Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004090.1 Hibiscus syriacus cultivar Beakdansim tig00008947_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: 62517
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2512 original size:18 final size:19
Alignment explanation
Indices: 2485--2521 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2475 ATATACAGAA
*
2485 AGTAAGTTAAT-TATAGTT
1 AGTAAATTAATATATAGTT
2503 AGTAAATTAATATATAGTT
1 AGTAAATTAATATATAGTT
2522 GATTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (19 bp):
AGTAAATTAATATATAGTT
Found at i:2550 original size:37 final size:37
Alignment explanation
Indices: 2450--2601 Score: 110
Period size: 45 Copynumber: 3.9 Consensus size: 37
2440 AAAAAGTTCT
* *
2450 TTAAAATATATTAATAAATTATTTAATATACAG-AAA
1 TTAAAATATATTAATAAATTATTTAATATATAGTTAA
* ** * * * * *
2486 GTAAGTTA-ATTATAGTTAGTAAATTAATATATAGTTGA
1 TTAAAATATATTA-A-TAAATTATTTAATATATAGTTAA
2524 TTAAAATATATTAATAAATTATTTAATATATAGAAAGTAAGTTAA
1 TTAAAATATATTAATAAATTATTT-A-ATAT----A-T-AGTTAA
2569 TTAAAATATATTAATAAATTATTTAATATATAG
1 TTAAAATATATTAATAAATTATTTAATATATAG
2602 AAAGTAAGTT
Statistics
Matches: 86, Mismatches: 18, Indels: 23
0.68 0.14 0.18
Matches are distributed among these distances:
35 4 0.05
36 6 0.07
37 22 0.26
38 9 0.10
39 9 0.10
43 5 0.06
44 2 0.02
45 29 0.34
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (37 bp):
TTAAAATATATTAATAAATTATTTAATATATAGTTAA
Found at i:2573 original size:45 final size:45
Alignment explanation
Indices: 2518--2648 Score: 181
Period size: 45 Copynumber: 2.7 Consensus size: 45
2508 ATTAATATAT
*
2518 AGTTGATTAAAATATATTAATAAATTATTTAATATATAGAAAGTA
1 AGTTAATTAAAATATATTAATAAATTATTTAATATATAGAAAGTA
2563 AGTTAATTAAAATATATTAATAAATTATTTAATATATAGAAAGTA
1 AGTTAATTAAAATATATTAATAAATTATTTAATATATAGAAAGTA
2608 AGTTAGTAAATTATTTAAAATATATTAATAAATTATTTAAT
1 AG-T--T--A--A-TTAAAATATATTAATAAATTATTTAAT
2649 TATTTAATAT
Statistics
Matches: 77, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
45 46 0.60
46 1 0.01
48 1 0.01
50 1 0.01
52 1 0.01
53 27 0.35
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (45 bp):
AGTTAATTAAAATATATTAATAAATTATTTAATATATAGAAAGTA
Found at i:2652 original size:30 final size:33
Alignment explanation
Indices: 2496--2684 Score: 123
Period size: 31 Copynumber: 5.8 Consensus size: 33
2486 GTAAGTTAAT
* * *
2496 TATAGTTAGTAAATTAATATATAGTTGA-TTAAAA
1 TATAGTTAATAAATTATTATA-AATT-ATTTAAAA
*
2530 TATA-TTAATAAATTATT-T-AA-TATATAGAAA
1 TATAGTTAATAAATTATTATAAATTATTTA-AAA
*
2560 GTA-AGTTAATTAAAATATATTAATAAATTATTTAATA
1 -TATAGTTAA-T-AAAT-TATT-ATAAATTATTTAAAA
* * *
2597 TATAG-AAAGTAAGTTA--GTAAATTATTTAAAA
1 TATAGTTAA-TAAATTATTATAAATTATTTAAAA
*
2628 TATA-TTAATAAATTATT-T-AATTATTTAATA
1 TATAGTTAATAAATTATTATAAATTATTTAAAA
*
2658 TATAGTTGATAAATTATTATAAATTAT
1 TATAGTTAATAAATTATTATAAATTAT
2685 GATGTATACA
Statistics
Matches: 122, Mismatches: 15, Indels: 37
0.70 0.09 0.21
Matches are distributed among these distances:
28 1 0.01
29 3 0.02
30 26 0.21
31 38 0.31
32 3 0.02
33 21 0.17
34 10 0.08
35 3 0.02
36 6 0.05
37 6 0.05
38 5 0.04
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (33 bp):
TATAGTTAATAAATTATTATAAATTATTTAAAA
Found at i:2671 original size:53 final size:53
Alignment explanation
Indices: 2540--2680 Score: 171
Period size: 53 Copynumber: 2.6 Consensus size: 53
2530 TATATTAATA
** * *
2540 AATTATTTAATATATAGAAAGTAAGTTAATTAAAATATATTAATAAATTATTT
1 AATTATTTAATATATAGTTAGTAAATTATTTAAAATATATTAATAAATTATTT
* *
2593 AA-TATATAGAAAGTA-AGTTAGTAAATTATTTAAAATATATTAATAAATTATTT
1 AATTATTTA-ATA-TATAGTTAGTAAATTATTTAAAATATATTAATAAATTATTT
2646 AATTATTTAATATATAGTT-GATAAATTATTATAAA
1 AATTATTTAATATATAGTTAG-TAAATTATT-TAAA
2681 TTATGATGTA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
52 8 0.11
53 55 0.74
54 11 0.15
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.43
Consensus pattern (53 bp):
AATTATTTAATATATAGTTAGTAAATTATTTAAAATATATTAATAAATTATTT
Found at i:4232 original size:74 final size:75
Alignment explanation
Indices: 4132--4328 Score: 238
Period size: 74 Copynumber: 2.6 Consensus size: 75
4122 GACCGTTGAA
* *
4132 CAGGGGGGAATCGGTACCCCCT-TGGGGGGATCGGTTCCCTCCGAGCATACT-AAAATTCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGAAAA-TCTCGGA
**
4195 ACAAAAATGTT
65 ACAAAAACATT
* * * * * *
4206 TA-GGGGGAATCGATTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGAAAATCTCGGAA
* *
4270 CCAAACCATT
66 CAAAAACATT
*
