Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001425.1 Hibiscus syriacus cultivar Beakdansim tig00002768_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: 95702
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:830 original size:23 final size:23
Alignment explanation
Indices: 799--871 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
789 ATAGGTAAAA
*
799 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
822 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
845 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
868 ATAT
1 ATAT
872 TGTAAAGTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2004 original size:28 final size:28
Alignment explanation
Indices: 1955--2029 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
1945 TTTATGTGTA
* **
1955 AATTAAATATTAAGACCATTTTTTGAAT-
1 AATTAAATATTAGGACTTTTTTTTG-ATG
1983 AATTAAATATTAGGACTTTTTTTTTGATG
1 AATTAAATATTAGGAC-TTTTTTTTGATG
*
2012 CATTAAATATTAGGACTT
1 AATTAAATATTAGGACTT
2030 GTGAAAGGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 19 0.46
29 22 0.54
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (28 bp):
AATTAAATATTAGGACTTTTTTTTGATG
Found at i:3462 original size:44 final size:39
Alignment explanation
Indices: 3392--3479 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 39
3382 ACTATCGCAA
3392 TGCGA-TTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTTCCAAATTCGTTGCGATAGTCCAAGTT--CGT
3432 TGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGT
1 TGCGATTT-TTCCAAATT--CGTTGCGATAGTCCAAGTTCGT
3474 TGCGAT
1 TGCGAT
3480 AGTCGAAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
40 5 0.11
41 2 0.05
42 18 0.41
44 19 0.43
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (39 bp):
TGCGATTTTTCCAAATTCGTTGCGATAGTCCAAGTTCGT
Found at i:3473 original size:63 final size:61
Alignment explanation
Indices: 3400--3668 Score: 258
Period size: 63 Copynumber: 4.3 Consensus size: 61
3390 AATGCGATTT
*
3400 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGATAG
* * * *
3463 TCCAAGTTCGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAGTTCGTTGCGATGG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
* * * * * *
3524 TCAAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTACGAT
1 TCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGA-
*
3585 TTAT
59 -TAG
* * *
3589 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATGTATTCCAAATTCGTTCCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
*
3650 TCGAAGTTCGCGTTGCGAT
1 TCCAAGTT--CGTTGCGAT
3669 TTATTCTAAG
Statistics
Matches: 170, Mismatches: 22, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
61 44 0.26
63 101 0.59
65 25 0.15
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (61 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
Found at i:3500 original size:84 final size:82
Alignment explanation
Indices: 3408--3702 Score: 371
Period size: 84 Copynumber: 3.5 Consensus size: 82
3398 TTTCCAAATT
* * *
3408 CGTTGCGA-TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTATTCCAAGTT--CGTTGCGA--TAGTCCAAATTCGCGTTGCGATTATTCCAAGTT
*
3471 CGTTGCGATAGTCGAAGTTTG
62 CGTTGCGATAGTCGAAGTTCG
*
3492 CGTTGCGATTTATTCCAAGTTCGTTGCGATGGT-CAAAGTTCGCGTTGCGATTTATTCCAAGTTC
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAA-TTCGCGTTGCGA-TTATTCCAAGTTC
3556 GTTGCGATAGTCGAAGTTCG
63 GTTGCGATAGTCGAAGTTCG
* * * *
3576 CGTTACGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATGTATTCCAAATTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAATTCGCGTTGCGAT-TATTCCAAGTTCG
*
3641 TTCCGATAGTCGAAGTTCG
64 TTGCGATAGTCGAAGTTCG
* *
3660 CGTTGCGATTTATTCTAAGTTCGTTGCGATAGTCCAAAATCGC
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAATTCGC
3703 AACGACTAGT
Statistics
Matches: 188, Mismatches: 16, Indels: 14
0.86 0.07 0.06
Matches are distributed among these distances:
81 4 0.02
82 14 0.07
83 1 0.01
84 157 0.84
85 2 0.01
86 10 0.05
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (82 bp):
CGTTGCGATTATTCCAAGTTCGTTGCGATAGTCCAAATTCGCGTTGCGATTATTCCAAGTTCGTT
GCGATAGTCGAAGTTCG
Found at i:3509 original size:42 final size:42
Alignment explanation
Indices: 3448--3693 Score: 397
Period size: 42 Copynumber: 5.9 Consensus size: 42
3438 TTATTCCAAA
*
3448 TTCGCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* * *
3488 TTTGCGTTGCGATTTATTCCAAGTTCGTTGCGATGGTCAAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
3530 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
3572 TTCGCGTTACGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* * *
