Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002826.1 Hibiscus syriacus cultivar Beakdansim tig00005811_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: 62928
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Found at i:681 original size:21 final size:21
Alignment explanation
Indices: 655--704 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
645 AAGGGGTATT
655 GATGCACCTAT-ATAGTGCACC
1 GATGCACCT-TGATAGTGCACC
676 GATGCACCTTGATAGTGCACC
1 GATGCACCTTGATAGTGCACC
697 GATGCACC
1 GATGCACC
705 ATGTTATGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (21 bp):
GATGCACCTTGATAGTGCACC
Found at i:3706 original size:18 final size:18
Alignment explanation
Indices: 3683--3740 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
3673 CAACAATTGG
3683 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
*
3701 TAACAATTGATATCATTCTGC
1 TAACAATTGATATC-TT-T-T
*
3722 TAACAATTGGTATCTTTT
1 TAACAATTGATATCTTTT
3740 T
1 T
3741 CATTAAACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 15 0.44
19 3 0.09
20 3 0.09
21 13 0.38
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.47
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Found at i:4012 original size:23 final size:20
Alignment explanation
Indices: 3961--4039 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
3951 AGGGTGTCAA
* * *
3961 AGTGCATCCATACACCCCTGC
1 AGTGCATCCATGCA-CCATGT
3982 AGTGCATCCATGCACC-TGGCACT
1 AGTGCATCCATGCACCAT-G---T
*
4005 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACCATGT
4025 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
4040 TCCATTTCGA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
19 1 0.02
20 18 0.37
21 13 0.27
23 16 0.33
24 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGT
Found at i:6178 original size:23 final size:23
Alignment explanation
Indices: 6134--6187 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
6124 TATATGATGG
6134 TATAAGAAATTATATGAATTAT-A
1 TATAAGAAATTATATG-ATTATGA
6157 TATAAGAACATGTATATG-TTATGA
1 TATAAGAA-AT-TATATGATTATGA
*
6181 GATAAGA
1 TATAAGA
6188 CCTATGACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 12 0.44
24 9 0.33
25 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (23 bp):
TATAAGAAATTATATGATTATGA
Found at i:6442 original size:30 final size:31
Alignment explanation
Indices: 6347--6465 Score: 136
Period size: 30 Copynumber: 3.8 Consensus size: 31
6337 CGAGGGTTAT
* * *
6347 CTATGTCTTTCGAGATATATGGATAGTTTAC
1 CTATGTCTTTCGGGACATATGGATAGATTAC
*
6378 CTATGTCTTTCGGGACATATGGACAAGATTAC
1 CTATGTCTTTCGGGACATATGGA-TAGATTAC
*
6410 CTATGT-TCTTCGGGATATATGGATAG-TTAC
1 CTATGTCT-TTCGGGACATATGGATAGATTAC
*
6440 CTATGT-TCTTCGGAACATATGGATAG
1 CTATGTCT-TTCGGGACATATGGATAG
6466 GTCCTTCGGG
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
30 28 0.36
31 24 0.31
32 26 0.33
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (31 bp):
CTATGTCTTTCGGGACATATGGATAGATTAC
Found at i:8989 original size:23 final size:23
Alignment explanation
Indices: 8959--9011 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
8949 TAAACTACCA
8959 AAAGGCAGAGAAAAATGTGCCAC
