Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006284.1 Hibiscus syriacus cultivar Beakdansim tig00014998_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: 108402
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1577 original size:11 final size:11
Alignment explanation
Indices: 1545--1578 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1535 AATGTGAAAA
1545 GTAAATGCAAT
1 GTAAATGCAAT
*
1556 GTAGATGCAAT
1 GTAAATGCAAT
*
1567 GTAAATACAAT
1 GTAAATGCAAT
1578 G
1 G
1579 CATGGTGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (11 bp):
GTAAATGCAAT
Found at i:7218 original size:23 final size:22
Alignment explanation
Indices: 7191--7237 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
7181 TGGGTCCTGT
7191 TGGGCTCTAGGTTTGAGTCTTGA
1 TGGGCTCTAGGTTTGAGT-TTGA
* *
7214 TGGGCTCTATGTTTGGGTTTGA
1 TGGGCTCTAGGTTTGAGTTTGA
7236 TG
1 TG
7238 TAACTTGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.11, C:0.11, G:0.36, T:0.43
Consensus pattern (22 bp):
TGGGCTCTAGGTTTGAGTTTGA
Found at i:8242 original size:2 final size:2
Alignment explanation
Indices: 8231--8269 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
8221 ATATAAGATG
8231 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8270 AAGCTAGAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:10454 original size:121 final size:122
Alignment explanation
Indices: 10073--10539 Score: 478
Period size: 124 Copynumber: 3.8 Consensus size: 122
10063 GATCGCTCTT
* * * * * * *
10073 AATCTAGTTATGATCTCACCCTTTCTTCTGAAAGACGTTGAGTCCTGTAACGATCTTACTCTTTC
1 AATCTGGTGATGATCTCACTCTTTCCTATGAAAGACGTTGAGTCATGGAACGATCTTACTC--TC
* * * * *
10138 ATCTGAAGGATGCTAAGTTGTAATTTGGGGTGATCCACTCCTTTTACTAAAGGATGATG
64 ATCTGAAGGATGTTAAGTCGTGATTCGGGGTGATCCACTTCTTTTACTAAAGGATGATG
* * * * **
10197 AATCTGGTGACGATCTCACTCTTTCTTATGAAAAATGTTGAGTTGTGGAACGATCTTACTCATTT
1 AATCTGGTGATGATCTCACTCTTTCCTATGAAAGACGTTGAGTCATGGAACGATCTTACTC---T
* * * *
10262 C-TCTGAAGGAT-TATATGTCATGATTCGGGGTGATACAC-TCATTTTACTAAAGGATGTTG
63 CATCTGAAGGATGT-TAAGTCGTGATTCGGGGTGATCCACTTC-TTTTACTAAAGGATGATG
* * *
10321 AATCTGGTGATGATCTCACTCTTTCCTATGGATGACGTTAAGTCATGGAACGATCTTACTC-CAT
1 AATCTGGTGATGATCTCACTCTTTCCTATGAAAGACGTTGAGTCATGGAACGATCTTACTCTCAT
* * * * * *
10385 CTAAATGATGTTAAGTCGTGATTCAGGGTGATCCACTTCTTTTACTGAATGATGGTG
66 CTGAAGGATGTTAAGTCGTGATTCGGGGTGATCCACTTCTTTTACTAAAGGATGATG
* * * *
10442 AATCTGGTGATGATATCACTCTTTCCTCTGAAAGAAGCTGAGTCATGG-ACGATCTTACTCCCTC
1 AATCTGGTGATGATCTCACTCTTTCCTATGAAAGACGTTGAGTCATGGAACGATCTTACT--CTC
* *
10506 CTCTGAAGGATGTTAAGTCGTTATTC-GGGTGATC
64 ATCTGAAGGATGTTAAGTCGTGATTCGGGGTGATC
10540 TATTACTGAG
Statistics
Matches: 286, Mismatches: 48, Indels: 20
0.81 0.14 0.06
Matches are distributed among these distances:
120 12 0.04
121 85 0.30
