Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015349.1 Corchorus olitorius cultivar O-4 contig15382, 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: 130237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1781 original size:17 final size:18
Alignment explanation
Indices: 1750--1784 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1740 TTAAATTCTA
*
1750 CAAAAAGATATAAAAGAG
1 CAAAAAGATAAAAAAGAG
1768 CAAAAA-ATAAAAAAGAG
1 CAAAAAGATAAAAAAGAG
1785 TATAACTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.06, G:0.14, T:0.09
Consensus pattern (18 bp):
CAAAAAGATAAAAAAGAG
Found at i:1860 original size:15 final size:15
Alignment explanation
Indices: 1840--1868 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1830 ATTATCATAC
1840 TATTACTATTACTAT
1 TATTACTATTACTAT
1855 TATTACTATTACTA
1 TATTACTATTACTA
1869 CTATATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTACTATTACTAT
Found at i:5746 original size:24 final size:24
Alignment explanation
Indices: 5709--5757 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5699 TAAAGATATC
*
5709 TCCAAACTAATGTATACTTAGTAT
1 TCCAAACTAATGTATACTCAGTAT
** *
5733 TCCAAACTGCTGTATGCTCAGTAT
1 TCCAAACTAATGTATACTCAGTAT
5757 T
1 T
5758 TGACTCCTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (24 bp):
TCCAAACTAATGTATACTCAGTAT
Found at i:5843 original size:13 final size:13
Alignment explanation
Indices: 5825--5849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5815 ATATTATTAC
5825 AAATAATATTTAT
1 AAATAATATTTAT
5838 AAATAATATTTA
1 AAATAATATTTA
5850 GAACATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:9410 original size:43 final size:43
Alignment explanation
Indices: 9344--9427 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
9334 TAAAAAAGAA
*
9344 TATTGAATATGGCTAATTATAACAACCTCACTCTTTTTGGGCC
1 TATTCAATATGGCTAATTATAACAACCTCACTCTTTTTGGGCC
9387 TATTCAATATGGCTAATTATAACAACCTCACTCTTTTTGGG
1 TATTCAATATGGCTAATTATAACAACCTCACTCTTTTTGGG
9428 TCATGGGCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (43 bp):
TATTCAATATGGCTAATTATAACAACCTCACTCTTTTTGGGCC
Found at i:12399 original size:46 final size:46
Alignment explanation
Indices: 12332--12426 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
12322 AGACACATAC
12332 ACAAAAAACTCATTATTGTATGATAAATGATTAAGAAATACAAGTG
1 ACAAAAAACTCATTATTGTATGATAAATGATTAAGAAATACAAGTG
12378 ACAAAAAACTCATTATTGTATGATAAATGATTAAGAAATACAAGTG
1 ACAAAAAACTCATTATTGTATGATAAATGATTAAGAAATACAAGTG
12424 ACA
1 ACA
12427 GATTGTGTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (46 bp):
ACAAAAAACTCATTATTGTATGATAAATGATTAAGAAATACAAGTG
Found at i:31205 original size:28 final size:26
Alignment explanation
Indices: 31169--31223 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
31159 ACAGTACGTT
*
31169 ATTGGCTTAACGGCGCGTGCACAACATG
1 ATTGACTTAA-GG-GCGTGCACAACATG
*
31197 ATTGACTTAATGGCGTGCACAACATG
1 ATTGACTTAAGGGCGTGCACAACATG
31223 A
1 A
31224 AAGGGTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.60
27 1 0.04
28 9 0.36
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (26 bp):
ATTGACTTAAGGGCGTGCACAACATG
Found at i:41812 original size:16 final size:17
Alignment explanation
Indices: 41793--41827 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
41783 TCGTTACTTA
41793 TCTACTC-TCTTACAAG
1 TCTACTCTTCTTACAAG
41809 TCTACTCTTTCTTACAAG
1 TCTACTC-TTCTTACAAG
41827 T
1 T
41828 TCAATAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.43
Consensus pattern (17 bp):
TCTACTCTTCTTACAAG
Found at i:43017 original size:2 final size:2
Alignment explanation
Indices: 43010--43052 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
43000 CATCATGGTG
* *
43010 TA TA TA TA TA TA TA TA TA TA TA TA TA -A CA TA TA -A TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43050 TA T
1 TA T
43053 TAGCATTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:43274 original size:15 final size:15
Alignment explanation
Indices: 43254--43294 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
43244 GCATGGGTAA
*
43254 ATAATGGTGATCATG
1 ATAATGATGATCATG
*
43269 ATAATGATGATGATG
1 ATAATGATGATCATG
*
43284 ATGATGATGAT
1 ATAATGATGAT
43295 GCATTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (15 bp):
ATAATGATGATCATG
Found at i:43280 original size:3 final size:3
Alignment explanation
Indices: 43261--43295 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
43251 TAAATAATGG
* *
43261 TGA TCA TGA TAA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
43296 CATTTTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:44521 original size:9 final size:9
