Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004099.1 Hibiscus syriacus cultivar Beakdansim tig00008964_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: 46711
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1021 original size:143 final size:144
Alignment explanation
Indices: 733--1021 Score: 491
Period size: 143 Copynumber: 2.0 Consensus size: 144
723 AAAATAAAAA
733 TTCAGAGTATGTGGAAGAAAGAGAAGTGGGGAGATCGAGAGGGAGGGAACGGTGCGGGTTTAAAG
1 TTCAGAGTATGTGGAAGAAAGAGAAGTGGGGAGATCGAGAGGGAGGGAACGGTGCGGGTTTAAAG
798 ATGAGAGAGGATTGGTCAAAAGGATACTGACGTCATAAATCATATTTTGTAAGAAATAATATTCT
66 AT-AGAGAGGATTGGTCAAAAGGATACTGACGTCATAAATCATATTTTGTAAGAAATAATATTCT
863 TTCCTTTTTTATTTT
130 TTCCTTTTTTATTTT
878 TTCAGAGTATGTGGAAGAAAGAG-A-TGGGGAGATCGAAGAGGGAGGGAACGGTGCGGGTTTAAA
1 TTCAGAGTATGTGGAAGAAAGAGAAGTGGGGAGATCG-AGAGGGAGGGAACGGTGCGGGTTTAAA
941 GAT-GAGAGGATTGGTC-AAAGGATACCTGACGTCATAAAATTCATA-TTTGTAAGAAATAATAT
65 GATAGAGAGGATTGGTCAAAAGGATA-CTGACGTCAT-AAA-TCATATTTTGTAAGAAATAATAT
1003 TCTTTCC-TTTTTATTTT
127 TCTTTCCTTTTTTATTTT
1020 TT
1 TT
1022 ACCTTTTATA
Statistics
Matches: 140, Mismatches: 0, Indels: 11
0.93 0.00 0.07
Matches are distributed among these distances:
141 8 0.06
142 35 0.25
143 38 0.27
144 36 0.26
145 23 0.16
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (144 bp):
TTCAGAGTATGTGGAAGAAAGAGAAGTGGGGAGATCGAGAGGGAGGGAACGGTGCGGGTTTAAAG
ATAGAGAGGATTGGTCAAAAGGATACTGACGTCATAAATCATATTTTGTAAGAAATAATATTCTT
TCCTTTTTTATTTT
Found at i:1106 original size:22 final size:21
Alignment explanation
Indices: 1071--1115 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
1061 AGATTAAGGA
*
1071 AAAATATATTTAAAATATTAT
1 AAAATATATCTAAAATATTAT
1092 AAAATATAATCTAAAATATTAT
1 AAAATAT-ATCTAAAATATTAT
1114 AA
1 AA
1116 CAACGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATATATCTAAAATATTAT
Found at i:2954 original size:2 final size:2
Alignment explanation
Indices: 2947--2984 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2937 GATCATGCCC
2947 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2985 GTGTGTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6083 original size:19 final size:19
Alignment explanation
Indices: 6059--6137 Score: 86
Period size: 19 Copynumber: 3.9 Consensus size: 19
6049 CGCGTTGCGA
6059 TTCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTCCAAG
* *
6078 TTCGTTGCGATGGTCAAAG
1 TTCGTTGCGATAGTCCAAG
* *
6097 TTCGCGTTGCGATTTATTCCAAA
1 TT--CGTTGCGA--TAGTCCAAG
6120 TTCGTTGCGATAGTCCAA
1 TTCGTTGCGATAGTCCAA
6138 AATCGCAACG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 26 0.53
21 16 0.33
23 7 0.14
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (19 bp):
TTCGTTGCGATAGTCCAAG
Found at i:6241 original size:6 final size:6
Alignment explanation
Indices: 6230--6269 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
6220 ACGTATGATT
6230 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGA
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGA
6270 GACGAGACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.35, C:0.47, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:7063 original size:42 final size:42
Alignment explanation
Indices: 7016--7213 Score: 328
Period size: 42 Copynumber: 4.8 Consensus size: 42
7006 TGCGATTTTG
* *
7016 GGACTATCGCAACGAATTTGGAATAAATTGCAACGAGAACTT
1 GGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTT
* *
