Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000456.1 Hibiscus syriacus cultivar Beakdansim tig00000846_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: 83798
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:62 original size:23 final size:24
Alignment explanation
Indices: 31--136 Score: 85
Period size: 23 Copynumber: 4.5 Consensus size: 24
21 CGAAGGGTCT
*
31 GTAGAATTTTTCCTAAAGGACCAC
1 GTAGAATTTGTCCTAAAGGACCAC
* * **
55 GTAG-ATTTGT-CTCGAAGGGCCGT
1 GTAGAATTTGTCCT-AAAGGACCAC
78 GTAGAATTTGTCCTAAAGGACCAC
1 GTAGAATTTGTCCTAAAGGACCAC
* ** *
102 ATAGAA-TTGTCCCGAATGACCAC
1 GTAGAATTTGTCCTAAAGGACCAC
*
125 ATAG-ATTTGTCC
1 GTAGAATTTGTCC
137 CGAAGGACTG
Statistics
Matches: 65, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
22 3 0.05
23 39 0.60
24 21 0.32
25 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
GTAGAATTTGTCCTAAAGGACCAC
Found at i:81 original size:47 final size:46
Alignment explanation
Indices: 18--117 Score: 146
Period size: 47 Copynumber: 2.2 Consensus size: 46
8 ACAGATTTTT
* * * *
18 TCCCGAAGGGTCTGTAGAATTTTTCCTAAAGGACCACGTAGATTTG
1 TCCCGAAGGGCCTGTAGAATTTGTCCTAAAGGACCACATAGAATTG
*
64 TCTCGAAGGGCCGTGTAGAATTTGTCCTAAAGGACCACATAGAATTG
1 TCCCGAAGGGCC-TGTAGAATTTGTCCTAAAGGACCACATAGAATTG
111 TCCCGAA
1 TCCCGAA
118 TGACCACATA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
46 10 0.21
47 37 0.79
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (46 bp):
TCCCGAAGGGCCTGTAGAATTTGTCCTAAAGGACCACATAGAATTG
Found at i:152 original size:23 final size:23
Alignment explanation
Indices: 46--144 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 23
36 ATTTTTCCTA
*
46 AAGGACCACGTAGATTTGTCTCG
1 AAGGACCACGTAGATTTGTCCCG
* ** **
69 AAGGGCCGTGTAGAATTTGTCCTA
1 AAGGACCACGTAG-ATTTGTCCCG
* *
93 AAGGACCACATAGAATTGTCCCG
1 AAGGACCACGTAGATTTGTCCCG
* *
116 AATGACCACATAGATTTGTCCCG
1 AAGGACCACGTAGATTTGTCCCG
139 AAGGAC
1 AAGGAC
145 TGCGTAGAAC
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
23 43 0.73
24 16 0.27
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.23
Consensus pattern (23 bp):
AAGGACCACGTAGATTTGTCCCG
Found at i:277 original size:15 final size:15
Alignment explanation
Indices: 253--287 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
243 GTGTGTCTTA
*
253 TTCACATAGGATATT
1 TTCACATAGGACATT
*
268 TTCACGTAGGACATT
1 TTCACATAGGACATT
283 TTCAC
1 TTCAC
288 TTAGAACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (15 bp):
TTCACATAGGACATT
Found at i:2207 original size:2 final size:2
Alignment explanation
Indices: 2181--2368 Score: 194
Period size: 2 Copynumber: 100.5 Consensus size: 2
2171 ATTAATAATA
* *
2181 AT AT AA AT A- AT AT AT A- AA AT A- AT AT AT AT AT AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
2221 -T AT -T AT AT AT AGT AT A- AT AT AT AT A- AT AT A- AT -T AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2258 AT A- AT AT A- AT AT AT AT AT ACT AT AT AT AT AT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
2297 AT A- AT AT AT ACT AT A- AT AT AT A- AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2336 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2369 CTAATTGTGT
Statistics
Matches: 160, Mismatches: 5, Indels: 42
0.77 0.02 0.20
Matches are distributed among these distances:
1 17 0.11
2 135 0.84
3 8 0.05
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2240 original size:29 final size:27
Alignment explanation
