Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000550.1 Hibiscus syriacus cultivar Beakdansim tig00001071_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: 77795
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2343 original size:16 final size:15
Alignment explanation
Indices: 2303--2344 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2293 ATGGTAGTAA
2303 AATATTATTTTAAAT
1 AATATTATTTTAAAT
*
2318 AAT-TACATTTTACAAT
1 AATAT-TATTTTA-AAT
2334 AATATTATTTT
1 AATATTATTTT
2345 GTAACTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
14 1 0.05
15 9 0.41
16 11 0.50
17 1 0.05
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATTATTTTAAAT
Found at i:2392 original size:21 final size:21
Alignment explanation
Indices: 2363--2404 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2353 TAAAATTATA
*
2363 AATAGTAAAATATTAAATATT
1 AATAGTAAAATATCAAATATT
* *
2384 AATATTAAATTATCAAATATT
1 AATAGTAAAATATCAAATATT
2405 TAAATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AATAGTAAAATATCAAATATT
Found at i:2494 original size:13 final size:13
Alignment explanation
Indices: 2476--2518 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
2466 TAATTTTGAG
2476 TAAAATATAAAAA
1 TAAAATATAAAAA
*
2489 TAAAATTTAAAAA
1 TAAAATATAAAAA
2502 -AAATATTATAAAAA
1 TAAA-A-TATAAAAA
2516 TAA
1 TAA
2519 TTCATTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 3 0.12
13 13 0.52
14 7 0.28
15 2 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAAATATAAAAA
Found at i:4738 original size:6 final size:6
Alignment explanation
Indices: 4727--4751 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4717 TCATTGTCTA
4727 CTGTTT CTGTTT CTGTTT CTGTTT C
1 CTGTTT CTGTTT CTGTTT CTGTTT C
4752 GATGTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.16, T:0.64
Consensus pattern (6 bp):
CTGTTT
Found at i:5643 original size:60 final size:61
Alignment explanation
Indices: 5518--5643 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 61
5508 ATATAATTTG
* * * * *
5518 GGATAAAATTGAAATGTTCAAAAAGTTTGGGGATCAATTTAGAATGAAGATAATAGTTTGG
1 GGATGAAATTGAAATATTCAAAAAGTTTGGGGATCAATTTAGAATCAAGATAATAGATTGA
* *
5579 GGATGAAATTGAAATATT-TAAAAGTTTAGGGG-TCAATTTAGAA-CAAGGATCATA-ATTGAA
1 GGATGAAATTGAAATATTCAAAAAGTTT-GGGGATCAATTTAGAATCAA-GATAATAGATTG-A
5639 GGATG
1 GGATG
5644 TGTGGTGTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
59 5 0.09
60 30 0.55
61 20 0.36
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.30
Consensus pattern (61 bp):
GGATGAAATTGAAATATTCAAAAAGTTTGGGGATCAATTTAGAATCAAGATAATAGATTGA
Found at i:7576 original size:29 final size:29
Alignment explanation
Indices: 7534--7597 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
7524 TAGACGAATT
*
7534 GAAGAAGGAGAAATGGGTTTATAGAAGAA
1 GAAGAAGAAGAAATGGGTTTATAGAAGAA
* *
7563 GAAGAAGAATAAATGGGTTTATGGAAGAA
1 GAAGAAGAAGAAATGGGTTTATAGAAGAA
*
7592 AAAGAA
1 GAAGAA
7598 AGGTTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (29 bp):
GAAGAAGAAGAAATGGGTTTATAGAAGAA
Found at i:7589 original size:23 final size:23
Alignment explanation
Indices: 7534--7801 Score: 167
Period size: 23 Copynumber: 11.5 Consensus size: 23
7524 TAGACGAATT
*
7534 GAAGAAGGAGAAATGGGTTTATAG
1 GAAGAAGAAGAAATGGGTTTAT-G
7558 AAGAAGAAGAAGAATAAATGGGTTTATG
1 --GAAGAAGAAG---AAATGGGTTTATG
* *
7586 GAAGAAAAAGAAA-GGTTTTTATGG
1 GAAGAAGAAGAAATGG-GTTTAT-G
*
7610 AAGAAGAAGAAGAAATGTGTTTATG
