Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001694.1 Hibiscus syriacus cultivar Beakdansim tig00003384_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: 81571
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:1494 original size:20 final size:21
Alignment explanation
Indices: 1450--1494 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
1440 TACTATGCTG
* *
1450 GAAA-TTAATGTTAGATTGTT
1 GAAATTTAATATTAGAATGTT
1470 G-AATTTAATATTAGAATG-T
1 GAAATTTAATATTAGAATGTT
1489 GAAATT
1 GAAATT
1495 GGACTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (21 bp):
GAAATTTAATATTAGAATGTT
Found at i:2793 original size:2 final size:2
Alignment explanation
Indices: 2788--2933 Score: 276
Period size: 2 Copynumber: 73.5 Consensus size: 2
2778 TATATATATA
2788 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2830 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
2871 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2913 TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG T
2934 ATGTATGATT
Statistics
Matches: 141, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
1 1 0.01
2 140 0.99
ACGTcount: A:0.01, C:0.00, G:0.49, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3347 original size:19 final size:19
Alignment explanation
Indices: 3309--3347 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3299 ATATGCACTG
*
3309 GCTATGAATTTGAAAATAA
1 GCTATGAATCTGAAAATAA
3328 GCTATGAATCT-AAAAGTAA
1 GCTATGAATCTGAAAA-TAA
3347 G
1 G
3348 TTACGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:3417 original size:13 final size:13
Alignment explanation
Indices: 3395--3434 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
3385 CTTGTTATGT
3395 AATG-AATATGAA
1 AATGAAATATGAA
*
3407 AGTGAAATATGAA
1 AATGAAATATGAA
*
3420 AATTAAATATGAA
1 AATGAAATATGAA
3433 AA
1 AA
3435 AAATATCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 3 0.12
13 21 0.88
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (13 bp):
AATGAAATATGAA
Found at i:3440 original size:11 final size:12
Alignment explanation
Indices: 3399--3440 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
3389 TTATGTAATG
*
3399 AATATGAAAGTGA
1 AATATGAAAAT-A
3412 AATATGAAAATTA
1 AATATGAAAA-TA
3425 AATATGAAAA-A
1 AATATGAAAATA
3436 AATAT
1 AATAT
3441 CTGAATGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 6 0.22
13 20 0.74
14 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (12 bp):
AATATGAAAATA
Found at i:3908 original size:46 final size:46
Alignment explanation
Indices: 3801--4509 Score: 882
Period size: 46 Copynumber: 15.5 Consensus size: 46
3791 AATAACTATA
*
3801 ATGAAAGGATGCCATAAATGAAAAT--AT-AACGTGCATT-TCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
*
3843 ATGAAAGGATGACATAAATGAAAATGCATAAAGGTGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
* * ** *
3889 ATGAAAGAATGCCAAAAATGAAAATGCATAACATCT-CATTATCGTC
1 ATGAAAGGATGCCATAAATGAAAATGCATAA-AGGTGCATTATCGGC
* * * *
3935 ATGAAAGGATGCCATATATGAGAATGCATAACGGTGCATTATTGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
* * *
3981 ATGAAATGATGCCATAAATGAAAATGCATAACGGTGCATTATCAGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
*
4027 ATGAAAGGATGCCGTAAATGAAAATGCATAACA-GTGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAA-AGGTGCATTATCGGC
* * * *
4073 ATGAAATGTTGTCATAAATGAAAATACATAAAGGTGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
* *
4119 AT-AAAGGGATGCCATAAATGAAAATGCATAACGGTTCATTATCGGC
1 ATGAAA-GGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
*
4165 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