Alignment explanation
Indices: 44498--44529 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
44488 GGAAATAAAT
44498 AGTGAAAAA
1 AGTGAAAAA
44507 AG-GAAAAA
1 AGTGAAAAA
44515 AGTG-AAAA
1 AGTGAAAAA
44523 AGTGAAA
1 AGTGAAA
44530 GGAAATGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.25, T:0.09
Consensus pattern (9 bp):
AGTGAAAAA
Found at i:54323 original size:22 final size:19
Alignment explanation
Indices: 54275--54325 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
54265 GTTAGTGATC
54275 TAAGT-AAAAATAAAAAAA
1 TAAGTAAAAAATAAAAAAA
54293 TAGAG-AAAAAATAATAATAAA
1 TA-AGTAAAAAATAA-AA-AAA
54314 TCAAGTAAAAAA
1 T-AAGTAAAAAA
54326 AGTAGTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 2 0.07
19 10 0.37
20 2 0.07
21 6 0.22
22 7 0.26
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.18
Consensus pattern (19 bp):
TAAGTAAAAAATAAAAAAA
Found at i:56092 original size:2 final size:2
Alignment explanation
Indices: 56085--56123 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
56075 AAATGAGTAG
* * *
56085 TA TA TA TA TA TA TA TA TA TA TA TA TT TG TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56124 TCCACGTTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (2 bp):
TA
Found at i:56433 original size:2 final size:2
Alignment explanation
Indices: 56428--56459 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
56418 AGAAGTCAAA
56428 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
56460 TGTTTAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57752 original size:2 final size:2
Alignment explanation
Indices: 57745--57792 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
57735 AAAATTGAGT
57745 TA TA 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 TA TA
57787 TA TA TA
1 TA TA TA
57793 AGATAATCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58773 original size:17 final size:18
Alignment explanation
Indices: 58746--58787 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
58736 TTTCGTCAGT
*
58746 TTTGTTTTGTTGAGTCAA
1 TTTGTTTTGTTCAGTCAA
58764 TTTG-TTTGTTCAGTCAA
1 TTTGTTTTGTTCAGTCAA
58781 TTT-TTTT
1 TTTGTTTT
58788 ACATAGTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.14, C:0.07, G:0.17, T:0.62
Consensus pattern (18 bp):
TTTGTTTTGTTCAGTCAA
Found at i:60177 original size:22 final size:22
Alignment explanation
Indices: 60142--60211 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
60132 ATATATATTA
60142 TTAAATAA-ATAATAAATATAGT
1 TTAAATAATA-AATAAATATAGT
*
60164 TTAAATAATAAAT-AAT-GAGT
1 TTAAATAATAAATAAATATAGT
*
60184 TCAAAATAAATAAATAATATATA-T
1 T-TAAAT-AATAAATAA-ATATAGT
60208 TTAA
1 TTAA
60212 TTACTAAACG
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
20 4 0.11
21 7 0.18
22 18 0.47
23 4 0.11
24 4 0.11
25 1 0.03
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (22 bp):
TTAAATAATAAATAAATATAGT
Found at i:71395 original size:80 final size:82
Alignment explanation
Indices: 71255--71409 Score: 244
Period size: 80 Copynumber: 1.9 Consensus size: 82
71245 TTAAAAAAAG
* *
71255 TGATCCAATGCACTTTGAGAGATCAAGCTTATATATTCTTTTATATTTTCGAAAGATACGTAACT
1 TGATCCAATGCACTTTGAGAGATCAAACTTATATATTCTTGTATATTTTCGAAAGATACGTAACT
71320 C-TTTTAAGTTACTAAA
66 CTTTTTAAGTTACTAAA
* *
71336 TGATCCCAATGCATTTTGAGAGATCAAAC-T-TATATTCTTGTATATTTTCGAAAGGTACGTAAC
1 TGAT-CCAATGCACTTTGAGAGATCAAACTTATATATTCTTGTATATTTTCGAAAGATACGTAAC
71399 TCTTTTTAAGT
65 TCTTTTTAAGT
71410 GACTTTGTAC
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
80 33 0.49
81 13 0.19
82 22 0.32
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.40
Consensus pattern (82 bp):
TGATCCAATGCACTTTGAGAGATCAAACTTATATATTCTTGTATATTTTCGAAAGATACGTAACT
CTTTTTAAGTTACTAAA
Found at i:83690 original size:5 final size:5
Alignment explanation
Indices: 83674--83707 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
83664 CTCGATCAGG
83674 TTTCT ATTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT -TTTCT TTTCT TTTCT TTTCT TTTCT TTT
83708 TTTAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:87348 original size:2 final size:2
Alignment explanation
Indices: 87341--87379 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
87331 TAATATGTAG
87341 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
87380 GCTAAACTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:96037 original size:36 final size:35
Alignment explanation
Indices: 95990--96086 Score: 131
Period size: 36 Copynumber: 2.7 Consensus size: 35
95980 TTTTGCACCT
*
95990 AAGAGATCAATGAGCAATTCAGAAGGCAGTGCTCC
1 AAGAGATCAATGAGCAATTCAGAAGGCACTGCTCC
*
96025 AAAGAGATCAATGAGCAATACAGAAGGCACTGCTCC
