Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002041.1 Hibiscus syriacus cultivar Beakdansim tig00004162_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: 69725
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4900 original size:28 final size:28
Alignment explanation
Indices: 4858--4913 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
4848 AGAGATCTTG
4858 CTAAGCATACATAGCATAATGCAACCTT
1 CTAAGCATACATAGCATAATGCAACCTT
**
4886 CTAAGCATATGTAGCATAATGCAACCTT
1 CTAAGCATACATAGCATAATGCAACCTT
4914 GAATAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (28 bp):
CTAAGCATACATAGCATAATGCAACCTT
Found at i:5416 original size:127 final size:123
Alignment explanation
Indices: 5183--5471 Score: 463
Period size: 127 Copynumber: 2.3 Consensus size: 123
5173 AAGCATTGGG
* * * * *
5183 TTCCCATAAGTTACAATT-ATTATCTATATCGGTAATTATGCTTTTATTTAAATACCTCCGTAGG
1 TTCCCATAAGTTGC-ATTGATTACCTACATCGGTAATTAGGCTTTTATTTAAAGACCTCCGTAGG
*
5247 TCGTCAGGTCCTCCGGGCGACCTCCATCCTCCAAACGTTCAAGCATTGGTTTCCTAGAT
65 TCGTCAGGTCCTCAGGGCGACCTCCATCCTCCAAACGTTCAAGCATTGGTTTCCTAGAT
*
5306 TTCCCATAAGTTGCATTGATTACCTACATCGGTAATTAGGCTTTTATTTAAAGACCTCTGTAGGT
1 TTCCCATAAGTTGCATTGATTACCTACATCGGTAATTAGGCTTTTATTTAAAGACCTC----CGT
5371 AGGTCGTCAGGTCCTCAGGGCGACCTCCATCCTCCAAACGTTCAAGCATTGGTTTCCTAGAT
62 AGGTCGTCAGGTCCTCAGGGCGACCTCCATCCTCCAAACGTTCAAGCATTGGTTTCCTAGAT
5433 TTCCCATAAGTTGCATTGATTACCTACATCGGTAATTAG
1 TTCCCATAAGTTGCATTGATTACCTACATCGGTAATTAG
5472 TGGTCCATAA
Statistics
Matches: 154, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
122 3 0.02
123 49 0.32
127 102 0.66
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (123 bp):
TTCCCATAAGTTGCATTGATTACCTACATCGGTAATTAGGCTTTTATTTAAAGACCTCCGTAGGT
CGTCAGGTCCTCAGGGCGACCTCCATCCTCCAAACGTTCAAGCATTGGTTTCCTAGAT
Found at i:8698 original size:36 final size:36
Alignment explanation
Indices: 8651--8725 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
8641 CCACAACTGA
*
8651 ACCAGAAGGCTTAACTGGAGTTGCCTTCATTTCAAC
1 ACCAGAAGGCTTAACTGGAGTTCCCTTCATTTCAAC
8687 ACCAGAAGGCTTAACTGGAGTTCCCTTCATTTCAAC
1 ACCAGAAGGCTTAACTGGAGTTCCCTTCATTTCAAC
8723 ACC
1 ACC
8726 TTCAAGCAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (36 bp):
ACCAGAAGGCTTAACTGGAGTTCCCTTCATTTCAAC
Found at i:10110 original size:2 final size:2
Alignment explanation
Indices: 10103--10127 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10093 TTATTATAGA
10103 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10128 ATTTTGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15711 original size:68 final size:68
Alignment explanation
Indices: 15502--15718 Score: 194
Period size: 69 Copynumber: 3.1 Consensus size: 68
15492 TCTAATCGGT
* * *
15502 AAGTATCGATATTTTTAT--ACAAATAT-AGATACTTTCGAATTAAAAAAAACATATAAAATAAG
1 AAGTATCAATATTTTT-TCCACAAATATCA-ATACTTTTGAATT-AAAAAAA-ATATAAAATGAG
* *
15564 AAGGTTATA
62 AA-GCT-CA
* * * * *
15573 AAATATCAATATTTTTTTCACAAATATCGATATTTTTTAATT-AAAAAAATGA-AAAATGAGAAG
1 AAGTATCAATATTTTTTCCACAAATATCAATACTTTTGAATTAAAAAAAAT-ATAAAATGAGAAG
15636 ACTTCA
65 -C-TCA
* *
15642 AAGTTTCAATA-TTTTTCCACACATATCAATACTTTTGAATTAAAAAAAATATAAAATGAGAATG