122 12 0.04
123 24 0.08
124 149 0.52
125 4 0.01
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (122 bp):
AATCTGGTGATGATCTCACTCTTTCCTATGAAAGACGTTGAGTCATGGAACGATCTTACTCTCAT
CTGAAGGATGTTAAGTCGTGATTCGGGGTGATCCACTTCTTTTACTAAAGGATGATG
Found at i:17560 original size:782 final size:783
Alignment explanation
Indices: 16056--17622 Score: 3064
Period size: 782 Copynumber: 2.0 Consensus size: 783
16046 TCATGAGCCT
16056 CCTCAGTGTGAACAGACTCATTCACCCTATTCTCGAGTTCACTCATCACTACAACCCTCTTCTTT
1 CCTCAGTGTGAACAGACTCATTCACCCTATTCTCGAGTTCACTCATCACTACAACCCTCTTCTTT
* *
16121 TTAACTAAGCCATGTGTATAACATCTATCAATCCTGGTGAAGCCCCCAACTTTATAAACTTCATC
66 TCAACTAAGCCATGTGTATAACATCTATCAATCCTGGTGAAGCCCCCAACTTCATAAACTTCATC
16186 TTTCTTATCTTCAGGAGTGTTAATTTGGCATGTGTAATTCCATGAAACCTTCCGTTGCTTGTATA
131 TTTCTTATCTTCAGGAGTGTTAATTTGGCATGTGTAATTCCATGAAACCTTCCGTTGCTTGTATA
16251 TACAAACGATGTTAGTGTTTGTATAAAACAATTTGGCATCGCCTGTCCTTTTTCATCTTATAGTT
196 TACAAACGATGTTAGTGTTTGTATAAAACAATTTGGCATCGCCTGTCCTTTTTCATCTTATAGTT
16316 TGGCTTGGATATAACCAACATTGGTTTCCTTATCTTTTTTTCAACCTTTTCCACATTCTATTCAG
261 TGGCTTGGATATAACCAACATTGGTTTCCTTATCTTTTTTTCAACCTTTTCCACATTCTATTCAG
16381 TTGCGTTCACATTTCCTTCACCATTCATAAGACTATCATCAAAAAATTGCATTTCTTTGGTGTCC
326 TTGCGTTCACATTTCCTTCACCATTCATAAGACTATCATCAAAAAATTGCATTTCTTTGGTGTCC
16446 ATCAGTCTTTGGACCAACCTTTTGAACTTTGTACAAGTCTGGATTTGGTAATCAGACTCACCATA
391 ATCAGTCTTTGGACCAACCTTTTGAACTTTGTACAAGTCTGGATTTGGTAATCAGACTCACCATA
*
16511 ATATTCATAAAACTACTTGGATTTCTCATCAGCGGATTCTTCCTTCGAACTTAATAATCTTCTTC
456 ATATTCATAAAACTACTTGGATTTCTCATCAGCGGATTCTTCCTTCGAACTTAAAAATCTTCTTC
16576 TGACCATTTATTTATACACCCAACTTAACAGTGTCTTAATCTCTTCCACCTTGTTTTAATTCTTC
521 TGACCATTTATTTATACACCCAACTTAACAGTGTCTTAATCTCTTCCACCTTGTTTTAATTCTTC
16641 GACCTTCATCAATGGCGTTGAATCCTTGATTTTGATGGTTTTGAAGTGGATCTGCAGCTGTACAA
586 GACCTTCATCAATGGCGTTGAATCCTTGATTTTGATGGTTTTGAAGTGGATCTGCAGCTGTACAA
*
16706 GGCATTTTTGAGTCATTAAATGATACCAACTTTCTCTTAATCAAATGCTCCACTACCCTTTTGAA
651 GGCATTTTCGAGTCATTAAATGATACCAACTTTCTCTTAATCAAATGCTCCACTACCCTTTTGAA
16771 AGAAGGGCAATTTTCAATGTTATGCCCTAAATATTAGCGTGGTACTTACAAGTCTCATTTTTATT
716 AGAAGGGCAATTTTCAATGTTATGCCCTAAATATTAGCGTGGTACTTACAAGTCTCATTTTTATT
16836 GCA
781 GCA
16839 CCTCAGTGTGAACAGACTCATTCACCCTATTCTCGAGTTCACTCATCACTACAACCCTCTTCTTT
1 CCTCAGTGTGAACAGACTCATTCACCCTATTCTCGAGTTCACTCATCACTACAACCCTCTTCTTT
16904 TCAACTAAGCCATGTGTATAACATCTATCAATCCTGGTGAAGCCCCCAACTTCATAAACTTCATC
66 TCAACTAAGCCATGTGTATAACATCTATCAATCCTGGTGAAGCCCCCAACTTCATAAACTTCATC
**
16969 TTTCTTATCTTCAGGAGTGTTAATTTGGCATGTGTAATTCCATGAAACCTTTTGTTGCTTGTATA
131 TTTCTTATCTTCAGGAGTGTTAATTTGGCATGTGTAATTCCATGAAACCTTCCGTTGCTTGTATA
17034 TACAAACGATGTTAGTGTTTGTATAAAACAA-TTGGCATCGCCTGTCCTTTTTCATCTTATAGTT
196 TACAAACGATGTTAGTGTTTGTATAAAACAATTTGGCATCGCCTGTCCTTTTTCATCTTATAGTT
