Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000473.1 Hibiscus syriacus cultivar Beakdansim tig00000881_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: 76860
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1532 original size:18 final size:18
Alignment explanation
Indices: 1509--1554 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1499 AATGTCGAGT
1509 TAATTTGTATAAGATTTA
1 TAATTTGTATAAGATTTA
*
1527 TAATTTGTATACGATTTA
1 TAATTTGTATAAGATTTA
*
1545 TATTTTGTAT
1 TAATTTGTAT
1555 GTGAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (18 bp):
TAATTTGTATAAGATTTA
Found at i:2565 original size:193 final size:198
Alignment explanation
Indices: 1669--2810 Score: 1951
Period size: 191 Copynumber: 5.9 Consensus size: 198
1659 CAATATGGCC
* *
1669 AACAGGGTGCACCCATAAAGTGTCGA-CC-TATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
1732 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
1797 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGAT-TTTTTTTCCAGAATGAA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
1861 TGGAA
194 TGGAA
1866 AACAGGGTGCACCCATAAA--G-CGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1927 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAA-CGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1990 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
2055 GAA
196 GAA
*
2058 AACAGGGTG----CATAAAGTGTCGATCCATATATAAAAAGTGTCAAT-CCAAAATCATCGAA-C
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2117 CAAAAGTATAATGT-ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
2181 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
*
2246 AAA
196 GAA
*
2249 AACAAGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
2312 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACAATTATACCGG-TTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
2376 AATATGTCTAAATAATG-GTCGACACT-ATATAGTTTGTGTCGATATTTTTTCCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
2439 GAA
196 GAA
* *
2442 AACA-GGTGCACCCATAAAGTATTGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2506 CAAAAGTATAAT-TAATATGTAATTTTTCAATC-AACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
2569 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGAT-TTTTTTCCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
2633 GAA
196 GAA
*
2636 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
2701 CAAAAAGTATAATGTAATATGT-A-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
66 C-AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
2764 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
2811 CTAATTTAAA
Statistics
Matches: 902, Mismatches: 17, Indels: 52
0.93 0.02 0.05
Matches are distributed among these distances:
188 6 0.01
189 8 0.01
190 28 0.03
191 201 0.22
192 95 0.11
193 130 0.14
194 130 0.14
195 146 0.16
196 131 0.15
197 27 0.03
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:4269 original size:6 final size:6
Alignment explanation
Indices: 4245--4333 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
4235 AGCGGTCGCA
* * * * * *
4245 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * *
4293 GGCGAT GAAGAT GATGACGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GAAGAT GA
4334 TGATCCAAAC
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
6 58 0.91
8 1 0.02
9 5 0.08
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:4280 original size:3 final size:3
Alignment explanation
Indices: 4260--4337 Score: 66
Period size: 3 Copynumber: 26.0 Consensus size: 3
4250 TGAAGCTGAC
* * * * * ** *
4260 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
4308 GAC GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
4338 CCAAACAAGT
Statistics
Matches: 56, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:4299 original size:36 final size:39
Alignment explanation
Indices: 4248--4329 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 39
4238 GGTCGCAGAA
4248 GATGAAGCTGACGATG-A-A-GATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGATGACGATGATGATGAC
* *
4284 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGATGACGATGATGATGAC
4323 GATGAAG
1 GATGAAG
4330 ATGATGATCC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
36 15 0.37
37 1 0.02
38 1 0.02
39 24 0.59
