Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006579.1 Hibiscus syriacus cultivar Beakdansim tig00016128_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: 129439
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2557 original size:30 final size:31
Alignment explanation
Indices: 2491--2562 Score: 94
Period size: 32 Copynumber: 2.4 Consensus size: 31
2481 TATTTATAAT
*
2491 CAAA-TTTAGGGTAAACTACACTAGATACCAC
1 CAAACTTTAGGATAAACTACACTA-ATACCAC
*
2522 CAAACTTTAGGATAAACTACACT-ATACCGC
1 CAAACTTTAGGATAAACTACACTAATACCAC
*
2552 TAAACTTTAGG
1 CAAACTTTAGG
2563 CATTGTATCG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 16 0.43
31 4 0.11
32 17 0.46
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.25
Consensus pattern (31 bp):
CAAACTTTAGGATAAACTACACTAATACCAC
Found at i:2750 original size:29 final size:29
Alignment explanation
Indices: 2717--2775 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2707 GTCATCAGCC
*
2717 ACGTCATCGCCGTTAACGATTTAACGGTT
1 ACGTCATCGCCGTTAACAATTTAACGGTT
2746 ACGTCATCGCCGTTAACAATTTAACGGTT
1 ACGTCATCGCCGTTAACAATTTAACGGTT
2775 A
1 A
2776 GTGGTCTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (29 bp):
ACGTCATCGCCGTTAACAATTTAACGGTT
Found at i:6273 original size:32 final size:32
Alignment explanation
Indices: 6226--6299 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
6216 TATTTATAAT
*
6226 CAAA-TTTAGGGTAAACTACACTAGATACCAC
1 CAAACTTTAGGATAAACTACACTAGATACCAC
*
6257 CAAACTTTAGGATAAACTACACTAGATACCGC
1 CAAACTTTAGGATAAACTACACTAGATACCAC
*
6289 TAAACTTTAGG
1 CAAACTTTAGG
6300 CATTGTATCG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 4 0.10
32 35 0.90
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (32 bp):
CAAACTTTAGGATAAACTACACTAGATACCAC
Found at i:6487 original size:29 final size:29
Alignment explanation
Indices: 6454--6512 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
6444 GTCATCAGCC
*
6454 ACGTCATCGCCGTTAACGATTTAACGGTT
1 ACGTCATCGCCGTTAACAATTTAACGGTT
6483 ACGTCATCGCCGTTAACAATTTAACGGTT
1 ACGTCATCGCCGTTAACAATTTAACGGTT
6512 A
1 A
6513 GTGGTCTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (29 bp):
ACGTCATCGCCGTTAACAATTTAACGGTT
Found at i:7372 original size:19 final size:21
Alignment explanation
Indices: 7348--7386 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7338 AATTATCAAT
7348 ATAGA-TAT-ATATAATACTA
1 ATAGATTATCATATAATACTA
*
7367 ATAGATTTTCATATAATACT
1 ATAGATTATCATATAATACT
7387 TTTACTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (21 bp):
ATAGATTATCATATAATACTA
Found at i:9208 original size:19 final size:18
Alignment explanation
Indices: 9184--9219 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9174 TGAATAATTA
*
9184 TAAAATATAAAAACTAAAT
1 TAAAATA-AAAAAATAAAT
9203 TAAAATAAAAAAATAAA
1 TAAAATAAAAAAATAAA
9220 AGGAAATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAAATAAAAAAATAAAT
Found at i:9564 original size:27 final size:27
Alignment explanation
Indices: 9526--9591 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
9516 CACATATAAA
9526 ATATA-TT-TATTTTTAATAAAAAAAT
1 ATATATTTATATTTTTAATAAAAAAAT
9551 ATATATTTATATTTTTAATAAAAAAAT
1 ATATATTTATATTTTTAATAAAAAAAT
9578 ATATATTTATATTT
1 ATATATTTATATTT
9592 AAACCACCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 5 0.13
26 2 0.05
27 32 0.82
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATATATTTATATTTTTAATAAAAAAAT
Found at i:11745 original size:2 final size:2
Alignment explanation
Indices: 11738--11775 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11728 TAGACAAAAC
11738 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
11776 CCAACCCTAA
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:12835 original size:16 final size:16
Alignment explanation
Indices: 12806--12839 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12796 AGGTAAACAT
*
12806 TTATAAATATATAAAA
1 TTATAAATAAATAAAA
*
12822 TTATACATAAATAAAA
1 TTATAAATAAATAAAA
12838 TT
1 TT
12840 TGAACTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TTATAAATAAATAAAA
Found at i:13777 original size:39 final size:36
Alignment explanation
Indices: 13734--13835 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 36
13724 AAGGAGAATG
* ** *
13734 AGGAGGTGGAGGTGGAGACTTGTACTTATATGGCTCCTT
1 AGGAGGAGGAGGTGGAGACTTGTACTTATA-AACT--GT
* *
13773 AGGAGGAGGAGGAGGAGACTTGTACTTGTAAACTGT
1 AGGAGGAGGAGGTGGAGACTTGTACTTATAAACTGT