4280 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGG-ATCGGTTCCCTCCGAGCA
4329 ATCTGTAATT
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
73 16 0.16
74 42 0.41
75 28 0.27
76 17 0.17
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23
Consensus pattern (75 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGAAAATCTCGGAA
CAAAAACATT
Found at i:6940 original size:21 final size:21
Alignment explanation
Indices: 6914--6953 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6904 CAGAACCCCA
*
6914 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
6935 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
6954 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:6982 original size:20 final size:21
Alignment explanation
Indices: 6936--6996 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
6926 TTCCCCTGTG
6936 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
6959 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
6979 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
6997 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:12866 original size:75 final size:76
Alignment explanation
Indices: 12758--12954 Score: 263
Period size: 75 Copynumber: 2.6 Consensus size: 76
12748 CCGTTGAACA
* * * *
12758 GGGGGAATCGGTACCCCCT-TGGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAAC
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAAC
** *
12822 AAAAATGTTTAG
65 AAAAACATTCAG
* * *
12834 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
*
12898 AAACCATTCAG
66 AAAACATTCAG
*
12909 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCA
12955 ATCTGTAATT
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
75 66 0.62
76 40 0.37
77 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
AAAACATTCAG
Found at i:13318 original size:53 final size:47
Alignment explanation
Indices: 13255--13376 Score: 158
Period size: 45 Copynumber: 2.5 Consensus size: 47
13245 TAAAATCATA
*
13255 AAATTATTTATTAATATATTTTAAAAAATTTACTAACTTACTTTCTATATATT
1 AAATAATTTATTAATATATTTT--AAAA--T--TAACTTACTTTCTATATATT
13308 AAATAATTTATTAATATATTTT--AATTAACTTACTTTCTATATATT
1 AAATAATTTATTAATATATTTTAAAATTAACTTACTTTCTATATATT
*
13353 AAGTAATTTATTAATATATTTTAA
1 AAATAATTTATTAATATATTTTAA
13377 TCAACTATAT
Statistics
Matches: 65, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
45 41 0.63
47 1 0.02
49 2 0.03
53 21 0.32
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.52
Consensus pattern (47 bp):
AAATAATTTATTAATATATTTTAAAATTAACTTACTTTCTATATATT
Found at i:13331 original size:22 final size:22
Alignment explanation
Indices: 13300--13451 Score: 90
Period size: 22 Copynumber: 6.5 Consensus size: 22
13290 ACTTACTTTC
13300 TATATATTAAATAATTTATTAA
1 TATATATTAAATAATTTATTAA
* * * **
13322 TATATTTTAATTAACTTACTTTC
1 TATATATTAAATAATTTA-TTAA
*
13345 TATATATTAAGTAATTTATTAA
1 TATATATTAAATAATTTATTAA
*
13367 TATAT-TTTAATCAACTATATATTAA
1 TATATATTAAAT-AA-T-T-TATTAA
* * * **
13392 TTTACTAACTATAATTAACTTACTTTC
1 TATA-T-A-T-TAAATAATTTA-TTAA
13419 TATATATTAAATAATTTATTAA
1 TATATATTAAATAATTTATTAA
*
13441 TATATTTTAAA
1 TATATATTAAA
13452 GAACTTTTTA
Statistics
Matches: 95, Mismatches: 24, Indels: 22
0.67 0.17 0.16
Matches are distributed among these distances:
21 4 0.04
22 36 0.38
23 27 0.28
24 2 0.02
25 10 0.11
26 4 0.04
27 6 0.06
29 3 0.03
30 3 0.03
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.51
Consensus pattern (22 bp):
TATATATTAAATAATTTATTAA
Found at i:13338 original size:45 final size:45
Alignment explanation
Indices: 13288--13382 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
13278 AAAAATTTAC
13288 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
1 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
*
13333 TAACTTACTTTCTATATATTAAGTAATTTATTAATATATTTTAAT
1 TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
*
13378 CAACT
1 TAACT
13383 ATATATTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (45 bp):
TAACTTACTTTCTATATATTAAATAATTTATTAATATATTTTAAT
Found at i:13414 original size:18 final size:19
Alignment explanation
Indices: 13379--13428 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
13369 TATTTTAATC
*
13379 AACTATATATTAATTTACT
1 AACTATATATTAACTTACT
13398 AACTATA-ATTAACTTACT
1 AACTATATATTAACTTACT
**
13416 TTCTATATATTAA
1 AACTATATATTAA
13429 ATAATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (19 bp):
AACTATATATTAACTTACT
Found at i:15297 original size:19 final size:18
Alignment explanation
