Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008424.1 Hibiscus syriacus cultivar Beakdansim tig00111207_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4198033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 16
Found at i:6759 original size:22 final size:22
Alignment explanation
Indices: 6729--6779 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
6719 CATGGGCCTA
* *
6729 ATGGGCCTAGTTGTAAGACCTT
1 ATGGACCTAGTTGTAAGACATT
*
6751 ATGGACCTATTTGTAAGACATT
1 ATGGACCTAGTTGTAAGACATT
6773 ATGGACC
1 ATGGACC
6780 CTAAGGTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (22 bp):
ATGGACCTAGTTGTAAGACATT
Found at i:8538 original size:3 final size:3
Alignment explanation
Indices: 8530--8556 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
8520 ATTAATGGCA
8530 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
8557 CACTACATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:9488 original size:21 final size:21
Alignment explanation
Indices: 9458--9530 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
9448 TAATATACTT
9458 TATA-TTTAATACTTATATTA
1 TATACTTTAATACTTATATTA
*
9478 TATACTTTAATACTTATATCCA
1 TATACTTTAATACTTATAT-TA
* * * *
9500 AACACTTTATTACTTTACATTA
1 TATACTTTAATAC-TTATATTA
9522 TATACTTTA
1 TATACTTTA
9531 TATATATATA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 4 0.10
21 14 0.33
22 19 0.45
23 5 0.12
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (21 bp):
TATACTTTAATACTTATATTA
Found at i:9673 original size:25 final size:24
Alignment explanation
Indices: 9626--9671 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
9616 TGATGAGGGA
9626 TGAAATTGAATTAATTATAAAATT
1 TGAAATTGAATTAATTATAAAATT
*
9650 TGAAGTTGATATTAA-TATAAAA
1 TGAAATTGA-ATTAATTATAAAA
9672 ATGGACGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (24 bp):
TGAAATTGAATTAATTATAAAATT
Found at i:10021 original size:24 final size:26
Alignment explanation
Indices: 9970--10033 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
9960 ATTGAAACAA
* * *
9970 TTATATATATATATATATATATGTATG
1 TTATGTATA-ATATGTATATATGAATG
9997 -TATGTATAATATGTATA-ATGAATG
1 TTATGTATAATATGTATATATGAATG
10021 TTATG-ATAATATG
1 TTATGTATAATATG
10034 ATGCATGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 14 0.42
25 12 0.36
26 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (26 bp):
TTATGTATAATATGTATATATGAATG
Found at i:10050 original size:20 final size:21
Alignment explanation
Indices: 9979--10048 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
9969 ATTATATATA
*
9979 TATATATATATATGTATGTATG
1 TATATATATATATG-ATGAATG
* *
10001 TATA-ATATGTATAATGAATG
1 TATATATATATATGATGAATG
*
10021 T-TATGATA-ATATGATGCATG
1 TATAT-ATATATATGATGAATG
10041 TATATATA
1 TATATATA
10049 ATGTACATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 2 0.05
20 20 0.51
21 13 0.33
22 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.44
Consensus pattern (21 bp):
TATATATATATATGATGAATG
Found at i:10110 original size:6 final size:6
Alignment explanation
Indices: 10068--10108 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
10058 ATACTTTATG
* *
10068 TATATA TATACA TATACA TATACA TATACA TATACT TATAC
1 TATACA TATACA TATACA TATACA TATACA TATACA TATAC
10109 TTTATAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (6 bp):
TATACA
Found at i:10675 original size:23 final size:23
Alignment explanation
Indices: 10613--10691 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
10603 TATGATGCAT
10613 GTATATATAATGTAAAATAT-AA
1 GTATATATAATGTAAAATATAAA
*
10635 GTATATATAAAGTGTAAACTATAAA
1 GTATATAT-AA-TGTAAAATATAAA
* * *
10660 GTATATATACTTTAAAGTATAAA
1 GTATATATAATGTAAAATATAAA
*
10683 ATATATATA
1 GTATATATA
10692 TATATATATA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.16
23 21 0.43
24 10 0.20
25 10 0.20
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.37
Consensus pattern (23 bp):
GTATATATAATGTAAAATATAAA
Found at i:10718 original size:587 final size:582
Alignment explanation
Indices: 9520--10725 Score: 1477
Period size: 587 Copynumber: 2.1 Consensus size: 582
9510 TACTTTACAT
* * *
9520 TATATACTTTATATATATATATAGATTATAT-ATGTATACAAATTGAACAAACATGAAATTGAAA
1 TATATA-TATATATATATATATATATTATATAAAGTATACAAATTGAACAAACATGAAATTGAAA
9584 ATAAAAAATTGAATAAATTAAACAACACACATTGATGAGGGATGAAATTGAATTAATTATAAAAT
65 ATAAAAAATTGAATAAATTAAACAACACACATTGATGAGGGATGAAATTGAATTAATTATAAAAT
* ** *
9649 TTGAAGTTGATATTAATATAAAAATGGACGAAATTGCATACATTTAAAAAGTTGGTGAACATAAT
130 GTGAAACTAATATTAATATAAAAATGGAC-AAATTGCATACATTTAAAAAGTTGGTGAACATAAT
*
9714 TTGAAAATAAATTTATTATGTGATTTACATTTTATAGGGTTTTAAGTAAATTACAAAAATATAAA
194 TTGAAAAGAAATTTATTATGTGATTTA-ATTTTATAGGGTTTTAAGTAAATTACAAAAATATAAA
* * * *
9779 TAAGTATGGGTCAATTTCAGATACAAATATACTTTGAAGGACTAAATTGAACAAATATGAAATTA
258 TAAGGATGGGTCAATTTCAGATACAAATATAATTTAAAGAACTAAATTGAACAAATATGAAATTA
* * * * * *
9844 AAAATAAAATTTTAAATAAATTAAAGAACACAAATGGATTAAATCGAAATAATTGTAAAATGTTA
323 AAAATAAAATTTTAAATAAAATAAAGAACACAAAAGGATCAAATC-AAAAAAATGTAAAATGTGA
* * * *
9909 AGAAATGTGTAAAATTAACTAAATTGCATTAATTTCAAAAGTTAAGAAAAAATTGAAACAATTAT
387 AGAAATGTATAAAATGAACTAAATTGCATTAATTTCAAAAATTAAGAAAAAATTAAAACAATTAT
9974 ATATATATATATATATATGTATGTATGTATAATATGTATAATGAATGTTATGATAATATGATGCA
452 ATATATATATATATATA-GTA-GTA-GTATAATA-GTATAATGAATGTTATGATAATATGATGCA
* * * * * *
10039 TGTATATATAATGTACATTATACTTTATGTATATATATACATATACATATACATATACATATACT
513 TGTATATATAATGTAAAATATACTTTATGTATAAATATAAATATACATATAAATATAAATATACT
10104 TATAC
578 TATAC
* * *
10109 T-T-TATAGT-T-TATAGTTTATATATGTATATAAAGTA-CCAAATTGAACAAACATGAAATTGG
1 TATATATA-TATATATA-TATATATAT-TATATAAAGTATACAAATTGAACAAACATGAAATTGA
*
10169 AAATAAAAAATTGAATAAATTAAGC-ACACACATTGATGAGGGATGAAATTGAATTAATTATAAA
63 AAATAAAAAATTGAATAAATTAAACAACACACATTGATGAGGGATGAAATTGAATTAATTATAAA
*
10233 ATGTGAAACTAATATTAATATAAAAATGGA-ATAATTGGATACATTTAAAAAGTTGGTGAACATA
128 ATGTGAAACTAATATTAATATAAAAATGGACA-AATTGCATACATTTAAAAAGTTGGTGAACATA
* *
10297 ATTTGAAAAGAAATTTATTGTGTGATTT-ATTTTATAGGGTTTGTTTTAAGTAAATTACTAAAAT
192 ATTTGAAAAGAAATTTATTATGTGATTTAATTTTATA-GG---GTTTTAAGTAAATTACAAAAAT
** *
10361 ATAAATAAGGATGGGTCAATTTCAGATATGAATATAATTTAAAGAACTAAATTGAACAAATCTGA
253 ATAAATAAGGATGGGTCAATTTCAGATACAAATATAATTTAAAGAACTAAATTGAACAAATATGA
* * * *
10426 AATTACAAATTTAAA-TTTAAATAAAATAAATAACATAAAAGGATCAAAT-AAAAAAATGTAAAA
318 AATTA-AAAATAAAATTTTAAATAAAATAAAGAACACAAAAGGATCAAATCAAAAAAATGTAAAA
* * * * * **
10489 TGTGAGGGAAAAT-TATAAAATGGATTGAATTGCATTAATTTCAAAAATT-GGGGAAAATTAAAA
382 TGTGA-AG-AAATGTATAAAATGAACTAAATTGCATTAATTTCAAAAATTAAGAAAAAATTAAAA
10552 CAATTATATATATATATATATATA-TA-TA-TAT-ATA-TATAATGAATG-T-T-ATAATATGAT
445 CAATTATATATATATATATATATAGTAGTAGTATAATAGTATAATGAATGTTATGATAATATGAT
* * *
10609 GCATGTATATATAATGTAAAATATAAGTATATATAAAGTGTAAACTATAAAGTATATATACTTTA
510 GCATGTATATATAATGTAAAATAT-ACT-T-TAT---GTATAAA-TATAAA-TATACATA---TA
10674 AAGTATAAAATATA-TATATA-
564 AA-TAT-AAATATACT-TATAC
10694 TATATATATATATATATATATATATATATATA
1 TATATATATATATATATATATATAT-TATATA
10726 TAAACTATAA
Statistics
Matches: 533, Mismatches: 54, Indels: 62
0.82 0.08 0.10
Matches are distributed among these distances:
573 32 0.06
574 3 0.01
575 2 0.00
576 14 0.03
578 3 0.01
579 8 0.02
580 5 0.01
581 9 0.02
583 10 0.02
584 6 0.01
585 116 0.22
586 117 0.22
587 191 0.36
588 16 0.03
589 1 0.00
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (582 bp):
TATATATATATATATATATATATATTATATAAAGTATACAAATTGAACAAACATGAAATTGAAAA
TAAAAAATTGAATAAATTAAACAACACACATTGATGAGGGATGAAATTGAATTAATTATAAAATG
TGAAACTAATATTAATATAAAAATGGACAAATTGCATACATTTAAAAAGTTGGTGAACATAATTT
GAAAAGAAATTTATTATGTGATTTAATTTTATAGGGTTTTAAGTAAATTACAAAAATATAAATAA
GGATGGGTCAATTTCAGATACAAATATAATTTAAAGAACTAAATTGAACAAATATGAAATTAAAA
ATAAAATTTTAAATAAAATAAAGAACACAAAAGGATCAAATCAAAAAAATGTAAAATGTGAAGAA
ATGTATAAAATGAACTAAATTGCATTAATTTCAAAAATTAAGAAAAAATTAAAACAATTATATAT
ATATATATATATAGTAGTAGTATAATAGTATAATGAATGTTATGATAATATGATGCATGTATATA
TAATGTAAAATATACTTTATGTATAAATATAAATATACATATAAATATAAATATACTTATAC
Found at i:11163 original size:2 final size:2
Alignment explanation
Indices: 10556--11146 Score: 129
Period size: 2 Copynumber: 302.0 Consensus size: 2
10546 TTAAAACAAT
*
10556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TGA -A TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* * * * *
10597 T- TA TA -A TA TGA TG CA TG TA TA TA TA -A TG TA -A AA TA TA -A
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
10635 GTA TA TA TA AA GTG TA AA CTA TA AA GTA TA TA TA CTT TA AA GTA
1 -TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA -TA TA TA -TA
*
10679 TA -A AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
10720 TA TA TA TA AA CTA TA -A GTA T- TA TT TA GTA TA TA TA AA T- TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * * *
10760 TA -A TA TA TA TT TT TA CTA -A AA CTT TA TA TA T- TA TA AA AA CTA
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* * * *
10802 TA TA TA AA GTA T- TA TA -A GGA CA -A AA TA TA TA TA TA -A TA TA
1 TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * *
10842 -A TA TA -A GTA TA -A GTA TA TA TA CA TA TA AA GTA -A AA GTA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * *
10882 TA -A AA TA AA TA TA TA TA TA TA TA TA TA TA TA -A GT- TC TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
10923 TA AA T- TA TA TA CA TA TA TA TA -A TA TA AA CTA TA -A GTA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
10963 TA TA TA -A TA -A AA GTA TA -A T- TA TA AA GA T- TA AA GTA TA T-
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
11001 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA CTC TA T- TC TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * *
11042 TA TA TA TA TA CTT TA T- TC TT TA TA -A T- TA TA CTC TA TT TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
11083 TG TA TA -A TA CT- TA TA T- TA TA TA T- TA T- TA TA TA TG TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
