Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold520
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: 155767
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:2465 original size:382 final size:389
Alignment explanation
Indices: 1854--2629 Score: 1325
Period size: 382 Copynumber: 2.0 Consensus size: 389
1844 CAGTTATTTG
*
1854 AAGATGTGAAGCTTGCAAATTTGCCTGAAGAGATTATCACCTAAGAGAGAGGTGGATAAGATTGA
1 AAGATGTGAAGCTTGCAAATTTGCCTGAAGAGATTACCACCTAAGAGAGAGGTGGATAAGATTGA
* *
1919 TGTATCAAACTTTGCTAGTAAAAGAGTCTTGATGCAAGATGGGCAGACCGAGAGAGGGAATGCAT
66 TGCATCAAACTTTGCTAGTAAAAGAGTCCTGATGCAAGAT--GCAGA-CGAGAGAGGGAATGCAT
* *
1984 TATTAGAGTTGAGTACAACACAGCATGACTGGCTAAAGTTGTTGGATATGGCCCAATTTTCTTAC
128 TATTAGAGTTGAGTACAACACAGCATGACTGGCCAAAGTTGTTGGATATAGCCCAATTTTCTTAC
* *
2049 AACTTGCAATGAAGTTACACGAGACTAAATCCAGCAGCTTACAAGTTCCTAAGCCATGGGAGGAG
193 AACTTGCAACGAAGTTACACGAGACTAAATCCAGCAGCTTACAAGTTCCTAAGCCATGAGAGGAG
* *
2114 CAGACTGACTTAGCTAGGGTTTATTTACACAAGGCAGGAAAGCGCACGAAGAA-TTAGGTAGATC
258 CAGACTGACTTAGCTAGGGTTTATTTACACAAGGCAGGAAAGCGCACGAAGAAGTGA-GCAGATC
*
2178 AGAAACATAGGGATGTATAGTTTCAGGTTGGAAACTTAGTCCTTGTTAAATTGCACTTGGTGTTA
322 AGAAACATAGGGATGTATAGTTTCAGGTTGGAAACTTAGTCCTTATTAAATTGCACTTGGTGTTA
2243 TGC
387 TGC
* *
2246 AAGATGTGAAGCTTGCAAATTTGCCT-AAGAGATTGCCACTTAAGAGAGAGGTGGATAAGATTGA
1 AAGATGTGAAGCTTGCAAATTTGCCTGAAGAGATTACCACCTAAGAGAGAGGTGGATAAGATTGA
2310 TGCATCAAACTTTGCTAGTAAAAGAGTCCTGATGC-AGAT-C-GA-GA-A-AGGGAATGCATTAT
66 TGCATCAAACTTTGCTAGTAAAAGAGTCCTGATGCAAGATGCAGACGAGAGAGGGAATGCATTAT
2369 TAGAGTTGAGTACAACACAGCATGACTGGCCAAAGTTGTTGGATATAGCCCAATTTTCTTACAAC
131 TAGAGTTGAGTACAACACAGCATGACTGGCCAAAGTTGTTGGATATAGCCCAATTTTCTTACAAC
2434 TTGCAACGAAGTTACACGAGACTAAATCCAGCAGCTTACAAGTTCCTAAGCCATGAGAGGAGCAG
196 TTGCAACGAAGTTACACGAGACTAAATCCAGCAGCTTACAAGTTCCTAAGCCATGAGAGGAGCAG
* *
2499 ACTGACTTAGCTAGGGTTTATTTACACAAGGTAGGAAAGCGCACGAAGAAGTGAGCAGTTCAGAA
261 ACTGACTTAGCTAGGGTTTATTTACACAAGGCAGGAAAGCGCACGAAGAAGTGAGCAGATCAGAA
*
2564 ACATAGGGATGTATAGTTTCAGGTTGGAAACTTAGTCCTTATTAAATTGTACTTGGTGTTATGC
326 ACATAGGGATGTATAGTTTCAGGTTGGAAACTTAGTCCTTATTAAATTGCACTTGGTGTTATGC
2628 AA
1 AA
2630 CCTATGCATG
Statistics
Matches: 368, Mismatches: 15, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
382 262 0.71
383 3 0.01
384 2 0.01
386 2 0.01
387 1 0.00
390 4 0.01
391 68 0.18
392 26 0.07
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (389 bp):
AAGATGTGAAGCTTGCAAATTTGCCTGAAGAGATTACCACCTAAGAGAGAGGTGGATAAGATTGA
TGCATCAAACTTTGCTAGTAAAAGAGTCCTGATGCAAGATGCAGACGAGAGAGGGAATGCATTAT
TAGAGTTGAGTACAACACAGCATGACTGGCCAAAGTTGTTGGATATAGCCCAATTTTCTTACAAC
TTGCAACGAAGTTACACGAGACTAAATCCAGCAGCTTACAAGTTCCTAAGCCATGAGAGGAGCAG
ACTGACTTAGCTAGGGTTTATTTACACAAGGCAGGAAAGCGCACGAAGAAGTGAGCAGATCAGAA
ACATAGGGATGTATAGTTTCAGGTTGGAAACTTAGTCCTTATTAAATTGCACTTGGTGTTATGC
Found at i:3650 original size:600 final size:600
Alignment explanation
Indices: 2510--3709 Score: 2319
Period size: 600 Copynumber: 2.0 Consensus size: 600
2500 CTGACTTAGC
2510 TAGGGTTTATTTACACAAGGTAGGAAAGCGCACGAAGAAGTGAGCAGTTCAGAAACATAGGGATG
1 TAGGGTTTATTTACACAAGGTAGGAAAGCGCACGAAGAAGTGAGCAGTTCAGAAACATAGGGATG
**
2575 TATAGTTTCAGGTTGGAAACTTAGTCCTTATTAAATTGTACTTGGTGTTATGCAACCTATGCATG
66 TATAGTTTCAGGTTGGAAACTTAGTCCTTATTAAATTAAACTTGGTGTTATGCAACCTATGCATG
2640 CACAAAGGGCTTGTGCGAAAATATGAAGGCCCTAAAGCTCAAGATACATCCCGTTTTTCATGTCA
131 CACAAAGGGCTTGTGCGAAAATATGAAGGCCCTAAAGCTCAAGATACATCCCGTTTTTCATGTCA
2705 CTATGCTTAAGCCATTCCATGAGGATCAAGAGGATCTAGACCGAGGCAAGTCACAACGTGCACCG
196 CTATGCTTAAGCCATTCCATGAGGATCAAGAGGATCTAGACCGAGGCAAGTCACAACGTGCACCG
2770 GTAGGAGTGAAGGCCTCCTACGACAAAGAGGTATAATGTATTCTTGTAGATTGAGTGGTACGACA
261 GTAGGAGTGAAGGCCTCCTACGACAAAGAGGTATAATGTATTCTTGTAGATTGAGTGGTACGACA
2835 AAGAGGTCATAGGCCAAGGCTTGAGTACTTTGTCCGATGGAAAGGACTACCCAACAGTGAGACGA
326 AAGAGGTCATAGGCCAAGGCTTGAGTACTTTGTCCGATGGAAAGGACTACCCAACAGTGAGACGA
*
2900 GTTGGGAGCCAGCTGAGGCATTATGGCAGTTCCAAGATAAGATCAAGCAGTTCCATTTAGAGGAT
391 GTTGGGAGCCAGCTGAGGCATTATGACAGTTCCAAGATAAGATCAAGCAGTTCCATTTAGAGGAT
2965 GCGATGAGGGCATCGCTGAAATAGGTGGGGGAGAATGTCACGAGCCACAAATTAACCTAGGCCCA
456 GCGATGAGGGCATCGCTGAAATAGGTGGGGGAGAATGTCACGAGCCACAAATTAACCTAGGCCCA
*
3030 ATGACCCAAATTACATGAAGTATTTGGCTCACCAAAATAATTCCAATACTTAGAGGATTCTAGAA
521 ATGACCCAAATTACATGAAGTATTTGGCTCACCAAAATAAGTCCAATACTTAGAGGATTCTAGAA
*
3095 AACCCAGTTTACTTA
586 AACCCAATTTACTTA
3110 TAGGGTTTATTTACACAAGGTAGGAAAGCGCACGAAGAAGTGAGCAGTTCAGAAACATAGGGATG
1 TAGGGTTTATTTACACAAGGTAGGAAAGCGCACGAAGAAGTGAGCAGTTCAGAAACATAGGGATG
*
3175 TATAGTTTCGGGTTGGAAACTTAGTCCTTATTAAATTAAACTTGGTGTTATGCAACCTATGCATG
66 TATAGTTTCAGGTTGGAAACTTAGTCCTTATTAAATTAAACTTGGTGTTATGCAACCTATGCATG
*
3240 CACAAAGGGCTTGTGTGAAAATATGAAGGCCCTAAAGCTCAAGATACATCCCGTTTTTCATGTCA
131 CACAAAGGGCTTGTGCGAAAATATGAAGGCCCTAAAGCTCAAGATACATCCCGTTTTTCATGTCA
3305 CTATGCTTAAGCCATTCCATGAGGATCAAGAGGATCTAGACCGAGGCAAGTCACAACGTGCACCG
196 CTATGCTTAAGCCATTCCATGAGGATCAAGAGGATCTAGACCGAGGCAAGTCACAACGTGCACCG
*
3370 GTAGGAGTGAAGGCCTCTTACGACAAAGAGGTATAATGTATTCTTGTAGATTGAGTGGTACGACA
261 GTAGGAGTGAAGGCCTCCTACGACAAAGAGGTATAATGTATTCTTGTAGATTGAGTGGTACGACA
3435 AAGAGGTCATAGGCCAAGGCTTGAGTACTTTGTCCGATGGAAAGGACTACCCAACAGTGAGACGA
326 AAGAGGTCATAGGCCAAGGCTTGAGTACTTTGTCCGATGGAAAGGACTACCCAACAGTGAGACGA
3500 GTTGGGAGCCAGCTGAGGCATTATGACAGTTCCAAGATAAGATCAAGCAGTTCCATTTAGAGGAT
391 GTTGGGAGCCAGCTGAGGCATTATGACAGTTCCAAGATAAGATCAAGCAGTTCCATTTAGAGGAT
*
3565 GCGATGAGGGCGTCGCTGAAATAGGTGGGGGAGAATGTCACGAGCCACAAATTAACCTAGGCCCA
456 GCGATGAGGGCATCGCTGAAATAGGTGGGGGAGAATGTCACGAGCCACAAATTAACCTAGGCCCA
3630 ATGACCCAAATTACATGAAGTATTTGGCTCACCAAAATAAGTCCAATACTTAGAGGATTCTAGAA
521 ATGACCCAAATTACATGAAGTATTTGGCTCACCAAAATAAGTCCAATACTTAGAGGATTCTAGAA
3695 AACCCAATTTACTTA
586 AACCCAATTTACTTA
3710 AAGTTTCTAA
Statistics
Matches: 591, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
600 591 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (600 bp):
TAGGGTTTATTTACACAAGGTAGGAAAGCGCACGAAGAAGTGAGCAGTTCAGAAACATAGGGATG
TATAGTTTCAGGTTGGAAACTTAGTCCTTATTAAATTAAACTTGGTGTTATGCAACCTATGCATG
CACAAAGGGCTTGTGCGAAAATATGAAGGCCCTAAAGCTCAAGATACATCCCGTTTTTCATGTCA
CTATGCTTAAGCCATTCCATGAGGATCAAGAGGATCTAGACCGAGGCAAGTCACAACGTGCACCG
GTAGGAGTGAAGGCCTCCTACGACAAAGAGGTATAATGTATTCTTGTAGATTGAGTGGTACGACA
AAGAGGTCATAGGCCAAGGCTTGAGTACTTTGTCCGATGGAAAGGACTACCCAACAGTGAGACGA
GTTGGGAGCCAGCTGAGGCATTATGACAGTTCCAAGATAAGATCAAGCAGTTCCATTTAGAGGAT
GCGATGAGGGCATCGCTGAAATAGGTGGGGGAGAATGTCACGAGCCACAAATTAACCTAGGCCCA
ATGACCCAAATTACATGAAGTATTTGGCTCACCAAAATAAGTCCAATACTTAGAGGATTCTAGAA
AACCCAATTTACTTA
Found at i:4854 original size:33 final size:33
Alignment explanation
Indices: 4784--4858 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 33
4774 AATTTGAAAC
* *
4784 ATAAATTTTTTTAATTTAAATTATTATTTAATA
1 ATAAATATTTTTAATTTAAATTATTATTAAATA
4817 ATAAAATATTTTT-ATTTAAATTTAATTA-TAAAT-
1 AT-AAATATTTTTAATTTAAA-TT-ATTATTAAATA
4850 ATAAATATT
1 ATAAATATT
4859 AATATTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
32 7 0.19
33 11 0.30
34 15 0.41
35 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
ATAAATATTTTTAATTTAAATTATTATTAAATA
Found at i:4871 original size:18 final size:18
Alignment explanation
Indices: 4833--4878 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
4823 TATTTTTATT
4833 TAAATTTAATTATAAATA
1 TAAATTTAATTATAAATA
4851 TAAATATTAA-TATTAAA-A
1 TAAAT-TTAATTA-TAAATA
4869 T-AATTTAATT
1 TAAATTTAATT
4879 TAATTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.16
17 4 0.16
18 9 0.36
19 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAATTTAATTATAAATA
Found at i:5110 original size:2 final size:2
Alignment explanation
Indices: 5103--5141 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5093 TTAATAGACA
5103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5142 GTTTGGTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7689 original size:13 final size:13
Alignment explanation
Indices: 7671--7700 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
7661 TCTACCAAAC
7671 ATAATATATATAT
1 ATAATATATATAT
7684 ATAATATATATAT
1 ATAATATATATAT
7697 ATAA
1 ATAA
7701 ACTTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:9890 original size:2 final size:2