17098 TGGCTTGGATATAACCAACATTGGTTTCCTTATCTTTTTTTCAACCTTTTCCACATTCTATTCAG
261 TGGCTTGGATATAACCAACATTGGTTTCCTTATCTTTTTTTCAACCTTTTCCACATTCTATTCAG
*
17163 TTGCGTTCACATTTCCTTCACCATTCATAAGACTATCATCAAAAAATTGTATTTCTTTGGTGTCC
326 TTGCGTTCACATTTCCTTCACCATTCATAAGACTATCATCAAAAAATTGCATTTCTTTGGTGTCC
17228 ATCAGTCTTTGGACCAACCTTTTGAACTTTGTACAAGTCTGGATTTGGTAATCAGACTCACCATA
391 ATCAGTCTTTGGACCAACCTTTTGAACTTTGTACAAGTCTGGATTTGGTAATCAGACTCACCATA
17293 ATATTCATAAAACTACTTGGATTTCTCATCAGCGGATTCTTCCTTCGAACTTAAAAATCTTCTTC
456 ATATTCATAAAACTACTTGGATTTCTCATCAGCGGATTCTTCCTTCGAACTTAAAAATCTTCTTC
17358 TGACCATTTATTTATACACCCAACTTAACAGTGTCTTAATCTCTTCCACCTTGTTTTAATTCTTC
521 TGACCATTTATTTATACACCCAACTTAACAGTGTCTTAATCTCTTCCACCTTGTTTTAATTCTTC
17423 GACCTTCATCAATGGCGTTGAATCCTTGATTTTGATGGTTTTGAAGTGGATCTGCAGCTGTACAA
586 GACCTTCATCAATGGCGTTGAATCCTTGATTTTGATGGTTTTGAAGTGGATCTGCAGCTGTACAA
17488 GGCATTTTCGAGTCATTAAATGATACCAACTTTCTCTTAATCAAATGCTCCACTACCCTTTTGAA
651 GGCATTTTCGAGTCATTAAATGATACCAACTTTCTCTTAATCAAATGCTCCACTACCCTTTTGAA
17553 AGAAGGGCAATTTTCAATGTTATGCCCTAAATATTAGCGTGGTACTTACAAGTCTCATTTTTATT
716 AGAAGGGCAATTTTCAATGTTATGCCCTAAATATTAGCGTGGTACTTACAAGTCTCATTTTTATT
17618 GCA
781 GCA
17621 CC
1 CC
17623 ATTTTAGATA
Statistics
Matches: 777, Mismatches: 7, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
782 555 0.71
783 222 0.29
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (783 bp):
CCTCAGTGTGAACAGACTCATTCACCCTATTCTCGAGTTCACTCATCACTACAACCCTCTTCTTT
TCAACTAAGCCATGTGTATAACATCTATCAATCCTGGTGAAGCCCCCAACTTCATAAACTTCATC
TTTCTTATCTTCAGGAGTGTTAATTTGGCATGTGTAATTCCATGAAACCTTCCGTTGCTTGTATA
TACAAACGATGTTAGTGTTTGTATAAAACAATTTGGCATCGCCTGTCCTTTTTCATCTTATAGTT
TGGCTTGGATATAACCAACATTGGTTTCCTTATCTTTTTTTCAACCTTTTCCACATTCTATTCAG
TTGCGTTCACATTTCCTTCACCATTCATAAGACTATCATCAAAAAATTGCATTTCTTTGGTGTCC
ATCAGTCTTTGGACCAACCTTTTGAACTTTGTACAAGTCTGGATTTGGTAATCAGACTCACCATA
ATATTCATAAAACTACTTGGATTTCTCATCAGCGGATTCTTCCTTCGAACTTAAAAATCTTCTTC
TGACCATTTATTTATACACCCAACTTAACAGTGTCTTAATCTCTTCCACCTTGTTTTAATTCTTC
GACCTTCATCAATGGCGTTGAATCCTTGATTTTGATGGTTTTGAAGTGGATCTGCAGCTGTACAA
GGCATTTTCGAGTCATTAAATGATACCAACTTTCTCTTAATCAAATGCTCCACTACCCTTTTGAA
AGAAGGGCAATTTTCAATGTTATGCCCTAAATATTAGCGTGGTACTTACAAGTCTCATTTTTATT
GCA
Found at i:18972 original size:16 final size:16
Alignment explanation
Indices: 18951--18982 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18941 ACTATTCACA
*
18951 TGAATAGTGAATTTCG
1 TGAATAGTGAAATTCG
18967 TGAATAGTGAAATTCG
1 TGAATAGTGAAATTCG
18983 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (16 bp):
TGAATAGTGAAATTCG
Found at i:20830 original size:21 final size:21
Alignment explanation
Indices: 20788--20830 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
20778 AGCGCATGAA
* *
20788 CAGAACTCTGAATGAACGTGC
