Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002535.1 Hibiscus syriacus cultivar Beakdansim tig00005151_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: 63838
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:957 original size:13 final size:13
Alignment explanation
Indices: 939--965 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
929 CTTAATTTAA
939 CTTATACCCAACT
1 CTTATACCCAACT
952 CTTATACCCAACT
1 CTTATACCCAACT
965 C
1 C
966 AACATGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.30
Consensus pattern (13 bp):
CTTATACCCAACT
Found at i:2039 original size:22 final size:21
Alignment explanation
Indices: 2002--2076 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 21
1992 TGTTGCACTT
*
2002 TTATCTTTGCTTTGTGACACG
1 TTATCTTTTCTTTGTGACACG
2023 TTATCTTTATCTTTGTGACACG
1 TTATCTTT-TCTTTGTGACACG
*
2045 TTATCTTTGTCTTTGTGGCACG
1 TTATCTTT-TCTTTGTGACACG
*
2067 TT-TTTTTTCT
1 TTATCTTTTCT
2077 CGATCTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
20 3 0.06
21 12 0.24
22 34 0.69
ACGTcount: A:0.12, C:0.17, G:0.16, T:0.55
Consensus pattern (21 bp):
TTATCTTTTCTTTGTGACACG
Found at i:6724 original size:3 final size:3
Alignment explanation
Indices: 6716--6770 Score: 74
Period size: 3 Copynumber: 17.7 Consensus size: 3
6706 TAAAATTAAA
* *
6716 ATT ATT ATT TTT ATT ATT ATT ATT AAT ATAT ATAT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT ATT ATT ATT
6763 ATT ATT AT
1 ATT ATT AT
6771 ATAAATAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
3 40 0.85
4 7 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:7175 original size:13 final size:13
Alignment explanation
Indices: 7157--7182 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7147 CGCAGCTATG
7157 GGGCGAGTCACCA
1 GGGCGAGTCACCA
7170 GGGCGAGTCACCA
1 GGGCGAGTCACCA
7183 CATAGTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.38, T:0.08
Consensus pattern (13 bp):
GGGCGAGTCACCA
Found at i:10741 original size:20 final size:20
Alignment explanation
Indices: 10713--10751 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10703 AATTTGCATT
*
10713 TTTATATTTACATTCACATA
1 TTTACATTTACATTCACATA
* *
10733 TTTACATTTGCATTTACAT
1 TTTACATTTACATTCACAT
10752 TTAGCATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTACATTTACATTCACATA
Found at i:10749 original size:12 final size:13
Alignment explanation
Indices: 10732--10760 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
10722 ACATTCACAT
10732 ATTTACATTT-GC
1 ATTTACATTTAGC
10744 ATTTACATTTAGC
1 ATTTACATTTAGC
10757 ATTT
1 ATTT
10761 TTTTTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (13 bp):
ATTTACATTTAGC
Found at i:17458 original size:22 final size:22
Alignment explanation
Indices: 17431--17504 Score: 130
Period size: 22 Copynumber: 3.4 Consensus size: 22
17421 TACACTCTTT
17431 AAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCTCTTTTC
*
17453 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTC
*
17475 AAAGATGATAGATTCTATTTTC
1 AAAGATGATAGATTCTCTTTTC
17497 AAAGATGA
1 AAAGATGA
17505 AAGCTTTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTC
Found at i:18279 original size:76 final size:76
Alignment explanation
Indices: 18180--18969 Score: 1454
Period size: 76 Copynumber: 10.4 Consensus size: 76
18170 CTATTTGCCA
18180 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18245 AGCCTTAGGGT
66 AGCCTTAGGGT
18256 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18321 AGCCTTAGGGT
66 AGCCTTAGGGT
*
18332 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAGGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18397 AGCCTTAGGGT
66 AGCCTTAGGGT
*
18408 CATCTGTAAGTCCTACAGTGCATGATGTTACCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
18473 AGCCTTAAGGT
66 AGCCTTAGGGT
18484 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18549 AGCCTTAGGGT
66 AGCCTTAGGGT
18560 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18625 AGCCTTAGGGT
66 AGCCTTAGGGT
*
