Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011353.1 Corchorus capsularis cultivar CVL-1 contig11374, 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: 45797
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3797 original size:21 final size:23
Alignment explanation
Indices: 3750--3797 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
3740 AACTGTTTTT
**
3750 TTTTTAAAAATCGGAAACCCTAA
1 TTTTTAAAAATCGGAAACAATAA
3773 -TTTTAAAAA-CGGAAA-AATAA
1 TTTTTAAAAATCGGAAACAATAA
3793 TTTTT
1 TTTTT
3798 TTTTTAATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.14
21 10 0.45
22 9 0.41
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.35
Consensus pattern (23 bp):
TTTTTAAAAATCGGAAACAATAA
Found at i:4171 original size:6 final size:6
Alignment explanation
Indices: 4162--4188 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4152 AAAGCAAAGC
4162 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
4189 GCAGATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:5156 original size:10 final size:10
Alignment explanation
Indices: 5141--5165 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5131 GAGGACTCTA
5141 GAATTTTCTG
1 GAATTTTCTG
5151 GAATTTTCTG
1 GAATTTTCTG
5161 GAATT
1 GAATT
5166 AAGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:7009 original size:41 final size:41
Alignment explanation
Indices: 6952--7059 Score: 189
Period size: 41 Copynumber: 2.6 Consensus size: 41
6942 AAGTAAAGTC
* *
6952 TTAATCCAGGGCGATTAAGAAGGTCAAACATAGTTAAGGTT
1 TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
6993 TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
1 TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
*
7034 TTAATCCAAGGCGATTAAGAAAGTCA
1 TTAATCCAGGGCGATTAAGAAAGTCA
7060 GATTAGTCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (41 bp):
TTAATCCAGGGCGATTAAGAAAGTCAAACACAGTTAAGGTT
Found at i:7147 original size:37 final size:37
Alignment explanation
Indices: 7068--7740 Score: 706
Period size: 37 Copynumber: 18.1 Consensus size: 37
7058 CAGATTAGTC
* * *
7068 AAAGAACTTAATTCATGGTGATTAAG-AAAAGCAGTC
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
*
7104 AAAGAACTTAATTCAGGGTAATTAAGTAAGAGCAGTT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
*
7141 AAAGAACTTAATTCAGGGTAATTAAGTAAGAGCAGTT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
*
7178 AAAGAACTTAATTCAGGGTAATTAAGTAAGAGCAGTT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
* *
7215 AAAGACCTTAATTCAGGGTAATTAAGTAAGAGCATGTT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCA-GTT
* *
7253 -AAGAACTTAATTCAGGGCAATTAAGTAAAAGCAGGT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
* *
7289 AAAGAACTTAATTCAAGGTAGTTAAGTAAAGGAGCAGTT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAA--AGCAGTT
* *
7328 -AAGAACTTAATTCAGGGTAGTTAA--AAGGAGCAGTT
1 AAAGAACTTAATTCAGGGTAATTAAGTAA-AAGCAGTT
* * *
7363 -GAGAACTTAATTCAGGGCAATTAAGTAAAAGCAGGT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
* ** ** *
7399 AAAAAACTTAATTCAGGACAATTAAGTAAAAATAGTC
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
* * *
7436 AAA-ATCTTAATTCAGGGCAATTAAGGAAAATAAACATAGTCAGTC
1 AAAGAACTTAATTCAGGGTAATTAA-G----T-AA-A-AG-CAGTT
* * * * *
7481 AAA-ATCTTAATTCAAGG-AAATAAGGTAAAAACAGTC
1 AAAGAACTTAATTCAGGGTAATTAA-GTAAAAGCAGTT
* * * *
7517 AAAGGAGCTTAATTCAGGGAAATTAAGTAAACA-CGGTC
1 AAA-GAACTTAATTCAGGGTAATTAAGTAAA-AGCAGTT
*
7555 AAAGAACTTAATTCAGGGTAATTAAGTAAAGAACAGTT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAA-AGCAGTT
**
7593 -AAGAACTTAATTCAGGACAATTAAGTAAAAGCAGTT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