Indices: 2202--2368 Score: 184
Period size: 29 Copynumber: 6.0 Consensus size: 27
2192 ATATAAAATA
*
2202 ATATATATATATATACTATTATTATATAT
1 ATATA-ATATATATA-TACTATTATATAT
2231 AGTATAATATATATAATA-TAATTATATAT
1 A-TATAATATATAT-ATACT-ATTATATAT
2260 AATATAATATATATATACTATATATATAT
1 -ATATAATATATATATACTAT-TATATAT
*
2289 AATATAATATAATATATACTATAATATAT
1 -ATATAATAT-ATATATACTATTATATAT
2318 A-ATAATATATATATA-TA-TATATAT
1 ATATAATATATATATACTATTATATAT
2342 ATATATATATATATATAC-A-TATATAT
1 ATATA-ATATATATATACTATTATATAT
2368 A
1 A
2369 CTAATTGTGT
Statistics
Matches: 126, Mismatches: 2, Indels: 23
0.83 0.01 0.15
Matches are distributed among these distances:
24 7 0.06
25 5 0.04
26 27 0.21
27 7 0.06
28 7 0.06
29 56 0.44
30 17 0.13
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (27 bp):
ATATAATATATATATACTATTATATAT
Found at i:4850 original size:16 final size:15
Alignment explanation
Indices: 4825--4856 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
4815 TATTATTTGA
4825 ATAATTGAATCGAAT
1 ATAATTGAATCGAAT
4840 ATAATTTGAATCGAAT
1 ATAA-TTGAATCGAAT
4856 A
1 A
4857 AATCTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (15 bp):
ATAATTGAATCGAAT
Found at i:5331 original size:26 final size:25
Alignment explanation
Indices: 5275--5327 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
5265 AACAAAATCC
*
5275 AAACAACCAAATATTCAAATCTGTT
1 AAACAACCAAATATTCAAATATGTT
5300 AAACAACCAAAT-TCATCAAA-ATGTT
1 AAACAACCAAATAT--TCAAATATGTT
5325 AAA
1 AAA
5328 ACAATGCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 1 0.04
25 19 0.76
26 5 0.20
ACGTcount: A:0.53, C:0.19, G:0.04, T:0.25
Consensus pattern (25 bp):
AAACAACCAAATATTCAAATATGTT
Found at i:7531 original size:15 final size:15
Alignment explanation
Indices: 7513--7546 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7503 ACATCTTCTT
*
7513 TAATGACATGATCTC
1 TAATGAAATGATCTC
*
7528 TAATGAAATGATGTC
1 TAATGAAATGATCTC
7543 TAAT
1 TAAT
7547 TTCAATATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (15 bp):
TAATGAAATGATCTC
Found at i:9578 original size:18 final size:18
Alignment explanation
Indices: 9549--9598 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
9539 GACTACATAT
*
9549 AACACATATGTCCCGAACG
1 AACAC-TATGTCCCAAACG
*
9568 AACACTATGTCCCAAAGG
1 AACACTATGTCCCAAACG
*
9586 ACCACTATGTCCC
1 AACACTATGTCCC
9599 TAATGACCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18
Consensus pattern (18 bp):
AACACTATGTCCCAAACG
Found at i:10395 original size:20 final size:22
Alignment explanation
Indices: 10370--10427 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
10360 TTTCCCTTGA
10370 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
10390 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
10413 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
10428 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:10489 original size:64 final size:63
Alignment explanation
Indices: 10415--10556 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 63
10405 TCTTTAACAT
* * *
10415 GTGCATCGATGCACTACC-CATGCATTGATAAACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATAAACAAATTACATTCGATG-TTTCATCTTTAAAGA
* ** * * *
10478 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATAAACAAATTACATTCGATGTTTCATCTTTAAAGA
10542 GTGCATCGATGCACT
1 GTGCATCGATGCACT
10557 TTGAATTTGC
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
63 22 0.33
64 45 0.67