Indices: 15252--15302 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
15242 TTGGACACTT
* *
15252 TTAATATTTATTATAAAG
1 TTAATTTTTATTTTAAAG
*
15270 TTTATTTTTATTTTAAAG
1 TTAATTTTTATTTTAAAG
15288 TATAATTTTTATTTT
1 T-TAATTTTTATTTT
15303 TGAAATCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (18 bp):
TTAATTTTTATTTTAAAG
Found at i:18480 original size:19 final size:19
Alignment explanation
Indices: 18456--18496 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
18446 ACGTGAAGAA
* *
18456 GAAGAAGGAACAAACACGT
1 GAAGAAGAAACAAACACAT
*
18475 GAAGAAGAAACAGACACAT
1 GAAGAAGAAACAAACACAT
18494 GAA
1 GAA
18497 TTTTTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.15, G:0.24, T:0.05
Consensus pattern (19 bp):
GAAGAAGAAACAAACACAT
Found at i:19105 original size:24 final size:23
Alignment explanation
Indices: 19078--19134 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
19068 TTTTATAGTG
* *
19078 ATAAAATTAAAATG-ATATTTGT
1 ATAAAATTAAAAAGTATATTTTT
* *
19100 GTATAATTAAAAAGTATATTTTT
1 ATAAAATTAAAAAGTATATTTTT
19123 ATTAAAATTAAA
1 A-TAAAATTAAA
19135 TTATTTTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 11 0.41
23 7 0.26
24 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (23 bp):
ATAAAATTAAAAAGTATATTTTT
Found at i:19161 original size:22 final size:21
Alignment explanation
Indices: 19114--19161 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
19104 AATTAAAAAG
19114 TATATTTTTATTAAAATTAAA
1 TATATTTTTATTAAAATTAAA
*
19135 T-TATTTTTATATTAAA-TAATA
1 TATATTTTTAT-TAAAATTAA-A
19156 TATATT
1 TATATT
19162 AAAATTGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 12 0.52
21 7 0.30
22 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATTTTTATTAAAATTAAA
Found at i:23359 original size:27 final size:28
Alignment explanation
Indices: 23329--23381 Score: 99
Period size: 27 Copynumber: 1.9 Consensus size: 28
23319 ACCACACAAA
23329 AGGTGGCTCTGAATGATA-TAACAGAAG
1 AGGTGGCTCTGAATGATACTAACAGAAG
23356 AGGTGGCTCTGAATGATACTAACAGA
1 AGGTGGCTCTGAATGATACTAACAGA
23382 TTAAGTGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (28 bp):
AGGTGGCTCTGAATGATACTAACAGAAG
Found at i:24250 original size:20 final size:20
Alignment explanation
Indices: 24225--24269 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
24215 GTCATCCAAT
24225 TTTTTAAACCCCATACAGGA
1 TTTTTAAACCCCATACAGGA
24245 TTTTTAAACCCCATACAGGA
1 TTTTTAAACCCCATACAGGA
24265 TTTTT
1 TTTTT
24270 TTCCAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (20 bp):
TTTTTAAACCCCATACAGGA
Found at i:24409 original size:20 final size:20
Alignment explanation
Indices: 24369--24410 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
24359 CGGTTATACT
* * *
24369 ATCCGGTTTTAAAATATCCG
1 ATCCGGTTTAAAAAAAACCG
24389 ATCCGGTTTAAAAAAAACCG
1 ATCCGGTTTAAAAAAAACCG
24409 AT
1 AT
24411 TTTTCCCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (20 bp):
ATCCGGTTTAAAAAAAACCG
Found at i:25194 original size:16 final size:16
Alignment explanation
Indices: 25173--25214 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
25163 TAAAGAGTCT
* *
25173 GACTCTTCCTTATTTA
1 GACTCTGCCTTACTTA
25189 GACTCTGCCTTACTTA
1 GACTCTGCCTTACTTA
25205 GACTCTGCCT
1 GACTCTGCCT
25215 CAATGCTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.17, C:0.31, G:0.12, T:0.40
Consensus pattern (16 bp):
GACTCTGCCTTACTTA
Found at i:28631 original size:21 final size:21
Alignment explanation
Indices: 28589--28641 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
28579 ATTCTGACTA
28589 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* ** *
28610 TCGCGTTGCGATTTTTCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
28631 TCGCAATGCGA
1 TCGCATTGCGA
28642 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:28656 original size:20 final size:20
Alignment explanation
Indices: 28631--28719 Score: 124
Period size: 20 Copynumber: 4.4 Consensus size: 20
28621 TTTTTCTAAT
28631 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
28651 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
28671 TCACAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
28692 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
28712 TCGCAATG
1 TCGCAATG
28720 TGGATCTGAC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 41 0.71
21 17 0.29
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:28693 original size:41 final size:40
Alignment explanation