3614 TTCGCGTTGCGATGTATTCCAAATTCGTTCCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
3656 TTCGCGTTGCGATTTATTCTAAGTTCGTTGCGATAGTC
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
3694 CAAAATCGCA
Statistics
Matches: 188, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 11 0.06
42 177 0.94
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (42 bp):
TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
Found at i:4471 original size:6 final size:6
Alignment explanation
Indices: 4455--4486 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4445 TCTCGTCTCG
4455 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
4487 AGTTGCGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:6395 original size:19 final size:19
Alignment explanation
Indices: 6371--6408 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
6361 CTTTAATTGA
6371 GAATTTATAATTAATATAG
1 GAATTTATAATTAATATAG
*
6390 GAATTTATAATTAGTATAG
1 GAATTTATAATTAATATAG
6409 TTTCTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (19 bp):
GAATTTATAATTAATATAG
Found at i:24397 original size:21 final size:21
Alignment explanation
Indices: 24371--24410 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24361 AACTACTATT
*
24371 TTTAATTTTTAATTTTTTAAA
1 TTTAATTTTGAATTTTTTAAA
*
24392 TTTAATTTTGATTTTTTTA
1 TTTAATTTTGAATTTTTTA
24411 TTAAACTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTAATTTTGAATTTTTTAAA
Found at i:33631 original size:21 final size:21
Alignment explanation
Indices: 33607--33659 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
33597 ACACTTAGGG
33607 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
33628 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
33649 TACCGATTCCC
1 AACCGATTCCC
33660 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:33870 original size:13 final size:13
Alignment explanation
Indices: 33852--33883 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
33842 CTCAAGTTCG
33852 TTAATTCAAATAC
1 TTAATTCAAATAC
*
33865 TTAATTGAAATAC
1 TTAATTCAAATAC
33878 TTAATT
1 TTAATT
33884 AACTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (13 bp):
TTAATTCAAATAC
Found at i:33990 original size:32 final size:33
Alignment explanation
Indices: 33894--33992 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
33884 AACTCAACAT
* * *
33894 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
33927 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
33960 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
33992 A
1 A
33993 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:34011 original size:21 final size:21
Alignment explanation
Indices: 33987--34026 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
33977 ACTTCAAGTT
33987 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
34008 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
34027 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:44516 original size:78 final size:78
Alignment explanation
Indices: 44360--44522 Score: 193
Period size: 78 Copynumber: 2.1 Consensus size: 78
44350 GTGCTGCCAC
* *
44360 CTTTTCTTGTAATGCCTGTGCAAAGGCATCTGAGGCATCACCTTTAGTCTCAACAGTATTTAAAT
1 CTTTTCTTGCAATGCCTGTGCAAAGGCATCTGAGGCATAACCTTTAGTCTCAACAGTATTTAAAT
* *
44425 CCAGCATACCCCT
66 ACAGCAAACCCCT
* * * * * *
44438 CTTTTCTTGCAATGCCTTTGCAAGGGCTTCTGAGGCATTAAGC-TTAGTCTCAGCAGTATTTGAA
1 CTTTTCTTGCAATGCCTGTGCAAAGGCATCTGAGGCA-TAACCTTTAGTCTCAACAGTATTTAAA
*
44502 TAGAGCAAATCCCTCT
65 TACAGCAAA-CCC-CT
44518 CTTTT
1 CTTTT
44523 ACCTCATCTT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
78 58 0.82
79 6 0.08
80 7 0.10
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (78 bp):
CTTTTCTTGCAATGCCTGTGCAAAGGCATCTGAGGCATAACCTTTAGTCTCAACAGTATTTAAAT
ACAGCAAACCCCT
Found at i:48731 original size:21 final size:21
Alignment explanation
Indices: 48689--48732 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
48679 AGTGACTAAC
* *
48689 CGATTAAACAAGTTAATAAAA
1 CGATTAAACAAATAAATAAAA
* *
48710 CGATTAATCAAATAAATTAAA
1 CGATTAAACAAATAAATAAAA
48731 CG
1 CG
48733 GAAAACTTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (21 bp):
CGATTAAACAAATAAATAAAA
Found at i:58403 original size:14 final size:11
Alignment explanation
Indices: 58371--58396 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
58361 TAACAAGTTA
58371 AATTTTATTAT
1 AATTTTATTAT
58382 AATTTTATTAT
1 AATTTTATTAT
58393 AATT
1 AATT
58397 AATTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AATTTTATTAT
Found at i:62436 original size:15 final size:15
