Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014901.1 Corchorus olitorius cultivar O-4 contig14934, 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: 100074
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:10913 original size:17 final size:16
Alignment explanation
Indices: 10859--10913 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
10849 TTTTAGCTAG
* *
10859 TTTGATTGAATTGATT
1 TTTGCTTGAATTTATT
*
10875 TTTGCTTGCATGTTATT
1 TTTGCTTGAAT-TTATT
*
10892 ATTGCTTGAATTTAGTT
1 TTTGCTTGAATTTA-TT
10909 TTTGC
1 TTTGC
10914 ATTTAGATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.18, C:0.07, G:0.18, T:0.56
Consensus pattern (16 bp):
TTTGCTTGAATTTATT
Found at i:13514 original size:10 final size:10
Alignment explanation
Indices: 13499--13523 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13489 AAATTGAGTC
13499 TTTAGCATGA
1 TTTAGCATGA
13509 TTTAGCATGA
1 TTTAGCATGA
13519 TTTAG
1 TTTAG
13524 TTCTTGAATT
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:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (10 bp):
TTTAGCATGA
Found at i:16433 original size:25 final size:26
Alignment explanation
Indices: 16400--16448 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
16390 ATTTATGAAG
*
16400 AGAGATAGTGAGTGGAG-GAGAAGAA
1 AGAGATAGTGAGAGGAGAGAGAAGAA
* *
16425 AGAGTTAGTGGGAGGAGAGAGAAG
1 AGAGATAGTGAGAGGAGAGAGAAG
16449 GAGGGCAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.47, T:0.12
Consensus pattern (26 bp):
AGAGATAGTGAGAGGAGAGAGAAGAA
Found at i:19920 original size:24 final size:25
Alignment explanation
Indices: 19892--19939 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
19882 AGAAACAATA
*
19892 AAAATAAATAAACAAGA-AAATAAT
1 AAAATAAAGAAACAAGATAAATAAT
* *
19916 AAAATTAAGCAACAAGATAAATAA
1 AAAATAAAGAAACAAGATAAATAA
19940 ATACTTCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (25 bp):
AAAATAAAGAAACAAGATAAATAAT
Found at i:21619 original size:15 final size:15
Alignment explanation
Indices: 21599--21628 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21589 ATCAGGCTGC
*
21599 CACGATACACGATAT
1 CACGATACACAATAT
21614 CACGATACACAATAT
1 CACGATACACAATAT
21629 TTCAACCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:26724 original size:16 final size:16
Alignment explanation
Indices: 26700--26754 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
26690 GGTTAAGTCA
26700 GGTTCGGGTATTTTCG
1 GGTTCGGGTATTTTCG
* *
26716 GGCTCGGGT-TATGTCG
1 GGTTCGGGTAT-TTTCG
26732 GGTTCGGGTATTTTCG
1 GGTTCGGGTATTTTCG
26748 GGTTCGG
1 GGTTCGG
26755 TCTCGGGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 31 0.94
17 1 0.03
ACGTcount: A:0.05, C:0.15, G:0.42, T:0.38
Consensus pattern (16 bp):
GGTTCGGGTATTTTCG
Found at i:26726 original size:32 final size:32
Alignment explanation
Indices: 26682--26754 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
26672 ATTGGGCGGG
26682 TCGGGTTC-GGTTAAGTCAGGTTCGGGTATTT
1 TCGGGTTCGGGTTAAGTCAGGTTCGGGTATTT
* * *
26713 TCGGGCTCGGGTTATGTCGGGTTCGGGTATTT
1 TCGGGTTCGGGTTAAGTCAGGTTCGGGTATTT
26745 TCGGGTTCGG
1 TCGGGTTCGG
26755 TCTCGGGTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 7 0.19
32 30 0.81
ACGTcount: A:0.08, C:0.15, G:0.40, T:0.37
Consensus pattern (32 bp):
TCGGGTTCGGGTTAAGTCAGGTTCGGGTATTT
Found at i:26753 original size:6 final size:6
Alignment explanation
Indices: 26744--26797 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
26734 TTCGGGTATT
* * *
26744 TTCGGG TTC-GG TCTCGGG -TAGGG TTCGGG TTCGGG CTCGGG -TCAGG
1 TTCGGG TTCGGG T-TCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