Indices: 28634--28719 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 40
28624 TTCTAATTCG
* *
28634 CAATGCGAATACGTAAATCGCAACGCGATTACGTAAATCA
1 CAATGCGAATACGAAAATCGCAACGCGAATACGTAAATCA
* * *
28674 CAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAATCG
1 CAATGCGAA-TACGAAAATCGCAACGCGAATACGTAAATCA
28715 CAATG
1 CAATG
28720 TGGATCTGAC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 9 0.22
41 31 0.77
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (40 bp):
CAATGCGAATACGAAAATCGCAACGCGAATACGTAAATCA
Found at i:29337 original size:14 final size:14
Alignment explanation
Indices: 29318--29378 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
29308 GGAAATGACT
*
29318 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
29332 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
29351 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
29365 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
29379 CCAAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:29355 original size:33 final size:33
Alignment explanation
Indices: 29297--29389 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
29287 CGAGAATGAA
**
29297 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
*
29331 AATCGCAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
29364 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
29390 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 43 0.80
34 11 0.20
ACGTcount: A:0.43, C:0.25, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:29426 original size:14 final size:14
Alignment explanation
Indices: 29407--29463 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
29397 TTTCATTTCG
*
29407 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
29421 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
29440 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
29454 CGTTGCGATT
1 CGTTGCGATT
29464 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:29432 original size:33 final size:33
Alignment explanation
Indices: 29390--29473 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 33
29380 CAAAATCGCA
*
29390 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
29423 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
29456 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
29474 ATTGTGATAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:29516 original size:20 final size:19
Alignment explanation
Indices: 29385--29530 Score: 132
Period size: 19 Copynumber: 8.1 Consensus size: 19
29375 GAAACCAAAA
*
29385 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
29404 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
29420 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29437 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
29451 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* * **
29470 TCGCATTGTGATAGTCATT
1 TCGCGTTGCGATTTTCATT
29489 TACGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
29509 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
29529 TC
1 TC
29531 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 18 0.18
16 8 0.08
17 8 0.08
19 35 0.35
20 31 0.31
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:31408 original size:94 final size:93
Alignment explanation
Indices: 31217--31780 Score: 938
Period size: 94 Copynumber: 6.1 Consensus size: 93
31207 TAGATTGCTT
* * *
31217 AGTAAATTTATTTGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
31278 ATTTGTATTTTGTTTTGTCTTTTGGTTGA
66 ATTTGT-CTTTGTTTTGTCTTTTGGTTGA
31307 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
31372 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
31401 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
31466 ATTTGTCTTTTGTTTTGTCTTTTGATTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
31495 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
31560 ATTTGTCTTTGTTTTGTCTTTTGTTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
31589 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
31654 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
31683 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
31748 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
31776 AGTAA
1 AGTAA
31781 TGCAATCCAT
Statistics
Matches: 453, Mismatches: 14, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
90 34 0.08
92 3 0.01
93 47 0.10
94 350 0.77
95 19 0.04
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:31901 original size:20 final size:20
