Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 18 of 75
Found at i:5113470 original size:44 final size:44
Alignment explanation
Indices: 5113415--5113943 Score: 289
Period size: 44 Copynumber: 11.3 Consensus size: 44
5113405 TCCCTAAGCA
* * *
5113415 ACAGTGGAGCAGATCGAAGCTAGAATTCTTATCTCCCTGAGGTT
1 ACAGCGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGGTT
* *
5113459 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCT-AGGATT
1 ACAGCGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGG-TT
* * ** * *
5113503 ACAGTGGAGCGGATT-AAAATA-AAGGATCTTATCTCTCTGAAGTT
1 ACAGCGGAGCAGATTGAAGCTAGAA--ATCTTATCTCCCTGAGGTT
* * * * *
5113547 ACAGCAGAGTAGATCGCATCAGATTAAAGCCAGAAATCTTATCTTCCTAAGATT
1 ACAGC---G--GA--G---CAGATTGAAGCTAGAAATCTTATCTCCCTGAGGTT
* *
5113601 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCT-AGGATT
1 ACAGCGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGG-TT
* * ** * *
5113645 ACAGTGGAGCGGATT-AAAATA-AAGGATCTTATCTCTCTGAAGTT
1 ACAGCGGAGCAGATTGAAGCTAGAA--ATCTTATCTCCCTGAGGTT
* * * *
5113689 ACAGCAGAGTAAATCGCATCAGATTGAAGCCAGAAATCTTATCTTCCTAAGATT
1 ACAGC-G-G---A--G---CAGATTGAAGCTAGAAATCTTATCTCCCTGAGGTT
* * *
5113743 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGCGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGGTT
* ** * * *
5113787 ACAGTGGAGCAGATT-AAAATAAAAGATCTTATCTCTCTGAAGTT
1 ACAGCGGAGCAGATTGAAGCTAGAA-ATCTTATCTCCCTGAGGTT
* *
5113831 ACAGCAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATT
1 ACAGC---G--GA--G---CAGATTGAAGCTAGAAATCTTATCTCCCTGAGGTT
* * *
5113885 ACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 ACAGCGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGGTT
*
5113929 ACAGCGGAGCGGATT
1 ACAGCGGAGCAGATT
5113944 AAGATAAAGG
Statistics
Matches: 368, Mismatches: 73, Indels: 88
0.70 0.14 0.17
Matches are distributed among these distances:
42 2 0.01
43 18 0.05
44 230 0.62
45 5 0.01
46 1 0.00
47 5 0.01
49 10 0.03
51 5 0.01
52 1 0.00
53 1 0.00
54 75 0.20
55 11 0.03
56 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (44 bp):
ACAGCGGAGCAGATTGAAGCTAGAAATCTTATCTCCCTGAGGTT
Found at i:5113647 original size:98 final size:94
Alignment explanation
Indices: 5113395--5113937 Score: 242
Period size: 98 Copynumber: 5.8 Consensus size: 94
5113385 GGAAAATTAC
* * * * * *
5113395 AAATCTTGTCTCCCTAAGCA--ACAGTGGAGCAGATCGAAGCTAGAATTCTTATCTCCCTGAGGT
1 AAATCTTATCTCCCTAAG-ATTACAGCGGAGCAGATTGAAGCTAGAAATCCTATCTCCCTG-GAT
* *
5113458 TACAGC--G-GA-G---CAGATTGAAGCTAG
64 TACAGCAGGAGACGCATCAGATTAAAGCCAG
* * * * * ** * * *
5113482 TAATCCTATCTCCCTAGGATTACAGTGGAGCGGATT-AAAATA-AAGGATCTTATCTCTCTGAAG
1 AAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGAA--ATCCTATCTCCCTGGA-
5113545 TTACAGCAGAGTAGATCGCATCAGATTAAAGCCAG
63 TTACAGCAG-G-AGA-CGCATCAGATTAAAGCCAG
* *
5113580 AAATCTTATCTTCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTAGGATT
1 AAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGAAATCCTATCTCCCT-GGATT
* * * * *
5113645 ACAG-TGGAG-CGGATTAAAATAAAG---G
65 ACAGCAGGAGACGCATCAGATTAAAGCCAG
* * *
5113670 --ATCTTATCTCTCTGAAG-TTACAGCAGAGTAAATCGCATCAGATTGAAGCCAGAAATCTTATC
1 AAATCTTATCTCCCT-AAGATTACAGC-G-G---A--G---CAGATTGAAGCTAGAAATCCTATC
* * * *
5113732 TTCCTAAGATTACAGC--G-GA-G---CAGATTGAAGCTAG
55 TCCCT-GGATTACAGCAGGAGACGCATCAGATTAAAGCCAG
* * * * ** * * * *
5113766 TAATCCTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAAAGATCTTATCTCTCTGAAGT
1 AAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGAA-ATCCTATCTCCCTGGA-T
*
5113830 TACAGCAGAGTAGATCGCATCAGATTGAAGCCAG
64 TACAGCAG-G-AGA-CGCATCAGATTAAAGCCAG
* *
5113864 AAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATT
1 AAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGAAATCCTATCTCCCTG-GATT
5113929 ACAGC-GGAG
65 ACAGCAGGAG
5113938 CGGATTAAGA
Statistics
Matches: 340, Mismatches: 65, Indels: 94
0.68 0.13 0.19
Matches are distributed among these distances:
86 3 0.01
87 24 0.07
88 74 0.22
89 4 0.01
90 2 0.01
91 3 0.01
93 23 0.07
95 7 0.02
96 6 0.02
97 6 0.02
98 175 0.51
99 12 0.04
100 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (94 bp):
AAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGAAATCCTATCTCCCTGGATTA
CAGCAGGAGACGCATCAGATTAAAGCCAG
Found at i:5113680 original size:142 final size:142
Alignment explanation
Indices: 5113424--5113994 Score: 966
Period size: 142 Copynumber: 4.0 Consensus size: 142
5113414 AACAGTGGAG
* * * * *
5113424 CAGATCGAAGCTAGAATTCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
5113489 ATCTCCCT-AGGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCA
66 ATCTCCCTGA-GATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCA
5113553 GAGTAGATCGCAT
130 GAGTAGATCGCAT
* *
5113566 CAGATTAAAGCCAGAAATCTTATCTTCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
5113631 ATCTCCCT-AGGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCA
66 ATCTCCCTGA-GATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCA
*
5113695 GAGTAAATCGCAT
130 GAGTAGATCGCAT
*
5113708 CAGATTGAAGCCAGAAATCTTATCTTCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
5113773 ATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGTTACAGCAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
5113838 AGTAGATCGCAT
131 AGTAGATCGCAT
*
5113850 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* * * *
5113915 ATCTCCCTGAGATTACAGCGGAGCGGATTAAGATAAAGGATCTTATCTCTCTAAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
5113980 AGTAGATCGCAT
131 AGTAGATCGCAT
5113992 CAG
1 CAG
5113995 GTCTTATCTC
Statistics
Matches: 408, Mismatches: 20, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
142 407 1.00
143 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAG
AGTAGATCGCAT
Found at i:5120956 original size:30 final size:30
Alignment explanation
Indices: 5120891--5120998 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 30
5120881 ACAATTGAAT
*
5120891 CAAAATCAAAGTTTTATGTGTATATTTCAAC
1 CAAAATCAAA-TTTTATGTGTATATTGCAAC
5120922 CAAAATCAAATTTTAATGTGTATAGTTGC-A-
1 CAAAATCAAATTTT-ATGTGTATA-TTGCAAC
* * * *
5120952 CAAAATCAAATATTATGTATCAAATTGCAAA
1 CAAAATCAAATTTTATGTGT-ATATTGCAAC
**
5120983 CTGAATCAAATTTTAT
1 CAAAATCAAATTTTAT
5120999 ATATAGTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
29 9 0.14
30 20 0.31
31 33 0.51
32 3 0.05
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (30 bp):
CAAAATCAAATTTTATGTGTATATTGCAAC
Found at i:5122643 original size:18 final size:18
Alignment explanation
Indices: 5122620--5122665 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
5122610 TAATTGGATG
*
5122620 CTTAAATATGTTTTAAAA
1 CTTAAATATGTTGTAAAA
*
5122638 CTTAAATATGTTGTAACA
1 CTTAAATATGTTGTAAAA
*
5122656 CATAAATATG
1 CTTAAATATG
5122666 GGGTGGTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (18 bp):
CTTAAATATGTTGTAAAA
Found at i:5123613 original size:30 final size:29
Alignment explanation
Indices: 5123548--5123620 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
5123538 ATGAATGAAA
*
5123548 TTTTTAACAAAAATGATTAATTTGCTCTT
1 TTTTTAACAAAAATGATTAATTTGATCTT
5123577 TGTTTTAACAAACAA-GAATTAATTT-ATCTAT
1 T-TTTTAACAAA-AATG-ATTAATTTGATCT-T
*
5123608 TTTTTAATAAAAA
1 TTTTTAACAAAAA
5123621 AATAAAATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 3 0.08
30 23 0.61
31 12 0.32
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.45
Consensus pattern (29 bp):
TTTTTAACAAAAATGATTAATTTGATCTT
Found at i:5128702 original size:5 final size:5
Alignment explanation
Indices: 5128692--5128728 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
5128682 TATATTTAAA
5128692 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
5128729 TTAACATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:5128704 original size:15 final size:15
Alignment explanation
Indices: 5128681--5128719 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5128671 AGTAAACAAA
5128681 TTATATTTAAATTATT
1 TTAT-TTTAAATTATT
**
5128697 TTATTTTATTTTATT
1 TTATTTTAAATTATT
5128712 TTATTTTA
1 TTATTTTA
5128720 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTTTAAATTATT
Found at i:5133405 original size:8 final size:7
Alignment explanation
Indices: 5133385--5133418 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
5133375 TTTTTAAATA
*
5133385 CATTTCT
1 CATTTCC
5133392 CATTTCCC
1 CATTT-CC
5133400 CATTTCC
1 CATTTCC
5133407 CATTTCC
1 CATTTCC
5133414 CATTT
1 CATTT
5133419 TTAAAATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.47
Consensus pattern (7 bp):
CATTTCC
Found at i:5133405 original size:15 final size:14
Alignment explanation
Indices: 5133385--5133418 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
5133375 TTTTTAAATA
*
5133385 CATTTCTCATTTCCC
1 CATTTCCCATTT-CC
5133400 CATTTCCCATTTCC
1 CATTTCCCATTTCC
5133414 CATTT
1 CATTT
5133419 TTAAAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.47
Consensus pattern (14 bp):
CATTTCCCATTTCC
Found at i:5138184 original size:2 final size:2
Alignment explanation
Indices: 5138177--5138209 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5138167 TTTTTCAGAT
*
5138177 TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5138210 TGTTCTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5138391 original size:13 final size:14
Alignment explanation
Indices: 5138362--5138403 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5138352 CCGGCCCAAT
5138362 ACCAAAA-ATAAATA
1 ACCAAAATATAAA-A
*
5138376 AACAAAATATAAAA
1 ACCAAAATATAAAA
5138390 ACCAAAA-ATAAAA
1 ACCAAAATATAAAA
5138403 A
1 A
5138404 AATCCAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.28
14 13 0.52
15 5 0.20
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (14 bp):
ACCAAAATATAAAA
Found at i:5138397 original size:15 final size:14
Alignment explanation
Indices: 5138362--5138404 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
5138352 CCGGCCCAAT
5138362 ACCAAAAATAAATAA
1 ACCAAAAATAAA-AA
5138377 A-C-AAAATATAAAA
1 ACCAAAAATA-AAAA
5138390 ACCAAAAATAAAAA
1 ACCAAAAATAAAAA
5138404 A
1 A
5138405 ATCCAAGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.36
14 9 0.36
15 7 0.28
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (14 bp):
ACCAAAAATAAAAA
Found at i:5138405 original size:15 final size:15
Alignment explanation
Indices: 5138362--5138410 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
5138352 CCGGCCCAAT
*
5138362 ACCAAAAATAAATAA
1 ACCAAAAATAAAAAA
*
5138377 A-C-AAAATATAAAA
