Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002668.1 Hibiscus syriacus cultivar Beakdansim tig00005480_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: 60612
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:778 original size:23 final size:23
Alignment explanation
Indices: 739--838 Score: 164
Period size: 23 Copynumber: 4.3 Consensus size: 23
729 CGAAGTGCCG
*
739 CGTAGAAATTGTCCCGAAAGACCA
1 CGTAGAAA-TGTCCCGAAGGACCA
*
763 CATAGAAATGTCCCGAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
786 CGTAGAAATGTCCCGAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
*
809 CGTAGAATTGTCCCGAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
832 CGTAGAA
1 CGTAGAA
839 GGAATGAGAT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
23 65 0.90
24 7 0.10
ACGTcount: A:0.36, C:0.25, G:0.24, T:0.15
Consensus pattern (23 bp):
CGTAGAAATGTCCCGAAGGACCA
Found at i:1693 original size:30 final size:29
Alignment explanation
Indices: 1659--1726 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 29
1649 CATAAAATTC
1659 TTATAATAATAATAATAATTATTATTATA
1 TTATAATAATAATAATAATTATTATTATA
1688 TTTATAATAATAATAATAATTATTATTATA
1 -TTATAATAATAATAATAATTATTATTATA
1718 TTATAATAA
1 TTATAATAA
1727 AGATTCTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.24
30 29 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TTATAATAATAATAATAATTATTATTATA
Found at i:2307 original size:142 final size:140
Alignment explanation
Indices: 1923--2375 Score: 664
Period size: 142 Copynumber: 3.2 Consensus size: 140
1913 ATTGTCTAAC
*
1923 TATATTTATA-TTATATTT-TA-TATATTTATATTT-TATTT-TATTTATATTTATATTTATATA
1 TATATTTATATTTATATTTATATTTTATTTATATTTATATTTATATTTATATTTATATTTATATA
* *
1983 T-TTATATTTATATTATA-TTATATTTATATTTATTATATTTATATTTATATTTATA-TTATATT
66 TATTATATTTATATTATATTTATATTTATATTTATTTTATATATATTTATATTTATATTTATATT
2045 ATATTTATATT
131 -TATTTATATT
2056 TATATTTATATTTATATTTATATTTTATTTATATTTATTTATATTATATTTATATTTATATTTAT
1 TATATTTATATTTATATTTATATTTTATTTATATTTA--TAT-TTATATTTATATTTATATTTAT
2121 ATATATTATATTTATATTTATATTTATATTTAT-TTATATTTTATATATATTTATATTTATATTT
63 ATATATTATATTTATA-TTATATTTATATTTATATT-TATTTTATATATATTTATATTTATATTT
2185 ATATTTATTTATATT
126 ATATTTATTTATATT
*
2200 TATATTTATATTTATATTTATATTTATATTTATATTTATATTTATATTTATA-TTATATTTTATT
1 TATATTTATATTTATATTTATATTT-TATTTATATTTATATTTATATTTATATTTATA-TTTATA
2264 TATATTATATTTTATATTATATTTATATTTATATTTATTTTATATTTATATTTATA-TTATATTT
64 TATATTATA-TTTATATTATATTTATATTTATATTTATTTTATA--TATATTTATATTTATATTT
2328 AGTA--TATTTATATT
126 A-TATTTATTTATATT
2342 TATATTTATATTTATATTTATA-TTTATTTATATT
1 TATATTTATATTTATATTTATATTTTATTTATATT
2376 GCACCGAAAT
Statistics
Matches: 296, Mismatches: 4, Indels: 33
0.89 0.01 0.10
Matches are distributed among these distances:
133 10 0.03
134 8 0.03
135 2 0.01
136 12 0.04
139 3 0.01
140 12 0.04
141 30 0.10
142 93 0.31
143 27 0.09
144 80 0.27
145 19 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.66
Consensus pattern (140 bp):
TATATTTATATTTATATTTATATTTTATTTATATTTATATTTATATTTATATTTATATTTATATA
TATTATATTTATATTATATTTATATTTATATTTATTTTATATATATTTATATTTATATTTATATT
TATTTATATT
