Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002329.1 Hibiscus syriacus cultivar Beakdansim tig00004754_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: 74827
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4770 original size:16 final size:16
Alignment explanation
Indices: 4745--4792 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
4735 AATCCATAAA
4745 ATTATTTTTATTATATT
1 ATTA-TTTTATTATATT
*
4762 -TTATATTTATAATATT
1 ATTAT-TTTATTATATT
4778 ATGTATTTTATTATA
1 AT-TATTTTATTATA
4793 ATATAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.04
16 13 0.50
17 9 0.35
18 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
ATTATTTTATTATATT
Found at i:18100 original size:16 final size:16
Alignment explanation
Indices: 18079--18109 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18069 CTTCTCCTGT
*
18079 GGTCCTAGCTCACTGC
1 GGTCCTACCTCACTGC
18095 GGTCCTACCTCACTG
1 GGTCCTACCTCACTG
18110 TTCTGTTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.39, G:0.23, T:0.26
Consensus pattern (16 bp):
GGTCCTACCTCACTGC
Found at i:18215 original size:6 final size:6
Alignment explanation
Indices: 18204--18235 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
18194 TAAATTTATT
*
18204 AAATTA AAATTA AAATTA AAATTA AAACTA AA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AA
18236 TAGATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATTA
Found at i:18561 original size:120 final size:119
Alignment explanation
Indices: 18344--18579 Score: 400
Period size: 120 Copynumber: 2.0 Consensus size: 119
18334 CTGTTTGAAA
*
18344 AAAATAGAAGAGCATTGGTCAACTTAGAATTTTTCTATAATTAAGTGGTCATAGGTGTAAGTTAC
1 AAAATAGAAGAGCATTGGTCAAATTAGAATTTTTCTATAATTAAGTGGTCATAGGTGTAAGTTAC
** *
18409 CCTAATTGTTTTTTACCCGAACTTCCTCAGCTAAAGACTTAAGAGTTAATTGGTG
66 CCTAATTGTTTTTTACCCGAACTTCCAAAGCTAAAGACTT-AGAATTAATTGGTG
* * *
18464 AAAATAGAAGATCATTGGTCAAATTAGAATTTTTCTATAATTATGTGGTCATAGGTGTAATTTAC
1 AAAATAGAAGAGCATTGGTCAAATTAGAATTTTTCTATAATTAAGTGGTCATAGGTGTAAGTTAC
18529 CCTAATTGTTTTTTACCCGAACTTCCAAAGCTAAAGACTTAGAATTAATTG
66 CCTAATTGTTTTTTACCCGAACTTCCAAAGCTAAAGACTTAGAATTAATTG
18580 CATCATAAGT
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 10 0.09
120 99 0.91
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (119 bp):
AAAATAGAAGAGCATTGGTCAAATTAGAATTTTTCTATAATTAAGTGGTCATAGGTGTAAGTTAC
CCTAATTGTTTTTTACCCGAACTTCCAAAGCTAAAGACTTAGAATTAATTGGTG
Found at i:18775 original size:59 final size:59
Alignment explanation
Indices: 18615--18778 Score: 190
Period size: 59 Copynumber: 2.8 Consensus size: 59
18605 CTTATTCTTG
* * * * *
18615 ATTAGTCCT-AAACTTTTAAATATTTTAATTTCATCCCTAACAATGACTATCATTCTAT
1 ATTAGTCCTCAAACTTTTGAACATTTTAATTTCATCCCAAACTATGACTATCATTCTAA
* * * *
18673 ATTAGTCCTCCAACTTTTGAACATTTTATTTTCATCCTTAAACTATGACCT-TCGTT-TAA
1 ATTAGTCCTCAAACTTTTGAACATTTTAATTTCATCC-CAAACTATGA-CTATCATTCTAA
*
18732 ATTAGTCCTCAAACTTTTTGAACATTTCAATTTCATCCCAAACTATG
1 ATTAGTCCTCAAAC-TTTTGAACATTTTAATTTCATCCCAAACTATG
18779 TGTATATAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
58 9 0.10
59 46 0.52
60 32 0.36
61 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.42
Consensus pattern (59 bp):
ATTAGTCCTCAAACTTTTGAACATTTTAATTTCATCCCAAACTATGACTATCATTCTAA
Found at i:26666 original size:2 final size:2
Alignment explanation
Indices: 26659--26692 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
26649 GATTCCTCAG
26659 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
26693 TTGTGAAAAG
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:31215 original size:13 final size:13
Alignment explanation
Indices: 31197--31222 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31187 TAAATTATTG
31197 GTATATTCCATTC
1 GTATATTCCATTC
31210 GTATATTCCATTC
1 GTATATTCCATTC
31223 TGATCACTAA
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:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
GTATATTCCATTC
Found at i:41488 original size:55 final size:54
Alignment explanation
Indices: 41404--41987 Score: 381
Period size: 51 Copynumber: 11.0 Consensus size: 54
41394 AAACTTGAAA
** * * *
41404 AATCTTCAAATGACGGGTCTGCTCCCTATTCTATCAGGGAGTATAAGACTCAAAC
1 AATCTTCAAAAAACGTGTCCGCTCCCTATTCT-TCAGAGAGTATAAGACTCAAAC