1 --GAAGAAGAAGAAATGGGTTTATG
* * * *
7635 GAAGAAAAACATAT-GTTTTATG
1 GAAGAAGAAGAAATGGGTTTATG
*
7657 GAAGAATAAGAAA-GTGGTTTATG
1 GAAGAAGAAGAAATG-GGTTTATG
* * * *
7680 AAAGAAGAATAAACGAGTTTATG
1 GAAGAAGAAGAAATGGGTTTATG
* * * *
7703 GAAGAAAAAGCAACGAGTTTATG
1 GAAGAAGAAGAAATGGGTTTATG
* * * *
7726 GAAAAAGAAGCAATGAGCTTATG
1 GAAGAAGAAGAAATGGGTTTATG
7749 GAAGAAGAAGAAAAT--GTTTATG
1 GAAGAAGAAG-AAATGGGTTTATG
*
7771 GAGGAAGAA-AAAT--G-TTATG
1 GAAGAAGAAGAAATGGGTTTATG
7790 GAAGAAGAAGAA
1 GAAGAAGAAGAA
7802 TGGTTCAGAA
Statistics
Matches: 197, Mismatches: 32, Indels: 32
0.75 0.12 0.12
Matches are distributed among these distances:
19 13 0.07
20 7 0.04
22 32 0.16
23 90 0.46
24 5 0.03
25 1 0.01
26 35 0.18
27 1 0.01
28 1 0.01
29 12 0.06
ACGTcount: A:0.48, C:0.02, G:0.28, T:0.22
Consensus pattern (23 bp):
GAAGAAGAAGAAATGGGTTTATG
Found at i:7668 original size:71 final size:68
Alignment explanation
Indices: 7580--7801 Score: 176
Period size: 68 Copynumber: 3.3 Consensus size: 68
7570 AATAAATGGG
* * *
7580 TTTATGGAAGAAAAAGAAAG-GTTTTTATGGAAGAAGAAGAAGAAATGTGTTTATGGAAGAAAAA
1 TTTATGGAAGAAAAAGAAAGTG-GTTTAT-G-A-AAGAAGAAGAAACGAGTTTATGGAAGAAAAA
7644 CATATGT
62 CATATGT
* *
7651 TTTATGGAAGAATAAGAAAGTGGTTTATGAAAGAAGAATAAACGAGTTTATGGAAGAAAAAGCA-
1 TTTATGGAAGAAAAAGAAAGTGGTTTATGAAAGAAGAAGAAACGAGTTTATGGAAGAAAAA-CAT
* *
7715 ACGAG
65 ATG-T
* * * *
7720 TTTATGGAA-AAAGAAGCAA-TGAGCTTATGGAAGAAGAAGAAA--ATGTTTATGGAGGAAGAAA
1 TTTATGGAAGAAA-AAGAAAGTG-GTTTATGAAAGAAGAAGAAACGA-GTTTATGGAAGAA-AAA
7781 -A-ATG-
62 CATATGT
*
7785 -TTATGGAAGAAGAAGAA
1 TTTATGGAAGAAAAAGAA
7802 TGGTTCAGAA
Statistics
Matches: 127, Mismatches: 16, Indels: 23
0.77 0.10 0.14
Matches are distributed among these distances:
64 12 0.09
65 2 0.02
67 4 0.03
68 46 0.36
69 37 0.29
70 1 0.01
71 24 0.19
72 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.27, T:0.23
Consensus pattern (68 bp):
TTTATGGAAGAAAAAGAAAGTGGTTTATGAAAGAAGAAGAAACGAGTTTATGGAAGAAAAACATA
TGT
Found at i:7687 original size:48 final size:47
Alignment explanation
Indices: 7560--7708 Score: 123
Period size: 49 Copynumber: 3.1 Consensus size: 47
7550 GTTTATAGAA
* *
7560 GAAGAAGAAGAATAAATGGGTTTATGGAAGAA-AAA-GAAAGGTTTTTATG
1 GAAGAAGAAGAAGAAATGTGTTTATGGAAGAATAAACG--A-G-TTTTATG
*
7609 GAAGAAGAAGAAGAAATGTGTTTATGGAAGAA-AAACATATGTTTTATG
1 GAAGAAGAAGAAGAAATGTGTTTATGGAAGAATAAAC-GA-GTTTTATG
* *
7657 GAAGAATAAG-A-AAGTG-GTTTATGAAAGAAGAATAAACGAG-TTTATG
1 GAAGAAGAAGAAGAAATGTGTTTATG---GAAGAATAAACGAGTTTTATG
7703 GAAGAA
1 GAAGAA
7709 AAAGCAACGA
Statistics
Matches: 87, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
45 7 0.08
46 16 0.18
47 2 0.02
48 23 0.26
49 39 0.45
ACGTcount: A:0.48, C:0.01, G:0.27, T:0.24
Consensus pattern (47 bp):
GAAGAAGAAGAAGAAATGTGTTTATGGAAGAATAAACGAGTTTTATG
Found at i:7779 original size:19 final size:18
Alignment explanation
Indices: 7752--7803 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 18
7742 GCTTATGGAA
7752 GAAGAAGAAAATGTTTATG
1 GAAGAAGAAAATG-TTATG
*
7771 GAGGAAGAAAAATGTTATG
1 GAAGAAG-AAAATGTTATG
7790 GAAGAAGAAGAATG
1 GAAGAAGAA-AATG
7804 GTTCAGAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 2 0.07
19 21 0.72
20 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (18 bp):
GAAGAAGAAAATGTTATG
Found at i:7779 original size:117 final size:117
Alignment explanation
Indices: 7564--7772 Score: 275
Period size: 117 Copynumber: 1.8 Consensus size: 117
