Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003930.1 Hibiscus syriacus cultivar Beakdansim tig00008494_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: 85520
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:287 original size:16 final size:16
Alignment explanation
Indices: 266--296 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
256 TAGTCTTAAG
*
266 AAAATAGAATTAGAAA
1 AAAATAGAAATAGAAA
282 AAAATAGAAATAGAA
1 AAAATAGAAATAGAA
297 TTTTTAGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (16 bp):
AAAATAGAAATAGAAA
Found at i:7757 original size:26 final size:25
Alignment explanation
Indices: 7728--7798 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 25
7718 TTGATTTAGC
*
7728 AAATAATGCTGAATGATTCAGCACAG
1 AAATAAT-CTAAATGATTCAGCACAG
7754 AAATATATCTAAATGATTCA-CACAG
1 AAATA-ATCTAAATGATTCAGCACAG
*
7779 AAATATTCTAAATGATTCAG
1 AAATAATCTAAATGATTCAG
7799 AGCCATTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
24 13 0.32
25 10 0.24
26 16 0.39
27 2 0.05
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (25 bp):
AAATAATCTAAATGATTCAGCACAG
Found at i:7793 original size:24 final size:26
Alignment explanation
Indices: 7739--7798 Score: 106
Period size: 24 Copynumber: 2.4 Consensus size: 26
7729 AATAATGCTG
7739 AATGATTCAGCACAGAAATATATCTA
1 AATGATTCAGCACAGAAATATATCTA
7765 AATGATTCA-CACAGAAATAT-TCTA
1 AATGATTCAGCACAGAAATATATCTA
7789 AATGATTCAG
1 AATGATTCAG
7799 AGCCATTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 13 0.39
25 11 0.33
26 9 0.27
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (26 bp):
AATGATTCAGCACAGAAATATATCTA
Found at i:17566 original size:42 final size:43
Alignment explanation
Indices: 17474--17949 Score: 636
Period size: 43 Copynumber: 11.1 Consensus size: 43
17464 GCAAAAACGA
* * * * *
17474 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCTAGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
* *
17518 TAAGGCTAACCCTTGCACACAGCAAAGGAACCT-GGGAAACTT
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
17560 TAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
* * *
17602 TAAGGCCTACCCTTGCATACAGTAAAGGAACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGGAAACTG
* * *
17646 TAAGGCCTACCCTTGCACACAG-ATAAGGGACCTGGGAAAACTG
1 TAAGGCTTACCCTTGCACACAGCA-AAGGAACCTGGGGAAACTG
* * *
17689 TAAGGCTTACTCTTGCACACAGCAAAGGGACCTGGGGAAACTA
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
* *
17732 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGGAAACTG
* * * *
17776 TAAGGCTTACCCTTGCACACAACAAAGGGATCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
* *
17819 TAAGGCTTACCCTTGTACACAGCAAAGGAACCT-GGGAAATTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
* *
17861 TAAGGCTTACCTTTGCACACAGCAAAGGAACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
* *
17904 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
17947 TAA
1 TAA
17950 CGGTAATTAA
Statistics
Matches: 391, Mismatches: 35, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
42 116 0.30
43 192 0.49
44 83 0.21
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTG
Found at i:20472 original size:18 final size:17
Alignment explanation
Indices: 20449--20506 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 17
20439 AACGGGTCAA
*
20449 CGGGTCGAGTCAATGGGT
1 CGGGTCG-GTCAACGGGT
20467 CGGGTCGGGTCAACGGGT
1 CGGGTC-GGTCAACGGGT
20485 CGGGTCGGATCAACGGGT
1 CGGGTCGG-TCAACGGGT
20503 CGGG
1 CGGG
20507 AGTTCCAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
17 2 0.05
18 34 0.92
19 1 0.03
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (17 bp):
CGGGTCGGTCAACGGGT
Found at i:22679 original size:43 final size:43
Alignment explanation
Indices: 22494--22969 Score: 656
Period size: 43 Copynumber: 11.1 Consensus size: 43
22484 GCAAAAACGA
* * * *
22494 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGCTTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGAAACTG
* * *
22538 TAAGGCTTACCATTGCACACAACAAAGGAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
* *
22580 TAAGGCTTACCCTTGCACACAGCAAATGAACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCT-GGGGAAACTG
* *
22624 TAAGGCCTACCCTTGCACACAGCAAAGGGACCTGGGAAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
22667 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