7058 GGACTATCGCAACGAATTTGGAATAAATCGCAACGTGAATTT
1 GGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTT
*
7100 GGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTT
1 GGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTT
*
7142 GGACTATCGTAACGAATTTGGAATAAATCGCAACGCGAACTT
1 GGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTT
7184 GGACTATCGCAACGAATTTGG-A-AAATCGCA
1 GGACTATCGCAACGAATTTGGAATAAATCGCA
7214 TTGCGATAGT
Statistics
Matches: 147, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 8 0.05
41 1 0.01
42 138 0.94
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (42 bp):
GGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTT
Found at i:8054 original size:2 final size:2
Alignment explanation
Indices: 8043--8084 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
8033 GAATATTAAC
8043 TA TA -A TA TA TA TA TA 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
8084 T
1 T
8085 CATTAATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8853 original size:21 final size:23
Alignment explanation
Indices: 8812--8872 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 23
8802 CATAAAGTTT
*
8812 AAAAAAA-TA-AATTACATAATTG
1 AAAAAAACTATAATTA-AAAATTG
*
8834 AAAAAAACT-T-ATTAAAAATTT
1 AAAAAAACTATAATTAAAAATTG
8855 AAAAAAACTATAATTAAA
1 AAAAAAACTATAATTAAA
8873 TTTCAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 14 0.42
22 12 0.36
23 7 0.21
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAAAAACTATAATTAAAAATTG
Found at i:8956 original size:39 final size:39
Alignment explanation
Indices: 8913--9023 Score: 156
Period size: 39 Copynumber: 2.8 Consensus size: 39
8903 GTTAAAAAAT
8913 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
*
8952 AATTTAGAATGTT-ATGGTGGCAA-AATTTAAGAAATTAAG
1 AATTTAGAATGTTAAT-GT-GAAATAATTTAAGAAATTAAG
*
8991 AATTTAGAATGTTAGA-GTGAAATAATTTGAGAA
1 AATTTAGAATGTTA-ATGTGAAATAATTTAAGAA
9024 TTATAAATAA
Statistics
Matches: 64, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
38 5 0.08
39 55 0.86
40 3 0.05
41 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.19, T:0.34
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
Found at i:9047 original size:6 final size:6
Alignment explanation
Indices: 9025--9113 Score: 62
Period size: 6 Copynumber: 15.2 Consensus size: 6
9015 ATTTGAGAAT
*
9025 TATAAA TA-AAA -AT-AA TATAAA TA-ATAA TATAAA TATATATA TATATA
1 TATAAA TATAAA TATAAA TATAAA TATA-AA TATAAA TATA-A-A TATAAA
* * * * *
9072 TATATA TATATA TATATA TATATA TATATA TATAAA TA-AAA T
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA T
9114 GGATACTGAG
Statistics
Matches: 74, Mismatches: 2, Indels: 15
0.81 0.02 0.16
Matches are distributed among these distances:
4 3 0.04
5 10 0.14
6 54 0.73
7 2 0.03
8 5 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
TATAAA
Found at i:9052 original size:12 final size:12
Alignment explanation
Indices: 9026--9110 Score: 63
Period size: 14 Copynumber: 7.1 Consensus size: 12
9016 TTTGAGAATT
9026 ATAA-ATAAA-A
1 ATAATATAAATA
9036 ATAATATAAATA
1 ATAATATAAATA
9048 ATAATATAAAT-
1 ATAATATAAATA
*
9059 AT-ATATATAT-
1 ATAATATAAATA
*
9069 ATATATATATATA
1 ATA-ATATAAATA
*
9082 TATATATATATATA
1 -ATA-ATATAAATA
9096 TATATATATAAATA
1 -ATA-ATATAAATA
9110 A
1 A
9111 AATGGATACT
Statistics
Matches: 67, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
10 13 0.19
11 7 0.10
12 20 0.30
13 1 0.01
14 26 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:9064 original size:2 final size:2
