Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018291.1 Corchorus olitorius cultivar O-4 contig18324, 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: 54293
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:77 original size:21 final size:21
Alignment explanation
Indices: 53--97 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43 GGCGCCCACA
* *
53 TGGTTTCCTTGAGCACCCATG
1 TGGTTTCCTTGAGAACCCAGG
*
74 TGGTTTGCTTGAGAACCCAGG
1 TGGTTTCCTTGAGAACCCAGG
95 TGG
1 TGG
98 GCAGTGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TGGTTTCCTTGAGAACCCAGG
Found at i:1317 original size:29 final size:29
Alignment explanation
Indices: 1274--1338 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
1264 TGCGAACTGA
1274 ATTGTTTAACTGGGATTGCATGTTGAGTTG
1 ATTG-TTAACTGGGATTGCATGTTGAGTTG
1304 ATTGTTAACTGGGATTGCATGTTGAGTTG
1 ATTGTTAACTGGGATTGCATGTTGAGTTG
1333 ATTGTT
1 ATTGTT
1339 GCCATCCTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.20, C:0.06, G:0.29, T:0.45
Consensus pattern (29 bp):
ATTGTTAACTGGGATTGCATGTTGAGTTG
Found at i:2386 original size:27 final size:29
Alignment explanation
Indices: 2355--2432 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 29
2345 GTGTGAACTT
*
2355 AAAATGGCCAAAATGCCCCT-GAAT-GTG
1 AAAATGACCAAAATGCCCCTAGAATCGTG
* * * * *
2382 CAAATGTCTAAAATGCCCCTAGATTCTTG
1 AAAATGACCAAAATGCCCCTAGAATCGTG
2411 AAAATGACCAAAATGCCCCTAG
1 AAAATGACCAAAATGCCCCTAG
2433 GTGATCCTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 17 0.41
28 3 0.07
29 21 0.51
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTAGAATCGTG
Found at i:4741 original size:21 final size:21
Alignment explanation
Indices: 4717--4780 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
4707 CCTTAGGCAA
4717 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAACCTT
*
4738 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACCTT
4759 CTCCAATGAGCTTGAAA-CTT
1 CTCCAATGAGCTTGAAACCTT
4779 CT
1 CT
4781 TTGTGAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 4 0.10
21 37 0.90
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACCTT
Found at i:22946 original size:128 final size:128
Alignment explanation
Indices: 22718--22955 Score: 449
Period size: 128 Copynumber: 1.9 Consensus size: 128
22708 AACGTTAGGT
*
22718 TGTGTATCACACGCATCTATTTTCTGTGTCAAAAAATCCAGCTCAGCATTCTATTAGCCAGCTGG
1 TGTGTATCACACGCATCTATGTTCTGTGTCAAAAAATCCAGCTCAGCATTCTATTAGCCAGCTGG
22783 TTATCTTTAATATTACATCAACCTTAATTTTTATATTTATATTTTCTGTATAAATATATTTTC
66 TTATCTTTAATATTACATCAACCTTAATTTTTATATTTATATTTTCTGTATAAATATATTTTC
*
22846 TGTGTATCACACGCATCTATGTTCTGTGTCAAAAAATCCTGCTCAGCATTCTATTAGCCAGCTGG
1 TGTGTATCACACGCATCTATGTTCTGTGTCAAAAAATCCAGCTCAGCATTCTATTAGCCAGCTGG
*
22911 TTATCTTTAGTATTACATCAACCTTAATTTTTATATTTATATTTT
66 TTATCTTTAATATTACATCAACCTTAATTTTTATATTTATATTTT
22956 TTTGTTTTTA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 107 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (128 bp):
