Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006063.1 Hibiscus syriacus cultivar Beakdansim tig00014340_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 152081
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:3762 original size:18 final size:17
Alignment explanation
Indices: 3742--3788 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
3732 AATATTTCAT
3742 TTTATTTTATTTTTACA
1 TTTATTTTATTTTTACA
* *
3759 TTT-TTGTATTTTTATAA
1 TTTATTTTATTTTTA-CA
*
3776 TTTACTTTATTTT
1 TTTATTTTATTTT
3789 ATTTTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTATTTTATTTTTACA
Found at i:3779 original size:23 final size:23
Alignment explanation
Indices: 3753--3802 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3743 TTATTTTATT
3753 TTTACATTT-TTGTATTTT-TATAA
1 TTTAC-TTTATTGTATTTTATA-AA
*
3776 TTTACTTTATTTTATTTTATAAA
1 TTTACTTTATTGTATTTTATAAA
3799 TTTA
1 TTTA
3803 AATACGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.12
23 19 0.79
24 2 0.08
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTACTTTATTGTATTTTATAAA
Found at i:6070 original size:49 final size:47
Alignment explanation
Indices: 6017--6157 Score: 139
Period size: 49 Copynumber: 3.0 Consensus size: 47
6007 ATTATTAGAT
6017 TATTAGATTAATATTAAATATATAA-ATATATTCATTATTAATAATTTAA
1 TATTAGATTAA-ATTAAATATATAATATATATT-ATTATTAATAATTT-A
* *
6066 TATTAGTATATGAAATT-AATAAATAATATAAATT-TTATTAATAATTTA
1 TATTAG-AT-T-AAATTAAATATATAATATATATTATTATTAATAATTTA
* * *
6114 TA-TATATTAAAATAAAAATATAATATAATATTATTA-TAATAATT
1 TATTAGATTAAATTAAATATATAATAT-ATATTATTATTAATAATT
6158 GATTATTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
44 4 0.05
45 11 0.14
46 14 0.18
47 5 0.06
48 3 0.04
49 19 0.24
50 10 0.13
51 10 0.13
52 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (47 bp):
TATTAGATTAAATTAAATATATAATATATATTATTATTAATAATTTA
Found at i:6187 original size:20 final size:20
Alignment explanation
Indices: 6140--6206 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
6130 AATATAATAT
* *
6140 AATATTATTATAATAATTGAT
1 AATATTATTATAAT-ATTAAA
*
6161 TAT-TTATTATAATATTAAA
1 AATATTATTATAATATTAAA
* *
6180 AATATTA-TATTATTATTAGA
1 AATATTATTA-TAATATTAAA
6200 AATATTA
1 AATATTA
6207 ATAAATAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 8 0.21
20 28 0.74
21 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
AATATTATTATAATATTAAA
Found at i:8396 original size:12 final size:12
Alignment explanation
Indices: 8379--8405 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
8369 AATATAAATA
8379 AAATATAATTTT
1 AAATATAATTTT
8391 AAATATAATTTT
1 AAATATAATTTT
8403 AAA
1 AAA
8406 AAAATAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATATAATTTT
Found at i:8432 original size:23 final size:24
Alignment explanation
Indices: 8389--8433 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
8379 AAATATAATT
*
8389 TTAAATATAATTTTAAAAAAATAG
1 TTAAATATAATTTCAAAAAAATAG
8413 TTAAA-ATAA-TTCAAATAAAAT
1 TTAAATATAATTTCAAA-AAAAT
8434 TAAAGTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
TTAAATATAATTTCAAAAAAATAG
Found at i:9470 original size:18 final size:17
Alignment explanation
Indices: 9418--9472 Score: 64
Period size: 13 Copynumber: 3.4 Consensus size: 17
9408 ACTCGAATCG
*
9418 ACTCAACTTGATCTAAT
1 ACTCAACTTGATTTAAT
9435 ACTC-AC-T--TTTAAT
1 ACTCAACTTGATTTAAT
9448 ACTCAACTTGATTTAACT
1 ACTCAACTTGATTTAA-T
9466 ACTCAAC
1 ACTCAAC
9473 AATATTGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
13 9 0.28
14 2 0.06
15 2 0.06
16 2 0.06
17 9 0.28
18 8 0.25
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (17 bp):
ACTCAACTTGATTTAAT
Found at i:26812 original size:185 final size:185
Alignment explanation
Indices: 26500--26869 Score: 686
Period size: 185 Copynumber: 2.0 Consensus size: 185
26490 CAAGCCAAAC
*
26500 TTTCGGTCTTTTAGGTTGTTCTAATTTCATTTCTCTAATTGCCCCCTCAAGTTTGGGTAAATAAA
1 TTTCGGTCCTTTAGGTTGTTCTAATTTCATTTCTCTAATTGCCCCCTCAAGTTTGGGTAAATAAA
26565 AAAATAGATAAACTATACAAATGATCACTAATATTTGAGTGAGTTTTCATTTTTGTCATTGAAGT
66 AAAATAGATAAACTATACAAATGATCACTAATATTTGAGTGAGTTTTCATTTTTGTCATTGAAGT
26630 TTCAAAATTAAAAATTTGATCAATAACGTTATGAATTTATAATAAATCAGTCGCT
131 TTCAAAATTAAAAATTTGATCAATAACGTTATGAATTTATAATAAATCAGTCGCT
*
26685 TTTCGGTCCTTTAGGTTGTTCTAATTTCATTTCTCTAGTTGCCCCCTCAAGTTTGGGTAAATAAA
1 TTTCGGTCCTTTAGGTTGTTCTAATTTCATTTCTCTAATTGCCCCCTCAAGTTTGGGTAAATAAA
* *
26750 AAAATAGATAAACTATACAGATGATCACTAATATTTTAGTGAGTTTTCATTTTTGTCATTGAAGT
66 AAAATAGATAAACTATACAAATGATCACTAATATTTGAGTGAGTTTTCATTTTTGTCATTGAAGT
* *
26815 TTCAAAATTAAAAATTTGATCAATAACGTTATGGATTTATAATAAATCGGTCGCT
131 TTCAAAATTAAAAATTTGATCAATAACGTTATGAATTTATAATAAATCAGTCGCT
26870 CGCCATTAAC
Statistics
Matches: 179, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
185 179 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (185 bp):
TTTCGGTCCTTTAGGTTGTTCTAATTTCATTTCTCTAATTGCCCCCTCAAGTTTGGGTAAATAAA
AAAATAGATAAACTATACAAATGATCACTAATATTTGAGTGAGTTTTCATTTTTGTCATTGAAGT
TTCAAAATTAAAAATTTGATCAATAACGTTATGAATTTATAATAAATCAGTCGCT
Found at i:27782 original size:16 final size:17
Alignment explanation
Indices: 27756--27811 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
27746 AAAATTGGAG
27756 TAAAGATAAAAAGTAAA
1 TAAAGATAAAAAGTAAA
27773 TAAA-ATAAAAAGTAAAGA
1 TAAAGATAAAAAGT-AA-A
*
27791 TAAAGACAATAAA-TAAA
1 TAAAGATAA-AAAGTAAA
27808 TAAA
1 TAAA
27812 TAAATATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 9 0.26
17 11 0.32
18 7 0.21
19 4 0.12
20 3 0.09
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (17 bp):
TAAAGATAAAAAGTAAA
Found at i:27786 original size:29 final size:30
Alignment explanation
Indices: 27754--27811 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
27744 AAAAAATTGG
*
27754 AGTAAAGATAAA-A-AGTAAATAAAATAAAA
1 AGTAAAGATAAAGACAATAAAT-AAATAAAA
27783 AGTAAAGATAAAGACAATAAATAAATAAA
1 AGTAAAGATAAAGACAATAAATAAATAAA
27812 TAAATATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.46
30 8 0.31
31 6 0.23
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (30 bp):
AGTAAAGATAAAGACAATAAATAAATAAAA
Found at i:27807 original size:4 final size:4
Alignment explanation
Indices: 27798--27907 Score: 62
Period size: 4 Copynumber: 25.5 Consensus size: 4
27788 AGATAAAGAC
* *
27798 AATA AATA AATA AATA AATA TGAATA AGTAA AACTA AGATA AAGAA AATA
1 AATA AATA AATA AATA AATA --AATA AAT-A AA-TA A-ATA AA-TA AATA
* * * *
27848 AAAA AATAA AATT AATA AAGA GAA-G AA-A AATA AATA AATA AATA AATAA
1 AATA AAT-A AATA AATA AATA -AATA AATA AATA AATA AATA AATA AAT-A
27897 AATA ATATA AA
1 AATA A-ATA AA
27908 GAAAAATAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
3 4 0.05
4 50 0.60
5 24 0.29
6 6 0.07
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:27901 original size:36 final size:34
Alignment explanation
Indices: 27801--27933 Score: 85
Period size: 36 Copynumber: 3.6 Consensus size: 34
27791 TAAAGACAAT
*
27801 AAATAAATAAATAAATATGAAT-AAGTAAAACTAAGATA
1 AAATAAATAAATAAATA--AATAAAATAAAA--AAGA-A
* *
27839 AAGA-AAATAAAAAAATAAA-ATTAATAAAGAGAAGAA
1 AA-ATAAATAAATAAATAAATA-AAATAAA-A-AAGAA
27875 AAATAAATAAATAAATAAATAAAATAATATAAAGAA
1 AAATAAATAAATAAATAAATAAAATAA-A-AAAGAA
*
27911 AAAT-AATAATAGTAAAGAAATAA
1 AAATAAATAA-A-TAAATAAATAA
27934 TATATATATA
Statistics
Matches: 78, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
35 6 0.08