* *
7629 -AAGAACTTAATTCAGGATAATCAAGTAAAAGCAGTT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
7665 -AAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
* * * *
7701 GAAGGACTTAAATCAGGGTAATTAAGTAAAAACAGTT
1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
7738 AAA
1 AAA
7741 AGGTAAGGAT
Statistics
Matches: 559, Mismatches: 54, Indels: 47
0.85 0.08 0.07
Matches are distributed among these distances:
35 28 0.05
36 135 0.24
37 295 0.53
38 54 0.10
39 14 0.03
40 1 0.00
41 1 0.00
42 2 0.00
43 1 0.00
44 8 0.01
45 20 0.04
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (37 bp):
AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
Found at i:7807 original size:41 final size:40
Alignment explanation
Indices: 7753--7965 Score: 249
Period size: 41 Copynumber: 5.3 Consensus size: 40
7743 GTAAGGATAG
*
7753 GCACAGACATAATTTCAAGGAAGGAAATTAGGTAAAGACAA
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-CAA
* * * * *
7794 TCATAGACTTAA-TTC--GG--GGTAATTAAGTAAAGTAA
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGCAA
7829 GCACAGACTTAATTTC-AGTGAAGGAAATTAGGTAAAGCAAA
1 GCACAGACTTAATTTCAAG-GAAGGAAATTAGGTAAAGC-AA
* *
7870 GCACCGACTTAATTTCAGGGAAGGAAATTAGGTAAAGCAAA
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGC-AA
*
7911 GCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGCAA
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA-GCAA
*
7952 GCACATACTTAATT
1 GCACAGACTTAATT
7966 CAGGGTAATT
Statistics
Matches: 146, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
35 12 0.08
36 16 0.11
37 1 0.01
38 3 0.02
40 16 0.11
41 95 0.65
42 3 0.02
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (40 bp):
GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGCAA
Found at i:7938 original size:82 final size:78
Alignment explanation
Indices: 7753--8002 Score: 264
Period size: 82 Copynumber: 3.2 Consensus size: 78
7743 GTAAGGATAG
* * * *
7753 GCACAGACATAATTTCAAGGAAGGAAATTAGGTAAAG-ACAATCATAGACTTAATTC--GGGGTA
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGCA-AAGCACAGACTTAATTCAGGGGGAA
*
7815 ATTAAGTAAAGTAA
65 ATTAAGTAAAGAAA
*
7829 GCACAGACTTAATTTC-AGTGAAGGAAATTAGGTAAAGCAAAGCACCGACTTAATTTCAGGGAAG
1 GCACAGACTTAATTTCAAG-GAAGGAAATTAGGTAAAGCAAAGCACAGACTTAA-TTCAGGG--G
*
7893 GAAATTAGGTAAAGCAAA
62 GAAATTAAGTAAAG-AAA
* * *
7911 GCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGGC-AAGCACATACTTAATTCA--GGGTA
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAA-GCAAAGCACAGACTTAATTCAGGGGGAA
**
7973 ATTAAGTAAA-TTA
65 ATTAAGTAAAGAAA
*
7986 GCAAAGACTTAATTTCA
1 GCACAGACTTAATTTCA
8003 TAAGAATTAA
Statistics
Matches: 149, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
75 19 0.13
76 44 0.30
77 16 0.11
79 3 0.02
81 17 0.11
82 46 0.31
83 4 0.03
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (78 bp):
GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGCAAAGCACAGACTTAATTCAGGGGGAAA
TTAAGTAAAGAAA
Found at i:8048 original size:36 final size:36
Alignment explanation
Indices: 7972--8057 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 36
7962 AATTCAGGGT
* * *
7972 AATTAAGT-AAATTAGCAAAGACTTAATTTCATAAG
1 AATTAAGTAAAATCATCAAAGACTTAATTCCATAAG
*
8007 AATTAATTAAAATCATCAAAGACTTAA-TCCA-AAG
1 AATTAAGTAAAATCATCAAAGACTTAATTCCATAAG
*
8041 ATGATTAAGTAAGATCA
1 A--ATTAAGTAAAATCA
8058 GAGAAAAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
34 4 0.10
35 10 0.24
36 28 0.67
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (36 bp):
AATTAAGTAAAATCATCAAAGACTTAATTCCATAAG
