Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009201.1 Hibiscus syriacus cultivar Beakdansim tig00112785_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: 119838
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4511 original size:29 final size:29
Alignment explanation
Indices: 4476--4557 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
4466 AAACTAAATT
* *
4476 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
4505 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
4534 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
4558 GTTATGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:9409 original size:51 final size:51
Alignment explanation
Indices: 9354--9663 Score: 291
Period size: 51 Copynumber: 6.1 Consensus size: 51
9344 GACGGGCGGC
* *
9354 GGAAGTAAA-GGGGTTGGGGGAAGAACGGGCGGCGGCAGAACGGGGTTCGGA
1 GGAAG-AAAGGGGGTTGGAGGAAGAACGGGCGGCGGAAGAACGGGGTTCGGA
* *
9405 GGAAGAAAGGGGGTTGGAGGAAGGACGGGCGGCTGAAGAACGGGGTTCGGA
1 GGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGAAGAACGGGGTTCGGA
* * * * * *
9456 GGAAG-AA-TGGG-CGGCGGCAGAACGGGGTTCGGAGGAAGAGAAGGGGTT-GGA
1 GGAAGAAAGGGGGTTGGAGGAAGAAC-GGG--CGGCGGAAGA-ACGGGGTTCGGA
* * ** * * *
9507 GGAAGAACGGGAGG-CGGTA-GAA-AGGGGGTTGGAGGAAGAAC-GGG--CGGC
1 GGAAGAAAGGG-GGTTGG-AGGAAGAACGGG-CGGCGGAAGAACGGGGTTCGGA
* *
9555 GGCAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGCAGAACGGGGTTCGGA
1 GGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGAAGAACGGGGTTCGGA
*
9606 GGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGCAGAACGGGGTTCGGA
1 GGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGAAGAACGGGGTTCGGA
9657 GGAAGAA
1 GGAAGAA
9664 TGGGCGGCGG
Statistics
Matches: 212, Mismatches: 31, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
47 3 0.01
48 33 0.16
49 16 0.08
50 6 0.03
51 134 0.63
52 11 0.05
53 2 0.01
54 7 0.03
ACGTcount: A:0.28, C:0.11, G:0.53, T:0.08
Consensus pattern (51 bp):
GGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGAAGAACGGGGTTCGGA
Found at i:9423 original size:84 final size:83
Alignment explanation
Indices: 9321--9729 Score: 460
Period size: 84 Copynumber: 4.9 Consensus size: 83
9311 GACGGGCGGC
*
9321 GGAAGAAAGGGGGTTGGAGGAAGGACGGGCGGCGGAAGTAAAGGGGTTGGGGGAAGAACGGGCGG
1 GGAAGAAAGGGGGTTGGAGGAAGGACGGGCGGCGGAAG-AAAGGGGTTGGAGGAAGAACGGGCGG
9386 CGGCAGAACGGGGTTCGGA
65 CGGCAGAACGGGGTTCGGA
* * *
9405 GGAAGAAAGGGGGTTGGAGGAAGGACGGGCGGCTGAAGAACGGGGTTCGGAGGAAGAATGGGCGG
1 GGAAGAAAGGGGGTTGGAGGAAGGACGGGCGGCGGAAGAAAGGGGTT-GGAGGAAGAACGGGCGG
9470 CGGCAGAACGGGGTTCGGA
65 CGGCAGAACGGGGTTCGGA
* * *
9489 GGAAGAGAA-GGGGTTGGAGGAAGAACGGGAGGCGGTAGAAAGGGGGTTGGAGGAAGAACGGGCG
1 GGAAGA-AAGGGGGTTGGAGGAAGGACGGGCGGCGGAAGAAA-GGGGTTGGAGGAAGAACGGGCG
*
9553 GCGGCAGAAAGGGGGTT-GGA
64 GCGGCAG-AACGGGGTTCGGA
* * * *
9573 GGAAGAACGGGCGG-CGGCA-GAACGG--GGTTCGGAGGAAGAAAGGGGGTTGGAGGAAGAACGG
1 GGAAGAAAGGG-GGTTGG-AGGAA-GGACGG-GCGGCGGAAGAAA-GGGGTTGGAGGAAGAACGG
9634 GCGGCGGCAGAACGGGGTTCGGA
61 GCGGCGGCAGAACGGGGTTCGGA
* * * *
9657 GGAAGAATGGGCGG-CGGCA-GAACGG--GGTTCGGAGGAAGAAAAGGGGTTGGAGGAAGAACGG
1 GGAAGAAAGGG-GGTTGG-AGGAA-GGACGG-GCGGCGGAAG-AAAGGGGTTGGAGGAAGAACGG
*
9718 GCGGCGGAAGAA
61 GCGGCGGCAGAA
9730 GCTGGTCCGG
Statistics
Matches: 293, Mismatches: 21, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
83 19 0.06
84 251 0.86
85 23 0.08
ACGTcount: A:0.28, C:0.11, G:0.53, T:0.08
Consensus pattern (83 bp):
GGAAGAAAGGGGGTTGGAGGAAGGACGGGCGGCGGAAGAAAGGGGTTGGAGGAAGAACGGGCGGC
GGCAGAACGGGGTTCGGA
Found at i:9529 original size:117 final size:117
Alignment explanation
Indices: 9297--9696 Score: 474
Period size: 117 Copynumber: 3.4 Consensus size: 117
9287 CGGCTGAAGT
* * * *
9297 GGGGTTGGAGGAAGGACGGGCGGCGGAAGAAAGGGGGTTGGAGGAAGGACGGGCGGCGGAAGTAA
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAACGGGGTTGGAGGAAGAACGGGCGGCGGCAG-AA
* * * * * * *
9362 AGGGGTT-GG-GGGA-AGAACGGG-CGGCGGCAGAACGGGGTTCGGAGGAAGAAAG
65 CGGGGTTCGGAGGAAGAGAAGGGGTTGGAGGAAGAAC-GGG--CGGCGGAAGAAAG
* * *
9414 GGGGTTGGAGGAAGGACGGGCGGCTGAAG-AACGGGGTTCGGAGGAAGAATGGGCGGCGGCAGAA
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAACGGGGTT-GGAGGAAGAACGGGCGGCGGCAGAA
* *
9478 CGGGGTTCGGAGGAAGAGAAGGGGTTGGAGGAAGAACGGGAGGCGGTAGAAAG
65 CGGGGTTCGGAGGAAGAGAAGGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAG
* *
9531 GGGGTTGGAGGAAGAACGGGCGGCGGCAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGCAGAAC
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAACGGGGTTGGAGGAAGAACGGGCGGCGGCAGAAC
* *
9596 GGGGTTCGGAGGAAGA-AAGGGGGTTGGAGGAAGAACGGGCGGCGGCAG-AAC
66 GGGGTTCGGAGGAAGAGAA-GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAG
* *
9647 GGGGTTCGGAGGAAGAATGGGCGGCGGCAG-AACGGGGTTCGGAGGAAGAA
1 GGGGTT-GGAGGAAGAACGGGCGGCGGAAGAAACGGGGTT-GGAGGAAGAA
9697 AAGGGGTTGG
Statistics
Matches: 250, Mismatches: 24, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
116 34 0.14
117 186 0.74
118 11 0.04
119 10 0.04
120 9 0.04
ACGTcount: A:0.27, C:0.11, G:0.54, T:0.08
Consensus pattern (117 bp):
GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAACGGGGTTGGAGGAAGAACGGGCGGCGGCAGAAC
GGGGTTCGGAGGAAGAGAAGGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAG
Found at i:9647 original size:15 final size:15
Alignment explanation
Indices: 9627--9682 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
9617 GGTTGGAGGA
9627 AGAACGGGCGGCGGC
1 AGAACGGGCGGCGGC
* *
9642 AGAACGGGGTTCGGAGGA
1 AGAAC-GGG--CGGCGGC
*
9660 AGAATGGGCGGCGGC
1 AGAACGGGCGGCGGC
9675 AGAACGGG
1 AGAACGGG
9683 GTTCGGAGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
15 17 0.53
16 3 0.09
17 3 0.09
18 9 0.28
ACGTcount: A:0.25, C:0.18, G:0.52, T:0.05
Consensus pattern (15 bp):
AGAACGGGCGGCGGC
Found at i:9648 original size:201 final size:201
Alignment explanation
Indices: 9297--9729 Score: 760
Period size: 201 Copynumber: 2.2 Consensus size: 201
9287 CGGCTGAAGT
* *
9297 GGGGTTGGAGGAAGGACGGGCGGCGGAAGAAAGGGGGTTGGAGGAAGGACGGGCGGCGGAAGTAA
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGAAGTAA
*
9362 AGGGGTTGGGGGAAGAACGGGCGGCGGCAGAACGGGGTTCGGAGGAAGAAAGGGGGTTGGAGGAA
66 AGGGGTTGGAGGAAGAACGGGCGGCGGCAGAACGGGGTTCGGAGGAAGAAAGGGGGTTGGAGGAA
* *
9427 GGACGGGCGGCTGAAGAACGGGGTTCGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGAGGA
131 GAACGGGCGGCGGAAGAACGGGGTTCGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGAGGA
*
9492 AGAGAA
196 AGAAAA
* * *
9498 GGGGTTGGAGGAAGAACGGGAGGCGGTAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGCAG-AA
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGAAGTAA
9562 AGGGGGTTGGAGGAAGAACGGGCGGCGGCAGAACGGGGTTCGGAGGAAGAAAGGGGGTTGGAGGA
66 A-GGGGTTGGAGGAAGAACGGGCGGCGGCAGAACGGGGTTCGGAGGAAGAAAGGGGGTTGGAGGA
*
9627 AGAACGGGCGGCGGCAGAACGGGGTTCGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGAGG
130 AGAACGGGCGGCGGAAGAACGGGGTTCGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGAGG
9692 AAGAAAA
