Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001441.1 Hibiscus syriacus cultivar Beakdansim tig00002790_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: 53659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4470 original size:15 final size:16
Alignment explanation
Indices: 4450--4482 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4440 AATTTTAAAT
*
4450 TTAAATTATGATT-TA
1 TTAAATTACGATTATA
4465 TTAAATTACGATTATA
1 TTAAATTACGATTATA
4481 TT
1 TT
4483 TTTAAGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (16 bp):
TTAAATTACGATTATA
Found at i:5372 original size:25 final size:25
Alignment explanation
Indices: 5337--5395 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
5327 GATGTAATAT
5337 TTTATCTTTAAAACTTAGAA-TTTTAA
1 TTTAT-TTTAAAACTT-GAAGTTTTAA
*
5363 TTTATTTTAATACTTGAAGTTTTAA
1 TTTATTTTAAAACTTGAAGTTTTAA
5388 TTT-TTTTA
1 TTTATTTTA
5396 TACCATAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 8 0.26
25 18 0.58
26 5 0.16
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (25 bp):
TTTATTTTAAAACTTGAAGTTTTAA
Found at i:7915 original size:41 final size:42
Alignment explanation
Indices: 7842--7935 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 42
7832 GACGAAAATA
* * * *
7842 TTTTGTCACTAGTCTCAGTTGGTAATTTGTGACGATAATTGT
1 TTTTGTCACTAATCTCAGTTAGTAATTTGTGACAATAATTAT
* *
7884 TTTTGTC-CTAATCTTAGTTAGTGATTTGTGACAATAATTAT
1 TTTTGTCACTAATCTCAGTTAGTAATTTGTGACAATAATTAT
*
7925 ATTTGTCACTA
1 TTTTGTCACTA
7936 TTGAAATAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 34 0.77
42 10 0.23
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (42 bp):
TTTTGTCACTAATCTCAGTTAGTAATTTGTGACAATAATTAT
Found at i:25250 original size:13 final size:13
Alignment explanation
Indices: 25232--25266 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
25222 TTTTTTAAAT
25232 AAAATATTATTTA
1 AAAATATTATTTA
*
25245 AAAATATTTTTTA
1 AAAATATTATTTA
25258 AAATATATT
1 AAA-ATATT
25267 CATATGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AAAATATTATTTA
Found at i:25260 original size:12 final size:13
Alignment explanation
Indices: 25231--25263 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
25221 TTTTTTTAAA
25231 TAAAATATTATTT
1 TAAAATATTATTT
*
25244 AAAAATATT-TTT
1 TAAAATATTATTT
25256 TAAAATAT
1 TAAAATAT
25264 ATTCATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAAATATTATTT
Found at i:26685 original size:15 final size:16
Alignment explanation
Indices: 26665--26697 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
26655 TTTTAGTCTG
26665 TTTTAA-TATTTAAAA
1 TTTTAATTATTTAAAA
*
26680 TTTTAATTTTTTAAAA
1 TTTTAATTATTTAAAA
26696 TT
1 TT
26698 ATATTTAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAATTATTTAAAA
Found at i:34910 original size:19 final size:19
Alignment explanation
Indices: 34884--34927 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
34874 ATTATATTTT
*
34884 TATT-TTAATAATATAATAA
1 TATTATTAATAAT-GAATAA
34903 -ATTATTAATAATGAATAA
1 TATTATTAATAATGAATAA
34921 TATTATT
1 TATTATT
34928 TATGTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTATTAATAATGAATAA
Found at i:35299 original size:14 final size:15
Alignment explanation
Indices: 35280--35351 Score: 58
Period size: 14 Copynumber: 4.7 Consensus size: 15
35270 CAAACAACAT
35280 AAAATATTTTCT-AA
1 AAAATATTTTCTAAA
* *
35294 AAAATATTTTTTTGAA
1 AAAATA-TTTTCTAAA
* *
35310 AATATAATTTATTTAAAA
1 AAAAT-ATTT-TCT-AAA
35328 AAAATATTTTCT-AA
1 AAAATATTTTCTAAA
35342 AAAATATTTT
1 AAAATATTTT
35352 GCAAAGGCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
14 18 0.38
15 5 0.10
16 11 0.23
17 8 0.17
18 6 0.12
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (15 bp):
AAAATATTTTCTAAA
Found at i:39260 original size:42 final size:39
Alignment explanation
Indices: 39202--39287 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 39
39192 CATCGACTTT
* * *
39202 AGCATAACTGAACTGCCTTGG-GAAACTAGGAATCTAGAAA
1 AGCATAACCGAACTGCCATGGTG-AACTAGAAATCTA-AAA
39242 GAGCATAACCCGAACTGCCATGGTGAACTAGAAATCTAAAA
1 -AGCATAA-CCGAACTGCCATGGTGAACTAGAAATCTAAAA
39283 AGCAT
1 AGCAT
39288 GACTCTAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
40 5 0.12
41 10 0.25
42 24 0.60
43 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.19
Consensus pattern (39 bp):
AGCATAACCGAACTGCCATGGTGAACTAGAAATCTAAAA
Found at i:43153 original size:8 final size:8
Alignment explanation
Indices: 43142--43170 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
43132 TCATTCATTC
43142 ATCTACCT
1 ATCTACCT
43150 ATCTACCT
1 ATCTACCT
43158 ATCTACCT
1 ATCTACCT
43166 ATCTA
1 ATCTA
43171 TTCATCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (8 bp):
ATCTACCT
Found at i:43177 original size:16 final size:16
Alignment explanation
Indices: 43138--43178 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
43128 GCATTCATTC
43138 ATTCATCTACCTATCT
1 ATTCATCTACCTATCT
*
43154 A-CCTATCTACCTATCT
