Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023751.1 Corchorus olitorius cultivar O-4 contig23784, 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: 57174
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1652 original size:16 final size:16
Alignment explanation
Indices: 1631--1665 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1621 TCTGAAAATA
1631 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
1647 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
1663 CTT
1 CTT
1666 TCTGAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:2742 original size:4 final size:5
Alignment explanation
Indices: 2703--2792 Score: 52
Period size: 5 Copynumber: 19.0 Consensus size: 5
2693 AAATATTTTC
* *
2703 TTATA TTATA TT-TA -TACA TTATA -TATA TTATA TTAT- TTATA -AAT-
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * *
2747 TTATAA ATATAA TAATA TTATA TTTATA TTATA --ATA CTATA TTATA
1 TTAT-A TTAT-A TTATA TTATA -TTATA TTATA TTATA TTATA TTATA
2793 AATATTATCT
Statistics
Matches: 66, Mismatches: 9, Indels: 20
0.69 0.09 0.21
Matches are distributed among these distances:
3 4 0.06
4 15 0.23
5 35 0.53
6 12 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (5 bp):
TTATA
Found at i:2775 original size:11 final size:11
Alignment explanation
Indices: 2703--2779 Score: 54
Period size: 11 Copynumber: 6.9 Consensus size: 11
2693 AAATATTTTC
2703 TTATATTATAT
1 TTATATTATAT
2714 TTATACATTATA-
1 TTAT--ATTATAT
2726 -TATATTATA-
1 TTATATTATAT
2735 TTAT-TTATAAAT
1 TTATATTAT--AT
* *
2747 TTATAAATATAA
1 TTAT-ATTATAT
*
2759 TAATATTATAT
1 TTATATTATAT
2770 TTATATTATA
1 TTATATTATA
2780 ATACTATATT
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
9 10 0.19
10 3 0.06
11 22 0.42
12 8 0.15
13 6 0.12
14 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATATTATAT
Found at i:2797 original size:22 final size:21
Alignment explanation
Indices: 2747--2825 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 21
2737 ATTTATAAAT
* *
2747 TTATAAATATAATAATATTATA
1 TTAT-AATATTATAATACTATA
2769 TT-T-ATATTATAATACTATA
1 TTATAATATTATAATACTATA
*
2788 TTATAAATATTATCTATACTA-A
1 TTAT-AATATTAT-AATACTATA
2810 TCTATAATATATATAA
1 T-TATAATAT-TATAA
2826 AAGTACGAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
19 16 0.34
20 1 0.02
21 1 0.02
22 17 0.36
23 12 0.26
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATAATATTATAATACTATA
Found at i:3932 original size:64 final size:64
Alignment explanation
Indices: 3831--3957 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
3821 GTATTAACGA
*
3831 ATTGGGTCTAAAAATATCAGATTTAGGCTTCAAGACATCTAGCTTGGCAATTTGGGTTTCATGT
1 ATTGGGTCTAAAAATATCAGATTTAGACTTCAAGACATCTAGCTTGGCAATTTGGGTTTCATGT
3895 ATTGGGTCTAAAAATATCAGATTTAGACTTCAAGACATCTAGCTTGGCAATTTGGGTTTCATG
1 ATTGGGTCTAAAAATATCAGATTTAGACTTCAAGACATCTAGCTTGGCAATTTGGGTTTCATG
3958 AACTCAAACG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35
Consensus pattern (64 bp):
ATTGGGTCTAAAAATATCAGATTTAGACTTCAAGACATCTAGCTTGGCAATTTGGGTTTCATGT
Found at i:8764 original size:218 final size:218
Alignment explanation
Indices: 8316--9297 Score: 1360
Period size: 218 Copynumber: 4.5 Consensus size: 218
8306 TGAGGCATAC
* *
8316 GCAAAATTCAGCATCCCCAAAGTGATATACTTTATACCCAAATCATTTCTCATCATTCCCAAATA
1 GCAAAATTCAGTATCCCCAAAGTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATA
* * * ** *
8381 ATCATAAGCACCAT-TCCCAAATTCATTCGAGATTGGGATTTTTTCTTATATATCCAAAATTGGC
66 ATCATATGCACCATCT-CCAAATTCTTTAGAGATTGACA-TTTTT-TTATATACCCAAAATTGGC
* ** * *
8445 TTCAAACGTTCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATGAATTT
128 TTTAAACGTGATTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCAGTCTAAATGAATTT
* *
8510 AGTGTCATGTAATAATTAAACAAAAT
193 AGTGCCATCTAATAATTAAACAAAAT
* * *
8536 GCAAAATTCAGTATCCCCAAACTGATATACTGTATACCCATATCATTTCTCATCATCCCCAAATA
1 GCAAAATTCAGTATCCCCAAAGTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATA
* * ** *
8601 ATCATATGCACCATCTTCAAATTTTTTAGAGATTGACATTTTTTTATATGTCCAAAATTGACTTT
66 ATCATATGCACCATCTCCAAATTCTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTT
*
8666 AAACGTGATTTAATCCATATTTTCATCCTAATTAATTGAATAAACGCAGTCTAAATGAATTTAGT
131 AAACGTGATTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCAGTCTAAATGAATTTAGT
8731 GCCATCTAATAATTAAACAAAAT
196 GCCATCTAATAATTAAACAAAAT
* * *
8754 GCAAAATTCAGTATCCCCAAAGTGATATATTTTATACCCAAATCATTTCTCATCATCCTCACATA
1 GCAAAATTCAGTATCCCCAAAGTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATA
* * * * * * *
8819 ATCCTATGTATCATCCCCAAATTCTTTAGAGATTGCCATTTTTTTATATACCCAAATTTGGGTTT
66 ATCATATGCACCATCTCCAAATTCTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTT
* *
8884 AAACATGTTTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCAGTCTAAATGAATTTAGT
131 AAACGTGATTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCAGTCTAAATGAATTTAGT
*
8949 GCCATCTAATATTTAAA-AGAAAT
196 GCCATCTAATAATTAAACA-AAAT
* * *
8972 GCAAAATTCAGTATCCCGAAAGTAATATACTTTATACCCAAATCATTTCTCATCATCCCCATATA
1 GCAAAATTCAGTATCCCCAAAGTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATA
* * * *
9037 ATCATATGCACTATCCCCAAATTCTTTAGAGATTGAC-CTTTTTTATATACCCAAAATTGGGTTT
66 ATCATATGCACCATCTCCAAATTCTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTT
* * *
9101 AAACGT-ATTTTAATCCATATTTTCATCCTAATTAATTGAATAGACCCTGTCTATATGAATTTAG
131 AAACGTGA-TTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCAGTCTAAATGAATTTAG
* * **
9165 TGTCTTCTAATGGTTAAACAAAAT
195 TGCCATCTAATAATTAAACAAAAT
* ** * * *
9189 ACAAAATTCAGTATCATCAAATTGACATACTTTATACCCAACTCATTTCTCATCATCCCCAAATA
1 GCAAAATTCAGTATCCCCAAAGTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATA
* *
9254 ATTATATGCACCATCTCCAAATTCTTTCGAGATTGACATTTTTT
66 ATCATATGCACCATCTCCAAATTCTTTAGAGATTGACATTTTTT
9298 GTACTTACTT
Statistics
Matches: 678, Mismatches: 79, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
217 191 0.28
218 392 0.58
219 5 0.01
220 89 0.13
221 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.36
Consensus pattern (218 bp):
GCAAAATTCAGTATCCCCAAAGTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATA
ATCATATGCACCATCTCCAAATTCTTTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTT
AAACGTGATTTAATCCATATTTTCATCCTAATTAATTGAATAAACCCAGTCTAAATGAATTTAGT
GCCATCTAATAATTAAACAAAAT
Found at i:9928 original size:16 final size:16
Alignment explanation
Indices: 9909--9947 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
9899 AAGAAATGGT
9909 TAAAAAAAATAGAGAA
1 TAAAAAAAATAGAGAA
* *
9925 TAAAAATATTAGAGAA
1 TAAAAAAAATAGAGAA
9941 -AAAAAAA
1 TAAAAAAA
9948 TAATAAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (16 bp):
TAAAAAAAATAGAGAA
Found at i:15081 original size:19 final size:19
Alignment explanation
Indices: 15044--15083 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
15034 GAAAACAATT
*
15044 AACAAAAAAACAGTGAATA
1 AACAAAAAAACAATGAATA
* *
15063 AACAAGAAAACAATTAATA
1 AACAAAAAAACAATGAATA
15082 AA
1 AA
15084 AACCTCCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.10, G:0.07, T:0.12
Consensus pattern (19 bp):
AACAAAAAAACAATGAATA
Found at i:19393 original size:258 final size:256
Alignment explanation
Indices: 18917--19423 Score: 924
Period size: 258 Copynumber: 2.0 Consensus size: 256