Alignment explanation
Indices: 9883--9917 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9873 TAAATTGGAA
9883 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9918 AACACTTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15153 original size:24 final size:25
Alignment explanation
Indices: 15126--15174 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
15116 ACAAGTAAAA
*
15126 TTAATAAATT-ATTATATATATTTT
1 TTAAAAAATTAATTATATATATTTT
* *
15150 TTAAAAAATTAATTTTTTATATTTT
1 TTAAAAAATTAATTATATATATTTT
15175 AAAAATATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAAAAAATTAATTATATATATTTT
Found at i:15697 original size:15 final size:16
Alignment explanation
Indices: 15676--15716 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
15666 TATGTAGTAA
15676 CAAAAATATTAA-AAT
1 CAAAAATATTAAGAAT
*
15691 TAAAAAT-TTAAGAAT
1 CAAAAATATTAAGAAT
15706 CAATAAATATT
1 CAA-AAATATT
15717 TATGTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 4 0.19
15 11 0.52
16 4 0.19
17 2 0.10
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (16 bp):
CAAAAATATTAAGAAT
Found at i:15885 original size:2 final size:2
Alignment explanation
Indices: 15878--15920 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
15868 TAAGTAGTAC
* * *
15878 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15920 T
1 T
15921 CTTCAAAAGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16617 original size:48 final size:48
Alignment explanation
Indices: 16546--16645 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
16536 TTCCTGTGTT
16546 TCTGAAATGGGACTCAAGATACAGGTACAATTTCACTATTTATATGCC
1 TCTGAAATGGGACTCAAGATACAGGTACAATTTCACTATTTATATGCC
16594 TCTGAAATGGGACTCAAGATACAGGTACAATTTCACTATTTATATGCC
1 TCTGAAATGGGACTCAAGATACAGGTACAATTTCACTATTTATATGCC
16642 TCTG
1 TCTG
16646 CAAGTCCCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (48 bp):
TCTGAAATGGGACTCAAGATACAGGTACAATTTCACTATTTATATGCC
Found at i:21600 original size:17 final size:17
Alignment explanation
Indices: 21570--21629 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
21560 TTTAAATTAA
*
21570 TAAATTTAAGATTAAAAT
1 TAAA-TTAATATTAAAAT
21588 TAAATTAATATTATAAAT
1 TAAATTAATATTA-AAAT
* *
21606 TATATAAAATATT-AAA-
1 TAAAT-TAATATTAAAAT
21622 TAAATTAA
1 TAAATTAA
21630 AAAATTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 2 0.06
16 4 0.11
17 11 0.31
18 12 0.34
19 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTAATATTAAAAT
Found at i:21626 original size:21 final size:20
Alignment explanation
Indices: 21600--21674 Score: 77
Period size: 21 Copynumber: 3.9 Consensus size: 20
21590 AATTAATATT
*
21600 ATAAATTATATAAAATATTAA
1 ATAAATAATATAAAA-ATTAA
*
21621 ATAAAT--TA-AAAAATTAT
1 ATAAATAATATAAAAATTAA
*
21638 ATATATAATATAAAAAATTAA
1 ATAAATAATAT-AAAAATTAA
21659 A-AAATAATATAAAAAT
1 ATAAATAATATAAAAAT
21675 AATTTATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
17 9 0.20
18 4 0.09
19 10 0.22
20 8 0.17
21 15 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATAATATAAAAATTAA
Found at i:21648 original size:31 final size:27
Alignment explanation
Indices: 21602--21676 Score: 98
Period size: 29 Copynumber: 2.7 Consensus size: 27
21592 TTAATATTAT
21602 AAATTATATAAAATATTAAATAAATTAAA
1 AAATTATATAAAATA-TAAA-AAATTAAA
21631 AAATTATATATATAATATAAAAAATTAAA
1 AAATTATATA-A-AATATAAAAAATTAAA
*
21660 AAATAATATAAAA-ATAA
1 AAATTATATAAAATATAA
21677 TTTATATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
26 4 0.09
27 2 0.05
28 1 0.02
29 27 0.63
30 5 0.12
31 4 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AAATTATATAAAATATAAAAAATTAAA
Found at i:21653 original size:22 final size:22
Alignment explanation
Indices: 21628--21693 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
21618 TAAATAAATT
21628 AAAAAATTATATATATAATAT-
1 AAAAAATTATATATATAATATA
* *
21649 AAAAAATTA-AAAAATAATATA
1 AAAAAATTATATATATAATATA
21670 AAAATAATT-TATATATAATATA
1 AAAA-AATTATATATATAATATA
21692 AA
1 AA
21694 TATATAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 9 0.24
21 13 0.34
22 16 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAAATTATATATATAATATA
Found at i:21665 original size:20 final size:20
Alignment explanation
Indices: 21602--21673 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
21592 TTAATATTAT
* *
21602 AAATTATATAAAATATT-AA
1 AAATAATATAAAAAATTAAA
* *
21621 ATA-AAT-TAAAAAATTATAT
1 AAATAATATAAAAAATTA-AA
*
21640 ATATAATATAAAAAATTAAA
1 AAATAATATAAAAAATTAAA
21660 AAATAATATAAAAA
1 AAATAATATAAAAA
21674 TAATTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
17 8 0.19
18 2 0.05
19 6 0.14
20 17 0.40
21 10 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATATAAAAAATTAAA
Found at i:21673 original size:40 final size:39
Alignment explanation
Indices: 21584--21693 Score: 109
Period size: 38 Copynumber: 2.8 Consensus size: 39
21574 TTTAAGATTA
* * * *
21584 AAATTAAATTAATAT-TATAAATTATATAAAATATTAAAT
1 AAATTAAA-AAATATATATATATAATATAAAAAATTAAAT
21623 AAATTAAAAAAT-TATATATATAATATAAAAAATTAAA-
1 AAATTAAAAAATATATATATATAATATAAAAAATTAAAT
*
21660 AAATAATATAAAAATAATTTATATATAATATAAA
1 AAAT--TA-AAAAAT-ATATATATATAATATAAA
21694 TATATAAATT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
37 5 0.08
38 23 0.38
39 10 0.17
40 6 0.10
42 16 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (39 bp):
AAATTAAAAAATATATATATATAATATAAAAAATTAAAT
Found at i:21677 original size:31 final size:30
Alignment explanation
Indices: 21585--21678 Score: 88
Period size: 29 Copynumber: 3.1 Consensus size: 30
21575 TTAAGATTAA
* *
21585 AATTAAATTAATATTATAAATTATAT-AAAAT
1 AATTAAA-TAA-ATTAAAAAATATATAAAAAT
* *
21616 -ATTAAATAAATTAAAAAAT-TATATATAT
1 AATTAAATAAATTAAAAAATATATAAAAAT
21644 AATATAAA-AAATTAAAAAATAATATAAAAAT
1 AAT-TAAATAAATTAAAAAAT-ATATAAAAAT
21675 AATT
1 AATT
21679 TATATATAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.06
28 11 0.21
29 17 0.33
30 11 0.21
31 10 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
AATTAAATAAATTAAAAAATATATAAAAAT
Found at i:21682 original size:13 final size:11
Alignment explanation
Indices: 21642--21693 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
21632 AATTATATAT
21642 ATAATATAAAA
1 ATAATATAAAA
*
21653 A-ATTA-AAAA
1 ATAATATAAAA
21662 ATAATATAAAA
1 ATAATATAAAA
* * *
21673 ATAATTTATAT
1 ATAATATAAAA
21684 ATAATATAAA
1 ATAATATAAA
21694 TATATAAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 5 0.16
10 6 0.19
11 21 0.66
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:21696 original size:11 final size:11
Alignment explanation
Indices: 21635--21697 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
21625 ATTAAAAAAT
*
21635 TATATATATAA
1 TATAAATATAA
21646 TATAAA-A-AA
1 TATAAATATAA
*
21655 T-TAAAAAATAA
1 TAT-AAATATAA
*
21666 TATAAAAATAA
1 TATAAATATAA
* *
21677 TTTATATATAA
1 TATAAATATAA
21688 TATAAATATA
1 TATAAATATA
21698 TAAATTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
8 1 0.02
9 6 0.14
10 2 0.05
11 32 0.76
12 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAAATATAA
Found at i:21720 original size:24 final size:24
Alignment explanation
Indices: 21675--21745 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
21665 ATATAAAAAT
* * *
21675 AATTTATATATAATATAAATATATA
1 AATTTAT-TAAAATTTATATATATA
21700 AATTTATTAAAATTTATATATA-A
1 AATTTATTAAAATTTATATATATA
*
21723 AAATTATTATAAATTT-TA-ATATA
1 AATTTATTA-AAATTTATATATATA
21746 GTAATACGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 3 0.08
23 12 0.30
24 18 0.45
25 7 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTTATTAAAATTTATATATATA
Found at i:22293 original size:2 final size:2
Alignment explanation
Indices: 22286--22311 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22276 TCAAAATTTA
22286 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
22312 TGTTTAAGCT
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:22579 original size:39 final size:40
Alignment explanation
Indices: 22532--22612 Score: 121
Period size: 39 Copynumber: 2.0 Consensus size: 40
22522 TATTATTTTA
* *
22532 AAAATATTTTTATATTAATATATAA-AA-TTAAATTTAAAT
1 AAAATATTTTTAT-TTAATAAATAATAATTTAAATTAAAAT
22571 AAAATATTTTTATTTAATAAATAATAATTTAAATTAAAAT