Alignment explanation
Indices: 31873--31934 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
31863 TTTTGGTTGA
*
31873 AATGAAAATCGCAACAAGAG
1 AATGAAAATCGCAACGAGAG
* *
31893 AATGGAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
31912 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
31932 AAT
1 AAT
31935 CGCAACGCGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.50, C:0.18, G:0.23, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:31919 original size:39 final size:33
Alignment explanation
Indices: 31871--31994 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 33
31861 TCTTTTGGTT
31871 GAAATGAAAATCGCAACAAGAGAATGGAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A--G-AATCGCAACGC
*
31910 GAAACGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
31943 GAAATGAAAATCGCAACGACAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
31976 GAAACCAAAAATCGCAACG
1 GAAA-TGAAAATCGCAACG
31995 CGAAACTATA
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
33 45 0.58
34 13 0.17
36 1 0.01
37 3 0.04
39 16 0.21
ACGTcount: A:0.48, C:0.23, G:0.21, T:0.08
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:31922 original size:19 final size:19
Alignment explanation
Indices: 31898--32000 Score: 100
Period size: 19 Copynumber: 5.9 Consensus size: 19
31888 AAGAGAATGG
31898 AAATCGCAACGCGAAACGA
1 AAATCGCAACGCGAAACGA
31917 AAATCGCAA--CG--A-GA
1 AAATCGCAACGCGAAACGA
* *
31931 GAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAACGA
31950 AAATCGCAA--CG--AC-A
1 AAATCGCAACGCGAAACGA
*
31964 AAATCGCAACGCGAAACCAA
1 AAATCGCAACGCGAAA-CGA
31984 AAATCGCAACGCGAAAC
1 AAATCGCAACGCGAAAC
32001 TATAATCGCG
Statistics
Matches: 70, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
14 20 0.29
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 21 0.30
20 17 0.24
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.07
Consensus pattern (19 bp):
AAATCGCAACGCGAAACGA
Found at i:31941 original size:33 final size:33
Alignment explanation
Indices: 31898--31994 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
31888 AAGAGAATGG
*
31898 AAATCGCAACGCGAAACGAAAATCGCAACGAGA
1 AAATCGCAACGCGAAACGAAAATCGCAACGACA
* *
31931 GAATCGCAACGCGAAATGAAAATCGCAACGACA
1 AAATCGCAACGCGAAACGAAAATCGCAACGACA
*
31964 AAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAATCGCAACGCGAAA-CGAAAATCGCAACG
31995 CGAAACTATA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.79
34 12 0.21
ACGTcount: A:0.47, C:0.26, G:0.20, T:0.07
Consensus pattern (33 bp):
AAATCGCAACGCGAAACGAAAATCGCAACGACA
Found at i:31986 original size:20 final size:20
Alignment explanation
Indices: 31963--32000 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
31953 TCGCAACGAC
31963 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
31983 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
32001 TATAATCGCG
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:0.50, C:0.29, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:32050 original size:19 final size:19
Alignment explanation
Indices: 32023--32112 Score: 83
Period size: 20 Copynumber: 4.6 Consensus size: 19
32013 GCGATTCTCT
* *
32023 CGTTACGATTTTCGTTTCG
1 CGTTGCGATTTTCATTTCG
*
32042 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
*
32062 CGTTGCGATTTTTATTTCG
1 CGTTGCGATTTTCATTTCG
** *
32081 -GTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCG
32101 CGTTGCGATTTT
1 CGTTGCGATTTT
32113 AAGTTCCAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
18 10 0.18
19 16 0.29
20 21 0.38
21 9 0.16
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:32071 original size:39 final size:38
Alignment explanation
Indices: 32016--32112 Score: 113
Period size: 39 Copynumber: 2.5 Consensus size: 38
32006 TCGCGTTGCG
* * **
32016 ATTCTCTCGTTACGATTTTCGTTTCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTCATTTCG-GTTGCGATAGTC
*
32055 ATTCTCTCGTTGCGATTTTTATTTCGGTTGCGATAGTC
1 ATTCTCTCGTTGCGATTTTCATTTCGGTTGCGATAGTC
* *
32093 ATTTTTCACGTTGCGATTTT
1 A-TTCTCTCGTTGCGATTTT
32113 AAGTTCCAGA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 11 0.22
39 39 0.78
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.49
Consensus pattern (38 bp):
ATTCTCTCGTTGCGATTTTCATTTCGGTTGCGATAGTC
Found at i:32629 original size:21 final size:21
Alignment explanation
Indices: 32570--32630 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
32560 CTCGAGAGTC
32570 CCCTCCCACCGTTCAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