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (39 bp):
GATGAAGCTGACGATGAAGATGATGACGATGATGATGAC
Found at i:4337 original size:12 final size:12
Alignment explanation
Indices: 4248--4333 Score: 91
Period size: 12 Copynumber: 6.9 Consensus size: 12
4238 GGTCGCAGAA
*
4248 GATGAAGCTGAC
1 GATGAAGATGAC
4260 GATGAAGATGAC
1 GATGAAGATGAC
*
4272 GATGATGATGAC
1 GATGAAGATGAC
* *
4284 GATGAAGCTGGC
1 GATGAAGATGAC
4296 GATGAAGATGATGAC
1 GATG-A-A-GATGAC
* *
4311 GATGATGATGAT
1 GATGAAGATGAC
4323 GATGAAGATGA
1 GATGAAGATGA
4334 TGATCCAAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
12 50 0.82
13 1 0.02
14 2 0.03
15 8 0.13
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:4337 original size:18 final size:18
Alignment explanation
Indices: 4248--4337 Score: 81
Period size: 18 Copynumber: 4.8 Consensus size: 18
4238 GGTCGCAGAA
* * *
4248 GATGAAGCTGACGATGAA
1 GATGAAGATGATGATGAT
* *
4266 GATGACGATGATGATGAC
1 GATGAAGATGATGATGAT
* *
4284 GATGAAGCTGGCGATGAAGAT
1 GATGAAGAT---GATGATGAT
*
4305 GATGACGATGATGATGAT
1 GATGAAGATGATGATGAT
4323 GATGAAGATGATGAT
1 GATGAAGATGATGAT
4338 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
18 43 0.75
21 14 0.25
ACGTcount: A:0.36, C:0.08, G:0.34, T:0.22
Consensus pattern (18 bp):
GATGAAGATGATGATGAT
Found at i:6368 original size:182 final size:182
Alignment explanation
Indices: 5801--6471 Score: 1198
Period size: 181 Copynumber: 3.7 Consensus size: 182
5791 TAAATTTGCA
* * *
5801 ATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTA
1 ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATA
* * *
5866 ATATTGTATCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGT
66 ATATTGTGTCGGTAC-TTATGTCCAGATTGGAATAAAAATGTGTCGATACGATTTAAAAAAGTGT
5931 CGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTGT-A-
130 CGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTGTAAT
5982 ATAA-CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAA-CTATATCGACACTTTATA
1 ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATA
6045 ATATTGTGTCGGTACTTATGTCCAGATTGGAATAAAAATGTGTCGATACGATTTAAAAAAGTGTC
66 ATATTGTGTCGGTACTTATGTCCAGATTGGAATAAAAATGTGTCGATACGATTTAAAAAAGTGTC
6110 GACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTGTAAT
131 GACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTGTAAT
6162 ATAACCGGTATAAATATA-CGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATA
1 ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATA
6226 ATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAAAATGTGTCGATACGATTTAAAAAAGTGT
66 ATATTGTGTCGGTAC-TTATGTCCAGATTGGAATAAAAATGTGTCGATACGATTTAAAAAAGTGT
6291 CGACA-TTTACACATCGGAACCCAT-ATTATAATGTAATAGATAATTTTGTAAT
130 CGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAA-TTTGTAAT
6343 ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATA
1 ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATA
6408 ATATTGTGTCGGTACTTATGTCCAGATTGGAATAAAAATGTGTCGATAC-ATTT-AAAAAGTGTC
66 ATATTGTGTCGGTACTTATGTCCAGATTGGAATAAAAATGTGTCGATACGATTTAAAAAAGTGTC
6471 G
131 G
6472 GTAATTTGAA
Statistics
Matches: 477, Mismatches: 6, Indels: 16
0.96 0.01 0.03
Matches are distributed among these distances:
178 97 0.20
179 43 0.09
180 93 0.19
181 129 0.27
182 115 0.24
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (182 bp):
ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATA
ATATTGTGTCGGTACTTATGTCCAGATTGGAATAAAAATGTGTCGATACGATTTAAAAAAGTGTC
GACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTGTAAT
Found at i:8955 original size:25 final size:24
Alignment explanation
Indices: 8921--8982 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 24
8911 TTATCATTAA
8921 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTAC-ATAACTACAT
8946 ATTTAGGTATGT---TAACTACAT
1 ATTTAGGTATGTACATAACTACAT
*
8967 ATTTAGGTATATACAT
1 ATTTAGGTATGTACAT
8983 CTTTTGAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 20 0.61
24 1 0.03
25 12 0.36
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (24 bp):
ATTTAGGTATGTACATAACTACAT
Found at i:9319 original size:21 final size:23
Alignment explanation
Indices: 9269--9330 Score: 83
Period size: 21 Copynumber: 2.8 Consensus size: 23
9259 ATAGGTAAAC
*
9269 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* *
9292 ATATAATGTAATAGGTA-TCGTT
1 ATATAATGTAATAGGTAGCCCTT