TGTGTATCACACGCATCTATGTTCTGTGTCAAAAAATCCAGCTCAGCATTCTATTAGCCAGCTGG
TTATCTTTAATATTACATCAACCTTAATTTTTATATTTATATTTTCTGTATAAATATATTTTC
Found at i:22963 original size:22 final size:23
Alignment explanation
Indices: 22938--22994 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
22928 TCAACCTTAA
*
22938 TTTTTATATTT-ATATTTTTTT-G
1 TTTTTAT-TTTCATATTTTTTTCC
*
22960 TTTTTATTTTCATCTTTTTTTCC
1 TTTTTATTTTCATATTTTTTTCC
22983 TTTTTATGTTTC
1 TTTTTAT-TTTC
22995 TCATCTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 3 0.10
22 16 0.53
23 7 0.23
24 4 0.13
ACGTcount: A:0.12, C:0.09, G:0.04, T:0.75
Consensus pattern (23 bp):
TTTTTATTTTCATATTTTTTTCC
Found at i:24354 original size:2 final size:2
Alignment explanation
Indices: 24347--24378 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24337 ATTCAATACT
24347 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
24379 AGTAACCTGA
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):
TA
Found at i:27281 original size:27 final size:26
Alignment explanation
Indices: 27251--27313 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
27241 TTAAAATTTT
* *
27251 ACCCTTGGATGGGTAAATTACTAAATC
1 ACCCTTGGAT-GCTAAATTACAAAATC
* *
27278 ACCCTTGAGATTCTAAATTACAAAATT
1 ACCCTTG-GATGCTAAATTACAAAATC
27305 ACCCTTGGA
1 ACCCTTGGA
27314 AGAATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 2 0.06
27 26 0.84
28 3 0.10
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (26 bp):
ACCCTTGGATGCTAAATTACAAAATC
Found at i:28398 original size:12 final size:13
Alignment explanation
Indices: 28355--28409 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
28345 TTGAGGAACT
*
28355 ATTTTATT-ACTG
1 ATTTTATTAAATG
28367 -TTTTATTAAATTG
1 ATTTTATTAAA-TG
*
28380 TTTTTA-TAAATG
1 ATTTTATTAAATG
*
28392 ATTTTATTAAATA
1 ATTTTATTAAATG
28405 ATTTT
1 ATTTT
28410 GGGTGCATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 7 0.19
12 8 0.22
13 16 0.44
14 5 0.14
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (13 bp):
ATTTTATTAAATG
Found at i:33165 original size:2 final size:2
Alignment explanation
Indices: 33160--33184 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33150 TCACTACAAG
33160 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
33185 CAATGTCCAT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:33829 original size:27 final size:26
Alignment explanation
Indices: 33799--33861 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
33789 TTACTATTTT
* *
33799 ACCCTTGGATAGGTAAATTACTAAATC
1 ACCCTTGGAT-GCTAAATTACAAAATC
* *
33826 ACCCTTGAGATTCTAAATTACAAAATT
1 ACCCTTG-GATGCTAAATTACAAAATC
33853 ACCCTTGGA
1 ACCCTTGGA
33862 AGAATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 2 0.06
27 26 0.84
28 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.30
Consensus pattern (26 bp):
ACCCTTGGATGCTAAATTACAAAATC
Found at i:34944 original size:12 final size:13