7554 ATAGAAGAAG
* * * ** *
7564 AAGAAGAATAAATGGGTTTATGGAAGAAAAAGAAAGGTTTTTATGGAAGAAGAAGAAGAAATGTG
1 AAGAAGAATAAACGAGTTTATGGAAGAAAAAGAAACGAGTTTATGGAAGAAGAAGAAGAAATGAG
* *
7629 TTTATGGAAGAAAAACATATGTTTTATGGAAGAATAAGAAAGTGGTTTATGA
66 CTTATGGAAGAAAAACAAATGTTTTATGGAAGAATAAGAAAGTGGTTTATGA
* *
7681 AAGAAGAATAAACGAGTTTATGGAAGAAAAAGCAACGAGTTTATGG-A-AA-AAGAAGCAATGAG
1 AAGAAGAATAAACGAGTTTATGGAAGAAAAAGAAACGAGTTTATGGAAGAAGAAGAAGAAATGAG
7743 CTTATGGAAGAAGAAGA-AAATG-TTTATGGA
66 CTTATGGAAGAA-AA-ACAAATGTTTTATGGA
7773 GGAAGAAAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
114 30 0.38
115 8 0.10
116 2 0.03
117 40 0.50
ACGTcount: A:0.47, C:0.03, G:0.26, T:0.23
Consensus pattern (117 bp):
AAGAAGAATAAACGAGTTTATGGAAGAAAAAGAAACGAGTTTATGGAAGAAGAAGAAGAAATGAG
CTTATGGAAGAAAAACAAATGTTTTATGGAAGAATAAGAAAGTGGTTTATGA
Found at i:9255 original size:22 final size:22
Alignment explanation
Indices: 9229--9270 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9219 AGTGCCTATA
9229 TTTTGTTATTT-CATAGTTTTTT
1 TTTTGTT-TTTGCATAGTTTTTT
*
9251 TTTTGTTTTTGCATCGTTTT
1 TTTTGTTTTTGCATAGTTTT
9271 GAGCTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.10, C:0.07, G:0.12, T:0.71
Consensus pattern (22 bp):
TTTTGTTTTTGCATAGTTTTTT
Found at i:13359 original size:31 final size:31
Alignment explanation
Indices: 13326--13547 Score: 390
Period size: 31 Copynumber: 7.2 Consensus size: 31
13316 GGTCACAATA
*
13326 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
13357 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
13388 CAAACTGTTCATATATGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
13419 TAAACTATTTATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
13450 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
13481 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
13512 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
13543 TAAAC
1 TAAAC
13548 CCTCGACTCT
Statistics
Matches: 182, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 182 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:13464 original size:15 final size:15
Alignment explanation
Indices: 13444--13527 Score: 50
Period size: 15 Copynumber: 5.5 Consensus size: 15
13434 TGCCTTTAAA
13444 CATATGTAAACTGTT
1 CATATGTAAACTGTT
**
13459 CATATGT-GCCT-TT
1 CATATGTAAACTGTT
13472 AAACATATGTAAACTGTT
1 ---CATATGTAAACTGTT
**
13490 CATATGT-GCCT-TT
1 CATATGTAAACTGTT
13503 AAACATATGTAAACTGTT
1 ---CATATGTAAACTGTT
13521 CATATGT
1 CATATGT
13528 GCCTTTAAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 21 0.41
16 14 0.27
17 4 0.08
18 4 0.08
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (15 bp):
CATATGTAAACTGTT
Found at i:15883 original size:31 final size:31
Alignment explanation
Indices: 15796--15926 Score: 142
Period size: 31 Copynumber: 4.2 Consensus size: 31
15786 AGAGTCGAGG
15796 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
15827 GAATTACCTATG-TCTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
* *
15859 GTATACCTATGTTCTAAGGAACATATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
15890 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
15921 GT-TACC
1 GTATACC
15927 AAGGATCTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
30 4 0.05
31 52 0.63
32 27 0.33
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:15954 original size:30 final size:30
Alignment explanation