* *
22710 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
* *
22753 TAAGGCTTACCCTTGCACACAGCAAAGTGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
22796 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGG-GGAAACTG
* * * *
22839 TAAGGCTTACCCTTGTACACAACAAAGGAACCT-GAGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
* * *
22881 TAAGGCTTACCTTTGCACACAACAAAGGAACCT-GGGAGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGA-AACTG
* *
22924 TAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
22967 TAA
1 TAA
22970 CGGTAATTAA
Statistics
Matches: 394, Mismatches: 31, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
41 1 0.00
42 79 0.20
43 264 0.67
44 50 0.13
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.18
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
Found at i:25463 original size:15 final size:15
Alignment explanation
Indices: 25443--25476 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
25433 GGTCAACGTC
25443 GGTCAACAGTCAACG
1 GGTCAACAGTCAACG
*
25458 GGTCAACGGTCAACG
1 GGTCAACAGTCAACG
25473 GGTC
1 GGTC
25477 GATTCAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.15
Consensus pattern (15 bp):
GGTCAACAGTCAACG
Found at i:25494 original size:18 final size:17
Alignment explanation
Indices: 25471--25531 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 17
25461 CAACGGTCAA
*
25471 CGGGTCGATTCAATGGGT
1 CGGGTCGA-TCAACGGGT
*
25489 CGGGTCGGGTCAACGGGT
1 CGGGTC-GATCAACGGGT
25507 CGGGTCAGATCAACGGGT
1 CGGGTC-GATCAACGGGT
25525 CGGGTCG
1 CGGGTCG
25532 GGTTGTGACC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 1 0.03
18 36 0.95
19 1 0.03
ACGTcount: A:0.15, C:0.21, G:0.44, T:0.20
Consensus pattern (17 bp):
CGGGTCGATCAACGGGT
Found at i:25505 original size:13 final size:13
Alignment explanation
Indices: 25489--25513 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25479 TTCAATGGGT
25489 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
25502 CGGGTCGGGTCA
1 CGGGTCGGGTCA
25514 GATCAACGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:27606 original size:43 final size:43
Alignment explanation
Indices: 27544--28061 Score: 685
Period size: 43 Copynumber: 12.1 Consensus size: 43
27534 GCAAAAACGA
* *
27544 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGCCTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAGCAAAGAGA-CCTGGGGAAACTG
27588 TAAGGCTTACCCTTGCACACAGCAAAG-GAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAG-ACCTGGGGAAACTG
* *
27630 TAAGGCTTACCCTTGCACACAACAAAG-GAACCT-AGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAG-ACCTGGGGAAACTG
*
27672 TAAGGCTTACCCTTGCACACAGTAAAG-GAACCTGGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAG-ACCT-GGGGAAACTG
* * *
27716 TAAGGCCTACCCTTGCACACAGCAAAGGGACCTGGGAAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
* *
27759 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
* * *
27802 TAAGGCTTACCCTTGCACACAGTAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
* * *
27845 TAAGGCTTACCCTTGCACACAGCAAAGGGACTTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
* * *
27888 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
27931 TAAGGCTTACCCTTGCACACAGCAAAG-GAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAG-ACCTGGGGAAACTG
* * *
27973 TAAGGCTTACCTTTGCACACAGCTAAG-GAACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAG-ACCTGGGGAAACTG
* *
28016 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
28059 TAA
1 TAA
28062 CGGTAATTAA
Statistics
Matches: 439, Mismatches: 27, Indels: 17
0.91 0.06 0.04
Matches are distributed among these distances:
42 120 0.27
43 274 0.62
44 44 0.10
45 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
Found at i:27796 original size:86 final size:86
Alignment explanation
Indices: 27544--28061 Score: 765
Period size: 86 Copynumber: 6.0 Consensus size: 86
27534 GCAAAAACGA
* * *
27544 TAAGGTCTTATCCTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACAC
1 TAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGAAACTGTAAGGCTTACCCTTGCACAC
27608 AGCAAAGGAACCT-GGGAAACTG
64 AGCAAAGGAACCTGGGGAAACTG
* * *
27630 TAAGGCTTACCCTTGCACACAACAAAGGAACCT-AGGAAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
*
27694 TAAAGGAACCTGGGGGAAACTG
66 CAAAGGAACCT-GGGGAAACTG
* * *