Alignment explanation
Indices: 34901--34955 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
34891 TTGAGGAACT
*
34901 ATTTTATT-ACTG
1 ATTTTATTAAATG
34913 -TTTTATTAAATTG
1 ATTTTATTAAA-TG
*
34926 TTTTTA-TAAATG
1 ATTTTATTAAATG
*
34938 ATTTTATTAAATA
1 ATTTTATTAAATG
34951 ATTTT
1 ATTTT
34956 GGGTGCATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 7 0.19
12 8 0.22
13 16 0.44
14 5 0.14
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (13 bp):
ATTTTATTAAATG
Found at i:37345 original size:42 final size:43
Alignment explanation
Indices: 37296--37397 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 43
37286 TTTTCGTCTC
*
37296 TGTGTGGTTAG-ACAAATTTCATAAGGAAGTTATCAATATTTCA
1 TGTGTGGTTAGCA-AAATTTCATAAGGAAGTTATCAAAATTTCA
** *
37339 T-TGTGGTTAGCAAAATTTCATGTGGAGGTTATCAAAATTTCA
1 TGTGTGGTTAGCAAAATTTCATAAGGAAGTTATCAAAATTTCA
*
37381 TGGTGTGGTTACCAAAA
1 T-GTGTGGTTAGCAAAA
37398 AGCTCATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
42 36 0.71
43 2 0.04
44 13 0.25
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (43 bp):
TGTGTGGTTAGCAAAATTTCATAAGGAAGTTATCAAAATTTCA
Found at i:37374 original size:22 final size:22
Alignment explanation
Indices: 37309--37648 Score: 87
Period size: 22 Copynumber: 15.4 Consensus size: 22
37299 GTGGTTAGAC
** *
37309 AAATTTCATAAGGAAGTTATCA
1 AAATTTCATGTGGAGGTTATCA
* * *
37331 ATATTTCAT-T-GTGGTTAGCA
1 AAATTTCATGTGGAGGTTATCA
37351 AAATTTCATGTGGAGGTTATCA
1 AAATTTCATGTGGAGGTTATCA
* *
37373 AAATTTCATG-GTGTGGTTACCAA
1 AAATTTCATGTG-GAGGTTATC-A
** * * *
37396 AAAGCTCATATAGAGGTTATAA
1 AAATTTCATGTGGAGGTTATCA
*
37418 GAAATTTCATAG-GGAGGTTATTA
1 -AAATTTCAT-GTGGAGGTTATCA
* ** *
37441 AAATTTTATAGT-TTGGTTACCA
1 AAATTTCAT-GTGGAGGTTATCA
* *
37463 AAATTTCATAG-GAAAGTTAT-A
1 AAATTTCAT-GTGGAGGTTATCA
** * *
37484 AAAAGTCACAGT-GTGGTTATCA
1 AAATTTCA-TGTGGAGGTTATCA
* *
37506 AAATTTCATAAT-GTGGTTATCA
1 AAATTTCAT-GTGGAGGTTATCA
* * * *
37528 AATTTTCATAG-AGAGATCATCA
1 AAATTTCAT-GTGGAGGTTATCA
*
37550 AAATTTCAT-TAGGA-GATATCAA
1 AAATTTCATGT-GGAGGTTATC-A
* *
37572 AAATTCATAATGTGGAAGGTTATTA
1 AAATT--TCATGTGG-AGGTTATCA
* ** * *
37597 AATTTTTTTATGGA-GTAATCA
1 AAATTTCATGTGGAGGTTATCA
**
37618 AAATTTCATAG-GGAGGTTATTG
1 AAATTTCAT-GTGGAGGTTATCA
37640 AAATTTCAT
1 AAATTTCAT
37649 AGTTTAGTTT
Statistics
Matches: 226, Mismatches: 68, Indels: 48
0.66 0.20 0.14
Matches are distributed among these distances:
20 15 0.07
21 32 0.14
22 128 0.57
23 35 0.15
24 5 0.02
25 7 0.03
26 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
AAATTTCATGTGGAGGTTATCA
Found at i:37523 original size:65 final size:68
Alignment explanation
Indices: 37362--37543 Score: 183
Period size: 65 Copynumber: 2.7 Consensus size: 68
37352 AATTTCATGT
* ** * * *
37362 GGAGGTTATCAAAATTTCATGGTGTGGTTACCAAAAAGCTCATA-TAGAGGTTATAAGAAATTTC
1 GGAGGTTATCAAAATTTCATAGTGTGGTTACC-AAAATTTCATAGGAGAAGTTATAAGAAATGTC
*
37426 ATAG
65 ACAG
* * *
