Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004825.1 Hibiscus syriacus cultivar Beakdansim tig00010870_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: 85672
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2271 original size:23 final size:23
Alignment explanation
Indices: 2208--2276 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
2198 CATTATTATA
2208 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * * *
2231 CGGCACTCCAGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
2254 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
2277 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:3409 original size:209 final size:208
Alignment explanation
Indices: 3048--3844 Score: 1091
Period size: 209 Copynumber: 3.8 Consensus size: 208
3038 TTTTTTCTCA
*
3048 ACTTATTACTTATTTATATTTATTAATTGGCCCATAACTTTTTAAA-TGAGTATAATTTAGTACA
1 ACTTATTACTTATTTCTATTT-TTAATTGGCCCATAACTTTTTAAATTG-GTATAATTTAGTACA
* *
3112 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTTGATTTGATCCCTTTTGTGTTGTATA
64 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTTTGTGTTGTTTA
*
3177 AAATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCA
129 ATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCA
**
3242 CCTGAAATTGACACAT
194 TATGAAATTGAC-CAT
* *
3258 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAAATTTTTAAATAGGTATAATTTAGTAC-T
1 ACTTATTACTTATTTCTATTTTT-AATTGGCCCATAACTTTTTAAATTGGTATAATTTAGTACAT
* *
3322 TTTTGTATTAATTTTAACCTCAAAATTTAAAATTATTTCGGTTTGATCCCTTTTGTGTTGTTTAA
65 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTTTGTGTTGTTTAA
*
3387 TATATTTAAATTTTTATTTGTAATTTCATATTTGTTTAATTTAGTCCTCCAAATTTTATTTGCAT
130 TATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCAT
3452 ATGAAATTGACCTAT
195 ATGAAATTGACC-AT
* * *
3467 ACTTATTACTTATTTCTATTTTTAAATTTGCCCATAACTTTTTAAATTGATATAATTTAGTACTT
1 ACTTATTACTTATTTCTATTTTT-AATTGGCCCATAACTTTTTAAATTGGTATAATTTAGTACAT
* * ** *** * *
3532 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCAT-CAATGTGT-G
65 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTTTGTGTTGTTTAA
* *
3595 T-TGTTT-AA--TTT-TTT-TAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCGT
130 TATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCAT
3654 ATGAAATTGATCCAT
195 ATGAAATTGA-CCAT
* **
3669 ACTTATTACTTGA-TT-T-TTTTTAATTGGCCCATAATTTTTTAAATTGGTATAATTTAGTATTT
1 ACTTATTACTT-ATTTCTATTTTTAATTGGCCCATAACTTTTTAAATTGGTATAATTTAGTACAT
* *
3731 TTTTGTATTAACTTCAACCTCATAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTT
65 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT--T---T-TGTGTT
3796 GTTTAATAT-TGTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
124 GTTTAATATAT-TTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
3845 ATTCTTAAAT
Statistics
Matches: 523, Mismatches: 43, Indels: 39
0.86 0.07 0.06
Matches are distributed among these distances:
199 85 0.16
200 5 0.01
201 1 0.00
202 68 0.13
203 6 0.01
204 3 0.01
205 1 0.00
206 6 0.01
207 6 0.01
208 5 0.01
209 203 0.39
210 104 0.20
211 4 0.01
212 3 0.01
213 23 0.04
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (208 bp):
ACTTATTACTTATTTCTATTTTTAATTGGCCCATAACTTTTTAAATTGGTATAATTTAGTACATT
TTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTTTTGTGTTGTTTAAT
ATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATA
TGAAATTGACCAT
Found at i:11414 original size:24 final size:24
Alignment explanation
Indices: 11352--11414 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
11342 CGTTCGTGAA
* *
11352 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTTGTTTATGTT
11376 CGTTCGATTATGTTTGTTTATGTT
1 CGTTCGATTATGTTTGTTTATGTT
*
11400 CTTTC-ATTTATGTTT
1 CGTTCGA-TTATGTTT