1 ATTC-ATCTACCTATCT
43170 ATTCATCTA
1 ATTCATCTA
43179 TTTCGTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTCATCTACCTATCT
Found at i:45589 original size:21 final size:22
Alignment explanation
Indices: 45560--45606 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
45550 ATTCTGACTA
45560 TCGCATTGCGATTTTCC-AAAT
1 TCGCATTGCGATTTTCCTAAAT
*
45581 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
45602 TCGCA
1 TCGCA
45607 ACGCGAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:46277 original size:20 final size:20
Alignment explanation
Indices: 46234--46301 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
46224 CGATTCTTGC
* *
46234 GTTGCGATAGTCAAATTT-GC
1 GTTGCGATAGTC-ATTTTCGT
46254 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
** *
46274 GTTGCGATTTTCATTTTCAT
1 GTTGCGATAGTCATTTTCGT
46294 GTTGCGAT
1 GTTGCGAT
46302 TTACAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 4 0.10
20 38 0.90
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.44
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:46311 original size:20 final size:20
Alignment explanation
Indices: 46268--46312 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
46258 CGATAGTCAT
* * *
46268 TTTCGTGTTGCGATTTTCAT
1 TTTCATGTTGCGATTTACAG
46288 TTTCATGTTGCGATTTACAG
1 TTTCATGTTGCGATTTACAG
46308 TTTCA
1 TTTCA
46313 GAAACTATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTCATGTTGCGATTTACAG
Found at i:47777 original size:6 final size:6
Alignment explanation
Indices: 47766--47801 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
47756 TTCTTCTGTT
47766 CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC
1 CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC
47802 GGGATGAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.67, G:0.00, T:0.17
Consensus pattern (6 bp):
CTCCAC
Found at i:48200 original size:20 final size:20
Alignment explanation
Indices: 48175--48277 Score: 112
Period size: 20 Copynumber: 5.5 Consensus size: 20
48165 AGAATAGTTT
48175 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
48195 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
48215 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
48231 A--ATCACAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
48248 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
48268 ACTATCGCAA
1 ACTATCGCAA
48278 CGAAGAATCG
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
14 6 0.09
16 6 0.09
17 4 0.06
18 2 0.03
19 10 0.14
20 42 0.60
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:48263 original size:53 final size:52
Alignment explanation
Indices: 48182--48314 Score: 185
Period size: 53 Copynumber: 2.5 Consensus size: 52
48172 TTTACTATCG
*
48182 CAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCA
1 CAATGCG-AAATGACTATCGCAATGCGAAAATGACTATCGCAACGA-AGAATCA
** *
48236 CAATGCGAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAGAATCG
1 CAATGCGAAATGACTATCGCAATGCGAAAATGACTATCGCAACGAAGAATCA
** *
48288 CAATGCGAAATGAAAATCGCATTGCGA
1 CAATGCGAAATGACTATCGCAATGCGA
48315 TTCTCTCGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 30 0.42
53 35 0.49
54 7 0.10
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (52 bp):
CAATGCGAAATGACTATCGCAATGCGAAAATGACTATCGCAACGAAGAATCA
Found at i:48375 original size:20 final size:20
Alignment explanation
Indices: 48323--48381 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
48313 GATTCTCTCG
**
48323 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
48343 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
48363 TTGCGATAGTCATTTTCGC
1 TTGCGATAGTCATTTTCGC
48382 GTTTGTGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:50326 original size:13 final size:14
Alignment explanation
Indices: 50310--50344 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
50300 ATTGTTTAAT
50310 TGATTTGTAAA-GA
1 TGATTTGTAAATGA
*
50323 TGATTTGTAAATGT
1 TGATTTGTAAATGA
50337 TGATTTGT
1 TGATTTGT
50345 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.49
Consensus pattern (14 bp):
TGATTTGTAAATGA
Found at i:50502 original size:33 final size:33
Alignment explanation
Indices: 50456--50539 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
50446 TCACAACGCA
** *
50456 GAAATGACTATCGCAACGAGAGAATCGTAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
*
50489 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
50522 GAAAAT-AAAATCGCAACG
1 G-AAATGAAAATCGCAACG
50540 CGAAACTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 42 0.91
34 4 0.09
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:50747 original size:233 final size:235
Alignment explanation
Indices: 50338--50803 Score: 789
Period size: 233 Copynumber: 2.0 Consensus size: 235
50328 TGTAAATGTT
50338 GATTTGTTTAATTGATGTGTACAAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGAT
1 GATTTGTTTAATTGATGTGTACAAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGAT
