Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003593.1 Hibiscus syriacus cultivar Beakdansim tig00007584_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: 119510
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:974 original size:30 final size:30
Alignment explanation
Indices: 918--974 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
908 GAGGATACGA
* * *
918 GGGGTCTGATGTAAATCCCGATGGATGCTG
1 GGGGTCGGATGTAAATCCCAAAGGATGCTG
948 GGGGTCGGATGTAAA-CCCAACAGGATG
1 GGGGTCGGATGTAAATCCCAA-AGGATG
975 TGACGATCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.25, C:0.18, G:0.37, T:0.21
Consensus pattern (30 bp):
GGGGTCGGATGTAAATCCCAAAGGATGCTG
Found at i:3204 original size:146 final size:146
Alignment explanation
Indices: 2940--3206 Score: 320
Period size: 146 Copynumber: 1.8 Consensus size: 146
2930 TAATTATTAT
* * ** *
2940 GATTTATTTTCTCTAATCTGTCGTCGTCCACTGTCTGATCGTCCTGATTTTTCAATATGTTGTTC
1 GATTTATTTTCTCTAATCTGCCATCGTCCACCATCCGATCGTCCTGATTTTTCAATATGTTGTTC
* * * ** * *
3005 GTATTGACGTCGCGCAACTTTTCACAGTTCGGAATGTTGATTAGAGATCCCGATCACCGGCAAGA
66 CTATTGACCTCACGCAACTTTTCACAGTTCAAAATGTTGATCAGACATCCCGATCACCGGCAAGA
3070 GGCCAAAAACCGTCCG
131 GGCCAAAAACCGTCCG
* * * *
3086 GATTTGTTTTCTTTGATCTGCCATCGTCCACCATCCGATCGTCCTGATTTTTCATTATGTTGTTC
1 GATTTATTTTCTCTAATCTGCCATCGTCCACCATCCGATCGTCCTGATTTTTCAATATGTTGTTC
* * * * * *
3151 CTGTTGGCCTTACGCAACTTTTGACCA-TTCAAAATGTTGATCGGACTTCCCGATCA
66 CTATTGACCTCACGCAACTTTTCA-CAGTTCAAAATGTTGATCAGACATCCCGATCA
3207 ATGACGAGAA
Statistics
Matches: 98, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
146 96 0.98
147 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (146 bp):
GATTTATTTTCTCTAATCTGCCATCGTCCACCATCCGATCGTCCTGATTTTTCAATATGTTGTTC
CTATTGACCTCACGCAACTTTTCACAGTTCAAAATGTTGATCAGACATCCCGATCACCGGCAAGA
GGCCAAAAACCGTCCG
Found at i:3499 original size:3 final size:3
Alignment explanation
Indices: 3491--3518 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3481 AGTGCTCGGG
3491 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3519 TTTTTGACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:7004 original size:25 final size:25
Alignment explanation
Indices: 6957--7024 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
6947 TAAGGGGCAC
6957 CATTTTTCAAAA--C-TTCATCAAA
1 CATTTTTCAAAATTCTTTCATCAAA
6979 CATTTTTCAAAATTCTTTCATCAAA
1 CATTTTTCAAAATTCTTTCATCAAA
7004 CATTTTTCAAAATTCTTTCAT
1 CATTTTTCAAAATTCTTTCAT
7025 TATTAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
22 12 0.28
24 1 0.02
25 30 0.70
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (25 bp):
CATTTTTCAAAATTCTTTCATCAAA
Found at i:7297 original size:19 final size:19
Alignment explanation
Indices: 7273--7309 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
7263 TGAATCATTT
7273 CAAGAAGATTCGACCTCCG
1 CAAGAAGATTCGACCTCCG
7292 CAAGAAGATTCGACCTCC
1 CAAGAAGATTCGACCTCC
7310 TGAAAAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.16
Consensus pattern (19 bp):
CAAGAAGATTCGACCTCCG
Found at i:7318 original size:22 final size:19
Alignment explanation
Indices: 7274--7318 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
7264 GAATCATTTC
*
7274 AAGAAGATTCGACCTCCGC
1 AAGAAGATTCGACCTCCGA
7293 AAGAAGATTCGACCTCCTGA
1 AAGAAGATTCGACCTCC-GA
7313 AA-AAGA
1 AAGAAGA
7319 CTTGTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (19 bp):
AAGAAGATTCGACCTCCGA
Found at i:10273 original size:2 final size:2
Alignment explanation
Indices: 10266--10299 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
10256 TAATTTTTCA
*
10266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10300 TAATACAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10691 original size:36 final size:35
Alignment explanation
Indices: 10644--10744 Score: 127
Period size: 34 Copynumber: 2.9 Consensus size: 35
10634 CATTTCAACA
*
10644 TTATCAAATATTTACAATTATCAGATGATTTTTTAG
1 TTATCAAATATTTACAGTTATCAGATGATTTTTT-G
* *
10680 TTATCATATATTTATAGTTATCAGATGA-TTTTTG
1 TTATCAAATATTTACAGTTATCAGATGATTTTTTG
*
10714 TTATCAGATGA-TTACAGTTATCAGATG-TTTT
1 TTATCAAAT-ATTTACAGTTATCAGATGATTTT
10745 ACAGTTATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
34 27 0.47
35 6 0.10
36 25 0.43
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.49
Consensus pattern (35 bp):
TTATCAAATATTTACAGTTATCAGATGATTTTTTG
Found at i:10699 original size:17 final size:17
Alignment explanation
Indices: 10644--10702 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
10634 CATTTCAACA
* *
10644 TTATCAAATATTTACAA
1 TTATCAAATATTTATAG
* *
10661 TTATCAGATGATTTTTTAG
1 TTATCAAAT-A-TTTATAG
*
10680 TTATCATATATTTATAG
1 TTATCAAATATTTATAG
10697 TTATCA
1 TTATCA
10703 GATGATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 20 0.59
18 2 0.06
19 12 0.35
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (17 bp):
TTATCAAATATTTATAG
Found at i:10716 original size:17 final size:17
Alignment explanation
Indices: 10661--10745 Score: 93
Period size: 17 Copynumber: 4.9 Consensus size: 17
10651 ATATTTACAA
10661 TTATCAGATGATTTTTTAG
1 TTATCAGATGA--TTTTAG
*
10680 TTATCATAT-ATTTATAG
1 TTATCAGATGATTT-TAG
*
10697 TTATCAGATGATTTTTG
1 TTATCAGATGATTTTAG
**
10714 TTATCAGATGATTACAG
1 TTATCAGATGATTTTAG
10731 TTATCAGATG-TTTTA
1 TTATCAGATGATTTTA
10746 CAGTTATTAG
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
16 6 0.11
17 37 0.66
18 5 0.09
19 8 0.14
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.49
Consensus pattern (17 bp):
TTATCAGATGATTTTAG
Found at i:10733 original size:34 final size:35
Alignment explanation
Indices: 10644--10744 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 35
10634 CATTTCAACA
* *
10644 TTATCAAATATTTACAATTATCAGATGATTTTTTAG
1 TTATCAGATATTTACAGTTATCAGATGA-TTTTTAG
* *
10680 TTATCATATATTTATAGTTATCAGATGATTTTT-G
1 TTATCAGATATTTACAGTTATCAGATGATTTTTAG
10714 TTATCAGATGA-TTACAGTTATCAGATG-TTTT
1 TTATCAGAT-ATTTACAGTTATCAGATGATTTT
10745 ACAGTTATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
33 4 0.07
34 24 0.41
35 6 0.10
36 25 0.42
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.49
Consensus pattern (35 bp):
TTATCAGATATTTACAGTTATCAGATGATTTTTAG
Found at i:12447 original size:233 final size:233
Alignment explanation
Indices: 12030--12476 Score: 594
Period size: 233 Copynumber: 1.9 Consensus size: 233
12020 TTTATATGCG
** * *
12030 ACTAGACGTCCTCATCAAGTAGGAACAATGTCATCCACTGACTAGACCTCATCAATATGAAGGGG
1 ACTAGACGTCCTCATCAAGTAGGAACAATGTCATCCACCAACTAGACCTCATCAACATGAAGGAG
* ** * *
12095 CAATGCTAACACCATATTTGACATCGAGCAAATCACCCCAAAGGCTGCCAGGTTCTCTTCATCGT
66 CAATGCTAACACCAGATTTGACATCGAGCAAATCACCCCAAAGGAGGCCAGATTCTCTTCAACGT
* * * ** * *
12160 CGGTGAGCATTGTAGCTTCCAACATCAAATTATCTATATGCAGTCAGATTTCCTCAACAAGAAGG
131 CGGTGAACAGTGTAGCTTCCAACATCAAATTATCTACAAACAATCAGATTTCCTCAACAAGAAGA
*
12225 AACAATGTTGTCTTCAGATGTGTAGTCACCCAAATACA
196 AACAATATTGTCTTCAGATGTGTAGTCACCCAAATACA
** * *
12263 ACTAGACGTCCTCATCAAGTAGGAACAATGTTGTCCACCAACTTGACCTCCTCAACATGAAGGAG
1 ACTAGACGTCCTCATCAAGTAGGAACAATGTCATCCACCAACTAGACCTCATCAACATGAAGGAG
* *
12328 CAATG-TCAGCACCAGATTTGACATTGAGCAAATCACCCCAAAGGAGGCCAGATTCTCTTCAACG
66 CAATGCT-AACACCAGATTTGACATCGAGCAAATCACCCCAAAGGAGGCCAGATTCTCTTCAACG
* * * *
12392 T-GGATGAATAGTGTCGTTTCCAACATCAAATTATCTCCAAACAATCA-ATTTTCCTCAACAAGA
130 TCGG-TGAACAGTGTAGCTTCCAACATCAAATTATCTACAAACAATCAGA-TTTCCTCAACAAGA
*
12455 ATAAACAATATTGTCTTCAGAT
193 AGAAACAATATTGTCTTCAGAT
12477 ACATAGTCAT
Statistics
Matches: 183, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
232 4 0.02
233 179 0.98
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (233 bp):
ACTAGACGTCCTCATCAAGTAGGAACAATGTCATCCACCAACTAGACCTCATCAACATGAAGGAG
CAATGCTAACACCAGATTTGACATCGAGCAAATCACCCCAAAGGAGGCCAGATTCTCTTCAACGT
CGGTGAACAGTGTAGCTTCCAACATCAAATTATCTACAAACAATCAGATTTCCTCAACAAGAAGA
AACAATATTGTCTTCAGATGTGTAGTCACCCAAATACA
Found at i:13537 original size:6 final size:6
Alignment explanation
Indices: 13519--13561 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
13509 AATAGAGAAC
* *
13519 AAAAAG AACAAG AAAAAG -AAAAG AAAAAG AAAAA- TAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
13562 TATTATCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:13542 original size:11 final size:11
Alignment explanation
