Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012754.1 Corchorus olitorius cultivar O-4 contig12787, 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: 54299
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7194 original size:33 final size:33
Alignment explanation
Indices: 7152--7223 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
7142 GAGGGAGAGC
* *
7152 AGATGTGCTTGTCCCACCGGGCGTGCCAAAAAG
1 AGATGTGCTTGTCCCACCGGACGTGACAAAAAG
*
7185 AGATGTGCTTGTCCCACTGGACGTGACAAAAAG
1 AGATGTGCTTGTCCCACCGGACGTGACAAAAAG
7218 AGATGT
1 AGATGT
7224 TGCGCCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (33 bp):
AGATGTGCTTGTCCCACCGGACGTGACAAAAAG
Found at i:9012 original size:19 final size:18
Alignment explanation
Indices: 8984--9027 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
8974 GGGATTTTTG
*
8984 ATAATAATTATTCAATAAA
1 ATAATTATTATTCAAT-AA
* *
9003 ATAATTATTATTTAATTA
1 ATAATTATTATTCAATAA
9021 ATAATTA
1 ATAATTA
9028 ATTTCAGTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTATTATTCAATAA
Found at i:11437 original size:14 final size:15
Alignment explanation
Indices: 11405--11436 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11395 GAGAACATGA
*
11405 TTTGAGAAAAACCTT
1 TTTGAAAAAAACCTT
11420 TTTGAAAAAAACCTT
1 TTTGAAAAAAACCTT
11435 TT
1 TT
11437 GTTACCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (15 bp):
TTTGAAAAAAACCTT
Found at i:13464 original size:22 final size:22
Alignment explanation
Indices: 13436--13478 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13426 CTTTTTTTTA
13436 GAGAGAGTAATCAAAAGAGAGG
1 GAGAGAGTAATCAAAAGAGAGG
* *
13458 GAGAGAGTAATCTAGAGAGAG
1 GAGAGAGTAATCAAAAGAGAG
13479 CTGTTCGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.37, T:0.12
Consensus pattern (22 bp):
GAGAGAGTAATCAAAAGAGAGG
Found at i:15164 original size:27 final size:27
Alignment explanation
Indices: 15129--15201 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
15119 AGTGAATTTA
*
15129 AAATGACCAAAATGCCCCTGAATATGC
1 AAATGACCAAAATGCCCCTGAACATGC
* * *
15156 AAATGACCAAAATGCCCTTGGACGTGC
1 AAATGACCAAAATGCCCCTGAACATGC
*
15183 AAATGACTAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
15202 AGGTGACCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.19
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAACATGC
Found at i:15757 original size:10 final size:10
Alignment explanation
Indices: 15742--15771 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
15732 AAGTAATACT
15742 TCCCCACTTA
1 TCCCCACTTA
15752 TCCCCACTTA
1 TCCCCACTTA
15762 TCCCCACTTA
1 TCCCCACTTA
15772 AGCAGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.50, G:0.00, T:0.30
Consensus pattern (10 bp):
TCCCCACTTA
Found at i:22003 original size:54 final size:54
Alignment explanation
Indices: 21932--23017 Score: 998
Period size: 54 Copynumber: 20.2 Consensus size: 54
21922 TATCAATTGG
* *
21932 AGATCAACTCTGATCATCGAAAACATCTTGAAATGACCGCACTGGATCATCTGA
1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* ** * *
21986 AGATCAACTCT-AGTCATCGAAAAGTTCTTGGAAAAATCGCACTGGATCAAT-TGG
1 AGATCAACTCTGA-TCATCGAAAACTTCTTGGAATGACCGCACTGGATC-ATCTGA
* * * * *
22040 AGATCAACTCTGATCATCGCAAATTTCTTGAAATGATCGCACTGGATCATCTGG
1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* *
22094 AGATCAACTCTGATCATTGAAAACTTCTTGAAATGACCGCACTGGATCATCTGA
1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* * * * * * * * *
22148 GGATTAACTCTAATCATTGAAAAATTCTTAGAATGACCGCATTGTATCAAT-TGG
1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATC-ATCTGA
