Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022687.1 Corchorus olitorius cultivar O-4 contig22720, 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: 60990
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--48 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC TC TC
1 TC TC TC
49 CAATTGTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3876 original size:13 final size:13
Alignment explanation
Indices: 3851--3901 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
3841 AGGAACTATT
3851 TTAATACTGTTTTA
1 TTAATA-TGTTTTA
3865 TTAATATGTTTTA
1 TTAATATGTTTTA
3878 -TAA-ATGGTTTTA
1 TTAATAT-GTTTTA
* *
3890 ATAAAATGTTTT
1 TTAATATGTTTT
3902 GGGTGCATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.26
13 15 0.44
14 8 0.24
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (13 bp):
TTAATATGTTTTA
Found at i:8660 original size:33 final size:33
Alignment explanation
Indices: 8623--8692 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
8613 AGCAAAACAA
8623 AGAACTAAAGAAAAAAACTAGAGAAAACTTAGG
1 AGAACTAAAGAAAAAAACTAGAGAAAACTTAGG
8656 AGAACTAAAGAAAAAAACTAGAGAAAACTTAGG
1 AGAACTAAAGAAAAAAACTAGAGAAAACTTAGG
8689 AGAA
1 AGAA
8693 AGGAGGGGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.61, C:0.09, G:0.19, T:0.11
Consensus pattern (33 bp):
AGAACTAAAGAAAAAAACTAGAGAAAACTTAGG
Found at i:9717 original size:46 final size:49
Alignment explanation
Indices: 9600--9719 Score: 142
Period size: 48 Copynumber: 2.5 Consensus size: 49
9590 CTTACCCAAT
* *
9600 AAAGTCCAAAACACATGCAACATAT-GTGCAACACTCTCAACAATAGCA
1 AAAGCCCAAAACACATGCAACACATAGTGCAACACTCTCAACAATAGCA
* * *
9648 AAAGTCCAAAACACATGCAACACATAG-GCAACATTCTCAA-AGT-GACA
1 AAAGCCCAAAACACATGCAACACATAGTGCAACACTCTCAACAATAG-CA
*
9695 AAA-CCCAAAACACATGTAACACATA
1 AAAGCCCAAAACACATGCAACACATA
9720 CTTTCTTATA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
46 21 0.32
47 7 0.11
48 36 0.55
49 1 0.02
ACGTcount: A:0.48, C:0.27, G:0.10, T:0.15
Consensus pattern (49 bp):
AAAGCCCAAAACACATGCAACACATAGTGCAACACTCTCAACAATAGCA
Found at i:10621 original size:28 final size:28
Alignment explanation
Indices: 10584--10652 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
10574 CCTAGGGGAT
*
10584 ATTCTAGTCATTTTGCACATCCAGGGGC
1 ATTCTGGTCATTTTGCACATCCAGGGGC
** *
10612 ATTCTGGTCA-TTTGCATGTTCAGGGGC
1 ATTCTGGTCATTTTGCACATCCAGGGGC
*
10639 ATTTTGGTCATTTT
1 ATTCTGGTCATTTT
10653 AGGTTCACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 23 0.66
28 12 0.34
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (28 bp):
ATTCTGGTCATTTTGCACATCCAGGGGC
Found at i:10954 original size:29 final size:29
Alignment explanation
Indices: 10912--10970 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
10902 AAGTGGAGAG
10912 TTGTATTTATTTATCAAGTAAGCCATTTT
1 TTGTATTTATTTATCAAGTAAGCCATTTT
*
10941 TTGTATTTATTTATTAAGTAAGCCATTTT
1 TTGTATTTATTTATCAAGTAAGCCATTTT
10970 T
1 T
10971 CATTTTTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.54
Consensus pattern (29 bp):
TTGTATTTATTTATCAAGTAAGCCATTTT
Found at i:13146 original size:169 final size:169
Alignment explanation
Indices: 12858--13641 Score: 1098
Period size: 169 Copynumber: 4.7 Consensus size: 169
12848 TCCATATAAG
* * * * *
12858 TTAAG-TTACAATCCTTGGTCAAGGTCACT-TGTCAGAGTTTACATTGGTAAGTCCTCCGGGCAC
1 TTAAGTTTAAAATCCTTGTTCAAGGTCTCTATTTAAGAGTTTACATTGGTAAGTCCTCCGGGCAC
12921 AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGT
66 AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGT
* *
12986 ACCATTTGATTTCATCAAGTTTTTCATCAAAAGTTCATGT
131 ACCATTTCATTTCATCAAG-TTTTCATCAAAAATTCATGT
* * *
