Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002615.1 Hibiscus syriacus cultivar Beakdansim tig00005293_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: 51005
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1340 original size:23 final size:25
Alignment explanation
Indices: 1296--1341 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
1286 CATAATATGT
1296 TTGAAACTCAAAATAAATAAAAGTG
1 TTGAAACTCAAAATAAATAAAAGTG
1321 TTGAAACTC-AAA-AAATAAAAG
1 TTGAAACTCAAAATAAATAAAAG
1342 GATCGTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 9 0.43
24 3 0.14
25 9 0.43
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.22
Consensus pattern (25 bp):
TTGAAACTCAAAATAAATAAAAGTG
Found at i:2253 original size:32 final size:32
Alignment explanation
Indices: 2217--2281 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2207 AAAACAACAC
* *
2217 AAATAGAAACTTAAAGGATTAAAATAATAAAA
1 AAATAGAAACTTAAAAGACTAAAATAATAAAA
* *
2249 AAATAGAAAGTTAAAAGACTAAAATAGTAAAA
1 AAATAGAAACTTAAAAGACTAAAATAATAAAA
2281 A
1 A
2282 TAGAAAGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.66, C:0.03, G:0.11, T:0.20
Consensus pattern (32 bp):
AAATAGAAACTTAAAAGACTAAAATAATAAAA
Found at i:3708 original size:3 final size:3
Alignment explanation
Indices: 3700--3740 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
3690 AAAAATAACC
3700 ATA ATA ATA ATA ATA ATA ATA ATA A-A TATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
3741 TTTTTTGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 3 0.09
3 31 0.89
4 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5719 original size:21 final size:21
Alignment explanation
Indices: 5677--5719 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5667 TATTTTGATA
*
5677 TTATGATTGATATTTATAAAT
1 TTATGATTGATATATATAAAT
* * *
5698 TTATGTTTGGTATATATTAAT
1 TTATGATTGATATATATAAAT
5719 T
1 T
5720 AATTCAAATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (21 bp):
TTATGATTGATATATATAAAT
Found at i:6165 original size:18 final size:18
Alignment explanation
Indices: 6144--6178 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6134 TTGGATATGA
*
6144 ATTGTATATTAAATTTGG
1 ATTGCATATTAAATTTGG
*
6162 ATTGCATATTGAATTTG
1 ATTGCATATTAAATTTG
6179 AGTTTTAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (18 bp):
ATTGCATATTAAATTTGG
Found at i:8324 original size:8 final size:8
Alignment explanation
Indices: 8313--8358 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
8303 TAATTAATCA
8313 ATTATTTT
1 ATTATTTT
8321 ATTATTATT
1 ATTATT-TT
8330 -TTATTTT
1 ATTATTTT
*
8337 AATA-TTT
1 ATTATTTT
*
8344 ATTATTTG
1 ATTATTTT
8352 ATTATTT
1 ATTATTT
8359 AATTGTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
7 8 0.25
8 22 0.69
9 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
ATTATTTT
Found at i:11537 original size:27 final size:26
Alignment explanation
Indices: 11507--11558 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
11497 GGTATGCTTT
* *
11507 ATGTCATGTTTAATATTTTGTTGTTTA
1 ATGTAATGTTT-ATAGTTTGTTGTTTA
*
11534 ATGTAATGTTTATGGTTTGTTGTTT
1 ATGTAATGTTTATAGTTTGTTGTTT
11559 TTATAGTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.19, C:0.02, G:0.19, T:0.60
Consensus pattern (26 bp):
ATGTAATGTTTATAGTTTGTTGTTTA
Found at i:12816 original size:83 final size:83
Alignment explanation
Indices: 12419--12815 Score: 465
Period size: 83 Copynumber: 4.8 Consensus size: 83
12409 ATTTCATGGT
* * *
