Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003071.1 Hibiscus syriacus cultivar Beakdansim tig00006400_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: 53901
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:354 original size:196 final size:197
Alignment explanation
Indices: 1--734 Score: 766
Period size: 200 Copynumber: 3.7 Consensus size: 197
* * * * *
1 AAAGTATCGATACCAAAAACATCGAAACCC-TTATTATAATGTAATAGGTGATTTTTCAATGTAA
1 AAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGT-AATTTTCAATGTAA
* *
65 CCGGTATAAATATA-C-ATGTTTATGCGAGAATATGTCTAC-ATATGTATCGACA-TATTTGAAT
65 CCGGTATAAATATATCGAT-TTTATGCGAGAATAGGTCTACAAAATGTATCGACACT-TTTGAAT
* * *
126 TGGTGTTGATA-ATTTTTGTCCAGAATGAATGCCCAAAATGGTGAATGCATAAGTGTCGATACAT
128 TTGTGTTGATACA-TTTTGTCCAGAATGAATGCCCAAAATGGTGCACGCATAAGTGTCGATACAT
190 TTTTAA
192 TTTTAA
* *
196 AAA-TGTCGATCCCAGAGACATCG-AACCCATAATTATAATGT-ATAGGTAATTTTGTAATGTAA
1 AAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTT-CAATGTAA
* * * *
258 CCGGTATAAATATATCGGTTTTATGTGAG-ATAGGTCTACAAAAATGTATTGACACTTTTTAATT
65 CCGGTATAAATATATCGATTTTATGCGAGAATAGGTCTAC-AAAATGTATCGACACTTTTGAA-T
*
322 TTGTGTTGATACATTTTGTCCATAATGAATGCCCAAAAAATTGGTGCACGCATAAAGTGTCGATA
128 TTGTGTTGATACATTTTGTCCAGAATGAATGCCC--AAAA-TGGTGCACGCAT-AAGTGTCGATA
*
387 CATTTATAA
189 CATTTTTAA
* *
396 AAAGTATCGAT-CCAGAAACATCGAAACCCAT-ATTATAATGTAATAGGTAATTTTCAATGTAAT
1 AAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTCAATGTAAC
* * * * * * *
459 CGCTATAAATATATCGGTTTTATGCGAGAATAGATTTAGAAAATATATCGACACTTATGGAATTT
66 CGGTATAAATATATCGATTTTATGCGAGAATAGGTCTACAAAATGTATCGACACTT-TTGAATTT
* * * * * * *
524 GTGTCGATACTTTTTGTCTAGAAGGAATG-CCAAAAGGGTGCACCCATTAAGTGTCAATACA-TT
130 GTGTTGATACATTTTGTCCAGAATGAATGCCCAAAATGGTGCACGCA-TAAGTGTCGATACATTT
587 TTAA
194 TTAA
* * ** *
591 AAAGTGTC-ATCCCAAAAACATTGAAACTGATAATTATAATGTAATAGGTAAATTTCCAA-GTAA
1 AAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGT-AATTTTCAATGTAA
* * * * * * *
654 CC-GTATAAATATACCGATTTTATGAGAAAATAGGTCAACATAAA-GTATCGACAATTGCTAAAT
65 CCGGTATAAATATATCGATTTTATGCGAGAATAGGTCTACA-AAATGTATCGACACTT-TTGAAT
*
717 TTGTGTCGATACCATTTT
128 TTGTGTTGATA-CATTTT
735 AAAAATTGCG
Statistics
Matches: 452, Mismatches: 63, Indels: 47
0.80 0.11 0.08
Matches are distributed among these distances:
192 5 0.01
193 41 0.09
194 39 0.09
195 101 0.22
196 83 0.18
197 14 0.03
198 4 0.01
199 12 0.03
200 118 0.26
201 35 0.08
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (197 bp):
AAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTCAATGTAAC
CGGTATAAATATATCGATTTTATGCGAGAATAGGTCTACAAAATGTATCGACACTTTTGAATTTG
TGTTGATACATTTTGTCCAGAATGAATGCCCAAAATGGTGCACGCATAAGTGTCGATACATTTTT
AA
Found at i:800 original size:15 final size:16
Alignment explanation
Indices: 774--806 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
764 TTATAGATAT
*
774 AATCGTACAAACTCTA
1 AATCGTACAAACCCTA
790 AATCG-ACAAACCCTA
1 AATCGTACAAACCCTA
805 AA
1 AA
807 CTTAAAGGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.18
Consensus pattern (16 bp):
AATCGTACAAACCCTA
Found at i:1066 original size:16 final size:17
Alignment explanation
Indices: 1034--1066 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1024 TCTTTTCAGG
1034 TCTTCTCAACCACAATCT
1 TCTTCTCAA-CACAATCT
1052 TCTTCTCAA-ACAATC
1 TCTTCTCAACACAATC
1067 GCTTCTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (17 bp):
TCTTCTCAACACAATCT
Found at i:2195 original size:3 final size:3