195 AAGAAAA
9699 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAA
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAA
9730 GCTGGTCCGG
Statistics
Matches: 219, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
200 3 0.01
201 216 0.99
ACGTcount: A:0.27, C:0.11, G:0.54, T:0.08
Consensus pattern (201 bp):
GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGAAGTAA
AGGGGTTGGAGGAAGAACGGGCGGCGGCAGAACGGGGTTCGGAGGAAGAAAGGGGGTTGGAGGAA
GAACGGGCGGCGGAAGAACGGGGTTCGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGAGGA
AGAAAA
Found at i:9709 original size:51 final size:51
Alignment explanation
Indices: 9297--9729 Score: 237
Period size: 51 Copynumber: 8.6 Consensus size: 51
9287 CGGCTGAAGT
* * *
9297 GGGGTT-GGAGGAAGGACGGGCGGCGGAAGAAAGGGGGTT-GGAGGAAGGAC
1 GGGGTTCGGAGGAAGAACGGGCGGCGGAAG-AACGGGGTTCGGAGGAAGAAC
* * * * * *
9347 -GGG--CGGCGGAAGTAAAGGGGTTGGGGGAAGAAC-GGG--CGGCGGCAGAAC
1 GGGGTTCGGAGGAAG--AACGGG-CGGCGGAAGAACGGGGTTCGGAGGAAGAAC
* * * * **
9395 GGGGTTCGGAGGAAGAAAGGG-GGTTGGAGGAA-GGACGG-GCGGCTGAAGAAC
1 GGGGTTCGGAGGAAGAACGGGCGG-CGGAAGAACGG--GGTTCGGAGGAAGAAC
* * *
9446 GGGGTTCGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGAGGAAGAGAA
1 GGGGTTCGGAGGAAGAACGGGCGGCGGAAGAACGGGGTTCGGAGGAAGA-AC
* * *
9498 GGGGTT-GGAGGAAGAACGGGAGGCGGTAGAAAGGGGGTT-GGAGGAAGAAC
1 GGGGTTCGGAGGAAGAACGGGCGGCGGAAG-AACGGGGTTCGGAGGAAGAAC
* ** * * * *
9548 GGGCG-GCGGCA-GAA-AGGGGGTTGGAGGAAGAAC-GGG--CGGCGGCAGAAC
1 GGG-GTTCGG-AGGAAGAACGGG-CGGCGGAAGAACGGGGTTCGGAGGAAGAAC
* * * * *
9596 GGGGTTCGGAGGAAGAAAGGGGGTTGGAGGAAGAAC-GGG--CGGCGGCAGAAC
1 GGGGTTCGGAGGAAG-AA-CGGG-CGGCGGAAGAACGGGGTTCGGAGGAAGAAC
* * *
9647 GGGGTTCGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGAGGAAGAAAA
1 GGGGTTCGGAGGAAGAACGGGCGGCGGAAGAACGGGGTTCGGAGGAAG-AAC
9699 GGGGTT-GGAGGAAGAACGGGCGGCGGAAGAA
1 GGGGTTCGGAGGAAGAACGGGCGGCGGAAGAA
9730 GCTGGTCCGG
Statistics
Matches: 303, Mismatches: 48, Indels: 63
0.73 0.12 0.15
Matches are distributed among these distances:
47 4 0.01
48 49 0.16
49 23 0.08
50 23 0.08
51 176 0.58
52 28 0.09
ACGTcount: A:0.27, C:0.11, G:0.54, T:0.08
Consensus pattern (51 bp):
GGGGTTCGGAGGAAGAACGGGCGGCGGAAGAACGGGGTTCGGAGGAAGAAC
Found at i:9727 original size:33 final size:33
Alignment explanation
Indices: 9297--9729 Score: 256
Period size: 33 Copynumber: 12.9 Consensus size: 33
9287 CGGCTGAAGT
* *
9297 GGGGTTGGAGGAAGGACGGGCGGCGGAAGAAAG
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAA
* *
9330 GGGGTTGGAGGAAGGACGGGCGGCGGAAGTAAA
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAA
* * *
9363 GGGGTTGGGGGAAGAACGGGCGGCGGCAG-AAC
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAA
* * * *
9395 GGGGTTCGGAGGAAGAAAGGG-GGTTGGAGGAAGGA
1 GGGGTT-GGAGGAAGAACGGGCGG-CGGAAGAA-AA
* * ** * *
9430 CGGG-CGGCTGAAGAACGGG-GTTCGGAGGAAGAA
1 GGGGTTGGAGGAAGAACGGGCG-GCGGAAGAA-AA
* * * * * *
9463 TGGG-CGGCGGCAGAACGGGGTTCGGAGGAAGAGAA
1 GGGGTTGGAGGAAGAAC-GGG--CGGCGGAAGAAAA
* * *
9498 GGGGTTGGAGGAAGAACGGGAGGCGGTAGAAAG
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAA
* *
9531 GGGGTTGGAGGAAGAACGGGCGGCGGCAGAAAG
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAA
* *
9564 GGGGTTGGAGGAAGAACGGGCGGCGGCAG-AAC
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAA
* * *
9596 GGGGTTCGGAGGAAGAAAGGG-GGTTGGAGGAAGAA
1 GGGGTT-GGAGGAAGAACGGGCGG-CGGAAGAA-AA
* * * * * *
9631 CGGG-CGGCGGCAGAACGGG-GTTCGGAGGAAGAA
1 GGGGTTGGAGGAAGAACGGGCG-GCGGAAGAA-AA
* * * * *
9664 TGGG-CGGCGGCAGAACGGGGTTCGGAGGAAGAAAA
1 GGGGTTGGAGGAAGAAC-GGG--CGGCGGAAGAAAA
9699 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAA
1 GGGGTTGGAGGAAGAACGGGCGGCGGAAGAA
9730 GCTGGTCCGG
Statistics
Matches: 319, Mismatches: 61, Indels: 40
0.76 0.15 0.10
Matches are distributed among these distances:
32 20 0.06
33 237 0.74
34 8 0.03
35 23 0.07
36 29 0.09
37 2 0.01
ACGTcount: A:0.27, C:0.11, G:0.54, T:0.08
Consensus pattern (33 bp):
GGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAA
Found at i:12757 original size:39 final size:34
Alignment explanation
Indices: 12699--12889 Score: 102
Period size: 38 Copynumber: 5.2 Consensus size: 34
12689 CGAAAATATT
* **
12699 TATATTATATAGTTTTTTAAAATGTTCTTGAAAGCTTA
1 TATAATATATAG--TTTTAAAACATT-TTGAAAG-TTA
*
12737 TATACAATATATAAGTTTTAAAGCATTTTGAAAGTTA
1 TAT--AATATAT-AGTTTTAAAACATTTTGAAAGTTA
* *
12774 TATAATATATAGTTTT-GATCATTTTGAAA---A
1 TATAATATATAGTTTTAAAACATTTTGAAAGTTA
* * *
12804 TATAATGTATAGTTTTAAAAAAATATTTTTGGAAAATTTA
1 TATAATATATAGTTTT---AAAACA-TTTT-G-AAAGTTA
* *
12844 TATAATATATAGTTTAAAAAAACATTTTGGAAAACTTA
1 TATAATATATAGTTT--TAAAACATTTT-G-AAAGTTA
12882 TATAATAT
1 TATAATAT
12890 TTTTAAAAAC
Statistics
Matches: 124, Mismatches: 14, Indels: 30
0.74 0.08 0.18
Matches are distributed among these distances:
30 16 0.13
33 11 0.09
34 8 0.06
35 11 0.09
36 1 0.01
37 9 0.07
38 31 0.25
39 14 0.11
40 21 0.17
41 2 0.02
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (34 bp):
TATAATATATAGTTTTAAAACATTTTGAAAGTTA
Found at i:12848 original size:40 final size:38
Alignment explanation
Indices: 12803--12914 Score: 131
Period size: 35 Copynumber: 3.0 Consensus size: 38
12793 CATTTTGAAA
* * *
12803 ATATAATGTATAGTTTTAAAAAAATATTTTTGGAAAATTT
1 ATATAATATATAG-TTTAAAAAAACA-TTTTGGAAAACTT
12843 ATATAATATATAGTTTAAAAAAACATTTTGGAAAACTT
1 ATATAATATATAGTTTAAAAAAACATTTTGGAAAACTT
** *
12881 ATATAATAT-T--TTTAAAAACTCATTTTTGAAAACT
1 ATATAATATATAGTTTAAAAAAACATTTTGGAAAACT
12915 ATCTTACCTC
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 21 0.32
37 1 0.02
38 21 0.32
39 11 0.17
40 12 0.18
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (38 bp):
ATATAATATATAGTTTAAAAAAACATTTTGGAAAACTT
Found at i:12872 original size:38 final size:40
Alignment explanation
Indices: 12803--12889 Score: 133
Period size: 38 Copynumber: 2.2 Consensus size: 40
12793 CATTTTGAAA
* * *
12803 ATATAATGTATAGTTTTAAAAAAATATTTTTGGAAAATTT
1 ATATAATATATAGTTTTAAAAAAACATTTTTGGAAAACTT
12843 ATATAATATATAG-TTTAAAAAAACA-TTTTGGAAAACTT
1 ATATAATATATAGTTTTAAAAAAACATTTTTGGAAAACTT
12881 ATATAATAT
1 ATATAATAT
12890 TTTTAAAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 21 0.48
39 11 0.25
40 12 0.27
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.41
Consensus pattern (40 bp):
ATATAATATATAGTTTTAAAAAAACATTTTTGGAAAACTT
Found at i:14306 original size:17 final size:16
Alignment explanation
Indices: 14264--14313 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
14254 TATTATTTTA
14264 TTTTTATTCAATTTGATCC
1 TTTTT-TTC-ATTT-ATCC
*
14283 TTTTTTTTATTTATCC
1 TTTTTTTCATTTATCC
14299 TTTGTTTTCATTTAT
1 TTT-TTTTCATTTAT
14314 TTTATTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.25
17 14 0.50
18 2 0.07
19 5 0.18
ACGTcount: A:0.16, C:0.12, G:0.04, T:0.68
Consensus pattern (16 bp):
TTTTTTTCATTTATCC
Found at i:14464 original size:15 final size:15
Alignment explanation
Indices: 14396--14466 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