1 ACCAAAAATAAAAAA
5138390 ACCAAAAATAAAAAA
1 ACCAAAAATAAAAAA
5138405 ATCCAA
1 A-CCAA
5138411 GTCCATTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.36
14 2 0.07
15 12 0.43
16 4 0.14
ACGTcount: A:0.73, C:0.14, G:0.00, T:0.12
Consensus pattern (15 bp):
ACCAAAAATAAAAAA
Found at i:5139690 original size:18 final size:21
Alignment explanation
Indices: 5139658--5139705 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
5139648 ATGGTGCCTC
*
5139658 TTTATTTACTAAAT-CTT-TTA
1 TTTATTT-TTAAATCCTTGTTA
5139678 TTT-TTTTTAAATCCTTGTTA
1 TTTATTTTTAAATCCTTGTTA
5139698 TTTATTTT
1 TTTATTTT
5139706 CTTTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.21
19 6 0.25
20 9 0.38
21 4 0.17
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTATTTTTAAATCCTTGTTA
Found at i:5139739 original size:15 final size:16
Alignment explanation
Indices: 5139707--5139747 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
5139697 ATTTATTTTC
*
5139707 TTTATTATTATGCATT
1 TTTATTATTATCCATT
*
5139723 TTTATT-TTATCC-CT
1 TTTATTATTATCCATT
5139737 TTTATTATTAT
1 TTTATTATTAT
5139748 TATTTCTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 7 0.32
15 9 0.41
16 6 0.27
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTATTATTATCCATT
Found at i:5139898 original size:12 final size:12
Alignment explanation
Indices: 5139883--5139907 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5139873 TCTTTTTTAT
5139883 TTTATTTATTCA
1 TTTATTTATTCA
5139895 TTTATTTATTCA
1 TTTATTTATTCA
5139907 T
1 T
5139908 CTATCATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTATTCA
Found at i:5150812 original size:35 final size:35
Alignment explanation
Indices: 5150773--5150843 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
5150763 GGCTCCAAAA
5150773 CGGTACCGTTTTGAGATTTAACCCGTGAGGTGACC
1 CGGTACCGTTTTGAGATTTAACCCGTGAGGTGACC
*
5150808 CGGTACCGTTTTGAGCTTTAACCCGTGAGGTGACC
1 CGGTACCGTTTTGAGATTTAACCCGTGAGGTGACC
5150843 C
1 C
5150844 AACCCGAGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (35 bp):
CGGTACCGTTTTGAGATTTAACCCGTGAGGTGACC
Found at i:5151200 original size:25 final size:26
Alignment explanation
Indices: 5151154--5151214 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
5151144 ATTAATTTGT
*
5151154 TTAATATTAGTTTATTAATATT-TTA
1 TTAATATTAGCTTATTAATATTATTA
*
5151179 TTAATATTAGCCTT-TTATTATTATTA
1 TTAATATTAG-CTTATTAATATTATTA
*
5151205 CTATATATTA
1 TTA-ATATTA
5151215 TTACTCTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 17 0.57
26 7 0.23
27 6 0.20
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (26 bp):
TTAATATTAGCTTATTAATATTATTA
Found at i:5151215 original size:13 final size:12
Alignment explanation
Indices: 5151194--5151229 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
5151184 ATTAGCCTTT
5151194 TATTATTATTAC
1 TATTATTATTAC
5151206 TATATATTATTAC
1 TAT-TATTATTAC
*
5151219 TCTTATTATTA
1 TATTATTATTA
5151230 TAGATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:5154585 original size:12 final size:10
Alignment explanation
Indices: 5154567--5154612 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 10
5154557 ACTTTAAGTC
5154567 AAAAAAAATG
1 AAAAAAAATG
*
5154577 ATGAAAAAATG
1 A-AAAAAAATG
5154588 AAAATAAAAATG
1 -AAA-AAAAATG
5154600 AAAAAAAATG
1 AAAAAAAATG
5154610 AAA
1 AAA
5154613 GTAAAAATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 11 0.35
11 12 0.39
12 8 0.26
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:5154618 original size:12 final size:11
Alignment explanation
Indices: 5154581--5154621 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
5154571 AAAATGATGA
5154581 AAAAATGAAAAT
1 AAAAATG-AAAT
5154593 AAAAATGAAA-
1 AAAAATGAAAT
5154603 AAAAATGAAAGT
1 AAAAATGAAA-T
5154615 AAAAATG
1 AAAAATG
5154622 GAGAGGCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.37
11 3 0.11
12 14 0.52
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (11 bp):
AAAAATGAAAT
Found at i:5154619 original size:22 final size:23
Alignment explanation
Indices: 5154570--5154621 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
5154560 TTAAGTCAAA
*
5154570 AAAAATGATGAAAAAATGAAAAT
1 AAAAATGATAAAAAAATGAAAAT
*
5154593 AAAAATGA-AAAAAAATGAAAGT
1 AAAAATGATAAAAAAATGAAAAT
5154615 AAAAATG
1 AAAAATG
5154622 GAGAGGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.15
Consensus pattern (23 bp):
AAAAATGATAAAAAAATGAAAAT
Found at i:5156019 original size:50 final size:50
Alignment explanation
Indices: 5155946--5156121 Score: 167
Period size: 50 Copynumber: 3.5 Consensus size: 50
5155936 GCAGTGGAAC
* *
5155946 AGATTAAAGCCACATCGGTGAATCTTGCTTCCTC-GACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCC-CAGACATTGCAGTTAAAA
* * * * * * * ** *
5155996 AGATTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGA-CGCAATGGAAC
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCAGAC-ATTGCAGTTAAAA
* * *
5156046 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCAGACATTGCAGTTAAAA
* *
5156096 AGATTAAAGCTACAATAGTGAATCTT
1 AGATTAAAGCCACAACAGTGAATCTT
5156122 AAATCCCAGA
Statistics
Matches: 94, Mismatches: 29, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
49 2 0.02
50 91 0.97
51 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGTGAATCTTGCTTCCCAGACATTGCAGTTAAAA
Found at i:5156093 original size:100 final size:100
Alignment explanation
Indices: 5155931--5156122 Score: 332
Period size: 100 Copynumber: 1.9 Consensus size: 100
5155921 TACTTCTCAA
* *
5155931 GCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCTCGACATTGCAGTTAAAA
1 GCGACGCAATGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCTCGACATTGCAGTTAAAA
5155996 AGATTAAAGCTACAACAGCGAATCTTACTCCCCAG
66 AGATTAAAGCTACAACAGCGAATCTTACTCCCCAG
5156031 GCGACGCAATGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCC-CTGACATTGCAGTTAAA
1 GCGACGCAATGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCTC-GACATTGCAGTTAAA
* *
5156095 AAGATTAAAGCTACAATAGTGAATCTTA
65 AAGATTAAAGCTACAACAGCGAATCTTA
5156123 AATCCCAGAC
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
99 1 0.01
100 86 0.99
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (100 bp):
GCGACGCAATGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCTCGACATTGCAGTTAAAA
AGATTAAAGCTACAACAGCGAATCTTACTCCCCAG
Found at i:5156169 original size:100 final size:100
Alignment explanation
Indices: 5155940--5156171 Score: 279
Period size: 100 Copynumber: 2.3 Consensus size: 100
5155930 AGCGATGCAG
* * *
5155940 TGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCTCGACATTGCAGTTAAAAAGATTAAAG
1 TGGAACAGATTAAAGCCACAGCAGCGAATCTTGCTTCCTCGACATTGCAGTTAAAAAGATTAAAG
* *
5156005 CTACAACAGCGAATCTTACTCCCCAGGCGACGCAA
66 CTACAACAGCGAATCTTAATCCCCAGACGACGCAA
* * *
5156040 TGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCC-CTGACATTGCAGTTAAAAAGATTAAA
1 TGGAACAGATTAAAGCCACAGCAGCGAATCTTGCTTCCTC-GACATTGCAGTTAAAAAGATTAAA
* * ** * *
5156104 GCTACAATAGTGAATCTTAAAT-CCCAGACGGTGTAC
65 GCTACAACAGCGAATCTT-AATCCCCAGACGACGCAA
* * *
5156140 TGGAACCGATTGAAGCTACAGCAGCGAATCTT
1 TGGAACAGATTAAAGCCACAGCAGCGAATCTT
5156172 ATTTCCCCGA
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
99 1 0.01
100 113 0.97
101 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (100 bp):
TGGAACAGATTAAAGCCACAGCAGCGAATCTTGCTTCCTCGACATTGCAGTTAAAAAGATTAAAG
CTACAACAGCGAATCTTAATCCCCAGACGACGCAA
Found at i:5157685 original size:13 final size:12
Alignment explanation
Indices: 5157650--5157699 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
5157640 ATATTTTTAT
5157650 TATTATTATTAGCC
1 TATTATTATTA--C
*
5157664 TTTTATTATTAC
1 TATTATTATTAC
5157676 TATATATTATTAC
1 TAT-TATTATTAC
*
5157689 TCTTATTATTA
1 TATTATTATTA
5157700 TAGATTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 11 0.34
13 11 0.34
14 10 0.31
ACGTcount: A:0.30, C:0.10, G:0.02, T:0.58
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:5157708 original size:25 final size:27
Alignment explanation
Indices: 5157651--5157710 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
5157641 TATTTTTATT
* *
5157651 ATTATTATTAGCCTTTTATTATTACTAT
1 ATTATTATTA-CCTCTTATTATTACTAG
5157679 A-TATTATTA-CTCTTATTATTA-TAG
1 ATTATTATTACCTCTTATTATTACTAG
5157703 ATTATTAT
1 ATTATTAT
5157711 ATTTATCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 3 0.10
25 17 0.59
27 8 0.28
28 1 0.03
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (27 bp):
ATTATTATTACCTCTTATTATTACTAG
Found at i:5161677 original size:23 final size:23
Alignment explanation
Indices: 5161644--5161688 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5161634 CATATTAAAT
*
5161644 CTACAAATCTTATCTCCCTGAAA
1 CTACAAATCTTATCCCCCTGAAA
*
5161667 CTACAAGTCTTATCCCCCTGAA
1 CTACAAATCTTATCCCCCTGAA
5161689 GTTGCAGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.33, G:0.07, T:0.29
Consensus pattern (23 bp):
CTACAAATCTTATCCCCCTGAAA
Found at i:5161730 original size:44 final size:44
Alignment explanation
Indices: 5161664--5161750 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
5161654 TATCTCCCTG
* * *
5161664 AAACTACAAGTCTTATCCCCCTGAAGTTGCAGTGGAGCTGATTA
1 AAACTACAAGTCTTATCCCCCTGAAGTTACAATGGAGCAGATTA
* *
5161708 AAACTACAAGTTTTATCTCCCTGAAGTTACAATGGAGCAGATT
1 AAACTACAAGTCTTATCCCCCTGAAGTTACAATGGAGCAGATT
5161751 GAAGCGACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (44 bp):
AAACTACAAGTCTTATCCCCCTGAAGTTACAATGGAGCAGATTA
Found at i:5161926 original size:138 final size:138
Alignment explanation
Indices: 5161672--5161926 Score: 294
Period size: 138 Copynumber: 1.8 Consensus size: 138
5161662 TGAAACTACA
* * * **
5161672 AGTCTTATCCCCCTGAAGTTGCAGTGGAGCTGATTAAAACTACAAGTTTTATCTCCCTGAAGTTA
1 AGTCTTATCCCCCTGAAGTAGCAGTGGAGCAGATTAAAACTACAAATCATATCTCCCTGAAGTTA
** * * * * * * *
5161737 CAATGGAGCAGATTGAAGCGACAAATCCTATGCCTCTGAATTTGTAGTGGGTCAGATTAAATCTA
66 CAACAGAGCAGAGTGAAACGACAAATCCTATACCCCTGAAGTTGAAATGGGTCAGATTAAATCTA
5161802 CCATAGCC
131 CCATAGCC
** * *
5161810 AGTCTTATTTCCCTGAAGTAGCAGTGGAGCAGATTAAAGCTACAAATCATATCTCCCTGAAGTTG
1 AGTCTTATCCCCCTGAAGTAGCAGTGGAGCAGATTAAAACTACAAATCATATCTCCCTGAAGTTA
* * * * * *
5161875 CAGCAGAGTAGAGTGAAACTACGATTCTTATACCCCTGAAGTTGAAATGGGT
66 CAACAGAGCAGAGTGAAACGACAAATCCTATACCCCTGAAGTTGAAATGGGT
5161927 TAGAATGAGA
Statistics
Matches: 93, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
138 93 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (138 bp):
AGTCTTATCCCCCTGAAGTAGCAGTGGAGCAGATTAAAACTACAAATCATATCTCCCTGAAGTTA
