Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002864.1 Hibiscus syriacus cultivar Beakdansim tig00005907_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: 59338
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:2701 original size:22 final size:20
Alignment explanation
Indices: 2669--2715 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
2659 GTTGAATATA
2669 TTGTTCCATACTATTATGGT
1 TTGTTCCATACTATTATGGT
*
2689 TTGTGTCCTATACTATTGTGGT
1 TTGT-TCC-ATACTATTATGGT
2711 TTGTT
1 TTGTT
2716 GAATATATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 16 0.67
ACGTcount: A:0.15, C:0.13, G:0.19, T:0.53
Consensus pattern (20 bp):
TTGTTCCATACTATTATGGT
Found at i:2790 original size:32 final size:32
Alignment explanation
Indices: 2702--2844 Score: 137
Period size: 32 Copynumber: 4.5 Consensus size: 32
2692 TGTCCTATAC
* * *
2702 TATTGTGGTTTGTTGAATATATTGTTTCATGC
1 TATTGTGGTTTGTTTAATATATTGTTTAATGT
* ** * *
2734 TATTCTTATTT-TTTAGTATATTGTTTAATAT
1 TATTGTGGTTTGTTTAATATATTGTTTAATGT
* *
2765 TATTGTGGGTTGTTTAATATATTGTTTAATGC
1 TATTGTGGTTTGTTTAATATATTGTTTAATGT
* * *
2797 TATTTTGATTTGTTTAATATACTT-CTTAATGT
1 TATTGTGGTTTGTTTAATATA-TTGTTTAATGT
*
2829 TGTTGTGGTTTGTTTA
1 TATTGTGGTTTGTTTA
2845 TTCGTAAACT
Statistics
Matches: 86, Mismatches: 23, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
31 22 0.26
32 62 0.72
33 2 0.02
ACGTcount: A:0.21, C:0.04, G:0.17, T:0.58
Consensus pattern (32 bp):
TATTGTGGTTTGTTTAATATATTGTTTAATGT
Found at i:6064 original size:139 final size:137
Alignment explanation
Indices: 5730--6119 Score: 414
Period size: 139 Copynumber: 2.8 Consensus size: 137
5720 AAGTGTAGGA
* * * *
5730 TCTAATATTAA-CCTAATTAATTTTAATCAATTATTGAATCAAATATTTGAAATGGAACCTCAGG
1 TCTAATATTAATCCTAATCAATTTTAATCAATTATTGAATCGAATAATTGAAATGGAACCTGA-G
* * * *
5794 CTTAAATGCAAGGACCAAAT-AAAATATTCTCTTAAATTAAGGGA-TAAAATTATAATTAAACTA
65 CATAAA-GCTAGGACCAAATCAAAA-ATTCTCCTAAATTAAGGGACTAAAATGATAATTAAACTA
*
5857 AAATAGAGGT
128 AAATAGAGAT
* * * **
5867 TCTAATATTAATCCTAACCAATTTTAGTTAATTATTGAATCGAGCAATTGAAATGGAACCATGAG
1 TCTAATATTAATCCTAATCAATTTTAATCAATTATTGAATCGAATAATTGAAATGGAACC-TGAG
* * * * *
5932 CAAAAAGGCTAGGACCAAATCAAAAATCCACCTAAATTAAGGGACTAAAGTGA-AATTAATCTAA
65 CATAAA-GCTAGGACCAAATCAAAAATTCTCCTAAATTAAGGGACTAAAATGATAATTAAACTAA
*
5996 AGT-GA-AT
129 AATAGAGAT
* *
6003 ACTCTAATTATTAATCCTAATCAGTTCTAATCAATTATTGAATCGAATAATTGAAATGGAACCTC
1 --TCTAA-TATTAATCCTAATCAATTTTAATCAATTATTGAATCGAATAATTGAAATGGAACCT-
* * * *
6068 GGGCATAAAGCTGATGACAAAATCAAGAATTCTCCTAAATTAAGGGACTAAA
62 GAGCATAAAGCT-AGGACCAAATCAAAAATTCTCCTAAATTAAGGGACTAAA
6120 TTTAAAGAAA
Statistics
Matches: 209, Mismatches: 35, Indels: 16
0.80 0.13 0.06
Matches are distributed among these distances:
136 1 0.00
137 13 0.06
138 94 0.45
139 101 0.48
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (137 bp):
TCTAATATTAATCCTAATCAATTTTAATCAATTATTGAATCGAATAATTGAAATGGAACCTGAGC
ATAAAGCTAGGACCAAATCAAAAATTCTCCTAAATTAAGGGACTAAAATGATAATTAAACTAAAA
TAGAGAT
Found at i:6155 original size:25 final size:26
Alignment explanation