14386 TTTCTTTGAC
14396 TTTTTATTTATATTTA
1 TTTTTATTTAT-TTTA
* *
14412 TATTTATTTATTTAA
1 TTTTTATTTATTTTA
**
14427 CATTTATTTATTGTTA
1 TTTTTATTTATT-TTA
*
14443 TTGTT-TTTATTTTA
1 TTTTTATTTATTTTA
*
14457 TTTTTTTTTA
1 TTTTTATTTA
14467 CTAACATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
14 7 0.16
15 24 0.53
16 14 0.31
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTTTATTTATTTTA
Found at i:14543 original size:6 final size:6
Alignment explanation
Indices: 14532--14558 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
14522 AATCGAATAT
14532 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
14559 TCAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:15036 original size:12 final size:12
Alignment explanation
Indices: 15019--15049 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
15009 TAATTATATT
15019 TTAAACTAATAC
1 TTAAACTAATAC
15031 TTAAACTAATAC
1 TTAAACTAATAC
15043 TTAAACT
1 TTAAACT
15050 TTAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (12 bp):
TTAAACTAATAC
Found at i:26335 original size:31 final size:31
Alignment explanation
Indices: 26294--26371 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
26284 CCATTACGTC
26294 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACGGACTAAATGTTG
*
26325 GGGGATCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACGGACTAAATGTTG
* **
26356 AGGGACTGTATTGCAA
1 GGGGACCATATTGCAA
26372 GTTTTAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGCAAACGGACTAAATGTTG
Found at i:26599 original size:16 final size:16
Alignment explanation
Indices: 26578--26634 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
26568 CCGGATAAAT
26578 TTATTAATTTAGAGAG
1 TTATTAATTTAGAGAG
* * *
26594 TTATTAGTTTATTGATAA
1 TTATTAATTTA--GAGAG
*
26612 TTATTAATTTAAAGAG
1 TTATTAATTTAGAGAG
*
26628 TTTTTAA
1 TTATTAA
26635 GTAATTATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 18 0.58
18 13 0.42
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (16 bp):
TTATTAATTTAGAGAG
Found at i:26969 original size:17 final size:17
Alignment explanation
Indices: 26935--26986 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
26925 ACCGGACAAA
* *
26935 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
26952 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
26969 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
26984 TTT
1 TTT
26987 CTACTGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:27573 original size:2 final size:2
Alignment explanation
Indices: 27566--27636 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
27556 TCTTAATCTT
27566 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27637 TGGAGTACTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27964 original size:20 final size:21
Alignment explanation
Indices: 27933--27986 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
27923 GATTCTTGAC
27933 AATCGCAATGCGATTTT-CAT
1 AATCGCAATGCGATTTTCCAT
* *
27953 ATTCGCATTGCGATTTTCCAT
1 AATCGCAATGCGATTTTCCAT
*
27974 AATCGCAACGCGA
1 AATCGCAATGCGA
27987 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
AATCGCAATGCGATTTTCCAT
Found at i:28048 original size:20 final size:20
Alignment explanation
Indices: 27974--28282 Score: 347
Period size: 20 Copynumber: 15.4 Consensus size: 20
27964 GATTTTCCAT
* ** *
27974 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
27994 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
28014 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28034 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28054 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28074 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28094 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28114 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* *
28134 AATCGCAACGAGAATCCGTA
1 AATCGCAACGCGTATCCGTA
28154 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28174 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28194 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
28214 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
28234 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
28254 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
28274 AATCACAAC
1 AATCGCAAC
28283 ACTGAAATTT
Statistics
Matches: 248, Mismatches: 33, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.01
20 243 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:28077 original size:80 final size:80
Alignment explanation
Indices: 27974--28282 Score: 399
Period size: 80 Copynumber: 3.9 Consensus size: 80
27964 GATTTTCCAT
* ** * * * *
27974 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTAAATC
1 AATCGCAACGAGAATCCGTAAATCGCAACGCGTATC-CGTATATCGCAACGCGTATCCGTAAATC
*
28038 GCAACG-TGTATCCGTA
65 GCAACGAT-AATCCGTA
* * * *
28054 AATCGTAACGCGTATCCGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTAAATCG
1 AATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTATATCGCAACGCGTATCCGTAAATCG
28119 CAACGATAATCCGTA
66 CAACGATAATCCGTA
28134 AATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTATATCGCAACGCGTATCCGTAAATCG
1 AATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTATATCGCAACGCGTATCCGTAAATCG
28199 CAACGATAATCCGTA
66 CAACGATAATCCGTA
* * * * * *
28214 AATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTAAATC
1 AATCGCAACGAGAATCCGTAAATCGCAACGCGT-ATCCGTATATCGCAACGCGTATCCGTAAATC
*
28278 ACAAC
65 GCAAC
28283 ACTGAAATTT
Statistics
Matches: 205, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
79 1 0.00
80 201 0.98
81 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (80 bp):
AATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTATATCGCAACGCGTATCCGTAAATCG
CAACGATAATCCGTA
Found at i:29013 original size:24 final size:24
Alignment explanation
Indices: 28974--29020 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28964 AAATTTGGTC
28974 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
28998 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
29021 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:29212 original size:12 final size:12
Alignment explanation
Indices: 29195--29219 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29185 ATATAATCCT
29195 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29207 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29219 G
1 G
29220 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:30323 original size:93 final size:93
Alignment explanation
Indices: 30164--30642 Score: 931
Period size: 93 Copynumber: 5.2 Consensus size: 93
30154 ATGGTTTATG
30164 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
1 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
*
30229 TACACAGTTTAGCAGAATTGACAGCAAC
66 TACACAGTTTAGCAGAATTGGCAGCAAC
30257 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
1 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