1 CAGAACTATGAATGAACATGC
20809 CAGAACTATGAA-GATACATGC
1 CAGAACTATGAATGA-ACATGC
20830 C
1 C
20831 GGCTTGCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (21 bp):
CAGAACTATGAATGAACATGC
Found at i:32724 original size:3 final size:3
Alignment explanation
Indices: 32716--32754 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
32706 TACTGTTTTC
* *
32716 ATT ATT ATT AGT ATT ATT ATC ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
32755 CTAGTTTACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:32909 original size:3 final size:3
Alignment explanation
Indices: 32885--32939 Score: 58
Period size: 3 Copynumber: 17.7 Consensus size: 3
32875 CATTTTCTTC
* *
32885 TTA TTT TTA TTTA TT- TTT TTA TTA TGTA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA TTA TTA
32932 TTA TTA TT
1 TTA TTA TT
32940 CCTTTTTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 34 0.76
4 9 0.20
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:32975 original size:11 final size:11
Alignment explanation
Indices: 32889--32971 Score: 60
Period size: 12 Copynumber: 6.9 Consensus size: 11
32879 TTCTTCTTAT
*
32889 TTTTATTTATTT
1 TTTTA-TTATTA
32901 TTTTATTATGTA
1 TTTTATTAT-TA
32913 TATATTATTATTA
1 T-T-TTATTATTA
32926 TTATTATTATTA
1 TT-TTATTATTA
* *
32938 TTCCTTTTTCTTCA
1 TT--TTATTATT-A
32952 TTTTATTATTA
1 TTTTATTATTA
32963 TTTT-TTATT
1 TTTTATTATT
32972 TATTGTATTC
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
10 5 0.08
11 9 0.15
12 26 0.43
13 10 0.17
14 10 0.17
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:33065 original size:18 final size:17
Alignment explanation
Indices: 33042--33077 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
33032 TCGTTCGTTT
*
33042 TTTATTTTCTTTATTTTA
1 TTTATTTTCATT-TTTTA
33060 TTTATTTTCATTTTTTA
1 TTTATTTTCATTTTTTA
33077 T
1 T
33078 CTAACACGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTCATTTTTTA
Found at i:37942 original size:40 final size:40
Alignment explanation
Indices: 37905--37983 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
37895 GAATCCTAAG
37905 TGATGAGAAGGTCTGGTCAGGGAATGACACGGTTCCTACA
1 TGATGAGAAGGTCTGGTCAGGGAATGACACGGTTCCTACA
* *
37945 TGATGAGGAGGTCTGGTCAGGGGATGACACGGTTCCTAC
1 TGATGAGAAGGTCTGGTCAGGGAATGACACGGTTCCTAC
37984 GCAATGAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (40 bp):
TGATGAGAAGGTCTGGTCAGGGAATGACACGGTTCCTACA
Found at i:39698 original size:21 final size:23
Alignment explanation
Indices: 39672--39718 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
39662 CTTCTTGTCC
*
39672 TTTTTTTCTTCGCTTTTT-TCTT
1 TTTTTTTCTTCGATTTTTCTCTT
*
39694 TTTTTTTCTTTGATTTTTCTCTT
1 TTTTTTTCTTCGATTTTTCTCTT
39717 TT
1 TT
39719 CTCTTTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (23 bp):
TTTTTTTCTTCGATTTTTCTCTT
