Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002937.1 Hibiscus syriacus cultivar Beakdansim tig00006066_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: 81661
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:707 original size:17 final size:16
Alignment explanation
Indices: 670--701 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
660 TATTAATTAC
670 AATAATATAATATAAT
1 AATAATATAATATAAT
686 AATAATAATAATATAA
1 AATAAT-ATAATATAA
702 CTATAACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAATATAATATAAT
Found at i:8880 original size:22 final size:23
Alignment explanation
Indices: 8855--8898 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
8845 AATATTTTAT
*
8855 TAATG-AATATGCTCAAAAAATA
1 TAATGTAATATGCTAAAAAAATA
8877 TAATGTAATATGCTAAAAAAAT
1 TAATGTAATATGCTAAAAAAAT
8899 GCTTATGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.30
Consensus pattern (23 bp):
TAATGTAATATGCTAAAAAAATA
Found at i:21590 original size:20 final size:20
Alignment explanation
Indices: 21565--21624 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
21555 TTTTTGTGCA
*
21565 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
21585 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
21606 GAATGGGAACCGATACCCC
1 G-A-GGGAACCGATACCCC
21625 ATGGGGTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
22 1 0.03
23 14 0.42
ACGTcount: A:0.27, C:0.32, G:0.25, T:0.17
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:25132 original size:24 final size:25
Alignment explanation
Indices: 25090--25140 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
25080 CACCTAAGTG
*
25090 CCGCGTAGAGATTTTTCCCGAAGGA
1 CCGCGTAGAGATTTGTCCCGAAGGA
25115 CCGCGTAGA-ATTTGTCCCGAAGGA
1 CCGCGTAGAGATTTGTCCCGAAGGA
25139 CC
1 CC
25141 ACATATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (25 bp):
CCGCGTAGAGATTTGTCCCGAAGGA
Found at i:25369 original size:29 final size:30
Alignment explanation
Indices: 25327--25396 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
25317 ACATAATTTA
* * *
25327 TATCGCATAGACATAACA-TTCCTTACCTT
1 TATCACATAAACATAACATTTCCATACCTT
**
25356 TATCACATAAACATTTCATTTTCCATACCTT
1 TATCACATAAACATAACA-TTTCCATACCTT
*
25387 TATCCCATAA
1 TATCACATAA
25397 TTCATATAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 14 0.42
31 19 0.58
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (30 bp):
TATCACATAAACATAACATTTCCATACCTT
Found at i:31945 original size:24 final size:25
Alignment explanation
Indices: 31907--31953 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
31897 TAAGTGCCGC
* *
31907 GTAGAGATTTGTCCCGAATGACCGG
1 GTAGAGATTTATCCCGAAGGACCGG
31932 GTAGA-ATTTATCCCGAAGGACC
1 GTAGAGATTTATCCCGAAGGACC
31954 ACATATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (25 bp):
GTAGAGATTTATCCCGAAGGACCGG
Found at i:32184 original size:29 final size:29
Alignment explanation
Indices: 32142--32210 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
32132 ACATAATTTA
* *
32142 TATCGCATAGACATAACA-TTCCATACCTT
1 TATCACATAAACATAACATTTCCATACC-T
**
32171 TATCACATAAACATTTCATTTTCCATACCT
1 TATCACATAAACATAACA-TTTCCATACCT
*
32201 TATCCCATAA
1 TATCACATAA
32211 TTCATATAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 14 0.42
30 10 0.30
31 9 0.27
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.35