Indices: 13519--13561 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
13509 AATAGAGAAC
13519 AAAAAGAACAAG
1 AAAAAGAA-AAG
13531 AAAAAGAAAAG
1 AAAAAGAAAAG
13542 AAAAAGAAAA-
1 AAAAAGAAAAG
13552 ATAAAAGAAA
1 A-AAAAGAAA
13562 TATTATCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 1 0.03
11 21 0.70
12 8 0.27
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:13542 original size:17 final size:17
Alignment explanation
Indices: 13520--13561 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
13510 ATAGAGAACA
*
13520 AAAAGAACAAGAAAAAG
1 AAAAGAAAAAGAAAAAG
*
13537 AAAAGAAAAAGAAAAAT
1 AAAAGAAAAAGAAAAAG
13554 AAAAGAAA
1 AAAAGAAA
13562 TATTATCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAAG
Found at i:14168 original size:2 final size:2
Alignment explanation
Indices: 14161--14219 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
14151 TATTCACCTT
14161 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
14203 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
14220 TGTACCCATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18062 original size:19 final size:19
Alignment explanation
Indices: 18035--18078 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
18025 GATGAATCAT
*
18035 ATTTTATAACTCAAACTTG
1 ATTTAATAACTCAAACTTG
* *
18054 ATTTAATAACTCAAATTTT
1 ATTTAATAACTCAAACTTG
18073 ATTTAA
1 ATTTAA
18079 ATTTAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (19 bp):
ATTTAATAACTCAAACTTG
Found at i:23204 original size:9 final size:8
Alignment explanation
Indices: 23187--23303 Score: 65
Period size: 9 Copynumber: 13.2 Consensus size: 8
23177 CATATATTAC
23187 TTTTTATT
1 TTTTTATT
23195 TTTCTTATTT
1 TTT-TTA-TT
23205 TATTTTATTT
1 T-TTTTA-TT
23215 TATTTTATT
1 T-TTTTATT
* *
23224 CTTTTCTT
1 TTTTTATT
*
23232 ATTTTATT
1 TTTTTATT
23240 TTTTTATGT
1 TTTTTAT-T
*
23249 CTTTTATT
1 TTTTTATT
*
23257 TATCTTATT
1 T-TTTTATT
23266 TTCCTTT-TT
1 TT--TTTATT
*
23275 TCATTTATTT
1 T-TTTTA-TT
23285 TTTTTATT
1 TTTTTATT
23293 TCTTTTATT
1 T-TTTTATT
23302 TT
1 TT
23304 ATTTTTCTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
8 30 0.34
9 34 0.39
10 21 0.24
11 2 0.02
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.78
Consensus pattern (8 bp):
TTTTTATT
Found at i:23207 original size:5 final size:5
Alignment explanation
Indices: 23188--23322 Score: 88
Period size: 5 Copynumber: 27.6 Consensus size: 5
23178 ATATATTACT
*
23188 TTTTA TTTT- TCTTA TTTTA TTTTA TTTTA TTTTA TTCTT- TTCTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TT-TTA TTTTA
* * * * * *
23238 TTTTT TTATGTC TTTTA -TTTA TCTTA TTTTC CTTT- TTTCA -TTTA TTTT-
1 TTTTA TT-T-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* *
23286 TTTTA -TTTC TTTTA TTTTA TTTT- TCTTTA GTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTT
23323 ATCTTCATTG
Statistics
Matches: 102, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
4 20 0.20
5 73 0.72
6 6 0.06
7 3 0.03
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:23232 original size:31 final size:29
Alignment explanation
Indices: 23188--23308 Score: 101
Period size: 31 Copynumber: 4.1 Consensus size: 29
23178 ATATATTACT
23188 TTTTA-TTTTTCTTATTTTATTTTATTTTA
1 TTTTATTTTTTCTTATTTTATTTT-TTTTA
23217 TTTTATTCTTTTCTTATTTTA-TTTTTTTA
1 TTTTATT-TTTTCTTATTTTATTTTTTTTA
** *
23246 TGTCTT-TTATTTATCTTATTTTCCTTTTTTCA
1 T-T-TTATT-TTT-TCTTATTTTATTTTTTTTA
*
23278 -TTTATTTTTT-TTATTTCT-TTTATTTTA
1 TTTTATTTTTTCTTATTT-TATTTTTTTTA
23305 TTTT
1 TTTT
23309 TCTTTAGTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
27 12 0.16
28 5 0.06
29 16 0.21
30 13 0.17
31 24 0.31
32 7 0.09
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.78
Consensus pattern (29 bp):
TTTTATTTTTTCTTATTTTATTTTTTTTA
Found at i:23233 original size:26 final size:25
Alignment explanation
Indices: 23188--23308 Score: 95
Period size: 23 Copynumber: 5.2 Consensus size: 25
23178 ATATATTACT
23188 TTTTA-TTT-TTCTTATTTTATTTTA
1 TTTTATTTTATTCTT-TTTTATTTTA
23212 TTTTATTTTATTCTTTTCTTATTTTA
1 TTTTATTTTATTCTTTT-TTATTTTA
23238 -TTT-TTTTATGTC--TTTTA-TTTA
1 TTTTATTTTAT-TCTTTTTTATTTTA
* *
23259 TCTTA-TTT-TCCTTTTTTCA-TTTA
1 TTTTATTTTATTCTTTTTT-ATTTTA
*
23282 TTTT-TTTTATT-TCTTTTATTTTA
1 TTTTATTTTATTCTTTTTTATTTTA
23305 TTTT
1 TTTT
23309 TCTTTAGTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 25
0.73 0.05 0.23
Matches are distributed among these distances:
20 1 0.01
21 5 0.06
22 13 0.16
23 26 0.32
24 12 0.15
25 10 0.12
26 13 0.16
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.78
Consensus pattern (25 bp):
TTTTATTTTATTCTTTTTTATTTTA
Found at i:23320 original size:65 final size:70
Alignment explanation
Indices: 23190--23340 Score: 172
Period size: 65 Copynumber: 2.2 Consensus size: 70
23180 ATATTACTTT
* * * **
23190 TTATTTTTCTTATTTTATTTTATTTTATTTTATTCTTTTCTTATTTTATTTTTTTATGTCTTTTA
1 TTATTTTCCTT-TTTTATTTTATTTTATTTTATTCTCTTCTTATTTTATTTTTCTATGTAGTTTA
23255 TTTATC
65 TTTATC
23261 TTATTTTCCTTTTTTCA-TTTATTTT-TTTTATT-TCTT-TTATTTTATTTTTCT-T-TAGTTTA
1 TTATTTTCCTTTTTT-ATTTTATTTTATTTTATTCTCTTCTTATTTTATTTTTCTATGTAGTTTA
23320 TTTATC
65 TTTATC
*
23326 TTCA-TTGCCTTTTTT
1 TT-ATTTTCCTTTTTT
23341 TCTAACATGC
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
65 23 0.32
66 2 0.03
67 14 0.19
68 3 0.04
69 7 0.10
70 12 0.17
71 11 0.15
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (70 bp):
TTATTTTCCTTTTTTATTTTATTTTATTTTATTCTCTTCTTATTTTATTTTTCTATGTAGTTTAT
TTATC
Found at i:24056 original size:17 final size:17
Alignment explanation
Indices: 24031--24075 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
24021 TCAGATTCAT
24031 ATTCCAATTCCTGACAG
1 ATTCCAATTCCTGACAG
*
24048 ATTCTAATTCCTGACAG
1 ATTCCAATTCCTGACAG
24065 ATTCCAATTCC
1 ATTCCAATTCC
24076 CTCAGAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (17 bp):
ATTCCAATTCCTGACAG
Found at i:27835 original size:5 final size:5
Alignment explanation
Indices: 27825--27854 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
27815 GGGGATCAAG
27825 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
27855 AAAGCAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:29350 original size:5 final size:6
Alignment explanation
Indices: 29335--29359 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29325 TGCACTTATA
29335 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
29360 GTACAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:32307 original size:28 final size:25
Alignment explanation
Indices: 32260--32310 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
32250 AAATATCATA
*
32260 TAAATAATTAAAAAAATATAATATT
1 TAAATATTTAAAAAAATATAATATT
* *
32285 TAAATATTTAAATAAATATTATATT
1 TAAATATTTAAAAAAATATAATATT
32310 T
1 T
32311 TTTAATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAATATTTAAAAAAATATAATATT
Found at i:32314 original size:20 final size:20
Alignment explanation
Indices: 32291--32346 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
32281 TATTTAAATA
32291 TTTAAATAAATATTATATTT
1 TTTAAATAAATATTATATTT
* **
32311 TTTAATTATTTATGTA-ATTT
1 TTTAAATAAATAT-TATATTT
*
32331 TTTAAAAAAAT-TTATA
1 TTTAAATAAATATTATA
32347 ATTATTTTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 5
0.69 0.18 0.13
Matches are distributed among these distances:
18 2 0.07
19 2 0.07
20 21 0.78
21 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTAAATAAATATTATATTT
Found at i:32481 original size:12 final size:11
Alignment explanation
Indices: 32478--32605 Score: 88
Period size: 11 Copynumber: 13.8 Consensus size: 11
32468 TATTTTAAAA
32478 TTTAAAATTAT
1 TTTAAAATTAT
32489 TTT-AAA--A-
1 TTTAAAATTAT
32496 TTTAAAATTAT
1 TTTAAAATTAT
32507 TTT--AA--AT
1 TTTAAAATTAT
32514 TTTAAAATTAT
1 TTTAAAATTAT
32525 TTT--AA--AT
1 TTTAAAATTAT
32532 TTTAAAATTAT
1 TTTAAAATTAT
32543 TTT--AA--AT
1 TTTAAAATTAT
32550 TTTAAAATTAT
1 TTTAAAATTAT
32561 TTT--AA--AT
1 TTTAAAATTAT
32568 TTTAAAATTAT
1 TTTAAAATTAT
32579 TTT--AA--AT
1 TTTAAAATTAT
32586 TTTAAAATTAT
1 TTTAAAATTAT
32597 TTTAAAATT
1 TTTAAAATT
32606 TAAAATTTAA
Statistics
Matches: 93, Mismatches: 0, Indels: 48
0.66 0.00 0.34
Matches are distributed among these distances:
7 28 0.30
8 4 0.04
9 20 0.22
10 4 0.04
11 37 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTAAAATTAT
Found at i:32490 original size:18 final size:18
