Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022517.1 Corchorus olitorius cultivar O-4 contig22550, 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: 73887
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:194 original size:35 final size:35
Alignment explanation
Indices: 155--229 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
145 TTATATAAAC
155 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
190 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
225 GAACA
1 GAACA
230 TAAACGAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGTCTGTTCGT
Found at i:2756 original size:12 final size:12
Alignment explanation
Indices: 2741--2766 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2731 ATATATATAT
2741 ATATTAGCACTA
1 ATATTAGCACTA
2753 ATATTAGCACTA
1 ATATTAGCACTA
2765 AT
1 AT
2767 TACCTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATATTAGCACTA
Found at i:8501 original size:15 final size:16
Alignment explanation
Indices: 8481--8511 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
8471 GGTCTACTGC
8481 TCTCATCAAC-ACCTT
1 TCTCATCAACAACCTT
8496 TCTCATCAACAACCTT
1 TCTCATCAACAACCTT
8512 ACACGACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (16 bp):
TCTCATCAACAACCTT
Found at i:9950 original size:45 final size:45
Alignment explanation
Indices: 9832--10052 Score: 329
Period size: 45 Copynumber: 4.9 Consensus size: 45
9822 TACTATGAAC
* ** *
9832 CAACAAATCCCTTCCATAACAAACAAATCCAGTGAAATGAGCCAAA
1 CAACAAACCCCTTCCCCAACAAACAAACCCAGTGAAATGAGCC-AA
* *
9878 CTACATGAA--TCTTCCCCAACAAACAAACCCAGTGAAATGAGCCAA
1 CAACA--AACCCCTTCCCCAACAAACAAACCCAGTGAAATGAGCCAA
*
9923 CAACAAACCTCTTCCCCAACAAACAAACCCAGTGAAATGAGCCAA
1 CAACAAACCCCTTCCCCAACAAACAAACCCAGTGAAATGAGCCAA
9968 CAACAAACCCCTTCCCCAACAAACAAACCCAGTGAAATGAGCCAA
1 CAACAAACCCCTTCCCCAACAAACAAACCCAGTGAAATGAGCCAA
*
10013 CAACAAACCCCTTCCCCAACAAACAAACCCAATGAAATGA
1 CAACAAACCCCTTCCCCAACAAACAAACCCAGTGAAATGA
10053 ATCAAGCTAC
Statistics
Matches: 163, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
43 2 0.01
45 125 0.77
46 34 0.21
48 2 0.01
ACGTcount: A:0.45, C:0.34, G:0.09, T:0.12
Consensus pattern (45 bp):
CAACAAACCCCTTCCCCAACAAACAAACCCAGTGAAATGAGCCAA
Found at i:9968 original size:26 final size:25
Alignment explanation
Indices: 9938--10022 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
9928 AACCTCTTCC
9938 CCAACAAACAAACCCAGTGAAATGAG
1 CCAAC-AACAAACCCAGTGAAATGAG
* **
9964 CCAACAACAAACCC-CT----T-CC
1 CCAACAACAAACCCAGTGAAATGAG
9983 CCAACAAACAAACCCAGTGAAATGAG
1 CCAAC-AACAAACCCAGTGAAATGAG
10009 CCAACAACAAACCC
1 CCAACAACAAACCC
10023 CTTCCCCAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
19 5 0.11
20 10 0.22
21 1 0.02
24 1 0.02
25 19 0.41
26 10 0.22
ACGTcount: A:0.47, C:0.36, G:0.09, T:0.07
Consensus pattern (25 bp):
CCAACAACAAACCCAGTGAAATGAG
Found at i:10124 original size:35 final size:35
Alignment explanation
Indices: 10076--10145 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
10066 ATTAGCTACA
*
10076 ATACATTTCTGTAAATCTATGAGCCAACAAACCCC
