Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018096.1 Corchorus olitorius cultivar O-4 contig18129, 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: 39557
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1351 original size:22 final size:23
Alignment explanation
Indices: 1323--1397 Score: 102
Period size: 22 Copynumber: 3.4 Consensus size: 23
1313 AAAGTTTCAT
1323 ATTTCAT-AGGTGAATTATCAAA
1 ATTTCATAAGGTGAATTATCAAA
* *
1345 ATTTCATAACGTG-GTTATCAAA
1 ATTTCATAAGGTGAATTATCAAA
*
1367 ATTTAATAAGGT-AATTATCAAA
1 ATTTCATAAGGTGAATTATCAAA
1389 ATTTCATAA
1 ATTTCATAA
1398 AAATATTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 41 0.91
23 4 0.09
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (23 bp):
ATTTCATAAGGTGAATTATCAAA
Found at i:1461 original size:2 final size:2
Alignment explanation
Indices: 1454--1481 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1444 GCTAAAACTA
1454 AT AT AT AT 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
1482 TAGTTTTACC
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):
AT
Found at i:3924 original size:21 final size:22
Alignment explanation
Indices: 3890--3930 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3880 GGCTCCATGT
*
3890 ATTTATATAGCCTTCTTGTATA
1 ATTTAAATAGCCTTCTTGTATA
*
3912 ATTTAAAT-GCCTTGTTGTA
1 ATTTAAATAGCCTTCTTGTA
3931 GCATTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (22 bp):
ATTTAAATAGCCTTCTTGTATA
Found at i:6654 original size:84 final size:84
Alignment explanation
Indices: 6559--6729 Score: 324
Period size: 84 Copynumber: 2.0 Consensus size: 84
6549 ACGAGTATAT
6559 ATTAAACCTACTATTAATTTTATGAACAAGGTCCTCATGGAGCGCCACATGGCATTTGGTTTCTT
1 ATTAAACCTACTATTAATTTTATGAACAAGGTCCTCATGGAGCGCCACATGGCATTTGGTTTCTT
6624 TGACAAGTGTCAATAGTTA
66 TGACAAGTGTCAATAGTTA
* *
6643 ATTAAATCTACTATTAATTTTATGAACAAGGTCCTCATGGAGCGTCACATGGCATTTGGTTTCTT
1 ATTAAACCTACTATTAATTTTATGAACAAGGTCCTCATGGAGCGCCACATGGCATTTGGTTTCTT
6708 TGACAAGTGTCAATAGTTA
66 TGACAAGTGTCAATAGTTA
6727 ATT
1 ATT
6730 TTCTAATGTT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (84 bp):
ATTAAACCTACTATTAATTTTATGAACAAGGTCCTCATGGAGCGCCACATGGCATTTGGTTTCTT
TGACAAGTGTCAATAGTTA
Found at i:6850 original size:11 final size:11
Alignment explanation
Indices: 6807--6844 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6797 TTCCTATATA
*
6807 AAATAAATTAT
1 AAATTAATTAT
6818 CAAA-TAATTAT
1 -AAATTAATTAT
6829 AAATTAATTAT
1 AAATTAATTAT
6840 AAATT
1 AAATT
6845 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:15829 original size:31 final size:30
Alignment explanation
Indices: 15791--15928 Score: 107
Period size: 31 Copynumber: 4.5 Consensus size: 30
15781 ATCGTCTGCG
* *
15791 AAAATGCTTAAATAAGGGCTCAAAGAAAACA
1 AAAATGCTCAAATAAGGGCCCAAAG-AAACA
* * * *** *
15822 AAAATGCTTAAATCAGGGCCCAACGTTTGCG
1 AAAATGCTCAAATAAGGGCCCAAAG-AAACA
*
15853 AAAATGCTCAAATAAGTGCCCAAAGAAA-A
1 AAAATGCTCAAATAAGGGCCCAAAGAAACA
* * * *
15882 AAAATGCTCAAATAAGGGTCCAACGATTAGA
1 AAAATGCTCAAATAAGGGCCCAAAGA-AACA
*
15913 AAATTGCTCAAATAAG
1 AAAATGCTCAAATAAG
15929 TCTCAGCTGT
Statistics
Matches: 84, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
29 23 0.27
30 1 0.01
31 60 0.71
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (30 bp):
AAAATGCTCAAATAAGGGCCCAAAGAAACA
Found at i:15891 original size:29 final size:30
Alignment explanation
Indices: 15853--15929 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