* * * * *
4211 ATGAATGGAATGACATAAATAAAAATGCATAATGGTGCATTATCAGC
1 ATGAAAGG-ATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
* * * * *
4258 ATAAAAGAATGACATAAATGAAAATG-A-ACA-GTTCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
* *
4301 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
* * **
4347 ATGAAAGGATGTCATAAATGAAAATGCATAACGGTGCATTATCAAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
*
4393 ATGAAAGGATGCCATAAATGAAAATGCATAACA-ATGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAA-AGGTGCATTATCGGC
* * ** *
4439 ATAAAAGGATGCCATAAATGGAAATGCATAACTGTGCATAATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
* *
4485 ATGAAAGGATGCTACAAATGAAAAT
1 ATGAAAGGATGCCATAAATGAAAAT
4510 ATATAGCGGT
Statistics
Matches: 577, Mismatches: 74, Indels: 28
0.85 0.11 0.04
Matches are distributed among these distances:
42 24 0.04
43 34 0.06
44 4 0.01
45 16 0.03
46 455 0.79
47 44 0.08
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (46 bp):
ATGAAAGGATGCCATAAATGAAAATGCATAAAGGTGCATTATCGGC
Found at i:8267 original size:46 final size:46
Alignment explanation
Indices: 8200--8691 Score: 691
Period size: 46 Copynumber: 10.7 Consensus size: 46
8190 GAGATTCAAA
* * *
8200 ATGAAAGGATGTCATAAATGAAAATGCATGACGGTGTATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * *
8246 ATGAAAGGTTGCCATAAATGAAAATGCATCACGATGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* *
8292 ACGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
8338 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* *
8384 ATGAAAGGATGCCATAAATGAAAATGCATAACGTTGCATTATCGAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
** *
8430 ATGAAAGGATAACATAAATGAAAAATGCATAACAGTGCATTATCGGC
1 ATGAAAGGATGCCATAAATG-AAAATGCATAACGGTGCATTATCGGC
* *
8477 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTACATTATCGAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* ** **
8523 ATAAAAGGATGCCATAAATGAAAATGCATAATAGTATATTATCGGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
**
8569 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCTTC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
* * * * *
8615 -CGAAAGGATGCCATAAATGAAAAAGAATAATGGTG-AGTTATCAGC
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCA-TTATCGGC
* *
8660 ATGAAAGGATGTCATAAATGAAAATGTATAAC
1 ATGAAAGGATGCCATAAATGAAAATGCATAAC
8692 TGTTGAAAAC
Statistics
Matches: 396, Mismatches: 47, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
44 1 0.00
45 37 0.09
46 317 0.80
47 41 0.10
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (46 bp):
ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
Found at i:8519 original size:185 final size:184
Alignment explanation
Indices: 8200--8691 Score: 704
Period size: 185 Copynumber: 2.7 Consensus size: 184
8190 GAGATTCAAA
* * * * *
8200 ATGAAAGGATGTCATAAATGAAAATGCATGACGGTGTATTATCGGCATGAAAGGTTGCCATAAAT
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAAT
* * *
8265 G-AAAATGCATCACGATGCATTATCGGCACGAAAGGATGCCATAAATGAAAATGCATAACGGTGC
66 GAAAAATGCATAACG-TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTAC
* * *
8329 ATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGC
130 ATTATCGACATAAAAGGATGCCATAAATGAAAATGCATAACAGTACATTATCGGC
* **
8384 ATGAAAGGATGCCATAAATGAAAATGCATAACGTTGCATTATCGACATGAAAGGATAACATAAAT
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAAT
8449 GAAAAATGCATAACAGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTAC
66 GAAAAATGCATAAC-GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTAC
* *
8514 ATTATCGACATAAAAGGATGCCATAAATGAAAATGCATAATAGTATATTATCGGC