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATAAACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:10888 original size:17 final size:17
Alignment explanation
Indices: 10868--10900 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10858 GATTTCACTT
10868 ATTCCTCTCT-TTCTTTA
1 ATTCC-CTCTATTCTTTA
10885 ATTCCCTCTATTCTTT
1 ATTCCCTCTATTCTTT
10901 CATCTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.12, C:0.30, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTCCCTCTATTCTTTA
Found at i:12111 original size:65 final size:64
Alignment explanation
Indices: 11993--12198 Score: 204
Period size: 65 Copynumber: 3.2 Consensus size: 64
11983 ATTTTCATAG
* * * * **
11993 TGATGCACCGATGCACCAATTCATGCATCGATGCAC-CATGAAATAAATT-AAACATCGAATGCA
1 TGATGCATCGATGCACCAA-CCATACATCGATGCACTCA-G-CATATTTTGAAACATCGAATGCA
12056 TT
63 TT
* * *
12058 TCATGCATCGATGCA-CATACCATACATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATACATCGATGCACTCAGCATATTT-TG-AAACATCGAATGCA
12121 TT
63 TT
* * * * *
12123 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGCCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATACATCGATGCACTCAGCATATTTTGAAACATCGAATGCATT
12187 TGATGCATCGAT
1 TGATGCATCGAT
12199 ACACTCGTAG
Statistics
Matches: 118, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 44 0.37
65 65 0.55
66 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATACATCGATGCACTCAGCATATTTTGAAACATCGAATGCATT
Found at i:17993 original size:20 final size:21
Alignment explanation
Indices: 17968--18131 Score: 107
Period size: 23 Copynumber: 7.4 Consensus size: 21
17958 TTGTGCTTAA
17968 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-AG
*
17988 TGCATCGATGCATCCTTGAAAG
1 TGCATCGATACA-CCTTGAAAG
**
18010 TGCATCGATACACCACGAAAG
1 TGCATCGATACACCTTGAAAG
* * *
18031 TGCACCGAGGCACACCTTGAATG
1 TGCATCGA--TACACCTTGAAAG
* * *
18054 TGCATCAATGCACGCCTTGAATG
1 TGCATCGAT--ACACCTTGAAAG
* *
18077 TGCATCGATGCATGCCTTGAATG
1 TGCATCGATACA--CCTTGAAAG
* *
18100 TGCATCGATGCACGCCTTGAATG
1 TGCATCGAT--ACACCTTGAAAG
18123 TGCATCGAT
1 TGCATCGAT
18132 GCACAAGGTC
Statistics
Matches: 115, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.10
21 17 0.15
22 14 0.12
23 72 0.63
25 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (21 bp):
TGCATCGATACACCTTGAAAG
Found at i:18031 original size:21 final size:20
Alignment explanation
Indices: 17968--18034 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
17958 TTGTGCTTAA
*
17968 TGCATCGATACACCTA-ACAG
1 TGCATCGATACACC-AGAAAG
* *
17988 TGCATCGATGCATCCTTGAAAG
1 TGCATCGATACA-CC-AGAAAG
18010 TGCATCGATACACCACGAAAG
1 TGCATCGATACACCA-GAAAG
18031 TGCA
1 TGCA
18035 CCGAGGCACA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.28
21 14 0.36
22 14 0.36
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (20 bp):
TGCATCGATACACCAGAAAG
Found at i:18056 original size:23 final size:23
Alignment explanation
Indices: 17987--18135 Score: 180
Period size: 23 Copynumber: 6.6 Consensus size: 23
17977 ACACCTAACA
* *
17987 GTGCATCGATGCA-TCCTTGAAA
1 GTGCATCGATGCACGCCTTGAAT
* *
18009 GTGCATCGATACAC-CAC--GAAA
1 GTGCATCGATGCACGC-CTTGAAT
* * *
18030 GTGCACCGAGGCACACCTTGAAT
1 GTGCATCGATGCACGCCTTGAAT
*
18053 GTGCATCAATGCACGCCTTGAAT
1 GTGCATCGATGCACGCCTTGAAT
*
18076 GTGCATCGATGCATGCCTTGAAT
1 GTGCATCGATGCACGCCTTGAAT
18099 GTGCATCGATGCACGCCTTGAAT
1 GTGCATCGATGCACGCCTTGAAT
18122 GTGCATCGATGCAC
1 GTGCATCGATGCAC
18136 AAGGTCATGC
Statistics
