Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000970.1 Hibiscus syriacus cultivar Beakdansim tig00001939_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: 76117
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:629 original size:20 final size:20
Alignment explanation
Indices: 606--643 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
596 TCTTACTTCA
* *
606 TTACTATTTTTTTTCTTTTT
1 TTACTAATTTTTTGCTTTTT
626 TTACTAATTTTTTGCTTT
1 TTACTAATTTTTTGCTTT
644 CGTGTTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.11, G:0.03, T:0.74
Consensus pattern (20 bp):
TTACTAATTTTTTGCTTTTT
Found at i:10931 original size:41 final size:41
Alignment explanation
Indices: 10817--10936 Score: 98
Period size: 41 Copynumber: 2.9 Consensus size: 41
10807 GAAGGGGCCC
** * * * *
10817 TCCACGATTTCAACTCCGA-ACGGAGCATATCGTACCCACAA
1 TCCACGATTTCAACTCAAAGACGAAGGATATCATGCCCAC-A
* * * *
10858 GTCCACGATTTCAACTCCACGATGGAGGATATCATGCCCACA
1 -TCCACGATTTCAACTCAAAGACGAAGGATATCATGCCCACA
* * *
10900 TCCACGATTTCAACTTAAAGACGAAGTATATCGTGCC
1 TCCACGATTTCAACTCAAAGACGAAGGATATCATGCC
10937 AACTCTAGAT
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 30 0.47
42 18 0.28
43 16 0.25
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (41 bp):
TCCACGATTTCAACTCAAAGACGAAGGATATCATGCCCACA
Found at i:11825 original size:12 final size:12
Alignment explanation
Indices: 11787--11836 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
11777 CAAACGTTAT
11787 TATATTATATAA
1 TATATTATATAA
11799 TATA-TAT-T--
1 TATATTATATAA
11807 TATATTATA-AA
1 TATATTATATAA
11818 TCATATTATATAA
1 T-ATATTATATAA
11831 TATATT
1 TATATT
11837 CATCTATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
8 4 0.12
9 3 0.09
10 1 0.03
11 4 0.12
12 17 0.53
13 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATTATATAA
Found at i:13084 original size:16 final size:17
Alignment explanation
Indices: 13063--13117 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
13053 TTAACATATA
13063 TATTTTACTTT-TTTTT
1 TATTTTACTTTATTTTT
* *
13079 TATTTTGCTTTATTTTC
1 TATTTTACTTTATTTTT
* *
13096 TATCTT-CATTTATTTTC
1 TATTTTAC-TTTATTTTT
13113 TATTT
1 TATTT
13118 CCTTATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 11 0.33
17 22 0.67
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.73
Consensus pattern (17 bp):
TATTTTACTTTATTTTT
Found at i:13186 original size:16 final size:17
Alignment explanation
Indices: 13143--13183 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
13133 GTTTCTCTTT
*
13143 TTATTTTTATTTTTTTG
1 TTATATTTATTTTTTTG
13160 TTATATTTATTTTTTTG
1 TTATATTTATTTTTTTG
*
13177 TTCTATT
1 TTATATT
13184 ATTATCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (17 bp):
TTATATTTATTTTTTTG
Found at i:13188 original size:19 final size:18
Alignment explanation
Indices: 13143--13188 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
13133 GTTTCTCTTT
13143 TTAT-TTTTATTTTTTTG
1 TTATATTTTATTTTTTTG
13160 TTATA-TTTATTTTTTTG
1 TTATATTTTATTTTTTTG
*
13177 TTCTATTATTAT
1 TTATATT-TTAT
13189 CAAGTTCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 20 0.80
18 1 0.04
19 4 0.16
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.76
Consensus pattern (18 bp):
TTATATTTTATTTTTTTG
Found at i:13244 original size:22 final size:22
Alignment explanation
Indices: 13226--13274 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
13216 TGTTTTTTTA
*
13226 CTTTTATTTCTTTTATTTTCTT
1 CTTTTATCTCTTTTATTTTCTT
* *
13248 TTTTTATCTCTTTT-TGTTTATT
1 CTTTTATCTCTTTTAT-TTTCTT
13270 CTTTT
1 CTTTT
13275 TGTTTATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.78
