Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000455.1 Hibiscus syriacus cultivar Beakdansim tig00000844_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: 78000
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1695 original size:19 final size:19
Alignment explanation
Indices: 1671--1717 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1661 AATGTAGGGT
1671 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1690 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1709 TAATTTTGT
1 TAATTTTGT
1718 GTGTGAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2257 original size:16 final size:16
Alignment explanation
Indices: 2236--2267 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2226 TTTGTCCAGA
2236 ATGAATGCCCAAAATG
1 ATGAATGCCCAAAATG
2252 ATGAATGCCCAAAATG
1 ATGAATGCCCAAAATG
2268 GTGAGCGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (16 bp):
ATGAATGCCCAAAATG
Found at i:2447 original size:215 final size:214
Alignment explanation
Indices: 2067--2957 Score: 659
Period size: 198 Copynumber: 4.4 Consensus size: 214
2057 GTAAAAAGAT
2067 GTGTCGATACATTTATAAAAGTATCGACCCCAAAAACATTGAAACCCATAATTATAATGTAATAG
1 GTGTCGATACATTTATAAAAGTATCGACCCCAAAAACATTGAAACCCATAATTATAATGTAATAG
* ** ** * *
2132 GTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTTGTGAGAATAGGTCTACATAATGTAT
66 GTAAATTTACAATATAACCGAAATAAATATACCGATTTTTGAGAGAATAGGTCTACATAATGTAT
* * *
2197 CGACACTTTTGAAATTGATGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGATGAATGCCC
131 CGACACTTTGGAAATTGATGTCGATACTGTTTGTCCAGAAGGAATGCCCAAAATGATGAATGCCC
2262 AAAATGGTGAGCGCATAAA
196 AAAATGGTGAGCGCATAAA
* * *
2281 GTGTCGATACATTTATAAAAAGTATTGATCCCAGAAACATTGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTAT-AAAAGTATCGACCCCAAAAACATTGAAACCCATAATTATAATGTAATA
* * * *
2346 GGTAAATTTACAATGTAACCGAAATAACTTTACCGATTTTATGAGAGAATATGTCTACATAATGT
65 GGTAAATTTACAATATAACCGAAATAAATATACCGATTTT-TGAGAGAATAGGTCTACATAATGT
*
2411 ATCGACACTTATGGAATTTG-TGT-GATACTGTTTGTCCAGAAGGAATGCCCAAAA-G--G---G
129 ATCGACACTT-TGGAAATTGATGTCGATACTGTTTGTCCAGAAGGAATGCCCAAAATGATGAATG
* *
2468 -------T-G-CA-CCCATAAA
193 CCCAAAATGGTGAGCGCATAAA
* * * * * *
2480 GTGTCGATATATTTTTTAAAAGTGTCGATCCCAAAGACATCGAAAC-CATAATTATAATGTAATA
1 GTGTCGATACA-TTTATAAAAGTATCGACCCCAAAAACATTGAAACCCATAATTATAATGTAATA
* * ** * ** * * *
2544 AGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGTGAAAATAGGTCTACATAATGT
65 GGTAAATTTACAATATAACCGAAATAAATATACCGATTTT-TGAGAGAATAGGTCTACATAATGT
* * * *
2609 ATCGACAAATTT--AAATTGGTATCGATACT-TTT-T-------G--T--CC-AGA--ATGAATG
129 ATCGAC-ACTTTGGAAATTGATGTCGATACTGTTTGTCCAGAAGGAATGCCCAAAATGATGAATG
*
2656 CCCAAAATGGTGAACGCATAAA
193 CCCAAAATGGTGAGCGCATAAA
* * * * * * *
2678 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAGACATCG-AACCCATAATTATAATATAATA
1 GTGTCGATACATTTAT-AAAAGTATCGACCCCAAAAACATTGAAACCCATAATTATAATGTAATA
* ** * ** * * *
2742 GGTAATTTTGTAATGTAACCGGTATAAATATAGCGATTTATGTGAGAATAGGTCTACATAATGTA
65 GGTAAATTTACAATATAACCGAAATAAATATACCGATTTTTGAGAGAATAGGTCTACATAATGTA
** * * *
2807 TCGACACTTT-TTAATT-ATGCGTCGATACAT-TTTATCCACAATGAATGCCC---A--A--AA-
130 TCGACACTTTGGAAATTGAT--GTCGATAC-TGTTTGTCCAGAAGGAATGCCCAAAATGATGAAT
*
2861 ---C--AATAGTGCA-CGCATAAA
192 GCCCAAAATGGTG-AGCGCATAAA
* * * * *
2879 GTGTCGATACATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTAT-AAAAGTATCGACCCCAAAAACATTGAAACCCATAATTATAATGTAATA
* *
2944 GGTAATTTTTCAAT
65 GGTAAATTTACAAT
2958 GTAATTGGTA
Statistics
Matches: 569, Mismatches: 66, Indels: 96
0.78 0.09 0.13
Matches are distributed among these distances:
184 2 0.00
185 3 0.01
187 1 0.00
188 1 0.00
189 1 0.00
195 1 0.00
196 12 0.02
197 47 0.08
198 185 0.33
199 48 0.08
200 6 0.01
201 53 0.09
202 34 0.06
203 1 0.00
207 3 0.01
209 4 0.01
211 2 0.00
212 1 0.00
214 17 0.03
215 105 0.18
216 35 0.06
217 7 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (214 bp):
GTGTCGATACATTTATAAAAGTATCGACCCCAAAAACATTGAAACCCATAATTATAATGTAATAG
GTAAATTTACAATATAACCGAAATAAATATACCGATTTTTGAGAGAATAGGTCTACATAATGTAT
CGACACTTTGGAAATTGATGTCGATACTGTTTGTCCAGAAGGAATGCCCAAAATGATGAATGCCC
AAAATGGTGAGCGCATAAA
Found at i:2602 original size:198 final size:196
Alignment explanation
Indices: 2252--2985 Score: 922
Period size: 198 Copynumber: 3.7 Consensus size: 196
2242 GCCCAAAATG
*
2252 ATGAATGCCCAAAATGGTG-AGCGCATAAAGTGTCGATACATTTATAAAAAGTATTGATCCCAGA
1 ATGAATGCCCAAAATGGTGCA-CGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGA
* * ** ** * *
2316 AACATTGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGAAATAACTTTACCG
65 AACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCG
* * *
2381 ATTTTATGAGAGAATATGTCTACATAATGTATCGACACTTATGGAATTTGTGT-GATACTGTTTG
