Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006933.1 Hibiscus syriacus cultivar Beakdansim tig00017795_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: 57392
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2976 original size:18 final size:19
Alignment explanation
Indices: 2940--2989 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
2930 TAAGAAAAAT
* *
2940 AAAAAGTAAAACTATATAA
1 AAAAAGTAAAAATAAATAA
2959 AAAAAG-AAAAATAAATAA
1 AAAAAGTAAAAATAAATAA
*
2977 GTAAAA-TAAAAAT
1 -AAAAAGTAAAAAT
2990 GCTATGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (19 bp):
AAAAAGTAAAAATAAATAA
Found at i:21116 original size:68 final size:68
Alignment explanation
Indices: 20993--21123 Score: 208
Period size: 68 Copynumber: 1.9 Consensus size: 68
20983 ATATATATAA
* * * * * *
20993 AATTTTTAAATAAAAAATGGTATAAATACAATTTTAGGATGGATATTATCCGTAAATTAAGTATG
1 AATTTTTAAATAAAAAATGGTACAAATACAATTTTAGGATGAACATCATCAGTAAAATAAGTATG
21058 TAG
66 TAG
21061 AATTTTTAAATAAAAAATGGTACAAATACAATTTTAGGATGAACATCATCAGTAAAATAAGTA
1 AATTTTTAAATAAAAAATGGTACAAATACAATTTTAGGATGAACATCATCAGTAAAATAAGTA
21124 ACTAATTGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 57 1.00
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (68 bp):
AATTTTTAAATAAAAAATGGTACAAATACAATTTTAGGATGAACATCATCAGTAAAATAAGTATG
TAG
Found at i:24886 original size:22 final size:22
Alignment explanation
Indices: 24855--24903 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
24845 CAAAGGGATC
*
24855 CCACCGTTTGTGTGGAGTCATT
1 CCACCATTTGTGTGGAGTCATT
*
24877 CCACCATTTGTGTGGAGTTATT
1 CCACCATTTGTGTGGAGTCATT
24899 CCACC
1 CCACC
24904 TTCAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.35
Consensus pattern (22 bp):
CCACCATTTGTGTGGAGTCATT
Found at i:26458 original size:125 final size:125
Alignment explanation
Indices: 26252--26501 Score: 464
Period size: 125 Copynumber: 2.0 Consensus size: 125
26242 TTGGTTCGCC
26252 TATGTAGGCTTTCTTATAAACTGGTTTGGGGATTATTGTAGGGCTAGGGTATAAAATGTATGTTG
1 TATGTAGGCTTTCTTATAAACTGGTTTGGGGATTATTGTAGGGCTAGGGTATAAAATGTATGTTG
26317 TAAGAATTCTTGTGTATTAGTTCCCTACCACCTCAAGGTGCACTATTTTTCCTCCATTTA
66 TAAGAATTCTTGTGTATTAGTTCCCTACCACCTCAAGGTGCACTATTTTTCCTCCATTTA
* **
26377 TATGTAGGCTTTCTTATAAACTGGTTTGGGGATTATTGTAGGGCTGGGGTATGGAATGTATGTTG
1 TATGTAGGCTTTCTTATAAACTGGTTTGGGGATTATTGTAGGGCTAGGGTATAAAATGTATGTTG
*
26442 TAAGAATTCTTGTGTATTAGTTCCCTACCACCTCAAGGTGCACTCTTTTTCCTCCATTTA
66 TAAGAATTCTTGTGTATTAGTTCCCTACCACCTCAAGGTGCACTATTTTTCCTCCATTTA
26502 GGATTAAGGA
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 121 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (125 bp):
TATGTAGGCTTTCTTATAAACTGGTTTGGGGATTATTGTAGGGCTAGGGTATAAAATGTATGTTG
TAAGAATTCTTGTGTATTAGTTCCCTACCACCTCAAGGTGCACTATTTTTCCTCCATTTA
Found at i:26913 original size:7 final size:7
Alignment explanation
Indices: 26903--26930 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
26893 AATTATTTGC
26903 AATTTTA
1 AATTTTA
26910 AATTTTA
1 AATTTTA
26917 AATTTTA
1 AATTTTA
26924 AATTTTA
1 AATTTTA
26931 TAAATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATTTTA
Found at i:29756 original size:31 final size:31
Alignment explanation
Indices: 29699--29781 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
29689 TTAAAAAGTT
* * * *
29699 AAATTCAAGTATCTAA-TAAGAGATTAAAATG
1 AAATTCAAGTATCAAATTGA-ACATTAAAATC
*
29730 AAGATT-AAGTATCACATTGAACATTAAAATC
1 AA-ATTCAAGTATCAAATTGAACATTAAAATC
29761 AAATTCAAGTATCAAATTGAA
1 AAATTCAAGTATCAAATTGAA
29782 ACCAAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
30 3 0.07
31 35 0.81
32 5 0.12
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.29
Consensus pattern (31 bp):
AAATTCAAGTATCAAATTGAACATTAAAATC