13809 AGGAGGAGGAGGTGGAGACTTGTACTT
1 AGGAGGAGGAGGTGGAGACTTGTACTT
13836 GTACATCTCC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
36 27 0.48
38 2 0.04
39 27 0.48
ACGTcount: A:0.25, C:0.10, G:0.39, T:0.25
Consensus pattern (36 bp):
AGGAGGAGGAGGTGGAGACTTGTACTTATAAACTGT
Found at i:13797 original size:87 final size:85
Alignment explanation
Indices: 13652--13816 Score: 224
Period size: 87 Copynumber: 1.9 Consensus size: 85
13642 CTTGTAAACG
* * *
13652 GGTGGGGTGGAGATTTGTACTTGTATGCCTCCTCCTTGGGGGGAGGAGGAGACTTGTACTTATAA
1 GGTGGGGTGGAGACTTGTACTTATATGCCTCCT-CTAGGGGGGAGGAGGAGACTTGTACTTATAA
13717 ACTGGAGAAGGAGAATGAGGA
65 ACTGGAGAAGGAGAATGAGGA
* *
13738 GGTGGAGGTGGAGACTTGTACTTATATGGCTCCT-TAGGAGGAGGAGGAGGAGACTTGTACTTGT
1 GGTGG-GGTGGAGACTTGTACTTATATGCCTCCTCTAGG-GG-GGAGGAGGAGACTTGTACTTAT
* *
13802 AAACTGTAGGAGGAG
63 AAACTGGAGAAGGAG
13817 GAGGTGGAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
85 3 0.04
86 7 0.10
87 59 0.86
ACGTcount: A:0.25, C:0.11, G:0.39, T:0.25
Consensus pattern (85 bp):
GGTGGGGTGGAGACTTGTACTTATATGCCTCCTCTAGGGGGGAGGAGGAGACTTGTACTTATAAA
CTGGAGAAGGAGAATGAGGA
Found at i:13812 original size:36 final size:36
Alignment explanation
Indices: 13772--13891 Score: 136
Period size: 36 Copynumber: 3.3 Consensus size: 36
13762 TATGGCTCCT
13772 TAGGAGGAGGAGGAGGAGACTTGTACTTGTAAACTG
1 TAGGAGGAGGAGGAGGAGACTTGTACTTGTAAACTG
* * *
13808 TAGGAGGAGGAGGTGGAGACTTGTACTTGTACATCTCC
1 TAGGAGGAGGAGGAGGAGACTTGTACTTGTA-AACT-G
* * *
13846 T-TG-GGAGGGGGAGGAGATTTGTACTTGTAAACTG
1 TAGGAGGAGGAGGAGGAGACTTGTACTTGTAAACTG
* *
13880 GAGGAGGTGGAG
1 TAGGAGGAGGAG
13892 ACTTGTACTT
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
35 4 0.06
36 58 0.87
37 4 0.06
38 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.41, T:0.24
Consensus pattern (36 bp):
TAGGAGGAGGAGGAGGAGACTTGTACTTGTAAACTG
Found at i:13815 original size:30 final size:31
Alignment explanation
Indices: 13779--14156 Score: 164
Period size: 30 Copynumber: 11.8 Consensus size: 31
13769 CCTTAGGAGG
*
13779 AGGAGGAGGAGACTTGTACTTGTAAACTGTAGG
1 AGGAGGAGGAGACTTGTACTTGTAAACTG--GT
* *
13812 AGGAGGAGGTGGAGACTTGTACTTGTACATCTCCTTGGG
1 AGGAGGA---GGAGACTTGTACTTGTA-A---AC-TGGT
* *
13851 AGGGGGAGGAGATTTGTACTTGTAAACTGG-
1 AGGAGGAGGAGACTTGTACTTGTAAACTGGT
* ** **
13881 AGGAGGTGGAGACTTGTACTTGTATGCCTCCTT
1 AGGAGGAGGAGACTTGTACTTGTA-AACT-GGT
* *
13914 AGGGGGAGGAGGAGATTTGTACTTATAAACTGGT
1 A---GGAGGAGGAGACTTGTACTTGTAAACTGGT
* *** *
13948 -GGAGGTGGAGACTTGTA--TGTCTCCTTGGG
1 AGGAGGAGGAGACTTGTACTTGTAAAC-TGGT
* *
13977 AGGGGGAGGAGATTTGTACTTGTAAACTGGT
1 AGGAGGAGGAGACTTGTACTTGTAAACTGGT
* * ** *
14008 -GGAGGTGGAGACTCGTACTTGTATTCCTCCTTGGG
1 AGGAGGAGGAGACTTGTACTTGTA----AAC-TGGT
* * * * *
14043 GGGAGGAGGAGATTTGTACTTATAGACCGGT
1 AGGAGGAGGAGACTTGTACTTGTAAACTGGT
* ** *
14074 -GGAGGTGGAGACTTGTA--TGCT-TCCTTGGG
1 AGGAGGAGGAGACTTGTACTTG-TAAAC-TGGT
*
14103 AGGAGGAGGAGATTTGTACTTGTAAACTGGT
1 AGGAGGAGGAGACTTGTACTTGTAAACTGGT
*
14134 -GGAGGTGGAGACTTGTACTTGTA
1 AGGAGGAGGAGACTTGTACTTGTA
14157 TGCCTCCTTG
Statistics
Matches: 254, Mismatches: 61, Indels: 63
0.67 0.16 0.17
Matches are distributed among these distances:
28 5 0.02
29 6 0.02
30 120 0.47
31 14 0.06
32 9 0.04
33 8 0.03
34 2 0.01
35 6 0.02
36 72 0.28
37 1 0.00
39 8 0.03
40 1 0.00
41 2 0.01
ACGTcount: A:0.22, C:0.11, G:0.37, T:0.29
Consensus pattern (31 bp):
AGGAGGAGGAGACTTGTACTTGTAAACTGGT
Found at i:13889 original size:66 final size:65
Alignment explanation
Indices: 13738--14316 Score: 681
Period size: 66 Copynumber: 8.9 Consensus size: 65
13728 AGAATGAGGA
* * *
13738 GGTGGAGGTGGAGACTTGTACTTATATGGCTCCTTAGGAGGAGGAGGAGGAGACTTGTACTTGTA
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTT--G-GG-GGAGGAGGAGATTTGTACTTGTA
13803 AACTGT
62 AAC--T
* *** *
13809 AGGAGGAGGAGGTGGAGACTTGTACTTGTACATCTCCTTGGGAGGGGGAGGAGATTTGTACTTGT
1 ----GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTGGG-GGAGGAGGAGATTTGTACTTGT
13874 AAACT
61 AAACT
* *
13879 GGAGGAGGTGGAGACTTGTACTTGTATGCCTCCTTAGGGGGAGGAGGAGATTTGTACTTATAAAC
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTT-GGGGGAGGAGGAGATTTGTACTTGTAAAC
13944 T
65 T
*
13945 GGTGGAGGTGGAGACTTGTA--TG--T--CTCCTTGGGAGGGGGAGGAGATTTGTACTTGTAAAC
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTGGG-GGAGGAGGAGATTTGTACTTGTAAAC
14004 T
65 T
* * * *
14005 GGTGGAGGTGGAGACTCGTACTTGTATTCCTCCTTGGGGGGAGGAGGAGATTTGTACTTATAGAC