Indices: 6127--6179 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
6117 AAATTTAAAG
*
6127 AAACCAAAATTTAAA-GGCCAAACCT
1 AAACCAAAACTTAAAGGGCCAAACCT
*
6152 AAACCTAAACTTAAAGGGCCAAACCT
1 AAACCAAAACTTAAAGGGCCAAACCT
6178 AA
1 AA
6180 GTGTTAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.51, C:0.25, G:0.09, T:0.15
Consensus pattern (26 bp):
AAACCAAAACTTAAAGGGCCAAACCT
Found at i:9522 original size:22 final size:22
Alignment explanation
Indices: 9491--9536 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
9481 CATATACAGT
*
9491 ATACAGAGGTCCTTCGGGACAA
1 ATACAGAGGTCCTTCGAGACAA
* *
9513 ATACATAGGTCTTTCGAGACAA
1 ATACAGAGGTCCTTCGAGACAA
9535 AT
1 AT
9537 TTCATATGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (22 bp):
ATACAGAGGTCCTTCGAGACAA
Found at i:10327 original size:20 final size:20
Alignment explanation
Indices: 10302--10341 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10292 GCCGAAATTA
*
10302 CTGTAGCAGTGCATCGGTAC
1 CTGTAGCAATGCATCGGTAC
*
10322 CTGTAGTAATGCATCGGTAC
1 CTGTAGCAATGCATCGGTAC
10342 ACAATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.28
Consensus pattern (20 bp):
CTGTAGCAATGCATCGGTAC
Found at i:10390 original size:21 final size:21
Alignment explanation
Indices: 10364--10404 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10354 CGATGTTTTT
10364 GTGCATCGGTACACTATAGCA
1 GTGCATCGGTACACTATAGCA
* *
10385 GTGCATTGGTACACTGTAGC
1 GTGCATCGGTACACTATAGC
10405 GCTGTTCACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
GTGCATCGGTACACTATAGCA
Found at i:10460 original size:19 final size:19
Alignment explanation
Indices: 10436--10486 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
10426 TACTGTTCAC
* **
10436 AGTACTGTTCATACCGTAT
1 AGTACTATTCATACAATAT
10455 AGTACTATTCATACAATAT
1 AGTACTATTCATACAATAT
10474 AGTACTATTCATA
1 AGTACTATTCATA
10487 AAAATGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (19 bp):
AGTACTATTCATACAATAT
Found at i:10980 original size:44 final size:44
Alignment explanation
Indices: 10803--10986 Score: 158
Period size: 44 Copynumber: 4.2 Consensus size: 44
10793 TGGAATTGAA
* *
10803 CAAAAGGGTGAAATTGATCCAATTTCTTATGTGATAGAATCAAG
1 CAAAAGGGTGATATTGATCCAACTTCTTATGTGATAGAATCAAG
* * * * * * *
10847 CGAAATGGTAATGCTT-ATCCAACTCCTTAGGTGAT-GTAATCGAG
1 CAAAAGGGTGAT-ATTGATCCAACTTCTTATGTGATAG-AATCAAG
* * * ** * *
10891 AAAAATGGTGATGTTGATCCAAC-TCTTTATGTGACGGACTTAAG
1 CAAAAGGGTGATATTGATCCAACTTC-TTATGTGATAGAATCAAG
* *
10935 CAAAAGGGTGATATTGATCCAGCTTCTTATGTAATAGAATCAAG
1 CAAAAGGGTGATATTGATCCAACTTCTTATGTGATAGAATCAAG
10979 CAAAAGGG
1 CAAAAGGG
10987 AATGTAGATC
Statistics
Matches: 106, Mismatches: 28, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
43 4 0.04
44 97 0.92
45 5 0.05
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (44 bp):
CAAAAGGGTGATATTGATCCAACTTCTTATGTGATAGAATCAAG
Found at i:18252 original size:19 final size:19
Alignment explanation
Indices: 18228--18265 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18218 CTTAGATAGA
*
18228 GGTATCGGTACCCTCTGGG
