Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004444.1 Hibiscus syriacus cultivar Beakdansim tig00009753_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: 69487
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6432 original size:82 final size:82
Alignment explanation
Indices: 6330--6584 Score: 261
Period size: 82 Copynumber: 3.2 Consensus size: 82
6320 TGGCATAGTG
* * * * * *
6330 TTTTCCATTATTATTCAGAGAATCTTTGCCATGTCATAGAGTTTCGTCCCATCCGAAATGAAAGG
1 TTTTCCATTATTATTTAGAGAATCTATGCCATGTCATAGTGTTCCATCCTATCCGAAATGAAAGG
*
6395 CGTGTTACAAGGGAAGCA
66 CGCGTT-CAAGGGAAGCA
* * * * *
6413 TTTTCCA-TATTATTTAGAGAATATCTACCATATCATAGTGTTCCATCCTATCCAAAATGAAAGG
1 TTTTCCATTATTATTTAGAGAATCTATGCCATGTCATAGTGTTCCATCCTATCCGAAATGAAAGG
* * *
6477 CACATTCCAGGGGAAG--
66 CGCGTT-CAAGGGAAGCA
* * **
6493 TTTTCCATTATTA-TT-CA-AATCTATGCTATGTCATAGTGTTCCATCCTATCCGAAATGAAAAA
1 TTTTCCATTATTATTTAGAGAATCTATGCCATGTCATAGTGTTCCATCCTATCCGAAATGAAAGG
* *
6555 CGCGTTCTAGGGAATCA
66 CGCGTTCAAGGGAAGCA
6572 TTTTCCATTATTA
1 TTTTCCATTATTA
6585 GAATCTATGC
Statistics
Matches: 140, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
77 6 0.04
78 41 0.29
79 14 0.10
80 9 0.06
81 5 0.04
82 58 0.41
83 7 0.05
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (82 bp):
TTTTCCATTATTATTTAGAGAATCTATGCCATGTCATAGTGTTCCATCCTATCCGAAATGAAAGG
CGCGTTCAAGGGAAGCA
Found at i:6662 original size:16 final size:17
Alignment explanation
Indices: 6631--6663 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6621 TCCTCGACCC
*
6631 TCAATATCTTAAACTCT
1 TCAATATCTAAAACTCT
6648 TCAAT-TCTAAAACTCT
1 TCAATATCTAAAACTCT
6664 GTATCTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.39
Consensus pattern (17 bp):
TCAATATCTAAAACTCT
Found at i:7683 original size:13 final size:13
Alignment explanation
Indices: 7665--7708 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
7655 GTTCATAATA
7665 TATGACGCGCATT
1 TATGACGCGCATT
*
7678 TATGA--CACATT
1 TATGACGCGCATT
7689 TATGACGCGCATT
1 TATGACGCGCATT
*
7702 AATGACG
1 TATGACG
7709 TTCATTGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 10 0.38
13 16 0.62
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:7807 original size:84 final size:84
Alignment explanation
Indices: 7686--7917 Score: 267
Period size: 84 Copynumber: 2.8 Consensus size: 84
7676 TTTATGACAC
* * *
7686 ATTTATGACGCGCAT-TAATGACGTT-CATTGAGTGTCATTGAAGCCCCCGTCATAATTAAGATG
1 ATTTATGACACGCATGT-ATGAC-TTACATTGCGTGTCATTGAAGCCCCCGTCATAAATAAGATG
7749 ACACACATTTGTGCGTCATAA
64 ACACACATTTGTGCGTCATAA
* ****
7770 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATCTTCTGAC
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATAAGATGAC
* *
7835 ATACATTTGTGTGTCATAA
66 ACACATTTGTGCGTCATAA
* * * * *
7854 ATTTAT-ACA--CATGTATGACTTACATTGCGTGTCATTAAAGCACACGTCATTAAAAAAGACGA
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCA-TAAATAAGATGA
7916 CA
65 CA
7918 AACGTTGGTT
Statistics
Matches: 125, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
81 36 0.29
82 8 0.06
83 5 0.04
84 75 0.60
85 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (84 bp):
ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATAAGATGAC
ACACATTTGTGCGTCATAA
Found at i:7957 original size:2 final size:2
Alignment explanation
Indices: 7950--7974 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7940 ATTTCGTAAT
7950 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 T
