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 63 of 75
Found at i:20092829 original size:17 final size:17
Alignment explanation
Indices: 20092807--20092840 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20092797 CAATGAGATA
20092807 GACAATACCCAAGAAAG
1 GACAATACCCAAGAAAG
20092824 GACAATACCCAAGAAAG
1 GACAATACCCAAGAAAG
20092841 AATCCACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.24, G:0.18, T:0.06
Consensus pattern (17 bp):
GACAATACCCAAGAAAG
Found at i:20093542 original size:30 final size:30
Alignment explanation
Indices: 20093508--20093565 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
20093498 CATGGGCTGG
20093508 CACATGGGCGTGTGGCCAGCCCGTGTGGCT
1 CACATGGGCGTGTGGCCAGCCCGTGTGGCT
** *
20093538 CACATGGTTGTGTGTCCAGCCCGTGTGG
1 CACATGGGCGTGTGGCCAGCCCGTGTGG
20093566 ATCCTGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.10, C:0.28, G:0.38, T:0.24
Consensus pattern (30 bp):
CACATGGGCGTGTGGCCAGCCCGTGTGGCT
Found at i:20096671 original size:2 final size:2
Alignment explanation
Indices: 20096664--20096698 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
20096654 TTCTAGTTTT
*
20096664 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20096699 TGTTCTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20117256 original size:32 final size:32
Alignment explanation
Indices: 20117220--20117285 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
20117210 TAAAATAGGG
**
20117220 TTTTAGGTTTCTTAAAAGTT-GAAGAAAAAAAT
1 TTTTAGGTCCCTTAAAAGTTGGAA-AAAAAAAT
*
20117252 TTTTAGGTCCCTTAAAAGTTGGTAAAAAAAAT
1 TTTTAGGTCCCTTAAAAGTTGGAAAAAAAAAT
20117284 TT
1 TT
20117286 GGGCCCTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 28 0.93
33 2 0.07
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (32 bp):
TTTTAGGTCCCTTAAAAGTTGGAAAAAAAAAT
Found at i:20119406 original size:29 final size:29
Alignment explanation
Indices: 20119356--20119411 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
20119346 GTTCAACATG
* *
20119356 TAATGTTATATATGAACTTTTATTTTGTA
1 TAATGTTATATATGAACGTTTAATTTGTA
*
20119385 TAATTTTATATATG-ACAGTTTAATTTG
1 TAATGTTATATATGAAC-GTTTAATTTG
20119412 ATTTTCACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54
Consensus pattern (29 bp):
TAATGTTATATATGAACGTTTAATTTGTA
Found at i:20119558 original size:54 final size:54
Alignment explanation
Indices: 20119496--20119612 Score: 211
Period size: 54 Copynumber: 2.2 Consensus size: 54
20119486 TATTATTTAT
20119496 ATAATATAAAATAAATGGTTGTATTCATTTTTTAATGTGTAAAA-TTAATAAAAA
1 ATAATATAAAATAAATGGTTGTATTCATTTTTTAATGTGTAAAATTTAAT-AAAA
20119550 ATAATATAAAATAAATGGTTGTATTCATTTTTTAATGTGTAAAATTTAATAAAA
1 ATAATATAAAATAAATGGTTGTATTCATTTTTTAATGTGTAAAATTTAATAAAA
20119604 AT-ATATAAA
1 ATAATATAAA
20119613 TATATTTAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
53 7 0.11
54 50 0.81
55 5 0.08
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.41
Consensus pattern (54 bp):
ATAATATAAAATAAATGGTTGTATTCATTTTTTAATGTGTAAAATTTAATAAAA
Found at i:20122208 original size:21 final size:23
Alignment explanation
Indices: 20122175--20122221 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
20122165 ATACCTTCTG
*
20122175 AAAAATACATATTTTAA-AAGAA
1 AAAAATACATATTCTAATAAGAA
*
20122197 AAAAATA-TTATTCTAATAAGAA
1 AAAAATACATATTCTAATAAGAA
20122219 AAA
1 AAA
20122222 CTGAAATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAAATACATATTCTAATAAGAA
Found at i:20125026 original size:24 final size:24
Alignment explanation
Indices: 20124973--20125054 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
20124963 GTCTTCATCT
** *
20124973 TCTTCATCTTCCCCTCGACCCCCG
1 TCTTCATCTTCATCTCGACCCTCG
*
20124997 TATTCATCTTCATCTCGACCCTCG
1 TCTTCATCTTCATCTCGACCCTCG
* * *
20125021 CCTTCATTTTCATCTCCA-CCTCCG
1 TCTTCATCTTCATCTCGACCCT-CG
20125045 TCTTCATCTT
1 TCTTCATCTT
20125055 TGTCTACATC
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.12, C:0.44, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTTCATCTTCATCTCGACCCTCG
Found at i:20126015 original size:7 final size:7
Alignment explanation
Indices: 20126003--20126028 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20125993 TGTTAGTTAC
20126003 AAAATTT
1 AAAATTT
20126010 AAAATTT
1 AAAATTT
20126017 AAAATTT
1 AAAATTT
20126024 AAAAT
1 AAAAT
20126029 CATTGCGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAAATTT
Found at i:20127020 original size:16 final size:17
Alignment explanation
Indices: 20126987--20127023 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
20126977 ATAAAATAGT
20126987 TTAAAATATTTTAGAAA
1 TTAAAATATTTTAGAAA
*
20127004 TTAAAATTTTTTA-AAA
1 TTAAAATATTTTAGAAA
20127020 TTAA
1 TTAA
20127024 CTTAATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAAATATTTTAGAAA
Found at i:20128769 original size:18 final size:16
Alignment explanation
Indices: 20128737--20128770 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
20128727 CAAAATATCT
20128737 AAAAATTTTAAATTTA
1 AAAAATTTTAAATTTA
20128753 AAAAATTATTAAAATTTA
1 AAAAATT-TT-AAATTTA
20128771 CTTTAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAATTTTAAATTTA
Found at i:20128977 original size:5 final size:5
Alignment explanation
Indices: 20128967--20128997 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
20128957 TTAATTTAGA
20128967 TATAT TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT T
20128998 TTTTTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:20129502 original size:17 final size:17
Alignment explanation
Indices: 20129480--20129513 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20129470 TTAGATCTAT
20129480 TCTATCGAGTTATTTGA
1 TCTATCGAGTTATTTGA
20129497 TCTATCGAGTTATTTGA
1 TCTATCGAGTTATTTGA
20129514 AGATGCACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (17 bp):
TCTATCGAGTTATTTGA
Found at i:20129646 original size:19 final size:19
Alignment explanation
Indices: 20129622--20129661 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
20129612 TTTATTTTTT
*
20129622 ATTAGAACT-GAAAAGTTTA
1 ATTAGAA-TGGAAAAGTATA
20129641 ATTAGAATGGAAAAGTATA
1 ATTAGAATGGAAAAGTATA
20129660 AT
1 AT
20129662 AAAAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (19 bp):
ATTAGAATGGAAAAGTATA
Found at i:20130679 original size:15 final size:15
Alignment explanation
Indices: 20130655--20130688 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
20130645 GATCTTTTTG
*
20130655 ACATTTTAATTCCAT
1 ACATTATAATTCCAT
20130670 ACATTATAATTCCAT
1 ACATTATAATTCCAT
20130685 ACAT
1 ACAT
20130689 AGACATAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (15 bp):
ACATTATAATTCCAT
Found at i:20134505 original size:16 final size:16
Alignment explanation
Indices: 20134480--20134513 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20134470 TGGCATAATG
20134480 ATTACCCATAATGCGC
1 ATTACCCATAATGCGC
* *
20134496 ATTACTCATAATGTGC
1 ATTACCCATAATGCGC
20134512 AT
1 AT
20134514 CCAAATATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (16 bp):
ATTACCCATAATGCGC
Found at i:20134646 original size:188 final size:188
Alignment explanation
Indices: 20134323--20134681 Score: 693
Period size: 188 Copynumber: 1.9 Consensus size: 188
20134313 AAATTTTAAT
20134323 CATCCAAATATCATACATATTATAATTTAATAAAAGAATCTTAGTTTAAAAGAAACCTTAAAGTA
1 CATCCAAATATCATACATATTATAATTTAATAAAAGAATCTTAGTTTAAAAGAAACCTTAAAGTA
20134388 ATAATATTTTGCATAAAATAATTTTACCAAAAATCAATCAACAAAGGAGAAAAACATGTCACGCA
66 ATAATATTTTGCATAAAATAATTTTACCAAAAATCAATCAACAAAGGAGAAAAACATGTCACGCA
20134453 AGGATTATAT-ATTTTTTTGGCATAATGATTACCCATAATGCGCATTACTCATAATGTG
131 AGGATTATATAATTTTTTT-GCATAATGATTACCCATAATGCGCATTACTCATAATGTG
20134511 CATCCAAATATCATACATATTATAATTTAATAAAAGAATCTTAGTTTAAAAGAAACCTTAAAGTA
1 CATCCAAATATCATACATATTATAATTTAATAAAAGAATCTTAGTTTAAAAGAAACCTTAAAGTA
*
20134576 ATAATATTTTGCATAAAATAATTTTACCAAAAATCAATCAACAAAGGAGAAAAACATGTCACGTA
66 ATAATATTTTGCATAAAATAATTTTACCAAAAATCAATCAACAAAGGAGAAAAACATGTCACGCA
20134641 AGGATTATATAATTTTTTTGCATAATGATTACCCATAATGC
131 AGGATTATATAATTTTTTTGCATAATGATTACCCATAATGC
20134682 ACGTGTCTCA
Statistics
Matches: 169, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
188 161 0.95
189 8 0.05
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (188 bp):
CATCCAAATATCATACATATTATAATTTAATAAAAGAATCTTAGTTTAAAAGAAACCTTAAAGTA
ATAATATTTTGCATAAAATAATTTTACCAAAAATCAATCAACAAAGGAGAAAAACATGTCACGCA
AGGATTATATAATTTTTTTGCATAATGATTACCCATAATGCGCATTACTCATAATGTG
Found at i:20136204 original size:61 final size:61