1 GGTATCGATACCCTCTGGG
18247 GGTATCGATACCCTCTGGG
1 GGTATCGATACCCTCTGGG
18266 CAATCTGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (19 bp):
GGTATCGATACCCTCTGGG
Found at i:18668 original size:19 final size:17
Alignment explanation
Indices: 18630--18664 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18620 TTATTACTCC
18630 CCCTTACTATAACACTT
1 CCCTTACTATAACACTT
18647 CCCTTACTATAACACTT
1 CCCTTACTATAACACTT
18664 C
1 C
18665 TCCCCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (17 bp):
CCCTTACTATAACACTT
Found at i:20396 original size:13 final size:13
Alignment explanation
Indices: 20380--20404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20370 TTGAAAAACT
20380 ATGTTTGAAAATA
1 ATGTTTGAAAATA
20393 ATGTTTGAAAAT
1 ATGTTTGAAAAT
20405 CAATATATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
ATGTTTGAAAATA
Found at i:20976 original size:22 final size:23
Alignment explanation
Indices: 20899--20970 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
20889 CACGTGTGGT
20899 TATCGGTACCCATTCAAAGAGGG
1 TATCGGTACCCATTCAAAGAGGG
20922 TATCGGTACCCATTCAAAGAGGG
1 TATCGGTACCCATTCAAAGAGGG
* *
20945 TATCGGTACCCATAC-AAGGGGG
1 TATCGGTACCCATTCAAAGAGGG
20967 TATC
1 TATC
20971 AATACCTAGC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
22 10 0.21
23 37 0.79
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (23 bp):
TATCGGTACCCATTCAAAGAGGG
Found at i:25038 original size:6 final size:5
Alignment explanation
Indices: 25031--25167 Score: 59
Period size: 5 Copynumber: 26.2 Consensus size: 5
25021 CATTTTTTTC
*
25031 TCTTT CTCTTT CTCCTTT TCTTT TCTTT TCATTT TCTGTT T-TTT TTTCTT
1 TCTTT -TCTTT -T-CTTT TCTTT TCTTT TC-TTT TCT-TT TCTTT TCT-TT
* * *
25081 TCTTC T-TTT TCTTT TCTTT T-TTT CTCTTT CTGTTT TTTTT TCTATT
1 TCTTT TCTTT TCTTT TCTTT TCTTT -TCTTT -TCTTT TCTTT TCT-TT
* * * * *
25127 TATTT T-TTT CCTCT ACGTTT TCTTTT TCTTT T-TAT TCTTT T
1 TCTTT TCTTT TCTTT TC-TTT TC-TTT TCTTT TCTTT TCTTT T
25168 TTATTCTCTT
Statistics
Matches: 104, Mismatches: 15, Indels: 25
0.72 0.10 0.17
Matches are distributed among these distances:
4 15 0.14
5 45 0.43
6 40 0.38
7 4 0.04
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:25060 original size:46 final size:45
Alignment explanation
Indices: 25006--25138 Score: 126
Period size: 46 Copynumber: 2.9 Consensus size: 45
24996 TATATATATA
25006 TTTTTTTTCA-TCTCTCATTTTTTTCTCTTTC-TCTTTCTCCTTTTC
1 TTTTTTTTCATTCTCT-ATTTTTTTCTCTTTCTTCTTT-TCCTTTTC
* * * *
25051 TTTTCTTTTCATTTTCTGTTTTTTTTTCTTTCTTCTTTTTCTTTTC
1 TTTT-TTTTCATTCTCTATTTTTTTCTCTTTCTTCTTTTCCTTTTC
* * * * * *
25097 TTTTTTTCTCTTTCTGTTTTTTTTTCTATTTATTTTTTTCCT
1 TTTTTTT-TCATTCTCTATTTTTTTCTCTTTCTTCTTTTCCT
25139 CTACGTTTTC
Statistics
Matches: 71, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
45 7 0.10
46 55 0.77
47 9 0.13
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.75
Consensus pattern (45 bp):
TTTTTTTTCATTCTCTATTTTTTTCTCTTTCTTCTTTTCCTTTTC
Found at i:25078 original size:28 final size:28
Alignment explanation
Indices: 25046--25134 Score: 85
