Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003962.1 Hibiscus syriacus cultivar Beakdansim tig00008578_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: 50918
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:3054 original size:4 final size:5
Alignment explanation
Indices: 3028--3065 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
3018 AAAACAATAA
3028 AAATT AAATT AAAGTT AAATT -AATT AAATT AAATT AAA
1 AAATT AAATT AAA-TT AAATT AAATT AAATT AAATT AAA
3066 AAAAATAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.13
5 22 0.71
6 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:4404 original size:12 final size:13
Alignment explanation
Indices: 4371--4408 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
4361 AAACAAACAA
*
4371 ATAAATAAATATAT
1 ATAAA-AAATATAC
4385 ATAAAAAATATAC
1 ATAAAAAATATAC
4398 A-AAAAAATATA
1 ATAAAAAATATA
4409 TTTCGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 8 0.35
14 5 0.22
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAAAAATATAC
Found at i:4582 original size:38 final size:37
Alignment explanation
Indices: 4440--4798 Score: 359
Period size: 38 Copynumber: 9.8 Consensus size: 37
4430 CCTATATATC
* *
4440 AAACTATATATTATATAAATTTTCAAAAACGTTTT-A
1 AAACTATATATTATATATATTTTCAAAAATGTTTTCA
* ** *
4476 AAACTATGTATTATAT-T-TTTTTGAAAATG-TTTCC
1 AAACTATATATTATATATATTTTCAAAAATGTTTTCA
4510 AAACTATATA-T-TATATATTTTCAAAAATGTTTTTCA
1 AAACTATATATTATATATATTTTCAAAAATG-TTTTCA
* *
4546 AAACTAAATATTATATATTTGATTTC-AAAATGTTTTCA
1 AAACTATATATTATATATAT--TTTCAAAAATGTTTTCA
*
4584 AAACTATATATTATATATATTTTCAAAAAAATGTATTCA
1 AAACTATATATTATATATATTTTC--AAAAATGTTTTCA
*
4623 AAACCATATATTATATATATATATTC-AAAATGTTTTCA
1 AAACTATATATTATATATAT-T-TTCAAAAATGTTTTCA
4661 AAACTATATATTATATATATTTTCAAAAAATGTTTTCA
1 AAACTATATATTATATATATTTTC-AAAAATGTTTTCA
* *
4699 AAACTAT-TAATTATATGTATTTTCAAAATTGTTTTCA
1 AAACTATAT-ATTATATATATTTTCAAAAATGTTTTCA
* * * *
4736 AAA-T-TATATAATATATGTTTT-TAAATTGTATTTTCA
1 AAACTATATATTATATATATTTTCAAAAATG--TTTTCA
* *
4772 AAAC--CATATTACATATATTTTCAAAAA
1 AAACTATATATTATATATATTTTCAAAAA
4799 CTGATCATTT
Statistics
Matches: 271, Mismatches: 30, Indels: 43
0.79 0.09 0.12
Matches are distributed among these distances:
32 3 0.01
33 5 0.02
34 34 0.13
35 12 0.04
36 59 0.22
37 21 0.08
38 93 0.34
39 36 0.13
40 5 0.02
41 3 0.01
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (37 bp):
AAACTATATATTATATATATTTTCAAAAATGTTTTCA
Found at i:4637 original size:77 final size:74
Alignment explanation
Indices: 4440--4751 Score: 379
Period size: 77 Copynumber: 4.2 Consensus size: 74
4430 CCTATATATC
* * * *
4440 AAACTATATATTATATAAATTTTCAAAAACGTTTT-AAAACTATGTATTATAT-TTT-TTTGAAA
1 AAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATTTATTTCAAA
*
4502 ATG-TTTCC
66 ATGTTTTCA
*
4510 AAACTATATA-T-TATATATTTTCAAAAATGTTTTTCAAAACTAAATATTATATATTTGATTTCA