130 ATTATCGACATAAAAGGATGCCATAAATGAAAATGCATAACAGTACATTATCGGC
** *
8569 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCTTC-CGAAAGGATGCCATAAAT
1 ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAAT
* * * * *
8633 GAAAAA-GAATAATGGTG-AGTTATCAGCATGAAAGGATGTCATAAATGAAAATGTATAAC
66 GAAAAATGCATAA-CGTGCA-TTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
8692 TGTTGAAAAC
Statistics
Matches: 277, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
182 1 0.00
183 45 0.16
184 79 0.29
185 151 0.55
186 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (184 bp):
ATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAAT
GAAAAATGCATAACGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACGGTACA
TTATCGACATAAAAGGATGCCATAAATGAAAATGCATAACAGTACATTATCGGC
Found at i:14828 original size:21 final size:21
Alignment explanation
Indices: 14802--14841 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14792 CCCCCTTTGA
*
14802 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
14823 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
14842 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:18262 original size:46 final size:46
Alignment explanation
Indices: 18189--18578 Score: 505
Period size: 46 Copynumber: 8.5 Consensus size: 46
18179 TAACTCAACA
* * * *
18189 ATAACGATGCATTATCGACTTGAAAGGATGCTATAAATGAAAATAC
1 ATAACGGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGC
* ** *
18235 ATAACGGTGCATTATCGGCATTTAAGGATGCAATAAATGAAAATGC
1 ATAACGGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGC
* *
18281 ATAACGGTGCATTATTGACATGAAAGGATGCCATAAATGAAAATGG
1 ATAACGGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGC
* *
18327 ATAACAGTGCATTATTGACATGAAAGGATGCCATAAATGAAAATGC
1 ATAACGGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGC
* *
18373 ATAACGATGCATTATC-AGCATGAAAGGATGCCATAAATGGAAATGC
1 ATAACGGTGCATTATCGA-CATGAAAGGATGCCATAAATGAAAATGC
*
18419 ATAACGGTGCATTATC-AGCATGAAAGGATGCCATAAATGAAAATGA
1 ATAACGGTGCATTATCGA-CATGAAAGGATGCCATAAATGAAAATGC
* * *
18465 ATAACAGTGTATTATCGACATGAAAGGATGCCATAAATGGAAATGC
1 ATAACGGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGC
* * * * * *
18511 ATAACGGTGCATAATCGGCATGAAAGGATGCTACAAATTAAAATAC
1 ATAACGGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGC
* * *
18557 ATAATGGTGTATTAACGACATG
1 ATAACGGTGCATTATCGACATG
18579 TTAGGTGCCA
Statistics
Matches: 302, Mismatches: 40, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
45 1 0.00
46 300 0.99
47 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (46 bp):
ATAACGGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGC
Found at i:22979 original size:20 final size:20
Alignment explanation
Indices: 22935--22979 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
22925 TACTATGCTA
*
22935 GAAATTAATGTTAGATTGTT
1 GAAATTAATGTTAGAATGTT
22955 G-AATTAAATGTTAGAATG-T
1 GAAATT-AATGTTAGAATGTT
22974 GAAATT
1 GAAATT
22980 GGACTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGTT
Found at i:24270 original size:2 final size:2
Alignment explanation
Indices: 24263--24300 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24253 GATGATCATG
24263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24301 TATGTGGGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24677 original size:19 final size:19
Alignment explanation
Indices: 24653--24705 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
24643 TATGCATTGG
*
24653 GCTATGAATTTGAAAATAA
1 GCTATGAATATGAAAATAA
*
24672 GCTATGAATATGAAATTAA
1 GCTATGAATATGAAAATAA
* *
24691 GTTATTAATAT-AAAA
1 GCTATGAATATGAAAA