*** * ** * **
41459 AATCTTCGGCAAACGTGTCTGCTCCCTATTCAGCCAGGGAGTATAAGACTTGAAC
1 AATCTTCAAAAAACGTGTCCGCTCCCTATTC-TTCAGAGAGTATAAGACTCAAAC
* * *
41514 AATCTTCAATAAAACG-GATCCACTCTCTATTCCTTTAGAGAGTAT-AGAACTCAGAA-
1 AATCTTCAA-AAAACGTG-TCCGCTCCCTATT-CTTCAGAGAGTATAAG-ACTCA-AAC
* * * *
41570 AATCTTCAATAAACGAGTCCGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAAC
1 AATCTTCAAAAAACGTGTCCGCTCCCTATTC-TTCAGAGAGTATAAG-ACTCAAAC
* * * *
41625 AATCTTCATAAAATGTGTCCGCTCTCTAATCCTTCAGAGAGTATATA-ACTCAAAC
1 AATCTTCAAAAAACGTGTCCGCTCCCT-ATTCTTCAGAGAGTATA-AGACTCAAAC
** * * *
41680 AATCTTCAACGAACTTGCCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----C
1 AATCTTCAAAAAACGTGTCCGCTCCCTATT-CTTCAGAGAGTATAAGACTCAAAC
** * *
41731 AATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----C
1 AATCTTCAAAAAACGTGTCCGCTCCCTATT-CTTCAGAGAGTATAAGACTCAAAC
** * *
41782 AATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----C
1 AATCTTCAAAAAACGTGTCCGCTCCCTATT-CTTCAGAGAGTATAAGACTCAAAC
** * * *
41833 AATCTTCAACGAACTTGTCCACTCCCTATTCCTTCAGAGAGTATAGGACT----C
1 AATCTTCAAAAAACGTGTCCGCTCCCTATT-CTTCAGAGAGTATAAGACTCAAAC
** * *
41884 AATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT----C
1 AATCTTCAAAAAACGTGTCCGCTCCCTATTC-TTCAGAGAGTATAAGACTCAAAC
** * *
41935 AATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAA
1 AATCTTCAAAAAACGTGTCCGCTCCCTATTC-TTCAGAGAGTATAAGACTCAA
41988 TCTTCAACAA
Statistics
Matches: 463, Mismatches: 48, Indels: 37
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.00
51 250 0.54
54 5 0.01
55 164 0.35
56 39 0.08
57 4 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (54 bp):
AATCTTCAAAAAACGTGTCCGCTCCCTATTCTTCAGAGAGTATAAGACTCAAAC
Found at i:41687 original size:110 final size:110
Alignment explanation
Indices: 41424--41987 Score: 434
Period size: 102 Copynumber: 5.3 Consensus size: 110
41414 TGACGGGTCT
* * ** *
41424 GCTCCCTATT-CTATCAGGGAGTATA-AGACTCAAACAATCTTCGGCAAACGTGTCTGCTCCCTA
1 GCTCTCTATTCCT-TCAGAGAGTATAGA-ACTCAAACAATCTTCAACAAACGTGTCCGCTCCCTA
*** * * *
41487 TTCAGCCAGGGAGTATA-AGACTTGAACAATCTTCAATAAAACG-GATCC
64 TTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTC-ATAAAATGTG-TCC
* * * *
41535 ACTCTCTATTCCTTTAGAGAGTATAGAACTCAGAA-AATCTTCAATAAACGAGTCCGCTCCCTAT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCA-AACAATCTTCAACAAACGTGTCCGCTCCCTAT
* *
41599 TCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAATGTGTCC
65 TCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAATGTGTCC
* * * * *
41645 GCTCTCTAATCCTTCAGAGAGTATATAACTCAAACAATCTTCAACGAACTTGCCCGCTCCCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAACAAACGTGTCCGCTCCCTATT
* *
41710 CCTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACT-TGTCC
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCATA--AAATGTGTCC
* * * *
41751 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCCGCTCCCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAACAAACGTGTCCGCTCCCTATT
* *
41812 CCTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACT-TGTCC
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCATA--AAATGTGTCC
* * * * *
41853 ACTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCCGCTCCCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAACAAACGTGTCCGCTCCCTATT
* * *
41914 CATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACT-TGTCC
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCATA--AAATGTGTCC
* * *
41955 GCTCCCTATTCATTCAGAGAGTATAGGACTCAA
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAA
41988 TCTTCAACAA
Statistics
Matches: 406, Mismatches: 36, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
102 199 0.49
105 1 0.00
106 40 0.10
107 3 0.01
109 2 0.00
110 80 0.20
111 75 0.18
112 6 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (110 bp):
GCTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAACAAACGTGTCCGCTCCCTATT
CCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAATGTGTCC
Found at i:41755 original size:51 final size:51
Alignment explanation
Indices: 41540--41995 Score: 610
Period size: 51 Copynumber: 8.7 Consensus size: 51
41530 GATCCACTCT
* * ** **
41540 CTATTCCTTTAGAGAGTATAGAACTCAGAAAATCTTCAATAAACGAGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTTGTCCGCTCC
* * * * *
41595 CTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATA--AAATGTGTCCGCTCT
1 CTATTCCTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACT-TGTCCGCTCC
* ** *
41650 CTAATCCTTCAGAGAGTATATAACTCAAACAATCTTCAACGAACTTGCCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCCGCTCC
41705 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCC
41756 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCC
*
41807 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCACTCC
1 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCC
41858 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCC
*
41909 CTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCC
1 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCC
*
41960 CTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
1 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
41996 AAACGAATTT
Statistics
Matches: 371, Mismatches: 22, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
51 262 0.71
54 3 0.01
55 101 0.27
56 4 0.01
59 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (51 bp):
CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCC
Found at i:43330 original size:27 final size:27
Alignment explanation
Indices: 43311--43391 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 27
43301 TTTTATTTCT
*
43311 CTTTTTTCATTT-TTCTCTTTTTCTTC
1 CTTTTTCCATTTGTTCTCTTTTTCTTC
43337 CTTTTTCCATTTGTTCTC---TTC--C
1 CTTTTTCCATTTGTTCTCTTTTTCTTC
* *
43359 CTTTTT-CATTTTTTCTTCTTTTTCTTT
1 CTTTTTCCATTTGTTC-TCTTTTTCTTC
43386 CTTTTT
1 CTTTTT
43392 GTTTTTCCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
21 8 0.18
22 9 0.20
24 3 0.07
25 3 0.07
26 11 0.24
27 11 0.24
ACGTcount: A:0.04, C:0.23, G:0.01, T:0.72
Consensus pattern (27 bp):
CTTTTTCCATTTGTTCTCTTTTTCTTC
Found at i:43358 original size:21 final size:19
Alignment explanation
Indices: 43328--43382 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 19
43318 CATTTTTCTC
43328 TTTTTCTTCCTTTTTCCAT
1 TTTTTCTTCCTTTTTCCAT
43347 TTGTTCTCTTCCCTTTTT-CAT
1 TT-TT-TCTT-CCTTTTTCCAT
43368 TTTTTCTT-CTTTTTC
1 TTTTTCTTCCTTTTTC
43383 TTTCTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
17 6 0.19
19 6 0.19
20 4 0.12
21 9 0.28
22 7 0.22
ACGTcount: A:0.04, C:0.25, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTCTTCCTTTTTCCAT
Found at i:53152 original size:44 final size:47
Alignment explanation
Indices: 53088--53184 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 47
53078 TGTTATCCAT
53088 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC-TTATTC-
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
* *
53133 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
53180 AAAAA
1 AAAAA
53185 ACGAAAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
44 28 0.60
45 8 0.17
46 6 0.13
47 5 0.11
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:57283 original size:36 final size:36
Alignment explanation
Indices: 57202--57418 Score: 323
Period size: 36 Copynumber: 6.1 Consensus size: 36
57192 AGATGAACAA
* *
57202 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTC-AC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
*
57237 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
57273 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCATT-
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-TTC
* *
57309 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
* *
57345 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTC-AC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
*
57380 TTTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
1 -TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
57417 TT
1 TT
57419 CCTCACCTTC
Statistics
Matches: 164, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
35 34 0.21
36 127 0.77
37 3 0.02
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (36 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCTTC
Found at i:57342 original size:72 final size:71
Alignment explanation
Indices: 57202--57418 Score: 380
Period size: 72 Copynumber: 3.0 Consensus size: 71
57192 AGATGAACAA
* *
57202 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCATTTGAATCGAAAGTGCCGATGCTTCCTTTCG