11415 AACCCAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (24 bp):
CGTTCGATTATGTTTGTTTATGTT
Found at i:12412 original size:10 final size:10
Alignment explanation
Indices: 12394--12468 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
12384 GGGTCTCCAA
*
12394 CGTTGATGTT
1 CGTTTATGTT
12404 CGTTTATGTT
1 CGTTTATGTT
12414 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
12425 ATGTTCATGTT
1 -CGTTTATGTT
12436 CGTTTATGTT
1 CGTTTATGTT
12446 CG----TGTT
1 CGTTTATGTT
12452 CGTTTATGTT
1 CGTTTATGTT
12462 CGTTTAT
1 CGTTTAT
12469 TTATTAAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 6 0.12
10 35 0.67
11 7 0.13
12 4 0.08
ACGTcount: A:0.11, C:0.12, G:0.21, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:12425 original size:16 final size:16
Alignment explanation
Indices: 12400--12464 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
12390 CCAACGTTGA
12400 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
12416 TGTTCATTTATGTTCA
1 TGTTCGTTTATGTTCG
12432 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
12448 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
12464 T
1 T
12465 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:12555 original size:16 final size:16
Alignment explanation
Indices: 12534--12566 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12524 AAAAAAATTT
12534 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
12550 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
12566 T
1 T
12567 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:13007 original size:9 final size:9
Alignment explanation
Indices: 12993--13022 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
12983 CATATACAGA
12993 CATTAATAT
1 CATTAATAT
13002 CATTAATAT
1 CATTAATAT
13011 CATTAATAT
1 CATTAATAT
13020 CAT
1 CAT
13023 ATGCGCGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (9 bp):
CATTAATAT
Found at i:17637 original size:1 final size:1
Alignment explanation
Indices: 17631--17657 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
17621 GAGAGTAGAA
17631 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
17658 AAAGGATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:24481 original size:16 final size:16
Alignment explanation
Indices: 24456--24498 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
24446 ATTGAAACTT
* * *
24456 GAACTAAAAAAGGATC
1 GAACTCAAAAAGCATA
24472 GAACTCAAAAAGCATA
1 GAACTCAAAAAGCATA
*
24488 GAATTCAAAAA
1 GAACTCAAAAA
24499 AAAAATTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (16 bp):
GAACTCAAAAAGCATA
Found at i:43026 original size:42 final size:42
Alignment explanation
Indices: 42965--43052 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
42955 CTGCAAGGAA
*
42965 GAAAAACAGAAACTTGAAGCATCTTTGCATA-AATGTAATGAG
1 GAAAAACAGAAACTAGAAGCATCTTTGCA-AGAATGTAATGAG
*
43007 GAAAAACAGAAACTAGAAGCGTCTTTGCAAGAATGTAATGAG
1 GAAAAACAGAAACTAGAAGCATCTTTGCAAGAATGTAATGAG
43049 GAAA
1 GAAA
43053 TATCTAGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.20
Consensus pattern (42 bp):
GAAAAACAGAAACTAGAAGCATCTTTGCAAGAATGTAATGAG
Found at i:48327 original size:2 final size:2
Alignment explanation
Indices: 48320--48353 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
48310 GAACAATTTA
48320 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
48354 TAAAACTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50004 original size:21 final size:22
Alignment explanation
Indices: 49975--50019 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
49965 GTGATGTTGT
**
49975 AAATATAAACGAGAAGATAAAC
1 AAATATAAAAAAGAAGATAAAC
*
49997 AAAT-TAAAAAAGATGATAAAC
1 AAATATAAAAAAGAAGATAAAC
50018 AA
1 AA
50020 TAAACTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.16
