Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016309.1 Corchorus olitorius cultivar O-4 contig16342, 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: 64637
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3699 original size:52 final size:52
Alignment explanation
Indices: 3617--3928 Score: 392
Period size: 52 Copynumber: 6.0 Consensus size: 52
3607 TTTTTTTTTA
* *
3617 GCCTT-ACTTTTGCCTAGGCCGCCCCAATGGGGTTTTCAACCTAGCAGGCTT
1 GCCTTAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAGGCTT
*
3668 GCCTTAACTTTTGCCTAAGCCGCCCCGATGGGGTTTTCAACTTAGCA-----
1 GCCTTAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAGGCTT
3715 G---TAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAGGCATTTTTTTTTTT
1 GCCTTAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAGGC----------TT
* *
3774 AAGCCTT-ACTTTTGCCTAGGCCGCCCCAATGGGGTTTTCAACCTAGCAGGCTT
1 --GCCTTAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAGGCTT
*
3827 GCCTTAACTTTTGCCTAAGCCGCCCCGATGGGGTTTTCAACTTAGCAGGCTT
1 GCCTTAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAGGCTT
3879 GCCTTAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAGGC
1 GCCTTAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAGGC
3929 ATTTTTTTTA
Statistics
Matches: 229, Mismatches: 10, Indels: 43
0.81 0.04 0.15
Matches are distributed among these distances:
44 42 0.18
47 1 0.00
51 10 0.04
52 130 0.57
53 2 0.01
61 1 0.00
63 42 0.18
64 1 0.00
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (52 bp):
GCCTTAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAGGCTT
Found at i:3735 original size:44 final size:44
Alignment explanation
Indices: 3672--3759 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
3662 AGGCTTGCCT
*
3672 TAACTTTTGCCTAAGCCGCCCCGATGGGGTTTTCAACTTAGCAG
1 TAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAG
3716 TAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAG
1 TAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAG
3760 GCATTTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.30
Consensus pattern (44 bp):
TAACTTTTGCCTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAG
Found at i:3803 original size:159 final size:160
Alignment explanation
Indices: 3605--3937 Score: 589
Period size: 159 Copynumber: 2.0 Consensus size: 160
3595 TTTGCTTTGC
3605 TTTTTTTTTTTAGCCTTACTTTTGCCTAGGCCGCCCCAATGGGGTTTTCAACCTAGCAGGCTTGC
1 TTTTTTTTTTTAGCCTTACTTTTGCCTAGGCCGCCCCAATGGGGTTTTCAACCTAGCAGGCTTGC
3670 CTTAACTTTTGCCTAAGCCGCCCCGATGGGGTTTTCAACTTAGCA-G-TAACTTTTGCCTAAGCC
66 CTTAACTTTTGCCTAAGCCGCCCCGATGGGGTTTTCAACTTAGCAGGCTAACTTTTGCCTAAGCC
3733 GCCCCAATGGGGTTTTCAACTTAGCAGGCA
131 GCCCCAATGGGGTTTTCAACTTAGCAGGCA
3763 TTTTTTTTTTTAAGCCTTACTTTTGCCTAGGCCGCCCCAATGGGGTTTTCAACCTAGCAGGCTTG
1 TTTTTTTTTTT-AGCCTTACTTTTGCCTAGGCCGCCCCAATGGGGTTTTCAACCTAGCAGGCTTG
3828 CCTTAACTTTTGCCTAAGCCGCCCCGATGGGGTTTTCAACTTAGCAGGCTTGCCTTAACTTTTGC
65 CCTTAACTTTTGCCTAAGCCGCCCCGATGGGGTTTTCAACTTAGCA-G---G-C-TAACTTTTGC
3893 CTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAGGCA
124 CTAAGCCGCCCCAATGGGGTTTTCAACTTAGCAGGCA
3930 TTTTTTTT
1 TTTTTTTT
3938 AAATTTGTGT
Statistics
Matches: 166, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
158 11 0.07
159 99 0.60
164 1 0.01
167 55 0.33
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (160 bp):
TTTTTTTTTTTAGCCTTACTTTTGCCTAGGCCGCCCCAATGGGGTTTTCAACCTAGCAGGCTTGC
CTTAACTTTTGCCTAAGCCGCCCCGATGGGGTTTTCAACTTAGCAGGCTAACTTTTGCCTAAGCC
GCCCCAATGGGGTTTTCAACTTAGCAGGCA
Found at i:11844 original size:13 final size:12
Alignment explanation
Indices: 11764--11957 Score: 71
Period size: 13 Copynumber: 15.7 Consensus size: 12
11754 TAGATTGGTG
11764 GAAAA-TTTGAT
1 GAAAACTTTGAT
11775 GAAGAAC--TGAGT
1 GAA-AACTTTGA-T
*
11787 GAAAACTTGTTGAA
1 GAAAAC-T-TTGAT
11801 GAACAAC-TTGAT
1 GAA-AACTTTGAT
* *
11813 GAAGAC-TTGTT
1 GAAAACTTTGAT
11824 GAAGAACTTTGAT
1 GAA-AACTTTGAT
*
11837 GAATAACTTTGGT
1 GAA-AACTTTGAT
* * *
11850 GGAGACTTGTTGAA
1 GAAAAC-T-TTGAT
11864 GAACAAC-TTGAT
1 GAA-AACTTTGAT
* *
11876 GAAGAC-TTGTT
1 GAAAACTTTGAT
11887 GAAGAACTTTGAT
1 GAA-AACTTTGAT
*
11900 GAATAACTTTGGT
1 GAA-AACTTTGAT
* * *
11913 GGAGAC-TTGTT
1 GAAAACTTTGAT
11924 GAAGAACTTTGAT
1 GAA-AACTTTGAT
*
11937 GAATAATTTTGAT
1 GAA-AACTTTGAT
*
11950 GAAGACTT
1 GAAAACTT
11958 GTTTCACTCT
Statistics
Matches: 135, Mismatches: 31, Indels: 33
0.68 0.16 0.17
Matches are distributed among these distances:
11 33 0.24
12 33 0.24
13 53 0.39
14 8 0.06
15 8 0.06
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (12 bp):
GAAAACTTTGAT
Found at i:11862 original size:63 final size:63
Alignment explanation
Indices: 11791--11930 Score: 280
Period size: 63 Copynumber: 2.2 Consensus size: 63
11781 CTGAGTGAAA
11791 ACTTGTTGAAGAACAACTTGATGAAGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGGAG
1 ACTTGTTGAAGAACAACTTGATGAAGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGGAG
11854 ACTTGTTGAAGAACAACTTGATGAAGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGGAG
1 ACTTGTTGAAGAACAACTTGATGAAGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGGAG
11917 ACTTGTTGAAGAAC
1 ACTTGTTGAAGAAC
11931 TTTGATGAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 77 1.00
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (63 bp):
ACTTGTTGAAGAACAACTTGATGAAGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGGAG
Found at i:11919 original size:37 final size:37
Alignment explanation
Indices: 11871--11960 Score: 153
Period size: 37 Copynumber: 2.4 Consensus size: 37
11861 GAAGAACAAC
11871 TTGATGAAGACTTGTTGAAGAACTTTGATGAATAACT
1 TTGATGAAGACTTGTTGAAGAACTTTGATGAATAACT
* * *
11908 TTGGTGGAGACTTGTTGAAGAACTTTGATGAATAATT
1 TTGATGAAGACTTGTTGAAGAACTTTGATGAATAACT
11945 TTGATGAAGACTTGTT
1 TTGATGAAGACTTGTT
11961 TCACTCTTGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.38
Consensus pattern (37 bp):
TTGATGAAGACTTGTTGAAGAACTTTGATGAATAACT
Found at i:11953 original size:63 final size:62
Alignment explanation
Indices: 11791--11954 Score: 231
Period size: 63 Copynumber: 2.6 Consensus size: 62
11781 CTGAGTGAAA
* *