Matches: 110, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
21 16 0.15
22 14 0.13
23 80 0.73
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACGCCTTGAAT
Found at i:20460 original size:33 final size:34
Alignment explanation
Indices: 20405--20489 Score: 138
Period size: 34 Copynumber: 2.6 Consensus size: 34
20395 AAACAAAAAG
* *
20405 GGGGAGAAGTGTT-AAGTGTTAAAATG-TTTATA
1 GGGGAGAAGTGTTAAAGTATTAAAATGTTTTAAA
20437 GGGGAGAAGTGTTAAAGTATTAAAATGTTTTAAA
1 GGGGAGAAGTGTTAAAGTATTAAAATGTTTTAAA
20471 GGGGAGAAGTGTTAAAGTA
1 GGGGAGAAGTGTTAAAGTA
20490 AGGGGGAGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 13 0.27
33 12 0.24
34 24 0.49
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.31
Consensus pattern (34 bp):
GGGGAGAAGTGTTAAAGTATTAAAATGTTTTAAA
Found at i:20969 original size:46 final size:45
Alignment explanation
Indices: 20918--21021 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
20908 ACATACCATA
* *
20918 CATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATG
1 CATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTGATG
* *
20964 CATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATG
1 CATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATG
21009 CATCGATGCACTC
1 CATCGATGCACTC
21022 GTAGTGCACC
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
45 33 0.62
46 17 0.32
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (45 bp):
CATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATG
Found at i:23342 original size:33 final size:33
Alignment explanation
Indices: 23305--23372 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
23295 GAAAGAAGCT
23305 TTAAGATCATCAATTTTCTTTTGATGATCATCA
1 TTAAGATCATCAATTTTCTTTTGATGATCATCA
23338 TTAAGATCATCAATTTTCTTTTGATGATCATCA
1 TTAAGATCATCAATTTTCTTTTGATGATCATCA
23371 TT
1 TT
23373 GACTCTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (33 bp):
TTAAGATCATCAATTTTCTTTTGATGATCATCA
Found at i:25617 original size:18 final size:19
Alignment explanation
Indices: 25590--25625 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
25580 TACTACTATA
*
25590 TATAAGGGTATCGGTACCG
1 TATAAGGGTATCAGTACCG
25609 TATAA-GGTATCAGTACC
1 TATAAGGGTATCAGTACC
25626 AAAATTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (19 bp):
TATAAGGGTATCAGTACCG
Found at i:25837 original size:20 final size:20
Alignment explanation
Indices: 25796--25837 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
25786 GTAAAAATTG
* *
25796 ATATTTGAAAACTTTTAGTA
1 ATATTTGAAAACTTTGAATA
25816 ATATTTGAAATA-TTTGAATA
1 ATATTTGAAA-ACTTTGAATA
25836 AT
1 AT
25838 TGAATCGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (20 bp):
ATATTTGAAAACTTTGAATA
Found at i:27693 original size:30 final size:30
Alignment explanation
Indices: 27672--28238 Score: 408
Period size: 30 Copynumber: 18.9 Consensus size: 30
27662 AGAATGCGAT
* * *
27672 TGAATTTCGGGTCGAACTTGAGAGTTTGAC
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* * *
27702 TGAATTTCGGGTAGAACTTGAGAGTTCGGA
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* * *
27732 TGAATTACGGATAGAACTTGAGAGTTCGCC
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* * * *
27762 TGAACTACGGGTAGAACTTGAGATTTCGAC
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* * * **
27792 TAAATTACGGGTAGAACTTGAGAGTTTGTT
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* * * * * *
27822 TGAATTCCGGATTGAACTTGAGATTTTGGA