Alignment explanation
Indices: 62419--62448 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
62409 ATCTTTCTTT
62419 CCCGTTCTGGATTTTC
1 CCCG-TCTGGATTTTC
62435 CCCGTCTGGATTTT
1 CCCGTCTGGATTTT
62449 GATCTGCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.30, G:0.20, T:0.43
Consensus pattern (15 bp):
CCCGTCTGGATTTTC
Found at i:63041 original size:13 final size:14
Alignment explanation
Indices: 63010--63043 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
63000 TAGTTTTAAA
63010 TATAAAAAATAATT
1 TATAAAAAATAATT
*
63024 AATAAAAAAT-ATT
1 TATAAAAAATAATT
63037 TATAAAA
1 TATAAAA
63044 TTTAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TATAAAAAATAATT
Found at i:70089 original size:22 final size:22
Alignment explanation
Indices: 70064--70105 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
70054 ACATGCAGGC
70064 GACCTCTTCCGACGTGCATGAT
1 GACCTCTTCCGACGTGCATGAT
70086 GACCTCTTCCGACGTGCATG
1 GACCTCTTCCGACGTGCATG
70106 GCGCATGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.33, G:0.24, T:0.26
Consensus pattern (22 bp):
GACCTCTTCCGACGTGCATGAT
Found at i:70147 original size:31 final size:31
Alignment explanation
Indices: 70112--70204 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
70102 CATGGCGCAT
70112 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
70143 GCAAA-CTTTCATCCTCTCACCACAGCTCGTA
1 GCAAAGC-TTCATCCTCTCACCACAGCTCGTA
*
70174 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCACCACAGCTCGTA
70205 TAGAACACTT
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
30 1 0.02
31 57 0.97
32 1 0.02
ACGTcount: A:0.25, C:0.39, G:0.13, T:0.24
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCACCACAGCTCGTA
Found at i:80817 original size:22 final size:22
Alignment explanation
Indices: 80775--80817 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
80765 CTTCTTTAAA
*
80775 AACCTTAAACCACTAAGAAAAT
1 AACCTTAAACCACTAACAAAAT
*
80797 AACC-TAAACCATTAATCAAAA
1 AACCTTAAACCACTAA-CAAAA
80818 CCCTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.56, C:0.23, G:0.02, T:0.19
Consensus pattern (22 bp):
AACCTTAAACCACTAACAAAAT
Found at i:83613 original size:3 final size:3
Alignment explanation
Indices: 83605--83640 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
83595 AATATTATAC
83605 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
83641 ATTTTTTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:83727 original size:2 final size:2
Alignment explanation
Indices: 83720--83757 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
83710 AGTTTAGTCT
83720 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
83758 GTTGTACTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:91967 original size:2 final size:2
Alignment explanation
Indices: 91960--92012 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
91950 TCTTTTTAAA
91960 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
92002 AC AC AC AC AC A
1 AC AC AC AC AC A
92013 TATATATATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:92017 original size:2 final size:2
Alignment explanation
Indices: 92012--92036 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
92002 ACACACACAC
92012 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 A
92037 CTCCATCCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:92224 original size:24 final size:24
Alignment explanation
Indices: 92197--92294 Score: 90
Period size: 24 Copynumber: 4.1 Consensus size: 24
92187 TATATCAAAA
* *
92197 ATCAAAACATAATCCATGTCAAGT
1 ATCAAAACAGAATCCAGGTCAAGT
* *
92221 ATCAGATCAGAATCCAGGTCAAGT
1 ATCAAAACAGAATCCAGGTCAAGT
* *
92245 ATTC-GATCAGAATCCAGGTCAAGT
1 A-TCAAAACAGAATCCAGGTCAAGT
** * *
92269 ATCCGATCAGAATCCAGGTCATGT
1 ATCAAAACAGAATCCAGGTCAAGT
92293 AT
1 AT
92295 TTTAATAGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 2 0.03
24 63 0.94
25 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATCCAGGTCAAGT
Found at i:92304 original size:24 final size:24
Alignment explanation
Indices: 92207--92295 Score: 135
Period size: 24 Copynumber: 3.7 Consensus size: 24
92197 ATCAAAACAT
*
92207 AATCCATGTCAAGTA-TCAGATCAG
1 AATCCAGGTCAAGTATTC-GATCAG
92231 AATCCAGGTCAAGTATTCGATCAG
1 AATCCAGGTCAAGTATTCGATCAG
*
92255 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATTCGATCAG
*
92279 AATCCAGGTCATGTATT
1 AATCCAGGTCAAGTATT
92296 TTAATAGAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
24 58 0.97
25 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (24 bp):
AATCCAGGTCAAGTATTCGATCAG
Done.