Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000747.1 Hibiscus syriacus cultivar Beakdansim tig00001440_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: 67828
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:435 original size:18 final size:19
Alignment explanation
Indices: 412--456 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
402 TGATATAAAC
412 ATTTAAAATTTAAACAAT-
1 ATTTAAAATTTAAACAATA
* *
430 ATTT-AAATTTAAAGATTA
1 ATTTAAAATTTAAACAATA
448 ATTTAAAAT
1 ATTTAAAAT
457 ATATACCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 11 0.48
18 8 0.35
19 4 0.17
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTTAAAATTTAAACAATA
Found at i:6164 original size:19 final size:20
Alignment explanation
Indices: 6135--6176 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
6125 AAATCTATAT
6135 TTTTTTGAATAAAAATAATA
1 TTTTTTGAATAAAAATAATA
* *
6155 TTTTTT-AATAAATATATTA
1 TTTTTTGAATAAAAATAATA
6174 TTT
1 TTT
6177 CAGATCGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTTTGAATAAAAATAATA
Found at i:10408 original size:34 final size:34
Alignment explanation
Indices: 10370--10441 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
10360 GGACTCGACT
10370 CGAAAACTTTAAAATTGATTTCGTCGAAAACTCG
1 CGAAAACTTTAAAATTGATTTCGTCGAAAACTCG
10404 CGAAAACTTTAAAATTGATTTCGTCGAAAACTCG
1 CGAAAACTTTAAAATTGATTTCGTCGAAAACTCG
10438 CGAA
1 CGAA
10442 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (34 bp):
CGAAAACTTTAAAATTGATTTCGTCGAAAACTCG
Found at i:12606 original size:16 final size:16
Alignment explanation
Indices: 12585--12619 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
12575 GGTATTACCC
12585 GACCTGTTATCAACCT
1 GACCTGTTATCAACCT
*
12601 GACCTGTTATGAACCT
1 GACCTGTTATCAACCT
12617 GAC
1 GAC
12620 ATGTAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:13212 original size:22 final size:22
Alignment explanation
Indices: 13187--13230 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
13177 TGTAAGGTGT
13187 GTGTTTTATTAACATGTTAAGA
1 GTGTTTTATTAACATGTTAAGA
13209 GTGTTTTATTAACATGTTAAGA
1 GTGTTTTATTAACATGTTAAGA
13231 AAATTCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (22 bp):
GTGTTTTATTAACATGTTAAGA
Found at i:15101 original size:20 final size:20
Alignment explanation
Indices: 15084--15128 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
15074 GGGGTATCGA
15084 TACCAATAAGGAGGTATCAG
1 TACCAATAAGGAGGTATCAG
15104 TACCAATAAGGAGGTATCAG
1 TACCAATAAGGAGGTATCAG
15124 TACCA
1 TACCA
15129 TTCTTGCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (20 bp):
TACCAATAAGGAGGTATCAG
Found at i:16906 original size:23 final size:23
Alignment explanation
Indices: 16880--16948 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
16870 CACCACAGCT
* *
16880 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
16903 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* *
16926 TGTAGAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
16949 TATAAGGTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:18780 original size:21 final size:21
Alignment explanation
Indices: 18754--18798 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18744 GATTTCTGGG
* *
18754 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
18775 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
18796 CAA
1 CAA
18799 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:20209 original size:32 final size:31
Alignment explanation
Indices: 20167--20294 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
20157 AGAGTCGAGG
20167 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
20198 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
20230 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
