Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009256.1 Hibiscus syriacus cultivar Beakdansim tig00112904_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: 65801
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2456 original size:15 final size:16
Alignment explanation
Indices: 2425--2455 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2415 GACATTGACA
2425 AAAAAGTCAAATTTTT
1 AAAAAGTCAAATTTTT
*
2441 AAAAAGTCATATTTT
1 AAAAAGTCAAATTTT
2456 ATGTTTTTTT
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:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
AAAAAGTCAAATTTTT
Found at i:8454 original size:117 final size:119
Alignment explanation
Indices: 8290--8503 Score: 285
Period size: 117 Copynumber: 1.8 Consensus size: 119
8280 ATTTTCTTTT
**
8290 GAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATGTTGAAAAAGGAGTTAGAGAGCTTTT-AA
1 GAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATAATGAAAAAGGAGTTAGAGA--TTTTAAA
*
8354 AATGAAATGTGAAA-TCTTTGAAAAAG-AAATTTTCGAACTAAACAAACTTCTTCTA
64 AATGAAATGTGAAAGT-ATTGAAAAAGAAAATTTTCGAACTAAACAAACTTCTTCTA
* * * * *
8409 GAAA-CTAAAATGGA-TTTGAAAATCAAAATGAAATAATGAAGAAGGATTTAGAGATTTTAAAAA
1 GAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATAATGAAAAAGGAGTTAGAGATTTTAAAAA
*
8472 TGAAATTTGAAAGTATTGAAAAAGAAAATTTT
66 TGAAATGTGAAAGTATTGAAAAAGAAAATTTT
8504 GATTTGAAAG
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
115 4 0.05
116 24 0.29
117 42 0.51
118 9 0.11
119 4 0.05
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.28
Consensus pattern (119 bp):
GAAAGCTAAAATAGACTTGGAAAATAAAAATGAAATAATGAAAAAGGAGTTAGAGATTTTAAAAA
TGAAATGTGAAAGTATTGAAAAAGAAAATTTTCGAACTAAACAAACTTCTTCTA
Found at i:9545 original size:16 final size:16
Alignment explanation
Indices: 9520--9550 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9510 AGAGGATTGC
*
9520 CAAAGCTAAAATTTGA
1 CAAAGATAAAATTTGA
9536 CAAAGATAAAATTTG
1 CAAAGATAAAATTTG
9551 TGATGTATGT
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:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (16 bp):
CAAAGATAAAATTTGA
Found at i:28325 original size:12 final size:12
Alignment explanation
Indices: 28308--28333 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28298 CGAGTTTGTC
28308 TTTTTCATTTGA
1 TTTTTCATTTGA
28320 TTTTTCATTTGA
1 TTTTTCATTTGA
28332 TT
1 TT
28334 ATCAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTTTCATTTGA
Found at i:29223 original size:98 final size:97
Alignment explanation
Indices: 29047--29249 Score: 241
Period size: 98 Copynumber: 2.1 Consensus size: 97
29037 TAATTTACGA
* * * * * *
29047 CATAAAATTACGACACACAAATGTGTGTCATCTTTTTTAATGATGTGTGCTTCAATGACACGCAG
1 CATAAATTTACGACACACAAATGTGTGTCATCTTATTTAATGACGAGGGCTTCAATGACACGCAA
*
29112 CGTAAGTCGTAAAT-GTAAGTCATAAATGCGTGT
66 CGTAAGTCATAAATAGT--GTCATAAATGCGTGT
* *
29145 CATAAATTTATGACACACAAATGTGTGTCATCTTCATTT-ATGACGAGGGCTTCAATGACGCGCA
1 CATAAATTTACGACACACAAATGTGTGTCATCTT-ATTTAATGACGAGGGCTTCAATGACACGCA
* *
29209 ATGTGCA-TCATAAATACGTGTCATAAATGCGTGT
65 ACGT-AAGTCATAAATA-GTGTCATAAATGCGTGT
29243 CATAAAT
1 CATAAAT
29250 GCGCGTCATA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
98 84 0.93
99 4 0.04
100 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (97 bp):
CATAAATTTACGACACACAAATGTGTGTCATCTTATTTAATGACGAGGGCTTCAATGACACGCAA
CGTAAGTCATAAATAGTGTCATAAATGCGTGT
Found at i:29234 original size:13 final size:13