24706 GTGAGTTCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 3 0.10
19 26 0.90
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (19 bp):
GCTATGAATATGAAAATAA
Found at i:31276 original size:12 final size:12
Alignment explanation
Indices: 31259--31283 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31249 CTTTGTTTAT
31259 TCTAGTTAACAA
1 TCTAGTTAACAA
31271 TCTAGTTAACAA
1 TCTAGTTAACAA
31283 T
1 T
31284 GCTAAACTAC
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCTAGTTAACAA
Found at i:31383 original size:21 final size:20
Alignment explanation
Indices: 31330--31386 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
31320 TGATTTATTA
31330 TTATGGATTTCAAGTTGGTT
1 TTATGGATTTCAAGTTGGTT
*
31350 TTACGGATTTCAAGATT-GTT
1 TTATGGATTTCAAG-TTGGTT
*
31370 GTTATGGATGTCAAGTT
1 -TTATGGATTTCAAGTT
31387 TATAATTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.23, C:0.07, G:0.25, T:0.46
Consensus pattern (20 bp):
TTATGGATTTCAAGTTGGTT
Found at i:31816 original size:43 final size:42
Alignment explanation
Indices: 31734--31816 Score: 96
Period size: 43 Copynumber: 2.0 Consensus size: 42
31724 GTCATTTCTC
* * *
31734 AAAAAAGCCGCTAAATATCATAACATTTACATGCGTTTGTAG
1 AAAAAAGCCGCTAAAAATCATAACATTTACAGGCATTTGTAG
* *
31776 AAAAAATGCTGCTAAAAATCATAACCTTTAGC-GGCATTTGT
1 AAAAAA-GCCGCTAAAAATCATAACATTTA-CAGGCATTTGT
31817 GGACGATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
42 6 0.18
43 27 0.79
44 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (42 bp):
AAAAAAGCCGCTAAAAATCATAACATTTACAGGCATTTGTAG
Found at i:32858 original size:35 final size:35
Alignment explanation
Indices: 32811--32890 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
32801 AACACAGTCA
* *
32811 TCAATTATATTCTAAACCCCAAAATCCAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAACACT
* ** *
32846 TCAATTACATTCTAAACCTCAATTTTCAAAACACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAACACT
32881 TCAATTACAT
1 TCAATTACAT
32891 GCCCAACCCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAACACT
Found at i:33118 original size:148 final size:148
Alignment explanation
Indices: 32940--33229 Score: 490
Period size: 148 Copynumber: 2.0 Consensus size: 148
32930 ATAACAAAAT
*
32940 AGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGGTTATAAAATTTAAATCAAGTCGAA
1 AGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGGTTATAAAATTTAAATCAAGCCGAA
* * * * *
33005 TTGAATTTAATTTTCGAGTTTCTGTTTAAATTTAATTACAAATATTTATCATATTATAATATTAT
66 TTGAATTGAATTCTCGAGTTTCTGTTTAAATTTAATTACAAATATTTATAAAACTATAATATTAT
*
33070 TTGATTCTAATTCAGTTC
131 TTGATTATAATTCAGTTC
*
33088 AGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGCCGAA
1 AGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGGTTATAAAATTTAAATCAAGCCGAA
*
33153 TTGAATTGAATTCTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAAAACTATAATATTAT
66 TTGAATTGAATTCTCGAGTTTCTGTTTAAATTTAATTACAAATATTTATAAAACTATAATATTAT
*
33218 TTTATTATAATT
131 TTGATTATAATT
33230 TAAATAGTTT
Statistics
Matches: 132, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
148 132 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (148 bp):
AGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGGTTATAAAATTTAAATCAAGCCGAA
TTGAATTGAATTCTCGAGTTTCTGTTTAAATTTAATTACAAATATTTATAAAACTATAATATTAT
TTGATTATAATTCAGTTC
Found at i:33770 original size:36 final size:35
Alignment explanation
Indices: 33730--33807 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 35
33720 GTTGGTCATG
33730 TAATTGAAGTATTTTTGGAATTTA-AGGTTTAGAATA
1 TAATTGAAGTA-TTTTGGAATTTAGA-GTTTAGAATA
* *