1 AAAATATTTTTATTTAATAAATAATAATTTAAATTAAAAT
22611 AA
1 AA
22613 TTTTAATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 10 0.26
39 15 0.39
40 13 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (40 bp):
AAAATATTTTTATTTAATAAATAATAATTTAAATTAAAAT
Found at i:22591 original size:18 final size:18
Alignment explanation
Indices: 22532--22591 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 18
22522 TATTATTTTA
22532 AAAATATTTTTATATTAAT
1 AAAATATTTTTAT-TTAAT
* **
22551 ATATAA-AATTAAATTTAAAT
1 A-A-AATATTTTTATTT-AAT
22571 AAAATATTTTTATTTAAT
1 AAAATATTTTTATTTAAT
22589 AAA
1 AAA
22592 TAATAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
18 8 0.26
19 11 0.35
20 10 0.32
21 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATATTTTTATTTAAT
Found at i:23138 original size:32 final size:30
Alignment explanation
Indices: 23077--23180 Score: 88
Period size: 32 Copynumber: 3.4 Consensus size: 30
23067 TTTTTTTAAC
** *
23077 AAATTTAAATATTAAAAAATTATATAATTTAT
1 AAATTTAAATATT-AAATTTTATAGAATTT-T
23109 AAATTTAAATATTAAATTTTATACGAATTTT
1 AAATTTAAATATTAAATTTTATA-GAATTTT
*
23140 AGATATTTAAAT-TTAAATTTATTTA-AATTTT
1 A-A-ATTTAAATATTAAATTT-TATAGAATTTT
*
23171 -TATTTAAATA
1 AAATTTAAATA
23181 ATGTTAAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
28 8 0.13
31 16 0.26
32 27 0.44
33 11 0.18
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (30 bp):
AAATTTAAATATTAAATTTTATAGAATTTT
Found at i:23304 original size:17 final size:17
Alignment explanation
Indices: 23284--23319 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
23274 TAAAAATTTA
*
23284 ATTTAATTAATTTAAAT
1 ATTTAATAAATTTAAAT
23301 ATTTAATAAATTTAAAT
1 ATTTAATAAATTTAAAT
23318 AT
1 AT
23320 CTAACTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATAAATTTAAAT
Found at i:23315 original size:22 final size:22
Alignment explanation
Indices: 23272--23312 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
23262 ATTTTTATTT
*
23272 TTTAAAAATTTAATTTAATTAA
1 TTTAAAAATTTAATTAAATTAA
*
23294 TTTAAATATTTAA-TAAATT
1 TTTAAAAATTTAATTAAATT
23313 TAAATATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAAAAATTTAATTAAATTAA
Found at i:23371 original size:14 final size:13
Alignment explanation
Indices: 23348--23381 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
23338 TAAATTACAT
23348 ATAAATTTAAATA
1 ATAAATTTAAATA
23361 ATAATATTTAAATA
1 ATAA-ATTTAAATA
*
23375 AAAAATT
1 ATAAATT
23382 AATATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAATTTAAATA
Found at i:23407 original size:27 final size:27
Alignment explanation
Indices: 23377--23429 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
23367 TTTAAATAAA
* *
23377 AAATTA-ATATAAATAATTTTAGATTTT
1 AAATTATAT-TAAATAAATTTAAATTTT
23404 AAATTATATTAAATAAATTTAAATTT
1 AAATTATATTAAATAAATTTAAATTT
23430 AAAAAAATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
AAATTATATTAAATAAATTTAAATTTT
Found at i:23807 original size:11 final size:11
Alignment explanation
Indices: 23786--23815 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
23776 ATAATTTTTT
23786 AAAAT-AATTA
1 AAAATAAATTA
23796 AAAATAAATTA
1 AAAATAAATTA
23807 AAAATAAAT
1 AAAATAAAT
23816 ATATTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATAAATTA
Found at i:24064 original size:2 final size:2
Alignment explanation
Indices: 24057--24086 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24047 GCATCTTGTC
24057 AT AT 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 AT AT
24087 CAATTACTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24163 original size:14 final size:14
Alignment explanation
Indices: 24122--24162 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
24112 AATTTAAATA
24122 AAAATAATAAATTTT
1 AAAA-AATAAATTTT
*
24137 -AAGAATAAATTTT
1 AAAAAATAAATTTT
24150 AAAAAAT-AATTTT
1 AAAAAATAAATTTT
24163 TTATACGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
AAAAAATAAATTTT
Found at i:24382 original size:16 final size:16
Alignment explanation
Indices: 24362--24420 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
24352 AAATATTAAA
24362 AATATATTAAATTATT
1 AATATATTAAATTATT
* * * *
24378 TATATTTTAAAAATAATA
1 AATATATT--AAATTATT
24396 AATATATTAAATTATT
1 AATATATTAAATTATT
24412 AAT-TATTAA
1 AATATATTAA
24421 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
15 6 0.18
16 15 0.45
18 12 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATATTAAATTATT
Found at i:24397 original size:43 final size:43
Alignment explanation
Indices: 24349--24440 Score: 109
Period size: 43 Copynumber: 2.1 Consensus size: 43
24339 AATATTGTTG
*
24349 TATAAATAT-TAAAAATATATTAAATTATTTA-TATTTTAAAAATA
1 TATAAATATAT-AAAAT-TATT-AATTATTAATTATTTTAAAAATA
* *
24393 -ATAAATATATTAAATTATTAATTATTAATTTTTTTAAAAATA
1 TATAAATATATAAAATTATTAATTATTAATTATTTTAAAAATA
24435 TATAAA
1 TATAAA
24441 GTAATGTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
41 8 0.19
42 16 0.38
43 17 0.40
44 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (43 bp):
TATAAATATATAAAATTATTAATTATTAATTATTTTAAAAATA
Found at i:25760 original size:20 final size:20
Alignment explanation
Indices: 25731--25780 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 20
25721 AAATTTTAAA
25731 AATA-TATTTATTTATACAT
1 AATATTATTTATTTATACAT
*
25750 AATATTATTTA--TATTCAT
1 AATATTATTTATTTATACAT
25768 -ATATT-TTTATTTA
1 AATATTATTTATTTA
25781 AGATATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 4 0.15
17 5 0.19
18 8 0.30
19 4 0.15
20 6 0.22
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTATTTATTTATACAT
Found at i:25874 original size:2 final size:2
Alignment explanation
Indices: 25869--25899 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25859 ACACACACAC
25869 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
25900 AAATACTCAA
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:30531 original size:15 final size:15
Alignment explanation
Indices: 30501--30539 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
30491 GGTTACTTAG
*
30501 GAAAATAAAAAAAAAA
1 GAAAA-AAAAAGAAAA
*
30517 GAAAAGAAAAGAAAA
1 GAAAAAAAAAGAAAA
30532 GAAAAAAA
1 GAAAAAAA
30540 GTTACTAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
GAAAAAAAAAGAAAA
Found at i:30747 original size:34 final size:34
Alignment explanation
Indices: 30705--30821 Score: 216
Period size: 34 Copynumber: 3.4 Consensus size: 34
30695 GTGAAACATA
30705 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
*
30739 TTAAGTGTGTTAGGTGATGTATTTGGTGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
*
30773 TTAGGTGTGTTAGGTGATGCATTTGGTGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
30807 TTAGGTGTGTTAGGT
1 TTAGGTGTGTTAGGT
30822 AATATGTTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 80 1.00
ACGTcount: A:0.21, C:0.01, G:0.38, T:0.41
Consensus pattern (34 bp):
TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
Found at i:35524 original size:34 final size:34
Alignment explanation
Indices: 35486--35568 Score: 166
Period size: 34 Copynumber: 2.4 Consensus size: 34
35476 GTGAAGTATA
35486 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
35520 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
1 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
35554 TTAGGTGTGTTAGGT
1 TTAGGTGTGTTAGGT
35569 AATATGTTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.19, C:0.00, G:0.39, T:0.42
Consensus pattern (34 bp):
TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
Found at i:35582 original size:34 final size:34
Alignment explanation
Indices: 35472--35582 Score: 150
Period size: 34 Copynumber: 3.2 Consensus size: 34
35462 GTTAAGTGTG
* *
35472 TTAGGTGAAGTATATTAGGTGTGTTAGGTGATGTA
1 TTAGGTG-AGAATGTTAGGTGTGTTAGGTGATGTA
*
35507 TTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTA
1 TTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTA
* * * *
35541 TTTGGTGAGAATGTTAGGTGTGTTAGGTAATATG
1 TTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTA
35575 TTAGGTGA
1 TTAGGTGA
35583 ATAAGATATT
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
34 63 0.91
35 6 0.09
ACGTcount: A:0.23, C:0.00, G:0.36, T:0.41
Consensus pattern (34 bp):