* * *
22202 AGATCAACTCTGATCGTTGAAAACTTCTTGGAATAACCGCACTGGATCATCTGA
1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* * * * *
22256 GGATCAACTCTGATC-TCTGAAAACTTCTTAGAATGACCGCATTGTATCAAT-TGG
1 AGATCAACTCTGATCATC-GAAAACTTCTTGGAATGACCGCACTGGATC-ATCTGA
* *
22310 AGATCAACTCTGATCATTG-AAATTATCTTGGAATGACCGCACTGGATCATCT-A
1 AGATCAACTCTGATCATCGAAAACT-TCTTGGAATGACCGCACTGGATCATCTGA
* * * ** *
22363 AGGATCAACTCTAATC-TCTAAAAACTTTTTTTAATGACCGCACTGGATCATCTGG
1 A-GATCAACTCTGATCATC-GAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* *
22418 GGATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTG-
1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* * *
22471 GGAATCAACTCTGATC-TCTAAAAACTTTTTTGGAATGACCGCACTGGATCATCT-A
1 AG-ATCAACTCTGATCATC-GAAAAC-TTCTTGGAATGACCGCACTGGATCATCTGA
* * *
22526 GGAATCAACTCTGATCA-CTGAAAACTTCTCGGAATGATCGCACTGGATCATCTG-
1 AG-ATCAACTCTGATCATC-GAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* * * * * *
22580 GGAATCAACTCTGATC-TCTAAAAACTTC-TGTGAAAGACCGCACAGGATCATATGG
1 AG-ATCAACTCTGATCATC-GAAAACTTCTTG-GAATGACCGCACTGGATCATCTGA
* *
22635 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACTGCACCGGATCATCT-A
1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* * * * * * * *
22688 GGGTCAACTCCGATCATCGAAAACTTCATGAAATGACCACACTGAATCAAT-TGG
1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATC-ATCTGA
* *
22742 AGATCAACTATGATCATCGAAAACTTCTTGGAATAACCGCACTGGATCATCTGA
1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* * * * *
22796 GGATCAACTCTGATCA-CTAAGGACTTCTTGGAATGACCGCATTGGGTCATCT-A
1 AGATCAACTCTGATCATCGAA-AACTTCTTGGAATGACCGCACTGGATCATCTGA
* * * * *
22849 GGGATCAGCTCTGATC-TCCAAAAACTTTTTGGAATGACCGCACTGGGTCATCTG-
1 -AGATCAACTCTGATCAT-CGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* * ** * * *
22903 GGATCAAATCTGATCAAAGAAAACTTCTTGGAATGATCGCATTGTATCATCTG-
1 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* * * * * *
22956 -GATCAACTCTGATC-TCTGAAAGCATCTAT-GAAAGACCGCACAGGGTCATCTTA
1 AGATCAACTCTGATCATC-GAAAACTTCT-TGGAATGACCGCACTGGATCATCTGA
*
23009 AAATCAACT
1 AGATCAACT
23018 TAGACTTCTG
Statistics
Matches: 852, Mismatches: 140, Indels: 80
0.79 0.13 0.07
Matches are distributed among these distances:
52 37 0.04
53 107 0.13
54 637 0.75
55 71 0.08
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (54 bp):
AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
Found at i:23028 original size:54 final size:53
Alignment explanation
Indices: 22970--23195 Score: 231
Period size: 54 Copynumber: 4.2 Consensus size: 53
22960 AACTCTGATC
* * * *
22970 TCTGAAAGCATCTATGAAAGACCGCACAGGGTCATCTT-AAAATCAACTTAGACT
1 TCTGAAAACTTCTATGAAAGACCGCACAGGGTCAT-TTGAAGATCAACTTA-AAT
* * ** *
23024 TCTGAAAACTTCGAAGAAACCCCGCACAGGGTTATTTGAAGATCAACTTAAAT
1 TCTGAAAACTTCTATGAAAGACCGCACAGGGTCATTTGAAGATCAACTTAAAT
* * * *
23077 CTCTGAAAACTTCTATGAAAGACCGCATAGGCTCATCTGAAGATCAAATTAAAT
1 -TCTGAAAACTTCTATGAAAGACCGCACAGGGTCATTTGAAGATCAACTTAAAT
* * * **
23131 TTTGAAAACTTCTATGAAAGACCGCACATGGCCATTTGAACG-TCAACTTAGACC
1 TCTGAAAACTTCTATGAAAGACCGCACAGGGTCATTTGAA-GATCAACTTA-AAT
23185 TCTGAAAACTT
1 TCTGAAAACTT
23196 TAAAAGATCG
Statistics
Matches: 140, Mismatches: 28, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
53 45 0.32
54 95 0.68
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.26
Consensus pattern (53 bp):
TCTGAAAACTTCTATGAAAGACCGCACAGGGTCATTTGAAGATCAACTTAAAT
Found at i:23188 original size:107 final size:108
Alignment explanation
Indices: 22969--23195 Score: 269
Period size: 107 Copynumber: 2.1 Consensus size: 108