27716 TAAGGCCTACCCTTGCACACAGCAAAGGGACCTGGGAAAACTGTAAGGCTTACCCTTGCACACAA
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
*
27781 CAAAGGGACCTGGGGAAACTG
66 CAAAGGAACCTGGGGAAACTG
* *
27802 TAAGGCTTACCCTTGCACACAGTAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
* * *
27867 CAAAGGGACTTGGGGGAACTG
66 CAAAGGAACCTGGGGAAACTG
* *
27888 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
27953 CAAAGGAACCT-GGGAAACTG
66 CAAAGGAACCTGGGGAAACTG
* * * *
27973 TAAGGCTTACCTTTGCACACAGCTAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
* *
28038 CAAAGGGACCTGGGGGAACTG
66 CAAAGGAACCTGGGGAAACTG
28059 TAA
1 TAA
28062 CGGTAATTAA
Statistics
Matches: 394, Mismatches: 33, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
84 40 0.10
85 100 0.25
86 217 0.55
87 37 0.09
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (86 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
CAAAGGAACCTGGGGAAACTG
Found at i:27856 original size:129 final size:129
Alignment explanation
Indices: 27544--28061 Score: 799
Period size: 129 Copynumber: 4.0 Consensus size: 129
27534 GCAAAAACGA
* * * *
27544 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACACA
1 TAAGG-CTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACA
* *
27609 GCAAAGGAACCT-GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCT-AGGAAACTG
65 GCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
* *
27672 TAAGGCTTACCCTTGCACACAGTAAAGGAACCTGGGGGAAACTGTAAGGCCTACCCTTGCACACA
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGGAAACTGTAAGGCTTACCCTTGCACACA
* *
27737 GCAAAGGGACCTGGGAAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
65 GCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
* * *
27802 TAAGGCTTACCCTTGCACACAGTAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
* * * *
27867 CAAAGGGACTTGGGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGGAACTG
66 CAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
*
27931 TAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGGAAACTGTAAGGCTTACCTTTGCACACAG
1 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
* * * *
27995 CTAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTG
66 CAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
28059 TAA
1 TAA
28062 CGGTAATTAA
Statistics
Matches: 362, Mismatches: 25, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
127 23 0.06
128 138 0.38
129 161 0.44
130 40 0.11
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (129 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAG
CAAAGGAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
Found at i:30590 original size:18 final size:18
Alignment explanation
Indices: 30564--30633 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
30554 GGGTCAACGA
*
30564 GTCGAGTCAACGGGTCGG
1 GTCGGGTCAACGGGTCGG
30582 GTCGGGTCAACGGGTC--
1 GTCGGGTCAACGGGTCGG
*
30598 -T--GGTAAACGGGTCGG
1 GTCGGGTCAACGGGTCGG
*
30613 GTCGGATCAACGGGTCGG
1 GTCGGGTCAACGGGTCGG
30631 GTC
1 GTC
30634 AGGTTGTGAC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 11 0.26
15 1 0.02
16 1 0.02
18 30 0.70
ACGTcount: A:0.16, C:0.21, G:0.44, T:0.19
Consensus pattern (18 bp):
GTCGGGTCAACGGGTCGG
Found at i:30590 original size:31 final size:30
Alignment explanation
Indices: 30553--30630 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 30
30543 CAACAGTCAA
*
30553 CGGGTCAACGAGTCGAGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCG-GTCAACGGGTCGGGT
*
30584 CGGGTCAACGGGTCTGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTC-GGTCAACGGGTCGGGT
*
30615 CGGATCAACGGGTCGG
1 CGGGTCAACGGGTCGG
30631 GTCAGGTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.05
31 40 0.93
32 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.44, T:0.17
Consensus pattern (30 bp):
CGGGTCAACGGGTCGGTCAACGGGTCGGGT
Found at i:30595 original size:13 final size:13
Alignment explanation
Indices: 30579--30615 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
30569 GTCAACGGGT
30579 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
30592 CGGGTCTGGTAAA
1 CGGGTCGGGTCAA
30605 CGGGTCGGGTC
1 CGGGTCGGGTC
30616 GGATCAACGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.22, G:0.46, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:37294 original size:12 final size:12