12419 GTTTTCCATTATTATCCAGAGAATCTCTACCATGTCATAGTGTT-TCATCCTATCCGAAATGAAA
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCT-ATCCCATCCGAAATGAAA
** *
12483 GGCGCGCTCCAGGGGAAGT
65 GGCGCATTCCAGGGGAAGC
* * * *
12502 GCTTTCCATTATTATTCAGAGAATCTTTGTCATGTCATAGTGTT-TCATTCCATCCGAAATGAAA
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCT-ATCCCATCCGAAATGAAA
*
12566 GGCGCATTCCAGGGGAAAC
65 GGCGCATTCCAGGGGAAGC
* * * * *
12585 GTTTTCCATTATTATTCATAGAATCTCTGTCATGTCATAGTCTTCCATCCCATCCGAAAAGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCTATCCCATCCGAAATGAAAG
* ** * *
12650 GTGTGTTCTACGGGAAGC
66 GCGCATTCCAGGGGAAGC
* * * * * *
12668 ATTTTCCATTATTATTCATAGAATCTCTACCATGTCAGAGTGTTCTATCCCATCTGAAATAAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCTATCCCATCCGAAATGAAAG
* * *
12733 ACGCATTCTAGGAGAAGC
66 GCGCATTCCAGGGGAAGC
* * *
12751 GTTTTCCATTATTATTCCGAGAATCTCTGCCATATCATAGTGTTCTATGCCATCCGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCTATCCCATCCGAAATGAAAG
12816 AATCATGTTC
Statistics
Matches: 265, Mismatches: 48, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
83 265 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (83 bp):
GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCTATCCCATCCGAAATGAAAG
GCGCATTCCAGGGGAAGC
Found at i:15217 original size:49 final size:49
Alignment explanation
Indices: 15160--15405 Score: 411
Period size: 49 Copynumber: 5.0 Consensus size: 49
15150 ACTGCTCTAA
*
15160 AATGAAAGTTAAATGCATAAAGGTGCATTTCGGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
*
15209 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTACCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
* * *
15258 AATGAAAGTTAAATGCATAACAGTGCATTTTCGACATAAAAGGTGCCATT
1 AATGAAAGTTAAATGCATAACGGTGCA-TTTCGGCATAAAAGGTGCCACT
*
15308 AATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
* *
15357 AATGAAAGTTAAATGCATAGCGGTGCATTTCAGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
15406 CATGGTATTC
Statistics
Matches: 185, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
49 140 0.76
50 45 0.24
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (49 bp):
AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
Found at i:15436 original size:99 final size:97
Alignment explanation
Indices: 15160--15405 Score: 402
Period size: 99 Copynumber: 2.5 Consensus size: 97
15150 ACTGCTCTAA
*
15160 AATGAAAGTTAAATGCATAAAGGTGCATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGC
1 AATGAAAGTTAAATGCATAACGGTGCATTTC-GCATAAAAGGTGCCACTAATGAAAGTTAAATGC
*
15225 ATAACGGTGCATTTCGGCATAAAAGGTACCACT
65 ATAACGGTGCATTTCAGCATAAAAGGTACCACT
* *
15258 AATGAAAGTTAAATGCATAACAGTGCATTTTCGACATAAAAGGTGCCATTAATGAAAGTTAAATG
1 AATGAAAGTTAAATGCATAACGGTGCA-TTTCG-CATAAAAGGTGCCACTAATGAAAGTTAAATG
*
15323 CATAACGGTGCATTTCAGCATAAAAGGTGCCACT
64 CATAACGGTGCATTTCAGCATAAAAGGTACCACT
*
15357 AATGAAAGTTAAATGCATAGCGGTGCATTTCAGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTC-GCATAAAAGGTGCCACT
15406 CATGGTATTC
Statistics
Matches: 137, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
98 45 0.33
99 92 0.67
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (97 bp):
AATGAAAGTTAAATGCATAACGGTGCATTTCGCATAAAAGGTGCCACTAATGAAAGTTAAATGCA
TAACGGTGCATTTCAGCATAAAAGGTACCACT
Found at i:18818 original size:21 final size:21
Alignment explanation
Indices: 18765--18820 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
18755 GACGATTTTC
*
18765 ATTAAAATAA-TATTTTTATT