Alignment explanation
Indices: 32467--32612 Score: 265
Period size: 18 Copynumber: 8.1 Consensus size: 18
32457 ATGTAATATT
*
32467 TTATTTTAAAATTTAAAA
1 TTATTTTAAATTTTAAAA
*
32485 TTATTTTAAAATTTAAAA
1 TTATTTTAAATTTTAAAA
32503 TTATTTTAAATTTTAAAA
1 TTATTTTAAATTTTAAAA
32521 TTATTTTAAATTTTAAAA
1 TTATTTTAAATTTTAAAA
32539 TTATTTTAAATTTTAAAA
1 TTATTTTAAATTTTAAAA
32557 TTATTTTAAATTTTAAAA
1 TTATTTTAAATTTTAAAA
32575 TTATTTTAAATTTTAAAA
1 TTATTTTAAATTTTAAAA
*
32593 TTATTTTAAAATTTAAAA
1 TTATTTTAAATTTTAAAA
32611 TT
1 TT
32613 TAATTATAAA
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 126 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTTTAAATTTTAAAA
Found at i:33639 original size:31 final size:31
Alignment explanation
Indices: 33547--33640 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
33537 AAACAACATC
* * * *
33547 TTATTTTTATCAAAACTTAAATAAGATATTTT
1 TTATTCTTATCATAACTTAAA-AACATATATT
***
33579 TTATTCTTATCATAACTTAAAATTTTATATT
1 TTATTCTTATCATAACTTAAAAACATATATT
* **
33610 TTATTTTTATTTTAACTTAAAAACATATATT
1 TTATTCTTATCATAACTTAAAAACATATATT
33641 CACAGTATAC
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 31 0.62
32 19 0.38
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.53
Consensus pattern (31 bp):
TTATTCTTATCATAACTTAAAAACATATATT
Found at i:33713 original size:27 final size:26
Alignment explanation
Indices: 33683--33736 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
33673 AAAATACTTA
*
33683 ATTTCTATTCATAATTTAAAAATGTAT
1 ATTTCTATTCAT-ACTTAAAAATGTAT
* *
33710 ATTTTTATTTATACTTAAAAATGTAT
1 ATTTCTATTCATACTTAAAAATGTAT
33736 A
1 A
33737 AATACTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (26 bp):
ATTTCTATTCATACTTAAAAATGTAT
Found at i:33875 original size:32 final size:33
Alignment explanation
Indices: 33804--33875 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 33
33794 GTTTTAAAAT
33804 AAAATAAAAAATATACATTTTTAAGTTTTGATA
1 AAAATAAAAAATATACATTTTTAAGTTTTGATA
* *
33837 AGAATAAAAAATAT-C-TTATTTTAGTTTTGATA
1 AAAATAAAAAATATACATT-TTTAAGTTTTGATA
33869 AAAATAA
1 AAAATAA
33876 GATGATGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 2 0.06
32 20 0.57
33 13 0.37
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (33 bp):
AAAATAAAAAATATACATTTTTAAGTTTTGATA
Found at i:33978 original size:20 final size:21
Alignment explanation
Indices: 33939--33982 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
33929 TTAAAAACAT
33939 ATATTTTATAGAACTTAATAA
1 ATATTTTATAGAACTTAATAA
* *
33960 ATATTTT-TTGAAGTTAATAA
1 ATATTTTATAGAACTTAATAA
33980 ATA
1 ATA
33983 AAGTATTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATTTTATAGAACTTAATAA
Found at i:40262 original size:16 final size:16
Alignment explanation
Indices: 40243--40275 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40233 CTAAAACTTA
40243 ATTTTACTAATAATCC
1 ATTTTACTAATAATCC
40259 ATTTTACTAATAATCC
1 ATTTTACTAATAATCC
40275 A
1 A
40276 ATGATCGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTTACTAATAATCC
Found at i:40916 original size:24 final size:24
Alignment explanation
Indices: 40889--40941 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
40879 ACGTTCGTGA
*
40889 ATGTTCAG-TTATGTTCGTTCGA-TT
1 ATGTTC-GTTTATGTTCATTC-ATTT
40913 ATGTTCGTTTATGTTCATTCATTT
1 ATGTTCGTTTATGTTCATTCATTT
40937 ATGTT
1 ATGTT
40942 TAACCCAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (24 bp):
ATGTTCGTTTATGTTCATTCATTT
Found at i:42030 original size:16 final size:16
Alignment explanation
Indices: 42003--42077 Score: 123
Period size: 16 Copynumber: 4.7 Consensus size: 16
41993 CCAACGTTTA
42003 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
42019 TATTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
42035 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
42051 TGTTCGTTTATGTTCA
1 TGTTCGTTTATGTTCG
42067 TGTTCGTTTAT
1 TGTTCGTTTAT
42078 TTATTAAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 54 1.00
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:42166 original size:16 final size:16
Alignment explanation
Indices: 42142--42174 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42132 AAAAAAAAAT
*
42142 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
42158 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
42174 T
1 T
42175 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.24, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:43217 original size:5 final size:5
Alignment explanation
Indices: 43207--43267 Score: 50
Period size: 5 Copynumber: 10.8 Consensus size: 5
43197 GGATATATAA
*
43207 ATTTT ATTTT ATTTT ATTTATT ATTTT GGATATATAA ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT A-TT-TT ATTTT --AT-T-T-T ATTTT ATTTT ATTTT
43259 ATTTT ATTT
1 ATTTT ATTT
43268 CTTTAGTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
5 32 0.68
6 5 0.11
7 6 0.13
8 3 0.06
9 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.70
Consensus pattern (5 bp):
ATTTT
Found at i:43267 original size:42 final size:37
Alignment explanation
Indices: 43189--43262 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
43179 TCACACCAAA
43189 ATTATTTTGGATATATAAATTTTATTTTATTTTATTT
1 ATTATTTTGGATATATAAATTTTATTTTATTTTATTT
43226 ATTATTTTGGATATATAAATTTTATTTTATTTTATTT
1 ATTATTTTGGATATATAAATTTTATTTTATTTTATTT
43263 TATTTCTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (37 bp):
ATTATTTTGGATATATAAATTTTATTTTATTTTATTT
Found at i:43278 original size:37 final size:37
Alignment explanation
Indices: 43189--43278 Score: 130
Period size: 37 Copynumber: 2.4 Consensus size: 37
43179 TCACACCAAA
*
43189 ATTATTTTGGATATATAAATTTTATTTTATTTTATTT
1 ATTATTTTAGATATATAAATTTTATTTTATTTTATTT
*
43226 ATTATTTTGGATATATAAATTTTATTTTATTTTATTTT
1 ATTATTTTAGATATATAAATTTTATTTTATTTTA-TTT
43264 ATT-TCTTTAG-TATAT
1 ATTAT-TTTAGATATAT
43279 TTATTTATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
37 40 0.80
38 10 0.20
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (37 bp):
ATTATTTTAGATATATAAATTTTATTTTATTTTATTT
Found at i:46059 original size:23 final size:23
Alignment explanation
Indices: 46033--46077 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
46023 TATGGAAACA
*
46033 ATTTTGT-AATCTATTCCATATAC
1 ATTTTGTCAATCTAATCC-TATAC
*
46056 ATTTTTTCAATCTAATCCTATA
1 ATTTTGTCAATCTAATCCTATA
46078 ACAATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.31, C:0.18, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTTGTCAATCTAATCCTATAC
Found at i:46085 original size:24 final size:23
Alignment explanation
Indices: 46029--46085 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
46019 CTGATATGGA
*
46029 AACAATTTTGTAATCTATTCCAT
1 AACAATTTTGTAATCTAATCCAT
*
46052 ATAC-ATTTTTTCAATCTAATCCTAT
1 A-ACAATTTTGT-AATCTAATCC-AT
46077 AACAATTTT
1 AACAATTTT
46086 ATCCATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 7 0.25
24 13 0.46
25 8 0.29
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.46
Consensus pattern (23 bp):
AACAATTTTGTAATCTAATCCAT
Found at i:46580 original size:21 final size:20
Alignment explanation
Indices: 46500--46581 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
46490 CGCAAATCAG
46500 TTTCCAGATTCGCAATGCGAT
1 TTTCCA-ATTCGCAATGCGAT
* * *
46521 TAT-GACTATCGCAATGCGAT
1 TTTCCAAT-TCGCAATGCGAT
**
46541 TTTCCAATTTCGCGTTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
46562 TTTCCCAATTCGCAATGCGA
1 TTT-CCAATTCGCAATGCGA
46582 ATAAGTAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
19 1 0.02
20 15 0.32
21 26 0.55
22 5 0.11
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:46666 original size:21 final size:20
Alignment explanation
Indices: 46632--46683 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
46622 ATACTGACTA
* * *
46632 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTACCT-AT
*
46653 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACCTAT
*
46673 TCGCGTTGCGA
1 TCGCATTGCGA
46684 ATTTGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACCTAT
Found at i:46695 original size:103 final size:103
Alignment explanation
Indices: 46509--46725 Score: 278
Period size: 103 Copynumber: 2.1 Consensus size: 103
46499 GTTTCCAGAT
* * *
46509 TCGCAATGCGATTATGACTATCGCAATGCGATTTTCCAATTTCGCGTTGCGATTTTCCCAATTCG