9314 -TATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
9331 TGGTTATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.46
22 3 0.09
23 16 0.46
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:9337 original size:21 final size:21
Alignment explanation
Indices: 9293--9344 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
9283 GTAGCCCTTA
*
9293 TATAATGTAATAGGTATCGTT
1 TATAATGTAATAGGTATCGGT
9314 TATAATGTAATAGGTAGT-GGT
1 TATAATGTAATAGGTA-TCGGT
*
9335 TATATTGTAA
1 TATAATGTAA
9345 AGTGTCTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (21 bp):
TATAATGTAATAGGTATCGGT
Found at i:9637 original size:25 final size:25
Alignment explanation
Indices: 9603--9653 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
9593 ACAACAAATC
*
9603 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
9628 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
9653 A
1 A
9654 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:10282 original size:39 final size:39
Alignment explanation
Indices: 10239--10325 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
10229 TCCGATGCTC
*
10239 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
10278 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
10317 ATCAAAATC
1 ATCAAAATC
10326 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:10706 original size:21 final size:22
Alignment explanation
Indices: 10660--10709 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
10650 AAATTACATA
10660 ACTTTTAAAAAAAGTATCGATC
1 ACTTTTAAAAAAAGTATCGATC
* * *
10682 -CTTTTTATAAAAGTATGGA-C
1 ACTTTTAAAAAAAGTATCGATC
10702 ACTTTTAA
1 ACTTTTAA
10710 TATAATAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (22 bp):
ACTTTTAAAAAAAGTATCGATC
Found at i:10755 original size:23 final size:23
Alignment explanation
Indices: 10724--10787 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
10714 ATAGGTAAAC
*
10724 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
10747 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
10770 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
10788 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:10794 original size:23 final size:23
Alignment explanation
Indices: 10724--10796 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
10714 ATAGGTAAAC
* **
10724 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
10747 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
10770 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
10793 ATAT
1 ATAT
10797 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:11215 original size:21 final size:22
Alignment explanation
Indices: 11171--11216 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
11161 AAATAGGTAA
*
11171 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAGTA-ATT
11194 ATATAAGCGCTACCTAGT-ATT
1 ATATAAGCGCTACCTAGTAATT
11215 AT
1 AT
11217 TGTACTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
23 17 0.77
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (22 bp):
ATATAAGCGCTACCTAGTAATT
Found at i:13526 original size:6 final size:6
Alignment explanation
Indices: 13511--13541 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
13501 GAAATGATGA
*
13511 TAATGC TAATGG TAATGC TAATGC TAATGC T
1 TAATGC TAATGC TAATGC TAATGC TAATGC T
13542 GGTACTGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (6 bp):
TAATGC
Found at i:13646 original size:21 final size:21
Alignment explanation
Indices: 13622--13669 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
13612 AATATGGATA
**
13622 TGGATACACGCCTGGTTACCC
1 TGGATACACGCCAAGTTACCC
* *
13643 TGGATACATGCCAAGTTATCC
1 TGGATACACGCCAAGTTACCC
13664 TGGATA
1 TGGATA
13670 TGGGCAACCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (21 bp):
TGGATACACGCCAAGTTACCC
Found at i:15363 original size:9 final size:9
Alignment explanation
Indices: 15351--15375 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
15341 AATAATGTCA
15351 TGATGTGGT
1 TGATGTGGT
15360 TGATGTGGT
1 TGATGTGGT
15369 TGATGTG
1 TGATGTG
15376 CATGTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (9 bp):
TGATGTGGT
Found at i:17012 original size:17 final size:17
Alignment explanation
Indices: 16990--17029 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
16980 CTTCTTAAGA
16990 GACCCAGAGTGCTCGCC