CAACAGAGCAGAGTGAAACGACAAATCCTATACCCCTGAAGTTGAAATGGGTCAGATTAAATCTA
CCATAGCC
Found at i:5162099 original size:15 final size:14
Alignment explanation
Indices: 5162080--5162125 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
5162070 CGTCCGGCCC
5162080 AAAACCAAAAATAA
1 AAAACCAAAAATAA
5162094 ATAAA-C-AAAATATA
1 A-AAACCAAAAATA-A
5162108 AAAACCAAAAATAA
1 AAAACCAAAAATAA
5162122 AAAA
1 AAAA
5162126 ATTCAAGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.32
14 10 0.36
15 9 0.32
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAACCAAAAATAA
Found at i:5162126 original size:15 final size:15
Alignment explanation
Indices: 5162080--5162126 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
5162070 CGTCCGGCCC
5162080 AAAACCAAAAATAAA
1 AAAACCAAAAATAAA
* *
5162095 TAAA-C-AAAATATA
1 AAAACCAAAAATAAA
5162108 AAAACCAAAAATAAA
1 AAAACCAAAAATAAA
5162123 AAAA
1 AAAA
5162127 TTCAAGTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 10 0.38
14 2 0.08
15 14 0.54
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAACCAAAAATAAA
Found at i:5163604 original size:12 final size:12
Alignment explanation
Indices: 5163587--5163611 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5163577 CCTTTTTTAT
5163587 TTTATTTATTCA
1 TTTATTTATTCA
5163599 TTTATTTATTCA
1 TTTATTTATTCA
5163611 T
1 T
5163612 CTATCATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTATTCA
Found at i:5164375 original size:17 final size:16
Alignment explanation
Indices: 5164332--5164374 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
5164322 GTTTAACTGC
5164332 TTCTATTTTTCTCTAT
1 TTCTATTTTTCTCTAT
* *
5164348 TGTGTATTTTTCTTTAT
1 T-TCTATTTTTCTCTAT
5164365 TTCTATTTTT
1 TTCTATTTTT
5164375 TTTATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.12, C:0.12, G:0.05, T:0.72
Consensus pattern (16 bp):
TTCTATTTTTCTCTAT
Found at i:5165297 original size:3 final size:3
Alignment explanation
Indices: 5165289--5165319 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5165279 TATACATTTC
5165289 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5165320 GTGTTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5167721 original size:19 final size:19
Alignment explanation
Indices: 5167685--5167784 Score: 87
Period size: 19 Copynumber: 5.3 Consensus size: 19
5167675 AGTAGGGGAA
5167685 ACTGGCACACATAA-TGCAT
1 ACTGGCACACA-AAGTGCAT
*
5167704 ACTGGCACACGAAGTGCAT
1 ACTGGCACACAAAGTGCAT
* * *
5167723 CCTGACATACAAAGTGCAT
1 ACTGGCACACAAAGTGCAT
* * * * *
5167742 ATTGACGCACGAAGCGCAT
1 ACTGGCACACAAAGTGCAT
5167761 -CTTGGCACACAAAGTGCAT
1 AC-TGGCACACAAAGTGCAT
5167780 ACTGG
1 ACTGG
5167785 GAAAATTAGT
Statistics
Matches: 62, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
18 2 0.03
19 59 0.95
20 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (19 bp):
ACTGGCACACAAAGTGCAT
Found at i:5167741 original size:38 final size:38
Alignment explanation
Indices: 5167690--5167784 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
5167680 GGGAAACTGG
*
5167690 CACACATAA-TGCATACTGGCACACGAAGTGCATCCTGA
1 CACACA-AAGTGCATACTGGCACACGAAGCGCATCCTGA
* * * * * *
5167728 CATACAAAGTGCATATTGACGCACGAAGCGCATCTTGG
1 CACACAAAGTGCATACTGGCACACGAAGCGCATCCTGA
5167766 CACACAAAGTGCATACTGG
1 CACACAAAGTGCATACTGG
5167785 GAAAATTAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
37 2 0.04
38 44 0.96
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (38 bp):
CACACAAAGTGCATACTGGCACACGAAGCGCATCCTGA
Found at i:5173587 original size:10 final size:10
Alignment explanation
Indices: 5173569--5173602 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5173559 CCTTTTAGAA
* *
5173569 ACATCTATAG
1 ACATATATAT
5173579 ACATATATAT
1 ACATATATAT
5173589 ACATATATAT
1 ACATATATAT
5173599 ACAT
1 ACAT
5173603 GAAGTTGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (10 bp):
ACATATATAT
Found at i:5177958 original size:9 final size:9
Alignment explanation
Indices: 5177880--5177967 Score: 77
Period size: 9 Copynumber: 9.6 Consensus size: 9
5177870 ATTTATAAAA
*
5177880 TTTTATATT
1 TTTTATAAT
*
5177889 TTTTCTATAT
1 TTTTATA-AT
*
5177899 TTCTATAAT
1 TTTTATAAT
*
5177908 TTTTATGAT
1 TTTTATAAT
5177917 TTTTATAAT
1 TTTTATAAT
* *
5177926 TTTTTTAAA
1 TTTTATAAT
* *
5177935 TTTAATTAT
1 TTTTATAAT
*
5177944 TTTTATAAC
1 TTTTATAAT
5177953 TTTTATTAAT
1 TTTTA-TAAT
5177963 TTTTA
1 TTTTA
5177968 CTTTTTATCC
Statistics
Matches: 60, Mismatches: 17, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
9 46 0.77
10 14 0.23
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:5188292 original size:15 final size:14
Alignment explanation
Indices: 5188272--5188355 Score: 71
Period size: 15 Copynumber: 5.8 Consensus size: 14
5188262 AATGCACCAC
5188272 AAACCCTAAAACAT
1 AAACCCTAAAACAT
*
5188286 AAAACCCTAAAACCCT
1 -AAACCCTAAAA-CAT
* *
5188302 AAGCACT-AAACATT
1 AAACCCTAAAACA-T
5188316 AAACCCTAAAACTAT
1 AAACCCTAAAAC-AT
* * *
5188331 AAACCTTAAACCCT
1 AAACCCTAAAACAT
5188345 AAACCCTAAAA
1 AAACCCTAAAA
5188356 TTAATAAATA
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
13 1 0.02
14 19 0.35
15 31 0.57
16 3 0.06
ACGTcount: A:0.52, C:0.30, G:0.01, T:0.17
Consensus pattern (14 bp):
AAACCCTAAAACAT
Found at i:5188325 original size:7 final size:7
Alignment explanation
Indices: 5188272--5188354 Score: 58
Period size: 7 Copynumber: 11.4 Consensus size: 7
5188262 AATGCACCAC
5188272 AAACCCT
1 AAACCCT
* *
5188279 AAAACAT
1 AAACCCT
5188286 AAAACCCT
1 -AAACCCT
5188294 AAAACCCT
1 -AAACCCT
* *
5188302 AAGCACT
1 AAACCCT
**
5188309 AAACATT
1 AAACCCT
5188316 AAACCCT
1 AAACCCT
**
5188323 AAAACTAT
1 -AAACCCT
*
5188331 AAACCTT
1 AAACCCT
5188338 AAACCCT
1 AAACCCT
5188345 AAACCCT
1 AAACCCT
5188352 AAA
1 AAA
5188355 ATTAATAAAT
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
7 41 0.69
8 18 0.31
ACGTcount: A:0.52, C:0.30, G:0.01, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:5188340 original size:29 final size:29
Alignment explanation
Indices: 5188280--5188355 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
5188270 ACAAACCCTA
* * *
5188280 AAACATAAAACCCTAAAACCCTAAGCACT
1 AAACATTAAACCCTAAAACCATAAACACT
*
5188309 AAACATTAAACCCTAAAACTATAAAC-CTT
1 AAACATTAAACCCTAAAACCATAAACAC-T
**
5188338 AAACCCTAAACCCTAAAA
1 AAACATTAAACCCTAAAA
5188356 TTAATAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 1 0.03
29 39 0.98
ACGTcount: A:0.53, C:0.29, G:0.01, T:0.17
Consensus pattern (29 bp):
AAACATTAAACCCTAAAACCATAAACACT
Found at i:5196369 original size:19 final size:20
Alignment explanation
Indices: 5196341--5196387 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5196331 TTGAGAACTT
*
5196341 TTTGAG-AATTGGGAGA-AA
1 TTTGAGAAATTAGGAGAGAA
5196359 TTTGAGAAATTAGGAGAGAA
1 TTTGAGAAATTAGGAGAGAA
*
5196379 TTTGTGAAA
1 TTTGAGAAA
5196388 ATTGTGTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 9 0.36
20 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (20 bp):
TTTGAGAAATTAGGAGAGAA
Found at i:5202152 original size:72 final size:71
Alignment explanation
Indices: 5202004--5202181 Score: 198
Period size: 72 Copynumber: 2.5 Consensus size: 71
5201994 CGTTGGCTAG
* * * *
5202004 TAAAATCGACAAATGAGTGTGCCTAGCACTGGTCAGTATAATTGACAAATAAGTGCGCCTTGAGC
1 TAAAATCGAAAAATGAGTGTGCC-AGCACTGGTCAGTATAAATGAAAAACAAGTGCGCCTTGAGC
* *
5202069 TGGCCGG
65 TAGCCGA
*
5202076 TAAAATCAAAAAATGAGTGTGCTCAGCACTGGTCAGTATAAATGAAAAACAAGTGCGCAC-T-AC
1 TAAAATCGAAAAATGAGTGTGC-CAGCACTGGTCAGTATAAATGAAAAACAAGTGCGC-CTTGA-
*
5202139 GCTAGTCGA
63 GCTAGCCGA
* * *
5202148 TAAAATTGAAAAATGACTGTGCCCAACACTGGTC
1 TAAAATCGAAAAATGAGTGTG-CCAGCACTGGTC
5202182 GATATAACTA
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
71 1 0.01
72 86 0.96
73 3 0.03
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (71 bp):
TAAAATCGAAAAATGAGTGTGCCAGCACTGGTCAGTATAAATGAAAAACAAGTGCGCCTTGAGCT
AGCCGA
Found at i:5215125 original size:45 final size:45
Alignment explanation
Indices: 5215053--5215138 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
5215043 AAGGAGAAGG
*
5215053 GACCAAGGTGAAAACTAGCAAAAGGCACTTTGAGTCCTAAAAAGA
1 GACCAAGGTGAAAACCAGCAAAAGGCACTTTGAGTCCTAAAAAGA
* * *
5215098 GACCAAGGTGAAAACCCGTAAATGGCACTTTGAGTCCTAAA
1 GACCAAGGTGAAAACCAGCAAAAGGCACTTTGAGTCCTAAA
5215139 TAAAAGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (45 bp):
GACCAAGGTGAAAACCAGCAAAAGGCACTTTGAGTCCTAAAAAGA
Found at i:5215832 original size:24 final size:24
Alignment explanation
Indices: 5215800--5215857 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
5215790 ATGTCCCAAA
*
5215800 ATTATAGTGGATTGAACCTTGAAG
1 ATTACAGTGGATTGAACCTTGAAG
5215824 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAGTGGATTGAACCTTGAAG
5215848 ATTACAGTGG
1 ATTACAGTGG
5215858 GGGCAATCCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (24 bp):
ATTACAGTGGATTGAACCTTGAAG
Found at i:5216201 original size:51 final size:51
Alignment explanation
Indices: 5216146--5216313 Score: 220
Period size: 51 Copynumber: 3.4 Consensus size: 51
5216136 CCCTAACATG
* * *
5216146 GCAGTGGAACAGATTAAAGCTGAAGGCAACGAATCTTATCTCCCTAGCGTT
1 GCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTT
* * *
5216197 GCA---G--TAGATTAAAGTTGAAGGCAGCAAATCTTATTTCCTTAGCGTT
1 GCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTT
* * *
5216243 GCACTGGAATAAATTAAAGCTGAAGGCAGCGAATCTTATTTCTCTAGCGTT
1 GCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTT
5216294 GCAGTGGAATAGATTAAAGC
1 GCAGTGGAATAGATTAAAGC
5216314 CACAAATTAT
Statistics
Matches: 99, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
46 39 0.39
48 1 0.01
49 1 0.01
51 58 0.59
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (51 bp):
GCAGTGGAATAGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTT
Found at i:5216227 original size:46 final size:46
Alignment explanation
Indices: 5216156--5216298 Score: 178
Period size: 46 Copynumber: 3.0 Consensus size: 46
5216146 GCAGTGGAAC
* *
5216156 AGATTAAAGCTGAAGGCAACGAATCTTATCTCCCTAGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGCAGT
* * *
5216202 AGATTAAAGTTGAAGGCAGCAAATCTTATTTCCTTAGCGTTGCACTGGAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGCA---G--T
* *
5216253 AAATTAAAGCTGAAGGCAGCGAATCTTATTTCTCTAGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGCAGT
5216299 GGAATAGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
46 40 0.49
48 1 0.01
49 1 0.01
51 40 0.49
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (46 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGCAGT
Found at i:5217102 original size:14 final size:14
Alignment explanation
Indices: 5217083--5217123 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5217073 AGTTGTGTCG
*
5217083 TTTTTATTTTTTTA
1 TTTTTATTTATTTA
5217097 TTTTTATTTATTTA
1 TTTTTATTTATTTA
**
5217111 TTTACATTTATTT
1 TTTTTATTTATTT
5217124 TTAAACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:5217120 original size:18 final size:18
Alignment explanation
Indices: 5217085--5217123 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5217075 TTGTGTCGTT
* **
5217085 TTTATTTTTTTATTTTTA
1 TTTATTTATTTACATTTA
5217103 TTTATTTATTTACATTTA
1 TTTATTTATTTACATTTA
5217121 TTT
1 TTT
5217124 TTAAACAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTTATTTACATTTA
Found at i:5219152 original size:24 final size:23
Alignment explanation
Indices: 5219093--5219157 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
5219083 GAAATGTCTA
*
5219093 GTTTT-GACAACACTTAAAACAT
1 GTTTTGGACAACATTTAAAACAT
* **
5219115 GCTTTGGATGACATTTAAAACAT
1 GTTTTGGACAACATTTAAAACAT
*
5219138 ATTTTTGGACAACATTTAAA
1 -GTTTTGGACAACATTTAAA
5219158 CCTTACTTTG
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
22 4 0.12
23 14 0.42
24 15 0.45
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.35
Consensus pattern (23 bp):
GTTTTGGACAACATTTAAAACAT
Found at i:5219190 original size:23 final size:23
Alignment explanation
Indices: 5219126--5219208 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
5219116 CTTTGGATGA
* * *
5219126 CATTTAAAACATATTTTTGGACAA
1 CATTTAAACCATACTTTT-GACAG
*
5219150 CATTTAAACCTTAC-TTTGACAG
1 CATTTAAACCATACTTTTGACAG
*
5219172 CATTTGAAA-CATACTTTTGCCAG
1 CATTT-AAACCATACTTTTGACAG
*
5219195 CATTTAAAGCATAC
1 CATTTAAACCATAC
5219209 CAAATGTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
22 16 0.32
23 23 0.46
24 11 0.22
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (23 bp):
CATTTAAACCATACTTTTGACAG
Found at i:5222031 original size:12 final size:12
Alignment explanation
Indices: 5222002--5222040 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 12
5221992 AACATTTTCA
5222002 TAAT-AAAATAT
1 TAATAAAAATAT
5222013 TAATAAAAAT-T
1 TAATAAAAATAT
*
5222024 TAATTAAAATAT
1 TAATAAAAATAT
5222036 TAATA
1 TAATA
5222041 TTATAACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAAAAATAT
Found at i:5226423 original size:111 final size:111
Alignment explanation
Indices: 5226228--5226452 Score: 389
Period size: 111 Copynumber: 2.0 Consensus size: 111
5226218 CATATATGAT
*
5226228 CAAAATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATAATTTTTCATTACTGTAGGAGC
1 CAAAATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATAACTTTTCATTACTGTAGGAGC
*
5226293 CATTATTAATATTCAATACAGAACCATCTAATTAAGCAATGAATATC
66 CATTATTAATATTCAATACAGAACCATCT-ATTAAGCAATGAACATC
* * *
5226340 CAAAATATCTTAAAAGCTTGAAGAAG-AAAAAAGAACAATAGTCACTTTTCATTACTGTAGGAGC
1 CAAAATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATAACTTTTCATTACTGTAGGAGC
5226404 CATTATTAATATTCAATACAGAACCATCTATTAAGCAATGAACATC
66 CATTATTAATATTCAATACAGAACCATCTATTAAGCAATGAACATC
5226450 CAA
1 CAA
5226453 TAAACACTAA
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
110 19 0.18
111 63 0.58
112 26 0.24
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (111 bp):
CAAAATATCTTAAAAGCTTGAAGAAGAAAAAAAGAACAACAATAACTTTTCATTACTGTAGGAGC
CATTATTAATATTCAATACAGAACCATCTATTAAGCAATGAACATC
Found at i:5229081 original size:1 final size:1
Alignment explanation
Indices: 5229075--5229120 Score: 65
Period size: 1 Copynumber: 46.0 Consensus size: 1
5229065 TATGGTAGGG
* * *
5229075 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTATTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5229121 ACAGGTTGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.02, C:0.00, G:0.04, T:0.93
Consensus pattern (1 bp):
T
Found at i:5229577 original size:10 final size:9
Alignment explanation
Indices: 5229560--5229613 Score: 58
Period size: 10 Copynumber: 5.9 Consensus size: 9
5229550 AAATTTATAT
5229560 TTTAAAAAA
1 TTTAAAAAA
5229569 -TTATAAAAA
1 TTTA-AAAAA
5229578 TTCTAAAAAA
1 TT-TAAAAAA
5229588 TTTAAAAAAA
1 TTT-AAAAAA
*
5229598 TTT-AAAAT
1 TTTAAAAAA
5229606 TTTAAAAA
1 TTTAAAAA
5229614 TGTTCTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 10 0.26
9 10 0.26
10 17 0.44
11 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:5229596 original size:19 final size:19
Alignment explanation
Indices: 5229562--5229623 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
5229552 ATTTATATTT
5229562 TAAAAAA-TTATAAAAATTC
1 TAAAAAATTTA-AAAAATTC
5229581 TAAAAAATTTAAAAAAATT-
1 TAAAAAATTT-AAAAAATTC
* *
5229600 T-AAAATTTTAAAAATGTTC
1 TAAAAAATTTAAAAA-ATTC
5229619 TAAAA
1 TAAAA
5229624 TAATAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 5 0.14
18 9 0.25
19 9 0.25
20 12 0.33
21 1 0.03
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
TAAAAAATTTAAAAAATTC
Found at i:5229624 original size:19 final size:17
Alignment explanation
Indices: 5229565--5229624 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 17
5229555 TATATTTTAA
*
5229565 AAAATTATAAAAATTCT
1 AAAATTTTAAAAATTCT
*
5229582 AAAAAATTTAAAAAAATT-T
1 --AAAATTT-TAAAAATTCT
5229601 AAAATTTTAAAAATGTTCT
1 AAAATTTTAAAAA--TTCT
5229620 AAAAT
1 AAAAT
5229625 AATAATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 5 0.15
17 7 0.21
18 2 0.06
19 13 0.38
20 7 0.21
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAATTTTAAAAATTCT
Found at i:5230878 original size:10 final size:9
Alignment explanation
Indices: 5230861--5230914 Score: 58
Period size: 10 Copynumber: 5.9 Consensus size: 9
5230851 AAATTTATAT
5230861 TTTAAAAAA
1 TTTAAAAAA
5230870 -TTATAAAAA
1 TTTA-AAAAA
5230879 TTCTAAAAAA
1 TT-TAAAAAA
5230889 TTTAAAAAAA
1 TTT-AAAAAA
*
5230899 TTT-AAAAT
1 TTTAAAAAA
5230907 TTTAAAAA
1 TTTAAAAA
5230915 TGTTCTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
8 10 0.26
9 10 0.26
10 17 0.44
11 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:5230897 original size:19 final size:19
Alignment explanation
Indices: 5230863--5230924 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
5230853 ATTTATATTT
5230863 TAAAAAA-TTATAAAAATTC
1 TAAAAAATTTA-AAAAATTC
5230882 TAAAAAATTTAAAAAAATT-
1 TAAAAAATTT-AAAAAATTC
* *
5230901 T-AAAATTTTAAAAATGTTC
1 TAAAAAATTTAAAAA-ATTC
5230920 TAAAA
1 TAAAA
5230925 TAATAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 5 0.14
18 9 0.25
19 9 0.25
20 12 0.33
21 1 0.03
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
TAAAAAATTTAAAAAATTC
Found at i:5230925 original size:19 final size:17
Alignment explanation
Indices: 5230866--5230925 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 17
5230856 TATATTTTAA
*
5230866 AAAATTATAAAAATTCT
1 AAAATTTTAAAAATTCT
*
5230883 AAAAAATTTAAAAAAATT-T
1 --AAAATTT-TAAAAATTCT
5230902 AAAATTTTAAAAATGTTCT
1 AAAATTTTAAAAA--TTCT
5230921 AAAAT
1 AAAAT
5230926 AATAATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 5 0.15
17 7 0.21
18 2 0.06
19 13 0.38
20 7 0.21
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAATTTTAAAAATTCT
Found at i:5233535 original size:106 final size:106
Alignment explanation
Indices: 5233417--5233628 Score: 361
Period size: 106 Copynumber: 2.0 Consensus size: 106
5233407 CCTAGAAAAT
* * *
5233417 ATTTTGGCTTTGCCCCTCATGATGTCCTAAACTATTTCACAAAGAAAATTGAAATGTAGAAGAGA
1 ATTTTGGCTTTGCCCCTCATAATGTCCAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
* *
5233482 AGGGGAAAAAGAGTTTTTAATTAGTGCAAGTAGAGTGATAA
66 AAGGGAAAAAGAGTTTTTAATTAGTGCAAGCAGAGTGATAA
5233523 ATTTTGGCTTTGCCCCTCATAATGTCCAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
1 ATTTTGGCTTTGCCCCTCATAATGTCCAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
* *
5233588 AAGGGAAAAAGAGTTTTTGATTGGTGCAAGCAGAGTGATAA
66 AAGGGAAAAAGAGTTTTTAATTAGTGCAAGCAGAGTGATAA
5233629 GAGAAAGCCA
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (106 bp):
ATTTTGGCTTTGCCCCTCATAATGTCCAAAACTATTTCACAAAGAAAATTGAAATGTAAAAGAGA
AAGGGAAAAAGAGTTTTTAATTAGTGCAAGCAGAGTGATAA
Found at i:5234571 original size:125 final size:126
Alignment explanation
Indices: 5234326--5234890 Score: 766
Period size: 126 Copynumber: 4.5 Consensus size: 126
5234316 AAAATCAAAG
* * * * * * *
5234326 CAGGATGATTTATTAGAAGGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGTAGG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGG
* * *
5234391 TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGT-TTAAA-AACGCTTCAAC
66 TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAATATAAAACAACGCTGCAAC
* * *
5234450 CAGGATGCTTTATGAGAAGAATTTGTGAAATTGCGCCCTCGTAGACGCGCTTTTGCTACAGTTGG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGG
* * * * * *
5234515 TCTTGGAAGAAATAATTTTGAGTTAACGTTTCTGAGCAAATAGT-TTAAA-AACGCTTCAAC
66 TCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAATATAAAACAACGCTGCAAC
* *
5234575 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTTGACGCGCTTTTGCTACAGTAGG
1 CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGG
* * * *
5234640 TCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAATATAAAACAACTCTGCAAG
66 TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAATATAAAACAACGCTGCAAC
*
5234701 CAGGATGCTATT-TGAGAATAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
1 CAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
* * * *
5234765 GTACTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAATATAAAACAACTCTGCAAG
65 GTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAATATAAAACAACGCTGCAAC
*
5234827 CAGGATGCTATT-TGAGAATAATTTGTGAAATCGCGCCCAT-GTGGACGCGCTTTTGCTACAGTA
1 CAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCC-TCGTGGACGCGCTTTTGCTACAGTA
5234890 G
64 G
5234891 CATGTTTGGG
Statistics
Matches: 404, Mismatches: 32, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
124 95 0.24
125 120 0.30
126 186 0.46
127 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (126 bp):
CAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGG
TCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAATATAAAACAACGCTGCAAC
Found at i:5238179 original size:22 final size:22
Alignment explanation
Indices: 5238148--5238777 Score: 591
Period size: 22 Copynumber: 29.0 Consensus size: 22
5238138 NNNNNNNNNN
*
5238148 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
5238170 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