130 -TTTTATGTGAGAATAGGTCTACATAATGTATCGACACTT-T-AAATTTGTGTCGATACT-TTTG
2445 TCCAGA
191 TCCAGA
* * * * * * *
2451 AGGAATGCCCAAAAGGGTGCACCCATAAAGTGTCGATATATTTTTTAAAAGTGTCGATCCCA-AA
1 ATGAATGCCCAAAATGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAA
*
2515 GACATCGAAA-CCATAATTATAATGTAATAAGTAATTTTGTAATGTAACCGGTATAAATATACCG
66 -ACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACC-
* * * *
2579 GTTTTATGTGAAAATAGGTCTACATAATGTATCGACAAATTTAAATTGGTATCGATACTTTTTGT
129 GTTTTATGTGAGAATAGGTCTACATAATGTATCGAC-ACTTTAAATTTGTGTCGATAC-TTTTGT
2644 CCAGA
192 CCAGA
* * * *
2649 ATGAATGCCCAAAATGGTGAACGCATAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAG
1 ATGAATGCCCAAAATGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAA
* * *
2714 ACATCG-AACCCATAATTATAATATAATAGGTAATTTTGTAATGTAACCGGTATAAATATAGCGA
66 ACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGT
* * *
2778 TTTATGTGAGAATAGGTCTACATAATGTATCGACACTTTTTAATTATGCGTCGATACATTTTATC
131 TTTATGTGAGAATAGGTCTACATAATGTATCGACAC-TTTAAATT-TGTGTCGATAC-TTTTGTC
*
2843 CACA
193 CAGA
* *
2847 ATGAATGCCCAAAACAATAGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATTGATCCCA
1 ATGAATGCCC--AA-AATGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCA
* **
2912 GAAACATCGAAACCCATGATTATAATGTAATAGGTAATTTT-TCAATGTAATTGGTATAAATATA
63 GAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGT-AATGTAACCGGTATAAATATA
2976 CCGTTTTATG
127 CCGTTTTATG
2986 CTTTTTGTCC
Statistics
Matches: 464, Mismatches: 56, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
196 1 0.00
197 50 0.11
198 234 0.50
199 66 0.14
200 3 0.01
201 54 0.12
202 56 0.12
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (196 bp):
ATGAATGCCCAAAATGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAA
ACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGT
TTTATGTGAGAATAGGTCTACATAATGTATCGACACTTTAAATTTGTGTCGATACTTTTGTCCAG
A
Found at i:3094 original size:147 final size:148
Alignment explanation
Indices: 2866--3132 Score: 383
Period size: 147 Copynumber: 1.8 Consensus size: 148
2856 CAAAACAATA
* * * *
2866 GTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATGA
1 GTGCACCCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCAAAACCCATAA
* * **
2931 TTATAATGTAATAGGTAATTTTTCAATGTAATTGGTATAAATATACCGTTTTATGCTTTTTGTCC
66 TTATAATGTAATAGGTAAATTTCCAATGTAACCGGTATAAATATACCGTTTTATGCTTTTTGTCC
2996 AAAATGAATGCCAAATGG
131 AAAATGAATGCCAAATGG
* * * * **
3014 GTGCACCCATTAAGTGTCGATACATTTTTAAAAAGTGTCGATCTCA-AAACATCAAAACCGGTAA
1 GTGCACCCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCAAAACCCATAA
* *
3078 TTATAATGTAATAGGTAAATTTCCAATGTACCCGGTATAAATATACGGTTTTATG
66 TTATAATGTAATAGGTAAATTTCCAATGTAACCGGTATAAATATACCGTTTTATG
3133 AGAAAATAGA
Statistics
Matches: 103, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
147 63 0.61
148 40 0.39
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (148 bp):
GTGCACCCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCAAAACCCATAA
TTATAATGTAATAGGTAAATTTCCAATGTAACCGGTATAAATATACCGTTTTATGCTTTTTGTCC
AAAATGAATGCCAAATGG
Found at i:4694 original size:12 final size:12
Alignment explanation
Indices: 4659--4697 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4649 GGTCAATAAA
*
4659 GATGAATATGAC
1 GATGAATATGAT
*
4671 GATGAAGATGAT
1 GATGAATATGAT
*
4683 GATGATTATGAT
1 GATGAATATGAT
4695 GAT
1 GAT
4698 CCAAACAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (12 bp):
GATGAATATGAT
Found at i:6041 original size:30 final size:30
Alignment explanation
Indices: 5982--6042 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5972 ATTTCATATA
* * *
5982 TAATTGGAGTTTGAATTTTAATTTTAATTT
1 TAATTGGAGTTTGAATTTCAATATAAATTT
* *
6012 TAATTTGAGTTTGAATTTCGATATAAATTT
1 TAATTGGAGTTTGAATTTCAATATAAATTT
6042 T
1 T
6043 GGCTCCACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.54
Consensus pattern (30 bp):
TAATTGGAGTTTGAATTTCAATATAAATTT
Found at i:8295 original size:199 final size:198
Alignment explanation
Indices: 7375--8330 Score: 1168
Period size: 200 Copynumber: 4.9 Consensus size: 198
7365 TAAAGTTTCA
* *
7375 CATAAAGTGTCGATACATGTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
** * * *
7440 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAATTTTTTTGAGAAAATAGAT--AC
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACC-GGTTTTATGAGAGAATAGGTCAAC
* * * * *
7503 GTAATGTATCGATACTTATAGAATTTGTGTCGATGCTTTTTGTCCAAAATGAATGCC-AA-----
130 ATAATGTATCGACACTTTTA-AATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAGGGGT
7562 --ACG
194 GCACG
**
7565 --TAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACTATATAATTATAA
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAAC-CGATAATTATAA
* * ** * * * *
7628 TGTAATAGTTAATTTTGTAATATAACTGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTAC
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAAC
* * * **
7693 GTAATGTGTCGACACTTTTAAATTTTGTGTCGATACTTTTTGTCCAGAATGATTGCCCAAAATGG
130 ATAATGTATCGACACTTTTAAA-TTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAAGGGG
*
7758 TGAACG
193 TGCACG
* * * * *
7764 CATAAAGTGTTGATACATTTATAAAAAGTATCGATCCTAGAAACATCGAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* *
7829 GTAATAGGTAAATTTACAATGTAACCGGTATAACTATACCGGTTTTATGAGAGAATAGGTCTACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACA
** * * *
7894 TAATGTATCGACACTTGTGGAAGTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTT
131 TAATGTATCGACACTT-TTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCC-AAAGGGGT
7959 GCACG
194 GCACG
* * *
7964 TATAAAGTGTCGATACATTTTTAAAAAGTATC-AGTCCCAAAAATATCGAAACCGATAACTATAA
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGA-TCCCAAAAACATCGAAACCGATAATTATAA
* * * *
8028 TGTAATAGGTAAATTTACAATGTAACTGGTATAAATTTACCGGTTTTATGAGAAAATAGGTGAAC
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAAC
* * *
8093 ATAATGTATCGACACGTTTTAGATTTGTGTCGATACATTTTGTCCAGAATGAATGTCAAACGGGG
130 ATAATGTATCGACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAA-GGGG
*
8158 TGCAGG
193 TGCACG
* * ** * *
8164 CACAAAGTGTCGATACA-TTTGAAATTGTGTCGATCCCAAAAACATCGAAACCGATAATTATAAC
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* **
8228 GTAATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAGAATATATCAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACA
*
8293 TAATGTATCAACACTTTTAAATTTGTGTCGATA-TTTTT
131 TAATGTATCGACACTTTTAAATTTGTGTCGATACTTTTT
8331 AAATAACGTA
Statistics
Matches: 656, Mismatches: 89, Indels: 35
0.84 0.11 0.04
Matches are distributed among these distances:
188 63 0.10
189 46 0.07
190 48 0.07
191 2 0.00
192 2 0.00
197 4 0.01
198 18 0.03
199 118 0.18
200 304 0.46
201 51 0.08
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (198 bp):
CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCAACA
TAATGTATCGACACTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAGGGGTGC
ACG
Found at i:11930 original size:199 final size:197
Alignment explanation
Indices: 11485--12200 Score: 865
Period size: 199 Copynumber: 3.6 Consensus size: 197
11475 CCTAAATATA
11485 TGTCGATACATTT-TCTAAAAGTATCGA-CCCAAAAAACATCGAAACCAATAATTATAATGTAAT
1 TGTCGATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCAATAATTATAATGTAAT
* * * * * *
11548 AGGTAAATTAACAATGTAACCAGTATAAATATACC-GGTTAATTAGAAAACAAGTCAACATAATG
64 AGGTAAATTTACAATGTAACCGGTATAAATATACCTGGTTTATGAGAAAATAGGTC-ACATAATG
** * **
11612 TATCGACACTTGTGCAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAATGAATTGCAC
128 TATCGACACTTGTTAAATTTGTGTCGATACTT-TTGTCCAGAATGAATG-CCAAA-CAGGTGCAC
11677 GCATAAAG
190 GCATAAAG
*
11685 TGTCGATACATTTATTAAAAGTATCGATCCCAATAAA-ATCGAAACCGATAATTATAATGTAATA
1 TGTCGATACATTTATTAAAAGTATCGATCCCAA-AAACATCGAAACCAATAATTATAATGTAATA
* * *
11749 TGTAAATTTACAATGTAACCGGTATAAATATACCTGTTTTATGAGAAAATAGGTCAGCATAAAGT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCTGGTTTATGAGAAAATAGGTCA-CATAATGT
* *
11814 ATCGACACTTGTTAAATTTGTGTCGATACATTTTGTCCATAATGAATGCCAAACAGGTGCACACA
129 ATCGACACTTGTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACAGGTGCACGCA
11879 TAAAG
193 TAAAG
* * * *
11884 TGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTACAATATGATAG
1 TGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAG
* * * * *
11949 GTAAATTTACAATGTACCCGATAGAAATATATC-GGCTTTATGAGAAAATAGGTCTAAATAATGT
66 GTAAATTTACAATGTAACCGGTATAAATATACCTGG-TTTATGAGAAAATAGGTC-ACATAATGT
* * * * * *
12013 ATCAACACTTTTTAAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACGAGGTGCACGTA
129 ATCGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAAC-AGGTGCACGCA
12078 TAAAG
193 TAAAG
** * *
12083 TGTCGATACATTTCA--AATTGTATCGATCCAAAAAATATCGAAACCAATAATTATAATGTAATA
1 TGTCGATACATTT-ATTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
* * * * * *
12146 GGAAAATTTGCAATGTTA-CTGTATAAATATA-CTGGTTTACTTATAAAATAGGTCA
65 GGTAAATTTACAATGTAACCGGTATAAATATACCTGGTTTA-TGAGAAAATAGGTCA
12201 ATATAGGCGC
Statistics
Matches: 450, Mismatches: 53, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
196 6 0.01
197 24 0.05
198 79 0.18
199 176 0.39
200 92 0.20
201 71 0.16
202 2 0.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (197 bp):
TGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTATAAATATACCTGGTTTATGAGAAAATAGGTCACATAATGTAT
CGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACAGGTGCACGCATAA
AG
Found at i:17722 original size:26 final size:26
Alignment explanation
Indices: 17693--17742 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
17683 TAGTATGGCA
17693 GTAACTGCTGCAGAAATAGTTTGGTT
1 GTAACTGCTGCAGAAATAGTTTGGTT
17719 GTAACTGCTGCAGAAATAGTTTGG
1 GTAACTGCTGCAGAAATAGTTTGG
17743 CTGACAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (26 bp):
GTAACTGCTGCAGAAATAGTTTGGTT
Found at i:19613 original size:112 final size:113
Alignment explanation
Indices: 19431--19904 Score: 731
Period size: 112 Copynumber: 4.2 Consensus size: 113
19421 AACTTTCAAC
* * **
19431 AAAGTATCGATACATTTTTATAAAAAGTATTTATACTTTCAACATATCAGGTAAATTTTACCGGT
1 AAAGTATCGATACTTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
*
19496 TTTGTCATAATGAAAGTGGTTTTGTCATATTTTTACATGTTATATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
* * * *
19544 AAAGTATCGAT-CCTTTTTATAAAAATGATCGATACTTTCAACATATCAAGTAAATTTTACTGGT
1 AAAGTATCGATACTTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
* *
19608 TTTGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
* *
19656 AAAGTATTGAT-CTTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTATATTTTACCGGT
1 AAAGTATCGATACTTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
* *
19720 TTTGTCATAATGAAACTGGTTTTGTCATACTTTTA-ACTGCTATATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACA-TGTTATATTGT
* * *
19768 AAAGTATCAATATTTTTTTATAAAAAGGATCGATACTTTCAACATATCCGGTAAATTTTACCGGT
1 AAAGTATCGATACTTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
*
19833 TTTGTCATAACGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
19881 AAAGTATCGATA-TATTTTTATAAA
1 AAAGTATCGATACT-TTTTTATAAA
19905 GTATCGATAC
Statistics
Matches: 328, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
112 202 0.62
113 125 0.38
114 1 0.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.43
Consensus pattern (113 bp):
AAAGTATCGATACTTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
Found at i:19850 original size:225 final size:224
Alignment explanation
Indices: 19431--19904 Score: 725
Period size: 225 Copynumber: 2.1 Consensus size: 224
19421 AACTTTCAAC
* * **
19431 AAAGTATCGATACATTTTTATAAAAAGTATTTATACTTTCAACATATCAGGTAAATTTTACCGGT
1 AAAGTATCGAT-CTTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
* * * *
19496 TTTGTCATAATGAAAGTGGTTTTGTCATATTTTTACATGTTATATTGTAAAGTATCGATCCTTTT
65 TTTGTCATAATGAAACTGGTTTTGTCATATTTTAACATGCTATATTGTAAAGTATCAATCCTTTT
* * *
19561 TATAAAAATGATCGATACTTTCAACATATCAAGTAAATTTTACTGGTTTTGTCATAATGAAACTG
130 TATAAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCGGTTTTGTCATAACGAAACTG
*
19626 ATTTTGTCATATTTTTACCTGTTATATTGT
195 ATTTTGTCATATTTTTACATGTTATATTGT
* *
19656 AAAGTATTGATCTTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTATATTTTACCGGTT
1 AAAGTATCGATCTTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
**
19721 TTGTCATAATGAAACTGGTTTTGTCATACTTTTAAC-TGCTATATTGTAAAGTATCAATATTTTT
66 TTGTCATAATGAAACTGGTTTTGTCATA-TTTTAACATGCTATATTGTAAAGTATCAAT-CCTTT
**
19785 TTATAAAAAGGATCGATACTTTCAACATATCCGGTAAATTTTACCGGTTTTGTCATAACGAAACT
129 TTATAAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCGGTTTTGTCATAACGAAACT
*
19850 GGTTTTGTCATATTTTTACATGTTATATTGT
194 GATTTTGTCATATTTTTACATGTTATATTGT
*
19881 AAAGTATCGATATATTTTTATAAA
1 AAAGTATCGATCT-TTTTTATAAA
19905 GTATCGATAC
Statistics
Matches: 225, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
224 96 0.43
225 119 0.53
226 10 0.04
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.43
Consensus pattern (224 bp):
AAAGTATCGATCTTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
TTGTCATAATGAAACTGGTTTTGTCATATTTTAACATGCTATATTGTAAAGTATCAATCCTTTTT
ATAAAAAGGATCGATACTTTCAACATATCAAGTAAATTTTACCGGTTTTGTCATAACGAAACTGA
TTTTGTCATATTTTTACATGTTATATTGT
Found at i:20264 original size:76 final size:76
Alignment explanation
Indices: 20173--20326 Score: 245
Period size: 76 Copynumber: 2.0 Consensus size: 76
20163 ATATAATCGC
*
20173 TACCTATTACGTTATATAAGCGCTACCTAATATATTACTGTGCTTAATAATGTTTCCAGTAATTA
1 TACCTATTACATTATATAAGCGCTACCTAATATATTACTGTGCTTAATAATGTTTCCAGTAATTA
20238 ACATATTTTAT
66 ACATATTTTAT
* * * * *
20249 TACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCTTGATAATGTTTTCAGTAATTA
1 TACCTATTACATTATATAAGCGCTACCTAATATATTACTGTGCTTAATAATGTTTCCAGTAATTA
*
20314 ACCTATTTTAT
66 ACATATTTTAT
20325 TA
1 TA
20327 TATAAGTGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (76 bp):
TACCTATTACATTATATAAGCGCTACCTAATATATTACTGTGCTTAATAATGTTTCCAGTAATTA
ACATATTTTAT
Found at i:20847 original size:93 final size:92
Alignment explanation
Indices: 20738--20933 Score: 288
Period size: 92 Copynumber: 2.1 Consensus size: 92