20261 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
20292 GTT
1 GTT
20295 ACCGAGGATC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
31 54 0.66
32 28 0.34
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:20314 original size:30 final size:30
Alignment explanation
Indices: 20253--20349 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
20243 CTAAGGAACA
* * ***
20253 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
20284 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
20314 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
20344 TCTGGA
1 TATGGA
20350 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:20350 original size:30 final size:30
Alignment explanation
Indices: 20280--20352 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
20270 GGTTCTTCGG
* *
20280 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
20310 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
20340 GACCTCTGGATAG
1 GACCTCTGGATAG
20353 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:21557 original size:24 final size:20
Alignment explanation
Indices: 21504--21561 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
21494 TTCCCCTTGA
*
21504 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
21524 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
21547 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
21562 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:23184 original size:2 final size:2
Alignment explanation
Indices: 23177--23384 Score: 71
Period size: 2 Copynumber: 109.0 Consensus size: 2
23167 TACATACATG
*
23177 TA TA TA TA TA TA TA TA AA GTA TA TA GTA TA -A GTA TA TA -A T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA
23217 TA TA TA -A T- TA TA TA CT- TA TA TA TA -A T- 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
* *
23255 TA TA TA -A TA -A TA -A TA -A GTA TA TA CT- TA TT TA TA -A TG TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
* * * * * *
23293 TG CA T- TA GTA TA -A TA TA CA T- TA TA TA TA CA TG CA TCA TA T-
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* *
23333 TA TCA TA -A CA T- TCG TCA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA T-A TA TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA TA TA
23374 TA TA TA T- TA TA
1 TA TA TA TA TA TA
23385 ATTGTTTCAA
Statistics
Matches: 155, Mismatches: 20, Indels: 62
0.65 0.08 0.26
Matches are distributed among these distances:
1 21 0.14
2 118 0.76
3 16 0.10
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:24062 original size:15 final size:15
Alignment explanation
Indices: 24042--24074 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
24032 ATCATTTGAA
24042 CATAATTCAATATCC
1 CATAATTCAATATCC
24057 CATAATTCAATATCC
1 CATAATTCAATATCC
24072 CAT
1 CAT
24075 GATGTACTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.33
Consensus pattern (15 bp):
CATAATTCAATATCC
Found at i:32540 original size:408 final size:407
Alignment explanation
Indices: 31555--32749 Score: 2166
Period size: 408 Copynumber: 2.9 Consensus size: 407
31545 TTGTTTTTCC
31555 TATTCGATACACGAATCATCTAATTCCTTCCGTTTTCGCGTCGGGCATAGTGATATACATATTTT
1 TATTCGATACACGAATCATCTAATTCCTTCCGTTTTCGCGTCGGGCATAGTGATATACATATTTT
*
31620 TCTGTCGTGGAGCGGTCGACTCTGGATTGAACAGAATTACGGATATTGTAATTTTTTATAACCAT
66 TCTGTCGTGGAGCGGTCGACTATGGATTGAACAGAATTACGGATATTGTAATTTTTTATAACCAT
31685 GATCGCTTCTTCTTTGCTTGAAAACTCCATGCCTAAAGATAACTCACCATTATTTATTGATGAGT
131 GATCGCTTCTTCTTTGCTTGAAAACTCCATGCCTAAAGATAACTCACCATTATTTATTGATGAGT
* *
31750 AATATCTATAGTCACCGAGATGAGGTATATCCGTAAATTTTGGCCCGTACATTGTACCATAATCA
196 AATATCTATAGTCACCGAGATGAGGCATATCCGTAAATTCTGGCCCGTACATTGTACCATAATCA
31815 GCTTCATACATGTGTGCTGGAGGGTCAGTTTGTGCCACATTTGAGGGAACTTCATCT--A-CATC