5238191 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
* * * *
5238212 TTTAGTGTTTTAGGGTTTAAGGTA
1 TTTA-AG-TTAAGGGTTTAGGGTT
* * ***
5238236 TTTAATTTAAAGGTTTACAATT
1 TTTAAGTTAAGGGTTTAGGGTT
5238258 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
5238280 TTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
5238301 TTCAATTTAAGGGTTATA--ATT
1 TTTAAGTTAAGGGTT-TAGGGTT
*
5238322 TTTAAGTTAAGAGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
5238344 TTAAAGTTAA-GGATTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
5238365 TTTAAGTTTAA-GGTTTAGGGTT
1 TTTAAG-TTAAGGGTTTAGGGTT
*
5238387 TTTAAGCTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
* *
5238408 TTTAGGGTTTAA-GGTTTAAGGTT
1 TTTA-AG-TTAAGGGTTTAGGGTT
* * *
5238431 TTTAATTTAAGGGTTTACGATT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
5238453 TTTAAGTTAAGGTTTTAAGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
5238474 TTTAGAGTTAAGGG-TTAGGGTT
1 TTTA-AGTTAAGGGTTTAGGGTT
* *
5238496 TTTAATTTAAGGGTTATA--ATT
1 TTTAAGTTAAGGGTT-TAGGGTT
5238517 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
5238539 TTAAAGGTAAAGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
5238560 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
5238582 TTTAATTTAAGGGTTTATAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
5238604 TTTAGGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
5238626 TTCAAGTTAAGGG-TTAGAG-T
1 TTTAAGTTAAGGGTTTAGGGTT
*
5238646 TTTAATTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
* *
5238667 TTTAGGGTTTTAA-GGTTTAAGGTT
1 TTTA-AG--TTAAGGGTTTAGGGTT
* * *
5238691 TTTAATTTAAGGGGTTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
5238713 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
5238734 TTTAAGTTTAA-GG-TTAGGGTT
1 TTTAAG-TTAAGGGTTTAGGGTT
* *
5238755 TTTAGGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
5238777 T
1 T
5238778 GTCAATTAAA
Statistics
Matches: 495, Mismatches: 83, Indels: 60
0.78 0.13 0.09
Matches are distributed among these distances:
20 20 0.04
21 184 0.37
22 246 0.50
23 32 0.06
24 13 0.03
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.46
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:5238448 original size:195 final size:193
Alignment explanation
Indices: 5238162--5238777 Score: 830
Period size: 195 Copynumber: 3.2 Consensus size: 193
5238152 ATTTAAGGGT
* *
5238162 TTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAGTGTTTTAGG
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAG-GGTTTAAG
* * * *
5238226 GTTTAAGGTATTTAATTTAAAGGTTTACAATTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAG
65 GTTTAAGGTTTTTAATTTAAGGGTTTACGATTTTTAAGTTAAGGGTTTAGGGTTTTAGAGTTAAG
*
5238291 GGTTAGGGTTTTCAATTTAAGGGTTATAATTTTTAAGTTAAGAGTTTAGGGTTTTAAAGTTAAGG
130 GGTTAGGGTTTTTAATTTAAGGGTTATAATTTTTAAGTTAAG-GTTTAGGGTTTTAAAGTTAAGG
* *
5238356 ATTAGTGTTTTTAAGTTTAA-GGTTTAGGGTTTTTAAGCTAAGGGTTTAGGGTTTTAGGGTTTAA
1 -TTAGGGTTTTTAAG-TTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAGGGTTTAA
* *
5238420 GGTTTAAGGTTTTTAATTTAAGGGTTTACGATTTTTAAGTTAAGGTTTTAAGGTTTTAGAGTTAA
64 GGTTTAAGGTTTTTAATTTAAGGGTTTACGATTTTTAAGTTAAGGGTTTAGGGTTTTAGAGTTAA
*
5238485 GGGTTAGGGTTTTTAATTTAAGGGTTATAATTTTTAAGTTAAGGGTTTAGGGTTTTAAAGGTAAA
129 GGGTTAGGGTTTTTAATTTAAGGGTTATAATTTTTAAGTTAA-GGTTTAGGGTTTTAAA-GTTAA
5238550 GG
192 GG
* * *
5238552 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTTAAGGGTTTATAGTTTTTA-GG-TTAAG
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTA-GGGTTTTAGGGTTTAA-
* * * * *
5238615 GGTTTAAGGTTTTCAAGTTAAGGG-TTA-GAGTTTTAATTTAAGGGTTTAGGGTTTTAGGGTTTT
64 GGTTTAAGGTTTTTAATTTAAGGGTTTACGATTTTTAAGTTAAGGGTTTAGGGTTTTAGAG--TT
* * ** * *
5238678 AAGGTTTAAGGTTTTTAATTTAAGGGGTTAGGATTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTT
127 AAGGGTTAGGGTTTTTAATTTAA-GGGTTATAATTTTTAAGTTAAGGTTTAGGGTTTTAAAG-TT
5238743 AAGG
190 AAGG
* *
5238747 TTAGGGTTTTTAGGTTAAGGGTTTAAGGTTT
1 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTT
5238778 GTCAATTAAA
Statistics
Matches: 377, Mismatches: 33, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
193 27 0.07
194 12 0.03
195 269 0.71
196 69 0.18
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.46
Consensus pattern (193 bp):
TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTAGGGTTTAAGG
TTTAAGGTTTTTAATTTAAGGGTTTACGATTTTTAAGTTAAGGGTTTAGGGTTTTAGAGTTAAGG
GTTAGGGTTTTTAATTTAAGGGTTATAATTTTTAAGTTAAGGTTTAGGGTTTTAAAGTTAAGG
Found at i:5238678 original size:16 final size:16
Alignment explanation
Indices: 5238651--5238703 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
5238641 AGAGTTTTAA
*
5238651 TTTAAGGG-TTTAGGG
1 TTTAAGGGTTTTAAGG
*
5238666 TTTTAGGGTTTTAAGG
1 TTTAAGGGTTTTAAGG
*
5238682 TTTAAGGTTTTTAA--
1 TTTAAGGGTTTTAAGG
5238696 TTTAAGGG
1 TTTAAGGG
5238704 GTTAGGATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 7 0.22
15 7 0.22
16 18 0.56
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (16 bp):
TTTAAGGGTTTTAAGG
Found at i:5239305 original size:18 final size:18
Alignment explanation
Indices: 5239279--5239322 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5239269 AAATGGAAAA
* *
5239279 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
5239297 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
5239315 AGGAAACA
1 AGGAAACA
5239323 CAGCTGGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.27, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:5240979 original size:98 final size:98
Alignment explanation
Indices: 5240856--5241050 Score: 327
Period size: 98 Copynumber: 2.0 Consensus size: 98
5240846 AAAAATCATG
* * *
5240856 AAGGAAATATTTCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGCGTGATTTCTT
*
5240921 AAATCTTGGATAAGTGGATGTTCTTTTGAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
* *
5240954 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGCGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGCGTGATTTCTT
*
5241019 AAATCTTGGATGAGTGGATGTTCTTTTAAAGT
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGT
5241051 TTTATTGTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.36
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGCGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:5246173 original size:44 final size:44
Alignment explanation
Indices: 5246125--5246836 Score: 247
Period size: 44 Copynumber: 16.2 Consensus size: 44
5246115 AAGATTTCAG
* *
5246125 ATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
5246169 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * **
5246213 GCCTTATCTCCTTGAGCAGCAGTGGA-AAGGTTGAAGATTG-AA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* *
5246255 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
5246300 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * ***
5246344 GCCTTGTCTCCCTAAGCAGCAGTGGAGAAGGTTGAAGA-TTAAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* *
5246387 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * **
5246432 ATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACGGCAA
** * * * * * ***
5246476 GCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGA-TTAAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* *
5246519 GATCTTATCTCCCTAAACAGTAGTGGAGCAGATTGAAGACGGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * * **
5246564 ATCTTATCTTTCC-AAG--GTAGTGGAAAGTAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGTGG--AGCAGATTGAAGACGGCAA
** * * * * * * * **** *
5246608 GCCTTGTTTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTATAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * *
5246652 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * * **
5246696 ATCTTATCTTTCC-AAG--GTAGTGGAAAGTAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGTGG--AGCAGATTGAAGACGGCAA
** * * * * * * * **** *
5246740 GCCTTGTTTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTATAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
* * * *
5246784 ATATTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
5246828 ATCTTATCT
1 ATCTTATCT
5246837 TTCCAAGATA
Statistics
Matches: 459, Mismatches: 172, Indels: 74
0.65 0.24 0.10
Matches are distributed among these distances:
42 28 0.06
43 55 0.12
44 331 0.72
45 26 0.06
46 19 0.04
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
Found at i:5246438 original size:132 final size:132
Alignment explanation
Indices: 5246123--5246942 Score: 1324
Period size: 132 Copynumber: 6.2 Consensus size: 132
5246113 TAAAGATTTC
* *
5246123 AGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * *
5246188 GTGGGAAGCAGATTTAAGCCACCAAGCCTTATCTCCTTGAGCAGCAGTGGA-AAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATT
*
5246252 GA
131 AA
5246254 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* *
5246319 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGCAGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATT
5246384 AA
131 AA
5246386 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
*
5246451 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATT
5246516 AA
131 AA
* * *
5246518 AGATCTTATCTCCCTAAACAGTAGTGGAGCAGATTGAAGACGGCGAATCTTATCTTTCCAAGGTA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * * *
5246583 GTGGAAAGTAGATTTAAGCCACCAAGCCTTGTTTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATT
*
5246648 AT
131 AA
* *
5246650 AGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTTCCAAGGTA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * * *
5246715 GTGGAAAGTAGATTTAAGCCACCAAGCCTTGTTTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATT
*
5246780 AT
131 AA
* *
5246782 AGATATTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * * *
5246847 GTGGGAAGCAAATTTAAGCTACCAAGCCTTGTTTCCCTGAGCAGCAGCGGAGTA---TGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATT
**
5246909 GT
131 AA
5246911 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
5246943 GTCGTATCCA
Statistics
Matches: 660, Mismatches: 28, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
129 39 0.06
131 111 0.17
132 510 0.77
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
GTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAGATT
AA
Found at i:5249502 original size:7 final size:7
Alignment explanation
Indices: 5249490--5249514 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5249480 TTATATTCAT
5249490 AATACTA
1 AATACTA
5249497 AATACTA
1 AATACTA
5249504 AATACTA
1 AATACTA