20728 TAATGAAACT
*
20738 GATTTTGTCATCTTTTTA-ACTGTTATATTATAAAGTATCGAT-CTTTTTTATAAAAAAAGATTG
1 GATTTTGTCATCTTTTTACA-TGTTATATTATAAAGTATCGATAC-TTTTTAT-AAAAAAGATCG
20801 ATACTTTCAACATATCAAGTAAATTTTACC
63 ATACTTTCAACATATCAAGTAAATTTTACC
* * *
20831 GATTTTGTCATGTTTTTACATGTTATATTGTAAAGTATCGATACTTTTTATAAAAAGGATCGATA
1 GATTTTGTCATCTTTTTACATGTTATATTATAAAGTATCGATACTTTTTATAAAAAAGATCGATA
* *
20896 CTTTCAACATATTAGGTAAATTTTACC
66 CTTTCAACATATCAAGTAAATTTTACC
*
20923 GGTTTTGTCAT
1 GATTTTGTCAT
20934 AATGAAACTG
Statistics
Matches: 94, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 47 0.50
93 45 0.48
94 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (92 bp):
GATTTTGTCATCTTTTTACATGTTATATTATAAAGTATCGATACTTTTTATAAAAAAGATCGATA
CTTTCAACATATCAAGTAAATTTTACC
Found at i:21030 original size:112 final size:113
Alignment explanation
Indices: 20833--21348 Score: 828
Period size: 112 Copynumber: 4.6 Consensus size: 113
20823 ATTTTACCGA
* *
20833 TTTTGTCATGTTTTTACATGTTATATTGTAAAGTATCGATAC-TTTTTATAAAAAGGATCGATAC
1 TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACATTTTTATAAAAAGGATCGATAC
*
20897 TTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGG
66 TTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGG
* *
20945 TTTTGTCATATTTTTACCTATTATATTGTAAAGTATCGAT-CTTTTTTATAAAAAGGATCGATAC
1 TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACATTTTTATAAAAAGGATCGATAC
*
21009 TTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGA
66 TTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGG
*
21057 TTTTGTCATATTTTTACATGTTATATTGTAAAGTATCGAT-CATTTTTATAAAAAGGATCGATAC
1 TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACATTTTTATAAAAAGGATCGATAC
* * *
21121 TTTCAATATATCAGGTAAATTTTGCCGGTTTTGTCATAATGAAATTGG
66 TTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGG
* *
21169 TTTTGTTATATTTTTACCTGTTATATTGTAAAGTATCGATACATTTTTTTTAAAAAGGATCGATA
1 TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACA-TTTTTATAAAAAGGATCGATA
* *
21234 CTTTCAACATATCCGGTAAATTTTACCGGTTTTGTCATAATGAAAGTAGG
65 CTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACT-GG
* *
21284 -TTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACATATTTAT--AAAGTATCGATAC
1 TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACATTTTTATAAAAAGGATCGATAC
21346 TTT
66 TTT
21349 ATAGGCGCTA
Statistics
Matches: 377, Mismatches: 23, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
111 16 0.04
112 248 0.66
113 7 0.02
114 104 0.28
115 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (113 bp):
TTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACATTTTTATAAAAAGGATCGATAC
TTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGG
Found at i:21351 original size:18 final size:19
Alignment explanation
Indices: 21311--21351 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
21301 TGTTATATTG
21311 TAAAGTATCGATACATATTTA
1 TAAAGTATCGATAC--ATTTA
21332 TAAAGTATCGATAC-TTTA
1 TAAAGTATCGATACATTTA
21350 TA
1 TA
21352 GGCGCTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
21 14 0.70
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
TAAAGTATCGATACATTTA
Found at i:21569 original size:23 final size:23
Alignment explanation
Indices: 21543--21592 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
21533 ACATATTTTA
*
21543 TTATATAAGAGCTACCTATTATG
1 TTATATAAGAGCTACCTAATATG
*
21566 TTATATAAGCGCTACCTAATATG
1 TTATATAAGAGCTACCTAATATG
21589 TTAT
1 TTAT
21593 TGTGCTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATATAAGAGCTACCTAATATG
Found at i:21673 original size:87 final size:87
Alignment explanation
Indices: 21527--21871 Score: 591
Period size: 87 Copynumber: 4.0 Consensus size: 87
21517 ACAAATTAAA
* * **
21527 TAATTAACATATTTTATTATATAAGAGCTACCTATTATGTTATATAAGCGCTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
21592 TTGTGCTTGATAATGTTTCTAG
66 TTGTGCTTGATAATGTTTCTAG
* *
21614 TAATTAACTTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
*
21679 TTGTGCTTGATAATGTTTCCAG
66 TTGTGCTTGATAATGTTTCTAG
*
21701 TAATTAACCTATTTTATTATATAAGCACTACCTATTACATTATATAAGCGCTACCTAATATGTTA
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
21766 TTGTGCTTGATAATGTTTCTAG
66 TTGTGCTTGATAATGTTTCTAG
* * *
21788 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATATTT
1 TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
21853 TTGTGCTTGATAATGTTTC
66 TTGTGCTTGATAATGTTTC
21872 CGGTTAAATG
Statistics
Matches: 244, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 244 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.43
Consensus pattern (87 bp):
TAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTA
TTGTGCTTGATAATGTTTCTAG