36 34 0.44
37 22 0.28
38 15 0.19
39 1 0.01
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.20
Consensus pattern (34 bp):
AAATAAATAAATAAATAAATAAAATAAAAAAGAA
Found at i:27941 original size:36 final size:36
Alignment explanation
Indices: 27790--27943 Score: 98
Period size: 37 Copynumber: 4.1 Consensus size: 36
27780 AAAAGTAAAG
* * *
27790 ATAAAG-ACAATAAATAAATAAATAAATATGAATAAGT
1 ATAAAGAAAAATAAATAAATAAAGAAATA-AAATAA-T
** * * *
27827 A-AAACTAAGATAAAGAAAATAAAAAAATAAAATTAAT
1 ATAAAGAAAAATAAA-TAAATAAAGAAATAAAA-TAAT
* *
27864 AAAGAGAAGAAAAATAAATAAATAAATAAATAAAATAAT
1 --ATA-AAGAAAAATAAATAAATAAAGAAATAAAATAAT
*
27903 ATAAAGAAAAAT-AATAATAGTAAAGAAATAATATATAT
1 ATAAAGAAAAATAAATAA-A-TAAAGAAATAAAATA-AT
27941 ATA
1 ATA
27944 TATATATAAT
Statistics
Matches: 93, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
35 5 0.05
36 13 0.14
37 25 0.27
38 20 0.22
39 5 0.05
40 16 0.17
41 9 0.10
ACGTcount: A:0.69, C:0.01, G:0.07, T:0.22
Consensus pattern (36 bp):
ATAAAGAAAAATAAATAAATAAAGAAATAAAATAAT
Found at i:28246 original size:43 final size:40
Alignment explanation
Indices: 28191--28295 Score: 104
Period size: 43 Copynumber: 2.5 Consensus size: 40
28181 AAACATTAGG
* * *
28191 AAAACAAAATAAAAAGAAATAGAAAATATATATAATA-GATAT
1 AAAATAAAATAAAAA-AAATAGAAAATA-AAATAAAAGGAT-T
* *
28233 AAAAATAAAATAAACAAAAAAATAAAATAAAATAAAAGGATT
1 -AAAATAAAATAAA-AAAAATAGAAAATAAAATAAAAGGATT
28275 AAAATAAAATAGAAAAAAATA
1 AAAATAAAATA-AAAAAAATA
28296 TATATACAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
41 17 0.32
42 9 0.17
43 25 0.47
44 2 0.04
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (40 bp):
AAAATAAAATAAAAAAAATAGAAAATAAAATAAAAGGATT
Found at i:30335 original size:80 final size:81
Alignment explanation
Indices: 30111--31075 Score: 1047
Period size: 80 Copynumber: 11.8 Consensus size: 81
30101 CTGAATTTAA
* * * * *** * ** *
30111 TGTAATCGAACTCGAAGCTCTTTGATGATATAAAACCCTTCTCAACTTGAGTTATGCTATAAATA
1 TGTAATCGAACTCGAAGGTCTTTG--GACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATG
30176 ATGTGCCTTTGAGCTGAG
64 ATGTGCCTTTGAGCTGAG
* * ** * *
30194 TGTAATCAAACTCGAAGGTCTTTTGGA-AGATAGCTTTTCTTGCATTGAGCTAAGCTGCAAATGA
1 TGTAATCGAACTCGAAGGTC-TTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGA
*
30258 TGTACCTTTGAGCTGAG
65 TGTGCCTTTGAGCTGAG
*
30275 TGTAATCGAACTCGAAGGTCTTTGGA-AGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATAAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
*
30339 GTGCCTTTGAGCTAAG
66 GTGCCTTTGAGCTGAG
* * * * *
30355 TGTAATAGAACTTGAAGGTCTTT-GACAGATAACCCTTCTTCCCTTGAGCTATGCTGCAAATGAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
*
30419 GTGCCTTTGAGCTAAG
66 GTGCCTTTGAGCTGAG
* * * *
30435 TGTAATCGAACTCGAAAGTATTTTGATAACAGATAACCCTT-TTAGCCTTGAGTTATA-CTACAA
1 TGTAATCGAACTCGAAGGT-CTTTG--GACAGATAACCCTTCTT-GCCTTGAGTTA-AGCTGCAA
*
30498 ATGATATGCCTTTGAGCTGAG
61 ATGATGTGCCTTTGAGCTGAG
* * * * *
30519 TGTAATCGAACTCGAAGGTCTTT-GACAGATAACCCTTTTTGCCTTAAGCTATGCTGCAAATAAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
30583 GTGCCTTTGAGCTGAG
66 GTGCCTTTGAGCTGAG
** * *
30599 TGTAATTAAACTCGAAGGTATTTGG-CAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
*
30663 ATGCCTTTGAGCTGAG
66 GTGCCTTTGAGCTGAG
* * * * *
30679 TGTAATAGAACTCGAAGGTCTTTTGATAACAAATAACCCTT-TTAGCATTGATTTATA-CTGCAA
1 TGTAATCGAACTCGAAGGTC-TTTG--GACAGATAACCCTTCTT-GCCTTGAGTTA-AGCTGCAA
*
30742 ATGATGTGCCTCTGAGCTGAG
61 ATGATGTGCCTTTGAGCTGAG
* * * *
30763 TGTAATCGAACTCGAAGGTCTTTTGATGATAAATAACCCTT-TTAGCATTGATTTATA-CTGCAA
1 TGTAATCGAACTCGAAGGTC-TTTG--GACAGATAACCCTTCTT-GCCTTGAGTTA-AGCTGCAA
*
30826 ATGATGTGCCTCTGAGCTGAG
61 ATGATGTGCCTTTGAGCTGAG
* * * *
30847 TATAATCGAACTCGAAGGTATTTGG-CAGATAACTCTTCTTGCCTTGAGCTAAGCTGCAAATGAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
*
30911 GTGTCTTTGAGCTGAG
66 GTGCCTTTGAGCTGAG
* * *
30927 TGTAATCGAACTCGAATGTCTTTTGATGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 TGTAATCGAACTCGAAGGTC-TTTG--GACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAAT
* *
30992 GATGTGCCTCTAAGCTGAG
63 GATGTGCCTTTGAGCTGAG
* ** * *
31011 TGTAATCAAACTCGAAGGTCTTTGG-CAGATAACCCTTCTTGCCTTGAACTATGCTACAAATGAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
31075 G
66 G
31076 AGCCGATCAT
Statistics
Matches: 760, Mismatches: 99, Indels: 49
0.84 0.11 0.05
Matches are distributed among these distances:
79 3 0.00
80 367 0.48
81 76 0.10
82 2 0.00
83 34 0.04
84 278 0.37
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (81 bp):
TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
GTGCCTTTGAGCTGAG
Found at i:30531 original size:244 final size:245
Alignment explanation
Indices: 30156--31057 Score: 1196
Period size: 244 Copynumber: 3.7 Consensus size: 245
30146 CCCTTCTCAA
* ** * *
30156 CTTGAGTTATGCTATAAATAATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTG--
1 CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGAT
* * * * * * *
30219 GA-AGAT-AGCTTTTCTTGCATTGAGCTA-AGCTGCAAATGATGTACCTTTGAGCTGAGTGTAAT
66 AACAGATAACCCTTT-TAGCATTGAGTTATA-CTGCAAATGATGTGCCTCTGAGCTGAGTGTAAT
30281 CGAACTCGAAGGTCTTTGGA-AGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATAATGTGCCT
129 CGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATAATGTGCCT
* * * * *
30345 TTGAGCTAAGTGTAATAGAACTTGAAGGTCTTTGACAGATAACCCTTCTTCC
194 TTGAGCTGAGTGTAATAGAACTCGAAGGTATTTGGCAGATAACCCTTCTTGC
* * *
30397 CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTAAGTGTAATCGAACTCGAAAGTATTTTGAT
1 CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGAT
* * * *
30462 AACAGATAACCCTTTTAGCCTTGAGTTATACTACAAATGATATGCCTTTGAGCTGAGTGTAATCG
66 AACAGATAACCCTTTTAGCATTGAGTTATACTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCG
* * * *
30527 AACTCGAAGGTCTTT-GACAGATAACCCTTTTTGCCTTAAGCTATGCTGCAAATAATGTGCCTTT
131 AACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATAATGTGCCTTT
30591 GAGCTGAGTGTAATTA-AACTCGAAGGTATTTGGCAGATAACCCTTCTTGC
196 GAGCTGAGTGTAA-TAGAACTCGAAGGTATTTGGCAGATAACCCTTCTTGC
* * *
30641 CTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATAGAACTCGAAGGTCTTTTGAT
1 CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGAT
* *
30706 AACAAATAACCCTTTTAGCATTGATTTATACTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCG
66 AACAGATAACCCTTTTAGCATTGAGTTATACTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCG
* * * * *
30771 AACTCGAAGGTCTTTTGATGATAAATAACCCTT-TTAGCATTGATTTATA-CTGCAAATGATGTG
131 AACTCGAAGGTC-TTTG--GACAGATAACCCTTCTT-GCCTTGAGTTA-AGCTGCAAATAATGTG
* * * *
30834 CCTCTGAGCTGAGTATAATCGAACTCGAAGGTATTTGGCAGATAACTCTTCTTGC
191 CCTTTGAGCTGAGTGTAATAGAACTCGAAGGTATTTGGCAGATAACCCTTCTTGC
* * *
30889 CTTGAGCTAAGCTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTTGAT
1 CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGAT
* * * * * *
30954 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTCTAAGCTGAGTGTAATCA
66 AACAGATAACCCTTTTAGCATTGAGTTATACTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCG
31019 AACTCGAAGGTCTTTGG-CAGATAACCCTTCTTGCCTTGA
131 AACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGA
31058 ACTATGCTAC
Statistics
Matches: 579, Mismatches: 67, Indels: 27
0.86 0.10 0.04
Matches are distributed among these distances:
241 55 0.09
243 3 0.01
244 291 0.50
245 14 0.02
247 7 0.01
248 209 0.36
