Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007014.1 Hibiscus syriacus cultivar Beakdansim tig00018107_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: 76250
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9714 original size:20 final size:20
Alignment explanation
Indices: 9689--9732 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
9679 TTTGTTAAGA
9689 GAATTACGACATTCTGAGCT
1 GAATTACGACATTCTGAGCT
* *
9709 GAATTACGATATTCTGAGTT
1 GAATTACGACATTCTGAGCT
9729 GAAT
1 GAAT
9733 GTCAATTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (20 bp):
GAATTACGACATTCTGAGCT
Found at i:15099 original size:2 final size:2
Alignment explanation
Indices: 15092--15130 Score: 60
Period size: 2 Copynumber: 18.5 Consensus size: 2
15082 CCCTACATAC
15092 AT AT AT AT GAT AT AT AT AT AT AT AT AT AT AT AGT AT AT A
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
15131 GTGCAGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 31 0.89
3 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:22800 original size:30 final size:31
Alignment explanation
Indices: 22766--22833 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
22756 GATATAATTT
*
22766 TTAATTTAATTAT-TAAA-TTTAGATAAAATA
1 TTAATTTAA-CATCTAAATTTTAGATAAAATA
* *
22796 TTAATTTGACATCTAAATTTTAGATACAATA
1 TTAATTTAACATCTAAATTTTAGATAAAATA
22827 TT-ATTTA
1 TTAATTTA
22834 GACTCATGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 2 0.06
30 16 0.50
31 14 0.44
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (31 bp):
TTAATTTAACATCTAAATTTTAGATAAAATA
Found at i:23537 original size:20 final size:20
Alignment explanation
Indices: 23504--23541 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23494 ATGAAATATC
23504 TAATTATTTTTTTAATTATA
1 TAATTATTTTTTTAATTATA
23524 TAATT-TTTTGTTTAATTA
1 TAATTATTTT-TTTAATTA
23542 GTTGATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (20 bp):
TAATTATTTTTTTAATTATA
Found at i:23709 original size:12 final size:12
Alignment explanation
Indices: 23692--23721 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23682 GTATGAGCAT
23692 ATTATAAAAATA
1 ATTATAAAAATA
23704 ATTATAAAAATA
1 ATTATAAAAATA
*
23716 GTTATA
1 ATTATA
23722 CATATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
ATTATAAAAATA
Found at i:27713 original size:7 final size:7
Alignment explanation
Indices: 27699--27821 Score: 76
Period size: 7 Copynumber: 17.7 Consensus size: 7
27689 GTTAGATTAC
27699 ACCCTAA
1 ACCCTAA
*
27706 ATCCTAA
1 ACCCTAA
*
27713 A-CTTAA
1 ACCCTAA
27719 ACCCTAA
1 ACCCTAA
27726 ACCCTAA
1 ACCCTAA
27733 ACCCTAA
1 ACCCTAA
27740 ACCCTAA
1 ACCCTAA
27747 A--CTATA
1 ACCCTA-A
27753 ACCTCTAA
1 ACC-CTAA
*
27761 ACCTTAA
1 ACCCTAA
*
27768 TTCCC-AA
1 -ACCCTAA
*
27775 CCCCTGAA
1 ACCCT-AA
**
27783 A-TATAA
1 ACCCTAA
*
27789 ACCATAA
1 ACCCTAA
*
27796 ACCATAA
1 ACCCTAA
* *
27803 GCCCTAT
1 ACCCTAA
27810 ACCCTAA
1 ACCCTAA
27817 ACCCT
1 ACCCT
27822 TAATCTAATT
Statistics
Matches: 91, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
5 3 0.03
6 13 0.14
7 64 0.70
8 8 0.09
9 3 0.03
ACGTcount: A:0.41, C:0.36, G:0.02, T:0.21
Consensus pattern (7 bp):
ACCCTAA
Found at i:29722 original size:6 final size:6
Alignment explanation
Indices: 29711--29770 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
29701 GACACGTATT
* * *
29711 ACCACG ACCACG ACCACG ACCACG ACCTCG A-CTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
29758 ACCACG ACCACG A
1 ACCACG ACCACG A
29771 GCCGAGCCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.10
6 46 0.90
ACGTcount: A:0.30, C:0.48, G:0.17, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:29747 original size:23 final size:23