Alignment explanation
Indices: 20136139--20136266 Score: 134
Period size: 61 Copynumber: 2.1 Consensus size: 61
20136129 TGGTGGTTTT
*
20136139 TTTTTAATTTAAAAATTGAA-AAAAAAATCATTTTGTAAAGATTGAGTACTAAATTTATTG-A
1 TTTTT-ATTTAAAAATTGAACAAAAAAAT-ATTTTGTAAACATTGAGTACTAAATTTATTGAA
* * * ** ** *
20136200 TTTTTTTTTAGAATTTGAACTAAAATGATATTTTGTAAACATTGAGTGTTAAATTTGTTGAA
1 TTTTTATTTAAAAATTGAAC-AAAAAAATATTTTGTAAACATTGAGTACTAAATTTATTGAA
20136262 TTTTT
1 TTTTT
20136267 TATATTTAGG
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
60 11 0.20
61 32 0.58
62 12 0.22
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (61 bp):
TTTTTATTTAAAAATTGAACAAAAAAATATTTTGTAAACATTGAGTACTAAATTTATTGAA
Found at i:20144955 original size:12 final size:11
Alignment explanation
Indices: 20144938--20144979 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
20144928 AGTATTAAAT
20144938 TTATAAAATGTA
1 TTATAAAAT-TA
*
20144950 TTATAAAAATA
1 TTATAAAATTA
*
20144961 -TATATAATTA
1 TTATAAAATTA
20144971 TTATAAAAT
1 TTATAAAAT
20144980 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 9 0.36
12 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
TTATAAAATTA
Found at i:20144974 original size:21 final size:22
Alignment explanation
Indices: 20144934--20144978 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
20144924 TAAAAGTATT
*
20144934 AAATTTATAAAATGTATTATAA
1 AAATATATAAAATGTATTATAA
*
20144956 AAATATATATAAT-TATTATAA
1 AAATATATAAAATGTATTATAA
20144977 AA
1 AA
20144979 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATATAAAATGTATTATAA
Found at i:20157861 original size:21 final size:21
Alignment explanation
Indices: 20157814--20157867 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
20157804 ACCATTGTTT
** *
20157814 CTAATCTCATTGCTACAGTAT
1 CTAATCTCACCGCTACAGTAA
*
20157835 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAGTAA
*
20157856 CTAATCTTACCG
1 CTAATCTCACCG
20157868 TCACCGTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:20166156 original size:16 final size:16
Alignment explanation
Indices: 20166135--20166166 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20166125 ATAGGACTTA
20166135 AATCATTTGTCGTATT
1 AATCATTTGTCGTATT
*
20166151 AATCATTTGTTGTATT
1 AATCATTTGTCGTATT
20166167 GAAATTAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.53
Consensus pattern (16 bp):
AATCATTTGTCGTATT
Found at i:20185364 original size:15 final size:15
Alignment explanation
Indices: 20185346--20185391 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
20185336 GTAGGAGGCT
20185346 GAGCAATTGGTGGAG
1 GAGCAATTGGTGGAG
* * *
20185361 GAGCCATAGGTGGCG
1 GAGCAATTGGTGGAG
*
20185376 GAGCAAGTGGTGGAG
1 GAGCAATTGGTGGAG
20185391 G
1 G
20185392 GGGTGAGGGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.24, C:0.11, G:0.50, T:0.15
Consensus pattern (15 bp):
GAGCAATTGGTGGAG
Found at i:20189046 original size:10 final size:10
Alignment explanation
Indices: 20189027--20189055 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
20189017 TGCCAAAATC
20189027 TAAA-TAAAA
1 TAAATTAAAA
20189036 TAAATTAAAA
1 TAAATTAAAA
20189046 TAAATTAAAA
1 TAAATTAAAA
20189056 ACATAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAATTAAAA
Found at i:20193625 original size:24 final size:24
Alignment explanation
Indices: 20193598--20193649 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
20193588 AATCAAAGTC
* *
20193598 AAATATATTAT-GTTAATAAATGCT
1 AAATATATTATACTT-ATAAATACT
20193622 AAATATATTATACTTATAAATACT
1 AAATATATTATACTTATAAATACT
20193646 AAAT
1 AAAT
20193650 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTTATAAATACT
Found at i:20200768 original size:7 final size:7
Alignment explanation
Indices: 20200756--20200803 Score: 51
Period size: 7 Copynumber: 6.3 Consensus size: 7
20200746 ATAGAAATTT
20200756 TAAAATA
1 TAAAATA
20200763 TAAAATA
1 TAAAATA
20200770 TAAAATAA
1 TAAAAT-A
20200778 TTAAAACTGA
1 -TAAAA-T-A
20200788 TAAAATA
1 TAAAATA
*
20200795 TAGAATA
1 TAAAATA
20200802 TA
1 TA
20200804 TAGACTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
7 22 0.61
8 2 0.06
9 10 0.28
10 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (7 bp):
TAAAATA
Found at i:20200790 original size:25 final size:23
Alignment explanation
Indices: 20200755--20200801 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
20200745 GATAGAAATT
20200755 TTAAAATATAAAATATAAAATAA
1 TTAAAATATAAAATATAAAATAA
*
20200778 TTAAAACTGATAAAATATAGAATA
1 TTAAAA-T-ATAAAATATAAAATA
20200802 TATAGACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 1 0.05
25 14 0.67
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
TTAAAATATAAAATATAAAATAA
Found at i:20203637 original size:15 final size:16
Alignment explanation
Indices: 20203614--20203655 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
20203604 ATTTTAATTC
20203614 TTTTT-AAATT-TATT
1 TTTTTAAAATTATATT
20203628 TTTTTAAAATTCATATT
1 TTTTTAAAATT-ATATT
20203645 TTTTTATAAAT
1 TTTTTA-AAAT
20203656 ACTTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.21
15 5 0.21
17 10 0.42
18 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTAAAATTATATT
Found at i:20207664 original size:22 final size:21
Alignment explanation
Indices: 20207622--20207671 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
20207612 TTTTTATTAA
* *
20207622 ATATATATGAAAATTAAAAAT
1 ATATATATAAAAATCAAAAAT
*
20207643 ATATATATAAAAAATCAGAAAT
1 ATATATAT-AAAAATCAAAAAT
20207665 ATATATA
1 ATATATA
20207672 AATTAAGANN
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (21 bp):
ATATATATAAAAATCAAAAAT
Found at i:20209269 original size:18 final size:17
Alignment explanation
Indices: 20209242--20209284 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
20209232 ACTTACCAAT
20209242 AATATATAAAAATTAAA
1 AATATATAAAAATTAAA
20209259 AATATTATAAAAATTAAA
1 AATA-TATAAAAATTAAA
*
20209277 AAAATATA
1 AATATATA
20209285 TTTAAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATATAAAAATTAAA
Found at i:20214997 original size:24 final size:24
Alignment explanation
Indices: 20214969--20215020 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
20214959 TTCGTAGATA
* *
20214969 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
20214993 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
20215017 AAAT
1 AAAT
20215021 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:20216811 original size:13 final size:13
Alignment explanation
Indices: 20216786--20216819 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
20216776 AGTGAAGAGT
20216786 ACAAAAGTGTAAAC
1 ACAAAA-TGTAAAC
20216800 ACAAAATGTAAAC
1 ACAAAATGTAAAC
*
20216813 ATAAAAT
1 ACAAAAT
20216820 TCTCTAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.18
Consensus pattern (13 bp):
ACAAAATGTAAAC
Found at i:20218468 original size:275 final size:275
Alignment explanation
Indices: 20217977--20218515 Score: 997
Period size: 275 Copynumber: 2.0 Consensus size: 275
20217967 ATACACTTTT
*
20217977 AAAATACCATTTCACCACTGGTGTGATTAAATATAAAGGAGACCCAAGGCTTCCTTTGGATACCA
1 AAAATACCATTTCACCACTGGTGTGATTAAATATAAAGGAGACCCAAGGCTTCCTTTAGATACCA
* *
20218042 CTAAATCTGTGCATCACAACTTTCAAGATAGGAATAATTACACCCGAACCATTGTATGGTGTTGG
66 CTAAATATGTGCATCACAACTTTCAAGATAGGAATAATTACACCCGAACCATTGTATGGTGTTGA
*
20218107 ATAACATCCGTGAGATGAGATTTAAATAAATTGTCATGAGTCTAAATGAAATTAGGGATTTTGAG
131 ATAACATCCGTGAGATGAGATTTAAACAAATTGTCATGAGTCTAAATGAAATTAGGGATTTTGAG
*
20218172 AAAAAAGAACCCTAATTTTGGAAATTAAGGAAATGATGAGGAATAGATTGAGGGAAGGAAAGGTC
196 AAAAAAGAACCCTAATTTTGGAAATTAAGGAAATGATGAGGAATAGATTAAGGGAAGGAAAGGTC
20218237 GAGAGTTAATGGGAC
261 GAGAGTTAATGGGAC
*
20218252 AAAATACCATTTCACCACTGGTGTGATTGAATATAAAGGAGACCCAAGGCTTCCTTTAGATACCA
1 AAAATACCATTTCACCACTGGTGTGATTAAATATAAAGGAGACCCAAGGCTTCCTTTAGATACCA
*
20218317 TTAAATATGTGCATCACAACTTTCAAGATAGGAATAATTACACCCGAACCATTGTATGGTGTTGA
66 CTAAATATGTGCATCACAACTTTCAAGATAGGAATAATTACACCCGAACCATTGTATGGTGTTGA
*
20218382 ATAACATCCGTGAGATGAGATTTAAACAAATTGTCATGAGTCTGAATGAAATTAGGGATTTTGAG
131 ATAACATCCGTGAGATGAGATTTAAACAAATTGTCATGAGTCTAAATGAAATTAGGGATTTTGAG
*
20218447 AAAAAAGAACCCTAATTTTGGAAATTAAGGAAATGATGAGGAATAGATTAAGGTAAGGAAAGGTC
196 AAAAAAGAACCCTAATTTTGGAAATTAAGGAAATGATGAGGAATAGATTAAGGGAAGGAAAGGTC
20218512 GAGA
261 GAGA
20218516 ATGGGCCAAG
Statistics
Matches: 255, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
275 255 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (275 bp):