Indices: 15910--15980 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
15900 GTTCTTCGGA
* *
15910 ACCTATGGACAGTTACCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
* *
15940 ACCTCTGGATAGTTATCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATCTTTATG
15970 ACCTCTGGATA
1 ACCTCTGGATA
15981 TGTCCTTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATCTTTATG
Found at i:17125 original size:64 final size:65
Alignment explanation
Indices: 17017--17194 Score: 225
Period size: 64 Copynumber: 2.8 Consensus size: 65
17007 TAATGAAGGT
* * ** * **
17017 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-AATATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
* ** * *
17081 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
*
17145 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTA
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTA
17195 TTTATTTTAA
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
63 1 0.01
64 96 0.99
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
Found at i:17214 original size:64 final size:64
Alignment explanation
Indices: 17080--17241 Score: 211
Period size: 64 Copynumber: 2.5 Consensus size: 64
17070 ATATTGCTGG
* * *
17080 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
** *
17144 GATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGA
** *
17207 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
17242 ATTCAAACAA
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 2 0.02
64 79 0.92
65 5 0.06
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
Found at i:20334 original size:31 final size:31
Alignment explanation
Indices: 20299--20551 Score: 443
Period size: 31 Copynumber: 8.2 Consensus size: 31
20289 GGTCACAATA
20299 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
20330 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
20361 CAAACTGTTTATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
20392 TAAACTGTTTATATGTGCCTTTAAATATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
20423 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
20454 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
20485 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
20516 TAAACTGTTCATATGTTCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
20547 TAAAC
1 TAAAC
20552 CCTCGACTCT
Statistics
Matches: 211, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 211 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:21173 original size:64 final size:65
Alignment explanation
Indices: 21061--21238 Score: 207
Period size: 64 Copynumber: 2.8 Consensus size: 65
21051 TAATGAAGGT
* * ** * * **
21061 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTTGATGTAGT-AATATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
* ** * *
21125 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
* *
21189 ATGCATCGATGCACTACTTATCCATCGATGCATGAATTGCATTCGATGTA
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTA
21239 TTTATTTTAA
Statistics
Matches: 95, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
63 1 0.01
64 94 0.99
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGGG
Found at i:21258 original size:64 final size:64
Alignment explanation
Indices: 21124--21269 Score: 197
Period size: 64 Copynumber: 2.3 Consensus size: 64
21114 ATATTGCTGG
* * * *
21124 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGG
1 GATGCATCGATGCACTACTTATCCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
** *
21188 GATGCATCGATGCACTACTTATCCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAAA-A
1 GATGCATCGATGCACTACTTATCCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGA
21251 GAGTGCATCGATGCACTAC
1 GA-TGCATCGATGCACTAC
21270 CAATGCATCG
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
63 2 0.03
64 66 0.90
65 5 0.07
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATCCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
Found at i:26738 original size:12 final size:12
Alignment explanation
Indices: 26723--26752 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
26713 TTATTTAAAA
*
26723 GGGTATCGGGTC
1 GGGTATCGGGCC
26735 GGGTATCGGGCC
1 GGGTATCGGGCC
26747 GGGTAT
1 GGGTAT
26753 ATATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.17, G:0.50, T:0.23
Consensus pattern (12 bp):
GGGTATCGGGCC
Found at i:26823 original size:2 final size:2
Alignment explanation
Indices: 26816--26853 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
26806 TTATTAAATT
26816 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
26854 ATTTTTTTAA
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):
TA
Found at i:29479 original size:3 final size:3
Alignment explanation
Indices: 29465--29522 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
29455 TTTGCTCCTA
* *
29465 ATG ATT ATG ATG ATG ATA ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
29513 ATG ATG ATG A
1 ATG ATG ATG A
29523 GAGTGAGGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:29749 original size:25 final size:24
Alignment explanation
Indices: 29667--29749 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 24
29657 ATCAATTGTA
* *
29667 AATTTTTTATTTATTTTG-TTTCTT
1 AATTTTTTA-TTATTTAGTTTTTTT
* * * *
29691 AATTTTTTTATTACTTAATTGTTTG
1 AA-TTTTTTATTATTTAGTTTTTTT
29716 AATTGTTTTATTATTTAGTTCTTTTT
1 AATT-TTTTATTATTTAGTT-TTTTT
29742 AATTTTTT
1 AATTTTTT
29750 TGTTGTATCA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
24 9 0.20
25 29 0.64
26 7 0.16
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (24 bp):
AATTTTTTATTATTTAGTTTTTTT
Found at i:30204 original size:24 final size:20
Alignment explanation
Indices: 30177--30234 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
30167 ACACGGGTAC
30177 TGCATCGATGCACGTGCTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
30201 TGCATCGATGCACTGTTGAA
1 TGCATCGATGCACTGTAGAA
30221 TGCATCGATGCACT
1 TGCATCGATGCACT
30235 TCAAGGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:31376 original size:30 final size:30
Alignment explanation
Indices: 31315--31443 Score: 177
Period size: 30 Copynumber: 4.3 Consensus size: 30
31305 CTAAGGAACA
* * ***
31315 TATGGATAGTTTACCTAGGTTCTTCGGGACC
1 TATGGATAG-TTACCGAGGATCTTTATGACC
31346 TATGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
31376 TATGGATAGTTACCGTGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
31406 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
31436 TCTGGATA
1 TATGGATA
31444 AGTCATTCGG
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
30 81 0.90
31 9 0.10
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGATCTTTATGACC
Found at i:34968 original size:64 final size:63
Alignment explanation
Indices: 34854--34976 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 63
