Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000318.1 Hibiscus syriacus cultivar Beakdansim tig00000600_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: 79618
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:67 original size:29 final size:29
Alignment explanation
Indices: 25--81 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
15 GAGCAAGGGT
*
25 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
*
54 AGGTCTCCAGGAGTGCATGGCGACCTAC
1 AGGTCGCCAGGAGTGCATGGCGACCTAC
82 GGCTAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (29 bp):
AGGTCGCCAGGAGTGCATGGCGACCTACA
Found at i:11077 original size:17 final size:16
Alignment explanation
Indices: 11047--11080 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11037 CCCTAATTGT
*
11047 TTTGGGCCTTATCGGG
1 TTTGGGCCTGATCGGG
11063 TTTGGGCCTGGATCGGG
1 TTTGGGCCT-GATCGGG
11080 T
1 T
11081 CTGGATCAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.06, C:0.18, G:0.41, T:0.35
Consensus pattern (16 bp):
TTTGGGCCTGATCGGG
Found at i:14917 original size:3 final size:3
Alignment explanation
Indices: 14902--14971 Score: 115
Period size: 3 Copynumber: 23.7 Consensus size: 3
14892 TAAACACACT
*
14902 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
14950 TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
14972 TTTTTAACTT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 1 0.02
3 61 0.98
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:15272 original size:105 final size:105
Alignment explanation
Indices: 15138--15389 Score: 335
Period size: 105 Copynumber: 2.4 Consensus size: 105
15128 TCTCGTGGAT
* * * *
15138 GAGTTCTTCTCATTATGAACTCTTTTGGAAATGTTGATCCAAATCCTTTTGCGGTGGACTTAGAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCAAATCCATCTGCGGT-GAATTAGAA
* *
15203 A-GAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
65 AGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGAC
* * ** * *
15243 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCATCTGTGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAA
* *
15308 GGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGAT
66 GGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGAC
*
15348 GAGTTCTTCTCATTATGAACTCTTCATTGGAAATGTCGATCC
1 GAGTTCTTCTCATTATGAACTCTTC--TGGAAATGTTGATCC
15390 CTCAAGCGAG
Statistics
Matches: 127, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
104 8 0.06
105 107 0.84
107 12 0.09
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAA
GGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGAC
Found at i:15371 original size:16 final size:16
Alignment explanation
Indices: 15317--15372 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
15307 AGGAACAAGT
15317 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* *
15333 T-TTCTCCTTTATGATGAGT
1 TCTTCT-CATTATGA--A-C
15352 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
15368 TCTTC
1 TCTTC
15373 ATTGGAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 4 0.13
16 13 0.42
17 1 0.03
18 1 0.03
19 8 0.26
20 4 0.13
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:15698 original size:225 final size:223
Alignment explanation
Indices: 15309--15742 Score: 667
Period size: 225 Copynumber: 1.9 Consensus size: 223
15299 AATTTGAAAG
*
15309 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGATGAGTTCTTCTCATTATGAACTCTTCA
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCA
* * * * * * *
15374 TTGGAAATGTCGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCAAGTGATAGGT
66 CTGAAAATGTCAATCCCTCAAGCAAGGCGTCACTGATTCAAAATGTCATAAATCAAGTGATAGGT
*
15439 CAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAAC
131 CAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAAC
15504 TCTCCATTGAAAATGTTGATGCGAAGTT
196 TCTCCATTGAAAATGTTGATGCGAAGTT
15532 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTT-GGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGATGAGTTCTTCTCATTATGAACT
* *
15596 C-TC-CTGAAAATGTCAATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATAAATCGAGTGA
61 CTTCACTGAAAATGTCAATCCCTCAAGCAAGGCGTCACTGATTCAAAATGTCATAAATCAAGTGA
* * *
15659 TAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCATTA
126 TAGGTCAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTA
*
15724 TGAACTCTCCATTGGAAAT
191 TGAACTCTCCATTGAAAAT
15743 TTTGGTTCAC
Statistics
Matches: 191, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
223 24 0.13
224 1 0.01
225 133 0.70
226 6 0.03
227 25 0.13
228 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (223 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCA
CTGAAAATGTCAATCCCTCAAGCAAGGCGTCACTGATTCAAAATGTCATAAATCAAGTGATAGGT
CAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAAC
TCTCCATTGAAAATGTTGATGCGAAGTT
Found at i:16639 original size:20 final size:19
Alignment explanation
Indices: 16610--16671 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 19
16600 AATTCTCCTT
16610 TTTCTCTTTTT-ATTTTTTCA
1 TTTCT-TTTTTCA-TTTTTCA
16630 TTTCTTTTTTCATTTTTCA
1 TTTCTTTTTTCATTTTTCA
16649 -TT-TTTTTTC-TTTTTCA
1 TTTCTTTTTTCATTTTTCA
16665 TTT-TTTT
1 TTTCTTTT
16672 CATTTTCATC
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.17
17 13 0.32
18 2 0.05
19 12 0.30
20 6 0.15
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCTTTTTTCATTTTTCA
Found at i:16654 original size:9 final size:9
Alignment explanation
Indices: 16634--16677 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
16624 TTTTCATTTC
16634 TTTTTTCA-
1 TTTTTTCAT
16642 -TTTTTCAT
1 TTTTTTCAT
16650 TTTTTT--T
1 TTTTTTCAT
*
16657 CTTTTTCAT
1 TTTTTTCAT
16666 TTTTTTCAT
1 TTTTTTCAT
16675 TTT
1 TTT
16678 CATCTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
7 13 0.43
9 17 0.57
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:16655 original size:16 final size:16
Alignment explanation
Indices: 16634--16702 Score: 81
Period size: 15 Copynumber: 4.4 Consensus size: 16
16624 TTTTCATTTC
16634 TTTTTTCATTTTTCATT
1 TTTTTTCATTTTTCA-T
16651 TTTTTTC-TTTTTCAT
1 TTTTTTCATTTTTCAT
16666 TTTTTTCA-TTTTCAT
1 TTTTTTCATTTTTCAT
* *
16681 CTTTTT-ATTTGTTCCT
1 TTTTTTCATTT-TTCAT
16697 TTTTTT
1 TTTTTT
16703 TTCTTCAAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
14 1 0.02
15 22 0.48
16 16 0.35
17 7 0.15
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTTTCATTTTTCAT
Found at i:16700 original size:31 final size:32
Alignment explanation
Indices: 16634--16702 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
16624 TTTTCATTTC
* *
16634 TTTTTTCATTTTTCATTTTTTTTCTTTTTCAT
1 TTTTTTCATTTTTCATTTTTTATCTTGTTCAT
*
16666 TTTTTTCA-TTTTCATCTTTTTAT-TTGTTCCT
1 TTTTTTCATTTTTCAT-TTTTTATCTTGTTCAT
16697 TTTTTT
1 TTTTTT
16703 TTCTTCAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 19 0.58
32 14 0.42
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (32 bp):
TTTTTTCATTTTTCATTTTTTATCTTGTTCAT
Found at i:29989 original size:3 final size:3
Alignment explanation
Indices: 29974--30037 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
29964 TAAACACACT
*
29974 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
30022 TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TA
30038 TTTTTTAACT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
2 1 0.02
3 55 0.98
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:36116 original size:3 final size:3
Alignment explanation
Indices: 36108--36157 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
36098 AGATTAAAAC
36108 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36156 AA
1 AA
36158 AAGATTTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:38273 original size:26 final size:26
Alignment explanation
Indices: 38224--38274 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
38214 ATTCTAAATA
38224 GTAAATATATGACGAAATTATAGGAT
1 GTAAATATATGACGAAATTATAGGAT
38250 GTAAATATATGACGAAATTATAGGA
1 GTAAATATATGACGAAATTATAGGA
38275 AACTTCTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (26 bp):
GTAAATATATGACGAAATTATAGGAT
Found at i:46070 original size:30 final size:30
Alignment explanation
Indices: 46003--46060 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
45993 CAGCGGGTGT
*
46003 AATAAATTATTTATAGGATATAAAACTTGA
1 AATAAATTATTTACAGGATATAAAACTTGA
46033 AATAAATTATTTACAGGATATAAAACTT
1 AATAAATTATTTACAGGATATAAAACTT
46061 TAGGTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (30 bp):
AATAAATTATTTACAGGATATAAAACTTGA
Found at i:47728 original size:2 final size:2
Alignment explanation
Indices: 47721--47762 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
47711 AGACGGAGAA
47721 AT AT 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 AT AT
47763 GACAAATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48166 original size:23 final size:25
Alignment explanation
Indices: 48140--48193 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
48130 TTTGTTTTTT
* *
48140 ATTTTATAATTTGATGAT-TTT-AA
1 ATTTTATAATTTAATCATATTTAAA
*
48163 ATTTTGTAATTTAATCATATTTAAA
1 ATTTTATAATTTAATCATATTTAAA
48188 ATTTTA
1 ATTTTA
48194 ATAAATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 15 0.60
24 3 0.12
25 7 0.28
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (25 bp):
ATTTTATAATTTAATCATATTTAAA