261 GCTTCATACATGTGTGCTGGAGGGTCAGTTTGTGCCACATTTGAGGGAACTTCATCTACATCATC
*
31877 ATCATC--GGAGTTGAATTGCGGTGATTCTGGGTGAATGAATAGTCCAGTCTCAGCACATGACTC
326 ATCATCATGGAGTTGAATTGCGGTGATTCTGGGTGAATGAATAGTCCAGTCTCAGCACCTGACTC
31940 ACGAACCATCTAATTCA
391 ACGAACCATCTAATTCA
*
31957 TATTCGATACACGAATCATCTAATTTCTTCCGTTTTCGCGTCGGGCATAGTGATATACATATTTT
1 TATTCGATACACGAATCATCTAATTCCTTCCGTTTTCGCGTCGGGCATAGTGATATACATATTTT
* *
32022 TCTGTCGTGGAGCGATCGACTATGGATTAAACAGAATTACGGATATTGTAATTTTTTATAACCAT
66 TCTGTCGTGGAGCGGTCGACTATGGATTGAACAGAATTACGGATATTGTAATTTTTTATAACCAT
32087 GATCGCTTCTTCTTTGCTTGAAAACTCCATGCCTAAAGATAACTCACCATTATTTATTGATGAGT
131 GATCGCTTCTTCTTTGCTTGAAAACTCCATGCCTAAAGATAACTCACCATTATTTATTGATGAGT
32152 AATATCTATAGTCACCGAGATGAGGCATATCCGTAAATTCTGGCCCGTACATTGTACCATAATCA
196 AATATCTATAGTCACCGAGATGAGGCATATCCGTAAATTCTGGCCCGTACATTGTACCATAATCA
32217 GCTTCATACATGTGTGCTGGAGGGTCAGTTTGTGCCACATTTGAGGGAACTTCATCTACATCATC
261 GCTTCATACATGTGTGCTGGAGGGTCAGTTTGTGCCACATTTGAGGGAACTTCATCTACATCATC
* * *
32282 ATCATCATTGGAGTTGAATTGCAGTGATTCTGGGTGAATGAATAGTCTAGTCTCAGCACCTGGCT
326 ATCATCA-TGGAGTTGAATTGCGGTGATTCTGGGTGAATGAATAGTCCAGTCTCAGCACCTGACT
*
32347 CACGAACCATCTAATTCT
390 CACGAACCATCTAATTCA
*
32365 TATTCGATACACGAATCATCTAATTCCTTCCGTTTTCGCATCGGGCATAGTGATATACATATTTT
1 TATTCGATACACGAATCATCTAATTCCTTCCGTTTTCGCGTCGGGCATAGTGATATACATATTTT
* ** *
32430 TCTGTCGTGGAGCGGTCGACTTTGGATTGAACAGAATTACAAATATTGTGATTTTTTATAACCAT
66 TCTGTCGTGGAGCGGTCGACTATGGATTGAACAGAATTACGGATATTGTAATTTTTTATAACCAT
32495 GATCGCTTCTTCTTTGCTTGAAAACTCCATGCCTAAAGATAACTCACCATTATTTATTGATGAGT
131 GATCGCTTCTTCTTTGCTTGAAAACTCCATGCCTAAAGATAACTCACCATTATTTATTGATGAGT
*
32560 AATATCTATAGTCACCGAGATGAGACATATCCGTAAATTCTGGCCCGTACATTGTACCATAATCA
196 AATATCTATAGTCACCGAGATGAGGCATATCCGTAAATTCTGGCCCGTACATTGTACCATAATCA
32625 GCTTCATACATGTGTGCTGGAGGGTCAGTTTGTGCCACATTTGAGGGAACTTCATCTACATCATC
261 GCTTCATACATGTGTGCTGGAGGGTCAGTTTGTGCCACATTTGAGGGAACTTCATCTACATCATC
* *
32690 ATCATCATCGGAGTTAAATTACGGTGATTCTGGGTGAATGAATAGTCCAGTCTCAGCACC
326 ATCATCAT-GGAGTTGAATTGCGGTGATTCTGGGTGAATGAATAGTCCAGTCTCAGCACC
32750 ATCTGCACCT
Statistics
Matches: 762, Mismatches: 24, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
402 311 0.41
404 1 0.00
405 10 0.01
407 1 0.00
408 439 0.58
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (407 bp):
TATTCGATACACGAATCATCTAATTCCTTCCGTTTTCGCGTCGGGCATAGTGATATACATATTTT
TCTGTCGTGGAGCGGTCGACTATGGATTGAACAGAATTACGGATATTGTAATTTTTTATAACCAT
GATCGCTTCTTCTTTGCTTGAAAACTCCATGCCTAAAGATAACTCACCATTATTTATTGATGAGT
AATATCTATAGTCACCGAGATGAGGCATATCCGTAAATTCTGGCCCGTACATTGTACCATAATCA
GCTTCATACATGTGTGCTGGAGGGTCAGTTTGTGCCACATTTGAGGGAACTTCATCTACATCATC
ATCATCATGGAGTTGAATTGCGGTGATTCTGGGTGAATGAATAGTCCAGTCTCAGCACCTGACTC
ACGAACCATCTAATTCA
Found at i:34965 original size:30 final size:30
Alignment explanation
Indices: 34909--34967 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
34899 CAGTTGCAAC
*
34909 AATAAAGTCACTTAATATATTAATTATTAA
1 AATAAAGTCACTTAATATATCAATTATTAA
* *
34939 AATAAAGTCA-TTCAATTTATCGATTATTA
1 AATAAAGTCACTT-AATATATCAATTATTA
34968 TCATCAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (30 bp):
AATAAAGTCACTTAATATATCAATTATTAA
Found at i:38113 original size:2 final size:2
Alignment explanation
Indices: 38106--38133 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38096 ATTCAACTAC
38106 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
38134 GTGTGTGCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39076 original size:21 final size:21
Alignment explanation
Indices: 39046--39161 Score: 80
Period size: 21 Copynumber: 5.6 Consensus size: 21
39036 GATTTACATA
*
39046 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* * *
39067 TTCGCGTTGCGGTTTATTTC-AAA
1 TTCGCGTTGC-G-ATA-GTCGAAG