1 TCGCAATGCGATTATGACTATCGCAATGCAATTTTCCAATTTCGCATTGCGATTTTACCAATTCG
* *
46574 CAATGCGAATAAGTAAATCGTAATACGAATTTGGAAAA
66 CAATGCGAATAAGAAAATCGCAATACGAATTTGGAAAA
**
46612 TCGCAATGCGA-TACTGACTATCGCAATGCAATTTTCCTAA-TTCGCATTGCGA-TTTACGTATT
1 TCGCAATGCGATTA-TGACTATCGCAATGCAATTTTCC-AATTTCGCATTGCGATTTTACCAATT
** ** *
46674 CGCGTTGCGAATTTGGAAAATCGCAATGCGAATTTGGAAAA
64 CGCAATGCGAA-TAAGAAAATCGCAATACGAATTTGGAAAA
46715 TCGCAATGCGA
1 TCGCAATGCGA
46726 ATTTGGAAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
102 18 0.18
103 79 0.80
104 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (103 bp):
TCGCAATGCGATTATGACTATCGCAATGCAATTTTCCAATTTCGCATTGCGATTTTACCAATTCG
CAATGCGAATAAGAAAATCGCAATACGAATTTGGAAAA
Found at i:46697 original size:21 final size:21
Alignment explanation
Indices: 46679--46741 Score: 126
Period size: 21 Copynumber: 3.0 Consensus size: 21
46669 GTATTCGCGT
46679 TGCGAATTTGGAAAATCGCAA
1 TGCGAATTTGGAAAATCGCAA
46700 TGCGAATTTGGAAAATCGCAA
1 TGCGAATTTGGAAAATCGCAA
46721 TGCGAATTTGGAAAATCGCAA
1 TGCGAATTTGGAAAATCGCAA
46742 CGCGGTACTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCGAATTTGGAAAATCGCAA
Found at i:46760 original size:20 final size:20
Alignment explanation
Indices: 46736--46828 Score: 114
Period size: 20 Copynumber: 4.7 Consensus size: 20
46726 ATTTGGAAAA
* *
46736 TCGCAACGCGGTACTGACTA
1 TCGCAACGCGATACTGACTT
46756 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* * *
46776 TCGCAACTCGATACTTAATT
1 TCGCAACGCGATACTGACTT
* *
46796 TCGCAACTCAATACTGACTT
1 TCGCAACGCGATACTGACTT
*
46816 TCGCAACGAGATA
1 TCGCAACGCGATA
46829 ATACATAATC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:47360 original size:20 final size:20
Alignment explanation
Indices: 47337--47379 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
47327 GATAGTCAAA
47337 TTCGCGTTGCGATTATCATT
1 TTCGCGTTGCGATTATCATT
* *
47357 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTATCATT
47377 TTC
1 TTC
47380 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCGATTATCATT
Found at i:47570 original size:25 final size:24
Alignment explanation
Indices: 47516--47570 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
47506 TGTTTATTAT
* *
47516 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
47540 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
47566 TGTTT
1 TGTTT
47571 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:48721 original size:18 final size:18
Alignment explanation
Indices: 48700--48747 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
48690 TCCACTTTGG
48700 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
48718 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
48736 GAGCCATCACCT
1 GAGCCATCACCT
48748 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:49342 original size:19 final size:20
Alignment explanation
Indices: 49288--49343 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
49278 TAGTTTACTT
* *
49288 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
49308 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
49328 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
49344 AAATCGCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:49349 original size:19 final size:19
Alignment explanation
Indices: 49327--49390 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
49317 GGAAATGGCT
49327 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
49346 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
49360 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
49379 ATCGCAATGCGA
1 ATCGCAATGCGA
49391 TTTGTGTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 10 0.28
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 22 0.61
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:49481 original size:20 final size:20
Alignment explanation
Indices: 49449--49541 Score: 114
Period size: 20 Copynumber: 4.7 Consensus size: 20
49439 GCAATTTTCA
* *
49449 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGTCAT
* *
49469 TTCCGTGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
49489 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* * *
49509 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGATAGTCAT
*
49529 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
49542 AAGTAAATTA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:49922 original size:21 final size:20
Alignment explanation
Indices: 49896--49965 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
49886 CAGTCATTCC
49896 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
49917 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
*
49938 TCAAGAGTCCCCCTCCACCGT
1 TCAAGAGT-CCCCTCCATCGT
49959 TCAAGAG
1 TCAAGAG
49966 GCCACTGTCA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
21 32 0.84
22 6 0.16
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:49980 original size:21 final size:20
Alignment explanation
Indices: 49912--49992 Score: 54
Period size: 21 Copynumber: 3.9 Consensus size: 20
49902 GTCCCCTCCA
*
49912 ATCGTTCAAGAGGCCCCTATC
1 ATCGTTCAAGAGGCCACT-TC
** * * *
49933 ATCCCTCAAGAGTCCCCCTCC
1 ATCGTTCAAGAG-GCCACTTC
*
49954 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCCACT-TC
* *
49975 ATCGTTGAAGAGGTCACT
1 ATCGTTCAAGAGGCCACT
49993 CCCACCATTC
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
20 4 0.09
21 36 0.80
22 5 0.11
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGTTCAAGAGGCCACTTC
Found at i:49986 original size:42 final size:42
Alignment explanation
Indices: 49889--49977 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
49879 GACTCACCAG
* * *
49889 TCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
*
49931 TCATCCCTCAAGAGTCCCCCTCC-ACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGT-CCCCTCCAACCGTTCAAGAGGCCACTA
49973 TCATC
1 TCATC
49978 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 35 0.83
43 7 0.17
ACGTcount: A:0.22, C:0.40, G:0.15, T:0.22
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:51423 original size:14 final size:14
Alignment explanation
Indices: 51389--51427 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
51379 TTGATTGTTT
51389 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
51403 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
51417 TGTTGATTTGT
1 AATTGATTTGT
51428 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:51553 original size:20 final size:20
Alignment explanation
Indices: 51525--51567 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
51515 GTTGAAGGCA
*
51525 AAACAGACTATCGCAACACG
1 AAACAGACTATCGCAACAAG
*
51545 AAACTGACTATCGCAACAAG
1 AAACAGACTATCGCAACAAG
51565 AAA
1 AAA
51568 ATCGCAATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.26, G:0.14, T:0.12
Consensus pattern (20 bp):
AAACAGACTATCGCAACAAG
Found at i:51600 original size:19 final size:19
Alignment explanation
Indices: 51564--51600 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
51554 ATCGCAACAA
* *
51564 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
51583 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
51601 ATTGCAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:51644 original size:20 final size:20
Alignment explanation
Indices: 51621--51687 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
51611 GATTTTCTAG
51621 TTGCGATAGCCATTTTCGCA
1 TTGCGATAGCCATTTTCGCA
*** *
51641 TTGCGATTTTTCA-TTTCGAA
1 TTGCGA-TAGCCATTTTCGCA
*
51661 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCA
51681 TTGCGAT
1 TTGCGAT
51688 TTCCCCGTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 3 0.08
20 30 0.83
21 3 0.08
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCA
Found at i:52842 original size:24 final size:24
Alignment explanation
Indices: 52791--52844 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
52781 GTATTCGAAA
* * *
52791 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
52815 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
52839 TTTGAT
1 TTTGAT
52845 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:53036 original size:12 final size:12
Alignment explanation
Indices: 53019--53043 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53009 ATATAATCCT
53019 GAAGAAGAAAAA
1 GAAGAAGAAAAA
53031 GAAGAAGAAAAA