1 AAAGGCAGAGAAAAATGTGCCAC
* *
8982 AAAGGCAGAGATAAATGTGCCAT
1 AAAGGCAGAGAAAAATGTGCCAC
9005 AAAGGCA
1 AAAGGCA
9012 TATAATGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.47, C:0.15, G:0.26, T:0.11
Consensus pattern (23 bp):
AAAGGCAGAGAAAAATGTGCCAC
Found at i:10024 original size:22 final size:21
Alignment explanation
Indices: 9991--10040 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
9981 TTCATGTATT
9991 CATATCATTTCTCTTATGATCA
1 CATATCATTTCTCTTATG-TCA
*
10013 CATATC-TCTTCTCTTTTGTCA
1 CATATCAT-TTCTCTTATGTCA
10034 CATATCA
1 CATATCA
10041 CATGTATGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.24, C:0.26, G:0.04, T:0.46
Consensus pattern (21 bp):
CATATCATTTCTCTTATGTCA
Found at i:17147 original size:2 final size:2
Alignment explanation
Indices: 17140--17180 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
17130 TCAAAAATTG
17140 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17181 ATCAATGGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25617 original size:21 final size:21
Alignment explanation
Indices: 25591--25631 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
25581 ATATTAACAA
25591 AACAATAATAATAATAAATAT
1 AACAATAATAATAATAAATAT
25612 AACAATAATAATAATAAATA
1 AACAATAATAATAATAAATA
25632 ATATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (21 bp):
AACAATAATAATAATAAATAT
Found at i:25883 original size:40 final size:42
Alignment explanation
Indices: 25781--25892 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 42
25771 TTGTTGGTGG
* * *
25781 GGATGACATGACTCATACGTGATGAAGAGGTCTGGTCGTTTAAA
1 GGATGACACGACTCATACGTGATGAAGAGATCTGGTCGTGT--A
* * *
25825 GG-TGACACAACTCCTACGTGATGAGGAGATCTGGTCG-GT-
1 GGATGACACGACTCATACGTGATGAAGAGATCTGGTCGTGTA
*
25864 GGATGACACGGCTCATACGTGATGAAGAG
1 GGATGACACGACTCATACGTGATGAAGAG
25893 TTGTGGCCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
39 2 0.04
40 22 0.39
42 1 0.02
43 30 0.53
44 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (42 bp):
GGATGACACGACTCATACGTGATGAAGAGATCTGGTCGTGTA
Found at i:26041 original size:134 final size:134
Alignment explanation
Indices: 25825--26397 Score: 482
Period size: 130 Copynumber: 4.4 Consensus size: 134
25815 GTCGTTTAAA
* * *
25825 GGTGACACAACTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAA
1 GGTGACACAGCTCCTACGTGATAAGGAGGTCTGGTCGGTGGATGACACGGCTCATACGTGATGAA
* *
25890 GAGTTGTGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACGCGATGATGAAGGCTGGTTATC
66 GAGTTATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACGAGATGATGAAGGCTGGTTATC
25955 TAAG
131 TAAG
* * * * **
25959 GGTGACACAGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACATGGTTTGTACGTGATGAG
1 GGTGACACAGCTCCTACGTGATAAGGAGGTCTGGTCGGTGGATGACACGGCTCATACGTGATGA-
* ** * * * * ** *
26024 GACAG-TAT-GCCATCTTTA-G--GGATGATAACACGATTCCTACGTA-ATGAGGTCGGCTCGTT
65 -AGAGTTATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACG-AGATGATGAAGGCTGGTT
**
26083 AT-TCGG
128 ATCTAAG
* * *
26089 GGTAACAC-GACTCCTACGTGATAAGGAGGTCTGATC-G-GG-T-ACATGGCTCATACGTGATGA
1 GGTGACACAG-CTCCTACGTGATAAGGAGGTCTGGTCGGTGGATGACACGGCTCATACGTGATGA