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTT-GGGGGAGGAGGAGATTTGTACTTGTAAAC
*
14070 C
65 T
*
14071 GGTGGAGGT-G-GA---G-ACTTGTATGCTTCCTTGGGAGGAGGAGGAGATTTGTACTTGTAAAC
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTGGG-GGAGGAGGAGATTTGTACTTGTAAAC
14130 T
65 T
* * *
14131 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTGGGGGGAGGAGGAGATTTGTATTTATAAAT
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTT-GGGGGAGGAGGAGATTTGTACTTGTAAAC
14196 T
65 T
*
14197 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTGGGGGAGGA-G-GA---G-ACTTGTAAACC
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTGGGGGAGGAGGAGATTTGTACTTGTAAACT
* *
14256 GGTGGAGGTGGAGACTTGTACTTATATGCCTCCTTGGGGGAGGAGGAGACTTGTACTTGTA
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTGGGGGAGGAGGAGATTTGTACTTGTA
14317 TGTCTCTTTG
Statistics
Matches: 447, Mismatches: 34, Indels: 56
0.83 0.06 0.10
Matches are distributed among these distances:
59 56 0.13
60 99 0.22
61 4 0.01
62 5 0.01
63 2 0.00
64 7 0.02
65 18 0.04
66 188 0.42
67 9 0.02
70 1 0.00
72 27 0.06
73 1 0.00
75 30 0.07
ACGTcount: A:0.22, C:0.12, G:0.37, T:0.29
Consensus pattern (65 bp):
GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTGGGGGAGGAGGAGATTTGTACTTGTAAACT
Found at i:13922 original size:36 final size:35
Alignment explanation
Indices: 13741--14343 Score: 144
Period size: 30 Copynumber: 18.4 Consensus size: 35
13731 ATGAGGAGGT
* * *
13741 GGAGGTGGAGACTTGTACTTATATGGCTCCTTAGGAGGA
1 GGAGGAGGAGACTTGTACTTGTA--ACTCCTTA-G-GGA
*
13780 GGAGGAGGAGACTTGTACTTGTAAACT--GTAGGAGGA
1 GGAGGAGGAGACTTGTACTTGT-AACTCCTTA-G-GGA
*
13816 GGAGGTGGAGACTTGTACTTGTACATCTCCTT-GGGA
1 GGAGGAGGAGACTTGTACTTGTA-A-CTCCTTAGGGA
* * *
13852 GGGGGAGGAGATTTGTACTTGTAA--AC-T--GGA
1 GGAGGAGGAGACTTGTACTTGTAACTCCTTAGGGA
* *
13882 GGAGGTGGAGACTTGTACTTGTATGCCTCCTTAGGG-
1 GGAGGAGGAGACTTGTACTTGTA--ACTCCTTAGGGA
* * * *
13918 GGAGGAGGAGATTTGTACTTATAA--AC-T--GGT
1 GGAGGAGGAGACTTGTACTTGTAACTCCTTAGGGA
*
13948 GGAGGTGGAGACTTGTA--TGT--CTCCTT-GGGA
1 GGAGGAGGAGACTTGTACTTGTAACTCCTTAGGGA
* * * *
13978 GGGGGAGGAGATTTGTACTTGTAA--AC-T--GGT
1 GGAGGAGGAGACTTGTACTTGTAACTCCTTAGGGA
* * * *
14008 GGAGGTGGAGACTCGTACTTGTATTCCTCCTT-GGGG
1 GGAGGAGGAGACTTGTACTTGTA--ACTCCTTAGGGA
* * *
14044 GGAGGAGGAGATTTGTACTTATAGA--CC----GGT
1 GGAGGAGGAGACTTGTACTTGTA-ACTCCTTAGGGA
*
14074 GGAGGTGGAGACTTGTA--TG---CTTCCTT-GGGA
1 GGAGGAGGAGACTTGTACTTGTAAC-TCCTTAGGGA
* * *
14104 GGAGGAGGAGATTTGTACTTGTAA--AC-T--GGT
1 GGAGGAGGAGACTTGTACTTGTAACTCCTTAGGGA
* * *
14134 GGAGGTGGAGACTTGTACTTGTATGCCTCCTT-GGGG
1 GGAGGAGGAGACTTGTACTTGTA--ACTCCTTAGGGA
* * * * *
14170 GGAGGAGGAGATTTGTATTTATAA---ATT--GGT
1 GGAGGAGGAGACTTGTACTTGTAACTCCTTAGGGA
* *
14200 GGAGGTGGAGACTTGTACTTGTATGCCTCCTT-GGG-
1 GGAGGAGGAGACTTGTACTTGTA--ACTCCTTAGGGA
*
14235 GGAGGAGGAGACTTGTA-----AA--CC----GGT
1 GGAGGAGGAGACTTGTACTTGTAACTCCTTAGGGA
* * *
14259 GGAGGTGGAGACTTGTACTTATATGCCTCCTT-GGG-
1 GGAGGAGGAGACTTGTACTTGTA--ACTCCTTAGGGA
** *
14294 GGAGGAGGAGACTTGTACTTGTATGTCTCTTTGGGA
1 GGAGGAGGAGACTTGTACTTGTAACTC-CTTAGGGA
14330 GGAGGAGGAGACTT
1 GGAGGAGGAGACTT
14344 ATAAACAGGG
Statistics
Matches: 420, Mismatches: 78, Indels: 135
0.66 0.12 0.21
Matches are distributed among these distances:
23 2 0.00
24 16 0.04
26 2 0.00
27 2 0.00
28 4 0.01
29 4 0.01
30 154 0.37
31 6 0.01
32 9 0.02
33 6 0.01
34 6 0.01
35 47 0.11
36 133 0.32
37 5 0.01
38 2 0.00
39 21 0.05
40 1 0.00
ACGTcount: A:0.22, C:0.12, G:0.37, T:0.29
Consensus pattern (35 bp):
GGAGGAGGAGACTTGTACTTGTAACTCCTTAGGGA
Found at i:13991 original size:126 final size:128
Alignment explanation
Indices: 13738--14313 Score: 735
Period size: 126 Copynumber: 4.5 Consensus size: 128
13728 AGAATGAGGA
* * * *
13738 GGTGGAGGTGGAGACTTGTACTTATATGGCTCCTTAGGAGGAGGAGGAGGAGACTTGTACTTGTA
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTA-G-GG-GGAGGAGGAGATTTGTACTTATA
* *
13803 AACTGTAGGAGGAGGAGGTGGAGACTTGTACTTGTACATCTCCTTGGGAGGGGGAGGAGATTTGT
63 AAC--T----GGTGGAGGTGGAGACTTGTAC-TG---ATCTCCTTGGGAGGAGGAGGAGATTTGT
13868 ACTTGTAAACT
118 ACTTGTAAACT
*
13879 GGAGGAGGTGGAGACTTGTACTTGTATGCCTCCTTAGGGGGAGGAGGAGATTTGTACTTATAAAC
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTAGGGGGAGGAGGAGATTTGTACTTATAAAC
*
13944 TGGTGGAGGTGGAGACTTGTA-TG-TCTCCTTGGGAGGGGGAGGAGATTTGTACTTGTAAACT
66 TGGTGGAGGTGGAGACTTGTACTGATCTCCTTGGGAGGAGGAGGAGATTTGTACTTGTAAACT
* * * *