22959 CAACTCTGAT
* * * * * *
22969 CTCTGAAAGCATCTATGAAAGACCGCACAGGGTCATCTTAAAATCAACTTAGACTTCTGAAAACT
1 CTCTGAAAACTTCTATGAAAGACCGCACAGGCTCATCTGAAAATCAAATTAGAATTCTGAAAACT
* ** *
23034 TCGAAGAAACCCCGCACAGGGTTATTTGAAGATCAACTTAAAT
66 TCGAAGAAACACCGCACAGGGCCATTTGAAGATCAACTTAAAC
* * *
23077 CTCTGAAAACTTCTATGAAAGACCGCATAGGCTCATCTGAAGATCAAATTA-AATTTTGAAAACT
1 CTCTGAAAACTTCTATGAAAGACCGCACAGGCTCATCTGAAAATCAAATTAGAATTCTGAAAACT
* * * * *
23141 TCTATGAAAGACCGCACATGGCCATTTGAACG-TCAACTTAGAC
66 TCGAAGAAACACCGCACAGGGCCATTTGAA-GATCAACTTAAAC
23184 CTCTGAAAACTT
1 CTCTGAAAACTT
23196 TAAAAGATCG
Statistics
Matches: 100, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
107 55 0.55
108 45 0.45
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.26
Consensus pattern (108 bp):
CTCTGAAAACTTCTATGAAAGACCGCACAGGCTCATCTGAAAATCAAATTAGAATTCTGAAAACT
TCGAAGAAACACCGCACAGGGCCATTTGAAGATCAACTTAAAC
Found at i:25044 original size:11 final size:11
Alignment explanation
Indices: 25028--25055 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
25018 TCATAATTTC
25028 TTTTTTCCTTT
1 TTTTTTCCTTT
25039 TTTTTTCCTTT
1 TTTTTTCCTTT
25050 TTTTTT
1 TTTTTT
25056 GCTTGCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTCCTTT
Found at i:25077 original size:11 final size:12
Alignment explanation
Indices: 25024--25065 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
25014 TCTTTCATAA
25024 TTTCTTTTTTCC
1 TTTCTTTTTTCC
25036 TTT-TTTTTTCC
1 TTTCTTTTTTCC
*
25047 TTT-TTTTTTGC
1 TTTCTTTTTTCC
*
25058 TTGCTTTT
1 TTTCTTTT
25066 CTTTTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 20 0.74
12 7 0.26
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.79
Consensus pattern (12 bp):
TTTCTTTTTTCC
Found at i:27758 original size:15 final size:16
Alignment explanation
Indices: 27728--27767 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
27718 TTGCTTTGTT
*
27728 TTGTTTCCTAGTTTAA
1 TTGTTTTCTAGTTTAA
27744 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
27759 TTGTTTTCT
1 TTGTTTTCT
27768 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:28081 original size:30 final size:31
Alignment explanation
Indices: 28031--28091 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
28021 TTCTCTAGTC
*
28031 TCTGCGTTTTTTATCTAAAAAAAAATTGTTT
1 TCTGCGTTTTTTATCTAAAAAAAAAATGTTT
28062 TCTGCG-TTTTT-TCTAAAAAAAAAAATGTTT
1 TCTGCGTTTTTTATCT-AAAAAAAAAATGTTT
28092 GTTTTGCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 3 0.11
30 19 0.68
31 6 0.21
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (31 bp):
TCTGCGTTTTTTATCTAAAAAAAAAATGTTT
Found at i:28100 original size:32 final size:30
Alignment explanation
Indices: 28031--28105 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
28021 TTCTCTAGTC
*
28031 TCTGCGTTTTTTATCTAAAAAAAAATTGTTT
1 TCTGCG-TTTTTATCTAAAAAAAAAATGTTT
28062 TCTGCGTTTTT-TCTAAAAAAAAAAATGTTTGT
1 TCTGCGTTTTTATCT-AAAAAAAAAATG-TT-T
*
28094 TTTGCGTTTTTA
1 TCTGCGTTTTTA
28106 ATTTTTTGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 3 0.08
30 16 0.42
31 8 0.21
32 11 0.29
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.49
Consensus pattern (30 bp):
TCTGCGTTTTTATCTAAAAAAAAAATGTTT
Found at i:31074 original size:21 final size:21
Alignment explanation
Indices: 31050--31094 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31040 GCCCTGCTAG
* *
31050 CCGTGCCTTCCTCTGCGTCAT
1 CCGTGCCTTCCTCCGCGCCAT
*
31071 CCGTGCCTTCTTCCGCGCCAT
1 CCGTGCCTTCCTCCGCGCCAT
31092 CCG
1 CCG
31095 AGCCAAATGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.47, G:0.20, T:0.29