Alignment explanation
Indices: 2160--2209 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
2150 CAAGAGGTCA
* * * * *
2160 ATG AAG ATG AAG ATG ACG ATG AAG ATA ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
2208 AT
1 AT
2210 TATTATATGT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.42, C:0.02, G:0.30, T:0.26
Consensus pattern (3 bp):
ATG
Found at i:3572 original size:24 final size:24
Alignment explanation
Indices: 3520--3572 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
3510 TTTCATATGT
* *
3520 AATTGGAGTTTGAATTTAAATTTA
1 AATTTGAGTTTGAATTTAAATATA
*
3544 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
3568 AATTT
1 AATTT
3573 CGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:4156 original size:198 final size:197
Alignment explanation
Indices: 3803--4557 Score: 867
Period size: 198 Copynumber: 3.8 Consensus size: 197
3793 AGTTTCCCAT
3803 AAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATC-AAAACCGAAAATTATAATGT
1 AAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAAA-CGAAAATTATAATGT
* * * *
3867 AATAGGTAAATTTACAATGTGACCGTATAAATATACTGATTTTATGAGCAAATAGGTCAGCATAA
65 AATAGGTAAATTTACAATGTAACGGTATAAATATACTGATTTTATGAGAAAATAGGTCAACATAA
* * ** * **
3932 AGTATCGACACCTTTTAAATTTGTGTCGATACCTTTGACCAAGCCTTTGCTTAACGAGCTTCACG
130 TGTATCGACACCTTTTAAATTTGTGTCGATACATTTGACCAAGAATATGCAAAACGAG-TTCACG
3997 CATA
194 CATA
** * *
4001 AAAGTGTCGATACATTTA-AAATTGTATCGATCTAAAAAACATCGAAAACAAAAATTATAATGTA
1 AAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAAACGAAAATTATAATGTA
* * *
4065 ATAGGTAAATATACAATGTAATCGGTATAAATATA-TCGGTTTTAAGAGAAAATAGGT-ATACAT
66 ATAGGTAAATTTACAATGTAA-CGGTATAAATATACT-GATTTTATGAGAAAATAGGTCA-ACAT
* * * * * * *
4128 AATGTATTGATA-TTGTTTAAATTTGTGTCGATACATTTTGTCC-ATAATGAATGCCAAACGGGG
128 AATGTATCGACACCT-TTTAAATTTGTGTCGATACA-TTTGACCAAGAAT--ATGCAAAAC-GAG
*
4191 TGCACGCAT-
188 TTCACGCATA
* * *
4200 AAAGTGTCAATACATTT-TAAAAAGTATCGATCTC-AAAAACATCGAAACCGATAATTATAATGT
1 AAAGTGTCGATACATTTATAAAAAGTATCGATC-CAAAAAACATCGAAAACGAAAATTATAATGT
* * *
4263 AATAGGTAAATTTAAAATGTAACCGG--TAAGTATACT-AGTTTTATGAGAAAATAGGTGAACAT
65 AATAGGTAAATTTACAATGTAA-CGGTATAAATATACTGA-TTTTATGAGAAAATAGGTCAACAT
* * *
4325 AATGTATCGACACTTTTTAGATTTGTGTCGATACATTTTATCC-AGAATGAATGCAAAAC-AGTG
128 AATGTATCGACACCTTTTAAATTTGTGTCGATACATTTGA-CCAAGAAT--ATGCAAAACGAGT-
4388 TGCACGCATA
189 T-CACGCATA
* *
4398 AAA-TGTCGTTACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAATGTA
1 AAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAAACGAAAATTATAATGTA
* * *
4462 ATAGGTAAATTTACAATGTAACTGGTATAAATATACCGATTTTATGAGAAAATAGGTTAACATAG
66 ATAGGTAAATTTACAATGTAAC-GGTATAAATATACTGATTTTATGAGAAAATAGGTCAACATAA
4527 TGTATCGACA-CTTTTAAATTTGTGTCGATAC
130 TGTATCGACACCTTTTAAATTTGTGTCGATAC
4558 GTTTTTAAAT
Statistics
Matches: 475, Mismatches: 57, Indels: 49
0.82 0.10 0.08
Matches are distributed among these distances:
195 2 0.00
196 3 0.01
197 152 0.32
198 157 0.33
199 102 0.21
200 56 0.12
201 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (197 bp):
AAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAAACGAAAATTATAATGTA
ATAGGTAAATTTACAATGTAACGGTATAAATATACTGATTTTATGAGAAAATAGGTCAACATAAT
GTATCGACACCTTTTAAATTTGTGTCGATACATTTGACCAAGAATATGCAAAACGAGTTCACGCA
TA
Found at i:4413 original size:197 final size:198
Alignment explanation
Indices: 3800--4562 Score: 931
Period size: 197 Copynumber: 3.8 Consensus size: 198
3790 TAAAGTTTCC
* *