7975 TGTAGATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10443 original size:25 final size:25
Alignment explanation
Indices: 10375--10451 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
10365 TTTCCTTTGT
10375 AGTGTCCCTTCTCCTTTACCCTCTTC
1 AGTGTCCCTTCTCCTTT-CCCTCTTC
* * * * * *
10401 -CTTTTCTTTCTCTTTTTCCGTCTTC
1 AGTGTCCCTTCTC-CTTTCCCTCTTC
10426 AGTGTCCCTTCTCCTTTCTCCTCTTC
1 AGTGTCCCTTCTCCTTTC-CCTCTTC
10452 CTTTTCAACA
Statistics
Matches: 36, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
25 19 0.53
26 17 0.47
ACGTcount: A:0.04, C:0.39, G:0.06, T:0.51
Consensus pattern (25 bp):
AGTGTCCCTTCTCCTTTCCCTCTTC
Found at i:14291 original size:15 final size:15
Alignment explanation
Indices: 14266--14321 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
14256 GATGCTTTCT
*
14266 TTTTCCTTCTTTGACA
1 TTTT-CTTCTTTGACG
*
14282 TTTTCTTCTTTAACG
1 TTTTCTTCTTTGACG
*
14297 TTTTCTTCTTAGACG
1 TTTTCTTCTTTGACG
*
14312 TTGTCTTCTT
1 TTTTCTTCTT
14322 ACCCCATGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
15 31 0.89
16 4 0.11
ACGTcount: A:0.11, C:0.21, G:0.09, T:0.59
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:23871 original size:23 final size:24
Alignment explanation
Indices: 23845--23892 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
23835 GATCATTTGA
* *
23845 TCCTATGTTAGTGC-AATATGCAC
1 TCCTATATTAGTGCAAATATACAC
*
23868 TCCTGTATTAGTGCAAATATACAC
1 TCCTATATTAGTGCAAATATACAC
23892 T
1 T
23893 TCTGTATCAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (24 bp):
TCCTATATTAGTGCAAATATACAC
Found at i:23892 original size:24 final size:23
Alignment explanation
Indices: 23852--23905 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
23842 TGATCCTATG
*
23852 TTAGTGCAATATGCACTCCTGTA
1 TTAGTGCAATATACACTCCTGTA
*
23875 TTAGTGCAAATATACACTTCTGTA
1 TTAGTGC-AATATACACTCCTGTA
*
23899 TCAGTGC
1 TTAGTGC
23906 CGTCGAGCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 7 0.26
24 20 0.74
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (23 bp):
TTAGTGCAATATACACTCCTGTA
Found at i:24199 original size:18 final size:18
Alignment explanation
Indices: 24174--24220 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
24164 AAATTAAAAA
* *
24174 TATAGTAAAAAGATATAG
1 TATAGTAAAAAGACAAAG
*
24192 TATGGT-AAAAGACAAAG
1 TATAGTAAAAAGACAAAG
24209 TATAGTAAAAAG
1 TATAGTAAAAAG
24221 TACAGTACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.55, C:0.02, G:0.19, T:0.23
Consensus pattern (18 bp):
TATAGTAAAAAGACAAAG
Found at i:25373 original size:12 final size:12
Alignment explanation
Indices: 25356--25406 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
25346 TTCAAAGAGG
25356 TTTTATATTTAA
1 TTTTATATTTAA
25368 TTTTATA-TTATA
1 TTTTATATTTA-A
*
25380 TTTGAT-TTTAA
1 TTTTATATTTAA
25391 TTTTA-ATATTAA
1 TTTTATAT-TTAA
25403 TTTT
1 TTTT
25407 TAAATAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:25438 original size:14 final size:14
Alignment explanation
Indices: 25419--25520 Score: 69
Period size: 14 Copynumber: 7.8 Consensus size: 14
25409 AATAAATTAC
25419 ATATTAATTTTTTA
1 ATATTAATTTTTTA
* *
25433 ATATT-ATATTATA
1 ATATTAATTTTTTA
25446 GATATTAA--TTTTA
1 -ATATTAATTTTTTA
25459 ATATTAA-TTTTTA
1 ATATTAATTTTTTA
* *
25472 A-A-TAA--ATTAA
1 ATATTAATTTTTTA
25482 ATATTAATTTTTTA
1 ATATTAATTTTTTA
* *
25496 ATATT-ATATTATA
1 ATATTAATTTTTTA
25509 GATATTAATTTT
1 -ATATTAATTTT
25521 ATATCATATA
Statistics
Matches: 69, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
10 4 0.06