Found at i:21679 original size:23 final size:23
Alignment explanation
Indices: 21629--21673 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
21619 AACTTATTTT
*
21629 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
21652 ATTATATAAGCGGTACCTAATA
1 ATTATATAAGCGCTACCTAATA
21674 TGTTATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:21742 original size:23 final size:23
Alignment explanation
Indices: 21707--21757 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
21697 CCAGTAATTA
**
21707 ACCTATTTTATTATATAAGCACT
1 ACCTATTACATTATATAAGCACT
*
21730 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCACT
21753 ACCTA
1 ACCTA
21758 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCACT
Found at i:21829 original size:23 final size:23
Alignment explanation
Indices: 21794--21844 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
21784 CTAGTAATTA
**
21794 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
21817 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
21840 ACCTA
1 ACCTA
21845 ATATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:21923 original size:16 final size:16
Alignment explanation
Indices: 21904--21948 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
21894 CGGTCTAAAT
21904 TTTAACCGGTCACTTA
1 TTTAACCGGTCACTTA
* *
21920 TTTAACCGATCAATTA
1 TTTAACCGGTCACTTA
*
21936 TTTAACCAGTCAC
1 TTTAACCGGTCAC
21949 GCTGTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (16 bp):
TTTAACCGGTCACTTA
Found at i:24243 original size:104 final size:104
Alignment explanation
Indices: 24080--24276 Score: 238
Period size: 104 Copynumber: 1.9 Consensus size: 104
24070 TCCGAAGAAA
* * * *
24080 AACCCAAAATAGAAATCAGAAATCAAGATGGGGACATTACCTTCCACAGAGGAACCCAAATACAT
1 AACCCAAAATAGAAAACAGAAATCAAGATGGGGACATTACCCTCCACAGAGGAACCCAAACA-AA
* * **
24145 AAAATAGGAAATTGGATAGAGACGTTACCCTATGAAGAGG
65 AAAACAAGAAATAAGATAGAGACGTTACCCTATGAAGAGG
* * * *
24185 AACCC-AAATAGAAAACATGAAA-CATGATGTGGACATTACCCTCTGA-AGAGGAATCCAAACAA
1 AACCCAAAATAGAAAACA-GAAATCAAGATGGGGACATTACCCTC-CACAGAGGAACCCAAACAA
24247 AAAAACAAGAAATAAGATAGAGACGTTACC
64 AAAAACAAGAAATAAGATAGAGACGTTACC
24277 ATCCGAGGAG
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
103 26 0.33
104 42 0.54
105 10 0.13
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.16
Consensus pattern (104 bp):
AACCCAAAATAGAAAACAGAAATCAAGATGGGGACATTACCCTCCACAGAGGAACCCAAACAAAA
AAACAAGAAATAAGATAGAGACGTTACCCTATGAAGAGG
Found at i:25159 original size:35 final size:36
Alignment explanation
Indices: 25095--25165 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
25085 GTATGTACAG
25095 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
25131 GGGAACAGATTCCCCCT-GGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
25166 CTTAATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 18 0.51
36 17 0.49
ACGTcount: A:0.17, C:0.31, G:0.32, T:0.20
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
Found at i:25619 original size:23 final size:22
Alignment explanation
Indices: 25592--25666 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
25582 TGATATATGA
25592 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
* ** *
25615 ATATG-ATATGAAATGACATATG
1 ATATGAATACGTGAT-ACATGTG
25637 AATATGTAATACGTGATACATGTG
1 -ATATG-AATACGTGATACATGTG
25661 ATATGA
1 ATATGA
25667 TATGAAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
23 15 0.38
24 6 0.15
25 6 0.15
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Found at i:25625 original size:46 final size:46
Alignment explanation
Indices: 25574--25678 Score: 185
Period size: 46 Copynumber: 2.3 Consensus size: 46
25564 CTATATGACT
*
25574 ATATGAAATGATATATGAATATGCAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
*
25620 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
25666 ATATGAAAT-ACAT
1 ATATGAAATGACAT
25679 GGTTACACAT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 4 0.07
46 53 0.93
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
Found at i:25878 original size:17 final size:17
Alignment explanation
Indices: 25856--25955 Score: 119
Period size: 17 Copynumber: 5.6 Consensus size: 17
25846 ACAGATTACA
* *
25856 TCCTTCGGGATGACAGG
1 TCCTTCGGGACGATAGG
**
25873 TCCTTCGGGACACAGATGACA
1 TCCTTCGGG--AC-GAT-AGG
*
25894 TCCTTCGGGATGATAGG
1 TCCTTCGGGACGATAGG
25911 TCCTTCGGGACGATAGG
1 TCCTTCGGGACGATAGG
25928 TCCTTCGGGACGATAGG
1 TCCTTCGGGACGATAGG
25945 TCCTTCGGGAC
1 TCCTTCGGGAC
25956 ATTTATATGA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
17 54 0.76
18 3 0.04
19 2 0.03
20 2 0.03
21 10 0.14
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.24
Consensus pattern (17 bp):
TCCTTCGGGACGATAGG