1 GAAGAAGAAAAA
53043 G
1 G
53044 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:55355 original size:39 final size:36
Alignment explanation
Indices: 55312--55426 Score: 116
Period size: 33 Copynumber: 3.2 Consensus size: 36
55302 CTTAATGTCT
55312 ATCGCAACGCGGAAATTACTATCGCAATGCAAAATGAAA
1 ATCGCAACGC-GAAA-TA-TATCGCAATGCAAAATGAAA
* * * *
55351 ATCGCAA--CGAGAGA-ATCGCATTGCGAAATGAAA
1 ATCGCAACGCGAAATATATCGCAATGCAAAATGAAA
55384 ATCGCAACGCG-AAT-T-TCGCAATGCGAAAATGAAA
1 ATCGCAACGCGAAATATATCGCAATGC-AAAATGAAA
55418 ATCGCAACG
1 ATCGCAACG
55427 AGGGAATTGC
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
33 32 0.50
34 18 0.28
35 3 0.05
36 3 0.05
37 1 0.02
39 7 0.11
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.17
Consensus pattern (36 bp):
ATCGCAACGCGAAATATATCGCAATGCAAAATGAAA
Found at i:55395 original size:19 final size:19
Alignment explanation
Indices: 55312--55396 Score: 54
Period size: 19 Copynumber: 4.7 Consensus size: 19
55302 CTTAATGTCT
* **
55312 ATCGCAACGCGGAAATTACT
1 ATCGCAACGC-GAAATGAAA
* *
55332 ATCGCAATGCAAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
55351 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
**
55365 ATCGCATTGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
55384 ATCGCAACGCGAA
1 ATCGCAACGCGAA
55397 TTTCGCAATG
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 2 0.04
17 1 0.02
18 1 0.02
19 26 0.53
20 9 0.18
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:55419 original size:34 final size:34
Alignment explanation
Indices: 55332--55445 Score: 153
Period size: 33 Copynumber: 3.4 Consensus size: 34
55322 GGAAATTACT
55332 ATCGCAATGC-AAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
* *
55365 ATCGCATTGCG-AAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
* *
55397 TTTCGCAATGCGAAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
*
55432 ATTGCAATGCGAAA
1 ATCGCAATGCGAAA
55446 TTCACGTTGC
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
32 1 0.01
33 37 0.54
34 30 0.43
35 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:55474 original size:19 final size:19
Alignment explanation
Indices: 55452--55510 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
55442 GAAATTCACG
55452 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
55471 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
55485 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
55504 TTGCGAT
1 TTGCGAT
55511 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:55636 original size:14 final size:14
Alignment explanation
Indices: 55617--55653 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
55607 CATCAATTAA
55617 ACAAATCAACTTGT
1 ACAAATCAACTTGT
* *
55631 ACAAATCACCTTTT
1 ACAAATCAACTTGT
55645 ACAAATCAA
1 ACAAATCAA
55654 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.24, G:0.03, T:0.27
Consensus pattern (14 bp):
ACAAATCAACTTGT
Found at i:57086 original size:42 final size:42
Alignment explanation
Indices: 57040--57119 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
57030 CGATGACAGT
* * *
57040 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
57082 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
57120 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:57518 original size:91 final size:89
Alignment explanation
Indices: 57341--57524 Score: 280
Period size: 91 Copynumber: 2.0 Consensus size: 89
57331 ATTTCAAACT
*
57341 TTCAACCAAAAGACAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCA
1 TTCAACCAAAAGACAAAAAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGCA
57406 GAATTGGCAGCAACCGAATAAATTTAC
63 GAATTGGCAGCAACCGAATAAATTTAC
57433 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGAC--AA-AAAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
57497 GTATTGGCAGCAACTGAATAAATTTAC
63 GAATTGGCAGCAACCGAATAAATTTAC
57524 T
1 T
57525 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
91 41 0.48
92 14 0.16
94 2 0.02
95 29 0.34
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (89 bp):
TTCAACCAAAAGACAAAAAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGAA
TTGGCAGCAACCGAATAAATTTAC
Found at i:59244 original size:20 final size:19
Alignment explanation
Indices: 59213--59339 Score: 87
Period size: 20 Copynumber: 7.1 Consensus size: 19
59203 TCTTTTGGTT
59213 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
59232 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
59253 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
59272 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
59286 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
59305 G--A-G--AATCGCAAC-A
1 GAAATGAAAATCGCAACGA
59318 CGAAATGAAAATCGCAACGA
1 -GAAATGAAAATCGCAACGA
59338 GA
1 GA
59340 GAATCGCAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
13 1 0.01
14 19 0.23
16 4 0.05
17 4 0.05
19 24 0.29
20 30 0.36
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:59281 original size:14 final size:14
Alignment explanation
Indices: 59262--59350 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
59252 GGAAATGACT
59262 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
59276 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
59293 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
*
59309 ATCGCAACACGAAATGAAA
1 ATCGC-A-ACG--A-GAGA
59328 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
59342 ATCGCAACG
1 ATCGCAACG
59351 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 24 0.39
15 2 0.03
16 9 0.15
17 9 0.15
18 2 0.03
19 15 0.25
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:59295 original size:33 final size:33
Alignment explanation
Indices: 59238--59358 Score: 206
Period size: 33 Copynumber: 3.6 Consensus size: 33
59228 ACGAGATAAT
59238 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
59272 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
59305 GAGAATCGCAACACGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
59338 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
59359 AAGGTTTCGC
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
33 69 0.83
34 14 0.17
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:59387 original size:19 final size:19
Alignment explanation
Indices: 59363--59436 Score: 70
Period size: 19 Copynumber: 4.1 Consensus size: 19
59353 AAATGAAAGG
59363 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
59382 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* *
59398 --TCTCGTTGCGATAGTT-A
1 TTTCGCGTTGCGAT-TTTCA
59415 TTTCCGCGTTGCGATTTTCA
1 TTT-CGCGTTGCGATTTTCA
59435 TT
1 TT
59437 CTCGAAACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.23
17 5 0.11
19 16 0.36
20 13 0.30
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:59994 original size:20 final size:20
Alignment explanation
Indices: 59966--60059 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
59956 TGATAGTAAG
*
59966 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
59986 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
60006 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
60027 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
60047 ATTCGCATTGCGA
1 ATTCGCATTGCGA
60060 ATTATGAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 45 0.71
21 18 0.29
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:60017 original size:41 final size:40
Alignment explanation
Indices: 59966--60059 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
59956 TGATAGTAAG
* * *
59966 ATTCACATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
60006 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
60047 ATTCGCATTGCGA
1 ATTCGCATTGCGA
60060 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:60080 original size:21 final size:21
Alignment explanation
Indices: 60056--60111 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
60046 TATTCGCATT
*
60056 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
60077 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
60097 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
60112 TGTATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:60092 original size:61 final size:61
Alignment explanation
Indices: 59973--60093 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 61
