Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005558.1 Hibiscus syriacus cultivar Beakdansim tig00012886_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: 52161
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:16069 original size:37 final size:38
Alignment explanation
Indices: 16026--16102 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 38
16016 ATTGATGGAA
16026 TTGTAATATTTCTTTATTTCGATT-GAGTAAGAATTAC
1 TTGTAATATTTCTTTATTTCGATTGGAGTAAGAATTAC
*
16063 TTGTAATATTTCTTTATTTCGATTGGAGTAATAATTAC
1 TTGTAATATTTCTTTATTTCGATTGGAGTAAGAATTAC
16101 TT
1 TT
16103 AGCCAATTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 24 0.63
38 14 0.37
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.51
Consensus pattern (38 bp):
TTGTAATATTTCTTTATTTCGATTGGAGTAAGAATTAC
Found at i:23857 original size:2 final size:2
Alignment explanation
Indices: 23852--23877 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23842 TATATATATA
23852 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
23878 ACTTTCATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:25508 original size:2 final size:2
Alignment explanation
Indices: 25501--25529 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25491 TTCTATCGTT
25501 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25530 TTTCATGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25851 original size:12 final size:12
Alignment explanation
Indices: 25836--25880 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
25826 CGGTTTTTTT
*
25836 ACCGGATAAAAA
1 ACCGGTTAAAAA
25848 ACCGGTTTGAAAAA
1 ACCGG-TT-AAAAA
25862 ACCGGTTAAAAA
1 ACCGGTTAAAAA
25874 ACCGGTT
1 ACCGGTT
25881 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 17 0.57
13 3 0.10
14 10 0.33
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:25862 original size:14 final size:13
Alignment explanation
Indices: 25842--25881 Score: 64
Period size: 12 Copynumber: 3.1 Consensus size: 13
25832 TTTTACCGGA
25842 TAAAAAACCGGTT
1 TAAAAAACCGGTT
25855 TGAAAAAACCGG-T
1 T-AAAAAACCGGTT
25868 TAAAAAACCGGTT
1 TAAAAAACCGGTT
25881 T
1 T
25882 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.40
13 5 0.20
14 10 0.40
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:28197 original size:21 final size:21
Alignment explanation
Indices: 28173--28212 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28163 TTTATTTTAT
28173 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
28194 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
28213 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:28260 original size:33 final size:33
Alignment explanation
Indices: 28207--28305 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
28197 TTTGTTTCAA
28207 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
28239 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
28272 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
28305 T
1 T
28306 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:28334 original size:13 final size:13
Alignment explanation
Indices: 28291--28345 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
28281 TTGGAAGTAT
28291 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
28304 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
28318 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
28331 TTAAGTATTTGAA
1 TTAAGTATTTCAA
28344 TT
1 TT
28346 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:28803 original size:21 final size:18
Alignment explanation
Indices: 28758--28791 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28748 GGTTTTTTAT
28758 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
28775 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
28792 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:28911 original size:15 final size:17
Alignment explanation
Indices: 28885--28916 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28875 TTCTATGGGA
28885 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
28901 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
28917 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:29214 original size:18 final size:17
Alignment explanation
Indices: 29193--29227 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29183 AATTATTATC
*
29193 TTAATTTATTATTAATAA
1 TTAATGTATTA-TAATAA
29211 TTAATGTATTATAATAA
1 TTAATGTATTATAATAA
29228 AAAATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTAATGTATTATAATAA
Found at i:29602 original size:18 final size:16
Alignment explanation
Indices: 29556--29615 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 16
29546 ATCATACTAC