13026 TTAAGTTTAAAATCCTTGTTTAAGGTCTCAATTTAAG-GTTTGCATTGGTAAGTCCTCCGGGCAC
1 TTAAGTTTAAAATCCTTGTTCAAGGTCTCTATTTAAGAGTTTACATTGGTAAGTCCTCCGGGCAC
13090 AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGT
66 AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGT
* * * *
13155 ACCATTTCATTTGATCGAGTTTTTCATTAAAAATTCATAT
131 ACCATTTCATTTCATCAAG-TTTTCATCAAAAATTCATGT
* * *
13195 TTAAGTTTAAAATCTTTGGTCAAGGTCTCTA-TTCAGAGTTTACATTGGTATA-TCCTCCGGGCA
1 TTAAGTTTAAAATCCTTGTTCAAGGTCTCTATTTAAGAGTTTACATTGGTA-AGTCCTCCGGGCA
* * **
13258 CAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAGCCTTTGGG
65 CAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGG
* * * * *
13323 TATCATTTCATTTTATCAAGTTCTCATTAAAGATTCATGT
130 TACCATTTCATTTCATCAAGTTTTCATCAAAAATTCATGT
* * * **
13363 TTAAGTTTAAAATCCTTGTTTAAGGT-TCCTTTTTCAGAGTTCGCATTGGTAAGTCCTCCGGGCA
1 TTAAGTTTAAAATCCTTGTTCAAGGTCT-CTATTTAAGAGTTTACATTGGTAAGTCCTCCGGGCA
* * * * * *
13427 CAAATTCTGAAACCTTCGGGTATTAATTCTGATAAGTCCTCCGAGTAATTGATAAAACATCCAGG
65 CAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGG
*
13492 TACCATTTCATTTCATCGAGTTTTCATCAAAAATTCATGT
130 TACCATTTCATTTCATCAAGTTTTCATCAAAAATTCATGT
*
13532 TTAAGTTTAAAATCCTTAG-TCAAGGTCTCTATTCAA-AGTTTACATTGGTAAGTCCTCCGGGCA
1 TTAAGTTTAAAATCCTT-GTTCAAGGTCTCTATTTAAGAGTTTACATTGGTAAGTCCTCCGGGCA
* *
13595 CAATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCTGGCA
65 CAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCA
13642 GTTCATATTT
Statistics
Matches: 543, Mismatches: 64, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
167 1 0.00
168 118 0.22
169 417 0.77
170 7 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (169 bp):
TTAAGTTTAAAATCCTTGTTCAAGGTCTCTATTTAAGAGTTTACATTGGTAAGTCCTCCGGGCAC
AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGT
ACCATTTCATTTCATCAAGTTTTCATCAAAAATTCATGT
Found at i:13634 original size:337 final size:338
Alignment explanation
Indices: 12858--13641 Score: 1213
Period size: 338 Copynumber: 2.3 Consensus size: 338
12848 TCCATATAAG
* *
12858 TTAAG-TTACAATCCTTGGTCAAGGTCACT-TGTCAGAGTTTACATTGGTAAGTCCTCCGGGCAC
1 TTAAGTTTAAAATCCTTGGTCAAGGTCTCTAT-TCAGAGTTTACATTGGTAAGTCCTCCGGGCAC
12921 AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGT
65 AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGT
* *
12986 ACCATTTGATTTCATCAAGTTTTTCATCAAAAGTTCATGTTTAAGTTTAAAATCCTTGTTTAAGG
130 ACCATTTCATTTCATCAAGTTTCTCATCAAAAGTTCATGTTTAAGTTTAAAATCCTTGTTTAAGG
*
13051 TCTCAATTTAAGGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAAT
195 TCTCAATTTAAGGTTCGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAAT
* * * *
13116 TCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGTACCATTTCATTTGATCGAGTTTTTCA
260 TCTGATAAGTCCTCCGAGCAATTGATAAAACATCCAGGTACCATTTCATTTCATCGAGTTTTTCA
*
13181 TTAAAAATTCATAT
325 TCAAAAATTCATAT
*
13195 TTAAGTTTAAAATCTTTGGTCAAGGTCTCTATTCAGAGTTTACATTGGTATA-TCCTCCGGGCAC
1 TTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGGTA-AGTCCTCCGGGCAC
* * **
13259 AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAGCCTTTGGGT
65 AAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGT
* * *
13324 ATCATTTCATTTTATCAAG-TTCTCAT-TAAAGATTCATGTTTAAGTTTAAAATCCTTGTTTAAG
130 ACCATTTCATTTCATCAAGTTTCTCATCAAAAG-TTCATGTTTAAGTTTAAAATCCTTGTTTAAG
** * * *
13387 GT-TCCTTTTTCAGAGTTCGCATTGGTAAGTCCTCCGGGCACAAATTCTGAAACCTTCGGGTATT
194 GTCT-CAATTTAAG-GTTCGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATT
*
13451 AATTCTGATAAGTCCTCCGAGTAATTGATAAAACATCCAGGTACCATTTCATTTCATCGAG-TTT
257 AATTCTGATAAGTCCTCCGAGCAATTGATAAAACATCCAGGTACCATTTCATTTCATCGAGTTTT
*
13515 TCATCAAAAATTCATGT