1 GACCCAGAGTGCTCGCC
17007 GACCCAGAGTGCTCGCC
1 GACCCAGAGTGCTCGCC
17024 GACCCA
1 GACCCA
17030 ACCCCTCCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.42, G:0.28, T:0.10
Consensus pattern (17 bp):
GACCCAGAGTGCTCGCC
Found at i:17602 original size:14 final size:15
Alignment explanation
Indices: 17583--17640 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
17573 ATTATATTCA
17583 AAAATTTATAA-AAT
1 AAAATTTATAATAAT
*
17597 ATAATTTTATAATAAT
1 A-AAATTTATAATAAT
* *
17613 AAAATTAAT-TTAAT
1 AAAATTTATAATAAT
*
17627 AAAATTAATAATAA
1 AAAATTTATAATAA
17641 AATAATAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
14 14 0.39
15 18 0.50
16 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTTATAATAAT
Found at i:17623 original size:20 final size:21
Alignment explanation
Indices: 17590--17661 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 21
17580 TCAAAAATTT
*
17590 ATAAAATATAATTTTATAATA
1 ATAAAATATAATTTAATAATA
17611 ATAAAAT-TAATTTAATAA-A
1 ATAAAATATAATTTAATAATA
*
17630 AT--TA-ATAA--TAA-AATA
1 ATAAAATATAATTTAATAATA
17645 ATAAAATAT-ATTTAATA
1 ATAAAATATAATTTAATA
17662 TGTACAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 17
0.67 0.05 0.28
Matches are distributed among these distances:
14 2 0.05
15 6 0.15
17 6 0.15
18 2 0.05
19 6 0.15
20 11 0.28
21 7 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAAATATAATTTAATAATA
Found at i:17624 original size:34 final size:34
Alignment explanation
Indices: 17585--17661 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
17575 TATATTCAAA
** *
17585 AATTT-ATAAAATATAATTTTATAATAATAAAATT
1 AATTTAATAAAAT-TAATAATAAAATAATAAAATT
17619 AATTTAATAAAATTAATAATAAAATAATAAAA-T
1 AATTTAATAAAATTAATAATAAAATAATAAAATT
17652 ATATTTAATA
1 A-ATTTAATA
17662 TGTACAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 2 0.05
34 29 0.76
35 7 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AATTTAATAAAATTAATAATAAAATAATAAAATT
Found at i:21659 original size:60 final size:60
Alignment explanation
Indices: 21586--21703 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
21576 TATCTGAAGA
21586 GACTTGAGCAATAACAATCTGAAGGGGCAACCTTATCTTTTTGAAATCCCA-GAAAAAAGG
1 GACTTGAGCAATAACAATCTGAAGGGGCAACCTTATCTTTTTGAAAT-CCATGAAAAAAGG
*
21646 GACTTGAGCAATAACAATCTGAATGGGCAACCTTATCTTTTTGAAATCCATGAAAAAA
1 GACTTGAGCAATAACAATCTGAAGGGGCAACCTTATCTTTTTGAAATCCATGAAAAAA
21704 AGGGTAAACT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
59 3 0.05
60 53 0.95
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (60 bp):
GACTTGAGCAATAACAATCTGAAGGGGCAACCTTATCTTTTTGAAATCCATGAAAAAAGG
Found at i:24928 original size:2 final size:2
Alignment explanation
Indices: 24921--24946 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24911 GAATCCCATG
24921 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
24947 CTATTATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26429 original size:111 final size:111
Alignment explanation
Indices: 26164--26525 Score: 503
Period size: 109 Copynumber: 3.2 Consensus size: 111
26154 TTCAGGGAAG
*
26164 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAGAAGAGAGATT
1 ATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTG-A-AAGAGA-A--
* * * *
26229 TGTTCTGTTCCACTTCTTCTGAGGGAATATATCAGATCTAGGAAAGTTGATCC
61 GGATCTGTTCCACTTCTTCTGAGGG-A-ATATCAGATCTGGGAAAGTTGATTC
* * *
26282 ATTGAATCATGGTAGACTTGTTCCACTGTCGCTCAGGGAATATCAAATCTTGAAAGAGAAGGATC
1 ATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATC
** * * *
26347 TGTTCTGCTTCCTCTGAGGGAATATCATATCTGGGAAAGTTGATTT
66 TGTTCCACTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
* * *
26393 ATTGAATCAAGGTAGACTTGTTCCGCTGTCATTCAGGGAATATCAAATCTTG-AA-AGATGGATA
1 ATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATC
26456 TGTTCCACTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
66 TGTTCCACTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
26502 ATTGAATCAAGGTAGACTTGTTCC
1 ATTGAATCAAGGTAGACTTGTTCC
26526 ACTTACTCTG
Statistics
Matches: 221, Mismatches: 23, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
109 72 0.33
110 2 0.01
111 69 0.31
112 1 0.00
113 20 0.09
115 1 0.00
116 6 0.03
117 1 0.00
118 49 0.22
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (111 bp):
ATTGAATCAAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATC
TGTTCCACTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
Found at i:26585 original size:66 final size:66
Alignment explanation
Indices: 26456--27432 Score: 1746
Period size: 66 Copynumber: 14.8 Consensus size: 66
26446 AAGATGGATA
* * * *
26456 TGTTCCACTT-CTTCTG-AGGGAATATCAGATCTGGGA-AAGTTGATTCATTGAATC-AAGGTAG
1 TGTTCCACTTAC-TCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAA-GCAG
26517 ACT
64 ACT
* *
26520 TGTTCCACTTACTCTGAATGGAATATCAAATCTTGGAGAAATTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
26585 T
66 T
* *
26586 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGGTCAATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
26651 T
66 T
* *
26652 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGCAGAAGTTGATCCATTGAATCGAAGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
26717 T
66 T
*
26718 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCTATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
26783 T
66 T
*
26784 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
26849 T
66 T
*
26850 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAACAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
26915 T
66 T
*
26916 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
26981 T
66 T
26982 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
27047 T
66 T
*
27048 TTTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
27113 T
66 T
*
27114 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
27179 T
66 T
27180 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
27245 T
66 T
*
27246 TGTTCCACTTACTCTGAAGGTAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
27311 T
66 T
*
27312 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAATCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
27377 T
66 T
27378 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAAT
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAAT
27433 TGGGATCGAA
Statistics
Matches: 878, Mismatches: 31, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
64 14 0.02
65 18 0.02
66 844 0.96
67 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (66 bp):
TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
T
Found at i:28635 original size:21 final size:23
Alignment explanation
Indices: 28599--28648 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
28589 CCTTCTTTTA
28599 TTTTTCTTTTCTTTTTTCCTCAT
1 TTTTTCTTTTCTTTTTTCCTCAT
*
28622 TTTTTC-TTTCTTTTTT-TTCAT
1 TTTTTCTTTTCTTTTTTCCTCAT
28643 TTTTTC
1 TTTTTC
28649 CCATTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 10 0.38
22 10 0.38
23 6 0.23
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTCTTTTCTTTTTTCCTCAT
Found at i:28655 original size:14 final size:14
Alignment explanation
Indices: 28638--28674 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
28628 TTTCTTTTTT
28638 TTCATTTTTTCCCA
1 TTCATTTTTTCCCA
28652 TTCA-TTTTT-CCA
1 TTCATTTTTTCCCA
28664 TTCATTTTTTC
1 TTCATTTTTTC
28675 AGGCGAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 7 0.33
13 10 0.48
14 4 0.19
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (14 bp):
TTCATTTTTTCCCA
Found at i:28672 original size:12 final size:13
Alignment explanation
Indices: 28638--28672 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
28628 TTTCTTTTTT
28638 TTCATTTTTTCCCA
1 TTCA-TTTTTCCCA
28652 TTCATTTTT-CCA
1 TTCATTTTTCCCA
28664 TTCATTTTT
1 TTCATTTTT
28673 TCAGGCGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 5 0.24
14 4 0.19
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (13 bp):
TTCATTTTTCCCA
Found at i:32224 original size:25 final size:27
Alignment explanation
Indices: 32191--32251 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
32181 AATCTATCCC
* *
32191 ATATCAAAATAGAATGAAAT-AAT-AAT
1 ATAT-AAAAAAGAAAGAAATAAATAAAT
32217 ATATAAAAAAGAAAGAAATAAATAAAT
1 ATATAAAAAAGAAAGAAATAAATAAAT
*
32244 AAATAAAA
1 ATATAAAA
32252 GAATGGAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.43
26 7 0.23
27 10 0.33
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (27 bp):
ATATAAAAAAGAAAGAAATAAATAAAT
Found at i:38280 original size:3 final size:3
Alignment explanation
Indices: 38220--38264 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
38210 ACAAATGTAA
* * *