1 AAGTATCAATATTTTTTCCACAAATATCAATACTTTTGAATTAAAAAAAATATAAAATGAGAA-G
15706 CTCA
65 CTCA
15710 AAGTATCAA
1 AAGTATCAA
15719 ACTTTTAAAA
Statistics
Matches: 120, Mismatches: 17, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
68 38 0.32
69 40 0.33
70 10 0.08
71 14 0.12
72 18 0.15
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (68 bp):
AAGTATCAATATTTTTTCCACAAATATCAATACTTTTGAATTAAAAAAAATATAAAATGAGAAGC
TCA
Found at i:16043 original size:100 final size:95
Alignment explanation
Indices: 15917--16220 Score: 365
Period size: 100 Copynumber: 3.0 Consensus size: 95
15907 ATAGTGTAAT
* * * * *
15917 AATAATTATAACTTAACCGTTAAAAATAAAATATGTGCAACATATTACGTTAAACTAGCTATTGG
1 AATATTTACAACTTAACCGTT-AAAATAAAATA-GCGCAACTTATTGCGTTAAACTAGCTATT-G
15982 TTTGTTTAAATGTATAATAGTAATGTAAACACTAA
63 TTTGTTTAAATGTATAATA-TAATGTAAACA-TAA
*
16017 AATATTTACAACTTAACCAGTTAAAATAAAATAGGCGTAACTTATTGCGTTAAACTAGCTATCTG
1 AATATTTACAACTTAACC-GTTAAAATAAAATA-GCGCAACTTATTGCGTTAAACTAGCTAT-TG
*
16082 TTTGTTTAAATGTATAATTATAATGTAAATGATAA
63 TTTGTTTAAATGTATAA-TATAATGTAAA-CATAA
* * *
16117 AATATTTACAACTAAACCGGTTAAAATAAAATAGACGCTACTTATTGCGTTAAACTAGCTACTTA
1 AATATTTACAACTTAACC-GTTAAAATAAAATAG-CGCAACTTATTGCGTTAAACTAGCTA-TTG
* *
16182 TTTGTTTAAAGGTATAATAATAATGTAAACGGTAA
63 TTTGTTTAAATGTATAAT-ATAATGTAAAC-ATAA
16217 AATA
1 AATA
16221 AAATAGACGC
Statistics
Matches: 180, Mismatches: 16, Indels: 16
0.85 0.08 0.08
Matches are distributed among these distances:
99 2 0.01
100 170 0.94
101 8 0.04
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (95 bp):
AATATTTACAACTTAACCGTTAAAATAAAATAGCGCAACTTATTGCGTTAAACTAGCTATTGTTT
GTTTAAATGTATAATATAATGTAAACATAA
Found at i:16225 original size:76 final size:76
Alignment explanation
Indices: 16129--16296 Score: 246
Period size: 76 Copynumber: 2.2 Consensus size: 76
16119 TATTTACAAC
* * * * * *
16129 TAAACCGGTTAAAATAAAATAGACGCTACTTATTGCGTTAAACTAGCTACTTATTTGTTTAAAGG
1 TAAA-CGG-TAAAATAAAATAGACGCGACCTATTACGTTAAACTAACTAATGATTTGTTTAAAGG
16194 TATAATAATAATG
64 TATAATAATAATG
* *
16207 TAAACGGTAAAATAAAATAGACGCGACCTATTACGTTAAACTAACTAATGATTTTTTTAAAGTTA
1 TAAACGGTAAAATAAAATAGACGCGACCTATTACGTTAAACTAACTAATGATTTGTTTAAAGGTA
16272 TAATAATAATG
66 TAATAATAATG
16283 TAAACGGTAAAATA
1 TAAACGGTAAAATA
16297 TTTACAACTT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
76 75 0.91
77 3 0.04
78 4 0.05
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (76 bp):
TAAACGGTAAAATAAAATAGACGCGACCTATTACGTTAAACTAACTAATGATTTGTTTAAAGGTA
TAATAATAATG
Found at i:16249 original size:176 final size:176
Alignment explanation
Indices: 16038--16396 Score: 499
Period size: 176 Copynumber: 2.0 Consensus size: 176
16028 CTTAACCAGT
* * * * * * *
16038 TAAAATAAAATAGGCGTAACTTATTGCGTTAAACTAGCTATCTG-TTTGTTTAAA-TGTATAATT
1 TAAAATAAAATAGACGCAACCTATTACGTTAAACTAACTA-ATGATTTGTTTAAAGT-TATAATA
* * *
16101 ATAATGTAAATGATAAAATATTTACAACTAAACCGGTTAAAATAAAATA-GACGCTACTTATTGC
64 ATAATGTAAACGATAAAATATTTACAACTAAACCGGTTAAAATAAAATATG-CGCTACATATTAC
**
16165 GTTAAACTAGCTACTTATTTGTTTAAAGGTATAATAATAATGTAAACGG
128 GTTAAACTAGCTACCGATTTGTTTAAAGGTATAATAATAATGTAAACGG
* *
16214 TAAAATAAAATAGACGCGACCTATTACGTTAAACTAACTAATGATTTTTTTAAAGTTATAATAAT