AAAATACCATTTCACCACTGGTGTGATTAAATATAAAGGAGACCCAAGGCTTCCTTTAGATACCA
CTAAATATGTGCATCACAACTTTCAAGATAGGAATAATTACACCCGAACCATTGTATGGTGTTGA
ATAACATCCGTGAGATGAGATTTAAACAAATTGTCATGAGTCTAAATGAAATTAGGGATTTTGAG
AAAAAAGAACCCTAATTTTGGAAATTAAGGAAATGATGAGGAATAGATTAAGGGAAGGAAAGGTC
GAGAGTTAATGGGAC
Found at i:20221978 original size:34 final size:35
Alignment explanation
Indices: 20221934--20222000 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
20221924 CAGTAAAATA
* *
20221934 TTTTCCGTAAAATGGTTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
20221968 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
20222001 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:20223109 original size:27 final size:27
Alignment explanation
Indices: 20223078--20223130 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
20223068 TTGATCCTTG
20223078 GGGACAAGGATTGAATCAAGAAGGGGT
1 GGGACAAGGATTGAATCAAGAAGGGGT
20223105 GGGACAAGGATTGAATCAAGAAGGGG
1 GGGACAAGGATTGAATCAAGAAGGGG
20223131 GTATTGTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.42, T:0.13
Consensus pattern (27 bp):
GGGACAAGGATTGAATCAAGAAGGGGT
Found at i:20226407 original size:16 final size:16
Alignment explanation
Indices: 20226387--20226439 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
20226377 AAAAATTATG
*
20226387 TTTTCCATCCTTCTAG
1 TTTTCCATCCTTCTAA
* *
20226403 TTTTCTACCCCTTC-AA
1 TTTTCCA-TCCTTCTAA
*
20226419 TTTTCCATCCTCCTAA
1 TTTTCCATCCTTCTAA
20226435 TTTTC
1 TTTTC
20226440 TTTCCACTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 4 0.14
16 20 0.69
17 5 0.17
ACGTcount: A:0.15, C:0.34, G:0.02, T:0.49
Consensus pattern (16 bp):
TTTTCCATCCTTCTAA
Found at i:20232168 original size:64 final size:64
Alignment explanation
Indices: 20232099--20232228 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
20232089 GATTAGTAGC
20232099 AATACTTCATCTCTCCAGAAGTCAAATAAACAGTAAAGATTCATCAAAGAATTGTTTGAAAACT
1 AATACTTCATCTCTCCAGAAGTCAAATAAACAGTAAAGATTCATCAAAGAATTGTTTGAAAACT
20232163 AATACTTCATCTCTCCAGAAGTCAAATAAACAGTAAAGATTCATCAAAGAATTGTTTGAAAACT
1 AATACTTCATCTCTCCAGAAGTCAAATAAACAGTAAAGATTCATCAAAGAATTGTTTGAAAACT
20232227 AA
1 AA
20232229 AAAAACCCTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.28
Consensus pattern (64 bp):
AATACTTCATCTCTCCAGAAGTCAAATAAACAGTAAAGATTCATCAAAGAATTGTTTGAAAACT
Found at i:20248008 original size:34 final size:35
Alignment explanation
Indices: 20247964--20248030 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
20247954 CAGTAAAATA
* *
20247964 TTTTCCGTAAAATGGTTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
20247998 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
20248031 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:20248649 original size:8 final size:8
Alignment explanation
Indices: 20248636--20248679 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
20248626 AATTGAGAGA
20248636 AGAGAGGG
1 AGAGAGGG
20248644 AGAGA-GG
1 AGAGAGGG
20248651 -GAGAGGG
1 AGAGAGGG
*
20248658 AGGGAGGG
1 AGAGAGGG
*
20248666 AGGGAGGG
1 AGAGAGGG
20248674 AGAGAG
1 AGAGAG
20248680 AGGGAATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 4 0.12
7 4 0.12
8 24 0.75
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Found at i:20248662 original size:4 final size:4
Alignment explanation
Indices: 20248639--20248675 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
20248629 TGAGAGAAGA
*
20248639 GAGG GAGA GAGG GA-- GAGG GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG
20248676 AGAGAGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:20248665 original size:22 final size:22
Alignment explanation
Indices: 20248630--20248684 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
20248620 GTGTTAAATT
*
20248630 GAGAGA-AGAGAGGGAGAGAGG
1 GAGAGAGAGGGAGGGAGAGAGG
* *
20248651 GAGAGGGAGGGAGGGAGGGAGG
1 GAGAGAGAGGGAGGGAGAGAGG
20248673 GAGAGAGAGGGA
1 GAGAGAGAGGGA
20248685 ATGCAAGCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (22 bp):
GAGAGAGAGGGAGGGAGAGAGG
Found at i:20258116 original size:20 final size:20
Alignment explanation
Indices: 20258072--20258121 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
20258062 AGAGCCATTA
20258072 ATATCGATACCAAGAGAAAT
1 ATATCGATACCAAGAGAAAT
* *
20258092 TTATCGATACCAA-ATAGAAT
1 ATATCGATACCAAGAGA-AAT
20258112 ATATCGATAC
1 ATATCGATAC
20258122 TTGATAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (20 bp):
ATATCGATACCAAGAGAAAT
Found at i:20268412 original size:18 final size:18
Alignment explanation
Indices: 20268389--20268424 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20268379 CAACACCTCT
20268389 ACCTCTGCCACGATAACC
1 ACCTCTGCCACGATAACC
*
20268407 ACCTCTGCCATGATAACC
1 ACCTCTGCCACGATAACC
20268425 TCTTCTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.42, G:0.11, T:0.19
Consensus pattern (18 bp):
ACCTCTGCCACGATAACC
Found at i:20270016 original size:15 final size:15
Alignment explanation
Indices: 20269971--20270017 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
20269961 TCCTAAAATG
20269971 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
**
20269986 A-AGTCATTTATAATTT
1 ATA-AAATTT-TAATTT
20270002 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
20270017 A
1 A
20270018 GAAATAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 1 0.04
15 12 0.48
16 11 0.44
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
ATAAAATTTTAATTT
Found at i:20271039 original size:14 final size:13
Alignment explanation
Indices: 20270998--20271053 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
20270988 AGTAATTTAA
*
20270998 ATTTTTTTCTTTT
1 ATTTTTTTCCTTT
*
20271011 ATGTTTTTTAACTTT
1 AT-TTTTTT-CCTTT
20271026 ACTTTTTTTCCTTT
1 A-TTTTTTTCCTTT
*
20271040 -TTTTTTTCCATT
1 ATTTTTTTCCTTT
20271052 AT
1 AT
20271054 CTTCTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 11 0.31
13 3 0.09
14 10 0.29
15 10 0.29
16 1 0.03
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.73
Consensus pattern (13 bp):
ATTTTTTTCCTTT
Found at i:20272411 original size:17 final size:18
Alignment explanation
Indices: 20272380--20272415 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
20272370 AATTTAACTT
20272380 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
20272398 TAATT-AATTTTTTAAAA
1 TAATTAAATTATTTAAAA
20272415 T
1 T
20272416 TATAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:20272611 original size:14 final size:13
Alignment explanation
Indices: 20272598--20272640 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
20272588 AACATAGAAC
20272598 CCTGAATCTTGAA
1 CCTGAATCTTGAA
* *
20272611 CTTGAACCTTGAA
1 CCTGAATCTTGAA
*
20272624 CCTTAATTCTTGAA
1 CCTGAA-TCTTGAA
20272638 CCT
1 CCT
20272641 TGAGGTTTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (13 bp):
CCTGAATCTTGAA
Found at i:20272621 original size:7 final size:7
Alignment explanation
Indices: 20272594--20272643 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
20272584 CTCAAACATA
*
20272594 GAACCCT
1 GAACCTT
*
20272601 GAATCTT
1 GAACCTT
20272608 GAA-CTT
1 GAACCTT
20272614 GAACCTT
1 GAACCTT
20272621 GAACCTT
1 GAACCTT
*
20272628 -AATTCTT
1 GAA-CCTT
20272635 GAACCTT
1 GAACCTT
20272642 GA
1 GA
20272644 GGTTTAGGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 8 0.22
7 26 0.72
8 2 0.06
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (7 bp):
GAACCTT
Found at i:20273153 original size:21 final size:21
Alignment explanation
Indices: 20273095--20273187 Score: 57
Period size: 21 Copynumber: 4.4 Consensus size: 21
20273085 CTATTATGAT
* *
20273095 ATAAATATTAAAATAATATTA
1 ATAAATATAAAAATAAAATTA
* * *
20273116 AGATGAT-TATAAAA-AAATTTA
1 ATA-AATATA-AAAATAAAATTA
20273137 ATAAATA-AAAAATAAAATTA
1 ATAAATATAAAAATAAAATTA
* * * *
20273157 CTAAATATTAAAATAATATAA
1 ATAAATATAAAAATAAAATTA
20273178 TATAAATATA
1 -ATAAATATA
20273188 TTTTTAAAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
19 4 0.08
20 15 0.29
21 20 0.38
22 13 0.25
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAATATAAAAATAAAATTA
Found at i:20273211 original size:32 final size:32
Alignment explanation
Indices: 20273175--20273238 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
20273165 TAAAATAATA
* *
20273175 TAATATAAATATATTTTTAAA-AAATTTAAATT
1 TAATATAAATAGA-TTTAAAATAAATTTAAATT
*
20273207 TAATATAGATAGATTTAAAATAAATTTAAATT
1 TAATATAAATAGATTTAAAATAAATTTAAATT
20273239 CAAACCTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (32 bp):
