
544667 TTTATTTCTTCTGTATTTTCTAGTAGTAGGGTAG
1 TTTATTTCTTCTGTATTTTCTAGTAGTAGGGTAG
544701 GATGAACAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.19, C:0.09, G:0.21, T:0.51
Consensus pattern (36 bp):
TTTATTTCTTCTGTATTTTCTAGTAGTAGGGTAGAA
Found at i:544825 original size:16 final size:16
Alignment explanation
Indices: 544802--544838 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
544792 ACAGTTCTTC
544802 TTTTTTTTGTATT-TT
1 TTTTTTTTGTATTATT
544817 TTTTGTTTTGTATTATT
1 TTTT-TTTTGTATTATT
544834 TTTTT
1 TTTTT
544839 GGTATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 10 0.50
17 6 0.30
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (16 bp):
TTTTTTTTGTATTATT
Found at i:544835 original size:28 final size:28
Alignment explanation
Indices: 544802--544858 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
544792 ACAGTTCTTC
* *
544802 TTTTTTTTGTATTTTTTTTGTTTTGTATTA
1 TTTTTTTGGTA-TTTATTT-TTTTGTATTA
544832 TTTTTTTGGTATTTATTTTTTTGTATT
1 TTTTTTTGGTATTTATTTTTTTGTATT
544859 TCGTATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.36
29 6 0.24
30 10 0.40
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (28 bp):
TTTTTTTGGTATTTATTTTTTTGTATTA
Found at i:544851 original size:16 final size:15
Alignment explanation
Indices: 544802--544859 Score: 75
Period size: 14 Copynumber: 3.9 Consensus size: 15
544792 ACAGTTCTTC
*
544802 TTTTTTTTGTATTTT
1 TTTTTTTTGTATTTA
544817 TTTTGTTTTGTA-TTA
1 TTTT-TTTTGTATTTA
*
544832 TTTTTTTGGTATTTA
1 TTTTTTTTGTATTTA
544847 -TTTTTTTGTATTT
1 TTTTTTTTGTATTT
544860 CGTATAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
14 18 0.47
15 13 0.34
16 7 0.18
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (15 bp):
TTTTTTTTGTATTTA
Found at i:545110 original size:22 final size:23
Alignment explanation
Indices: 545080--545124 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
545070 AATCGAATTT
* *
545080 ATGCTCGAAGGTTTTACA-AATC
1 ATGCCCGAAGGTCTTACAGAATC
545102 ATGCCCGAAGGTCTTACAGAATC
1 ATGCCCGAAGGTCTTACAGAATC
545125 GATTGGGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (23 bp):
ATGCCCGAAGGTCTTACAGAATC
Found at i:545211 original size:110 final size:110
Alignment explanation
Indices: 545032--545234 Score: 284
Period size: 110 Copynumber: 1.8 Consensus size: 110
545022 ATGACATCGT
* * * * * * *
545032 AAGTTGAAAAATAATAAATTGATCGAGATAATATCGTGAATCGAATTTATGCTCGAAGGTTTTAC
1 AAGTTAAAAAATAATAAATCGATCGAGATAACACCGTGAATCAAATTTATGCTCGAAGGTCTTAA
545097 AAATCATGCCCGAAGGTCTTACAGAATCGATTGGGATAACACTGC
66 AAATCATGCCCGAAGGTCTTACAGAATCGATTGGGATAACACTGC
* *
545142 AAGTTAAAAAATAA-AGAATCGATCGGGATAACACCGTGAATCAAATTTATGC-CTGGAGGTCTT
1 AAGTTAAAAAATAATA-AATCGATCGAGATAACACCGTGAATCAAATTTATGCTC-GAAGGTCTT
*
545205 AAAAATCATGCCCGGAGGTCTTACAGAATC