1 TAAAATAAAATAGACGCAACCTATTACGTTAAACTAACTAATGATTTGTTTAAAGTTATAATAAT
* * *
16279 AATGTAAACGGTAAAATATTTACAACTTAACCGTTTAAAATAAAATATGCGCTACATATTACGTT
66 AATGTAAACGATAAAATATTTACAACTAAACCGGTTAAAATAAAATATGCGCTACATATTACGTT
* *
16344 AAACTATCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGG
131 AAACTAGCTACCGATTTGTTTAAAGGTATAATAATAATGTAAACGG
16390 TAAAATA
1 TAAAATA
16397 TTTACAACTT
Statistics
Matches: 161, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
175 2 0.01
176 157 0.98
177 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (176 bp):
TAAAATAAAATAGACGCAACCTATTACGTTAAACTAACTAATGATTTGTTTAAAGTTATAATAAT
AATGTAAACGATAAAATATTTACAACTAAACCGGTTAAAATAAAATATGCGCTACATATTACGTT
AAACTAGCTACCGATTTGTTTAAAGGTATAATAATAATGTAAACGG
Found at i:16348 original size:100 final size:100
Alignment explanation
Indices: 16214--16420 Score: 317
Period size: 100 Copynumber: 2.1 Consensus size: 100
16204 ATGTAAACGG
* * * *
16214 TAAAATAAAATAGACGCGACCTATTACGTTAAACTAACTAATGATTTTTTTAAAGTTATAATAAT
1 TAAAATAAAATAGACGCGACATATTACGTTAAACTAACTAACGATTTGTTTAAAGGTATAATAAT
*
16279 AATGTAAACGGTAAAATATTTACAACTTAACCGTT
66 AATGTAAACGGTAAAATATTTACAACTTAACCATT
* * * *
16314 TAAAATAAAATATG-CGCTACATATTACGTTAAACTATCTACCGGTTTGTTTAAAGGTATAATAA
1 TAAAATAAAATA-GACGCGACATATTACGTTAAACTAACTAACGATTTGTTTAAAGGTATAATAA
16378 TAATGTAAACGGTAAAATATTTACAACTTAACCATT
65 TAATGTAAACGGTAAAATATTTACAACTTAACCATT
16414 TAAAATA
1 TAAAATA
16421 TTTTTTTATA
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 96 0.99
101 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (100 bp):
TAAAATAAAATAGACGCGACATATTACGTTAAACTAACTAACGATTTGTTTAAAGGTATAATAAT
AATGTAAACGGTAAAATATTTACAACTTAACCATT
Found at i:17715 original size:2 final size:2
Alignment explanation
Indices: 17708--17743 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17698 TGATTTTTAA
17708 AT AT AT AT AT AT AT 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
17744 TCAAAGATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18134 original size:126 final size:126
Alignment explanation
Indices: 17909--18147 Score: 478
Period size: 126 Copynumber: 1.9 Consensus size: 126
17899 AGTAACTCCT
17909 TTAAGGTATATACATCAACTTCCCATCTTCATTTTATCCATTTCCATGGCTTTATCTTCTAGCTT
1 TTAAGGTATATACATCAACTTCCCATCTTCATTTTATCCATTTCCATGGCTTTATCTTCTAGCTT
17974 TTTATATATGTGTTTTCAGTTTGTTGCTGCTTCTTGTTCTTCAAAGTTGATGTTAGCTAGC
66 TTTATATATGTGTTTTCAGTTTGTTGCTGCTTCTTGTTCTTCAAAGTTGATGTTAGCTAGC
18035 TTAAGGTATATACATCAACTTCCCATCTTCATTTTATCCATTTCCATGGCTTTATCTTCTAGCTT
1 TTAAGGTATATACATCAACTTCCCATCTTCATTTTATCCATTTCCATGGCTTTATCTTCTAGCTT
18100 TTTATATATGTGTTTTCAGTTTGTTGCTGCTTCTTGTTCTTCAAAGTT
66 TTTATATATGTGTTTTCAGTTTGTTGCTGCTTCTTGTTCTTCAAAGTT
18148 ATCGAGGAAA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 113 1.00
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.49
Consensus pattern (126 bp):
TTAAGGTATATACATCAACTTCCCATCTTCATTTTATCCATTTCCATGGCTTTATCTTCTAGCTT
TTTATATATGTGTTTTCAGTTTGTTGCTGCTTCTTGTTCTTCAAAGTTGATGTTAGCTAGC
Found at i:28776 original size:26 final size:27
Alignment explanation
Indices: 28747--28816 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 27
28737 TATGGGTGGA
* *