26790 TTCGGG TT
1 TTCGGG TT
26798 TGATTTCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
5 11 0.28
6 26 0.67
7 2 0.05
ACGTcount: A:0.04, C:0.19, G:0.46, T:0.31
Consensus pattern (6 bp):
TTCGGG
Found at i:26774 original size:23 final size:23
Alignment explanation
Indices: 26744--26797 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
26734 TTCGGGTATT
*
26744 TTCGGGTTCGGTCTCGGGT-AGGG
1 TTCGGGTTCGGGCTCGGGTCA-GG
26767 TTCGGGTTCGGGCTCGGGTCAGG
1 TTCGGGTTCGGGCTCGGGTCAGG
26790 TTCGGGTT
1 TTCGGGTT
26798 TGATTTCGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.04, C:0.19, G:0.46, T:0.31
Consensus pattern (23 bp):
TTCGGGTTCGGGCTCGGGTCAGG
Found at i:26939 original size:5 final size:5
Alignment explanation
Indices: 26922--26978 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
26912 AAGTTTATTG
* *
26922 ATAAT AT-AT ATAAT AT-A- ATAAT ATAAT ATAAC ATTATT ATCAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT AT-AAT ATAAT
26971 AT-AT ATAA
1 ATAAT ATAA
26979 AGATTGAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
3 2 0.05
4 10 0.24
5 23 0.55
6 7 0.17
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:26947 original size:13 final size:14
Alignment explanation
Indices: 26922--26978 Score: 71
Period size: 13 Copynumber: 3.9 Consensus size: 14
26912 AAGTTTATTG
26922 ATAATATATATAAT
1 ATAATATATATAAT
26936 ATAATA-ATATAAT
1 ATAATATATATAAT
*
26949 ATAACATTATTATCAAT
1 ATAATA-TA-TAT-AAT
26966 ATAATATATATAA
1 ATAATATATATAA
26979 AGATTGAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 12 0.32
14 8 0.22
15 4 0.11
16 5 0.14
17 8 0.22
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAATATATATAAT
Found at i:26947 original size:22 final size:23
Alignment explanation
Indices: 26922--26978 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
26912 AAGTTTATTG
26922 ATAATATATATAATATAAT-AAT
1 ATAATATATATAATATAATCAAT
* * *
26944 ATAATATA-ACATTATTATCAAT
1 ATAATATATATAATATAATCAAT
26966 ATAATATATATAA
1 ATAATATATATAA
26979 AGATTGAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 7 0.25
22 19 0.68
23 2 0.07
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAATATATATAATATAATCAAT
Found at i:27510 original size:2 final size:2
Alignment explanation
Indices: 27505--27544 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
27495 TTATATAAGT
* *
27505 TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27545 GTTGTTTAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27622 original size:27 final size:27
Alignment explanation
Indices: 27592--27646 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
27582 TAATTGTGAA
27592 TGAATCATTTAATTATATAAATTTTAT
1 TGAATCATTTAATTATATAAATTTTAT
27619 TGAATCATTTAATTATATAAATTTTAT
1 TGAATCATTTAATTATATAAATTTTAT
27646 T
1 T
27647 ATATACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (27 bp):
TGAATCATTTAATTATATAAATTTTAT
Found at i:27647 original size:14 final size:14
Alignment explanation
Indices: 27598--27651 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
27588 TGAATGAATC
27598 ATTTAATTATATAA
1 ATTTAATTATATAA
* *
27612 ATTTTATTGA-AT-C
1 ATTTAATT-ATATAA
27625 ATTTAATTATATAA
1 ATTTAATTATATAA
*
27639 ATTTTATTATATA
1 ATTTAATTATATA
27652 CATATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 1 0.03
13 9 0.28
14 21 0.66
15 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (14 bp):
ATTTAATTATATAA
Found at i:27781 original size:6 final size:6
Alignment explanation
Indices: 27761--27807 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
27751 AATTATTTAT
* * *
27761 TCGGG- TCGGGA TCGGGC TCGGTC TCGGG- TCGGGT TCGGGC TCGGGC
