Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005131.1 Hibiscus syriacus cultivar Beakdansim tig00011550_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: 73899
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:2439 original size:183 final size:183
Alignment explanation
Indices: 2115--2605 Score: 882
Period size: 183 Copynumber: 2.7 Consensus size: 183
2105 TTAAAATTAC
*
2115 CGACACTTTTT-A-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTAACAAT-GTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAA
* * *
2178 TATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGT
65 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
2243 TATATTACAAATTTATCTATTACATTATAATTATGGGTT-CTGATGTGTAAATGT
130 TATATTACAAATTTATCTATTACATTATAATTATGGGTTAC-GATGTGTAAATGT
2297 CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
*
2362 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCAGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
2427 ATATTACAAATTTATCTATTACATTATAATTATGGGTTACGATGTGTAAATGT
131 ATATTACAAATTTATCTATTACATTATAATTATGGGTTACGATGTGTAAATGT
*
2480 CGACACTTTTTAACAATGTATCGAAACA-TTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
1 CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
2544 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
2606 ATAGCATTGC
Statistics
Matches: 299, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
182 108 0.36
183 187 0.63
184 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTAACAATGTATCGACACATTTTTTTTCCAATCTGGACATAAAGTACCGACACAAG
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAATTTATCTATTACATTATAATTATGGGTTACGATGTGTAAATGT
Found at i:4100 original size:3 final size:3
Alignment explanation
Indices: 4092--4172 Score: 81
Period size: 3 Copynumber: 27.0 Consensus size: 3
4082 ACTTGTTTGG
* * * **
4092 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * *
4140 AGC TTC ATC GTC ATC ATC ATC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
4173 GTCAGCTTCA
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:4109 original size:12 final size:12
Alignment explanation
Indices: 4096--4184 Score: 79
Period size: 12 Copynumber: 7.4 Consensus size: 12
4086 GTTTGGATCA
* *
4096 TCATCTTCATCA
1 TCATCATCATCT
*
4108 TCATCATCATCA
1 TCATCATCATCT
*
4120 TCGTCATCATCT
1 TCATCATCATCT
** *
4132 TCATCGCCAGCT
1 TCATCATCATCT
* *
4144 TCATCGTCATCA
1 TCATCATCATCT
4156 TCATCATCATCT
1 TCATCATCATCT
* *
4168 TCATCGTCAGCT
1 TCATCATCATCT
4180 TCATC
1 TCATC
4185 TTCTGCGACC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.22, C:0.35, G:0.07, T:0.36
Consensus pattern (12 bp):
TCATCATCATCT
Found at i:4148 original size:36 final size:36
Alignment explanation
Indices: 4108--4184 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
4098 ATCTTCATCA
*
4108 TCATCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* *
4144 TCATCGTCATCATCATCATCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
4180 TCATC
1 TCATC
4185 TTCTGCGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:5999 original size:199 final size:199
Alignment explanation
Indices: 5640--7403 Score: 3153
Period size: 199 Copynumber: 8.9 Consensus size: 199
5630 TTTAAATTAG
5640 TATCGACACAAACTAAA--ACGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
1 TATCGACACAAACTAAATTA-GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA-
* * *
5703 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGG
64 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGG
*
5767 ATCGACACTTTTTATATATGAATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAA
129 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAA
5832 CAAAAA
194 CAAAAA
*
5838 TATTGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA-A
* * * *
5903 ATTGTACCCGTTTGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
5967 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
6032 AAAAA
195 AAAAA
*
6037 TATCGACACAAACTAAATTAGTGCCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA-A
* *
6102 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
6166 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
6231 AAAAA
195 AAAAA
6236 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
6301 CTTG--CCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 -TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