Alignment explanation
Indices: 9039--9105 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
9029 AATAAAAATA
* *
9039 AT AT AA AT A- AT A- AT AT AA AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9079 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9106 AATAAAATGG
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:10512 original size:2 final size:2
Alignment explanation
Indices: 10505--10545 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
10495 ATTCATTCGT
*
10505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10546 TCAAACATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:11438 original size:40 final size:39
Alignment explanation
Indices: 11313--11438 Score: 116
Period size: 40 Copynumber: 3.2 Consensus size: 39
11303 ACACTATTGT
*
11313 TAAATTACATTAGGTTAATATTTATTATTAAGGTTTATA
1 TAAATTACATTAGGTTAATATTTATTATTAAGATTTATA
* * * *
11352 TTAATTAAGATTA---TATATATTTTATATGTTAATATTT-TA
1 TAAATT-ACATTAGGTTA-ATA-TTTAT-TATTAAGATTTATA
*
11391 AATAATTACATTAGGTTAATATTTATTATTAAGATTTATA
1 TA-AATTACATTAGGTTAATATTTATTATTAAGATTTATA
11431 CTAAATTA
1 -TAAATTA
11439 AATTTTGAAG
Statistics
Matches: 66, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
37 2 0.03
38 3 0.05
39 26 0.39
40 29 0.44
41 4 0.06
42 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (39 bp):
TAAATTACATTAGGTTAATATTTATTATTAAGATTTATA
Found at i:13510 original size:26 final size:24
Alignment explanation
Indices: 13448--13510 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
13438 CATTTTAATC
13448 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
13472 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
13495 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
13511 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:13512 original size:22 final size:23
Alignment explanation
Indices: 13482--13528 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
13472 AAAATATATT
13482 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
13505 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
13527 TA
1 TA
13529 AAACAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:13542 original size:32 final size:32
Alignment explanation
Indices: 13476--13555 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
13466 ATATTTAAAA
* * *
13476 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAACAATAT
13508 TATATTT-TTAATA-TTATAATAAAACAATCAAT
1 TATATTTATTAATATTTATAATAAAACAAT--AT
*
13540 TATATTATAATAATAT
1 TATATT-TATTAATAT
13556 AAGATATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 12 0.31
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.13
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAACAATAT
Found at i:13661 original size:27 final size:30
Alignment explanation
Indices: 13631--13704 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 30
13621 ATTTCATAGA
*
13631 AATAATATTATTAA-A-TTATTAATAAT-T
1 AATAATATTATTAATATTTAATAATAATAT
13658 AATAATATTATTTATATATTTAATAATAATAT
1 AATAATATTA-TTA-ATATTTAATAATAATAT
13690 AATAATATT-TTAATA
1 AATAATATTATTAATA
13705 AAGATATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 10 0.24
28 3 0.07
29 4 0.10
30 4 0.10
31 10 0.24
32 10 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
AATAATATTATTAATATTTAATAATAATAT
Found at i:13697 original size:21 final size:20
Alignment explanation