Found at i:25883 original size:38 final size:38
Alignment explanation
Indices: 25827--25956 Score: 178
Period size: 38 Copynumber: 3.5 Consensus size: 38
25817 TATAAGACAT
*
25827 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATTACATCCTTCGGG
* *
25865 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATTACATCCTTCGGG
**
25903 ATGATAGGTCCTTCGGG--AC-GA-TAGGTCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATTACATCCTTCGGG
*
25937 ACGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
25957 TTTATATGAG
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
34 26 0.32
35 2 0.02
36 3 0.04
38 51 0.62
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATTACATCCTTCGGG
Found at i:25899 original size:21 final size:21
Alignment explanation
Indices: 25835--25903 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
25825 ATATGATAGG
* *
25835 TCCTACGGGACACAGATTACA
1 TCCTTCGGGACACAGATGACA
*
25856 TCCTTCGGGATGACAG--G---
1 TCCTTCGGGA-CACAGATGACA
25873 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
25894 TCCTTCGGGA
1 TCCTTCGGGA
25904 TGATAGGTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Found at i:26146 original size:20 final size:21
Alignment explanation
Indices: 26110--26151 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
26100 TGACATTATT
*
26110 TATATATATGTCATATTGAAA
1 TATATACATGTCATATTGAAA
26131 TATATACATG-CATATTGAAA
1 TATATACATGTCATATTGAAA
26151 T
1 T
26152 GTTATGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (21 bp):
TATATACATGTCATATTGAAA
Found at i:31321 original size:20 final size:21
Alignment explanation
Indices: 31285--31326 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
31275 TGACATTATT
*
31285 TATATATATGTCATATTGAAA
1 TATATACATGTCATATTGAAA
31306 TATATACATG-CATATTGAAA
1 TATATACATGTCATATTGAAA
31326 T
1 T
31327 GTTATGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (21 bp):
TATATACATGTCATATTGAAA
Found at i:42507 original size:23 final size:23
Alignment explanation
Indices: 42481--42529 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
42471 ATAAAGAACC
*
42481 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
42504 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
42527 AAA
1 AAA
42530 CCAACCACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:52227 original size:23 final size:23
Alignment explanation
Indices: 52201--52249 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
52191 ATAAAGAACC
*
52201 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
52224 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
52247 AAA
1 AAA
52250 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:59882 original size:18 final size:20
Alignment explanation
Indices: 59832--59882 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 20
59822 TGTGTTTTCT
* *
59832 TTTTTAAAAATATATAATTT
1 TTTTTAAAATTATATAATTA
**
59852 TTTTTAATTTTATAT-A-TA
1 TTTTTAAAATTATATAATTA
59870 TTTTTAAAATTAT
1 TTTTTAAAATTAT
59883 CAGATTGTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 12 0.48
19 1 0.04
20 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTAAAATTATATAATTA
Found at i:60357 original size:15 final size:15
Alignment explanation
Indices: 60337--60387 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
60327 TTTTAAAAAA
60337 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
60352 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
*
60367 TGAATTACTGAAATT
1 TGAATTACTGGAATT
60382 TGAATT
1 TGAATT
60388 TTAAAAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:60427 original size:14 final size:14
Alignment explanation
Indices: 60405--60445 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
60395 ATGAATTACA
*
60405 TTTCTGGAAAATGT
1 TTTCCGGAAAATGT
*
60419 TTTCCGGAAAATAT
1 TTTCCGGAAAATGT
*
60433 TTTCCGTAAAATG
1 TTTCCGGAAAATG
60446 AATTACATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:60716 original size:23 final size:23
Alignment explanation
Indices: 60667--60717 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
60657 GTGTTATATT
**
60667 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
60690 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
60713 ATATT
1 ATATT
60718 ATTTGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:60756 original size:24 final size:26
Alignment explanation
Indices: 60729--60785 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
60719 TTTGATTATT
60729 ATATTA-A-TATTAAATATATAAATA
1 ATATTATATTATTAAATATATAAATA
60753 ATATTATTCATTATTAAATATATAAA-A
1 ATATTA-T-ATTATTAAATATATAAATA
60780 AT-TTAT
1 ATATTAT
60786 TATATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 6 0.21