1 ATACATTTCTGTAAATCTATGAACCAACAAACCCC
*
10111 ATACATTTTTGTAAATCTATGAACCAACAAACCCC
1 ATACATTTCTGTAAATCTATGAACCAACAAACCCC
10146 TTTCCACATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (35 bp):
ATACATTTCTGTAAATCTATGAACCAACAAACCCC
Found at i:10161 original size:90 final size:90
Alignment explanation
Indices: 10061--10240 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
10051 GAATCAAGCT
10061 ACATAATTAGCTACAATACATTTCTGTAAATCTATGAGCCAACAAACCCCATACATTTTTGTAAA
1 ACATAATTAGCTACAATACATTTCTGTAAATCTATGAGCCAACAAACCCCATACATTTTTGTAAA
10126 TCTATGAACCAACAAACCCCTTTCC
66 TCTATGAACCAACAAACCCCTTTCC
*
10151 ACATGATTAGCTACAATACATTTCTGTAAATCTATGAGCCAACAAACCCCATACATTTTTGTAAA
1 ACATAATTAGCTACAATACATTTCTGTAAATCTATGAGCCAACAAACCCCATACATTTTTGTAAA
10216 TCTATGAACCAACAAACCCCTTTCC
66 TCTATGAACCAACAAACCCCTTTCC
10241 CCCATACATT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (90 bp):
ACATAATTAGCTACAATACATTTCTGTAAATCTATGAGCCAACAAACCCCATACATTTTTGTAAA
TCTATGAACCAACAAACCCCTTTCC
Found at i:10214 original size:35 final size:35
Alignment explanation
Indices: 10166--10375 Score: 141
Period size: 35 Copynumber: 6.0 Consensus size: 35
10156 ATTAGCTACA
* *
10166 ATACATTTCTGTAAATCTATGAGCCAACAAACCCC
1 ATACATTTTTGTAAATCTATGAACCAACAAACCCC
10201 ATACATTTTTGTAAATCTATGAACCAACAAACCCCTTTCCCCC
1 ATACATTTTTGTAAATCTATGAACCAACAAA--------CCCC
10244 ATACATTTTTGTAAATCTATGAACCAACAAACCCC
1 ATACATTTTTGTAAATCTATGAACCAACAAACCCC
* ******
10279 -TTC--CCCAACAAA-C-A--AACC--CAAACCCAC
1 ATACATTTTTGTAAATCTATGAACCAACAAACCC-C
* ** * *
10306 AAACCCCTTCTGTAAATCTATGAGCCAACAAACCCC
1 ATA-CATTTTTGTAAATCTATGAACCAACAAACCCC
10342 ATACATTTTTGTAAATCTATGAACCAACAAACCC
1 ATACATTTTTGTAAATCTATGAACCAACAAACCC
10376 TTTCCCCAAC
Statistics
Matches: 134, Mismatches: 22, Indels: 38
0.69 0.11 0.20
Matches are distributed among these distances:
26 7 0.05
27 1 0.01
28 4 0.03
29 1 0.01
30 1 0.01
31 5 0.04
32 4 0.03
33 1 0.01
34 2 0.01
35 63 0.47
36 3 0.02
37 7 0.05
43 35 0.26
ACGTcount: A:0.38, C:0.32, G:0.06, T:0.24
Consensus pattern (35 bp):
ATACATTTTTGTAAATCTATGAACCAACAAACCCC
Found at i:10258 original size:43 final size:42
Alignment explanation
Indices: 10197--10284 Score: 167
Period size: 43 Copynumber: 2.1 Consensus size: 42
10187 AGCCAACAAA
10197 CCCCATACATTTTTGTAAATCTATGAACCAACAAACCCCTTTC
1 CCCCATACATTTTTGTAAATCTATGAACCAACAAACCCC-TTC
10240 CCCCATACATTTTTGTAAATCTATGAACCAACAAACCCCTTC
1 CCCCATACATTTTTGTAAATCTATGAACCAACAAACCCCTTC
10282 CCC
1 CCC
10285 AACAAACAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 6 0.13
43 39 0.87
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.28
Consensus pattern (42 bp):
CCCCATACATTTTTGTAAATCTATGAACCAACAAACCCCTTC
Found at i:10903 original size:23 final size:23
Alignment explanation
Indices: 10873--10918 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
10863 CCAACCACTT
10873 ATTAGTCATTTCTTCTAACTCTA
1 ATTAGTCATTTCTTCTAACTCTA
10896 ATTAGTCATTTCTTCTAACTCTA
1 ATTAGTCATTTCTTCTAACTCTA
10919 TCATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (23 bp):