Period size: 31 Copynumber: 3.1 Consensus size: 28
25036 CTCTTTCTCC
* *
25046 TTTTCTTTTCTTTTCATTTTCTGTTTTT
1 TTTTCTTTTCTTTTCTTTTTCTATTTTT
*
25074 TTTTC-TTTC--TTCTTTTTCTTTTCTTT
1 TTTTCTTTTCTTTTCTTTTTCTATT-TTT
*
25100 TTTTCTCTTTCTGTTTTTTTTTCTATTTATT
1 TTTTCT-TTTCT-TTTCTTTTTCTATTT-TT
25131 TTTT
1 TTTT
25135 TCCTCTACGT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
25 11 0.22
26 8 0.16
27 4 0.08
28 9 0.18
30 1 0.02
31 17 0.34
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (28 bp):
TTTTCTTTTCTTTTCTTTTTCTATTTTT
Found at i:25086 original size:7 final size:6
Alignment explanation
Indices: 25025--25159 Score: 80
Period size: 6 Copynumber: 21.8 Consensus size: 6
25015 ATCTCTCATT
* * *
25025 TTTTTC TCTTTCTC TTTCTC CTTTTC -TTTTC -TTTTC ATTTTC TGTTTT-
1 TTTTTC T-TTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC
* *
25073 TTTTTC TTTCTTC TTTTTC TTTTCTT TTTTTC TCTTTC TGTTTT- TTTTTC
1 TTTTTC TTT-TTC TTTTTC TTTT-TC TTTTTC TTTTTC T-TTTTC TTTTTC
* * * * *
25123 TATTTATT TTTTTC CTCTAC GTTTTC TTTTTC TTTTT
1 T-TTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
25160 ATTCTTTTTT
Statistics
Matches: 101, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
5 18 0.18
6 49 0.49
7 29 0.29
8 5 0.05
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:25089 original size:14 final size:13
Alignment explanation
Indices: 25046--25136 Score: 71
Period size: 14 Copynumber: 6.7 Consensus size: 13
25036 CTCTTTCTCC
25046 TTTTCTTTTCTTTT
1 TTTTC-TTTCTTTT
*
25060 CATTTTCTGT-TTTT
1 --TTTTCTTTCTTTT
*
25074 TTTTCTTTCTTCT
1 TTTTCTTTCTTTT
25087 TTTTCTTTTCTTTT
1 TTTTC-TTTCTTTT
*
25101 TTTCTCTTTCTGTT
1 TTT-TCTTTCTTTT
25115 TTTT-TTTCTATTT
1 TTTTCTTTCT-TTT
25128 ATTTT-TTTC
1 -TTTTCTTTC
25137 CTCTACGTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
12 12 0.19
13 11 0.17
14 32 0.50
15 4 0.06
16 5 0.08
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTCTTTCTTTT
Found at i:25089 original size:40 final size:42
Alignment explanation
Indices: 25037--25123 Score: 117
Period size: 44 Copynumber: 2.1 Consensus size: 42
25027 TTTCTCTTTC
25037 TCTTTCTCC-TTTTCTTTTC-TTTTCAT-TTTCTGTTTTTTTT
1 TCTTTCTCCTTTTTCTTTTCTTTTTC-TCTTTCTGTTTTTTTT
*
25077 TCTTTCTTCTTTTTCTTTTCTTTTTTTCTCTTTCTGTTTTTTTT
1 TCTTTCTCCTTTTTCTTTTC--TTTTTCTCTTTCTGTTTTTTTT
25121 TCT
1 TCT
25124 ATTTATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
40 8 0.20
41 10 0.24
43 1 0.02
44 22 0.54
ACGTcount: A:0.01, C:0.20, G:0.02, T:0.77
Consensus pattern (42 bp):
TCTTTCTCCTTTTTCTTTTCTTTTTCTCTTTCTGTTTTTTTT
Found at i:25111 original size:32 final size:30
Alignment explanation
Indices: 25047--25168 Score: 92
Period size: 32 Copynumber: 3.9 Consensus size: 30
25037 TCTTTCTCCT
*
25047 TTTC-TTTTC-TTTTCATTTTCTGTTTTTT--
1 TTTCTTTTTCTTTTTC-TTTTAT-TTTTTTCC
*
25075 TTTCTTTCTTCTTTTTCTTTTCTTTTTTTCTC
1 TTTCTTT-TTCTTTTTCTTTTATTTTTTTC-C
25107 TTTCTGTTTT-TTTTTCTATTTATTTTTTTCC
1 TTTCT-TTTTCTTTTTCT-TTTATTTTTTTCC
* *
25138 TCTACGTTTTCTTTTTCTTTTTATTCTTTTT
1 T-TTCTTTTTCTTTTTC-TTTTATT-TTTTT
25169 TATTCTCTTA