Found at i:50034 original size:5 final size:5
Alignment explanation
Indices: 50024--50080 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
50014 GTCCGTCCGT
* * * *
50024 CTCGG CTCGG CACGG CACGG CACGG CACGG CTCGG CTCGTG CTCGTG CTCGTG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG-G CTCG-G CTCG-G
50077 CTCG
1 CTCG
50081 TGGTCGAGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 32 0.65
6 17 0.35
ACGTcount: A:0.07, C:0.39, G:0.37, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:50069 original size:6 final size:6
Alignment explanation
Indices: 50053--50082 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
50043 GCACGGCACG
50053 GCTCG- GCTCGT GCTCGT GCTCGT GCTCGT G
1 GCTCGT GCTCGT GCTCGT GCTCGT GCTCGT G
50083 GTCGAGGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.33, G:0.37, T:0.30
Consensus pattern (6 bp):
GCTCGT
Found at i:50294 original size:6 final size:6
Alignment explanation
Indices: 50082--50290 Score: 319
Period size: 6 Copynumber: 34.8 Consensus size: 6
50072 TCGTGCTCGT
50082 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
50130 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
*
50178 GGTCGA GGTCGA GGTCGA GGTCGT GGTCGA GGTCGA GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* * * * * * * *
50226 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* *
50274 GGTCGT GGTCGT GGTCG
1 GGTCGA GGTCGA GGTCG
50291 TGGTAATACG
Statistics
Matches: 200, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 200 1.00
ACGTcount: A:0.11, C:0.17, G:0.50, T:0.22
Consensus pattern (6 bp):
GGTCGA
Found at i:50586 original size:22 final size:22
Alignment explanation
Indices: 50561--50615 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
50551 TCAGGAGTTA
* *
50561 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
50583 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
50605 CGGGAGTTATA
1 CAGGAGTTATA
50616 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:56149 original size:5 final size:5
Alignment explanation
Indices: 56135--56178 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
56125 GTCCGTCCGT
* * * *
56135 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
56179 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.07, C:0.41, G:0.36, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:56187 original size:6 final size:6
Alignment explanation
Indices: 56176--56236 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
56166 TCGGCTCGGC
* * * *
56176 TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
56224 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
56237 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.07, C:0.16, G:0.49, T:0.28
Consensus pattern (6 bp):
TCGTGG
Found at i:56536 original size:22 final size:22
Alignment explanation
Indices: 56511--56565 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
56501 TCAGGAGTTA
* *
56511 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
56533 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
56555 CGGGAGTTATA
1 CAGGAGTTATA
56566 ACAGTTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:63632 original size:20 final size:18
Alignment explanation
Indices: 63585--63657 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
63575 ACTGAATATT
*
63585 TGTCCCAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
63603 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
63622 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
63641 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
63658 GATAATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 31 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:64336 original size:64 final size:65
Alignment explanation
Indices: 64268--64390 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 65
64258 TCATAAATCT
* * * * *
64268 CATTCGATGTTTGTATTTTAAGGGGGTGCAACGATGCA-CTACTTGTGCATCGATACACTAATGA
1 CATTCGATGTTTGTATTTTAAAGGAGTGCAACGATACACCCACATGTGCATCGATACACTAATGA
* * *
64332 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATACACCCCCATGTGCATCGATACAC
1 CATTCGATGTTTGTATTTTAAAGGAGTGCAACGATACACCCACATGTGCATCGATACAC
64391 CTTGAACAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
64 33 0.66
65 17 0.34
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (65 bp):
CATTCGATGTTTGTATTTTAAAGGAGTGCAACGATACACCCACATGTGCATCGATACACTAATGA
Found at i:66024 original size:42 final size:42
Alignment explanation
Indices: 65973--66216 Score: 425
Period size: 42 Copynumber: 5.8 Consensus size: 42
65963 CATATTCGCA
65973 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* *