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* *
27852 TGAATTACGGGTAGAACTTGAGATTTCGGC
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* * *
27882 T-AAATAAGGGTAGAACTTGAGAGTTCGGC
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* * ** * * *
27911 TGAATTACAGATAAAATTTGAGATTTCGGT
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
*
27941 TGAATT-CTAGGTCGAACTTGAGAGTTCGGC
1 TGAATTAC-GGGTCGAACTTGAGAGTTCGGC
* * * *
27971 TGAACTGCGGGACGAACTTGAGAATTCGGC
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* * * *
28001 CGAATTCCGGGTCGAACTTGATATTTCGGC
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* * * *
28031 TGAATTTCGGGTTGAATTTGAGA-TTCCGAC
1 TGAATTACGGGTCGAACTTGAGAGTT-CGGC
* * * *
28061 TTAATTCCAGGTCGAACTTGAGAGTTCGGT
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* * *
28091 TGAACTGC-GGTACGAACTTGAGAGTTCGGT
1 TGAATTACGGGT-CGAACTTGAGAGTTCGGC
* * ** * *
28121 TGAAGTGCAAGTCGAACTTGAGAATTCGAC
1 TGAATTACGGGTCGAACTTGAGAGTTCGGC
* *
28151 TGAATT-CTAGGTCGAACTTGAGAATTCGGC
1 TGAATTAC-GGGTCGAACTTGAGAGTTCGGC
* * * *
28181 TGAATT-CTAGGCCGAAATTGAGAATTCGGC
1 TGAATTAC-GGGTCGAACTTGAGAGTTCGGC
* * *
28211 TGAATTCCGGGTTGAACTTGAGAATTCG
1 TGAATTACGGGTCGAACTTGAGAGTTCG
28239 ATTGACTCTT
Statistics
Matches: 441, Mismatches: 87, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
29 33 0.07
30 402 0.91
31 6 0.01
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAATTACGGGTCGAACTTGAGAGTTCGGC
Found at i:31815 original size:2 final size:2
Alignment explanation
Indices: 31808--31854 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
31798 TTAAAAAGAG
31808 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
31850 TA TA T
1 TA TA T
31855 TGCTTTGAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34847 original size:21 final size:21
Alignment explanation
Indices: 34823--34862 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34813 CTGATATGAC
* *
34823 GCTTCTTTCTGTGTTTCCGTT
1 GCTTCTTTATGTGCTTCCGTT
34844 GCTTCTTTATGTGCTTCCG
1 GCTTCTTTATGTGCTTCCG
34863 GTACTACTGT
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:0.03, C:0.25, G:0.20, T:0.53
Consensus pattern (21 bp):
GCTTCTTTATGTGCTTCCGTT
Found at i:43549 original size:40 final size:42
Alignment explanation
Indices: 43493--43588 Score: 126
Period size: 40 Copynumber: 2.3 Consensus size: 42
43483 GATGTAGCGC
** *
43493 CTATTGCGGTGTTTGTGAA-AAAATGCCACTAAA-ATATAATA
1 CTATTGCGACGTTTGTGAAGAAAACGCCACTAAATATA-AATA
*
43534 -TATTGCGACGTTTGTGAAGAAAACGCCACTATATATAAATA
1 CTATTGCGACGTTTGTGAAGAAAACGCCACTAAATATAAATA
43575 CTATTGCGACGTTT
1 CTATTGCGACGTTT
43589 TTATACAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 16 0.33
41 16 0.33
42 16 0.33
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (42 bp):
CTATTGCGACGTTTGTGAAGAAAACGCCACTAAATATAAATA
Found at i:48089 original size:46 final size:45
Alignment explanation
Indices: 47990--48093 Score: 131
Period size: 46 Copynumber: 2.3 Consensus size: 45
47980 ATAATACAAA
* *
47990 GTCTAATTCATAATTAGTGCTACAACACATCAAACTAACAATATT
1 GTCTAAGTCATAATTAGTACTACAACACATCAAACTAACAATATT
* *
48035 GT-TGAAGTCTATAATTAGTACTACAACACATTAGAGCTAA-AATATT
1 GTCT-AAGTC-ATAATTAGTACTACAACACATCA-AACTAACAATATT
48081 GTCTAAGTCATAA
1 GTCTAAGTCATAA
48094 ATAATTTTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
44 1 0.02
45 10 0.20
46 34 0.67
47 6 0.12
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (45 bp):
GTCTAAGTCATAATTAGTACTACAACACATCAAACTAACAATATT