Found at i:8185 original size:37 final size:37
Alignment explanation
Indices: 8080--8525 Score: 592
Period size: 37 Copynumber: 12.2 Consensus size: 37
8070 AACTCCGGGG
* * *
8080 ATTAAGTAAAGAAAAGGACTT-AGTTCAAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGA-TTCCAAGGAAGGGA
*
8117 ATTAAGT----T-AAGGTCTT-AGTTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGA-TTCCAAGGAAGGGA
*
8149 ATTGAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
*
8186 ATTAAGTAGAGCT-AAGGACTTGGTTCCAAGGAAGGGA
1 ATTAAGTAGAG-TAAAGGACTTGATTCCAAGGAAGGGA
* *
8223 ATTAAGTGGAGTAGAGGACTT-AGTTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGA-TTCCAAGGAAGGGA
*
8260 ATTAAGTAGAATAAAGGACTTGATTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
8297 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
*
8334 ATTAAGTAGAGCT-AAGGACTTGGTTCCAAGGAAGGGA
1 ATTAAGTAGAG-TAAAGGACTTGATTCCAAGGAAGGGA
8371 ATTAAGTAGAGTAAAGGACTTGA-TCCAAAGGAAGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCC-AAGGAAGGGA
* *
8408 ATTAAGTAGAGTTAAGGACTTGATTGCAAGGAA-GGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
*
8444 ATTAAGTAGAAGTAGAGGACTTGATTCCAAGGAAGGGA
1 ATTAAGTAG-AGTAAAGGACTTGATTCCAAGGAAGGGA
* * * *
8482 ATTAAGTAGAGTTAAGGACTTAATTTCAAGGAAGGAA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
8519 ATTAAGT
1 ATTAAGT
8526 CAAGTTAGGG
Statistics
Matches: 367, Mismatches: 26, Indels: 32
0.86 0.06 0.08
Matches are distributed among these distances:
32 28 0.08
36 18 0.05
37 303 0.83
38 18 0.05
ACGTcount: A:0.40, C:0.08, G:0.30, T:0.23
Consensus pattern (37 bp):
ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGA
Found at i:8563 original size:32 final size:32
Alignment explanation
Indices: 8522--8589 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
8512 GAAGGAAATT
8522 AAGTCAAGTTAGGGACTTAATTCAGGGTAATG
1 AAGTCAAGTTAGGGACTTAATTCAGGGTAATG
* *
8554 AAGTCAAGTTAGGGACTTAGTTCAGGGTAATT
1 AAGTCAAGTTAGGGACTTAATTCAGGGTAATG
8586 AAGT
1 AAGT
8590 AGTGTCAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (32 bp):
AAGTCAAGTTAGGGACTTAATTCAGGGTAATG
Found at i:8614 original size:36 final size:35
Alignment explanation
Indices: 8535--8718 Score: 155
Period size: 36 Copynumber: 5.2 Consensus size: 35
8525 TCAAGTTAGG
* **
8535 GACTTAATTCAGGGTAATGAAGTCA-AGT---TAGG
1 GACTTAATTCAGGGTAATTAAGT-AGAGTCAATAAA
* *
8567 GACTTAGTTCAGGGTAATTAAGTAGTGTCAATAAAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAAT-AAA
*
8603 GACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA
* ** **
8638 GAACTTAATCTAAAAG-AGATTAAGTA-AAACAATAAAA
1 G-ACTTAAT-TCAGGGTA-ATTAAGTAGAGTCAAT-AAA
*
8675 GACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA
8710 GAACTTAAT
1 G-ACTTAAT
8719 CTAAAAATAG
Statistics
Matches: 120, Mismatches: 20, Indels: 20
0.75 0.12 0.12
Matches are distributed among these distances:
31 1 0.01
32 23 0.19
35 19 0.16
36 63 0.52
37 14 0.12
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (35 bp):
GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA
Found at i:8679 original size:72 final size:73
Alignment explanation
Indices: 8595--8753 Score: 293
Period size: 72 Copynumber: 2.2 Consensus size: 73
8585 TAAGTAGTGT
8595 CAATAAAAGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCT-AAAAGAGATT
1 CAATAAAAGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATT
8659 AAGTAAAA
66 AAGTAAAA
*
8667 CAATAAAAGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAATAGATT
1 CAATAAAAGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATT
8732 AAGTAAAA
66 AAGTAAAA
8740 CAATAAAAGGACTT