TTAGGTGAGAATGTTAGGTGTGTTAGGTGATGTA
Found at i:37809 original size:20 final size:20
Alignment explanation
Indices: 37784--37832 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
37774 TAATTTAATT
37784 AAAATAATTTTGAATACTAA
1 AAAATAATTTTGAATACTAA
* **
37804 AAAAT-ATTTTTAATGTTAA
1 AAAATAATTTTGAATACTAA
37823 ATAAATAATT
1 A-AAATAATT
37833 AATAAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.50
20 9 0.38
21 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (20 bp):
AAAATAATTTTGAATACTAA
Found at i:38537 original size:15 final size:15
Alignment explanation
Indices: 38519--38550 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38509 TCGCATCTCA
*
38519 TTTTAAAAAATTATT
1 TTTTAAAAAATAATT
38534 TTTTAAAAAATAATT
1 TTTTAAAAAATAATT
38549 TT
1 TT
38551 AAATCAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAAAAAATAATT
Found at i:41284 original size:17 final size:17
Alignment explanation
Indices: 41232--41286 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
41222 ACGAATATCT
41232 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
41248 T-AAA-TTAT-TAACATA
1 TAAAATTTATATAA-ATA
41263 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
41281 TAAAAT
1 TAAAAT
41287 ACTTTAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 6 0.18
16 2 0.06
17 9 0.27
18 7 0.21
19 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:44785 original size:2 final size:2
Alignment explanation
Indices: 44778--44807 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44768 TTCATTTTAG
44778 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
44808 TGCTTACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:46583 original size:26 final size:28
Alignment explanation
Indices: 46554--46611 Score: 84
Period size: 26 Copynumber: 2.1 Consensus size: 28
46544 CTTATGTTTT
*
46554 AAATCATATTATTATTATCAA-T-AATA
1 AAATCATATTATTAGTATCAATTGAATA
*
46580 AAATCATATTATTAGTATTAATTGAATA
1 AAATCATATTATTAGTATCAATTGAATA
46608 AAAT
1 AAAT
46612 TCAAACCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 19 0.68
27 1 0.04
28 8 0.29
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (28 bp):
AAATCATATTATTAGTATCAATTGAATA
Found at i:46752 original size:24 final size:23
Alignment explanation
Indices: 46709--46754 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
46699 GAGTTAAGTG
*
46709 TAAAATAAATTTTAATTTTAATT
1 TAAAATAAATTTAAATTTTAATT
46732 TAAAA-AAATTATAAATATTTAAT
1 TAAAATAAATT-TAAAT-TTTAAT
46755 GCCTTACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAATAAATTTAAATTTTAATT
Found at i:47082 original size:25 final size:24
Alignment explanation
Indices: 47045--47092 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
47035 TTCATAAATA
47045 TTTTTAAATATAATTACAAGAATAAT
1 TTTTTAAATATAATTA-AA-AATAAT
47071 TTTTTAAA-ATAATTAAAAATAA
1 TTTTTAAATATAATTAAAAATAA
47093 ATTAAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.23
24 2 0.09
25 7 0.32
26 8 0.36
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
TTTTTAAATATAATTAAAAATAAT
Found at i:47462 original size:15 final size:14
Alignment explanation
Indices: 47431--47461 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
47421 AAATATTAAA
47431 TTTAAAAAATAATT
1 TTTAAAAAATAATT
47445 TTTAAAAAATAATT
1 TTTAAAAAATAATT
47459 TTT
1 TTT
47462 TTACACGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAAAAAATAATT
Found at i:47710 original size:43 final size:46
Alignment explanation
Indices: 47649--47738 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 46
47639 ATTATTGTAT
*
47649 AAATATTAAAAATATATTAAATTATTTA-TATTTTAAAAATA-ATAAA
1 AAATATT-AAAATATATT-AATTATTAATTATTTTAAAAATATATAAA
*
47695 AAATATT-AAAT-TATTAATTATTAATTTTTTTAAAAATATATAAA
1 AAATATTAAAATATATTAATTATTAATTATTTTAAAAATATATAAA
47739 GCAATGTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
42 8 0.20
43 16 0.40
44 9 0.22
46 7 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (46 bp):
AAATATTAAAATATATTAATTATTAATTATTTTAAAAATATATAAA
Found at i:47711 original size:27 final size:28
Alignment explanation
Indices: 47648--47711 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 28
47638 TATTATTGTA
* *
47648 TAAA-TATTAAAAATATATTAAATTATT
1 TAAATTATTAAAAATATATAAAAATATT
*
47675 TATATT-TTAAAAATA-ATAAAAA-ATAT
1 TAAATTATTAAAAATATATAAAAATAT-T
47701 TAAATTATTAA
1 TAAATTATTAA
47712 TTATTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
25 2 0.07
26 11 0.37
27 16 0.53
28 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAATTATTAAAAATATATAAAAATATT
Found at i:47984 original size:18 final size:17
Alignment explanation
Indices: 47963--48011 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
47953 TATTAATTAT
47963 AATTAAAATTTTAAAAGA
1 AATTAAAATTTTAAAA-A
* *
47981 AATTAAAATATATATAAA
1 AATTAAAAT-TTTAAAAA
*
47999 AATTAAATTTTTA
1 AATTAAAATTTTA
48012 CTAGTTCAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.69
19 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
AATTAAAATTTTAAAAA
Found at i:49236 original size:2 final size:2
Alignment explanation
Indices: 49229--49272 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
49219 AGCTAAATGC
49229 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
49271 AT
1 AT
49273 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53894 original size:22 final size:22
Alignment explanation
Indices: 53869--53931 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
53859 TTAATTTCTT
* * *
53869 TGTTAAGTGTATTTGGTGAGAA
1 TGTTAGGTGTGTTAGGTGAGAA
53891 TGTTAGGTGTGTTAGGTGAGAA
1 TGTTAGGTGTGTTAGGTGAGAA
53913 TGTTAGGTGTGTTAGGTGA
1 TGTTAGGTGTGTTAGGTGA
53932 TGTATTTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (22 bp):
TGTTAGGTGTGTTAGGTGAGAA
Found at i:58581 original size:22 final size:22
Alignment explanation
Indices: 58556--58618 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
58546 TTAATTTCTT
* * *
58556 TGTTAAGTGTATTTGGTGAGAA
1 TGTTAGGTGTGTTAGGTGAGAA
58578 TGTTAGGTGTGTTAGGTGAGAA
1 TGTTAGGTGTGTTAGGTGAGAA
58600 TGTTAGGTGTGTTAGGTGA
1 TGTTAGGTGTGTTAGGTGA
58619 TGTATTTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (22 bp):
TGTTAGGTGTGTTAGGTGAGAA
Found at i:61003 original size:20 final size:20
Alignment explanation
Indices: 60978--61026 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
60968 TAATTTAATT
60978 AAAATAATTTTGAATACTAA
1 AAAATAATTTTGAATACTAA
* **
60998 AAAAT-ATTTTTAATGTTAA
1 AAAATAATTTTGAATACTAA
61017 ATAAATAATT
1 A-AAATAATT
61027 AATAAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.50
20 9 0.38
21 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (20 bp):
AAAATAATTTTGAATACTAA
Found at i:71833 original size:51 final size:52
Alignment explanation
Indices: 71735--71833 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 52
71725 AAAGTAGTCA
* *
71735 TGATTCATGAATGGGAGAGGGGAGATGAATACATTTAATTTAATAATTAATG
1 TGATTCATGAATGGGAGAGAGGAGATGAATACATTTAATTAAATAATTAATG
* * *
71787 TGATTCATGTAT-GGAGAGAGGAGATGAGTGCATTTAA-TAAATTAATT
1 TGATTCATGAATGGGAGAGAGGAGATGAATACATTTAATTAAA-TAATT
71834 CGATTCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 3 0.07
51 27 0.66
52 11 0.27
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.33
Consensus pattern (52 bp):
TGATTCATGAATGGGAGAGAGGAGATGAATACATTTAATTAAATAATTAATG
Found at i:72586 original size:16 final size:17
Alignment explanation
Indices: 72567--72599 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
72557 TACCAAGTTA
*
72567 TTTTTATTTTA-ATAAT
1 TTTTTATGTTATATAAT
72583 TTTTTATGTTATATAAT
1 TTTTTATGTTATATAAT
72600 CATATAGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTTATGTTATATAAT
Found at i:79001 original size:22 final size:23
Alignment explanation
Indices: 78969--79024 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
78959 TGGACATGTT
*
78969 AAAAATACATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
78991 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
79014 AAAAATGCATG
1 AAAAATGCATG
79025 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 19 0.59
23 13 0.41
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:79982 original size:20 final size:20
Alignment explanation