Found at i:2375 original size:6 final size:6
Alignment explanation
Indices: 1923--2368 Score: 613
Period size: 6 Copynumber: 77.5 Consensus size: 6
1913 ATTGTCTAAC
*
1923 TATATT TATATT ATATTTT ATATATT TATATT T-TATT T-TATT TATATT
1 TATATT TATATT -TATATT -TATATT TATATT TATATT TATATT TATATT
1971 TATATTT ATATATT TATATT TATA-T TATA-T TATATT TATA-T T-TA-T
1 TATA-TT -TATATT TATATT TATATT TATATT TATATT TATATT TATATT
2016 TATATT TATATT TATATT TATA-T TATA-T TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
2062 TATATT TATATT TATATT T-TATT TATA-T T-TATT TATA-T TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
2106 TATATT TATATT TATA-- TATA-T TATATT TATATT TATATT TATA-T
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
*
2150 T-TATT TATATT T-TATA TATATT TATATT TATATT TATA-T T-TATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
2194 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
2242 TATATT TATA-T TATATT T-TATT TATA-T TATATT T-TATAT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATAT-T TATATT
2287 TATATT TATATT TAT-TT TATATT TATATT TATA-T TATATTT AGTATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATA-TT --TATATT
2336 TATATT TATATT TATATT TATATT TATATT TAT
1 TATATT TATATT TATATT TATATT TATATT TAT
2369 TTATATTGCA
Statistics
Matches: 407, Mismatches: 4, Indels: 58
0.87 0.01 0.12
Matches are distributed among these distances:
4 14 0.03
5 92 0.23
6 272 0.67
7 19 0.05
8 6 0.01
9 4 0.01
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:2776 original size:35 final size:36
Alignment explanation
Indices: 2713--2793 Score: 137
Period size: 35 Copynumber: 2.3 Consensus size: 36
2703 ATTATAACGT
2713 ACCAAAATATAGAGAAAAAAATTGGAGACAATAGCC
1 ACCAAAATATAGAGAAAAAAATTGGAGACAATAGCC
* *
2749 ACCAAAATATAGAG-AGAAAATTGGAGACAATAGTC
1 ACCAAAATATAGAGAAAAAAATTGGAGACAATAGCC
2784 ACCAAAATAT
1 ACCAAAATAT
2794 TCATATAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 29 0.67
36 14 0.33
ACGTcount: A:0.54, C:0.14, G:0.16, T:0.16
Consensus pattern (36 bp):
ACCAAAATATAGAGAAAAAAATTGGAGACAATAGCC
Found at i:4158 original size:28 final size:28
Alignment explanation
Indices: 4122--4191 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
4112 TTTCATATAA
* *
4122 GTACATAAATTATATTTA-GTTAAAATAG
1 GTACCTAAATTAT-TTTATGTCAAAATAG
*
4150 GTACCTAAAGTATTTTATGTCAAAATAG
1 GTACCTAAATTATTTTATGTCAAAATAG
*
4178 GTGCCTAAATTATT
1 GTACCTAAATTATT
4192 CAAATTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 4 0.11
28 32 0.89
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.39
Consensus pattern (28 bp):
GTACCTAAATTATTTTATGTCAAAATAG
Found at i:7197 original size:14 final size:13
Alignment explanation
Indices: 7172--7203 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
7162 AAGATAAATC
7172 ATTAATAATATTT
1 ATTAATAATATTT
7185 ATTAATAAATATTT
1 ATTAAT-AATATTT
7199 ATTAA
1 ATTAA
7204 AGAAAAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTAATAATATTT
Found at i:27739 original size:33 final size:34
Alignment explanation
Indices: 27694--27765 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
27684 CCTTTATAAC
* * *