Consensus pattern (22 bp):
CTTTTATCTCTTTTATTTTCTT
Found at i:13254 original size:13 final size:12
Alignment explanation
Indices: 13218--13307 Score: 63
Period size: 13 Copynumber: 6.8 Consensus size: 12
13208 TTTTTCCTTG
13218 TTTTTTTACTTTT
1 TTTTTTTA-TTTT
13231 ATTTCTTTTATTTT
1 -TTT-TTTTATTTT
13245 CTTTTTTTATCTCTT
1 -TTTTTTTAT-T-TT
*
13260 TTTGTTTATTCTT
1 TTTTTTTATT-TT
*
13273 TTTGTTTATTTGT
1 TTTTTTTATTT-T
*
13286 TTTCTTTATTTT
1 TTTTTTTATTTT
*
13298 ATTTATTTAT
1 -TTTTTTTAT
13308 GTTCATTATT
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
12 2 0.03
13 39 0.58
14 19 0.28
15 7 0.10
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (12 bp):
TTTTTTTATTTT
Found at i:13302 original size:22 final size:20
Alignment explanation
Indices: 13215--13305 Score: 56
Period size: 23 Copynumber: 4.1 Consensus size: 20
13205 TTTTTTTTCC
*
13215 TTGTTTTTTTACTTTTATTTCTT
1 TTGTTTTTTT--TTTTATTT-AT
* *
13238 TTATTTTCTTTTTTTATCTCTTT
1 TTGTTTT-TTTTTTTAT-T-TAT
* *
13261 TTGTTTATTCTTTTTGTTTAT
1 TTGTTT-TTTTTTTTATTTAT
13282 TTGTTTTCTTTATTTTATTTAT
1 TTGTTTT-TTT-TTTTATTTAT
13304 TT
1 TT
13306 ATGTTCATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
20 1 0.02
21 10 0.18
22 18 0.33
23 21 0.38
24 5 0.09
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.78
Consensus pattern (20 bp):
TTGTTTTTTTTTTTATTTAT
Found at i:13316 original size:22 final size:22
Alignment explanation
Indices: 13272--13317 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
13262 TGTTTATTCT
* * * *
13272 TTTTGTTTATTTGTTTTCTTTA
1 TTTTATTTATTTATGTTCATTA
13294 TTTTATTTATTTATGTTCATTA
1 TTTTATTTATTTATGTTCATTA
13316 TT
1 TT
13318 GTTTTCCTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.74
Consensus pattern (22 bp):
TTTTATTTATTTATGTTCATTA
Found at i:14656 original size:2 final size:2
Alignment explanation
Indices: 14598--14641 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
14588 TACGTGTGTG
14598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14640 TA
1 TA
14642 CCAAAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24765 original size:20 final size:20
Alignment explanation
Indices: 24720--24765 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
24710 TTTATTAATT
*
24720 TATATTATTTTAAACATACAC
1 TATA-TATTTTAAAAATACAC
*
24741 -A-ATATTTTAAAAATATAC
1 TATATATTTTAAAAATACAC
24759 TATATAT
1 TATATAT
24766 ATATATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
18 14 0.67
19 2 0.10
20 5 0.24
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (20 bp):
TATATATTTTAAAAATACAC
Found at i:25496 original size:24 final size:24
Alignment explanation
Indices: 25470--25556 Score: 138
Period size: 24 Copynumber: 3.6 Consensus size: 24
25460 AATTTGCATT
*
25470 GAAGTGCCACATAGAATATACACT
1 GAAGTGCCACATAGAATATACACC
*
25494 GAAGTGCCACGTAGAATATACACC
1 GAAGTGCCACATAGAATATACACC
* *
25518 AAAGTGCCACGTAGAATATACACC
1 GAAGTGCCACATAGAATATACACC
25542 GAAGTGCCACATAGA
1 GAAGTGCCACATAGA
25557 TTTGTCCCGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (24 bp):
GAAGTGCCACATAGAATATACACC
Found at i:29154 original size:41 final size:41
Alignment explanation
Indices: 29102--29184 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
29092 TTGGAATTAA
29102 TACCTTCTTTATTTTTCA-TTTGTCATTTTCACTTTCAACAT
1 TACCTTCTTTATTTTTCATTTTG-CATTTTCACTTTCAACAT
* * *
29143 TACCTTTTTTATTTTTTATTTTGCATTTTCACTTTCAGCAT
1 TACCTTCTTTATTTTTCATTTTGCATTTTCACTTTCAACAT
29184 T
1 T
29185 GCATTTATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 34 0.89
42 4 0.11
ACGTcount: A:0.18, C:0.19, G:0.04, T:0.59
Consensus pattern (41 bp):