* * * *
26149 AGAGTTATGGTCATCTTTAGGAAGAGCGATAACAAGGTTTCTACAAGATGATGAAGGTTGGTTAT
65 AGAGTTATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACGAGATGATGAAGGCTGGTTAT
26214 CTAAG
130 CTAAG
* * * * * *
26219 GGTGACACGGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCGTACGTGATGAG
1 GGTGACACAGCTCCTACGTGATAAGGAGGTCTGGTCGGTGGATGACACGGCTCATACGTGATGAA
** * * * * ** *
26284 GA-TAGTAT-GCCATCTTTA-G--GGATGATAACACGATTCCTACGTA-ATGAGGTCGGCTCGTT
66 GAGT--TATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACG-AGATGATGAAGGCTGGTT
**
26343 AT-TCGG
128 ATCTAAG
* * * * *
26349 GGTAACACGGCTCCTACGTGATAAGAAGGTCTGATCGGGGGATGACACG
1 GGTGACACAGCTCCTACGTGATAAGGAGGTCTGGTCGGTGGATGACACG
26398 ATTCCTACGC
Statistics
Matches: 345, Mismatches: 75, Indels: 42
0.75 0.16 0.09
Matches are distributed among these distances:
124 3 0.01
125 3 0.01
126 26 0.08
127 2 0.01
128 3 0.01
129 30 0.09
130 109 0.32
131 61 0.18
132 3 0.01
133 4 0.01
134 93 0.27
135 5 0.01
136 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (134 bp):
GGTGACACAGCTCCTACGTGATAAGGAGGTCTGGTCGGTGGATGACACGGCTCATACGTGATGAA
GAGTTATGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACGAGATGATGAAGGCTGGTTATC
TAAG
Found at i:26240 original size:130 final size:132
Alignment explanation
Indices: 25842--26303 Score: 442
Period size: 134 Copynumber: 3.5 Consensus size: 132
25832 CAACTCCTAC
* * * *
25842 GTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAAGAGTTGTGGCCATCTTT
1 GTGATAAGGAGGTCTGGTC-G-GGATGACATGGCTCATACGTGATGAAGAGTTATGGCCATCTTT
* ** *
25907 AGGAAGGGCGATAACAAGGTTTCTACGCGATGATGAAGGCTGGTTATCTAAGGGTGACACAGCTC
64 AGGAAGAGCGATAACAAGGTTTCTACAAGATGATGAAGGCTGGTTATCTAAGGGTGACACGGCTC
25972 TTAT
129 TTAT
* ** *
25976 GTGATAAGGAGGTCTGGTCGGTGGATGACATGGTTTGTACGTGATGAGGACAG-TAT-GCCATCT
1 GTGATAAGGAGGTCTGGTC-G-GGATGACATGGCTCATACGTGATGA--AGAGTTATGGCCATCT
* * * * * * ** * ** * *
26039 TTAGG--GA-TGATAACACGATTCCTACGTA-ATGAGGTCGGCTCGTTAT-TCGGGGTAACACGA
62 TTAGGAAGAGCGATAACAAGGTTTCTAC-AAGATGATGAAGGCTGGTTATCTAAGGGTGACACGG
* *
26099 CTCCTAC
126 CTCTTAT
* *
26106 GTGATAAGGAGGTCTGATCGGG-T-ACATGGCTCATACGTGATGAAGAGTTATGGTCATCTTTAG
1 GTGATAAGGAGGTCTGGTCGGGATGACATGGCTCATACGTGATGAAGAGTTATGGCCATCTTTAG
*
26169 GAAGAGCGATAACAAGGTTTCTACAAGATGATGAAGGTTGGTTATCTAAGGGTGACACGGCTCTT
66 GAAGAGCGATAACAAGGTTTCTACAAGATGATGAAGGCTGGTTATCTAAGGGTGACACGGCTCTT
26234 AT
131 AT
* * * *
26236 GTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCGTACGTGATGAGGA-TAGTAT-GCCATCT
1 GTGATAAGGAGGTCTGGTC-G-GGATGACATGGCTCATACGTGATGAAGAGT--TATGGCCATCT
26299 TTAGG
62 TTAGG
26304 GATGATAACA
Statistics
Matches: 258, Mismatches: 54, Indels: 32
0.75 0.16 0.09
Matches are distributed among these distances:
124 3 0.01
125 3 0.01
126 28 0.11
127 1 0.00
128 5 0.02
129 28 0.11
130 65 0.25
131 29 0.11
132 3 0.01
133 2 0.01
134 83 0.32
135 5 0.02
136 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.27
Consensus pattern (132 bp):
GTGATAAGGAGGTCTGGTCGGGATGACATGGCTCATACGTGATGAAGAGTTATGGCCATCTTTAG
GAAGAGCGATAACAAGGTTTCTACAAGATGATGAAGGCTGGTTATCTAAGGGTGACACGGCTCTT
AT
Found at i:26334 original size:260 final size:262