33766 TAATTAAAGTATTTTGGAATTTAGAGTTTAGAATG
1 TAATTGAAGTATTTTGGAATTTAGAGTTTAGAATA
33801 TAATTGA
1 TAATTGA
33808 TGATTGTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 27 0.71
36 11 0.29
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (35 bp):
TAATTGAAGTATTTTGGAATTTAGAGTTTAGAATA
Found at i:39036 original size:22 final size:23
Alignment explanation
Indices: 39004--39049 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
38994 TGATACGATT
39004 AATTTTCAGGGTGGACAC-CATA
1 AATTTTCAGGGTGGACACACATA
* *
39026 AATTTTTAGGGTGGGCACACATA
1 AATTTTCAGGGTGGACACACATA
39049 A
1 A
39050 CAATGAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (23 bp):
AATTTTCAGGGTGGACACACATA
Found at i:41830 original size:24 final size:25
Alignment explanation
Indices: 41803--41858 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
41793 AAATTAATTT
41803 TTTTAATAATTTAAT-T-TTGTAGTA
1 TTTTAATAATTTAATGTATT-TAGTA
*
41827 TTTTTAT-ATTTAATGTATTTAGTA
1 TTTTAATAATTTAATGTATTTAGTA
*
41851 TCTTAATA
1 TTTTAATA
41859 TTTTTAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 7 0.27
24 17 0.65
25 2 0.08
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (25 bp):
TTTTAATAATTTAATGTATTTAGTA
Found at i:45924 original size:17 final size:17
Alignment explanation
Indices: 45911--45945 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
45901 GAGTTATATA
45911 AAATATATTTTTATTAT
1 AAATATATTTTTATTAT
* *
45928 AATTATATTTTTTTTAT
1 AAATATATTTTTATTAT
45945 A
1 A
45946 GTTTAAATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
AAATATATTTTTATTAT
Found at i:45969 original size:24 final size:24
Alignment explanation
Indices: 45942--46018 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
45932 ATATTTTTTT
*
45942 TATAGTTTAAATGGATATAATTCA
1 TATAGTTTAAATAGATATAATTCA
* *
45966 TATA-TAATTAAA-AAAT-TAAATTTA
1 TATAGT--TTAAATAGATAT-AATTCA
*
45990 TTATAGTTTAAATTGATATAATTCA
1 -TATAGTTTAAATAGATATAATTCA
46015 TATA
1 TATA
46019 TAAGTGTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
23 2 0.05
24 20 0.50
25 16 0.40
26 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (24 bp):
TATAGTTTAAATAGATATAATTCA
Found at i:46012 original size:25 final size:25
Alignment explanation
Indices: 45941--46030 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 25
45931 TATATTTTTT
*
45941 TTATAGTTTAAATGGATATAATTCA
1 TTATAGTTTAAATAGATATAATTCA
* * *
45966 TATATA-ATTAAA-AAAT-TAAATTTA
1 T-TATAGTTTAAATAGATAT-AATTCA
*
45990 TTATAGTTTAAATTGATATAATTCA
1 TTATAGTTTAAATAGATATAATTCA
*
46015 TATATAAGTGTAAATA
1 T-TAT-AGTTTAAATA
46031 TAATTCAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
23 5 0.10
24 13 0.27
25 14 0.29
26 8 0.17
27 8 0.17
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (25 bp):
TTATAGTTTAAATAGATATAATTCA
Found at i:46203 original size:14 final size:13
Alignment explanation
Indices: 46153--46205 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 13
46143 TTTATACAAC
46153 ACTTTTAAAAGTT
1 ACTTTTAAAAGTT
* *
46166 CAATTTTACAA--T
1 -ACTTTTAAAAGTT
46178 ACTTTTAAAAGTT
1 ACTTTTAAAAGTT
46191 ACTTTTCAAAAGTT
1 ACTTTT-AAAAGTT
46205 A
1 A
46206 TATCAATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 8 0.25
12 1 0.03
13 7 0.22
14 16 0.50
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (13 bp):
ACTTTTAAAAGTT
Found at i:54391 original size:24 final size:21
Alignment explanation
Indices: 54364--54426 Score: 56
Period size: 24 Copynumber: 2.9 Consensus size: 21
54354 CACCGACGCA
54364 TAAGTAGTGCATCGATGCACCCG
1 TAAG-AGTGCATCGATGCA-CCG
* * *
54387 TTAAGGAATGCATCGATACACTG
1 -TAA-GAGTGCATCGATGCACCG