14005 GGTGGAGGTGGAGACTCGTACTTGTATTCCTCCTTGGGGGGAGGAGGAGATTTGTACTTATAGAC
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTAGGGGGAGGAGGAGATTTGTACTTATAAAC
* *
14070 CGGTGGAGGTGGAGACTTGTA-TGCT-TCCTTGGGAGGAGGAGGAGATTTGTACTTGTAAACT
66 TGGTGGAGGTGGAGACTTGTACTGATCTCCTTGGGAGGAGGAGGAGATTTGTACTTGTAAACT
* * *
14131 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTGGGGGGAGGAGGAGATTTGTATTTATAAAT
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTAGGGGGAGGAGGAGATTTGTACTTATAAAC
14196 TGGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTGGG-GGAGGA-G-GA---G-ACTTGTAAA
66 TGGTGGAGGTGGAGACTTGTAC-TG-AT--CTCCTTGGGAGGAGGAGGAGATTTGTACTTGTAAA
*
14254 CC
127 CT
* *
14256 GGTGGAGGTGGAGACTTGTACTTATATGCCTCCTT-GGGGGAGGAGGAGACTTGTACTT
1 GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTAGGGGGAGGAGGAGATTTGTACTT
14314 GTATGTCTCT
Statistics
Matches: 404, Mismatches: 24, Indels: 31
0.88 0.05 0.07
Matches are distributed among these distances:
124 21 0.05
125 44 0.11
126 236 0.58
127 1 0.00
128 2 0.00
129 3 0.01
130 3 0.01
131 6 0.01
132 27 0.07
136 1 0.00
138 24 0.06
139 2 0.00
140 1 0.00
141 33 0.08
ACGTcount: A:0.22, C:0.12, G:0.37, T:0.29
Consensus pattern (128 bp):
GGTGGAGGTGGAGACTTGTACTTGTATGCCTCCTTAGGGGGAGGAGGAGATTTGTACTTATAAAC
TGGTGGAGGTGGAGACTTGTACTGATCTCCTTGGGAGGAGGAGGAGATTTGTACTTGTAAACT
Found at i:15244 original size:13 final size:14
Alignment explanation
Indices: 15229--15270 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
15219 ATTGGTTATT
15229 AAAATAAATAAATA
1 AAAATAAATAAATA
** *
15243 AAAATTGAT-AATC
1 AAAATAAATAAATA
15256 AAAATAAATAAATA
1 AAAATAAATAAATA
15270 A
1 A
15271 TATAAATGAG
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (14 bp):
AAAATAAATAAATA
Found at i:15259 original size:27 final size:28
Alignment explanation
Indices: 15206--15272 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
15196 CTTTCTCAAA
* * * *
15206 AAATAAAAAATAAATTGGTTATTAAAAT
1 AAATAAATAATAAATTGATAATCAAAAT
15234 AAATAAATAA-AAATTGATAATCAAAAT
1 AAATAAATAATAAATTGATAATCAAAAT
15261 AAATAAATAATA
1 AAATAAATAATA
15273 TAAATGAGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 24 0.71
28 10 0.29
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (28 bp):
AAATAAATAATAAATTGATAATCAAAAT
Found at i:15976 original size:27 final size:27
Alignment explanation
Indices: 15913--15976 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
15903 TTCAGCTAAT
*
15913 TCGACCTGAAAAATATAAATTCTTCAC
1 TCGACTTGAAAAATATAAATTCTTCAC
*
15940 CCGA-TCTGAAAAATATAAATTCTTCAC
1 TCGACT-TGAAAAATATAAATTCTTCAC
15967 TCGACTTGAA
1 TCGACTTGAA
15977 TCAACCCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
TCGACTTGAAAAATATAAATTCTTCAC
Found at i:18095 original size:23 final size:23
Alignment explanation
Indices: 18069--18126 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
18059 TGTGACATGT
*
18069 TCTCTGCTTTTATGATACATTTA
1 TCTCTGCTTTTATGACACATTTA
* * * *
18092 TCTCTACCTTTATGACACGTTTT
1 TCTCTGCTTTTATGACACATTTA
18115 TCTCTGCCTTTT
1 TCTCTG-CTTTT
18127 GGTAGCTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.16, C:0.24, G:0.09, T:0.52
Consensus pattern (23 bp):
TCTCTGCTTTTATGACACATTTA
Found at i:21145 original size:27 final size:27
Alignment explanation
Indices: 21110--21181 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
21100 TGTAAATAAC
21110 AAAGCATGTTTGGGTAGAACTATTATA
1 AAAGCATGTTTGGGTAGAACTATTATA
21137 AAAGCATGTTTGGGTAGAACTATTATA
1 AAAGCATGTTTGGGTAGAACTATTATA
**
21164 AAAGCATGTCAGGGTAGA
1 AAAGCATGTTTGGGTAGA
21182 TACCATGTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (27 bp):
AAAGCATGTTTGGGTAGAACTATTATA
Found at i:26965 original size:20 final size:20
Alignment explanation
Indices: 26940--26996 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
26930 TCAAGACTGG
* *
26940 CTGGTCTCTATACCGAAGGA
1 CTGGTCTCCATACCGAAGAA
*
26960 CTGGTCTCCATACTGAAGAA
1 CTGGTCTCCATACCGAAGAA
*
26980 CTGGTCCCCATACCGAA
1 CTGGTCTCCATACCGAA
26997 AGATTGGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (20 bp):
CTGGTCTCCATACCGAAGAA
Found at i:27004 original size:20 final size:20
Alignment explanation
Indices: 26949--27004 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
26939 GCTGGTCTCT
* *
26949 ATACCGAAGGACTGGTCTCC
1 ATACCGAAAGACTGGTCCCC
*
26969 ATACTG-AAGAACTGGTCCCC
1 ATACCGAAAG-ACTGGTCCCC
*
26989 ATACCGAAAGATTGGT
1 ATACCGAAAGACTGGT
27005 ATCCAAACCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (20 bp):