37430 GGAGGTTATTAAAATTTTATAGTTTGGTTACCAAAATTTCATAGGA-AAGTTATAA-AAA-GTCA
1 GGAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGAGAAGTTATAAGAAATGTCA
37492 CAG
66 CAG
* * * * *
37495 TGTGGTTATCAAAATTTCATAATGTGGTTATCAAATTTTCATAGAGAGA
1 GGAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAG-GAGA
37544 TCATCAAAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
65 41 0.44
66 5 0.05
67 18 0.19
68 29 0.31
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (68 bp):
GGAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGAGAAGTTATAAGAAATGTCA
CAG
Found at i:37741 original size:22 final size:22
Alignment explanation
Indices: 37711--37753 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
37701 TTGTGTAGAT
**
37711 CAAAATTTCATAGCGAGGTTAA
1 CAAAATTTCATAAAGAGGTTAA
*
37733 CAAAGTTTCATAAAGAGGTTA
1 CAAAATTTCATAAAGAGGTTA
37754 TCTATAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (22 bp):
CAAAATTTCATAAAGAGGTTAA
Found at i:37846 original size:23 final size:24
Alignment explanation
Indices: 37789--37851 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
37779 AAATTTTTTA
*
37789 TTATCAAAATTCTAT-GGTAAGAT
1 TTATCAAAATTTTATAGGTAAGAT
*
37812 TTATCAAAATTTTATAGG-AAGGT
1 TTATCAAAATTTTATAGGTAAGAT
* *
37835 TTATCAACATTTCATAG
1 TTATCAAAATTTTATAG
37852 TGAGGTTATC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.40
Consensus pattern (24 bp):
TTATCAAAATTTTATAGGTAAGAT
Found at i:37857 original size:23 final size:24
Alignment explanation
Indices: 37811--37875 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
37801 TATGGTAAGA
* *
37811 TTTATCAAAATTTTATAG-GAAGG
1 TTTATCAACATTTCATAGTGAAGG
37834 TTTATCAACATTTCATAGTG-AGG
1 TTTATCAACATTTCATAGTGAAGG
37857 -TTATC-ACAATTTCATAGTG
1 TTTATCAAC-ATTTCATAGTG
37876 TGATAATCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 2 0.05
22 16 0.42
23 19 0.50
24 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (24 bp):
TTTATCAACATTTCATAGTGAAGG
Found at i:37868 original size:22 final size:23
Alignment explanation
Indices: 37789--37875 Score: 74
Period size: 23 Copynumber: 3.8 Consensus size: 23
37779 AAATTTTTTA
* * *
37789 TTATCAAAATTCTATGGT-AAGAT
1 TTATCAAATTTC-ATAGTGAAGGT
*
37812 TTATCAAAATTTTATAG-GAAGGT
1 TTATC-AAATTTCATAGTGAAGGT
37835 TTATCAACATTTCATAGTG-AGG-
1 TTATCAA-ATTTCATAGTGAAGGT
37857 TTATCACAATTTCATAGTG
1 TTATCA-AATTTCATAGTG
37876 TGATAATCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
22 19 0.35
23 29 0.54
24 6 0.11
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (23 bp):
TTATCAAATTTCATAGTGAAGGT
Found at i:37884 original size:22 final size:22
Alignment explanation
Indices: 37843--37892 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
37833 GTTTATCAAC
* *
37843 ATTTCATAGTGAGGTTATCACA
1 ATTTCATAGTGAGATAATCACA
* *
37865 ATTTCATAGTGTGATAATCATA
1 ATTTCATAGTGAGATAATCACA
37887 ATTTCA
1 ATTTCA
37893 CTGTGTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
ATTTCATAGTGAGATAATCACA