TACCTTCTTTATTTTTCATTTTGCATTTTCACTTTCAACAT
Found at i:31297 original size:15 final size:15
Alignment explanation
Indices: 31277--31308 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
31267 TTGATAATCA
31277 ATAAACTCATATTTT
1 ATAAACTCATATTTT
31292 ATAAACTCATATTTT
1 ATAAACTCATATTTT
31307 AT
1 AT
31309 GATTTGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAAACTCATATTTT
Found at i:31834 original size:61 final size:60
Alignment explanation
Indices: 31768--31899 Score: 158
Period size: 65 Copynumber: 2.1 Consensus size: 60
31758 GTTTCCCCTA
31768 TCTTGAGGATATCTTTAAAAA-CAATAAAAAATATTGTCTTTCTTAAGACTATTTTTACCTC
1 TCTTGAGGATATCTTTAAAAATCAATAAAAAATATTGTCTTTCTTAAG-CTATTTTT-CCTC
* * ** * *
31829 TCTTGAGGGTGTCTTTAAAAATTTTCTCTTAAAAATATTGTCTTTCTTAAGTTATTTTTCCTC
1 TCTTGAGGATATCTTTAAAAA---TCAATAAAAAATATTGTCTTTCTTAAGCTATTTTTCCTC
31892 TCTTGAGG
1 TCTTGAGG
31900 CTGTCTGAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
61 19 0.31
63 12 0.20
64 7 0.11
65 23 0.38
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.45
Consensus pattern (60 bp):
TCTTGAGGATATCTTTAAAAATCAATAAAAAATATTGTCTTTCTTAAGCTATTTTTCCTC
Found at i:31961 original size:38 final size:38
Alignment explanation
Indices: 31910--32028 Score: 134
Period size: 38 Copynumber: 3.1 Consensus size: 38
31900 CTGTCTGAAA
*
31910 ACTATTTTCCTAGAAACCTCAATCTTTTCTTCCTTAGG
1 ACTATTTTCCTAGAAACCTCAATCTTATCTTCCTTAGG
* * *
31948 ACTA-TTTCTCTAGAAATCTCAATCTTATCTTTCTTCA-A
1 ACTATTTTC-CTAGAAACCTCAATCTTATCTTCCTT-AGG
* ** *
31986 ACTATTTTCCTAGAAACCTTAATCTCGTCTTCCTAAGG
1 ACTATTTTCCTAGAAACCTCAATCTTATCTTCCTTAGG
32024 ACTAT
1 ACTAT
32029 GTAATGCCCT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
37 5 0.08
38 56 0.85
39 5 0.08
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.41
Consensus pattern (38 bp):
ACTATTTTCCTAGAAACCTCAATCTTATCTTCCTTAGG
Found at i:32856 original size:20 final size:20
Alignment explanation
Indices: 32831--32879 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
32821 GATTCAATCA
32831 GTATCGATACC-AAAGGAGAC
1 GTATCGATACCGAAAGGA-AC
* *
32851 GTATCGATACCGAATGGAAG
1 GTATCGATACCGAAAGGAAC
32871 GTATCGATA
1 GTATCGATA
32880 TCATTTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (20 bp):
GTATCGATACCGAAAGGAAC
Found at i:33440 original size:47 final size:47
Alignment explanation
Indices: 33371--33720 Score: 511
Period size: 47 Copynumber: 7.4 Consensus size: 47
33361 AAATCGAATT
* *
33371 CATAATTTAAAATGCATGAAAAGATGCTTTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGC
*
33418 CATAATTGAGAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGC
* *
33465 CATAATTCAAAATGCATGAAAAGATGCATTAAGTCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGC
*
33512 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGC
* * * * *
33559 CATAATTGAAAATGCATGAAAGGATGCATTGAGACATGAATGTATGC
1 CATAATTGAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGC
* * * * * *
33606 CATAATTTAAAATGCATGAAATGATACATTAAGGTATGAAAAGAAGC
1 CATAATTGAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGC
* *
33653 CATAATTGAAAATGCATGAAATGATACATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGC
* *
33700 CATAATTTAAAATGTATGAAA
1 CATAATTGAAAATGCATGAAA
33721 GGATAGATGT
Statistics
Matches: 274, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 274 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.24
Consensus pattern (47 bp):
CATAATTGAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGC
Found at i:33443 original size:27 final size:25
Alignment explanation
Indices: 33404--33585 Score: 142
Period size: 27 Copynumber: 7.6 Consensus size: 25