30322 TACACAGTTTAGCAGAATTGGCAGCAAC
66 TACACAGTTTAGCAGAATTGGCAGCAAC
30350 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
1 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
30415 TACACAGTTTAGCAGAATTGGCAGCAAC
66 TACACAGTTTAGCAGAATTGGCAGCAAC
30443 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
1 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
*
30508 TACACAGTTTAGCAGAATTGGTAGCAAC
66 TACACAGTTTAGCAGAATTGGCAGCAAC
30536 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
1 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
30601 TACACAGTTTAGCAGAATTGGCAGCAAC
66 TACACAGTTTAGCAGAATTGGCAGCAAC
*
30629 CGAATAAATTTACT
1 CGAACAAATTTACT
30643 AAGCAATCTA
Statistics
Matches: 382, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 382 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
TACACAGTTTAGCAGAATTGGCAGCAAC
Found at i:32371 original size:20 final size:20
Alignment explanation
Indices: 32340--32436 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
32330 TTTTGGTTGA
32340 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
32360 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
32380 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
32399 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
32414 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
32434 AAT
1 AAT
32437 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:32392 original size:21 final size:21
Alignment explanation
Indices: 32338--32402 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
32328 TCTTTTGGTT
32338 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
32359 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
32379 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
32400 GAA
1 GAA
32403 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:32406 original size:14 final size:14
Alignment explanation
Indices: 32387--32443 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
32377 GAGAAATGAA
32387 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
32401 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
32420 AATCGCAACGAGAG
1 AATCGCAACGAGAG
32434 AATCGCAACG
1 AATCGCAACG
32444 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:32419 original size:33 final size:33
Alignment explanation
Indices: 32338--32460 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
32328 TCTTTTGGTT
*
32338 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
32379 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
32412 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
32445 GAAATGAAAACCGCAA
1 GAAATGAAAATCGCAA
32461 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
33 49 0.61
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:32496 original size:14 final size:14
Alignment explanation
Indices: 32477--32533 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
32467 TTTGGTTTCG
32477 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
32491 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
32510 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
32524 CGTTGCGATT
1 CGTTGCGATT
32534 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:32509 original size:33 final size:33
Alignment explanation
Indices: 32461--32540 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
32451 AAAACCGCAA
**
32461 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
32494 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
32527 TGCGATTTTCATTT
1 TGCGATTTTCATTT
32541 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:32546 original size:21 final size:21
Alignment explanation
Indices: 32521--32594 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
32511 GTTGCGATTC
32521 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
32542 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
32563 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
32584 TCTCGTTGCGA
1 TCTCGTTGCGA
32595 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:32716 original size:33 final size:33
Alignment explanation
Indices: 32674--32744 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
32664 AATACTAACT
32674 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
32707 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
32740 TGAAA
1 TGAAA
32745 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:33149 original size:20 final size:20
Alignment explanation
Indices: 33124--33275 Score: 207
Period size: 20 Copynumber: 7.6 Consensus size: 20
33114 CTTTAAAAAT
33124 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
33144 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
33164 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
33184 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
33204 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
33224 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
33244 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
33264 CGCGTTGCGATT
1 CGCGTTGCGATT
33276 ATGGAAAATC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
20 117 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:33293 original size:21 final size:20
Alignment explanation
Indices: 33269--33316 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
33259 ATATTCGCGT
33269 TGCGATTATGGAAAATCGCAA
1 TGCGATTAT-GAAAATCGCAA
* *
33290 TGCGAATATGAAAATCGCAT
1 TGCGATTATGAAAATCGCAA
33310 TGCGATT
1 TGCGATT
33317 GTCAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCGATTATGAAAATCGCAA
Found at i:37261 original size:182 final size:180
Alignment explanation
Indices: 36954--37316 Score: 708
Period size: 182 Copynumber: 2.0 Consensus size: 180
36944 AATTTTCTCC
36954 ATTAGTATGTTCATCAACACTCGTGCACATTAATGGTTATTTTGTGTGTATAGTTTTTCATCTGG
1 ATTAGTATGTTCATCAACACTCGTGCACATTAATGGTTATTTTGTGTGTATAGTTTTTCATCTGG
37019 TTATCTAATGGGTTTGACCATGTTTGGCTGTTTCTTCTTAGACAATTTAACCACTTTTTTTTTTT
66 TTATCTAATGGGTTTGACCATGTTTGGCTGTTTCTTCTTAGACAATTTAACCAC--TTTTTTTTT
37084 GATAACGTAGGACCTCCCAAGGCCAGACTAAAGAACCCGACCCTACAAGGCA
129 GATAACGTAGGACCTCCCAAGGCCAGACTAAAGAACCCGACCCTACAAGGCA
37136 ATTAGTATGTTCATCAACACTCGTGCACATTAATGGTTATTTTGTGTGTATAGTTTTTCATCTGG
1 ATTAGTATGTTCATCAACACTCGTGCACATTAATGGTTATTTTGTGTGTATAGTTTTTCATCTGG
37201 TTATCTAATGGGTTTGACCATGTTTGGCTGTTTCTTCTTAGACAATTTAACCACTTTTTTTTTGA
66 TTATCTAATGGGTTTGACCATGTTTGGCTGTTTCTTCTTAGACAATTTAACCACTTTTTTTTTGA
37266 TAACGTAGGACCTCCCAAGGCCAGACTAAAGAACCCGACCCTACAAGGCA
131 TAACGTAGGACCTCCCAAGGCCAGACTAAAGAACCCGACCCTACAAGGCA
37316 A
1 A
37317 CCTCCGGAGG
Statistics
Matches: 181, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
180 62 0.34
182 119 0.66
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (180 bp):
ATTAGTATGTTCATCAACACTCGTGCACATTAATGGTTATTTTGTGTGTATAGTTTTTCATCTGG
TTATCTAATGGGTTTGACCATGTTTGGCTGTTTCTTCTTAGACAATTTAACCACTTTTTTTTTGA
TAACGTAGGACCTCCCAAGGCCAGACTAAAGAACCCGACCCTACAAGGCA