1 TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC
27807 T
1 T
27808 GTCTCGGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
5 10 0.28
6 26 0.72
ACGTcount: A:0.02, C:0.26, G:0.49, T:0.23
Consensus pattern (6 bp):
TCGGGC
Found at i:27791 original size:23 final size:23
Alignment explanation
Indices: 27761--27804 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
27751 AATTATTTAT
27761 TCGGGTCGGGATCGGGCTCGGTC
1 TCGGGTCGGGATCGGGCTCGGTC
*
27784 TCGGGTCGGGTTCGGGCTCGG
1 TCGGGTCGGGATCGGGCTCGG
27805 GCTGTCTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.02, C:0.25, G:0.50, T:0.23
Consensus pattern (23 bp):
TCGGGTCGGGATCGGGCTCGGTC
Found at i:27830 original size:16 final size:16
Alignment explanation
Indices: 27811--27854 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
27801 TCGGGCTGTC
*
27811 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTAATT
*
27827 TCGGGCTCGGGTAATT
1 TCGGGTTCGGGTAATT
27843 TCGGGTTCGGGT
1 TCGGGTTCGGGT
27855 TCGGGATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.16, G:0.41, T:0.36
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:27835 original size:32 final size:32
Alignment explanation
Indices: 27794--27854 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
27784 TCGGGTCGGG
*
27794 TTCGGGCTCGGGCT-GTCTCGGGTTCGGGTATT
1 TTCGGGCTCGGG-TAATCTCGGGTTCGGGTATT
*
27826 TTCGGGCTCGGGTAATTTCGGGTTCGGGT
1 TTCGGGCTCGGGTAATCTCGGGTTCGGGT
27855 TCGGGATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.05, C:0.20, G:0.41, T:0.34
Consensus pattern (32 bp):
TTCGGGCTCGGGTAATCTCGGGTTCGGGTATT
Found at i:29347 original size:23 final size:23
Alignment explanation
Indices: 29319--29362 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
29309 ATTTAGATTT
*
29319 AGCTCATATTAATTTAGTTGGGA
1 AGCTCATATTAATCTAGTTGGGA
29342 AGCTCATATTAATCTAGTTGG
1 AGCTCATATTAATCTAGTTGG
29363 ACTATGGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (23 bp):
AGCTCATATTAATCTAGTTGGGA
Found at i:37018 original size:42 final size:43
Alignment explanation
Indices: 36967--37060 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
36957 AGTGCATTAC
* *
36967 CTAA-ATTCTA-CTCCATCTTTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTGTAGATAATTCATCAAAATAAAG
*
37008 CTGATATTCTACTCCTCCATCTGTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTGTAGATAATTCATCAAAATAAAG
37053 CTAATATT
1 CTAATATT
37061 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.13
45 36 0.80
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTGTAGATAATTCATCAAAATAAAG
Found at i:38943 original size:19 final size:18
Alignment explanation
Indices: 38904--38953 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
38894 TCTGCATGTC
38904 TTTTTTTTTCTTTTCATGG
1 TTTTTTTTTCTTTT-ATGG
38923 TTTTTTTTTCTGTTT-TGGG
1 TTTTTTTTTCT-TTTAT-GG
*
38942 TTGTTTTTTCTT
1 TTTTTTTTTCTT
38954 CATCTTTCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.07
19 23 0.82
20 3 0.11
ACGTcount: A:0.02, C:0.08, G:0.14, T:0.76
Consensus pattern (18 bp):
TTTTTTTTTCTTTTATGG
Found at i:44729 original size:16 final size:16
Alignment explanation
Indices: 44704--44744 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
44694 TTTCATATAT
*
44704 TTATAGATTTTTATTA
1 TTATATATTTTTATTA
44720 TTATATATTTTTATTA
1 TTATATATTTTTATTA
44736 -TATAT-TTTT
1 TTATATATTTT
44745 ATTTTCTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 4 0.17
15 5 0.21
16 15 0.62
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TTATATATTTTTATTA
Found at i:44733 original size:13 final size:13
Alignment explanation