57267 TTCTTC
66 TTCTTC
*
57273 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCATTTTGAATCGAAAGTGCTGATGCTTCCTTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCA-TTTGAATCGAAAGTGCCGATGCTTCCTTTC
57338 GTTCTTC
65 GTTCTTC
*
57345 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCCGATGCTTCCTTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCA-TTTGAATCGAAAGTGCCGATGCTTCCTTTC
57410 GTTCTTC
65 GTTCTTC
57417 TT
1 TT
57419 CCTCACCTTC
Statistics
Matches: 139, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 33 0.24
72 106 0.76
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (71 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCATTTGAATCGAAAGTGCCGATGCTTCCTTTCG
TTCTTC
Found at i:61241 original size:19 final size:19
Alignment explanation
Indices: 61219--61297 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 19
61209 CGCGATTTTG
61219 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
61238 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
61258 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
*
61282 AAAAAGTGTTGCGATA
1 AAAATGTGTTGCGATA
61298 ATGAAAAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
19 26 0.52
20 3 0.06
22 8 0.16
24 3 0.06
25 10 0.20
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:61285 original size:22 final size:21
Alignment explanation
Indices: 61217--61304 Score: 62
Period size: 19 Copynumber: 4.3 Consensus size: 21
61207 CACGCGATTT
61217 TGAAAA-TG-TGTTGCGATAG
1 TGAAAAGTGTTGTTGCGATAG
* *
61236 TTAAAA-TG-TGTTGCGAGAG
1 TGAAAAGTGTTGTTGCGATAG
61255 TTTGAAAAACGTGTTGTTGCGATAG
1 --TG-AAAA-GTGTTGTTGCGATAG
* *
61280 TGAAAA-AG-TGTTGCGATAA
1 TGAAAAGTGTTGTTGCGATAG
61299 TGAAAA
1 TGAAAA
61305 ATCCAAAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
19 33 0.58
20 1 0.02
21 1 0.02
22 8 0.14
23 2 0.04
24 2 0.04
25 10 0.18
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (21 bp):
TGAAAAGTGTTGTTGCGATAG
Found at i:61302 original size:19 final size:19
Alignment explanation
Indices: 61269--61305 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
61259 AAAAACGTGT
*
61269 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAATGAAAAAG
61288 TGTTGCGATAATGAAAAA
1 TGTTGCGATAATGAAAAA
61306 TCCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAATGAAAAAG
Found at i:68799 original size:2 final size:2
Alignment explanation
Indices: 68792--68819 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
68782 TTTATAATTG
68792 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
68820 ATTTGAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71736 original size:18 final size:17
Alignment explanation
Indices: 71707--71752 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
71697 ATTTTCAAAG
71707 TAATAATTAAACCGATT
1 TAATAATTAAACCGATT
*
71724 TAATAACTTAAACTGA-T
1 TAATAA-TTAAACCGATT
71741 TAATTAATTAAA
1 TAA-TAATTAAA
71753 TAAACCACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (17 bp):
TAATAATTAAACCGATT
Found at i:71974 original size:21 final size:21
Alignment explanation
Indices: 71950--71989 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
71940 TGACTGAGGT
71950 TCACTTGATAATTGAGTTATG
1 TCACTTGATAATTGAGTTATG
71971 TCACTTGATAATTGAGTTA
1 TCACTTGATAATTGAGTTA
71990 CAGGTCAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (21 bp):
TCACTTGATAATTGAGTTATG
Found at i:72698 original size:21 final size:21
Alignment explanation
Indices: 72653--72698 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
72643 AAAGTTTTGT
*
72653 AGATTTTCAGGGAAGGACATG
1 AGATTTTCAGGGAAGGACATA
* *
72674 AGATTTTCAGTGAAGGACTTA
1 AGATTTTCAGGGAAGGACATA
72695 AGAT
1 AGAT
72699 GTTGGAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (21 bp):
AGATTTTCAGGGAAGGACATA
Found at i:73904 original size:16 final size:16
Alignment explanation
Indices: 73883--73926 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
73873 TCCAACTATC
73883 TAGTATTTTCGAGGTG
1 TAGTATTTTCGAGGTG
73899 TAGTA-TTTCGAGGTG
1 TAGTATTTTCGAGGTG
*
73914 CAGTATTTT-GAGG
1 TAGTATTTTCGAGG
73927 AAAATCCAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.20, C:0.07, G:0.32, T:0.41
Consensus pattern (16 bp):
TAGTATTTTCGAGGTG
Done.