Found at i:38144 original size:21 final size:21
Alignment explanation
Indices: 38113--38171 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
38103 TATAGGGTAA
38113 TTATCAAAATTTCATAAGGTGG
1 TTAT-AAAATTTCATAAGGTGG
38135 TTATAAAATTTCATAAGGTGG
1 TTATAAAATTTCATAAGGTGG
38156 TTATAAAATTTCATAA
1 TTATAAAATTTCATAA
38172 AAATATCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 33 0.89
22 4 0.11
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.39
Consensus pattern (21 bp):
TTATAAAATTTCATAAGGTGG
Found at i:40232 original size:132 final size:132
Alignment explanation
Indices: 39979--40237 Score: 394
Period size: 132 Copynumber: 2.0 Consensus size: 132
39969 ATAATTTTAT
* * *
39979 TTTATTTCTTCATGATTCATGCTTTGTAAATCTTATGCTGAATACTTAATACATCAGGGTGAGAA
1 TTTATATCTTCAGGATTCATGCTTTGTAAATCTTATGCTGAATACTTAATACATCAGAGTGAGAA
*
40044 GATTGTTAATTTGGATCTCTAATCTCTTTGAAATGGCTTCAGTCATCAAGTCGTTAAATGGATTG
66 GATTGTTAATTTGGATCTCTAATCTCTTTGAAATAGCTTCAGTCATCAAGTCGTTAAATGGATTG
40109 AC
131 AC
* *
40111 TTTATATCTTCAGGATTCATGCTTTGTAAATCTTATGCT-AAGTACTTAATATATCATAGTGAGA
1 TTTATATCTTCAGGATTCATGCTTTGTAAATCTTATGCTGAA-TACTTAATACATCAGAGTGAGA
* * * * * *
40175 AGATTGTTAATTTGGCTCTCTAATCTCTTTGAATTAGCTTTAGTCCTCCAGTTGTTAAATGGA
65 AGATTGTTAATTTGGATCTCTAATCTCTTTGAAATAGCTTCAGTCATCAAGTCGTTAAATGGA
40238 AATTAGTTGC
Statistics
Matches: 114, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
131 2 0.02
132 112 0.98
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (132 bp):
TTTATATCTTCAGGATTCATGCTTTGTAAATCTTATGCTGAATACTTAATACATCAGAGTGAGAA
GATTGTTAATTTGGATCTCTAATCTCTTTGAAATAGCTTCAGTCATCAAGTCGTTAAATGGATTG
AC
Found at i:45542 original size:24 final size:24
Alignment explanation
Indices: 45498--45543 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
45488 GGTTTATATT
* *
45498 CCATGCACTGTCAGTGTATAGAGG
1 CCATACACTGTCAGTGCATAGAGG
45522 CCATACACTGTCAG-GCCATAGA
1 CCATACACTGTCAGTG-CATAGA
45544 ATTATGCCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (24 bp):
CCATACACTGTCAGTGCATAGAGG
Found at i:49902 original size:49 final size:49
Alignment explanation
Indices: 49825--49929 Score: 192
Period size: 49 Copynumber: 2.1 Consensus size: 49
49815 TTTTGTTAGC
* *
49825 TTCAGCTTCTTGGGTTAACAGTTTGCACTTTTATTTTGATTCATATGTT
1 TTCATCTTCTTGGGTTAACAGTTTGCACTTTAATTTTGATTCATATGTT
49874 TTCATCTTCTTGGGTTAACAGTTTGCACTTTAATTTTGATTCATATGTT
1 TTCATCTTCTTGGGTTAACAGTTTGCACTTTAATTTTGATTCATATGTT
49923 TTCATCT
1 TTCATCT
49930 ACAACATGGG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.19, C:0.15, G:0.14, T:0.51
Consensus pattern (49 bp):
TTCATCTTCTTGGGTTAACAGTTTGCACTTTAATTTTGATTCATATGTT
Found at i:52906 original size:2 final size:2
Alignment explanation
Indices: 52899--52934 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
52889 CTAAAACTAG
52899 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52935 GAAATCAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.