Indices: 44717--44747 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
44707 TAGATTTTTA
44717 TTATTATATATTT
1 TTATTATATATTT
44730 TTATTATATATTT
1 TTATTATATATTT
44743 TTATT
1 TTATT
44748 TTCTTCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTATATATTT
Found at i:44782 original size:16 final size:18
Alignment explanation
Indices: 44761--44793 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44751 TTCAACTGTA
44761 AAAATT-TC-GGAAAATG
1 AAAATTGTCTGGAAAATG
44777 AAAATTGTCTGGAAAAT
1 AAAATTGTCTGGAAAAT
44794 TACTTCTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (18 bp):
AAAATTGTCTGGAAAATG
Found at i:57070 original size:10 final size:10
Alignment explanation
Indices: 56974--57075 Score: 68
Period size: 10 Copynumber: 10.3 Consensus size: 10
56964 TGACATATAA
56974 AAATATAATT
1 AAATATAATT
* *
56984 AAATCAAAATG
1 AAAT-ATAATT
*
56995 ACATATAA--
1 AAATATAATT
57003 AAATATAATT
1 AAATATAATT
* *
57013 AAATCAAAATG
1 AAAT-ATAATT
*
57024 ACATATAA--
1 AAATATAATT
57032 AAATATAATT
1 AAATATAATT
* *
57042 AAATCAAAATG
1 AAAT-ATAATT
*
57053 ATATATAATT
1 AAATATAATT
57063 AAATATAATT
1 AAATATAATT
57073 AAA
1 AAA
57076 GGAAAAAATG
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
8 14 0.20
10 34 0.49
11 21 0.30
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (10 bp):
AAATATAATT
Found at i:57070 original size:31 final size:29
Alignment explanation
Indices: 56958--57075 Score: 209
Period size: 29 Copynumber: 4.0 Consensus size: 29
56948 CAAAGTCAAT
56958 TCAAAATGACATATAAAAATATAATTAAA
1 TCAAAATGACATATAAAAATATAATTAAA
56987 TCAAAATGACATATAAAAATATAATTAAA
1 TCAAAATGACATATAAAAATATAATTAAA
57016 TCAAAATGACATATAAAAATATAATTAAA
1 TCAAAATGACATATAAAAATATAATTAAA
*
57045 TCAAAATGATATATAATTAAATATAATTAAA
1 TCAAAATGACATATAA--AAATATAATTAAA
57076 GGAAAAAATG
Statistics
Matches: 86, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
29 73 0.85
31 13 0.15
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (29 bp):
TCAAAATGACATATAAAAATATAATTAAA
Found at i:72948 original size:44 final size:44
Alignment explanation
Indices: 72865--72949 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
72855 TAAATTTCAT
* * *
72865 AATTATAGTCGATCTAGAATTTTATTTCATAATTTAAAAAATAC
1 AATTATAGTAGATCTAGAATTCTATTTCATAATTGAAAAAATAC
* * *
72909 AATTATAGTAGATTTAGAATATCT-TTTCGTAGTTGAAAAAA
1 AATTATAGTAGATCTAGAAT-TCTATTTCATAATTGAAAAAA
72950 CAAAGTGGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 32 0.94
45 2 0.06
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (44 bp):
AATTATAGTAGATCTAGAATTCTATTTCATAATTGAAAAAATAC
Found at i:76596 original size:20 final size:21
Alignment explanation
Indices: 76558--76596 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
76548 CATTTTATTG
76558 ATAAAAAACCAAACATTTTCA
1 ATAAAAAACCAAACATTTTCA
*
76579 ATAAAAATCCAAAC-TTTT
1 ATAAAAAACCAAACATTTT
76597 AGCAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAAAAAACCAAACATTTTCA
Found at i:76985 original size:21 final size:21
Alignment explanation
Indices: 76959--77000 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
76949 ACACAAAGAA
76959 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
76980 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
77001 CCTAAGGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Found at i:77148 original size:21 final size:21
Alignment explanation
Indices: 77115--77156 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
77105 TGAAGAGCTA
*
77115 AAGGCCATCGGAGTTCATTTG
1 AAGGCCATCGGAGATCATTTG
* *
77136 AAGGGCATTGGAGATCATTTG
1 AAGGCCATCGGAGATCATTTG