11791 ACTTGTTGAAGAACAACTTGATGAAGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGGAG
1 ACTTGTTGAAGAAC-ACTTGATGAAAACTTGATGAAGAACTTTGATGAATAACTTTGGTGGAG
* *
11854 ACTTGTTGAAGAACAACTTGATGAAGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGGAG
1 ACTTGTTGAAGAAC-ACTTGATGAAAACTTGATGAAGAACTTTGATGAATAACTTTGGTGGAG
* *
11917 ACTTGTTGAAGAAC-TTTGATGAATAATTTTGATGAAGA
1 ACTTGTTGAAGAACACTTGATGAA-AA-CTTGATGAAGA
11955 CTTGTTTCAC
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
61 8 0.08
62 1 0.01
63 86 0.91
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (62 bp):
ACTTGTTGAAGAACACTTGATGAAAACTTGATGAAGAACTTTGATGAATAACTTTGGTGGAG
Found at i:12263 original size:19 final size:19
Alignment explanation
Indices: 12243--12279 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12233 AATTAATTAT
12243 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
12261 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
12280 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:14203 original size:18 final size:18
Alignment explanation
Indices: 14180--14215 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
14170 TACAAAAATT
14180 AAAATTGTTCATAAACAA
1 AAAATTGTTCATAAACAA
*
14198 AAAATTGTTCATGAACAA
1 AAAATTGTTCATAAACAA
14216 TGTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.11, G:0.08, T:0.28
Consensus pattern (18 bp):
AAAATTGTTCATAAACAA
Found at i:14271 original size:2 final size:2
Alignment explanation
Indices: 14254--14292 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
14244 AATGAACAAA
14254 AT AT -T AT AT A- AT -T AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14292 A
1 A
14293 CTAGTACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.12
2 29 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:14526 original size:23 final size:22
Alignment explanation
Indices: 14500--14545 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
14490 ACCCAATGAA
14500 ATTTTTGT-TAACCACCCTTCTGT
1 ATTTTT-TATAACCACCCTT-TGT
*
14523 ATTTTTTATAACCATCCTTTGT
1 ATTTTTTATAACCACCCTTTGT
14545 A
1 A
14546 ATCTTGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.50
Consensus pattern (22 bp):
ATTTTTTATAACCACCCTTTGT
Found at i:14621 original size:68 final size:68
Alignment explanation
Indices: 14549--14758 Score: 238
Period size: 68 Copynumber: 3.1 Consensus size: 68
14539 CTTTGTAATC
14549 TTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTGTTGATAACTGCCCTTTGAG
1 TTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTGTTGATAACTGCCCTTTGAG
14614 ATT
66 ATT
* * * * * ***
14617 TTGATAATC--TCG--AT-T-AGAATTTTTACAATTGTCCTATATAAT-TATGATAACCATCCTT
1 TTGATAATCAAACGCCATATCA-AATTTTGATAATCGCCCTATAT--TGT-TGATAACTGCCCTT
*
14675 TGTA-ATC
62 TG-AGATT
14682 TTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTGTTGATAACTGCCCTTTGAG
1 TTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTGTTGATAACTGCCCTTTGAG
14747 ATT
66 ATT
14750 TTGATAATC
1 TTGATAATC
14759 TTGATTAGAA
Statistics
Matches: 111, Mismatches: 18, Indels: 26
0.72 0.12 0.17
Matches are distributed among these distances:
62 1 0.01
63 19 0.17
64 3 0.03
65 25 0.23
66 3 0.03
67 3 0.03
68 34 0.31
69 3 0.03
70 19 0.17
71 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (68 bp):
TTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTGTTGATAACTGCCCTTTGAG
ATT
Found at i:14686 original size:65 final size:66
Alignment explanation
Indices: 14530--14864 Score: 223
Period size: 65 Copynumber: 5.1 Consensus size: 66
14520 TGTATTTTTT
* * * *
14530 ATAACCATCCTTTGTAATCTTGATAATCAAACGCCATATCA-AATTTTGATAATCGCCCTATAT-
1 ATAACCATCCTTTGTAATTTTGATAATC-ATCG--AT-T-AGAATTTTGACAATTGCCCTATATA
14593 -TGT-TG
61 AT-TATG
*** * *
14598 ATAACTGCCCTTTG-AGATTTTGATAATC-TCGATTAGAATTTTTACAATTGTCCTATATAATTA
1 ATAACCATCCTTTGTA-ATTTTGATAATCATCGATTAGAATTTTGACAATTGCCCTATATAATTA
14661 TG
65 TG
* * * *
14663 ATAACCATCCTTTGTAATCTTGATAATCAAACGCCATATCA-AATTTTGATAATCGCCCTATAT-
1 ATAACCATCCTTTGTAATTTTGATAATC-ATCG--AT-T-AGAATTTTGACAATTGCCCTATATA
14726 -TGT-TG
61 AT-TATG
*** * *
14731 ATAACTGCCCTTTG-AGATTTTGATAATC-TTGATTAGAATTTTGACAATTGTCCTATATAATTA
1 ATAACCATCCTTTGTA-ATTTTGATAATCATCGATTAGAATTTTGACAATTGCCCTATATAATTA
14794 TG
65 TG
* * *
14796 ATAACCATCCTTTATAATTTTAATAA-CTTCGATT-GAAATTTTGACAATTGCCCTATGA-AATT
1 ATAACCATCCTTTGTAATTTTGATAATCATCGATTAG-AATTTTGACAATTGCCCTAT-ATAATT
*
14858 TTG
64 ATG
14861 ATAA
1 ATAA
14865 TTACTGTTTG
Statistics
Matches: 210, Mismatches: 35, Indels: 47
0.72 0.12 0.16
Matches are distributed among these distances:
62 2 0.01
63 39 0.19
64 8 0.04
65 81 0.39
66 6 0.03
67 4 0.02
68 47 0.22
69 3 0.01
70 19 0.09
71 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (66 bp):
ATAACCATCCTTTGTAATTTTGATAATCATCGATTAGAATTTTGACAATTGCCCTATATAATTAT
G
Found at i:14768 original size:133 final size:133
Alignment explanation
Indices: 14530--14813 Score: 541
Period size: 133 Copynumber: 2.1 Consensus size: 133
14520 TGTATTTTTT
14530 ATAACCATCCTTTGTAATCTTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTG
1 ATAACCATCCTTTGTAATCTTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTG
*
14595 TTGATAACTGCCCTTTGAGATTTTGATAATCTCGATTAGAATTTTTACAATTGTCCTATATAATT
66 TTGATAACTGCCCTTTGAGATTTTGATAATCTCGATTAGAATTTTGACAATTGTCCTATATAATT
14660 ATG
131 ATG
14663 ATAACCATCCTTTGTAATCTTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTG
1 ATAACCATCCTTTGTAATCTTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTG
*
14728 TTGATAACTGCCCTTTGAGATTTTGATAATCTTGATTAGAATTTTGACAATTGTCCTATATAATT
66 TTGATAACTGCCCTTTGAGATTTTGATAATCTCGATTAGAATTTTGACAATTGTCCTATATAATT
14793 ATG
131 ATG
*
14796 ATAACCATCCTTTATAAT
1 ATAACCATCCTTTGTAAT
14814 TTTAATAACT
Statistics
Matches: 148, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 148 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (133 bp):
ATAACCATCCTTTGTAATCTTGATAATCAAACGCCATATCAAATTTTGATAATCGCCCTATATTG
TTGATAACTGCCCTTTGAGATTTTGATAATCTCGATTAGAATTTTGACAATTGTCCTATATAATT
ATG
Found at i:14821 original size:22 final size:22
Alignment explanation
Indices: 14781--14822 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
14771 TTGACAATTG
*