11 4 0.06
12 11 0.16
13 22 0.32
14 23 0.33
15 5 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATATTAATTTTTTA
Found at i:25451 original size:28 final size:28
Alignment explanation
Indices: 25419--25520 Score: 105
Period size: 28 Copynumber: 3.4 Consensus size: 28
25409 AATAAATTAC
25419 ATATTAATTTTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTATATTATAG
* * * *
25447 ATATTAATTTTAATATTAATTTTTAAATAAATTAA
1 ATATTAA-TTT--T-TTAA-TATTATAT-TA-TAG
25482 ATATTAATTTTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTATATTATAG
25510 ATATTAATTTT
1 ATATTAATTTT
25521 ATATCATATA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
28 20 0.34
29 4 0.07
30 6 0.10
31 5 0.08
32 5 0.08
33 6 0.10
34 4 0.07
35 9 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTAATTTTTTAATATTATATTATAG
Found at i:25465 original size:63 final size:63
Alignment explanation
Indices: 25368--25521 Score: 269
Period size: 63 Copynumber: 2.5 Consensus size: 63
25358 TTATATTTAA
* *
25368 TTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTAAATAAATTACATATTAATT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATT
25428 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATT
25491 TTTTAATATTATATTATAGATATTAATTTTA
1 TTTTAATATTATATTATAGATATTAATTTTA
25522 TATCATATAA
Statistics
Matches: 89, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
60 4 0.04
61 10 0.11
62 1 0.01
63 74 0.83
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (63 bp):
TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTAATT
Found at i:25522 original size:20 final size:20
Alignment explanation
Indices: 25493--25543 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
25483 TATTAATTTT
* * *
25493 TTAATATTATATTATAGATA
1 TTAATTTTATATCATAGAAA
*
25513 TTAATTTTATATCATATAAA
1 TTAATTTTATATCATAGAAA
25533 TT-ATTTTATAT
1 TTAATTTTATAT
25544 ATTATTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TTAATTTTATATCATAGAAA
Found at i:25552 original size:20 final size:20
Alignment explanation
Indices: 25516--25577 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
25506 ATAGATATTA
25516 ATTTTATATCA-TA-TAAATT
1 ATTTTATAT-ATTATTAAATT
25535 ATTTTATATATTATTAAA--
1 ATTTTATATATTATTAAATT
*
25553 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA-TTAAATT
25573 ATTTT
1 ATTTT
25578 GATTTAAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 3 0.08
18 14 0.38
19 11 0.30
20 9 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTATATATTATTAAATT
Found at i:26080 original size:31 final size:31
Alignment explanation
Indices: 26043--26102 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
26033 TAGTTGTATG
* *
26043 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
26074 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
26103 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:27209 original size:2 final size:2
Alignment explanation
Indices: 27202--27252 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
27192 TAAAATAAAT
27202 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
27244 TA TA TA TA T
1 TA TA TA TA T
27253 TATTTAATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27378 original size:2 final size:2
Alignment explanation
Indices: 27371--27396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27361 TAAAATTTGG
27371 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
27397 CAAACACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28836 original size:19 final size:21