15843 AACGTTTGCG
15853 AAAATGCTCAAATAAGTGCCCAAAGA-AAA
1 AAAATGCTCAAATAAGTGCCCAAAGATAAA
* * * *
15882 AAAATGCTCAAATAAGGGTCCAACGATTAGA
1 AAAATGCTCAAATAAGTGCCCAAAGA-TAAA
*
15913 AAATTGCTCAAATAAGT
1 AAAATGCTCAAATAAGT
15930 CTCAGCTGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 23 0.57
31 17 0.43
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (30 bp):
AAAATGCTCAAATAAGTGCCCAAAGATAAA
Found at i:15921 original size:60 final size:62
Alignment explanation
Indices: 15790--15929 Score: 178
Period size: 60 Copynumber: 2.3 Consensus size: 62
15780 CATCGTCTGC
* * * * * * *
15790 GAAAATGCTTAAATAAGGGCTCAAAGAAAACAAAAATGCTTAAATCAGGGCCCAACGTTTGC
1 GAAAATGCTCAAATAAGTGCCCAAAGAAAACAAAAATGCTCAAATAAGGGCCCAACGATTGA
*
15852 GAAAATGCTCAAATAAGTGCCCAAAG-AAA-AAAAATGCTCAAATAAGGGTCCAACGATT-A
1 GAAAATGCTCAAATAAGTGCCCAAAGAAAACAAAAATGCTCAAATAAGGGCCCAACGATTGA
15911 GAAAATTGCTCAAATAAGT
1 GAAAA-TGCTCAAATAAGT
15930 CTCAGCTGTC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 5 0.07
60 38 0.55
61 3 0.04
62 23 0.33
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.19
Consensus pattern (62 bp):
GAAAATGCTCAAATAAGTGCCCAAAGAAAACAAAAATGCTCAAATAAGGGCCCAACGATTGA
Found at i:15977 original size:22 final size:22
Alignment explanation
Indices: 15949--16000 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
15939 CACTGTGTGG
15949 TTATCAAAATTCCATAAT-AAGA
1 TTATCAAAATTCCAT-ATGAAGA
* *
15971 TTATCAAAATTTCATATGGAGA
1 TTATCAAAATTCCATATGAAGA
15993 TTATCAAA
1 TTATCAAA
16001 TTTTCATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTCCATATGAAGA
Found at i:24118 original size:42 final size:42
Alignment explanation
Indices: 24056--24136 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
24046 GCTAAGTCTT
24056 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
* * *
24098 GAAAATTTTTTGTAACTTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
24137 TTAATCCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:24304 original size:56 final size:57
Alignment explanation
Indices: 24202--24312 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 57
24192 TTTATTTTGT
*
24202 AGAATAATTAAGTAGAGATAGGGGGGATATGATTTATTATAACATTTATAGTGTGGA
1 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATAGTGTGGA
*
24259 AGAATAATTAAGTAGAGATA-GGGGGATAGGATTTATTATAACATTTATTGTGTG
1 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATAGTGTG
24313 AAAGGAAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
56 32 0.62
57 20 0.38
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATAGTGTGGA
Found at i:28458 original size:31 final size:31
Alignment explanation
Indices: 28418--28494 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
28408 CTTAAAAAGT
* * * *
28418 GATCGATTTAGTTCATGTATTCATAAGATTG
1 GATCAATTTAGTCCATATACTCATAAGATTG
* *
28449 GGTCAATTTAGTCCCTATACTCATAAGATTG
1 GATCAATTTAGTCCATATACTCATAAGATTG
*
28480 GATCAATTGAGTCCA
1 GATCAATTTAGTCCA
28495 ATCGATATTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (31 bp):
GATCAATTTAGTCCATATACTCATAAGATTG
Found at i:28563 original size:31 final size:31
Alignment explanation
Indices: 28513--28589 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
28503 TGGCACAATG
* *
28513 AGGACTCAATTGA-CACAATCATATGAGTATT
1 AGGACTAAATTGATCACAATCATATGAGTA-C
* *
28544 AGGACTAAATTGATC-CAATCTTGTGAGTAC
1 AGGACTAAATTGATCACAATCATATGAGTAC
*
28574 ATGAACTAAATTGATC