1 ATTATAATAATTATTTTTATT
*
18785 ATTTTAA-ATATTATTTTTAATT
1 ATTATAATA-ATTATTTTT-ATT
18807 A-TATAATAATTATT
1 ATTATAATAATTATT
18821 AAAAAAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.03
20 6 0.21
21 17 0.59
22 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATAATAATTATTTTTATT
Found at i:20107 original size:18 final size:19
Alignment explanation
Indices: 20086--20127 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 19
20076 TTTTTATTAT
20086 TTATTATTT-ATATT-TTAA
1 TTATT-TTTCATATTCTTAA
20104 TTATTTTTCATATTGCTTAA
1 TTATTTTTCATATT-CTTAA
20124 TTAT
1 TTAT
20128 ATTAGGGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.14
18 10 0.48
20 8 0.38
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTTTTCATATTCTTAA
Found at i:20770 original size:76 final size:75
Alignment explanation
Indices: 20639--20780 Score: 203
Period size: 76 Copynumber: 1.9 Consensus size: 75
20629 TTAACTTTGC
* * * *
20639 ATTTTACTCAATTGAATATCTTGACTACAATTGTTTCCAATTTCTTTTTCTCATAAATTAATTAA
1 ATTTTACTCAATTGAATATCTTGACTACAATTGTTTACAAATTATTTTTCCCATAAA-TAATTAA
20704 CTTTTCAAATT
65 CTTTTCAAATT
* * * *
20715 ATTTTACTCAATTGAGTCTCTTGATTGCAATTGTTTACAAATTATTTTTCCCATAAATAATTAAC
1 ATTTTACTCAATTGAATATCTTGACTACAATTGTTTACAAATTATTTTTCCCATAAATAATTAAC
20780 T
66 T
20781 CTTTTATACT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
75 9 0.16
76 49 0.84
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.47
Consensus pattern (75 bp):
ATTTTACTCAATTGAATATCTTGACTACAATTGTTTACAAATTATTTTTCCCATAAATAATTAAC
TTTTCAAATT
Found at i:33866 original size:16 final size:16
Alignment explanation
Indices: 33845--33878 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33835 CTTAAATAAT
33845 AATATTACTCTCCTAA
1 AATATTACTCTCCTAA
* *
33861 AATATTATTTTCCTAA
1 AATATTACTCTCCTAA
33877 AA
1 AA
33879 ATAACTAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATTACTCTCCTAA
Found at i:38482 original size:14 final size:16
Alignment explanation
Indices: 38458--38490 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
38448 AAACAGTTGG
38458 AAAAGAAAT-AAAAAT
1 AAAAGAAATAAAAAAT
38473 AAAA-AAATAAAAAAT
1 AAAAGAAATAAAAAAT
38488 AAA
1 AAA
38491 CTTAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAGAAATAAAAAAT
Found at i:38516 original size:43 final size:45
Alignment explanation
Indices: 38468--38577 Score: 120
Period size: 45 Copynumber: 2.4 Consensus size: 45
38458 AAAAGAAATA
*
38468 AAAATAAAAAAATAAAAAATAAACTTAATTA-AAAAATGAT-AAA-
1 AAAATAAAAAAATAAAAAATAAAC-TAATAAGAAAAATGATAAAAG
* *
38511 TAAATAAATAAAGAGAAAAAA-AAACTAATAAGAAAAATGATAAAAG
1 AAAATAAA-AAA-ATAAAAAATAAACTAATAAGAAAAATGATAAAAG
*
38557 AAAAGAAAAGAAATAAAAAAT
1 AAAATAAAA-AAATAAAAAAT
38578 GATAATAAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
43 12 0.22
44 16 0.30
45 18 0.33
46 8 0.15
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (45 bp):
AAAATAAAAAAATAAAAAATAAACTAATAAGAAAAATGATAAAAG
Found at i:38547 original size:44 final size:43
Alignment explanation
Indices: 38469--38554 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
38459 AAAGAAATAA
* *
38469 AAATAAAAAAATAAAAAATAAACTTAATTAAAAAATGATAAAT
1 AAATAAAAAAAGAAAAAATAAACTTAATAAAAAAATGATAAAT
38512 AAATAAATAAAGAGAAAAAA-AAAC-TAATAAGAAAAATGATAAA
1 AAATAAA-AAA-AGAAAAAATAAACTTAATAA-AAAAATGATAAA
38555 AGAAAAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
43 12 0.32
44 19 0.50
45 7 0.18
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (43 bp):