Alignment explanation
Indices: 28798--28841 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
28788 AGTTTGATTA
28798 ATTTTTTTTAAAAAAATTAG-
1 ATTTTTTTTAAAAAAATTAGT
* *
28818 ATTTTTTTT-ACAAATTTAGT
1 ATTTTTTTTAAAAAAATTAGT
28838 ATTT
1 ATTT
28842 ATTTAATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTTTTTTTAAAAAAATTAGT
Found at i:28952 original size:26 final size:24
Alignment explanation
Indices: 28908--28962 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
28898 AAATGTAAAG
28908 TAAAT-TAAAAATTAT-AAAATAAT
1 TAAATATAAAAATTATAAAAAT-AT
*
28931 TAAATATAAAAATATTTAAAAAATAT
1 TAAATATAAAAAT-TAT-AAAAATAT
28957 TAAATA
1 TAAATA
28963 ATTGAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.19
24 7 0.26
25 2 0.07
26 8 0.30
27 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TAAATATAAAAATTATAAAAATAT
Found at i:29032 original size:19 final size:20
Alignment explanation
Indices: 29013--29063 Score: 84
Period size: 22 Copynumber: 2.5 Consensus size: 20
29003 AAGAAAATAT
29013 AAAAATAATTTAAAATTATAA
1 AAAAATAATTTAAAATTAT-A
29034 AAATAATAATTTAAAATTATA
1 AAA-AATAATTTAAAATTATA
29055 AAAAATAAT
1 AAAAATAAT
29064 AATTTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.21
21 7 0.24
22 16 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATAATTTAAAATTATA
Found at i:29044 original size:22 final size:23
Alignment explanation
Indices: 29016--29073 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
29006 AAAATATAAA
29016 AATAATTTAAAATTAT-AAAAAT
1 AATAATTTAAAATTATAAAAAAT
29038 AATAATTTAAAATTATAAAAAAT
1 AATAATTTAAAATTATAAAAAAT
29061 AATAATTTAAAAT
1 AATAATTTAAAAT
29074 GTTAACTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AATAATTTAAAATTATAAAAAAT
Found at i:29049 original size:13 final size:13
Alignment explanation
Indices: 29033--29073 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
29023 TAAAATTATA
29033 AAAATAATAATTT
1 AAAATAATAATTT
*
29046 AAAATTATAA---
1 AAAATAATAATTT
29056 AAAATAATAATTT
1 AAAATAATAATTT
29069 AAAAT
1 AAAAT
29074 GTTAACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
10 9 0.39
13 14 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAATAATAATTT
Found at i:35942 original size:21 final size:20
Alignment explanation
Indices: 35900--35947 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
35890 CTTTCATGTC
* *
35900 TTTTTTTTCGAACAGTTTTT
1 TTTTTTTTCGAACAGCTATT
*
35920 TTTCTTTTTCGAACTGCTATT
1 TTT-TTTTTCGAACAGCTATT
35941 TTTTTTT
1 TTTTTTT
35948 CAACATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.12, C:0.12, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTTTTTTCGAACAGCTATT
Found at i:37350 original size:17 final size:17
Alignment explanation
Indices: 37306--37351 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
37296 AACATGCTTG
37306 AATG-AATAAAAATAAA
1 AATGAAATAAAAATAAA
*
37322 AATGAAACAAAAAGTAAA
1 AATGAAATAAAAA-TAAA
*
37340 GAT-AAATAAAAA
1 AATGAAATAAAAA
37352 AAATATGACG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 4 0.16
17 15 0.60
18 6 0.24
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (17 bp):
AATGAAATAAAAATAAA
Found at i:44237 original size:30 final size:30
Alignment explanation
Indices: 44203--44305 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
44193 GGTTCTTCGG
* *
44203 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
44233 GACCTCTGGATTGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