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (245 bp):
CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGAT
AACAGATAACCCTTTTAGCATTGAGTTATACTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCG
AACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATAATGTGCCTTT
GAGCTGAGTGTAATAGAACTCGAAGGTATTTGGCAGATAACCCTTCTTGC
Found at i:30539 original size:164 final size:164
Alignment explanation
Indices: 30050--31075 Score: 1146
Period size: 164 Copynumber: 6.3 Consensus size: 164
30040 GACAATTTTG
* * * * * * * ** * *
30050 TTGACAAATAACCCTTATTACCTTGAGCTATGTTGTAAATTTGATTTGCCTCTGAATTTAATGTA
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTA
* * * * * * * * ** *
30115 ATCGAACTCGAAGCT-CTTTGATGATATAAAACCCTTCTCA-ACTTGAGTTATGCTATAAATAAT
64 ATCGAACTCGAAGGTATTTTGATGACAGATAACCCTT-TTAGCCTTGAGTTATACTGCAAATGAT
*
30178 GTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTT
128 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-T
* ** * * *
30216 TTGGA-AGATAGCTTTTCTTGCATTGAGCTAAGCTGCAAATGATGTACCTTTGAGCTGAGTGTAA
1 TT-GACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAA
* *
30280 TCGAACTCGAAGGT-CTTTG--GA-AGATAACCCTTCTT-GCCTTGAGTTA-AGCTGCAAATAAT
65 TCGAACTCGAAGGTATTTTGATGACAGATAACCCTT-TTAGCCTTGAGTTATA-CTGCAAATGAT
* * *
30339 GTGCCTTTGAGCTAAGTGTAATAGAACTTGAAGGTCT
128 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* *
30376 TTGACAGATAACCCTTCTTCCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTAAGTGTAAT
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
* * * *
30441 CGAACTCGAAAGTATTTTGATAACAGATAACCCTTTTAGCCTTGAGTTATACTACAAATGATATG
66 CGAACTCGAAGGTATTTTGATGACAGATAACCCTTTTAGCCTTGAGTTATACTGCAAATGATGTG
30506 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
131 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* * *
30540 TTGACAGATAACCCTTTTTGCCTTAAGCTATGCTGCAAATAATGTGCCTTTGAGCTGAGTGTAAT
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
** * *
30605 TAAACTCGAAGGTA-TTTG--G-CAGATAACCCTTCTT-GCCTTGAGTTATGCTGCAAATGATAT
66 CGAACTCGAAGGTATTTTGATGACAGATAACCCTT-TTAGCCTTGAGTTATACTGCAAATGATGT
*
30665 GCCTTTGAGCTGAGTGTAATAGAACTCGAAGGTCTT
130 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-T
* * ** * *
30701 TTGATAACAAATAACCCTT-TTAGCATTGATTTATACTGCAAATGATGTGCCTCTGAGCTGAGTG
1 TTG---ACAGATAACCCTTCTT-GCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* * * * *
30765 TAATCGAACTCGAAGGTCTTTTGATGATAAATAACCCTTTTAGCATTGATTTATACTGCAAATGA
62 TAATCGAACTCGAAGGTATTTTGATGACAGATAACCCTTTTAGCCTTGAGTTATACTGCAAATGA
* * *
30830 TGTGCCTCTGAGCTGAGTATAATCGAACTCGAAGGTAT
127 TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* * * *
30868 TTGGCAGATAACTCTTCTTGCCTTGAGCTAAGCTGCAAATGATGTGTCTTTGAGCTGAGTGTAAT
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
* * * *
30933 CGAACTCGAATGTCTTTTGATGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
66 CGAACTCGAAGGTATTTTGATGACAGATAACCCTTTTAGCCTTGAGTTATACTGCAAATGATGTG
* * *
30998 CCTCTAAGCTGAGTGTAATCAAACTCGAAGGTCT
131 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* * *
31032 TTGGCAGATAACCCTTCTTGCCTTGAACTATGCTACAAATGATG
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
31076 AGCCGATCAT
Statistics
Matches: 734, Mismatches: 104, Indels: 46
0.83 0.12 0.05
Matches are distributed among these distances:
159 2 0.00
160 136 0.19
161 71 0.10
162 2 0.00
163 9 0.01
164 410 0.56
165 7 0.01
166 26 0.04
167 9 0.01
168 62 0.08
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (164 bp):
TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
CGAACTCGAAGGTATTTTGATGACAGATAACCCTTTTAGCCTTGAGTTATACTGCAAATGATGTG
CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
Found at i:32376 original size:95 final size:95
Alignment explanation
Indices: 32167--32427 Score: 314
Period size: 95 Copynumber: 2.7 Consensus size: 95
32157 GACTAGCTGG
* * * *
32167 ATCCATAAAGCCAGGACGTTTAACCAATTGCTCT-AGGGGACAGCTCAAT--ATTATTGTATAGA
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAAAGGGACAACTC-ATGCTTTATTG--T--A
* *
32229 TATTACAATCGCCTTTAGCAGGCTAGCTGAATATT
61 TATTATAATCACCTTTAGCAGGCTAGCTGAATATT
* *
32264 ATACATAAGGCCAGGGCGTTTAACCAATTGCTCTAAAGGGACAACTCATGCTTTATTGTATATTA
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAAAGGGACAACTCATGCTTTATTGTATATTA
* * *
32329 TAATCACCTTTATCTGGCTAGCTGAATCTT
66 TAATCACCTTTAGCAGGCTAGCTGAATATT
* * * *
32359 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATA-TA
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAAAGGGACAACTCATGCTTTATTGTATATTA
32423 TAATC
66 TAATC
32428 TGGGTATACG
Statistics
Matches: 144, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
94 7 0.05
95 87 0.60
97 34 0.24
98 10 0.07
99 6 0.04
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (95 bp):
ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAAAGGGACAACTCATGCTTTATTGTATATTA
TAATCACCTTTAGCAGGCTAGCTGAATATT
Found at i:34288 original size:32 final size:34
Alignment explanation
Indices: 34247--34316 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
34237 ACCTTACAAC
*
34247 TCCCTAGCTTTT-C-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
*
34279 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
34313 TCCC
1 TCCC
34317 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 12 0.35
33 1 0.03
34 21 0.62
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:34556 original size:20 final size:22
Alignment explanation
Indices: 34531--34570 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
34521 AGTCGTATAT
34531 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
34551 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
34571 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:34622 original size:21 final size:21
Alignment explanation
Indices: 34598--34640 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
34588 CCCAGAATAG
*
34598 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
*
34619 AGGGAATTGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
34640 A
1 A
34641 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:34773 original size:15 final size:15
Alignment explanation
Indices: 34753--34797 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
34743 AACCTGCATG
34753 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
34768 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
34783 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
34798 CCTGGGGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:34807 original size:21 final size:21
Alignment explanation
Indices: 34783--34824 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34773 ATCTGTACCC
* *
34783 GGGGTATCTGTACCCCCTGGG
1 GGGGAATCTATACCCCCTGGG
34804 GGGGAATCTATACCCCCTGGG
1 GGGGAATCTATACCCCCTGGG
34825 CAATCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.29, G:0.36, T:0.21
Consensus pattern (21 bp):
GGGGAATCTATACCCCCTGGG
Found at i:34947 original size:29 final size:31
Alignment explanation
Indices: 34915--34972 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
34905 AACTTTGAAT
34915 AATTCAATT-AAGTCCAAAAA-CATTTTGTA
1 AATTCAATTCAAGTCCAAAAACCATTTTGTA
34944 AATTCAATTCAAGTCCAAAAACCATTTTG
1 AATTCAATTCAAGTCCAAAAACCATTTTG
34973 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 9 0.33
30 11 0.41
31 7 0.26
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