*
39090 TT--TGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* ** * *
39109 TTCGCGTTGTGATTTTCCAAA
1 TTCGCGTTGCGATAGTCGAAG
39130 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
39149 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
39162 TTATTCCAAA
Statistics
Matches: 68, Mismatches: 19, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
18 2 0.03
19 20 0.29
20 1 0.01
21 36 0.53
22 1 0.01
23 6 0.09
24 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:39099 original size:42 final size:42
Alignment explanation
Indices: 39052--39177 Score: 193
Period size: 42 Copynumber: 3.0 Consensus size: 42
39042 CATATTCGCA
* *
39052 TTGCGATAGTCGAAGTTCGCGTTGCGGTTTATTTCAAATTTG
1 TTGCGATAGTCGAAGTTCGCGTTGCGGTTTATTCCAAATTCG
* *
39094 TTGCGATAGTCGAAGTTCGCGTTG-TGATT-TTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGGTTTATTCCAAATTCG
*
39134 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGGTTTATTCCAAATTCG
39176 TT
1 TT
39178 AACGACAGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 33 0.44
41 5 0.07
42 37 0.49
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.39
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGGTTTATTCCAAATTCG
Found at i:39152 original size:19 final size:19
Alignment explanation
Indices: 39093--39152 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
39083 TTTCAAATTT
39093 GTTGCGATAGTCGAAGTTCGC
1 GTTGCGATAGTCGAAGTT--C
* ** * *
39114 GTTGTGATTTTCCAAATTC
1 GTTGCGATAGTCGAAGTTC
39133 GTTGCGATAGTCGAAGTTC
1 GTTGCGATAGTCGAAGTTC
39152 G
1 G
39153 CGTTGCGATT
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (19 bp):
GTTGCGATAGTCGAAGTTC
Found at i:39177 original size:21 final size:19
Alignment explanation
Indices: 39081--39177 Score: 50
Period size: 21 Copynumber: 4.8 Consensus size: 19
39071 CGTTGCGGTT
* *
39081 TATTTCAAATTTGTTGCGA
1 TATTCCAAATTCGTTGCGA
* * * *
39100 TAGTCGAAGTTCGCGTTGTGA
1 TATTCCAAATT--CGTTGCGA
*
39121 TTTTCCAAATTCGTTGCGA
1 TATTCCAAATTCGTTGCGA
* * *
39140 TAGTCGAAGTTCGCGTTGCGA
1 TATTCCAAATT--CGTTGCGA
39161 TTTATTCCAAATTCGTT
1 --TATTCCAAATTCGTT
39178 AACGACAGGT
Statistics
Matches: 54, Mismatches: 18, Indels: 10
0.66 0.22 0.12
Matches are distributed among these distances:
19 21 0.39
21 25 0.46
23 8 0.15
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (19 bp):
TATTCCAAATTCGTTGCGA
Found at i:39271 original size:6 final size:6
Alignment explanation
Indices: 39260--39297 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
39250 AGACACGTAT
39260 GACCAC GACCAC GACCAC GACCAC GACC-C GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
39298 CGAGACGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:40029 original size:63 final size:63
Alignment explanation
Indices: 39930--40064 Score: 225
Period size: 63 Copynumber: 2.1 Consensus size: 63
39920 TTTGGAATAA
* * *
39930 ATCGCAATGCGAACTTCGACTATCGCAATGAACTTGGAATAAATCGTAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
* *
39993 ATCGCAACGCGAACTTTGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
40056 ATCGCAACG
1 ATCGCAACG
40065 AATTTGGAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (63 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:40039 original size:42 final size:42
Alignment explanation
Indices: 39993--40144 Score: 254
Period size: 42 Copynumber: 3.7 Consensus size: 42
39983 AACTTCGACT
* *
39993 ATCGCAACGCGAACTTTGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
40035 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
*
40077 ATCGCAACGCGAACTTTGACTATCGCAACGAATTTGG-A-AA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
*
40117 ATCGCAACGCGAACTTGGACTTTCGCAA
1 ATCGCAACGCGAACTTGGACTATCGCAA
40145 TGCAAATATG
Statistics
Matches: 105, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 28 0.27