Consensus pattern (29 bp):
TATCACATAAACATAACATTTCCATACCT
Found at i:32645 original size:21 final size:21
Alignment explanation
Indices: 32627--32684 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
32617 TCGTTTGAGG
*
32627 GGGTATCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
32648 GGGTACCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
32669 GGGTACCGATTCCCCT
1 GGGTACCGATTCCCCT
32685 AGCCCAGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.29
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:33961 original size:2 final size:2
Alignment explanation
Indices: 33954--34034 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
33944 ACCCTAAAGC
33954 TA TA 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 TA TA
33996 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
34035 TAAGTCTTTA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36456 original size:16 final size:17
Alignment explanation
Indices: 36435--36468 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
36425 ATTTTTTATT
*
36435 ATTTAACATG-AAAATA
1 ATTTAAAATGTAAAATA
36451 ATTTAAAATGTAAAATA
1 ATTTAAAATGTAAAATA
36468 A
1 A
36469 AAATAGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (17 bp):
ATTTAAAATGTAAAATA
Found at i:38123 original size:36 final size:36
Alignment explanation
Indices: 38083--38155 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
38073 TTAACGTTGG
*
38083 CTTTCCACTCTTTTTACCCATCTTTAGCCCCTCCCC
1 CTTTCCACTCTTTTTACCCATCTTTAACCCCTCCCC
38119 CTTTCCACTCTTTTTACCCATCTTTAACCCCTCCCC
1 CTTTCCACTCTTTTTACCCATCTTTAACCCCTCCCC
38155 C
1 C
38156 CCTTTCTCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.12, C:0.48, G:0.01, T:0.38
Consensus pattern (36 bp):
CTTTCCACTCTTTTTACCCATCTTTAACCCCTCCCC
Found at i:39879 original size:23 final size:23
Alignment explanation
Indices: 39848--39933 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
39838 TGTTTGTGTT
39848 TGTTTATTTAGA-GTTCGTGAATA
1 TGTTTATTTA-ACGTTCGTGAATA
* * **
39871 TGTTGATTTAACGTTCATGAGCA
1 TGTTTATTTAACGTTCGTGAATA
* *
39894 AGTTCATTTAACGTTCGTGAATA
1 TGTTTATTTAACGTTCGTGAATA
*
39917 TGTTTATTTAATGTTCG
1 TGTTTATTTAACGTTCG
39934 GCAGTGAACA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 1 0.02
23 49 0.98
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (23 bp):
TGTTTATTTAACGTTCGTGAATA
Found at i:42383 original size:21 final size:22
Alignment explanation
Indices: 42350--42404 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
42340 AATAAAAAAT
42350 AATATATATATATATTTAAATTAA
1 AATA-ATA-ATATATTTAAATTAA
*
42374 AATAA-AATATTTTTAAATTAA
1 AATAATAATATATTTAAATTAA
*
42395 ATTAATAATA
1 AATAATAATA
42405 AAATATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 18 0.64
22 5 0.18
23 1 0.04
24 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATAATAATATATTTAAATTAA
Found at i:42415 original size:27 final size:27
Alignment explanation
Indices: 42347--42463 Score: 91
Period size: 27 Copynumber: 4.4 Consensus size: 27
42337 AAGAATAAAA
* * *
42347 AATAATATATATATATATTTAAATTAA-
1 AATAAAATATATTTA-AATTAAATTAAT
*
42374 AATAAAATATTTTTAAATTAAATTAAT
1 AATAAAATATATTTAAATTAAATTAAT
*
42401 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATATATTTAAATTAAATTAAT
* * *
42426 ATACAAAATATTTCTTAAATTTAA-T-AT
