Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007810.1 Hibiscus syriacus cultivar Beakdansim tig00110134_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: 70660
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:4624 original size:15 final size:15
Alignment explanation
Indices: 4601--4640 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
4591 TTTCTCACCT
*
4601 CTGAATGATTCAGTG
1 CTGACTGATTCAGTG
4616 CTGACTGATTCAGTG
1 CTGACTGATTCAGTG
*
4631 TTGACTGATT
1 CTGACTGATT
4641 TAGCATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (15 bp):
CTGACTGATTCAGTG
Found at i:4741 original size:16 final size:16
Alignment explanation
Indices: 4720--4766 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
4710 ATACAGAGCC
4720 TTTGAATCATTCAGCA
1 TTTGAATCATTCAGCA
*
4736 TTTGAATCATTCAACA
1 TTTGAATCATTCAGCA
4752 TTTGAATCATTCAGC
1 TTTGAATCATTCAGC
4767 GCTTAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (16 bp):
TTTGAATCATTCAGCA
Found at i:15905 original size:34 final size:33
Alignment explanation
Indices: 15829--15935 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
15819 GTGGTAAGAA
* *
15829 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
15863 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
15898 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
15932 ATTT
1 ATTT
15936 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:15917 original size:36 final size:34
Alignment explanation
Indices: 15862--15940 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
15852 TTTAAATAGT
*
15862 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
15894 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
15928 TATTATTTATTTA
1 TATTATTTTTTTA
15941 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:17695 original size:21 final size:21
Alignment explanation
Indices: 17665--17712 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
17655 GCAGGGGTAC
* *
17665 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
17686 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
17707 ATGCCA
1 ATGCCA
17713 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:17727 original size:21 final size:21
Alignment explanation
Indices: 17703--17809 Score: 94
Period size: 21 Copynumber: 5.1 Consensus size: 21
17693 GCCCACCAGT
*
17703 TTATATGCC-ATCTCCGCAGGG
1 TTATATGCCGAGC-CCGCAGGG
*
17724 TTATATTCCGAGCCCGCAGGG
1 TTATATGCCGAGCCCGCAGGG
* *
17745 TTACATTCCGAGCCCGCAGGG
1 TTATATGCCGAGCCCGCAGGG
* * *
17766 TTACATTCCTAGCCCGCTA-GG
1 TTATATGCCGAGCCCGC-AGGG
*
17787 TTACT-TGCCTAGCCCGCAGGG
1 TTA-TATGCCGAGCCCGCAGGG
17808 TT
1 TT
17810 TTATACCATA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
20 1 0.01
21 72 0.95
22 3 0.04
ACGTcount: A:0.18, C:0.31, G:0.25, T:0.26
Consensus pattern (21 bp):
TTATATGCCGAGCCCGCAGGG
Found at i:17763 original size:42 final size:42
Alignment explanation
Indices: 17716--17809 Score: 129
Period size: 42 Copynumber: 2.2 Consensus size: 42
17706 TATGCCATCT
*
17716 CCGCAGGGTTATATTCCGAGCCCGC-AGGGTTACATT-CCGAGC
1 CCGCAGGGTTACATTCCGAGCCCGCTA-GGTTAC-TTGCCGAGC
* *
17758 CCGCAGGGTTACATTCCTAGCCCGCTAGGTTACTTGCCTAGC
1 CCGCAGGGTTACATTCCGAGCCCGCTAGGTTACTTGCCGAGC
17800 CCGCAGGGTT
1 CCGCAGGGTT
17810 TTATACCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
41 2 0.04
42 44 0.94
43 1 0.02
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (42 bp):
CCGCAGGGTTACATTCCGAGCCCGCTAGGTTACTTGCCGAGC
Found at i:18389 original size:27 final size:28
Alignment explanation
Indices: 18327--18405 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
18317 GATAAATGTT
* *
18327 TTTAAAATAAAAATTATATTATTTGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
18355 TTTAAAATAAAAATAATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
*
18383 TTTAAATTTAAAATATAA-ATTAT
1 TTTAAA-ATAAAA-ATAATATTAT
18406 AGTATTCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 32 0.70
29 10 0.22
30 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (28 bp):
TTTAAAATAAAAATAATATTATTCGAAA
Found at i:18417 original size:28 final size:28
Alignment explanation
Indices: 18327--18421 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 28
18317 GATAAATGTT
**
18327 TTTAAAATAAAAATTATATTATTTGAAA
1 TTTAAAATAAAAATTATATTATTCAAAA
*
18355 TTTAAAATAAAAATAATATTATTCGAAATTTAAA
1 TTTAAAATAAAAATTATATTATTC---A---AAA
* *
18389 TTTAAAATATAAATTATAGTATTCAAAA
1 TTTAAAATAAAAATTATATTATTCAAAA
18417 TTTAA
1 TTTAA
18422 CATTAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
28 30 0.55
31 1 0.02
34 24 0.44
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (28 bp):
TTTAAAATAAAAATTATATTATTCAAAA
Found at i:18428 original size:34 final size:34
Alignment explanation
Indices: 18347--18421 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
18337 AAATTATATT
* *
18347 ATTTGAAATTTAAAATAAAAATAATATTATTCGAA
1 ATTT-AAATTTAAAATAAAAATAATAGTATTCAAA
* *
18382 ATTTAAATTTAAAATATAAATTATAGTATTCAAA
1 ATTTAAATTTAAAATAAAAATAATAGTATTCAAA
18416 ATTTAA
1 ATTTAA
18422 CATTAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 32 0.89
35 4 0.11
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (34 bp):
ATTTAAATTTAAAATAAAAATAATAGTATTCAAA
Found at i:19050 original size:128 final size:128
Alignment explanation
Indices: 18822--19706 Score: 1497
Period size: 128 Copynumber: 6.9 Consensus size: 128