6363 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
6428 AAAAA
195 AAAAA
6433 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
6497 CTTGTACCGGTT--ATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 -TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
6560 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
6625 AAAAA
195 AAAAA
6630 TATCGACAC-AACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
6694 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 -TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
6759 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
6824 -AAAA
195 AAAAA
6828 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA-A
*
6893 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
6958 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGGAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAA
7023 -AAAAA
194 CAAAAA
7028 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA-A
*
7093 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
7158 TCGGCATTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAC
7223 AAAAA
195 AAAAA
7228 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGA
1 TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA-A
*
7293 CTTGTACC-GTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
7357 TTGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
7404 GGCCATATTG
Statistics
Matches: 1532, Mismatches: 19, Indels: 29
0.97 0.01 0.02
Matches are distributed among these distances:
196 90 0.06
197 298 0.19
198 37 0.02
199 831 0.54
200 276 0.18
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTAAATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAA
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAACA
AAAA
Found at i:7568 original size:19 final size:19
Alignment explanation
Indices: 7522--7570 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
7512 TTATATTCAC
*
7522 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
7541 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
7560 ATACAAAATTA
1 ATACAAAATTA
7571 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:9482 original size:21 final size:21
Alignment explanation
Indices: 9457--9521 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
9447 CCCCTTATGC
* *
9457 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
9478 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
9499 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
9520 CT
1 CT
9522 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:11764 original size:17 final size:18
Alignment explanation
Indices: 11742--11784 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
11732 ATATATCCGG
11742 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
11759 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
11779 TATCAT
1 TATCAT
11785 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:11802 original size:20 final size:19
Alignment explanation
Indices: 11747--11793 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
11737 TCCGGTATCA
11747 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
11766 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
11787 TTTTACC
1 TTTTACC
11794 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:11958 original size:20 final size:20
Alignment explanation
Indices: 11927--11973 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
11917 TCCGGTAACG
11927 TTTTACCAGTTTTATCAT-T
1 TTTTACCAGTTTTATCATAT
*
11946 TTGTTACCGGTTTTATCATAT
1 TT-TTACCAGTTTTATCATAT
11967 TTTTACC
1 TTTTACC
11974 TGGTATATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTACCAGTTTTATCATAT
Found at i:12138 original size:182 final size:181
Alignment explanation
Indices: 11714--12185 Score: 687
Period size: 182 Copynumber: 2.6 Consensus size: 181
11704 CGTACTTACG
* * *
11714 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
11779 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATA-TTTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
11843 AGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATAT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATAT
* * *