Statistics
Matches: 79, Mismatches: 3, Indels: 19
0.78 0.03 0.19
Matches are distributed among these distances:
28 4 0.05
29 8 0.10
30 9 0.11
31 18 0.23
32 32 0.41
33 8 0.10
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.77
Consensus pattern (30 bp):
TTTCTTTTTCTTTTTCTTTTATTTTTTTCC
Found at i:25134 original size:44 final size:45
Alignment explanation
Indices: 25006--25123 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 45
24996 TATATATATA
* * * *
25006 TTTT-TTTTCATCTCTCATTTTTTTCTCTTTC-TCTTTCTCCTTTTC
1 TTTTCTTTTCATTTCT-GTTTTTTTTTCTTTCTTCTTT-TTCTTTTC
25051 TTTTCTTTTCATTTTCTGTTTTTTTTTCTTTCTTCTTTTTCTTTTC
1 TTTTCTTTTCA-TTTCTGTTTTTTTTTCTTTCTTCTTTTTCTTTTC
25097 TTTT-TTTCTC-TTTCTGTTTTTTTTTCT
1 TTTTCTTT-TCATTTCTGTTTTTTTTTCT
25124 ATTTATTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
44 17 0.26
45 7 0.11
46 32 0.49
47 9 0.14
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (45 bp):
TTTTCTTTTCATTTCTGTTTTTTTTTCTTTCTTCTTTTTCTTTTC
Found at i:31637 original size:22 final size:21
Alignment explanation
Indices: 31595--31634 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31585 AAGACTATTT
31595 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
31616 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
31635 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:33605 original size:20 final size:20
Alignment explanation
Indices: 33580--33619 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
33570 ATCTTACATA
33580 GGGTATCGATACCCTCTGGG
1 GGGTATCGATACCCTCTGGG
*
33600 GGGTATCGGTACCCTCTGGG
1 GGGTATCGATACCCTCTGGG
33620 CAATCTGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCCTCTGGG
Found at i:36203 original size:2 final size:2
Alignment explanation
Indices: 36196--36240 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
36186 TGGACCACCA
*
36196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36238 AT A
1 AT A
36241 ACTCACCAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37777 original size:18 final size:18
Alignment explanation
Indices: 37754--37788 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
37744 TACCAAAAGT
37754 GAATTTCTCACTCCATTG
1 GAATTTCTCACTCCATTG
37772 GAATTTCTCACTCCATT
1 GAATTTCTCACTCCATT
37789 CTTAGCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.40
Consensus pattern (18 bp):
GAATTTCTCACTCCATTG
Found at i:41128 original size:11 final size:11
Alignment explanation
Indices: 41112--41138 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41102 TGGATTTATT
41112 AAACCTCCCAA
1 AAACCTCCCAA
41123 AAACCTCCCAA
1 AAACCTCCCAA
41134 AAACC
1 AAACC
41139 CATTTTGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.44, G:0.00, T:0.07
Consensus pattern (11 bp):
AAACCTCCCAA
Found at i:41938 original size:40 final size:40
Alignment explanation
Indices: 41803--42068 Score: 182
Period size: 40 Copynumber: 6.5 Consensus size: 40
41793 AAAATGGGTT
*
41803 TTTAGCGGCGTATTTTGA-ACAAACGCCACTAAATACTATAC
1 TTTAGTGGCGT-TTTT-ATACAAACGCCACTAAATACTATAC
* * * * * * *