Indices: 79935--80009 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
79925 AAAAAGACAT
*
79935 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
79954 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
79975 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
79995 AATGTATCGATACAT
1 AATGTATCGATACAT
80010 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:80003 original size:40 final size:39
Alignment explanation
Indices: 79932--80009 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
79922 GGTAAAAAGA
* *
79932 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
79971 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
80010 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:80626 original size:32 final size:32
Alignment explanation
Indices: 80583--81614 Score: 1042
Period size: 32 Copynumber: 33.6 Consensus size: 32
80573 GGTGCCACTA
80583 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* * *
80615 ACTCGTATGGGCTTTGAAAAGAG-TGCCACTG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
*
80646 AC-T-TGTGGGCTTTGAAAAGAG-TGCCACTG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* * *
80675 A-AT-TGTGGGCTTTG-AAAG-GGTGCCACTG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* * *
80703 AC-T-TGTGGGCTTTG-AAAG-GGTGACACTG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* * **
80731 A-TT-TGTAGGCTTTG-AAAG-GGTGCCACTA
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* *
80759 AC-T-TGTGGGCTTTG-AAAG-GGTGCCACTG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
*
80787 AC-T-TGTGGGCTTTGAAAAGAG-TGCCACTG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
80816 AC-T-TGTGGGCTTTGAAAAGAGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* * *
80846 ACTCGTGTGGGCTTTG-AAAG-GGTGCCACTG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
*
80876 AC-T-TGTGGGCTTTGAAAAGAG-TGCCACTG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* **
80905 AC-T-TGTGGGCTTTG-AAAG-GGTGCCACTA
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
*
80933 AC-T-TGTGGGCTTTGAAAAGAG-TGCCACTG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
*
80962 AC-T-TGTGGGCTTTGAAAAGAG-TGCCACCA
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
*
80991 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* * * *
81023 ACTTGTGTGGGCTTTCAAATGGGTTGCCACCA
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* *
81055 ACTTGTGTAGGCTTTGAAATGAGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* * * *
81087 ACTTGTGTGGGCTTTCAAATGGGTTGCCACCA
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* *
81119 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* * *
81151 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCA
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* *
81183 ACTTGTGTGGGCTTTGAAATGAGTTACCACCG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* *
81215 ACTTGTGTGGGCTTTCAAATAG-GTTGCCACCA
1 ACTTGTGTGGGCTTTGAAA-AGAGTTGCCACCG
* * *
81247 ACTTGTGTGGGCTTTGAAATGGGTTGCCACAG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* * *
81279 ACTTGTGTGGGCTTTGAAATGGGTTGCCACAG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* *
81311 ATTTGTGTGGGCTTTGAAATGAGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
*
81343 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* **
81375 ACTTGTGTGGGCTTTCAAATAG-GTTGCCACAT
1 ACTTGTGTGGGCTTTGAAA-AGAGTTGCCACCG
**
81407 ACTTGTGTGGGCTTTGAAATAG-GTTGCCACAA
1 ACTTGTGTGGGCTTTGAAA-AGAGTTGCCACCG
*
81439 ACTTGTGTGGGCTTTGAAATGAGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* **
81471 ACTTGTGTGGGCTTTCAAATAG-GTTGCCACAT
1 ACTTGTGTGGGCTTTGAAA-AGAGTTGCCACCG
* * *
81503 ACTTGTGTGGGCTTTGAAATGGGTTGCCACAG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* * *
81535 ACTTGTGTGGGCTTTGAAATGGGTTGCCACTG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
* * *
81567 ACTTGTGTGGGCTTTGAGAAG-GATGCCACTG
1 ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
81598 AC-T-TGTGGGCTTTGAAA
1 ACTTGTGTGGGCTTTGAAA
81615 GGTGCCACGG
Statistics
Matches: 904, Mismatches: 72, Indels: 51
0.88 0.07 0.05
Matches are distributed among these distances:
27 2 0.00
28 137 0.15
29 150 0.17
30 24 0.03
31 44 0.05
32 544 0.60
33 3 0.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (32 bp):
ACTTGTGTGGGCTTTGAAAAGAGTTGCCACCG
Found at i:81060 original size:64 final size:64
Alignment explanation
Indices: 80575--81614 Score: 1175
Period size: 64 Copynumber: 16.9 Consensus size: 64
80565 AAAAAAATGG
* * * * * *
80575 TGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTATGGGCTTTGAAAAGAG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
** * * *
80638 TGCCACTGAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGA-AT-TGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
** * * * *
80695 TGCCACTGAC-T-TGTGGGCTTTGAAA-G-GGTGACACTGA-TT-TGTAGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * * * *
80751 TGCCACTAAC-T-TGTGGGCTTTGAAA-G-GGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
** * *
80808 TGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
** * *
80868 TGCCACTGAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T-TGTGGGCTTTGAAA-GGG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * * * *
80925 TGCCACTAAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T-TGTGGGCTTTGAAAAGAG-
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
*
80983 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTCAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* *
81047 TGCCACCAACTTGTGTAGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTCAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
*
81111 TGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * *
81175 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTACCACCGACTTGTGTGGGCTTTCAAATAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* *
81239 TGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACAGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* *
81303 TGCCA-CAGATTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGAGT
1 TGCCACCA-ACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * ** *
81367 TGCCACCGACTTGTGTGGGCTTTCAAAT-AGGTTGCCACATACTTGTGTGGGCTTTGAAATAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGA-GTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* * *
81431 TGCCACAAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTCAAATAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
* *
81495 TGCCA-CATACTTGTGTGGGCTTTGAAATGGGTTGCCACAGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCA-ACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
** * *
81559 TGCCACTGACTTGTGTGGGCTTTGAGAA-G-GATGCCACTGAC-T-TGTGGGCTTTGAAA
1 TGCCACCAACTTGTGTGGGCTTTGA-AATGAGTTGCCACCGACTTGTGTGGGCTTTGAAA
81615 GGTGCCACGG
Statistics
Matches: 889, Mismatches: 67, Indels: 44
0.89 0.07 0.04
Matches are distributed among these distances:
55 1 0.00
56 75 0.08
57 123 0.14
58 25 0.03
59 20 0.02
60 56 0.06
61 55 0.06
62 3 0.00
63 38 0.04
64 489 0.55
65 4 0.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (64 bp):
TGCCACCAACTTGTGTGGGCTTTGAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGT
Found at i:81630 original size:27 final size:27
Alignment explanation
Indices: 81585--81997 Score: 523
Period size: 27 Copynumber: 15.1 Consensus size: 27
81575 GGGCTTTGAG
* * * *
81585 AAGGATGCCACTGACTTGTGGGCTTTGA
1 AAGG-TGCCACGGAGTTGTGGACTTTAA
81613 AAGGTGCCACGGAGTTGTGGAC-TTAA
1 AAGGTGCCACGGAGTTGTGGACTTTAA
*
81639 AAGGATGCCATGGAGTTGTGGA-TTTAA
1 AAGG-TGCCACGGAGTTGTGGACTTTAA
*
81666 GAGGGTGCCACGGAGTTGTGGACTTTAA
1 -AAGGTGCCACGGAGTTGTGGACTTTAA
* *
81694 AAGAGCGCTACGGAGTTGTGGAC-TTAA
1 AAG-GTGCCACGGAGTTGTGGACTTTAA
*
81721 AAGGGTGCCACGGAGTTGTGGACTTTGA
1 AA-GGTGCCACGGAGTTGTGGACTTTAA
*
81749 AAGGTGCCACAGAGTTGTGGAC-TTAA
1 AAGGTGCCACGGAGTTGTGGACTTTAA
81775 AAGGGTGCCACGGAGTTGTGGACTTTAA
1 AA-GGTGCCACGGAGTTGTGGACTTTAA
*
81803 AAGTGTGCCACGGAGTTGTGGACTTTAC
1 AAG-GTGCCACGGAGTTGTGGACTTTAA
*
81831 AAGTGTGCCACGGAGTTGTGGACTTTGA
1 AAG-GTGCCACGGAGTTGTGGACTTTAA
*
81859 AGGGTGCCACGGAGTTGTGGAC-TTAA
1 AAGGTGCCACGGAGTTGTGGACTTTAA
*
81885 AAGGGTGCTACGGAGTTGTGGACTTTAA