28747 AATATATATTAATAATATTTTTATA-G
1 AATATATATTAATAAAATTTTAATATG
*
28773 AATATATATAAATAAAATTTTAATATG
1 AATATATATTAATAAAATTTTAATATG
*
28800 AATAT-TAATAATAAAAT
1 AATATATATTAATAAAAT
28817 GAATAAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 32 0.84
27 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (27 bp):
AATATATATTAATAAAATTTTAATATG
Found at i:30533 original size:21 final size:20
Alignment explanation
Indices: 30500--30538 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
30490 ACTTGTATAT
30500 AGTCGTTGGGATG-TTTTGG
1 AGTCGTTGGGATGATTTTGG
30519 AGTCGTTTGGGGATGATTTT
1 AGTCG-TT-GGGATGATTTT
30539 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 6 0.35
22 4 0.24
ACGTcount: A:0.13, C:0.05, G:0.38, T:0.44
Consensus pattern (20 bp):
AGTCGTTGGGATGATTTTGG
Found at i:30738 original size:20 final size:21
Alignment explanation
Indices: 30707--30749 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
30697 AATTTTGAGC
30707 ATCGGATACTGTTCAAACAGT
1 ATCGGATACTGTTCAAACAGT
30728 ATCGG-TACTGTTCAAACAGT
1 ATCGGATACTGTTCAAACAGT
30748 AT
1 AT
30750 AGTTACTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
ATCGGATACTGTTCAAACAGT
Found at i:30756 original size:20 final size:20
Alignment explanation
Indices: 30713--30756 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
30703 GAGCATCGGA
*
30713 TACTGTTCAAACAGTATCGG
1 TACTGTTCAAACAGTATAGG
*
30733 TACTGTTCAAACAGTATAGT
1 TACTGTTCAAACAGTATAGG
30753 TACT
1 TACT
30757 ATTTAGACAG
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:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (20 bp):
TACTGTTCAAACAGTATAGG
Found at i:32748 original size:14 final size:14
Alignment explanation
Indices: 32729--32760 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
32719 TTAAATTATA
32729 AACGAACACAAATG
1 AACGAACACAAATG
*
32743 AACGAACATAAATG
1 AACGAACACAAATG
32757 AACG
1 AACG
32761 GATGTAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.19, G:0.16, T:0.09
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:32770 original size:24 final size:24
Alignment explanation
Indices: 32743--32801 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
32733 AACACAAATG
* * *
32743 AACGAACATAAATGAACGGATGTA
1 AACGAACACAAATGAACGAACGTA
32767 AACGAACACAAATGAACGAACGTA
1 AACGAACACAAATGAACGAACGTA
32791 AACGAACACAA
1 AACGAACACAA
32802 TAAATAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.54, C:0.19, G:0.17, T:0.10
Consensus pattern (24 bp):
AACGAACACAAATGAACGAACGTA
Found at i:32814 original size:10 final size:10
Alignment explanation
Indices: 32801--32839 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
32791 AACGAACACA
*
32801 ATAAATAAAC
1 ATAAATGAAC
32811 ATAAATGAAC
1 ATAAATGAAC
* *
32821 GTAAACGAAC
1 ATAAATGAAC
32831 ATAAATGAA
1 ATAAATGAA
32840 AATATATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:33065 original size:14 final size:14
Alignment explanation
Indices: 33048--33088 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
33038 ACTTGCGAAC
33048 ATAAACGAACATAA
1 ATAAACGAACATAA
*
33062 ATAAACAAACATAA
1 ATAAACGAACATAA
*
33076 ATGAACGAACATA
1 ATAAACGAACATA