* ** * *
32591 CACTGTCATCGTTGAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
*
32612 CCCTCCCACCATTCAAGAG
1 CCCTCCCACCGTTCAAGAG
32631 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
CCCTCCCACCGTTCAAGAGGT
Found at i:33999 original size:14 final size:14
Alignment explanation
Indices: 33980--34015 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
33970 ATTGTTTAAT
33980 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
33994 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
34008 TGATTTGT
1 TGATTTGT
34016 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:34182 original size:19 final size:19
Alignment explanation
Indices: 34160--34310 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
34150 CGAAACTAAA
*
34160 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
34179 TTCGCTTTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
* *
34194 -CCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
34212 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
34228 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
34245 TTCGCATTGTGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
34261 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
34278 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
*
34297 TTCTGCGTTGCGAT
1 TTC-GCATTGCGAT
34311 AGACATTAAG
Statistics
Matches: 101, Mismatches: 15, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
14 19 0.19
16 17 0.17
17 17 0.17
19 39 0.39
20 9 0.09
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:34208 original size:33 final size:33
Alignment explanation
Indices: 34164--34290 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
34154 ACTAAATTCG
* *
34164 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
34197 CATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
34230 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
34263 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
34291 AGTCATTTCT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:34309 original size:20 final size:19
Alignment explanation
Indices: 34263--34317 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
34253 GTGATTCTCT
**
34263 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
34282 CATTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTC-G
*
34302 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
34318 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:34356 original size:20 final size:20
Alignment explanation
Indices: 34284--34356 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
34274 TCATTTCGCA
* *
34284 TTGCGATAGTCATTTCTGCG
1 TTGCGATAGTCATTTCAGTG
* *
34304 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCAG-TG
*
34324 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCAGTG
34345 TTGCGATAGTCA
1 TTGCGATAGTCA
34357 AATGAATGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTCAGTG
Found at i:36831 original size:24 final size:24
Alignment explanation
Indices: 36797--36850 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
36787 CTGAAAAATC
36797 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
36821 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
36845 ATCAAA
1 ATCAAA
36851 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:36864 original size:24 final size:24
Alignment explanation
Indices: 36797--36864 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
36787 CTGAAAAATC
* * *
36797 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
36821 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
36845 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
36865 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:37750 original size:21 final size:21
Alignment explanation
Indices: 37726--37781 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
37716 GCGATTACGT
*
37726 AAATCGCATTGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * * *
37747 AAATCACAACGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
37768 AAATCGCAATGCGA
1 AAATCGCAATGCGA
37782 TAGTCAGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:38611 original size:35 final size:33
Alignment explanation
Indices: 38527--38611 Score: 80
Period size: 35 Copynumber: 2.4 Consensus size: 33
38517 AATATATTTT
* *
38527 TTATTCAAAAAAATACTACTTTATACTCATTGAA
1 TTATT-AAAAAAATACTACTTTATAATCATTCAA
* * *
38561 TGTGTATACACAAATACTACTTTATAATCACCTTCAA