1 AAACTATATATTATATATATTTTCAAAAATG-TTTTCAAAACTATATATTATATATTT-ATTTCA
4573 AAATGTTTTCA
64 AAATGTTTTCA
* * *
4584 AAACTATATATTATATATATTTTCAAAAAAATGTATTCAAAACCATATATTATATATATATATTC
1 AAACTATATATTATATATATTTTC--AAAAATGTTTTCAAAACTATATATTATATATTTAT-TTC
4649 AAAATGTTTTCA
63 AAAATGTTTTCA
* *
4661 AAACTATATATTATATATATTTTCAAAAAATGTTTTCAAAACTAT-TAAT-TATATGTATTTTCA
1 AAACTATATATTATATATATTTTC-AAAAATGTTTTCAAAACTATATATTATATATTTA-TTTCA
4724 AAATTGTTTTCA
64 AAA-TGTTTTCA
* *
4736 AAATTATATAATATAT
1 AAACTATATATTATAT
4752 GTTTTTAAAT
Statistics
Matches: 213, Mismatches: 16, Indels: 21
0.85 0.06 0.08
Matches are distributed among these distances:
68 16 0.08
69 5 0.02
70 25 0.12
71 3 0.01
73 9 0.04
74 28 0.13
75 27 0.13
76 32 0.15
77 61 0.29
78 7 0.03
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (74 bp):
AAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATTTATTTCAAA
ATGTTTTCA
Found at i:11631 original size:5 final size:5
Alignment explanation
Indices: 11621--11679 Score: 50
Period size: 5 Copynumber: 12.0 Consensus size: 5
11611 TGAGGGTTAG
* * * *
11621 AATAA AATAA AA-AA AATTA AATTA AATTA AATAA AAGTAA AAT-A AATGA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA-TAA AATAA AATAA
*
11670 AGTAA AATAA
1 AATAA AATAA
11680 CATTCAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
4 8 0.17
5 33 0.72
6 5 0.11
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (5 bp):
AATAA
Found at i:11652 original size:15 final size:15
Alignment explanation
Indices: 11621--11679 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 15
11611 TGAGGGTTAG
*
11621 AATAAAA-TAAAAAA
1 AATAAAAGTAAAATA
* * *
11635 AATTAAATTAAATTA
1 AATAAAAGTAAAATA
11650 AATAAAAGTAAAATA
1 AATAAAAGTAAAATA
*
11665 AAT-GAAGTAAAATA
1 AATAAAAGTAAAATA
11679 A
1 A
11680 CATTCAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
14 17 0.46
15 20 0.54
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (15 bp):
AATAAAAGTAAAATA
Found at i:13105 original size:36 final size:37
Alignment explanation
Indices: 13063--13231 Score: 247
Period size: 36 Copynumber: 4.6 Consensus size: 37
13053 CCTATATATC
*
13063 AAACTATATATTATATATATTTTCAAAAACGTTTT-A
1 AAACTATATATTATATATATTTTCAAAAATGTTTTCA
* *
13099 AAACTATATATTATATATTTTTTGAAAAATGTTTTCA
1 AAACTATATATTATATATATTTTCAAAAATGTTTTCA
13136 AAACTATATATTATATATATTTT--AAAATGTTTTCA
1 AAACTATATATTATATATATTTTCAAAAATGTTTTCA
* *
13171 AAACTATATTATATATATATATATTC-AAAATATTTTCA
1 AAACTATA-TAT-TATATATATTTTCAAAAATGTTTTCA
13209 AAACTATATATTATATATATTTT
1 AAACTATATATTATATATATTTT
13232 TTAAAAAAAA
Statistics
Matches: 122, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
35 20 0.16
36 46 0.38
37 37 0.30
38 19 0.16
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (37 bp):
AAACTATATATTATATATATTTTCAAAAATGTTTTCA
Found at i:13142 original size:73 final size:73
Alignment explanation
Indices: 13063--13231 Score: 245
Period size: 73 Copynumber: 2.3 Consensus size: 73