44263 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
44293 GACCTTTGGATAG
1 GACCTCTGGATAG
44306 GTCCTTCGGA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:47840 original size:64 final size:63
Alignment explanation
Indices: 47708--47868 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
47698 AATTGTTCAG
* * * * *
47708 TGTGTATCGATGCACAGGAAGTGCATCGATGCACCTATTAAAATGGAAACATCGAATGCAATT
1 TGTGCATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATT
* * **
47771 GGTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATT
1 TGTGCATCGATGCA-AAGGAAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATT
** * *
47835 TGTGCATCGATGCACGGGTACTGCATCGATGCAC
1 TGTGCATCGATGCAAAGGAAGTGCATCGATGCAC
47869 ATGCTAAAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 29 0.35
64 53 0.65
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (63 bp):
TGTGCATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATT
Found at i:47902 original size:20 final size:20
Alignment explanation
Indices: 47837--47913 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
47827 AGGTGATTTG
* * *
47837 TGCATCGATGCACGGGT-AC
1 TGCATCGATGCACTGTTGAA
*
47856 TGCATCGATGCACATGCTAAAGAA
1 TGCATCGATGCAC-TG-T--TGAA
47880 TGCATCGATGCACTGTTGAA
1 TGCATCGATGCACTGTTGAA
47900 TGCATCGATGCACT
1 TGCATCGATGCACT
47914 TCAAGAGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 13 0.27
20 18 0.38
22 1 0.02
23 2 0.04
24 14 0.29
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (20 bp):
TGCATCGATGCACTGTTGAA
Found at i:49058 original size:30 final size:30
Alignment explanation
Indices: 49024--49126 Score: 143
Period size: 30 Copynumber: 3.4 Consensus size: 30
49014 GGTTCTTCGG
* * *
49024 GACCTATGGACAGTTACCAAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
49054 GACCTCTGGATTGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
49084 TACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
49114 GACCTCTGGATAG
1 GACCTCTGGATAG
49127 GTCCTTCGGA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:51551 original size:27 final size:27
Alignment explanation
Indices: 51521--51591 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
51511 AGAACTCGAT
*
51521 GATATTTCAATCATTTTAAAG-TCTTAG
1 GATATTTCAATCATTTTAAAGCTC-AAG
*** *
51548 GATATTTTGGTAATTTTAAAGCTCAAG
1 GATATTTCAATCATTTTAAAGCTCAAG
*
51575 GGTATTTCAATCATTTT
1 GATATTTCAATCATTTT
51592 TAATAAATTC
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (27 bp):
GATATTTCAATCATTTTAAAGCTCAAG
Found at i:52904 original size:24 final size:24
Alignment explanation
Indices: 52861--52925 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
52851 CACTGAAGTG
52861 CCACATAG-ATTTGTCCCGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
* *
52884 CCGCATAGAATTTGTCTCGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
52908 CCACATAGAAATTTGTCC
1 CCACATAG-AATTTGTCC
52926 TGAATGATCG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 7 0.19
24 21 0.58
25 8 0.22
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (24 bp):
CCACATAGAATTTGTCCCGAAGGA
Found at i:52939 original size:25 final size:24
Alignment explanation
Indices: 52864--52939 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
52854 TGAAGTGCCA
*
52864 CATAG-ATTTGTCCCGAAGGACCG
1 CATAGAATTTGTCCTGAAGGACCG
*
52887 CATAGAATTTGT-CTCGAAGGACCA
1 CATAGAATTTGTCCT-GAAGGACCG
* *
52911 CATAGAAATTTGTCCTGAATGATCG
1 CATAG-AATTTGTCCTGAAGGACCG
52936 CATA
1 CATA