Indices: 13650--13705 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
13640 ATTAAATTAT
* * *
13650 TAATAATTAATAATATTATT
1 TAATATTTAATAATAATATA
13670 TATATATTTAATAATAATATAA
1 TA-ATATTTAATAATAATAT-A
13692 TAATATTTTAATAA
1 TAATA-TTTAATAA
13706 AGATATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 18 0.60
22 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATTTAATAATAATATA
Found at i:13703 original size:11 final size:11
Alignment explanation
Indices: 13656--13705 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
13646 TTATTAATAA
13656 TTAATAATATT
1 TTAATAATATT
*
13667 ATTTAT-ATA-T
1 -TTAATAATATT
*
13677 TTAATAATAAT
1 TTAATAATATT
*
13688 ATAATAATATT
1 TTAATAATATT
13699 TTAATAA
1 TTAATAA
13706 AGATATTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
9 4 0.13
10 4 0.13
11 19 0.61
12 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTAATAATATT
Found at i:13726 original size:23 final size:24
Alignment explanation
Indices: 13700--13745 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
13690 AATAATATTT
13700 TAATAAAGA-TATTTAAAATATAC
1 TAATAAAGATTATTTAAAATATAC
* * *
13723 TAATTAATATTTTTTAAAATATA
1 TAATAAAGATTATTTAAAATATA
13746 ATATAATACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TAATAAAGATTATTTAAAATATAC
Found at i:14457 original size:5 final size:5
Alignment explanation
Indices: 14447--14484 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
14437 CATCGCTCGA
14447 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTC
14485 AAATGTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTCTC
Found at i:19014 original size:17 final size:17
Alignment explanation
Indices: 18994--19027 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18984 TTACTATTCA
18994 TGTGAATAGTGAAATTT
1 TGTGAATAGTGAAATTT
19011 TGTGAATAGTGAAATTT
1 TGTGAATAGTGAAATTT
19028 GGTCGGCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (17 bp):
TGTGAATAGTGAAATTT
Found at i:26780 original size:18 final size:17
Alignment explanation
Indices: 26759--26800 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
26749 TTAAAATTAG
26759 ATATTATTTTA-AATAAT
1 ATATT-TTTTATAATAAT
26776 -TATATTTTTATAATAAT
1 ATAT-TTTTTATAATAAT
26793 ATATTTTT
1 ATATTTTT
26801 ACCTCATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 8 0.36
17 11 0.50
18 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTTTTTATAATAAT
Found at i:26795 original size:16 final size:16
Alignment explanation
Indices: 26765--26801 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
26755 TTAGATATTA
26765 TTTTAAATAATTATAT
1 TTTTAAATAATTATAT
26781 TTTTATAATAA-TATAT
1 TTTTA-AATAATTATAT
26797 TTTTA
1 TTTTA
26802 CCTCATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAAATAATTATAT
Found at i:28715 original size:82 final size:81
Alignment explanation
Indices: 28567--28870 Score: 321
Period size: 82 Copynumber: 3.7 Consensus size: 81
28557 TTTGTTGTAA
* * * *
28567 AAACGCTGCAATAGAGTTGACATATAGTGGTGTTTTTACAACAAACGCCGCAATAGAGTGGTAAA
1 AAACGCCGCAATAGA-TTAACATATAGTGGCGTTTTTACAA-AAACGCCGCAATAGA-TGATAAA
28632 TTAGCGGCGTTTATACCAC
63 TTAGCGGCGTTTATACCAC
*
28651 AAACGCCGCAATAGATTAACATATAGTGGCG-TTTTAGCCAAAACGCCGCAATAGATCGATAAAT
1 AAACGCCGCAATAGATTAACATATAGTGGCGTTTTTA-CAAAAACGCCGCAATAGAT-GATAAAT
*
28715 TAGCGGTGTTTATACCAC
64 TAGCGGCGTTTATACCAC
* * * * *
28733 AAACGCCACAATAGATTACACATATAGTGGCATTTATT-CTTAAAACGCCGCAATATTTATAATA
1 AAACGCCGCAATAGATTA-ACATATAGTGGCGTTT-TTAC-AAAAACGCCGCAATA--GATGATA