34844 ATGCACAGAA
* *
34854 AGTGCATCGATGCACCTATTAAAATAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG
1 AGTGCATCGATGCACCCATTAAAATAGAAACATCGAAGGCAATTGGTGCATCGATGCATAAGG
* ** *
34917 AGTGCATCGATGCATCCCCTTAAAAT-GAAAACATCGAAGGTGATTTGTGCATCGATGCAT
1 AGTGCATCGATGCA-CCCATTAAAATAG-AAACATCGAAGGCAATTGGTGCATCGATGCAT
34977 GGGTACTACA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 15 0.29
64 37 0.71
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (63 bp):
AGTGCATCGATGCACCCATTAAAATAGAAACATCGAAGGCAATTGGTGCATCGATGCATAAGG
Found at i:34989 original size:64 final size:63
Alignment explanation
Indices: 34858--34995 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 63
34848 ACAGAAAGTG
* * * *
34858 CATCGATGCACCTATTAAAATAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGGAGTG
1 CATCGATGCACCCATTAAAATAGAAACATCGAAGGCAATTGGTGCATCGATGCATAAGGACTA
* ** * *
34921 CATCGATGCATCCCCTTAAAAT-GAAAACATCGAAGGTGATTTGTGCATCGATGCAT-GGGTACT
1 CATCGATGCA-CCCATTAAAATAG-AAACATCGAAGGCAATTGGTGCATCGATGCATAAGG-ACT
34984 A
63 A
34985 CATCGATGCAC
1 CATCGATGCAC
34996 ATGCTAAAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
63 14 0.22
64 49 0.78
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (63 bp):
CATCGATGCACCCATTAAAATAGAAACATCGAAGGCAATTGGTGCATCGATGCATAAGGACTA
Found at i:35012 original size:24 final size:20
Alignment explanation
Indices: 35003--35040 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34993 CACATGCTAA
35003 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
35023 TGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
35041 TCAAGGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:35782 original size:2 final size:2
Alignment explanation
Indices: 35775--35845 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
35765 AGTATACGTG
35775 AT AT 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 AT AT
*
35817 AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35846 AGTTATTGGA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:36227 original size:30 final size:30
Alignment explanation
Indices: 36166--36294 Score: 150
Period size: 30 Copynumber: 4.3 Consensus size: 30
36156 CTAAGGAACA
* * ***
36166 TATGGATAGTTTACCTAGGTTCTTCGGGACC
1 TATGGATA-TTTACCGAGGATCTTTATGACC
*
36197 TATGGATATTTACCCAGGATCTTTATGACC
1 TATGGATATTTACCGAGGATCTTTATGACC
*
36227 TATGGATAATTACCGAGGATCTTTATGACC
1 TATGGATATTTACCGAGGATCTTTATGACC
* * *
36257 TCTGAATAGTTACCGAGGATCTTTATGACC
1 TATGGATATTTACCGAGGATCTTTATGACC
*
36287 TCTGGATA
1 TATGGATA
36295 GGTCATTCGG
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
30 79 0.91
31 8 0.09
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (30 bp):
TATGGATATTTACCGAGGATCTTTATGACC
Found at i:38239 original size:60 final size:59
Alignment explanation
Indices: 38143--38260 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 59
38133 CTCTACAATG
* * * *
38143 TCGACATTTAGGTCGAACAAGCTGGTAGTTGCATGTCTTTCCCTT-GAACTTGAAGGCATA
1 TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGTC--TCCCTTAGAACTTGAAGGCATA
* *
38203 TCGACATTGAGGTCGAAGAAGCTCGCAGTTGAATGTCTCCCTTAGAGCTTGAAGGCAT
1 TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGTCTCCCTTAGAACTTGAAGGCAT
38261 CGTGTCAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 6 0.12
59 13 0.25
60 32 0.63
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (59 bp):
TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGTCTCCCTTAGAACTTGAAGGCATA
Found at i:39269 original size:23 final size:24
Alignment explanation
Indices: 39212--39277 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
39202 ACATTACAAT
39212 AAAAATAGAAGGAATTGATGAAGC
1 AAAAATAGAAGGAATTGATGAAGC
*
39236 AAAAATTGAAGGAATTGATGAAG-
1 AAAAATAGAAGGAATTGATGAAGC
*
39259 TAAAATAGAAGGAATTGAT
1 AAAAATAGAAGGAATTGAT
39278 TTGATGATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 17 0.44
24 22 0.56
ACGTcount: A:0.53, C:0.02, G:0.24, T:0.21
Consensus pattern (24 bp):
AAAAATAGAAGGAATTGATGAAGC
Found at i:50564 original size:16 final size:16
Alignment explanation
Indices: 50543--50581 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
50533 GGTGATGCAT
50543 TATTAAATCTCTCAAC
1 TATTAAATCTCTCAAC
50559 TATTAAATCTCTCAAC
1 TATTAAATCTCTCAAC
50575 TATTAAA
1 TATTAAA
50582 AGTTATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (16 bp):
TATTAAATCTCTCAAC
Found at i:54806 original size:33 final size:33
Alignment explanation
Indices: 54725--54786 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
54715 TATTTCAGAT
*
54725 TTTCAGTTCTTTTTTTCCCCTCGTCTTTTTCAG
1 TTTCAGTTCTTTTTTTCCCCTAGTCTTTTTCAG
54758 TTTCAGTTCTTTTTTT-CCCTAGTCTTTTT
1 TTTCAGTTCTTTTTTTCCCCTAGTCTTTTT
54787 AGTACTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.06, C:0.24, G:0.08, T:0.61
Consensus pattern (33 bp):
TTTCAGTTCTTTTTTTCCCCTAGTCTTTTTCAG
Found at i:59775 original size:21 final size:22
Alignment explanation
Indices: 59738--59784 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
59728 ATTTTTCAAA
59738 ATAT-ATTTATTATATTTATAT
1 ATATAATTTATTATATTTATAT
59759 ATATAATTTATTA-ATTTATAT
1 ATATAATTTATTATATTTATAT
59780 ATATA
1 ATATA
59785 TATATAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATAATTTATTATATTTATAT
Found at i:59800 original size:27 final size:27
Alignment explanation
Indices: 59747--59801 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
59737 AATATATTTA
* * *
59747 TTATATTTATATATATAATTTATTAAT
1 TTATATATATATATATAATTCACTAAT
59774 TTATATATATATATATAA-TCACCTAAT
1 TTATATATATATATATAATTCA-CTAAT
59801 T
1 T
59802 CATGAGATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATATATATATATATAATTCACTAAT
Found at i:68867 original size:14 final size:15
Alignment explanation
Indices: 68850--68878 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
68840 TTTATTGTGT
68850 TATATT-TTCATTTA
1 TATATTATTCATTTA
68864 TATATTATTCATTTA
1 TATATTATTCATTTA
68879 ATCAGGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTATTCATTTA
Found at i:72008 original size:13 final size:13
Alignment explanation
Indices: 71990--72015 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71980 CAAAAAGTAT
71990 TAAATGGTAAATG
1 TAAATGGTAAATG
72003 TAAATGGTAAATG
1 TAAATGGTAAATG
72016 ATAACCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
TAAATGGTAAATG
Found at i:74358 original size:21 final size:19
Alignment explanation
Indices: 74334--74385 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
74324 AATTAAATAC
*
74334 AATAAATAATTTAAATACTTA
1 AATAAATAATATAAATA--TA
74355 AATAAACTAAATATAAATATA
1 AATAAA-T-AATATAAATATA
74376 AATATAATAA
1 AATA-AATAA
74386 AATATACCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 2 0.07
21 13 0.48
22 3 0.11
23 9 0.33
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAAATAATATAAATATA
Done.