3800 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCAAAACCGAAAATTATAAT
1 CATAAAATGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* * * *
3865 GTAATAGGTAAATTTACAATGTGACCGTATAAATATACTGATTTTATGAGCAAATAGGTCAGCAT
66 GTAATAGGTAAATTTACAATGTAACCGGATAAATATACTGATTTTATGAGAAAATAGGT-AACAT
* * * * ** * **
3930 AAAGTATCGACACCTTTTAAATTTGTGTCGATACCTTTGA-CCAAGCCT--TTGCTTAACGAGCT
130 AATGTATCGACACTTTTTAAATTTGTGTCGATACATTTTATCC-AGAATGAATGCAAAAC-AG-T
3992 -T-CACG
192 GTGCACG
** * * *
3997 CATAAAAGTGTCGATACATTTA-AAATTGTATCGATCTAAAAAACATCGAAAACAAAAATTATAA
1 CATAAAA-TGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAA
* * * *
4061 TGTAATAGGTAAATATACAATGTAATCGGTATAAATATA-TCGGTTTTAAGAGAAAATAGGTATA
65 TGTAATAGGTAAATTTACAATGTAACCGG-ATAAATATACT-GATTTTATGAGAAAATAGGTA-A
* * * * * *
4125 CATAATGTATTGATA-TTGTTTAAATTTGTGTCGATACATTTTGTCCATAATGAATGCCAAACGG
127 CATAATGTATCGACACTT-TTTAAATTTGTGTCGATACATTTTATCCAGAATGAATGCAAAACAG
*
4189 GGTGCACG
191 TGTGCACG
* * *
4197 CATAAAGTGTCAATACATTT-TAAAAAGTATCGATCTC-AAAAACATCGAAACCGATAATTATAA
1 CATAAAATGTCGATACATTTATAAAAAGTATCGATC-CAAAAAACATCGAAACCGAAAATTATAA
* *
4260 TGTAATAGGTAAATTTAAAATGTAACCGG-TAAGTATACT-AGTTTTATGAGAAAATAGGTGAAC
65 TGTAATAGGTAAATTTACAATGTAACCGGATAAATATACTGA-TTTTATGAGAAAATAGGT-AAC
*
4323 ATAATGTATCGACACTTTTTAGATTTGTGTCGATACATTTTATCCAGAATGAATGCAAAACAGTG
128 ATAATGTATCGACACTTTTTAAATTTGTGTCGATACATTTTATCCAGAATGAATGCAAAACAGTG
4388 TGCACG
193 TGCACG
*
4394 CATAAAATGTCGTTACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
1 CATAAAATGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* *
4459 GTAATAGGTAAATTTACAATGTAACTGGTATAAATATACCGATTTTATGAGAAAATAGGTTAACA
66 GTAATAGGTAAATTTACAATGTAACCGG-ATAAATATACTGATTTTATGAGAAAATAGG-TAACA
* *
4524 TAGTGTATCGACAC-TTTTAAATTTGTGTCGATACGTTTT
129 TAATGTATCGACACTTTTTAAATTTGTGTCGATACATTTT
4563 TAAATTACGC
Statistics
Matches: 481, Mismatches: 63, Indels: 42
0.82 0.11 0.07
Matches are distributed among these distances:
197 174 0.36
198 147 0.31
199 100 0.21
200 58 0.12
201 2 0.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (198 bp):
CATAAAATGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGATAAATATACTGATTTTATGAGAAAATAGGTAACATA
ATGTATCGACACTTTTTAAATTTGTGTCGATACATTTTATCCAGAATGAATGCAAAACAGTGTGC
ACG
Found at i:8672 original size:198 final size:200
Alignment explanation
Indices: 8197--8719 Score: 668
Period size: 199 Copynumber: 2.6 Consensus size: 200
8187 TGTCCAAAAT
* * *
8197 ATAAAGTGTCGATACATTTATTAAAAGTATCGATCCTAATAACATAGAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTA-TAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATG
* * * * *
8262 TAATAGGTAAATTTACAATGTAACTGGTATAAATATACC-AGTTTTATAAGAAAATATGTCAGCA
65 TAATAGGTAAATTTACAATGTATCCGGTATAAATATACCGAGTTTTATAAGAAAAAAGGTCAGAA
* * *
8326 TAAAGTATTAACACTATTTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGCCAAACGAGGT
130 TAAAGTATCAACACTATTTAAATTTGCGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGT
8391 GCATGC
195 GCATGC
* * *
8397 ATAAA-TGTCGATACATTTATTAAAAGTATCGATCCCACAAACATCGAAACCGATAATTACAATG
1 ATAAAGTGTCGATACATTTA-TAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATG
* * * *
8461 TGATAGGTAAATTTACAATGTATCCGATAGAAATATACCGA-TTTTATGAGAAAAAAGGTCTA-A
65 TAATAGGTAAATTTACAATGTATCCGGTATAAATATACCGAGTTTTATAAGAAAAAAGGTC-AGA
* * * * *
8524 ATAATGTATCGACACTTTTTAAGTTTGCGTCGATACTTTTT-TCCAGAATGAATGCCCAACGAGG
129 ATAAAGTATCAACACTATTTAAATTTGCGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGG
8588 TGCATGC
194 TGCATGC
* *
8595 ATAAAGTGTCAATACATTTA-AAATTGTATCGATCCAAAAAACATCGAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTATAAA-AGTATCGATCCAAAAAACATCGAAACCGATAATTATAATG
* * * *
8659 TAATAGATAAATTTGCAATGT-TACCGGTATAAATATACCG-G-TTTACTTAGAAAATAGGTCA
65 TAATAGGTAAATTTACAATGTAT-CCGGTATAAATATACCGAGTTTTA-TAAGAAAAAAGGTCA
8720 ATATAAGCGC
Statistics
Matches: 282, Mismatches: 34, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
197 9 0.03
198 114 0.40
199 152 0.54
200 7 0.02
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (200 bp):
ATAAAGTGTCGATACATTTATAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGT
AATAGGTAAATTTACAATGTATCCGGTATAAATATACCGAGTTTTATAAGAAAAAAGGTCAGAAT
AAAGTATCAACACTATTTAAATTTGCGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGTG
CATGC
Found at i:8815 original size:87 final size:87
Alignment explanation
Indices: 8720--8882 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
8710 AAATAGGTCA
*
8720 ATATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATATTATTGTACTTGATAATATTT
8785 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
*
8807 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATATTATTGTACTTGATAATATTT
*
8872 TCGGTTAAATG
66 CCGGTTAAATG
8883 ATATAACATA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCACTACCTAATATATTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:8822 original size:23 final size:23
Alignment explanation
Indices: 8796--8854 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
8786 CGGTTAAATG
*
8796 CCTATTTTATTATATAAGCGCTA
1 CCTATTATATTATATAAGCGCTA
*
8819 CCTATTACATTATATAAGCGCTA
1 CCTATTATATTATATAAGCGCTA
*
8842 CCTAATATATTAT
1 CCTATTATATTAT
8855 TGTACTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.41
Consensus pattern (23 bp):
CCTATTATATTATATAAGCGCTA
Found at i:8985 original size:13 final size:13
Alignment explanation
Indices: 8967--8995 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
8957 GCGCCGCACC
8967 GCAGAAGTTGCCT
1 GCAGAAGTTGCCT
8980 GCAGAAGTTGCCT
1 GCAGAAGTTGCCT
8993 GCA
1 GCA
8996 AGTTAACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (13 bp):
GCAGAAGTTGCCT
Found at i:18832 original size:15 final size:15
Alignment explanation
Indices: 18812--18867 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
18802 TAACCGGTTT
18812 CGGTTTTAAAAAATC
1 CGGTTTTAAAAAATC
*
18827 CGGTTTTTTTAAAAATC
1 CGG--TTTTAAAAAATC
* *
18844 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAATC
*
18859 CGATTTTAA
1 CGGTTTTAA
18868 TATTATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 19 0.58
17 14 0.42
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (15 bp):
CGGTTTTAAAAAATC
Found at i:18840 original size:17 final size:17
Alignment explanation
Indices: 18815--18848 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18805 CCGGTTTCGG
18815 TTTTAAAAAATCCGGTT
1 TTTTAAAAAATCCGGTT
*
18832 TTTTTAAAAATCCGGTT
1 TTTTAAAAAATCCGGTT
18849 ATAAAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (17 bp):
TTTTAAAAAATCCGGTT
Found at i:18945 original size:32 final size:33
Alignment explanation
Indices: 18909--19017 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 33
18899 ACAAAGTTTA
*
18909 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
18941 CGATAAATTAAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
18974 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
19006 CGAT-AATTGAAA
1 CGATAAATTGAAA