38220 AAT ATT AAT AAT AAT AAT AAT AAT -AT AGT AGT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
38265 TTATTATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:38700 original size:90 final size:90
Alignment explanation
Indices: 38512--38783 Score: 427
Period size: 90 Copynumber: 3.0 Consensus size: 90
38502 AATGCTTACA
* * *
38512 GATGACCTGAAGGATTTAAAAATCAAGAAAACCCCGAAGGCTTAGTTTCTTAAAATCTCATTTGA
1 GATGACCCGAAGGACTTAAAAATCAAGAAAACCCCGAAGGCTTAGTTTC-TAAAATTTCATTTGA
* *
38577 AAACATGCTGCACTGAAGGTCTTATG
65 AAACATACTGCAATGAAGGTCTTATG
* *
38603 GATGACCCGAAGGACTTAAAAATTAAGAAAACCCCGAAGGCTTAGTTTCTAAAATTTCATTTAAA
1 GATGACCCGAAGGACTTAAAAATCAAGAAAACCCCGAAGGCTTAGTTTCTAAAATTTCATTTGAA
* *
38668 AACATCCTGCATTGAAGGTCTTATG
66 AACATACTGCAATGAAGGTCTTATG
* *
38693 GATGACCCGAAGGACTTAGAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATTTCATTTGAA
1 GATGACCCGAAGGACTTAAAAATCAAGAAAACCCCGAAGGCTTAGTTTCTAAAATTTCATTTGAA
*
38758 AACATACTGTAATGAAGGTCTTATG
66 AACATACTGCAATGAAGGTCTTATG
38783 G
1 G
38784 GTCAAGAAAC
Statistics
Matches: 167, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
90 121 0.72
91 46 0.28
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (90 bp):
GATGACCCGAAGGACTTAAAAATCAAGAAAACCCCGAAGGCTTAGTTTCTAAAATTTCATTTGAA
AACATACTGCAATGAAGGTCTTATG
Found at i:38937 original size:43 final size:43
Alignment explanation
Indices: 38864--39104 Score: 272
Period size: 43 Copynumber: 5.6 Consensus size: 43
38854 CAAGTGTTCA
* * * *
38864 TCAAGTTTATCATCAAGGAACCCCTACATATCACTATGGTCCT
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCT
* * * * *
38907 TCAAACTTGTCCTCAAGAAACCCTTGCATATCACGATTGT-CT
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCT
* *
38949 CTCAAGCTTTTCATCAA-AGAACCCCTACATATCACGATGGACCT
1 -TCAAGCTTGTCATCAAGA-AACCCCTACATATCACGATGGTCCT
* * *
38993 TCAAGCTTGTCATGAAGGAACTCCTACATATCACGATGGTCCT
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCT
*
39036 TCAAGCTTGTCCTCAAGAAACCCCTACATATCACGATGGT-CT
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCT
* * *
39078 CTCAAGCTTTTCTTTAAGAAACCCCTA
1 -TCAAGCTTGTCATCAAGAAACCCCTA
39105 AAAATCAGGC
Statistics
Matches: 165, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
42 5 0.03
43 158 0.96
44 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (43 bp):
TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCT
Found at i:39496 original size:40 final size:40
Alignment explanation
Indices: 39159--39487 Score: 500
Period size: 40 Copynumber: 8.2 Consensus size: 40
39149 TATCTCAAGC
* ** *
39159 GAGATAAAATCTTATGTTTCAAGTG--AAACAATCTCAAGC
1 GAGATAAAATCTTCTGTTTCAAG-GAAAAACAATCTTGAGT
* **
39198 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
39238 GAGATAAAATCTTCTATTTCAAGGAAAAACAAACTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
39278 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
39318 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
**
39358 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
39398 GAGATAAAATCTTCTGATTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
39438 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
39478 CAAATAAAAT
1 GAGATAAAAT
39488 ATCTTGTTTT
Statistics
Matches: 267, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
38 1 0.00
39 22 0.08
40 244 0.91
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:39521 original size:120 final size:119
Alignment explanation
Indices: 39145--39521 Score: 426
Period size: 120 Copynumber: 3.2 Consensus size: 119
39135 GTTTCGAGTT
* * * ** *
39145 AAACTATCTCAAGCGAGATAAAATCTTATGTTTCAAGTG--AAACAATCTCAAGCGAGATAAAAT
1 AAACAATCTCGAGCGAGATAAAATCTTCTGTTTCAAG-GAAAAACAATCTTGAGTGAGATAAAAT
* * *
39208 CTTTTGTTTCAAGGAAAAACAATCTTGA-ACGAGAT-AAA-ATCTTCTATTTCAAGGAA
65 CTTCTGTTTCAAGGAAAAACAATCTTGAGTC-AGATAAAATATCTTGT-TTT-AA-GAA
* * * *
39264 AAACAAACTTGAGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAATGAGATAAAATC
1 AAACAATCTCGAGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATC
* * *
39329 TTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCT-TCTGTTTCAAGGAA
66 TTCTGTTTCAAGGAAAAACAATCTTGAGTCAGATAAAATATCT-TGTTTTAA-GAA
* * *
39384 AAACAATCTTGAACGAGATAAAATCTTCTGATTCAAGGAAAAACAATCTTGAGTGAGATAAAATC
1 AAACAATCTCGAGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATC
*