27694 TCCCTAGTTTTTCATGGGCTAAACTAGAACC-TT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTTT
*
27727 TCCCTAGCTTTTCACGGGATCAACTAGAACCTTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTTT
27761 TCCCT
1 TCCCT
27766 TTACAAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 27 0.79
34 7 0.21
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.35
Consensus pattern (34 bp):
TCCCTAGCTTTTCACGGGATAAACTAGAACCTTT
Found at i:28207 original size:35 final size:35
Alignment explanation
Indices: 28133--28197 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
28123 GAGCTAGGGG
28133 GTATTGATACCCATAAAGGGGTATCGGTACCCAAC
1 GTATTGATACCCATAAAGGGGTATCGGTACCCAAC
*
28168 GTATTGATA-CC-TATAGGGGTATCGGTACCC
1 GTATTGATACCCATAAAGGGGTATCGGTACCC
28198 TTTTTGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 18 0.62
34 2 0.07
35 9 0.31
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (35 bp):
GTATTGATACCCATAAAGGGGTATCGGTACCCAAC
Found at i:28278 original size:23 final size:22
Alignment explanation
Indices: 28221--28311 Score: 110
Period size: 22 Copynumber: 4.1 Consensus size: 22
28211 TGTTTGAGCC
* *
28221 TTCATAGGAGTATTGATACCCA
1 TTCATAGGGGTATCGATACCCA
* *
28243 GTCATAGGGGTATCGTTACCCA
1 TTCATAGGGGTATCGATACCCA
* *
28265 TTCATAAGGGGTATTGATACCTA
1 TTCAT-AGGGGTATCGATACCCA
*
28288 TTCATAGGGGTATCGGTACCCA
1 TTCATAGGGGTATCGATACCCA
28310 TT
1 TT
28312 TGCATTTTTG
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 38 0.67
23 19 0.33
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (22 bp):
TTCATAGGGGTATCGATACCCA
Found at i:28285 original size:45 final size:44
Alignment explanation
Indices: 28221--28311 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
28211 TGTTTGAGCC
*
28221 TTCATAGGAGTATTGATACCCAGTCATAGGGGTATCGTTACCCA
1 TTCATAGGAGTATTGATACCCAGTCATAGGGGTATCGGTACCCA
* * *
28265 TTCATAAGGGGTATTGATACCTATTCATAGGGGTATCGGTACCCA
1 TTCAT-AGGAGTATTGATACCCAGTCATAGGGGTATCGGTACCCA
28310 TT
1 TT
28312 TGCATTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 5 0.12
45 37 0.88
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (44 bp):
TTCATAGGAGTATTGATACCCAGTCATAGGGGTATCGGTACCCA
Found at i:30281 original size:10 final size:9
Alignment explanation
Indices: 30244--30275 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
30234 TGCCTACCTC
30244 TTTCTT-TT
1 TTTCTTGTT
30252 TTTCTTGTT
1 TTTCTTGTT
30261 TTTCTTGTT
1 TTTCTTGTT
30270 TTTCTT
1 TTTCTT
30276 CATTTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (9 bp):
TTTCTTGTT
Found at i:30281 original size:18 final size:17
Alignment explanation
Indices: 30244--30285 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
30234 TGCCTACCTC
**
30244 TTTCTTTTTTTCTTGTT
1 TTTCTTTTTTTCTTCAT
30261 TTTCTTGTTTTTCTTCAT
1 TTTCTT-TTTTTCTTCAT
30279 TTTCTTT
1 TTTCTTT
30286 CTCTTCCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTCTTTTTTTCTTCAT
Found at i:31319 original size:33 final size:33
Alignment explanation
Indices: 31264--31330 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
31254 TTACAACTCT
* *
31264 CTAGTTTTTCACGAGCTAAACTAGAACATTTCC
1 CTAGCTTTTCACGAGATAAACTAGAACATTTCC
* * *