TAATATAAATAGATTTAAAATAAATTTAAATT
Found at i:20277940 original size:10 final size:10
Alignment explanation
Indices: 20277910--20277950 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
20277900 ATCACAAGTC
20277910 TTGTGATATA
1 TTGTGATATA
*
20277920 GTGTGATATA
1 TTGTGATATA
20277930 TTGTGATATA
1 TTGTGATATA
*
20277940 TATATGATATA
1 T-TGTGATATA
20277951 AGTAGAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (10 bp):
TTGTGATATA
Found at i:20282572 original size:51 final size:51
Alignment explanation
Indices: 20282496--20282599 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
20282486 TTTTTGGGAC
20282496 TTAACAATTGAAATTGAGTCTTATTTGGGAAAGGAAGAAAGAATTCTACTA
1 TTAACAATTGAAATTGAGTCTTATTTGGGAAAGGAAGAAAGAATTCTACTA
20282547 TTAACAATTGAAATTGAGTCTTATTTGGGAAAGGAAGAAAGAATTCTACTA
1 TTAACAATTGAAATTGAGTCTTATTTGGGAAAGGAAGAAAGAATTCTACTA
20282598 TT
1 TT
20282600 CTTTTGGAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (51 bp):
TTAACAATTGAAATTGAGTCTTATTTGGGAAAGGAAGAAAGAATTCTACTA
Found at i:20285734 original size:17 final size:17
Alignment explanation
Indices: 20285694--20285742 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
20285684 TTTAGATAGT
*
20285694 AAAAGAAAAAGAAGAGG
1 AAAAGAAAAAGAAGAAG
** *
20285711 AGGAGAAGAAGAAGAAG
1 AAAAGAAAAAGAAGAAG
*
20285728 AAAAGAAAAATAAGA
1 AAAAGAAAAAGAAGA
20285743 GAAGAAATAG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAGAAGAAG
Found at i:20286829 original size:21 final size:21
Alignment explanation
Indices: 20286805--20286875 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
20286795 TGTTGATGAG
*
20286805 TTGGGGCAGCTTTTTGCTGAA
1 TTGGGGCAGCTTATTGCTGAA
* * *
20286826 TTGGAGTAGCTTATTGCTGAG
1 TTGGGGCAGCTTATTGCTGAA
*
20286847 TTGGGGCAGCTTCTTGCTGAA
1 TTGGGGCAGCTTATTGCTGAA
*
20286868 TCGGGGCA
1 TTGGGGCA
20286876 ACCTTGATTA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.34
Consensus pattern (21 bp):
TTGGGGCAGCTTATTGCTGAA
Found at i:20289376 original size:26 final size:27
Alignment explanation
Indices: 20289341--20289455 Score: 90
Period size: 27 Copynumber: 4.3 Consensus size: 27
20289331 CAAAAGGGCA
* **
20289341 TTCTCTTCATAAATCGCC-CAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
* * * *
20289367 TTCTTTTCATAGATAGCTATAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
* *
20289394 GTCTTTTCA-AAGATAACCATAAAGGCT
1 TTCTTTTCATAA-ATAACCACAAAGGCT
* * *
20289421 TCCTTTTCATAGATCACCACAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
*
20289448 TCCTTTTC
1 TTCTTTTC
20289456 TAGCGTGTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
26 15 0.21
27 56 0.78
28 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (27 bp):
TTCTTTTCATAAATAACCACAAAGGCT
Found at i:20289390 original size:27 final size:27
Alignment explanation
Indices: 20289360--20289455 Score: 120
Period size: 27 Copynumber: 3.6 Consensus size: 27
20289350 TAAATCGCCC
* *
20289360 AAAGGCTTTCTTTTCATAGATAGCTAT
1 AAAGGCTTTCTTTTCATAGATAACCAT
* *
20289387 AAAGGCTGTCTTTTCAAAGATAACCAT
1 AAAGGCTTTCTTTTCATAGATAACCAT
* * *
20289414 AAAGGCTTCCTTTTCATAGATCACCAC
1 AAAGGCTTTCTTTTCATAGATAACCAT
*
20289441 AAAGGCTTCCTTTTC
1 AAAGGCTTTCTTTTC
20289456 TAGCGTGTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (27 bp):
AAAGGCTTTCTTTTCATAGATAACCAT
Found at i:20292162 original size:25 final size:25
Alignment explanation
Indices: 20292133--20292220 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
20292123 TGTACAATAG
20292133 CCAAACAATAATCATGCACTTTAAT
1 CCAAACAATAATCATGCACTTTAAT
* * *
20292158 CCAAAACAGT-ATCATGTACATGGTAGACAAT
1 CC-AAACAATAATCATGCAC-T--T---TAAT
20292189 AACCAAACAATAATCATGCACTTTAAT
1 --CCAAACAATAATCATGCACTTTAAT
20292216 CCAAA
1 CCAAA
20292221 TCATATTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 20
0.64 0.08 0.27
Matches are distributed among these distances:
25 15 0.32
26 7 0.15
27 3 0.06
28 1 0.02
30 1 0.02
31 3 0.06
32 7 0.15
33 10 0.21
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (25 bp):
CCAAACAATAATCATGCACTTTAAT
Found at i:20293051 original size:45 final size:45
Alignment explanation
Indices: 20292987--20293104 Score: 168
Period size: 45 Copynumber: 2.6 Consensus size: 45
20292977 GGAAGGAAGA
* *
20292987 ATTAGTGGCTTCGTCCACAACCTACAT-GACAGCTTGTCTATGAAT
1 ATTAGTGGCTTCATCCACAACCTACATAG-CAACTTGTCTATGAAT
* *
20293032 ATTAGTGGCTTCATCCACAACCTACATAGCAACTTGTTTGTGAAT
1 ATTAGTGGCTTCATCCACAACCTACATAGCAACTTGTCTATGAAT
*
20293077 ATTAGTGG-TTTATCCACAACCTACATAG
1 ATTAGTGGCTTCATCCACAACCTACATAG
20293105 TAGCTTATCT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 19 0.28
45 47 0.70
46 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (45 bp):
ATTAGTGGCTTCATCCACAACCTACATAGCAACTTGTCTATGAAT
Found at i:20305126 original size:167 final size:168
Alignment explanation
Indices: 20304850--20305185 Score: 665
Period size: 167 Copynumber: 2.0 Consensus size: 168
20304840 CATGTTATTT
20304850 AAACAGATTGATCCATATATTGAATGACATGTCATGTTTTAGTACTACTATCATATTGTATTTTT
1 AAACAGATTGATCCATATATTGAATGACATGTCATGTTTTAGTACTACTATCATATTGTATTTTT
20304915 GTCTATCTAATTCATATCATATTTTATATAATTTATCAGAATTATTATTAAATTTTAAATTATGT
66 GTCTATCTAATTCATATCATATTTTATATAATTTATCAGAATTATTATTAAATTTTAAATTATGT
20304980 ATGTATAATATAAAAATATTTAAATAT-TAAATAATAG
131 ATGTATAATATAAAAATATTTAAATATGTAAATAATAG
20305017 AAACAGATTGATCCATATATTGAATGACATGTCATGTTTTAGTACTACTATCATATTGTATTTTT
1 AAACAGATTGATCCATATATTGAATGACATGTCATGTTTTAGTACTACTATCATATTGTATTTTT
20305082 GTCTATCTAATTCATATCATATTTTATATAATTTATCAGAATTATTATTAAATTTTAAATTATGT
66 GTCTATCTAATTCATATCATATTTTATATAATTTATCAGAATTATTATTAAATTTTAAATTATGT
20305147 ATGTATAATATAAAAATATTTAAATATGTAAATAATAG
131 ATGTATAATATAAAAATATTTAAATATGTAAATAATAG
20305185 A
1 A
20305186 TATTTAATAT
Statistics
Matches: 168, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
167 157 0.93
168 11 0.07
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (168 bp):
AAACAGATTGATCCATATATTGAATGACATGTCATGTTTTAGTACTACTATCATATTGTATTTTT
GTCTATCTAATTCATATCATATTTTATATAATTTATCAGAATTATTATTAAATTTTAAATTATGT
ATGTATAATATAAAAATATTTAAATATGTAAATAATAG
Found at i:20308103 original size:139 final size:139
Alignment explanation
Indices: 20307842--20308114 Score: 354
Period size: 139 Copynumber: 2.0 Consensus size: 139
20307832 AAACTTAGGC
* * *
20307842 TTAATATATAGATTGGCTCCTAAACTTGGCAACTTTTCTCAAATTAGCTCCTAAACTTTTTTTTG
1 TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAGCCCCTAAACTTTTTTTTG
* * * * * *
20307907 GATCACATCTGTCCCTAAGGTTGGCATCCGTTACACAAATTGGTCCCTATAGTTAACACCGTTAG
66 GATCACATCGGTCCCTAAGGTTGGCATCCATTACACAAATTAGTCCCTACAGCTAACACAGTTAG
20307972 TTTTAAGGT
131 TTTTAAGGT
* *
20307981 TTAATATACAGATTGGCCCCTAAACTTGGCAGCTTTTCTCACATT-GTCCCCTAAACTCTTTTTT
1 TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAG-CCCCTAAACT-TTTTTT
* * * *
20308045 TGGGTCATAGT-GGTCCCTAAGGTTGGCATCCATTGCATAAATTAGTCCCTACA-CTAACACAGT
64 TGGATCACA-TCGGTCCCTAAGGTTGGCATCCATTACACAAATTAGTCCCTACAGCTAACACAGT
*
20308108 TTGTTTT
128 TAGTTTT
20308115 TGAAGATTTT
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
138 1 0.01
139 64 0.56
140 49 0.43
141 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (139 bp):
TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAGCCCCTAAACTTTTTTTTG
GATCACATCGGTCCCTAAGGTTGGCATCCATTACACAAATTAGTCCCTACAGCTAACACAGTTAG
TTTTAAGGT
Found at i:20308747 original size:35 final size:35
Alignment explanation
Indices: 20308675--20308748 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
20308665 AAATTTGATA
* * *
20308675 TTTTTATTTTCAATTTATACATATTCTTTTTTATT
1 TTTTTATTTTCAATTTATACATATTATATTCTATT
20308710 TTTTTATTTTCAATTTATATACATA-TATATTCT-TT
1 TTTTTATTTTCAA-TT-TATACATATTATATTCTATT
20308745 TTTT
1 TTTT
20308749 AAAGTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 19 0.56
36 7 0.21
37 8 0.24
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (35 bp):
TTTTTATTTTCAATTTATACATATTATATTCTATT
Found at i:20309226 original size:19 final size:19
Alignment explanation
Indices: 20309184--20309251 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 19
20309174 ATTACAAAAT
20309184 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
20309204 AATTCAAAATAAGTTTT-AA
1 AATTCAAAATAA-TTTTAAA
20309223 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
20309242 AATTCTAAAA
1 AATTC-AAAA
20309252 ATTATATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.07
18 2 0.05
19 19 0.43
20 16 0.36
21 4 0.09
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.35