Alignment explanation
Indices: 25829--26397 Score: 935
Period size: 260 Copynumber: 2.2 Consensus size: 262
25819 TTTAAAGGTG
* * * *
25829 ACACAACTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGGCTCATACGTGATGAAGAGT
1 ACACGACTCCTACGTGATAAGGAGGTCTGATC-G-GGATGACACGGCTCATACGTGATGAAGAGT
* * **
25894 TGTGGCCATCTTTAGGAAGGGCGATAACAAGGTTTCTACGCGATGATGAAGGCTGGTTATCTAAG
64 TATGGCCATCTTTAGGAAGAGCGATAACAAGGTTTCTACAAGATGATGAAGGCTGGTTATCTAAG
* *
25959 GGTGACACAGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACATGGTTTGTACGTGATGAG
129 GGTGACACAGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCGTACGTGATGAG
26024 GACAGTATGCCATCTTTAGGGATGATAACACGATTCCTACGTAATGAGGTCGGCTCGTTATTCGG
194 GACAGTATGCCATCTTTAGGGATGATAACACGATTCCTACGTAATGAGGTCGGCTCGTTATTCGG
26089 GGTA
259 GGTA
*
26093 ACACGACTCCTACGTGATAAGGAGGTCTGATCGGG-T-ACATGGCTCATACGTGATGAAGAGTTA
1 ACACGACTCCTACGTGATAAGGAGGTCTGATCGGGATGACACGGCTCATACGTGATGAAGAGTTA
* *
26156 TGGTCATCTTTAGGAAGAGCGATAACAAGGTTTCTACAAGATGATGAAGGTTGGTTATCTAAGGG
66 TGGCCATCTTTAGGAAGAGCGATAACAAGGTTTCTACAAGATGATGAAGGCTGGTTATCTAAGGG
*
26221 TGACACGGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCGTACGTGATGAGGA
131 TGACACAGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCGTACGTGATGAGGA
*
26286 TAGTATGCCATCTTTAGGGATGATAACACGATTCCTACGTAATGAGGTCGGCTCGTTATTCGGGG
196 CAGTATGCCATCTTTAGGGATGATAACACGATTCCTACGTAATGAGGTCGGCTCGTTATTCGGGG
26351 TA
261 TA
* *
26353 ACACGGCTCCTACGTGATAAGAAGGTCTGATCGGGGGATGACACG
1 ACACGACTCCTACGTGATAAGGAGGTCTGATC--GGGATGACACG
26398 ATTCCTACGC
Statistics
Matches: 283, Mismatches: 18, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
260 243 0.86
261 1 0.00
262 5 0.02
263 2 0.01
264 32 0.11
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.27
Consensus pattern (262 bp):
ACACGACTCCTACGTGATAAGGAGGTCTGATCGGGATGACACGGCTCATACGTGATGAAGAGTTA
TGGCCATCTTTAGGAAGAGCGATAACAAGGTTTCTACAAGATGATGAAGGCTGGTTATCTAAGGG
TGACACAGCTCTTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGGTTCGTACGTGATGAGGA
CAGTATGCCATCTTTAGGGATGATAACACGATTCCTACGTAATGAGGTCGGCTCGTTATTCGGGG
TA
Found at i:26609 original size:66 final size:63
Alignment explanation
Indices: 26533--26754 Score: 238
Period size: 66 Copynumber: 3.4 Consensus size: 63
26523 TTCAAAGATG
* *
26533 TTTTGTTTCAAGGGAAACAAACTCAAAG-TTAGGTGTTTGTAAAAGAAACTGTCTCGAGAGACAA
1 TTTTGTTTCAAGAGAAACAAACTCAAAGATT---T-TTTCTAAAAGAAACTGTCTCGAGAGACAA
26597 AA
62 AA
*
26599 TTTTGTTTCAA-AGGAAACAAACTCAAAGATTTTTTTCCTCAAAAGAAATTGTCTCAAGAGAGAC
1 TTTTGTTTCAAGA-GAAACAAACTCAAAGA-TTTTTT-CT-AAAAGAAACTGTCTC--GAGAGAC
26663 AAAA
60 AAAA
* * * * *
26667 ATTTGTTTCTAGAGAAATAGACTCAAAGATTTTTTTTAAAAGAAACTGTCTCGAGAGACAAAA
1 TTTTGTTTCAAGAGAAACAAACTCAAAGATTTTTTCTAAAAGAAACTGTCTCGAGAGACAAAA
*
26730 --TTGTTTCAATAGAAAC-AACTCAAAG
1 TTTTGTTTCAAGAGAAACAAACTCAAAG
26755 GATACTGATA
Statistics
Matches: 135, Mismatches: 13, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
60 8 0.06
61 13 0.10
63 11 0.08
64 3 0.02
65 16 0.12
66 41 0.30
67 6 0.04
68 36 0.27
69 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (63 bp):