54410 T-AGAGTGCATCGATGCA
1 TAAGAGTGCATCGATGCA
54427 TACCCTCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 13 0.39
21 1 0.03
22 1 0.03
23 2 0.06
24 15 0.45
25 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (21 bp):
TAAGAGTGCATCGATGCACCG
Found at i:55014 original size:22 final size:22
Alignment explanation
Indices: 54934--55010 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
54924 TTGAGGGTAT
*
54934 AGTGGTCCTTCAGGATGTATTC
1 AGTGGTCCTTCAGGACGTATTC
* *
54956 AATGGTCATTCAGGACGTATTC
1 AGTGGTCCTTCAGGACGTATTC
* *
54978 AGTGGTCCTTCGGGACGTATCC
1 AGTGGTCCTTCAGGACGTATTC
55000 AGTGGTCCTTC
1 AGTGGTCCTTC
55011 GGGATAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.32
Consensus pattern (22 bp):
AGTGGTCCTTCAGGACGTATTC
Found at i:61786 original size:21 final size:21
Alignment explanation
Indices: 61760--61816 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
61750 ATATGTGTTT
61760 ATATGAAAAGTGATGAAAGAG
1 ATATGAAAAGTGATGAAAGAG
61781 ATATGAAAAGTGATGAAAGAG
1 ATATGAAAAGTGATGAAAGAG
61802 ATAT-AAAA-TGA-GAAA
1 ATATGAAAAGTGATGAAA
61817 TGTATTCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.11
19 3 0.08
20 4 0.11
21 25 0.69
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (21 bp):
ATATGAAAAGTGATGAAAGAG
Found at i:61930 original size:22 final size:22
Alignment explanation
Indices: 61905--61973 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
61895 GGTCCTTCAA
61905 GACGTATTCAAG-GGTCATTCGG
1 GACGTATTC-AGTGGTCATTCGG
*
61927 GACGTATTCAGTGGTCCTTCGG
1 GACGTATTCAGTGGTCATTCGG
* * *
61949 GACGTATCCAGTGGTCTTTTGG
1 GACGTATTCAGTGGTCATTCGG
61971 GAC
1 GAC
61974 AAATACTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 2 0.05
22 40 0.95
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.30
Consensus pattern (22 bp):
GACGTATTCAGTGGTCATTCGG
Found at i:68512 original size:20 final size:20
Alignment explanation
Indices: 68489--68610 Score: 99
Period size: 20 Copynumber: 6.0 Consensus size: 20
68479 AGTTTCCAAT
68489 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* **
68509 TTCGC-GCTGCGATTTTCCAAA
1 TTCGCAAC-GCGATAGT-CAAA
* *
68530 TTCGCAACGGGAATTTGT-AAA
1 TTCGCAACGCG-A-TAGTCAAA
*
68551 -TCGCAACACAGA-AGTCAAA
1 TTCGCAACGC-GATAGTCAAA
68570 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* *
68590 TTTGCAACGCGAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
68610 T
1 T
68611 GTTTTTACGC
Statistics
Matches: 81, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 53 0.65
21 15 0.19
22 2 0.02
23 3 0.04
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGATAGTCAAA
Found at i:68756 original size:22 final size:22
Alignment explanation
Indices: 68731--68788 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
68721 TCACTCTCTA
*
68731 CGACGACATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
68753 CGACGAAATCCGTCCCCATTTC
1 CGACGAAATCCGTCCCCATCTC
68775 CGACGAAATCCGTC
1 CGACGAAATCCGTC
68789 TATCTCCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.22, C:0.43, G:0.16, T:0.19
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:69087 original size:19 final size:20
Alignment explanation
Indices: 69047--69089 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
69037 CACACCAAAT
69047 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
69067 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
69086 TCGC
1 TCGC
69090 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:69127 original size:20 final size:20
Alignment explanation
Indices: 69086--69127 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
69076 GAAACTAAAA
