Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019731.1 Corchorus olitorius cultivar O-4 contig19764, 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: 62141
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1179 original size:31 final size:32
Alignment explanation
Indices: 1126--1190 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
1116 TTCTCAGATT
*
1126 ATTCGGGTTTCGGCTCATCTGGATTCA-GGTC
1 ATTCGGGTCTCGGCTCATCTGGATTCAGGGTC
* *
1157 ATTCGGGTCTCGGGTC-TGCTGGATTTAGGGTC
1 ATTCGGGTCTCGGCTCAT-CTGGATTCAGGGTC
1189 AT
1 AT
1191 GCAGGTTCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 22 0.76
32 6 0.21
ACGTcount: A:0.12, C:0.20, G:0.32, T:0.35
Consensus pattern (32 bp):
ATTCGGGTCTCGGCTCATCTGGATTCAGGGTC
Found at i:1201 original size:31 final size:31
Alignment explanation
Indices: 1144--1202 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1134 TTCGGCTCAT
* *
1144 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
*
1175 CTGGATTTAGGGTCATGCAGGT-TCGGGT
1 CTGGATTCA-GGTCATGCAGGTCTCGGGT
1203 TTTGGCCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32
Consensus pattern (31 bp):
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
Found at i:2369 original size:10 final size:10
Alignment explanation
Indices: 2354--2403 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
2344 CCGTTTAATA
2354 ATTATATATT
1 ATTATATATT
2364 ATTATATATGT
1 ATTATATAT-T
2375 AATTATATA-T
1 -ATTATATATT
2385 ATCTA-ATATT
1 AT-TATATATT
*
2395 ATTTTATAT
1 ATTATATAT
2404 ATATAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
9 6 0.18
10 19 0.56
11 1 0.03
12 8 0.24
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTATATATT
Found at i:2379 original size:12 final size:11
Alignment explanation
Indices: 2352--2427 Score: 52
Period size: 12 Copynumber: 6.7 Consensus size: 11
2342 AACCGTTTAA
2352 TAATTATATAT
1 TAATTATATAT
2363 T-ATTATATAT
1 TAATTATATAT
2373 GTAATTATATA-
1 -TAATTATATAT
2384 T-ATCTA-ATAT
1 TAAT-TATATAT
*
2394 TATTTTATATAT
1 TA-ATTATATAT
*
2406 ATAAAATATATATT
1 -T-AATTATATA-T
2420 TAATTATA
1 TAATTATA
2428 AATATTACTA
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
9 5 0.10
10 13 0.25
11 4 0.08
12 19 0.37
13 8 0.16
14 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (11 bp):
TAATTATATAT
Found at i:2407 original size:14 final size:14
Alignment explanation
Indices: 2356--2407 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 14
2346 GTTTAATAAT
2356 TATATATTATTATA
1 TATATATTATTATA
*
2370 TATGTAATTATATATA
1 TATAT-ATTAT-TATA
* *
2386 TCTAATATTATTTTA
1 TAT-ATATTATTATA
2401 TATATAT
1 TATATAT
2408 AAAATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 8 0.27
15 10 0.33
16 11 0.37
17 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (14 bp):
TATATATTATTATA
Found at i:2413 original size:21 final size:21
Alignment explanation
Indices: 2377--2434 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
2367 ATATATGTAA
*
2377 TTATATATATCTAATATTAT-T
1 TTATATATAT-AAATATTATAT
2398 TTATATATATAAA-ATATATAT
1 TTATATATATAAATAT-TATAT
2419 TTA-AT-TATAAATATTA
1 TTATATATATAAATATTA
2435 CTAAACGGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 10 0.30
20 9 0.27
21 14 0.42
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATATATATAAATATTATAT
Found at i:11049 original size:41 final size:40
Alignment explanation
Indices: 10943--11183 Score: 257
Period size: 43 Copynumber: 5.7 Consensus size: 40
10933 CCAATAACTA
* *
10943 AAAGTCCCCAAACAAAATTATAACACAGGGGCAATTCTCTTTC
1 AAAGT-CCCAAACACAATTATAACACAGGGGC-A-TCTCTATC
* * *
10986 TAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATC
1 -AAAGTCC-CAAACACAATTATAACACAGGGGCATCTCTATC
11028 AAAGTCTCCAAACACAATTATAACACAGGGGCATCTCTATTCC