ATTAGTCATTTCTTCTAACTCTA
Found at i:10924 original size:18 final size:20
Alignment explanation
Indices: 10875--10924 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 20
10865 AACCACTTAT
10875 TAGTCATTTCTTCTAACTCTAA
1 TAGTCATTTCTTCTAACTC--A
10897 TTAGTCATTTCTTCTAACTC-
1 -TAGTCATTTCTTCTAACTCA
10917 TA-TCATTT
1 TAGTCATTT
10925 TTTTCCTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.22
19 2 0.07
23 19 0.70
ACGTcount: A:0.24, C:0.22, G:0.04, T:0.50
Consensus pattern (20 bp):
TAGTCATTTCTTCTAACTCA
Found at i:18453 original size:39 final size:39
Alignment explanation
Indices: 18409--18486 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
18399 GTGTGTCACC
*
18409 TTGTTGAGCTAATTGCAAAGTATTGATGAGCTCATGTGA
1 TTGTTGAGCTAATTACAAAGTATTGATGAGCTCATGTGA
** *
18448 TTGTTGAGCTAATTACAGTGTATTGATGGGCTCATGTGA
1 TTGTTGAGCTAATTACAAAGTATTGATGAGCTCATGTGA
18487 GTCGGTGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.26, C:0.10, G:0.27, T:0.37
Consensus pattern (39 bp):
TTGTTGAGCTAATTACAAAGTATTGATGAGCTCATGTGA
Found at i:21304 original size:4 final size:4
Alignment explanation
Indices: 21295--21322 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
21285 TCAAAACAAT
21295 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
21323 AATCCAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:25495 original size:17 final size:17
Alignment explanation
Indices: 25473--25507 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
25463 GTTTAATTTG
25473 TTATTTATTATTATTAT
1 TTATTTATTATTATTAT
*
25490 TTATTTATTTTTATTAT
1 TTATTTATTATTATTAT
25507 T
1 T
25508 ATTGTCATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTTATTATTATTAT
Found at i:25909 original size:17 final size:18
Alignment explanation
Indices: 25869--25915 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
25859 TTCCTTCAAA
25869 CTTCAAATTTT-TCAATT
1 CTTCAAATTTTCTCAATT
25886 CTCTCAAATTTTCTCAATT
1 CT-TCAAATTTTCTCAATT
*
25905 -TTCAAACTTTC
1 CTTCAAATTTTC
25916 AAACCTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 11 0.41
18 10 0.37
19 6 0.22
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (18 bp):
CTTCAAATTTTCTCAATT
Found at i:27213 original size:12 final size:12
Alignment explanation
Indices: 27196--27220 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27186 ATATATACTC
27196 GGGCAATTTGAT
1 GGGCAATTTGAT
27208 GGGCAATTTGAT
1 GGGCAATTTGAT
27220 G
1 G
27221 AGACAATGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.36, T:0.32
Consensus pattern (12 bp):
GGGCAATTTGAT
Found at i:48723 original size:72 final size:72
Alignment explanation
Indices: 48606--48750 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
48596 ATTAAATTAC
48606 TAAAGAGTAAAAGTTCTATAAGGTCTGCCTATAAAACTATGGGTTTACACCCTCCAATAATATTA
1 TAAAGAGTAAAAGTTCTATAAGGTCTGCCTATAAAACTATGGGTTTACACCCTCCAATAATATTA
48671 TGCCACA
66 TGCCACA
48678 TAAAGAGTAAAAGTTCTATAAGGTCTGCCTATAAAACTATGGGTTTACACCCTCCAATAATATTA
1 TAAAGAGTAAAAGTTCTATAAGGTCTGCCTATAAAACTATGGGTTTACACCCTCCAATAATATTA
48743 TGCCACA