25 1 0.03
26 3 0.10
27 4 0.14
28 15 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTATATTATTAAATATATAAATA
Found at i:60832 original size:23 final size:23
Alignment explanation
Indices: 60806--60856 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
60796 TTAAAATAAA
*
60806 AATATAATATCTTATATTATTAT
1 AATATAATATATTATATTATTAT
* *
60829 AATATAATTTATTATTTTATTAT
1 AATATAATATATTATATTATTAT
60852 AATAT
1 AATAT
60857 TAAAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:60885 original size:22 final size:20
Alignment explanation
Indices: 60853--60908 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
60843 TTTTATTATA
* *
60853 ATATTAAAAATATAATATAAT
1 ATATTATAAATATAACA-AAT
60874 ATTATTATAAATATTAACAAAT
1 A-TATTATAAATA-TAACAAAT
*
60896 ATATTTTAAATAT
1 ATATTATAAATAT
60909 TTTAATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.03
21 11 0.37
22 14 0.47
23 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTATAAATATAACAAAT
Found at i:61211 original size:42 final size:42
Alignment explanation
Indices: 61122--61211 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
61112 TTTCTTCAAT
* * *
61122 CAAACACTGAAAAATATTTTTCTAAAAATGAATTACGTGAAA
1 CAAACACTGAAAAATATTTTTCTAAAAACGAATTACATAAAA
61164 CAAACAC-GAAAAA-ATATTTTCTAAAAAACGAATTACATAAAA
1 CAAACACTGAAAAATAT-TTTTCT-AAAAACGAATTACATAAAA
*
61206 TAAACA
1 CAAACA
61212 TTAAATTTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 2 0.05
41 12 0.29
42 28 0.67
ACGTcount: A:0.56, C:0.13, G:0.07, T:0.24
Consensus pattern (42 bp):
CAAACACTGAAAAATATTTTTCTAAAAACGAATTACATAAAA
Found at i:62695 original size:36 final size:36
Alignment explanation
Indices: 62648--62732 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
62638 AAGAGAATAA
* * *
62648 TTTCCCTGCACCCCCAGCACCGGTTCTACTCGATAG
1 TTTCCCTGCACCACCAGCACCAGTTCCACTCGATAG
62684 TTTCCCTGCACCACCAGCACCAGTTCCACTCGATAG
1 TTTCCCTGCACCACCAGCACCAGTTCCACTCGATAG
62720 TTTCCCTGCACCA
1 TTTCCCTGCACCA
62733 GCACTGGTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.19, C:0.42, G:0.14, T:0.25
Consensus pattern (36 bp):
TTTCCCTGCACCACCAGCACCAGTTCCACTCGATAG
Found at i:62743 original size:33 final size:34
Alignment explanation
Indices: 62661--62745 Score: 118
Period size: 36 Copynumber: 2.5 Consensus size: 34
62651 CCCTGCACCC
*
62661 CCAGCACCGGTTCTACTCGATAGTTTCCCTGCACCA
1 CCAGCACCGGTTCCACTCGATAGTTTCCCTG--CCA
*
62697 CCAGCACCAGTTCCACTCGATAGTTTCCCTG-CA
1 CCAGCACCGGTTCCACTCGATAGTTTCCCTGCCA
*
62730 CCAGCACTGGTTCCAC
1 CCAGCACCGGTTCCAC
62746 CCGGCAGTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
33 16 0.36
36 29 0.64
ACGTcount: A:0.20, C:0.40, G:0.16, T:0.24
Consensus pattern (34 bp):
CCAGCACCGGTTCCACTCGATAGTTTCCCTGCCA
Found at i:64727 original size:18 final size:18
Alignment explanation
Indices: 64701--64754 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
64691 AGCAGAAGAC
64701 ATCTAAAGGATCAGCCAA
1 ATCTAAAGGATCAGCCAA
* **
64719 ATCTCAAGGATCAGCTGA
1 ATCTAAAGGATCAGCCAA
64737 ATCTAAAGGATCAGCCAA
1 ATCTAAAGGATCAGCCAA
64755 GCCTAAGCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (18 bp):
ATCTAAAGGATCAGCCAA
Found at i:71408 original size:22 final size:21
Alignment explanation
Indices: 71369--71409 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
71359 GTAAAACTTG
* *
71369 ACTTGAAAAGTTGATTTTTTA
1 ACTTAAAAAATTGATTTTTTA
71390 ACTTAAAAAATTGATTTTTT
1 ACTTAAAAAATTGATTTTTT
71410 GGCTCGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (21 bp):
ACTTAAAAAATTGATTTTTTA
Found at i:72043 original size:2 final size:2
Alignment explanation
Indices: 72036--72068 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
72026 TAAAAATAAG
72036 AT AT AT 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 AT AT AT A
72069 AATTCAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72123 original size:13 final size:13
Alignment explanation
Indices: 72105--72145 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
72095 AATAAATATT
72105 TATAAATTAAAAA
1 TATAAATTAAAAA
**
72118 TATAAATTATGAA
1 TATAAATTAAAAA
72131 -ATAAATTAAAAA
1 TATAAATTAAAAA
72143 TAT
1 TAT
72146 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
TATAAATTAAAAA
Found at i:72153 original size:21 final size:23
Alignment explanation
Indices: 72106--72155 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
72096 ATAAATATTT
*
72106 ATAAATTAAAAATATAAATTATGAA
1 ATAAATTAAAAATAT--ATTATAAA
72131 ATAAATTAAAAATAT-TTA-AAA
1 ATAAATTAAAAATATATTATAAA
72152 ATAA
1 ATAA
72156 TAATTTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.25
22 3 0.12
25 15 0.62
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
ATAAATTAAAAATATATTATAAA
Done.