33394 ATGCTTTAAG
33404 GCATGAAAGGATGCCATAATTGAGAAT
1 GCATGAAAGGATGCCATAATT-A-AAT
* *
33431 GCATGAAAAGATG-C---ATT-AAG
1 GCATGAAAGGATGCCATAATTAAAT
33451 GCATGAAAGGATGCCATAATTCAAAAT
1 GCATGAAAGGATGCCATAATT--AAAT
* *
33478 GCATGAAAAGATG-C---ATTAAGT
1 GCATGAAAGGATGCCATAATTAAAT
33499 -CATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCCATAATT--AAAT
*
33525 GCATGAAAGGATG-C---ATT-AAG
1 GCATGAAAGGATGCCATAATTAAAT
33545 GCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCCATAATT--AAAT
33572 GCATGAAAGGATGC
1 GCATGAAAGGATGC
33586 ATTGAGACAT
Statistics
Matches: 124, Mismatches: 10, Indels: 42
0.70 0.06 0.24
Matches are distributed among these distances:
20 40 0.32
21 6 0.05
23 9 0.07
24 9 0.07
26 6 0.05
27 54 0.44
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (25 bp):
GCATGAAAGGATGCCATAATTAAAT
Found at i:33550 original size:20 final size:20
Alignment explanation
Indices: 33384--33558 Score: 89
Period size: 20 Copynumber: 7.7 Consensus size: 20
33374 AATTTAAAAT
* *
33384 GCATGAAAAGATGCTTTAAG
1 GCATGAAAGGATGCATTAAG
*
33404 GCATGAAAGGATGCCATAATTGAGAAT
1 GCATGAAAGGATG-C---ATT---AAG
*
33431 GCATGAAAAGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
33451 GCATGAAAGGATGCCATAATTCAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
*
33478 GCATGAAAAGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
33498 TCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
33525 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
33545 GCATGAAAGGATGC
1 GCATGAAAGGATGC
33559 CATAATTGAA
Statistics
Matches: 120, Mismatches: 14, Indels: 42
0.68 0.08 0.24
Matches are distributed among these distances:
20 55 0.46
21 3 0.03
23 9 0.08
24 8 0.07
26 3 0.03
27 42 0.35
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:33598 original size:20 final size:20
Alignment explanation
Indices: 33526--33598 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 20
33516 ATTGAAAATG
* *
33526 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTGAGA
*
33546 CATGAAAGGATGCCATAATTGAAAA
1 CATGAAAGGATG-C---ATTG-AGA
33571 TGCATGAAAGGATGCATTGAGA
1 --CATGAAAGGATGCATTGAGA
33593 CATGAA
1 CATGAA
33599 TGTATGCCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
20 18 0.43
21 1 0.02
22 2 0.05
23 4 0.10
24 3 0.07
25 1 0.02
26 1 0.02
27 12 0.29
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (20 bp):
CATGAAAGGATGCATTGAGA
Found at i:37694 original size:20 final size:20
Alignment explanation
Indices: 37656--37694 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
37646 CGTTATCACC
*
37656 GGATATAAAGGACTCGATTT
1 GGATATAAAGGACTAGATTT
37676 GGATAATAAAGGAC-AGATT
1 GGAT-ATAAAGGACTAGATT
37695 GACCAAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.41, C:0.08, G:0.26, T:0.26
Consensus pattern (20 bp):
GGATATAAAGGACTAGATTT
Found at i:39580 original size:19 final size:19
Alignment explanation
Indices: 39537--39580 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
39527 GAATGTAAAA
39537 ATGGTATCGATATCATAAT
1 ATGGTATCGATATCATAAT
* *
39556 AGGGTATCGATATCATAGT
1 ATGGTATCGATATCATAAT
39575 ATGGTA
1 ATGGTA
39581 GTATCGATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (19 bp):
ATGGTATCGATATCATAAT
Found at i:40082 original size:47 final size:47
Alignment explanation
Indices: 40007--40453 Score: 707
Period size: 47 Copynumber: 9.5 Consensus size: 47
39997 ACTGAATTCG
* *
40007 TAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGCCA
1 TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
* *
40054 TACTTGAAAATGCATGAAAAGATGCATTAAGGCATGAAAGGATGCCA