41 1 0.01
42 76 0.72
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
Found at i:40041 original size:105 final size:105
Alignment explanation
Indices: 39905--40106 Score: 341
Period size: 105 Copynumber: 1.9 Consensus size: 105
39895 TGCGATTTTG
* * *
39905 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCGCAATGAACTTGGAAT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
*
39970 AAATCGTAACGCGAACTTCGACTATCGCAACGCGAACTTT
66 AAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTT
* *
40010 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
*
40075 AAATCGCAACGCGAACTTTGACTATCGCAACG
66 AAATCGCAACGCGAACTTCGACTATCGCAACG
40107 AATTTGGAAA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
105 90 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (105 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAAT
AAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTT
Found at i:40130 original size:105 final size:104
Alignment explanation
Indices: 39909--40135 Score: 323
Period size: 105 Copynumber: 2.2 Consensus size: 104
39899 ATTTTGGACT
* * *
39909 ATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCGCAATGAACTTGGAATAAAT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAAT
* **
39974 CGTAACGCGAACTTCGACTATCGCAACGCGAACTTTGACT
66 CGCAACGCGAACTTCGACTATCGCAAC-CGAACTTTGAAA
* *
40014 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAAT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAAT
*
40079 CGCAACGCGAACTTTGACTATCGCAA-CGAA-TTTGGAAA
66 CGCAACGCGAACTTCGACTATCGCAACCGAACTTT-GAAA
40117 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
40136 CTTTCGCAAT
Statistics
Matches: 110, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
102 3 0.03
103 13 0.12
105 94 0.85
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (104 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAAT
CGCAACGCGAACTTCGACTATCGCAACCGAACTTTGAAA
Found at i:40142 original size:21 final size:21
Alignment explanation
Indices: 39902--40144 Score: 191
Period size: 21 Copynumber: 11.7 Consensus size: 21
39892 CGTTGCGATT
*
39902 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
39921 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
39944 TTCGACTATCGCAA--TGAAC
1 TTGGACTATCGCAACGCGAAC
* *
39963 TTGGAATAAATCGTAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
39986 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
40007 TTTGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
40026 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
40049 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
40068 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
40091 TTTGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
40110 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
40131 TTGGACTTTCGCAA
1 TTGGACTATCGCAA
40145 TGCAAATATG
Statistics
Matches: 177, Mismatches: 29, Indels: 34
0.74 0.12 0.14
Matches are distributed among these distances:
19 50 0.28
21 89 0.50
23 38 0.21
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:41593 original size:22 final size:22
Alignment explanation
Indices: 41568--41609 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41558 ATGAGTTATT
* *
41568 TGATTTAATTCCAGGGGTTACA
1 TGATATAATTCCAGGAGTTACA
*
41590 TGATATAATTTCAGGAGTTA
1 TGATATAATTCCAGGAGTTA
41610 TAACAGCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (22 bp):
TGATATAATTCCAGGAGTTACA
Found at i:47034 original size:22 final size:22
Alignment explanation
Indices: 47009--47063 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
46999 CCAGGAGTTA
* *
47009 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
47031 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