11894 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCAGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
11959 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * *
12024 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATA-T
* * * * *
12076 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
12140 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
12186 AATTTGGATC
Statistics
Matches: 261, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
180 96 0.37
181 67 0.26
182 97 0.37
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATAT
Found at i:12187 original size:181 final size:180
Alignment explanation
Indices: 11714--12187 Score: 680
Period size: 180 Copynumber: 2.6 Consensus size: 180
11704 CGTACTTACG
* * *
11714 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* ** *
11779 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATTTTTTTTAAAGTATCGACACATTATA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATA
* *
11844 GGCGCTATAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATAT
131 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATAT
* * *
11894 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCAGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
11959 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTAAAAGTATCGACACATTAT
** * *
12024 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATA-T
* * * * *
12076 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
12140 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTAA
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
12188 TTTGGATCGA
Statistics
Matches: 262, Mismatches: 29, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
180 96 0.37
181 73 0.28
182 92 0.35
183 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (180 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATAT
Found at i:12653 original size:229 final size:228
Alignment explanation
Indices: 12252--12738 Score: 893
Period size: 229 Copynumber: 2.1 Consensus size: 228
12242 ACCTACTTTT
*
12252 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
12317 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
*
12382 ATATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
* *
12447 CAAATATAATAATAAATATGTTTTCAACAGTGAA
196 CAAAGATAATAATAAATATATTTTC-ACAGTGAA
12481 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
* *
12546 ATTTTTTTAATAGTGTTTCATGTTTTCCACTTACAATATTAATTTAATAATTTCATTTACACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
12611 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
*
12676 TAAAGATAATAATAAATATATTTTCACAGTGAA
196 CAAAGATAATAATAAATATATTTTCACAGTGAA
*
12709 ATAAGTATGGACACTTTTATAAAAAGGATA
1 ATAAGTATGGACACTTTTATAAAAATGATA
12739 GATAATTTAT
Statistics
Matches: 250, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
228 37 0.15
229 213 0.85
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (228 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
CAAAGATAATAATAAATATATTTTCACAGTGAA
Found at i:13464 original size:17 final size:18
Alignment explanation
Indices: 13432--13465 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13422 TATTTTATTA
13432 TATTTTAGTCTTAAAATT
1 TATTTTAGTCTTAAAATT
*
13450 TATTTT-GTTTTAAAAT
1 TATTTTAGTCTTAAAAT
13466 CATGCAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (18 bp):
TATTTTAGTCTTAAAATT
Found at i:14131 original size:29 final size:30
Alignment explanation
Indices: 14096--14152 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
14086 TGATCATAAT
* * *
14096 TATTTAAA-GTTTTAAATTTTTATAAAATA
1 TATTTAAACGTTATAAATATTTAAAAAATA
14125 TATTTAAACGTTATAAATATTTAAAAAA
1 TATTTAAACGTTATAAATATTTAAAAAA
14153 AAACTAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (30 bp):
TATTTAAACGTTATAAATATTTAAAAAATA
Found at i:17071 original size:21 final size:20
Alignment explanation
Indices: 17045--17091 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
17035 GCGATGGTAC
17045 CGATACTAAGCAATTTACTAT
1 CGATACTAA-CAATTTACTAT
** *
17066 CGATACTAACCCTTTATTAT
1 CGATACTAACAATTTACTAT
17086 CGATAC
1 CGATAC
17092 CCACTCTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (20 bp):
CGATACTAACAATTTACTAT
Found at i:19320 original size:6 final size:6
Alignment explanation
Indices: 19309--19348 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