14781 TCCTATATAATTATGATAACCA
1 TCCTATATAATTATAATAACCA
* *
14803 TCCTTTATAATTTTAATAAC
1 TCCTATATAATTATAATAAC
14823 TTCGATTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (22 bp):
TCCTATATAATTATAATAACCA
Found at i:15026 original size:22 final size:22
Alignment explanation
Indices: 14996--15054 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
14986 CATAAAGTGT
*
14996 TTATGAAAATTACAAAGGATAG
1 TTATCAAAATTACAAAGGATAG
* *
15018 TTATCAAAATGACAAAGGATTG
1 TTATCAAAATTACAAAGGATAG
15040 TTATCAAAATT-CAAA
1 TTATCAAAATTACAAA
15055 ACCTCATAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (22 bp):
TTATCAAAATTACAAAGGATAG
Found at i:18625 original size:12 final size:13
Alignment explanation
Indices: 18597--18623 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18587 TCTTTCTCTC
18597 TTCTTCTTTTTTT
1 TTCTTCTTTTTTT
18610 TTCTTCTTTTTTT
1 TTCTTCTTTTTTT
18623 T
1 T
18624 CTGGTTCGGA
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTCTTCTTTTTTT
Found at i:21842 original size:16 final size:16
Alignment explanation
Indices: 21821--21852 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21811 TTTATAATTT
21821 TTATTAATAATATATA
1 TTATTAATAATATATA
*
21837 TTATTATTAATATATA
1 TTATTAATAATATATA
21853 AATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:21845 original size:19 final size:19
Alignment explanation
Indices: 21821--21868 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
21811 TTTATAATTT
* *
21821 TTATTAATAATATATATTA
1 TTATTAATAATATAAATAA
21840 TTATTAAT-ATATAAATAA
1 TTATTAATAATATAAATAA
21858 TTATATAATAA
1 TTAT-TAATAA
21869 ATGAACGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.48
19 12 0.48
20 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATAAATAA
Found at i:30513 original size:28 final size:27
Alignment explanation
Indices: 30476--30531 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 27
30466 TAAAAGATTG
30476 TATACATCTTAATATCTTAGACAAATA
1 TATACATCTTAATATCTTAGACAAATA
30503 TATATCATCTTAATATCTTAGACAAATA
1 TATA-CATCTTAATATCTTAGACAAATA
30531 T
1 T
30532 CACATGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (27 bp):
TATACATCTTAATATCTTAGACAAATA
Found at i:34437 original size:2 final size:2
Alignment explanation
Indices: 34389--34418 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34379 AATCATACAG
34389 AT AT AT A- 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 A
34419 GAAAACATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:45498 original size:31 final size:33
Alignment explanation
Indices: 45455--45533 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 33
45445 TTCAAGTCCG
* *
45455 GACATTTTGCCCCCTAAAC-TT-CCAAATTCAA
1 GACATTTAGCCCCCTAAACTTTCCCAAAGTCAA
45486 GACATTTAGCCCCCT--ACTTTCCCAAAGTCAA
1 GACATTTAGCCCCCTAAACTTTCCCAAAGTCAA
45517 GACATTTTA-CCCCCTAA
1 GACA-TTTAGCCCCCTAA
45534 TGGAGGGGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 2 0.05
30 2 0.05
31 33 0.80
32 4 0.10
ACGTcount: A:0.30, C:0.34, G:0.08, T:0.28
Consensus pattern (33 bp):
GACATTTAGCCCCCTAAACTTTCCCAAAGTCAA
Done.