11121 TA TA CTT TA TA GTA TA TA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA
11147 CTTTATATTC
Statistics
Matches: 433, Mismatches: 79, Indels: 154
0.65 0.12 0.23
Matches are distributed among these distances:
1 45 0.10
2 354 0.82
3 34 0.08
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:11163 original size:59 final size:56
Alignment explanation
Indices: 10996--11328 Score: 155
Period size: 59 Copynumber: 5.9 Consensus size: 56
10986 AAGATTAAAG
* * * *
10996 TATATTA-TATATATTATATAT-ATATATATATATATACTCTATTCTTTATA-TATA
1 TATATTATTATATATTATATATAATTTATATATATATA-TATATACTTTATATTTTA
* * * * * * *
11050 TACT-TTATTCTTTATAAT-TATACTCTATTTATATGTATA-ATAC-TTATA--TTA
1 TA-TATTATTATATATTATATATAATTTATATATATATATATATACTTTATATTTTA
*
11101 TATATTATTATATATGTATATATACTTTATAGTATATATATATATACTTTATATTCTTA
1 TATATTATTATATAT-TATATATAATTTATA-TATATATATATATACTTTATATT-TTA
* * *
11160 TATACTT-GTATAT-TTACTTATATATTTTATAT-TATATACTTAGATACTTTATA--TTA
1 TATA-TTATTATATATTA--TATATAATTTATATATATATA--TATATACTTTATATTTTA
*
11216 TATGATTA-TATACT-TTATCTTTATAATTATACTATATATATATATTATACTTTATATTATTA
1 TAT-ATTATTATA-TATTA--TATATAATT-TA-TATATATATATA-TATACTTTATATT-TTA
* * *
11278 TAT-GTA-TATACT-TTATACTAAAACTTTATATACATATATATACATACTTTA
1 TATATTATTATA-TATTATA-TATAA-TTTATAT--ATATATATATATACTTTA
11329 CTTTATAGTT
Statistics
Matches: 220, Mismatches: 28, Indels: 57
0.72 0.09 0.19
Matches are distributed among these distances:
50 1 0.00
51 13 0.06
52 7 0.03
53 12 0.05
54 18 0.08
55 23 0.10
56 17 0.08
57 20 0.09
58 10 0.05
59 63 0.29
60 30 0.14
62 6 0.03
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (56 bp):
TATATTATTATATATTATATATAATTTATATATATATATATATACTTTATATTTTA
Found at i:11175 original size:95 final size:87
Alignment explanation
Indices: 11005--11296 Score: 216
Period size: 81 Copynumber: 3.3 Consensus size: 87
10995 GTATATTATA
* *
11005 TATATTATATATATATATATATATATACTCTATTCTTTATATATATACTTTATTCTTTATAATTA
1 TATATTATATATATATATATATATATACTCTATTATATATATATATACTTTATTCTTTATAATTA
11070 TACTCTATTTATATGTATAATACT
66 TA--CTATTTATATGTATAATACT
*
11094 TATATTATATATTATTATATATGTATATATACTTTATAGTATATATATATATACTTTATATTCTT
1 TATATTATATA-TA-TATATA--TATATATACTCTAT--TATATATATATATAC-TT-TATTCTT
* * *
11159 ATATACTTGTA-TATTTA-CT-TAT-ATA--
58 -TATAATTATACTATTTATATGTATAATACT
* * *
11184 T-T-TTATAT-TATATA-CT-TAGATACTTTA-TATTATATGATTATATACTTTA-TCTTTATAA
1 TATATTATATATATATATATATATATACTCTATTA-TATAT-A-TATATACTTTATTCTTTATAA
* * *
11242 TTATACTATATATATATATTATACTT
63 TTATACTATTTATATGTATAATAC-T
* *
11268 TATATTAT-TATATGTATATACTTTATACT
1 TATATTATATATATATATATA-TATATACT
11297 AAAACTTTAT
Statistics
Matches: 162, Mismatches: 16, Indels: 50
0.71 0.07 0.22
Matches are distributed among these distances:
77 8 0.05
78 11 0.07
79 8 0.05
80 6 0.04
81 20 0.12
82 1 0.01
84 1 0.01
85 6 0.04
86 11 0.07
87 1 0.01
88 6 0.04
89 18 0.11
90 3 0.02
91 6 0.04
92 3 0.02
93 16 0.10
94 1 0.01
95 19 0.12
96 2 0.01
97 7 0.04
98 8 0.05
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.54
Consensus pattern (87 bp):
TATATTATATATATATATATATATATACTCTATTATATATATATATACTTTATTCTTTATAATTA
TACTATTTATATGTATAATACT
Found at i:11178 original size:51 final size:49
Alignment explanation
Indices: 10994--11200 Score: 140
Period size: 49 Copynumber: 4.4 Consensus size: 49
10984 TAAAGATTAA
* * *
10994 AGTATAT-TATATATA--TTATA-T-ATATATATATATATATACTCTAT
1 AGTATATATATATATACTTTATATTCTTATATATGTATATATACTTTAT
* * *
11038 --TCTTTATATATATAC-TT-TATTCTT-TATAAT-TATACTCTA-TTTAT
1 AGTATATATATATATACTTTATATTCTTATAT-ATGTATA-TATACTTTAT
*
11082 ATGTATA-ATACT-TATA-TTATATATTATTATATATGTATATATACTTTAT
1 A-GTATATATA-TATATACTT-TATATTCTTATATATGTATATATACTTTAT
*
11131 AGTATATATATATATACTTTATATTCTTATATACTTGTATATTTACTTATAT
1 AGTATATATATATATACTTTATATTCTTATATA--TGTATATATACTT-TAT
* *
11183 ATTTTATAT-TATATACTT
1 AGTATATATATATATACTT
11201 AGATACTTTA
Statistics
Matches: 128, Mismatches: 13, Indels: 37
0.72 0.07 0.21
Matches are distributed among these distances:
42 3 0.02
43 10 0.08
44 14 0.11
45 6 0.05
46 8 0.06
47 4 0.03
48 17 0.13
49 33 0.26
50 2 0.02
51 21 0.16
52 10 0.08
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (49 bp):
AGTATATATATATATACTTTATATTCTTATATATGTATATATACTTTAT
Found at i:11199 original size:22 final size:22
Alignment explanation
Indices: 11149--11294 Score: 101
Period size: 22 Copynumber: 6.7 Consensus size: 22
11139 TATATATACT
* *
11149 TTATATTCTTATATACTTGTATA
1 TTATATACTTATATA-TTTTATA
11172 -T-T-TACTTATATATTTTATA
1 TTATATACTTATATATTTTATA
* *
11191 TTATATACTTAGATACTTTATA
1 TTATATACTTATATATTTTATA
* *
11213 TTATATGA-TTATATACTTTATC
1 TTATAT-ACTTATATATTTTATA
* *
11235 TT-TATAATTATACTA-TATATA
1 TTATATACTTATA-TATTTTATA
11256 TATATTATACTT-TATATTATTATA
1 T-TA-TATACTTATATATT-TTATA
11280 TGTATATACTT-TATA
1 T-TATATACTTATATA
11295 CTAAAACTTT
Statistics
Matches: 101, Mismatches: 11, Indels: 22
0.75 0.08 0.16
Matches are distributed among these distances:
19 6 0.06
20 11 0.11
21 15 0.15
22 41 0.41
23 15 0.15
24 13 0.13
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (22 bp):
TTATATACTTATATATTTTATA
Found at i:11294 original size:30 final size:28
Alignment explanation
Indices: 11121--11296 Score: 136
Period size: 30 Copynumber: 6.2 Consensus size: 28
11111 TATATGTATA
*
11121 TATACTTTATAGTATATATATATATACTT
1 TATACTTTATATTATATAT-TATATACTT
* *
11150 TATA-TTCT-TA-TATA-CTTGTATA-TT
1 TATACTT-TATATTATATATTATATACTT
* *
11174 TACT--TATATATTTTATATTATATACTT
1 TA-TACTTTATATTATATATTATATACTT
*
11201 AGATACTTTATATTATATGATTATATACTT
1 -TATACTTTATATTATAT-ATTATATACTT
11231 TAT-CTTTATAATTATACTATATATATA-TAT
1 TATACTTTAT-ATTATA-TAT-TATATACT-T
11261 TATACTTTATATTATTATATGTATATACTT
1 TATACTTTATATTA-TATAT-TATATACTT
11291 TATACT
1 TATACT
11297 AAAACTTTAT
Statistics
Matches: 119, Mismatches: 11, Indels: 33
0.73 0.07 0.20
Matches are distributed among these distances:
23 1 0.01
24 7 0.06
25 9 0.08
26 7 0.06
27 7 0.06
28 11 0.09
29 26 0.22
30 42 0.35
31 9 0.08
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (28 bp):
TATACTTTATATTATATATTATATACTT
Found at i:11488 original size:28 final size:25
Alignment explanation
Indices: 11448--11535 Score: 72
Period size: 28 Copynumber: 3.4 Consensus size: 25
11438 TAAAAGTATG
11448 TATATATATATATAATTTATAGTTTA
1 TATATATATATATAATTTATA-TTTA
*
11474 TATATATACTCATATACTTTATATTTA
1 TATATATA-T-ATATAATTTATATTTA
* * **
11501 AACTATATAATTTATAA-TTATACATA
1 TA-TATAT-ATATATAATTTATATTTA
11527 TATA-ATATA
1 TATATATATA
11536 AGTTGTATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
23 2 0.04
24 2 0.04
25 2 0.04
26 16 0.32
27 10 0.20
28 17 0.34
29 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (25 bp):
TATATATATATATAATTTATATTTA
Found at i:11530 original size:21 final size:20
Alignment explanation
Indices: 11485--11532 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
11475 ATATATACTC
* *
11485 ATATACTTTATATTTAAACT
1 ATATAATTTATAATTAAACT
*
11505 ATATAATTTATAATTATACAT
1 ATATAATTTATAATTAAAC-T
11526 ATATAAT
1 ATATAAT
11533 ATAAGTTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATAATTTATAATTAAACT
Found at i:11698 original size:44 final size:49
Alignment explanation
Indices: 11633--11760 Score: 124
Period size: 47 Copynumber: 2.7 Consensus size: 49
11623 TAGTTCATGG
* * *
11633 TATATATAGTTTATAC-ATATATATATATATAT-ATATATAGTTTATAATA
1 TATATATAATATATACTATATATATATATATATAATATATA--ATATAATA
*
11682 -ATATA-AATA-A-ACTATATAGTTTATATAATATAATATATAATATAATA
1 TATATATAATATATACTATATA-TATATAT-ATATAATATATAATATAATA
* *
11729 TATATATAATATATACTTTATATATTTATATA
1 TATATATAATATATACTATATATATATATATA
11761 ATTTTATGTA
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
45 2 0.03
46 6 0.09
47 15 0.23
48 14 0.22
49 14 0.22
50 6 0.09
51 7 0.11
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (49 bp):
TATATATAATATATACTATATATATATATATATAATATATAATATAATA
Found at i:11764 original size:9 final size:9
Alignment explanation
Indices: 11656--11779 Score: 51
Period size: 9 Copynumber: 13.7 Consensus size: 9
11646 TACATATATA
*
11656 TATATATATA
1 TATATA-ATT
*
11666 TATATAGTT
1 TATATAATT
*
11675 TATAATAATA
1 TAT-ATAATT
* **
11685 TAAATAAAC
1 TATATAATT
*
11694 TATATAGTT
1 TATATAATT
11703 TATATAATAT
1 TATATAAT-T
*
11713 AATATATAATA
1 --TATATAATT
*
11724 TA-AT-ATA
1 TATATAATT
11731 TATATAA--
1 TATATAATT
*
11738 TATATACTT
1 TATATAATT
11747 TATAT-ATT
1 TATATAATT
11755 TATATAATTT
1 TATATAA-TT
* *
11765 TATGTAGTT
1 TATATAATT
11774 TATATA
1 TATATA
11780 GTATATATTA
Statistics
Matches: 86, Mismatches: 18, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
7 11 0.13
8 11 0.13
9 36 0.42
10 20 0.23
12 8 0.09
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (9 bp):
TATATAATT
Found at i:11777 original size:71 final size:72
Alignment explanation
Indices: 11634--11793 Score: 175
Period size: 71 Copynumber: 2.2 Consensus size: 72
11624 AGTTCATGGT
*
11634 ATATATAGTTTATACATATATATATATATATATATATAGTTTATAATAATATAAATAAACTATAT
1 ATATATA--TTATA-ATATATATATATATATATATATACTTTATAATAATATAAATAAACTATAT
11699 AGTTTATATA
63 AGTTTATATA
* * ** *
11709 ATATA-ATATATAATATA-ATATATATATAATATATACTTTAT-AT-ATTTATATAATTTTATGT
1 ATATATAT-TATAATATATATATATATAT-ATATATACTTTATAATAATATAAATAA-ACTATAT
11770 AGTTTATATA
63 AGTTTATATA
*
11780 GTATATATTATAAT
1 ATATATATTATAAT
11794 TGTTTAAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
70 8 0.11
71 36 0.49
72 20 0.27
73 4 0.05
74 1 0.01
75 5 0.07
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (72 bp):
ATATATATTATAATATATATATATATATATATATACTTTATAATAATATAAATAAACTATATAGT
TTATATA
Found at i:11779 original size:2 final size:2
Alignment explanation
Indices: 11633--11760 Score: 90
Period size: 2 Copynumber: 65.0 Consensus size: 2
11623 TAGTTCATGG
* * *
11633 TA TA TA TA GTT TA TA CA TA TA TA TA TA TA TA TA TA TA TA GTT TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
11677 TA -A TA -A TA TA AA TA AA CTA TA TA GTT TA TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* *