* * *
28797 AA-TAGTGGCGTTTTTA-GAC
61 AATTAGCGGCGTTTATACCAC
* *
28816 AAACGTCGCAATAGTGTTAATCA-ATAGTGGCGTTTTTACAAAAACGCCGCAATAG
1 AAACGCCGCAATAG-ATTAA-CATATAGTGGCGTTTTTACAAAAACGCCGCAATAG
28871 TTTTAATCAA
Statistics
Matches: 188, Mismatches: 21, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
81 1 0.01
82 76 0.40
83 56 0.30
84 46 0.24
85 7 0.04
86 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (81 bp):
AAACGCCGCAATAGATTAACATATAGTGGCGTTTTTACAAAAACGCCGCAATAGATGATAAATTA
GCGGCGTTTATACCAC
Found at i:28769 original size:42 final size:41
Alignment explanation
Indices: 28567--28891 Score: 231
Period size: 42 Copynumber: 7.8 Consensus size: 41
28557 TTTGTTGTAA
* * * * *
28567 AAACGCTGCAATAGAGTTGACATATAGTGGTGTTTTTACAAC
1 AAACGCCGCAATAGA-TTAACATATAGTGGCGTTTATACCAC
*
28609 AAACGCCGCAATAGAGTGGTAA-AT-TAGCGGCGTTTATACCAC
1 AAACGCCGCAATAGA-T--TAACATATAGTGGCGTTTATACCAC
28651 AAACGCCGCAATAGATTAACATATAGTGGCGTTT-TAGCCA-
1 AAACGCCGCAATAGATTAACATATAGTGGCGTTTATA-CCAC
* *
28691 AAACGCCGCAATAGATCGATAA-AT-TAGCGGTGTTTATACCAC
1 AAACGCCGCAATAGAT---TAACATATAGTGGCGTTTATACCAC
* * * *
28733 AAACGCCACAATAGATTACACATATAGTGGCATTTATTCTTA-
1 AAACGCCGCAATAGATTA-ACATATAGTGGCGTTTATAC-CAC
** * * * *
28775 AAACGCCGCAATATTTATAATAAATAGTGGCGTTTTTA-GAC
1 AAACGCCGCAATAGAT-TAACATATAGTGGCGTTTATACCAC
* * * *
28816 AAACGTCGCAATAGTGTTAATCA-ATAGTGGCGTTTTTA-CAA
1 AAACGCCGCAATAG-ATTAA-CATATAGTGGCGTTTATACCAC
*
28857 AAACGCCGCAATAGTTTTAATCA-ATAGTGGCGTTT
1 AAACGCCGCAATAG-ATTAA-CATATAGTGGCGTTT
28892 TTTTAATAAA
Statistics
Matches: 233, Mismatches: 32, Indels: 37
0.77 0.11 0.12
Matches are distributed among these distances:
39 5 0.02
40 22 0.09
41 92 0.39
42 104 0.45
43 8 0.03
44 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (41 bp):
AAACGCCGCAATAGATTAACATATAGTGGCGTTTATACCAC
Found at i:28842 original size:41 final size:40
Alignment explanation
Indices: 28774--28934 Score: 182
Period size: 41 Copynumber: 4.0 Consensus size: 40
28764 ATTTATTCTT
* *
28774 AAAACGCCGCAATA-TTTATAATAAATAGTGGCGTTTTTAGA
1 AAAACGCCGCAATAGTGT-TAATCAATAGTGGCGTTTTTA-A
* *
28815 CAAACGTCGCAATAGTGTTAATCAATAGTGGCGTTTTTACA
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTA-A
*
28856 AAAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTTTTAA
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCG--TTTTTAA
* * * *
28898 TAAACGCCACAATAATG-TAATCAATAGTGGAGTTTTT
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTT
28935 TGTATAAACG
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
39 5 0.05
41 77 0.74
42 16 0.15
43 6 0.06
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (40 bp):
AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAA
Found at i:28935 original size:41 final size:41
Alignment explanation
Indices: 28775--28955 Score: 174
Period size: 41 Copynumber: 4.4 Consensus size: 41
28765 TTTATTCTTA
* * * *
28775 AAACGCCGCAATATTTATAATAAATAGTGGCG--TTTTTAGAC
1 AAACGCCGCAATA-ATGTAATCAATAGTGGCGTTTTTTTA-AT
* * **
28816 AAACGTCGCAATAGTGTTAATCAATAGTGGCGTTTTTACAA-
1 AAACGCCGCAATAATG-TAATCAATAGTGGCGTTTTTTTAAT
* *
28857 AAACGCCGCAATAGTTTTAATCAATAGTGGCGTTTTTTTAAT
1 AAACGCCGCAATA-ATGTAATCAATAGTGGCGTTTTTTTAAT
* *
28899 AAACGCCACAATAATGTAATCAATAGTGGAGTTTTTTGT-AT
1 AAACGCCGCAATAATGTAATCAATAGTGGCGTTTTTT-TAAT
28940 AAACGCCGCAA-AATGT
1 AAACGCCGCAATAATGT
28956 TAAATATATA
Statistics
Matches: 118, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