Alignment explanation
Indices: 37277--37302 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37267 AAATAAACTC
37277 ATCAATTTTAAT
1 ATCAATTTTAAT
37289 ATCAATTTTAAT
1 ATCAATTTTAAT
37301 AT
1 AT
37303 AAAGGATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
ATCAATTTTAAT
Found at i:37836 original size:20 final size:20
Alignment explanation
Indices: 37811--37884 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
37801 TTTTCCCAAT
*
37811 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
37831 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
37852 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
37872 TCGCAACGCGAAT
1 TCGCAACGCGAAT
37885 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:37903 original size:21 final size:21
Alignment explanation
Indices: 37828--37895 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
37818 GCGAATAAGT
37828 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
37849 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
37869 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
37890 AAATCG
1 AAATCG
37896 TAATGCGATA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:37918 original size:41 final size:41
Alignment explanation
Indices: 37811--37903 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
37801 TTTTCCCAAT
37811 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
37852 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
37893 TCGTAATGCGA
1 TCGCAATGCGA
37904 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:37920 original size:20 final size:20
Alignment explanation
Indices: 37900--38006 Score: 108
Period size: 20 Copynumber: 5.3 Consensus size: 20
37890 AAATCGTAAT
*
37900 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
37920 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
* * *
37941 GAGATACTTACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
*
37961 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* *
37981 GCGATTCTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
38001 GCGATA
1 GCGATA
38007 ATACATAATC
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 56 0.77
21 13 0.18
22 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:37934 original size:41 final size:41
Alignment explanation
Indices: 37889--38020 Score: 142
Period size: 41 Copynumber: 3.2 Consensus size: 41
37879 GCGAATTGGG
* * * *
37889 AAAATCGTAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
37930 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
37972 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
*
38011 ATAATCGCAA
1 AAAATCGCAA
38021 TGCAATTTTC
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.42
41 38 0.52
42 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:38222 original size:22 final size:22
Alignment explanation
Indices: 38194--38237 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
38184 CACTCTCTCA
38194 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
38216 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
38238 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:38526 original size:20 final size:20
Alignment explanation
Indices: 38501--38538 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38491 CGATTCTCTC
38501 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
38521 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
38539 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:40205 original size:20 final size:19
Alignment explanation
Indices: 40174--40348 Score: 92
Period size: 20 Copynumber: 9.8 Consensus size: 19
40164 TCTTTTGGTT
40174 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
40193 GATAATGAGAATCGCAACGTG
1 GA-AATGAAAATCGCAACG-A
**
40214 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
40233 G--A-G--AATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
40247 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
40261 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
40277 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
* *
40294 CAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
*
40314 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
40333 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
40349 TGCGATTTTT
Statistics