64 AAAAATCATGCCCGAAGGTCTTACAGAATC
545235 ATGTCTGGAG
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
109 2 0.02
110 79 0.98
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (110 bp):
AAGTTAAAAAATAATAAATCGATCGAGATAACACCGTGAATCAAATTTATGCTCGAAGGTCTTAA
AAATCATGCCCGAAGGTCTTACAGAATCGATTGGGATAACACTGC
Found at i:545244 original size:23 final size:23
Alignment explanation
Indices: 545190--545257 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
545180 AATCAAATTT
*
545190 ATGCCTGGAGGTCTTA-AAAATC
1 ATGCCTGGAGGTCTTACAGAATC
*
545212 ATGCCCGGAGGTCTTACAGAATC
1 ATGCCTGGAGGTCTTACAGAATC
*
545235 ATGTCTGGAGGTCTTACAGAATC
1 ATGCCTGGAGGTCTTACAGAATC
545258 GACTGGGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 15 0.37
23 26 0.63
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (23 bp):
ATGCCTGGAGGTCTTACAGAATC
Found at i:545358 original size:22 final size:22
Alignment explanation
Indices: 545333--545380 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
545323 ATGCCAAAAA
*
545333 GTCTTAAAAATCATGCCCGGAG
1 GTCTTAAAAATCATGCCCGAAG
*
545355 GTCTTAAAAATCATGCCTGAAG
1 GTCTTAAAAATCATGCCCGAAG
545377 GTCT
1 GTCT
545381 CACAGAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (22 bp):
GTCTTAAAAATCATGCCCGAAG
Found at i:545448 original size:132 final size:132
Alignment explanation
Indices: 545088--545492 Score: 567
Period size: 132 Copynumber: 3.1 Consensus size: 132
545078 TTATGCTCGA
* * * * * * *
545088 AGGTTTTACAAATCATGCCCGAAGGTCTTACAGAATCGATTGGGATAACACTGCAAGTTAAAAAA
1 AGGTCTTAAAAATCATGCCTGAAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAGA
*
545153 TAAAGAATCGATCGGGATAACACCGTGAATCAAATTTATGCCTGGAGGTCTTAAAAATCATGCCC
66 TAAAGAATCGATCGGGATAACACCGTGAATCAAATTTATGCCAGGAGGTCTTAAAAATCATGCCC
545218 GG
131 GG
* * * *
545220 AGGTCTTACAGAATCATGTCTGGAGGTCTTACAGAATCGACTGGGATAACATCGCAAGTCAAAAG
1 AGGTCTTA-AAAATCATGCCTGAAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAG
* ** *
545285 ATAAAGAATCGATCGGGATAACACCGTGAATCGAATTTATGCCAAAAAGTCTTAAAAATCATGCC
65 ATAAAGAATCGATCGGGATAACACCGTGAATCAAATTTATGCCAGGAGGTCTTAAAAATCATGCC
545350 CGG
130 CGG
* * *
545353 AGGTCTTAAAAATCATGCCTGAAGGTCTCACAGAATTGACTGGGATAACACCACAAGTCAAAAGA
1 AGGTCTTAAAAATCATGCCTGAAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAGA
* * * * * *
545418 TAAAGCATTGATCGGGATAACACCGCGAATCAAATTTATGCCCGGAGGTCTTAGAAATCATACCC
66 TAAAGAATCGATCGGGATAACACCGTGAATCAAATTTATGCCAGGAGGTCTTAAAAATCATGCCC
*
545483 GA
131 GG
545485 AGGTCTTA
1 AGGTCTTA
545493 GAGATTATGC
Statistics
Matches: 238, Mismatches: 34, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
132 121 0.51
133 117 0.49
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (132 bp):
AGGTCTTAAAAATCATGCCTGAAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAAAGA
TAAAGAATCGATCGGGATAACACCGTGAATCAAATTTATGCCAGGAGGTCTTAAAAATCATGCCC
GG
Found at i:545483 original size:22 final size:22
Alignment explanation
Indices: 545458--545520 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
545448 CAAATTTATG
545458 CCCGGAGGTCTTAGAAATCATA
1 CCCGGAGGTCTTAGAAATCATA
* * * *
545480 CCCGAAGGTCTTAGAGATTATG
1 CCCGGAGGTCTTAGAAATCATA
* *
545502 CCCAGAGGTCTTACAAATC
1 CCCGGAGGTCTTAGAAATC
545521 TCAAAATCTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
CCCGGAGGTCTTAGAAATCATA
Found at i:546294 original size:66 final size:66
Alignment explanation
Indices: 546218--546361 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
546208 CTTTTTTTTG
* * * * *
546218 GGCCAAATAAACTGGGTTTAAAT-TTTA-TTGAAGGCCAGCTAAAACTGGGCTTAAAACCTCATT
1 GGCCAGATAAACTAGGCTTAAATCTTCATTTG-AGGCCAGAT-AAACTGGGCTTAAAACCTCA-T
546281 TGA-
63 TGAT
* *
546284 GGCTAGATAAAATAGGCTTAAATCTTCATTTGAGGCCAGATAAACTGGGCTTAAAACCTCATTGA
1 GGCCAGATAAACTAGGCTTAAATCTTCATTTGAGGCCAGATAAACTGGGCTTAAAACCTCATTGA
546349 T
66 T
546350 GGCCAGATAAAC
1 GGCCAGATAAAC
546362 CGGGCCAGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
65 4 0.06
66 48 0.73
67 11 0.17
68 3 0.05
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (66 bp):
GGCCAGATAAACTAGGCTTAAATCTTCATTTGAGGCCAGATAAACTGGGCTTAAAACCTCATTGA
T
Found at i:546361 original size:33 final size:33
Alignment explanation
Indices: 546249--546366 Score: 148
Period size: 33 Copynumber: 3.5 Consensus size: 33
546239 ATTTTATTGA
*
546249 AGGCCAGCTAAAACTGGGCTTAAAACCTCATTTG
1 AGGCCAGAT-AAACTGGGCTTAAAACCTCATTTG
* * * * *
546283 AGGCTAGATAAAATAGGCTTAAATCTTCATTTG
1 AGGCCAGATAAACTGGGCTTAAAACCTCATTTG
546316 AGGCCAGATAAACTGGGCTTAAAACCTCA-TTG
1 AGGCCAGATAAACTGGGCTTAAAACCTCATTTG
*
546348 ATGGCCAGATAAACCGGGC
1 A-GGCCAGATAAACTGGGC
546367 CAGATAAATT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
32 4 0.06
33 60 0.85
34 7 0.10
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (33 bp):
AGGCCAGATAAACTGGGCTTAAAACCTCATTTG
Found at i:546371 original size:47 final size:47
Alignment explanation
Indices: 546317--546408 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 47
546307 CTTCATTTGA
*
546317 GGCCAGATAAACTGGGCTTAAAACCTCATTGATGGCCAGATAAACCG
1 GGCCAGATAAACTGGGCTTAAAACCTCATTAATGGCCAGATAAACCG
* * *
546364 GGCCAGATAAATTGGGCTTAAAACTTTATTAATGGCCAGATAAAC
1 GGCCAGATAAACTGGGCTTAAAACCTCATTAATGGCCAGATAAAC
546409 TGGGTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (47 bp):
GGCCAGATAAACTGGGCTTAAAACCTCATTAATGGCCAGATAAACCG
Found at i:546406 original size:33 final size:33
Alignment explanation
Indices: 546364--546472 Score: 155
Period size: 33 Copynumber: 3.3 Consensus size: 33
546354 AGATAAACCG
* * * **
546364 GGCCAGATAAATTGGGCTTAAAACTTTATTAAT
1 GGCCAGATAAACTGGGTTTAAAGCTTCGTTAAT