AATTCAATTCAAGTCCAAAAACCATTTTGTA
Found at i:36255 original size:19 final size:19
Alignment explanation
Indices: 36212--36259 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
36202 TCTAAATCCT
*
36212 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATCTCATTTTG
36231 TCTTTCAAAATCT-ATTTTTG
1 T-TTTCAAAATCTCA-TTTTG
36251 TTTTCAAAA
1 TTTTCAAAA
36260 GAAAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTCAAAATCTCATTTTG
Found at i:37184 original size:34 final size:34
Alignment explanation
Indices: 37119--37222 Score: 176
Period size: 34 Copynumber: 3.1 Consensus size: 34
37109 ACCTTACAAC
* *
37119 TCCCTAGCTTTT-C-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
37151 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
37185 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
37219 TCCC
1 TCCC
37223 CTTTACAAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 12 0.18
33 1 0.01
34 55 0.81
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
Found at i:37462 original size:20 final size:22
Alignment explanation
Indices: 37437--37476 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
37427 AGTCGTATAT
37437 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
37457 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
37477 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:37528 original size:21 final size:21
Alignment explanation
Indices: 37504--37546 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
37494 CCCAGAATAG
* *
37504 AGGGAATCGGTACCTCTTCAT
1 AGGGAATCGATACCCCTTCAT
37525 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
37546 A
1 A
37547 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:37608 original size:21 final size:21
Alignment explanation
Indices: 37582--37624 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
37572 CTGTTGAACA
37582 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
37603 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
37624 G
1 G
37625 AACATTCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:37681 original size:15 final size:15
Alignment explanation
Indices: 37661--37690 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
37651 AACCTGCATG
37661 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
37676 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
37691 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:37700 original size:21 final size:21
Alignment explanation
Indices: 37676--37717 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
37666 ATCTGTACCC
* *
37676 GGGGTATCTGTACCCCCTGGG
1 GGGGAATCTATACCCCCTGGG
37697 GGGGAATCTATACCCCCTGGG
1 GGGGAATCTATACCCCCTGGG
37718 CAATCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.29, G:0.36, T:0.21
Consensus pattern (21 bp):
GGGGAATCTATACCCCCTGGG
Found at i:37840 original size:29 final size:31
Alignment explanation
Indices: 37808--37865 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
37798 AACTTTGAAT
37808 AATTCAATT-AAGTCCAAAAA-CATTTTGTA
1 AATTCAATTCAAGTCCAAAAACCATTTTGTA
37837 AATTCAATTCAAGTCCAAAAACCATTTTG
1 AATTCAATTCAAGTCCAAAAACCATTTTG
37866 CCAAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 9 0.33
30 11 0.41
31 7 0.26
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
AATTCAATTCAAGTCCAAAAACCATTTTGTA
Found at i:39151 original size:19 final size:19
Alignment explanation
Indices: 39108--39155 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
39098 TCTAAATCCT
*
39108 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATCTCATTTTG
39127 TCTTTCAAAATCT-ATTTTTG
1 T-TTTCAAAATCTCA-TTTTG
39147 TTTTCAAAA
1 TTTTCAAAA
39156 GAAAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTCAAAATCTCATTTTG
Found at i:40058 original size:32 final size:34
Alignment explanation
Indices: 40015--40084 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
40005 ACCTTACAAC
* *
40015 TCCCTAGCTTTT-C-CGGGCTAAACTAGAACCTT
1 TCCCTAACTTTTACACGGGATAAACTAGAACCTT
*
40047 TCCCTAACTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAACTTTTACACGGGATAAACTAGAACCTT
40081 TCCC
1 TCCC
40085 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.30
Consensus pattern (34 bp):
TCCCTAACTTTTACACGGGATAAACTAGAACCTT
Found at i:40324 original size:20 final size:22
Alignment explanation
Indices: 40299--40338 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40289 AGTCGTATAT
40299 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
40319 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
40339 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:40390 original size:21 final size:21
Alignment explanation
Indices: 40366--40408 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
40356 CCCAGAATAG
*
40366 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
40387 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
40408 A
1 A
40409 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:40483 original size:20 final size:21
Alignment explanation
Indices: 40444--40486 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
40434 CTGTTGAACA
*
40444 GGGGGGGAATCGGTACCCCCT
1 GGGGAGGAATCGGTACCCCCT
40465 GGGGAGGAATCGGTACCCCCT
1 GGGGAGGAATCGGTACCCCCT
40486 G
1 G
40487 AACATTCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.28, G:0.42, T:0.14
Consensus pattern (21 bp):
GGGGAGGAATCGGTACCCCCT
Found at i:40566 original size:15 final size:15
Alignment explanation
Indices: 40546--40574 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40536 CCCCTGGGGC
40546 GGGTATCTGTACCCG
1 GGGTATCTGTACCCG
40561 GGGTATCTGTACCC
1 GGGTATCTGTACCC
40575 CCTGGGCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.28
Consensus pattern (15 bp):
GGGTATCTGTACCCG
Found at i:40703 original size:29 final size:31
Alignment explanation
Indices: 40671--40728 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
40661 AACTTTGAAT
40671 AATTCAATT-AAGTCCAAAAA-CATTTTGTA
1 AATTCAATTCAAGTCCAAAAACCATTTTGTA
40700 AATTCAATTCAAGTCCAAAAACCATTTTG
1 AATTCAATTCAAGTCCAAAAACCATTTTG
40729 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 9 0.33
30 11 0.41
31 7 0.26
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
AATTCAATTCAAGTCCAAAAACCATTTTGTA
Found at i:42006 original size:18 final size:18
Alignment explanation
Indices: 41965--42009 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
41955 TCTAAATCCT
*
41965 TTTTCAAATTTCATTTTG
1 TTTTCAAATCTCATTTTG
41983 TCTTTCAAATCT-ATTTTTG
1 T-TTTCAAATCTCA-TTTTG
42002 TTTTCAAA
1 TTTTCAAA
42010 AGAAAATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.24, C:0.13, G:0.04, T:0.58
Consensus pattern (18 bp):
TTTTCAAATCTCATTTTG
Found at i:42911 original size:32 final size:34
Alignment explanation
Indices: 42870--42939 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
42860 ACCTTACAAC
* *
42870 TCCCTAGCTTTT-C-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
*
42902 TCCCTAGCTTTTACACGGGATAAGCTAGAACATT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
42936 TCCC
1 TCCC
42940 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.36
33 1 0.03
34 20 0.61
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACATT
Found at i:43205 original size:21 final size:20
Alignment explanation
Indices: 43158--43213 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 20
