Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003851.1 Hibiscus syriacus cultivar Beakdansim tig00008265_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: 66070
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1083 original size:26 final size:26
Alignment explanation
Indices: 1036--1085 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1026 TCGTTGAAAA
**
1036 GGATACATATTTTTTATATTTAATAT
1 GGATACATATTTTACATATTTAATAT
1062 GGATATCATATTTTACAT-TTTAAT
1 GGATA-CATATTTTACATATTTAAT
1086 TTAATTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (26 bp):
GGATACATATTTTACATATTTAATAT
Found at i:2251 original size:24 final size:23
Alignment explanation
Indices: 2208--2253 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
2198 ACAATCAAAA
*
2208 TATTTTAAACTCTTCGGGAGTTT
1 TATTTTAAACTCTTCAGGAGTTT
*
2231 TATTTTAAAGCTCTTTAGGAGTT
1 TATTTTAAA-CTCTTCAGGAGTT
2254 CCAATTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (23 bp):
TATTTTAAACTCTTCAGGAGTTT
Found at i:3313 original size:19 final size:19
Alignment explanation
Indices: 3273--3314 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3263 TAATTCAAAC
*
3273 ATTTAATCGATTAAATTTT
1 ATTTAATCGATTAAATTAT
3292 ATTTAATCGATTAACA-TAT
1 ATTTAATCGATTAA-ATTAT
3311 ATTT
1 ATTT
3315 TATTTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (19 bp):
ATTTAATCGATTAAATTAT
Found at i:9582 original size:27 final size:27
Alignment explanation
Indices: 9552--9608 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
9542 AAGCTACAAG
* *
9552 AAAACATAAATAATAGAAAGAAACCCT
1 AAAACACAAATAACAGAAAGAAACCCT
* **
9579 AAAACACAAATTACAGGGAGAAACCCT
1 AAAACACAAATAACAGAAAGAAACCCT
9606 AAA
1 AAA
9609 TACGCTATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.60, C:0.18, G:0.11, T:0.12
Consensus pattern (27 bp):
AAAACACAAATAACAGAAAGAAACCCT
Found at i:10308 original size:19 final size:20
Alignment explanation
Indices: 10284--10329 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
10274 CACTTGTGTT
*
10284 ATCATTTTATTAAG-TTTTA
1 ATCATTATATTAAGTTTTTA
10303 ATCATTATATTAAGTTTTTA
1 ATCATTATATTAAGTTTTTA
10323 ATCATTA
1 ATCATTA
10330 GTACATTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (20 bp):
ATCATTATATTAAGTTTTTA
Found at i:13973 original size:26 final size:26
Alignment explanation
Indices: 13944--13994 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
13934 GGTTGGTCTG
* *
13944 GGCCGGTTCTGTTTTATTTGTAACTT
1 GGCCGGTCCAGTTTTATTTGTAACTT
*
13970 GGCCGGTCCAGTTTTGTTTGTAACT
1 GGCCGGTCCAGTTTTATTTGTAACT
13995 GTTTGTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.12, C:0.18, G:0.25, T:0.45
Consensus pattern (26 bp):
GGCCGGTCCAGTTTTATTTGTAACTT
Found at i:14010 original size:3 final size:3
Alignment explanation
Indices: 14002--14069 Score: 84
Period size: 3 Copynumber: 22.7 Consensus size: 3
13992 ACTGTTTGTA
* *
14002 AAT AAT AAT TAT AAT -AT AAT AAT AAT ATTT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
**
14047 AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
14070 AAACAAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.93
4 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:14066 original size:24 final size:25
Alignment explanation
Indices: 14007--14069 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
13997 TTGTAAATAA
*
14007 TAATTATAAT-ATAATAATAATATT
1 TAATAATAATAATAATAATAATATT
14031 TAATAATAATAATAATAATAAT-TT
1 TAATAATAATAATAATAATAATATT
14055 TAATAATAATAATAA
1 TAATAATAATAATAA
14070 AAACAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
24 26 0.70
25 11 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TAATAATAATAATAATAATAATATT
Found at i:14785 original size:301 final size:303
Alignment explanation
Indices: 14220--15154 Score: 1745
Period size: 301 Copynumber: 3.1 Consensus size: 303
14210 TAGGTCTTAA
14220 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
* *
14285 AGGCTTTTCGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
14350 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTT
14415 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
*
14480 CCTAAGGCTTTAAAAACATCAAAAAGCTCCCGACGGC-TTTTGG
261 CCTAAGGCTTTAAAAACATCAAAAAGCT-CCGAAGGCTTTTTGG
*
14523 AAACATCATGCACTGCAGGAC-TACAGATGACCCTAAGATTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
14587 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGA-CCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
14651 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTT
14716 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
*
14781 CCTAAGGCTTTAAAAACATCAAAAACCTCCGAAGGCTTTTTGG
261 CCTAAGGCTTTAAAAACATCAAAAAGCTCCGAAGGCTTTTTGG
* *
14824 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
14888 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
14953 AAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTT
15017 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
*
15082 CCTAAGGCTTTGAAAACATCAAAAAGCTCCGAAGGCTTTTTGG
261 CCTAAGGCTTTAAAAACATCAAAAAGCTCCGAAGGCTTTTTGG
*
15125 AAACACCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
15155 TGGGAAATAG
Statistics
Matches: 618, Mismatches: 11, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
300 7 0.01
301 435 0.70
302 155 0.25
303 21 0.03
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (303 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTT
GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
CCTAAGGCTTTAAAAACATCAAAAAGCTCCGAAGGCTTTTTGG
Found at i:15181 original size:75 final size:76
Alignment explanation
Indices: 14220--15154 Score: 1722
Period size: 76 Copynumber: 12.4 Consensus size: 76
14210 TAGGTCTTAA
*
14220 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
14285 AGGCTTTTCGG
66 AGGCTTTTTGG
*
14296 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
14361 AGGCTTTTTGG
66 AGGCTTTTTGG
14372 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
14437 AGGCTTTTTGG
66 AGGCTTTTTGG
*
14448 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
14513 CGGC-TTTTGG
66 AGGCTTTTTGG
**
14523 AAACATCATGCACTGCAGGAC-TACAGATGACCCTAAGATTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
14587 AGGCTTTTTGG
66 AGGCTTTTTGG
14598 AAACATCATGCACTGCAGGACTTACAGATGA-CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
14662 AGGCTTTTTGG
66 AGGCTTTTTGG
14673 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
14738 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
14749 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAACCT-CCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
14813 AGGCTTTTTGG
66 AGGCTTTTTGG
*
14824 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
14888 AGGCTTTTTGG
66 AGGCTTTTTGG
14899 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
14964 AGGC-TTTTGG
66 AGGCTTTTTGG
14974 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
15039 AGGCTTTTTGG
66 AGGCTTTTTGG
15050 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
15114 AGGCTTTTTGG
66 AGGCTTTTTGG
*
15125 AAACACCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
15155 TGGGAAATAG
Statistics
Matches: 839, Mismatches: 15, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
74 43 0.05
75 394 0.47
76 402 0.48
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:16180 original size:22 final size:22
Alignment explanation
Indices: 16155--16209 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
16145 CATAAAGCTT
16155 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
16177 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
16199 TCATCTTTGAA
1 TCATCTTTGAA
16210 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:18870 original size:113 final size:113
Alignment explanation
Indices: 18701--19030 Score: 516
Period size: 113 Copynumber: 2.9 Consensus size: 113
18691 ATCATGCAGC
* * * * * * * *
18701 TCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACCGAATCAGATCAGATAACTCAAAGAA
1 TCATCTTTCAAATCCAATGATT-ATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
* *
18766 TACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAAT
65 CACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCAAAT
18815 TCATCTTTCAAATCCAATGATTATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
1 TCATCTTTCAAATCCAATGATTATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
* *
18880 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAT
66 ACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCAAAT
*
18928 TCATCTTTCAAATCCAATGATTAGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
1 TCATCTTTCAAATCCAATGATTA-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
*
18993 CACTTCCAGAAGATGCTATTGGGTCTCTTTATTTCTAC
65 CACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTAC
19031 TACGAGAACA
Statistics
Matches: 200, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 104 0.52
114 96 0.48
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (113 bp):
TCATCTTTCAAATCCAATGATTATTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
ACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCAAAT
Found at i:23686 original size:26 final size:26
Alignment explanation
Indices: 23657--23711 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
23647 TCTGGTTGGT
* *
23657 CTGGGCCGATTCTGTTTTGTTTGTAA
1 CTGGGCCGATCCAGTTTTGTTTGTAA
* *
23683 CTGGGTCGGTCCAGTTTTGTTTGTAA
1 CTGGGCCGATCCAGTTTTGTTTGTAA
23709 CTG
1 CTG
23712 TCGACACATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.11, C:0.16, G:0.29, T:0.44
Consensus pattern (26 bp):
CTGGGCCGATCCAGTTTTGTTTGTAA
Found at i:25112 original size:25 final size:24
Alignment explanation
Indices: 25059--25116 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
25049 GTATTTTACC
* *
25059 CTATTTCTTTACTTCTTTATTATT
1 CTATTTATTTACTTATTTATTATT
* *
25083 ATATTTATTTACATTATTTATTTTT
1 CTATTTATTTAC-TTATTTATTATT
25108 CTATTTATT
1 CTATTTATT
25117 ATATTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.67
Consensus pattern (24 bp):
CTATTTATTTACTTATTTATTATT
Found at i:26426 original size:10 final size:10
Alignment explanation
Indices: 26411--26444 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
26401 TTCATTTACC
26411 ATTTATTTTT
1 ATTTATTTTT
26421 ATTTATTTTT
1 ATTTATTTTT
* *
26431 ATCTATTTAT
1 ATTTATTTTT
26441 ATTT
1 ATTT
26445 TACTAACCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:35909 original size:52 final size:51
Alignment explanation
Indices: 35828--35925 Score: 142
Period size: 52 Copynumber: 1.9 Consensus size: 51
35818 AATACTTCGC
* * *
35828 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAAAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATT-AAAAAAAAAAAAAAACGT
* *
35880 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAAAAAAA
35926 GAGGAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 12 0.29
52 29 0.71
ACGTcount: A:0.49, C:0.14, G:0.22, T:0.14
Consensus pattern (51 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAAAAAAAAACGT
Found at i:36868 original size:105 final size:105
Alignment explanation
Indices: 36686--37563 Score: 1593
Period size: 105 Copynumber: 8.4 Consensus size: 105
36676 CAGGTTTTAC
**
36686 TCAGAGCCAATTTCAACTTCACAACGGGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
36751 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
*
36791 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
36856 GACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAAT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
*
36896 TCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
36961 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
*
37001 TTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
37066 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
*
37106 TCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
37171 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
*
37211 TCAGAGCCAATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
37276 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
37316 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
37381 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
*
37421 TCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* * * *
37486 GGCGAAGGGACCGCTGGTTGTCAACAAACAACTTCACAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAAT
37527 TC----CCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
37564 TGAACAATAC
Statistics
Matches: 752, Mismatches: 20, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
102 35 0.05
105 707 0.94
106 10 0.01
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT
Found at i:39371 original size:2 final size:2
Alignment explanation
Indices: 39364--39399 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39354 ACTTATATGT
39364 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
39400 CACATTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39472 original size:22 final size:20
Alignment explanation
Indices: 39430--39488 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 20
39420 ATTTCTTTAC
*
39430 TTCT-TTATTATTATATTTA
1 TTCTATTATTATTATATTTT
*
39449 TT-TA-CATTATT-TATTTT
1 TTCTATTATTATTATATTTT
39466 TTCTATTATTATTATATTTT
1 TTCTATTATTATTATATTTT
39486 TTC
1 TTC
39489 CTCCCTCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 7 0.21
18 9 0.27
19 8 0.24
20 9 0.27
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (20 bp):
TTCTATTATTATTATATTTT
Found at i:40217 original size:3 final size:3
Alignment explanation
Indices: 40209--40273 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
40199 ACTGTTTGTA
*
40209 AAT AAT AAT TAT AAT -AT AAT AAT AAT AATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
**
40254 AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
40274 AAACAAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:54929 original size:29 final size:29
Alignment explanation
Indices: 54893--54960 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
54883 CATTTTACAC
* *
54893 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
* *
54922 AAATAGCACCCATTTCAAATTAATTTCCA
1 AAATAGCACCCATTTCAAAATAATTACCA
* *
54951 GAATAACACC
1 AAATAGCACC
54961 AAAACCGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATTACCA
Found at i:55025 original size:13 final size:13
Alignment explanation
Indices: 55007--55053 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
54997 GGTCAACGAT
55007 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
55020 CGGGTCCGGT---
1 CGGGTCGGGTCAA
*
55030 CGGGTTGGGTCAA
1 CGGGTCGGGTCAA
55043 CGGGTCGGGTC
1 CGGGTCGGGTC
55054 GTGACCGGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
10 8 0.30
13 19 0.70
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:55039 original size:23 final size:23
Alignment explanation
Indices: 55006--55054 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
54996 CGGTCAACGA
55006 TCGGGTCGGGTCAACGGGTCCGG
1 TCGGGTCGGGTCAACGGGTCCGG
* *
55029 TCGGGTTGGGTCAACGGGTCGGG
1 TCGGGTCGGGTCAACGGGTCCGG
55052 TCG
1 TCG
55055 TGACCGGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.08, C:0.22, G:0.49, T:0.20
Consensus pattern (23 bp):
TCGGGTCGGGTCAACGGGTCCGG
Found at i:55063 original size:23 final size:23
Alignment explanation
Indices: 54987--55065 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 23
54977 CCAGAATAGC
*
54987 ACCGGTCAAC-GGTCAACGATCGGG
1 ACCGGTCAACGGGTC--CGGTCGGG
* *
55011 TCGGGTCAACGGGTCCGGTCGGG
1 ACCGGTCAACGGGTCCGGTCGGG
*** * *
55034 TTGGGTCAACGGGTCGGGTCGTG
1 ACCGGTCAACGGGTCCGGTCGGG
55057 ACCGGTCAA
1 ACCGGTCAA
55066 ACCGGTCAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 33 0.73
24 8 0.18
25 4 0.09
ACGTcount: A:0.16, C:0.25, G:0.41, T:0.18
Consensus pattern (23 bp):
ACCGGTCAACGGGTCCGGTCGGG
Found at i:62236 original size:17 final size:18
Alignment explanation
Indices: 62214--62248 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
62204 ACCAGTCAAC
62214 GGTCAAC-GATCGGGTCG
1 GGTCAACGGATCGGGTCG
*
62231 GGTCAACGGGTCGGGTCG
1 GGTCAACGGATCGGGTCG
62249 TGACCGGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCAACGGATCGGGTCG
Done.