546397 GGCCAGATAAACTGGGTTTAAAGCTTCGTTAAT
1 GGCCAGATAAACTGGGTTTAAAGCTTCGTTAAT
* *
546430 GGCCAGATAAACTAGGTTTAAAGCTTCGTTGAT
1 GGCCAGATAAACTGGGTTTAAAGCTTCGTTAAT
546463 GGCCAGATAA
1 GGCCAGATAA
546473 GTTGGGGGCC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (33 bp):
GGCCAGATAAACTGGGTTTAAAGCTTCGTTAAT
Found at i:546500 original size:82 final size:82
Alignment explanation
Indices: 546397--546636 Score: 381
Period size: 82 Copynumber: 2.9 Consensus size: 82
546387 CTTTATTAAT
* * * * *
546397 GGCCAGATAAACTGGGTTTAAAGCTTCGTTAATGGCCAGATAAACTAGGTTTAAAGCTTCGTTGA
1 GGCCAGATAAACTGGGCTTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGCTTCATTGA
* *
546462 TGGCCAGATAAGTTGGG
66 TGGCCAGATAAGCTAGG
* *
546479 GGCCAGATAAACTGGACTTAAAGCTTCATTGATGGCCAGATAAACTGGGCTTAAAGCTTCATTGA
1 GGCCAGATAAACTGGGCTTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGCTTCATTGA
546544 TGGCCAGATAAGCTAGG
66 TGGCCAGATAAGCTAGG
* *
546561 GGCCAGATAAATTGGGCTTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAACTTCATTGA
1 GGCCAGATAAACTGGGCTTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGCTTCATTGA
546626 TGGCCAGATAA
66 TGGCCAGATAA
546637 ACTGGGCTTA
Statistics
Matches: 145, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 145 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (82 bp):
GGCCAGATAAACTGGGCTTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAGCTTCATTGA
TGGCCAGATAAGCTAGG
Found at i:546521 original size:33 final size:33
Alignment explanation
Indices: 546479--546554 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
546469 ATAAGTTGGG
546479 GGCCAGATAAACTGGACTTAAAGCTTCATTGAT
1 GGCCAGATAAACTGGACTTAAAGCTTCATTGAT
*
546512 GGCCAGATAAACTGGGCTTAAAGCTTCATTGAT
1 GGCCAGATAAACTGGACTTAAAGCTTCATTGAT
546545 GGCCAGATAA
1 GGCCAGATAA
546555 GCTAGGGGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (33 bp):
GGCCAGATAAACTGGACTTAAAGCTTCATTGAT
Found at i:546533 original size:115 final size:114
Alignment explanation
Indices: 546250--546702 Score: 443
Period size: 115 Copynumber: 4.0 Consensus size: 114
546240 TTTTATTGAA
* * * * * *
546250 GGCCAGCTAAAACTGGGCTTAAAACCTCATTTGA-GGCTAGATAAAATAGGCTTAAATCTTCATT
1 GGCCAGAT-AAACTGGGCTTAAAACTTCA-TTGATGGCCAGATAAACTGGGCTTAAAGCTTCA-T
* * * *
546314 TGA-GGCCAGATAAACTGGGCTTAAAACCTCATTGATGGCCAGATAA--ACCG
63 TAATGGCCAGATAAACTAGGCTTAAAACTTCATTGATGGCCAGATAATTA-AG
* * * * *
546364 GGCCAGATAAATTGGGCTTAAAACTTTATTAATGGCCAGATAAACTGGGTTTAAAGCTTCGTTAA
1 GGCCAGATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAACTGGGCTTAAAGCTTCATTAA
* * * **
546429 TGGCCAGATAAACTAGGTTTAAAGCTTCGTTGATGGCCAGATAAGTTGGG
66 TGGCCAGATAAACTAGGCTTAAAACTTCATTGATGGCCAGATAA-TTAAG
* * *
546479 GGCCAGATAAACTGGACTTAAAGCTTCATTGATGGCCAGATAAACTGGGCTTAAAGCTTCATTGA