19299 AATAGAATAC
19309 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATAC
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATAC
19349 CATCATCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:21008 original size:21 final size:21
Alignment explanation
Indices: 20982--21035 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
20972 AATTTTGTCT
*
20982 TAGTGCATCGGTACACACTCA
1 TAGTGCATCGATACACACTCA
21003 TAGTGCATCGATACACACTCA
1 TAGTGCATCGATACACACTCA
21024 TAGTGCATCGAT
1 TAGTGCATCGAT
21036 GCACCTGCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
TAGTGCATCGATACACACTCA
Found at i:22072 original size:31 final size:29
Alignment explanation
Indices: 22019--22084 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
22009 GTAAGTTTTG
* * *
22019 AAAGTTTAGAGGCCAAAGTATAAACTTTGTA
1 AAAGTTTAGAGACAAAAATAT-AA-TTTGTA
*
22050 AAAGTTTAGAGACAAAAATATAATTTTTA
1 AAAGTTTAGAGACAAAAATATAATTTGTA
22079 AAAGTT
1 AAAGTT
22085 ATATATTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 11 0.35
30 2 0.06
31 18 0.58
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (29 bp):
AAAGTTTAGAGACAAAAATATAATTTGTA
Found at i:23705 original size:18 final size:17
Alignment explanation
Indices: 23672--23705 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
23662 AACTTACTCA
*
23672 TTTTGTAATTTATTTAT
1 TTTTGTAATATATTTAT
23689 TTTTGTAAATATATTTA
1 TTTTGT-AATATATTTA
23706 GGGTAAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTGTAATATATTTAT
Found at i:23826 original size:21 final size:21
Alignment explanation
Indices: 23801--23840 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
23791 CGATGTTAAA
23801 AACTTAACGCGTTTAGTACCC
1 AACTTAACGCGTTTAGTACCC
23822 AACTTAACGCGTTTAGTAC
1 AACTTAACGCGTTTAGTAC
23841 ATAAACTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (21 bp):
AACTTAACGCGTTTAGTACCC
Found at i:28408 original size:28 final size:28
Alignment explanation
Indices: 28376--28435 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
28366 ATATTGTACT
28376 ATTAAAAAATATCATAATTGATAATCAC
1 ATTAAAAAATATCATAATTGATAATCAC
28404 ATTAAAAAATATCATAATTGATAATCAC
1 ATTAAAAAATATCATAATTGATAATCAC
28432 ATTA
1 ATTA
28436 TTATAGGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (28 bp):
ATTAAAAAATATCATAATTGATAATCAC
Found at i:28816 original size:21 final size:21
Alignment explanation
Indices: 28783--28827 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28773 AATTTTGAAA
*
28783 AAAATTGAAAGTTTAGGTACT
1 AAAACTGAAAGTTTAGGTACT
* *
28804 AAAACTGATAGTTTAGTTACT
1 AAAACTGAAAGTTTAGGTACT
28825 AAA
1 AAA
28828 CACGTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (21 bp):
AAAACTGAAAGTTTAGGTACT
Found at i:33926 original size:2 final size:2
Alignment explanation
Indices: 33919--33953 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
33909 TTCTTTACAT
33919 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33954 GAGAGCACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40087 original size:15 final size:15
Alignment explanation
Indices: 40067--40098 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40057 AAAATCTTTC
*
40067 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTAGAT
40082 TTTCCCGTTCTAGAT
1 TTTCCCGTTCTAGAT
40097 TT
1 TT
40099 CGATCTGGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.25, G:0.12, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTAGAT
Found at i:41501 original size:8 final size:8
Alignment explanation
Indices: 41488--41517 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
41478 TTATCAATAA
41488 AAAAATTT
1 AAAAATTT
41496 AAAAATTT
1 AAAAATTT
41504 AAAAATTT
1 AAAAATTT
41512 AAAAAT
1 AAAAAT
41518 AGTATATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAAATTT
Found at i:43938 original size:18 final size:16
Alignment explanation
Indices: 43871--43945 Score: 64
Period size: 17 Copynumber: 4.5 Consensus size: 16
43861 CGGTAAGAAT
43871 TTTAAATTCTATTTTAA
1 TTTAAATT-TATTTTAA
43888 TTTAAA-TTATTGTTAA
1 TTTAAATTTATT-TTAA
**
43904 TATTTTATTTA-TTTAA
1 T-TTAAATTTATTTTAA
43920 TTTAAAATTCTATTTTAA
1 TTT-AAATT-TATTTTAA
*
43938 TTTTAATT
1 TTTAAATT
43946 ATTGTCCAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
15 6 0.13
16 14 0.30
17 16 0.34
18 11 0.23