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:20309256 original size:18 final size:18
Alignment explanation
Indices: 20309221--20309288 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
20309211 AATAAGTTTT
20309221 AAAATTC-AAAATATTTATA
1 AAAATTCTAAAA-A-TTATA
20309240 AAAATTCTAAAAATTATA
1 AAAATTCTAAAAATTATA
**** **
20309258 TTTTTTAAAAAAATTATA
1 AAAATTCTAAAAATTATA
20309276 AAAATT-TAAAAAT
1 AAAATTCTAAAAAT
20309289 AAATTCTAAA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
17 6 0.16
18 19 0.51
19 8 0.22
20 4 0.11
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTCTAAAAATTATA
Found at i:20310568 original size:15 final size:17
Alignment explanation
Indices: 20310542--20310579 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
20310532 AGCTCAAAGC
20310542 ATAAGTAGAAAAGAAAT
1 ATAAGTAGAAAAGAAAT
*
20310559 A-AAGTA-AAAATAAAT
1 ATAAGTAGAAAAGAAAT
20310574 ATAAGT
1 ATAAGT
20310580 TGTAGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 9 0.47
17 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (17 bp):
ATAAGTAGAAAAGAAAT
Found at i:20314056 original size:27 final size:27
Alignment explanation
Indices: 20314026--20314092 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
20314016 CCTATCAGGT
*
20314026 AGGCGCCAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGCGCCTCACAGAG
*
20314053 AGGCGCCAATGAAGGCGCCTCATAGAG
1 AGGCGCCAATGAAGGCGCCTCACAGAG
20314080 AGGCGCCAATGAA
1 AGGCGCCAATGAA
20314093 TATTGTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.31, C:0.25, G:0.33, T:0.10
Consensus pattern (27 bp):
AGGCGCCAATGAAGGCGCCTCACAGAG
Found at i:20314085 original size:15 final size:15
Alignment explanation
Indices: 20314042--20314086 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
20314032 CAATGAAGGT
*
20314042 GCCTCACAGAGAGGC
1 GCCTCATAGAGAGGC
*
20314057 GCC-AAT-GA-AGGC
1 GCCTCATAGAGAGGC
20314069 GCCTCATAGAGAGGC
1 GCCTCATAGAGAGGC
20314084 GCC
1 GCC
20314087 AATGAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.29
13 4 0.17
14 3 0.12
15 10 0.42
ACGTcount: A:0.27, C:0.31, G:0.33, T:0.09
Consensus pattern (15 bp):
GCCTCATAGAGAGGC
Found at i:20314191 original size:21 final size:21
Alignment explanation
Indices: 20314162--20314205 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
20314152 TGGATTAGTA
*
20314162 TTTTGTATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
20314183 TTTTATATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
20314204 TT
1 TT
20314206 GTGTTTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
TTTTATATGAATATTGTAATT
Found at i:20314463 original size:19 final size:19
Alignment explanation
Indices: 20314439--20314572 Score: 105
Period size: 19 Copynumber: 6.7 Consensus size: 19
20314429 NNNNNNNNNN
20314439 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
20314458 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
20314479 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
* * *
20314498 A-TACTA-ATCCAAAACTATAA
1 ATTACAATATTC-ATAC-A-AA
*
20314518 A-TACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATACAA-A
*
20314540 ATTACAATATTAATACAAA
1 ATTACAATATTCATACAAA
20314559 ATTACAATATTCAT
1 ATTACAATATTCAT
20314573 TGGCGCCTCT
Statistics
Matches: 93, Mismatches: 9, Indels: 26
0.73 0.07 0.20
Matches are distributed among these distances:
17 3 0.03
18 7 0.08
19 38 0.41
20 12 0.13
21 21 0.23
22 5 0.05
23 5 0.05
25 2 0.02
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:20314481 original size:21 final size:21
Alignment explanation
Indices: 20314439--20314498 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
20314429 NNNNNNNNNN
20314439 ATTACAATATTCATAC--AAA
1 ATTACAATATTCATACAAAAA
20314458 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATACAAAAA
20314479 ATTACAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
20314499 TACTAATCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.41
21 23 0.59
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (21 bp):
ATTACAATATTCATACAAAAA
Found at i:20314699 original size:27 final size:27
Alignment explanation
Indices: 20314568--20314684 Score: 225
Period size: 27 Copynumber: 4.3 Consensus size: 27
20314558 AATTACAATA
*
20314568 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTGTGAGGCACC
20314595 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTGTGAGGCACC
20314622 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTGTGAGGCACC
20314649 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTGTGAGGCACC
20314676 TTCATTGGC
1 TTCATTGGC
20314685 ACCTACCTGA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
27 89 1.00
ACGTcount: A:0.12, C:0.32, G:0.25, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTGTGAGGCACC
Found at i:20315231 original size:12 final size:13
Alignment explanation
Indices: 20315213--20315246 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
20315203 CTTAAATTAA
*
20315213 AATTTTTAAAAGT
1 AATTTTTAAAAAT
20315226 -ATTTTTAAAAAT
1 AATTTTTAAAAAT
20315238 AATTTTTAA
1 AATTTTTAA
20315247 GCAATGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
AATTTTTAAAAAT
Found at i:20319549 original size:51 final size:51
Alignment explanation
Indices: 20319466--20319644 Score: 207
Period size: 51 Copynumber: 3.4 Consensus size: 51
20319456 ACTTCTGATC
* * *
20319466 AGTGATAAGTGATAAGT-AGTAGCTTCAACTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGA-TAGCTTTAGCTACACTTATCTGATCAGTGACA
*
20319517 AGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
20319568 GGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGAT-A--GCT---TTAGCTACACTTATCTGATCAGTGACA
* * *
20319625 AGAGATAAATGATAAGTGAT
1 AGTGACAAGTGATAAGTGAT
20319645 TCCGTGTAAG
Statistics
Matches: 110, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
51 63 0.57
52 2 0.02
54 2 0.02
57 43 0.39
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:20319573 original size:58 final size:57
Alignment explanation
Indices: 20319511--20319624 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 57
20319501 TATCTGATCA
*
20319511 GTGACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAG
1 GTGACAAGTGACAAGTGATAAGTGATAGC-TTAGCTACACTTATCTGATCAGTGACAG
* *
20319569 GTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
1 GTGACAAGTGACAAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAGTGACA
20319625 AGAGATAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 27 0.51
58 26 0.49
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (57 bp):
GTGACAAGTGACAAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAGTGACAG
Found at i:20319638 original size:57 final size:58
Alignment explanation
Indices: 20319523--20319644 Score: 192
Period size: 57 Copynumber: 2.1 Consensus size: 58
20319513 GACAAGTGGC
* * *
20319523 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAGGTGACAAGTGAT
1 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGAGACAAATGAT
* *
20319581 AAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACAAGAGATAAATGAT
1 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGAGACAAATGAT
20319638 AAGTGAT
1 AAGTGAT
20319645 TCCGTGTAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
57 43 0.73
58 16 0.27
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (58 bp):
AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGAGACAAATGAT
Found at i:20322331 original size:13 final size:13
Alignment explanation
Indices: 20322308--20322349 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
20322298 CTGGCTTTCT
*
20322308 TACACAAATAATA
1 TACAAAAATAATA
*
20322321 TATAAAAATAAT-
1 TACAAAAATAATA
20322333 TACAAAAATAAGTA
1 TACAAAAATAA-TA
20322347 TAC
1 TAC
20322350 TGAACAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.42
13 11 0.46
14 3 0.12
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (13 bp):
TACAAAAATAATA
Found at i:20322801 original size:17 final size:18
Alignment explanation
Indices: 20322764--20322804 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20322754 GTATATTATT
**
20322764 AAAAAAAAGTTGAAAATA
1 AAAAAAAAACTGAAAATA
20322782 AAAAAAAAACTGAAAA-A
1 AAAAAAAAACTGAAAATA
20322799 AAAAAA
1 AAAAAA
20322805 GAAGGGAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.10
Consensus pattern (18 bp):
AAAAAAAAACTGAAAATA
Found at i:20323700 original size:26 final size:27
Alignment explanation
Indices: 20323648--20323700 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