13053 CCTATATATC
* *
13063 AAACTATATATTATATATATTTTCAAAAACGTTTT-AAAACTATA-TAT-TATATATTTTTTGAA
1 AAACTATATATTATATATATTTT--AAAACGTTTTCAAAACTATATTATATATATATATATT-AA
*
13125 AAATGTTTTCA
63 AAATATTTTCA
* *
13136 AAACTATATATTATATATATTTTAAAATGTTTTCAAAACTATATTATATATATATATATTCAAAA
1 AAACTATATATTATATATATTTTAAAACGTTTTCAAAACTATATTATATATATATATATTAAAAA
13201 TATTTTCA
66 TATTTTCA
13209 AAACTATATATTATATATATTTT
1 AAACTATATATTATATATATTTT
13232 TTAAAAAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
71 9 0.10
72 9 0.10
73 60 0.68
74 10 0.11
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (73 bp):
AAACTATATATTATATATATTTTAAAACGTTTTCAAAACTATATTATATATATATATATTAAAAA
TATTTTCA
Found at i:13260 original size:73 final size:73
Alignment explanation
Indices: 13063--13261 Score: 233
Period size: 73 Copynumber: 2.7 Consensus size: 73
13053 CCTATATATC
* * * * *
13063 AAACTATATATTATATATATTTTCAAAAACGTTTTAAAACTATATATTATATATTTTTTGAAAAA
1 AAACTATATATTATATATATTTTTAAAAAAGTTTTAAAACTATATAATATATATATATTGAAAAA
*
13128 TGTTTTCA
66 TATTTTCA
* *
13136 AAACTATATATTATATATA-TTTT-AAAATGTTTTCAAAACTATATTATATATATATATATT-CA
1 AAACTATATATTATATATATTTTTAAAAAAGTTTT-AAAACTATA-TA-ATATATATATATTGAA
13198 AAATATTTTCA
63 AAATATTTTCA
*** *
13209 AAACTATATATTATATATATTTTTTAAAAAAAAATTAAAATTATATAATATAT
1 AAACTATATATTATATATA-TTTTTAAAAAAGTTTTAAAACTATATAATATAT
13262 GTTTTTAAAT
Statistics
Matches: 108, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
71 9 0.08
72 12 0.11
73 57 0.53
74 12 0.11
75 12 0.11
76 6 0.06
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.46
Consensus pattern (73 bp):
AAACTATATATTATATATATTTTTAAAAAAGTTTTAAAACTATATAATATATATATATTGAAAAA
TATTTTCA
Found at i:14566 original size:13 final size:14
Alignment explanation
Indices: 14548--14580 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
14538 TGCATGCTTA
14548 TATTTT-AAAAAAT
1 TATTTTAAAAAAAT
14561 TATTTTAAAAAAAT
1 TATTTTAAAAAAAT
14575 TATTTT
1 TATTTT
14581 TATTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTTTAAAAAAAT
Found at i:17841 original size:23 final size:22
Alignment explanation
Indices: 17814--17857 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17804 TTGAGTCTCC
*
17814 TTACATCCAATTGTCTAGATTAT
1 TTACAT-CAATGGTCTAGATTAT
*
17837 TTACATCGATGGTCTAGATTA
1 TTACATCAATGGTCTAGATTA
17858 AAAATATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (22 bp):
TTACATCAATGGTCTAGATTAT
Found at i:18563 original size:44 final size:44
Alignment explanation
Indices: 18514--18906 Score: 326
Period size: 44 Copynumber: 8.9 Consensus size: 44
18504 TTCTTCATAC
* * *
18514 GACTCCCCTTCGTGGGTTTAAGCCATGTTAAGGATTCTTTGGAT
1 GACTCCCCTTCGTGGGTTTAAGCCAAGTAAATGATTCTTTGGAT
* ** * *
18558 GACTCCCCTTCGTAGGTTTAAGTTAGGTGAAATGATTCTTTAGAT
1 GACTCCCCTTCGTGGGTTTAAGCCAAGT-AAATGATTCTTTGGAT
* * * *
18603 GACTCCCCCTCGTTGGTTTAAGCCAGGTGAA-GAATTCTTTGGAT
1 GACTCCCCTTCGTGGGTTTAAGCCAAGTAAATG-ATTCTTTGGAT