Found at i:41914 original size:4 final size:4
Alignment explanation
Indices: 41907--41961 Score: 83
Period size: 4 Copynumber: 13.8 Consensus size: 4
41897 ATAAGTGCAT
* * *
41907 ATAC ATAC ATTC ATAC ATTC ATAC ATAC ATAC ATAC ATTC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
41955 ATAC ATA
1 ATAC ATA
41962 TATATATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:41932 original size:20 final size:20
Alignment explanation
Indices: 41907--41961 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
41897 ATAAGTGCAT
*
41907 ATACATACATTCATACATTC
1 ATACATACATACATACATTC
41927 ATACATACATACATACATTC
1 ATACATACATACATACATTC
41947 ATACATACATACATA
1 ATACATACATACATA
41962 TATATATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (20 bp):
ATACATACATACATACATTC
Found at i:45486 original size:14 final size:13
Alignment explanation
Indices: 45435--45489 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 13
45425 ACTTCTAGAC
45435 TATTATTAA-ATT
1 TATTATTAAGATT
*
45447 ATATTAGGTTAATATT
1 -TATTA--TTAAGATT
45463 TATTATTAAGATT
1 TATTATTAAGATT
45476 TATTAATTAAGATT
1 TATT-ATTAAGATT
45490 AGATATTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
13 16 0.43
14 9 0.24
15 9 0.24
16 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATTATTAAGATT
Found at i:50812 original size:22 final size:22
Alignment explanation
Indices: 50765--50812 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
50755 TATTGATATT
*
50765 TTAATTTAGTTAATTTGATCAT
1 TTAATTTAGTTAATTTGATCAA
* *
50787 TTAA-TTATTTAATTATTATCAA
1 TTAATTTAGTTAATT-TGATCAA
50809 TTAA
1 TTAA
50813 GTCACTTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (22 bp):
TTAATTTAGTTAATTTGATCAA
Found at i:53716 original size:4 final size:4
Alignment explanation
Indices: 53709--53735 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
53699 TGAATGGTGG
53709 CTCC CTCC CTCC CTCC CTCC CTCC CTC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTC
53736 TCTATCTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.74, G:0.00, T:0.26
Consensus pattern (4 bp):
CTCC
Found at i:55829 original size:6 final size:6
Alignment explanation
Indices: 55818--55842 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55808 TTTTCTAATT
55818 ATATTC ATATTC ATATTC ATATTC A
1 ATATTC ATATTC ATATTC ATATTC A
55843 AGATGTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTC
Found at i:56298 original size:25 final size:26
Alignment explanation
Indices: 56244--56295 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
56234 TATAAACATC
*
56244 AAATACAATAACTAATACTATTTATT
1 AAATAAAATAACTAATACTATTTATT
*
56270 -AATAAAATAA-TAATATTATTT-TT
1 AAATAAAATAACTAATACTATTTATT
56293 AAA
1 AAA
56296 ATACTAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
23 2 0.09
24 12 0.52
25 9 0.39
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATAAAATAACTAATACTATTTATT
Found at i:56466 original size:44 final size:44
Alignment explanation
Indices: 56406--56489 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
56396 AAAGTAAAAT
*
56406 TATTATAAAGTATATTAATTATTTATTAAAATAAGAATATAATA
1 TATTATAAAGTATATTAATTACTTATTAAAATAAGAATATAATA
* * *
56450 TATTATTAATTATATTAATTACTTATTAAAATAATAATAT
1 TATTATAAAGTATATTAATTACTTATTAAAATAAGAATAT
56490 TATTAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (44 bp):
TATTATAAAGTATATTAATTACTTATTAAAATAAGAATATAATA
Found at i:56494 original size:17 final size:17
Alignment explanation
Indices: 56444--56499 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
56434 AAATAAGAAT
*
56444 ATAAT-ATATTATTAATT
1 ATAATAATATTATTAA-A
*
56461 ATATTAATTACTTATTAAA
1 ATAATAA-TA-TTATTAAA
56480 ATAATAATATTATTAAA
1 ATAATAATATTATTAAA
56497 ATA
1 ATA
56500 TTGAAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 15 0.45
18 3 0.09
19 8 0.24
20 7 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAATAATATTATTAAA
Found at i:56511 original size:48 final size:44
Alignment explanation
Indices: 56416--56501 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
56406 TATTATAAAG
* * *
56416 TATATTAATTATTTATTAAAATAAGAATATAATATATTATTAAT
1 TATATTAATTACTTATTAAAATAAGAATATAATAAAATATTAAT
* *
56460 TATATTAATTACTTATTAAAATAATAATATTATTAAAATATT
1 TATATTAATTACTTATTAAAATAAGAATA-TAATAAAATATT
56502 GAAAATTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 27 0.75
45 9 0.25
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (44 bp):
TATATTAATTACTTATTAAAATAAGAATATAATAAAATATTAAT
Found at i:56528 original size:14 final size:14
Alignment explanation
Indices: 56473--56531 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
56463 ATTAATTACT
56473 TATTAAAATAATAA
1 TATTAAAATAATAA
*
56487 TATT--ATTAA-AA
1 TATTAAAATAATAA
*
56498 TATTGAAAATTATAA
1 TATT-AAAATAATAA
*
56513 TATTAAAATAAGAA
1 TATTAAAATAATAA
56527 TATTA
1 TATTA
56532 TGTTATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
14 20 0.56
15 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
TATTAAAATAATAA
Found at i:56774 original size:30 final size:28
Alignment explanation
Indices: 56739--56794 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 28
56729 ATGACTATTT
56739 TATTAAAATGATACTAAAATAAT-ATATTAA
1 TATT-AAAT-ATA-TAAAATAATAATATTAA
56769 TATTAAATATATAAAATAATAATATT
1 TATTAAATATATAAAATAATAATATT
56795 TTGAATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.36
28 8 0.32
29 4 0.16
30 4 0.16
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
TATTAAATATATAAAATAATAATATTAA
Found at i:57336 original size:59 final size:60
Alignment explanation
Indices: 57196--57339 Score: 166
Period size: 59 Copynumber: 2.4 Consensus size: 60
57186 AATCTTATTT
* * * * ** *
57196 TAAATTGATCCTTAAACTTTTGAATATTCCATTTTAATCCCTAAACTTTGACTTTCATTC
1 TAAATTGATCCTTAAACTTTTGAACATTCAATTTTAATACCTAAACTATGACACTCATAC
* *
57256 TAAATTAATCCTTAAAATTTTGAACATTCTAATTTT-ATACC-AAACTATGACACTCATAC
1 TAAATTGATCCTTAAACTTTTGAACATTC-AATTTTAATACCTAAACTATGACACTCATAC
* *
57315 TAAATTGATCATCAAACTTTTGAAC
1 TAAATTGATCCTTAAACTTTTGAAC
57340 CTTTTTCATC
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
59 35 0.50
60 30 0.43
61 5 0.07
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (60 bp):
TAAATTGATCCTTAAACTTTTGAACATTCAATTTTAATACCTAAACTATGACACTCATAC
Found at i:57834 original size:20 final size:20
Alignment explanation
Indices: 57790--58069 Score: 137
Period size: 20 Copynumber: 13.8 Consensus size: 20
57780 AATGACCAAC
* *
57790 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
57809 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* **
57829 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
**
57849 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
**
57869 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* ***
57890 AAGAATCGCAATGCGAGCCA-
1 AA-AATCGCAACGCGATTTAG
*** *
57910 AAGAATCGCGTTGCGATTCCA-
1 AA-AATCGCAACGCGATT-TAG
* * *
57931 AGAATCGCAATGCGATCTTCG
1 AAAATCGCAACGCGAT-TTAG