41844 --TAGTAGCGATTTAAGCACAAATGTCTCTAAATACTCATAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCACTAAATACT-ATAC
* * *
41884 TTTAGTGGCATTTTTATATAAATGCCACTAAATACTATAC
1 TTTAGTGGCGTTTTTATACAAACGCCACTAAATACTATAC
* ** * * * *
41924 TTTAGTGACGTTTTTATACAAACGCGGCTGAAGACTTGTAA
1 TTTAGTGGCGTTTTTATACAAACGCCACTAAATAC-TATAC
** * *
41965 TTTAGTGGTTTTTTTATATATAAACGCCACTAAATGA-TGTAC
1 TTTAGTGG-CGTTTT-TATACAAACGCCACTAAAT-ACTATAC
* * * *
42007 TTTAGTGGCGTTTTTATACAGACGACGCTAAAGACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGCCACTAAATACT-ATAC
42048 TTTAGTGGC-TTTTTATACAAA
1 TTTAGTGGCGTTTTTATACAAA
42069 TGCCGCAATT
Statistics
Matches: 171, Mismatches: 43, Indels: 23
0.72 0.18 0.10
Matches are distributed among these distances:
37 1 0.01
38 3 0.02
39 23 0.13
40 61 0.36
41 42 0.25
42 26 0.15
43 14 0.08
44 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (40 bp):
TTTAGTGGCGTTTTTATACAAACGCCACTAAATACTATAC
Found at i:42008 original size:83 final size:82
Alignment explanation
Indices: 41823--42061 Score: 229
Period size: 83 Copynumber: 2.9 Consensus size: 82
41813 TATTTTGAAC
* * * * * * * *
41823 AAACGCCACTAAATACTATAC--TAGT-AGCGATTTAAGCACAAATGTCTCTAAATACTCATACT
1 AAACGCCACTAAATACTATACTTTAGTGA-CGTTTTTA-TACAAACGACGCTAAAGACTCATAAT
*
41885 TTAGTGGC-ATTTTTATAT
64 TTAGTGGCTTTTTTTATAT
* * **
41903 AAATGCCACTAAATACTATACTTTAGTGACGTTTTTATACAAACG-CGGCTGAAGACTTGTAATT
1 AAACGCCACTAAATACTATACTTTAGTGACGTTTTTATACAAACGAC-GCTAAAGACTCATAATT
*
41967 TAGTGGTTTTTTTATATAT
65 TAGTGGCTTTTTT-TATAT
* * * *
41986 AAACGCCACTAAATGA-TGTACTTTAGTGGCGTTTTTATACAGACGACGCTAAAGACTCATACTT
1 AAACGCCACTAAAT-ACTATACTTTAGTGACGTTTTTATACAAACGACGCTAAAGACTCATAATT
42050 TAGTGGCTTTTT
65 TAGTGGCTTTTT
42062 ATACAAATGC
Statistics
Matches: 129, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
80 21 0.16
81 23 0.18
82 14 0.11
83 69 0.53
84 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (82 bp):
AAACGCCACTAAATACTATACTTTAGTGACGTTTTTATACAAACGACGCTAAAGACTCATAATTT
AGTGGCTTTTTTTATAT
Found at i:43508 original size:17 final size:16
Alignment explanation
Indices: 43486--43529 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
43476 GTTTTTTCGG
43486 TTCGGTTCGGTTTTTT
1 TTCGGTTCGGTTTTTT
*
43502 TTACGGTTCGG--GTTT
1 TT-CGGTTCGGTTTTTT
43517 TTCGGTTCGGTTT
1 TTCGGTTCGGTTT
43530 GGTTCGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 8 0.35
15 5 0.22
16 2 0.09
17 8 0.35
ACGTcount: A:0.02, C:0.14, G:0.30, T:0.55
Consensus pattern (16 bp):
TTCGGTTCGGTTTTTT
Found at i:51148 original size:9 final size:9
Alignment explanation
Indices: 51116--51150 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
51106 TAGAAGATAT
*
51116 TTTTATTAA
1 TTTTATTTA
*
51125 TTTTAATTA
1 TTTTATTTA
51134 TTTTATTTA
1 TTTTATTTA
51143 TTTTATTT
1 TTTTATTT
51151 TGCATTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:51488 original size:18 final size:20
Alignment explanation
Indices: 51453--51489 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
51443 TTTTTATAAC
*
51453 TATATATAAATATTATTAAT
1 TATATATAAATATAATTAAT
51473 TATAT-TAAATA-AATTAA