18636 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18701 AGCCTTAGGGT
66 AGCCTTAGGGT
*
18712 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
18777 AACCTTAGGGT
66 AGCCTTAGGGT
* *
18788 CATCTGTAAGTCCTGCAGTGTATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
18853 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
18864 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
18929 AACCTTAGGGT
66 AGCCTTAGGGT
* **
18940 CATCTGTAAGCCCTTTAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
18970 TCAATATTTC
Statistics
Matches: 698, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 698 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:19110 original size:3 final size:3
Alignment explanation
Indices: 19102--19155 Score: 99
Period size: 3 Copynumber: 17.7 Consensus size: 3
19092 TTTTATTAAA
19102 ATT ATT ATT ATT ATT ATT ATT ATAT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
19148 ATT ATT AT
1 ATT ATT AT
19156 ATAAATTACA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:23307 original size:2 final size:2
Alignment explanation
Indices: 23300--23356 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
23290 TATTAAGGAA
23300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23342 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
23357 CTGTAATAGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26196 original size:30 final size:31
Alignment explanation
Indices: 26145--26213 Score: 122
Period size: 30 Copynumber: 2.2 Consensus size: 31
26135 CCTCGCTATT
26145 CTAAGCTTTACCCTTTCTCTCTAATAGCTTTG
1 CTAAGCTTTACCC-TTCTCTCTAATAGCTTTG
26177 CTAAGCTTTACCC-TCTCTCTAATAGCTTTG
1 CTAAGCTTTACCCTTCTCTCTAATAGCTTTG
26207 CTAAGCT
1 CTAAGCT
26214 ATTATTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 24 0.65
32 13 0.35
ACGTcount: A:0.20, C:0.29, G:0.10, T:0.41
Consensus pattern (31 bp):
CTAAGCTTTACCCTTCTCTCTAATAGCTTTG
Found at i:27347 original size:30 final size:31
Alignment explanation
Indices: 27291--27366 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 31
27281 CGCTATTCTA
27291 AGCTTTGCTAAGCTTTACCCTTTCTCTCTAAT
1 AGCTTTGCTAAGCTTTACCC-TTCTCTCTAAT
* *
27323 AGCTTTTCTAGGCTTTACCC-TCTCTCTAAT
1 AGCTTTGCTAAGCTTTACCCTTCTCTCTAAT
*
27353 AGCTTTCCTAAGCT
1 AGCTTTGCTAAGCT
27367 ATTATTCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 22 0.55
32 18 0.45
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (31 bp):
AGCTTTGCTAAGCTTTACCCTTCTCTCTAAT
Found at i:28181 original size:55 final size:55
Alignment explanation
Indices: 28098--28206 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 55
28088 AGGAATATGA
* * * * * *
28098 GAAAAGGCTTAGAAAAGCCAGAATGAGAAATAGCTTAGCAAAGCTATTAGAGAAT
1 GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAACTTAGAAAAGCTATGAGAGAAT
* *
28153 GAAAAAGCTTAGCAAAGCAAGGACGAGAAATAACTTAGAAAAGCTATGAGAGAA
1 GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAACTTAGAAAAGCTATGAGAGAA
28207 AAGGTGAAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.50, C:0.11, G:0.24, T:0.16
Consensus pattern (55 bp):
GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAACTTAGAAAAGCTATGAGAGAAT
Found at i:28720 original size:30 final size:31
Alignment explanation
Indices: 28684--28751 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 31
28674 ATAGCTTAGG
28684 AAAGCTATTAGAGAG-AGGGTAAAGCCTAGC
1 AAAGCTATTAGAGAGAAGGGTAAAGCCTAGC
*
28714 AAAGCTATTAGAGAGAAAGGGTAAAGCTTAGC
1 AAAGCTATTAGAGAG-AAGGGTAAAGCCTAGC
28746 AAAGCT
1 AAAGCT
28752 TAGAATAGCG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 15 0.43
32 20 0.57
ACGTcount: A:0.43, C:0.12, G:0.28, T:0.18
Consensus pattern (31 bp):
AAAGCTATTAGAGAGAAGGGTAAAGCCTAGC
Found at i:28755 original size:30 final size:29
Alignment explanation
Indices: 28676--28755 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
28666 AATGAATAAT
*
28676 AGCTTAGGAAAGCTATTAGAGAGAGGGTAA
1 AGCTTAGCAAAGC-ATTAGAGAGAGGGTAA
*
28706 AGCCTAGCAAAGCTATTAGAGAGAAAGGGTAA