43148 GTATATAGCT
*
43158 GTTGGGGATGTTTTGGAGCC
1 GTTGGGGATGTTTTGAAGCC
43178 GTTGGGGATGTTTTGAAGCC
1 GTTGGGGATGTTTTGAAGCC
43198 GTTTGGGGATGATTTT
1 G-TTGGGGATG-TTTT
43214 TATACTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 20 0.61
21 9 0.27
22 4 0.12
ACGTcount: A:0.12, C:0.07, G:0.41, T:0.39
Consensus pattern (20 bp):
GTTGGGGATGTTTTGAAGCC
Found at i:43265 original size:21 final size:21
Alignment explanation
Indices: 43241--43283 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
43231 CCCAGAATAG
*
43241 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
43262 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
43283 A
1 A
43284 ATATTCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:43345 original size:21 final size:21
Alignment explanation
Indices: 43319--43361 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
43309 CTGTTGAATA
43319 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
43340 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
43361 G
1 G
43362 AACATTCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:43563 original size:29 final size:31
Alignment explanation
Indices: 43531--43588 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
43521 AACTTTGAAT
43531 AATTCAATT-AAGTCCAAAAA-CATTTTGTA
1 AATTCAATTCAAGTCCAAAAACCATTTTGTA
43560 AATTCAATTCAAGTCCAAAAACCATTTTG
1 AATTCAATTCAAGTCCAAAAACCATTTTG
43589 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 9 0.33
30 11 0.41
31 7 0.26
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
AATTCAATTCAAGTCCAAAAACCATTTTGTA
Found at i:44871 original size:19 final size:19
Alignment explanation
Indices: 44828--44875 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
44818 TCTAAATCCT
*
44828 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATCTCATTTTG
44847 TCTTTCAAAATCT-ATTTTTG
1 T-TTTCAAAATCTCA-TTTTG
44867 TTTTCAAAA
1 TTTTCAAAA
44876 GAAAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTCAAAATCTCATTTTG
Found at i:45776 original size:32 final size:34
Alignment explanation
Indices: 45735--45804 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
45725 ACCTTACAAC
* *
45735 TCCCTAGCTTTT-C-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
*
45767 TCCCTAGCTTTTACACGGGATAAGCTAGAACATT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACATT
45801 TCCC
1 TCCC
45805 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 12 0.36
33 1 0.03
34 20 0.61
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACATT
Found at i:46044 original size:20 final size:22
Alignment explanation
Indices: 46019--46058 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
46009 AGTCGTATAT
46019 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
46039 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
46059 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:46110 original size:21 final size:21
Alignment explanation
Indices: 46086--46128 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
46076 CCCATAATAG
*
46086 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
46107 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
46128 A
1 A
46129 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:46190 original size:21 final size:21
Alignment explanation
Indices: 46164--46206 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
46154 CTGTTGAACA
46164 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
46185 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
46206 G
1 G
46207 AACATTCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:46268 original size:21 final size:20
Alignment explanation
Indices: 46242--46319 Score: 85
Period size: 20 Copynumber: 4.1 Consensus size: 20
46232 AAACCTGCAT
46242 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCT-G
46263 GGGGGTATCTGTA--CCC--
1 GGGGGTATCTGTACCCCCTG
*
46279 -GAGGTATCTGTACCCCCTG
1 GGGGGTATCTGTACCCCCTG
* *
46298 GGGGGAATCTATACCCCCTG
1 GGGGGTATCTGTACCCCCTG
46318 GG
1 GG
46320 CAATCTTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
15 11 0.23
17 3 0.06
19 3 0.06
20 18 0.38
21 13 0.27
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.23
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCCTG
Found at i:46313 original size:35 final size:36
Alignment explanation
Indices: 46245--46313 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
46235 CCTGCATGGG
* *
46245 GGTATCTGTACCCCCTGGGGGGGTATCTGTACCCGA
1 GGTATCTGTACCCCCTGGGGGGGAATCTATACCCGA
46281 GGTATCTGTACCCCCT-GGGGGGAATCTATACCC
1 GGTATCTGTACCCCCTGGGGGGGAATCTATACCC
46314 CCTGGGCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 15 0.48
36 16 0.52
ACGTcount: A:0.16, C:0.29, G:0.30, T:0.25
Consensus pattern (36 bp):
GGTATCTGTACCCCCTGGGGGGGAATCTATACCCGA
Found at i:46442 original size:29 final size:31
Alignment explanation
Indices: 46410--46467 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
46400 AACTTTGAAT
46410 AATTCAATT-AAGTCCAAAAA-CATTTTGTA
1 AATTCAATTCAAGTCCAAAAACCATTTTGTA
46439 AATTCAATTCAAGTCCAAAAACCATTTTG
1 AATTCAATTCAAGTCCAAAAACCATTTTG
46468 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 9 0.33
30 11 0.41
31 7 0.26
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
AATTCAATTCAAGTCCAAAAACCATTTTGTA
Found at i:47679 original size:22 final size:22
Alignment explanation
Indices: 47654--47733 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 22
47644 TTTAAATCAA
47654 AATTTTCTTTTTCAAAACTTTC
1 AATTTTCTTTTTCAAAACTTTC
* * * *
47676 AATTTTTATTTTTGAAAGCTCT-
1 AA-TTTTCTTTTTCAAAACTTTC
*
47698 AA-ATTCTTTTTCAAAA-TTTC
1 AATTTTCTTTTTCAAAACTTTC
* *
47718 -ATTTTGTCTTTCAAAA
1 AATTTTCTTTTTCAAAA
47734 TCTATTTTTG
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
19 3 0.07
20 21 0.49
22 4 0.09
23 15 0.35
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.53
Consensus pattern (22 bp):
AATTTTCTTTTTCAAAACTTTC
Found at i:47748 original size:19 final size:19
Alignment explanation
Indices: 47705--47752 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
47695 TCTAAATTCT
*
47705 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATCTCATTTTG
47724 TCTTTCAAAATCT-ATTTTTG
1 T-TTTCAAAATCTCA-TTTTG
47744 TTTTCAAAA
1 TTTTCAAAA
47753 GAAAATCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTCAAAATCTCATTTTG
Found at i:48469 original size:32 final size:34
Alignment explanation
Indices: 48428--48497 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
48418 ACCTTACAAC
*
48428 TCCCTAGCTTTT-C-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
*
48460 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
48494 TCCC
1 TCCC
48498 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 12 0.35
33 1 0.03
34 21 0.62
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:48737 original size:20 final size:22
Alignment explanation
Indices: 48712--48751 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
48702 AGTCGTATAT
48712 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
48732 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
48752 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:48803 original size:21 final size:21
Alignment explanation
Indices: 48779--48821 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
48769 CCCAGAATAG
*