1 TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
* *
40101 TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAATGGAAT-TCA
1 TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGG-ATGCCA
*
40148 TAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCA
1 TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
* * *
40195 TAATTTAAAATGCATGAAAGGATGCATTAAGTCATGAAAAGATGCCA
1 TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
* *
40242 TAATTGAAAATGCATGAAATGATGCATTAAGACATGAAAGGATGCCA
1 TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
* * * *
40289 TAATTTAAAATGCATGAAAGGATGCGTTAAGGCATGAAAAGATGTCA
1 TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
40336 TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
1 TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
**
40383 TAATTGAAAATATATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
1 TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
*
40430 TAATTTAAAATGCATGAAAGGATG
1 TAATTGAAAATGCATGAAAGGATG
40454 GATGTGTTAA
Statistics
Matches: 364, Mismatches: 34, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
46 2 0.01
47 360 0.99
48 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.24
Consensus pattern (47 bp):
TAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
Found at i:40265 original size:27 final size:26
Alignment explanation
Indices: 40011--40453 Score: 213
Period size: 27 Copynumber: 18.8 Consensus size: 26
40001 AATTCGTAAT
40011 TTAAAATGCATGAAAGGATG-C---A
1 TTAAAATGCATGAAAGGATGCCATAA
* * *
40033 TT--AAGGCATGAAAGAATGCCATAC
1 TTAAAATGCATGAAAGGATGCCATAA
*
40057 TTGAAAATGCATGAAAAGATG-C---A
1 TT-AAAATGCATGAAAGGATGCCATAA
*
40080 TT--AAGGCATGAAAGGATGCCATAA
1 TTAAAATGCATGAAAGGATGCCATAA
40104 TTGAAAATGCATGAAAGGATG-C---A
1 TT-AAAATGCATGAAAGGATGCCATAA
* * *
40127 TT--AAGGCATGAATGGAAT-TCATAA
1 TTAAAATGCATGAAAGG-ATGCCATAA
*
40151 TTGAAAATGCATGAAATGATG-C---A
1 TT-AAAATGCATGAAAGGATGCCATAA
*
40174 TT--AAGGCATGAAAGGATGCCATAA
1 TTAAAATGCATGAAAGGATGCCATAA
40198 TTTAAAATGCATGAAAGGATG-C---A
1 -TTAAAATGCATGAAAGGATGCCATAA
* *
40221 TT-AAGT-CATGAAAAGATGCCATAA
1 TTAAAATGCATGAAAGGATGCCATAA
*
40245 TTGAAAATGCATGAAATGATG-C---A
1 TT-AAAATGCATGAAAGGATGCCATAA
*
40268 TTAAGA--CATGAAAGGATGCCATAA
1 TTAAAATGCATGAAAGGATGCCATAA
*
40292 TTTAAAATGCATGAAAGGATG-C---G
1 -TTAAAATGCATGAAAGGATGCCATAA
* * *
40315 TT--AAGGCATGAAAAGATGTCATAA
1 TTAAAATGCATGAAAGGATGCCATAA
40339 TTGAAAATGCATGAAAGGATG-C---A
1 TT-AAAATGCATGAAAGGATGCCATAA
*
40362 TT--AAGGCATGAAAGGATGCCATAA
1 TTAAAATGCATGAAAGGATGCCATAA
**
40386 TTGAAAATATATGAAAGGATG-C---A
1 TT-AAAATGCATGAAAGGATGCCATAA
*
40409 TT--AAGGCATGAAAGGATGCCATAA
1 TTAAAATGCATGAAAGGATGCCATAA
40433 TTTAAAATGCATGAAAGGATG
1 -TTAAAATGCATGAAAGGATG
40454 GATGTGTTAA
Statistics
Matches: 317, Mismatches: 39, Indels: 125
0.66 0.08 0.26
Matches are distributed among these distances:
20 117 0.37
21 14 0.04
22 9 0.03
23 18 0.06
24 19 0.06
25 9 0.03
26 13 0.04
27 118 0.37
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.24
Consensus pattern (26 bp):
TTAAAATGCATGAAAGGATGCCATAA
Found at i:41556 original size:17 final size:16
Alignment explanation
Indices: 41533--41576 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
41523 ATTATTAGTA
*
41533 ATATTTATTACTTATT
1 ATATTTATTACTTACT
*
41549 ATTATTTACTACTTACT
1 A-TATTTATTACTTACT
41566 ATATATTATTA
1 ATAT-TTATTA
41577 TTAAATTGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTTATTACTTACT
Found at i:41881 original size:23 final size:22
Alignment explanation
Indices: 41855--41914 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
41845 AGTATTTATT