Found at i:29897 original size:6 final size:6
Alignment explanation
Indices: 29886--29913 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29876 TATCAAAATG
29886 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
29914 TATGAAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:32767 original size:24 final size:24
Alignment explanation
Indices: 32740--32789 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
32730 TGGTGGTTGA
*
32740 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAAATTTATT
*
32764 TTTAATGGTGTATTTAAATTTATT
1 TTTAATGGTGTATTGAAATTTATT
32788 TT
1 TT
32790 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAAATTTATT
Found at i:42685 original size:25 final size:25
Alignment explanation
Indices: 42656--42715 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
42646 CCAAGGAATG
42656 GCAAGCTAGGCGCCGAAAGGAGCTA
1 GCAAGCTAGGCGCCGAAAGGAGCTA
42681 GCAAGCTAGGCGCCGAAAGGAGCTA
1 GCAAGCTAGGCGCCGAAAGGAGCTA
*
42706 GCGAGCTAGG
1 GCAAGCTAGG
42716 TGGTTCACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.30, C:0.23, G:0.38, T:0.08
Consensus pattern (25 bp):
GCAAGCTAGGCGCCGAAAGGAGCTA
Found at i:42917 original size:24 final size:24
Alignment explanation
Indices: 42890--42939 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
42880 TGGTGGTTGA
42890 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
42914 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
42938 TT
1 TT
42940 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:44469 original size:25 final size:25
Alignment explanation
Indices: 44420--44474 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
44410 AACTATGAAA
*
44420 CAAAACAATTAAAAATAAAATTAAT
1 CAAAACAATTAAAAACAAAATTAAT
*
44445 CAAAATAATT-AAAACAAAATATAAT
1 CAAAACAATTAAAAACAAAAT-TAAT
*
44470 AAAAA
1 CAAAA
44475 ACAGTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (25 bp):
CAAAACAATTAAAAACAAAATTAAT
Found at i:44485 original size:20 final size:18
Alignment explanation
Indices: 44460--44500 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
44450 TAATTAAAAC
44460 AAAATATAATAAAAAACAGT
1 AAAATATAA-AAAAAACA-T
*
44480 AAAATATAAAATAAACAT
1 AAAATATAAAAAAAACAT
44498 AAA
1 AAA
44501 TAGAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 9 0.45
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAATATAAAAAAAACAT
Found at i:44501 original size:17 final size:17
Alignment explanation
Indices: 44456--44516 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
44446 AAAATAATTA
*
44456 AAACA-AAATATAATAAA
1 AAACATAAATATAA-AAT
44473 AAACAGTAAAATATAAAAT
1 AAACA-T-AAATATAAAAT
*
44492 AAACATAAATAGAAAAT
1 AAACATAAATATAAAAT
44509 AAA-ATAAA
1 AAACATAAA
44517 CATGCACTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.13
17 18 0.46
18 1 0.03
19 7 0.18
20 8 0.21
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (17 bp):
AAACATAAATATAAAAT
Found at i:47139 original size:23 final size:22
Alignment explanation
Indices: 47112--47154 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
47102 AATGAAATAA
47112 AATTAAAATTATAAATATAATTG
1 AATTAAAATTA-AAATATAATTG
*
47135 AATTAAAATTAAAATTTAAT
1 AATTAAAATTAAAATATAAT
47155 CTACAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTAAAATTAAAATATAATTG
Found at i:47162 original size:29 final size:29
Alignment explanation
Indices: 47104--47163 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
47094 TGCGTAGGAA
*
47104 TGAAATAAAATTAAAATTATAAATATAAT
1 TGAAATAAAATTAAAATTATAAATACAAT
* *
47133 TGAATTAAAATTAAAATT-TAATCTACAAT
1 TGAAATAAAATTAAAATTATAA-ATACAAT
47162 TG
1 TG
47164 TACAAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (29 bp):
TGAAATAAAATTAAAATTATAAATACAAT
Found at i:51287 original size:20 final size:19