1 GGCCAGATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAACTGGGCTTAAAGCTTCATTAA
* **** * ** * * * *
546544 TGGCCAGATAAGCTAGGGGCCAGA-TAAATTG--GGCTTAAAGCTTCATTAAT
66 TGGCCAGATAAACTAGGCTTAAAACTTCATTGATGGC---CAG-ATAATTAAG
*
546594 GGCCAGATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAACTGGGCTTAAAGTTTCATTAA
1 GGCCAGATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAACTGGGCTTAAAGCTTCATTAA
*
546659 TGGCCAGATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAA
66 TGGCCAGATAAACTAGGCTTAAAACTTCATTGATGGCCAGATAA
546703 ACTGGGCTTA
Statistics
Matches: 268, Mismatches: 59, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
112 9 0.03
113 77 0.29
114 13 0.05
115 159 0.59
116 7 0.03
118 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (114 bp):
GGCCAGATAAACTGGGCTTAAAACTTCATTGATGGCCAGATAAACTGGGCTTAAAGCTTCATTAA
TGGCCAGATAAACTAGGCTTAAAACTTCATTGATGGCCAGATAATTAAG
Found at i:546603 original size:33 final size:33
Alignment explanation
Indices: 546561--546715 Score: 256
Period size: 33 Copynumber: 4.7 Consensus size: 33
546551 ATAAGCTAGG
*
546561 GGCCAGATAAATTGGGCTTAAAGCTTCATTAAT
1 GGCCAGATAAACTGGGCTTAAAGCTTCATTAAT
* *
546594 GGCCAGATAAACTGGGCTTAAAACTTCATTGAT
1 GGCCAGATAAACTGGGCTTAAAGCTTCATTAAT
*
546627 GGCCAGATAAACTGGGCTTAAAGTTTCATTAAT
1 GGCCAGATAAACTGGGCTTAAAGCTTCATTAAT
* *
546660 GGCCAGATAAACTGGGCTTAAAACTTCATTGAT
1 GGCCAGATAAACTGGGCTTAAAGCTTCATTAAT
546693 GGCCAGATAAACTGGGCTTAAAG
1 GGCCAGATAAACTGGGCTTAAAG
546716 TTTTTCTTTT
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 112 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
GGCCAGATAAACTGGGCTTAAAGCTTCATTAAT
Found at i:546667 original size:66 final size:66
Alignment explanation
Indices: 546561--546718 Score: 298
Period size: 66 Copynumber: 2.4 Consensus size: 66
546551 ATAAGCTAGG
* *
546561 GGCCAGATAAATTGGGCTTAAAGCTTCATTAATGGCCAGATAAACTGGGCTTAAAACTTCATTGA
1 GGCCAGATAAACTGGGCTTAAAGTTTCATTAATGGCCAGATAAACTGGGCTTAAAACTTCATTGA
546626 T
66 T
546627 GGCCAGATAAACTGGGCTTAAAGTTTCATTAATGGCCAGATAAACTGGGCTTAAAACTTCATTGA
1 GGCCAGATAAACTGGGCTTAAAGTTTCATTAATGGCCAGATAAACTGGGCTTAAAACTTCATTGA
546692 T
66 T
546693 GGCCAGATAAACTGGGCTTAAAGTTT
1 GGCCAGATAAACTGGGCTTAAAGTTT
546719 TTCTTTTTTT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 90 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (66 bp):
GGCCAGATAAACTGGGCTTAAAGTTTCATTAATGGCCAGATAAACTGGGCTTAAAACTTCATTGA
T
Found at i:547989 original size:11 final size:10
Alignment explanation
Indices: 547973--548026 Score: 58
Period size: 11 Copynumber: 5.4 Consensus size: 10
547963 TCATAACCAA
*
547973 TTTTTTCTTC
1 TTTTTTTTTC
547983 -TTTTTTTTC
1 TTTTTTTTTC
547992 TTTTTTTTCTC
1 TTTTTTTT-TC
*
548003 TTTTTTTGTTG
1 TTTTTTT-TTC
548014 TTTTTTTTT-
1 TTTTTTTTTC
548023 TTTT
1 TTTT