31297 CTAGCTTTTCACGGGATCAACTAGAACCTTTCC
1 CTAGCTTTTCACGAGATAAACTAGAACATTTCC
31330 C
1 C
31331 CTTTACAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.31
Consensus pattern (33 bp):
CTAGCTTTTCACGAGATAAACTAGAACATTTCC
Found at i:31810 original size:22 final size:22
Alignment explanation
Indices: 31785--31827 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
31775 GTTTGAGTCT
*
31785 TCATAAGGGTATTGATACCCAA
1 TCATAAGGGTATCGATACCCAA
* *
31807 TCATATGGGTATCGGTACCCA
1 TCATAAGGGTATCGATACCCA
31828 GGGTATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (22 bp):
TCATAAGGGTATCGATACCCAA
Found at i:31856 original size:23 final size:22
Alignment explanation
Indices: 31828--31889 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 22
31818 TCGGTACCCA
31828 GGGTATTTATACCCATTCATAAG
1 GGGTATTTATACCCATTCAT-AG
* ** *
31851 GGGTATTGATATTCATTCATAT
1 GGGTATTTATACCCATTCATAG
* *
31873 GGGTATCTGTACCCATT
1 GGGTATTTATACCCATT
31890 TGCATTTTTG
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (22 bp):
GGGTATTTATACCCATTCATAG
Found at i:32540 original size:13 final size:13
Alignment explanation
Indices: 32502--32534 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
32492 GTTATAAATC
32502 TATGACGAGCATT
1 TATGACGAGCATT
*
32515 TATGACTAGCATT
1 TATGACGAGCATT
32528 TATGACG
1 TATGACG
32535 CACATTGAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (13 bp):
TATGACGAGCATT
Found at i:40966 original size:16 final size:16
Alignment explanation
Indices: 40945--40976 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40935 AAATATAATT
*
40945 AATATAATATTTAAAA
1 AATATAAAATTTAAAA
40961 AATATAAAATTTAAAA
1 AATATAAAATTTAAAA
40977 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATAAAATTTAAAA
Found at i:40979 original size:23 final size:24
Alignment explanation
Indices: 40934--40982 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
40924 TATATATATT
*
40934 AAAATATAATTAATATAATATTTAA
1 AAAATATAA-TAATATAAAATTTAA
*
40959 AAAATATAA-AATTTAAAATTTAA
1 AAAATATAATAATATAAAATTTAA
40982 A
1 A
40983 TTAAACTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
25 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATATAATAATATAAAATTTAA
Found at i:43733 original size:2 final size:2
Alignment explanation
Indices: 43726--43755 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43716 TTTATTTTGT
43726 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
43756 GGTTGTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47120 original size:27 final size:27
Alignment explanation
Indices: 47081--47143 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
47071 AAACTGGCCC
*
47081 AAAAAT-TATACCATCTTCCCGACCTG
1 AAAAATATACACCATCTTCCCGACCTG
47107 AAAAATATACACCATCTTCCCGACCTG
1 AAAAATATACACCATCTTCCCGACCTG
47134 AAAAATATAC
1 AAAAATATAC
47144 CTTCCACTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (27 bp):
AAAAATATACACCATCTTCCCGACCTG
Found at i:49781 original size:21 final size:21
Alignment explanation
Indices: 49757--49796 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49747 TCCAATAGAA
*
49757 CGTTACTTAAAATGTTAATTT
1 CGTTACCTAAAATGTTAATTT
*
49778 CGTTACCTAATATGTTAAT