1 A-GGACTAAATTGATC
28590 TGTTTTTTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 1 0.03
31 37 0.95
32 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (31 bp):
AGGACTAAATTGATCACAATCATATGAGTAC
Found at i:29549 original size:42 final size:43
Alignment explanation
Indices: 29502--29597 Score: 131
Period size: 47 Copynumber: 2.2 Consensus size: 43
29492 GAATTGTAAT
*
29502 GAGATTT-CACTGGGTTTGTTCCTTGGGGAAGGGCTAATCATA
1 GAGATTTGAACTGGGTTTGTTCCTTGGGGAAGGGCTAATCATA
*
29544 GAGATTTATTTGAATTGGGTTTGTTCCTTGGGGAAGGGCTAATCATA
1 GAG----ATTTGAACTGGGTTTGTTCCTTGGGGAAGGGCTAATCATA
29591 GAGATTT
1 GAGATTT
29598 ATTTGAATTG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
42 3 0.06
43 4 0.09
46 4 0.09
47 36 0.77
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.36
Consensus pattern (43 bp):
GAGATTTGAACTGGGTTTGTTCCTTGGGGAAGGGCTAATCATA
Found at i:29581 original size:47 final size:47
Alignment explanation
Indices: 29512--29607 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
29502 GAGATTTCAC
29512 TGGGTTTGTTCCTTGGGGAAGGGCTAATCATAGAGATTTATTTGAAT
1 TGGGTTTGTTCCTTGGGGAAGGGCTAATCATAGAGATTTATTTGAAT
29559 TGGGTTTGTTCCTTGGGGAAGGGCTAATCATAGAGATTTATTTGAAT
1 TGGGTTTGTTCCTTGGGGAAGGGCTAATCATAGAGATTTATTTGAAT
29606 TG
1 TG
29608 TAATGAGATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.23, C:0.08, G:0.30, T:0.39
Consensus pattern (47 bp):
TGGGTTTGTTCCTTGGGGAAGGGCTAATCATAGAGATTTATTTGAAT
Found at i:29739 original size:37 final size:37
Alignment explanation
Indices: 29689--29762 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
29679 GTTTGTAATC
29689 CCAATCTCTTTAAGAAATGAAAATGATTCAGTGTACG
1 CCAATCTCTTTAAGAAATGAAAATGATTCAGTGTACG
29726 CCAATCTCTTTAAGAAATGAAAATGATTCAGTGTACG
1 CCAATCTCTTTAAGAAATGAAAATGATTCAGTGTACG
29763 GATCTTCCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (37 bp):
CCAATCTCTTTAAGAAATGAAAATGATTCAGTGTACG
Found at i:29778 original size:97 final size:101
Alignment explanation
Indices: 29659--29922 Score: 367
Period size: 108 Copynumber: 2.6 Consensus size: 101
29649 TCATGTAGCG
*
29659 GTGTACGGGTCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCAGTGTA
1 GTGTACGGGTCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCAATG-A
29724 CGCCAATCTCTTT-AA-G-AA-A-TGAAAATGATTCA
65 CGCCAATCTCTTTAAATGAAAGATTGAAAATGATTCA
* *
29756 GTGTACGGATCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTGAAAATG
1 GTGTACGGGTCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATT--CAATG
*
29821 ATGCCAATCTCTTTAAGAAATGAAAATGATTGAAAATGATTCA
64 ACGCCAATCTCTTT---AAATG-AAA-GATTGAAAATGATTCA
* *
29864 GTGTGCGGGTCTTCCTGTGCATTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTC
1 GTGTACGGGTCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTC
29923 TTATCTCTAA
Statistics
Matches: 147, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
97 57 0.39
98 13 0.09
99 3 0.02
102 2 0.01
103 1 0.01
105 2 0.01
107 1 0.01
108 68 0.46
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (101 bp):
GTGTACGGGTCTTCCTGTGCGTTTGTAATCCCAATCTCTTTAAGAAATGAAAATGATTCAATGAC
GCCAATCTCTTTAAATGAAAGATTGAAAATGATTCA
Found at i:29837 original size:38 final size:38
Alignment explanation
Indices: 29786--29860 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
29776 GTTTGTAATC
29786 CCAATCTCTTTAAGAAATGAAAATGATTGAAAATGATG
1 CCAATCTCTTTAAGAAATGAAAATGATTGAAAATGATG
29824 CCAATCTCTTTAAGAAATGAAAATGATTGAAAATGAT