Matches: 126, Mismatches: 17, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 31 0.25
15 1 0.01
16 4 0.03
17 4 0.03
18 1 0.01
19 36 0.29
20 47 0.37
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:40242 original size:14 final size:14
Alignment explanation
Indices: 40223--40259 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
40213 GGAAATGACT
40223 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
40237 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
40251 ATCGCAACG
1 ATCGCAACG
40260 CGAAATGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.27, T:0.08
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:40273 original size:47 final size:48
Alignment explanation
Indices: 40199--40292 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 48
40189 ACGAGATAAT
* * *
40199 GAGAATCGCAACGTGGAAATGACTATCGCAACGAGAGAATCGCAACGA
1 GAGAATCGCAACGTCGAAATGACTATCGCAACCAGACAATCGCAACGA
*
40247 GAGAATCGCAACG-CGAAATGACTATCGCGACCAGACAATCGCAACG
1 GAGAATCGCAACGTCGAAATGACTATCGCAACCAGACAATCGCAACG
40293 CCAAATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 29 0.69
48 13 0.31
ACGTcount: A:0.38, C:0.24, G:0.26, T:0.12
Consensus pattern (48 bp):
GAGAATCGCAACGTCGAAATGACTATCGCAACCAGACAATCGCAACGA
Found at i:40307 original size:19 final size:19
Alignment explanation
Indices: 40283--40353 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
40273 GCGACCAGAC
*
40283 AATCGCAACGCCAAATGAA
1 AATCGCAACGCGAAATGAA
40302 AATCGCAACCGCGAAATGAA
1 AATCGCAA-CGCGAAATGAA
40322 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
40341 AATCGCAATGCGA
1 AATCGCAACGCGA
40354 TTTTTTGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 31 0.63
20 18 0.37
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:40307 original size:33 final size:33
Alignment explanation
Indices: 40236--40348 Score: 100
Period size: 33 Copynumber: 3.2 Consensus size: 33
40226 GCAACGAGAG
* * * *
40236 AATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACCAGACAATCGCAACGCCAAATGAA
* *
40269 TATCGCGACCAGACAATCGCAACGCCAAATGAA
1 AATCGCAACCAGACAATCGCAACGCCAAATGAA
* *
40302 AATCGCAACCGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAA-C-C---A-GACAATCGCAACGCCAAATGAA
40341 AATCGCAA
1 AATCGCAA
40349 TGCGATTTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
33 33 0.52
34 1 0.02
35 1 0.02
38 1 0.02
39 28 0.44
ACGTcount: A:0.43, C:0.26, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACCAGACAATCGCAACGCCAAATGAA
Found at i:40378 original size:19 final size:20
Alignment explanation
Indices: 40349--40394 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
40339 AAAATCGCAA
*
40349 TGCGATTTTTTGTTTCGCGT
1 TGCGATTTTTTATTTCGCGT
40369 TGCG-TTTTTTATTTCGCGT
1 TGCGATTTTTTATTTCGCGT
*
40388 TACGATT
1 TGCGATT
40395 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.09, C:0.15, G:0.22, T:0.54
Consensus pattern (20 bp):
TGCGATTTTTTATTTCGCGT
Found at i:40973 original size:20 final size:20
Alignment explanation
Indices: 40948--41020 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
40938 GCGCTATGTA
40948 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
40968 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
40988 AATCGCGTTGAGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
41008 TATCTCGTTGCGA
1 AATCGCGTTGCGA
41021 TTTTGTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:41054 original size:20 final size:20
Alignment explanation
Indices: 41029--41082 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
41019 GATTTTGTAT
41029 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
41049 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
*
41069 TATCACATTGCGAT
1 TATCGCATTGCGAT
41083 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:41054 original size:61 final size:61
Alignment explanation
Indices: 40969--41085 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
40959 GAAAGTCAGA
* * * * *
40969 ATCGCGTTGCGAAAGTCAGAATCGCGTTGAGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGAGAAAGTCAGTATCACATTGCGATTTTGTATT
* * * *
41030 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCACATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGAGAAAGTCAGTATCACATTGCGATTTT
41086 CCCAATTTGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGAGAAAGTCAGTATCACATTGCGATTTTGTATT