1 AGCTTAGCAAAGC-ATTAGAGAG--AGGGTAA
28738 AGCTTAGCAAAGC-TTAGA
1 AGCTTAGCAAAGCATTAGA
28756 ATAGCGAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
30 26 0.58
32 19 0.42
ACGTcount: A:0.41, C:0.11, G:0.29, T:0.19
Consensus pattern (29 bp):
AGCTTAGCAAAGCATTAGAGAGAGGGTAA
Found at i:29881 original size:55 final size:55
Alignment explanation
Indices: 29798--29906 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 55
29788 AGGAATATGA
* * * * * *
29798 GAAAAGGCTTAGAAAAGCCAGAATGAGAAATAGCTTAGCAAAGCTATTAGAGAAT
1 GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAACTTAGAAAAGCTATGAGAGAAT
* *
29853 GAAAAAGCTTAGCAAAGCAAGGACGAGAAATAACTTAGAAAAGCTATGAGAGAA
1 GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAACTTAGAAAAGCTATGAGAGAA
29907 AATGTGAAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.50, C:0.11, G:0.24, T:0.16
Consensus pattern (55 bp):
GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAACTTAGAAAAGCTATGAGAGAAT
Found at i:29909 original size:26 final size:26
Alignment explanation
Indices: 29825--29909 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
29815 CCAGAATGAG
* *
29825 AAATAGCTTAGCAAAGCTATTAGAGA
1 AAATAACTTAGCAAAGCTATGAGAGA
* * *
29851 ATGAAAAAGCTTAGCAAAGCAAGGACGAG-
1 A--AATAA-CTTAGCAAAGCTATGA-GAGA
*
29880 AAATAACTTAGAAAAGCTATGAGAGA
1 AAATAACTTAGCAAAGCTATGAGAGA
29906 AAAT
1 AAAT
29910 GTGAAGCTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
25 3 0.07
26 18 0.40
27 4 0.09
28 3 0.07
29 14 0.31
30 3 0.07
ACGTcount: A:0.51, C:0.11, G:0.21, T:0.18
Consensus pattern (26 bp):
AAATAACTTAGCAAAGCTATGAGAGA
Found at i:36359 original size:2 final size:2
Alignment explanation
Indices: 36352--36376 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36342 ATACAAAACA
36352 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
36377 AACTTTAGTA
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:39223 original size:22 final size:21
Alignment explanation
Indices: 39182--39223 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
39172 GGAAGATGAA
*
39182 TTATAAATTTTATGAATAAAT
1 TTATAAATTTTAAGAATAAAT
*
39203 TTATAAAATTTTAAGAGTAAA
1 TTAT-AAATTTTAAGAATAAA
39224 ATGTATTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
TTATAAATTTTAAGAATAAAT
Found at i:46748 original size:18 final size:19
Alignment explanation
Indices: 46716--46752 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
46706 ATATATTTGA
*
46716 TTATCTTATTTATCTAATT
1 TTATCTTATTGATCTAATT
46735 TTAT-TTATTGATCTAATT
1 TTATCTTATTGATCTAATT
46753 CTCTCGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (19 bp):
TTATCTTATTGATCTAATT
Found at i:46975 original size:20 final size:20
Alignment explanation
Indices: 46946--46983 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
46936 ACATTCAAAT
*
46946 AAAATGCAATATTATAACAC
1 AAAATACAATATTATAACAC
46966 AAAATACAATATTATAAC
1 AAAATACAATATTATAAC
46984 TTGCTGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAATACAATATTATAACAC
Found at i:48221 original size:23 final size:21
Alignment explanation
Indices: 48161--48226 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 21
48151 ATAAGAATAA
*
48161 TTATGTCTTTGTGACATGTTT
1 TTATGTCTTTGTGACACGTTT
* *
48182 TT-TGTCTTTATAACACGTTT
1 TTATGTCTTTGTGACACGTTT
*
48202 ATCTATGTCTTTGTGGCACGTTT
1 -T-TATGTCTTTGTGACACGTTT
48225 TT
1 TT
48227 CTCTGCCTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 15 0.42
21 4 0.11
22 2 0.06
23 15 0.42
ACGTcount: A:0.15, C:0.14, G:0.17, T:0.55
Consensus pattern (21 bp):
TTATGTCTTTGTGACACGTTT
Found at i:49769 original size:23 final size:23
Alignment explanation
Indices: 49743--49788 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
49733 TTTTTAATTC
49743 GATAGCATCATTTAACTTTCCAA
1 GATAGCATCATTTAACTTTCCAA
49766 GATAGCATCATTTAACTTTCCAA
1 GATAGCATCATTTAACTTTCCAA
49789 CGTTGATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (23 bp):
GATAGCATCATTTAACTTTCCAA
Found at i:50650 original size:2 final size:2