11717 TA TA -A TA TA -A TA TA TA TA TA -A TA TA TA CTT TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
11757 TA TA
1 TA TA
11761 ATTTTATGTA
Statistics
Matches: 98, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
1 7 0.07
2 86 0.88
3 5 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:13450 original size:80 final size:80
Alignment explanation
Indices: 13325--13620 Score: 443
Period size: 80 Copynumber: 3.7 Consensus size: 80
13315 CAATAAAAAG
* * * * *
13325 GGGAGCCAATCTAAGGATATACCTT-GGATCTACCCAAGGACATCCTTAGATCCGTAGGGTTACC
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
* * *
13389 TTAAGCACACAACTAA
65 TTATGCACACAGCAAA
*
13405 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
13470 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* *
13485 GGGAACCAACCTAAGGATATACCTTGGTACCTACCCAAGATATCCTTAGGTCCGTAAGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
13550 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* *
13565 GGGAACCAACCTAAGGATATGCCTTGGGGCCT-CCCTAAGATATCCTTAGGTCCGTA
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCC-AAGATATCCTTAGGTCCGTA
13621 ATGACTTACA
Statistics
Matches: 199, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
79 3 0.02
80 186 0.93
81 10 0.05
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TATGCACACAGCAAA
Found at i:18230 original size:16 final size:17
Alignment explanation
Indices: 18197--18240 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
18187 CCGGTTTCGG
18197 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
18214 TTTTTAAAAAACC-G-T
1 TTTTAAAAAAACCGGTT
*
18229 TTATAAAAAAAC
1 TTTTAAAAAAAC
18241 TGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
16 1 0.04
17 12 0.50
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:19432 original size:32 final size:33
Alignment explanation
Indices: 19336--19434 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
19326 AACTCAACAT
* * *
19336 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
19369 AATCCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
19402 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
19434 A
1 A
19435 TTGAAAAAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 12 0.20
33 49 0.80
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.31
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:21885 original size:19 final size:20
Alignment explanation
Indices: 21856--21894 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
21846 GTTAAAATAA
*
21856 CCGGTTTAAAAAAATCCGAT
1 CCGGTTTAAAAAAAACCGAT
21876 CCGG-TTAAAAAAAACCGAT
1 CCGGTTTAAAAAAAACCGAT
21895 TTTTCCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (20 bp):
CCGGTTTAAAAAAAACCGAT
Found at i:25602 original size:23 final size:23
Alignment explanation
Indices: 25520--25594 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
25510 TTTATTATTT
*
25520 TATTAATTAGGATTCTAGTTTGT
1 TATTAATTAGGATTCTAGTTTGC
*
25543 TATTAATTAGGATTCTAATTTGC
1 TATTAATTAGGATTCTAGTTTGC
25566 TATT-ATGTAGGATTCTAGTTTGC
1 TATTAAT-TAGGATTCTAGTTTGC
25589 TATTAA
1 TATTAA
25595 ATACGATTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
22 2 0.04
23 44 0.94
24 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (23 bp):
TATTAATTAGGATTCTAGTTTGC
Found at i:25915 original size:19 final size:19
Alignment explanation
Indices: 25891--25928 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
25881 CTTTGTATTT
*
25891 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
25910 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
25929 AATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:25938 original size:43 final size:42
Alignment explanation
Indices: 25890--26020 Score: 111
Period size: 43 Copynumber: 3.3 Consensus size: 42
25880 TCTTTGTATT
25890 TTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGAATA
1 TTATTTTAAATAGGTTTTAGTATTTTAATT-AGTTTTAGAATA
* * * *
25933 TTATTTT-TATA---TTT--TA-TCT--TT-GTTTTAGGTATT
1 TTATTTTAAATAGGTTTTAGTATTTTAATTAGTTTTA-GAATA
* *
25966 TTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATA
1 TTATTTTAAATAGGTTTTAGTATTTTAATTA-GTTTTAGAATA
26009 TTATTTTAAATA
1 TTATTTTAAATA
26021 TTATTTTTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 24
0.65 0.11 0.24
Matches are distributed among these distances:
32 6 0.09
33 9 0.14
34 5 0.08
36 2 0.03
37 5 0.08
39 5 0.08
40 2 0.03
42 5 0.08
43 21 0.32
44 5 0.08
ACGTcount: A:0.31, C:0.01, G:0.11, T:0.56
Consensus pattern (42 bp):
TTATTTTAAATAGGTTTTAGTATTTTAATTAGTTTTAGAATA
Found at i:25966 original size:76 final size:72
Alignment explanation
Indices: 25849--26068 Score: 262
Period size: 76 Copynumber: 3.0 Consensus size: 72
25839 TAAACCCAAG
* * * ** *
25849 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTATTTTAAATAGGTTTTAGTATT
1 TTTAGAATATTATTTTAAATATTAT-TTTT-T-TAGGTATTTTAGTTTAAATAGGTTTTAGTATT
*
25914 TTAATTAAGT
63 TTAATTAAGA
* *
25924 TTTAGAATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAT
1 TTTAGAATATTA-TTTTAAATATTA--TTT-TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAT
*
25989 TTTAATTAGGA
62 TTTAATTAAGA
*
26000 TTTAGAATATTATTTTAAATATTATTTTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTT
1 TTTAGAATATTATTTTAAATATTATTTTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTT
26064 AATTA
65 AATTA
26069 GAATTTAAGA
Statistics
Matches: 127, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
71 5 0.04
72 35 0.28
73 3 0.02
75 20 0.16
76 58 0.46
77 3 0.02
78 3 0.02
ACGTcount: A:0.30, C:0.01, G:0.11, T:0.57
Consensus pattern (72 bp):
TTTAGAATATTATTTTAAATATTATTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTA
ATTAAGA
Found at i:26775 original size:19 final size:19
Alignment explanation
Indices: 26751--26791 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
26741 TATTTATTAT
*
26751 TTTATTATTTTCCT-TTTTA
1 TTTATTATTAT-CTATTTTA
26770 TTTATTATTATCTATTTTA
1 TTTATTATTATCTATTTTA
26789 TTT
1 TTT
26792 TACTAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTATTATCTATTTTA
Found at i:32251 original size:5 final size:5
Alignment explanation
Indices: 32225--32283 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
32215 ACCCATTTCG
* * * *
32225 TTTTA -TTT- TTTTA TTTCA TTTTA TTTTCG TTCTA TTTCA TTTTA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA -TTTTA
32275 TTTTA TTTT
1 TTTTA TTTT
32284 TAGAAAACTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
4 6 0.14
5 28 0.67
6 8 0.19
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:32252 original size:11 final size:11
Alignment explanation
Indices: 32233--32283 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
32223 CGTTTTATTT
32233 TTTTA-TTTCA
1 TTTTATTTTCA
*
32243 TTTTATTTTCG
1 TTTTATTTTCA
*
32254 TTCTA-TTTCA
1 TTTTATTTTCA
*
32264 TTTTATTTTTA
1 TTTTATTTTCA
32275 TTTTATTTT
1 TTTTATTTT
32284 TAGAAAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 13 0.38
11 21 0.62
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:32261 original size:16 final size:16
Alignment explanation
Indices: 32233--32283 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
32223 CGTTTTATTT
*
32233 TTTTATTTC-ATTTTA
1 TTTTAGTTCTATTTTA
* *
32248 TTTTCGTTCTATTTCA
1 TTTTAGTTCTATTTTA
* *
32264 TTTTATTTTTATTTTA
1 TTTTAGTTCTATTTTA
32280 TTTT
1 TTTT
32284 TAGAAAACTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTTAGTTCTATTTTA
Found at i:32262 original size:21 final size:18
Alignment explanation
Indices: 32219--32273 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 18
32209 GAGGCAACCC
*
32219 ATTTCGTTTTATTTTTTT
1 ATTTCATTTTATTTTTTT
32237 ATTTCATTTTATTTTCGTTCT
1 ATTTCATTTTATTTT--TT-T
32258 ATTTCATTTTATTTTT
1 ATTTCATTTTATTTTT
32274 ATTTTATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 14 0.42
19 1 0.03
20 2 0.06
21 16 0.48
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.73
Consensus pattern (18 bp):
ATTTCATTTTATTTTTTT
Found at i:32281 original size:21 final size:21
Alignment explanation
Indices: 32233--32282 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
32223 CGTTTTATTT
*
32233 TTTTATTTCATTTTATTTTCG
1 TTTTATTTCATTTTATTTTCA
* *
32254 TTCTATTTCATTTTATTTTTA
1 TTTTATTTCATTTTATTTTCA
32275 TTTTATTT
1 TTTTATTT
32283 TTAGAAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTATTTCATTTTATTTTCA
Found at i:32284 original size:11 final size:11
Alignment explanation
Indices: 32225--32285 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
32215 ACCCATTTCG
*
32225 TTTTATTTTTT
1 TTTTATTTTAT
32236 TATTTCATTTTAT
1 T-TTT-ATTTTAT
** *
32249 TTTCGTTCTA-
1 TTTTATTTTAT
*
32259 TTTCATTTTAT
1 TTTTATTTTAT
32270 TTTTATTTTAT
1 TTTTATTTTAT
32281 TTTTA
1 TTTTA
32286 GAAAACTTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
10 8 0.20
11 20 0.50
12 5 0.12
13 7 0.17
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:34004 original size:19 final size:19
Alignment explanation
Indices: 33980--34017 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
33970 CTTTGTATTT
*
33980 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
33999 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
34018 GATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:34027 original size:43 final size:42
Alignment explanation
Indices: 33979--34109 Score: 102
Period size: 43 Copynumber: 3.3 Consensus size: 42
33969 TCTTTGTATT
33979 TTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATA
1 TTATTTTAAATAGGTTTTAGTATTTTAATT-AGTTTTAGGATA
* * *
34022 TTATTTT-TATA---TTT--TA-TCT--TT-GTTTTAGGTATT
1 TTATTTTAAATAGGTTTTAGTATTTTAATTAGTTTTAGG-ATA
* * **
34055 TTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTATAATA
1 TTATTTTAAATAGGTTTTAGTATTTTAATTA-GTTTTAGGATA
34098 TTATTTTAAATA
1 TTATTTTAAATA
34110 TTATTTTTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 24
0.65 0.11 0.24
Matches are distributed among these distances:
32 8 0.12
33 8 0.12
34 5 0.08
36 2 0.03
37 5 0.08
39 5 0.08
40 2 0.03
42 5 0.08
43 20 0.31
44 5 0.08
ACGTcount: A:0.31, C:0.01, G:0.11, T:0.57