TTTTGTTTCAAGAGAAACAAACTCAAAGATTTTTTCTAAAAGAAACTGTCTCGAGAGACAAAA
Found at i:26692 original size:68 final size:61
Alignment explanation
Indices: 26572--26754 Score: 226
Period size: 68 Copynumber: 2.9 Consensus size: 61
26562 TAGGTGTTTG
*
26572 TAAAAGAAACTGTCTCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTT
1 TAAAAGAAACTGTCTCGAGAGACAAAAATTTGTTTCAAA-GAAAC-AACTCAAAGATTTTTTT
* * *
26635 CCTCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTTTCTAGAGAAATAGACTCAAAGATTTT
1 --T-AAAAGAAACTGTCTC--GAGAGACAAAAATTTGTTTC-AAAGAAACA-ACTCAAAGATTTT
26700 TTT
59 TTT
26703 TAAAAGAAACTGTCTCGAGAGAC-AAAA-TTGTTTCAATAGAAACAACTCAAAG
1 TAAAAGAAACTGTCTCGAGAGACAAAAATTTGTTTCAA-AGAAACAACTCAAAG
26755 GATACTGATA
Statistics
Matches: 105, Mismatches: 7, Indels: 17
0.81 0.05 0.13
Matches are distributed among these distances:
60 9 0.09
61 13 0.12
62 4 0.04
63 7 0.07
65 15 0.14
66 15 0.14
67 1 0.01
68 39 0.37
69 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.28
Consensus pattern (61 bp):
TAAAAGAAACTGTCTCGAGAGACAAAAATTTGTTTCAAAGAAACAACTCAAAGATTTTTTT
Found at i:27960 original size:26 final size:25
Alignment explanation
Indices: 27931--28005 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 25
27921 CATGTTCTTC
27931 TTGTCTTCTTTCTCTTTGTTTTTTCT
1 TTGT-TTCTTTCTCTTTGTTTTTTCT
27957 TTGTTT-TCTTC-C-TT-TTTTTTCT
1 TTGTTTCT-TTCTCTTTGTTTTTTCT
* *
27979 TTCTTTTTTTCTCTTTGTTTTTTCT
1 TTGTTTCTTTCTCTTTGTTTTTTCT
28004 TT
1 TT
28006 TTTTTCTCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
22 16 0.37
23 4 0.09
24 4 0.09
25 15 0.35
26 4 0.09
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.77
Consensus pattern (25 bp):
TTGTTTCTTTCTCTTTGTTTTTTCT
Found at i:27965 original size:22 final size:21
Alignment explanation
Indices: 27939--28046 Score: 92
Period size: 22 Copynumber: 4.7 Consensus size: 21
27929 TCTTGTCTTC
27939 TTTCTCTTTGTTTTTTCTTTGT
1 TTTCTCTTTGTTTTTTCTTT-T
*
27961 TTTCTTCCTTTTTTTTCTTTCTTTT
1 TTTC-T-C-TTTGTTT-TTTCTTTT
27986 TTTCTCTTTGTTTTTTCTTTTT
1 TTTCTCTTTGTTTTTTC-TTTT
*
28008 TTTCTCTCTCTGCTTTGTTTC-TCT
1 TTTCTCT-T-TG-TTT-TTTCTTTT
*
28032 TTGCTCTTTGTTTTT
1 TTTCTCTTTGTTTTT
28047 CCCTTTTCTT
Statistics
Matches: 73, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
20 2 0.03
21 7 0.10
22 23 0.32
23 4 0.05
24 12 0.16
25 14 0.19
26 11 0.15
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.75
Consensus pattern (21 bp):
TTTCTCTTTGTTTTTTCTTTT
Found at i:27971 original size:13 final size:12
Alignment explanation
Indices: 27939--28012 Score: 77
Period size: 11 Copynumber: 6.4 Consensus size: 12
27929 TCTTGTCTTC
27939 TTTC-TCTTTGT
1 TTTCTTCTTTGT
27950 TTT-TTCTTTGT
1 TTTCTTCTTTGT
*
27961 TTTCTTCCTTTTT
1 TTTCTT-CTTTGT
27974 TTTCTTTCTTT-T
1 TTTC-TTCTTTGT
27986 TTTC-TCTTTGT
1 TTTCTTCTTTGT
*
27997 TTT-TTCTTTTT
1 TTTCTTCTTTGT
28008 TTTCT
1 TTTCT
28013 CTCTCTGCTT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
10 5 0.09
11 26 0.48
12 8 0.15
13 13 0.24
14 2 0.04
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (12 bp):
TTTCTTCTTTGT
Found at i:28028 original size:26 final size:25
Alignment explanation