Alignment explanation
Indices: 29216--29259 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
29206 GCAATGTGCA
*
29216 TCATAAATACGTG
1 TCATAAATGCGTG
29229 TCATAAATGCGTG
1 TCATAAATGCGTG
*
29242 TCATAAATGCGCG
1 TCATAAATGCGTG
29255 TCATA
1 TCATA
29260 GATGTATGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (13 bp):
TCATAAATGCGTG
Found at i:35134 original size:18 final size:19
Alignment explanation
Indices: 35099--35141 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
35089 TGAATAGATA
*
35099 AATAAATATATAAATAATG
1 AATAAAAATATAAATAATG
35118 AATAAAAATAT-AATAATG
1 AATAAAAATATAAATAATG
35136 AATAAA
1 AATAAA
35142 GTAGATAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AATAAAAATATAAATAATG
Found at i:37256 original size:46 final size:46
Alignment explanation
Indices: 37187--37516 Score: 536
Period size: 46 Copynumber: 7.2 Consensus size: 46
37177 AATATAATCT
* *
37187 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTAGCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
37232 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
37278 CTTACCATCTAATACCATAAGATCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
37324 CTTACCATTTAATACCATAAGCTAGTAAGCTTATTTTACCAATACA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
37370 CTTTCCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
37416 TTTACCATTTAATAGCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
37462 CTTACCATTTAATACCATAAGTTCTTAAGCTTATTTTACCAATACA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
37508 CTTGCCATT
1 CTTACCATT
37517 ATTCTATAAC
Statistics
Matches: 264, Mismatches: 20, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
45 10 0.04
46 254 0.96
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.38
Consensus pattern (46 bp):
CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:37716 original size:61 final size:61
Alignment explanation
Indices: 37607--37721 Score: 167
Period size: 61 Copynumber: 1.9 Consensus size: 61
37597 GTAGTACTAA
* *
37607 ACCTGCACTAAGCTTACGCCATAGTGCTAATCCAGATATGACACATAAGGTCGTGCCCACC
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTCGTGCCCACC
* * * * *
37668 ACCTACACTAAGCTTACGCTATAGTGCTACTCCGGACATGATATATAAGGTCGT
1 ACCTACACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTCGT
37722 ATCCACCTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (61 bp):
ACCTACACTAAGCTTACGCCATAGTGCTAATCCAGACATGACACATAAGGTCGTGCCCACC
Found at i:39612 original size:13 final size:13
Alignment explanation
Indices: 39580--39626 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
39570 AACGGTCAAC
39580 GGTCAACGGGTCG
1 GGTCAACGGGTCG
39593 GGT---CGGGTCG
1 GGTCAACGGGTCG
39603 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
39616 GGTAAACGGGT
1 GGTCAACGGGT
39627 AAACGGGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:39659 original size:10 final size:10
Alignment explanation
Indices: 39642--39693 Score: 63
Period size: 10 Copynumber: 5.3 Consensus size: 10
39632 GGTCGTGACA
39642 GGTC-AAACC
1 GGTCAAAACC
39651 GGTCAAAACC
1 GGTCAAAACC
*
39661 GATTCAAAACC
1 G-GTCAAAACC
*
39672 GGT-TAAACC
1 GGTCAAAACC
39681 GGTCAAAACC
1 GGTCAAAACC
39691 GGT
1 GGT
39694 TTCCAGCGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 12 0.33
10 15 0.42
11 9 0.25
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.15
Consensus pattern (10 bp):
GGTCAAAACC
Found at i:46886 original size:13 final size:13