18812 TTACCTGATT
*
18822 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * * *** * *
18887 TGACAAAATAATGGAAGTCGCACCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATATG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* * *
18950 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
* * * *** *
19014 ATGACAAAATAATGGAAGGCGCGCCCCCGAGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
65 CTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
*
19078 TACTGGTATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
19143 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
19206 TATTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
19271 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTTATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
19334 TACTGATATATCTAGTGTCCCAGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
19399 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
19462 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
19527 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
19590 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
19655 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCATTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
19707 ACTCCGATTA
Statistics
Matches: 726, Mismatches: 28, Indels: 6
0.96 0.04 0.01
Matches are distributed among these distances:
127 2 0.00
128 723 1.00
129 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:27461 original size:68 final size:68
Alignment explanation
Indices: 27352--27508 Score: 298
Period size: 68 Copynumber: 2.3 Consensus size: 68
27342 ATTTTATATT
27352 TTAAAAAGTAATTGAATTCCAAGAAAGAAGTTATGATCTAATTTAGCTAGTTTCAAAATTTAGAG
1 TTAAAAAGTAATTGAATTCCAAGAAAGAAGTTATGATCTAATTTAGCTAGTTTCAAAATTTAGAG
27417 GAC
66 GAC
27420 TTAAAAAGTAATTGAATTCCAAGAAAGAAGTTATGATCTAATTTAGCTAGTTTCAAAATTTAGAG
1 TTAAAAAGTAATTGAATTCCAAGAAAGAAGTTATGATCTAATTTAGCTAGTTTCAAAATTTAGAG
27485 GAC
66 GAC
*
27488 TTAAAAAATAATTGAA-TCCAA
1 TTAAAAAGTAATTGAATTCCAA
27509 AAAATTAAGG
Statistics
Matches: 88, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
67 5 0.06
68 83 0.94
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.32
Consensus pattern (68 bp):
TTAAAAAGTAATTGAATTCCAAGAAAGAAGTTATGATCTAATTTAGCTAGTTTCAAAATTTAGAG
GAC
Found at i:29390 original size:31 final size:31
Alignment explanation
Indices: 29295--29382 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 31
29285 ATCTGACATC
* * *
29295 TAAATTTTAGACAACATA-CAA-TTGATCCT-
1 TAAATTTTAGATAAAATATTAATTTGAT-CTA
29324 TAAATTTTAGATAAAATATTAATTTGATCTA
1 TAAATTTTAGATAAAATATTAATTTGATCTA
29355 TAAATTTTAGATAAAATATTAATTTGAT
1 TAAATTTTAGATAAAATATTAATTTGAT
29383 TCGTAAATCT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 16 0.30
30 4 0.08
31 33 0.62
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (31 bp):
TAAATTTTAGATAAAATATTAATTTGATCTA
Found at i:29874 original size:20 final size:20
Alignment explanation
Indices: 29780--30148 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
29770 GATTTTCCAT
* ** *
29780 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
29800 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
29820 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29840 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
29860 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
29880 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29900 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
29920 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
29940 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
29960 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
29980 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
30000 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
30020 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
30040 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
30060 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
30080 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
30100 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
30120 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
30140 AATCACAAC
1 AATCGCAAC
30149 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:30869 original size:24 final size:24
Alignment explanation
Indices: 30830--30876 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
30820 AAATTTGGTC
30830 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
30854 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
30877 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:31068 original size:12 final size:12
Alignment explanation
Indices: 31051--31075 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31041 ATATAATCCT
31051 GAAGAAGAAAAA
1 GAAGAAGAAAAA
31063 GAAGAAGAAAAA
1 GAAGAAGAAAAA
31075 G
1 G
31076 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:33379 original size:19 final size:19
Alignment explanation
Indices: 33357--33677 Score: 369
Period size: 19 Copynumber: 18.4 Consensus size: 19
33347 CGGAAAATAC
*
33357 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33376 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
33390 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
33410 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