1 T-TAT-TAAAAAAATACTACTTTATAATCA--TTCAA
38598 TTATTAAAAAAATA
1 TTATTAAAAAAATA
38612 TTTTCTAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
34 1 0.03
35 30 0.77
36 3 0.08
37 5 0.13
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (33 bp):
TTATTAAAAAAATACTACTTTATAATCATTCAA
Found at i:39276 original size:15 final size:15
Alignment explanation
Indices: 39239--39310 Score: 65
Period size: 15 Copynumber: 4.7 Consensus size: 15
39229 AAATAGTTAT
* *
39239 TATTTTTTATATTAA
1 TATTATTTATATAAA
*
39254 TA-TATTTATGTAAA
1 TATTATTTATATAAA
39268 TATTATTTATTATTAAAA
1 TATTATTTA-TA-T-AAA
* *
39286 TAATATTTATATAAT
1 TATTATTTATATAAA
39301 TATTATTTAT
1 TATTATTTAT
39311 TTAGAATTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
14 11 0.24
15 19 0.41
16 2 0.04
17 3 0.07
18 11 0.24
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (15 bp):
TATTATTTATATAAA
Found at i:41168 original size:126 final size:126
Alignment explanation
Indices: 40943--41296 Score: 690
Period size: 126 Copynumber: 2.8 Consensus size: 126
40933 CAATATCATC
40943 GTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGG
1 GTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGG
*
41008 CGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGT
66 CGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGT
41069 GTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGG
1 GTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGG
*
41134 CGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTATTGATATATCTAGT
66 CGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGT
41195 GTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGG
1 GTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGG
41260 CGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 CGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
41297 CCGATTATAG
Statistics
Matches: 226, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 226 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (126 bp):
GTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGG
CGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGT
Found at i:44419 original size:12 final size:13
Alignment explanation
Indices: 44386--44423 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
44376 AAATACATAA
44386 ATATATTTAATAT
1 ATATATTTAATAT
*
44399 ATTTATTTAATAT
1 ATATATTTAATAT
44412 A-ATATTTAATAT
1 ATATATTTAATAT
44424 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:44475 original size:23 final size:23
Alignment explanation
Indices: 44437--44494 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
44427 TAGTTATAAT
44437 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
44458 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
44481 TTTTACATAATATA
1 TTTTACATAATATA
44495 TTATTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:51295 original size:8 final size:8
Alignment explanation
Indices: 51279--51316 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
51269 CTGACCTCCA
*
51279 TTGTGAAT
1 TTGTAAAT
51287 TTGTAAAT
1 TTGTAAAT
51295 TTGTAAAT
1 TTGTAAAT
51303 TTGTAAAT
1 TTGTAAAT
51311 TTGTAA
1 TTGTAA
51317 TTGTTATTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (8 bp):
TTGTAAAT
Found at i:55422 original size:16 final size:16
Alignment explanation
Indices: 55396--55430 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
55386 CATTAGGGGA
55396 GAAAATAAAT-AGTTG
1 GAAAATAAATAAGTTG
55411 GAAAACTAAATAAGTTG
1 GAAAA-TAAATAAGTTG
55428 GAA
1 GAA
55431 TGAATTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 5 0.28
17 8 0.44
ACGTcount: A:0.54, C:0.03, G:0.20, T:0.23
Consensus pattern (16 bp):
GAAAATAAATAAGTTG
Found at i:55786 original size:21 final size:22
Alignment explanation
Indices: 55754--55802 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
55744 TGGTCTGATC
*
55754 GAAGA-ATCTAAAAAATTTCTA
1 GAAGATATCTAAAAAATCTCTA
*
55775 GAAGATAT-TAAAAGATCTCTA
1 GAAGATATCTAAAAAATCTCTA
55796 GAAGATA
1 GAAGATA
55803 AATTTGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (22 bp):
GAAGATATCTAAAAAATCTCTA
Found at i:59983 original size:20 final size:20
Alignment explanation
Indices: 59958--59998 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
59948 ACTTCTTATC
*
59958 TATAAGAATATTCTGTTAAT
1 TATAAGAATATTATGTTAAT
59978 TATAAGAATATTATGTTAAT
1 TATAAGAATATTATGTTAAT
59998 T
1 T
59999 TATGTCCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (20 bp):
TATAAGAATATTATGTTAAT
Done.