1 CCAATCTCTTTAAGAAATGAAAATGATTGAAAATGAT
29861 TCAGTGTGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (38 bp):
CCAATCTCTTTAAGAAATGAAAATGATTGAAAATGATG
Found at i:30745 original size:47 final size:47
Alignment explanation
Indices: 30676--30876 Score: 215
Period size: 47 Copynumber: 4.0 Consensus size: 47
30666 CAGGAAGACC
30676 CGTACACTGAATCATTTTCAATCATTTTCATTTCTTAAAGAGATTGG
1 CGTACACTGAATCATTTTCAATCATTTTCATTTCTTAAAGAGATTGG
30723 CGTACACTGAATCATTTTCAATCATTTTCATTTCTTAAAGAGATTGG
1 CGTACACTGAATCATTTTCAATCATTTTCATTTCTTAAAGAGATTGG
* * *** *
30770 -GATTACAAACGCACAGGAAGACCCGTACACTGAATCATTTTCATTTCTTAAAGAGATTGG
1 CG--T----A--CAC-TG-A-A-TC--ATTTTCAATCATTTTCATTTCTTAAAGAGATTGG
30830 CGTACACTGAATCATTTTCAATCATTTTCATTTCTTAAAGAGATTGG
1 CGTACACTGAATCATTTTCAATCATTTTCATTTCTTAAAGAGATTGG
30877 GATATGGATA
Statistics
Matches: 127, Mismatches: 12, Indels: 30
0.75 0.07 0.18
Matches are distributed among these distances:
46 1 0.01
47 77 0.61
48 1 0.01
49 1 0.01
50 1 0.01
51 1 0.01
52 2 0.02
53 3 0.02
54 3 0.02
55 2 0.02
56 1 0.01
57 1 0.01
58 1 0.01
59 1 0.01
60 30 0.24
61 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (47 bp):
CGTACACTGAATCATTTTCAATCATTTTCATTTCTTAAAGAGATTGG
Found at i:37000 original size:62 final size:62
Alignment explanation
Indices: 36909--37238 Score: 282
Period size: 62 Copynumber: 5.3 Consensus size: 62
36899 GATGTTGCAA
* * *
36909 TTGACACCAGAAGTTGTCATATTATATTATTATCTTGACACCAGAAGTTGTCATGAAAATTT
1 TTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATAAAAATTT
*
36971 TTGACACTAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATAAAAATTT
1 TTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATAAAAATTT
* *
37033 TTGACACCAGAAGTTGTC--ATGAAA--ATTA--TTGACACCAGAAGTTGTTATAGCAAATTATT
1 TTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATA--AAA--ATT
37092 AT
62 -T
* *
37094 CTTAACACCAGAAGTTGTC--ATGAAA--ATT-T-TTGACACCAGAAGTTGTCATATCAAATTAT
1 -TTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATA--AAA--AT
37153 TAT
61 T-T
*
37156 CTTGACACCAGAAGTTGTC--ATGAAA--ATTA--TTGACACCAGAAGTTGTCATAGCAAATTAT
1 -TTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATA--AAA--AT
37215 TAT
61 T-T
*
37218 CTTGACACCAAAAGTTGTCAT
1 -TTGACACCAGAAGTTGTCAT
37239 GCTGAGGAAA
Statistics
Matches: 245, Mismatches: 13, Indels: 18
0.89 0.05 0.07
Matches are distributed among these distances:
56 20 0.08
58 7 0.03
60 8 0.03
61 1 0.00
62 209 0.85
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (62 bp):
TTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATAAAAATTT
Found at i:37053 original size:90 final size:93
Alignment explanation
Indices: 36909--37271 Score: 381
Period size: 90 Copynumber: 3.8 Consensus size: 93
36899 GATGTTGCAA
* *
36909 TTGACACCAGAAGTTGTCATATTATATTATTATCTTGACACCAGAAGTTGTCATGAAAATTTTTG
1 TTGACACCAGAAGTTGTCATA-TA-A-AATTATCTTGACACCAGAAGTTGTCATGAAAATTATTG
*
36974 ACACTAGAAGTTGTCATATCAAATTATTATC
63 ACACCAGAAGTTGTCATATCAAATTATTATC
37005 TTGACACCAGAAGTTGTCATA-AAAATT-T-TTGACACCAGAAGTTGTCATGAAAATTATTGACA
1 TTGACACCAGAAGTTGTCATATAAAATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACA
* *
37067 CCAGAAGTTGTTATAGCAAATTATTATC
66 CCAGAAGTTGTCATATCAAATTATTATC
* * *
37095 TTAACACCAGAAGTTGTCAT-GAAAATT-T-TTGACACCAGAAGTTGTCATATCAAATTATTATC
1 TTGACACCAGAAGTTGTCATATAAAATTATCTTGACACCAGAAGTTGTC--ATGAAA--ATTA--
*
37157 TTGACACCAGAAGTTGTC--ATGAAA--ATTA--
60 TTGACACCAGAAGTTGTCATATCAAATTATTATC