1 CAATAAAA-GACTT
8754 GATTTATAAA
Statistics
Matches: 84, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
72 54 0.64
73 25 0.30
74 5 0.06
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (73 bp):
CAATAAAAGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGAGATT
AAGTAAAA
Found at i:16383 original size:19 final size:18
Alignment explanation
Indices: 16359--16395 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
16349 TTAAAGATTT
16359 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
16378 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
16396 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:21331 original size:9 final size:8
Alignment explanation
Indices: 21297--21330 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
21287 GAATCGGTTA
21297 TGAATTTT
1 TGAATTTT
*
21305 TGAAGTTTC
1 TGAA-TTTT
21314 TGAATTTT
1 TGAATTTT
21322 TGAATTTT
1 TGAATTTT
21330 T
1 T
21331 TTCAAGGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:33818 original size:200 final size:200
Alignment explanation
Indices: 33470--33878 Score: 782
Period size: 200 Copynumber: 2.0 Consensus size: 200
33460 ATTATTCGGT
*
33470 TTAATTATAATTATAATTAAGAAGTTGATATCAGGCCGCCTATTAACATCCAGCCGTAAGGTAGA
1 TTAA-TATAATTATAATTAAGAAGTTGATATCAGGCCGCCTATTAACATCCAGCCGTAAGATAGA
33535 TCAGCCGCTACACAAATAATATAACAACTTAATTCACTTTGACAATCTCATATATAGATATATAC
65 TCAGCCGCTACACAAATAATATAACAACTTAATTCACTTTGACAATCTCATATATAGATATATAC
*
33600 TTTTACACATCTGATAAGAAAGTTTCATTTGATCGATTATTTAATTTTGGGCAGATTCTTTTTCA
130 TTTTACACATCTGATAAGAAAGTTTCATTTGATCGATTATTTAATTTTGGACAGATTCTTTTTCA
33665 TGAATA
195 TGAATA
33671 TTAATATAATTATAATTAAGAAGTTGATATCAGGCCGCCTATTAACATCCAGCCGTAAGATAGAT
1 TTAATATAATTATAATTAAGAAGTTGATATCAGGCCGCCTATTAACATCCAGCCGTAAGATAGAT
33736 CAGCCGCTACACAAATAATATAACAACTTAATTCACTTTGACAATCTCATATATAGATATATACT
66 CAGCCGCTACACAAATAATATAACAACTTAATTCACTTTGACAATCTCATATATAGATATATACT
33801 TTTACACATCTGATAAGAAAGTTTCATTTGATCGATTATTTAATTTTGGACAGATTCTTTTTCAT
131 TTTACACATCTGATAAGAAAGTTTCATTTGATCGATTATTTAATTTTGGACAGATTCTTTTTCAT
*
33866 GAGTA
196 GAATA
33871 TTAATATA
1 TTAATATA
33879 TAATTTTATA
Statistics
Matches: 205, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
200 201 0.98
201 4 0.02
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (200 bp):
TTAATATAATTATAATTAAGAAGTTGATATCAGGCCGCCTATTAACATCCAGCCGTAAGATAGAT
CAGCCGCTACACAAATAATATAACAACTTAATTCACTTTGACAATCTCATATATAGATATATACT
TTTACACATCTGATAAGAAAGTTTCATTTGATCGATTATTTAATTTTGGACAGATTCTTTTTCAT
GAATA
Found at i:38984 original size:13 final size:13
Alignment explanation
Indices: 38976--39039 Score: 69
Period size: 15 Copynumber: 4.8 Consensus size: 13
38966 ACTATAGTAT
38976 TATTATATATATA
1 TATTATATATATA
38989 TATATAATATATATA
1 TAT-T-ATATATATA
*
39004 TATTATAGA-ATA
1 TATTATATATATA
39016 TATGCTATATATATA
1 TAT--TATATATATA
39031 TA-TATATAT
1 TATTATATAT
39040 GTAAGCGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
12 13 0.30
13 7 0.16
14 7 0.16
15 17 0.39
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (13 bp):
TATTATATATATA
Found at i:38986 original size:2 final size:2
Alignment explanation
Indices: 38979--39039 Score: 74
Period size: 2 Copynumber: 31.5 Consensus size: 2
38969 ATAGTATTAT
*
38979 TA TA TA TA TA TA TA TA -A TA TA TA TA TA T- TA TA GA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
39018 TGC TA TA TA TA TA TA TA TA TA T
1 T-A TA TA TA TA TA TA TA TA TA T
39040 GTAAGCGAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
1 3 0.06
2 48 0.92
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Done.