1 A-ATAAAATATAT-TTAAATTAAATTAAT
42453 ATATAAAATAT
1 A-ATAAAATAT
42464 TATGATATAA
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
25 9 0.12
26 21 0.28
27 39 0.53
28 3 0.04
29 2 0.03
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (27 bp):
AATAAAATATATTTAAATTAAATTAAT
Found at i:42868 original size:21 final size:21
Alignment explanation
Indices: 42842--42900 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
42832 ATTATCCAAT
*
42842 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
42863 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
42884 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
42901 TAATAAATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.51, C:0.22, G:0.07, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:45203 original size:25 final size:25
Alignment explanation
Indices: 45175--45222 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
45165 GAAAAACGAG
45175 CAAGAACATATAAATTCACGATTGT
1 CAAGAACATATAAATTCACGATTGT
45200 CAAGAACATATAAATTCACGATT
1 CAAGAACATATAAATTCACGATT
45223 CCCTTACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (25 bp):
CAAGAACATATAAATTCACGATTGT
Found at i:46840 original size:41 final size:41
Alignment explanation
Indices: 46795--47003 Score: 226
Period size: 41 Copynumber: 5.1 Consensus size: 41
46785 CCTATTATGG
* *
46795 CGTTTGTATAAAAATGCCACTGAAGTTCGAGTCTTTAGCGA
1 CGTTTGTATAAAAATACCACTAAAGTTCGAGTCTTTAGCGA
* * *
46836 CGTTTGTATAAAAACACCACTAAAGTACGAGTCTATAGC-A
1 CGTTTGTATAAAAATACCACTAAAGTTCGAGTCTTTAGCGA
*
46876 CGTTTGTATAAAAATACCACTAAAGTAT-GAGTCTTTAGTGA
1 CGTTTGTATAAAAATACCACTAAAGT-TCGAGTCTTTAGCGA
* * * * *
46917 CATTTGTATACAAACACCACTAAAGTGCGAGTCTTTAGTGA
1 CGTTTGTATAAAAATACCACTAAAGTTCGAGTCTTTAGCGA
* * * * * *
46958 CGTTTATATAAAAGTGCCACTAAAATAT-GAGTATTTAGCGG
1 CGTTTGTATAAAAATACCACTAAAGT-TCGAGTCTTTAGCGA
46999 CGTTT
1 CGTTT
47004 TTGCTTAAAA
Statistics
Matches: 140, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
40 35 0.25
41 105 0.75
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (41 bp):
CGTTTGTATAAAAATACCACTAAAGTTCGAGTCTTTAGCGA
Found at i:46844 original size:205 final size:206
Alignment explanation
Indices: 46463--46869 Score: 531
Period size: 205 Copynumber: 2.0 Consensus size: 206
46453 GTAAACTTGC
46463 GGTGTTTGTAAATACAAACACCACTAATGTACAGATAAATTACGACATTTAGTCAAAAAGCGCCA
1 GGTGTTTGT-AATACAAACACCACTAATGTACAGATAAATTACGACATTTAGTCAAAAAGCGCCA
* *
46528 TTACAGTATGAATCTCTTACGACATTTTTTCAAAAACGCTATTTACATATGTCCTATTATGGCGT
65 TTACAGTATGAATCTCTTACGACATTTTTTCAAAAACACCATTTACATATGTCCTATTATGGCGT
* * *
46593 TCGTATAAAAACGCCACTAAAGTCTGAGTCTATATCAGCATTTGTATAAAAACGCTACTAAAATA
130 TCGTATAAAAACGCCACTAAAGTCTGAGTCTATAGCAGCATTTGTATAAAAACACCACTAAAATA
46658 CGAGTCTTTAGT
195 CGAGTCTTTAGT
* ** * *
46670 GGTGTTTGT-ATACAAACGCCACTAATGTATTGATAAATT--GTAGCGTTTATTCAAAAA-CGCC
1 GGTGTTTGTAATACAAACACCACTAATGTACAGATAAATTACG-A-CATTTAGTCAAAAAGCGCC
* * *
46731 ATTATAGTATGAATCTCTTACGGCATTTTTTCAAAAACACCA-TTATATATGTGCCCTATTATGG
64 ATTACAGTATGAATCTCTTACGACATTTTTTCAAAAACACCATTTACATATGT--CCTATTATGG
* * * * *
46795 CGTTTGTATAAAAATGCCACTGAAGT-TCGAGTCTTTAGC-GACGTTTGTATAAAAACACCACTA
127 CGTTCGTATAAAAACGCCACTAAAGTCT-GAGTCTATAGCAG-CATTTGTATAAAAACACCACTA
*
46858 AAGTACGAGTCT
190 AAATACGAGTCT
46870 ATAGCACGTT