40 6 0.05
41 93 0.79
42 15 0.13
43 4 0.03
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (41 bp):
AAACGCCGCAATAATGTAATCAATAGTGGCGTTTTTTTAAT
Found at i:28950 original size:83 final size:82
Alignment explanation
Indices: 28774--28934 Score: 220
Period size: 82 Copynumber: 2.0 Consensus size: 82
28764 ATTTATTCTT
* * *
28774 AAAACGCCGCAATATTTATAATAAATAGTGGCGTTTTTAGACAAACGTCGCAATAGTGTTAATCA
1 AAAACGCCGCAATATTTATAATAAATAGTGGCGTTTTTAGACAAACGCCACAATAATGTTAATCA
*
28839 ATAGTGGCGTTTTTACA
66 ATAGTGGAGTTTTTACA
* *
28856 AAAACGCCGCAATAGTTT-TAATCAATAGTGGCGTTTTTTTA-ATAAACGCCACAATAATG-TAA
1 AAAACGCCGCAATA-TTTATAATAAATAGTGGCG--TTTTTAGACAAACGCCACAATAATGTTAA
28918 TCAATAGTGGAGTTTTT
63 TCAATAGTGGAGTTTTT
28935 TGTATAAACG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
82 47 0.67
83 17 0.24
84 6 0.09
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (82 bp):
AAAACGCCGCAATATTTATAATAAATAGTGGCGTTTTTAGACAAACGCCACAATAATGTTAATCA
ATAGTGGAGTTTTTACA
Found at i:28967 original size:83 final size:81
Alignment explanation
Indices: 28774--28967 Score: 198
Period size: 83 Copynumber: 2.3 Consensus size: 81
28764 ATTTATTCTT
* * *
28774 AAAACGCCGCAATAT-TTATAATAAATAGTGGCGTTTTTAGACAAACGTCGCAATAGTGTTAATC
1 AAAACGCCGCAATATGTTA-AAT-AATAGTGGCGTTTTTAGACAAACGCCACAATAATGTTAATC
*
28838 AATAGTGGCGTTTTTACA
64 AATAGTGGAGTTTTTACA
* *
28856 AAAACGCCGCAATA-GTTTTAATCAATAGTGGCGTTTTTTTA-ATAAACGCCACAATAATG-TAA
1 AAAACGCCGCAATATG-TTAAAT-AATAGTGGCG--TTTTTAGACAAACGCCACAATAATGTTAA
**
28918 TCAATAGTGGAGTTTTTTGTA
62 TCAATAGTGGAG-TTTTTACA
* *
28939 TAAACGCCGCAAAATGTTAAATATATAGT
1 AAAACGCCGCAATATGTTAAATA-ATAGT
28968 CCTCCTTTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
82 42 0.45
83 44 0.47
84 7 0.08
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (81 bp):
AAAACGCCGCAATATGTTAAATAATAGTGGCGTTTTTAGACAAACGCCACAATAATGTTAATCAA
TAGTGGAGTTTTTACA
Found at i:29132 original size:41 final size:41
Alignment explanation
Indices: 29000--29297 Score: 321
Period size: 41 Copynumber: 7.2 Consensus size: 41
28990 CCTAAAATCA
**
29000 TTTAGTGGGGTTTTTATACAAACGCCGCTAAAGACTCGTAC
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * * *
29041 TTTAATGGCATTTTTTGTACAAACGCCGCTAAA-AATGAGTTC
1 TTTAGTGGCA-TTTTTATACAAACGCCGCTAAAGACT-CGTAC
* * *
29083 ATTA-TGGCATTTTTGTACAAACGCCGCTAACGACTCGTAC
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTAC
* * ** * *
29123 TTTAGTGGCATTTGTGTTTACAAATGTTGCTAAAGACTTGTAA
1 TTTAGTGGCATTT-T-TATACAAACGCCGCTAAAGACTCGTAC
* * * *
29166 TTCAGTGGCATTTTTATATAAACGCCGCTATAGACTCATAC
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTAC
* * *
29207 TTCAGTGGCGTTTTTATACAAACGTCGCTAAAGACTCGTAC
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTAC
* *
29248 TTCAGTGGCATTTTTATACAAACGCCGCTAAAGACTTGTAC
1 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTAC
29289 TTTAGTGGC
1 TTTAGTGGC
29298 GTTTGTAAAC
Statistics
Matches: 212, Mismatches: 39, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
40 27 0.13
41 124 0.58
42 29 0.14
43 32 0.15
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (41 bp):
TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTAC
Found at i:32086 original size:43 final size:43
Alignment explanation
Indices: 31967--32147 Score: 211
Period size: 43 Copynumber: 4.2 Consensus size: 43
31957 ACCAGATCTT
** * * * * *
31967 TTGCGGCGTTTGTGGGAAAAATGCCACAAAATCTCAAGACATA