29556 TTCATTTAAGCATG-A
1 TTCATTTAAGCATGCA
29571 GTTCATTTAAGCATGCA
1 -TTCATTTAAGCATGCA
29588 TTGCATTTAAAGCAT-CTA
1 TT-CATTT-AAGCATGC-A
29606 TTTCATTTAA
1 -TTCATTTAA
29616 TAAAGTTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
16 16 0.41
17 9 0.23
18 12 0.31
19 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.42
Consensus pattern (16 bp):
TTCATTTAAGCATGCA
Found at i:29642 original size:17 final size:17
Alignment explanation
Indices: 29622--29674 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
29612 TTAATAAAGT
29622 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
29639 TAGTTCATAAATCAAAC
1 TAGTTCATTAATTAAAC
*
29656 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
29673 TA
1 TA
29675 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:32889 original size:15 final size:16
Alignment explanation
Indices: 32859--32892 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
32849 AATTATTCAC
32859 TTTAATATTTTAAAAT
1 TTTAATATTTTAAAAT
*
32875 TTTAAT-TTTTTAAAT
1 TTTAATATTTTAAAAT
32890 TTT
1 TTT
32893 GACACTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAATATTTTAAAAT
Found at i:32951 original size:39 final size:39
Alignment explanation
Indices: 32843--32952 Score: 118
Period size: 39 Copynumber: 2.8 Consensus size: 39
32833 TTATTCACAA
* *
32843 TCTTCAAATTA-TTCACTTTAATATTTTAAAATTTTAATT
1 TCTT-AAATTATTTCACATTAATATTTTAAATTTTTAATT
* * *
32882 TTTTAAA-T-TTTGACACTATAATATTCTAAATTTTTAATT
1 TCTTAAATTATTTCACA-T-TAATATTTTAAATTTTTAATT
*
32921 TCTTAAATTATTTCACATTAACATTTTAAATT
1 TCTTAAATTATTTCACATTAATATTTTAAATT
32953 ATTTTTTAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
37 5 0.09
38 4 0.07
39 40 0.70
40 2 0.04
41 6 0.11
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.53
Consensus pattern (39 bp):
TCTTAAATTATTTCACATTAATATTTTAAATTTTTAATT
Found at i:33222 original size:21 final size:22
Alignment explanation
Indices: 33198--33256 Score: 84
Period size: 21 Copynumber: 2.6 Consensus size: 22
33188 AAACTATATA
33198 TATATTAACTTAAAATAT-TTT
1 TATATTAACTTAAAATATATTT
33219 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAATATATTT
33243 TACTATTAACTTAA
1 TA-TATTAACTTAA
33257 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.35
23 7 0.21
24 5 0.15
25 10 0.29
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:33240 original size:25 final size:27
Alignment explanation
Indices: 33202--33270 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 27
33192 TATATATATA
*
33202 TTAACTTAAAATATTTTTA-TATTAAC
1 TTAATTTAAAATATTTTTACTATTAAC
33228 TT-A-TT-AAATATATTTTACTATTAAC
1 TTAATTTAAAATAT-TTTTACTATTAAC
33253 TTAATTTAAAAATATTTT
1 TTAATTT-AAAATATTTT
33271 ATTTTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
23 6 0.16
24 7 0.19
25 10 0.27
26 3 0.08
27 2 0.05
28 3 0.08
29 6 0.16
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAATTTAAAATATTTTTACTATTAAC
Found at i:33268 original size:27 final size:24
Alignment explanation
Indices: 33198--33272 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 24
33188 AAACTATATA
*
33198 TATATTAACTTA--AAATAT-TTT
1 TATATTAACTTATTAAAAATATTT
*
33219 TATATTAACTTATTAAATATATTT
1 TATATTAACTTATTAAAAATATTT
33243 TACTATTAACTTAATTTAAAAATATTT
1 TA-TATTAACTT-A-TTAAAAATATTT
33270 TAT
1 TAT
33273 TTTTATTTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
21 12 0.26
23 6 0.13
24 5 0.11
25 9 0.19
26 2 0.04
27 13 0.28
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (24 bp):
TATATTAACTTATTAAAAATATTT
Found at i:43467 original size:2 final size:2
Alignment explanation
Indices: 43460--43494 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
43450 CTTGTATACA
*
43460 AT AT AT AT A- AT CT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43495 TTATTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48275 original size:22 final size:22
Alignment explanation
Indices: 48250--48300 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
48240 CTACGGCGAC
48250 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
48272 ATCCATCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
48294 ATCCGTC
1 ATCCGTC
48301 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.45, G:0.14, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:48777 original size:20 final size:20
Alignment explanation
Indices: 48706--48794 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
48696 GATTTTCTCA
*
48706 TTGCGGTTTTCA-TTTCGCG
1 TTGCGATTTTCATTTTCGCG
** **
48725 TTGCGATAGTCAAATTCGCG
1 TTGCGATTTTCATTTTCGCG
** *
48745 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCATTTTCGCG
*
48765 TTGCGATTTTCATTTTCGTG
1 TTGCGATTTTCATTTTCGCG