Statistics
Matches: 175, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
203 10 0.06
204 45 0.26
205 111 0.63
207 9 0.05
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (206 bp):
GGTGTTTGTAATACAAACACCACTAATGTACAGATAAATTACGACATTTAGTCAAAAAGCGCCAT
TACAGTATGAATCTCTTACGACATTTTTTCAAAAACACCATTTACATATGTCCTATTATGGCGTT
CGTATAAAAACGCCACTAAAGTCTGAGTCTATAGCAGCATTTGTATAAAAACACCACTAAAATAC
GAGTCTTTAGT
Found at i:46908 original size:81 final size:82
Alignment explanation
Indices: 46795--47003 Score: 278
Period size: 81 Copynumber: 2.6 Consensus size: 82
46785 CCTATTATGG
*
46795 CGTTTGTATAAAAATGCCACTGAAGT-TCGAGTCTTTAGCGACGTTTGTATAAAAACACCACTAA
1 CGTTTGTATAAAAATGCCACTAAAGTAT-GAGTCTTTAGCGACGTTTGTATAAAAACACCACTAA
46859 AGTACGAGTCTATAG-CA
65 AGTACGAGTCTATAGTCA
* * * *
46876 CGTTTGTATAAAAATACCACTAAAGTATGAGTCTTTAGTGACATTTGTATACAAACACCACTAAA
1 CGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTAGCGACGTTTGTATAAAAACACCACTAAA
* * *
46941 GTGCGAGTCTTTAGTGA
66 GTACGAGTCTATAGTCA
* * * * *
46958 CGTTTATATAAAAGTGCCACTAAAATATGAGTATTTAGCGGCGTTT
1 CGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTAGCGACGTTT
47004 TTGCTTAAAA
Statistics
Matches: 110, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
81 70 0.64
82 40 0.36
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (82 bp):
CGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTAGCGACGTTTGTATAAAAACACCACTAAA
GTACGAGTCTATAGTCA
Found at i:47211 original size:13 final size:13
Alignment explanation
Indices: 47193--47220 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47183 TTAGTATAAC
47193 TTTAAAAGTCACT
1 TTTAAAAGTCACT
47206 TTTAAAAGTCACT
1 TTTAAAAGTCACT
47219 TT
1 TT
47221 AATTGTTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (13 bp):
TTTAAAAGTCACT
Found at i:47221 original size:12 final size:12
Alignment explanation
Indices: 47191--47222 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
47181 GTTTAGTATA
47191 ACTTTAAAAGTC
1 ACTTTAAAAGTC
47203 ACTTTTAAAAGTC
1 AC-TTTAAAAGTC
47216 ACTTTAA
1 ACTTTAA
47223 TTGTTGGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.38
Consensus pattern (12 bp):
ACTTTAAAAGTC
Found at i:48600 original size:71 final size:71
Alignment explanation
Indices: 48484--48623 Score: 208
Period size: 71 Copynumber: 2.0 Consensus size: 71
48474 AAGGATTCAG
* * * * *
48484 GTACATTGGAGCATGCCACACGTTGGGACAGTTTGGTGGAGCATTTGAAAGACATATACAGCTCA
1 GTACATTGGAGCATGACACACATTGGAACAGCTTGGTGGAGCATTTGAAAGACATATACAACTCA
48549 CAAATA
66 CAAATA
* **
48555 GTACATTGGAGCATGACACACATTGGAATAGCTTGGTGGAGCATTTGGGAGACATATACAACTCA
1 GTACATTGGAGCATGACACACATTGGAACAGCTTGGTGGAGCATTTGAAAGACATATACAACTCA
48620 CAAA
66 CAAA
48624 CAACTCTCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.24
Consensus pattern (71 bp):
GTACATTGGAGCATGACACACATTGGAACAGCTTGGTGGAGCATTTGAAAGACATATACAACTCA
CAAATA
Found at i:55971 original size:56 final size:56
Alignment explanation
Indices: 55731--55971 Score: 376
Period size: 56 Copynumber: 4.3 Consensus size: 56
55721 CTATATGGTA
* *
55731 ATTCATCAACTCATGAATAAATTTCGTGGA-TTTGCACACATAGTGCCTGTACGACT
1 ATTCATCAACTCATG-ATGAATTCCGTGGATTTTGCACACATAGTGCCTGTACGACT
* * * *
55787 ATTCATCAACTCATAATGAATTCCGTGAAATTTGCACACATAGTGTCTGTACGACT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCCTGTACGACT
* * *
55843 ATTCATCAACTCATGATGAATTCTGTGGATTTTGCACACATAGTGCATGTACGGCT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCCTGTACGACT
*
55899 ATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCCTGTACGGCT
1 ATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCCTGTACGACT
55955 ATTCATCAACTCATGAT
1 ATTCATCAACTCATGAT
55972 TGCACACATA
Statistics
Matches: 170, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
55 11 0.06
56 159 0.94
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (56 bp):
ATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCCTGTACGACT
Found at i:55991 original size:41 final size:41
Alignment explanation
Indices: 55930--56012 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
55920 TCCGTGGATT
*
55930 TTGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGA
1 TTGCACACATAGTGCATGTACGGCTATTCATCAACTCATGA
* *
55971 TTGCACACATAGTGCATGTACGGTTTTTCATCAACTCATGA
1 TTGCACACATAGTGCATGTACGGCTATTCATCAACTCATGA
56012 T
1 T
56013 GAATTATGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (41 bp):
TTGCACACATAGTGCATGTACGGCTATTCATCAACTCATGA
Found at i:56040 original size:97 final size:97
Alignment explanation
Indices: 55874--56069 Score: 329
Period size: 97 Copynumber: 2.0 Consensus size: 97
55864 TCTGTGGATT
*
55874 TTGCACACATAGTGCATGTACGGCTATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACA
1 TTGCACACATAGTGCATGTACGGCTATTCATCAACTCATGATGAATTACGTGGATTTTGCACACA
55939 TAGTGCCTGTACGGCTATTCATCAACTCATGA
66 TAGTGCCTGTACGGCTATTCATCAACTCATGA
* * * *
55971 TTGCACACATAGTGCATGTACGGTTTTTCATCAACTCATGATGAATTATGTGGATTTTGTACACA
1 TTGCACACATAGTGCATGTACGGCTATTCATCAACTCATGATGAATTACGTGGATTTTGCACACA
**
56036 TAGTGCCTGTGTGGCTATTCATCAACTCATGA
66 TAGTGCCTGTACGGCTATTCATCAACTCATGA
56068 TT
1 TT
56070 CCGTGGAATT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 92 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (97 bp):
TTGCACACATAGTGCATGTACGGCTATTCATCAACTCATGATGAATTACGTGGATTTTGCACACA
TAGTGCCTGTACGGCTATTCATCAACTCATGA
Found at i:56561 original size:19 final size:19
Alignment explanation
Indices: 56522--56570 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
56512 TTCGAAATGA
* *
56522 TATCGATACCTTCCTTTCGG
1 TATCGATA-CTCCCATTCGG
56542 TATCGATACTCCCATTCGG
1 TATCGATACTCCCATTCGG
56561 TATCGATACT
1 TATCGATACT
56571 GATTGAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.37
Consensus pattern (19 bp):
TATCGATACTCCCATTCGG
Found at i:62760 original size:56 final size:56
Alignment explanation
Indices: 62699--63022 Score: 397
Period size: 56 Copynumber: 5.8 Consensus size: 56
62689 ACGGTAATTG
* * * *
62699 ATCAACTCTTGAATGAATTTCATGGA-TTTGCACACATAGTGCATGTACGACTATTC
1 ATCAACTCATG-ATGAATTCCGTGGATTTTGCACACATAGTGCTTGTACGACTATTC
* * *
62755 ATCAACTCATGATGAATTCCGTGGAATTTGCATACATAGTGCTTGTATGACTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCTTGTACGACTATTC
* *
62811 ATCAACTCATGATGAATTCCGTGGATTTTGCAC-CATACTGCCTGTACGACTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCTTGTACGACTATTC
* * * *
62866 ATTAACTCATGATGAATTCCGTGTATTTTCCACACATATTGCTTGTACGACTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCTTGTACGACTATTC
* * * *
62922 ATCAAATCATGATGAATTCCGTGGATTTTG--TATATAGTGCTTGTACGGCTATTC
1 ATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCTTGTACGACTATTC
* * * * *
62976 ATCCACTCATGATGAATTCTC-TAGAATTTGCACATATAGTGCATGTA
1 ATCAACTCATGATGAATTC-CGTGGATTTTGCACACATAGTGCTTGTA
63023 GTACACTTAG
Statistics
Matches: 233, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
54 44 0.19
55 62 0.27
56 127 0.55
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (56 bp):
ATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCTTGTACGACTATTC
Found at i:62866 original size:111 final size:111
Alignment explanation
Indices: 62699--63022 Score: 411
Period size: 111 Copynumber: 2.9 Consensus size: 111
62689 ACGGTAATTG
* * *
62699 ATCAACTCTTGAATGAATTTCATGGA-TTTGCACACATAGTGCATGTACGACTATTCATCAACTC
1 ATCAACTCATG-ATGAATTCCGTGGATTTTGCAC-CATAGTGCATGTACGACTATTCATCAACTC
* *
62763 ATGATGAATTCCGTGGAATTTGCATACATAGTGCTTGTATGACTATTC
64 ATGATGAATTCCGTGGAATTTGCACACATAGTGCTTGTACGACTATTC
* * *
62811 ATCAACTCATGATGAATTCCGTGGATTTTGCACCATACTGCCTGTACGACTATTCATTAACTCAT
1 ATCAACTCATGATGAATTCCGTGGATTTTGCACCATAGTGCATGTACGACTATTCATCAACTCAT
* * * *
62876 GATGAATTCCGTGTATTTTCCACACATATTGCTTGTACGACTATTC
66 GATGAATTCCGTGGAATTTGCACACATAGTGCTTGTACGACTATTC
* * * * * *
62922 ATCAAATCATGATGAATTCCGTGGATTTTGTA-TATAGTGCTTGTACGGCTATTCATCCACTCAT
1 ATCAACTCATGATGAATTCCGTGGATTTTGCACCATAGTGCATGTACGACTATTCATCAACTCAT
* * *
62986 GATGAATTCTC-TAGAATTTGCACATATAGTGCATGTA
66 GATGAATTC-CGTGGAATTTGCACACATAGTGCTTGTA
63023 GTACACTTAG
Statistics
Matches: 183, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
110 54 0.30
111 112 0.61
112 17 0.09
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (111 bp):
ATCAACTCATGATGAATTCCGTGGATTTTGCACCATAGTGCATGTACGACTATTCATCAACTCAT
GATGAATTCCGTGGAATTTGCACACATAGTGCTTGTACGACTATTC
Found at i:64362 original size:47 final size:47
Alignment explanation
Indices: 64308--64404 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
64298 CATCTAACTA
64308 GAAAAATAATTGTCTTGACGTAAGATGATATATATATATATATATAT
1 GAAAAATAATTGTCTTGACGTAAGATGATATATATATATATATATAT
64355 GAAAAATAATTGTCTTGACGTAAGATGATATATATATATATATATAT
1 GAAAAATAATTGTCTTGACGTAAGATGATATATATATATATATATAT
64402 GAA
1 GAA
64405 TATTTCTAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.37
Consensus pattern (47 bp):
GAAAAATAATTGTCTTGACGTAAGATGATATATATATATATATATAT
Found at i:68275 original size:18 final size:17
Alignment explanation
Indices: 68254--68288 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
68244 CCGAGCTTTC
68254 AAAATTGAAAAATGAAAA
1 AAAATTGAAAAAT-AAAA
68272 AAAATTGAAAAATAAAA
1 AAAATTGAAAAATAAAA
68289 TTTTGTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
AAAATTGAAAAATAAAA
Found at i:73181 original size:2 final size:2
Alignment explanation
Indices: 73174--73248 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
73164 TTTCGTAAAT
73174 TA TA 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 TA TA
73216 TA TA TA TA 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 TA TA TA TA T
73249 TGTAGATTGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:73309 original size:2 final size:2
Alignment explanation
Indices: 73302--73338 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
73292 ATAATACTAA
73302 AT AT AT AT AT AT AT AT AT AT AT AT CAT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT A
73339 AGCAATCCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.