548027 ATGCCCCCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 12 0.31
10 9 0.23
11 17 0.44
12 1 0.03
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:547992 original size:9 final size:9
Alignment explanation
Indices: 547973--548026 Score: 65
Period size: 10 Copynumber: 5.8 Consensus size: 9
547963 TCATAACCAA
547973 TTTTTTCTTC
1 TTTTTT-TTC
547983 TTTTTTTTC
1 TTTTTTTTC
547992 TTTTTTTTC
1 TTTTTTTTC
*
548001 TCTTTTTTTG
1 T-TTTTTTTC
548011 TTGTTTTTT-
1 TT-TTTTTTC
548020 TTTTTTT
1 TTTTTTT
548027 ATGCCCCCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
8 5 0.12
9 16 0.39
10 20 0.49
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:553705 original size:64 final size:64
Alignment explanation
Indices: 553637--553768 Score: 257
Period size: 64 Copynumber: 2.1 Consensus size: 64
553627 TGTCAATGTC
553637 TCTAAACAGTAAGTATGAATTAAATATGCATATATAATAATTTATGGAGAGGAATCAGCTTACA
1 TCTAAACAGTAAGTATGAATTAAATATGCATATATAATAATTTATGGAGAGGAATCAGCTTACA
553701 TCTAAACAGTAAGTATGAATTAAATATGCATATATAATAATTTATGGAGAGGAATCAGCTTACA
1 TCTAAACAGTAAGTATGAATTAAATATGCATATATAATAATTTATGGAGAGGAATCAGCTTACA
553765 -CTAA
1 TCTAA
553769 TTTAAAACTA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
63 4 0.06
64 64 0.94
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (64 bp):
TCTAAACAGTAAGTATGAATTAAATATGCATATATAATAATTTATGGAGAGGAATCAGCTTACA
Found at i:555645 original size:18 final size:19
Alignment explanation
Indices: 555624--555668 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
555614 GCAAAGCTAT
555624 TTAATTATGT-AAAAATAA
1 TTAATTATGTGAAAAATAA
*
555642 TTAATTTTTTGTGAAAAATAA
1 TTAA--TTATGTGAAAAATAA
555663 TTAATT
1 TTAATT
555669 TTTTGTGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 2 0.09
20 5 0.22
21 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (19 bp):
TTAATTATGTGAAAAATAA
Found at i:555671 original size:22 final size:22
Alignment explanation
Indices: 555634--555682 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
555624 TTAATTATGT
555634 AAAAATAATTAATTTTTTGT-G
1 AAAAATAATTAATTTTTTGTGG
555655 AAAAATAATTAATTTTTTGTGG
1 AAAAATAATTAATTTTTTGTGG
555677 AAAAAT
1 AAAAAT
555683 CATTTTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (22 bp):
AAAAATAATTAATTTTTTGTGG
Found at i:557264 original size:22 final size:22
Alignment explanation
Indices: 557193--557263 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
557183 AATTATTTAA
557193 AATTATTATTTTATTTTTAAAAT
1 AATTATTATTTTATTTTT-AAAT
*
557216 AATTATT-TTTTATTATTTAATT
1 AATTATTATTTTATT-TTTAAAT
557238 AATT-TTATTCTTATTTTTAAAT
1 AATTATTATT-TTATTTTTAAAT
557260 AATT
1 AATT
557264 TGATAAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.05
22 26 0.60
23 15 0.35
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (22 bp):
AATTATTATTTTATTTTTAAAT
Done.