1 AA-GGTGCCACGGAGTTGTGGACTTTAA
*
81913 AAGAGTGCCACAGAGTTGTGGA-TTTAA
1 AAG-GTGCCACGGAGTTGTGGACTTTAA
*
81940 AAGGGTGCCACAGAGTTGTGGACTTTAA
1 AA-GGTGCCACGGAGTTGTGGACTTTAA
*
81968 AAGGATGCCACGGAGTTGTGGACTTCAA
1 AAGG-TGCCACGGAGTTGTGGACTTTAA
81996 AA
1 AA
81998 AGAAATGCCA
Statistics
Matches: 342, Mismatches: 27, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
26 16 0.05
27 181 0.53
28 145 0.42
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.25
Consensus pattern (27 bp):
AAGGTGCCACGGAGTTGTGGACTTTAA
Found at i:81715 original size:82 final size:82
Alignment explanation
Indices: 81585--81992 Score: 542
Period size: 82 Copynumber: 5.0 Consensus size: 82
81575 GGGCTTTGAG
* * * * *
81585 AAGGATGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACGGAGTTGTGGACTTAAAAGGATGCCA
1 AAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCA
*
81649 TGGAGTTGTGGA-TTTA
66 CGGAGTTGTGGACTTTA
* * * * *
81665 AGAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGCGCTACGGAGTTGTGGACTTAAAAGGGTGCC
1 A-AGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCC
81730 ACGGAGTTGTGGACTTTGA
65 ACGGAGTTGTGGACTTT-A
81749 AA-GGTGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGTG-TGC
1 AAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAG-GATGC
81811 CACGGAGTTGTGGACTTTA
64 CACGGAGTTGTGGACTTTA
* * * * *
81830 CAAGTGTGCCACGGAGTTGTGGACTTT-GAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCT
1 -AAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCC
81894 ACGGAGTTGTGGACTTTAA
65 ACGGAGTTGTGGACTTT-A
* *
81913 AAGAGTGCCACAGAGTTGTGGA-TTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGATGCC
1 AAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGATGCC
81977 ACGGAGTTGTGGACTT
65 ACGGAGTTGTGGACTT
81993 CAAAAAGAAA
Statistics
Matches: 291, Mismatches: 24, Indels: 23
0.86 0.07 0.07
Matches are distributed among these distances:
80 1 0.00
81 53 0.18
82 159 0.55
83 74 0.25
84 4 0.01
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.26
Consensus pattern (82 bp):
AAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCA
CGGAGTTGTGGACTTTA
Found at i:81726 original size:55 final size:55
Alignment explanation
Indices: 81615--81997 Score: 551
Period size: 55 Copynumber: 7.0 Consensus size: 55
81605 GGCTTTGAAA
* * *
81615 GGTGCCACGGAGTTGTGGAC-TTAAAAG-GATGCCATGGAGTTGTGGATTTAAGAG
1 GGTGCCACGGAGTTGTGGACTTTAAAAGAG-TGCCACGGAGTTGTGGACTTAAAAG
* *
81669 GGTGCCACGGAGTTGTGGACTTTAAAAGAGCGCTACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAG
* *
81724 GGTGCCACGGAGTTGTGGACTTTGAAAG-GTGCCACAGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAG
* *
81778 GGTGCCACGGAGTTGTGGACTTTAAAAGTGTGCCACGGAGTTGTGGACTTTACAAG
1 GGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAG
* * *
81834 TGTGCCACGGAGTTGTGGACTTT-GAAGGGTGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAG
* * *
81888 GGTGCTACGGAGTTGTGGACTTTAAAAGAGTGCCACAGAGTTGTGGATTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAG
*
81943 GGTGCCACAGAGTTGTGGACTTTAAAAG-GATGCCACGGAGTTGTGGACTTCAAAA
1 GGTGCCACGGAGTTGTGGACTTTAAAAGAG-TGCCACGGAGTTGTGGACTT-AAAA
81998 AGAAATGCCA
Statistics
Matches: 296, Mismatches: 26, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
54 98 0.33
55 165 0.56
56 33 0.11
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.25
Consensus pattern (55 bp):
GGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAG
Found at i:83063 original size:6 final size:6
Alignment explanation
Indices: 83048--83079 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
83038 GTGAAAAGGG
83048 TTTT-T TTTTGT TTTTGT TTTTGT TTTT-T TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
83080 AGGATTGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (6 bp):
TTTTGT
Found at i:83350 original size:24 final size:24
Alignment explanation
Indices: 83321--83379 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
83311 CATGTCCTCG
* *
83321 TTTTTTATTTTTCTTGTT-CTCTTT
1 TTTTTTATTTTGCTT-TTGCACTTT
83345 TTTTTTATTTTGCTTTTGCACTTT
1 TTTTTTATTTTGCTTTTGCACTTT
*
83369 TTTTTTCTTTT
1 TTTTTTATTTT
83380 CATTTTTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 2 0.06
24 29 0.94
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (24 bp):
TTTTTTATTTTGCTTTTGCACTTT
Found at i:83372 original size:40 final size:39
Alignment explanation
Indices: 83328--83410 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
83318 TCGTTTTTTA
* * * *
83328 TTTTTCTTGTTCTC-TTTTTTTTTATTTTGCTTTTGCACT
1 TTTTTTTTCTTCTCATTTTTTGTGATTTTGCTTTTG-ACT
* *
83367 TTTTTTTTCTTTTCATTTTTTGTGCTTTTGCTTTTGACT
1 TTTTTTTTCTTCTCATTTTTTGTGATTTTGCTTTTGACT
83406 TTTTT
1 TTTTT
83411 GTCATTTTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 19 0.51
40 18 0.49
ACGTcount: A:0.05, C:0.13, G:0.08, T:0.73
Consensus pattern (39 bp):
TTTTTTTTCTTCTCATTTTTTGTGATTTTGCTTTTGACT
Found at i:83395 original size:23 final size:23
Alignment explanation
Indices: 83370--83412 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
83360 TTGCACTTTT
*
83370 TTTTTCTTTTCA-TTTTTTGTGC
1 TTTTGCTTTTCACTTTTTTGTGC
*
83392 TTTTGCTTTTGACTTTTTTGT
1 TTTTGCTTTTCACTTTTTTGT
83413 CATTTTGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.05, C:0.12, G:0.12, T:0.72
Consensus pattern (23 bp):
TTTTGCTTTTCACTTTTTTGTGC
Found at i:89559 original size:22 final size:23
Alignment explanation
Indices: 89527--89582 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
89517 TGGACATGTT
*
89527 AAAAATACATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
89549 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
89572 AAAAATGCATG
1 AAAAATGCATG
89583 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 19 0.59
23 13 0.41
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:90518 original size:20 final size:20
Alignment explanation
Indices: 90493--90618 Score: 74
Period size: 20 Copynumber: 5.8 Consensus size: 20
90483 AAAAAGACAT
90493 AATGTATCGATACATTGTAG
1 AATGTATCGATACATTGTAG
90513 AATGTATCGATACATTTAGGTAAAAAG
1 AATGTATCGATACA-TT--GT----AG
90540 ACATAATGTATCGATACATTGTAG
1 ----AATGTATCGATACATTGTAG
* *
90564 AATATATCGATACATTCATA-
1 AATGTATCGATACATT-GTAG
* * * *
90584 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGTAG
*
90604 AATGTATTGATACAT
1 AATGTATCGATACAT
90619 CAGGGTATGA
Statistics
Matches: 83, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
19 1 0.01
20 54 0.65
21 4 0.05
23 2 0.02
24 2 0.02
27 2 0.02
28 2 0.02
30 2 0.02
31 14 0.17
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTGTAG
Found at i:90519 original size:51 final size:51
Alignment explanation
Indices: 90443--90579 Score: 238
Period size: 51 Copynumber: 2.7 Consensus size: 51
90433 TTTTAACTAG
* **
90443 ATGTATCGATACATTATTCAATGTATCGATACATTTAGGTAAAAAGACATA
1 ATGTATCGATACATTGTAGAATGTATCGATACATTTAGGTAAAAAGACATA
90494 ATGTATCGATACATTGTAGAATGTATCGATACATTTAGGTAAAAAGACATA
1 ATGTATCGATACATTGTAGAATGTATCGATACATTTAGGTAAAAAGACATA
*
90545 ATGTATCGATACATTGTAGAATATATCGATACATT
1 ATGTATCGATACATTGTAGAATGTATCGATACATT
90580 CATACATGTA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 82 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (51 bp):
ATGTATCGATACATTGTAGAATGTATCGATACATTTAGGTAAAAAGACATA
Found at i:90616 original size:40 final size:39
Alignment explanation
Indices: 90541--90618 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
90531 GGTAAAAAGA
* *
90541 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* * *
90580 CATACATGTATCGATATATTGAAAAATGTATTGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
90619 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:91463 original size:38 final size:38
Alignment explanation
Indices: 91372--91502 Score: 99
Period size: 38 Copynumber: 3.4 Consensus size: 38
91362 CAAGTTATGA
* * *
91372 ACAAAAATCACTATTTTAAATCGATGGCATTG-TTCGAA-
1 ACAAAAATTACTATTCTAAATCGATGGCA-CGATTC-AAT
* ** *
91410 ACGAAAACCATTATTCTAAA-CTGATGGCACGATTCGAA-
1 ACAAAAATTACTATTCTAAATC-GATGGCACGATTC-AAT
* * *
91448 ACAAAATTTACTATTCTAAATCGATGGTACGGTTCAAT
1 ACAAAAATTACTATTCTAAATCGATGGCACGATTCAAT
*
91486 ATAAAAATTACTATTCT
1 ACAAAAATTACTATTCT
91503 TATCCAGTGA