Alignment explanation
Indices: 29711--29765 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
29701 GACACGTATT
*
29711 ACCACGACCACGACCACGACCACG
1 ACCACGA-CTCGACCACGACCACG
* *
29735 ACCTCGACTCGACCTCGACCACG
1 ACCACGACTCGACCACGACCACG
29758 ACCACGAC
1 ACCACGAC
29766 CACGAGCCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.29, C:0.49, G:0.16, T:0.05
Consensus pattern (23 bp):
ACCACGACTCGACCACGACCACG
Found at i:29778 original size:5 final size:5
Alignment explanation
Indices: 29768--29821 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
29758 ACCACGACCA
* * * *
29768 CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
29818 CGAG
1 CGAG
29822 ACGGACGGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.17, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:35665 original size:6 final size:6
Alignment explanation
Indices: 35654--35840 Score: 257
Period size: 6 Copynumber: 31.2 Consensus size: 6
35644 GACACGTATT
35654 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* *
35702 ACCACG ACCACG ACCTCG ACCACG ACCACG ACCACG ACCACG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * * * * * * *
35750 ACCTCG ACCTCG ACCTCG ACCTCG ACCTCG ACCTCG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * *
35798 ACCTCG ACCTCG ACCTCG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
35841 GCCGAGCCGA
Statistics
Matches: 177, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 177 1.00
ACGTcount: A:0.27, C:0.50, G:0.17, T:0.07
Consensus pattern (6 bp):
ACCACG
Found at i:35848 original size:5 final size:5
Alignment explanation
Indices: 35838--35881 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
35828 ACCACGACCA
* * *
35838 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
35882 ACGGACGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.18, C:0.36, G:0.41, T:0.05
Consensus pattern (5 bp):
CGAGC
Found at i:37334 original size:86 final size:87
Alignment explanation
Indices: 37190--37434 Score: 326
Period size: 86 Copynumber: 2.9 Consensus size: 87
37180 TATGTTATAT
* * * * *
37190 CATTTAACCGGAAATA-T-T-AAGCACAATAACATATTACGCAACACTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATA-GT
*
37252 AGCGCTTT-TATAAT-AAATAGG
65 AGCGCTTTATATAATAAAATAAG
*
37273 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATATAATAGTA
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGTA
37338 GCG-TTTATATAATAAAATAAG
66 GCGCTTTATATAATAAAATAAG
*
37359 CATTTAACC-AGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAAG
1 CATTTAACCGA-AAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAAT-AG
*
37423 TAACGC-TTATAT
64 TAGCGCTTTATAT
37435 TGACCTATTT
Statistics
Matches: 144, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
83 15 0.10
84 4 0.03
85 14 0.10
86 99 0.69
87 12 0.08
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.32
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGTA
GCGCTTTATATAATAAAATAAG
Found at i:37364 original size:20 final size:21
Alignment explanation
Indices: 37320--37364 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
37310 TAGGTAACGC
* *
37320 TTATATAATATAATAGTAGCGT
1 TTATATAATAAAATAG-AGCAT
37342 TTATATAATAAAATA-AGCAT
1 TTATATAATAAAATAGAGCAT
37362 TTA
1 TTA
37365 ACCAGAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
22 14 0.67
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (21 bp):
TTATATAATAAAATAGAGCAT
Found at i:38345 original size:3 final size:3
Alignment explanation
Indices: 38339--38433 Score: 66
Period size: 3 Copynumber: 29.7 Consensus size: 3