1 CGTTACCTAAAATGTTAAT
49797 ATTTTAACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (21 bp):
CGTTACCTAAAATGTTAATTT
Found at i:50119 original size:40 final size:40
Alignment explanation
Indices: 49993--50362 Score: 179
Period size: 41 Copynumber: 9.2 Consensus size: 40
49983 TTTTTTGAAC
* * * *
49993 AAACGCCGGTAAATACTTGTTCTTTAGTGACGTTTTTGTAT
1 AAACGCCGCTAAATACATGTACTTTAGTGGCG-TTTTGTAT
*
50034 AAACGCCGCTAAA-AGATAGTACTTTAGTGGCGTGTTTGTAT
1 AAACGCCGCTAAATACAT-GTACTTTAGTGGCGT-TTTGTAT
* * *
50075 AAACGCCGCTAAATA-ATGTACTTTAGTGGCGTTTAAGCAA
1 AAACGCCGCTAAATACATGTACTTTAGTGGCGTTT-TGTAT
* * * ** *
50115 AAACGCCGCCAAAGAGTCA--TACTTTAGTGGTGTTTCTAAAC
1 AAACGCCGCTAAATA--CATGTACTTTAGTGGCGTTT-TGTAT
**
50156 AAACGCCGCTAAATACCCGTA-TTGTAGTGGCG-TTT-TAT
1 AAACGCCGCTAAATACATGTACTT-TAGTGGCGTTTTGTAT
* * * * *
50194 --ACGCCGGTAAATACTTGTTCTTTAGTGGCGTTTCTATAC
1 AAACGCCGCTAAATACATGTACTTTAGTGGCGTTT-TGTAT
* * ** * *
50233 AAACGCCGCCAAAGACCCGTACTTTCGTGGCATTTT-TAT
1 AAACGCCGCTAAATACATGTACTTTAGTGGCGTTTTGTAT
* * * ** *
50272 ACAAAGCCGCCAAAGACCCGTACTTTCGTGGCGTTTT-TAT
1 A-AACGCCGCTAAATACATGTACTTTAGTGGCGTTTTGTAT
* * ** * * *
50312 ACAAACGCCGCCAAAGACCCGTACTTTATTGGCTTTTTTGAAT
1 --AAACGCCGCTAAATACATGTACTTTAGTGGC-GTTTTGTAT
50355 -AACGCCGC
1 AAACGCCGC
50363 AATTTATTAG
Statistics
Matches: 265, Mismatches: 43, Indels: 43
0.75 0.12 0.12
Matches are distributed among these distances:
36 23 0.09
37 4 0.02
38 2 0.01
39 9 0.03
40 82 0.31
41 136 0.51
42 6 0.02
43 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACGCCGCTAAATACATGTACTTTAGTGGCGTTTTGTAT
Found at i:50119 original size:81 final size:81
Alignment explanation
Indices: 49990--50171 Score: 192
Period size: 81 Copynumber: 2.2 Consensus size: 81
49980 GCGTTTTTTG
* * * ** * *
49990 AACAAACGCCGGTAAATACTTGTTCTTTAGTGACGTTTTTGTATAAACGCCGCTAAAAGA-T-AG
1 AACAAACGCCGCTAAATACATGTACTTTAGTGACGTTTAAGCAAAAACGCCGC-AAAAGAGTCA-
*
50053 TACTTTAGTGGCGTGTTTGT
64 TACTTTAGT-G-GTGTTTCT
* * *
50073 -ATAAACGCCGCTAAATA-ATGTACTTTAGTGGCGTTTAAGCAAAAACGCCGCCAAAGAGTCATA
1 AACAAACGCCGCTAAATACATGTACTTTAGTGACGTTTAAGCAAAAACGCCGCAAAAGAGTCATA
50136 CTTTAGTGGTGTTTCT
66 CTTTAGTGGTGTTTCT
50152 AAACAAACGCCGCTAAATAC
1 -AACAAACGCCGCTAAATAC
50172 CCGTATTGTA
Statistics
Matches: 82, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
79 7 0.09
80 6 0.07
81 53 0.65
82 16 0.20
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (81 bp):
AACAAACGCCGCTAAATACATGTACTTTAGTGACGTTTAAGCAAAAACGCCGCAAAAGAGTCATA
CTTTAGTGGTGTTTCT
Found at i:50362 original size:81 final size:81
Alignment explanation
Indices: 50119--50350 Score: 249
Period size: 81 Copynumber: 2.9 Consensus size: 81
50109 AAGCAAAAAC
** * * * * *
50119 GCCGCCAAAGAGTCATACTTTAGTGGTGTTTCTAAACAAACGCCGCTAAATACCCGTA-TTGTAG
1 GCCGCCAAAGACCCGTACTTTAGTGGCGTTTCTATACAAACGCCGCCAAAGACCCGTACTT-TAG
*
50183 TGGC-GTTTTATAC---
65 TGGCATTTTTATACAAA
** * ** * *
50196 GCCGGTAAATACTTGTTCTTTAGTGGCGTTTCTATACAAACGCCGCCAAAGACCCGTACTTTCGT
1 GCCGCCAAAGACCCGTACTTTAGTGGCGTTTCTATACAAACGCCGCCAAAGACCCGTACTTTAGT
50261 GGCATTTTTATACAAA
66 GGCATTTTTATACAAA
* * *
50277 GCCGCCAAAGACCCGTACTTTCGTGGCGTTTTTATACAAACGCCGCCAAAGACCCGTACTTTATT