1 -AAGAGATCAATGAGCAATTCAGAAGGCACTGCTCC
* **
96061 TAGCAGATCAACAAGCAATTCAGAAG
1 AAG-AGATCAATGAGCAATTCAGAAG
96087 ATGATAAAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 2 0.04
36 52 0.96
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (35 bp):
AAGAGATCAATGAGCAATTCAGAAGGCACTGCTCC
Found at i:104258 original size:1 final size:1
Alignment explanation
Indices: 104252--104276 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
104242 CTTTCTCATG
104252 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
104277 AAATTCTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:105017 original size:29 final size:30
Alignment explanation
Indices: 104984--105047 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
104974 CGTTTAGACG
* *
104984 TTTTATCTATTGAATTTCAATTTT-GGACA
1 TTTTATCCACTGAATTTCAATTTTGGGACA
* *
105013 TTTTATCCCCTGAATTTCAATTTTGGGACG
1 TTTTATCCACTGAATTTCAATTTTGGGACA
105043 TTTTA
1 TTTTA
105048 CCCGTTCAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.23, C:0.14, G:0.12, T:0.50
Consensus pattern (30 bp):
TTTTATCCACTGAATTTCAATTTTGGGACA
Found at i:110061 original size:9 final size:9
Alignment explanation
Indices: 110049--110084 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
110039 AATATTTCAT
110049 TCATCAATA
1 TCATCAATA
110058 TCATCAATCA
1 TCATCAAT-A
*
110068 CCATCAATA
1 TCATCAATA
110077 TCATCAAT
1 TCATCAAT
110085 CATTTACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.31
Consensus pattern (9 bp):
TCATCAATA
Found at i:110074 original size:19 final size:19
Alignment explanation
Indices: 110050--110086 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
110040 ATATTTCATT
110050 CATCAATATCATCAATCAC
1 CATCAATATCATCAATCAC
110069 CATCAATATCATCAATCA
1 CATCAATATCATCAATCA
110087 TTTACTTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (19 bp):
CATCAATATCATCAATCAC
Found at i:114414 original size:2 final size:2
Alignment explanation
Indices: 114407--114432 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
114397 TAGGTTTTTC
114407 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
114433 TACATGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:123170 original size:20 final size:20
Alignment explanation
Indices: 123145--123184 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
123135 AATTACAAAC
123145 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
123165 AAACTCACATTCCGTGAGAG
1 AAACTCACATTCCGTGAGAG
123185 TTGAACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAACTCACATTCCGTGAGAG
Found at i:123415 original size:19 final size:19
Alignment explanation
Indices: 123391--123429 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
123381 GAAAAAAATC
123391 TACCATTATATATCTCCCA
1 TACCATTATATATCTCCCA
123410 TACCATTATATATCTCCCA
1 TACCATTATATATCTCCCA
123429 T
1 T
123430 TTATGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (19 bp):
TACCATTATATATCTCCCA
Found at i:125115 original size:19 final size:19
Alignment explanation
Indices: 125078--125115 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
125068 AAATGAATGG
*
125078 ATGATAAATCTAATCTAAT
1 ATGATAAATCTAATATAAT
*
125097 ATGATAAATCTCATATAAT
1 ATGATAAATCTAATATAAT
125116 TGGTCTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (19 bp):
ATGATAAATCTAATATAAT
Found at i:128081 original size:3 final size:3
Alignment explanation
Indices: 128073--128100 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
128063 ATCTACTATA
128073 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
128101 TATTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:130091 original size:20 final size:21
Alignment explanation
Indices: 130054--130096 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
130044 ATCTCACACA
130054 AAGATTATCAAAAATCATAGG
1 AAGATTATCAAAAATCATAGG
*
130075 AAGATTA-CAAAATTCATAGG
1 AAGATTATCAAAAATCATAGG
130095 AA
1 AA
130097 AGTTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (21 bp):
AAGATTATCAAAAATCATAGG
Found at i:130216 original size:22 final size:21
Alignment explanation
Indices: 130144--130220 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 21
130134 CTTTTGGAGT
* *
130144 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTAATAGGTAA
* **
130165 TTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTAATA-GGTAA
* *
130187 TTACCAAAATTTAATAGGGCAA
1 TTATCAAAATTTAATA-GGTAA
130209 TTATCAAAATTT
1 TTATCAAAATTT
130221 CATAAAAATA
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
21 14 0.32
22 30 0.68
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TTATCAAAATTTAATAGGTAA
Done.