Consensus pattern (42 bp):
TTATTTTAAATAGGTTTTAGTATTTTAATTAGTTTTAGGATA
Found at i:34063 original size:76 final size:72
Alignment explanation
Indices: 33938--34164 Score: 240
Period size: 76 Copynumber: 3.1 Consensus size: 72
33928 TAAACTCAAG
* * * ** *
33938 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTATTTTAAATAGGTTTTAGTATT
1 TTTAGAATATTATTTTAAATATTAT-TTTT-T-TAGGTATTTTAGTTTAAATAGGTTTTAGTATT
*
34003 TTAATTAAGT
63 TTAATTAAGA
* * *
34013 TTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAT
1 TTTAGAATATTA-TTTTAAATATTA--TTT-TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTAT
*
34078 TTTAATTAGGA
62 TTTAATTAAGA
* *
34089 TTTATAATATTATTTTAAATATTATTTTTTTAGGTATTTTGGTTTAAATA-GTTTTAAGTATTTT
1 TTTAGAATATTATTTTAAATATTATTTTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTT
* *
34153 AACTAGGA
65 AATTAAGA
34161 TTTA
1 TTTA
34165 AGATGTTTTA
Statistics
Matches: 132, Mismatches: 15, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
71 5 0.04
72 41 0.31
73 3 0.02
75 21 0.16
76 56 0.42
77 3 0.02
78 3 0.02
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (72 bp):
TTTAGAATATTATTTTAAATATTATTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTA
ATTAAGA
Found at i:34160 original size:72 final size:75
Alignment explanation
Indices: 33974--34164 Score: 255
Period size: 76 Copynumber: 2.6 Consensus size: 75
33964 TTTTATCTTT
* * * * * *
33974 GTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTAT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATTTTTAAATATTA-
34039 CTTTGTTTTAG
65 CTTTGTTTTAG
*
34050 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTATAATATTA-TTTTAAATATTA-
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATTTTTAAATATTAC
34113 TTT-TTTTAG
66 TTTGTTTTAG
* *
34122 GTATTTTGGTTTAAATA-GTTTTAAGTATTTTAACTAGGATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTA
34165 AGATGTTTTA
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
71 5 0.05
72 41 0.39
73 3 0.03
75 10 0.10
76 46 0.44
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.57
Consensus pattern (75 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATTTTTAAATATTAC
TTTGTTTTAG
Found at i:34852 original size:22 final size:24
Alignment explanation
Indices: 34831--34874 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
34821 TATTACTATT
*
34831 TATTATT-T-TATTTTTTTTTATT
1 TATTATTATCTATTTTATTTTATT
34853 TATTATTATCTATTTTATTTTA
1 TATTATTATCTATTTTATTTTA
34875 CTAAATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 11 0.58
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (24 bp):
TATTATTATCTATTTTATTTTATT
Found at i:37403 original size:29 final size:28
Alignment explanation
Indices: 37329--37419 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
37319 AAAAAAAATC
*
37329 GTAATTTTTTAAAAAAAAATGATATTTTA
1 GTAATTTTTT-AAAAATAATGATATTTTA
* * *
37358 GTAATTATTTTGAAAATAGTGATATTTTG
1 GTAATT-TTTTAAAAATAATGATATTTTA
* * *
37387 GTAATTGTTTTAAAAATGATGTTATTTTC
1 GTAATT-TTTTAAAAATAATGATATTTTA
37416 GTAA
1 GTAA
37420 AATGGTTGTT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.47
Consensus pattern (28 bp):
GTAATTTTTTAAAAATAATGATATTTTA
Found at i:45215 original size:21 final size:23
Alignment explanation
Indices: 45191--45242 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
45181 AGGAAATCAA
45191 TCCCCCCATG-A-GGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
**
45212 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
45235 TCCCCCCA
1 TCCCCCCA
45243 CAGGGGAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 1 0.04
23 16 0.64
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.17
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCGAT
Found at i:45669 original size:25 final size:26
Alignment explanation
Indices: 45620--45669 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
45610 AGAATTTTTC
*
45620 AAAAAAATTTTTAAATTTTCGAAATA
1 AAAAAAATTGTTAAATTTTCGAAATA
45646 AAAAAAATGTGTT-AATTTTC-AAAT
1 AAAAAAAT-TGTTAAATTTTCGAAAT
45670 TATTGTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 15 0.68
27 3 0.14
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (26 bp):
AAAAAAATTGTTAAATTTTCGAAATA
Found at i:47567 original size:20 final size:20
Alignment explanation
Indices: 47542--47582 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
47532 GGGGAGTAAT
47542 TTCAAAACTTGATTTCAAAA
1 TTCAAAACTTGATTTCAAAA
47562 TTCAAAACTTGATTTCAAAA
1 TTCAAAACTTGATTTCAAAA
47582 T
1 T
47583 CTTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (20 bp):
TTCAAAACTTGATTTCAAAA
Found at i:51730 original size:14 final size:14
Alignment explanation
Indices: 51711--51740 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
51701 TTTGGTCAAT
51711 GGTCAAAGTCAACA
1 GGTCAAAGTCAACA
*
51725 GGTCAAAGTTAACA
1 GGTCAAAGTCAACA
51739 GG
1 GG
51741 GTTGACTCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.27, T:0.17
Consensus pattern (14 bp):
GGTCAAAGTCAACA
Found at i:55816 original size:22 final size:24
Alignment explanation
Indices: 55771--55834 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 24
55761 TTCAGAGAAA
*
55771 AATAAAATAAAATTAA-GCATATG
1 AATAAAATAAAATAAATGCATATG
*
55794 -ATAAAATAAAATAAATGGA-ATG
1 AATAAAATAAAATAAATGCATATG
*
55816 AAATAAATTAAAATGAAAT
1 -AATAAAATAAAAT-AAAT
55835 AAAGTTTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 17 0.50
23 2 0.06
24 11 0.32
25 4 0.12
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (24 bp):
AATAAAATAAAATAAATGCATATG
Found at i:61794 original size:24 final size:25
Alignment explanation
Indices: 61761--61821 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
61751 TACATATTTG
61761 AAAAT-AAAACTT-AAAA-ATAAAGA
1 AAAATGAAAACTTGAAAAGA-AAAGA
61784 AAAATGAAAACTTGAAAAGAAAAGA
1 AAAATGAAAACTTGAAAAGAAAAGA
61809 AAAGA-GAAAACTT
1 AAA-ATGAAAACTT
61822 TATAAAACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.15
24 7 0.21
25 20 0.59
26 2 0.06
ACGTcount: A:0.69, C:0.05, G:0.11, T:0.15
Consensus pattern (25 bp):
AAAATGAAAACTTGAAAAGAAAAGA
Found at i:62124 original size:22 final size:22
Alignment explanation
Indices: 62094--62141 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
62084 TCCATTCGTT
*
62094 CTTCTAGAAGCGCTGACTAGAC
1 CTTCCAGAAGCGCTGACTAGAC
*
62116 CTTCCAGAAGCGCTGACTGGAC
1 CTTCCAGAAGCGCTGACTAGAC
62138 CTTC
1 CTTC
62142 TAGAGGGTGC
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:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (22 bp):
CTTCCAGAAGCGCTGACTAGAC
Found at i:64579 original size:21 final size:22
Alignment explanation
Indices: 64553--64593 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
64543 AATAGCGATC
64553 AATGACATAAACTAT-AAATCA
1 AATGACATAAACTATGAAATCA
* *
64574 AATGACTTAATCTATGAAAT
1 AATGACATAAACTATGAAAT
64594 TTACTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (22 bp):
AATGACATAAACTATGAAATCA
Found at i:66876 original size:21 final size:21
Alignment explanation
Indices: 66852--66904 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
66842 GCTTTGGAAT
*
66852 TTTTCCTGTGATACAACTAGC
1 TTTTCCTGTGATACAACCAGC
* **
66873 TTTTCCTGAGATTTAACCAGC
1 TTTTCCTGTGATACAACCAGC
*
66894 TTTTCTTGTGA
1 TTTTCCTGTGA
66905 AATTACTAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (21 bp):
TTTTCCTGTGATACAACCAGC
Found at i:68734 original size:21 final size:22
Alignment explanation
Indices: 68703--68759 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
68693 TAGCATATTT
68703 GAAAAT-AAAACTT-AAAATAAA
1 GAAAATGAAAACTTGAAAA-AAA
68724 -AAAATGAAAACTTGAAAAAAA
1 GAAAATGAAAACTTGAAAAAAA
*
68745 GAAAAGAGAAAACTT
1 GAAAA-TGAAAACTT
68760 TATAAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 5 0.16
21 10 0.32
22 8 0.26
23 8 0.26
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16
Consensus pattern (22 bp):
GAAAATGAAAACTTGAAAAAAA
Found at i:68766 original size:23 final size:24
Alignment explanation
Indices: 68729--68776 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
68719 ATAAAAAAAT
68729 GAAAACTTGAAAAAA-AGAAAAGA
1 GAAAACTTGAAAAAACAGAAAAGA
* *
68752 GAAAACTTTATAAAACTAGAAAAGA
1 GAAAACTTGAAAAAAC-AGAAAAGA
68777 AGAATAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
25 8 0.38
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.15
Consensus pattern (24 bp):
GAAAACTTGAAAAAACAGAAAAGA
Found at i:68898 original size:20 final size:22
Alignment explanation
Indices: 68848--68900 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
68838 ATAGCCTTCA
68848 AAATCCTAAAAACAAGGTAAAT
1 AAATCCTAAAAACAAGGTAAAT
68870 ATAATTCCTAAAATA-AA-G-AAAT
1 A-AA-TCCTAAAA-ACAAGGTAAAT
68892 AAATCCTAA
1 AAATCCTAA
68901 TGAAAATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 6 0.21
23 3 0.11
24 10 0.36
25 1 0.04
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (22 bp):
AAATCCTAAAAACAAGGTAAAT
Found at i:73375 original size:21 final size:22
Alignment explanation
Indices: 73349--73389 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
73339 AATAGCGATC
73349 AATGACATAAACTAT-AAATCA
1 AATGACATAAACTATGAAATCA
* *
73370 AATGACTTAATCTATGAAAT
1 AATGACATAAACTATGAAAT
73390 TTACTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (22 bp):
AATGACATAAACTATGAAATCA
Found at i:90371 original size:23 final size:23
Alignment explanation
Indices: 90345--90406 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
90335 CCATAAACAA
90345 AACCCGACCCGGAGCCCAAAAAG
1 AACCCGACCCGGAGCCCAAAAAG
* * * *
90368 AACCCAACACGAAGCCCAAAATG
1 AACCCGACCCGGAGCCCAAAAAG
*
90391 AACCCGACCCAGAGCC
1 AACCCGACCCGGAGCC
90407 TACCCTAACC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.40, G:0.18, T:0.02
Consensus pattern (23 bp):
AACCCGACCCGGAGCCCAAAAAG
Found at i:90776 original size:14 final size:15
Alignment explanation
Indices: 90747--90779 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
90737 ATTTTGATCC
*
90747 GAAAATCAAGAAAAA
1 GAAAAGCAAGAAAAA
90762 GAAAAGCAA-AAAAA
1 GAAAAGCAAGAAAAA