1 TATATATAAATATAATTAA
51490 AATTATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 6 0.38
20 5 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATATAAATATAATTAAT
Found at i:51744 original size:12 final size:13
Alignment explanation
Indices: 51722--51750 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
51712 GTCGATTCTC
51722 TTTTCTCTTTGTT
1 TTTTCTCTTTGTT
51735 TTTTCT-TTTGTT
1 TTTTCTCTTTGTT
51747 TTTT
1 TTTT
51751 AATAAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:52313 original size:21 final size:21
Alignment explanation
Indices: 52252--52313 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
52242 CTTGATAAAA
52252 TTAAATTTTAAATTAATT-TT
1 TTAAATTTTAAATTAATTATT
* * *
52272 TATACATATTAAATTTATTATT
1 T-TAAATTTTAAATTAATTATT
*
52294 TTAAATTTTATATTAATTAT
1 TTAAATTTTAAATTAATTAT
52314 ATTTTAAAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.88
22 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAAATTTTAAATTAATTATT
Found at i:53908 original size:64 final size:64
Alignment explanation
Indices: 53776--53917 Score: 182
Period size: 64 Copynumber: 2.2 Consensus size: 64
53766 CGCACTAAGG
** * ***
53776 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGTCTGGGTGTATCGATGCATGTTTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGAGTGTATCGATGCATGTGAA
53840 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGCT-TCGATGCATG-G
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAACCTGAGTG-TATCGATGCATGTG
53902 AA
63 AA
53904 GTGCATCGATGCAT
1 GTGCATCGATGCAT
53918 GGAAGTGCAC
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
64 43 0.62
65 23 0.33
66 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGAGTGTATCGATGCATGTGAA
Found at i:53912 original size:18 final size:18
Alignment explanation
Indices: 53885--53935 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
53875 TAAAAACCTG
*
53885 AGTGCTTCGATGCATGGA
1 AGTGCATCGATGCATGGA
53903 AGTGCATCGATGCATGGA
1 AGTGCATCGATGCATGGA
*
53921 AGTGCACCGATGCAT
1 AGTGCATCGATGCAT
53936 AAAATGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (18 bp):
AGTGCATCGATGCATGGA
Found at i:56548 original size:23 final size:23
Alignment explanation
Indices: 56520--56600 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
56510 GCATGGCATT
56520 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
56543 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
*
56565 -TGTATCGATGCACATTCAAGG-
1 GTGCATCGATGCACATTCAAGGA
56586 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
56601 TATGCAACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 1 0.02
21 13 0.28
22 5 0.11
23 27 0.57
24 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:56999 original size:15 final size:15
Alignment explanation
Indices: 56981--57015 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
56971 AACAACATCT
56981 TCTAGCGACATGGTC
1 TCTAGCGACATGGTC
56996 TCTAGCGACATGGTC
1 TCTAGCGACATGGTC
57011 TCTAG
1 TCTAG
57016 TCTATTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (15 bp):
TCTAGCGACATGGTC
Done.