ATACCGAAAGACTGGTCCCC
Found at i:29957 original size:23 final size:23
Alignment explanation
Indices: 29898--29961 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
29888 CTGAATGATT
29898 CAGTGCTGATTGATTCAGTAAAA
1 CAGTGCTGATTGATTCAGTAAAA
**
29921 CAGTATTGATTGATTCAGTAAAA
1 CAGTGCTGATTGATTCAGTAAAA
* *
29944 CAGTGCTAAATGATTCAG
1 CAGTGCTGATTGATTCAG
29962 CACAGAAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (23 bp):
CAGTGCTGATTGATTCAGTAAAA
Found at i:30952 original size:19 final size:19
Alignment explanation
Indices: 30928--30964 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
30918 ATGACCAACA
30928 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
30947 AAATCGCAACGCGGTCTC
1 AAATCGCAACGCGATCTC
30965 CAGTACCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:33145 original size:14 final size:14
Alignment explanation
Indices: 33126--33162 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
33116 TCCAGTGGCA
33126 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
33140 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
33154 TTCTTCTTC
1 TT-TTCTTC
33163 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:33391 original size:24 final size:24
Alignment explanation
Indices: 33364--33410 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
33354 CAAAATCCGA
33364 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
33388 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
33411 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:33419 original size:24 final size:24
Alignment explanation
Indices: 33368--33419 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
33358 ATCCGAGTAT
** *
33368 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
33392 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
33416 TGAC
1 TGAC
33420 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:34251 original size:20 final size:20
Alignment explanation
Indices: 34226--34294 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
34216 GAAATTCAGT
* *
34226 GTTGCGACAGTCAGAATCGA
1 GTTGCGATAGTCAGAATCGC
**
34246 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
34267 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
34287 GTTGCGAT
1 GTTGCGAT
34295 TTACATATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 23 0.57
21 13 0.32
22 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:34334 original size:21 final size:21
Alignment explanation
Indices: 34310--34356 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
34300 TATTCGCATT
*
34310 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCGAAAATCGCAAC
* * *
34331 GCGAATTTGGAAAATCGCAAT
1 GCGATTTTCGAAAATCGCAAC
34352 GCGAT
1 GCGAT
34357 AGTCAAAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GCGATTTTCGAAAATCGCAAC
Found at i:34376 original size:41 final size:41
Alignment explanation
Indices: 34269--34384 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 41
34259 ATTATCGCGT
* ** * * *
34269 TGCGATAGTCAGAATCGCGTTGCG-ATTTACATATTCGCAT
1 TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAATCGCAA
** ***
34309 TGCGATTTTCTAAAATCGCAACGCGAATTTGGAAAATCGCAA
1 TGCGATAGTC-AAAATCGCGTTGCGAATTTGGAAAATCGCAA
*
34351 TGCGATAGTCAAAATCGCGTTGCGAATCTGGAAA
1 TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAA
34385 CTGGTTTGCG
Statistics
Matches: 57, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
40 8 0.14
41 30 0.53
42 19 0.33
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (41 bp):
TGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAATCGCAA
Found at i:35474 original size:23 final size:22
Alignment explanation
Indices: 35442--35485 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
35432 GACTCAACTA
35442 TAATTATAAATTAGTTGAAAATT
1 TAATTATAAATTA-TTGAAAATT
* *
35465 TAATTGTAAATTATTTAAAAT
1 TAATTATAAATTATTGAAAAT
35486 AAAAGGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (22 bp):
TAATTATAAATTATTGAAAATT
Found at i:44942 original size:13 final size:14
Alignment explanation
Indices: 44913--44946 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
44903 TGTTATTTTC
*
44913 TTTAAATTATATGT
1 TTTAATTTATATGT
44927 TTTAATTTATAT-T
1 TTTAATTTATATGT
44940 TTTAATT
1 TTTAATT
44947 CATCACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TTTAATTTATATGT
Found at i:47793 original size:3 final size:3
Alignment explanation