Alignment explanation
Indices: 51245--51288 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
51235 TTTCTTTAAT
51245 TATTTTAAATTTAGTTGTA
1 TATTTTAAATTTAGTTGTA
51264 -ATTTTATAATTTTA-TTGTA
1 TATTTTA-AA-TTTAGTTGTA
51283 TATTTT
1 TATTTT
51289 TATATTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (19 bp):
TATTTTAAATTTAGTTGTA
Found at i:52336 original size:25 final size:25
Alignment explanation
Indices: 52308--52359 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
52298 ATATTAAAAA
52308 ATTGTGCAACCGGCAAACTTAACTT
1 ATTGTGCAACCGGCAAACTTAACTT
52333 ATTGTGCAACCGGCAAACTTAACTT
1 ATTGTGCAACCGGCAAACTTAACTT
52358 AT
1 AT
52360 CGGTTCGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (25 bp):
ATTGTGCAACCGGCAAACTTAACTT
Found at i:52798 original size:20 final size:19
Alignment explanation
Indices: 52775--52821 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
52765 CGATATAACA
52775 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
52795 GGTATCAAAATGATGAAACC
1 GGTA-AAAAATGATAAAACC
52815 GGTAAAA
1 GGTAAAA
52822 CGCTATCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:52888 original size:181 final size:181
Alignment explanation
Indices: 52381--53015 Score: 960
Period size: 182 Copynumber: 3.6 Consensus size: 181
52371 GATCCAAATT
* * * **
52381 AAAAATGTATCGATCCACAACGATATAACAGGTAAAACTATGACAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
52446 AAACCGGTAAAGCGGTACCGGATATATTTAAAGTGTCGGTACTTTAATATAAAGATCGACACTTT
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATA-TTTTATATAAAGATCGACACTTT
* *
52511 GTTAATTTAAAAGAGAATCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
130 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * *
52563 AAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGATATCAAAATGATG
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
52628 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTTGATACTTTATATAAGGATCGACACTTTG
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATATTTTATATAAAGATCGACACTTTG
52693 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
131 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTT-AA
*
52745 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATG
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
52810 AAACCGGTAAAACGCTATCGGATATATTGAAAGTGTCGATATTTTATATAAAGATCGACACTTTG
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATATTTTATATAAAGATCGACACTTTG
52875 TGAATTT--AA-AG-AG-A-----AGCGCCTATAAAGTGTCGATACTTT-A
131 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
52915 AAAAATGTATCGATCCACAACGATATAACAGGT---AA-ATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
52976 AAACC-GTAAAACGCTACCGGATATATTGAAAGTGTCGATA
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATA
53016 CTTTCGTAGT
Statistics
Matches: 426, Mismatches: 26, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
165 34 0.08
166 30 0.07
167 2 0.00
170 34 0.08
172 25 0.06
177 1 0.00
178 2 0.00
179 2 0.00
180 2 0.00
181 68 0.16
182 226 0.53
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (181 bp):
AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATATTTTATATAAAGATCGACACTTTG
TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:53755 original size:35 final size:35
Alignment explanation
Indices: 53709--53777 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
53699 CAAAGGGTGA
53709 ATATATGTACTTCTAGTAAGTATCAATGTCTTTTG
1 ATATATGTACTTCTAGTAAGTATCAATGTCTTTTG
53744 ATATATGTACTTCTAGTAAGTATCAATGTCTTTT
1 ATATATGTACTTCTAGTAAGTATCAATGTCTTTT
53778 TGTTATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (35 bp):
ATATATGTACTTCTAGTAAGTATCAATGTCTTTTG
Found at i:55161 original size:14 final size:14