39449 TTCTGTTTCAAGGAAAAACAATCTTGAGTCAAATAAAATATCTTGTTTTAA-ATA
66 TTCTGTTTCAAGGAAAAACAATCTTGAGTCAGATAAAATATCTTGTTTTAAGA-A
* *
39503 AAACATGTCTCCAGCGAGA
1 AAACA-ATCTCGAGCGAGA
39522 CAAATATTGT
Statistics
Matches: 220, Mismatches: 29, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
118 2 0.01
119 37 0.17
120 171 0.78
121 7 0.03
122 3 0.01
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (119 bp):
AAACAATCTCGAGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATC
TTCTGTTTCAAGGAAAAACAATCTTGAGTCAGATAAAATATCTTGTTTTAAGAA
Found at i:39527 original size:39 final size:39
Alignment explanation
Indices: 39484--39701 Score: 154
Period size: 37 Copynumber: 5.7 Consensus size: 39
39474 GAGTCAAATA
*
39484 AAATATCTTGTTTTAAATAAAACATGTCTCCAGCGAGAC
1 AAATATCTTGTTTTGAATAAAACATGTCTCCAGCGAGAC
* * * * *
39523 AAATA--TTGTTTTGAA-AAAA-ATAATCTTCAGTGAAATA
1 AAATATCTTGTTTTGAATAAAACAT-GTCTCCAGCGAGA-C
* * *
39560 AAATGTCTTGTTTTGAATAAAACATGTCTCTAGCTAGAC
1 AAATATCTTGTTTTGAATAAAACATGTCTCCAGCGAGAC
* ** * *
39599 -AA-ATCTTGTTTTGAGA-AAAACA-ATCTTGAGTC-AAATA
1 AAATATCTTGTTTTGA-ATAAAACATGTCTCCAG-CGAGA-C
*
39636 AAATGTCTTGTTTTGAATAAAACATGTCTCCAGCGAGAC
1 AAATATCTTGTTTTGAATAAAACATGTCTCCAGCGAGAC
*
39675 -AA-ATCTTGTTTTGAGAAAAAACA-GTCT
1 AAATATCTTGTTTTGA-ATAAAACATGTCT
39702 TGAGTCAAAT
Statistics
Matches: 136, Mismatches: 28, Indels: 32
0.69 0.14 0.16
Matches are distributed among these distances:
35 2 0.01
36 20 0.15
37 46 0.34
38 15 0.11
39 33 0.24
40 18 0.13
41 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (39 bp):
AAATATCTTGTTTTGAATAAAACATGTCTCCAGCGAGAC
Found at i:39559 original size:76 final size:76
Alignment explanation
Indices: 39462--39776 Score: 420
Period size: 76 Copynumber: 4.1 Consensus size: 76
39452 TGTTTCAAGG
*
39462 AAAAACAATCTTGAGTCAAATAAAATATCTTGTTTTAAATAAAACATGTCTCCAGCGAGACAAAT
1 AAAAACAATCTTGAGTCAAATAAAATGTCTTGTTTTAAATAAAACATGTCTCCAGCGAGACAAAT
*
39527 ATTGTTTTGAA
66 CTTGTTTTGAA
* * * * * *
39538 AAAAATAATCTTCAGTGAAATAAAATGTCTTGTTTTGAATAAAACATGTCTCTAGCTAGACAAAT
1 AAAAACAATCTTGAGTCAAATAAAATGTCTTGTTTTAAATAAAACATGTCTCCAGCGAGACAAAT
*
39603 CTTGTTTTGAG
66 CTTGTTTTGAA
*
39614 AAAAACAATCTTGAGTCAAATAAAATGTCTTGTTTTGAATAAAACATGTCTCCAGCGAGACAAAT
1 AAAAACAATCTTGAGTCAAATAAAATGTCTTGTTTTAAATAAAACATGTCTCCAGCGAGACAAAT
39679 CTTGTTTTGAGA
66 CTTGTTTTGA-A
* * * * * * *
39691 AAAAACAGTCTTGAGTCAAATGAAATGTCTTCTTTCAAGTAAAACA-GTCTCAAGTGAGACAAAG
1 AAAAACAATCTTGAGTCAAATAAAATGTCTTGTTTTAAATAAAACATGTCTCCAGCGAGACAAA-
39755 T-TTGTTTT-AA
65 TCTTGTTTTGAA
*
39765 GAAAAATAATCT
1 -AAAAACAATCT
39777 CCAGTTAGAT
Statistics
Matches: 211, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
74 1 0.00
75 10 0.05
76 159 0.75
77 41 0.19
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (76 bp):
AAAAACAATCTTGAGTCAAATAAAATGTCTTGTTTTAAATAAAACATGTCTCCAGCGAGACAAAT
CTTGTTTTGAA
Found at i:42642 original size:19 final size:19
Alignment explanation
Indices: 42614--42650 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42604 AAAATCGGTC
* *
42614 ACTAATCATAAATGAATTG
1 ACTAAACATAAATCAATTG
42633 ACTAAACATAAATCAATT
1 ACTAAACATAAATCAATT
42651 TATCGATAAA
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:0.14, G:0.05, T:0.30
Consensus pattern (19 bp):
ACTAAACATAAATCAATTG
Found at i:49447 original size:22 final size:22
Alignment explanation
Indices: 49414--49465 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
49404 CTCGGAGGGA
49414 ACCGA-TTCCCCCCAAAGGGGT
1 ACCGATTTCCCCCCAAAGGGGT
*
49435 ACCGATTTCCCCCCAAGGGGGT
1 ACCGATTTCCCCCCAAAGGGGT
49457 ACCGATTTC
1 ACCGATTTC
49466 TCCTGTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.19
Consensus pattern (22 bp):
ACCGATTTCCCCCCAAAGGGGT
Found at i:53589 original size:21 final size:21
Alignment explanation
Indices: 53565--53623 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
53555 ACAAAAATGA
53565 AGCAAGAGAAGCAGAGAGAGC
1 AGCAAGAGAAGCAGAGAGAGC
* **
53586 AGCAACAGAAGCAGCTAGAGC
1 AGCAAGAGAAGCAGAGAGAGC
*
53607 AG-TAGCAGAAGCAGAGA
1 AGCAAG-AGAAGCAGAGA
53624 AAGAAACAAC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.46, C:0.17, G:0.34, T:0.03
Consensus pattern (21 bp):
AGCAAGAGAAGCAGAGAGAGC
Found at i:54328 original size:43 final size:43
Alignment explanation
Indices: 54122--54366 Score: 223