Indices: 47785--47817 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
47775 TGTATTGCAA
*
47785 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
47818 GCAAAAGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:48104 original size:2 final size:2
Alignment explanation
Indices: 48099--48141 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
48089 TATCAAAAAT
48099 TA TA TA 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
48141 T
1 T
48142 GTGTGTGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51231 original size:21 final size:20
Alignment explanation
Indices: 51188--51304 Score: 153
Period size: 20 Copynumber: 5.8 Consensus size: 20
51178 AGATTGCTCA
*
51188 GGGGTACAGATTCCCCCCAG
1 GGGGAACAGATTCCCCCCAG
51208 GGGGAACAGATTCCCCCCAG
1 GGGGAACAGATTCCCCCCAG
* *
51228 GGGGAACAGATTCCGCCCAA
1 GGGGAACAGATTCCCCCCAG
* *
51248 GGGGTACTGATTCCCTCCCAG
1 GGGGAACAGATTCCC-CCCAG
51269 GGGGAACAGATTCCCCCCCAG
1 GGGGAACAGATT-CCCCCCAG
* *
51290 GGGGTACCGATTCCC
1 GGGGAACAGATTCCC
51305 TCTGTCTAAC
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
20 52 0.62
21 29 0.35
22 3 0.04
ACGTcount: A:0.21, C:0.34, G:0.30, T:0.15
Consensus pattern (20 bp):
GGGGAACAGATTCCCCCCAG
Found at i:54712 original size:21 final size:21
Alignment explanation
Indices: 54688--54760 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
54678 CTCAGGAGGT
*
54688 ACAGATTCCCCCCCAGGGGGA
1 ACAGATTCCCCCCAAGGGGGA
54709 ACAGATTCCCCCCAAGGGGGA
1 ACAGATTCCCCCCAAGGGGGA
* *
54730 ACAGATTCCCCCCTAGGGGGT
1 ACAGATTCCCCCCAAGGGGGA
*
54751 ACCGATTCCC
1 ACAGATTCCC
54761 TCTGTCTTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.23, C:0.37, G:0.26, T:0.14
Consensus pattern (21 bp):
ACAGATTCCCCCCAAGGGGGA
Found at i:58883 original size:16 final size:18
Alignment explanation
Indices: 58862--58908 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
58852 AAACAAGTTT
*
58862 CAGATTTTAATT-CTT-A
1 CAGATTCTAATTCCTTCA
58878 CAGATTCTAATTCCTTCA
1 CAGATTCTAATTCCTTCA
*
58896 CAGATTCCAATTC
1 CAGATTCTAATTC
58909 ACACATAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 13 0.48
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (18 bp):
CAGATTCTAATTCCTTCA
Found at i:81157 original size:83 final size:82
Alignment explanation
Indices: 80995--81243 Score: 324
Period size: 83 Copynumber: 3.0 Consensus size: 82
80985 TACCATGCGG
* * * *
80995 TTGATATGCCTATGAGCTGAATGAAATCGAACTCGAAGGTCTTTGATGACAGATAGCCCTTATCG
1 TTGATATGCCT-TGAGCTGAATGTAATCGAACTCGAAGG-GTTTGTTGACAGATAACCCTTATCG
*
81060 CCTTGAGCTATGCTGTAAA
64 CCTTGAGTTATGCTGTAAA
*
81079 TTTGATATGCCATTGAGCTGAATGTAATCGAACTC-AAGGGTTTGTTGACAGATAACCCTTCTCG
1 -TTGATATGCC-TTGAGCTGAATGTAATCGAACTCGAAGGGTTTGTTGACAGATAACCCTTATCG
*
81143 CCTTGAGTTATGCTGCAAA
64 CCTTGAGTTATGCTGTAAA
* * *
81162 -TGATGTGCCTTTGAGCTGAATGTAATCGAACTCGAA-GGTCTTGGTTGACATACAACCCTTATC
1 TTGATATGCC-TTGAGCTGAATGTAATCGAACTCGAAGGGT-TT-GTTGACAGATAACCCTTATC
81225 GCCTTGAGTTATGCTGTAA
63 GCCTTGAGTTATGCTGTAA
81244 CTGGGCTGGG
Statistics
Matches: 147, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
81 34 0.23
82 4 0.03
83 73 0.50
84 4 0.03
85 31 0.21
86 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (82 bp):
TTGATATGCCTTGAGCTGAATGTAATCGAACTCGAAGGGTTTGTTGACAGATAACCCTTATCGCC
TTGAGTTATGCTGTAAA
Found at i:81680 original size:170 final size:170
Alignment explanation
Indices: 81477--81819 Score: 535
Period size: 170 Copynumber: 2.0 Consensus size: 170
81467 TCAAAAGATG
* *
81477 AATGTTGCTGGTGGACACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGTTTTGAGTCAAAT
1 AATGTTGCTGGTGGACACGATATCCTTCGTCGTGAAGTTAAAATCATGGATGTTTCGAGTCAAAT
*
81542 ATCCTTCGTCGTGAAGTTGAAATTGACTCTGAATGAATCTGGGAAGCCCCTTCACTGT-GATGTT
66 ATCCTTCGTCGTGAAGTTGAAATTGACTCTGAATGAAACTGGGAAGCCCCTTCACTGTGGA-GTT
* * *
81606 GAGCTTTGAATTGGATATCCTTCGCTGTGAAGTTGAAATCC
130 GAGCTTTGAATTGGATATCATTCGCTATAAAGTTGAAATCC
* * * * *
81647 AATGTTGTTTGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGTTTCGAGTCCAAT
1 AATGTTGCTGGTGGACACGATATCCTTCGTCGTGAAGTTAAAATCATGGATGTTTCGAGTCAAAT
* * *
81712 ATCCTTCGTCGTGAAGTTGAAATTGGCTTTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTG
66 ATCCTTCGTCGTGAAGTTGAAATTGACTCTGAATGAAACTGGGAAGCCCCTTCACTGTGGAGTTG
*
81777 AGCTTTGAATTGGATATCATTCGTTATAAAGTTGAAATCC
131 AGCTTTGAATTGGATATCATTCGCTATAAAGTTGAAATCC
81817 AAT
1 AAT
81820 CTTCAGTATA
Statistics