* * * *
18647 GACTCCCTTTCGTGGGTTTAAGTCAAGTGAAATGATTATTTGGAA
1 GACTCCCCTTCGTGGGTTTAAGCCAAGT-AAATGATTCTTTGGAT
* ** ** * * * *
18692 GACT-CCCTTCATTAGTTTAAGTTAGGCGAAATGATTCTTTAGAA
1 GACTCCCCTTCGTGGGTTTAAGCCAAG-TAAATGATTCTTTGGAT
* * * *
18736 GACTCCCCTTCGCGGGTTTAAGTCAAGTGAGTGATTCTTTGGAT
1 GACTCCCCTTCGTGGGTTTAAGCCAAGTAAATGATTCTTTGGAT
* * * *
18780 GACTTCTCTTCGCGGGTTTAAGCCAAGTAAAATG-TTCTTTAGAT
1 GACTCCCCTTCGTGGGTTTAAGCCAAGT-AAATGATTCTTTGGAT
* * * * *
18824 GACTCCCCTTAGAGGGTTTAAGGCAGGTGAATGATTCTTTGGAT
1 GACTCCCCTTCGTGGGTTTAAGCCAAGTAAATGATTCTTTGGAT
* * * *
18868 GACTCTCATTCGCGGGTTTAACCCAAGTGAAA-GATTCTT
1 GACTCCCCTTCGTGGGTTTAAGCCAAGT-AAATGATTCTT
18907 CGAACGACTT
Statistics
Matches: 277, Mismatches: 63, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
43 5 0.02
44 198 0.71
45 73 0.26
46 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (44 bp):
GACTCCCCTTCGTGGGTTTAAGCCAAGTAAATGATTCTTTGGAT
Found at i:18586 original size:89 final size:89
Alignment explanation
Indices: 18486--18862 Score: 300
Period size: 89 Copynumber: 4.3 Consensus size: 89
18476 CTTCGCGAGC
* * * * *
18486 TTAAGTCAGGTGAAATGATTCTTCATACGACTCCCCTTCGTGGGTTTAAGCCATGTTAAGGATTC
1 TTAAGTCAGGTGAAATGATTCTTCAGACGACTCCCCCTCGTGGGTTTAAGCCAGGTGAAGAATTC
18551 TTTGGATGACTCCCCTTCGTAGGT
66 TTTGGATGACTCCCCTTCGTAGGT
* * * *
18575 TTAAGTTAGGTGAAATGATTCTTTAGATGACTCCCCCTCGTTGGTTTAAGCCAGGTGAAGAATTC
1 TTAAGTCAGGTGAAATGATTCTTCAGACGACTCCCCCTCGTGGGTTTAAGCCAGGTGAAGAATTC
* *
18640 TTTGGATGACTCCCTTTCGTGGGT
66 TTTGGATGACTCCCCTTCGTAGGT
* * ** * * * ** ** *
18664 TTAAGTCAAGTGAAATGATTATTTGGAAGACT-CCCTTCATTAGTTTAAGTTAGGCGAA-ATGAT
1 TTAAGTCAGGTGAAATGATTCTTCAGACGACTCCCCCTCGTGGGTTTAAGCCAGGTGAAGA--AT
* * **
18727 TCTTTAGAAGACTCCCCTTCGCGGGT
64 TCTTTGGATGACTCCCCTTCGTAGGT
* * ** * * * * * *
18753 TTAAGTCAAGTG-AGTGATTCTTTGGATGACTTCTCTTCGCGGGTTTAAGCCAAGT-AA-AATGT
1 TTAAGTCAGGTGAAATGATTCTTCAGACGACTCCCCCTCGTGGGTTTAAGCCAGGTGAAGAA--T
* *
18815 TCTTTAGATGACTCCCCTTAG-AGGGT
64 TCTTTGGATGACTCCCCTTCGTA-GGT
*
18841 TTAAGGCAGGTG-AATGATTCTT
1 TTAAGTCAGGTGAAATGATTCTT
18863 TGGATGACTC
Statistics
Matches: 238, Mismatches: 44, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
86 1 0.00
87 1 0.00
88 81 0.34
89 155 0.65
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (89 bp):
TTAAGTCAGGTGAAATGATTCTTCAGACGACTCCCCCTCGTGGGTTTAAGCCAGGTGAAGAATTC
TTTGGATGACTCCCCTTCGTAGGT
Found at i:18712 original size:133 final size:133
Alignment explanation
Indices: 18514--18897 Score: 422
Period size: 133 Copynumber: 2.9 Consensus size: 133
18504 TTCTTCATAC
* * * * *
18514 GACTCCCCTTCGTGGGTTTAAGCCATGTTAAGGATTCTTTGGATGACTCCCCTTCGTAGGTTTAA
1 GACTCCCTTTCGTGGGTTTAAGCCAAGTAAATGATTCTTTGGATGACTCCCCTTCATAGGTTTAA
** *
18579 GTTAGGTGAAATGATTCTTTAGATGACTCCCCCTCGTTGGTTTAAGCCAGGTGAAG-AATTCTTT
66 GTTAGGTGAAATGATTCTTTAGATGACTCCCCCTCGCGGGTTTAAGCCAAGTG-AGTAATTCTTT
18643 GGAT
130 GGAT
* * *