Found at i:39767 original size:16 final size:16
Alignment explanation
Indices: 39707--39771 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 16
39697 TTTTCTTTGA
*
39707 TTTTTCTCTTTTCTCT
1 TTTTTTTCTTTTCTCT
*
39723 TTGTTATTT-TTTTCT-A
1 TT-TT-TTTCTTTTCTCT
*
39739 TTTGTTTCTTTTCTCT
1 TTTTTTTCTTTTCTCT
39755 TTTTTTTCTTTTCTCT
1 TTTTTTTCTTTTCTCT
39771 T
1 T
39772 CGCTTTGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
14 3 0.08
15 7 0.17
16 20 0.50
17 8 0.20
18 2 0.05
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTTTCTTTTCTCT
Found at i:41056 original size:21 final size:20
Alignment explanation
Indices: 41031--41070 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
41021 AAAAAATAAA
*
41031 ATGCAGATGCAAAATGCAAAG
1 ATGCAAATGC-AAATGCAAAG
*
41052 ATGCAAATGCATATGCAAA
1 ATGCAAATGCAAATGCAAA
41071 AAATGTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.17
Consensus pattern (20 bp):
ATGCAAATGCAAATGCAAAG
Found at i:50863 original size:12 final size:13
Alignment explanation
Indices: 50846--50875 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
50836 ATGAAAATAT
50846 TAAAAAA-TCAAA
1 TAAAAAATTCAAA
50858 TAAAAAATTCAAA
1 TAAAAAATTCAAA
50871 TAAAA
1 TAAAA
50876 TATAAATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAAAATTCAAA
Found at i:51841 original size:16 final size:16
Alignment explanation
Indices: 51816--51846 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51806 AACAGTCCTC
51816 ATGGAACTCGTCACGT
1 ATGGAACTCGTCACGT
*
51832 ATGGAGCTCGTCACG
1 ATGGAACTCGTCACG
51847 CATGAGATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.23
Consensus pattern (16 bp):
ATGGAACTCGTCACGT
Found at i:52344 original size:90 final size:93
Alignment explanation
Indices: 52134--52387 Score: 336
Period size: 90 Copynumber: 2.7 Consensus size: 93
52124 ATAAATTTAA
*
52134 TCTAAGTAGTATCGATATCATATATGGTATCGGTACCATTTTATCATTCTGTTTTGACAGTATCG
1 TCTAAGTAGTATCGATATCATATATGGTATCGGTACCA-TTTAGCATTCTGTTTTGACAGTATCG
* *
52199 GTACTGCATCAGCAGTATTGGTACTACTAC
65 GTACTGCATCAG-AGTATCGGTACTACAAC
* * * * *
52229 TCTATGTAGTATCGATATCACATATGTTATCGTTACCATTTAGCATTCT-TTTTGACATTATCGG
1 TCTAAGTAGTATCGATATCATATATGGTATCGGTACCATTTAGCATTCTGTTTTGACAGTATCGG
* *
52293 TACT-CCTGAG-GTATCGGTACTACAAC
66 TACTGCATCAGAGTATCGGTACTACAAC
* *
52319 TCTAAGTAGTATCAATATCATATATGGTATTGGTACCAATTTAGCATTCTGTTTTGACAAGTA-C
1 TCTAAGTAGTATCGATATCATATATGGTATCGGTACC-ATTTAGCATTCTGTTTTGAC-AGTATC
52383 GGTAC
64 GGTAC
52388 CAGAACTCAG
Statistics
Matches: 139, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
90 45 0.32
91 12 0.09
92 17 0.12
93 21 0.15
94 10 0.07
95 34 0.24
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (93 bp):
TCTAAGTAGTATCGATATCATATATGGTATCGGTACCATTTAGCATTCTGTTTTGACAGTATCGG