Found at i:41193 original size:21 final size:21
Alignment explanation
Indices: 41153--41193 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41143 ATTGTATACC
**
41153 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
41174 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
41194 GTGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:42171 original size:7 final size:7
Alignment explanation
Indices: 42159--42289 Score: 56
Period size: 7 Copynumber: 18.9 Consensus size: 7
42149 AGATTACACC
42159 CTAAACT
1 CTAAACT
42166 CTAAACT
1 CTAAACT
*
42173 TTAAACT
1 CTAAACT
* *
42180 ATAAACC
1 CTAAACT
*
42187 CTAAAGT
1 CTAAACT
42194 -TAAAC-
1 CTAAACT
*
42199 CTTAAATT
1 C-TAAACT
*
42207 CTAAAAT
1 CTAAACT
* *
42214 ATAAACC
1 CTAAACT
*
42221 CTAAATT
1 CTAAACT
*
42228 CTAAACA
1 CTAAACT
42235 CTAAA-T
1 CTAAACT
42241 CCTAAACT
1 -CTAAACT
*
42249 ATAAAC-
1 CTAAACT
*
42255 CATAAATT
1 C-TAAACT
* *
42263 ATAAACC
1 CTAAACT
42270 CT-AACT
1 CTAAACT
*
42276 CCTAAACC
1 -CTAAACT
42284 CTAAAC
1 CTAAAC
42290 CCTTAATCCA
Statistics
Matches: 88, Mismatches: 27, Indels: 18
0.66 0.20 0.14
Matches are distributed among these distances:
6 7 0.08
7 76 0.86
8 5 0.06
ACGTcount: A:0.48, C:0.24, G:0.01, T:0.27
Consensus pattern (7 bp):
CTAAACT
Found at i:42279 original size:35 final size:34
Alignment explanation
Indices: 42174--42292 Score: 139
Period size: 35 Copynumber: 3.4 Consensus size: 34
42164 CTCTAAACTT
* * *
42174 TAAACTATAAACCCTAAAGTTAAACCTTAAATTC
1 TAAACTATAAACCCTAAATTTAAACCCTAAATCC
* *
42208 TAAAATATAAACCCTAAATTCTAAACACTAAATCC
1 TAAACTATAAACCCTAAATT-TAAACCCTAAATCC
* *
42243 TAAACTATAAACCATAAATTATAAACCCTAACTCC
1 TAAACTATAAACCCTAAATT-TAAACCCTAAATCC
**
42278 TAAACCCTAAACCCT
1 TAAACTATAAACCCT
42293 TAATCCAATT
Statistics
Matches: 71, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
34 18 0.25
35 53 0.75
ACGTcount: A:0.48, C:0.25, G:0.01, T:0.26
Consensus pattern (34 bp):
TAAACTATAAACCCTAAATTTAAACCCTAAATCC
Found at i:42836 original size:84 final size:83
Alignment explanation
Indices: 42696--42863 Score: 282
Period size: 84 Copynumber: 2.0 Consensus size: 83
42686 CCCTCTTTGC
*
42696 ACATTCTTGTGTTAACAAGATAAGACAAAGAAGAAAAAGACAACCAATTTTTGTCCGATAAATGA
1 ACATTCTTGTGTTAACAAGATAAGACAAAGAAGAAAAAGACAAACAATTTTTGTCCGATAAATGA
42761 AACATGTGACATAAACAA
66 AACATGTGACATAAACAA
* * * *
42779 ACATTCTTGTGTTAATAACGATATGACAAAGACGAAAAAGACAAACAGTTTTTGTCCGATAAATG
1 ACATTCTTGTGTTAACAA-GATAAGACAAAGAAGAAAAAGACAAACAATTTTTGTCCGATAAATG
42844 AAACATGTGACATAAACAA
65 AAACATGTGACATAAACAA
42863 A
1 A
42864 AATATATCTG
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
83 17 0.22
84 62 0.78
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (83 bp):
ACATTCTTGTGTTAACAAGATAAGACAAAGAAGAAAAAGACAAACAATTTTTGTCCGATAAATGA
AACATGTGACATAAACAA
Found at i:42883 original size:17 final size:17
Alignment explanation
Indices: 42861--42895 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
42851 TGACATAAAC
*
42861 AAAAATATATCTGATAA
1 AAAAATATATCCGATAA
42878 AAAAATATATCCGATAA
1 AAAAATATATCCGATAA
42895 A
1 A
42896 TTTTACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAAATATATCCGATAA
Found at i:43054 original size:16 final size:16
Alignment explanation
Indices: 43030--43061 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43020 ATAATGCCTG
43030 ATTCACTTCCCAATCA
1 ATTCACTTCCCAATCA
*
43046 ATTCCCTTCCCAATCA
1 ATTCACTTCCCAATCA
43062 TCGAAAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.41, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTCACTTCCCAATCA
Found at i:43357 original size:25 final size:25
Alignment explanation
Indices: 43329--43381 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
43319 AATAATATGA
*
43329 TTATTTATC-TAATTTAAATATATTT
1 TTATCTATCTTAATTT-AATATATTT
43354 TTATCTATCTTATAATTTAATATATTT
1 TTATCTATC-T-TAATTTAATATATTT
43381 T
1 T
43382 AACTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.33
27 10 0.42
28 6 0.25
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATCTATCTTAATTTAATATATTT
Found at i:62949 original size:148 final size:147
Alignment explanation
Indices: 62744--63035 Score: 431
Period size: 148 Copynumber: 2.0 Consensus size: 147
62734 AAATACTCAA
*
62744 TTCAGTTTATAAAATAGTTGACTAAAAAAAATTCGATTTGAGTTTATAAAATTTAAATCAAATCA