Consensus pattern (22 bp):
AAATATAAAAAAGAAGATAAAC
Found at i:54828 original size:20 final size:19
Alignment explanation
Indices: 54803--54842 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
54793 ATACAATTAG
54803 AATTTTAAAAATATACAAAT
1 AATTTTAAAAATATA-AAAT
*
54823 AATTTTAATAATATAAAAT
1 AATTTTAAAAATATAAAAT
54842 A
1 A
54843 TTAGATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTTTAAAAATATAAAAT
Found at i:56807 original size:13 final size:13
Alignment explanation
Indices: 56791--56835 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
56781 TAAAATTAAT
56791 TTAATGATTATAA
1 TTAATGATTATAA
56804 TTAA-GATTTATAA
1 TTAATGA-TTATAA
*
56817 TGTAAAGATTATAA
1 T-TAATGATTATAA
56831 TTAAT
1 TTAAT
56836 ATATAAAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 2 0.07
13 14 0.50
14 10 0.36
15 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (13 bp):
TTAATGATTATAA
Found at i:56846 original size:25 final size:27
Alignment explanation
Indices: 56796--56847 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
56786 TTAATTTAAT
* *
56796 GATTATAATTAAGATTTATAATGTAAA
1 GATTATAATTAAGATATATAAAGTAAA
56823 GATTATAATT-A-ATATATAAAGTAAA
1 GATTATAATTAAGATATATAAAGTAAA
56848 TTTATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 1 0.04
27 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (27 bp):
GATTATAATTAAGATATATAAAGTAAA
Found at i:65252 original size:24 final size:25
Alignment explanation
Indices: 65223--65270 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
65213 TATACTTAAA
65223 TTTATAATACTCTTA-ATTCAAAAT
1 TTTATAATACTCTTATATTCAAAAT
*
65247 TTTATAATACTCTTATATTTAAAA
1 TTTATAATACTCTTATATTCAAAA
65271 ATTTCGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTATAATACTCTTATATTCAAAAT
Found at i:66054 original size:17 final size:17
Alignment explanation
Indices: 66025--66059 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
66015 TTTTGAAAAT
66025 AAATTGAAGAAAAATAA
1 AAATTGAAGAAAAATAA
66042 AAATGTGAA-AAAAATAA
1 AAAT-TGAAGAAAAATAA
66059 A
1 A
66060 GGCCAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (17 bp):
AAATTGAAGAAAAATAA
Found at i:67337 original size:11 final size:10
Alignment explanation
Indices: 67316--67375 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
67306 CTTTTTTTAA
67316 AAAAATAAAT
1 AAAAATAAAT
67326 AAAAATACAAT
1 AAAAATA-AAT
*
67337 AAAAATGAATT
1 AAAAAT-AAAT
*
67348 AAAAAATGAAT
1 -AAAAATAAAT
* *
67359 AAAATTCAAT
1 AAAAATAAAT
67369 AAAAATA
1 AAAAATA
67376 TAATGTAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
10 20 0.50
11 13 0.32
12 7 0.17
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:67934 original size:11 final size:10
Alignment explanation
Indices: 67899--67962 Score: 67
Period size: 11 Copynumber: 6.1 Consensus size: 10
67889 TTAGCTTTAC
67899 ATTATATTTTT
1 ATTA-ATTTTT
67910 ATTGAA-TTTT
1 ATT-AATTTTT
67920 ATTAATTTTT
1 ATTAATTTTT
67930 AATTAATTTTT
1 -ATTAATTTTT
*
67941 ATTGCATTTTT
1 ATT-AATTTTT
*
67952 ATTTATTTTT
1 ATTAATTTTT
67962 A
1 A
67963 AAAAAATGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
9 2 0.04
10 21 0.45
11 23 0.49
12 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (10 bp):
ATTAATTTTT
Found at i:67940 original size:21 final size:20
Alignment explanation
Indices: 67899--67962 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
67889 TTAGCTTTAC
67899 ATTATATTTTTATTGAA-TTTT
1 ATTA-ATTTTTATT-AATTTTT
67920 ATTAATTTTTAATTAATTTTT
1 ATTAATTTTT-ATTAATTTTT
* *
67941 ATTGCATTTTTATTTATTTTT
1 ATT-AATTTTTATTAATTTTT
67962 A
1 A
67963 AAAAAATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.21
21 24 0.63
22 6 0.16
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (20 bp):
ATTAATTTTTATTAATTTTT