77157 CCAAGGAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (21 bp):
AAGGCCATCGGAGATCATTTG
Found at i:78866 original size:15 final size:15
Alignment explanation
Indices: 78846--78874 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
78836 TGGAGGTTCG
78846 AAATCAACAAGCTCA
1 AAATCAACAAGCTCA
78861 AAATCAACAAGCTC
1 AAATCAACAAGCTC
78875 CACTTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.28, G:0.07, T:0.14
Consensus pattern (15 bp):
AAATCAACAAGCTCA
Found at i:79505 original size:33 final size:32
Alignment explanation
Indices: 79460--79539 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 32
79450 GTGTTTTAGA
* *
79460 TGTTGTTAGTGATGATACTAAACCTAATTTAAG
1 TGTTGTTTGTGATGACACTAAACCT-ATTTAAG
* * *
79493 TGTTGTTTGTGATGACACTAAATCTGTTTAGG
1 TGTTGTTTGTGATGACACTAAACCTATTTAAG
*
79525 TGTTGTTTATGATGA
1 TGTTGTTTGTGATGA
79540 AACAACTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 19 0.46
33 22 0.54
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (32 bp):
TGTTGTTTGTGATGACACTAAACCTATTTAAG
Found at i:81431 original size:21 final size:21
Alignment explanation
Indices: 81405--81446 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
81395 ACACAAAGAA
*
81405 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCAACGGAGTTG
81426 GTTTCAAGCTCAACGGAGTTG
1 GTTTCAAGCTCAACGGAGTTG
81447 CCTAAGGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (21 bp):
GTTTCAAGCTCAACGGAGTTG
Found at i:82289 original size:21 final size:20
Alignment explanation
Indices: 82242--82289 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
82232 AGATTCGTAT
82242 CAAACTCCCTCTTCTTCCTC
1 CAAACTCCCTCTTCTTCCTC
* * *
82262 GACACTCTCTTCTTCTTCCTC
1 CAAACTC-CCTCTTCTTCCTC
82283 CAAACTC
1 CAAACTC
82290 GACCCAAACC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.17, C:0.46, G:0.02, T:0.35
Consensus pattern (20 bp):
CAAACTCCCTCTTCTTCCTC
Found at i:84965 original size:27 final size:27
Alignment explanation
Indices: 84893--84968 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
84883 AGTGAACTTA
* * *
84893 AAATGACCAAAATGCCCCCGAATATGC
1 AAATGACCAAAATGCCCCTGGACATGC
* *
84920 AAATGACCAAAATACCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTGGACATGC
*
84947 AAATGACTAAAATGCCCCTGGA
1 AAATGACCAAAATGCCCCTGGA
84969 TGACCCTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGACATGC
Found at i:85571 original size:21 final size:21
Alignment explanation
Indices: 85547--85586 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
85537 CACATACCGC
* *
85547 ATTTTATAATTAATTATATAT
1 ATTTAATAATTAAATATATAT
*
85568 ATTTAATATTTAAATATAT
1 ATTTAATAATTAAATATAT
85587 TTCCTAAGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTAATAATTAAATATATAT
Found at i:88833 original size:15 final size:16
Alignment explanation
Indices: 88803--88835 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
88793 TTTACAAAAG
88803 AAACAACTACCAAGCT
1 AAACAACTACCAAGCT
*
88819 AAACAACT-TCAAGCT
1 AAACAACTACCAAGCT
88834 AA
1 AA
88836 TTGTAAGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.27, G:0.06, T:0.15
Consensus pattern (16 bp):
AAACAACTACCAAGCT
Found at i:90461 original size:18 final size:17
Alignment explanation
Indices: 90438--90474 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
90428 CTATCCCTAA
90438 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
*
90456 AACTAGAAGAGAAATAG
1 AACTAGAAGAAAAATAG
90473 AA
1 AA
90475 GAAGAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.62, C:0.08, G:0.19, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:96688 original size:13 final size:13
Alignment explanation