322 TCATCAAAAATTCATAT
* *
13532 TTAAGTTTAAAATCCTTAGTCAAGGTCTCTATTCAAAGTTTACATTGGTAAGTCCTCCGGGCACA
1 TTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCGGGCACA
* *
13597 ATTTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCTGGCA
66 AATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCA
13642 GTTCATATTT
Statistics
Matches: 410, Mismatches: 30, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
336 6 0.01
337 171 0.42
338 231 0.56
339 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (338 bp):
TTAAGTTTAAAATCCTTGGTCAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCGGGCACA
AATTCAGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGTA
CCATTTCATTTCATCAAGTTTCTCATCAAAAGTTCATGTTTAAGTTTAAAATCCTTGTTTAAGGT
CTCAATTTAAGGTTCGCATTGGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATT
CTGATAAGTCCTCCGAGCAATTGATAAAACATCCAGGTACCATTTCATTTCATCGAGTTTTTCAT
CAAAAATTCATAT
Found at i:13750 original size:39 final size:39
Alignment explanation
Indices: 13688--13872 Score: 235
Period size: 39 Copynumber: 4.7 Consensus size: 39
13678 TTATGCTTCA
* * ** *
13688 ATTCCGATCATGATTTTTGATTATTGCTTTGTCAGTTTT
1 ATTCCAATCCTGATTTAGGATTATTGCTTTATCAGTTTT
* *
13727 ATTTCAATCCTGATTTAGTATTATTGCTTTATCAGTTTT
1 ATTCCAATCCTGATTTAGGATTATTGCTTTATCAGTTTT
* *
13766 ATTCCAATCCTGGTTTAGGATTATTGCTTTATCAGTCTT
1 ATTCCAATCCTGATTTAGGATTATTGCTTTATCAGTTTT
* *
13805 ATTCCAATCCTGATTTAGGATTATTGCTTTGTCAATTTT
1 ATTCCAATCCTGATTTAGGATTATTGCTTTATCAGTTTT
* * * *
13844 ATTTCGATCCTGATTTAGAATCATTGCTT
1 ATTCCAATCCTGATTTAGGATTATTGCTT
13873 ATAAGTTAAT
Statistics
Matches: 127, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 127 1.00
ACGTcount: A:0.22, C:0.15, G:0.14, T:0.50
Consensus pattern (39 bp):
ATTCCAATCCTGATTTAGGATTATTGCTTTATCAGTTTT
Found at i:14554 original size:29 final size:29
Alignment explanation
Indices: 14512--14570 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
14502 AAGTGGAGAG
14512 TTGTATTTATTTATCAAGTAAGCCATTTT
1 TTGTATTTATTTATCAAGTAAGCCATTTT
*
14541 TTGTATTTATTTATTAAGTAAGCCATTTT
1 TTGTATTTATTTATCAAGTAAGCCATTTT
14570 T
1 T
14571 CATTTTTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.54
Consensus pattern (29 bp):
TTGTATTTATTTATCAAGTAAGCCATTTT
Found at i:21473 original size:8 final size:8
Alignment explanation
Indices: 21460--21484 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21450 TTTTCAAGAG
21460 GAAGAATT
1 GAAGAATT
21468 GAAGAATT
1 GAAGAATT
21476 GAAGAATT
1 GAAGAATT
21484 G
1 G
21485 GAGTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (8 bp):
GAAGAATT
Found at i:22076 original size:15 final size:15
Alignment explanation
Indices: 22046--22087 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
22036 TTTTAGATCT
22046 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
22062 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
22077 TTGTTTTCTGT
1 TTGTTTTCTGT
22088 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:22636 original size:15 final size:14
Alignment explanation
Indices: 22616--22645 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
22606 ATCTCTTTAA
22616 TTTTCCTTGTATTAT
1 TTTTCCTTG-ATTAT
22631 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
22645 T
1 T
22646 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:33016 original size:21 final size:20
Alignment explanation
Indices: 32986--33027 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
32976 CTAGAGATAG
32986 AAAAAGGAAAAAATCAAAAA
1 AAAAAGGAAAAAATCAAAAA
33006 AAAAAGTGAAAAAATCAGAAAA
1 AAAAAG-GAAAAAATCA-AAAA
33028 TTAAAAGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAAAGGAAAAAATCAAAAA
Found at i:35561 original size:19 final size:19
Alignment explanation
Indices: 35537--35573 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35527 AAATAGCAGG
35537 TAGAAATAAAATTTGCATA
1 TAGAAATAAAATTTGCATA
*
35556 TAGAAATAGAATTTGCAT
1 TAGAAATAAAATTTGCAT
35574 CGGCATGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (19 bp):
TAGAAATAAAATTTGCATA
Found at i:35737 original size:27 final size:27
Alignment explanation
Indices: 35707--35758 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
35697 CCATTTGCAT
35707 AAATAGAATTTGCACTTCCTAAAATGC
1 AAATAGAATTTGCACTTCCTAAAATGC
35734 AAATAGAATTTGCACTTCCTAAAAT
1 AAATAGAATTTGCACTTCCTAAAAT
35759 TACCTGCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATAGAATTTGCACTTCCTAAAATGC
Found at i:46583 original size:24 final size:24
Alignment explanation
Indices: 46551--46598 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
46541 TTGAGTTCCA
46551 TCATGCTCATCTCGAATTCTCCCT
1 TCATGCTCATCTCGAATTCTCCCT
46575 TCATGCTCATCTCGAATTCTCCCT
1 TCATGCTCATCTCGAATTCTCCCT
46599 GCATTTCTTT
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:0.17, C:0.38, G:0.08, T:0.38
Consensus pattern (24 bp):
TCATGCTCATCTCGAATTCTCCCT
Found at i:48005 original size:2 final size:2
Alignment explanation
Indices: 47998--48027 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
47988 AAATAATTAA
*
47998 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48028 TAACTAACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55767 original size:29 final size:29
Alignment explanation
Indices: 55716--55798 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
55706 CTTTGACACG
* *
55716 AGTGCA-AACCCACACTCAAAACAATCCCA
1 AGTGCACAACCCACACT-TAAACAAACCCA
* *
55745 AGTGCACAACCCACACTTGAACAAACGCA
1 AGTGCACAACCCACACTTAAACAAACCCA
* *
55774 AGTTCACAACCCGCACTTAAACAAA
1 AGTGCACAACCCACACTTAAACAAA
55799 ATACAGAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
29 36 0.78
30 10 0.22
ACGTcount: A:0.43, C:0.35, G:0.10, T:0.12
Consensus pattern (29 bp):
AGTGCACAACCCACACTTAAACAAACCCA
Found at i:58701 original size:151 final size:154
Alignment explanation
Indices: 58458--58827 Score: 606
Period size: 151 Copynumber: 2.4 Consensus size: 154
58448 TATAATGTAA
*
58458 CATGGATGGATTATCAAACTCATAATGTCCTTAATCAAAGTAATGATCATATCACATGTAAAATC
1 CATGGATGGATTATCAAACTCATAATGTCCTTAATCAAAGTGATGATCATATCACATGTAAAATC
* *
58523 ATAATGTAACATATATATTAACAAAAGTTTTAAGA-T-T-TATCTATGAGATCAATTAGAGTATA
66 ATAATGTAACATATATATTAACAAAAGTTTTAAGATTATCTATATATGAGATCAATTAGAGTACA
58585 ATGT-ACATGGATGAAAGTTCTAC
131 ATGTAACATGGATGAAAGTTCTAC
*
58608 CATGGATGG-TTATCAAACTCATAATGTCCTTAATCAAAGTGATGATCATATATCACATGTATAA
1 CATGGATGGATTATCAAACTCATAATGTCCTTAATCAAAGTGATGATC--ATATCACATGTAAAA
* *
58672 TCATAATGTAACATATATATTTATAAAAGTTTTAAGATTGATCTATATATGAGATCAATTAGAGT
64 TCATAATGTAACATATATATTAACAAAAGTTTTAAGATT-ATCTATATATGAGATCAATTAGAGT
58737 ACAATGTAACATGGATGAAAGTTCTAC
128 ACAATGTAACATGGATGAAAGTTCTAC
*
58764 CATGGATGGGTTTATCAAACTCATAATGTCCTTAATCAAAGTGATGATCATATCACATGTAAAA
1 CATGGAT-GGATTATCAAACTCATAATGTCCTTAATCAAAGTGATGATCATATCACATGTAAAA
58828 ACTACAAATA
Statistics
Matches: 204, Mismatches: 7, Indels: 12
0.91 0.03 0.05
Matches are distributed among these distances:
149 37 0.18
150 9 0.04
151 49 0.24
152 1 0.00
154 1 0.00
155 27 0.13
156 40 0.20
157 2 0.01
158 38 0.19
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (154 bp):
CATGGATGGATTATCAAACTCATAATGTCCTTAATCAAAGTGATGATCATATCACATGTAAAATC
ATAATGTAACATATATATTAACAAAAGTTTTAAGATTATCTATATATGAGATCAATTAGAGTACA
ATGTAACATGGATGAAAGTTCTAC
Done.