66015 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
66057 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * *
66099 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATCCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
66141 TTGCGATAGTCCAAGTTCGCGTTGTGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
66183 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTC
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTC
66217 ATTTATTCCA
Statistics
Matches: 189, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 189 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:66093 original size:84 final size:84
Alignment explanation
Indices: 65973--66216 Score: 470
Period size: 84 Copynumber: 2.9 Consensus size: 84
65963 CATATTCGCA
65973 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
*
66038 GCGATTTATTCCAAATTCG
66 GCGATTTATTCCAAATCCG
66057 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
66122 GCGATTTATTCCAAATCCG
66 GCGATTTATTCCAAATCCG
*
66141 TTGCGATAGTCCAAGTTCGCGTTGTGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
66206 GCGATTTATTC
66 GCGATTTATTC
66217 ATTTATTCCA
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 158 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (84 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATCCG
Found at i:66270 original size:50 final size:49
Alignment explanation
Indices: 66167--66270 Score: 111
Period size: 50 Copynumber: 2.1 Consensus size: 49
66157 TCGCGTTGTG
* ** ** **
66167 ATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTC
1 ATTTATTCCAAGTTCGTTGCGATAGTCCAAAATCGCG-AACGAGGTATTC
66217 ATTTATTCCAAGTTCGTTGCGATAGTCCAAAATCGC-AACGACGGTATTGC
1 ATTTATTCCAAGTTCGTTGCGATAGTCCAAAATCGCGAACGA-GGTATT-C
66267 ATTT
1 ATTT
66271 GTTTCTTAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
48 3 0.07
49 4 0.09
50 38 0.84
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (49 bp):
ATTTATTCCAAGTTCGTTGCGATAGTCCAAAATCGCGAACGAGGTATTC
Found at i:66857 original size:5 final size:5
Alignment explanation
Indices: 66847--66871 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
66837 CCGCCGTCGT
66847 CCGTC CCGTC CCGTC CCGTC CCGTC
1 CCGTC CCGTC CCGTC CCGTC CCGTC
66872 TCGAGTCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.20, T:0.20
Consensus pattern (5 bp):
CCGTC
Found at i:68712 original size:90 final size:92
Alignment explanation
Indices: 68597--68770 Score: 284
Period size: 94 Copynumber: 1.9 Consensus size: 92
68587 TTGTCAGCAT
68597 TTTTCCTTAAAAATATATTACTAATTTAG-TAAATTTGTGAT-A-AA-AATAAAAATAAAAAAAG
1 TTTTCCTTAAAAATATATTACTAATTTAGATAAATTTGTGATAATAATAATAAAAAT-AAAAAAG
68658 ATTTACTGACAAAATGGTAAGCATTTGC
65 ATTTACTGACAAAATGGTAAGCATTTGC
68686 TTTTCCTTAAAATATATATTACTAATTTAGTATAAATTTGTGATAATAATAATAAAAATAAAAAA
1 TTTTCCTTAAAA-ATATATTACTAATTTAG-ATAAATTTGTGATAATAATAATAAAAATAAAAAA
*
68751 TATTTACTGACAAAATGGTA
64 GATTTACTGACAAAATGGTA
68771 GGATACAAGA
Statistics
Matches: 78, Mismatches: 1, Indels: 7
0.91 0.01 0.08
Matches are distributed among these distances:
89 12 0.15
90 17 0.22
92 12 0.15
93 1 0.01
94 27 0.35
95 9 0.12
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (92 bp):
TTTTCCTTAAAAATATATTACTAATTTAGATAAATTTGTGATAATAATAATAAAAATAAAAAAGA
TTTACTGACAAAATGGTAAGCATTTGC
Found at i:69631 original size:21 final size:20
Alignment explanation
Indices: 69573--69632 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
69563 AACTTAATAT
*
69573 TATTATTTTTAAATATTAAAA
1 TATT-TTTTTTAATATTAAAA
* *
69594 TAATTTATTT-ATGATTAAAA
1 TATTTTTTTTAAT-ATTAAAA
69614 TATTGTTTTTTAATATTAA
1 TATT-TTTTTTAATATTAA
69633 TAAAAATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 2 0.06
20 14 0.45
21 13 0.42
22 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TATTTTTTTTAATATTAAAA
Found at i:69938 original size:22 final size:22
Alignment explanation
Indices: 69913--69962 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
69903 TATATAATTG
*
69913 ATATTTTATTATAATATTAAAA
1 ATATTATATTATAATATTAAAA
* * * *
69935 ATATAATATTATATTGTTAGAA
1 ATATTATATTATAATATTAAAA
69957 ATATTA
1 ATATTA
69963 ATAAATGTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
ATATTATATTATAATATTAAAA
Found at i:70002 original size:26 final size:25
Alignment explanation
Indices: 69973--70022 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
69963 ATAAATGTAT
* *
69973 TTAAATATTTTAATAATTATATTTTG
1 TTAAAAATGTTAATAA-TATATTTTG
*
69999 TTAAAAATGTTATTAATATATTTT
1 TTAAAAATGTTAATAATATATTTT
70023 ATAATATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
TTAAAAATGTTAATAATATATTTTG
Done.