48785 TTGCGATTTT
1 TTGCGATTTT
48795 AAGTTTCAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 9 0.15
20 51 0.85
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATTTTCGCG
Found at i:48801 original size:20 final size:20
Alignment explanation
Indices: 48758--48801 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
48748 CGATAGTCAT
* *
48758 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
48778 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
48798 TTTC
1 TTTC
48802 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:50403 original size:21 final size:21
Alignment explanation
Indices: 50379--50434 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
50369 TGGTGCATGG
* * *
50379 CGTGATGAGGTATCTACTTTA
1 CGTGATGAGGTAGCGACTCTA
*
50400 CGTGGTGAGGTAGCGACTCTA
1 CGTGATGAGGTAGCGACTCTA
50421 CGTGA-GATGGTAGC
1 CGTGATGA-GGTAGC
50435 ATCATTGCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (21 bp):
CGTGATGAGGTAGCGACTCTA
Found at i:50701 original size:20 final size:20
Alignment explanation
Indices: 50672--50737 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
50662 TGCAGAAGAA
* * *
50672 GCAACACGAAACTTAAAATC
1 GCAACGCGAAAATGAAAATC
**
50692 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGAAAATC
**
50712 GCAACGCG-AAATGACCATC
1 GCAACGCGAAAATGAAAATC
50731 GCAACGC
1 GCAACGC
50738 AATTTGACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 17 0.43
20 23 0.57
ACGTcount: A:0.41, C:0.29, G:0.18, T:0.12
Consensus pattern (20 bp):
GCAACGCGAAAATGAAAATC
Found at i:50725 original size:19 final size:20
Alignment explanation
Indices: 50689--50737 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
50679 GAAACTTAAA
*
50689 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACC
50709 ATCGCAACGCG-AAATGACC
1 ATCGCAACGCGAAAATGACC
50728 ATCGCAACGC
1 ATCGCAACGC
50738 AATTTGACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.37, C:0.31, G:0.20, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACC
Found at i:50792 original size:32 final size:33
Alignment explanation
Indices: 50756--50817 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
50746 TATCAACGAT
50756 AATCGCAATGCG-AAATAAAAATCGCAACGTAA
1 AATCGCAATGCGAAAATAAAAATCGCAACGTAA
* *
50788 AATCGCATTGCGAAAATGAAAATCGCAACG
1 AATCGCAATGCGAAAATAAAAATCGCAACG
50818 AAATTTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.16
Consensus pattern (33 bp):
AATCGCAATGCGAAAATAAAAATCGCAACGTAA
Found at i:50850 original size:19 final size:20
Alignment explanation
Indices: 50821--50859 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
50811 CGCAACGAAA
*
50821 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
50841 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
50860 ACTTGTTGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:50889 original size:20 final size:20
Alignment explanation
Indices: 50864--50911 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
50854 GCGATTACTT
50864 GTTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTTCCGC
*
50884 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTCCGC
50904 GTTGCGAT
1 GTTGCGAT
50912 TTTAAGTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGC
Found at i:50921 original size:20 final size:20
Alignment explanation
Indices: 50898--50941 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
50888 CGATAGTCAT
50898 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
50918 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
50938 TTTC
1 TTTC
50942 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:51439 original size:21 final size:21
Alignment explanation
Indices: 51415--51484 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
51405 CTATCATCCC
51415 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* * ** *
51436 TCAAGAGGCCCATGTCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* *
51457 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCGT
51478 TCAAGAG
1 TCAAGAG
51485 CCTGATTCAC
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:51454 original size:42 final size:42
Alignment explanation
Indices: 51391--51484 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
51381 CACCTGTCAT
*
51391 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCCATATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
51433 CGTTCAAGAGGCCCATGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCATATCATCCCTCAAGAGGTCCCTCCCAC
*
51475 CATTCAAGAG
1 CGTTCAAGAG
51485 CCTGATTCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 43 0.96
43 2 0.04
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCCATATCATCCCTCAAGAGGTCCCTCCCAC
Done.