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (16 bp):
TTTAAATTTATTTTAA
Found at i:44811 original size:15 final size:17
Alignment explanation
Indices: 44791--44830 Score: 66
Period size: 15 Copynumber: 2.5 Consensus size: 17
44781 TTTTATTGAA
44791 TATATTTAAAA-A-TAT
1 TATATTTAAAATAGTAT
44806 TATATTTAAAATAGTAT
1 TATATTTAAAATAGTAT
44823 TATATTTA
1 TATATTTA
44831 CTAGATACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.48
16 1 0.04
17 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATATTTAAAATAGTAT
Found at i:45000 original size:57 final size:57
Alignment explanation
Indices: 44917--45026 Score: 136
Period size: 57 Copynumber: 1.9 Consensus size: 57
44907 ACTTTGTCTA
* *
44917 AAAATATATTTTAGGTATCTAAATAAAAATTGAATA-CTTTAAA-TATTTATTTTGATC
1 AAAATATATTTTAAGTATCTAAATAAAAA-T-AATATATTTAAAGTATTTATTTTGATC
* *
44974 AAAATATATTTTAAGTA-CTTAGATAAATATAATATATTTAAAGTATTTATTTT
1 AAAATATATTTTAAGTATC-TAAATAAAAATAATATATTTAAAGTATTTATTTT
45027 TGAATTAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
55 4 0.09
56 8 0.17
57 34 0.74
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (57 bp):
AAAATATATTTTAAGTATCTAAATAAAAATAATATATTTAAAGTATTTATTTTGATC
Found at i:46400 original size:17 final size:17
Alignment explanation
Indices: 46378--46435 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
46368 TTGTGAAAGG
46378 TCTGATATCTGTAAATA
1 TCTGATATCTGTAAATA
*
46395 TCTGATAACTGT-AATCA
1 TCTGATATCTGTAAAT-A
* *
46412 TCTTATATATGTAAATA
1 TCTGATATCTGTAAATA
*
46429 TTTGATA
1 TCTGATA
46436 ACTGAAACCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 3 0.09
17 27 0.82
18 3 0.09
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (17 bp):
TCTGATATCTGTAAATA
Found at i:46459 original size:34 final size:35
Alignment explanation
Indices: 46382--46459 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 35
46372 GAAAGGTCTG
* * *
46382 ATAT-CTGTAAATATCTGATAACTGTAATCATCTT
1 ATATACTGTAAATATCTGATAACTGAAACCATCTA
*
46416 ATATA-TGTAAATATTTGATAACTGAAACCATCTA
1 ATATACTGTAAATATCTGATAACTGAAACCATCTA
46450 ATA-ACTGTAA
1 ATATACTGTAA
46460 TAATTTAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 1 0.03
34 37 0.97
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (35 bp):
ATATACTGTAAATATCTGATAACTGAAACCATCTA
Found at i:50490 original size:16 final size:16
Alignment explanation
Indices: 50471--50501 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50461 GATGAAAACA
*
50471 AATATTTAATTTTATT
1 AATATTTAAATTTATT
50487 AATATTTAAATTTAT
1 AATATTTAAATTTAT
50502 AGGACCTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATATTTAAATTTATT
Found at i:58392 original size:14 final size:14
Alignment explanation
Indices: 58373--58400 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58363 TCGATAATCT
58373 GTTCATTTATGTTC
1 GTTCATTTATGTTC
58387 GTTCATTTATGTTC
1 GTTCATTTATGTTC
58401 ATTTGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:58409 original size:14 final size:14
Alignment explanation
Indices: 58374--58413 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
58364 CGATAATCTG
*
58374 TTCATTTATGTTCG
1 TTCATTTATGTTCA
58388 TTCATTTATGTTCA
1 TTCATTTATGTTCA
**
58402 TTTGTTTATGTT
1 TTCATTTATGTT
58414 TGTTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (14 bp):
TTCATTTATGTTCA
Found at i:61831 original size:26 final size:26
Alignment explanation
Indices: 61795--61874 Score: 151
Period size: 26 Copynumber: 3.1 Consensus size: 26
61785 TTTGTTTGGT
61795 TAAAATTAAATAAACGAATATGAACA
1 TAAAATTAAATAAACGAATATGAACA
61821 TAAAATTAAATAAACGAATATGAACA
1 TAAAATTAAATAAACGAATATGAACA
*
61847 TAAAATTAAATAAACGAATACGAACA
1 TAAAATTAAATAAACGAATATGAACA
61873 TA
1 TA
61875 CCCTCATTCG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.61, C:0.09, G:0.07, T:0.23
Consensus pattern (26 bp):
TAAAATTAAATAAACGAATATGAACA
Found at i:63912 original size:3 final size:3
Alignment explanation
Indices: 63904--63938 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
63894 GAAAGGTTAG
63904 CTT CTT CTT CTT CTT CCTT CTT CTT CTT CCTT CTT
1 CTT CTT CTT CTT CTT -CTT CTT CTT CTT -CTT CTT
63939 TTTCCTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.80
4 6 0.20
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:63925 original size:10 final size:9
Alignment explanation