AAATAAAAAAAGAAAAAATAAACTTAATAAAAAAATGATAAAT
Found at i:38559 original size:31 final size:30
Alignment explanation
Indices: 38518--38582 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
38508 AAATAAATAA
*
38518 ATAAAGAGAAAAAAAAACTAATAAGAAAAATG
1 ATAAAGAGAAAAAAAAACAAAT-A-AAAAATG
* *
38550 ATAAA-AGAAAAGAAAAGAAATAAAAAATG
1 ATAAAGAGAAAAAAAAACAAATAAAAAATG
38579 ATAA
1 ATAA
38583 TAAAGTAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 11 0.37
30 1 0.03
31 13 0.43
32 5 0.17
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (30 bp):
ATAAAGAGAAAAAAAAACAAATAAAAAATG
Found at i:38575 original size:44 final size:43
Alignment explanation
Indices: 38463--38576 Score: 110
Period size: 44 Copynumber: 2.6 Consensus size: 43
38453 GTTGGAAAAG
*
38463 AAATAAAAATAAAA-AAATAAAAAATAAACTTAATTAAAAAATGAT
1 AAATAAAAA-AAAAGAAAT-AAAAA-AAACTTAATAAAAAAATGAT
*
38508 AAATAAATAAATAAAGAGA-AAAAAAAAC-TAATAAGAAAAATGAT
1 AAATAAA-AAA-AAAGAAATAAAAAAAACTTAATAA-AAAAATGAT
38552 AAA-AGAAAAGAAAAGAAATAAAAAA
1 AAATA-AAAA-AAAAGAAATAAAAAA
38577 TGATAATAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
43 14 0.24
44 25 0.42
45 13 0.22
46 5 0.08
47 2 0.03
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (43 bp):
AAATAAAAAAAAAGAAATAAAAAAAACTTAATAAAAAAATGAT
Found at i:38613 original size:21 final size:20
Alignment explanation
Indices: 38589--38628 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
38579 ATAATAAAGT
*
38589 AAGGTTAAAAACAATTAAAAA
1 AAGGGTAAAAACAA-TAAAAA
*
38610 AAGGGTAAAAGCAATAAAA
1 AAGGGTAAAAACAATAAAA
38629 TTTAAAGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.65, C:0.05, G:0.15, T:0.15
Consensus pattern (20 bp):
AAGGGTAAAAACAATAAAAA
Found at i:39137 original size:33 final size:29
Alignment explanation
Indices: 39085--39183 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
39075 ATAAAATGAA
**
39085 AATAA-AAAAATAATAATATATCTATATGT
1 AATAATAAAAATAATAATATA-AAATATGT
*
39114 ATATATATAAGAAATAATGATATAAAATATGT
1 A-ATA-ATAA-AAATAATAATATAAAATATGT
*
39146 AATAATAAAAATAATAATAATAAAA-ATAT
1 AATAATAAAAATAATAAT-ATAAAATATGT
39175 AATATATAA
1 AATA-ATAA
39184 TAAACATAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
29 17 0.29
30 17 0.29
31 4 0.07
32 9 0.15
33 12 0.20
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (29 bp):
AATAATAAAAATAATAATATAAAATATGT
Found at i:39153 original size:3 final size:3
Alignment explanation
Indices: 39145--39186 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
39135 ATAAAATATG
* *
39145 TAA TAA TAA AAA TAA TAA TAA TAA AAA T-A TAA TATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
39187 ACATAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:39153 original size:15 final size:14
Alignment explanation
Indices: 39135--39201 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 14
39125 AAATAATGAT
*
39135 ATAAAATATGTAATA
1 ATAAAA-ATATAATA
39150 ATAAAAATAATAATA
1 ATAAAAAT-ATAATA
39165 ATAAAAATATAATA
1 ATAAAAATATAATA
*
39179 TATAATAAACATAAATA
1 -ATAA-AAATAT-AATA
39196 A-AAAAA
1 ATAAAAA
39202 AAAAAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
14 11 0.24
15 25 0.54
16 6 0.13
17 4 0.09
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (14 bp):
ATAAAAATATAATA
Found at i:40373 original size:20 final size:19
Alignment explanation
Indices: 40334--40373 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40324 AAACATGTAA
*
40334 AAATAGTAAAATAAATAAT
1 AAATAATAAAATAAATAAT
*