19018 CAAAGTTTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 7 0.10
32 14 0.19
33 51 0.71
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (33 bp):
CGATAAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:19030 original size:21 final size:21
Alignment explanation
Indices: 19006--19047 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
18996 ACTTCAAGTT
*
19006 CGATAATTGAAACAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
*
19027 CGATAATTAAAATAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
19048 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTAAAACAAAGTTTA
Found at i:21465 original size:19 final size:20
Alignment explanation
Indices: 21427--21465 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
21417 GTTAAAATAA
**
21427 CCGGTTTAAAAAAATCCGAT
1 CCGGTTTAAAAAAAAACGAT
21447 CCGG-TTAAAAAAAAACGAT
1 CCGGTTTAAAAAAAAACGAT
21466 TTTTCCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (20 bp):
CCGGTTTAAAAAAAAACGAT
Found at i:23597 original size:20 final size:20
Alignment explanation
Indices: 23558--23615 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
23548 TGCGTGTTTG
* **
23558 TCAAATTATGAAAAAGATTA
1 TCAAATTATGCAAATTATTA
23578 TCAAATTATGCAAATTATTA
1 TCAAATTATGCAAATTATTA
*
23598 -CAACATTTTGCATAATTA
1 TCAA-ATTATGCA-AATTA
23616 CTACATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.09
20 24 0.75
21 5 0.16
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (20 bp):
TCAAATTATGCAAATTATTA
Found at i:34172 original size:32 final size:31
Alignment explanation
Indices: 34136--34211 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
34126 CGGGGCCGTG
*
34136 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
34168 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
34199 GAGCCTACCTAAG
1 GGGCCTACCTAAG
34212 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:34195 original size:63 final size:63
Alignment explanation
Indices: 34089--34211 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
34079 ACCTAAGGGA
* * ** *
34089 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
34152 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
34212 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:37047 original size:15 final size:16
Alignment explanation
Indices: 37014--37051 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
37004 TTTTGGTCAA
37014 CAACGGTCAACGTGGGT
1 CAACGGTCAACG-GGGT
37031 CAACGGTCAAC-GGGT
1 CAACGGTCAACGGGGT
37046 CAACGG
1 CAACGG
37052 GTCGGGTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
17 11 0.52
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.13
Consensus pattern (16 bp):
CAACGGTCAACGGGGT
Found at i:37048 original size:8 final size:8
Alignment explanation
Indices: 37014--37054 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
37004 TTTTGGTCAA
37014 CAAC-GGT
1 CAACGGGT
37021 CAACGTGGGT
1 CAAC--GGGT
37031 CAAC-GGT
1 CAACGGGT
37038 CAACGGGT
1 CAACGGGT
37046 CAACGGGT
1 CAACGGGT
37054 C
1 C
37055 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 11 0.37
8 12 0.40
10 7 0.23
ACGTcount: A:0.24, C:0.27, G:0.34, T:0.15
Consensus pattern (8 bp):
CAACGGGT
Found at i:37059 original size:13 final size:13
Alignment explanation
Indices: 37054--37102 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
37044 GTCAACGGGT
*
37054 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
37067 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
37080 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