Matches: 157, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
170 155 0.99
171 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (170 bp):
AATGTTGCTGGTGGACACGATATCCTTCGTCGTGAAGTTAAAATCATGGATGTTTCGAGTCAAAT
ATCCTTCGTCGTGAAGTTGAAATTGACTCTGAATGAAACTGGGAAGCCCCTTCACTGTGGAGTTG
AGCTTTGAATTGGATATCATTCGCTATAAAGTTGAAATCC
Found at i:81927 original size:14 final size:14
Alignment explanation
Indices: 81908--81945 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
81898 TTATACATAT
81908 ATGCGATGCTATGG
1 ATGCGATGCTATGG
81922 ATGCGATGCTATGG
1 ATGCGATGCTATGG
*
81936 ATGCAATGCT
1 ATGCGATGCT
81946 CTTAGGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.29
Consensus pattern (14 bp):
ATGCGATGCTATGG
Found at i:89461 original size:39 final size:39
Alignment explanation
Indices: 89414--89488 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
89404 TAGATGCAGA
* *
89414 TTTCCCTTTGGTAGATGATGAGTCACCGGGTAATGCAAC
1 TTTCCCTTTAGTAGAGGATGAGTCACCGGGTAATGCAAC
* *
89453 TTTCCCTTTAGTAGCGGATGAGTCCCCGGGTAATGC
1 TTTCCCTTTAGTAGAGGATGAGTCACCGGGTAATGC
89489 TCCGGGTGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.31
Consensus pattern (39 bp):
TTTCCCTTTAGTAGAGGATGAGTCACCGGGTAATGCAAC
Found at i:99952 original size:23 final size:23
Alignment explanation
Indices: 99922--99982 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
99912 CTCGTATAAA
*
99922 TGCACCGAAGTGCCACTTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
99945 TGCACCGAAGTGTCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
99968 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
99983 TATAAGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:101741 original size:64 final size:65
Alignment explanation
Indices: 101573--101742 Score: 170
Period size: 65 Copynumber: 2.6 Consensus size: 65
101563 GACAATTATT
* * *
101573 CTTTTGAATATGTCAAATTAAAAGGTATTCATTATTTATTTAACTTTGAATATTAAGAGATAATT
1 CTTTTGAATATTTCAAATTAAAA--TA-T-ATTATTTATTTAACTTTGAATATAAAAAGAT-ATT
*
101638 GTATA
61 ATATA
* * *
101643 CTTTTGAATATTTCAAA-AATAAAT-TAATATTTATTTAAGTTTGAATAGTAAAAAGAGT-TTAT
1 CTTTTGAATATTTCAAATTA-AAATATATTATTTATTTAACTTTGAATA-TAAAAAGA-TATTAT
101705 ATA
63 ATA
101708 -TTTTGAATATTTCAAATTAAAATATATTA-TTATTT
1 CTTTTGAATATTTCAAATTAAAATATATTATTTATTT
101743 GTTTACATTT
Statistics
Matches: 86, Mismatches: 9, Indels: 16
0.77 0.08 0.14
Matches are distributed among these distances:
64 26 0.30
65 31 0.36
66 7 0.08
67 1 0.01
68 1 0.01
69 1 0.01
70 19 0.22
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (65 bp):
CTTTTGAATATTTCAAATTAAAATATATTATTTATTTAACTTTGAATATAAAAAGATATTATATA
Found at i:104624 original size:2 final size:2
Alignment explanation
Indices: 104617--104647 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
104607 ACTAAAAACA
*
104617 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
104648 ATTAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:104913 original size:60 final size:59
Alignment explanation
Indices: 104815--105003 Score: 159
Period size: 60 Copynumber: 3.1 Consensus size: 59
104805 GCATCATATG
* * * * *
104815 TCCCTAAAATATAACTCTCATTTTAAATTGGTCCTTAAACTTTGGAATATTCTAATTACA
1 TCCCCAAAATATGACCCTCATTCTAAATTAGTCCTTAAACTTTGGAATATTCTAATT-CA
*
104875 TCCCCAAAATATGACCCTCATTCTAAATTAATCCTTAAACTTTTGGACATA--CTAATTTCA
1 TCCCCAAAATATGACCCTCATTCTAAATTAGTCCTTAAAC-TTTGGA-ATATTCTAA-TTCA
* * * * * ** *
104935 TACCTAAACTATGACCAT-ATTTCTAAATTTGTCCCCCAAACTTTTGAATATTCCTAATTCA
1 TCCCCAAAATATGACCCTCA-TTCTAAATTAGT-CCTTAAACTTTGGAATATT-CTAATTCA
*
104996 TCCTCAAA
1 TCCCCAAA
105004 TTCATCCAAA
Statistics
Matches: 103, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
59 4 0.04
60 69 0.67
61 23 0.22
62 7 0.07
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.37
Consensus pattern (59 bp):
TCCCCAAAATATGACCCTCATTCTAAATTAGTCCTTAAACTTTGGAATATTCTAATTCA
Found at i:105254 original size:52 final size:52
Alignment explanation
Indices: 105155--105254 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
105145 GGAATGTTAA
* *
105155 AAAAGTTTGGGACCAATTTAGAAATGAATGTCATAGTTTGGCGATGAATTTC
1 AAAAGTTTGGGACCAATTTAGAAATGAATATCATAGTTTGGCAATGAATTTC
* * *
105207 AAAAGTTTGGGGACTAATTTAG-AATTATTATCATAGTTTTGG-AATGAA
1 AAAAGTTT-GGGACCAATTTAGAAATGAATATCATAG-TTTGGCAATGAA
105255 ATTGAACCAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
52 24 0.59
53 17 0.41
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (52 bp):