18907 TTCGTGCAAA
* *
18917 AAACTAAGCTCCGTGCTTATTCTCTCTGGCCCTGCGCCACTTTCTGCAGCAACCCTGCAAAATCT
1 AAACTAAGCTCCATGCTTATTCTCTCTGGCCCTACGCCACTTTCTGCAGCAACCCTGCAAAATCT
*
18982 ATCTTTTTTCAACACGAGTCAGCATCATTCTTCAATTTTTCTCAACTTCAATTTCGTCTCAGGAC
66 ATCTTTTTTCAACACGAGTCAGCATCATTCTTCAATTTTTCTCAACTTCAATTTCGTCTCAAGAC
*
19047 GTTAAATCAACTCTCTGCGAGTTTTTCTTCTCTTTCAATTTCGTCTCAAGACGTTAAACATTTAA
131 GTTAAATCAACTCTCTGCGAGTTTTTCTTCTCTTTCAATCTCGTCTCAAGACGTTAAACATTTAA
*
19112 TTTTCTGTTTTTCATATGAATAACAACCAGCTTGTTATTTCAATCTCTTTTTCTTAGGAAG
196 TTTTCTGTTTTTCATATGAATAACAACCAGCTTGTAATTTCAATCTCTTTTTCTTAGGAAG
19173 AAACTAAGCTCCATGCTTATTTTCTCTCTGGCCCTACGCCACTTTCTGCAGCAACCCTGCAAAAT
1 AAACTAAGCTCCATGCTTA--TTCTCTCTGGCCCTACGCCACTTTCTGCAGCAACCCTGCAAAAT
* * *
19238 CTATCTTTTTTCCACACGAGTCAGCCTCGTTCTTCAATTTTTCTCAACTTCAATTTCGTCTCAAG
64 CTATCTTTTTTCAACACGAGTCAGCATCATTCTTCAATTTTTCTCAACTTCAATTTCGTCTCAAG
19303 ACGTTAAATCAACTCTCTGCGAGTTTTTCTTCTCTTTCAATCTCGTCTCAAGACGTTAAACATTT
129 ACGTTAAATCAACTCTCTGCGAGTTTTTCTTCTCTTTCAATCTCGTCTCAAGACGTTAAACATTT
19368 AATTTTCTGTTTTTCATATGAATAACAACCAGCTTGTAATTTCAATCTCTTTTTCT
194 AATTTTCTGTTTTTCATATGAATAACAACCAGCTTGTAATTTCAATCTCTTTTTCT
19424 CAGCAAAAAA
Statistics
Matches: 241, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
256 18 0.07
258 223 0.93
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (256 bp):
AAACTAAGCTCCATGCTTATTCTCTCTGGCCCTACGCCACTTTCTGCAGCAACCCTGCAAAATCT
ATCTTTTTTCAACACGAGTCAGCATCATTCTTCAATTTTTCTCAACTTCAATTTCGTCTCAAGAC
GTTAAATCAACTCTCTGCGAGTTTTTCTTCTCTTTCAATCTCGTCTCAAGACGTTAAACATTTAA
TTTTCTGTTTTTCATATGAATAACAACCAGCTTGTAATTTCAATCTCTTTTTCTTAGGAAG
Found at i:22178 original size:19 final size:18
Alignment explanation
Indices: 22156--22207 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
22146 GGGCTGAAAT
22156 TAATTGATTATTAAATAAA
1 TAATT-ATTATTAAATAAA
* * *
22175 TAATTATTATTTTATTGAA
1 TAATTATTA-TTAAATAAA
22194 TAATTATTATTAAA
1 TAATTATTATTAAA
22208 AATCCCATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TAATTATTATTAAATAAA
Found at i:22189 original size:23 final size:22
Alignment explanation
Indices: 22163--22205 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
22153 AATTAATTGA
22163 TTATTAAATAAATAATTATTATT
1 TTATTAAAT-AATAATTATTATT
* *
22186 TTATTGAATAATTATTATTA
1 TTATTAAATAATAATTATTA
22206 AAAATCCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATTAAATAATAATTATTATT
Found at i:23671 original size:51 final size:50
Alignment explanation
Indices: 23570--23675 Score: 119
Period size: 51 Copynumber: 2.1 Consensus size: 50
23560 ATACTTCATA
* **
23570 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
*
23620 TTTTCTCTTGTTTCA-ATCTTGTCTCTGGACATAT-AAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACA-ATCAAACACTCGTACA-GTGT
23671 TTTTC
1 TTTTC
23676 ATTCAGAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
50 7 0.15
51 38 0.79
52 3 0.06
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Found at i:27457 original size:21 final size:20
Alignment explanation
Indices: 27431--27475 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
27421 TAATTTTGTG
*
27431 TTTTGCGTCAAAGAAAAAAAA
1 TTTTGCGCCAAA-AAAAAAAA
*
27452 TTTTGCGCCATAAAAAAAAA
1 TTTTGCGCCAAAAAAAAAAA
27472 TTTT
1 TTTT
27476 TTTTTTGTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (20 bp):
TTTTGCGCCAAAAAAAAAAA
Found at i:30422 original size:16 final size:15
Alignment explanation
Indices: 30384--30425 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
30374 ACAGAGATTG
*
30384 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