*
37093 TGGGTCGGGT
1 CGGGTCGGGT
37103 CGGGTCGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.16, C:0.16, G:0.47, T:0.20
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:37064 original size:18 final size:18
Alignment explanation
Indices: 37041--37076 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
37031 CAACGGTCAA
37041 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
37059 CGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGT
37077 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.19
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:39241 original size:32 final size:31
Alignment explanation
Indices: 39205--39280 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
39195 CGGGGCCGTG
*
39205 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
39237 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
39268 GAGCCTACCTAAG
1 GGGCCTACCTAAG
39281 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:39264 original size:63 final size:63
Alignment explanation
Indices: 39158--39280 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
39148 ACCTAAGGGA
* * ** *
39158 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
39221 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
39281 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:42124 original size:8 final size:8
Alignment explanation
Indices: 42096--42130 Score: 56
Period size: 7 Copynumber: 4.6 Consensus size: 8
42086 TGGTCAACGT
42096 GGGTCAAC
1 GGGTCAAC
42104 -GGTCAAC
1 GGGTCAAC
42111 -GGTCAAC
1 GGGTCAAC
42118 GGGTCAAC
1 GGGTCAAC
42126 GGGTC
1 GGGTC
42131 GGGTCGGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 14 0.54
8 12 0.46
ACGTcount: A:0.23, C:0.26, G:0.37, T:0.14
Consensus pattern (8 bp):
GGGTCAAC
Found at i:42124 original size:15 final size:14
Alignment explanation
Indices: 42097--42127 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
42087 GGTCAACGTG
42097 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
42111 GGTCAACGGGTCAAC
1 GGTCAAC-GGTCAAC
42126 GG
1 GG
42128 GTCGGGTCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (14 bp):
GGTCAACGGTCAAC
Found at i:42135 original size:13 final size:13
Alignment explanation
Indices: 42130--42166 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
42120 GTCAACGGGT
42130 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
42143 CTGGTCGGGTAAA
1 CGGGTCGGGTCAA
42156 CGGGTCGGGTC
1 CGGGTCGGGTC
42167 GGGTCGGGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.22, G:0.46, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:42140 original size:18 final size:18
Alignment explanation
Indices: 42117--42171 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
42107 CAACGGTCAA
42117 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
42135 CGGGTCAAC---T--GGT
1 CGGGTCAACGGGTCGGGT
*
42148 CGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
42166 CGGGTC
1 CGGGTC
42172 GGGTTATGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 11 0.37
15 1 0.03
16 1 0.03
18 17 0.57
ACGTcount: A:0.13, C:0.22, G:0.47, T:0.18
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:44395 original size:2 final size:2
Alignment explanation
Indices: 44388--44413 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44378 CTTCCATGAT
44388 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
44414 GTGGTGCGTT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.