40353 AAATAATAAATATATATAAT
1 AAATAATAAA-ATAAATAAT
40373 A
1 A
40374 TATGTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
AAATAATAAAATAAATAAT
Found at i:40392 original size:14 final size:14
Alignment explanation
Indices: 40363--40410 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
40353 AAATAATAAA
40363 TATATATAATATATG
1 TATATAT-ATATATG
*
40378 TTTAT-TATAATATG
1 TATATATAT-ATATG
40392 TATATATATATATG
1 TATATATATATATG
*
40406 AATAT
1 TATAT
40411 TATTAATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 2 0.07
14 19 0.68
15 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
TATATATATATATG
Found at i:41105 original size:19 final size:19
Alignment explanation
Indices: 41081--41117 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41071 TCGAATGCAT
41081 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
41100 TCCATGCATCGATGCACT
1 TCCATGCACCGATGCACT
41118 TTGAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:41244 original size:64 final size:65
Alignment explanation
Indices: 41067--41229 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
41057 GAATTAATTG
* * * ***
41067 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTTTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACCAGGAATATTTTCAA
* ** *
41132 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACCAGG-CTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACCAGGAATA-TTTTCA
41195 A
65 A
41196 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
41230 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 34 0.40
65 50 0.60
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACCAGGAATATTTTCAA
Found at i:42783 original size:117 final size:117
Alignment explanation
Indices: 42572--42785 Score: 256
Period size: 117 Copynumber: 1.8 Consensus size: 117
42562 ATCTTATTTT
*
42572 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGGAGTTAGAGCTTTCAAAAA
1 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGAAGTTAGAGCTTTCAAAAA
*
42637 TAAAATCGAAAAACTTTGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
66 TAAAATCGAAAAAC-TGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
* * * * *
42690 GAAA-CTAAAATGGATTTTGAAAA-ACAAAATGAAAT-TTCGAAGAAGAATTTAGAGCTTTCAAA
1 GAAAGCTAAAAAGGACTTGGAAAATA-AAAATGAAATGTT-GAAAAAGAAGTTAGAGCTTTCAAA
* * * *
42752 GATAAAATTTGAAAGTA-TGGAAAAGGAAATTTTC
64 AATAAAA-TCGAAA-AACTGGAAAAAGAAATTTTC
42786 GATTTAGAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
116 3 0.04
117 68 0.84
118 9 0.11
119 1 0.01
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (117 bp):
GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGAAGTTAGAGCTTTCAAAAA
TAAAATCGAAAAACTGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
Found at i:43349 original size:20 final size:21
Alignment explanation
Indices: 43316--43355 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
43306 TTTTAACGTA
43316 ATTGATATTCATTTT-AAACC
1 ATTGATATTCATTTTCAAACC
43336 ATTGATA-TCAATTTTCAAAC
1 ATTGATATTC-ATTTTCAAAC
43356 AATTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATTCATTTTCAAACC
Found at i:43363 original size:22 final size:20
Alignment explanation
Indices: 43315--43359 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
43305 ATTTTAACGT
43315 AATTGATATTCATTTTAAAC
1 AATTGATATTCATTTTAAAC
*
43335 CATTGATA-TCAATTTTCAAAC
1 AATTGATATTC-ATTTT-AAAC
43356 AATT
1 AATT
43360 TGATTTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.57
21 7 0.33