38329 ATTATTATTC
* * * *
38339 CTT CTT CTTT CGT CTT CTT CTT CATT CTTT ATT CTTT CTT TTT CTT TTT
1 CTT CTT C-TT CTT CTT CTT CTT C-TT C-TT CTT C-TT CTT CTT CTT CTT
* *
38388 CTTT CTT TTT CTT -TT CTT CTT CCTT CTT CTAT CAT CTT CTT CTT CT
1 C-TT CTT CTT CTT CTT CTT CTT -CTT CTT CT-T CTT CTT CTT CTT CT
38434 ATTCACCATT
Statistics
Matches: 72, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
2 2 0.03
3 51 0.71
4 19 0.26
ACGTcount: A:0.04, C:0.27, G:0.01, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:38366 original size:10 final size:10
Alignment explanation
Indices: 38339--38433 Score: 66
Period size: 10 Copynumber: 8.8 Consensus size: 10
38329 ATTATTATTC
38339 CTTCTTCTTT
1 CTTCTTCTTT
*
38349 CGTCTTC-TT
1 CTTCTTCTTT
38358 CTTCATTCTTT
1 CTTC-TTCTTT
*
38369 ATTCTTTCTTTTT
1 CTTC-TTC--TTT
*
38382 CTTTTTCTTT
1 CTTCTTCTTT
*
38392 CTTTTTCTTTT
1 CTTCTTC-TTT
*
38403 CTTCTTCCTT
1 CTTCTTCTTT
38413 CTTCTATCATCTT
1 CTTCT-TC-T-TT
38426 CTTCTTCT
1 CTTCTTCT
38434 ATTCACCATT
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
9 5 0.07
10 26 0.38
11 20 0.29
12 5 0.07
13 12 0.18
ACGTcount: A:0.04, C:0.27, G:0.01, T:0.67
Consensus pattern (10 bp):
CTTCTTCTTT
Found at i:38391 original size:16 final size:16
Alignment explanation
Indices: 38363--38402 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 16
38353 TTCTTCTTCA
38363 TTCTTTATTCTTTCTTT
1 TTCTTT-TTCTTTCTTT
38380 TTCTTTTTCTTTCTTT
1 TTCTTTTTCTTTCTTT
38396 TTCTTTT
1 TTCTTTT
38403 CTTCTTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
TTCTTTTTCTTTCTTT
Found at i:39998 original size:13 final size:14
Alignment explanation
Indices: 39980--40008 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39970 TACTTTACCC
39980 AAAAAT-AAAATAA
1 AAAAATAAAAATAA
39993 AAAAATAAAAATAA
1 AAAAATAAAAATAA
40007 AA
1 AA
40009 TTAAGAGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:41855 original size:16 final size:17
Alignment explanation
Indices: 41819--41858 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
41809 TAATTATACG
* *
41819 TTAAATATTTTATAATT
1 TTAAATTTTTTATAATA
41836 TTAAATTTTTTATAA-A
1 TTAAATTTTTTATAATA
41852 TTAAATT
1 TTAAATT
41859 AATGGTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTATAATA
Found at i:42237 original size:18 final size:18
Alignment explanation
Indices: 42214--42248 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42204 AAGGCTAGTA
*
42214 ATTTTTTAATATATTTAT
1 ATTTTTTAAAATATTTAT
42232 ATTTTTTAAAATATTTA
1 ATTTTTTAAAATATTTA
42249 ATATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTTAAAATATTTAT
Found at i:43220 original size:34 final size:32
Alignment explanation
Indices: 43167--43236 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
43157 ACCTTACAAC
*
43167 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
43199 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
43233 TCCC
1 TCCC
43237 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:43547 original size:20 final size:21
Alignment explanation
Indices: 43510--43550 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
43500 CCAGAATGGG
*
43510 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
43531 GGGAATCGATA-CCCTTCATA
1 GGGAATCGATACCCCTTCATA
43551 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:43681 original size:19 final size:19
Alignment explanation
Indices: 43657--43719 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
43647 AGCTCGGGTA
*
43657 TGTTCAAACAGTGATTTAC
1 TGTTCAAACAGTAATTTAC
*
43676 TGTTCAAATAGTAATTTAC
1 TGTTCAAACAGTAATTTAC
* *
43695 TGTTCAAATAGTAAATTAC
1 TGTTCAAACAGTAATTTAC