33424 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33443 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33462 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33481 AATCGCAA--CG--A-GAT
1 AATCGCAATGCGAAATGAA
33495 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33514 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
33533 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
33547 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
33566 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33585 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
33599 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33618 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
33632 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33651 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33670 AATCGCAA
1 AATCGCAA
33678 CGAGATAATC
Statistics
Matches: 261, Mismatches: 10, Indels: 62
0.78 0.03 0.19
Matches are distributed among these distances:
14 56 0.21
15 2 0.01
16 22 0.08
17 20 0.08
18 3 0.01
19 145 0.56
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:33444 original size:33 final size:33
Alignment explanation
Indices: 33357--33658 Score: 323
Period size: 33 Copynumber: 8.8 Consensus size: 33
33347 CGGAAAATAC
* *
33357 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
33390 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
33424 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
33462 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
33495 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
33533 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
33566 AATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
33598 GAATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 -AATCGCAATGCGAAATGAAAATCGCAACGAGAA
33631 GAATCGCAATGCGAAATGAAAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
33659 TGCGAAATGA
Statistics
Matches: 242, Mismatches: 9, Indels: 36
0.84 0.03 0.13
Matches are distributed among these distances:
32 2 0.01
33 141 0.58
34 31 0.13
35 10 0.04
36 9 0.04
37 2 0.01
38 47 0.19
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:33499 original size:52 final size:52
Alignment explanation
Indices: 33357--33677 Score: 378
Period size: 52 Copynumber: 6.2 Consensus size: 52
33347 CGGAAAATAC
* *
33357 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
*
33410 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
*
33462 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAA
* * *
33514 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAA
33566 AATCGCAATGCGAAATGAAAATCGCAACGA-AAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA-AATCGCAATGCGAAATGAA
33618 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
33670 AATCGCAA
1 AATCGCAA
33678 CGAGATAATC
Statistics
Matches: 242, Mismatches: 9, Indels: 35
0.85 0.03 0.12
Matches are distributed among these distances:
47 8 0.03
48 9 0.04
49 4 0.02
50 6 0.02
51 4 0.02
52 169 0.70
53 27 0.11
54 2 0.01
55 2 0.01
56 1 0.00
57 10 0.04
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:33604 original size:14 final size:14
Alignment explanation
Indices: 33585--33639 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
33575 GCGAAATGAA
33585 AATCGCAACGAAAG
1 AATCGCAACGAAAG
33599 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
33616 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
33632 AATCGCAA
1 AATCGCAA
33640 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 16 0.44
16 6 0.17
17 6 0.17
19 8 0.22
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:33659 original size:85 final size:85
Alignment explanation
Indices: 33385--33699 Score: 442
Period size: 85 Copynumber: 3.6 Consensus size: 85
33375 AAATCCCAAC
*
33385 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCA
33450 ATGCGAAATGAAAATCGCAATGCGAA
65 A--CGAAA-G--AATCGCAATGCGAA
*
33476 ATGAAAATCGCAA--CG--A-GATAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAAT
*
33536 CGCAACGACAGAATCGCAATGCGAA
61 CGCAACGAAAGAATCGCAATGCGAA
*
33561 ATTAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAA
33626 CGAAAGAATCGCAATGCGAA
66 CGAAAGAATCGCAATGCGAA
* *
33646 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
33700 TATAAACGCA
Statistics
Matches: 205, Mismatches: 9, Indels: 26
0.85 0.04 0.11
Matches are distributed among these distances:
85 133 0.65
86 1 0.00
87 8 0.04
88 11 0.05
89 2 0.01
90 37 0.18
91 13 0.06
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (85 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAA
CGAAAGAATCGCAATGCGAA
Found at i:33815 original size:19 final size:19
Alignment explanation
Indices: 33706--33807 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
33696 AAATTATAAA
33706 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
33725 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
33745 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
33761 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
33778 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
33797 CGCATTGCGAT
1 CGCATTGCGAT
33808 AGTCATTTTG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:33932 original size:14 final size:14
Alignment explanation
Indices: 33913--33949 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
33903 CATCAATTAC