1 AAAGTC-CCAAACACAATTATAACACAGGGGCATCTCTA-T-C
* * * *
11071 AAAGTCGTCAAACACATTTATAACACAGAGGCATCTATATC
1 AAAGTC-CCAAACACAATTATAACACAGGGGCATCTCTATC
* *
11112 AAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCTA
1 AAAGT-CCCAAACACAATTATAACACAGGGGC-A-TCTCTATC
*
11155 AAAGTCCTCAAACACATTTATAACACAGG
1 AAAGTCC-CAAACACAATTATAACACAGG
11184 CATCCATACT
Statistics
Matches: 169, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
41 62 0.37
42 13 0.08
43 68 0.40
44 26 0.15
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.23
Consensus pattern (40 bp):
AAAGTCCCAAACACAATTATAACACAGGGGCATCTCTATC
Found at i:11083 original size:43 final size:42
Alignment explanation
Indices: 10943--11183 Score: 265
Period size: 41 Copynumber: 5.7 Consensus size: 42
10933 CCAATAACTA
* * * *
10943 AAAGTCCCCAAACAAAATTATAACACAGGGGCAATTCTCTTTCT
1 AAAGTCCTCAAACACAATTATAACACAGGGGC-A-TCTCTATCC
* * *
10987 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATAT-C
1 AAAGTCCTCAAACACAATTATAACACAGGGGCATCTCTATCC
11028 AAAGT-CTCCAAACACAATTATAACACAGGGGCATCTCTATTCC
1 AAAGTCCT-CAAACACAATTATAACACAGGGGCATCTCTA-TCC
* * * *
11071 AAAGTCGTCAAACACATTTATAACACAGAGGCATCTATAT-C
1 AAAGTCCTCAAACACAATTATAACACAGGGGCATCTCTATCC
* * *
11112 AAAGTCCCCAAACACAATTATAACACAGGGGCAAT-TCTCTCTA
1 AAAGTCCTCAAACACAATTATAACACAGGGGC-ATCTCTATC-C
*
11155 AAAGTCCTCAAACACATTTATAACACAGG
1 AAAGTCCTCAAACACAATTATAACACAGG
11184 CATCCATACT
Statistics
Matches: 167, Mismatches: 23, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
40 2 0.01
41 65 0.39
42 9 0.05
43 62 0.37
44 29 0.17
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.23
Consensus pattern (42 bp):
AAAGTCCTCAAACACAATTATAACACAGGGGCATCTCTATCC
Found at i:11102 original size:84 final size:84
Alignment explanation
Indices: 10943--11182 Score: 385
Period size: 84 Copynumber: 2.8 Consensus size: 84
10933 CCAATAACTA
* *
10943 AAAGTCCCCAAACAAAATTATAACACAGGGGCAATTCTCTTTCTAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAA-TCTCTTTCAAAAGTCCTCAAACACATTTAT
11008 AACACAGAGGCATCTATATC
65 AACACAGAGGCATCTATATC
* * *
11028 AAAGTCTCCAAACACAATTATAACACAGGGGC-ATCTCTATTCCAAAGTCGTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCT-TTCAAAAGTCCTCAAACACATTTAT
11092 AACACAGAGGCATCTATATC
65 AACACAGAGGCATCTATATC
*
11112 AAAGTCCCCAAACACAATTATAACACAGGGGCAAT-TCTCTCTAAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTTTC-AAAAGTCCTCAAACACATTTAT
11176 AACACAG
65 AACACAG
11183 GCATCCATAC
Statistics
Matches: 144, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
83 7 0.05
84 105 0.73
85 32 0.22
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.23
Consensus pattern (84 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTTTCAAAAGTCCTCAAACACATTTATA
ACACAGAGGCATCTATATC
Found at i:14906 original size:18 final size:18
Alignment explanation
Indices: 14883--14917 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14873 GCAATCTGAT
14883 TTTGTCAGAGGTGATGAC
1 TTTGTCAGAGGTGATGAC
* *
14901 TTTGTCGGTGGTGATGA
1 TTTGTCAGAGGTGATGA
14918 TATGCCGGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.09, G:0.37, T:0.37
Consensus pattern (18 bp):
TTTGTCAGAGGTGATGAC
Found at i:16821 original size:12 final size:12
Alignment explanation
Indices: 16804--16852 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
16794 ATTTAACAAC
16804 AATAAATAAACT
1 AATAAATAAACT
*
16816 AATAAATAAAGT
1 AATAAATAAACT
*
16828 AAGT---CAAACT
1 AA-TAAATAAACT
16838 AATAAATAAACT
1 AATAAATAAACT
16850 AAT
1 AAT
16853 TAAGAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
9 1 0.03
10 6 0.21
12 21 0.72
13 1 0.03
ACGTcount: A:0.63, C:0.08, G:0.04, T:0.24
Consensus pattern (12 bp):
AATAAATAAACT
Found at i:16912 original size:23 final size:22