1 GCCGCCAAAGACCCGTACTTTAGTGGCGTTTCTATACAAACGCCGCCAAAGACCCGTACTTTAGT
*
50342 GGCTTTTTT
66 GGCATTTTT
50351 GAATAACGCC
Statistics
Matches: 126, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
77 53 0.42
78 10 0.08
81 63 0.50
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (81 bp):
GCCGCCAAAGACCCGTACTTTAGTGGCGTTTCTATACAAACGCCGCCAAAGACCCGTACTTTAGT
GGCATTTTTATACAAA
Found at i:52536 original size:22 final size:23
Alignment explanation
Indices: 52505--52558 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
52495 TTTTAAAACC
*
52505 TTTATATAAT-TTTTAATAATTA
1 TTTATTTAATCTTTTAATAATTA
*
52527 TTTATTTAATCTTTTAATATTTA
1 TTTATTTAATCTTTTAATAATTA
*
52550 TTTTTTTAA
1 TTTATTTAA
52559 CCTTAATAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTATTTAATCTTTTAATAATTA
Found at i:54469 original size:21 final size:20
Alignment explanation
Indices: 54445--54539 Score: 54
Period size: 21 Copynumber: 4.7 Consensus size: 20
54435 ATGAAGCAAG
54445 GGAAACAGAGAGAGCAGCAGC
1 GGAAACAGAGAGAG-AGCAGC
** **
54466 GGAAGTAGCTAGAGCAGCAGC
1 GGAAACAGAGAGAG-AGCAGC
*
54487 -G-AGCAGAGAGA-AGCAGC
1 GGAAACAGAGAGAGAGCAGC
*
54504 GGCAGCACAGAGAGAG-GCAGC
1 GG-A-AACAGAGAGAGAGCAGC
54525 GGCAGAACAGAGAGA
1 GG-A-AACAGAGAGA
54540 AGTAATATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
17 6 0.10
18 1 0.02
19 7 0.12
20 1 0.02
21 44 0.75
ACGTcount: A:0.39, C:0.19, G:0.40, T:0.02
Consensus pattern (20 bp):
GGAAACAGAGAGAGAGCAGC
Found at i:54517 original size:23 final size:21
Alignment explanation
Indices: 54490--54539 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
54480 CAGCAGCGAG
* *
54490 CAGAGAGAAGCAGCGGCAGCA
1 CAGAGAGAGGCAGCGGCAGAA
54511 CAGAGAGAGGCAGCGGCAGAA
1 CAGAGAGAGGCAGCGGCAGAA
54532 CAGAGAGA
1 CAGAGAGA
54540 AGTAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (21 bp):
CAGAGAGAGGCAGCGGCAGAA
Found at i:54988 original size:42 final size:42
Alignment explanation
Indices: 54872--55009 Score: 120
Period size: 42 Copynumber: 3.2 Consensus size: 42
54862 CATACATTTA
* * * * *
54872 GCGGCGTTTTTG-ATAAAACGCCGCGAAATCTCAAGACATATTCT
1 GCGGCGTTTTTGAAGAAAACGCCGCTAAA-AT-AA-ACATCTACT
* * *
54916 GCGGCGTTTGT-AGGAAAACGCCGGTAAAAATAAACATCTACT
1 GCGGCGTTTTTGAAGAAAACGCCGCT-AAAATAAACATCTACT
* *
54958 GCGGCGTTTTTGAAGAAAACGCCGCTAAAATCAACGA-CTATT
1 GCGGCGTTTTTGAAGAAAACGCCGCTAAAATAAAC-ATCTACT
55000 GCGGCGTTTT
1 GCGGCGTTTT
55010 GTCTGCCAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
42 39 0.51
43 15 0.19
44 20 0.26
45 3 0.04
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (42 bp):
GCGGCGTTTTTGAAGAAAACGCCGCTAAAATAAACATCTACT
Found at i:56103 original size:23 final size:24
Alignment explanation
Indices: 56070--56130 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
56060 TCTATATCAT
*
56070 AAACAAACTTATAAATAAATCGAC
1 AAACAAACTTATAAATAAATCGAA
*
56094 AAAC-AACTTATAAATAACTCGAA
1 AAACAAACTTATAAATAAATCGAA
* *
56117 AAACTATCTTATAA
1 AAACAAACTTATAA
56131 TCGAGCTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 21 0.64
24 12 0.36
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (24 bp):
AAACAAACTTATAAATAAATCGAA
Done.