66 TGCCACA
48750 T
1 T
48751 CAGATTTTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (72 bp):
TAAAGAGTAAAAGTTCTATAAGGTCTGCCTATAAAACTATGGGTTTACACCCTCCAATAATATTA
TGCCACA
Found at i:49280 original size:16 final size:15
Alignment explanation
Indices: 49254--49284 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49244 AAGTCCTTCA
49254 ATTTTTCTTTTTGCT
1 ATTTTTCTTTTTGCT
*
49269 ATTTTTTTTTTTGCT
1 ATTTTTCTTTTTGCT
49284 A
1 A
49285 CTCTTTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.74
Consensus pattern (15 bp):
ATTTTTCTTTTTGCT
Found at i:49291 original size:15 final size:15
Alignment explanation
Indices: 49261--49299 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
49251 TCAATTTTTC
* *
49261 TTTTTGCTATTTTTT
1 TTTTTGCTACTCTTT
49276 TTTTTGCTACTCTTT
1 TTTTTGCTACTCTTT
*
49291 TGTTTGCTA
1 TTTTTGCTA
49300 TTCTGTTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.13, G:0.10, T:0.69
Consensus pattern (15 bp):
TTTTTGCTACTCTTT
Found at i:60196 original size:48 final size:48
Alignment explanation
Indices: 59878--60183 Score: 372
Period size: 48 Copynumber: 6.4 Consensus size: 48
59868 AGACGCCTTA
* * *
59878 TGCCATCGCTGCCTTCCTC-TCGAGCCTCATCCATATCAGAATCATTTAG
1 TGCCATCACTGCCTTGCTCTTCGA-ACTCATCCATATCAGAATCATTT-G
* * * *
59927 T-CCATCA-TCGTCTTGCTCTTC-AGCCTCATCCATATCAAAATCATTTA
1 TGCCATCACT-GCCTTGCTCTTCGA-ACTCATCCATATCAGAATCATTTG
* *
59974 AGCCATCACTGCCTTGCTCTTCGAACTTATCCATATCAGAATCATTT-
1 TGCCATCACTGCCTTGCTCTTCGAACTCATCCATATCAGAATCATTTG
* * * *
60021 TGGCCATCACTGCTTTGCTCTTCGAACTCATCCATATCAAAATAATCTG
1 T-GCCATCACTGCCTTGCTCTTCGAACTCATCCATATCAGAATCATTTG
*
60070 TGCCATCACTGCCTTGCTCTTCGAACTCATCGATATCAGAATCATTTAG
1 TGCCATCACTGCCTTGCTCTTCGAACTCATCCATATCAGAATCATTT-G
* *
60119 -GCCATCACTGCCTTGCTCTTCGAACTCATCCATATCATAATAATTTG
1 TGCCATCACTGCCTTGCTCTTCGAACTCATCCATATCAGAATCATTTG
60166 TGCCATCACTGCCTTGCT
1 TGCCATCACTGCCTTGCT
60184 TTTGAGCTTC
Statistics
Matches: 224, Mismatches: 24, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
47 2 0.01
48 215 0.96
49 7 0.03
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (48 bp):
TGCCATCACTGCCTTGCTCTTCGAACTCATCCATATCAGAATCATTTG
Found at i:60196 original size:96 final size:97
Alignment explanation
Indices: 59878--60196 Score: 425
Period size: 96 Copynumber: 3.3 Consensus size: 97
59868 AGACGCCTTA
* * * * * *
59878 TGCCATCGCTGCCTTCCTC-TCGAGCCTCATCCATATCAGAATCATTTAGTCCATCA-TCGTCTT
1 TGCCATCACTGCCTTGCTCTTCGAACTTCATCCATATCAGAATCATTTAGGCCATCACT-GCCTT
* * *
59941 GCTCTTC-AGCCTCATCCATATCAAAATCATTTA
65 GCTCTTCGA-ACTCATCCATATCAAAATAATTTG
* * *
59974 AGCCATCACTGCCTTGCTCTTCGAACTT-ATCCATATCAGAATCATTTTGGCCATCACTGCTTTG
1 TGCCATCACTGCCTTGCTCTTCGAACTTCATCCATATCAGAATCATTTAGGCCATCACTGCCTTG
*
60038 CTCTTCGAACTCATCCATATCAAAATAATCTG
66 CTCTTCGAACTCATCCATATCAAAATAATTTG
*
60070 TGCCATCACTGCCTTGCTCTTCGAAC-TCATCGATATCAGAATCATTTAGGCCATCACTGCCTTG
1 TGCCATCACTGCCTTGCTCTTCGAACTTCATCCATATCAGAATCATTTAGGCCATCACTGCCTTG
*
60134 CTCTTCGAACTCATCCATATCATAATAATTTG
66 CTCTTCGAACTCATCCATATCAAAATAATTTG
* *