Alignment explanation
Indices: 16860--16921 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 22
16850 AATTAAGAAT
*
16860 AATTAATTTTAATTAAATTTCAA
1 AATTAA-TTTAATTAAATGTCAA
16883 AATTTAATTTAATTAACA-GTCATA
1 AA-TTAATTTAATTAA-ATGTCA-A
*
16907 AATTAA-CTAATTAAA
1 AATTAATTTAATTAAA
16922 ACTAATAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
21 1 0.03
22 7 0.21
23 18 0.53
24 8 0.24
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
AATTAATTTAATTAAATGTCAA
Found at i:16929 original size:22 final size:22
Alignment explanation
Indices: 16811--16940 Score: 61
Period size: 22 Copynumber: 6.0 Consensus size: 22
16801 AACAATAAAT
* * * *
16811 AAACTAATAAATAAAGTAAGTC
1 AAACTAATAAATTAACTAATTA
*
16833 AAACTAATAAATAAACTAATTA
1 AAACTAATAAATTAACTAATTA
* *
16855 AGAA-TAATTAATT--TTAATTA
1 A-AACTAATAAATTAACTAATTA
** * *
16875 AATTTCAA-AATTTAATTTAATTA
1 AAACT-AATAAATTAA-CTAATTA
* * *
16898 ACAGTCATAAATTAACTAATTA
1 AAACTAATAAATTAACTAATTA
* *
16920 AAACTAATAAACTAAGTAATT
1 AAACTAATAAATTAACTAATT
16941 CATTAATTTT
Statistics
Matches: 81, Mismatches: 20, Indels: 14
0.70 0.17 0.12
Matches are distributed among these distances:
19 1 0.01
20 11 0.14
21 2 0.02
22 50 0.62
23 17 0.21
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.34
Consensus pattern (22 bp):
AAACTAATAAATTAACTAATTA
Found at i:17019 original size:25 final size:26
Alignment explanation
Indices: 16997--17049 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
16987 TTAATTAATT
* *
16997 AAATGTTTAATATTTTTTTTTAAAAA
1 AAATATTTAATATTTGTTTTTAAAAA
17023 AAATATTTAATATTTG-TTTTAAAAA
1 AAATATTTAATATTTGTTTTTAAAAA
17048 AA
1 AA
17050 TTGGGCATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
AAATATTTAATATTTGTTTTTAAAAA
Found at i:17026 original size:26 final size:25
Alignment explanation
Indices: 16997--17049 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
16987 TTAATTAATT
* *
16997 AAATGTTTAATATTTTTTTTTAAAAA
1 AAATATTTAATA-TTTGTTTTAAAAA
17023 AAATATTTAATATTTGTTTTAAAAA
1 AAATATTTAATATTTGTTTTAAAAA
17048 AA
1 AA
17050 TTGGGCATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
AAATATTTAATATTTGTTTTAAAAA
Found at i:17375 original size:2 final size:2
Alignment explanation
Indices: 17368--17395 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17358 CTTATTTAGT
17368 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
17396 AAAGAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24537 original size:145 final size:143
Alignment explanation
Indices: 24252--24520 Score: 360
Period size: 145 Copynumber: 1.9 Consensus size: 143
24242 TTATTTTTCG
* * *
24252 AATATATTTCATATATGATATTGTTCAAACTTTTATAGTTTTATCAACTAAAAACTCTATTTTTA
1 AATATATTTCATAAATAACATTGTTCAAACTTTTATAGTTTTATCAACTAAAAACTCTATTTTTA
** * ** * * *
24317 TTTAATTAAATTTAATATCTTTATTCTATTTTATTTTTACTGTTTTAATTAAAAACTTATATATA
66 TTTAATTAAATTTAATATCTTTATAATATTTTATTTTAACCATTTCAATTAAAAAATTATAGATA
24382 TTAGGATTTTTAA
131 TTAGGATTTTTAA
* * *
24395 AATATATTTCTTAAATAACATTGTTTAAACTTTTATAGTTTTTATTATACTAAAAACTCTATTTT
1 AATATATTTCATAAATAACATTGTTCAAACTTTTATAG-TTTTATCA-ACTAAAAACTCTATTTT
*
24460 TATTTAATTAAATTTAATATTTTTATAAATATTTTA-TTTAACCATTTCAATTTAAAAAATT
64 TATTTAATTAAATTTAATATCTTTAT-AATATTTTATTTTAACCATTTCAA-TTAAAAAATT
24521 GAAGACTTTT
Statistics
Matches: 108, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
143 33 0.31
144 7 0.06
145 52 0.48
146 16 0.15
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (143 bp):
AATATATTTCATAAATAACATTGTTCAAACTTTTATAGTTTTATCAACTAAAAACTCTATTTTTA
TTTAATTAAATTTAATATCTTTATAATATTTTATTTTAACCATTTCAATTAAAAAATTATAGATA
TTAGGATTTTTAA
Found at i:27242 original size:60 final size:60
Alignment explanation