33089 TTATCGAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (14 bp):
ATAAACGAACATAA
Found at i:33072 original size:24 final size:23
Alignment explanation
Indices: 33007--33081 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 23
32997 GATTGTGCTA
*
33007 AACATAAATGAACACACATAAACG
1 AACATAAAT-AACAAACATAAACG
* ** *
33031 AAAATAAACTTGCGAACATAAACG
1 AACATAAA-TAACAAACATAAACG
*
33055 AACATAAATAAACAAACATAAATG
1 AACATAAAT-AACAAACATAAACG
33079 AAC
1 AAC
33082 GAACATATTA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
23 1 0.03
24 37 0.95
25 1 0.03
ACGTcount: A:0.60, C:0.17, G:0.08, T:0.15
Consensus pattern (23 bp):
AACATAAATAACAAACATAAACG
Found at i:37605 original size:239 final size:239
Alignment explanation
Indices: 37186--37664 Score: 958
Period size: 239 Copynumber: 2.0 Consensus size: 239
37176 TGCCAATCTC
37186 TTTGTCAAGAACCAGGCTGGACACTTGGTTGGAGGGAATCTTCAGTCCATTTGGGAATATTCTTT
1 TTTGTCAAGAACCAGGCTGGACACTTGGTTGGAGGGAATCTTCAGTCCATTTGGGAATATTCTTT
37251 ACTGTAAGATCGCCGAAGAAAATGGCAAGATCGGTCTCCATGATACCATGCTTAAAGGAAAGAAA
66 ACTGTAAGATCGCCGAAGAAAATGGCAAGATCGGTCTCCATGATACCATGCTTAAAGGAAAGAAA
37316 TTCTCTTTCTTCTTTTTTTAGTCTAATTTATGCACATCAGAGGAATGTCTATATTTTTATGATAA
131 TTCTCTTTCTTCTTTTTTTAGTCTAATTTATGCACATCAGAGGAATGTCTATATTTTTATGATAA
37381 AGAGTTTGGAGAGTTAAGTAGCTTGAATATATCACAATTCATCA
196 AGAGTTTGGAGAGTTAAGTAGCTTGAATATATCACAATTCATCA
37425 TTTGTCAAGAACCAGGCTGGACACTTGGTTGGAGGGAATCTTCAGTCCATTTGGGAATATTCTTT
1 TTTGTCAAGAACCAGGCTGGACACTTGGTTGGAGGGAATCTTCAGTCCATTTGGGAATATTCTTT
37490 ACTGTAAGATCGCCGAAGAAAATGGCAAGATCGGTCTCCATGATACCATGCTTAAAGGAAAGAAA
66 ACTGTAAGATCGCCGAAGAAAATGGCAAGATCGGTCTCCATGATACCATGCTTAAAGGAAAGAAA
37555 TTCTCTTTCTTCTTTTTTTAGTCTAATTTATGCACATCAGAGGAATGTCTATATTTTTATGATAA
131 TTCTCTTTCTTCTTTTTTTAGTCTAATTTATGCACATCAGAGGAATGTCTATATTTTTATGATAA
37620 AGAGTTTGGAGAGTTAAGTAGCTTGAATATATCACAATTCATCA
196 AGAGTTTGGAGAGTTAAGTAGCTTGAATATATCACAATTCATCA
37664 T
1 T
37665 ATCAATGATG
Statistics
Matches: 240, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
239 240 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (239 bp):
TTTGTCAAGAACCAGGCTGGACACTTGGTTGGAGGGAATCTTCAGTCCATTTGGGAATATTCTTT
ACTGTAAGATCGCCGAAGAAAATGGCAAGATCGGTCTCCATGATACCATGCTTAAAGGAAAGAAA
TTCTCTTTCTTCTTTTTTTAGTCTAATTTATGCACATCAGAGGAATGTCTATATTTTTATGATAA
AGAGTTTGGAGAGTTAAGTAGCTTGAATATATCACAATTCATCA
Found at i:44692 original size:2 final size:2
Alignment explanation
Indices: 44685--44720 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
44675 ACAAAAATTC
44685 AT AT AT AT AT AT AT 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
44721 TCGAATATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52968 original size:34 final size:34
Alignment explanation
Indices: 52925--52990 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
52915 CGTCAAGTCC
52925 AGTAAGGCCCTGAGCACACAGCCGAAGAGCCTGA
1 AGTAAGGCCCTGAGCACACAGCCGAAGAGCCTGA
*
52959 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCT
1 AGTAAGGCCCTGAGCACACAGCCGAAGAGCCT
52991 TCATGTATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.30, T:0.09
Consensus pattern (34 bp):
AGTAAGGCCCTGAGCACACAGCCGAAGAGCCTGA
Found at i:53085 original size:24 final size:24