Indices: 96670--96695 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
96660 TATATAGCAT
96670 GTAAGATAAGATA
1 GTAAGATAAGATA
96683 GTAAGATAAGATA
1 GTAAGATAAGATA
96696 TATTGAAATA
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:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (13 bp):
GTAAGATAAGATA
Found at i:98179 original size:19 final size:20
Alignment explanation
Indices: 98149--98212 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
98139 TTGACACTGT
98149 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
*
98170 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATGAGA
* *
98189 TTAGGTACTGTACAAATGAGA
1 TTA-GCACTGTACAGATGAGA
98210 TTA
1 TTA
98213 TTAGAGTAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:98200 original size:21 final size:19
Alignment explanation
Indices: 98155--98212 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
98145 CTGTTTAGCA
98155 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
98174 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
*
98195 ACTGTACAAATGAGATTA
1 ACTGTACAGATGAGATTA
98213 TTAGAGTAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:98480 original size:215 final size:214
Alignment explanation
Indices: 98109--98528 Score: 615
Period size: 215 Copynumber: 2.0 Consensus size: 214
98099 GACTAGATGT
* * * *
98109 GTTTAGTAGATCGGTGCGATAGTGGTGTGATTGACACTGTTTAGCAACTGTACAGATGAGATTAC
1 GTTTAGTAAAACGGTGCGATAGCGGTGCGATTGACACTGTTTAGCAACTGTACAGATGAGATTAC
* * *
98174 ACTGTACAGATTAGATTAGGTACTGTACAAATGAGATTATTAGAGTAGCGATTGAAACGGAGTTT
66 ACTGTACAGATTAAATTAGGTACTGTACAAATGAGATTATTAGAGCAGCGATTGAAACGAAGTTT
* * * * *
98239 ACACTTAAACTCCGTTTGGACCCAAAATGGTGGTGAAAAGGTCAAACGGTGGTGAAAAAGGTTAC
131 ACACTTAAACTCCGTTTGGACCCAAAACGGTAGTGAAAAGATCAAACGATGGTG-AAAAGATTAC
98304 AGATAAGAAGCATAGGCTGC
195 AGATAAGAAGCATAGGCTGC
* * *
98324 GTTTAGTAAAACGGTGCGGTAGCGGTGCGATTGACACTGTTTAGCAATTGTATAGATGAGATTAC
1 GTTTAGTAAAACGGTGCGATAGCGGTGCGATTGACACTGTTTAGCAACTGTACAGATGAGATTAC
* * *
98389 ACTGTATAGATTAAATTAGGTACTGTACAGATGAGATTGTTAGAGCAGCGATTGAAACGAAGTTT
66 ACTGTACAGATTAAATTAGGTACTGTACAAATGAGATTATTAGAGCAGCGATTGAAACGAAGTTT
* * * * *
98454 ACACTTAAACTCTGTTTGGTCCCAAAACGGTAGTGAAATGATTAAACGATGGTGAAACGATTACA
131 ACACTTAAACTCCGTTTGGACCCAAAACGGTAGTGAAAAGATCAAACGATGGTGAAAAGATTACA
*
98519 TATAAGAAGC
196 GATAAGAAGC
98529 CTAGTTGAAA
Statistics
Matches: 181, Mismatches: 24, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
214 18 0.10
215 163 0.90
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.28
Consensus pattern (214 bp):
GTTTAGTAAAACGGTGCGATAGCGGTGCGATTGACACTGTTTAGCAACTGTACAGATGAGATTAC
ACTGTACAGATTAAATTAGGTACTGTACAAATGAGATTATTAGAGCAGCGATTGAAACGAAGTTT
ACACTTAAACTCCGTTTGGACCCAAAACGGTAGTGAAAAGATCAAACGATGGTGAAAAGATTACA
GATAAGAAGCATAGGCTGC
Found at i:99481 original size:80 final size:79
Alignment explanation
Indices: 99348--99506 Score: 273
Period size: 80 Copynumber: 2.0 Consensus size: 79
99338 AAAGTGGTTT
99348 CGGATCTTAGACGACTTTTGAAGATAAGTTGCCTGGAAAACCTATTTTGGGAAGGGAAATAAAAA
1 CGGATCTTAGACGACTTTTGAAGATAAGTTGCCTGGAAAACCTATTTTGGGAAGGGAAATAAAAA
99413 CGAGGGGGAGTTGCA
66 CGA-GGGGAGTTGCA
** * *
99428 CGGATCTTAGACGACTTTTGAAGATGGGTTGGCTGGAAAACCTATTTTGGGAAGGGAAATGAAAA
1 CGGATCTTAGACGACTTTTGAAGATAAGTTGCCTGGAAAACCTATTTTGGGAAGGGAAATAAAAA
99493 CGAGGGGAGTTGCA
66 CGAGGGGAGTTGCA
99507 TAACGAATGC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
79 11 0.15
80 64 0.85
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (79 bp):
CGGATCTTAGACGACTTTTGAAGATAAGTTGCCTGGAAAACCTATTTTGGGAAGGGAAATAAAAA
CGAGGGGAGTTGCA
Done.