20323638 ATTTTAAAAT
* *
20323648 ATTTTTAAAATACTTTTTTTATTTTTA
1 ATTTTTAAAATACTTTTTTGATGTTTA
*
20323675 ATTTTTAAAATA-TTTTTTGGTGTTTA
1 ATTTTTAAAATACTTTTTTGATGTTTA
20323701 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.28, C:0.02, G:0.06, T:0.64
Consensus pattern (27 bp):
ATTTTTAAAATACTTTTTTGATGTTTA
Found at i:20326024 original size:16 final size:13
Alignment explanation
Indices: 20325998--20326045 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
20325988 TTTTATAGAT
20325998 ATTTTTCTTTTTC
1 ATTTTTCTTTTTC
20326011 ATGTTCTCTCTTTTTC
1 AT-TT-T-TCTTTTTC
20326027 ATTTTTCTTTTTC
1 ATTTTTCTTTTTC
20326040 -TTTTTC
1 ATTTTTC
20326046 CTACCCTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.19
13 10 0.31
14 3 0.09
15 3 0.09
16 10 0.31
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (13 bp):
ATTTTTCTTTTTC
Found at i:20327199 original size:20 final size:19
Alignment explanation
Indices: 20327161--20327205 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
20327151 AATAATAATT
20327161 TAATATTTTACTAAAAATAA
1 TAATATTTTACTAAAAAT-A
*
20327181 TAATATTTTA-TAAGTAATA
1 TAATATTTTACTAA-AAATA
20327200 TAATAT
1 TAATAT
20327206 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
TAATATTTTACTAAAAATA
Found at i:20327204 original size:19 final size:18
Alignment explanation
Indices: 20327152--20327205 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
20327142 TTTTTGTTAA
*
20327152 ATAATAATTTAATATTTT
1 ATAATAATATAATATTTT
*
20327170 ACTAAAAATAATAATATTTT
1 A-TAATAAT-ATAATATTTT
20327190 ATAAGTAATATAATAT
1 ATAA-TAATATAATAT
20327206 ATATATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.03
19 16 0.53
20 13 0.43
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
ATAATAATATAATATTTT
Found at i:20328581 original size:27 final size:27
Alignment explanation
Indices: 20328543--20328607 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 27
20328533 CGAATATAAT
*
20328543 AAATATTATTTTTA-TTTTTTATTTTTA
1 AAATATT-TTTTTATTTTTTTATTGTTA
20328570 AAATACTTTTTTTATTTTTTTATTGTTA
1 AAATA-TTTTTTTATTTTTTTATTGTTA
20328598 AAATATTTTT
1 AAATATTTTT
20328608 AAAATATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (27 bp):
AAATATTTTTTTATTTTTTTATTGTTA
Found at i:20328604 original size:11 final size:11
Alignment explanation
Indices: 20328590--20328629 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
20328580 TTTATTTTTT
*
20328590 TATTGTTAAAA
1 TATTTTTAAAA
20328601 TATTTTTAAAA
1 TATTTTTAAAA
20328612 TATATTTTAAAA
1 TAT-TTTTAAAA
20328624 T-TTTTT
1 TATTTTT
20328630 TTGGTGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 4 0.15
11 14 0.52
12 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:20328621 original size:12 final size:12
Alignment explanation
Indices: 20328590--20328624 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
20328580 TTTATTTTTT
20328590 TATTGTTAAAATA
1 TATT-TTAAAATA
20328603 T-TTTTAAAATA
1 TATTTTAAAATA
20328614 TATTTTAAAAT
1 TATTTTAAAAT
20328625 TTTTTTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.43
12 11 0.52
13 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
TATTTTAAAATA
Found at i:20328903 original size:34 final size:34
Alignment explanation
Indices: 20328840--20328904 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
20328830 TGTATGTTTA
* * *
20328840 AATCAATTGTCATGTTGTAATACTGCTTCTTTTG
1 AATCAATTGTCATGGTGGAATACTACTTCTTTTG
* *
20328874 AATCAATTGTTATGGTGGAATATTACTTCTT
1 AATCAATTGTCATGGTGGAATACTACTTCTT
20328905 CTTCTTTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.46
Consensus pattern (34 bp):
AATCAATTGTCATGGTGGAATACTACTTCTTTTG
Found at i:20340338 original size:9 final size:9
Alignment explanation
Indices: 20340324--20340408 Score: 116
Period size: 9 Copynumber: 9.4 Consensus size: 9
20340314 TTTGGTTAAA
20340324 AATTAACCG
1 AATTAACCG
*
20340333 AATTAACCA
1 AATTAACCG
20340342 AATTAACCG
1 AATTAACCG
*
20340351 AATTACCCG
1 AATTAACCG
20340360 AATTAACCG
1 AATTAACCG
*
20340369 AATTACCCG
1 AATTAACCG
*
20340378 AATTACCCG
1 AATTAACCG
*
20340387 AATTACCCG
1 AATTAACCG
*
20340396 AATTAACCT
1 AATTAACCG
20340405 AATT
1 AATT
20340409 GAATCATACC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 69 1.00
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:20340346 original size:18 final size:18
Alignment explanation
Indices: 20340324--20340408 Score: 134
Period size: 18 Copynumber: 4.7 Consensus size: 18
20340314 TTTGGTTAAA
* *
20340324 AATTAACCGAATTAACCA
1 AATTAACCGAATTACCCG
20340342 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
20340360 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
20340378 AATTACCCGAATTACCCG
1 AATTAACCGAATTACCCG
*
20340396 AATTAACCTAATT
1 AATTAACCGAATT
20340409 GAATCATACC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:20347408 original size:2 final size:2
Alignment explanation
Indices: 20347403--20347433 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20347393 CTAAGCTTGC
20347403 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20347434 ATCTGTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20379899 original size:492 final size:492
Alignment explanation
Indices: 20378975--20379960 Score: 1972
Period size: 492 Copynumber: 2.0 Consensus size: 492
20378965 TAAGAAAATA
20378975 GCATGCAGAATTTGTCTTCAGGTTACAACATATCATAGAAGCTACCATCTAATACTAGGTTCAAA
1 GCATGCAGAATTTGTCTTCAGGTTACAACATATCATAGAAGCTACCATCTAATACTAGGTTCAAA
20379040 ATTATATTTCTTACCAGGTAAATCCCTTCTTGGGGACCTCCGGAAGTAAGTGCAGTGTCTTCCAT
66 ATTATATTTCTTACCAGGTAAATCCCTTCTTGGGGACCTCCGGAAGTAAGTGCAGTGTCTTCCAT
20379105 GCTCTGAGGAGTAAGGTGGTGATAAAATATCAAAAATAGCACAGGGAGTCCGTGCCCTGAAACAA
131 GCTCTGAGGAGTAAGGTGGTGATAAAATATCAAAAATAGCACAGGGAGTCCGTGCCCTGAAACAA
20379170 TGGATGTTGCCTCCACTTGTGGGATAAAGTACTGTTGTTGCACAAGGGGCTGTCATCTCAGTATC
196 TGGATGTTGCCTCCACTTGTGGGATAAAGTACTGTTGTTGCACAAGGGGCTGTCATCTCAGTATC
20379235 CTTGACAAGTTTTGCAGCTCTTGCTACAAACCACCAAAAATAAGCAAATCAGAGTCAAAGACTGA
261 CTTGACAAGTTTTGCAGCTCTTGCTACAAACCACCAAAAATAAGCAAATCAGAGTCAAAGACTGA
20379300 AGAATATACAATAAGTGCCCTATACCCTAGGAAGGGTGAGGAGAAAACGCATTATTTAAAATAAG
326 AGAATATACAATAAGTGCCCTATACCCTAGGAAGGGTGAGGAGAAAACGCATTATTTAAAATAAG
20379365 ATACATCACCACTTTGTCCATGAATAAATTATCAATACCATTACATCAGTTGAACAAGCAACTAC
391 ATACATCACCACTTTGTCCATGAATAAATTATCAATACCATTACATCAGTTGAACAAGCAACTAC
20379430 TTCAGTTGCGATTGGTGACAGATAGGCAGGTTTAGCT
456 TTCAGTTGCGATTGGTGACAGATAGGCAGGTTTAGCT
20379467 GCATGCAGAATTTGTCTTCAGGTTACAACATATCATAGAAGCTACCATCTAATACTAGGTTCAAA
1 GCATGCAGAATTTGTCTTCAGGTTACAACATATCATAGAAGCTACCATCTAATACTAGGTTCAAA
20379532 ATTATATTTCTTACCAGGTAAATCCCTTCTTGGGGACCTCCGGAAGTAAGTGCAGTGTCTTCCAT
66 ATTATATTTCTTACCAGGTAAATCCCTTCTTGGGGACCTCCGGAAGTAAGTGCAGTGTCTTCCAT
20379597 GCTCTGAGGAGTAAGGTGGTGATAAAATATCAAAAATAGCACAGGGAGTCCGTGCCCTGAAACAA
131 GCTCTGAGGAGTAAGGTGGTGATAAAATATCAAAAATAGCACAGGGAGTCCGTGCCCTGAAACAA
20379662 TGGATGTTGCCTCCACTTGTGGGATAAAGTACTGTTGTTGCACAAGGGGCTGTCATCTCAGTATC
196 TGGATGTTGCCTCCACTTGTGGGATAAAGTACTGTTGTTGCACAAGGGGCTGTCATCTCAGTATC
20379727 CTTGACAAGTTTTGCAGCTCTTGCTACAAACCACCAAAAATAAGCAAATCAGAGTCAAAGACTGA
261 CTTGACAAGTTTTGCAGCTCTTGCTACAAACCACCAAAAATAAGCAAATCAGAGTCAAAGACTGA
20379792 AGAATATACAATAAGTGCCCTATACCCTAGGAAGGGTGAGGAGAAAACGCATTATTTAAAATAAG
326 AGAATATACAATAAGTGCCCTATACCCTAGGAAGGGTGAGGAGAAAACGCATTATTTAAAATAAG
20379857 ATACATCACCACTTTGTCCATGAATAAATTATCAATACCATTACATCAGTTGAACAAGCAACTAC
391 ATACATCACCACTTTGTCCATGAATAAATTATCAATACCATTACATCAGTTGAACAAGCAACTAC
20379922 TTCAGTTGCGATTGGTGACAGATAGGCAGGTTTAGCT
456 TTCAGTTGCGATTGGTGACAGATAGGCAGGTTTAGCT
20379959 GC
1 GC
20379961 CATAGGCCAC
Statistics
Matches: 494, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
492 494 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (492 bp):
GCATGCAGAATTTGTCTTCAGGTTACAACATATCATAGAAGCTACCATCTAATACTAGGTTCAAA
ATTATATTTCTTACCAGGTAAATCCCTTCTTGGGGACCTCCGGAAGTAAGTGCAGTGTCTTCCAT
GCTCTGAGGAGTAAGGTGGTGATAAAATATCAAAAATAGCACAGGGAGTCCGTGCCCTGAAACAA
TGGATGTTGCCTCCACTTGTGGGATAAAGTACTGTTGTTGCACAAGGGGCTGTCATCTCAGTATC
CTTGACAAGTTTTGCAGCTCTTGCTACAAACCACCAAAAATAAGCAAATCAGAGTCAAAGACTGA
AGAATATACAATAAGTGCCCTATACCCTAGGAAGGGTGAGGAGAAAACGCATTATTTAAAATAAG
ATACATCACCACTTTGTCCATGAATAAATTATCAATACCATTACATCAGTTGAACAAGCAACTAC
TTCAGTTGCGATTGGTGACAGATAGGCAGGTTTAGCT
Found at i:20384247 original size:6 final size:6
Alignment explanation
Indices: 20384236--20384260 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20384226 AAGTGTCAAT