Alignment explanation
Indices: 53058--53181 Score: 90
Period size: 24 Copynumber: 5.2 Consensus size: 24
53048 TATATCAAAA
53058 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
53082 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
53106 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
53130 ATCAGATCAGAATCCATGTC-AGAT
1 ATCAAAACAAAATCCAGGTCAAG-T
* * * *
53154 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
53178 ATCA
1 ATCA
53182 TATCAGAATT
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
23 6 0.07
24 83 0.91
25 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:53186 original size:24 final size:24
Alignment explanation
Indices: 53075--53190 Score: 171
Period size: 24 Copynumber: 4.8 Consensus size: 24
53065 CATAAATCAG
* * *
53075 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
53099 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
53123 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
53147 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
*
53171 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCAGATCAGAAT
53191 TCAAATCGAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:53206 original size:48 final size:47
Alignment explanation
Indices: 53075--53208 Score: 169
Period size: 48 Copynumber: 2.8 Consensus size: 47
53065 CATAAATCAG
* *
53075 GTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAAGTCAA-TATCAGATCAGAATCCAA
* * *
53123 GTCAAGTATCAGATCAGAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAAGTCA-ATATCAGATCAGAATCCAA
* * *
53171 GTCAAGTATCATATCAGAATTCAAATCGAAAATCAGAT
1 GTCAAGTATCATATCAGAATCCAAGTC-AATATCAGAT
53209 AAAATATTCA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
48 73 0.97
49 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (47 bp):
GTCAAGTATCATATCAGAATCCAAGTCAATATCAGATCAGAATCCAA
Found at i:54967 original size:36 final size:36
Alignment explanation
Indices: 54915--54987 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
54905 GATAAATTAT
54915 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
*
54951 AATCTACATATTCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
54987 A
1 A
54988 TTCCAGAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:65148 original size:120 final size:120
Alignment explanation
Indices: 64935--65176 Score: 484
Period size: 120 Copynumber: 2.0 Consensus size: 120
64925 ATCAAAATCA
64935 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
1 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
65000 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
66 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
65055 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
1 CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
65120 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
66 ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
65175 CA
1 CA
65177 ATAGGAAGGT
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 122 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (120 bp):
CAGTGCACAATTTTGCAGCATCTTTCACTCACCTAGCAAAGCTATCAGACATCACATTTACACTC
ATAAAACTTCAAATACTGTTTATAACGGTGATTAAAACTACATATACGAGGTGTC
Done.