48779 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
48800 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
48821 A
1 A
48822 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:48938 original size:20 final size:20
Alignment explanation
Indices: 48913--48988 Score: 90
Period size: 21 Copynumber: 4.0 Consensus size: 20
48903 AAACCTGCAT
48913 GGGGGTATCTGTACCCCCTG
1 GGGGGTATCTGTACCCCCTG
48933 GGGGGTATCTGTA--CCC--
1 GGGGGTATCTGTACCCCCTG
48949 -GGGGTATCTGTACCCCCTG
1 GGGGGTATCTGTACCCCCTG
* *
48968 GGTGGGAATCTATACCCCCTG
1 GG-GGGTATCTGTACCCCCTG
48989 AGCAATCTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
15 12 0.25
17 3 0.06
18 3 0.06
20 14 0.29
21 16 0.33
ACGTcount: A:0.13, C:0.29, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCCTG
Found at i:48953 original size:35 final size:36
Alignment explanation
Indices: 48914--48984 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
48904 AACCTGCATG
* *
48914 GGGGTATCTGTACCCCCTGGG-GGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGTGGGAATCTATACCC
48949 GGGGTATCTGTACCCCCTGGGTGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGTGGGAATCTATACCC
48985 CCTGAGCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 21 0.64
36 12 0.36
ACGTcount: A:0.14, C:0.28, G:0.32, T:0.25
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGTGGGAATCTATACCC
Found at i:48954 original size:15 final size:15
Alignment explanation
Indices: 48934--48963 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
48924 TACCCCCTGG
48934 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
48949 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
48964 CCTGGGTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:49113 original size:29 final size:31
Alignment explanation
Indices: 49081--49138 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
49071 AACTTTGAAT
49081 AATTCAATT-AAGTCCAAAAA-CATTTTGTA
1 AATTCAATTCAAGTCCAAAAACCATTTTGTA
49110 AATTCAATTCAAGTCCAAAAACCATTTTG
1 AATTCAATTCAAGTCCAAAAACCATTTTG
49139 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 9 0.33
30 11 0.41
31 7 0.26
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
AATTCAATTCAAGTCCAAAAACCATTTTGTA
Found at i:53201 original size:65 final size:63
Alignment explanation
Indices: 53113--53234 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
53103 CCCATTCAAA
* * * *
53113 AGGTATCGATACCCTCTCAAACGAAAAGAATCACAGAATGTAATGAGGGTACCGATACCCCAGTT
1 AGGTACCGATACCCTCTCAAACG-AAA-AATAACAGAATGCAATAAGGGTACCGATACCCCAGTT
** * *
53178 AGGTACCGATACCCTCTTGAACGAAAACTAACAGAATGCAGTAAGGGTACCGATACC
1 AGGTACCGATACCCTCTCAAACGAAAAATAACAGAATGCAATAAGGGTACCGATACC
53235 TCAAGGGGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 26 0.53
64 3 0.06
65 20 0.41
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (63 bp):
AGGTACCGATACCCTCTCAAACGAAAAATAACAGAATGCAATAAGGGTACCGATACCCCAGTT
Found at i:58317 original size:45 final size:45
Alignment explanation
Indices: 58233--58320 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 45
58223 AAAACAAATA
* *
58233 AGATACAAAAAATAGATTAAAGAAAAAAATGAAGTAAATAAAACG
1 AGATACAAAAAATAGAGTAAAGAAAAAAATGAAATAAATAAAACG
* *
58278 AGATA-AAAAAATGGAGTAAAGATAAAAA-GTAAATAAAATAAAA
1 AGATACAAAAAATAGAGTAAAGAAAAAAATG-AAAT-AAATAAAA
58321 ATAAAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 1 0.03
44 23 0.62
45 13 0.35
ACGTcount: A:0.68, C:0.02, G:0.14, T:0.16
Consensus pattern (45 bp):
AGATACAAAAAATAGAGTAAAGAAAAAAATGAAATAAATAAAACG
Found at i:58319 original size:22 final size:21
Alignment explanation
Indices: 58294--58353 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
58284 AAAAATGGAG
* *
58294 TAAAGATAAAAAGTAAATAAAA
1 TAAAAATAAAAA-TAAAGAAAA
*
58316 TAAAAATAAAAATAACGAAAA
1 TAAAAATAAAAATAAAGAAAA
*
58337 TAAAAAGTAAAGATAAA
1 TAAAAA-TAAAAATAAA
58354 TACAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 13 0.41
22 19 0.59
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (21 bp):
TAAAAATAAAAATAAAGAAAA
Found at i:58381 original size:4 final size:4
Alignment explanation
Indices: 58349--58489 Score: 56
Period size: 4 Copynumber: 33.0 Consensus size: 4
58339 AAAAGTAAAG
* *
58349 ATAA ATACA A-AA ATAA ACAA ATGA ATAA ATAA ATAA ATAA ATATGA ATAA
1 ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA
* * * * *
58399 GTAAA ACGAA GATAA AGAAA ATAAA ATAA AGAGA A-GA A-AA ATAA ATAA
1 AT-AA A-TAA -ATAA A-TAA AT-AA ATAA ATA-A ATAA ATAA ATAA ATAA
* *
58447 ATAAA ATAA ATAA GATAA AGAA A-AA ATAA TAGTAA AGAA ATAA
1 AT-AA ATAA ATAA -ATAA ATAA ATAA ATAA -A-TAA ATAA ATAA
58490 TATATATATA
Statistics
Matches: 105, Mismatches: 16, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
3 9 0.09
4 61 0.58
5 27 0.26
6 8 0.08
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (4 bp):
ATAA
Found at i:58842 original size:11 final size:11
Alignment explanation
Indices: 58772--58984 Score: 53
Period size: 11 Copynumber: 17.9 Consensus size: 11
58762 AACAATAGGA
58772 AAAAATAAAA-
1 AAAAATAAAAT
*
58782 AGAAAT-AAAT
1 AAAAATAAAAT
58792 AAAATATATATAAT
1 AAAA-ATA-A-AAT
*
58806 -AAGATATAAA-
1 AAAAATA-AAAT
*
58816 AAAAATAAACAA
1 AAAAATAAA-AT
58828 AAAAATAAAAT
1 AAAAATAAAAT
58839 AAAAGGATTAAAAT
1 AAAA--A-TAAAAT
*
58853 AGAAATAGAAAT
1 AAAAATA-AAAT
*
58865 AAATATATATATAT
1 AAA-A-ATA-AAAT
* * *
58879 AATAACGTTTAAAC
1 AA-AA--ATAAAAT
58893 AAAATATTAAAAT
1 AAAA-A-TAAAAT
58906 -AAAATAATAAT
1 AAAAATAA-AAT
* *
58917 AGGAAATAAAAC
1 A-AAAATAAAAT
58929 AAAAATAAAAT
1 AAAAATAAAAT
58940 GAACAAATAAAA-
1 -AA-AAATAAAAT
*
58952 AATAATAAAA-
1 AAAAATAAAAT
*
58962 AGAATAATAAAAG
1 A-AA-AATAAAAT
*
58975 AATAATAAAA
1 AAAAATAAAA
58985 GGACTAAATT
Statistics
Matches: 153, Mismatches: 25, Indels: 49
0.67 0.11 0.22
Matches are distributed among these distances:
9 3 0.02
10 21 0.14
11 39 0.25
12 37 0.24
13 26 0.17
14 25 0.16
15 2 0.01
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:58927 original size:76 final size:74
Alignment explanation
Indices: 58765--58933 Score: 177
Period size: 76 Copynumber: 2.3 Consensus size: 74
58755 ATACACAAAC
58765 AATAGGAA-AAAATAAAAAGAAATAAATAAAATATATATAATAAGATATAAAAAAAATAAACAAA
1 AATAGGAATAAAATAAAAAGAAATAAATAAAATATATATAATAAGATATAAAAAAAATAAACAAA
58829 AAAATAAAAT
66 AAAAT-AAAT
* * * * *
58839 AAAAGGATTAAAATAGAAATAGAAATAAAT-ATATATATATAATAACG-TTTAAACAAAATATTA
1 AATAGGAATAAAATA-AAA-AGAAATAAATAAAATATATATAATAA-GATATAAA-AAAA-ATAA
*
58902 A-AATAAAAT-AAT
61 ACAAAAAAATAAAT
*
58914 AATAGGAAATAAAACAAAAA
1 AATAGG-AATAAAATAAAAA
58934 TAAAATGAAC
Statistics
Matches: 79, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
74 7 0.09
75 17 0.22
76 29 0.37
77 22 0.28
78 4 0.05
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (74 bp):
AATAGGAATAAAATAAAAAGAAATAAATAAAATATATATAATAAGATATAAAAAAAATAAACAAA
AAAATAAAT
Found at i:58978 original size:23 final size:23
Alignment explanation
Indices: 58920--58984 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
58910 TAATAATAGG
* *
58920 AAATAAAACAAAAATAAAATGAAC
1 AAATAAAA-AATAATAAAAAGAAC
58944 AAATAAAAAATAATAAAAAGAA-
1 AAATAAAAAATAATAAAAAGAAC
*
58966 TAATAAAAGAATAATAAAA
1 AAATAAAA-AATAATAAAA
58985 GGACTAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.19
23 22 0.59
24 8 0.22
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (23 bp):
AAATAAAAAATAATAAAAAGAAC