Alignment explanation
Indices: 46847--46898 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
46837 ACCGGTCAAC
46847 GGTCAACGGGTCG
1 GGTCAACGGGTCG
**
46860 GGTCGGGTCGGGTCG
1 GGTC--AACGGGTCG
46875 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
46888 GGTAAACGGGT
1 GGTCAACGGGT
46899 AAACGGGTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 21 0.66
15 11 0.34
ACGTcount: A:0.13, C:0.19, G:0.50, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:46890 original size:5 final size:5
Alignment explanation
Indices: 46853--46878 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46843 CAACGGTCAA
46853 CGGGT CGGGT CGGGT CGGGT CGGGT C
1 CGGGT CGGGT CGGGT CGGGT CGGGT C
46879 AACGGGTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.58, T:0.19
Consensus pattern (5 bp):
CGGGT
Found at i:46924 original size:10 final size:10
Alignment explanation
Indices: 46911--46956 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
46901 ACGGGTCGTG
46911 ACCGGTCAAA
1 ACCGGTCAAA
46921 ACCGGTTCAAA
1 ACCGG-TCAAA
*
46932 ACCGGT-TAA
1 ACCGGTCAAA
46941 ACCGGTCAAA
1 ACCGGTCAAA
46951 ACCGGT
1 ACCGGT
46957 TTCCAGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 8 0.25
10 14 0.44
11 10 0.31
ACGTcount: A:0.35, C:0.28, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:46932 original size:11 final size:11
Alignment explanation
Indices: 46911--46957 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
46901 ACGGGTCGTG
46911 ACCGG-TCAAA
1 ACCGGTTCAAA
46921 ACCGGTTCAAA
1 ACCGGTTCAAA
46932 ACCGGTT--AA
1 ACCGGTTCAAA
46941 ACCGG-TCAAA
1 ACCGGTTCAAA
46951 ACCGGTT
1 ACCGGTT
46958 TCCAGCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 1 0.03
9 7 0.21
10 12 0.36
11 13 0.39
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (11 bp):
ACCGGTTCAAA
Found at i:46951 original size:19 final size:20
Alignment explanation
Indices: 46919--46957 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
46909 TGACCGGTCA
46919 AAACCGGTTCAAAACCGGTT
1 AAACCGGTTCAAAACCGGTT
46939 AAACCGG-TCAAAACCGGTT
1 AAACCGGTTCAAAACCGGTT
46958 TCCAGCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
AAACCGGTTCAAAACCGGTT
Found at i:50985 original size:6 final size:5
Alignment explanation
Indices: 50978--51041 Score: 58
Period size: 5 Copynumber: 12.2 Consensus size: 5
50968 CATTTTTTTC
* * *
50978 TCTTT CTCTTTT TCTTT TCTTT TCTTT T-TTT CCATT TCTTT TTTTT TCGTTT
1 TCTTT -TCT-TT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TC-TTT
51030 TCTTTT TCTTT T
1 TC-TTT TCTTT T
51042 TATTCTCTCT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
4 3 0.06
5 27 0.56
6 16 0.33
7 2 0.04
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:50991 original size:14 final size:13
Alignment explanation
Indices: 50972--51059 Score: 58
Period size: 13 Copynumber: 6.8 Consensus size: 13
50962 ATCTATCATT
50972 TTTTTCTCTTTCTC
1 TTTTTCT-TTTCTC
50986 TTTTTCTTTTCT-
1 TTTTTCTTTTCTC
*
50998 TTTCTTTTTTTC-C
1 TTT-TTCTTTTCTC
* *
51011 ATTTCTTTTTTTTTC
1 -TTT-TTCTTTTCTC
*
51026 GTTTTCTTTT-TC
1 TTTTTCTTTTCTC
* *
51038 TTTTTATTCTCTC
1 TTTTTCTTTTCTC
51051 TTTTT-TTTT
1 TTTTTCTTTT
51060 TAACTCTTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
12 15 0.25
13 25 0.41
14 20 0.33
15 1 0.02
ACGTcount: A:0.02, C:0.18, G:0.01, T:0.78
Consensus pattern (13 bp):
TTTTTCTTTTCTC
Found at i:50995 original size:19 final size:18
Alignment explanation
Indices: 50973--51059 Score: 67