*
57952 AAGAATCGCAATGCGATTCTA-
1 AA-AATCGCAACGCGATT-TAG
* *
57973 AGAATCGCAATGCGATTCTA-
1 AAAATCGCAACGCGATT-TAG
* *
57993 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
58013 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* *
58033 ATAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
58053 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
58070 CCAAGAATCG
Statistics
Matches: 211, Mismatches: 34, Indels: 31
0.76 0.12 0.11
Matches are distributed among these distances:
18 1 0.00
19 19 0.09
20 150 0.71
21 13 0.06
22 28 0.13
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:57937 original size:62 final size:62
Alignment explanation
Indices: 57871--58082 Score: 211
Period size: 62 Copynumber: 3.5 Consensus size: 62
57861 GTCAAAAGAA
**
57871 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAGAATCGCGTTGCGATTCCAAG
1 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAGAATCGCAATGCGATTCCAAG
* * ** * *
57933 AATCGCAATGCGATCTTCGAAGAATCGCAATGCGATTCTAAGAATCGCAATGCGATTCTAAG
1 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAGAATCGCAATGCGATTCCAAG
*** * * * * * *
57995 AATCGCAACGCGAT-TGAGAA-AATCGCAACGCGATTCC-AATAATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGA-GCCAAAGAATCGCAATGCGATTCCA-AG
58055 AATCGCAACGCGA--TTCCAAGAATCGCAA
1 AATCGCAACGCGATCTTCCAAGAATCGCAA
58083 AACGGCAAAA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
59 4 0.03
60 50 0.39
61 6 0.05
62 67 0.53
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (62 bp):
AATCGCAACGCGATCTTCCAAGAATCGCAATGCGAGCCAAAGAATCGCAATGCGATTCCAAG
Found at i:58048 original size:60 final size:61
Alignment explanation
Indices: 57792--58082 Score: 181
Period size: 62 Copynumber: 4.8 Consensus size: 61
57782 TGACCAACAA
* * ****
57792 AATCGCAACGCGATAT-CAA-AATCGCAACGCGATTTAGAA-AATCGCAACGTTGAAAAGAA-
1 AATCGCAACGCGAT-TCCAAGAATCGCAACGCGATTGAGAAGAATCGCAACG-CGATTCCAAG
* *** * *
57851 AATCGCAACG-G--TCAAAAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGA-GCCAAA
1 AATCGCAACGCGATTC-CAAG--AATCGCAACGCGAT-TGAGAAGAATCGCAACGCGATTCC-AA
57912 G
61 G
*** * ** * *
57913 AATCGCGTTGCGATTCCAAGAATCGCAATGCGATCTTCGAAGAATCGCAATGCGATTCTAAG
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGAT-TGAGAAGAATCGCAACGCGATTCCAAG
* * *
57975 AATCGCAATGCGATTCTAAGAATCGCAACGCGATTGAGAA-AATCGCAACGCGATTCCAAT
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAAGAATCGCAACGCGATTCCAAG
* * **
58035 AATCGCAACGCGATT-GAGAAAATCGCAACGCGATT-CCAAGAATCGCAA
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTGAGAAGAATCGCAA
58083 AACGGCAAAA
Statistics
Matches: 187, Mismatches: 30, Indels: 29
0.76 0.12 0.12
Matches are distributed among these distances:
55 1 0.01
57 2 0.01
58 1 0.01
59 13 0.07
60 69 0.37
61 12 0.06
62 82 0.44
63 2 0.01
64 3 0.02
65 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (61 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAAGAATCGCAACGCGATTCCAAG
Found at i:58078 original size:20 final size:20
Alignment explanation
Indices: 57871--58082 Score: 196
Period size: 20 Copynumber: 10.4 Consensus size: 20
57861 GTCAAAAGAA
57871 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
57893 AATCGCAATGCGA-GCCAAAG
1 AATCGCAACGCGATTCC-AAG
***
57913 AATCGCGTTGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
* *
57933 AATCGCAATGCGATCTTCGAAG
1 AATCGCAACGCGA--TTCCAAG
* *
57955 AATCGCAATGCGATTCTAAG
1 AATCGCAACGCGATTCCAAG
* *
57975 AATCGCAATGCGATTCTAAG
1 AATCGCAACGCGATTCCAAG
* *
57995 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
*
58015 AATCGCAACGCGATTCCAAT
1 AATCGCAACGCGATTCCAAG
* *
58035 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
58055 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
58075 AATCGCAA
1 AATCGCAA
58083 AACGGCAAAA
Statistics
Matches: 164, Mismatches: 18, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.02
20 125 0.76
21 4 0.02
22 31 0.19
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:58206 original size:6 final size:6
Alignment explanation
Indices: 58195--58251 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
58185 GACACGTATT
58195 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
58243 ACCACG ACC
1 ACCACG ACC
58252 CGAGACGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:59017 original size:6 final size:6
Alignment explanation
Indices: 59006--59032 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
58996 TCTCGTCTCG
59006 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
59033 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:59168 original size:20 final size:20
Alignment explanation
Indices: 59143--59232 Score: 101
Period size: 20 Copynumber: 4.4 Consensus size: 20
59133 TTTTGCCGTT
59143 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCA
* *
59163 TTGCGATTCCTGGAATCGCG
1 TTGCGATTCTTGGAATCGCA
**
59183 TTGCGATT-TTCTCAATCGCA
1 TTGCGATTCTT-GGAATCGCA
*
59203 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCA
59225 TTGCGATT
1 TTGCGATT
59233 TTCTTTTGAC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.70
21 3 0.05
22 13 0.23
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCA
Found at i:59200 original size:40 final size:42
Alignment explanation
Indices: 59156--59236 Score: 139
Period size: 40 Copynumber: 2.0 Consensus size: 42
59146 CGATTCTTGG
59156 AATCGCATTGCGATTCCTGG-A-ATCGCGTTGCGATTTTCTC
1 AATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
*
59196 AATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 AATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCT
59237 TTTGACCGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 19 0.50
41 1 0.03
42 18 0.47
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (42 bp):
AATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
Found at i:59248 original size:20 final size:20
Alignment explanation
Indices: 59223--59276 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
59213 TGGAAGATCG
* *
59223 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
59243 CGTTGCGATTTTCTTTTCAA
1 CGTTGCGATTTTCTTTTCAA
*
59263 CATTGCGATTTTCT
1 CGTTGCGATTTTCT
59277 AAATCGCGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:59288 original size:20 final size:19
Alignment explanation
Indices: 59176--59294 Score: 78
Period size: 20 Copynumber: 5.9 Consensus size: 19
59166 CGATTCCTGG
59176 AATCGCGTTGCGATTTTCT
1 AATCGCGTTGCGATTTTCT
* **
59195 CAATCGCATTGCGATTCTTGGA
1 -AATCGCGTTGCGATT-TT-CT
59217 AGATCGCGTTGCGATTTTCT
1 A-ATCGCGTTGCGATTTTCT
* *
59237 -TTTGACCGTTGCGATTTTCT
1 AATCG--CGTTGCGATTTTCT
** * *
59257 TTTCAACATTGCGATTTTCT
1 AATC-GCGTTGCGATTTTCT
59277 AAATCGCGTTGCGATTTT
1 -AATCGCGTTGCGATTTT
59295 TGTTTCGCAT
Statistics
Matches: 76, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
18 2 0.03
20 52 0.68
21 9 0.12
22 13 0.17
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (19 bp):
AATCGCGTTGCGATTTTCT