TACTGCATCAGAGTATCGGTACTACAAC
Found at i:56278 original size:15 final size:15
Alignment explanation
Indices: 56258--56287 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
56248 CCTAATGGGC
56258 TAAATAATTTACCCG
1 TAAATAATTTACCCG
56273 TAAATAATTTACCCG
1 TAAATAATTTACCCG
56288 GGATCGACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (15 bp):
TAAATAATTTACCCG
Found at i:66575 original size:26 final size:26
Alignment explanation
Indices: 66542--66594 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
66532 TATGCCGCCG
* *
66542 CTTCTTTT-TGTTTTTTGTGTCTTCTT
1 CTTCTTTTACGTTTTTTGTCT-TTCTT
66568 CTTCTTTTACGTTTTTTGTCTTTCTT
1 CTTCTTTTACGTTTTTTGTCTTTCTT
66594 C
1 C
66595 CGTGATAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.02, C:0.19, G:0.09, T:0.70
Consensus pattern (26 bp):
CTTCTTTTACGTTTTTTGTCTTTCTT
Found at i:82035 original size:24 final size:24
Alignment explanation
Indices: 82008--82095 Score: 124
Period size: 24 Copynumber: 3.7 Consensus size: 24
81998 TTCTATTATA
82008 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
82032 ATACTTGACCTGGATTCTGATTGA
1 ATACTTGACCTGGATTCTGATCGG
*
82056 ATACTTGACCTGGATT-TCGATCTG
1 ATACTTGACCTGGATTCT-GATCGG
*
82080 ATACTTGACTTGGATT
1 ATACTTGACCTGGATT
82096 ATGTTATGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
23 1 0.02
24 56 0.98
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:82105 original size:24 final size:24
Alignment explanation
Indices: 82008--82105 Score: 110
Period size: 24 Copynumber: 4.1 Consensus size: 24
81998 TTCTATTATA
**
82008 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATATG
82032 ATACTTGACCTGGATTCTGAT-TG
1 ATACTTGACCTGGATTCTGATATG
*
82055 AATACTTGACCTGGATT-TCGATCTG
1 -ATACTTGACCTGGATTCT-GATATG
* * *
82080 ATACTTGACTTGGATTATGTTATG
1 ATACTTGACCTGGATTCTGATATG
82104 AT
1 AT
82106 TTTTTTATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
23 2 0.03
24 61 0.92
25 3 0.05
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.39
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATATG
Found at i:84206 original size:18 final size:18
Alignment explanation
Indices: 84182--84273 Score: 86
Period size: 18 Copynumber: 5.2 Consensus size: 18
84172 GTCATAACCC
84182 GACCCGACCTGACCCGTT
1 GACCCGACCTGACCCGTT
* *
84200 TA--C--CC-GACCCATT
1 GACCCGACCTGACCCGTT
* *
84213 GACCCGACCCGACCTGTT
1 GACCCGACCTGACCCGTT
84231 GACCCGACCTGACCCGTT
1 GACCCGACCTGACCCGTT
84249 GACCCGACCCGTTGACCCGTT
1 GACCCGA-CC--TGACCCGTT
84270 GACC
1 GACC
84274 GGCGTTGACC
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
13 8 0.14
14 2 0.03
15 1 0.02
16 1 0.02
17 2 0.03
18 30 0.51
19 2 0.03
21 13 0.22
ACGTcount: A:0.17, C:0.45, G:0.21, T:0.17
Consensus pattern (18 bp):
GACCCGACCTGACCCGTT
Found at i:84252 original size:13 final size:13