* *
37185 TTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAAAAGTTGTCATGCTGAGGAAAT
1 TTGACACCAGAAGTTGTCATA-TAAA--ATTATCTTGACACCAGAAGTTGTCA---TGA--AAAT
*
37250 TATTGACACTAGAAGTTGTCAT
58 TATTGACACCAGAAGTTGTCAT
37272 CCTAAGATTG
Statistics
Matches: 232, Mismatches: 15, Indels: 39
0.81 0.05 0.14
Matches are distributed among these distances:
90 121 0.52
91 1 0.00
92 15 0.06
93 1 0.00
94 13 0.06
95 18 0.08
96 55 0.24
97 6 0.03
99 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (93 bp):
TTGACACCAGAAGTTGTCATATAAAATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACA
CCAGAAGTTGTCATATCAAATTATTATC
Found at i:37157 original size:152 final size:151
Alignment explanation
Indices: 36878--37215 Score: 532
Period size: 152 Copynumber: 2.2 Consensus size: 151
36868 TCTACTTACA
** ** *
36878 ATTGACACCAGAAGTTGTCATGATGTTGCAATTGACACCAGAAGTTGTCATATTATATTATTATC
1 ATTGACACCAGAAGTTGTCATGAAATT---ATTGACACCAGAAGTTGTCATAGCAAATTATTATC
* *
36943 TTGACACCAGAAGTTGTCATGAAAATTTTTGACACTAGAAGTTGTCATATCAAATTATTATCTTG
63 TTAACACCAGAAGTTGTCATGAAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATCTTG
37008 ACACCAGAAGTTGTCATAAAAATT
128 ACACCAGAAGTTGTCATAAAAATT
* *
37032 TTTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTTATAGCAAATTATTATCTT
1 ATTGACACCAGAAGTTGTCATG-AAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCTT
37097 AACACCAGAAGTTGTCATGAAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATCTTGAC
65 AACACCAGAAGTTGTCATGAAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATCTTGAC
*
37162 ACCAGAAGTTGTCATGAAAATT
130 ACCAGAAGTTGTCATAAAAATT
37184 ATTGACACCAGAAGTTGTCATAGCAAATTATT
1 ATTGACACCAGAAGTTGTCAT-G-AAATTATT
37216 ATCTTGACAC
Statistics
Matches: 170, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
152 137 0.81
153 9 0.05
154 21 0.12
155 3 0.02
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (151 bp):
ATTGACACCAGAAGTTGTCATGAAATTATTGACACCAGAAGTTGTCATAGCAAATTATTATCTTA
ACACCAGAAGTTGTCATGAAAATTTTTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACA
CCAGAAGTTGTCATAAAAATT
Found at i:37239 original size:62 final size:62
Alignment explanation
Indices: 36943--37271 Score: 403
Period size: 62 Copynumber: 5.3 Consensus size: 62
36933 TATTATTATC
* *
36943 TTGACACCAGAAGTTGTCAT-G-AAA--ATT-T-TTGACACTAGAAGTTGTCATATCAAATTATT
1 TTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTC--ATGAAA--ATT
37002 A
62 A
37003 TCTTGACACCAGAAGTTGTCATA--AAA--ATT-T-TTGACACCAGAAGTTGTCATGAAAATTA
1 --TTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTA
* * *
37061 TTGACACCAGAAGTTGTTATAGCAAATTATTATCTTAACACCAGAAGTTGTCATGAAAATTT
1 TTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTA
*
37123 TTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTA
1 TTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTA
*
37185 TTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAAAAGTTGTCATGCTGAGGAAAT
1 TTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTCA---TGA--AAAT
37250 TA
61 TA
*
37252 TTGACACTAGAAGTTGTCAT
1 TTGACACCAGAAGTTGTCAT
37272 CCTAAGATTG
Statistics
Matches: 243, Mismatches: 12, Indels: 19
0.89 0.04 0.07
Matches are distributed among these distances:
56 20 0.08
58 7 0.03
60 8 0.03
61 1 0.00
62 179 0.74
65 3 0.01
67 25 0.10
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (62 bp):
TTGACACCAGAAGTTGTCATAGCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTA
Done.