Found at i:67960 original size:32 final size:32
Alignment explanation
Indices: 67894--67963 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
67884 TATTTTTAGC
67894 TTTACATTATATTTTTATTGAATTTTATTAATT
1 TTTA-ATTATATTTTTATTGAATTTTATTAATT
* *
67927 TTTAATTA-ATTTTTATTGCATTTTTATTTATT
1 TTTAATTATATTTTTATTG-AATTTTATTAATT
67959 TTTAA
1 TTTAA
67964 AAAAATGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 10 0.29
32 20 0.59
33 4 0.12
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (32 bp):
TTTAATTATATTTTTATTGAATTTTATTAATT
Found at i:74784 original size:19 final size:21
Alignment explanation
Indices: 74745--74790 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
74735 AAATAACACT
74745 AATAA-ATAATATTTGATTAA
1 AATAATATAATATTTGATTAA
*
74765 ATTAATATAATATTT-A-TAA
1 AATAATATAATATTTGATTAA
74784 AATAATA
1 AATAATA
74791 ATATTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 9 0.39
20 5 0.22
21 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATAATATAATATTTGATTAA
Found at i:74817 original size:23 final size:24
Alignment explanation
Indices: 74772--74818 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
74762 TAAATTAATA
74772 TAATATTTATAAAATAATAATATT
1 TAATATTTATAAAATAATAATATT
* *
74796 TAATTTTTATAATA-AATAATATT
1 TAATATTTATAAAATAATAATATT
74819 ATTATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATATTTATAAAATAATAATATT
Found at i:74829 original size:23 final size:23
Alignment explanation
Indices: 74772--74818 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
74762 TAAATTAATA
*
74772 TAATATTTATAAAATAATAATATT
1 TAAT-TTTATATAATAATAATATT
74796 TAATTTT-TATAATAAATAATATT
1 TAATTTTATATAAT-AATAATATT
74819 ATTATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 12 0.57
24 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATTTTATATAATAATAATATT
Found at i:75068 original size:21 final size:21
Alignment explanation
Indices: 75043--75085 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
75033 AAAATAAATT
**
75043 ACTGGAATTTGAATTACTGGA
1 ACTGGAAAATGAATTACTGGA
75064 ACTGGAAAATGAATTACTGGA
1 ACTGGAAAATGAATTACTGGA
75085 A
1 A
75086 TTTGAATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (21 bp):
ACTGGAAAATGAATTACTGGA
Found at i:75082 original size:15 final size:15
Alignment explanation
Indices: 75064--75108 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
75054 AATTACTGGA
75064 ACTGGAAAATGAATT
1 ACTGGAAAATGAATT
**
75079 ACTGGAATTTGAATT
1 ACTGGAAAATGAATT
*
75094 -CTAGAAAATGAATT
1 ACTGGAAAATGAATT
75108 A
1 A
75109 TATTTCTGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (15 bp):
ACTGGAAAATGAATT
Found at i:75135 original size:14 final size:14
Alignment explanation
Indices: 75118--75151 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
75108 ATATTTCTGG
75118 AAAATGTTTTCCGA
1 AAAATGTTTTCCGA
*
75132 AAAATGTTTTCCGT
1 AAAATGTTTTCCGA
75146 AAAATG
1 AAAATG
75152 AATTATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (14 bp):
AAAATGTTTTCCGA
Found at i:75338 original size:27 final size:27
Alignment explanation
Indices: 75299--75350 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
75289 ATCATAAAAC
75299 ATAATATTATTATT-TTAAAATATTAAA
1 ATAATATTATTATTATT-AAATATTAAA
75326 ATAAT-TTATTTATTATTAAATATTA
1 ATAATATTA-TTATTATTAAATATTA
75351 TTTTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 3 0.13
27 18 0.78
28 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATAATATTATTATTATTAAATATTAAA
Found at i:75502 original size:23 final size:23
Alignment explanation
Indices: 75453--75515 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
75443 GTATTATATT
* **
75453 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