90776 GAAA
1 GAAA
90780 GATAGAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.03
Consensus pattern (15 bp):
GAAAAGCAAGAAAAA
Found at i:93920 original size:27 final size:27
Alignment explanation
Indices: 93848--93941 Score: 125
Period size: 27 Copynumber: 3.5 Consensus size: 27
93838 CTTTAGGTAT
* *
93848 TTTGGTCATTTTGGAGTTCAAAGATAA
1 TTTGGTCATTTTGGAGTTTAAGGATAA
*
93875 TTTGGTCATTTTGGTGTTTAAGGATAA
1 TTTGGTCATTTTGGAGTTTAAGGATAA
* * *
93902 TTTGGTCATTTTGGAGTTTAGGGGTAT
1 TTTGGTCATTTTGGAGTTTAAGGATAA
*
93929 TTTAGTCATTTTG
1 TTTGGTCATTTTG
93942 TTCAATTCAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.48
Consensus pattern (27 bp):
TTTGGTCATTTTGGAGTTTAAGGATAA
Found at i:94740 original size:19 final size:19
Alignment explanation
Indices: 94716--94756 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
94706 CTTGGCATCA
* *
94716 CTCGGTTCGACTCAAGTGG
1 CTCGGTTCAACTCAAATGG
94735 CTCGGTTCAACTCAAATGG
1 CTCGGTTCAACTCAAATGG
94754 CTC
1 CTC
94757 AGTTTGGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (19 bp):
CTCGGTTCAACTCAAATGG
Found at i:94813 original size:19 final size:18
Alignment explanation
Indices: 94771--94814 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
94761 TGGCTTGGCG
94771 GTTTAGACCAATTTAGCC
1 GTTTAGACCAATTTAGCC
*
94789 GATTTAGAGCAATTTAGCC
1 G-TTTAGACCAATTTAGCC
94808 AGTTTAG
1 -GTTTAG
94815 TTTGTTCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 21 0.91
20 1 0.04
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (18 bp):
GTTTAGACCAATTTAGCC
Found at i:98237 original size:45 final size:46
Alignment explanation
Indices: 98149--98237 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 46
98139 TTGAAAAAGC
* * * * *
98149 CTGATTGCATCAATGCATGGTCTTGTGCATCGATGCATCAAATGAA
1 CTGAGTGCATCAATGCATGGTCATATGCATCAATGCATAAAATGAA
*
98195 CTGAGTGCATCGATGCATGGT-ATATGCATCAATGCATAAAATG
1 CTGAGTGCATCAATGCATGGTCATATGCATCAATGCATAAAATG
98238 CATTCGATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 18 0.49
46 19 0.51
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (46 bp):
CTGAGTGCATCAATGCATGGTCATATGCATCAATGCATAAAATGAA
Found at i:101448 original size:21 final size:22
Alignment explanation
Indices: 101408--101448 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
101398 CTAAAGGTTT
* *
101408 TGTAAAGATATCCACTAATTGG
1 TGTAAAGATATCAACAAATTGG
101430 TGTAAA-ATATCAACAAATT
1 TGTAAAGATATCAACAAATT
101449 TTAGAACTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (22 bp):
TGTAAAGATATCAACAAATTGG
Found at i:104780 original size:20 final size:20
Alignment explanation
Indices: 104743--104781 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
104733 GAGGTTTTAA
** *
104743 GATCATCATTTTCTTTTGAT
1 GATCATCATTGACCTTTGAT
104763 GATCATCATTGACCTTTGA
1 GATCATCATTGACCTTTGA
104782 AAGTAAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (20 bp):
GATCATCATTGACCTTTGAT
Found at i:104925 original size:21 final size:21
Alignment explanation
Indices: 104891--104930 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
104881 GAGTTTATTT
*
104891 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTAAAAACA
104912 TCATTTTT-ATATTTAAAAA
1 TCATTTTTCA-ATTTAAAAA
104931 AAAATTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (21 bp):
TCATTTTTCAATTTAAAAACA
Found at i:106852 original size:26 final size:25
Alignment explanation
Indices: 106821--106869 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
106811 GCATGGTCTT
*
106821 GTGCATCGATGCATCAAATGCATTGA
1 GTGCATCGATGCA-AAAATGCATTGA
106847 GTGCATCGATGCAAAAATGCATT
1 GTGCATCGATGCAAAAATGCATT
106870 CGATGTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (25 bp):
GTGCATCGATGCAAAAATGCATTGA
Found at i:106911 original size:20 final size:20
Alignment explanation
Indices: 106886--106923 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
106876 TTGAAAATTA
106886 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
106906 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
106924 CACTTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:108941 original size:31 final size:31
Alignment explanation
Indices: 108906--108976 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
108896 TTCTTATTAG
*
108906 CTTCTAATTCCCCTATTTTTGCCTTTCCCAA
1 CTTCTAACTCCCCTATTTTTGCCTTTCCCAA
108937 CTTCTAACTCCCCTATTTTTGCCTTTCCCAA
1 CTTCTAACTCCCCTATTTTTGCCTTTCCCAA
108968 CTTCTAACT
1 CTTCTAACT
108977 TCTGAATTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.17, C:0.37, G:0.03, T:0.44
Consensus pattern (31 bp):
CTTCTAACTCCCCTATTTTTGCCTTTCCCAA
Found at i:117466 original size:138 final size:137
Alignment explanation
Indices: 117133--117473 Score: 359
Period size: 137 Copynumber: 2.5 Consensus size: 137
117123 AACATAGGGG
* * * * * * *
117133 ATTAAACCTAAAAATGTAGG-TCTAATATTAATCCAAATCATTTTTAATAAATTATTGAGTCGAA
1 ATTAAGCCT-AAAATGAAGGCTCTAATATTAACCCTAATCAATTTTAATAAATTATTGATTCAAA
* * * * *
117197 TAATCAAAGTGGAACCTCAAGAATAAGCGAGGACCAAATTAAGAATTCCCTTAAATTAAAGGATT
65 TAATCAAAATGGAACCTCAAGAATAAGCGAGGACCAAATTAAAAATTCCCATAAATTAAAAGACT
117262 GAAATGAA
130 GAAATGAA
* * * *
117270 ATT-AGATCTAAAGTGAAGACTCTAATATTAACCCTAATCAATTTTAATTAATTATTGATTCAAA
1 ATTAAG-CCTAAAATGAAGGCTCTAATATTAACCCTAATCAATTTTAATAAATTATTGATTCAAA
* * * *
117334 TGATTAAAATGGAACCTCAAGTAA-AAGCGATGACCAAATTAAAAATTCTCATAAATTAAAAGAC
65 TAATCAAAATGGAACCTCAAG-AATAAGCGAGGACCAAATTAAAAATTCCCATAAATTAAAAGAC
*
117398 T-AAGTTTGAA
129 TGAA--ATGAA
* * ** *
117408 ATTAAGCCTAAAATGGAGGCTCTAATTATTAA-CTTAATCAATTTTAACCAATTATTGATTCGAA
1 ATTAAGCCTAAAATGAAGGCTCTAA-TATTAACCCTAATCAATTTTAATAAATTATTGATTCAAA
117472 TA
65 TA
117474 TTGGCGATGA
Statistics
Matches: 167, Mismatches: 30, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
136 10 0.06
137 96 0.57
138 53 0.32
139 8 0.05
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (137 bp):
ATTAAGCCTAAAATGAAGGCTCTAATATTAACCCTAATCAATTTTAATAAATTATTGATTCAAAT
AATCAAAATGGAACCTCAAGAATAAGCGAGGACCAAATTAAAAATTCCCATAAATTAAAAGACTG
AAATGAA
Found at i:117506 original size:117 final size:117
Alignment explanation
Indices: 117360--117589 Score: 352
Period size: 117 Copynumber: 2.0 Consensus size: 117
117350 TCAAGTAAAA
**
117360 GCGATGACCAAATTAAAAATTCTCATAAATTAAAAGACTAAGTTTGAAATTAAGCCTAAAATGGA
1 GCGATGACCAAATTAAAAATTCTCATAAATTAAAAGACTAAGTTTGAAATTAAGAATAAAATGGA
* *
117425 GGCTCTAATTATTAACTTAATCAATTTTAACCAATTATTGATTCGAATATTG
66 AGCTCTAATTATTAACCTAATCAATTTTAACCAATTATTGATTCGAATATTG
* * * * *
117477 GCGATGACCAAATTAAGAATTTTCCTAAATTAAAGGATTAAGTTTGAAATTAAGAATAAAATGGA
1 GCGATGACCAAATTAAAAATTCTCATAAATTAAAAGACTAAGTTTGAAATTAAGAATAAAATGGA
* * *
117542 AGCTCTAATTATTAACCTAGTCAATTTTAACTAATTATTGATTTGAAT
66 AGCTCTAATTATTAACCTAATCAATTTTAACCAATTATTGATTCGAAT
117590 GATTAAAATA
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 101 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (117 bp):
GCGATGACCAAATTAAAAATTCTCATAAATTAAAAGACTAAGTTTGAAATTAAGAATAAAATGGA
AGCTCTAATTATTAACCTAATCAATTTTAACCAATTATTGATTCGAATATTG
Found at i:117678 original size:255 final size:254
Alignment explanation
Indices: 117223--117717 Score: 678
Period size: 255 Copynumber: 1.9 Consensus size: 254
117213 TCAAGAATAA
* *
117223 GCGAGGACCAAATTAAGAATTCCCTTAAATTAAAGGATTGAAATGAAATTAGATCTAAAGTGAAG
1 GCGAGGACCAAATTAAGAATTCCCTTAAATTAAAGGATTGAAATGAAATTAGATATAAAATGAAG
* *
117288 ACTCTAATATTAACCCTAATCAATTTTAATTAATTATTGATTCAAATGATTAAAATGGAACCTCA
66 ACTCTAATATTAACCCTAATCAATTTTAACTAATTATTGATTCAAATGATTAAAATAGAACCTCA
* * * *
117353 AGTAAAAGCGATGACCAAATTAAAAATTCTCATAAATTAAAAGACTAAGTTTGAAATTAAGCCTA
131 AGCAAAAGCGAGGACCAAATTAAAAATTCTCATAAATTAAAAGACTAAGTTTGAAATTAAACATA
* *
117418 AAATGGAGGCTCTAATTATTAACTTAATCAATTTTAACCAATTATTGATTCGAATATTG
196 AAATGGAGGATCTAATTATTAACCTAATCAATTTTAACCAATTATTGATTCGAATATTG
* * *
117477 GCGATGACCAAATTAAGAATTTTCC-TAAATTAAAGGATT-AAGTTTGAAATTAAGA-ATAAAAT
1 GCGAGGACCAAATTAAGAA-TTCCCTTAAATTAAAGGATTGAA--ATGAAATT-AGATATAAAAT
* **
117539 GGAAG-CTCTAATTATTAA-CCTAGTCAATTTTAACTAATTATTGATTTGAATGATTAAAATAGA
62 -GAAGACTCTAA-TATTAACCCTAATCAATTTTAACTAATTATTGATTCAAATGATTAAAATAGA
* * * *
117602 ACCTCGAGCAAAAGTGAGGACCAAATTAAAAATTTGTC-TAAATTAAAGGACTAAGTTTGAAATT
125 ACCTCAAGCAAAAGCGAGGACCAAATTAAAAA-TTCTCATAAATTAAAAGACTAAGTTTGAAATT
* * *
117666 AAATATAAAATGGAGGATTTAATTATTAACCTAATCAATTTTAATCAATTAT
189 AAACATAAAATGGAGGATCTAATTATTAACCTAATCAATTTTAACCAATTAT
117718 CGAATATTTA
Statistics
Matches: 211, Mismatches: 23, Indels: 13
0.85 0.09 0.05
Matches are distributed among these distances:
253 2 0.01
254 32 0.15
255 160 0.76
256 17 0.08
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (254 bp):
GCGAGGACCAAATTAAGAATTCCCTTAAATTAAAGGATTGAAATGAAATTAGATATAAAATGAAG
ACTCTAATATTAACCCTAATCAATTTTAACTAATTATTGATTCAAATGATTAAAATAGAACCTCA
AGCAAAAGCGAGGACCAAATTAAAAATTCTCATAAATTAAAAGACTAAGTTTGAAATTAAACATA
AAATGGAGGATCTAATTATTAACCTAATCAATTTTAACCAATTATTGATTCGAATATTG
Found at i:124189 original size:2 final size:2
Alignment explanation
Indices: 124182--124218 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
124172 AAGTAAAAGA
124182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
124219 ATCAAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:130018 original size:4 final size:4
Alignment explanation
Indices: 130009--130042 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
129999 CTCGAATATA
130009 AAAT AAAT AAAT AAAT AAAT -AAT AAAT -AAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
130043 TAGCGGTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:130032 original size:7 final size:8
Alignment explanation
Indices: 130009--130042 Score: 54
Period size: 7 Copynumber: 4.5 Consensus size: 8
129999 CTCGAATATA
130009 AAATAAAT
1 AAATAAAT
130017 AAATAAAT
1 AAATAAAT
130025 AAAT-AAT
1 AAATAAAT
130032 AAAT-AAT
1 AAATAAAT
130039 AAAT
1 AAAT
130043 TAGCGGTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 14 0.54
8 12 0.46
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AAATAAAT