30399 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
30414 ACTAGAAAACAA
1 AC-AGAAAACAA
30426 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:31203 original size:11 final size:11
Alignment explanation
Indices: 31187--31212 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31177 CCTTTGCCTA
31187 AAAACTAGAAG
1 AAAACTAGAAG
31198 AAAACTAGAAG
1 AAAACTAGAAG
31209 AAAA
1 AAAA
31213 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:32556 original size:21 final size:21
Alignment explanation
Indices: 32513--32562 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
32503 CGCCCATTCA
**
32513 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
32534 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
32555 CCGAGCCA
1 CCGTGCCA
32563 TCGCCATTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.48, G:0.24, T:0.10
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:33182 original size:16 final size:16
Alignment explanation
Indices: 33161--33193 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33151 CATGCATCAT
33161 AATCTTAATATATGCC
1 AATCTTAATATATGCC
33177 AATCTTAATATATGCC
1 AATCTTAATATATGCC
33193 A
1 A
33194 TAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (16 bp):
AATCTTAATATATGCC
Found at i:35090 original size:11 final size:11
Alignment explanation
Indices: 35074--35099 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35064 GTTTTAGATA
35074 TTTTCTTCTAG
1 TTTTCTTCTAG
35085 TTTTCTTCTAG
1 TTTTCTTCTAG
35096 TTTT
1 TTTT
35100 TTAGGCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:48256 original size:5 final size:5
Alignment explanation
Indices: 48246--48278 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
48236 TTCCCTCCCA
*
48246 TTTCC TTTCC TTTCC TTTCC TTCCC TTTCC TTT
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTT
48279 AATTACTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTCC
Found at i:48525 original size:13 final size:13
Alignment explanation
Indices: 48507--48532 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48497 CTTGGCATGA
48507 GTGATGATTTTTG
1 GTGATGATTTTTG
48520 GTGATGATTTTTG
1 GTGATGATTTTTG
48533 TTGCTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:50119 original size:18 final size:18
Alignment explanation
Indices: 50073--50122 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
50063 GGTTTTAGGC
50073 AGATATCACTCATCTC-A
1 AGATATCACTCATCTCAA
*
50090 A-A-ACCA-TC-TCTCAA
1 AGATATCACTCATCTCAA
50104 AGATATCACTCATCTCAA
1 AGATATCACTCATCTCAA
50122 A
1 A
50123 AACCAGCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
13 4 0.15
14 4 0.15
15 4 0.15
16 4 0.15
17 3 0.12
18 7 0.27
ACGTcount: A:0.40, C:0.30, G:0.04, T:0.26
Consensus pattern (18 bp):
AGATATCACTCATCTCAA
Found at i:50348 original size:51 final size:50
Alignment explanation
Indices: 50243--50348 Score: 110
Period size: 51 Copynumber: 2.1 Consensus size: 50
50233 GCTCTTCATA
* ** *
50243 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGC
*
50293 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACT-GTACACGTGC
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGC
50344 TTTTC
1 TTTTC
50349 ATTTAGAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
50 9 0.19
51 37 0.79
52 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGC
Found at i:55062 original size:2 final size:2
Alignment explanation
Indices: 55055--55091 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
55045 CATTTCATGC
55055 AT AT AT AT AT AT AT 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 AT AT AT A
55092 CACAAACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.