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
37 4 0.05
38 70 0.93
39 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (38 bp):
ACAAAAATTACTATTCTAAATCGATGGCACGATTCAAT
Found at i:91557 original size:38 final size:38
Alignment explanation
Indices: 91472--91557 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
91462 TCTAAATCGA
* *
91472 TGGTACGGTTCAATATAAAAATTACTATTCTTATCCAG
1 TGGTACGGTTCAATACAAAAATCACTATTCTTATCCAG
* *
91510 TGACT-CGGTTGAATACAAAAATCACTATTCTTATCCAG
1 TG-GTACGGTTCAATACAAAAATCACTATTCTTATCCAG
91548 TGGTACGGTT
1 TGGTACGGTT
91558 TGAAACCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 1 0.02
38 39 0.95
39 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (38 bp):
TGGTACGGTTCAATACAAAAATCACTATTCTTATCCAG
Found at i:93724 original size:2 final size:2
Alignment explanation
Indices: 93717--93753 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
93707 TTCATAATTC
93717 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93754 ACTAGAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:95808 original size:2 final size:2
Alignment explanation
Indices: 95795--95824 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
95785 ATCTAATCCC
*
95795 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
95825 AACTATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:95985 original size:22 final size:21
Alignment explanation
Indices: 95943--95986 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
95933 CCGCCATCCA
95943 CTTAAAACAATTTTTCGAAAAT
1 CTTAAAAC-ATTTTTCGAAAAT
95965 CTTAAAAC-TTTTATCGTAAAAT
1 CTTAAAACATTTT-TCG-AAAAT
95987 ATTATCATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.20
21 3 0.15
22 13 0.65
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (21 bp):
CTTAAAACATTTTTCGAAAAT
Found at i:97642 original size:20 final size:20
Alignment explanation
Indices: 97614--97657 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
97604 ATAGAGACTT
*
97614 CCTCCTCCCTCTCAAGTATC
1 CCTCATCCCTCTCAAGTATC
**
97634 CCTCATCCCTCTCTTGTATC
1 CCTCATCCCTCTCAAGTATC
97654 CCTC
1 CCTC
97658 TTCAATTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.50, G:0.05, T:0.34
Consensus pattern (20 bp):
CCTCATCCCTCTCAAGTATC
Found at i:102098 original size:28 final size:27
Alignment explanation
Indices: 102039--102107 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
102029 CACCCATTTG
* *
102039 TTTGTCAAAAATGGTAGTTATTTTGTG
1 TTTGTCAAAAATGGTAGTTATTTTATA
102066 TTTGTCAAAAATGGTAGTT-TCCTTTATA
1 TTTGTCAAAAATGGTAGTTAT--TTTATA
*
102094 TTTGTCAAATATGG
1 TTTGTCAAAAATGG
102108 AGGCTTGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.51
28 17 0.46
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTAGTTATTTTATA
Found at i:102214 original size:20 final size:20
Alignment explanation
Indices: 102186--102229 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
102176 ATAGAGACTT
*
102186 CCTCCTCCCTCTCAAGTATC
1 CCTCATCCCTCTCAAGTATC
**
102206 CCTCATCCCTCTCTTGTATC
1 CCTCATCCCTCTCAAGTATC
102226 CCTC
1 CCTC
102230 TTCAATTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.50, G:0.05, T:0.34
Consensus pattern (20 bp):
CCTCATCCCTCTCAAGTATC
Found at i:103175 original size:19 final size:20
Alignment explanation
Indices: 103147--103196 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
103137 GATACGAAAG
*
103147 AATAACTAAAAT-ACGATATAA
1 AATAA-TAAAATGAC-ATAAAA
103168 AAT-ATAAAATGACATAAAA
1 AATAATAAAATGACATAAAA
103187 AATAATAAAA
1 AATAATAAAA
103197 ATATTGCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 14 0.54
20 9 0.35
21 3 0.12
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.22
Consensus pattern (20 bp):
AATAATAAAATGACATAAAA
Found at i:107137 original size:2 final size:2
Alignment explanation
Indices: 107132--107164 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
107122 AGGAAAAAAA
107132 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
107165 ATATTCCGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:108213 original size:1 final size:1
Alignment explanation
Indices: 108202--108293 Score: 139
Period size: 1 Copynumber: 92.0 Consensus size: 1
108192 ACAAACAACA
* ** *
108202 CCCCACCCCCCCCCCCCCAACCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
*
108267 CCCCCCCCCCCCCACCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
108294 GAAAAAAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 83 1.00
ACGTcount: A:0.05, C:0.95, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:108231 original size:21 final size:20
Alignment explanation
Indices: 108200--108293 Score: 163
Period size: 20 Copynumber: 4.8 Consensus size: 20
108190 ACACAAACAA
*
108200 CACCCCACCCCCCCCCCCCC
1 CACCCCCCCCCCCCCCCCCC
*
108220 AACCCCCCCCCCCCCCCCCC
1 CACCCCCCCCCCCCCCCCCC
108240 CACCCCCCCCCCCCCCCCCC
1 CACCCCCCCCCCCCCCCCCC
108260 C-CCCCCCCCCCCCCCCCCC
1 CACCCCCCCCCCCCCCCCCC
108279 CACCCCCCCCCCCCC
1 CACCCCCCCCCCCCC
108294 GAAAAAAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 19 0.27
20 51 0.73
ACGTcount: A:0.06, C:0.94, G:0.00, T:0.00
Consensus pattern (20 bp):
CACCCCCCCCCCCCCCCCCC
Found at i:108653 original size:13 final size:13
Alignment explanation
Indices: 108631--108664 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
108621 TTCAGTTTTC
* *
108631 TTTATCATTGATT
1 TTTATTATTGATA
108644 TTTATTATTGATA
1 TTTATTATTGATA
108657 TTTATTAT
1 TTTATTAT
108665 AATAGATCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (13 bp):
TTTATTATTGATA
Found at i:113680 original size:19 final size:21
Alignment explanation
Indices: 113652--113707 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 21
113642 TATGTAAATA
113652 ATATAAATATGATATAA-TTT
1 ATATAAATATGATATAATTTT
* *
113672 ATA-AAATATGTTAAAATTTT
1 ATATAAATATGATATAATTTT
*
113692 ATATAAATATCATATA
1 ATATAAATATGATATA
113708 TATATATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 11 0.38
20 9 0.31
21 9 0.31
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
ATATAAATATGATATAATTTT
Found at i:113699 original size:49 final size:47
Alignment explanation
Indices: 113639--113731 Score: 116
Period size: 49 Copynumber: 1.9 Consensus size: 47
113629 ATTTTGTATT
* *
113639 TTTTATGTAAATAAT-ATAAATATGATATAATTTATAAAATATGTTAAAA
1 TTTTATATAAAT-ATCATAAATAT-ATAT-ATATATAAAATATGTTAAAA
* *
113688 TTTTATATAAATATCATATATATATATATATATTAAATATGTTA
1 TTTTATATAAATATCATAAATATATATATATATAAAATATGTTA
113732 TGTTCATCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 15 0.38
48 6 0.15
49 18 0.46
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (47 bp):
TTTTATATAAATATCATAAATATATATATATATAAAATATGTTAAAA
Found at i:118579 original size:12 final size:12
Alignment explanation
Indices: 118563--118609 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
118553 TGATGAAAAA
*
118563 GATGAATATGAT
1 GATGAAGATGAT
*
118575 TATGAAGATGAT
1 GATGAAGATGAT
*
118587 GATGATGATGAT
1 GATGAAGATGAT
*
118599 GATGATGATGA
1 GATGAAGATGA
118610 AAATGATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:118589 original size:3 final size:3
Alignment explanation
Indices: 118570--118619 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
118560 AAAGATGAAT
* * **
118570 ATG ATT ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG ATG AAA ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
118618 AT
1 AT
118620 CATTTATTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:120746 original size:2 final size:2
Alignment explanation
Indices: 120739--120771 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
120729 TATAGCCATT
120739 TA TA TA TA TA TA 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 T
120772 TCCTTTCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:120873 original size:23 final size:24
Alignment explanation
Indices: 120842--120893 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
120832 TTTACTTTGA
*
120842 AAAAAAAATCTAT-TTAAAACTTG
1 AAAAAAAATATATATTAAAACTTG
* * *
120865 AAAATAAATATATATTCAAATTTG
1 AAAAAAAATATATATTAAAACTTG
120889 AAAAA
1 AAAAA
120894 CATGATTACA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAAAAAATATATATTAAAACTTG
Found at i:120893 original size:25 final size:24