Found at i:58985 original size:11 final size:11
Alignment explanation
Indices: 58908--58985 Score: 70
Period size: 11 Copynumber: 7.0 Consensus size: 11
58898 ATTAAAATAA
*
58908 AATAATAATAG
1 AATAATAAAAG
* *
58919 GA-AATAAAAC
1 AATAATAAAAG
*
58929 AAAAATAAAATG
1 AATAATAAAA-G
*
58941 AACAAATAAAA-
1 AA-TAATAAAAG
58952 AATAATAAAAAG
1 AATAAT-AAAAG
58964 AATAATAAAAG
1 AATAATAAAAG
58975 AATAATAAAAG
1 AATAATAAAAG
58986 GACTAAATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
10 10 0.18
11 30 0.54
12 8 0.14
13 8 0.14
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.17
Consensus pattern (11 bp):
AATAATAAAAG
Found at i:65465 original size:6 final size:6
Alignment explanation
Indices: 65454--65481 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
65444 TTTTCTTCCC
65454 GGGGTG GGGGTG GGGGTG GGGGTG GGGG
1 GGGGTG GGGGTG GGGGTG GGGGTG GGGG
65482 AGGAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.86, T:0.14
Consensus pattern (6 bp):
GGGGTG
Found at i:74579 original size:40 final size:40
Alignment explanation
Indices: 74533--74689 Score: 153
Period size: 40 Copynumber: 4.0 Consensus size: 40
74523 CCTTTTTAGT
* *
74533 GTGGAACTTTTATGTAAATTAGGTTAACTGCATTTTCCAC
1 GTGGAACTTTTACGTAAACTAGGTTAACTGCATTTTCCAC
* *
74573 GTGGAACTTTTACGTAAACTAGGTTAACTTCATTTTCCAT
1 GTGGAACTTTTACGTAAACTAGGTTAACTGCATTTTCCAC
** * * * *
74613 GTAAAAC--TTAGGCT-CACTCTGGTT--TTGCATTTTCCCAC
1 GTGGAACTTTTACG-TAAACT-AGGTTAACTGCATTTT-CCAC
*
74651 GTGGAACTTTTACGTAAACTAGGTTAACTTCATTTTCCA
1 GTGGAACTTTTACGTAAACTAGGTTAACTGCATTTTCCA
74690 TGTAAAACTT
Statistics
Matches: 90, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
37 7 0.08
38 15 0.17
39 10 0.11
40 51 0.57
41 7 0.08
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (40 bp):
GTGGAACTTTTACGTAAACTAGGTTAACTGCATTTTCCAC
Found at i:74656 original size:78 final size:77
Alignment explanation
Indices: 74561--74717 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 77
74551 TTAGGTTAAC
74561 TGCATTTTCCACGTGGAACTTTTACGTAAACTAGGTTAACTTCATTTTCCATGTAAAACTTAGGC
1 TGCATTTTCCACGTGGAACTTTTACGTAAACTAGGTTAACTTCATTTTCCATGTAAAACTTAGGC
74626 TCACTCTGGTTT
66 TCACTCTGGTTT
74638 TGCATTTTCCCACGTGGAACTTTTACGTAAACTAGGTTAACTTCATTTTCCATGTAAAACTTAGG
1 TGCATTTT-CCACGTGGAACTTTTACGTAAACTAGGTTAACTTCATTTTCCATGTAAAACTTAGG
74703 CTCACTCTGGTTT
65 CTCACTCTGGTTT
74716 TG
1 TG
74718 AAGATAGAAG
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 8 0.10
78 71 0.90
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (77 bp):
TGCATTTTCCACGTGGAACTTTTACGTAAACTAGGTTAACTTCATTTTCCATGTAAAACTTAGGC
TCACTCTGGTTT
Found at i:79615 original size:18 final size:19
Alignment explanation
Indices: 79587--79624 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
79577 AACTAGTAAA
79587 GCAGAGGAAAGATCAGAAG
1 GCAGAGGAAAGATCAGAAG
79606 GCAG-GGAAAGATCAGAAG
1 GCAGAGGAAAGATCAGAAG
79624 G
1 G
79625 AAGGCATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.45, C:0.11, G:0.39, T:0.05
Consensus pattern (19 bp):
GCAGAGGAAAGATCAGAAG
Found at i:80015 original size:3 final size:3
Alignment explanation
Indices: 80007--80033 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
79997 GGAACTCTTC
80007 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
80034 AGATAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:80972 original size:24 final size:24
Alignment explanation
Indices: 80939--81020 Score: 139
Period size: 24 Copynumber: 3.5 Consensus size: 24
80929 TTTTTCGGAT
* *
80939 AAAAAA-CGGTTTTTTAACCAGTA
1 AAAAAACCGGTTTTTTATCCGGTA
80962 AAAAAACCGGTTTTTTATCCGGTA
1 AAAAAACCGGTTTTTTATCCGGTA
80986 AAAAAACCGGTTTTTTATCCGGTA
1 AAAAAACCGGTTTTTTATCCGGTA
81010 AAAAAACCGGT
1 AAAAAACCGGT
81021 CGTCCAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
23 6 0.11
24 50 0.89
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
AAAAAACCGGTTTTTTATCCGGTA
Found at i:87771 original size:84 final size:84
Alignment explanation
Indices: 87626--87794 Score: 293
Period size: 84 Copynumber: 2.0 Consensus size: 84
87616 CTGCCGAAAA
* *
87626 GTGTTTGCGACACTTTGGAAAAGTTTATTCGTAGATTTGTGTGGAATGCAAATAGAAGTTCAAAT
1 GTGTTTGCGACACTTTGGAAAAGCTTATTCGTAGATTTGTGCGGAATGCAAATAGAAGTTCAAAT
87691 AGCCTTGCGTTAATTAAAT
66 AGCCTTGCGTTAATTAAAT
* * *
87710 GTGTTTGCGATACTTTGGAAAAGCTTATTCGTAGATTTGTGCGGAATGCAAATGGAGGTTCAAAT
1 GTGTTTGCGACACTTTGGAAAAGCTTATTCGTAGATTTGTGCGGAATGCAAATAGAAGTTCAAAT
87775 AGCCTTGCGTTAATTAAAT
66 AGCCTTGCGTTAATTAAAT
87794 G
1 G
87795 GGACACAGCT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (84 bp):
GTGTTTGCGACACTTTGGAAAAGCTTATTCGTAGATTTGTGCGGAATGCAAATAGAAGTTCAAAT
AGCCTTGCGTTAATTAAAT
Found at i:100487 original size:28 final size:26
Alignment explanation
Indices: 100429--100501 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 26
100419 TTTTTTATTT
* *
100429 TATTTTATTGATAATATTCATCATGA
1 TATTTTATTTATAATATTCATCATAA
100455 TATTTTATTTATAATTACTTCATC-TAA
1 TATTTTATTTATAA-TA-TTCATCATAA
100482 TAATTTTATATTATTAATAT
1 T-ATTTTAT-TTA-TAATAT
100502 ATGTGTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 13 0.32
27 5 0.12
28 14 0.35
29 5 0.12
30 3 0.08
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.55
Consensus pattern (26 bp):
TATTTTATTTATAATATTCATCATAA
Found at i:101958 original size:363 final size:365
Alignment explanation
Indices: 101279--102007 Score: 1417
Period size: 363 Copynumber: 2.0 Consensus size: 365
101269 AAATGAAGCA
101279 TTTTCAGATAATTAAAGGAAACTTTTTATGTTAGCAAATGTGTGATTCCTTTTTTTTAAAAATTT
1 TTTTCAGATAATTAAAGGAAACTTTTTATGTTAGCAAATGTGTGATTCCTTTTTTTTAAAAATTT
101344 AATTCTCTAGAAAAACTTCAGAATCCACCTTTGGGATTTAGTTGATTTTGTTTCTGATATGCTAA
66 AATTCTCTAGAAAAACTTCAGAATCCACCTTTGGGATTTAGTTGATTTTGTTTCTGATATGCTAA
101409 AATGAGTGACCTCTTTAATTTTCGTATTATTTCCTATTTTTCTTTTTTTTTTTCAACTGATTTAT
131 AATGAGTGACCTCTTTAATTTTCGTATTATTTCCTATTTTTC-TTTTTTTTTTCAACTGATTTAT
101474 ACAAAAGGAGTGATAGTTTTTCCTCCTTTTTCTTTTTTAATATCTAATTTTTGGAGTTTAGATCA
195 ACAAAAGGAGTGATAGTTTTTCCTCCTTTTTCTTTTTTAATATCTAATTTTTGGAGTTTAGATCA
101539 AACTTGAATCTATAGGTTTTTTCAGTGTGTTGACTTTTGATTTTAGATTTCTCCATAGTTGTTTA
260 AACTTGAATCTATAGGTTTTTTCAGTGTGTTGACTTTTGATTTTAGATTTCTCCATAGTTGTTTA
101604 TAATATGCTAATTGTTTCTATTTCTATTGAATTTTGCAGTT
325 TAATATGCTAATTGTTTCTATTTCTATTGAATTTTGCAGTT
**
101645 TTTTCAGATAATTAAAGGAAACTTTTTATGTTAGC-AATGTGTGATTCCTTTTTTTTTTAAATTT
1 TTTTCAGATAATTAAAGGAAACTTTTTATGTTAGCAAATGTGTGATTCCTTTTTTTTAAAAATTT
101709 AATTCTCTAGAAAAACTTCAGAATCCACCTTTGGGATTTAGTTGATTTTGTTTCTGATATGCTAA
66 AATTCTCTAGAAAAACTTCAGAATCCACCTTTGGGATTTAGTTGATTTTGTTTCTGATATGCTAA
101774 AATGAGTGACCTCTTTAATTTTCGTATTATTTCCTATTTTTC-TTTTTTTTTCAACTGATTTATA
131 AATGAGTGACCTCTTTAATTTTCGTATTATTTCCTATTTTTCTTTTTTTTTTCAACTGATTTATA
101838 CAAAAGGAGTGATAGTTTTTCCTCCTTTTTCTTTTTTAATATCTAATTTTTGGAGTTTAGATCAA
196 CAAAAGGAGTGATAGTTTTTCCTCCTTTTTCTTTTTTAATATCTAATTTTTGGAGTTTAGATCAA
101903 ACTTGAATCTATAGGTTTTTTCAGTGTGTTGACTTTTGATTTTAGATTTCTCCATAGTTGTTTAT
261 ACTTGAATCTATAGGTTTTTTCAGTGTGTTGACTTTTGATTTTAGATTTCTCCATAGTTGTTTAT
101968 AATATGCTAATTGTTTCTATTTCTATTGAATTTTGCAGTT
326 AATATGCTAATTGTTTCTATTTCTATTGAATTTTGCAGTT
102008 AAGATTTGAA
Statistics
Matches: 361, Mismatches: 2, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
363 192 0.53
365 134 0.37
366 35 0.10
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.50