* * *
69086 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTAAGTT
69106 TCGCGTTGCGAATTTAAGTT
1 TCGCGTTGCGAATTTAAGTT
69126 TC
1 TC
69128 AGAAACTTCT
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:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAAGTT
Found at i:73331 original size:19 final size:20
Alignment explanation
Indices: 73307--73358 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
73297 ACTAAAACAT
73307 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
** *
73326 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGA
73346 GTTGCGAATTTGA
1 GTTGCGAATTTGA
73359 CTATCGCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:73351 original size:20 final size:20
Alignment explanation
Indices: 73307--73377 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
73297 ACTAAAACAT
** *
73307 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGACTTTCGC
73326 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCGC
*
73346 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTCGC
* *
73366 TTTACGAATTTG
1 GTTGCGAATTTG
73378 GAAAATCGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
19 16 0.36
20 29 0.64
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTCGC
Found at i:73430 original size:20 final size:20
Alignment explanation
Indices: 73401--73454 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
73391 CGATTTACAT
73401 ATTCGCGTTGCGAAATTGGAA
1 ATTCGCGTTGCGAAATTGG-A
* *
73422 ATT-GGGTTGAGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
73441 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
73455 TTTATTGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 21 0.75
21 3 0.11
ACGTcount: A:0.28, C:0.11, G:0.31, T:0.30
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:74548 original size:13 final size:13
Alignment explanation
Indices: 74521--74562 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
74511 AGGGTCTATT
74521 TGTTTTACTGAAAA
1 TGTTTT-CTGAAAA
74535 TGTTTT-TGGAAAA
1 TGTTTTCT-GAAAA
74548 TGTTTTCTGAAAA
1 TGTTTTCTGAAAA
74561 TG
1 TG
74563 AATTACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.04
13 18 0.69
14 7 0.27
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (13 bp):
TGTTTTCTGAAAA
Found at i:74673 original size:14 final size:13
Alignment explanation
Indices: 74656--74702 Score: 62
Period size: 12 Copynumber: 3.7 Consensus size: 13
74646 GCAAATTTTC
74656 TATAAATTATTTAT
1 TATAAA-TATTTAT
74670 TATAAATATTT-T
1 TATAAATATTTAT
*
74682 TATTAA-ATTTAT
1 TATAAATATTTAT
74694 TATAAATAT
1 TATAAATAT
74703 CAAATACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 4 0.14
12 12 0.41
13 7 0.24
14 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATAAATATTTAT
Found at i:74688 original size:27 final size:24
Alignment explanation
Indices: 74650--74702 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 24
74640 CAAATGGCAA
74650 ATTTTCTATAAATTATTTATTATAAAT
1 ATTTTCTAT-AA--ATTTATTATAAAT
74677 ATTTT-TATTAAATTTATTATAAAT
1 ATTTTCTA-TAAATTTATTATAAAT
74701 AT
1 AT
74703 CAAATACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 15 0.60
26 4 0.16
27 6 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTCTATAAATTTATTATAAAT
Found at i:81039 original size:17 final size:18
Alignment explanation
Indices: 81017--81053 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
81007 GAATATGTCA
81017 TATGTCT-GAAGGACCAC
1 TATGTCTCGAAGGACCAC
81034 TATGTCTCGAAGGACCAC
1 TATGTCTCGAAGGACCAC
81052 TA
1 TA
81054 ATAATCCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (18 bp):
TATGTCTCGAAGGACCAC
Done.