5249511 AATA
1 AATA
5249515 ACAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:5252666 original size:22 final size:22
Alignment explanation
Indices: 5252616--5252666 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 22
5252606 CGCACTTGGT
*
5252616 TTACACTTTTGTGTCATGCTTC
1 TTACATTTTTGTGTCATGCTTC
5252638 TTAACATTTTTGTGTCATGCTTC
1 TT-ACATTTTTGTGTCATGCTTC
5252661 TTACAT
1 TTACAT
5252667 GGGGAATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.51
Consensus pattern (22 bp):
TTACATTTTTGTGTCATGCTTC
Found at i:5254538 original size:59 final size:60
Alignment explanation
Indices: 5254474--5254597 Score: 173
Period size: 58 Copynumber: 2.1 Consensus size: 60
5254464 TTATTAATCC
* *
5254474 ATATTTTAAAAATAATTATATTAAGAATGTTATTAAATTATAT-ATTA-TTTTATTAAATT
1 ATATTTTAAAAATAACTATATTAA-AATATTATTAAATTATATCATTACTTTTATTAAATT
* * *
5254533 GTA-TTTAATAATAACTATTTTAAAATATTATTAAATTATATCATTACTTTTATTAAATT
1 ATATTTTAAAAATAACTATATTAAAATATTATTAAATTATATCATTACTTTTATTAAATT
5254592 ATATTT
1 ATATTT
5254598 AGTAATAATC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
57 17 0.30
58 21 0.38
59 16 0.29
60 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (60 bp):
ATATTTTAAAAATAACTATATTAAAATATTATTAAATTATATCATTACTTTTATTAAATT
Found at i:5254615 original size:59 final size:58
Alignment explanation
Indices: 5254478--5254617 Score: 187
Period size: 59 Copynumber: 2.4 Consensus size: 58
5254468 TAATCCATAT
* * *
5254478 TTTAAAAATAAT-TATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTGTA
1 TTTAATAATAATCTATATTAA-AATATTATTAAATTATATATTATTTTATTAAATTATA
*
5254536 TTTAATAATAA-CTATTTTAAAATATTATTAAATTATATCATTACTTTTATTAAATTATA
1 TTTAATAATAATCTATATTAAAATATTATTAAATTATAT-ATTA-TTTTATTAAATTATA
*
5254595 TTTAGTAATAATCT-TATTAAAAT
1 TTTAATAATAATCTATATTAAAAT
5254618 TTAATAACAA
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
57 17 0.24
58 21 0.29
59 32 0.44
60 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (58 bp):
TTTAATAATAATCTATATTAAAATATTATTAAATTATATATTATTTTATTAAATTATA
Found at i:5257557 original size:14 final size:14
Alignment explanation
Indices: 5257540--5257567 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5257530 CTCACATTTC
5257540 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
5257554 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
5257568 GATTTCTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:5257558 original size:19 final size:18
Alignment explanation
Indices: 5257520--5257564 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
5257510 TACGATACGC
5257520 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
5257537 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
5257556 TTCTTTTCT
1 TTCTTTTCT
5257565 CCAGATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:5259274 original size:12 final size:12
Alignment explanation
Indices: 5259257--5259281 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5259247 TTGCAGGCGC
5259257 AGTCTCCTAACT
1 AGTCTCCTAACT
5259269 AGTCTCCTAACT
1 AGTCTCCTAACT
5259281 A
1 A
5259282 CAATGCTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (12 bp):
AGTCTCCTAACT
Found at i:5261686 original size:35 final size:37
Alignment explanation
Indices: 5261647--5261723 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 37
5261637 TTATTAAATT
5261647 ATATTTAATAATA-ATTATGTTAA-AATATGATTAAA
1 ATATTTAATAATATATTATGTTAATAATATGATTAAA
* * * *
5261682 ATATTT-ATATTATATTATTTTAATAATCTTATTAAA
1 ATATTTAATAATATATTATGTTAATAATATGATTAAA
5261718 AT-TTTA
1 ATATTTA
5261724 TAACAAAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 5 0.14
35 18 0.51
36 12 0.34
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (37 bp):
ATATTTAATAATATATTATGTTAATAATATGATTAAA
Found at i:5262654 original size:18 final size:18
Alignment explanation
Indices: 5262594--5262659 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
5262584 TTTTAACTTT
5262594 TTTTAATATATTTTT-TAA
1 TTTTAA-ATATTTTTATAA
**
5262612 TTTTAAA-ATTTTTATTC
1 TTTTAAATATTTTTATAA
* * *
5262629 GTTAAAATATTTTTAGAA
1 TTTTAAATATTTTTATAA
5262647 TTTTAAATTATTT
1 TTTTAAA-TATTT
5262660 GTTAATGTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
16 6 0.17
17 7 0.19
18 18 0.50
19 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTAAATATTTTTATAA
Found at i:5267124 original size:3 final size:3
Alignment explanation
Indices: 5267116--5267142 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5267106 GAATCTGCAA
5267116 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
5267143 TAGCATGTAT
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:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:5269836 original size:18 final size:18
Alignment explanation
Indices: 5269809--5269843 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5269799 TAATCTATTT
*
5269809 AAGTAGTATATATAAAAG
1 AAGTAATATATATAAAAG
5269827 AAGTAATATATATAAAA
1 AAGTAATATATATAAAA
5269844 TGAGGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
AAGTAATATATATAAAAG
Found at i:5270177 original size:15 final size:16
Alignment explanation
Indices: 5270157--5270190 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5270147 AAAGAGGAAT
*
5270157 TTTAAA-ATAAATTAA
1 TTTAAAGATAAATAAA
5270172 TTTAAAGATAAATAAA
1 TTTAAAGATAAATAAA
5270188 TTT
1 TTT
5270191 TGAAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
TTTAAAGATAAATAAA
Found at i:5271066 original size:7 final size:7
Alignment explanation
Indices: 5271042--5271079 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
5271032 AAAAGATGAA
*
5271042 TTTCCTT
1 TTTCTTT
5271049 TTTCTTCT
1 TTTCTT-T
5271057 TTTCTTT
1 TTTCTTT
5271064 TTTC-TT
1 TTTCTTT
5271070 TTTCTTT
1 TTTCTTT
5271077 TTT
1 TTT
5271080 TTGTTGCCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 6 0.21
7 15 0.54
8 7 0.25
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTCTTT
Found at i:5271081 original size:15 final size:15
Alignment explanation
Indices: 5271042--5271079 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
5271032 AAAAGATGAA
*
5271042 TTTCCTTTTTCTTCT
1 TTTCTTTTTTCTTCT
5271057 TTTCTTTTTTC-T-T
1 TTTCTTTTTTCTTCT
5271070 TTTCTTTTTT
1 TTTCTTTTTT
5271080 TTGTTGCCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.50
14 1 0.05
15 10 0.45
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTTTTTTCTTCT
Found at i:5276743 original size:18 final size:19
Alignment explanation
Indices: 5276720--5276755 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5276710 ATATTTTTTA
5276720 TTTTTTA-TTTTAAAATAC
1 TTTTTTATTTTTAAAATAC
5276738 TTTTTTATTTTTAAAATA
1 TTTTTTATTTTTAAAATA
5276756 AATTTTGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTTATTTTTAAAATAC
Found at i:5276761 original size:19 final size:18
Alignment explanation
Indices: 5276721--5276761 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
5276711 TATTTTTTAT
**
5276721 TTTTTATTTTAAAATACT
1 TTTTTATTTTAAAATAAA
5276739 TTTTTATTTTTAAAATAAA
1 TTTTTA-TTTTAAAATAAA
5276758 TTTT
1 TTTT
5276762 GGTGTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTATTTTAAAATAAA
Found at i:5278349 original size:21 final size:21
Alignment explanation
Indices: 5278319--5278369 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
5278309 GGCAGCCTGT
5278319 TGAGTTGGGGTA-CTCTCTTGC
1 TGAGTTGGGGTAGCT-TCTTGC
* *
5278340 TGATTTGGGGTAGCTTGTTGC
1 TGAGTTGGGGTAGCTTCTTGC
5278361 TGAGTTGGG
1 TGAGTTGGG
5278370 ACACCAACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.10, C:0.12, G:0.39, T:0.39
Consensus pattern (21 bp):
TGAGTTGGGGTAGCTTCTTGC
Found at i:5279066 original size:28 final size:28
Alignment explanation
Indices: 5279026--5279079 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
5279016 CACACACCTA
* * *
5279026 AAAAAATAGTCACTATATGCATATTATT
1 AAAAAATACTCACTACAAGCATATTATT
5279054 AAAAAATACTCACTACAAGCATATTA
1 AAAAAATACTCACTACAAGCATATTA
5279080 AAAAATAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.30
Consensus pattern (28 bp):
AAAAAATACTCACTACAAGCATATTATT
Found at i:5281305 original size:6 final size:6
Alignment explanation
Indices: 5281290--5281371 Score: 92
Period size: 6 Copynumber: 13.7 Consensus size: 6
5281280 AACCAAACCG
* * * * * **
5281290 AAATCC AAATCA AAATCT AAATCA AAATCT AAATCG AGATCA AAATTG
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
*
5281338 AAATGA AAATCA AAATCA AAATCA AAATCA AAAT
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
5281372 TGAAATTGAA
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.60, C:0.15, G:0.05, T:0.21
Consensus pattern (6 bp):
AAATCA
Found at i:5281383 original size:18 final size:18
Alignment explanation
Indices: 5281288--5281383 Score: 79
Period size: 18 Copynumber: 5.3 Consensus size: 18
5281278 ATAACCAAAC
* **
5281288 CGAAATCCAAATCAAAAT
1 CGAAATCAAAATTGAAAT
*
5281306 CTAAATCAAAATCT-AAAT
1 CGAAATCAAAAT-TGAAAT
*
5281324 CGAGATCAAAATTGAAAT
1 CGAAATCAAAATTGAAAT
**
5281342 -GAAAATCAAAATCAAAAT
1 CG-AAATCAAAATTGAAAT
*
5281360 CAAAATCAAAATTGAAAT
1 CGAAATCAAAATTGAAAT
*
5281378 TGAAAT
1 CGAAAT
5281384 AACCCTAAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
17 2 0.03
18 59 0.97
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.22
Consensus pattern (18 bp):
CGAAATCAAAATTGAAAT
Found at i:5281868 original size:21 final size:21
Alignment explanation
Indices: 5281844--5281883 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5281834 AATGTGGCAA
5281844 GTTAACTTGCCACATCAGCTG
1 GTTAACTTGCCACATCAGCTG
*
5281865 GTTAACTTGCCACGTCAGC
1 GTTAACTTGCCACATCAGC
5281884 GGTCCCGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (21 bp):
GTTAACTTGCCACATCAGCTG
Found at i:5282438 original size:9 final size:9
Alignment explanation
Indices: 5282424--5282450 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5282414 CTTTAGAGTT
5282424 TTTTTAAAA
1 TTTTTAAAA
5282433 TTTTTAAAA
1 TTTTTAAAA
5282442 TTTTTAAAA
1 TTTTTAAAA
5282451 ATACAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:5283772 original size:5 final size:5
Alignment explanation
Indices: 5283762--5283791 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
5283752 AAAATATGAG
5283762 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
5283792 TTTATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:5284580 original size:19 final size:19
Alignment explanation
Indices: 5284556--5284594 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5284546 AGGAAAAAAT
*