Found at i:132006 original size:61 final size:58
Alignment explanation
Indices: 131935--132144 Score: 210
Period size: 61 Copynumber: 3.5 Consensus size: 58
131925 CAATCTACTT
*
131935 CTTCATGTTGAGGAGATCTAGTTGTTCTTAAAAAGTTGTGAATATGAAGACAACATTGTTC
1 CTTCTTGTTGAGGAGATCTAGTT-TTCTTAAAAA-TTGTGAAT-TGAAGACAACATTGTTC
* * ** * *
131996 CTTCTTGTTGAGGA-AGTCTAATTTTCTGAAGATAACTT-TGCCTTCGAAAACAACATTGCTC
1 CTTCTTGTTGAGGAGA-TCTAGTTTTCTTAA-A-AA-TTGTGAATT-GAAGACAACATTGTTC
132057 CTTCATT-TTGAGGAGATCTAGTTGTTCTTACAAAATTGTGAATCTGAAGACAACATTGTTC
1 CTTC-TTGTTGAGGAGATCTAGTT-TTCTTA-AAAATTGTGAAT-TGAAGACAACATTGTTC
* *
132118 CTTCTTGCTGAGGAAATCTAGTTTTCT
1 CTTCTTGTTGAGGAGATCTAGTTTTCT
132145 GAAGATGATT
Statistics
Matches: 122, Mismatches: 16, Indels: 23
0.76 0.10 0.14
Matches are distributed among these distances:
60 16 0.13
61 91 0.75
62 14 0.11
63 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (58 bp):
CTTCTTGTTGAGGAGATCTAGTTTTCTTAAAAATTGTGAATTGAAGACAACATTGTTC
Found at i:132158 original size:122 final size:122
Alignment explanation
Indices: 131935--132194 Score: 396
Period size: 122 Copynumber: 2.1 Consensus size: 122
131925 CAATCTACTT
*
131935 CTTCATGTTGAGGAGATCTAGTTGTTCTTAAAAAGTTGTGAATATGAAGACAACATTGTTCCTTC
1 CTTCATTTTGAGGAGATCTAGTTGTTCTTAAAAAGTTGTGAATATGAAGACAACATTGTTCCTTC
* *
132000 TTGTTGAGGAAGTCTAATTTTCTGAAGATAACTTTGCCTTCGAAAACAACATTGCTC
66 TTGCTGAGGAAATCTAATTTTCTGAAGATAACTTTGCCTTCGAAAACAACATTGCTC
*
132057 CTTCATTTTGAGGAGATCTAGTTGTTCTTACAAAA-TTGTGAATCTGAAGACAACATTGTTCCTT
1 CTTCATTTTGAGGAGATCTAGTTGTTCTTA-AAAAGTTGTGAATATGAAGACAACATTGTTCCTT
* * * * * **
132121 CTTGCTGAGGAAATCTAGTTTTCTGAAGATGATTTTGCTTTTGAAAATGACATTGCTC
65 CTTGCTGAGGAAATCTAATTTTCTGAAGATAACTTTGCCTTCGAAAACAACATTGCTC
*
132179 CTTAATTTTGAGGAGA
1 CTTCATTTTGAGGAGA
132195 GCTAATCTTT
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
122 121 0.97
123 4 0.03
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (122 bp):
CTTCATTTTGAGGAGATCTAGTTGTTCTTAAAAAGTTGTGAATATGAAGACAACATTGTTCCTTC
TTGCTGAGGAAATCTAATTTTCTGAAGATAACTTTGCCTTCGAAAACAACATTGCTC
Found at i:132174 original size:61 final size:61
Alignment explanation
Indices: 131935--132181 Score: 189
Period size: 61 Copynumber: 4.0 Consensus size: 61
131925 CAATCTACTT
* * * * * * * *
131935 CTTCATGTTGAGGAGATCTAGTTGTTCTTAA-A-AAGTTGTGAATATGAAGACAACATTGTTC
1 CTTCTTGTTGAGGAAATCTAGTT-TTCTGAAGATAA-TTTTGCATTTGAAAACAACATTGCTC
* * * * *
131996 CTTCTTGTTGAGGAAGTCTAATTTTCTGAAGATAACTTTGCCTTCGAAAACAACATTGCTC
1 CTTCTTGTTGAGGAAATCTAGTTTTCTGAAGATAATTTTGCATTTGAAAACAACATTGCTC
* * * * * * *
132057 CTTCATT-TTGAGGAGATCTAGTTGTTCTTACA-A-AATTGTGAATCTGAAGACAACATTGTTC
1 CTTC-TTGTTGAGGAAATCTAGTT-TTCTGA-AGATAATTTTGCATTTGAAAACAACATTGCTC
* * * **
132118 CTTCTTGCTGAGGAAATCTAGTTTTCTGAAGATGATTTTGCTTTTGAAAATGACATTGCTC
1 CTTCTTGTTGAGGAAATCTAGTTTTCTGAAGATAATTTTGCATTTGAAAACAACATTGCTC
132179 CTT
1 CTT
132182 AATTTTGAGG
Statistics
Matches: 141, Mismatches: 37, Indels: 16
0.73 0.19 0.08
Matches are distributed among these distances:
59 1 0.01
60 14 0.10
61 115 0.82
62 10 0.07
63 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (61 bp):
CTTCTTGTTGAGGAAATCTAGTTTTCTGAAGATAATTTTGCATTTGAAAACAACATTGCTC
Found at i:134200 original size:12 final size:11
Alignment explanation
Indices: 134179--134323 Score: 59
Period size: 11 Copynumber: 12.6 Consensus size: 11
134169 GCTTTCAGTT
134179 TTCTTGTTTTTC
1 TTCTT-TTTTTC
*
134191 TTCTTATTTTCC
1 TTCTT-TTTTTC
134203 TTCTTTTTCTCTC
1 TTCTTTTT-T-TC
*
134216 TTCTTATTCTT-
1 TTCTT-TTTTTC
*
134227 TTC-TTTTCTC
1 TTCTTTTTTTC
*
134237 TTCTTATTTT-
1 TTCTTTTTTTC
134247 TTCTTTCTTTT-
1 TTCTTT-TTTTC
*
134258 TT-TCTTTTTC
1 TTCTTTTTTTC
**
134268 AACTTTTTTTC
1 TTCTTTTTTTC
* *
134279 TTTCTTTCTCTC
1 -TTCTTTTTTTC
134291 TAT-TTTCTTTCTC
1 T-TCTTT-TTT-TC
134304 TCTCTCTTTTTTC
1 T-TCT-TTTTTTC
134317 TTCTTTT
1 TTCTTTT
134324 CTTCAGGTGT
Statistics
Matches: 99, Mismatches: 20, Indels: 29
0.67 0.14 0.20
Matches are distributed among these distances:
9 7 0.07
10 11 0.11
11 30 0.30
12 29 0.29
13 14 0.14
14 6 0.06
15 2 0.02
ACGTcount: A:0.04, C:0.23, G:0.01, T:0.72
Consensus pattern (11 bp):
TTCTTTTTTTC
Found at i:134221 original size:25 final size:25
Alignment explanation
Indices: 134188--134263 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
134178 TTTCTTGTTT
134188 TTCTTCTTATTTTCCTTCTTTTTCTC
1 TTCTTCTTATTTT-CTTCTTTTTCTC
134214 -TCTTCTTATTCTT-TTC-TTTTCTC
1 TTCTTCTTATT-TTCTTCTTTTTCTC
* *
134237 TTCTTATT-TTTTCTTTCTTTTTTTC
1 TTCTTCTTATTTTC-TTCTTTTTCTC
134262 TT
1 TT
134264 TTTCAACTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
22 2 0.05
23 9 0.21
24 12 0.28
25 18 0.42
26 2 0.05
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (25 bp):
TTCTTCTTATTTTCTTCTTTTTCTC
Found at i:134227 original size:19 final size:19
Alignment explanation
Indices: 134203--134267 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 19
134193 CTTATTTTCC
134203 TTCTTTTTCTCTCTTCTTA
1 TTCTTTTTCTCTCTTCTTA
*
134222 TTCTTTTCTTTTCTCTTCTTA
1 TTC-TTT-TTCTCTCTTCTTA
* *
134243 -T-TTTTTCTTTCTT-TTT
1 TTCTTTTTCTCTCTTCTTA
134259 TTCTTTTTC
1 TTCTTTTTC
134268 AACTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
16 2 0.05
17 8 0.21
18 9 0.24
19 3 0.08
20 4 0.11
21 12 0.32
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (19 bp):
TTCTTTTTCTCTCTTCTTA
Found at i:134248 original size:15 final size:13
Alignment explanation
Indices: 134222--134285 Score: 56
Period size: 15 Copynumber: 4.5 Consensus size: 13
134212 TCTCTTCTTA
134222 TTCTTTTCTTTTCT
1 TTCTTTT-TTTTCT
134236 CTTCTTATTTTTTCT
1 -TTCTT-TTTTTTCT
*
134251 TTCTTTTTTTCTTT
1 TTCTTTTTTT-TCT
*
134265 TTCAACTTTTTTTCT
1 TTC--TTTTTTTTCT
134280 TTCTTT
1 TTCTTT
134286 CTCTCTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 7 0.17
14 10 0.24
15 16 0.39
16 8 0.20
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTTTTTTTCT
Found at i:134253 original size:24 final size:24
Alignment explanation
Indices: 134177--134257 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
134167 ATGCTTTCAG
*
134177 TTTTC-TTGTTTT-TCTTCTTATT
1 TTTTCTTTCTTTTCTCTTCTTATT
*
134199 TTCCTTCTTT-TTCTCTCTTCTTA--
1 TT--TTCTTTCTTTTCTCTTCTTATT
*
134222 TTCT-TTTCTTTTCTCTTCTTATT
1 TTTTCTTTCTTTTCTCTTCTTATT
134245 TTTTCTTTCTTTT
1 TTTTCTTTCTTTT
134258 TTTCTTTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
20 3 0.06
21 13 0.28
22 2 0.04
23 5 0.11
24 14 0.30
25 10 0.21
ACGTcount: A:0.04, C:0.21, G:0.01, T:0.74
Consensus pattern (24 bp):
TTTTCTTTCTTTTCTCTTCTTATT
Found at i:134296 original size:19 final size:19
Alignment explanation
Indices: 134274--134322 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
134264 TTTCAACTTT
134274 TTTTCTTTCTTTCTCTCTA
1 TTTTCTTTCTTTCTCTCTA
* *
134293 TTTTCTTTCTCTCTCTCTT
1 TTTTCTTTCTTTCTCTCTA
134312 TTTTC-TTCTTT
1 TTTTCTTTCTTT
134323 TCTTCAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCTTTCTTTCTCTCTA
Found at i:134316 original size:15 final size:16
Alignment explanation
Indices: 134277--134317 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
134267 CAACTTTTTT
134277 TCTTTCTTTCTCTCTA
1 TCTTTCTTTCTCTCTA
*
134293 T-TTTCTTTCTCTCTC
1 TCTTTCTTTCTCTCTA
134308 TCTTT-TTTCT
1 TCTTTCTTTCT
134318 TCTTTTCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.68
Consensus pattern (16 bp):
TCTTTCTTTCTCTCTA
Found at i:134326 original size:15 final size:15
Alignment explanation
Indices: 134222--134326 Score: 61
Period size: 17 Copynumber: 6.7 Consensus size: 15
134212 TCTCTTCTTA
*
134222 TTCTTTTCTTTTCTC
1 TTCTTTTCTTTTTTC
*
134237 TTCTTATTTTTTCTTTC
1 TTCTT-TTCTTT-TTTC
* *
134254 TTTTTTTCTTTTTCAAC
1 TTCTTTTCTTTTT--TC
*
134271 TTTTTTTCTTTCTTTC
1 TTCTTTTCTTT-TTTC
* *
134287 TCTCTATT-TTCTTTC
1 T-TCTTTTCTTTTTTC
*
134302 -TCTCTCTCTTTTTTC
1 TTCT-TTTCTTTTTTC
134317 TTCTTTTCTT
1 TTCTTTTCTT
134327 CAGGTGTAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
13 3 0.04
14 1 0.01
15 22 0.32
16 17 0.25
17 23 0.34
18 2 0.03
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (15 bp):
TTCTTTTCTTTTTTC
Found at i:139062 original size:45 final size:45
Alignment explanation
Indices: 139007--139154 Score: 251
Period size: 45 Copynumber: 3.3 Consensus size: 45
138997 ATTATTCATT
139007 ATTTCTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTC-ATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
*
139053 ATTTCATTTATGGCATACTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* **
139098 ATTTCATTTATGGCACCCTTTCATGCCTTTAATGCACATTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
139143 ATTTCATTTATG
1 ATTTCATTTATG
139155 TAATGGAAAC
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 92 0.95
46 5 0.05
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:139660 original size:19 final size:17
Alignment explanation
Indices: 139613--139662 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
139603 ACCTTTCTCT
139613 TAGTATCGATACTACTA
1 TAGTATCGATACTACTA
* * *
139630 TGGTACCGATACTCACTT
1 TAGTATCGATACT-ACTA
139648 TCAGTATCGATACTA
1 T-AGTATCGATACTA
139663 TTTTAGTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 11 0.42
18 5 0.19
19 10 0.38
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (17 bp):
TAGTATCGATACTACTA
Found at i:139675 original size:91 final size:90
Alignment explanation
Indices: 139534--139714 Score: 251
Period size: 91 Copynumber: 2.0 Consensus size: 90
139524 GATACTTTTA
* * * *
139534 TACTATGGTACCGATACTCCCTTTTAGTATCGTTACCATTTCTACGTTATGTAATTCCATGGTAT
1 TACTATGGTACCGATACTCACTTTCAGTATCGATACCATTTCTACGTTATGTAA-TCCATGGAAT
139599 CAATACCTTT-CTCTTAGTATCGATAC
65 CAATA-CTTTCCTCTTAGTATCGATAC
*
139625 TACTATGGTACCGATACTCACTTTCAGTATCGATACTATTT-TA-GTATTATGTAATCCATGGAA
1 TACTATGGTACCGATACTCACTTTCAGTATCGATACCATTTCTACG--TTATGTAATCCATGGAA
*
139688 TCAATACTTTCCTTTTAGTATCGATAC
64 TCAATACTTTCCTCTTAGTATCGATAC
139715 CCCATCAGTA
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
89 5 0.06
90 31 0.38
91 45 0.56
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (90 bp):