Alignment explanation
Indices: 50638--50709 Score: 58
Period size: 2 Copynumber: 36.0 Consensus size: 2
50628 TTTTATAACC
* ** * *
50638 AT AT A- AT AT AT AT AT AT AT AT AT AT TT CC AT AT -T TT TT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
*
50679 AT GT GAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
50710 CATACAAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
1 2 0.03
2 54 0.93
3 2 0.03
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:51039 original size:23 final size:23
Alignment explanation
Indices: 51013--51066 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
51003 ACAATTTCAG
*
51013 GAGCTCG-TTTGAAGCTCGAACTC
1 GAGCTCGATTT-AAGCTCAAACTC
*
51036 GAGCTTGATTTAAGCTCAAACTC
1 GAGCTCGATTTAAGCTCAAACTC
*
51059 AAGCTCGA
1 GAGCTCGA
51067 ATATGAACCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (23 bp):
GAGCTCGATTTAAGCTCAAACTC
Found at i:51376 original size:31 final size:33
Alignment explanation
Indices: 51310--51380 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
51300 TATATCTTAT
* * *
51310 TTTACTTACAAAAATAATAGCAACGTGTTCAGA
1 TTTACTTACAAAAATAACAGCAACATATTCAGA
51343 TTTACTTA-AAAAATAACAGCAACATATTC-GA
1 TTTACTTACAAAAATAACAGCAACATATTCAGA
51374 TTTACTT
1 TTTACTT
51381 GTAAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 9 0.26
32 18 0.51
33 8 0.23
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.34
Consensus pattern (33 bp):
TTTACTTACAAAAATAACAGCAACATATTCAGA
Found at i:58544 original size:20 final size:21
Alignment explanation
Indices: 58519--58562 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
58509 GATTTCTGGG
*
58519 CAAGGGGAATCG-TACCCATT
1 CAAGGGGAACCGATACCCATT
*
58539 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
58560 CAA
1 CAA
58563 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:60158 original size:144 final size:146
Alignment explanation
Indices: 59971--60277 Score: 519
Period size: 146 Copynumber: 2.1 Consensus size: 146
59961 GTCGAGGGTC
* *
59971 TACGCGGTCCTTCGGGACATATGTATATCTTTGGAACATGTGTGAAGTCTTGAAAG-ACATACTT
1 TACGC-GTCCTTCGGGACATATATATATCTGTGGAACATGTGTGAAGTCTTGAAAGAACATACTT
60035 GATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATG
65 GATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATG
60100 GCACTACGGTGCAATTA
130 GCACTACGGTGCAATTA
*
60117 TACGCGTCCTTCGGGATATATATAT-TCTGTGGAACATGTGTGAAGTCTTGAAAGAAACATACTT
1 TACGCGTCCTTCGGGACATATATATATCTGTGGAACATGTGTGAAGTCTTGAAAG-AACATACTT
60181 GATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATG
65 GATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATG
* *
60246 GTACTACGGTGCAATTC
130 GCACTACGGTGCAATTA
*
60263 TACGCGGCACTTCGG
1 TACGCGTC-CTTCGG
60278 TGCAATTATA
Statistics
Matches: 152, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
144 28 0.18
145 18 0.12
146 100 0.66
147 6 0.04
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (146 bp):
TACGCGTCCTTCGGGACATATATATATCTGTGGAACATGTGTGAAGTCTTGAAAGAACATACTTG
ATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGG
CACTACGGTGCAATTA
Found at i:61734 original size:22 final size:23
Alignment explanation
Indices: 61688--61736 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
61678 AATAACATAT
**
61688 TAGGTAGCGCTTAGATAATGTAA
1 TAGGTAGCGCTTAGATAATAAAA
*
61711 TAGGTA-CGCTTATATAATAAAA
1 TAGGTAGCGCTTAGATAATAAAA
61733 TAGG
1 TAGG
61737 CATTTAACCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (23 bp):
TAGGTAGCGCTTAGATAATAAAA
Found at i:61791 original size:23 final size:21
Alignment explanation
Indices: 61765--61810 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
61755 ATCAAGTACA
*
61765 ATAACAAATTAGGTAGTGCTTAT
1 ATAA-AAA-TAGGTAGCGCTTAT
*
61788 ATAATAATAGGTAGCGCTTAT
1 ATAAAAATAGGTAGCGCTTAT
61809 AT
1 AT
61811 TGACCTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 2 0.10
23 4 0.19
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (21 bp):
ATAAAAATAGGTAGCGCTTAT
Done.