*
43714 TATTCA
1 TGTTCA
43720 TAAAAACATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (19 bp):
TGTTCAAACAGTAATTTAC
Found at i:43835 original size:30 final size:31
Alignment explanation
Indices: 43784--43874 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
43774 AAATTTTGAA
*
43784 TAAATTCAATT-AAGTCTAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
43813 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
43844 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
43875 CCTTAAATTG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 10 0.17
31 38 0.64
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:44483 original size:18 final size:18
Alignment explanation
Indices: 44460--44516 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
44450 GTGACAAACA
44460 ATATCATACATAATAGTC
1 ATATCATACATAATAGTC
*
44478 ATATCAAACATGAA-A--C
1 ATATCATACAT-AATAGTC
44494 ATAT-AT--ATAATAGTC
1 ATATCATACATAATAGTC
44509 ATATCATA
1 ATATCATA
44517 TTCTTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 13
0.67 0.04 0.28
Matches are distributed among these distances:
12 2 0.06
13 3 0.10
15 6 0.19
16 7 0.23
18 11 0.35
19 2 0.06
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (18 bp):
ATATCATACATAATAGTC
Found at i:44618 original size:28 final size:25
Alignment explanation
Indices: 44564--44619 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 25
44554 CATTTTCATC
44564 TTTCACTTTCATATTCACTTTCACA
1 TTTCACTTTCATATTCACTTTCACA
*
44589 TTTCATTTTCATAATTCATACTTTCACA
1 TTTCACTTTCAT-ATTC--ACTTTCACA
44617 TTT
1 TTT
44620 AAGAACTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 11 0.41
26 4 0.15
28 12 0.44
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTCACTTTCATATTCACTTTCACA
Found at i:55128 original size:18 final size:18
Alignment explanation
Indices: 55105--55143 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
55095 TTTTGGGTAC
*
55105 TGTAATGTGCTTACACTT
1 TGTAATGTACTTACACTT
55123 TGTAATGTACTTACACTT
1 TGTAATGTACTTACACTT
55141 TGT
1 TGT
55144 TTGAGTTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (18 bp):
TGTAATGTACTTACACTT
Found at i:60375 original size:3 final size:3
Alignment explanation
Indices: 60369--60397 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
60359 AAGAAGAGAC
60369 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
60398 ATATCTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:64360 original size:16 final size:17
Alignment explanation
Indices: 64326--64361 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
64316 TTACTTTTAT
64326 TAAAAATAAAAAATATA
1 TAAAAATAAAAAATATA
*
64343 TAAAATTAAAAAAT-TA
1 TAAAAATAAAAAATATA
64359 TAA
1 TAA
64362 GTATAACGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAATAAAAAATATA
Found at i:64360 original size:18 final size:18
Alignment explanation
Indices: 64322--64360 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
64312 ATAGTTACTT
64322 TTAT-TAAAAATAAAAAA
1 TTATATAAAAATAAAAAA
*
64339 -TATATAAAATTAAAAAA
1 TTATATAAAAATAAAAAA
64356 TTATA
1 TTATA
64361 AGTATAACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 3 0.16
17 12 0.63
18 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TTATATAAAAATAAAAAA
Found at i:68415 original size:18 final size:19
Alignment explanation
Indices: 68388--68427 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
68378 CCGAAAATTC
68388 ATTAAATATACA-TTTTTA
1 ATTAAATATACATTTTTTA
* *
68406 ATTAATTATATATTTTTTA
1 ATTAAATATACATTTTTTA
68425 ATT
1 ATT
68428 TTTATTGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTAAATATACATTTTTTA
Done.