Found at i:63537 original size:17 final size:18
Alignment explanation
Indices: 63515--63557 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
63505 GGTCAACAGT
* *
63515 GGTCAACATC-GGTCAAC
1 GGTCAACAGCAGGTCAAA
63532 GGTCAAC-GCAGGTCAAA
1 GGTCAACAGCAGGTCAAA
63549 GGTCAACAG
1 GGTCAACAG
63558 TAGACCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 20 0.91
18 1 0.05
ACGTcount: A:0.33, C:0.26, G:0.28, T:0.14
Consensus pattern (18 bp):
GGTCAACAGCAGGTCAAA
Found at i:63649 original size:22 final size:23
Alignment explanation
Indices: 63619--63669 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
63609 CACATTCTGT
*
63619 AAATATTTACGA-AACTAACACCC
1 AAATATTTAC-ACAAATAACACCC
*
63642 AAAT-TTTACACAAATAGCACCC
1 AAATATTTACACAAATAACACCC
63664 AAATAT
1 AAATAT
63670 AAATAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 18 0.75
23 5 0.21
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.24
Consensus pattern (23 bp):
AAATATTTACACAAATAACACCC
Found at i:73656 original size:22 final size:22
Alignment explanation
Indices: 73626--73688 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
73616 TATAACTCAC
* *
73626 AACTAAAGCCTTATTGCTAACA
1 AACTCAAGCCTTACTGCTAACA
*
73648 AGCTCAAGCCTTACTGCTAACA
1 AACTCAAGCCTTACTGCTAACA
*
73670 AACTCAAGCCTAACTGCTA
1 AACTCAAGCCTTACTGCTA
73689 CTAACAACTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.24
Consensus pattern (22 bp):
AACTCAAGCCTTACTGCTAACA
Found at i:77547 original size:131 final size:131
Alignment explanation
Indices: 77306--77672 Score: 488
Period size: 132 Copynumber: 2.8 Consensus size: 131
77296 ATTTTAAGAT
* * *
77306 AGAAAATAATAATATCTAATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAGAGCA-AT
1 AGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGA-CTCTCATGCCTTAAAGCATA-
* * *
77370 CATTTATTACTCCAACCGAAATGAAAAGATATTACTATTTCGTCTT-AAAATTCAATATTGATTT
64 CATTTATTACTCCAACCGAAATGAAGAGATATTACTATTTCGTCTTAAAAAATCAATATTGATTC
77434 GAG
129 GAG
* * *
77437 CGAAAACAATAATATCTAATGATTTCCAATCGATAATAAATGATCTCTCATGCCTTAAAGCATAC
1 AGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGA-CTCTCATGCCTTAAAGCATAC
* * *
77502 ATTTATTACTCTAATCGAAATGAAGAGATATCACTATTCTC-TCTTAAAAAATCAATATTGATTC
65 ATTTATTACTCCAACCGAAATGAAGAGATATTACTATT-TCGTCTTAAAAAATCAATATTGATTC
77566 GAG
129 GAG
* * * * * *
77569 AGAAAACAATAATATCTAATTATTTTCAATAGAGAATAACTGACATCTCATGTCTTAAAGAATTC
1 AGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGAC-TCTCATGCCTTAAAGCATAC
* *
77634 ATTTATTTCTCCAACCGAAACGAAGAGATATTACTATTT
65 ATTTATTACTCCAACCGAAATGAAGAGATATTACTATTT
77673 TCAATATGGA
Statistics
Matches: 205, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
131 96 0.47
132 109 0.53
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (131 bp):
AGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACTCTCATGCCTTAAAGCATACA
TTTATTACTCCAACCGAAATGAAGAGATATTACTATTTCGTCTTAAAAAATCAATATTGATTCGA
G
Found at i:78305 original size:2 final size:2
Alignment explanation
Indices: 78298--78346 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
78288 CATGCATACA
78298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78339 AT A- AT AT A
1 AT AT AT AT A
78347 GAATATAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:78355 original size:12 final size:13
Alignment explanation
Indices: 78297--78353 Score: 82
Period size: 12 Copynumber: 4.5 Consensus size: 13
78287 ACATGCATAC