TACTATGGTACCGATACTCACTTTCAGTATCGATACCATTTCTACGTTATGTAATCCATGGAATC
AATACTTTCCTCTTAGTATCGATAC
Found at i:139732 original size:90 final size:91
Alignment explanation
Indices: 139541--139732 Score: 223
Period size: 90 Copynumber: 2.1 Consensus size: 91
139531 TTATACTATG
* * * *
139541 GTACCGATACTCCCTTTTAGTATCGTTACCATTTCTACGTTATGTAATTCCATGGTATCAATACC
1 GTACCGATACTCACTTTCAGTATCGATACCATTTCTACGTTATGTAATTCCATGGAATCAATACC
* *
139606 TTTCTCTTAGTATCGATACTACTATG
66 TTTCTCTTAGTATCGATACTACCATA
*
139632 GTACCGATACTCACTTTCAGTATCGATACTATTT-TA-GTATTATGTAA-TCCATGGAATCAATA
1 GTACCGATACTCACTTTCAGTATCGATACCATTTCTACG--TTATGTAATTCCATGGAATCAATA
* *
139694 -CTTTCCTTTTAGTATCGATAC-CCCATCA
64 CCTTT-CTCTTAGTATCGATACTACCAT-A
*
139722 GTATCGATACT
1 GTACCGATACT
139733 AATTGCATAA
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
89 8 0.09
90 41 0.47
91 38 0.44
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (91 bp):
GTACCGATACTCACTTTCAGTATCGATACCATTTCTACGTTATGTAATTCCATGGAATCAATACC
TTTCTCTTAGTATCGATACTACCATA
Found at i:140242 original size:8 final size:8
Alignment explanation
Indices: 140231--140303 Score: 52
Period size: 8 Copynumber: 10.0 Consensus size: 8
140221 GAAAATATTT
140231 ATATATAA
1 ATATATAA
140239 ATATA-AA
1 ATATATAA
140246 A-ATATAA
1 ATATATAA
140253 A-AT-T-A
1 ATATATAA
140258 ATATATAA
1 ATATATAA
*
140266 TTATATAA
1 ATATATAA
*
140274 A-AAATAA
1 ATATATAA
* *
140281 AAAT-TAT
1 ATATATAA
*
140288 ATATATAT
1 ATATATAA
140296 ATATATAA
1 ATATATAA
140304 TCGGGGGGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
5 2 0.04
6 6 0.12
7 20 0.38
8 24 0.46
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATATAA
Found at i:142206 original size:22 final size:22
Alignment explanation
Indices: 142150--142199 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
142140 ATATGGAATG
* *
142150 AATGAAACAATAAAAATGTTAAA
1 AATGAAATAA-AAGAATGTTAAA
142173 AATGAAATAAAAGAATG-TAAA
1 AATGAAATAAAAGAATGTTAAA
142194 TAATGA
1 -AATGA
142200 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 11 0.46
23 9 0.38
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.22
Consensus pattern (22 bp):
AATGAAATAAAAGAATGTTAAA
Found at i:147114 original size:21 final size:21
Alignment explanation
Indices: 147089--147131 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
147079 TCGTTGAATT
147089 TTAAAGGTAAAAAATAT-TAAA
1 TTAAA-GTAAAAAATATATAAA
* *
147110 TTAAATTTAAAAATATATAAA
1 TTAAAGTAAAAAATATATAAA
147131 T
1 T
147132 CTTAAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (21 bp):
TTAAAGTAAAAAATATATAAA
Found at i:154359 original size:91 final size:91
Alignment explanation
Indices: 154253--154437 Score: 370
Period size: 91 Copynumber: 2.0 Consensus size: 91
154243 AGAAAAAGGT
154253 GATAACTTTTCTTGCTTTAAGAGTTTCAGCTATGGAGGAAAAAGAGATAAGAAGAAGATGAAAAT
1 GATAACTTTTCTTGCTTTAAGAGTTTCAGCTATGGAGGAAAAAGAGATAAGAAGAAGATGAAAAT
154318 GAAAAGTTGAAAGAAATAATGAGAGA
66 GAAAAGTTGAAAGAAATAATGAGAGA
154344 GATAACTTTTCTTGCTTTAAGAGTTTCAGCTATGGAGGAAAAAGAGATAAGAAGAAGATGAAAAT
1 GATAACTTTTCTTGCTTTAAGAGTTTCAGCTATGGAGGAAAAAGAGATAAGAAGAAGATGAAAAT
154409 GAAAAGTTGAAAGAAATAATGAGAGA
66 GAAAAGTTGAAAGAAATAATGAGAGA
154435 GAT
1 GAT
154438 GAAGTGAGTG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (91 bp):
GATAACTTTTCTTGCTTTAAGAGTTTCAGCTATGGAGGAAAAAGAGATAAGAAGAAGATGAAAAT
GAAAAGTTGAAAGAAATAATGAGAGA
Found at i:154585 original size:18 final size:19
Alignment explanation
Indices: 154551--154596 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
154541 GGAGAGAGAG
154551 AAATAAAAATAAGGAAATA
1 AAATAAAAATAAGGAAATA
154570 AAATAAAAGA-AA-GAAATA
1 AAATAAAA-ATAAGGAAATA
*
154588 AAGTAAAAA
1 AAATAAAAA
154597 GGAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 13 0.52
19 10 0.40
20 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (19 bp):
AAATAAAAATAAGGAAATA
Found at i:187906 original size:18 final size:18
Alignment explanation
Indices: 187883--187939 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
187873 AAACATCACT
187883 GGTTTAAGCTCAAAATGC
1 GGTTTAAGCTCAAAATGC
*
187901 GGTTTAAGCTCAAAATAC
1 GGTTTAAGCTCAAAATGC
187919 GGTTTAAGCTCAAAATG-
1 GGTTTAAGCTCAAAATGC
187936 GGTT
1 GGTT
187940 GTTTGTATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
17 4 0.11
18 33 0.89
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (18 bp):
GGTTTAAGCTCAAAATGC
Found at i:188214 original size:21 final size:22
Alignment explanation
Indices: 188170--188214 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
188160 TAAGTAAATA
*
188170 TATGGTGACAAGAAAAACTTGT
1 TATGGTGACAAGAAAAAATTGT
188192 TATGGTGA-AA-AAAAAATTAGT
1 TATGGTGACAAGAAAAAATT-GT
188213 TA
1 TA
188215 GTTGTCAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 6 0.29
22 8 0.38
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (22 bp):
TATGGTGACAAGAAAAAATTGT
Found at i:191264 original size:53 final size:48
Alignment explanation
Indices: 191199--191323 Score: 166
Period size: 45 Copynumber: 2.6 Consensus size: 48
191189 AAAAATCATA
* *
191199 AAATTATTTATTAATATATTTTAAATAATTTACTAACTTACTTTCTATATATT
1 AAATAATTTATTAATATATTTT-AATAA--T--TAACTTACTTTCTATACATT
191252 AAATAATTTATTAATATA-TTT--TAATTAACTTACTTTCTATACATT
1 AAATAATTTATTAATATATTTTAATAATTAACTTACTTTCTATACATT
191297 AAATAATTTATTAATATATTTTAATAA
1 AAATAATTTATTAATATATTTTAATAA
191324 ACTATATATT
Statistics
Matches: 67, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
45 37 0.55
46 3 0.04
47 1 0.01
48 3 0.04
49 3 0.04
52 3 0.04
53 17 0.25
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.51
Consensus pattern (48 bp):
AAATAATTTATTAATATATTTTAATAATTAACTTACTTTCTATACATT
Found at i:191275 original size:22 final size:22
Alignment explanation
Indices: 191244--191320 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
191234 ACTTACTTTC
191244 TATATATTAAATAATTTATTAA
1 TATATATTAAATAATTTATTAA
* * * **
191266 TATATTTTAATTAACTTACTTTC
1 TATATATTAAATAATTTA-TTAA
*
191289 TATACATTAAATAATTTATTAA
1 TATATATTAAATAATTTATTAA
*
191311 TATATTTTAA
1 TATATATTAA
191321 TAAACTATAT
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
22 25 0.61
23 16 0.39
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
TATATATTAAATAATTTATTAA
Found at i:191282 original size:45 final size:45
Alignment explanation
Indices: 191232--191326 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
191222 AATAATTTAC
*
191232 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
1 TAACTTACTTTCTATACATTAAATAATTTATTAATATATTTTAAT
191277 TAACTTACTTTCTATACATTAAATAATTTATTAATATATTTTAAT
1 TAACTTACTTTCTATACATTAAATAATTTATTAATATATTTTAAT
*
191322 AAACT
1 TAACT
191327 ATATATTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (45 bp):
TAACTTACTTTCTATACATTAAATAATTTATTAATATATTTTAAT
Found at i:191358 original size:18 final size:19
Alignment explanation
Indices: 191323--191372 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
191313 TATTTTAATA
*
191323 AACTATATATTAATTTACT
1 AACTATATATTAACTTACT
191342 AACTATA-ATTAACTTACT
1 AACTATATATTAACTTACT
**
191360 TTCTATATATTAA
1 AACTATATATTAA
191373 ATTATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (19 bp):
AACTATATATTAACTTACT
Found at i:194033 original size:19 final size:18
Alignment explanation
Indices: 193994--194038 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
193984 ACTTTTGATA
* *
193994 TTTATTATAAAGTTTATT
1 TTTATTTTAAAGTTAATT
194012 TTTATTTTAAAGTATAATT
1 TTTATTTTAAAGT-TAATT
194031 TTTATTTT
1 TTTATTTT
194039 TGAAATCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTATTTTAAAGTTAATT
Found at i:195323 original size:194 final size:192
Alignment explanation
Indices: 194926--195326 Score: 493
Period size: 194 Copynumber: 2.1 Consensus size: 192
194916 CTGACATTAT
* * * *
194926 ATATGGTGACGTTATGCATGATCATCATTCATAATATTATTAGGTAATGACATATTATGTCACTA
1 ATATAGTGACGTTATGCATAAACATCATTAATAATATTATTAGGTAATGACATATTATGTCACTA
*
194991 AAAATGTGACAATATCTCTTTCGTCACATATAAGGTGATTTAATGCATTATTTGTGACAATATAA
66 AAAATGTGACAATATCTCTTTCGTCACATATAAGGTGATTTAATGCATTATCTGTGACAATATAA
* ** * *
195056 ATTATCAATAACGAAATCTTATTTAATTTAGTGACGTAACCAACTCTCATAGAATATAAATT
131 ATCATCAATAACGAAATCTTACATAATTTAGTGACATAACCAACTCTCATAGAATATAAATC
* * **
195118 ATAAAGTGACGTTATGCATAAACGTCATTAATAATATTATTAGGTAACAT-TTATATTATGTCAC
1 ATATAGTGACGTTATGCATAAACATCATTAATAATATTATTAGGT-A-ATGACATATTATGTCAC
* * * *
195182 TAAAAATTTGACAATATCTCTTTCGTCACATA-CAGGTTGATTTTAATGTATTATCCT-TGACGA
64 TAAAAATGTGACAATATCTCTTTCGTCACATATAAGG-TGA-TTTAATGCATTAT-CTGTGACAA
* * ** ** * * *
195245 TATAAATCATCAATAATGAAATTTTACATAATTTAGTGACATAATTAGTTGTCATTGAATATTAA
126 TATAAATCATCAATAACGAAATCTTACATAATTTAGTGACATAACCAACTCTCATAGAATATAAA
195310 TC
191 TC
195312 ATATAGTGACGTTAT
1 ATATAGTGACGTTAT
195327 ATATAAATGT
Statistics
Matches: 176, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
192 42 0.24
193 47 0.27
194 86 0.49
195 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (192 bp):
ATATAGTGACGTTATGCATAAACATCATTAATAATATTATTAGGTAATGACATATTATGTCACTA
AAAATGTGACAATATCTCTTTCGTCACATATAAGGTGATTTAATGCATTATCTGTGACAATATAA
ATCATCAATAACGAAATCTTACATAATTTAGTGACATAACCAACTCTCATAGAATATAAATC
Found at i:195355 original size:194 final size:192
Alignment explanation
Indices: 194956--195408 Score: 484
Period size: 194 Copynumber: 2.3 Consensus size: 192
194946 ATCATCATTC
* * *
194956 ATAATATTATTAGGTAATGACATATTATGTCACTAAAAATGTGACAATATCTCTTTCGTCACATA
1 ATAATACTATTAGGTAACGATATATTATGTCACTAAAAATGTGACAATATCTCTTTCGTCACATA
* * **
195021 TAAGGTGATTTAATGCATTATTTGTGACAATATAAATTATCAATAACGAAATCTTATTTAATTTA
66 TAAGGTGATTTAATGCATTATCTGTGACAATATAAATCATCAATAACGAAATCTTACATAATTTA
* * * *
195086 GTGACGTAACCAACTCTCATAGAATATAAATTATAAAGTGACGTTATGCATAAACGTCATTA
131 GTGACATAACCAACTCTCATAGAATATAAATCATAAAGTGACGTTATACATAAACGTCATCA
* *
195148 ATAATATTATTAGGTAAC-ATTTATATTATGTCACTAAAAATTTGACAATATCTCTTTCGTCACA
1 ATAATACTATTAGGTAACGA--TATATTATGTCACTAAAAATGTGACAATATCTCTTTCGTCACA
* * * * *