33913 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
33927 ACAAATCATCTTTT
1 ACAAATCAACTTTT
33941 ACAAATCAA
1 ACAAATCAA
33950 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:35943 original size:14 final size:14
Alignment explanation
Indices: 35924--35980 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35914 GCGAAATGAA
*
35924 AATCGCAACGACAG
1 AATCGCAACGAAAG
35938 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
35955 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
35971 AATCGCAACG
1 AATCGCAACG
35981 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:35951 original size:33 final size:33
Alignment explanation
Indices: 35905--35997 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
35895 GCGAAACCAA
*
35905 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
35938 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
35971 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
35998 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:35962 original size:19 final size:19
Alignment explanation
Indices: 35868--36002 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
35858 TAGTTTACTT
* *
35868 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
35888 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
35907 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
35926 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
35940 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
35959 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
35973 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
35992 TCGCAATGCGA
1 TCGCAACGCGA
36003 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:36020 original size:19 final size:19
Alignment explanation
Indices: 35998--36126 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
35988 AAAATCGCAA
35998 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
36017 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
36031 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
36050 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
36064 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
36083 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
36102 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
36122 TGCGA
1 TGCGA
36127 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:36040 original size:33 final size:33
Alignment explanation
Indices: 35998--36089 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
35988 AAAATCGCAA
35998 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
36031 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
36064 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
36090 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:36317 original size:93 final size:93
Alignment explanation
Indices: 36158--36624 Score: 918
Period size: 93 Copynumber: 5.0 Consensus size: 93
36148 GCAAATTGAA
36158 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
36223 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
36251 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
36316 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
36344 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
36409 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
36437 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
36501 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
36529 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
36594 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
36622 ACT
1 ACT
36625 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.25
93 280 0.75
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:36595 original size:185 final size:186
Alignment explanation
Indices: 36158--36624 Score: 918
Period size: 185 Copynumber: 2.5 Consensus size: 186
36148 GCAAATTGAA
36158 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
36223 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
36288 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
36344 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
36409 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
36473 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
36529 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
36594 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
36625 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
185 154 0.55
186 126 0.45
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:38348 original size:14 final size:14
Alignment explanation
Indices: 38329--38415 Score: 75
Period size: 14 Copynumber: 5.5 Consensus size: 14
38319 TTGAAATGAA
38329 AATCGCAACGAGAG
1 AATCGCAACGAGAG
38343 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
38360 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
38376 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
38395 AATCGCAACGAGAG
1 AATCGCAACGAGAG
38409 AATCGCA
1 AATCGCA
38416 GCGCGAAATG
Statistics
Matches: 61, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
14 25 0.41
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 18 0.30
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:38366 original size:33 final size:33
Alignment explanation
Indices: 38321--38435 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
38311 TCTTTTGGTT