5284556 AAATAAATAAA-TAAATAAG
1 AAATAAA-AAAGTAAACAAG
5284575 AAATAAAAAAGTAAACAAG
1 AAATAAAAAAGTAAACAAG
5284594 A
1 A
5284595 TCTACCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (19 bp):
AAATAAAAAAGTAAACAAG
Found at i:5285059 original size:5 final size:5
Alignment explanation
Indices: 5285049--5285073 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5285039 GTGTAATGAG
5285049 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
5285074 TTTATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:5285862 original size:19 final size:19
Alignment explanation
Indices: 5285838--5285876 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5285828 AGGAAAAAAT
*
5285838 AAATAAATAAA-TAAATAAG
1 AAATAAA-AAAGTAAACAAG
5285857 AAATAAAAAAGTAAACAAG
1 AAATAAAAAAGTAAACAAG
5285876 A
1 A
5285877 TCTACCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (19 bp):
AAATAAAAAAGTAAACAAG
Found at i:5286531 original size:45 final size:44
Alignment explanation
Indices: 5286425--5286536 Score: 111
Period size: 45 Copynumber: 2.5 Consensus size: 44
5286415 TCGTTCTAAC
* * * *
5286425 CCGCTGCTACTTCAGGGAGATGAGACTTGTGGTTTTAGCCTACT
1 CCGCTGCAACTTCAGGGAGATAAGACTCGTGATTTTAGCCTACT
** * *
5286469 CCATTGCAACCTT-AGGGAGATAAGACTCGCT-ATCTTTAGTCTGCT
1 CCGCTGCAA-CTTCAGGGAGATAAGACTCG-TGAT-TTTAGCCTACT
5286514 CCGCTGCAACTTCAGGGAGATAA
1 CCGCTGCAACTTCAGGGAGATAA
5286537 AGTTGGTGGC
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
44 24 0.44
45 30 0.56
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (44 bp):
CCGCTGCAACTTCAGGGAGATAAGACTCGTGATTTTAGCCTACT
Found at i:5286924 original size:143 final size:143
Alignment explanation
Indices: 5286482--5286925 Score: 604
Period size: 143 Copynumber: 3.1 Consensus size: 143
5286472 TTGCAACCTT
* * * * * *
5286482 AGGGAGATAAGACTCGCTATCTTTAGTCTGCTCCGCTGCAACTTCAGGGAGATAAAGTTGGTGGC
1 AGGGAAATAAGATTCTCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGTTGGTGGC
* *
5286547 TTCAATCTGCTCCACTGTAACTTCATGAAGATAAGATCTACCGTAACTTGTAGCTTTAATCTGTT
66 TTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTACCGTAACTTGTAGCTTTAATCTGTT
*
5286612 CCACTACAACGCC
131 CCACTGCAACGCC
* *
5286625 AGGGAAATAAGA-TCTGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAAGGAGATAAGGCTGGTGG
1 AGGGAAATAAGATTCT-CTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGTTGGTGG
* * * * *
5286689 CTTTAATCTACTCCACTGCAACTTCAGGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGT
65 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTACCGTAACTTGTAGCTTTAATCTGT
* * *
5286754 TCTACTGCAACACT
130 TCCACTGCAACGCC
*
5286768 AGGGAAAGAAGATTCAT-TGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGTTGGTGG
1 AGGGAAATAAGATTC-TCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGTTGGTGG
* * * * * * *
5286832 CTTCAATCTGCTTCGCTACAACCTCAGGAAAATAAGATTTACCGTAACTTGTAACTTTAATCTGT
65 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTACCGTAACTTGTAGCTTTAATCTGT
*
5286897 TCCACTGCAATGCC
130 TCCACTGCAACGCC
5286911 AGGGAAATAAGATTC
1 AGGGAAATAAGATTC
5286926 GCCATAATGA
Statistics
Matches: 260, Mismatches: 38, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
142 2 0.01
143 255 0.98
144 2 0.01
145 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (143 bp):
AGGGAAATAAGATTCTCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGTTGGTGGC
TTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTACCGTAACTTGTAGCTTTAATCTGTT
CCACTGCAACGCC
Found at i:5290092 original size:47 final size:47
Alignment explanation
Indices: 5290023--5290255 Score: 349
Period size: 47 Copynumber: 4.8 Consensus size: 47
5290013 NNNNNNNNNN
*
5290023 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTCGAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATCGAGC
* * *
5290070 CGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCAAAACTAATCTCGAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACT-G-ACT-----CTCATATCGAGC
*
5290124 CGATGCCATGTCCCAAACATGGTCTTACACTGACTCTCATATCGAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATCGAGC
*
5290171 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATTGAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATCGAGC
5290218 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTC
5290256 TCACATATCA
Statistics
Matches: 171, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
47 123 0.72
48 1 0.01
49 3 0.02
52 3 0.02
53 1 0.01
54 40 0.23
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATCGAGC
Found at i:5290198 original size:101 final size:94
Alignment explanation
Indices: 5290023--5290255 Score: 358
Period size: 101 Copynumber: 2.4 Consensus size: 94
5290013 NNNNNNNNNN
*
5290023 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTCGAGCCGATGCCATGTCCCAGAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATCGAGCCGATGCCATGTCCCAGAC
*
5290088 ATGGTCTTACACTGGCACTCAAAACTAATCTCGAGT
66 ATGGTCTTACACT-G-ACTC-AAA-T-AT-T-GAGC
*
5290124 CGATGCCATGTCCCAAACATGGTCTTACACTGACTCTCATATCGAGCCGATGCCATGTCCCAGAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATCGAGCCGATGCCATGTCCCAGAC
**
5290189 ATGGTCTTACACTGACTCTCATATTGAGC
66 ATGGTCTTACACTGACTCAAATATTGAGC
5290218 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTC
5290256 TCACATATCA
Statistics
Matches: 126, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
94 40 0.32
95 1 0.01
96 2 0.02
97 1 0.01
98 1 0.01
99 4 0.03
100 1 0.01
101 76 0.60
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (94 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATATCGAGCCGATGCCATGTCCCAGAC
ATGGTCTTACACTGACTCAAATATTGAGC
Found at i:5303183 original size:9 final size:9
Alignment explanation
Indices: 5303169--5303213 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
5303159 ATTTTAGAAT
5303169 TCGAATAAC
1 TCGAATAAC
*
5303178 TCGAATAAT
1 TCGAATAAC
5303187 TCGAATAAC
1 TCGAATAAC
*
5303196 TCGAATAAT
1 TCGAATAAC
5303205 TCGAATAAC
1 TCGAATAAC
5303214 ATATTGGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (9 bp):
TCGAATAAC
Found at i:5303187 original size:18 final size:18
Alignment explanation
Indices: 5303166--5303213 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
5303156 TGAATTTTAG
5303166 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
5303184 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
5303202 AATTCGAATAAC
1 AATTCGAATAAC
5303214 ATATTGGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:5303542 original size:14 final size:14
Alignment explanation
Indices: 5303525--5303563 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5303515 TTAATATTTT
* *
5303525 TAATTTAATTCGAA
1 TAATTTAACTCAAA
5303539 TAATTTAACTCAAA
1 TAATTTAACTCAAA
*
5303553 TAATTTCACTC
1 TAATTTAACTC
5303564 GGTTCAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (14 bp):
TAATTTAACTCAAA
Found at i:5306647 original size:41 final size:41
Alignment explanation
Indices: 5306602--5306682 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
5306592 AAAGAATATC
* **
5306602 TAAAATTAAAATGTGGTATATATAATTGTTTAAAATTAAAG
1 TAAAATTAAAATGTGATATATATAATTGCATAAAATTAAAG
* *
5306643 TAAAATTTAAATGTTATATATATAATTGCATAAAATTAAA
1 TAAAATTAAAATGTGATATATATAATTGCATAAAATTAAA
5306683 ATTTACGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.40
Consensus pattern (41 bp):
TAAAATTAAAATGTGATATATATAATTGCATAAAATTAAAG
Found at i:5308467 original size:23 final size:23
Alignment explanation
Indices: 5308417--5308480 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
5308407 ATTTACACCA
*
5308417 AAGTGCCACTGTCACTTGCACGG
1 AAGTGCCACTATCACTTGCACGG
*
5308440 GAGTGCCACTATCACTTGCATC-G
1 AAGTGCCACTATCACTTGCA-CGG
*
5308463 AAGTGCCACCATCACTTG
1 AAGTGCCACTATCACTTG
5308481 TGCGCGTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.23
Consensus pattern (23 bp):
AAGTGCCACTATCACTTGCACGG
Found at i:5310202 original size:301 final size:300
Alignment explanation
Indices: 5309649--5310221 Score: 753
Period size: 301 Copynumber: 1.9 Consensus size: 300
5309639 TATTTATCTA
* *
5309649 TACTATTATTTAAACTTCTGATTGAGTTGGTGTCACAAGTCAACTGAACACCAACTCAGTTAGGA
1 TACTATTAGTTAAACTTCTGATTGAGTTGGTGTCACAAGTCAACTGAACACCAACTCAGTTAGAA
* * *
5309714 AATTATGAGTATGTCCTTCCGTAATTAAACTAAGTAATATTATTTGAGAGGGTATTTTAGTCTTT
66 AATTATGAGTATGCCCTTCCATAATTAAAATAAGTAATATTATTT-AGAGGGTATTTTAGTCTTT
* * * *
5309779 TCACTTAAAAAATTAATAAAAAATTACATTCAGTGGGATTTGAACTCAAGATAATTACATTAGTA
130 TCACTTAAAAAATCAATAAAAAATTACATTCAGTGAGATTTGAACCCAAGACAATTACATTAGTA
* * * *
5309844 AATCCTTTAATTTACTACTCAACTAAAGCTTTATTTTAATCTTTTAATATATTTTAATTTTATTA
195 AATCCTTTAATTTACTACTCAACCAAAGATTTATTTAAATCTTTTAATATATTTTAATTTTATAA
*
5309909 TGTACACTTTATCACCACTATCAGTAGTATATATCTATACT
260 TGCACACTTTATCACCACTATCAGTAGTATATATCTATACT
* * * ** * *
5309950 TACTATTAGTTGAAC-TCTTGATTGATTTGGTGTCACGAGTCAACTGGGCACTAACTCGGTTAGA
1 TACTATTAGTTAAACTTC-TGATTGAGTTGGTGTCACAAGTCAACTGAACACCAACTCAGTTAGA
* *
5310014 AAATTGT-AGGTATGCCCTTCCATAATTAAAATAAGTAATATTATTT-GAGGGTATTTTCGTCTT
65 AAATTATGA-GTATGCCCTTCCATAATTAAAATAAGTAATATTATTTAGAGGGTATTTTAGTCTT
* * * * *
5310077 TTCACTTAAAAAATCAATTAAAATTTGCATTTAGTGAGATTTGAACCCACA-CCAATTACATTAG
129 TTCACTTAAAAAATCAATAAAAAATTACATTCAGTGAGATTTGAACCCA-AGACAATTACATTAG
* * *
5310141 TAAAAT-CTTTAATTTAGTACTCAACCAAA-ATTCTATATTAAATTTTTTTTATATATTTTAATT
193 T-AAATCCTTTAATTTACTACTCAACCAAAGATT-TAT-TTAAA-TCTTTTAATATATTTTAATT
5310204 TTATAATGCACACTTTAT
254 TTATAATGCACACTTTAT
5310222 TACTTCCATA
Statistics
Matches: 234, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
298 2 0.01
299 94 0.40
300 12 0.05
301 126 0.54
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (300 bp):
TACTATTAGTTAAACTTCTGATTGAGTTGGTGTCACAAGTCAACTGAACACCAACTCAGTTAGAA
AATTATGAGTATGCCCTTCCATAATTAAAATAAGTAATATTATTTAGAGGGTATTTTAGTCTTTT
CACTTAAAAAATCAATAAAAAATTACATTCAGTGAGATTTGAACCCAAGACAATTACATTAGTAA
ATCCTTTAATTTACTACTCAACCAAAGATTTATTTAAATCTTTTAATATATTTTAATTTTATAAT
GCACACTTTATCACCACTATCAGTAGTATATATCTATACT
Found at i:5313616 original size:21 final size:21
Alignment explanation
Indices: 5313575--5313616 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5313565 ATTTTAGAAA
**
5313575 AAAAACAAAAATTAGTTGTCG
1 AAAAACAAAAATTAGGAGTCG
*
5313596 AAAAACAAAAATTGGGAGTCG
1 AAAAACAAAAATTAGGAGTCG
5313617 CAACCAATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (21 bp):
AAAAACAAAAATTAGGAGTCG
Found at i:5315635 original size:21 final size:19
Alignment explanation
Indices: 5315598--5315672 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