1 TTCAGTTTATAAAATAGTTGACTAAAAAAAATTCAATTTGAGTTTATAAAATTTAAATCAAATCA
* * *
62809 AATTGAATTGAATTTTCGAGTTTATATTTAAATTTAATTATAAATATTTATTATATTATGATATT
66 AATTGAATTGAATTTTCGAGTTTATATTTAAATTTAATTATAAATATTTATAATACTATAATATT
*
62874 ATTTTATTCTAATTCAG
131 ATTTGATTCTAATTCAG
* **** *
62891 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGTTTATAAAATAGTTGACT-AAAAAAAATTCAATTTGAGTTTATAAAATTTAAATCAAATC
* * * * *
62956 GAATTGAATTGAATTTTCTAGTTTCTGTTTAAATTTAATTATGAATATTTATAATACTATAATAT
65 AAATTGAATTGAATTTTCGAGTTTATATTTAAATTTAATTATAAATATTTATAATACTATAATAT
63021 TATTTGATTCTAATT
130 TATTTGATTCTAATT
63036 TAAATAATTT
Statistics
Matches: 128, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
147 23 0.18
148 105 0.82
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (147 bp):
TTCAGTTTATAAAATAGTTGACTAAAAAAAATTCAATTTGAGTTTATAAAATTTAAATCAAATCA
AATTGAATTGAATTTTCGAGTTTATATTTAAATTTAATTATAAATATTTATAATACTATAATATT
ATTTGATTCTAATTCAG
Found at i:63594 original size:35 final size:36
Alignment explanation
Indices: 63536--63613 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 36
63526 GTTGGTCATG
* *
63536 TAATTAAAGTATTTTTGAAATTTGAGGTTTATAATA
1 TAATTGAAGTATTTTTGAAATTTGAGGTTTAGAATA
* * *
63572 TAATTGAAGTA-TTTTGGAATTTGGGGTTTAGAATG
1 TAATTGAAGTATTTTTGAAATTTGAGGTTTAGAATA
63607 TAATTGA
1 TAATTGA
63614 TGACTGTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 27 0.73
36 10 0.27
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.45
Consensus pattern (36 bp):
TAATTGAAGTATTTTTGAAATTTGAGGTTTAGAATA
Found at i:66623 original size:21 final size:21
Alignment explanation
Indices: 66599--66645 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
66589 TCAACATATG
66599 CATCTGAAGATTATTACCATA
1 CATCTGAAGATTATTACCATA
*
66620 CATCTGAAGATTATTACCATG
1 CATCTGAAGATTATTACCATA
66641 CATCT
1 CATCT
66646 CAGGCTAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (21 bp):
CATCTGAAGATTATTACCATA
Found at i:68991 original size:57 final size:60
Alignment explanation
Indices: 68913--69047 Score: 204
Period size: 57 Copynumber: 2.3 Consensus size: 60
68903 TTTCCGTCTA
* * *
68913 TCTTATTTCGGTCACTGATTTTGAAAAAGTTACA-TTTGATCACTTTTA-TTTTTATCTT
1 TCTTATTTTGGTCATTGATTTTGAAAAAGTTACATTTTGATCACTTTTATTTTTTATATT
* *
68971 TCTT-TTTTGTTCATTGATTTTGAAAAGGTTACATTTTGATCACTTTTATTTTTTATATT
1 TCTTATTTTGGTCATTGATTTTGAAAAAGTTACATTTTGATCACTTTTATTTTTTATATT
69030 TCTTATTTTGGTCATTGA
1 TCTTATTTTGGTCATTGA
69048 GCAGTTTACT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
57 25 0.37
58 18 0.26
59 13 0.19
60 12 0.18
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (60 bp):
TCTTATTTTGGTCATTGATTTTGAAAAAGTTACATTTTGATCACTTTTATTTTTTATATT
Found at i:72769 original size:6 final size:6
Alignment explanation
Indices: 72752--72783 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
72742 GTACCTTGTC
72752 TTAATCA TTAATA TTAATA TTAATA TTAATA T
1 TTAAT-A TTAATA TTAATA TTAATA TTAATA T
72784 ACTTAATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:74356 original size:21 final size:21
Alignment explanation
Indices: 74323--74362 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
74313 CTACCCCTAA
* *
74323 CTTAAATCATAAAATATAAAT
1 CTTAAACCATAAAACATAAAT
*
74344 CTTAAACCCTAAAACATAA
1 CTTAAACCATAAAACATAA
74363 CTTCATAACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (21 bp):
CTTAAACCATAAAACATAAAT
Found at i:77376 original size:3 final size:3
Alignment explanation
Indices: 77368--77392 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
77358 GAGGAGATCT
77368 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
77393 AGGGTTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:81174 original size:2 final size:2
Alignment explanation
Indices: 81160--81215 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
81150 AAACTATAAA
*
81160 AT AT AT CT A- 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
81201 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
81216 AAAATTTAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84929 original size:2 final size:2
Alignment explanation
Indices: 84922--84951 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
84912 AACTAAAGAA
84922 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
84952 TTGCTAATTA
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
Done.