Found at i:60105 original size:6 final size:6
Alignment explanation
Indices: 60094--60122 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
60084 GCACACCATG
60094 TCAATC TCAATC TCAATC TCAATC T-AATC
1 TCAATC TCAATC TCAATC TCAATC TCAATC
60123 GCTGTTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (6 bp):
TCAATC
Found at i:62918 original size:27 final size:28
Alignment explanation
Indices: 62869--62926 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
62859 AGGGGTGCAC
62869 AAAAAATCCGAATATCCGATTTTGCGAA
1 AAAAAATCCGAATATCCGATTTTGCGAA
* *
62897 AAAAATATCCGAA-AT-CGGTTTTGGGAA
1 AAAAA-ATCCGAATATCCGATTTTGCGAA
62924 AAA
1 AAA
62927 TCGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 13 0.48
28 7 0.26
29 7 0.26
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGCGAA
Found at i:62949 original size:20 final size:20
Alignment explanation
Indices: 62926--62965 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
62916 TTTGGGAAAA
* *
62926 ATCGGTTTTTTTTTAACCGG
1 ATCGGATTTTTTTAAACCGG
62946 ATCGGATTTTTTTAAACCGG
1 ATCGGATTTTTTTAAACCGG
62966 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (20 bp):
ATCGGATTTTTTTAAACCGG
Found at i:63025 original size:12 final size:12
Alignment explanation
Indices: 63010--63055 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
63000 CGGTTTTTTT
*
63010 ACCGGATAAAAA
1 ACCGGTTAAAAA
63022 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
63037 ACCGGTTAAAAA
1 ACCGGTTAAAAA
63049 ACCGGTT
1 ACCGGTT
63056 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:63037 original size:15 final size:13
Alignment explanation
Indices: 63016--63056 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
63006 TTTTACCGGA
63016 TAAAAAACCGGTT
1 TAAAAAACCGGTT
63029 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
63043 TAAAAAACCGGTT
1 TAAAAAACCGGTT
63056 T
1 T
63057 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:65385 original size:21 final size:21
Alignment explanation
Indices: 65361--65400 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
65351 TTTATTTTAT
65361 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
65382 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
65401 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:65463 original size:34 final size:34
Alignment explanation
Indices: 65395--65489 Score: 158
Period size: 34 Copynumber: 2.9 Consensus size: 34
65385 TTTGTTTCAA
65395 TTATCGAACTT-GAAGTTTTTAAGTA-TTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTTGAAT
65427 TTATCGAACTTGGAAGTTTTTAAGTATTTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTTGAAT
* *
65461 TTATCAAACTTGGAAGTATTTAAGTATTT
1 TTATCGAACTTGGAAGTTTTTAAGTATTT
65490 CAATTATGTT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 11 0.19
33 14 0.24
34 34 0.58
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (34 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTTGAAT
Found at i:65523 original size:13 final size:13
Alignment explanation
Indices: 65480--65534 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
65470 TTGGAAGTAT
65480 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
65493 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
65507 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
65520 TTAAGTATTTGAA
1 TTAAGTATTTCAA
65533 TT
1 TT
65535 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:65957 original size:15 final size:15
Alignment explanation
Indices: 65932--65987 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
65922 ATCTGGAATA
*
65932 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
65947 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
65962 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
65979 TTAAAACCG
1 TTAAAACCG
65988 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:65996 original size:21 final size:18
Alignment explanation
Indices: 65951--65984 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
65941 GTTTTTTTAT
65951 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
65968 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
65985 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:66105 original size:15 final size:17
Alignment explanation
Indices: 66079--66110 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
66069 TTCTATGGGA
66079 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
66095 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
66111 CAGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:69643 original size:2 final size:2
Alignment explanation
Indices: 69636--69664 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
69626 CATAATCATA
69636 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
69665 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:81786 original size:24 final size:23
Alignment explanation
Indices: 81756--81820 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
81746 CGAATATATT
*
81756 AATATTTTAAAATAATTAAAATA
1 AATATTTTAAAATAATAAAAATA
*
81779 ATATATTTTATAAT-ATAAAAATA
1 A-ATATTTTAAAATAATAAAAATA
*
81802 AAAATTCTTAAAATAATAA
1 AATATT-TTAAAATAATAA
81821 TTATAATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 4 0.11
23 16 0.46
24 15 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATTTTAAAATAATAAAAATA
Found at i:81821 original size:3 final size:3
Alignment explanation
Indices: 81813--81858 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
81803 AAATTCTTAA
* *
81813 AAT AAT AAT TAT AAT -AT GAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
81859 CTAGACTGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:84730 original size:3 final size:3
Alignment explanation
Indices: 84722--84754 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
84712 AATAAAACAT
84722 TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
84755 TTTTTTAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:85843 original size:106 final size:106
Alignment explanation
Indices: 85535--86661 Score: 1597
Period size: 106 Copynumber: 11.0 Consensus size: 106
85525 GCATTGTTCC
* * **
85535 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * *
85599 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
85641 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT-TAA-T--GAAA-T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * ** *
85700 TCAGCCGCCCCTTCGTCGTGAAGTTGGGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
85742 G-GTCCAAGATCCTTTGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
85806 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
85847 GAGTCCAATATCCTTCGCTGTGAAGTTGAAACTGGCTCTGAAATTGGGAAATTG-TTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
85911 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
85952 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGAAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