59963 AAGATTCACA
* * * ** * *
59973 TTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTTAATCGCG
1 TTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAATCGCG
*
60034 TTGCGATTTACGTATTCGCATTGCGAATTAT-GAAAATCGCAACGCGA-ATACGTAAATCGC
1 TTGCGATTTACGTATTCGCATTGCG-ATTATCCAAAATCGCAACGCGATATAC-TAAATCGC
60094 AATGCGAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 3 0.06
61 43 0.86
62 4 0.08
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (61 bp):
TTGCGATTTACGTATTCGCATTGCGATTATCCAAAATCGCAACGCGATATACTAAATCGCG
Found at i:68906 original size:6 final size:6
Alignment explanation
Indices: 68895--68920 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
68885 AAAAATTATC
68895 TTTAAA TTTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
68921 AAAAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:69046 original size:2 final size:2
Alignment explanation
Indices: 69039--69065 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
69029 GAATTTTGAA
69039 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
69066 AGCTATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70199 original size:20 final size:20
Alignment explanation
Indices: 70159--70199 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
70149 TTTGATCATG
*
70159 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
70179 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
70199 A
1 A
70200 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:72073 original size:19 final size:20
Alignment explanation
Indices: 72036--72073 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
72026 GTATGCTCAG
72036 AGGGAACCGATTCCCCCCCA
1 AGGGAACCGATTCCCCCCCA
*
72056 AGGGTACCGATTCCCCCC
1 AGGGAACCGATTCCCCCC
72074 TGTTCAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.13
Consensus pattern (20 bp):
AGGGAACCGATTCCCCCCCA
Found at i:77864 original size:19 final size:19
Alignment explanation
Indices: 77826--77887 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
77816 ACCCCTTTGA
* *
77826 AGGGGAACCGATTTCCCCCT
1 AGGGGAATCGA-TACCCCCT
77846 AGGGGAATCGATACCCCCT
1 AGGGGAATCGATACCCCCT
* *
77865 AAGGGAATCGATACCCCCA
1 AGGGGAATCGATACCCCCT
77884 AGGG
1 AGGG
77888 TTCTGGTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 27 0.73
20 10 0.27
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (19 bp):
AGGGGAATCGATACCCCCT
Found at i:77881 original size:18 final size:19
Alignment explanation
Indices: 77840--77887 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
77830 GAACCGATTT
*
77840 CCCCCTAGGGGAATCGATA
1 CCCCCTAAGGGAATCGATA
77859 CCCCCTAAGGGAATCGATA
1 CCCCCTAAGGGAATCGATA
77878 CCCCC-AAGGG
1 CCCCCTAAGGG
77888 TTCTGGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.27, C:0.35, G:0.25, T:0.12
Consensus pattern (19 bp):
CCCCCTAAGGGAATCGATA
Found at i:90136 original size:35 final size:36
Alignment explanation
Indices: 90067--90137 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
90057 CATCTTCATG
*
90067 GGGTATCGATACTAAAAGGGCTAGTATCGATACCAT
1 GGGTATCGATACCAAAAGGGCTAGTATCGATACCAT
*
90103 GGGTATCGATACCATAA-GGC-AGGTATCGATACCAT
1 GGGTATCGATACCAAAAGGGCTA-GTATCGATACCAT
90138 TTTTGAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 1 0.03
35 16 0.50
36 15 0.47
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (36 bp):
GGGTATCGATACCAAAAGGGCTAGTATCGATACCAT
Found at i:90774 original size:21 final size:21
Alignment explanation
Indices: 90725--90801 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
90715 GAGGGTCCAC
90725 GTGGT-CTTTCGGAACATATAT
1 GTGGTCCTTT-GGAACATATAT
**
90746 GTAATCCTTTGGAACATATAT
1 GTGGTCCTTTGGAACATATAT
*
90767 GCGGTCCTTTGAGACACATAT-T
1 GTGGTCCTTTG-GA-ACATATAT
90789 -TGGTCCTTTGGAA
1 GTGGTCCTTTGGAA
90802 TATGTATATG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 31 0.66
22 7 0.15
23 6 0.13
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (21 bp):
GTGGTCCTTTGGAACATATAT
Found at i:92339 original size:105 final size:105
Alignment explanation
Indices: 92215--92418 Score: 300
Period size: 105 Copynumber: 1.9 Consensus size: 105
92205 TATTGCTAAT
* * *
92215 AGTATTGAACATTTGGTCACTAAAAAACACTTAGTGTGACAATATTAATCGTCACAAAATATACT
1 AGTATCGAACATTTGGTCACTAAAAAACACTTAGTATAACAATATTAATCGTCACAAAATATACT
* * *
92280 TTCAGTGTCAAATAAATTCATCACAATTTCTATTGATAGC
66 TTCAGTGTCAAAAAAATTAATCACAATTTATATTGATAGC
* * * * *
92320 AGTATCGAATATTTGGTCACTAAAAAATACTTAGTATAACAATATTGATGGTCACAAAATATATT
1 AGTATCGAACATTTGGTCACTAAAAAACACTTAGTATAACAATATTAATCGTCACAAAATATACT
*
92385 TTTAGTGTCAAAAAAATTAATCACAATTTATATT
66 TTCAGTGTCAAAAAAATTAATCACAATTTATATT
92419 AATAATTGTG
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
105 87 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (105 bp):
AGTATCGAACATTTGGTCACTAAAAAACACTTAGTATAACAATATTAATCGTCACAAAATATACT
TTCAGTGTCAAAAAAATTAATCACAATTTATATTGATAGC
Found at i:95313 original size:51 final size:51
Alignment explanation
Indices: 95235--95459 Score: 268
Period size: 51 Copynumber: 4.5 Consensus size: 51
95225 AAAAATGTTC
* * * *
95235 CACTTAACACATACATACACTGATGTAAGTGAATAAAATAAACAAGTGTAG
1 CACTTAACACATACTTACACAGGTGTAAGTGAATAAAATAAAAAAGTGTAG
* * *
95286 CACTTAATACATACTTACACAGGTGTAAGTGAATAAAACAAAAAAATGTAG
1 CACTTAACACATACTTACACAGGTGTAAGTGAATAAAATAAAAAAGTGTAG
* * * *
95337 CAATTAGCACATAC-TACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAA
1 CACTTAACACATACTTACACAGGTGTAAGTGAATAAAATAAAAAAGTGTAG
*
95387 CACTTAACACATACTTACA-ACGGTGT-A---AAT-AAATAAATAA-TGTAG
1 CACTTAACACATACTTACACA-GGTGTAAGTGAATAAAATAAAAAAGTGTAG
*
95432 CACTTAACACATACTTACACAGATGTAA
1 CACTTAACACATACTTACACAGGTGTAA
95460 ATATTTACAT
Statistics
Matches: 150, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
45 27 0.18
46 11 0.07
47 3 0.02
50 45 0.30
51 64 0.43
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (51 bp):
CACTTAACACATACTTACACAGGTGTAAGTGAATAAAATAAAAAAGTGTAG
Found at i:95399 original size:101 final size:102
Alignment explanation
Indices: 95224--95423 Score: 278
Period size: 101 Copynumber: 2.0 Consensus size: 102
95214 TTCATATTAC
* * * * *
95224 AAAAAATGTTCCACTTAACACATACATACACTGATGTAAGTGAATAAAATAAACAAGTGTAGCAC
1 AAAAAATGTACCAATTAACACATACATACACCGATGTAAGTGAATAAAATAAAAAAGTGTAACAC
* * *
95289 TTAATACATACTTAC-ACAGGTGTAAGTGAATAAAACA
66 TTAACACATACTTACAAC-GGTGTAAATAAATAAAACA
* * *
95326 AAAAAATGTAGCAATTAGCACATAC-TACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAACAC
1 AAAAAATGTACCAATTAACACATACATACACCGATGTAAGTGAATAAAATAAAAAAGTGTAACAC
95390 TTAACACATACTTACAACGGTGTAAATAAATAAA
66 TTAACACATACTTACAACGGTGTAAATAAATAAA
95424 TAATGTAGCA
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
101 63 0.73
102 23 0.27
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.23
Consensus pattern (102 bp):
AAAAAATGTACCAATTAACACATACATACACCGATGTAAGTGAATAAAATAAAAAAGTGTAACAC
TTAACACATACTTACAACGGTGTAAATAAATAAAACA
Found at i:96548 original size:50 final size:51
Alignment explanation
Indices: 96427--96554 Score: 177
Period size: 51 Copynumber: 2.5 Consensus size: 51
96417 TTAACAGTAA
* * **
96427 AGCGTGCCCCCTACACCGCGCTATACGATGATTTGGCGCCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
* *
96478 AGCGCGCCCCCTGAACCGCGCTATACGGTGAGCTGGCGCCACGT-GGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
* *
96528 AGCGCGGCCCCTGCAGCGCGCTATACG
1 AGCGCGCCCCCTGCACCGCGCTATACG
96555 CCACGTAGGG
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 30 0.44
51 38 0.56
ACGTcount: A:0.16, C:0.34, G:0.32, T:0.17
Consensus pattern (51 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTAT
Found at i:96644 original size:49 final size:49
Alignment explanation
Indices: 96566--96685 Score: 181
Period size: 49 Copynumber: 2.4 Consensus size: 49
96556 CACGTAGGGG
**
96566 TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCTA-ATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCC-ACATAATTTTA
*
96615 TCTAGCGCGGGGCAGGTACCGCGAC-ATACCTTTACTCCACATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCG-CTATACCTTTACTCCACATAATTTTA
96664 TATAGCGCGGGGCAGGTACCGC
1 TATAGCGCGGGGCAGGTACCGC
96686 ATTTTGTATA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
48 1 0.02
49 63 0.97
50 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (49 bp):
TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCCACATAATTTTA
Found at i:100376 original size:205 final size:207
Alignment explanation
Indices: 99979--100394 Score: 727
Period size: 205 Copynumber: 2.0 Consensus size: 207
99969 ACAATTGATG
99979 AGGAAATGATGTATTTATTGTCAAATAATAATTCTTCTACTTTAATTTGCATTACTTCAAGTTAA
1 AGGAAATGATGTATTTATTGTCAAATAATAATTCTTCTACTTTAATTTGCATTACTTCAAGTTAA
100044 TGTCATTTGATTATCACCGATGAAGATTAAAAAAACAAACACAATCATTAAATTTTAACAAACTA
66 TGTCATTTGA-TATCACCGATGAAGATTAAAAAAACAAACACAATCATTAAATTTTAACAAAC--
100109 ATAACAATAAGTATTAAATGTAAATGATAACCAAAATTACAATAACTGATATTAAATGGTAATAA
128 ATAACAATAAGTATTAAATGTAAATGATAACCAAAATTACAATAACTGATATTAAATGGTAATAA
100174 AAAAAACGAACTGAA
193 AAAAAACGAACTGAA
100189 AGGAAATGATGTATTTTATTGTCAAATAATAATTCTTCTACTTTAATTTGCATTTACTTCAAGTT
1 AGGAAATGATGTA-TTTATTGTCAAATAATAATTCTTCTACTTTAATTTGCA-TTACTTCAAGTT
100254 AATGTCATTT-A-ATCACCGATGAAGATT-AAAAAA-AAACACACATCATTAAATTTTAACAAAC
64 AATGTCATTTGATATCACCGATGAAGATTAAAAAAACAAACACA-ATCATTAAATTTTAACAAAC
100315 -TAACAATAAGTATTAAATGGTAAATGATAACC-AAATTACAATAACTGATATTAAATGGTAATA
128 ATAACAATAAGTATTAAAT-GTAAATGATAACCAAAATTACAATAACTGATATTAAATGGTAATA
100378 AAAAAAACGAACTGAA
192 AAAAAAACGAACTGAA
100394 A
1 A
100395 TACATTAAAA
Statistics
Matches: 202, Mismatches: 0, Indels: 13
0.94 0.00 0.06
Matches are distributed among these distances:
205 66 0.33
206 13 0.06
207 7 0.03
208 26 0.13
209 16 0.08
210 13 0.06
211 39 0.19
212 22 0.11
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.32
Consensus pattern (207 bp):
AGGAAATGATGTATTTATTGTCAAATAATAATTCTTCTACTTTAATTTGCATTACTTCAAGTTAA
TGTCATTTGATATCACCGATGAAGATTAAAAAAACAAACACAATCATTAAATTTTAACAAACATA
ACAATAAGTATTAAATGTAAATGATAACCAAAATTACAATAACTGATATTAAATGGTAATAAAAA
AAACGAACTGAA
Found at i:100442 original size:26 final size:26
Alignment explanation
Indices: 100413--100485 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 26
100403 AAAATCCAAC
**
100413 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAAAAATT
*
100439 AAA-TGAGA-AATAATAAA--AAAAATT
1 AAATTTA-ACAA-AATAAAGTAAAAATT
100463 ACAATTTAACAAAATAAAGTAAA
1 A-AATTTAACAAAATAAAGTAAA
100486 TACAAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 13
0.68 0.08 0.25
Matches are distributed among these distances:
24 6 0.17
25 13 0.36
26 14 0.39
27 3 0.08
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (26 bp):
AAATTTAACAAAATAAAGTAAAAATT
Found at i:100644 original size:12 final size:12
Alignment explanation
Indices: 100613--100655 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
100603 GTCATCGTCA
*
100613 TCGTCGTCATCG
1 TCGTCGTTATCG
100625 TCGTCGTTATCG
1 TCGTCGTTATCG
* * *
100637 TTGTCGTTGTCA
1 TCGTCGTTATCG
100649 TCGTCGT
1 TCGTCGT
100656 CTTGCGCAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.26, G:0.26, T:0.42
Consensus pattern (12 bp):
TCGTCGTTATCG
Found at i:100651 original size:15 final size:15
Alignment explanation
Indices: 100602--100656 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
100592 GACTCCTCGC
*
100602 TGTCATCGTCATCGT
1 TGTCATCGTCGTCGT
*
100617 CGTCATCGTCGTCG-
1 TGTCATCGTCGTCGT
*
100631 T-T-ATCGTTGTCGT
1 TGTCATCGTCGTCGT
100644 TGTCATCGTCGTC
1 TGTCATCGTCGTC
100657 TTGCGCAGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 9 0.28
13 2 0.06
14 1 0.03
15 20 0.62
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (15 bp):
TGTCATCGTCGTCGT
Found at i:102670 original size:110 final size:111
Alignment explanation
Indices: 102476--102696 Score: 372
Period size: 110 Copynumber: 2.0 Consensus size: 111
102466 ATTACAAAAA
* * * *
102476 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
102541 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
102587 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
102651 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
102697 ATGATTTCTA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 70 0.68
111 33 0.32
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:102862 original size:10 final size:10
Alignment explanation
Indices: 102821--102862 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
102811 ACCTTAAAAA
*
102821 GAGAGTATTT
1 GAGAGAATTT
102831 GAGAGAAATTT
1 GAGAG-AATTT
*
102842 -AGAGAAATT
1 GAGAGAATTT
102851 GAGAGAATTT
1 GAGAGAATTT
102861 GA
1 GA
102863 TGTAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 4 0.15
10 19 0.70
11 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:102997 original size:50 final size:50
Alignment explanation
Indices: 102942--103095 Score: 136
Period size: 51 Copynumber: 3.1 Consensus size: 50
102932 CACCCTGCAT
* *
102942 CGCGCTATACCCCACGTG-T-CAGATATACATGTATAGCGCGCTGC-AGGGG
1 CGCGCTATACCCCACGTGCTCCAGAT-CAC-CGTATAGCGCGCTGCAAGGGG
* *
102991 CCGCGCTATA-CCCACGTGGCTCCAGCTCACCGTATAGCGCGGTGCAAGGGG
1 -CGCGCTATACCCCACGT-GCTCCAGATCACCGTATAGCGCGCTGCAAGGGG
* * * * * * *
103042 CGCGCTATACCTCACGTGGCGCCAAATCATCGTATAACGCGATGCAGGGGG
1 CGCGCTATACCCCACGT-GCTCCAGATCACCGTATAGCGCGCTGCAAGGGG
103093 CGC
1 CGC
103096 ACTTTACTGC
Statistics
Matches: 87, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
49 7 0.08
50 32 0.37
51 44 0.51
52 4 0.05
ACGTcount: A:0.21, C:0.32, G:0.30, T:0.18
Consensus pattern (50 bp):
CGCGCTATACCCCACGTGCTCCAGATCACCGTATAGCGCGCTGCAAGGGG
Found at i:103076 original size:51 final size:50
Alignment explanation
Indices: 102972--103095 Score: 151
Period size: 51 Copynumber: 2.5 Consensus size: 50
102962 AGATATACAT
* * **
102972 GTATAGCGCGCTGC-AGGGGCCGCGCTATACCCACGTGGCTCCAGCTCACC
1 GTATAGCGCGATGCAAGGGG-CGCGCTATACCCACGTGGCGCCAAATCACC
* *
103022 GTATAGCGCGGTGCAAGGGGCGCGCTATACCTCACGTGGCGCCAAATCATC
1 GTATAGCGCGATGCAAGGGGCGCGCTATACC-CACGTGGCGCCAAATCACC
* *
103073 GTATAACGCGATGCAGGGGGCGC
1 GTATAGCGCGATGCAAGGGGCGC
103096 ACTTTACTGC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 24 0.38
51 40 0.62
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.16
Consensus pattern (50 bp):
GTATAGCGCGATGCAAGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:103518 original size:16 final size:16
Alignment explanation
Indices: 103497--103533 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
103487 TTTTTTGTGA
103497 CACTTTAAAAGAATGC
1 CACTTTAAAAGAATGC
103513 CACTTTAAAAGAATGC
1 CACTTTAAAAGAATGC
103529 CACTT
1 CACTT
103534 GGATTTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.27
Consensus pattern (16 bp):
CACTTTAAAAGAATGC
Found at i:105818 original size:21 final size:22
Alignment explanation
Indices: 105774--105844 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
105764 GGTATAACTC
*
105774 TAAAATAATAATAAAATGATTA
1 TAAAATAATAATAAAATAATTA
105796 TAAAAT-A-AATAAAATTAATTA
1 TAAAATAATAATAAAA-TAATTA
*
105817 TAAAA-AATAACTATAATAAAATTA
1 TAAAATAATAA-TA-AA-ATAATTA
105841 TAAA
1 TAAA
105845 TATTTTGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
20 7 0.17
21 12 0.29
22 8 0.20
23 2 0.05
24 11 0.27
25 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (22 bp):
TAAAATAATAATAAAATAATTA
Found at i:105819 original size:16 final size:15
Alignment explanation
Indices: 105803--105840 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
105793 TTATAAAATA
*
105803 AATAAAATTAATTAT
1 AATAAAATTAACTAT
105818 AA-AAAA-TAACTAT
1 AATAAAATTAACTAT
105831 AATAAAATTA
1 AATAAAATTA
105841 TAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 8 0.40
14 8 0.40
15 4 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAAATTAACTAT
Found at i:105823 original size:23 final size:23
Alignment explanation
Indices: 105774--105844 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
105764 GGTATAACTC
*
105774 TAAAATAAT-AATAAAA-TGATTA
1 TAAAA-AATAAATAAAATTAATTA
105796 T--AAAATAAATAAAATTAATTA
1 TAAAAAATAAATAAAATTAATTA
* * *
105817 TAAAAAATAACTATAATAAAATTA
1 TAAAAAATAAATAAAAT-TAATTA
105841 TAAA
1 TAAA
105845 TATTTTGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 3 0.08
20 9 0.22
21 6 0.15
22 1 0.03
23 12 0.30
24 9 0.22
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (23 bp):
TAAAAAATAAATAAAATTAATTA
Found at i:106686 original size:29 final size:29
Alignment explanation
Indices: 106644--106718 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
106634 AACCCAACCA
**
106644 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
106673 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