52940 TAACTCTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 6 0.14
24 19 0.43
25 17 0.39
26 2 0.05
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (24 bp):
CATAGAATTTGTCCTGAAGGACCG
Found at i:53090 original size:15 final size:15
Alignment explanation
Indices: 53044--53095 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
53034 ACATGTCTTT
53044 TATTCACATAGACCA
1 TATTCACATAGACCA
* ** * *
53059 CATTCATGTAAATCA
1 TATTCACATAGACCA
*
53074 TATTCACATAGAGCA
1 TATTCACATAGACCA
53089 TATTCAC
1 TATTCAC
53096 TTATAACACA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (15 bp):
TATTCACATAGACCA
Found at i:53615 original size:20 final size:20
Alignment explanation
Indices: 53564--53621 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
53554 ATTTCATCCT
* *
53564 CAATAATAGTATTGATACCT
1 CAATATTAGTATTGATACCC
* * * *
53584 TACTCTTGGTATTGATACCC
1 CAATATTAGTATTGATACCC
*
53604 CAATATTAGTATCGATAC
1 CAATATTAGTATTGATAC
53622 TACTTCAATC
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
CAATATTAGTATTGATACCC
Found at i:59868 original size:48 final size:49
Alignment explanation
Indices: 59807--59904 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
59797 TGCCACATAG
** * *
59807 ATTTGTCCCGAAGGACTGCGTAG-AATTTGTCCCGAAGGACTGCGTAGA
1 ATTTGTCCCGAAGGACCACGTAGAAATTTGTCCCAAAGGACCGCGTAGA
* *
59855 ATTTGTCTCGAAGGACCACGTAGAAATTTGTCTCAAAGGACCGCGTAGA
1 ATTTGTCCCGAAGGACCACGTAGAAATTTGTCCCAAAGGACCGCGTAGA
59904 A
1 A
59905 CCCTCGACTC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
48 20 0.47
49 23 0.53
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (49 bp):
ATTTGTCCCGAAGGACCACGTAGAAATTTGTCCCAAAGGACCGCGTAGA
Found at i:59888 original size:25 final size:24
Alignment explanation
Indices: 59807--59904 Score: 133
Period size: 24 Copynumber: 4.0 Consensus size: 24
59797 TGCCACATAG
*
59807 ATTTGTCCCGAAGGACTGCGTAGA
1 ATTTGTCCCGAAGGACCGCGTAGA
*
59831 ATTTGTCCCGAAGGACTGCGTAGA
1 ATTTGTCCCGAAGGACCGCGTAGA
* *
59855 ATTTGTCTCGAAGGACCACGTAGAA
1 ATTTGTCCCGAAGGACCGCGTAG-A
* *
59880 ATTTGTCTCAAAGGACCGCGTAGA
1 ATTTGTCCCGAAGGACCGCGTAGA
59904 A
1 A
59905 CCCTCGACTC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
24 46 0.68
25 22 0.32
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (24 bp):
ATTTGTCCCGAAGGACCGCGTAGA
Found at i:65944 original size:26 final size:26
Alignment explanation
Indices: 65897--65947 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
65887 AATTTTGTAA
*
65897 AAAATTATATAAAATTTAATAAATTT
1 AAAATTATATAAAATATAATAAATTT
*
65923 AAAATT-TTTAAAATATATATAAATT
1 AAAATTATATAAAATATA-ATAAATT
65948 AATTACGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAAATTATATAAAATATAATAAATTT
Found at i:66020 original size:2 final size:2
Alignment explanation
Indices: 66013--66052 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
66003 TAGAATTTAA
*
66013 AT AT AT AT AT AT AT AT AC AT -T AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66053 ATAAGGATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:67255 original size:22 final size:24
Alignment explanation
Indices: 67230--67273 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
67220 ATAAATTTGA
*
67230 TTATTTAA-AT-TTATTTTTTTTT
1 TTATTTAATATATTAATTTTTTTT
67252 TTATTTAATATATTAATTTTTT
1 TTATTTAATATATTAATTTTTT
67274 ATAATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 2 0.11
24 9 0.47
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (24 bp):
TTATTTAATATATTAATTTTTTTT
Done.