86017 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
86058 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
86123 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
86164 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
86229 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
86270 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
86335 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
86376 GAGTCCAATATCCTTCG-T-T---G-CG-AA----CT-TGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
86429 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
86470 GAGTCCAATATCCTTCG-T-T---G-CG-AA---G-T-TGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
86523 CCAGCGGTCCCTCCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
86564 GAGTCCAATATCCTT--CT-T--TG-TG-AA---G-T-TGAAATTGGAAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
86617 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
86658 GAGT
1 GAGT
86662 GGCACGATAT
Statistics
Matches: 955, Mismatches: 53, Indels: 38
0.91 0.05 0.04
Matches are distributed among these distances:
93 2 0.00
94 246 0.26
95 2 0.00
99 2 0.00
100 77 0.08
101 6 0.01
102 5 0.01
104 5 0.01
105 108 0.11
106 501 0.52
107 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:86469 original size:94 final size:94
Alignment explanation
Indices: 86308--86661 Score: 627
Period size: 94 Copynumber: 3.8 Consensus size: 94
86298 AAATTGGCTC
*
86308 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
86373 CTGGAGTCCAATATCCTTCGTTGCGAACT
66 CTGGAGTCCAATATCCTTCGTTGCGAAGT
86402 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
86467 CTGGAGTCCAATATCCTTCGTTGCGAAGT
66 CTGGAGTCCAATATCCTTCGTTGCGAAGT
* *
86496 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTCCGTCGTGAAGTTGAACTTGCATTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
86561 CTGGAGTCCAATATCCTTCTTTGTGAAGT
66 CTGGAGTCCAATATCCTTCGTTGCGAAGT
* *
86590 TGAAATTGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
86655 CTCGAGT
66 CTGGAGT
86662 GGCACGATAT
Statistics
Matches: 249, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 249 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (94 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGCGAAGT
Found at i:89510 original size:20 final size:20
Alignment explanation
Indices: 89487--89526 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
89477 CATCCAGCTC
*
89487 AGCTAGGGTTTCTCCATCTT
1 AGCTAGGGTTTCGCCATCTT
89507 AGCTAGGGTTTCGCCATCTT
1 AGCTAGGGTTTCGCCATCTT
89527 GTTCTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.38
Consensus pattern (20 bp):
AGCTAGGGTTTCGCCATCTT
Found at i:92475 original size:3 final size:3
Alignment explanation
Indices: 92467--92505 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
92457 AATAAAACAT
92467 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
92506 TTTTTTAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:94422 original size:23 final size:23
Alignment explanation
Indices: 94395--94452 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
94385 TAAGCTACCA
94395 AAAGGCAGAGAAAAACGAGCCAC
1 AAAGGCAGAGAAAAACGAGCCAC
* * *** *
94418 AAAGGCATAGATAAATTTGCCAT
1 AAAGGCAGAGAAAAACGAGCCAC
94441 AAAGGCAGAGAA
1 AAAGGCAGAGAA
94453 TATGTCACAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.16, G:0.24, T:0.10
Consensus pattern (23 bp):
AAAGGCAGAGAAAAACGAGCCAC
Found at i:95595 original size:17 final size:15
Alignment explanation
Indices: 95566--95612 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 15
95556 ATAAACCGAA
95566 CCGAACC-AAAAAAC
1 CCGAACCGAAAAAAC
*
95580 CCGAACCGTTAAAAAAA
1 CCGAACCG--AAAAAAC
*
95597 CTGAACCGAAAAAAC
1 CCGAACCGAAAAAAC
95612 C
1 C
95613 GATTTCGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 7 0.26
15 7 0.26
17 13 0.48
ACGTcount: A:0.53, C:0.30, G:0.11, T:0.06
Consensus pattern (15 bp):
CCGAACCGAAAAAAC
Found at i:97337 original size:23 final size:22
Alignment explanation
Indices: 97297--97339 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
97287 AAGAATATAA
* *
97297 TTATTTTTATTATGTTTTATGT
1 TTATTTTTATAATATTTTATGT
97319 TTATTTTTAATAATATTTTAT
1 TTATTTTT-ATAATATTTTAT
97340 AATGTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (22 bp):
TTATTTTTATAATATTTTATGT
Found at i:97770 original size:19 final size:19
Alignment explanation
Indices: 97735--97773 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
97725 AATAGTATCT
*
97735 TATATTAATTAATATATAA
1 TATATTAAATAATATATAA
97754 TATATTAAAATAA-ATATAA
1 TATATT-AAATAATATATAA
97773 T
1 T
97774 TCCATATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATATTAAATAATATATAA
Found at i:99061 original size:3 final size:3
Alignment explanation
Indices: 99053--99087 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
99043 GTAATGATAT
99053 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
99088 CATGTCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:101079 original size:24 final size:23
Alignment explanation
Indices: 101036--101096 Score: 106
Period size: 24 Copynumber: 2.7 Consensus size: 23
101026 CCGTTCAAAC
101036 TTCAAATTCA-TTTTTTAGTGAA
1 TTCAAATTCATTTTTTTAGTGAA
101058 TTCAAATTCATTTTTTTGAGTGAA
1 TTCAAATTCATTTTTTT-AGTGAA
101082 TTCAAATTCATTTTT
1 TTCAAATTCATTTTT
101097 AATTTATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.27
23 6 0.16
24 21 0.57
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (23 bp):
TTCAAATTCATTTTTTTAGTGAA
Found at i:101110 original size:24 final size:22
Alignment explanation
Indices: 101036--101106 Score: 65
Period size: 24 Copynumber: 3.1 Consensus size: 22
101026 CCGTTCAAAC
*
101036 TTCAAATTCATTTTTTAGTGA-A
1 TTCAAATTCA-TTTTTATTGATA
101058 TTCAAATTCATTTTT-TTGAGTGAA
1 TTCAAATTCATTTTTATTGA-T--A
*
101082 TTCAAATTCATTTTTAATTTATA
1 TTCAAATTCATTTTT-ATTGATA
101105 TT
1 TT
101107 TCAATCAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
20 3 0.07
21 5 0.12
22 10 0.24
23 3 0.07
24 16 0.39
25 1 0.02
26 3 0.07
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.54
Consensus pattern (22 bp):
TTCAAATTCATTTTTATTGATA
Found at i:102922 original size:25 final size:25
Alignment explanation
Indices: 102889--102938 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
102879 AATTTATGAT
102889 ATATTTCAATATGTTACATTAGTGG
1 ATATTTCAATATGTTACATTAGTGG
102914 ATATTTCAATATGTTACATTAGTGG
1 ATATTTCAATATGTTACATTAGTGG
102939 TATGTCTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (25 bp):
ATATTTCAATATGTTACATTAGTGG
Found at i:114069 original size:16 final size:16
Alignment explanation
Indices: 114048--114084 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
114038 TAAGTCGAGG
*
114048 ATGCCGCCAGAAGAGA
1 ATGCCGCCAAAAGAGA
114064 ATGCCGCCAAAAGAGA
1 ATGCCGCCAAAAGAGA
114080 ATGCC
1 ATGCC
114085 TTATTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.27, G:0.27, T:0.08
Consensus pattern (16 bp):
ATGCCGCCAAAAGAGA
Done.