Consensus pattern (365 bp):
TTTTCAGATAATTAAAGGAAACTTTTTATGTTAGCAAATGTGTGATTCCTTTTTTTTAAAAATTT
AATTCTCTAGAAAAACTTCAGAATCCACCTTTGGGATTTAGTTGATTTTGTTTCTGATATGCTAA
AATGAGTGACCTCTTTAATTTTCGTATTATTTCCTATTTTTCTTTTTTTTTTCAACTGATTTATA
CAAAAGGAGTGATAGTTTTTCCTCCTTTTTCTTTTTTAATATCTAATTTTTGGAGTTTAGATCAA
ACTTGAATCTATAGGTTTTTTCAGTGTGTTGACTTTTGATTTTAGATTTCTCCATAGTTGTTTAT
AATATGCTAATTGTTTCTATTTCTATTGAATTTTGCAGTT
Found at i:110725 original size:22 final size:23
Alignment explanation
Indices: 110700--110743 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
110690 AAACATTTTA
* *
110700 AAACTT-AGCTCAATTGAAGCTC
1 AAACTTGAGCACAATTCAAGCTC
110722 AAACTTGAGCACAATTCAAGCT
1 AAACTTGAGCACAATTCAAGCT
110744 AGAACTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (23 bp):
AAACTTGAGCACAATTCAAGCTC
Found at i:110966 original size:16 final size:16
Alignment explanation
Indices: 110939--110977 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
110929 AGAACTCGAG
110939 TCAAATTCAAGCTTGAA
1 TCAAA-TCAAGCTTGAA
110956 TCAAATCAAGCTTGAA
1 TCAAATCAAGCTTGAA
110972 TCAAAT
1 TCAAAT
110978 TGAGTCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (16 bp):
TCAAATCAAGCTTGAA
Found at i:112994 original size:12 final size:12
Alignment explanation
Indices: 112977--113064 Score: 67
Period size: 12 Copynumber: 7.6 Consensus size: 12
112967 GGATTTTTTT
112977 ATTAATTAATCG
1 ATTAATTAATCG
** **
112989 ATTAATTTTTTT
1 ATTAATTAATCG
113001 ATTAATTAATCG
1 ATTAATTAATCG
113013 ATTAATT--T--
1 ATTAATTAATCG
113021 ATTAATTAATCG
1 ATTAATTAATCG
** **
113033 ATTAATTTTTTTT
1 ATTAA-TTAATCG
113046 ATTAATTAATCG
1 ATTAATTAATCG
113058 ATTAATT
1 ATTAATT
113065 TTTTATCCAG
Statistics
Matches: 55, Mismatches: 16, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
8 7 0.13
10 2 0.04
12 38 0.69
13 8 0.15
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (12 bp):
ATTAATTAATCG
Found at i:113001 original size:24 final size:24
Alignment explanation
Indices: 112969--113068 Score: 163
Period size: 24 Copynumber: 4.3 Consensus size: 24
112959 ATTGAATCGG
112969 ATTTTTTTATTAATTAATCGATTA
1 ATTTTTTTATTAATTAATCGATTA
112993 ATTTTTTTATTAATTAATCGATTA
1 ATTTTTTTATTAATTAATCGATTA
113017 A----TTTATTAATTAATCGATTA
1 ATTTTTTTATTAATTAATCGATTA
113037 ATTTTTTTTATTAATTAATCGATTA
1 A-TTTTTTTATTAATTAATCGATTA
113062 ATTTTTT
1 ATTTTTT
113069 ATCCAGTCGA
Statistics
Matches: 71, Mismatches: 0, Indels: 10
0.88 0.00 0.12
Matches are distributed among these distances:
20 20 0.28
24 31 0.44
25 20 0.28
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (24 bp):
ATTTTTTTATTAATTAATCGATTA
Found at i:113079 original size:45 final size:44
Alignment explanation
Indices: 112974--113082 Score: 157
Period size: 45 Copynumber: 2.5 Consensus size: 44
112964 ATCGGATTTT
*
112974 TTTATTAATTAATCGATTAATTTTTTTATTAATTAATCGATTAA
1 TTTATTAATCAATCGATTAATTTTTTTATTAATTAATCGATTAA
*
113018 TTTATTAATTAATCGATTAATTTTTTTTATTAATTAATCGATTAA
1 TTTATTAATCAATCGATTAA-TTTTTTTATTAATTAATCGATTAA
* *
113063 TTT-TTTATCCAGTCGATTAA
1 TTTATTAAT-CAATCGATTAA
113083 CAATTAAATA
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
44 24 0.40
45 36 0.60
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (44 bp):
TTTATTAATCAATCGATTAATTTTTTTATTAATTAATCGATTAA
Found at i:120764 original size:18 final size:18
Alignment explanation
Indices: 120738--120774 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
120728 TCAACTAAAC
*
120738 AACACCCTATAGTTTGGG
1 AACACCCTATAATTTGGG
*
120756 AACATCCTATAATTTGGG
1 AACACCCTATAATTTGGG
120774 A
1 A
120775 CCGTTCTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (18 bp):
AACACCCTATAATTTGGG
Found at i:126846 original size:20 final size:20
Alignment explanation
Indices: 126821--126875 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
126811 TTTTACATAC
126821 GAGTATCGAAACTCAACAGT
1 GAGTATCGAAACTCAACAGT
126841 GAGTATCGAAACTCAACAGT
1 GAGTATCGAAACTCAACAGT
126861 GAGTATCGAAACTCA
1 GAGTATCGAAACTCA
126876 CATGTTGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
GAGTATCGAAACTCAACAGT
Found at i:127386 original size:21 final size:21
Alignment explanation
Indices: 127362--127422 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
127352 AAACATCTAC
127362 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
**
127383 CAAA----G--AAACATTTAC
1 CAAACTTTGAAAAACATTTTT
*
127398 CAAACTTTAAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
127419 CAAA
1 CAAA
127423 GTTGGTTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 12 0.41
17 1 0.03
21 16 0.55
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.31
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:127399 original size:36 final size:36
Alignment explanation
Indices: 127344--127423 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
127334 CCCATTCCTA
* *
127344 TTTTC-AACAAACATCTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTAAAAAACAT
*
127379 TTTTCAAAGAAACATTTACCAAACTTTAAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTAAAAAACAT
127415 TTTTCAAAG
1 TTTTCAAAG
127424 TTGGTTGCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 5 0.12
36 36 0.88
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (36 bp):
TTTTCAAAGAAACATCTACCAAACTTTAAAAAACAT
Found at i:130720 original size:15 final size:15
Alignment explanation
Indices: 130700--130731 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
130690 AAAATATTTC
*
130700 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
130715 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
130730 TT
1 TT
130732 GGATCTGCCA
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:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:131957 original size:21 final size:21
Alignment explanation
Indices: 131933--132001 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
131923 CAAACTTTAC
131933 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
* * **
131954 CAAATTTTCAAAGAAACATTTAC
1 CAAACTTT-GAA-AAACATTTTT
131977 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
131998 CAAA
1 CAAA
132002 GTTGGTTGCC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 19 0.50
22 4 0.11
23 15 0.39
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.33
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:132475 original size:21 final size:22
Alignment explanation
Indices: 132422--132480 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
132412 AGTAGGCATC
* *
132422 GAGTTGT-AGTCTTTTCCTAATT
1 GAGTTGTAACTCTTTT-TTAATT
*
132444 GAGTTGTAACTTTTTTTTAATT
1 GAGTTGTAACTCTTTTTTAATT
*
132466 GTGTTG-AACTCTTTT
1 GAGTTGTAACTCTTTT
132481 CTTCAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 8 0.26
22 17 0.55
23 6 0.19
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.54
Consensus pattern (22 bp):
GAGTTGTAACTCTTTTTTAATT
Found at i:144569 original size:24 final size:24
Alignment explanation
Indices: 144511--144569 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
144501 TCTCAGCTCT
*
144511 AAGGATGTTGATGAAAAGGTTGAG
1 AAGGATGTTGATGAAAAGGTTAAG
**
144535 AAGGACATTGATGAAAAGGTTAAG
1 AAGGATGTTGATGAAAAGGTTAAG
144559 AAGGATGTTGA
1 AAGGATGTTGA
144570 GGCTGATGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.41, C:0.02, G:0.34, T:0.24
Consensus pattern (24 bp):
AAGGATGTTGATGAAAAGGTTAAG
Done.