20384236 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
20384261 ATAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:20397546 original size:166 final size:167
Alignment explanation
Indices: 20397262--20397594 Score: 659
Period size: 166 Copynumber: 2.0 Consensus size: 167
20397252 TATTATAAAT
20397262 TAAAAACCCAAATAAACTCCAATATTAAAATATAAACATAATTGATGAGGTGATAATTTATGTTG
1 TAAAAACCCAAATAAACTCCAATATTAAAATATAAACATAATTGATGAGGTGATAATTTATGTTG
20397327 GAGAGGGTTGATAGAATAGACATAGAAGTAATTTTTAATGTAAAAACTTTAGAGGATGATATAGT
66 GAGAGGGTTGATAGAATAGACATAGAAGTAATTTTTAATGTAAAAACTTTAGAGGATGATATAGT
20397392 TCTAAAAGAAAAAAAAAATAGGTATTTGAATTCAATC
131 TCTAAAAGAAAAAAAAAATAGGTATTTGAATTCAATC
20397429 TAAAAACCC-AATAAACTCCAATATTAAAATATAAACATAATTGATGAGGTGATAATTTATGTTG
1 TAAAAACCCAAATAAACTCCAATATTAAAATATAAACATAATTGATGAGGTGATAATTTATGTTG
20397493 GAGAGGGTTGATAGAATAGACATAGAAGTAATTTTTAATGTAAAAACTTTAGAGGATGATATAGT
66 GAGAGGGTTGATAGAATAGACATAGAAGTAATTTTTAATGTAAAAACTTTAGAGGATGATATAGT
20397558 TCTAAAAGAAAAAAAAAATAGGTATTTGAATTCAATC
131 TCTAAAAGAAAAAAAAAATAGGTATTTGAATTCAATC
20397595 ACAACTCTAG
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
166 157 0.95
167 9 0.05
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (167 bp):
TAAAAACCCAAATAAACTCCAATATTAAAATATAAACATAATTGATGAGGTGATAATTTATGTTG
GAGAGGGTTGATAGAATAGACATAGAAGTAATTTTTAATGTAAAAACTTTAGAGGATGATATAGT
TCTAAAAGAAAAAAAAAATAGGTATTTGAATTCAATC
Found at i:20397868 original size:23 final size:23
Alignment explanation
Indices: 20397833--20397882 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
20397823 TAACACAGTT
**
20397833 CGGATTCCTCAATCCTATATCTA
1 CGGATTCAACAATCCTATATCTA
20397856 CGGATTCAACAATCCTATATCTA
1 CGGATTCAACAATCCTATATCTA
20397879 CGGA
1 CGGA
20397883 GCCTTGCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (23 bp):
CGGATTCAACAATCCTATATCTA
Found at i:20402575 original size:2 final size:2
Alignment explanation
Indices: 20402568--20402593 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20402558 AAAATTATTC
20402568 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
20402594 TCTTACGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20410901 original size:29 final size:28
Alignment explanation
Indices: 20410863--20410918 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
20410853 TTGTGTTAAT
20410863 AATTTAC-AAATCAAAATCCCATGTATAA
1 AATTTACAAAATCAAAAT-CCATGTATAA
*
20410891 AATTTCACAAAATCAAAATTCATGTATA
1 AATTT-ACAAAATCAAAATCCATGTATA
20410919 GTTTTGGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 10 0.40
30 10 0.40
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (28 bp):
AATTTACAAAATCAAAATCCATGTATAA
Found at i:20417139 original size:24 final size:22
Alignment explanation
Indices: 20417110--20417190 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 22
20417100 CTATATAGCG
20417110 GGAAGCTCATAAGAGCCATAAT
1 GGAAGCTCATAAGAGCCATAAT
**
20417132 CAGGAAGCTCATGCGAGCCAATAAT
1 --GGAAGCTCATAAGAGCC-ATAAT
20417157 GGATAGCTCCA-AAGAGCCATTAATT
1 GGA-AGCT-CATAAGAGCCA-TAA-T
20417182 GGAAAGCTC
1 GG-AAGCTC
20417191 TGGACAATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
23 4 0.09
24 28 0.60
25 14 0.30
26 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (22 bp):
GGAAGCTCATAAGAGCCATAAT
Found at i:20417255 original size:26 final size:26
Alignment explanation
Indices: 20417219--20417273 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
20417209 GAAGCTCCGG
*
20417219 AGAGCCTTTAATCAGGAAGCTCACAA
1 AGAGCCCTTAATCAGGAAGCTCACAA
* *
20417245 AGAGCCCTTAATCATGAAGCTCACGA
1 AGAGCCCTTAATCAGGAAGCTCACAA
20417271 AGA
1 AGA
20417274 ACCATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
AGAGCCCTTAATCAGGAAGCTCACAA
Found at i:20417939 original size:20 final size:20
Alignment explanation
Indices: 20417901--20417940 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20417891 CCATGTGTTT
* *
20417901 CATAAAATTTAGAATTTTTC
1 CATAAAATTTACAACTTTTC
*
20417921 CATAAATTTTACAACTTTTC
1 CATAAAATTTACAACTTTTC
20417941 AATTTAGTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (20 bp):
CATAAAATTTACAACTTTTC
Found at i:20419061 original size:24 final size:24
Alignment explanation
Indices: 20419015--20419066 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
20419005 ATTTTTATTT
* **
20419015 AAATAATTCTTTAAATTTGTATAA
1 AAATAATTATTTAAATTAATATAA
* *
20419039 AAATAATTATTTACATTAATATAT
1 AAATAATTATTTAAATTAATATAA
20419063 AAAT
1 AAAT
20419067 TTCTAATGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (24 bp):
AAATAATTATTTAAATTAATATAA
Found at i:20428478 original size:24 final size:22
Alignment explanation
Indices: 20428449--20428529 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 22
20428439 CTATATAGCG
20428449 GGAAGCTCATAAGAGCCATAAT
1 GGAAGCTCATAAGAGCCATAAT
**
20428471 CAGGAAGCTCATGCGAGCCAATAAT
1 --GGAAGCTCATAAGAGCC-ATAAT
20428496 GGATAGCTCCA-AAGAGCCATTAATT
1 GGA-AGCT-CATAAGAGCCA-TAA-T
20428521 GGAAAGCTC
1 GG-AAGCTC
20428530 TGGACAATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
23 4 0.09
24 28 0.60
25 14 0.30
26 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (22 bp):
GGAAGCTCATAAGAGCCATAAT
Found at i:20428594 original size:26 final size:26
Alignment explanation
Indices: 20428558--20428612 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
20428548 GAAGCTCCGG
*
20428558 AGAGCCTTTAATCAGGAAGCTCACAA
1 AGAGCCCTTAATCAGGAAGCTCACAA
* *
20428584 AGAGCCCTTAATCATGAAGCTCACGA
1 AGAGCCCTTAATCAGGAAGCTCACAA
20428610 AGA
1 AGA
20428613 ACCATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
AGAGCCCTTAATCAGGAAGCTCACAA
Found at i:20429278 original size:20 final size:20
Alignment explanation
Indices: 20429240--20429279 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20429230 CCATGTGTTT
* *
20429240 CATAAAATTTAGAATTTTTC
1 CATAAAATTTACAACTTTTC
*
20429260 CATAAATTTTACAACTTTTC
1 CATAAAATTTACAACTTTTC
20429280 AATTTAGTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (20 bp):
CATAAAATTTACAACTTTTC
Found at i:20430400 original size:24 final size:24
Alignment explanation
Indices: 20430354--20430405 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
20430344 ATTTTTATTT
* **
20430354 AAATAATTCTTTAAATTTGTATAA
1 AAATAATTATTTAAATTAATATAA
* *
20430378 AAATAATTATTTACATTAATATAT
1 AAATAATTATTTAAATTAATATAA
20430402 AAAT
1 AAAT
20430406 TTCTAATGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (24 bp):
AAATAATTATTTAAATTAATATAA
Found at i:20451915 original size:36 final size:36
Alignment explanation
Indices: 20451867--20451960 Score: 118
Period size: 37 Copynumber: 2.6 Consensus size: 36
20451857 GGGTCTCCAA
* *
20451867 AATCACATTTCAATTCAATTTCACTTTTTCACTTTC
1 AATCACAATTCAATTCAATTTCACTTTTCCACTTTC
* *
20451903 AATCACAATTCAATTCAAAATTCACTTTTCCATTTTC
1 AATCACAATTCAATTC-AATTTCACTTTTCCACTTTC
20451940 AAGTCA-ATATTCAATTCAATT
1 AA-TCACA-ATTCAATTCAATT
20451961 CCACACATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
36 15 0.30
37 23 0.46
38 12 0.24
ACGTcount: A:0.34, C:0.22, G:0.01, T:0.43
Consensus pattern (36 bp):
AATCACAATTCAATTCAATTTCACTTTTCCACTTTC
Found at i:20451989 original size:23 final size:22
Alignment explanation
Indices: 20451946--20451989 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
20451936 TTTCAAGTCA
20451946 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
20451969 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
20451990 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:20452274 original size:17 final size:18
Alignment explanation
Indices: 20452242--20452275 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20452232 ATTTTCTTTT
20452242 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
20452260 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
20452276 TATTAAAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:20452320 original size:4 final size:4
Alignment explanation
Indices: 20452311--20452344 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
20452301 TTAGTTTTTC
20452311 CTTT CTTT CTTT CTTTT CTTT CTTT CCTTT CTTT
1 CTTT CTTT CTTT C-TTT CTTT CTTT -CTTT CTTT
20452345 TCTCCCTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:20452328 original size:9 final size:9
Alignment explanation
Indices: 20452306--20452347 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
20452296 AAACTTTAGT
20452306 TTTTCCTTTC
1 TTTT-CTTTC
20452316 -TTTCTTTC
1 TTTTCTTTC
20452324 TTTTCTTTC
1 TTTTCTTTC
*
20452333 TTTCCTTTC