60166 TGCCATCACTGCCTTGCT-TTTGAGCTTCATC
1 TGCCATCACTGCCTTGCTCTTCGAACTTCATC
60197 TATAACACCA
Statistics
Matches: 197, Mismatches: 21, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
95 6 0.03
96 183 0.93
97 8 0.04
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.34
Consensus pattern (97 bp):
TGCCATCACTGCCTTGCTCTTCGAACTTCATCCATATCAGAATCATTTAGGCCATCACTGCCTTG
CTCTTCGAACTCATCCATATCAAAATAATTTG
Found at i:62341 original size:31 final size:31
Alignment explanation
Indices: 62306--62369 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
62296 TTGTATGTCA
*
62306 TCTAGGCAAACAGTTGTTCTTGAACTTAATC
1 TCTAGGCAAACAATTGTTCTTGAACTTAATC
62337 TCTAGGCAAACAATTGTTCTTGAACTTAATC
1 TCTAGGCAAACAATTGTTCTTGAACTTAATC
62368 TC
1 TC
62370 CTCAAGCTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (31 bp):
TCTAGGCAAACAATTGTTCTTGAACTTAATC
Found at i:62464 original size:24 final size:24
Alignment explanation
Indices: 62437--62485 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
62427 CCGAGTCTGA
62437 CAGTTTTAGTATCGAAGCATATTT
1 CAGTTTTAGTATCGAAGCATATTT
62461 CAGTTTTAGTATCGAAGCATATTT
1 CAGTTTTAGTATCGAAGCATATTT
62485 C
1 C
62486 TGTTGGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (24 bp):
CAGTTTTAGTATCGAAGCATATTT
Found at i:71462 original size:18 final size:18
Alignment explanation
Indices: 71439--71474 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
71429 TGACTGGTGG
*
71439 TGATGATGTGCAAATGAT
1 TGATGATGTGAAAATGAT
71457 TGATGATGTGAAAATGAT
1 TGATGATGTGAAAATGAT
71475 GGGAGATGAC
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:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (18 bp):
TGATGATGTGAAAATGAT
Found at i:71721 original size:135 final size:135
Alignment explanation
Indices: 71479--71721 Score: 355
Period size: 135 Copynumber: 1.8 Consensus size: 135
71469 AATGATGGGA
** * *
71479 GATGACCTTCTGTCTAAAGATGATTCAACTGTAGTGTCGCATGAAAATCCAGAAATGGCGGCGAA
1 GATGACCTTCCATCTAAAGATGATTCAACTGTAGTGTCACATCAAAATCCAGAAATGGCGGCGAA
71544 CCAATTGGATCAGAATTCTATACTGGTTGAAAACAAGGAGGCCATTGGTGAACATAGCCGAATGG
66 CCAATTGGATCAGAATTCTATACTGGTTGAAAACAAGGAGGCCATTGGTGAACATAGCCGAATGG
71609 CAGGC
131 CAGGC
* * * *
71614 GATGACCTTCCATCTGAAGATGATTCAACTGTGGTGTCACATCAAAATCCA-AATATGGTGGTGA
1 GATGACCTTCCATCTAAAGATGATTCAACTGTAGTGTCACATCAAAATCCAGAA-ATGGCGGCGA
* * *
71678 ACCAATTGGATCGGGATGT-TGTACTGGTTGAAAACAAGGAGGCC
65 ACCAATTGGATCAGAAT-TCTATACTGGTTGAAAACAAGGAGGCC
71722 CTTGTCGATG
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
134 2 0.02
135 92 0.97
136 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (135 bp):
GATGACCTTCCATCTAAAGATGATTCAACTGTAGTGTCACATCAAAATCCAGAAATGGCGGCGAA
CCAATTGGATCAGAATTCTATACTGGTTGAAAACAAGGAGGCCATTGGTGAACATAGCCGAATGG
CAGGC
Found at i:72493 original size:5 final size:5
Alignment explanation
Indices: 72483--72508 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
72473 GTAAAGATAA
72483 AATAT AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT A
72509 GGTCCTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Done.