Alignment explanation
Indices: 120837--120893 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
120827 TCATATTTAC
*
120837 TTTGAAAAAAAAATCTATTTAAAA
1 TTTGAAAAAAAAATATATTTAAAA
* * *
120861 CTTG-AAAATAAATATATATTCAAA
1 TTTGAAAAAAAAATATAT-TTAAAA
120885 TTTGAAAAA
1 TTTGAAAAA
120894 CATGATTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.42
24 11 0.42
25 4 0.15
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (24 bp):
TTTGAAAAAAAAATATATTTAAAA
Found at i:122833 original size:77 final size:77
Alignment explanation
Indices: 122705--122874 Score: 225
Period size: 77 Copynumber: 2.2 Consensus size: 77
122695 TCCTTTAGGG
* * *
122705 AACTTTCATGTCACACGTGTACATTAAGTGTACGCTACTCATTTAAACTTAAAACCGAGTCCTTT
1 AACTTTCATGTCACACGCGTACATGAAGGGTACGCTACTCATTTAAACTTAAAACCGAGTCCTTT
122770 AAGCTC-ATGTAC
66 AAGCTCGAT-TAC
* * * * * * *
122782 AACTTTCATGTCACATGCGTATATGAAGGGTATGTTATTCATTTTACCTTAAAACCGAGTCCTTT
1 AACTTTCATGTCACACGCGTACATGAAGGGTACGCTACTCATTTAAACTTAAAACCGAGTCCTTT
*
122847 AAGCTCGCTTAC
66 AAGCTCGATTAC
122859 AACTTTCATGTCACAC
1 AACTTTCATGTCACAC
122875 AGTTACTTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
77 79 0.99
78 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (77 bp):
AACTTTCATGTCACACGCGTACATGAAGGGTACGCTACTCATTTAAACTTAAAACCGAGTCCTTT
AAGCTCGATTAC
Found at i:125798 original size:2 final size:2
Alignment explanation
Indices: 125791--125821 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
125781 TTCATAATTC
*
125791 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
125822 ACTAGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:126262 original size:2 final size:2
Alignment explanation
Indices: 126214--126243 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
126204 ACATACATAC
126214 AT AT 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 AT AT
126244 GAGAGATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127807 original size:40 final size:40
Alignment explanation
Indices: 127758--127838 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
127748 AATTGTATAG
*
127758 TAAAAATTTATTTAAATATAATAA-AAATAAAATAA-AATTT
1 TAAAAATTTATCT-AATATAATAATAAA-AAAATAAGAATTT
* **
127798 TAAACATTTATCTAATATTTTAATAAAAAAATAAGAATTT
1 TAAAAATTTATCTAATATAATAATAAAAAAATAAGAATTT
127838 T
1 T
127839 CGTTTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
39 15 0.43
40 20 0.57
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (40 bp):
TAAAAATTTATCTAATATAATAATAAAAAAATAAGAATTT
Found at i:129056 original size:20 final size:20
Alignment explanation
Indices: 129028--129076 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
129018 AGAAAGAATT
129028 GAAGAGGGATACAAGAGAGG
1 GAAGAGGGATACAAGAGAGG
* **
129048 GATGAGGGATACTTGAGAGG
1 GAAGAGGGATACAAGAGAGG
129068 GAAGAGGGA
1 GAAGAGGGA
129077 GCCTCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.47, T:0.10
Consensus pattern (20 bp):
GAAGAGGGATACAAGAGAGG
Found at i:129213 original size:27 final size:27
Alignment explanation
Indices: 129152--129222 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
129142 AAACAAGCCT
* *
129152 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
*
129180 CTATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
129207 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
129223 AATGGGTGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:133630 original size:20 final size:20
Alignment explanation
Indices: 133602--133650 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
133592 AGAAAGAATT
133602 GAAGAGGGATACAAGAGAGG
1 GAAGAGGGATACAAGAGAGG
* **
133622 GATGAGGGATACTTGAGAGG
1 GAAGAGGGATACAAGAGAGG
133642 GAAGAGGGA
1 GAAGAGGGA
133651 GCCTCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.47, T:0.10
Consensus pattern (20 bp):
GAAGAGGGATACAAGAGAGG
Found at i:133767 original size:28 final size:27
Alignment explanation
Indices: 133706--133797 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 27
133696 TAGCCACAAA
* * *
133706 TTTTGACAAATA-AACA-AGCCTCCAT
1 TTTTGACAAATACAAAATAACCACCAT
* *
133731 ATTTGACAAATACAAAGGA-AACCACTAT
1 TTTTGACAAATACAAA--ATAACCACCAT
*
133759 TTTTGACAAACACAAAATAACCACCAT
1 TTTTGACAAATACAAAATAACCACCAT
133786 TTTTGACAAATA
1 TTTTGACAAATA
133798 AATGGGTGGC
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.06
27 19 0.35
28 21 0.39
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.26
Consensus pattern (27 bp):
TTTTGACAAATACAAAATAACCACCAT
Found at i:133788 original size:27 final size:27
Alignment explanation
Indices: 133727--133795 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
133717 AAACAAGCCT
* *
133727 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
*
133755 CTATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
133782 CCATTTTTGACAAA
1 CCATTTTTGACAAA
133796 TAAATGGGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 18 0.50
28 17 0.47
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:134498 original size:20 final size:20
Alignment explanation
Indices: 134473--134512 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
134463 TGTAGAAGAG
134473 AAAAAATGAGCTTACAAATT
1 AAAAAATGAGCTTACAAATT
134493 AAAAAATGAGCTTACAAATT
1 AAAAAATGAGCTTACAAATT
134513 CTGAGGGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (20 bp):
AAAAAATGAGCTTACAAATT
Found at i:139789 original size:2 final size:2
Alignment explanation
Indices: 139784--139822 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
139774 AAAGGAAAAA
139784 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
139823 ATATTCCGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:141177 original size:28 final size:28
Alignment explanation
Indices: 141116--141169 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
141106 AAATGCTACT
*
141116 CTTTGTATTTATCAAATATGGTGGTTTC
1 CTTTGTATTTGTCAAATATGGTGGTTTC
141144 CTTTGTATTTGTCAAATATGGTGGTT
1 CTTTGTATTTGTCAAATATGGTGGTT
141170 ATTTTTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.50
Consensus pattern (28 bp):
CTTTGTATTTGTCAAATATGGTGGTTTC
Found at i:141210 original size:24 final size:24
Alignment explanation
Indices: 141151--141219 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
141141 TTCCTTTGTA
* * *
141151 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
*
141177 TTTGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
*
141201 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAAATGGTGGCT
141220 AATTTTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
24 22 0.59
26 15 0.41
ACGTcount: A:0.22, C:0.06, G:0.26, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:146931 original size:2 final size:2
Alignment explanation
Indices: 146926--146958 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
146916 TTGGCGTGTG
*
146926 TA TA TA TA TA TA TA TG 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 T
146959 TAAATAGATT
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:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:149967 original size:2 final size:2
Alignment explanation
Indices: 149960--150004 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
149950 TTCATAGTTC
149960 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
150002 AT A
1 AT A
150005 GCTAGAGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:152063 original size:2 final size:2
Alignment explanation
Indices: 152050--152090 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
152040 ATCTAACCCC
*
152050 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
152091 AAAGACTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:152185 original size:20 final size:20
Alignment explanation
Indices: 152162--152223 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
152152 TAGCGCATAT
152162 GATAAAATTTTGAAGCATTG
1 GATAAAATTTTGAAGCATTG
* * **
152182 GAT--AA-GTGGGCGCATAT-
1 GATAAAATTTTGAAGCAT-TG
152199 GATAAAATTTTGAAGCATTG
1 GATAAAATTTTGAAGCATTG
152219 GATAA
1 GATAA
152224 CTAACATAGT
Statistics
Matches: 29, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 9 0.31
18 3 0.10
19 3 0.10
20 14 0.48
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (20 bp):
GATAAAATTTTGAAGCATTG
Done.