Period size: 18 Copynumber: 4.9 Consensus size: 18
50963 TCTATCATTT
50973 TTTTCTCTTTCTCTTTTTC
1 TTTTCTCTTT-TCTTTTTC
*
50992 TTTTCT-TTTCTTTTTTTC
1 TTTTCTCTTT-TCTTTTTC
**
51010 CATT-TCTTTT-TTTTTC
1 TTTTCTCTTTTCTTTTTC
*
51026 GTTTTCT-TTTTCTTTTTA
1 -TTTTCTCTTTTCTTTTTC
*
51044 TTCTCTCTTTT-TTTTT
1 TTTTCTCTTTTCTTTTT
51060 TAACTCTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
16 6 0.11
17 18 0.32
18 26 0.46
19 6 0.11
ACGTcount: A:0.02, C:0.18, G:0.01, T:0.78
Consensus pattern (18 bp):
TTTTCTCTTTTCTTTTTC
Found at i:51042 original size:6 final size:6
Alignment explanation
Indices: 50972--51060 Score: 60
Period size: 6 Copynumber: 14.8 Consensus size: 6
50962 ATCTATCATT
* **
50972 TTTTTC TCTTTCTC TTTTTC -TTTTC TTTTCTT TTTTTC CATTTC -TTTT-
1 TTTTTC T-TTT-TC TTTTTC TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC
* * *
51020 TTTTTC GTTTTC TTTTTC TTTTTA TTCTCTC TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TTTTT
51061 AACTCTTATA
Statistics
Matches: 65, Mismatches: 11, Indels: 15
0.71 0.12 0.16
Matches are distributed among these distances:
5 17 0.26
6 30 0.46
7 15 0.23
8 3 0.05
ACGTcount: A:0.02, C:0.18, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:51042 original size:35 final size:34
Alignment explanation
Indices: 50976--51059 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 34
50966 ATCATTTTTT
50976 TCTCTTTCTCTTTTTCTTTTCTTTTCTTTTTT-TCC
1 TCTCTTT-T-TTTTTCTTTTCTTTTCTTTTTTATCC
* *
51011 ATTTCTTTTTTTTTCGTTTTCTTTT-TCTTTTTATTC
1 -TCTCTTTTTTTTTC-TTTTCTTTTCT-TTTTTATCC
51047 TCTCTTTTTTTTT
1 TCTCTTTTTTTTT
51060 TAACTCTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
34 7 0.17
35 27 0.64
36 8 0.19
ACGTcount: A:0.02, C:0.19, G:0.01, T:0.77
Consensus pattern (34 bp):
TCTCTTTTTTTTTCTTTTCTTTTCTTTTTTATCC
Found at i:51066 original size:17 final size:19
Alignment explanation
Indices: 51030--51066 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
51020 TTTTTCGTTT
*
51030 TCTTTTTCTTTTTATTCTC
1 TCTTTTTCTTTTTATACTC
51049 TCTTTTT-TTTTTA-ACTC
1 TCTTTTTCTTTTTATACTC
51066 T
1 T
51067 TATACCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 6 0.35
19 7 0.41
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (19 bp):
TCTTTTTCTTTTTATACTC
Found at i:53306 original size:13 final size:13
Alignment explanation
Indices: 53288--53319 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53278 TTATGAATAT
*
53288 TGAACAGTACTAG
1 TGAACAGTACCAG
53301 TGAACAGTACCAG
1 TGAACAGTACCAG
53314 TGAACA
1 TGAACA
53320 ATGAACAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (13 bp):
TGAACAGTACCAG
Found at i:53421 original size:21 final size:21
Alignment explanation
Indices: 53397--53438 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
53387 AAAATTGTGT
*
53397 ATCGATGCACTGCTACATTGC
1 ATCGATGCACTACTACATTGC
53418 ATCGATGCACTACTACATTGC
1 ATCGATGCACTACTACATTGC
53439 TGCTACAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (21 bp):
ATCGATGCACTACTACATTGC
Found at i:53909 original size:46 final size:46
Alignment explanation
Indices: 53840--54169 Score: 527
Period size: 46 Copynumber: 7.2 Consensus size: 46
53830 TATATAATCT
* *
53840 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATG
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
53885 CTTACCATTTAATACCATAAGCTCGTAAGCTTAATTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
53931 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