106702 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
106719 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:106724 original size:29 final size:29
Alignment explanation
Indices: 106645--106732 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
106635 ACCCAACCAT
* * ****
106645 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
106674 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
106703 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
106732 A
1 A
106733 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:107000 original size:29 final size:29
Alignment explanation
Indices: 106934--107004 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
106924 AGGTCGTTGG
106934 CTGGTAGGTCGCAGGGCATGCATGGCGAC
1 CTGGTAGGTCGCAGGGCATGCATGGCGAC
*** * *
106963 CTACCAGGTCGCTGGGCGTGCATGGCGAC
1 CTGGTAGGTCGCAGGGCATGCATGGCGAC
106992 CTGGTAGGTCGCA
1 CTGGTAGGTCGCA
107005 CCCTTTGGAC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.15, C:0.27, G:0.39, T:0.18
Consensus pattern (29 bp):
CTGGTAGGTCGCAGGGCATGCATGGCGAC
Found at i:111617 original size:38 final size:39
Alignment explanation
Indices: 111575--111667 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 39
111565 AGCAATATAG
* *
111575 TATAATTTTTGAAAATGCTTT-TAAAAAAATATGTAATA
1 TATAATTTTTGAAAATGCTTTCCAAAAAAATATATAATA
* * * *
111613 TATAATTTTTAGAAAATGGTTTCCGAAAATATATATATTA
1 TATAATTTTT-GAAAATGCTTTCCAAAAAAATATATAATA
111653 TATAATTTTTGAAAA
1 TATAATTTTTGAAAA
111668 CATTTTTAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 10 0.21
39 15 0.32
40 22 0.47
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (39 bp):
TATAATTTTTGAAAATGCTTTCCAAAAAAATATATAATA
Found at i:111684 original size:40 final size:40
Alignment explanation
Indices: 111575--111934 Score: 98
Period size: 39 Copynumber: 9.2 Consensus size: 40
111565 AGCAATATAG
*** * *
111575 TATAATTTTTGAAAATGCTTTTAAAA-AA-ATATGTAATA
1 TATAATTTTTGAAAACATTTTTAAAATAATATATATATTA
*** ***
111613 TATAATTTTTAGAAAATGGTTTCCGAA-AATATATATATTA
1 TATAATTTTT-GAAAACATTTTTAAAATAATATATATATTA
*
111653 TATAATTTTTGAAAACATTTTTAAAATAATATATGGT-TT-
1 TATAATTTTTGAAAACATTTTTAAAATAATATAT-ATATTA
* * * ** *
111692 TGAAAATGTTTTTGCAAATACATATATATTAT-ATATAT-TTTTA
1 T-ATAA--TTTTTG-AAA-ACATTTTTAAAATAATATATATATTA
* * *
111735 -AAACATTTTTGAAAAC----TT-ATATAATATATAGT-TTT
1 TATA-ATTTTTGAAAACATTTTTAAAATAATATATA-TATTA
* * * * *
111770 TAAAATATTTTG-AAATATATAT-ATATA-TATATATATTA
1 TATAAT-TTTTGAAAACATTTTTAAAATAATATATATATTA
* * ** **
111808 TATAGTTTTTAAAAACATTTTTTGAA-AACGTATA-A-TA
1 TATAATTTTTGAAAACATTTTTAAAATAATATATATATTA
* * * *
111845 TATAGTTTTT-AAAACATTTTGAAAA-CATATAAATATTA
1 TATAATTTTTGAAAACATTTTTAAAATAATATATATATTA
** *
111883 TATAAGGTTTGAAAACATTTTTAAAAATATATAATATATAATA
1 TATAATTTTTGAAAACATTTTT-AAAATA-AT-ATATATATTA
111926 TATAATTTT
1 TATAATTTT
111935 CAAAAACGTT
Statistics
Matches: 240, Mismatches: 50, Indels: 59
0.69 0.14 0.17
Matches are distributed among these distances:
33 3 0.01
34 7 0.03
35 7 0.03
36 25 0.10
37 18 0.08
38 42 0.17
39 49 0.20
40 40 0.17
41 5 0.02
42 11 0.05
43 24 0.10
44 9 0.04
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (40 bp):
TATAATTTTTGAAAACATTTTTAAAATAATATATATATTA
Found at i:111704 original size:30 final size:32
Alignment explanation
Indices: 111659--111718 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
111649 ATTATATAAT
111659 TTTTGAAAACATTTTT-AAAATA-ATATATGG
1 TTTTGAAAACATTTTTGAAAATACATATATGG
** *
111689 TTTTGAAAATGTTTTTGCAAATACATATAT
1 TTTTGAAAACATTTTTGAAAATACATATAT
111719 ATTATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.56
31 5 0.20
32 6 0.24
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (32 bp):
TTTTGAAAACATTTTTGAAAATACATATATGG
Found at i:111756 original size:36 final size:36
Alignment explanation
Indices: 111713--111803 Score: 114
Period size: 36 Copynumber: 2.5 Consensus size: 36
111703 TTGCAAATAC
111713 ATATATATTATATATATTTTTAAAACATTTTTGAAA-
1 ATATATATTATATATATTTTTAAAACA-TTTTGAAAT
* *
111749 ACT-TATATAATATATAGTTTTTAAAATATTTTGAAAT
1 A-TATATATTATATATA-TTTTTAAAACATTTTGAAAT
111786 ATATATATATATATATAT
1 ATATATAT-TATATATAT
111804 ATTATATAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
36 22 0.47
37 18 0.38
38 7 0.15
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (36 bp):
ATATATATTATATATATTTTTAAAACATTTTGAAAT
Found at i:111757 original size:38 final size:39
Alignment explanation
Indices: 111700--111806 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 39
111690 TTTGAAAATG
*
111700 TTTTTGCAAATACATATATATTATATATATTTTTAAAACA
1 TTTTTG-AAATACTTATATATTATATATATTTTTAAAACA
*
111740 TTTTTGAAA-ACTTATATA--ATATATAGTTTTTAAAATA
1 TTTTTGAAATACTTATATATTATATATA-TTTTTAAAACA
111777 -TTTTGAAATA-TATATATATATATATATATT
1 TTTTTGAAATACT-TATATAT-TATATATATT
111807 ATATAGTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
36 16 0.27
37 17 0.29
38 8 0.14
39 5 0.08
40 13 0.22
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (39 bp):
TTTTTGAAATACTTATATATTATATATATTTTTAAAACA
Found at i:111853 original size:84 final size:83
Alignment explanation
Indices: 111707--111886 Score: 249
Period size: 84 Copynumber: 2.2 Consensus size: 83
111697 ATGTTTTTGC
* *
111707 AAATACATATATATTATATATATTTTTAAAACATTTTTGAAAACTTATATAATATATAGTTTTTA
1 AAATATATATATATTATATATATTTTAAAAACATTTTTGAAAAC-TATATAATATATAGTTTTTA
* *
111772 AAATATTTTGAAATATATAT
65 AAACATTTTGAAA-ACATAT
* *
111792 ATATATATATATATTATATAGT-TTTTAAAAACATTTTTTGAAAAC-GTATAATATATAGTTTTT
1 AAATATATATATATTATATA-TATTTTAAAAACA-TTTTTGAAAACTATATAATATATAGTTTTT
111855 AAAACATTTTGAAAACATAT
64 AAAACATTTTGAAAACATAT
111875 AAATAT-TATATA
1 AAATATATATATA
111887 AGGTTTGAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
82 6 0.07
83 10 0.12
84 30 0.35
85 28 0.33
86 12 0.14
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (83 bp):
AAATATATATATATTATATATATTTTAAAAACATTTTTGAAAACTATATAATATATAGTTTTTAA
AACATTTTGAAAACATAT
Found at i:111855 original size:37 final size:34
Alignment explanation
Indices: 111800--111922 Score: 111
Period size: 37 Copynumber: 3.4 Consensus size: 34
111790 ATATATATAT
*
111800 ATATATTATATAGTTTTTAAAAACATTTTTTGAAAAC
1 ATATAATATATAGTTTTT-AAAACA--TTTTGAAAAC
*
111837 GTATAATATATAGTTTTTAAAACATTTTGAAAAC
1 ATATAATATATAGTTTTTAAAACATTTTGAAAAC
* * * *
111871 ATATAAATATTATATAAGGTTTGAAAACATTTTTAAAAAT
1 ATAT--A-A-TATAT-AGTTTTTAAAACA-TTTTGAAAAC
111911 ATATAATATATA
1 ATATAATATATA
111923 ATATATAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
34 13 0.18
35 1 0.01
36 12 0.16
37 18 0.25
38 6 0.08
39 11 0.15
40 12 0.16
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (34 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAAC
Found at i:111953 original size:43 final size:41
Alignment explanation
Indices: 111838--111963 Score: 123
Period size: 43 Copynumber: 3.0 Consensus size: 41
111828 TTTGAAAACG
* * *
111838 TATAATATATAGTTTTTAAAACATTTTGAAAACATATAA-A
1 TATAATATATAATTTTAAAAACATTTTGAAAATATATAATA
* * *
111878 TAT--TATATAAGGTTTGAAAACATTTTTAAAAATATATAATA
1 TATAATATATAA-TTTTAAAAACA-TTTTGAAAATATATAATA
* *
111919 TATAATATATAATTTTCAAAAACGTTTTGGAAAATATATTATA
1 TATAATATATAATTTT-AAAAACATTTT-GAAAATATATAATA
111962 TA
1 TA
111964 ATTTTAAAAG
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
38 6 0.09
39 9 0.13
40 17 0.25
41 4 0.06
42 7 0.10
43 26 0.38
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.41
Consensus pattern (41 bp):
TATAATATATAATTTTAAAAACATTTTGAAAATATATAATA
Found at i:116499 original size:75 final size:76
Alignment explanation
Indices: 116376--116527 Score: 288
Period size: 75 Copynumber: 2.0 Consensus size: 76
116366 ATAGGTTGGA
116376 GTTCAAATTGGTACATTTAAGCTGCCACAAAATTATAAAGATTACACTT-AAAAAAAACTCGTTG
1 GTTCAAATTGGTACATTTAAGCTGCCACAAAATTATAAAGATTACACTTAAAAAAAAACTCGTTG
116440 AAGTGAGATAG
66 AAGTGAGATAG
116451 GTTCAAATTGGTACATTTAAGCTGCCACAAAATTATAAAGATTACACTTAAAAAAAAAACTCGTT
1 GTTCAAATTGGTACATTTAAGCTGCCACAAAATTATAAAGATTACACTT-AAAAAAAAACTCGTT
116516 GAAGTGAGATAG
65 GAAGTGAGATAG
116528 ACACAAAGAA
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
75 49 0.65
77 26 0.35
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (76 bp):
GTTCAAATTGGTACATTTAAGCTGCCACAAAATTATAAAGATTACACTTAAAAAAAAACTCGTTG
AAGTGAGATAG
Done.