Indices: 27178--27292 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
27168 ACACCAGCAA
27178 GGCCAAATCCTATCCATGAGCAATCAG-A-A-AAATATCACCTTGAAAAAACGACACCTAAAG
1 GGCCAAATCCTATCCAT--G-AATCAGCATACAAATATCACCTTGAAAAAACGACACCTAAAG
* *
27238 GGCCAAATCCTATCCATGAATCAGCATACAAATATCACCTTTAAAGAACGACACC
1 GGCCAAATCCTATCCATGAATCAGCATACAAATATCACCTTGAAAAAACGACACC
27293 AGGTTGGTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
57 6 0.12
58 2 0.04
59 1 0.02
60 41 0.82
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (60 bp):
GGCCAAATCCTATCCATGAATCAGCATACAAATATCACCTTGAAAAAACGACACCTAAAG
Found at i:27306 original size:60 final size:58
Alignment explanation
Indices: 27143--27295 Score: 152
Period size: 60 Copynumber: 2.6 Consensus size: 58
27133 ATGATTTATC
* * * *
27143 GAACAAATATCGCCTTAAAAGAGCAACACCAGCAAGGCCAAATCCTATCCATGAGCAATCA
1 GAACAAATATCACCTTAAAAGAACGACACCAG--GGGCCAAATCCTATCCAT-AGCAATCA
*
27204 GAA-AAATATCACCTTGAAAA-AACGACACCTAAAGGGCCAAATCCTATCCAT-G-AATCA
1 GAACAAATATCACCTT-AAAAGAACGACACC--AGGGGCCAAATCCTATCCATAGCAATCA
*
27261 GCATACAAATATCACCTTTAAAGAACGACACCAGG
1 G-A-ACAAATATCACCTTAAAAGAACGACACCAGG
27296 TTGGTCAAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
57 6 0.08
58 4 0.05
59 4 0.05
60 56 0.72
61 7 0.09
62 1 0.01
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.16
Consensus pattern (58 bp):
GAACAAATATCACCTTAAAAGAACGACACCAGGGGCCAAATCCTATCCATAGCAATCA
Found at i:37569 original size:24 final size:24
Alignment explanation
Indices: 37541--37588 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
37531 TTATAACGTT
37541 AGCAGTGACAAGACATCTTAATGC
1 AGCAGTGACAAGACATCTTAATGC
37565 AGCAGTGACAAGACATCTTAATGC
1 AGCAGTGACAAGACATCTTAATGC
37589 CACAAGCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
AGCAGTGACAAGACATCTTAATGC
Found at i:44663 original size:2 final size:2
Alignment explanation
Indices: 44656--44691 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
44646 AATTTATAAA
*
44656 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
44692 ACAGTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:50403 original size:15 final size:15
Alignment explanation
Indices: 50383--50416 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
50373 GATCTTGGAT
*
50383 GTTTGAGTCAGTTTA
1 GTTTGAGTCAGTTGA
50398 GTTTGAGTCAGTTGA
1 GTTTGAGTCAGTTGA
50413 GTTT
1 GTTT
50417 ATTGAGTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.29, T:0.47
Consensus pattern (15 bp):
GTTTGAGTCAGTTGA
Found at i:50866 original size:15 final size:17
Alignment explanation
Indices: 50846--50882 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
50836 TCTCTTCGGG
50846 GAAAAAA-AAAGAA-AA
1 GAAAAAAGAAAGAAGAA
50861 GAAAAAAAGAAAGAAGAA
1 G-AAAAAAGAAAGAAGAA
50879 GAAA
1 GAAA
50883 GCCCACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.05
16 6 0.32
17 9 0.47
18 3 0.16
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
GAAAAAAGAAAGAAGAA
Found at i:50873 original size:17 final size:17
Alignment explanation
Indices: 50847--50882 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
50837 CTCTTCGGGG
50847 AAAAAAAAAGAA-AAGA
1 AAAAAAAAAGAAGAAGA
50863 AAAAAAGAAAGAAGAAGA
1 AAAAAA-AAAGAAGAAGA
50881 AA
1 AA
50883 GCCCACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 6 0.33
18 6 0.33
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAGAAGA
Found at i:59466 original size:15 final size:16
Alignment explanation
Indices: 59433--59472 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
59423 TTACTTTGCT
59433 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
59449 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTATAA
*
59464 TTGCTTTCT
1 TTGTTTTCT
59473 TTCAATCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Done.