Alignment explanation
Indices: 84236--84267 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
84226 CTGTTGACCC
*
84236 GACCTGACCCGTT
1 GACCCGACCCGTT
84249 GACCCGACCCGTT
1 GACCCGACCCGTT
84262 GACCCG
1 GACCCG
84268 TTGACCGGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.25, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:86823 original size:29 final size:24
Alignment explanation
Indices: 86738--86819 Score: 121
Period size: 24 Copynumber: 3.4 Consensus size: 24
86728 TTTCTATTAT
*
86738 AATACCTGACCTGGATTCTGATTG
1 AATACTTGACCTGGATTCTGATTG
*
86762 GATACTTGACCTGGATTCTGATTG
1 AATACTTGACCTGGATTCTGATTG
*
86786 AATACTTGACCTGGATTTTGATCTG
1 AATACTTGACCTGGATTCTGAT-TG
86811 -ATACTTGAC
1 AATACTTGAC
86820 TTGAATTATG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 51 0.96
25 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (24 bp):
AATACTTGACCTGGATTCTGATTG
Found at i:88630 original size:2 final size:2
Alignment explanation
Indices: 88623--88750 Score: 119
Period size: 2 Copynumber: 68.0 Consensus size: 2
88613 TCGGGCCAGG
* *
88623 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA AA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
88664 AA TA TA TA AA TA T- TA TA TA TA TA T- TT TA -A TT TA AA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
88702 AA TT TA T- TA -A TA T- TA TA TA TA TA TA TA 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
88741 TA TA TA TA TA
1 TA TA TA TA TA
88751 ATTATTTTTA
Statistics
Matches: 101, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
1 8 0.08
2 93 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:90993 original size:17 final size:18
Alignment explanation
Indices: 90968--91008 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
90958 TTTTCATCAT
* *
90968 AAATATTTT-AAATAATA
1 AAATTTTTTAAAATAAAA
90985 AAATTTTTTAAAATAAAA
1 AAATTTTTTAAAATAAAA
91003 AAATTT
1 AAATTT
91009 AGTAGAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTTTTTAAAATAAAA
Found at i:98175 original size:17 final size:17
Alignment explanation
Indices: 98153--98187 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
98143 TTAATGCATT
98153 TTATTCCATCATGAGCA
1 TTATTCCATCATGAGCA
98170 TTATTCCATCATGAGCA
1 TTATTCCATCATGAGCA
98187 T
1 T
98188 ACACTTACAT
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:0.23, G:0.11, T:0.37
Consensus pattern (17 bp):
TTATTCCATCATGAGCA
Found at i:99757 original size:17 final size:16
Alignment explanation
Indices: 99735--99768 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
99725 TAAAGACAGT
99735 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
99752 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
99768 A
1 A
99769 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Done.