Indices: 63904--63938 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
63894 GAAAGGTTAG
63904 CTTCTTCTT
1 CTTCTTCTT
63913 CTTCTTCCTT
1 CTTCTT-CTT
63923 CTTCTTCTT
1 CTTCTTCTT
63932 CCTTCTT
1 -CTTCTT
63939 TTTCCTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (9 bp):
CTTCTTCTT
Found at i:63925 original size:13 final size:13
Alignment explanation
Indices: 63907--63938 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
63897 AGGTTAGCTT
63907 CTTCTTCTTCTTC
1 CTTCTTCTTCTTC
63920 CTTCTTCTTCTTC
1 CTTCTTCTTCTTC
63933 CTTCTT
1 CTTCTT
63939 TTTCCTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTCTTCTTCTTC
Found at i:63943 original size:10 final size:10
Alignment explanation
Indices: 63904--63944 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
63894 GAAAGGTTAG
63904 CTTCTTCTT-
1 CTTCTTCTTC
63913 CTTCTTCCTT-
1 CTTCTT-CTTC
63923 CTTCTTCTTC
1 CTTCTTCTTC
*
63933 CTTCTTTTTC
1 CTTCTTCTTC
63943 CT
1 CT
63945 ATATAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (10 bp):
CTTCTTCTTC
Found at i:66094 original size:21 final size:19
Alignment explanation
Indices: 66058--66097 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
66048 TTTCCATGGT
*
66058 AAAATTTTGCATCATTATG
1 AAAATTTTACATCATTATG
66077 AAAATATTTACATCCATTATG
1 AAAAT-TTTACAT-CATTATG
66098 TTTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (19 bp):
AAAATTTTACATCATTATG
Found at i:67815 original size:12 final size:12
Alignment explanation
Indices: 67797--67827 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
67787 ATGTGAATCT
67797 AAAATGAGACTG
1 AAAATGAGACTG
*
67809 GAAATGAGACTG
1 AAAATGAGACTG
67821 AAAATGA
1 AAAATGA
67828 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.26, T:0.16
Consensus pattern (12 bp):
AAAATGAGACTG
Found at i:71811 original size:255 final size:253
Alignment explanation
Indices: 71351--72089 Score: 992
Period size: 255 Copynumber: 2.9 Consensus size: 253
71341 ATTAAAATTT
* * * * *
71351 CTCAAGAAACAATTGAAATCATATCATATCAATCCAAAAACTAAATTCCTTACATAGGATTACAA
1 CTCAAGAAACAATTGAACTCATAT-ATATCAATCCCAAAACTTAATTCCTTATAGAGGATTACAA
* *
71416 AATGTAGCATCATTTACTGAACCTTCAGGTACCAATAAAATACAGAGGTTCACCCAAGAACAATG
65 AATGTAGCATCATTTACTGAACCTTCAGGCACCAATAAAATCCAGAGGTTCACCCAAGAACAATG
** * * * * * *
71481 CACGGGTAATTTTGCTGAAGTTTAAGAGAATCTAGTTCACAAAAGGAAACATGACCCTTCTTTTT
130 CACAAGTAATTTTCCTGAAGTTTACGAGAACCTAGTTCACAAAAGGCAACAAGACCCTGCTTTTT
* * *
71546 TACATCAGGTTTAGGAATCCAAAATCTCAGCCAAAAATAGGACCA-AAAAAATCAAAACGC
195 CAC-TCAGGTTTA-GAATCCAAAATCTCAGCCAAAAATAGGACCAGAAAAAAGCAAAACAC
* *
71606 CTCAAGAAACAATTTAACTCATATATGTATCAATCCCAAAACTTAATTCCTTATAGAGGAATACA
1 CTCAAGAAACAATTGAACTCATATA--TATCAATCCCAAAACTTAATTCCTTATAGAGGATTACA
*
71671 AAATGTAGCATCATTTACTGAACCTTCAGGCACCAAT-AAATCCAGAGGCTCACCCAAGAACAAT
64 AAATGTAGCATCATTTACTGAACCTTCAGGCACCAATAAAATCCAGAGGTTCACCCAAGAACAAT
*
71735 GCACAAGTAATTTTCCTGAAGTTTACGAGAACCTAGTTCACAAAAGGCAACAAGGCCCTGCTTTT
129 GCACAAGTAATTTTCCTGAAGTTTACGAGAACCTAGTTCACAAAAGGCAACAAGACCCTGCTTTT
* * * * * *
71800 TCACGTCAGGTTTAAGAACCCAAAATCTCAGCCAAAAAGAGGATCAGACAACAGCAGAACAC
194 TCAC-TCAGGTTT-AGAATCCAAAATCTCAGCCAAAAATAGGACCAGAAAAAAGCAAAACAC
*
71862 CTCAATAAACAATTGAACTC----ATATCAA-CCCGAAAACTTAATTCCTTATAGAGGATTACAA
1 CTCAAGAAACAATTGAACTCATATATATCAATCCC-AAAACTTAATTCCTTATAGAGGATTACAA
*
71922 AATGTAGCATCATTTACTGAACCTTCAAGCACCAATAAAATCCAGAGGTTCACCCAAGAACAATG
65 AATGTAGCATCATTTACTGAACCTTCAGGCACCAATAAAATCCAGAGGTTCACCCAAGAACAATG
* * * *
71987 CACAAGTAATTTCCCTGAAGTTTACGAGAGCCTAGTTCACAAAAAGGCAAAAAAACCCTGCTTTC
130 CACAAGTAATTTTCCTGAAGTTTACGAGAACCTAGTTCAC-AAAAGGCAACAAGACCCTGCTTT-
* *
72052 TTCA-TCAGGTTTATAATCCAAATAT-TCAGCAAAAAATA
193 TTCACTCAGGTTTAGAATCCAAA-ATCTCAGCCAAAAATA
72090 AATCTATAAC
Statistics
Matches: 432, Mismatches: 43, Indels: 23
0.87 0.09 0.05
Matches are distributed among these distances:
249 3 0.01
250 88 0.20
251 75 0.17
252 21 0.05
253 4 0.01
254 1 0.00
255 142 0.33
256 98 0.23
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (253 bp):
CTCAAGAAACAATTGAACTCATATATATCAATCCCAAAACTTAATTCCTTATAGAGGATTACAAA
ATGTAGCATCATTTACTGAACCTTCAGGCACCAATAAAATCCAGAGGTTCACCCAAGAACAATGC
ACAAGTAATTTTCCTGAAGTTTACGAGAACCTAGTTCACAAAAGGCAACAAGACCCTGCTTTTTC
ACTCAGGTTTAGAATCCAAAATCTCAGCCAAAAATAGGACCAGAAAAAAGCAAAACAC
Done.