Alignment explanation
Indices: 55142--55188 Score: 76
Period size: 14 Copynumber: 3.3 Consensus size: 14
55132 TGGTTGTATT
55142 AGGGGATGACGGTG
1 AGGGGATGACGGTG
55156 AGGGGATGACGGTG
1 AGGGGATGACGGTG
*
55170 AGGGGGACGACGGTG
1 A-GGGGATGACGGTG
55185 AGGG
1 AGGG
55189 AAAACAGAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.21, C:0.09, G:0.60, T:0.11
Consensus pattern (14 bp):
AGGGGATGACGGTG
Found at i:55181 original size:15 final size:15
Alignment explanation
Indices: 55143--55188 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
55133 GGTTGTATTA
55143 GGGGATGACGGTGA-
1 GGGGATGACGGTGAG
55157 GGGGATGACGGTGAG
1 GGGGATGACGGTGAG
*
55172 GGGGACGACGGTGAG
1 GGGGATGACGGTGAG
55187 GG
1 GG
55189 AAAACAGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 14 0.47
15 16 0.53
ACGTcount: A:0.20, C:0.09, G:0.61, T:0.11
Consensus pattern (15 bp):
GGGGATGACGGTGAG
Found at i:55330 original size:20 final size:21
Alignment explanation
Indices: 55273--55334 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
55263 GACAATCAAA
*
55273 AGTCGAAGAGAAACTTGATAG
1 AGTCGAAGAGAAACTTGAGAG
55294 AGTCGAAGAGAAACTTGAGAG
1 AGTCGAAGAGAAACTTGAGAG
*
55315 AGTCGAAG-GTAACTTGAGAG
1 AGTCGAAGAGAAACTTGAGAG
55335 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 11 0.28
21 28 0.72
ACGTcount: A:0.40, C:0.10, G:0.32, T:0.18
Consensus pattern (21 bp):
AGTCGAAGAGAAACTTGAGAG
Found at i:55409 original size:33 final size:33
Alignment explanation
Indices: 55367--55432 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
55357 AAATAGATGG
* *
55367 AGTGGTGAAAGAAGTTGATGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
55400 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
55433 TCTTAATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
Found at i:55658 original size:12 final size:11
Alignment explanation
Indices: 55641--55703 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 11
55631 AGAGGAGGAA
55641 GAAGAAGAGATG
1 GAAGAAGAGA-G
*
55653 GAAGAAAAGAG
1 GAAGAAGAGAG
*
55664 G--GAAGAGGAA
1 GAAGAAGA-GAG
55674 GAAGAAGAGATG
1 GAAGAAGAGA-G
55686 GAAGAA-ATGAG
1 GAAGAAGA-GAG
55697 GAAGAAG
1 GAAGAAG
55704 GAAGTCAATG
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
9 4 0.10
10 3 0.07
11 12 0.29
12 22 0.54
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (11 bp):
GAAGAAGAGAG
Found at i:55658 original size:33 final size:33
Alignment explanation
Indices: 55620--55707 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
55610 AAAATATGAA
*
55620 GAAGAAAAGAGAGAGGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGAGAAGAGGAAGAAGAAGAGATG
*
55653 GAAGAAAAGAGGGAAGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGAGAAGAGGAAGAAGAAGAGATG
*
55686 GAAGAAATGAG-GAAGAAGGAAG
1 GAAGAAAAGAGAGAAG-AGGAAG
55708 TCAATGTCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 4 0.08
33 47 0.92
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (33 bp):
GAAGAAAAGAGAGAAGAGGAAGAAGAAGAGATG
Found at i:56655 original size:4 final size:4
Alignment explanation
Indices: 56646--56670 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
56636 GCTAAGATTG
56646 GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
56671 AAAGGACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:57287 original size:17 final size:19
Alignment explanation
Indices: 57249--57295 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
57239 AATGTAGGGT
57249 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
57268 TAA-TTTGTATACGA-TTA
1 TAATTTTGTATAAGATTTA
57285 TAATTTTGTAT
1 TAATTTTGTAT
57296 GTGAATGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 17 0.65
19 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Done.