AAAAGTTTGGGACCAATTTAGAAATGAATATCATAGTTTGGCAATGAATTTC
Found at i:106200 original size:31 final size:31
Alignment explanation
Indices: 106165--106245 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
106155 AACGACATCC
106165 GTCCGTTCGATTTAAGTCTCC-AACATTATCG
1 GTCCGTTCGATTTAAGTC-CCTAACATTATCG
* * *
106196 GTCCGTCCGATTTCAGTCCCTAACATTATTG
1 GTCCGTTCGATTTAAGTCCCTAACATTATCG
106227 GT-CGTTCGATTTAA-TCCCT
1 GTCCGTTCGATTTAAGTCCCT
106246 CATCCATGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
29 5 0.11
30 12 0.27
31 27 0.61
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (31 bp):
GTCCGTTCGATTTAAGTCCCTAACATTATCG
Found at i:107267 original size:23 final size:23
Alignment explanation
Indices: 107241--107287 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
107231 AATATTTAAG
*
107241 AAATAGGTTAAATTAATAAAAAA
1 AAATAAGTTAAATTAATAAAAAA
*
107264 AAATAAGTTAATTTAATAAAAAA
1 AAATAAGTTAAATTAATAAAAAA
107287 A
1 A
107288 TTACTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (23 bp):
AAATAAGTTAAATTAATAAAAAA
Found at i:107663 original size:22 final size:21
Alignment explanation
Indices: 107629--107671 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
107619 TAAAAAAATT
107629 ATTTTTAGATATAATTTTAAC
1 ATTTTTAGATATAATTTTAAC
* *
107650 ATTTCTTATATATATTTTTAAC
1 ATTT-TTAGATATAATTTTAAC
107672 TTATGACGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTTAGATATAATTTTAAC
Found at i:108578 original size:4 final size:4
Alignment explanation
Indices: 108569--108600 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
108559 TATCCCATAT
*
108569 TTTA TTTA TTTA TTGA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
108601 AGTAGATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:115288 original size:39 final size:36
Alignment explanation
Indices: 115232--115305 Score: 87
Period size: 39 Copynumber: 2.0 Consensus size: 36
115222 TTATATATTT
*
115232 AATATTAATATATTATTTTAGTG-TCATTTTAATAAA
1 AATATTAATATATTA-TTTAGTGATAATTTTAATAAA
*
115268 AATATTAATTATTATATATTTATTGATAATTTTAATAA
1 AATATTAA-TA-TAT-TATTTAGTGATAATTTTAATAA
115306 TATGATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 8 0.25
37 2 0.06
38 9 0.28
39 13 0.41
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (36 bp):
AATATTAATATATTATTTAGTGATAATTTTAATAAA
Found at i:115365 original size:30 final size:30
Alignment explanation
Indices: 115331--115388 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
115321 TATTCTATTA
115331 TTATAATTATATTATC-ATAAAATATAATTT
1 TTATAATTATATT-TCAATAAAATATAATTT
* *
115361 TTATAATTTTATTTCAATAATATATAAT
1 TTATAATTATATTTCAATAAAATATAAT
115389 AAATTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (30 bp):
TTATAATTATATTTCAATAAAATATAATTT
Found at i:115696 original size:20 final size:19
Alignment explanation
Indices: 115671--115711 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
115661 TTGACATAAA
115671 ATAATATTAAATAAATAATT
1 ATAATATTAAA-AAATAATT
* *
115691 ATAATATTTAAAAATTATT
1 ATAATATTAAAAAATAATT
115710 AT
1 AT
115712 TATTATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATATTAAAAAATAATT
Found at i:115753 original size:29 final size:29
Alignment explanation
Indices: 115695--115753 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
115685 ATAATTATAA
* *
115695 TATTTAAAAATTATTATTATTATTATTAT
1 TATTTAAAAATTAATATTATTATTAGTAT
115724 TATTTAATAAA-TAATATTATTTATT-GTAT
1 TATTTAA-AAATTAATATTA-TTATTAGTAT
115753 T
1 T
115754 TAACGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
TATTTAAAAATTAATATTATTATTAGTAT
Found at i:124516 original size:27 final size:27
Alignment explanation
Indices: 124478--124531 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
124468 CCGAAGGTGC
*
124478 AACTTTGATGATCAAGATCTTTCCTTT
1 AACTTTAATGATCAAGATCTTTCCTTT
*
124505 AACTTTAATGATTAAGATCTTTCCTTT
1 AACTTTAATGATCAAGATCTTTCCTTT
124532 TACGTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (27 bp):
AACTTTAATGATCAAGATCTTTCCTTT
Found at i:126783 original size:29 final size:28
Alignment explanation
Indices: 126751--126809 Score: 100
Period size: 29 Copynumber: 2.1 Consensus size: 28
126741 TAATTCTAAT
126751 AACTTAAATATAACTCAAATTTAAAAAAA
1 AACTTAAATATAACTCAAA-TTAAAAAAA
*
126780 AACTTAAATTTAACTCAAATTAAAAAAA
1 AACTTAAATATAACTCAAATTAAAAAAA
126808 AA
1 AA
126810 TGTTTGTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (28 bp):
AACTTAAATATAACTCAAATTAAAAAAA
Done.