Indices: 27928--28029 Score: 90
Period size: 25 Copynumber: 4.2 Consensus size: 25
27918 TTGCATGTTC
27928 TTCTTGTCTTCTTTCTCT-T-TGTTTT
1 TTCTT-TCTT-TTTCTCTCTCTGTTTT
* *
27953 TTCTTT-GTTTTCT-TC-CTTTTTT
1 TTCTTTCTTTTTCTCTCTCTGTTTT
* *
27975 TTCTTTCTTTTTTTCTCTTTGTTTT
1 TTCTTTCTTTTTCTCTCTCTGTTTT
28000 TTCTTT-TTTTTCTCTCTCTGCTTTGT
1 TTCTTTCTTTTTCTCTCTCTG-TTT-T
28026 TTCT
1 TTCT
28030 CTTTGCTCTT
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
21 1 0.02
22 16 0.26
23 6 0.10
24 15 0.24
25 19 0.31
26 5 0.08
ACGTcount: A:0.00, C:0.20, G:0.06, T:0.75
Consensus pattern (25 bp):
TTCTTTCTTTTTCTCTCTCTGTTTT
Found at i:48076 original size:34 final size:34
Alignment explanation
Indices: 48015--48082 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
48005 TTTATTATCG
* * * *
48015 AGGGTTAGAGTGTTATGTTTATCTTATGTTATTC
1 AGGGTTAGAATGTTATGTGTATATTATGTAATTC
48049 AGGGTTAGAATG-TATTGTGTATATTATGTAATTC
1 AGGGTTAGAATGTTA-TGTGTATATTATGTAATTC
48083 TGGTCTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 2 0.07
34 27 0.93
ACGTcount: A:0.25, C:0.04, G:0.24, T:0.47
Consensus pattern (34 bp):
AGGGTTAGAATGTTATGTGTATATTATGTAATTC
Found at i:54673 original size:48 final size:48
Alignment explanation
Indices: 54604--54706 Score: 152
Period size: 48 Copynumber: 2.1 Consensus size: 48
54594 TTCAAATCAT
* * *
54604 CCCCTGTGATTATAATGTCATCTACATACACTAATAAGGCAATAACTC
1 CCCCTGTGACTATAATGTCATCTACATAAACCAATAAGGCAATAACTC
* *
54652 CCCCTTTGACTATAATGTCATCTACATAAACCAATAAGGCAGTAACTC
1 CCCCTGTGACTATAATGTCATCTACATAAACCAATAAGGCAATAACTC
*
54700 CCACTGT
1 CCCCTGT
54707 AGCAGGATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (48 bp):
CCCCTGTGACTATAATGTCATCTACATAAACCAATAAGGCAATAACTC
Found at i:60811 original size:21 final size:19
Alignment explanation
Indices: 60770--60812 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
60760 TAACCAAAGC
*
60770 AAAAGAAATATTATAAAAA
1 AAAAGAAATATTACAAAAA
*
60789 AAAAGCAAATTATTACAACAA
1 AAAAG-AAA-TATTACAAAAA
60810 AAA
1 AAA
60813 TATTTAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 12 0.60
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAAGAAATATTACAAAAA
Found at i:62445 original size:15 final size:15
Alignment explanation
Indices: 62425--62473 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
62415 TCTCCTTGAT
62425 TTTCTCCAAGATCCC
1 TTTCTCCAAGATCCC
**
62440 TTTCTCCTTGAT---
1 TTTCTCCAAGATCCC
62452 TTTCTCCAAGATCCC
1 TTTCTCCAAGATCCC
62467 TTTCTCC
1 TTTCTCC
62474 TTAGACTCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 10 0.37
15 17 0.63
ACGTcount: A:0.14, C:0.37, G:0.06, T:0.43
Consensus pattern (15 bp):
TTTCTCCAAGATCCC
Found at i:62445 original size:27 final size:27
Alignment explanation
Indices: 62414--62475 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
62404 CCCTGGAATC
62414 TTCTCCTTGATTTTCTCCAAGATCCCT
1 TTCTCCTTGATTTTCTCCAAGATCCCT
62441 TTCTCCTTGATTTTCTCCAAGATCCCT
1 TTCTCCTTGATTTTCTCCAAGATCCCT
62468 TTCTCCTT
1 TTCTCCTT
62476 AGACTCACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.13, C:0.34, G:0.06, T:0.47
Consensus pattern (27 bp):
TTCTCCTTGATTTTCTCCAAGATCCCT
Done.