Period size: 43 Copynumber: 5.8 Consensus size: 43
54112 ACGATAAAAT
* * * * **
54122 CGCCACTAAATCTCAACACTTATTGTGGCGTTTGAGATAA-AAA
1 CGCCGCTAAATATCAACACCTATTGCGGCGTTTG-TCTAACAAA
* * * * **
54165 CGTCGCTAAATCTCAACACCTACTGTGGCGTTTGTGGGAA-AAA
1 CGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-CTAACAAA
* * * *
54208 CACCACTAAACATCAACACCTATTGCGGTGTTTGTCTAACAAA
1 CGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTAACAAA
* * *
54251 CGCTGCTAAATATCAACACCTATTGCAGTGTTTGTCTAACAAA
1 CGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTAACAAA
54294 CGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-T--CAAA
1 CGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTAACAAA
* * *
54334 CACCGCTATATATCGTA-ACCTATTGCGGCGTTT
1 CGCCGCTAAATATC-AACACCTATTGCGGCGTTT
54367 TTCGTTAACA
Statistics
Matches: 171, Mismatches: 28, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
40 32 0.19
41 1 0.01
42 3 0.02
43 135 0.79
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (43 bp):
CGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTAACAAA
Found at i:54943 original size:2 final size:2
Alignment explanation
Indices: 54938--54970 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
54928 TCTCAAGAAA
*
54938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54971 AGTGGAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:60071 original size:19 final size:19
Alignment explanation
Indices: 60044--60090 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
60034 GGAGAAATTG
*
60044 TCTTTTGCAACATCACCCT
1 TCTTCTGCAACATCACCCT
60063 TCTTCTGCAACATCACCCT
1 TCTTCTGCAACATCACCCT
60082 TCTTCTGCA
1 TCTTCTGCA
60091 GGGTACTAAG
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:0.19, C:0.38, G:0.06, T:0.36
Consensus pattern (19 bp):
TCTTCTGCAACATCACCCT
Found at i:66278 original size:24 final size:23
Alignment explanation
Indices: 66242--66289 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
66232 CAGTTGATTA
* *
66242 GTTGTAACTGTTTCTGGTTAAGTT
1 GTTGCAACCGTTTCTGGTT-AGTT
*
66266 GTTGCAACCGTTTCTTGTTAGTT
1 GTTGCAACCGTTTCTGGTTAGTT
66289 G
1 G
66290 GGTTGTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.48
Consensus pattern (23 bp):
GTTGCAACCGTTTCTGGTTAGTT
Found at i:71202 original size:24 final size:24
Alignment explanation
Indices: 71149--71205 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
71139 CACCACAACT
* * *
71149 CATATAAATTGCACCGAAGTGTCG
1 CATAGAAATTGCACCGAAGTGCCA
*
71173 CGTAGAAATTGCACCGAAGTGCCA
1 CATAGAAATTGCACCGAAGTGCCA
71197 CATAGAAAT
1 CATAGAAAT
71206 GTTCCGAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
CATAGAAATTGCACCGAAGTGCCA
Found at i:71221 original size:23 final size:23
Alignment explanation
Indices: 71194--71283 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 23
71184 CACCGAAGTG
* *
71194 CCACATAGAAATGTTCCGAAGGA
1 CCACATAGAAATGTCCCGAAGAA
* * *
71217 TCACATAGTATTGTCCCGAAGAA
1 CCACATAGAAATGTCCCGAAGAA
*
71240 CCACGTAGAAATGTCCCGAA-ATA
1 CCACATAGAAATGTCCCGAAGA-A
* *
71263 CCACTTAGAATTGTCCCGAAG
1 CCACATAGAAATGTCCCGAAG
71284 GACCGTGTAG
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
22 1 0.02
23 53 0.98
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAAGAA
Found at i:71294 original size:23 final size:23
Alignment explanation
Indices: 71226--71295 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
71216 ATCACATAGT
*
71226 ATTGTCCCGAAGAACCACGTAGA
1 ATTGTCCCGAAGAACCATGTAGA
*
71249 AATGTCCCGAA-ATACCACT-TAGA
1 ATTGTCCCGAAGA-ACCA-TGTAGA
* *
71272 ATTGTCCCGAAGGACCGTGTAGA
1 ATTGTCCCGAAGAACCATGTAGA
71295 A
1 A
71296 CTCTCGACTC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
22 2 0.05
23 36 0.95
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.20
Consensus pattern (23 bp):
ATTGTCCCGAAGAACCATGTAGA
Found at i:71295 original size:46 final size:46
Alignment explanation
Indices: 71194--71283 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 46
71184 CACCGAAGTG
* * * * *
71194 CCACATAGAAATGTTCCGAAGGATCACATAGTATTGTCCCGAAGAA
1 CCACGTAGAAATGTCCCGAAAGACCACATAGAATTGTCCCGAAGAA
* *
71240 CCACGTAGAAATGTCCCGAAATACCACTTAGAATTGTCCCGAAG
1 CCACGTAGAAATGTCCCGAAAGACCACATAGAATTGTCCCGAAG
71284 GACCGTGTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (46 bp):
CCACGTAGAAATGTCCCGAAAGACCACATAGAATTGTCCCGAAGAA
Done.