47053 CAGGAGTTATA
1 CAGGAGTTATA
47064 ACAGCTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:50303 original size:22 final size:22
Alignment explanation
Indices: 50278--50327 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
50268 AGTGTTCGTA
50278 CGTTAACACTGTTAAAAATCTC
1 CGTTAACACTGTTAAAAATCTC
*
50300 CGTTAACACTGTTAAAAATCTT
1 CGTTAACACTGTTAAAAATCTC
50322 CGTTAA
1 CGTTAA
50328 ATGACACGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (22 bp):
CGTTAACACTGTTAAAAATCTC
Found at i:56740 original size:42 final size:42
Alignment explanation
Indices: 56693--56807 Score: 176
Period size: 42 Copynumber: 2.7 Consensus size: 42
56683 CCGAATTCTT
*
56693 GTGTTTATTTCACGTAATTCATTTTTCGGAAAATATTTTCCC
1 GTGTTTGTTTCACGTAATTCATTTTTCGGAAAATATTTTCCC
* * *
56735 GTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTTTTCTC
1 GTGTTTGTTTCACGTAATTCATTTTTCGGAAAATATTTTCCC
* *
56777 GTGTTTGTTTTACGTAATTGATTTTTCGGAA
1 GTGTTTGTTTCACGTAATTCATTTTTCGGAA
56808 TGTAATTCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCATTTTTCGGAAAATATTTTCCC
Found at i:57051 original size:30 final size:30
Alignment explanation
Indices: 56978--57061 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 30
56968 CATTTTCATC
*
56978 AAAATAATTTTATTTATTAATATTTATAAT
1 AAAATAATTATATTTATTAATATTTATAAT
*
57008 AATATAATATATATTT-TTAATATTATATAA-
1 AAAATAAT-TATATTTATTAATATT-TATAAT
*
57038 AAAATCAATTATATTATAATAATA
1 AAAAT-AATTATATT-TATTAATA
57062 AGATATTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 25 0.56
31 15 0.33
32 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
AAAATAATTATATTTATTAATATTTATAAT
Found at i:57125 original size:17 final size:17
Alignment explanation
Indices: 57103--57137 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
57093 AATTTTTTTA
*
57103 TATATAATGAATAATAT
1 TATATAATAAATAATAT
*
57120 TATATATTAAATAATAT
1 TATATAATAAATAATAT
57137 T
1 T
57138 TAATAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TATATAATAAATAATAT
Found at i:57282 original size:28 final size:31
Alignment explanation
Indices: 57217--57284 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
57207 TAATATATTT
*
57217 ATAATA-TTTTATTTCACTAAAATATAAAAA
1 ATAATATTTTTATTTCAATAAAATATAAAAA
*
57247 ATTAATATTTTTA-TT-AATAAATTAT-AAAA
1 A-TAATATTTTTATTTCAATAAAATATAAAAA
57276 ATAATATTT
1 ATAATATTT
57285 AATAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.24
29 5 0.15
30 9 0.26
31 7 0.21
32 5 0.15
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
ATAATATTTTTATTTCAATAAAATATAAAAA
Found at i:57557 original size:15 final size:15
Alignment explanation
Indices: 57515--57558 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
57505 TTCCAGAAAT
*
57515 GTAATTCATTTTTCA
1 GTAATTCATTTTCCA
**
57530 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
57544 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
57559 ATTCTAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:57561 original size:21 final size:21
Alignment explanation
Indices: 57537--57578 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
57527 TCAGAATTCA
*
57537 AATTCCAGTAATTCATTTTCC
1 AATTCCAATAATTCATTTTCC
*
57558 AATTCTAATAATTCATTTTCC
1 AATTCCAATAATTCATTTTCC
57579 GGAAAACCAA
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:0.31, C:0.21, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTCCAATAATTCATTTTCC
Found at i:59025 original size:25 final size:21
Alignment explanation
Indices: 59008--59048 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
58998 TTAAAATGGA
59008 ATTTTATTATTTTCATTAAAT
1 ATTTTATTATTTTCATTAAAT
59029 ATTTTATTATTTT--TTAAAT
1 ATTTTATTATTTTCATTAAAT
59048 A
1 A
59049 ATAAAATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTATTATTTTCATTAAAT
Done.