78297 AATATATATATAT
1 AATATATATATAT
78310 -ATATATATATAT
1 AATATATATATAT
78322 ATATATATATATAT
1 A-ATATATATATAT
*
78336 AATATA-ATATAG
1 AATATATATATAT
78348 AATATA
1 AATATA
78354 ATTACATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
12 23 0.56
13 5 0.12
14 13 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
AATATATATATAT
Found at i:79296 original size:19 final size:20
Alignment explanation
Indices: 79269--79306 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
79259 AATCTAGTGT
* *
79269 GTTTTTTTTTTCT-TTTTTG
1 GTTTGTTTTCTCTGTTTTTG
79288 GTTTGTTTTCTCTGTTTTT
1 GTTTGTTTTCTCTGTTTTT
79307 TGAACCCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.00, C:0.08, G:0.13, T:0.79
Consensus pattern (20 bp):
GTTTGTTTTCTCTGTTTTTG
Found at i:80649 original size:243 final size:241
Alignment explanation
Indices: 80187--80984 Score: 1014
Period size: 243 Copynumber: 3.3 Consensus size: 241
80177 CATCTGCCCG
* * * * * * *
80187 AAGGTCTTATAGATGGCCCAAAGGACTT-ATCATCTTGCTCGAAAGACTAACAGATGGCTCGAAG
1 AAGG-CTTATAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
* ** * * * * *
80251 GTCTTAGTAATTTTAGAAGTAGTTTAATAGGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCA
65 GACTTACCAATTTTGGAAATAGTTTACTAGGTAAG-AACTTTGAAAATC-ATTT-TTACTTTTCA
* *
80316 AAAACTTCAATTTTCAGATTTAAATGAGAAA-TTTTTCTTA-TTTTCAAAAACATGTGAAAACAT
127 AAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTTCTCATTTTTCAAAAACATGTGAAAACAT
*
80379 CCTGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGA
192 CCTGCCCGAAGGTCTTGTGGATGGCCCGAAAGACTTATCATCTTGCTCGA
* * * * *
80429 AAGGCTTATAGATGATCCGAAGGATTTACTCGTCATACTCAAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTATAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
*
80494 ACTTACCAATTTTGGAAATATTTTACTAGGTAAGAACTTTGAAAATCATTTATTACTTTTCAAAA
66 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAACTTTGAAAATCATTT-TTACTTTTCAAAA
80559 ATTTCAATTTTCAGATTTAAATGAGAAACTTTTTCTCATTTTTCAAAAAACATGTGAAAACATCC
130 ATTTCAATTTTCAGATTTAAATGAGAAACTTTTTCTCATTTTTC-AAAAACATGTGAAAACATCC
* * * * *
80624 TGCCCGAAGATCTTGTGGATGGCCCGAAGGACTTATTATATTGCTAGA
194 TGCCCGAAGGTCTTGTGGATGGCCCGAAAGACTTATCATCTTGCTCGA
* * *
80672 AAGGCTTATAGATGACCCGAAGGATTTAATCATAATGCTGGGAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTATAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* * *
80737 ACATACCAA-TTTGGAAATAGTTTACTAGGTAAGAATTTTGAAAATCGTTTTCCTACTTTTCAAA
66 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAACTTTGAAAATCATTTT--TACTTTTCAAA
* * * *
80801 AATTTTAATTTTTAGATTTAAATGAGAAAC-TTTTCTCATTTTTTTGAAAAATATGTGAAAACAT
129 AATTTCAATTTTCAGATTTAAATGAGAAACTTTTTCTCA--TTTTTCAAAAACATGTGAAAACAT
* * * *
80865 ACTGTCCGAAGGTCTTGTAGTTGGCCC-AAAGGACTTATCATCTTGCTCGA
192 CCTGCCCGAAGGTCTTGTGGATGGCCCGAAA-GACTTATCATCTTGCTCGA
* * * * * *
80915 AAGGGTTATAGATAACCCGAAGGATTTAATCATCATGCTTGAAAGACTTACTAATGACCCGAATG
1 AAGGCTTATAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
80980 ACTTA
66 ACTTA
80985 TTATGTAAGA
Statistics
Matches: 483, Mismatches: 64, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
240 43 0.09
241 40 0.08
242 113 0.23
243 282 0.58
244 5 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (241 bp):
AAGGCTTATAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAACTTTGAAAATCATTTTTACTTTTCAAAAA
TTTCAATTTTCAGATTTAAATGAGAAACTTTTTCTCATTTTTCAAAAACATGTGAAAACATCCTG
CCCGAAGGTCTTGTGGATGGCCCGAAAGACTTATCATCTTGCTCGA
Done.