75476 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
75499 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
75516 AAATAATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:75554 original size:27 final size:27
Alignment explanation
Indices: 75500--75596 Score: 92
Period size: 27 Copynumber: 3.5 Consensus size: 27
75490 TTTATTAAAA
75500 TATTATTTAAATATAT-AAATAATATAT
1 TATTA-TTAAATATATAAAATAATATAT
* *
75527 TCATTATTAAATATATAAAAT-TTTTAT
1 T-ATTATTAAATATATAAAATAATATAT
* *
75554 TATATATTAAA-ATAAAAATATAATATCT
1 TAT-TATTAAATATATAAA-ATAATATAT
75582 TATTATTATAATATA
1 TATTATTA-AATATA
75597 ATTGATTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
26 8 0.14
27 30 0.53
28 16 0.28
29 3 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TATTATTAAATATATAAAATAATATAT
Found at i:75555 original size:23 final size:27
Alignment explanation
Indices: 75500--75653 Score: 80
Period size: 27 Copynumber: 5.9 Consensus size: 27
75490 TTTATTAAAA
75500 TATTATTTAAATATATAAATAATATATT
1 TATTA-TTAAATATATAAATAATATATT
* * *
75528 CATTATTAAATATAT-AA-AATTTTTAT
1 TATTATTAAATATATAAATAATATAT-T
*
75554 TATATATTAAA-ATAAAAAT-ATAATATCT
1 TAT-TATTAAATATATAAATAAT-ATAT-T
* * *
75582 TATTATTATA-ATATAATTGAT-TA-T
1 TATTATTAAATATATAAATAATATATT
75606 T-TTA-TATAATAT-TAAA-AATATATAT
1 TATTATTA-AATATATAAATAATATAT-T
*
75631 TATTATTATAA-ATATTAATAATA
1 TATTATTA-AATATATAAATAATA
75654 AATAAATATT
Statistics
Matches: 96, Mismatches: 15, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
22 4 0.04
23 9 0.09
24 4 0.04
25 7 0.07
26 15 0.16
27 41 0.43
28 16 0.17
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (27 bp):
TATTATTAAATATATAAATAATATATT
Found at i:75619 original size:15 final size:17
Alignment explanation
Indices: 75572--75641 Score: 60
Period size: 16 Copynumber: 4.3 Consensus size: 17
75562 AAAATAAAAA
*
75572 TATAATAT-CTTATTAT
1 TATAATATAATTATTAT
75588 TATAATATAATTGATTAT
1 TATAATATAATT-ATTAT
*
75606 T-TTATATAA-TATTA-
1 TATAATATAATTATTAT
*
75620 -AAAATATATATTATTAT
1 TATAATATA-ATTATTAT
75637 TATAA
1 TATAA
75642 ATATTAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
14 5 0.12
15 5 0.12
16 14 0.33
17 9 0.21
18 9 0.21
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
TATAATATAATTATTAT
Found at i:75912 original size:42 final size:43
Alignment explanation
Indices: 75866--75960 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 43
75856 TGCGTGAAAT
*
75866 AAACACGGA-AAAACATTTTCCGAAAAATAAATTACGTAAAAC
1 AAACACGGAGAAAACATTTTCCAAAAAATAAATTACGTAAAAC
* *
75908 AAACAC-GAGAAAACATTTTCCAAAAAATGAATTACGTGAAAC
1 AAACACGGAGAAAACATTTTCCAAAAAATAAATTACGTAAAAC
75950 AAACAC-GAGAA
1 AAACACGGAGAA
75961 TTCAAAGAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
41 2 0.04
42 47 0.96
ACGTcount: A:0.55, C:0.17, G:0.12, T:0.17
Consensus pattern (43 bp):
AAACACGGAGAAAACATTTTCCAAAAAATAAATTACGTAAAAC
Found at i:81421 original size:92 final size:87
Alignment explanation
Indices: 81280--81447 Score: 216
Period size: 92 Copynumber: 1.9 Consensus size: 87
81270 TGACTAATGC
*
81280 TTCAATTCAGTGTTGACAAAGGTGATATGTACATGAATGTTAAGTACATTTCT-GCTCTGTTATT
1 TTCAATTCAGTGTTGACAAAGGTGATATGTACATGAATGTTAAGTACATTT-TAGCTCTGTTACT
81344 TTTGGTGGTCCTTCGAATTTGTTT
65 TTT-GTGGTCCTTCGAATTTGTTT
* *
81368 TTCAATTCAGTGTTGACAAAAGGAAT-ATAACTGTACATGAATGTTTCA-TACATTTTAGCTGTG
1 TTCAATTCAGTGTTGAC-AAAGG--TGAT-A-TGTACATGAATG-TTAAGTACATTTTAGCTCTG
81431 TTACTTTTGTGGTCCTT
60 TTACTTTTGTGGTCCTT
81448 TCAATAGTTG
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
88 17 0.24
89 5 0.07
90 2 0.03
91 12 0.17
92 31 0.44
93 3 0.04
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (87 bp):
TTCAATTCAGTGTTGACAAAGGTGATATGTACATGAATGTTAAGTACATTTTAGCTCTGTTACTT
TTGTGGTCCTTCGAATTTGTTT
Done.