**
41855 TTATTATTATATATTATATAGTA
1 TTATTATTAT-TATTATATACCA
*
41878 TTATCTATTATTCTTATATACCA
1 TTAT-TATTATTATTATATACCA
*
41901 TTATTGTTATTATT
1 TTATTATTATTATT
41915 TATGTTTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 8 0.26
23 17 0.55
24 6 0.19
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (22 bp):
TTATTATTATTATTATATACCA
Found at i:43307 original size:21 final size:22
Alignment explanation
Indices: 43261--43307 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
43251 CATTCTTAAT
** *
43261 TTTTTTCTTCATATTATTTTAG
1 TTTTTTCTTCATATTATTAAAC
43283 TTTTTT-TTCATATTATTAAAC
1 TTTTTTCTTCATATTATTAAAC
43304 TTTT
1 TTTT
43308 CATATTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTTTCTTCATATTATTAAAC
Found at i:46352 original size:15 final size:15
Alignment explanation
Indices: 46332--46360 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46322 ATACCAAAGG
46332 AAGGGTATCGATACC
1 AAGGGTATCGATACC
46347 AAGGGTATCGATAC
1 AAGGGTATCGATAC
46361 TAATGCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (15 bp):
AAGGGTATCGATACC
Found at i:47098 original size:16 final size:16
Alignment explanation
Indices: 47046--47099 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
47036 GACAAGGAAT
**
47046 TATGTGATTATATGTC
1 TATGTGATTATATGAA
*
47062 TATGTGA-TA-CTGAA
1 TATGTGATTATATGAA
47076 CTATGTGATTATATGAA
1 -TATGTGATTATATGAA
47093 TATGTGA
1 TATGTGA
47100 AATGTGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 2 0.06
15 9 0.29
16 16 0.52
17 4 0.13
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (16 bp):
TATGTGATTATATGAA
Found at i:47367 original size:24 final size:24
Alignment explanation
Indices: 47316--47361 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
47306 CCTTTGGGAC
* *
47316 ATTTTTATGTGGCACTTCGGTGTA
1 ATTTCTATGCGGCACTTCGGTGTA
47340 ATTTCTATGCGGCACTTCGGTG
1 ATTTCTATGCGGCACTTCGGTG
47362 CTATTTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.26, T:0.41
Consensus pattern (24 bp):
ATTTCTATGCGGCACTTCGGTGTA
Found at i:47486 original size:6 final size:6
Alignment explanation
Indices: 47475--47532 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
47465 TAATGAACTG
* * * **
47475 TGATAA TGATAA TTATAA TGACAA TGATGA TGATGT TGATAA TGATAA
1 TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA
*
47523 TGATGA TGAT
1 TGATAA TGAT
47533 GAGGAGGATA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (6 bp):
TGATAA
Found at i:47507 original size:24 final size:24
Alignment explanation
Indices: 47475--47532 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
47465 TAATGAACTG
*
47475 TGATAATGATAATT-ATAATGACAA
1 TGATGATGAT-ATTGATAATGACAA
* *
47499 TGATGATGATGTTGATAATGATAA
1 TGATGATGATATTGATAATGACAA
47523 TGATGATGAT
1 TGATGATGAT
47533 GAGGAGGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (24 bp):
TGATGATGATATTGATAATGACAA
Found at i:52147 original size:20 final size:20
Alignment explanation
Indices: 52122--52163 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
52112 TGATGGTAAA
* *
52122 AAAAGAAAAAGAAGATGAAG
1 AAAAGAAAAACAAGAAGAAG
*
52142 AAAAGAATAACAAGAAGAAG
1 AAAAGAAAAACAAGAAGAAG
52162 AA
1 AA
52164 TGAGGTAGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAACAAGAAGAAG
Found at i:61194 original size:21 final size:20
Alignment explanation
Indices: 61166--61204 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
61156 CATTGCAAGA
*
61166 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCCACAAAAG
*
61186 ATTTCATGGCTTCCACAAA
1 ATTT-ATGGCCTCCACAAA
61205 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCCACAAAAG
Done.