1 TTGCGGCGTTTGTGAAAAAAAAGCCGCTAAATCTCAACACCTA
* * * * *
32010 TTGTGGTGTTTGTGTAAAAAAACGCTGCTAAATCTCAATACCTA
1 TTGCGGCGTTTGTG-AAAAAAAAGCCGCTAAATCTCAACACCTA
32054 TTGCGGCGTTTGTGAAAAAAAAGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGAAAAAAAAGCCGCTAAATCTCAACACCTA
* *
32097 TTGCGGCGTTTGTTGGAAAAACA-CCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTG-TGAAAAAAAAGCCGCTAAATCTCAACACCTA
32140 TTGCGGCG
1 TTGCGGCG
32148 CGAACTTTAG
Statistics
Matches: 119, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
43 78 0.66
44 41 0.34
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
TTGCGGCGTTTGTGAAAAAAAAGCCGCTAAATCTCAACACCTA
Found at i:32086 original size:87 final size:86
Alignment explanation
Indices: 31967--32147 Score: 229
Period size: 87 Copynumber: 2.1 Consensus size: 86
31957 ACCAGATCTT
** * * * * *
31967 TTGCGGCGTTTGTGGGAAAAATGCCACAAAATCTCAAGACATATTGTGGTGTTTG-TGTAAAAAA
1 TTGCGGCGTTTGTGAAAAAAAAGCCACAAAATCTCAACACATATTGCGGCGTTTGTTGGAAAAAA
*
32031 ACGCTGCTAAATCTCAATACCTA
66 AC-C-GCTAAATCTCAACACCTA
* * * *
32054 TTGCGGCGTTTGTGAAAAAAAAGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGGAAAAAC
1 TTGCGGCGTTTGTGAAAAAAAAGCCACAAAATCTCAACACATATTGCGGCGTTTGTTGGAAAAAA
32119 ACCGCTAAATCTCAACACCTA
66 ACCGCTAAATCTCAACACCTA
32140 TTGCGGCG
1 TTGCGGCG
32148 CGAACTTTAG
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
86 25 0.31
87 47 0.58
88 9 0.11
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (86 bp):
TTGCGGCGTTTGTGAAAAAAAAGCCACAAAATCTCAACACATATTGCGGCGTTTGTTGGAAAAAA
ACCGCTAAATCTCAACACCTA
Found at i:35087 original size:27 final size:27
Alignment explanation
Indices: 35057--35118 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
35047 GATTTATCAT
35057 TTATATTTTTAATTATA-ATTTTACTTA
1 TTATATTTTTAATT-TACATTTTACTTA
** *
35084 TTATATTTTTTCTTTACTTTTTACTTA
1 TTATATTTTTAATTTACATTTTACTTA
35111 TTATATTT
1 TTATATTT
35119 CAGCTGTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 2 0.06
27 29 0.94
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (27 bp):
TTATATTTTTAATTTACATTTTACTTA
Found at i:38879 original size:39 final size:39
Alignment explanation
Indices: 38835--38922 Score: 149
Period size: 39 Copynumber: 2.3 Consensus size: 39
38825 CAACGAGGCA
38835 AGCAATGAGCATCAAGCTTAACAGATAACGAGCTTGATG
1 AGCAATGAGCATCAAGCTTAACAGATAACGAGCTTGATG
* *
38874 AGCAATGAGCATCAAGCTTAATAGATAACGAGCTTGATT
1 AGCAATGAGCATCAAGCTTAACAGATAACGAGCTTGATG
*
38913 AGCAACGAGC
1 AGCAATGAGC
38923 TTCACGAGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (39 bp):
AGCAATGAGCATCAAGCTTAACAGATAACGAGCTTGATG
Found at i:40503 original size:20 final size:21
Alignment explanation
Indices: 40475--40525 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
40465 CCAAGTGGAG
*
40475 TATCAATACTGCAGG-GCCAA
1 TATCGATACTGCAGGTGCCAA
* *
40495 TATCGATACT-CAGGTGTCAG
1 TATCGATACTGCAGGTGCCAA
40515 TATCGATACTG
1 TATCGATACTG
40526 AGGCCCCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (21 bp):
TATCGATACTGCAGGTGCCAA
Found at i:44020 original size:19 final size:20
Alignment explanation
Indices: 43983--44021 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43973 CAACATTAGC
43983 CATGTTTTTATATTTTAATT
1 CATGTTTTTATATTTTAATT
44003 CATGTTTATT-TA-TTTAATT
1 CATGTTT-TTATATTTTAATT
44022 TTATGCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 9 0.50
21 2 0.11
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
CATGTTTTTATATTTTAATT
Done.