38321 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
38354 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
38387 GAAATGAAAATCGCAACGAGAGAATCGCAGCGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
38420 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
38436 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:38367 original size:19 final size:18
Alignment explanation
Indices: 38328--38440 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
38318 GTTGAAATGA
38328 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
38343 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
38360 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
38376 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
38393 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
* *
38409 -AATCGCAGCGCGAAATG
1 AAATCGCAACGCGAGATG
*
38426 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
38441 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 26
0.71 0.06 0.24
Matches are distributed among these distances:
14 23 0.30
16 15 0.19
17 12 0.16
19 27 0.35
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:38471 original size:14 final size:14
Alignment explanation
Indices: 38452--38506 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
38442 TTTGGTTTCG
38452 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
38466 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
38485 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
38499 CGTTGCGA
1 CGTTGCGA
38507 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:38484 original size:33 final size:33
Alignment explanation
Indices: 38436--38506 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
38426 AAAATCGCAA
**
38436 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
38469 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
38502 TGCGA
1 TGCGA
38507 CAGTCATTCT
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:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:38514 original size:33 final size:33
Alignment explanation
Indices: 38447--38528 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
38437 GCGATTTTGG
***
38447 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
38480 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
38513 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
38529 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:38533 original size:20 final size:20
Alignment explanation
Indices: 38459--38534 Score: 67
Period size: 20 Copynumber: 4.2 Consensus size: 20
38449 TCGCGTTGCG
38459 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
38479 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
38492 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
38512 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
38532 ATT
1 ATT
38535 TATCTTGTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
13 3 0.07
14 9 0.20
19 9 0.20
20 23 0.52
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:38665 original size:33 final size:33
Alignment explanation
Indices: 38623--38693 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
38613 AATATTAACT
*
38623 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
38656 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
38689 TGAAA
1 TGAAA
38694 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:38926 original size:22 final size:22
Alignment explanation
Indices: 38874--38928 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
38864 TGGTTGTGAG
**
38874 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
38896 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
38918 GGATTTCTTCG
1 GGATTTCTTCG
38929 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:39099 original size:20 final size:20
Alignment explanation
Indices: 39074--39266 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
39064 CTTTAAATAT
39074 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
39094 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
39116 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
39135 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
39155 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
39175 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
39195 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
39215 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
39235 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
39255 CGCGTTGCGATT
1 CGCGTTGCGATT
39267 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:39261 original size:60 final size:60
Alignment explanation
Indices: 39074--39266 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
39064 CTTTAAATAT
**
39074 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
39135 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
39195 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
39255 CGCGTTGCGATT
1 CGCGTTGCGATT
39267 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:39347 original size:20 final size:20
Alignment explanation
Indices: 39322--39373 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
39312 AAGAATCGCG
*
39322 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
39342 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
39362 TTGCGATTCTGG
1 TTGCGATTCTGG