1 TTTTCTTTC
20452342 TTTTCT
1 TTTTCT
20452348 CCCTGTTTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 5 0.17
9 24 0.83
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:20452328 original size:13 final size:13
Alignment explanation
Indices: 20452307--20452344 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
20452297 AACTTTAGTT
20452307 TTTCCTTTCTTTC
1 TTTCCTTTCTTTC
*
20452320 TTTCTTTTCTTTC
1 TTTCCTTTCTTTC
20452333 TTTCCTTTCTTT
1 TTTCCTTTCTTT
20452345 TCTCCCTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCCTTTCTTTC
Found at i:20456891 original size:14 final size:14
Alignment explanation
Indices: 20456872--20456900 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20456862 TTGAAAACAA
20456872 TTTTTATTTATTGT
1 TTTTTATTTATTGT
20456886 TTTTTATTTATTGT
1 TTTTTATTTATTGT
20456900 T
1 T
20456901 CTTCAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTATTTATTGT
Found at i:20460446 original size:6 final size:6
Alignment explanation
Indices: 20460437--20460469 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
20460427 TTAAATTAAT
20460437 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
20460470 CGTAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:20460615 original size:17 final size:17
Alignment explanation
Indices: 20460577--20460609 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20460567 AATAAAAAAT
*
20460577 ATTTATAAAAATTATAG
1 ATTTATAAAAAATATAG
20460594 ATTTATAAAAAATATA
1 ATTTATAAAAAATATA
20460610 TTTTTAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTTATAAAAAATATAG
Found at i:20461896 original size:17 final size:17
Alignment explanation
Indices: 20461858--20461890 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20461848 AATAAAAAAT
*
20461858 ATTTATAAAAATTATAG
1 ATTTATAAAAAATATAG
20461875 ATTTATAAAAAATATA
1 ATTTATAAAAAATATA
20461891 TTTTTAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTTATAAAAAATATAG
Found at i:20466658 original size:105 final size:105
Alignment explanation
Indices: 20466543--20466784 Score: 265
Period size: 105 Copynumber: 2.3 Consensus size: 105
20466533 CGCAACTACG
*
20466543 AAACAGCTCGCAGACTTATGTTCTCAGTTGATGTTTAAAGGTTAGTTGCA-TTAAGTTCGCAACC
1 AAACAGCTCGCAGACTTATGTTCTCAGTTGATGTTTAAAGGTTAGTTG-AGTTAAGCTCGCAACC
* * * * * ***
20466607 TCTAGATTATTCGAGTTAACTTAGTTAAGCTTGTAACTCTA
65 TCCAAATTATTCAAGTTAACTGAATTAAGCTCACAACTCTA
* * * ** *
20466648 AAACAACTCGCAAACTTACGTT-TCCAACTGATGTTTAAAGGTTAGTTGAGTTAAGCTCGCAGCC
1 AAACAGCTCGCAGACTTATGTTCT-CAGTTGATGTTTAAAGGTTAGTTGAGTTAAGCTCGCAACC
* *
20466712 TCCAAATTATTCAAGTTAGCTGAATTAAGCTCACAACTCTG
65 TCCAAATTATTCAAGTTAACTGAATTAAGCTCACAACTCTA
* *
20466753 AAACAGCTCGC-GAACCTATGTTCCCAGTTGAT
1 AAACAGCTCGCAG-ACTTATGTTCTCAGTTGAT
20466785 TCTACTAAGG
Statistics
Matches: 109, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
104 2 0.02
105 107 0.98
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (105 bp):
AAACAGCTCGCAGACTTATGTTCTCAGTTGATGTTTAAAGGTTAGTTGAGTTAAGCTCGCAACCT
CCAAATTATTCAAGTTAACTGAATTAAGCTCACAACTCTA
Found at i:20467296 original size:104 final size:103
Alignment explanation
Indices: 20467163--20467523 Score: 359
Period size: 104 Copynumber: 3.5 Consensus size: 103
20467153 ACAGCTCACA
* * * ** *
20467163 AACCTACGTTCCCAGCTCAT-TCTACTAAGGTTTACTGAATTAAGATCGCAATCTCCGATTATTT
1 AACCTACGTTCACAGCTGATAT-TACTAAGGCTCGCTGATTTAAGATCGCAATCTCCGATTATTT
* *
20467227 AAGTTCACTGATTTAAGATCGCAACTCTTAACAACTTACT
65 GAGTTCACTGATTTAAGATCGCAACTC-TAACAACTTGCT
* * * *
20467267 AACCTACGTTCACAGCTGATATTACTAAGGCTCGTTGATTTAAGATGGCAACCTCCAATTATTTG
1 AACCTACGTTCACAGCTGATATTACTAAGGCTCGCTGATTTAAGATCGCAATCTCCGATTATTTG
* * *
20467332 AGTTCGCTGATTTAAGAACGCAACTGCTAACAACTCGCT
66 AGTTCACTGATTTAAGATCGCAACT-CTAACAACTTGCT
* ** * * * * * * *
20467371 GATTTATGTTCACAACTGATGTTACTAAGGCTCGCTGATTTAATATTGCAGTTTCCGATTATTTG
1 AACCTACGTTCACAGCTGATATTACTAAGGCTCGCTGATTTAAGATCGCAATCTCCGATTATTTG
* *
20467436 AGTT-AGTTGATTTAAGATCGCAATTCCTAACAACTTGCT
66 AGTTCA-CTGATTTAAGATCGCAACT-CTAACAACTTGCT
* * * * * *
20467475 GACATACGTTCAGAGTTGATATTACTAAAGCTCG-TGATTTGAGATCGCA
1 AACCTACGTTCACAGCTGATATTACTAAGGCTCGCTGATTTAAGATCGCA
20467524 GCCTCCGAAT
Statistics
Matches: 209, Mismatches: 45, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
103 12 0.06
104 195 0.93
105 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (103 bp):
AACCTACGTTCACAGCTGATATTACTAAGGCTCGCTGATTTAAGATCGCAATCTCCGATTATTTG
AGTTCACTGATTTAAGATCGCAACTCTAACAACTTGCT
Found at i:20471173 original size:11 final size:11
Alignment explanation
Indices: 20471159--20471217 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
20471149 AATTATTTTA
20471159 TCAATTTCCTC
1 TCAATTTCCTC
*
20471170 TCAATTTCCTT
1 TCAATTTCCTC
* *
20471181 TCAAATTGCTC
1 TCAATTTCCTC
*
20471192 TCAATTTCCTT
1 TCAATTTCCTC
20471203 TCAAATTT-CTC
1 TC-AATTTCCTC
20471214 TCAA
1 TCAA
20471218 ATCCATATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
10 2 0.05
11 32 0.82
12 5 0.13
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.46
Consensus pattern (11 bp):
TCAATTTCCTC
Found at i:20471192 original size:22 final size:22
Alignment explanation
Indices: 20471167--20471217 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
20471157 TATCAATTTC
20471167 CTCTCAATTTCCTTTCAAATTG
1 CTCTCAATTTCCTTTCAAATTG
*
20471189 CTCTCAATTTCCTTTCAAATTT
1 CTCTCAATTTCCTTTCAAATTG
20471211 CTCTCAA
1 CTCTCAA
20471218 ATCCATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.45
Consensus pattern (22 bp):
CTCTCAATTTCCTTTCAAATTG
Found at i:20471255 original size:29 final size:28
Alignment explanation
Indices: 20471206--20471260 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
20471196 TTTCCTTTCA
*
20471206 AATTTCTCTCAAATCCATATTTAATCTC
1 AATTTCTCTCAAATCCATATTAAATCTC
*
20471234 AATTTGCTCTCAATTTCC-TATTAAATC
1 AATTT-CTCTCAA-ATCCATATTAAATC
20471261 CCTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.22
29 15 0.65
30 3 0.13
ACGTcount: A:0.31, C:0.24, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTTCTCTCAAATCCATATTAAATCTC
Found at i:20471260 original size:40 final size:40
Alignment explanation
Indices: 20471190--20471267 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
20471180 TTCAAATTGC
* *
20471190 TCTCAATTTCCTTTCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTCCTCTCAAATTTCTATCAAATCCATATTTAA
* * *
20471230 TCTCAATTTGCTCTC-AATTTCCTATTAAATCCCTATTT
1 TCTCAATTTCCTCTCAAATTT-CTATCAAATCCATATTT
20471268 TTAATTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 5 0.16
40 27 0.84
ACGTcount: A:0.27, C:0.26, G:0.01, T:0.46
Consensus pattern (40 bp):
TCTCAATTTCCTCTCAAATTTCTATCAAATCCATATTTAA
Found at i:20473278 original size:24 final size:24
Alignment explanation
Indices: 20473239--20473295 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
20473229 TTCCTTTTAC
* * *
20473239 CAAACACCATCACCGTATGG-GTTT
1 CAAACACCTTCACCGT-TGGTGATG
*
20473263 CAAACACCTTCGCCGTTGGTGATG
1 CAAACACCTTCACCGTTGGTGATG
20473287 CAAACACCT
1 CAAACACCT
20473296 CCACATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.23
Consensus pattern (24 bp):
CAAACACCTTCACCGTTGGTGATG
Found at i:20476290 original size:7 final size:7
Alignment explanation
Indices: 20476278--20476306 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
20476268 AAAACCCTAA
20476278 AAACCCT
1 AAACCCT
20476285 AAACCCT
1 AAACCCT
20476292 AAACCCT
1 AAACCCT
20476299 -AACCCT
1 AAACCCT
20476305 AA
1 AA
20476307 TCCTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:20487523 original size:93 final size:91
Alignment explanation
Indices: 20487358--20487546 Score: 236
Period size: 93 Copynumber: 2.1 Consensus size: 91
20487348 TGAAATTGAG
* ** * *
20487358 TTTCATATGATAATGGCTTCTTGCTTTCTTCCCCATGTTTATTTTCTTCTTATTTATACTGATGT
1 TTTCATATGATAACGGCTTCTTGCTTTCTTCCCCATCATTATTTGCTTCTTATCTATACTGATGT
* * *
20487423 TTGATAGTTAATTTTTTTTTTGTAGATAT
66 TTAATAG-T--TGTTTCTTTTGTAGATAT
* ** *
20487452 TTTCATATGATAACGGC-TCTTGCTTTCTTCCCCCTCATTATTTGCTTCTTATCTATTTTGATTT
1 TTTCATATGATAACGGCTTCTTGCTTTCTTCCCCATCATTATTTGCTTCTTATCTATACTGATGT
20487516 TTAATAGTTGTTTCTTTTGTAGATAT
66 TTAATAGTTGTTTCTTTTGTAGATAT
20487542 TTTCA
1 TTTCA
20487547 CTTTAATCTA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
90 21 0.25
92 1 0.01
93 45 0.54
94 16 0.19
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (91 bp):
TTTCATATGATAACGGCTTCTTGCTTTCTTCCCCATCATTATTTGCTTCTTATCTATACTGATGT
TTAATAGTTGTTTCTTTTGTAGATAT
Done.