*
50403 TTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGACTATCACAACGCAGAAATGACTATC
66 TTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGAATATCACAACGCAGAAATGACTATC
* *
50468 GCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAAT-AAAA
131 ACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAA
50532 TCGCAACGCGAAACTAATTTCGCGTTGCGATTTTCATTTTC
196 TCGCAACGCGAAACTAATTTCGCGTTGCGA-TTTCATTTTC
*
50573 GATTTG-TTAATTGATGTGTACATAATATTTGTTCTTGTTTAATTGATTGAAATGTAATAGTTGA
1 GATTTGTTTAATTGATGTGTACA-AATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGA
*
50637 TTT-TTGATTTCAATCTGCATTAT-TTGAATGCAAAACAGAATATCGCAACGC-GAAAATGACTA
65 TTTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGAATATCACAACGCAG-AAATGACTA
* * *
50699 TCACAACGAGAGATTCGCAATGCGAAATTAAAATCGCAATGAGTGAATCGCAATGCGAAAATGAA
129 TCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAA
*
50764 AATCGCAACGCGAAACTAATTTCGCGTTGTGATTTCATTT
194 AATCGCAACGCGAAACTAATTTCGCGTTGCGATTTCATTT
50804 CGCATTGCGA
Statistics
Matches: 219, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
232 1 0.00
233 100 0.46
234 69 0.32
235 49 0.22
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (235 bp):
GATTTGTTTAATTGATGTGTACAAATATTTGTGCTTGTTTAATTGATTGAAATGTAATAGTTGAT
TTGTTGATTTCAATCTGCATTATGTTGAATGCAAAACAGAATATCACAACGCAGAAATGACTATC
ACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAA
TCGCAACGCGAAACTAATTTCGCGTTGCGATTTCATTTTC
Found at i:50771 original size:34 final size:34
Alignment explanation
Indices: 50678--50773 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 34
50668 AAAACAGAAT
* ** *
50678 ATCGCAACGCGAAAATGACTATCACAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
* * * *
50712 TTCGCAATGCG-AAATTAAAATCGCAATGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
50745 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
50774 CGAAACTAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
33 26 0.52
34 24 0.48
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:50815 original size:18 final size:18
Alignment explanation
Indices: 50782--50848 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
50772 CGCGAAACTA
* *
50782 ATTTCGCGTTGTGATTTC
1 ATTTCGCATTGCGATTTC
50800 ATTTCGCATTGCGA-TTC
1 ATTTCGCATTGCGATTTC
*
50817 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA-TTTC
*
50833 ATTTCGCATTACGATT
1 ATTTCGCATTGCGATT
50849 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 7 0.18
18 14 0.36
19 5 0.13
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (18 bp):
ATTTCGCATTGCGATTTC
Found at i:50838 original size:33 final size:33
Alignment explanation
Indices: 50788--50870 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
50778 ACTAATTTCG
* *
50788 CGTTGTGA-TTTCATTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTCGCATTACGATTCACT
*
50820 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTACGATTCACT
**
50853 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
50871 CGCGCTGCGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 7 0.16
33 38 0.84
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTACGATTCACT
Found at i:50881 original size:20 final size:20
Alignment explanation
Indices: 50853--50964 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
50843 ACGATTCTCT
50853 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
50873 CGCTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
50893 CATTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
50913 C-ATGCGATAGTTATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
50932 TGTTG-GATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
*
50951 CGTTACGATAGTCA
1 CGTTGCGATAGTCA
50965 ATGAATGTCT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 28 0.36
20 49 0.64
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:50931 original size:39 final size:40
Alignment explanation
Indices: 50855--50966 Score: 122
Period size: 39 Copynumber: 2.9 Consensus size: 40
50845 GATTCTCTCG
* *
50855 TTGCGATAGTCATTTCCGCGCTGCGATAGTCAATTCCGCA
1 TTGCGATAGTCAATTCCGCGATGCGATAGTCAATTCCGCA
* * **
50895 TTGCGATAGTCAATTCCGC-ATGCGATAGTTATTTCCGTG
1 TTGCGATAGTCAATTCCGCGATGCGATAGTCAATTCCGCA
* *
50934 TTG-GATAGTCATATT-CGCGTTACGATAGTCAAT
1 TTGCGATAGTCA-ATTCCGCGATGCGATAGTCAAT
50967 GAATGTCTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
38 11 0.18
39 31 0.52
40 18 0.30
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.34
Consensus pattern (40 bp):
TTGCGATAGTCAATTCCGCGATGCGATAGTCAATTCCGCA
Found at i:53375 original size:24 final size:24
Alignment explanation
Indices: 53324--53375 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
53314 ATCCAAGTAT
** *
53324 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
53348 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
53372 TGAC
1 TGAC
53376 TATACTCACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Done.