39374 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:39401 original size:19 final size:19
Alignment explanation
Indices: 39377--39429 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
39367 ATTCTGGGGA
39377 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
39396 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
39415 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
39430 GTTGGTCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.09, C:0.17, G:0.23, T:0.51
Consensus pattern (19 bp):
TCGCGTTGCGATTTTTATT
Found at i:43249 original size:14 final size:15
Alignment explanation
Indices: 43230--43258 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43220 TTTGATATGA
43230 AAATAAA-TTTAAAT
1 AAATAAATTTTAAAT
43244 AAATAAATTTTAAAT
1 AAATAAATTTTAAAT
43259 GATAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATAAATTTTAAAT
Found at i:46535 original size:13 final size:13
Alignment explanation
Indices: 46517--46543 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46507 TTGCTAAACC
46517 TTAAGAACACATT
1 TTAAGAACACATT
46530 TTAAGAACACATT
1 TTAAGAACACATT
46543 T
1 T
46544 GCTAAAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (13 bp):
TTAAGAACACATT
Found at i:49361 original size:18 final size:18
Alignment explanation
Indices: 49338--49395 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
49328 TTTATGAGGA
49338 AATTGGAATCTGTGAAGG
1 AATTGGAATCTGTGAAGG
*
49356 AATTGGAATCTGTGAAAG
1 AATTGGAATCTGTGAAGG
*
49374 AATT-GAGATCTGT-CAGG
1 AATTGGA-ATCTGTGAAGG
49391 AATTG
1 AATTG
49396 TAATTCAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.23
18 27 0.77
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.29
Consensus pattern (18 bp):
AATTGGAATCTGTGAAGG
Found at i:59650 original size:68 final size:64
Alignment explanation
Indices: 59523--59669 Score: 154
Period size: 67 Copynumber: 2.2 Consensus size: 64
59513 ATTAAAGAGT
* * * *
59523 TAAAATATAATAGTTTCCTTATCATGAATTAAAAAATTATTCTCCATTACTGAATATTTAAATGA
1 TAAAATATAA-AGTTTCCTCATCATGAATTAAAAAATAATTCTCCATTACCGAATATTT-AATCA
59588 A
64 A
*
59589 TAAAATATAAAGTTTCCTCATCAAT-ATATTAAAAAAATAAATAT-TCCATTACCGAGTATTTAA
1 TAAAATATAAAGTTTCCTCATC-ATGA-ATT-AAAAAAT-AAT-TCTCCATTACCGAATATTTAA
59652 TCAA
61 TCAA
* *
59656 TTAGATATAAAGTT
1 TAAAATATAAAGTT
59670 CTAAGTTTCC
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
65 12 0.17
66 15 0.22
67 24 0.35
68 17 0.25
69 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (64 bp):
TAAAATATAAAGTTTCCTCATCATGAATTAAAAAATAATTCTCCATTACCGAATATTTAATCAA
Found at i:59819 original size:14 final size:13
Alignment explanation
Indices: 59800--59848 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
59790 TATTGACCAA
59800 ATATTTAATATAAT
1 ATATTT-ATATAAT
59814 ATATTTATAATAAT
1 ATATTTAT-ATAAT
59828 AT-TTTATATAAT
1 ATATTTATATAAT
*
59840 -TATTGATAT
1 ATATTTATAT
59849 TGAATTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 1 0.03
12 11 0.34
13 7 0.22
14 13 0.41
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
ATATTTATATAAT
Found at i:59838 original size:12 final size:12
Alignment explanation
Indices: 59799--59839 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
59789 ATATTGACCA
*
59799 AATATTTAATAT
1 AATATTTTATAT
59811 AATATATTTATAAT
1 AATAT-TTTAT-AT
59825 AATATTTTATAT
1 AATATTTTATAT
59837 AAT
1 AAT
59840 TATTGATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 10 0.38
13 9 0.35
14 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AATATTTTATAT
Found at i:62296 original size:23 final size:23
Alignment explanation
Indices: 62266--62309 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
62256 TAAACTCGAT
62266 ACTTGCTTAAGTGATATTACACC
1 ACTTGCTTAAGTGATATTACACC
62289 ACTTGCTTAAGTGATATTACA
1 ACTTGCTTAAGTGATATTACA
62310 ATACTTACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (23 bp):
ACTTGCTTAAGTGATATTACACC
Found at i:62315 original size:23 final size:23
Alignment explanation
Indices: 62264--62315 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
62254 CTTAAACTCG
62264 ATACTTGCTTAAGTGATATTACA
1 ATACTTGCTTAAGTGATATTACA
**
62287 CCACTTGCTTAAGTGATATTACA
1 ATACTTGCTTAAGTGATATTACA
62310 ATACTT
1 ATACTT
62316 ACCACTTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (23 bp):
ATACTTGCTTAAGTGATATTACA
Found at i:63290 original size:16 final size:18
Alignment explanation
Indices: 63269--63301 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
63259 TACGTAGAAG
63269 TTTT-AATT-TATTTTAT
1 TTTTAAATTATATTTTAT
63285 TTTTAAATTATATTTTA
1 TTTTAAATTATATTTTA
63302 ATTAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTAAATTATATTTTAT
Found at i:67748 original size:20 final size:20
Alignment explanation
Indices: 67723--67760 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
67713 TTTGGTTCAC
67723 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
67743 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
67761 AGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:67987 original size:37 final size:37
Alignment explanation
Indices: 67914--67988 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
67904 GTTGGAAAAT
* *
67914 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
67951 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
67988 A
1 A
67989 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Done.