18647 GACTCCCTTTCGTGGGTTTAAGTCAAGTGAAATGATTATTTGGAAGACT-CCCTTCATTA-GTTT
1 GACTCCCTTTCGTGGGTTTAAGCCAAGT-AAATGATTCTTTGGATGACTCCCCTTCA-TAGGTTT
* * * * *
18710 AAGTTAGGCGAAATGATTCTTTAGAAGACTCCCCTTCGCGGGTTTAAGTCAAGTGAGTGATTCTT
64 AAGTTAGGTGAAATGATTCTTTAGATGACTCCCCCTCGCGGGTTTAAGCCAAGTGAGTAATTCTT
18775 TGGAT
129 TGGAT
* * * *
18780 GACT-TCTCTTCGCGGGTTTAAGCCAAGTAAAATG-TTCTTTAGATGACTCCCCTT-AGAGGGTT
1 GACTCCCT-TTCGTGGGTTTAAGCCAAGT-AAATGATTCTTTGGATGACTCCCCTTCATA-GGTT
** * * ** *
18842 TAAGGCAGGTG-AATGATTCTTTGGATGACTCTCATTCGCGGGTTTAACCCAAGTGA
63 TAAGTTAGGTGAAATGATTCTTTAGATGACTCCCCCTCGCGGGTTTAAGCCAAGTGA
18898 AAGATTCTTC
Statistics
Matches: 211, Mismatches: 33, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
131 1 0.00
132 55 0.26
133 137 0.65
134 18 0.09
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (133 bp):
GACTCCCTTTCGTGGGTTTAAGCCAAGTAAATGATTCTTTGGATGACTCCCCTTCATAGGTTTAA
GTTAGGTGAAATGATTCTTTAGATGACTCCCCCTCGCGGGTTTAAGCCAAGTGAGTAATTCTTTG
GAT
Found at i:22108 original size:2 final size:2
Alignment explanation
Indices: 22103--22129 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22093 GAAGCAAATA
22103 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
22130 CACACACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25524 original size:23 final size:22
Alignment explanation
Indices: 25497--25540 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25487 TTAAGCCTCC
*
25497 TTACATCTAATGGTTTAGATTAT
1 TTACATC-AACGGTTTAGATTAT
*
25520 TTACATCGACGGTTTAGATTA
1 TTACATCAACGGTTTAGATTA
25541 AAATCATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (22 bp):
TTACATCAACGGTTTAGATTAT
Found at i:27366 original size:22 final size:21
Alignment explanation
Indices: 27340--27382 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
27330 AAAAAATATA
27340 TAACAATGACTAAATTAGAAAC
1 TAACAATGACTAAATTA-AAAC
*
27362 TAACAGTGACTAAATTAAAAC
1 TAACAATGACTAAATTAAAAC
27383 AAAACAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.23
Consensus pattern (21 bp):
TAACAATGACTAAATTAAAAC
Found at i:29791 original size:59 final size:59
Alignment explanation
Indices: 29669--29806 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 59
29659 AGAAAAAAAC
* * *
29669 ATAATTTTAAGATTTATTTTGATGAAAAATAATTTAACTACCTAAAATAATTACATATA
1 ATAATTTAAAGATTTATTTTAATGAAAAATAATTTAACAACCTAAAATAATTACATATA
* * * * *
29728 ATAATTTAAAGATTTATTTTAACT-AAAAATAATTTAAGAACTTAAAGTAA-TATATTTA
1 ATAATTTAAAGATTTATTTTAA-TGAAAAATAATTTAACAACCTAAAATAATTACATATA
* *
29786 TATAATTTAAATACTTATTTT
1 -ATAATTTAAAGATTTATTTT
29807 TAGTTTAAGC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 6 0.09
59 60 0.90
60 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (59 bp):
ATAATTTAAAGATTTATTTTAATGAAAAATAATTTAACAACCTAAAATAATTACATATA
Found at i:34446 original size:39 final size:39
Alignment explanation
Indices: 34392--34523 Score: 228