195212 TA-CAGGTTGATTTTAATGTATTATCCT-TGACGATATAAATCATCAATAATGAAATTTTACATA
64 TATAAGG-TGA-TTTAATGCATTAT-CTGTGACAATATAAATCATCAATAACGAAATCTTACATA
** ** * * * * * *
195275 ATTTAGTGACATAATTAGTTGTCATTGAATATTAATCATATAGTGACGTTATATATAAATGTCAT
126 ATTTAGTGACATAACCAACTCTCATAGAATATAAATCATAAAGTGACGTTATACATAAACGTCAT
*
195340 CC
191 CA
* * * * * * *
195342 ATGCA-ACTATTAGGTGACGATATACTACGTCACTAACAATGTGACAAT-TTTCTTTTCGTCACG
1 AT-AATACTATTAGGTAACGATATATTATGTCACTAAAAATGTGACAATATCTC-TTTCGTCACA
195405 TATA
64 TATA
195409 CAATGAAATT
Statistics
Matches: 215, Mismatches: 37, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
191 1 0.00
192 23 0.11
193 81 0.38
194 107 0.50
195 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (192 bp):
ATAATACTATTAGGTAACGATATATTATGTCACTAAAAATGTGACAATATCTCTTTCGTCACATA
TAAGGTGATTTAATGCATTATCTGTGACAATATAAATCATCAATAACGAAATCTTACATAATTTA
GTGACATAACCAACTCTCATAGAATATAAATCATAAAGTGACGTTATACATAAACGTCATCA
Found at i:196656 original size:22 final size:22
Alignment explanation
Indices: 196630--196678 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
196620 ACCTCATATG
196630 AGAGAAAGGGGTGGAAGAAAAT
1 AGAGAAAGGGGTGGAAGAAAAT
*
196652 AGAGAAAGGGGTGTAAGAAAAT
1 AGAGAAAGGGGTGGAAGAAAAT
196674 AGAGA
1 AGAGA
196679 TTATCAAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.39, T:0.10
Consensus pattern (22 bp):
AGAGAAAGGGGTGGAAGAAAAT
Found at i:207321 original size:20 final size:20
Alignment explanation
Indices: 207283--207334 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
207273 AGAAGAGTAT
207283 AATAATAAAAAT-GTCAAGAC
1 AATAA-AAAAATGGTCAAGAC
*
207303 AATGAAAAAAATGGT-AAGAT
1 AAT-AAAAAAATGGTCAAGAC
*
207323 AATAAATAAATG
1 AATAAAAAAATG
207335 ATAGTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 8 0.29
20 16 0.57
21 4 0.14
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.21
Consensus pattern (20 bp):
AATAAAAAAATGGTCAAGAC
Found at i:212110 original size:21 final size:21
Alignment explanation
Indices: 212086--212126 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
212076 GTAAATCACA
212086 TTGTGATTTTCCAAATTCGCG
1 TTGTGATTTTCCAAATTCGCG
212107 TTGTGATTTTCCAAATTCGC
1 TTGTGATTTTCCAAATTCGC
212127 AACGCGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44
Consensus pattern (21 bp):
TTGTGATTTTCCAAATTCGCG
Found at i:212919 original size:21 final size:21
Alignment explanation
Indices: 212893--212976 Score: 105
Period size: 21 Copynumber: 4.0 Consensus size: 21
212883 ATCAGATTGT
212893 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
* *
212914 CCAGGGGGTACCGATTTCCCC
1 CCAGGGGGTACAGATTCCCCC
* * *
212935 CCAGAGAGAACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
* *
212956 CCAGGGGTTACCGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
212977 TGTCTAACGG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.20, C:0.39, G:0.25, T:0.15
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:214260 original size:19 final size:20
Alignment explanation
Indices: 214236--214283 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
214226 AATGATTTTC
*
214236 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
214255 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
214275 TTTTGAAAA
1 TTTTGAAAA
214284 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:214338 original size:15 final size:17
Alignment explanation
Indices: 214306--214338 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
214296 TTTCAAAAAT
214306 AAAAATTAAAAGTTTTG
1 AAAAATTAAAAGTTTTG
214323 AAAAA-TAAAA-TTTTG
1 AAAAATTAAAAGTTTTG
214338 A
1 A
214339 TTTAAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (17 bp):
AAAAATTAAAAGTTTTG
Found at i:215719 original size:41 final size:42
Alignment explanation
Indices: 215671--215773 Score: 147
Period size: 41 Copynumber: 2.5 Consensus size: 42
215661 ATCAGATTGT
* * *
215671 CCAGGGGGTACAGATTCCCCCCCA-AGGGTACAGATTCCCCC
1 CCAGGGGGTACCGATTCCCCCCCAGAGGGAACAAATTCCCCC
* *
215712 CTAGGGGGTACCGATT-CCCCCCAGGGGGAACAAATTCCCCC
1 CCAGGGGGTACCGATTCCCCCCCAGAGGGAACAAATTCCCCC
215753 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
215774 TGTCTAAAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
40 7 0.13
41 43 0.80
42 4 0.07
ACGTcount: A:0.20, C:0.39, G:0.26, T:0.15
Consensus pattern (42 bp):
CCAGGGGGTACCGATTCCCCCCCAGAGGGAACAAATTCCCCC
Found at i:215720 original size:21 final size:21
Alignment explanation
Indices: 215671--215773 Score: 138
Period size: 21 Copynumber: 5.0 Consensus size: 21
215661 ATCAGATTGT
215671 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
215692 CCA-AGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
* *
215712 CTAGGGGGTACCGATT-CCCC
1 CCAGGGGGTACAGATTCCCCC
* *
215732 CCAGGGGGAACAAATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
215753 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
215774 TGTCTAAAGG
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
20 34 0.49
21 35 0.51
ACGTcount: A:0.20, C:0.39, G:0.26, T:0.15
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:216525 original size:20 final size:19
Alignment explanation
Indices: 216490--216543 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
216480 AAATCGCAAC
216490 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
216509 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
* *
216529 GTGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
216544 AGAAACTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:218520 original size:4 final size:4
Alignment explanation
Indices: 218511--218553 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
218501 TTTTTCGGAA
* * * *
218511 TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
218554 CAACGGACCG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (4 bp):
TTAT
Found at i:218737 original size:21 final size:21
Alignment explanation
Indices: 218702--218778 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
218692 CCTATCATCA
**
218702 TTCAAGAGGTGCCTCCTATCC
1 TTCAAGAGGCCCCTCCTATCC
218723 TTCAAGAGGCCCCT-CTCAT-C
1 TTCAAGAGGCCCCTCCT-ATCC
* * * * *
218743 ATCGAATAAGCCCCTCCCACCC
1 TTC-AAGAGGCCCCTCCTATCC
218765 TTCAAGAGGCCCCT
1 TTCAAGAGGCCCCT
218779 ATCATTGTTC
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 5 0.12
21 33 0.79
22 4 0.10
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.22
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCTATCC
Found at i:218743 original size:42 final size:42
Alignment explanation
Indices: 218692--218812 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 42
218682 GCCCGATGCA
* * *
218692 CCTATCATCATTCAAGAGGTGCCTCCTATCCTTCAAGAGGCC
1 CCTATCATCATTCAAGAGGTCCCTCCCACCCTTCAAGAGGCC
* * * *
218734 CCTCTCATCA-TCGAATAAGCCCCTCCCACCCTTCAAGAGGCC
1 CCTATCATCATTC-AAGAGGTCCCTCCCACCCTTCAAGAGGCC
** * * *
218776 CCTATCATTGTTCAAGAGGTCCCGCCCGCCGTTCAAG
1 CCTATCATCATTCAAGAGGTCCCTCCCACCCTTCAAG
218813 TGCCGATTCA
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
41 2 0.03
42 57 0.93
43 2 0.03
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCATTCAAGAGGTCCCTCCCACCCTTCAAGAGGCC
Found at i:220238 original size:14 final size:14
Alignment explanation
Indices: 220219--220255 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
220209 GCTTGTTTAA
*
220219 TTGATTTGTAAAAG
1 TTGATTTGTAAAAC
220233 TTGATTTGTAAAAC
1 TTGATTTGTAAAAC
220247 TTGATTTGT
1 TTGATTTGT
220256 TTAATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAC
Found at i:220264 original size:28 final size:28
Alignment explanation
Indices: 220219--220272 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
220209 GCTTGTTTAA
*
220219 TTGATTTGTAAAAGTTGATTTGTAAAAC
1 TTGATTTGTAAAAGTTGATGTGTAAAAC
** *
220247 TTGATTTGTTTAATTTGATGTGTAAA
1 TTGATTTGTAAAAGTTGATGTGTAAA
220273 TAAGAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (28 bp):
TTGATTTGTAAAAGTTGATGTGTAAAAC
Found at i:220285 original size:79 final size:79
Alignment explanation
Indices: 220169--220321 Score: 272
Period size: 80 Copynumber: 1.9 Consensus size: 79
220159 ACATTGAAAG
220169 TTGATTTGTTTAATTGATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTAATTGATTTGTAAAAG
1 TTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTAAAAG
220233 TTGATTTGTAAAAC
66 TTGATTTGTAAAAC
* *
220247 TTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTAAAA
1 TTGATTTGTTTAA-TTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTAAAA
220312 GTTGATTTGT
65 GTTGATTTGT
220322 TGTTTTAAAT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
78 13 0.18
79 19 0.27
80 39 0.55
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (79 bp):
TTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTAAAAG
TTGATTTGTAAAAC
Found at i:220428 original size:20 final size:20
Alignment explanation
Indices: 220377--220452 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
220367 TTGAAGGTAC
*
220377 AAATTCGCAACACGAAAGGT
1 AAATTCGCAACGCGAAAGGT
220397 AAATTCGCAACGCGAAAGGT
1 AAATTCGCAACGCGAAAGGT
*
220417 AAATTCGCAACGC-AAAAGT
1 AAATTCGCAACGCGAAAGGT
* **
220436 CAATTTACAACGCGAAA
1 AAATTCGCAACGCGAAA
220453 TAAGCGTTGC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
19 15 0.30
20 35 0.70
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAGGT
Found at i:223111 original size:24 final size:24
Alignment explanation
Indices: 223084--223137 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
223074 CCATCACATC
*
223084 ATCAAAATCTTAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
223108 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
223132 ATCAAA
1 ATCAAA
223138 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:223283 original size:12 final size:12
Alignment explanation
Indices: 223262--223295 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
223252 GGTTGTGGGT
*
223262 TTTGAGATTGTG
1 TTTGATATTGTG
223274 TTTGATATTGTG
1 TTTGATATTGTG
*
223286 TTTGGTATTG
1 TTTGATATTG
223296 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Done.