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (20 bp):
AATTGATATTCATTTTAAAC
Found at i:48245 original size:19 final size:19
Alignment explanation
Indices: 48221--48257 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
48211 TCGAATGCAT
48221 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
48240 TCCATGCATCGATGCACT
1 TCCATGCACCGATGCACT
48258 ATATTTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:48380 original size:64 final size:61
Alignment explanation
Indices: 48207--48365 Score: 212
Period size: 61 Copynumber: 2.6 Consensus size: 61
48197 GAATTAATTG
* * * *
48207 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACCATATTTTCAA
* **
48268 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACCA---TA-TTTTCAA
48332 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
48366 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
61 45 0.54
64 34 0.40
65 5 0.06
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (61 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACCATATTTTCAA
Found at i:49456 original size:59 final size:65
Alignment explanation
Indices: 49358--49508 Score: 190
Period size: 65 Copynumber: 2.4 Consensus size: 65
49348 TTGTGGGCAC
* * * *
49358 GATATCCTTCGTCATGAAGTTGAAATCGTGGATG-GCCC-C-TTC-GA-GTTGAGCCTTGAATTG
1 GATATCCTTCGTCGTGAAATTGAAATCGTGGATGACCCCTCGTTCTGACGTTGAGCATTGAATTG
*
49418 GATATCCTTCGTCGT-AAATTGAAATCGTGGATGACCCCTTCGTTCTGACGTTGAGTATTGAATT
1 GATATCCTTCGTCGTGAAATTGAAATCGTGGATGACCCC-TCGTTCTGACGTTGAGCATTGAATT
49482 G
65 G
*
49483 GATATCCTTCGTCGTGAAGTT-AAATC
1 GATATCCTTCGTCGTGAAATTGAAATC
49509 CAAGTATTGT
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
59 17 0.22
60 17 0.22
62 1 0.01
63 3 0.04
64 2 0.03
65 34 0.44
66 4 0.05
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (65 bp):
GATATCCTTCGTCGTGAAATTGAAATCGTGGATGACCCCTCGTTCTGACGTTGAGCATTGAATTG
Found at i:50357 original size:1 final size:1
Alignment explanation
Indices: 50351--50395 Score: 63
Period size: 1 Copynumber: 45.0 Consensus size: 1
50341 ACCCACCTTA
* * *
50351 TTTTTTTTTTTTTTTCTTTTTTTTTTTTTCTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
50396 AATTTAGGGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:50372 original size:14 final size:14
Alignment explanation
Indices: 50353--50394 Score: 75
Period size: 14 Copynumber: 2.9 Consensus size: 14
50343 CCACCTTATT
50353 TTTTTTTTTTTTTC
1 TTTTTTTTTTTTTC
50367 TTTTTTTTTTTTTC
1 TTTTTTTTTTTTTC
50381 TTTTTTCTTTTTTT
1 TTTTTT-TTTTTTT
50395 TAATTTAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTTTTTTTTTTC
Found at i:50377 original size:21 final size:21
Alignment explanation
Indices: 50351--50395 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
50341 ACCCACCTTA
50351 TTTTTTTTT-TTTTTTCTTTT
1 TTTTTTTTTCTTTTTTCTTTT
50371 TTTTTTTTTCTTTTTTCTTTT
1 TTTTTTTTTCTTTTTTCTTTT
50392 TTTT
1 TTTT
50396 AATTTAGGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (21 bp):
TTTTTTTTTCTTTTTTCTTTT
Found at i:50455 original size:17 final size:16
Alignment explanation
Indices: 50432--50474 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
50422 ACCCTAAACG
*
50432 TTTTTCTCTTTTTTGT
1 TTTTTCTCTTTTTTAT
50448 TCTTTTCT-TTTTTTAT
1 T-TTTTCTCTTTTTTAT
*
50464 TTTTTTTCTTT
1 TTTTTCTCTTT
50475 GACTTAGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.22
16 12 0.52
17 6 0.26
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (16 bp):
TTTTTCTCTTTTTTAT
Done.