Period size: 39 Copynumber: 3.4 Consensus size: 39
34382 ATCGATTAAA
*
34392 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAG
1 CACTTCGGTGCATATGGTGGCCACGACCTTATGTGTAAG
34431 CACTTCGGTGCATATGGTGGCCACGACCTTATGTGTAAG
1 CACTTCGGTGCATATGGTGGCCACGACCTTATGTGTAAG
*
34470 CACTTCGGTGCATATGGTGGCCACGACCTTATATGTAAG
1 CACTTCGGTGCATATGGTGGCCACGACCTTATGTGTAAG
* *
34509 CACTACGATGCATAT
1 CACTTCGGTGCATAT
34524 ATTTGACTCG
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.28
Consensus pattern (39 bp):
CACTTCGGTGCATATGGTGGCCACGACCTTATGTGTAAG
Found at i:36417 original size:2 final size:2
Alignment explanation
Indices: 36410--36434 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36400 ATTTCCAAGG
36410 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
36435 GTCACACCCC
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:37148 original size:18 final size:19
Alignment explanation
Indices: 37125--37160 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
37115 GTCAAATGTT
*
37125 TTGTTT-GGTTGTTTTAAA
1 TTGTTTAGGTTGATTTAAA
37143 TTGTTTAGGTTGATTTAA
1 TTGTTTAGGTTGATTTAA
37161 TGGTTGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.58
Consensus pattern (19 bp):
TTGTTTAGGTTGATTTAAA
Found at i:41043 original size:2 final size:2
Alignment explanation
Indices: 41036--41067 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
41026 TTATTTAATA
41036 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41068 CTTATTTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41073 original size:15 final size:15
Alignment explanation
Indices: 41036--41067 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
41026 TTATTTAATA
41036 ATATATA-TATATAT
1 ATATATATTATATAT
41050 ATATATATTATATAT
1 ATATATATTATATAT
41065 ATA
1 ATA
41068 CTTATTTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATATTATATAT
Found at i:48972 original size:3 final size:3
Alignment explanation
Indices: 48964--48995 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
48954 GTAGATGTAT
48964 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
48996 TATATTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:49001 original size:9 final size:10
Alignment explanation
Indices: 48961--48998 Score: 51
Period size: 9 Copynumber: 3.7 Consensus size: 10
48951 TGAGTAGATG
48961 TATTTATTAT
1 TATTTATTAT
48971 TA-TTATTAT
1 TATTTATTAT
48980 TATTATTATTAT
1 TA-T-TTATTAT
48992 TATTTAT
1 TATTTAT
48999 ATTTAGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 9 0.36
10 6 0.24
11 1 0.04
12 9 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATTTATTAT
Found at i:50420 original size:2 final size:2
Alignment explanation
Indices: 50413--50463 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
50403 AAGGATATTA
50413 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
50455 AT AT AT AT A
1 AT AT AT AT A
50464 ATCATTTTAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.