** * *
53977 CTTACCATTTAATATAATAAGCTCGTAAGCTTATTTTACCGATACA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
54023 CTTACCATTTCATACCATAAGATCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
54069 TTTACCATTTAATACCATAAGCTCATAAGTTTATTTTACCAATATA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
54115 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATACA
1 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
*
54161 CTTGCCATT
1 CTTACCATT
54170 ATTCCATAAC
Statistics
Matches: 260, Mismatches: 24, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
45 10 0.04
46 250 0.96
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (46 bp):
CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:56064 original size:6 final size:7
Alignment explanation
Indices: 56047--56071 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56037 GAAAATAATT
56047 TTTTTTA
1 TTTTTTA
56054 TTTTTTA
1 TTTTTTA
56061 TTTTTTA
1 TTTTTTA
56068 TTTT
1 TTTT
56072 CATGACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:61394 original size:21 final size:21
Alignment explanation
Indices: 61365--61415 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
61355 AATAATGAAC
*
61365 TATCAATACCGTTTAAAGAAG
1 TATCGATACCGTTTAAAGAAG
61386 TATCGATACCGTTTAAAGAAG
1 TATCGATACCGTTTAAAGAAG
61407 TATCGATAC
1 TATCGATAC
61416 TGAGGTGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (21 bp):
TATCGATACCGTTTAAAGAAG
Found at i:61922 original size:54 final size:53
Alignment explanation
Indices: 61840--62051 Score: 298
Period size: 54 Copynumber: 3.9 Consensus size: 53
61830 TACTATTGGC
61840 ACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCAGA
1 ACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC-GA
* *
61894 ACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTTTGC
1 ACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCA-TTTCGA
* * * * *
61948 ACTATGTATACAATCCATGGAATTCATAATGAGATGGTGAATTACCATTTCGA
1 ACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGA
* * * *
62001 CACTATGTGTGCAAACCATAGAATTCATAATTAGTTTGTAAATTACCATTT
1 -ACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCATTT
62052 TGGCACTTAG
Statistics
Matches: 139, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
53 4 0.03
54 132 0.95
55 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (53 bp):
ACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGA
Found at i:62027 original size:108 final size:108
Alignment explanation
Indices: 61835--62058 Score: 342
Period size: 108 Copynumber: 2.1 Consensus size: 108
61825 ATATGTACTA
* * * *
61835 TTGGCACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCAGAACTATG
1 TTGGCACTATGTATACAACCCATGGAATTCATAATGAGATGGTGAATTACCATTTCAGAACTATG
* * *
61900 TGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCATT
66 TGTGCAAACCATAGAATTCATAATGAGTTTGTAAATTACCATT
* *
61943 TTTGCACTATGTATACAATCCATGGAATTCATAATGAGATGGTGAATTACCATTTC-GACACTAT
1 TTGGCACTATGTATACAACCCATGGAATTCATAATGAGATGGTGAATTACCATTTCAGA-ACTAT
*
62007 GTGTGCAAACCATAGAATTCATAATTAGTTTGTAAATTACCATT
65 GTGTGCAAACCATAGAATTCATAATGAGTTTGTAAATTACCATT
62051 TTGGCACT
1 TTGGCACT
62059 TAGGTGCAAC
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
107 2 0.02
108 102 0.98
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (108 bp):
TTGGCACTATGTATACAACCCATGGAATTCATAATGAGATGGTGAATTACCATTTCAGAACTATG
TGTGCAAACCATAGAATTCATAATGAGTTTGTAAATTACCATT
Done.