5315588 AATCATATCT
5315598 TCCAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
5315617 TCCAAGATTGCATATATCATA
1 TCCAAGATTGC--ATATCATA
*
5315638 TCTAAGATTGCATATCATA
1 TCCAAGATTGCATATCATA
*
5315657 TCTAAGATTGCATATC
1 TCCAAGATTGCATATC
5315673 CTTGAAGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 35 0.66
21 18 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (19 bp):
TCCAAGATTGCATATCATA
Found at i:5316267 original size:89 final size:89
Alignment explanation
Indices: 5316019--5316297 Score: 429
Period size: 89 Copynumber: 3.2 Consensus size: 89
5316009 AAGACTTGTA
* *
5316019 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTACCTTTGATCTATTTCATGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTATTTCACGCC
*
5316084 AATACATGAAGACAAGATCTGCTT
66 AATACATGAAGAAAAGATCTGCTT
*** *
5316108 TCTTCGATCTACTTCGCCA--A-TACATGAAGACAAGATCTGCTATCTTTGATCTATTTCGCGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTATTTCACGCC
*
5316170 AATACATGAAGATAAGATCTGCTT
66 AATACATGAAGAAAAGATCTGCTT
* *
5316194 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTATTTCACGCC
*
5316259 AATACATGAAGAAAAAATCTGCTT
66 AATACATGAAGAAAAGATCTGCTT
*
5316283 TCTTCGATCCACTTC
1 TCTTCGATCTACTTC
5316298 ACGACAACCC
Statistics
Matches: 171, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
86 78 0.46
87 1 0.01
88 1 0.01
89 91 0.53
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (89 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTATTTCACGCC
AATACATGAAGAAAAGATCTGCTT
Found at i:5316298 original size:44 final size:44
Alignment explanation
Indices: 5316019--5316299 Score: 278
Period size: 44 Copynumber: 6.4 Consensus size: 44
5316009 AAGACTTGTA
* * *** *
5316019 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTC-ACACCAATACATGAAGACAAGATCTGCTT
* * * **
5316064 CCTTTGATCTATTTCATGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTT
* *
5316108 TCTTCGATCTACTT--CGCCAATACATGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTT
* * * * *
5316150 TCTTTGATCTATTTCGCGCCAATACATGAAGATAAGATCTGCTT
1 TCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTT
* * *** *
5316194 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTC-ACACCAATACATGAAGACAAGATCTGCTT
* * *
5316239 TCTTTGATCTACTTCACACCAATACATGAAGAAAAAATCTGCTT
1 TCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTT
*
5316283 TCTTCGATCCACTTCAC
1 TCTTCGATCTACTTCAC
5316300 GACAACCCAG
Statistics
Matches: 192, Mismatches: 41, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
42 38 0.20
44 107 0.56
45 47 0.24
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (44 bp):
TCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTT
Found at i:5316361 original size:44 final size:44
Alignment explanation
Indices: 5316307--5316450 Score: 146
Period size: 44 Copynumber: 3.3 Consensus size: 44
5316297 CACGACAACC
* *
5316307 CAGGGAGGCAAGGCTGGTATTTTTGATCTGCTTCACTGTCGGTA
1 CAGGAAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTA
* * ** * * ****
5316351 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTTCACT-ACAACC
1 CAGGAAGGCAAG-GCTGGTATCTTTGATCTGCTTCACTGTCGGTA
* *
5316395 CAGGGAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTG
1 CAGGAAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTA
5316439 CAGGAAGGCAAG
1 CAGGAAGGCAAG
5316451 ATCTGCTATC
Statistics
Matches: 74, Mismatches: 24, Indels: 4
0.73 0.24 0.04
Matches are distributed among these distances:
43 20 0.27
44 35 0.47
45 19 0.26
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTA
Found at i:5316385 original size:45 final size:45
Alignment explanation
Indices: 5316334--5316476 Score: 155
Period size: 45 Copynumber: 3.2 Consensus size: 45
5316324 TATTTTTGAT
5316334 CTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAAC
1 CTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAAC
* **** * * * ** *
5316379 CTGCTTCACT-ACAACCCAGGGAGGCAAG-GCTGGTATCTTTGAT
1 CTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAAC
*
5316422 CTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATCTTCAAC
1 CTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAAC
*
5316467 CTGCTCCACT
1 CTGCTTCACT
5316477 ACAACCCAGG
Statistics
Matches: 73, Mismatches: 23, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
43 20 0.27
44 24 0.33
45 29 0.40
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (45 bp):
CTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAAC
Found at i:5316393 original size:88 final size:88
Alignment explanation
Indices: 5316294--5316493 Score: 364
Period size: 88 Copynumber: 2.3 Consensus size: 88
5316284 CTTCGATCCA
* *
5316294 CTTCACGACAACCCAGGGAGGCAAGGCTGGTATTTTTGATCTGCTTCACTGTCGGTACAGGAAGG
1 CTTCACTACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTACAGGAAGG
5316359 CAAGATCTGCTATCTTCAACCTG
66 CAAGATCTGCTATCTTCAACCTG
*
5316382 CTTCACTACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTGCAGGAAGG
1 CTTCACTACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTACAGGAAGG
5316447 CAAGATCTGCTATCTTCAACCTG
66 CAAGATCTGCTATCTTCAACCTG
*
5316470 CTCCACTACAACCCAGGGAGGCAA
1 CTTCACTACAACCCAGGGAGGCAA
5316494 TCAGTGCAGG
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 108 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (88 bp):
CTTCACTACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTACAGGAAGG
CAAGATCTGCTATCTTCAACCTG
Found at i:5316426 original size:43 final size:43
Alignment explanation
Indices: 5316294--5316431 Score: 141
Period size: 43 Copynumber: 3.2 Consensus size: 43
5316284 CTTCGATCCA
* *
5316294 CTTCACGACAACCCAGGGAGGCAAGGCTGGTATTTTTGATCTG
1 CTTCACTACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTG
* **** * * * ** *
5316337 CTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAACCTG
1 CTTCACT-ACAACCCAGGGAGGCAAG-GCTGGTATCTTTGATCTG
5316382 CTTCACTACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTG
1 CTTCACTACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTG
5316425 CTTCACT
1 CTTCACT
5316432 GTCGGTGCAG
Statistics
Matches: 69, Mismatches: 24, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
43 26 0.38
44 24 0.35
45 19 0.28
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (43 bp):
CTTCACTACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTG
Found at i:5316492 original size:44 final size:44
Alignment explanation
Indices: 5316351--5316493 Score: 153
Period size: 44 Copynumber: 3.2 Consensus size: 44
5316341 ACTGTCGGTA
5316351 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTTCACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTTCACTACAACC
* * * ** * * ****
5316395 CAGGGAGGCAAG-GCTGGTATCTTTGATCTGCTTCACTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTTCACT-ACAACC
*
5316439 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTTCACTACAACC
*
5316483 CAGGGAGGCAA
1 CAGGAAGGCAA
5316494 TCAGTGCAGG
Statistics
Matches: 73, Mismatches: 24, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
43 20 0.27
44 34 0.47
45 19 0.26
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTTCACTACAACC
Found at i:5316531 original size:61 final size:61
Alignment explanation
Indices: 5316436--5316554 Score: 229
Period size: 61 Copynumber: 2.0 Consensus size: 61
5316426 TTCACTGTCG
*
5316436 GTGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAATCA
1 GTGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGGCAATCA
5316497 GTGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGGCAA
1 GTGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGGCAA
5316555 GGTTGGTATC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.29, C:0.30, G:0.23, T:0.18
Consensus pattern (61 bp):
GTGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGGCAATCA
Found at i:5316624 original size:149 final size:149
Alignment explanation
Indices: 5316351--5316638 Score: 486
Period size: 149 Copynumber: 1.9 Consensus size: 149
5316341 ACTGTCGGTA
* *
5316351 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTTCACTACAACCCAGGGAGGCAAGGCTGGTATC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGGCAAGGCTGGTATC
* * *
5316416 TTTGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAA
66 TTCGATCTGCTTCACTGTCGATGCAGGAAGACAAGATCTGCTATCTTCAACCTGCTCCACTACAA
5316481 CCCAGGGAGGCAATCAGTG
131 CCCAGGGAGGCAATCAGTG
*
5316500 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGGCAAGGTTGGTATC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGGCAAGGCTGGTATC
** *
5316565 TTCGATCTGCTTCGTTGTCGATGCAGGAAGACAAGATCTGCTATCTTCAACCTGTTCCACTACAA
66 TTCGATCTGCTTCACTGTCGATGCAGGAAGACAAGATCTGCTATCTTCAACCTGCTCCACTACAA
*
5316630 CCTAGGGAG
131 CCCAGGGAG
5316639 ACAAGGCTGG
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
149 129 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (149 bp):
CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGGCAAGGCTGGTATC
TTCGATCTGCTTCACTGTCGATGCAGGAAGACAAGATCTGCTATCTTCAACCTGCTCCACTACAA
CCCAGGGAGGCAATCAGTG
Found at i:5316680 original size:88 final size:88
Alignment explanation
Indices: 5316494--5316710 Score: 274
Period size: 88 Copynumber: 2.5 Consensus size: 88
5316484 AGGGAGGCAA
* * *
5316494 TCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGGCAAGGTT
1 TCAGTGCAGGAAGACAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGACAAGGCT
* ***
5316559 GGTATCTTCGATCTGCTTCGTTG
66 GGTATCTTCGAGCTGCTTCACCG
* * *
5316582 TC-GATGCAGGAAGACAAGATCTGCTATCTTCAACCTGTTCCACTACAACCTAGGGAGACAAGGC
1 TCAG-TGCAGGAAGACAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGACAAGGC
5316646 TGGTATCTTCGAGCTGCTTCACCG
65 TGGTATCTTCGAGCTGCTTCACCG
* * * * * *
5316670 TCAGTACAGGAAGTCAAGATCTGTTATTTTTAACCTACTCC
1 TCAGTGCAGGAAGACAAGATCTGCTATCTTCAACCTGCTCC
5316711 GCTGCAAACC
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
87 1 0.01
88 108 0.98
89 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (88 bp):
TCAGTGCAGGAAGACAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCACGGAGACAAGGCT
GGTATCTTCGAGCTGCTTCACCG
Found at i:5318924 original size:25 final size:26
Alignment explanation
Indices: 5318873--5318933 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
5318863 AAGAAAGTCC
* **
5318873 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
*
5318899 AAAAGAATGAAAAAAT-ATTGGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
5318924 AAAATGAATG
1 AAAA-GAATG
5318934 CAAAGATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Done.