Consensus pattern (21 bp):
CCGTGCCTTCCTCCGCGCCAT
Found at i:34613 original size:15 final size:16
Alignment explanation
Indices: 34583--34615 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
34573 TTGCTTTGTT
34583 TTGTTTCCTAGTTTAA
1 TTGTTTCCTAGTTTAA
*
34599 TTGTTTTCT-GTTTAA
1 TTGTTTCCTAGTTTAA
34614 TT
1 TT
34616 CATTTCTTTC
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:0.15, C:0.09, G:0.12, T:0.64
Consensus pattern (16 bp):
TTGTTTCCTAGTTTAA
Found at i:37611 original size:15 final size:16
Alignment explanation
Indices: 37591--37623 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
37581 TATCATTCAT
37591 AATATATCC-TTAAAA
1 AATATATCCTTTAAAA
37606 AATATATCCTTTAAAA
1 AATATATCCTTTAAAA
37622 AA
1 AA
37624 ATACATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (16 bp):
AATATATCCTTTAAAA
Found at i:37826 original size:19 final size:19
Alignment explanation
Indices: 37808--37844 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
37798 TATTAATTAT
*
37808 TTTA-ATATTATATTTTTA
1 TTTATATATTACATTTTTA
37826 TTTATATATTACATTTTTA
1 TTTATATATTACATTTTTA
37845 CTTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTACATTTTTA
Found at i:37981 original size:13 final size:13
Alignment explanation
Indices: 37963--37989 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37953 AAATATAATA
37963 AATATGATTTATG
1 AATATGATTTATG
37976 AATATGATTTATG
1 AATATGATTTATG
37989 A
1 A
37990 GGTTATAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
AATATGATTTATG
Found at i:40048 original size:39 final size:37
Alignment explanation
Indices: 40005--40320 Score: 268
Period size: 39 Copynumber: 8.7 Consensus size: 37
39995 TACTTTGTCA
* *
40005 ATTTCGATCATGGTTTAGGATCATTGCTTTGTCAGTTTT
1 ATTTCGATCCTGGTTTAGGATCATTGCTTT-TTAG-TTT
40044 ATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTT
1 ATTTCGATCCTGGTTTAGGATCATTGCTTT-TTAGTTT
* * *
40082 ATTTCGATCCTAGTTTAGGATCATTTCCTTTTTTGCTTT
1 ATTTCGATCCTGGTTTAGGATCA-TTGCTTTTTAG-TTT
* *
40121 ATTTCGATCCTGGTTTAGGGTCATTGC--TTTA--TG
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTTTAGTTT
* * *
40154 AGTTCAATCCTGGTTTACGATCATTG---TTTA--TT
1 ATTTCGATCCTGGTTTAGGATCATTGCTTTTTAGTTT
* *
40186 -TTTCAATCCTGGTTTAGGATCATTGCTTTATCAGTTT
1 ATTTCGATCCTGGTTTAGGATCATTGCTTT-TTAGTTT
*
40223 ATTTTCAATCCTGGTTTAGGATCATTG---TTTA--TT
1 A-TTTCGATCCTGGTTTAGGATCATTGCTTTTTAGTTT
* * *
40256 -TCTCAATCCTGGTTTTAGGATCATTGCTTTATCAGTTT
1 ATTTCGATCCTGG-TTTAGGATCATTGCTTT-TTAGTTT
* *
40294 ATTTTCAATCCTAGTTTAGGATCATTG
1 A-TTTCGATCCTGGTTTAGGATCATTG
40321 TTTATTTCTC
Statistics
Matches: 234, Mismatches: 24, Indels: 38
0.79 0.08 0.13
Matches are distributed among these distances:
31 34 0.15
32 18 0.08
33 25 0.11
34 1 0.00
35 5 0.02
36 6 0.03
37 2 0.01
38 33 0.14
39 100 0.43
40 10 0.04
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (37 bp):
ATTTCGATCCTGGTTTAGGATCATTGCTTTTTAGTTT
Found at i:40132 original size:77 final size:73
Alignment explanation
Indices: 40045--40329 Score: 274
Period size: 71 Copynumber: 4.0 Consensus size: 73
40035 GTCAGTTTTA
* * * *
40045 TTTCGATCCTGGTTTAGGATCATTGCTTTATTAGTTTATTTCGATCCTAGTTTAGGATCATTTCC
1 TTTCAATCCTGGTTTAGGATCATTGCTTTATCAGTTTATTTCAATCCTGGTTTAGGATCATTT--
40110 TTTTTTGCTTT
64 TTTTTT-CTTT
* * * *
40121 ATTTCGATCCTGGTTTAGGGTCATTGCTTTAT--G---AGTTCAATCCTGGTTTACGATCA---T
1 -TTTCAATCCTGGTTTAGGATCATTGCTTTATCAGTTTATTTCAATCCTGGTTTAGGATCATTTT
* *
40178 TGTTT-ATT
65 TTTTTCTTT
40186 TTTCAATCCTGGTTTAGGATCATTGCTTTATCAGTTTATTTTCAATCCTGGTTTAGGATCATTGT
1 TTTCAATCCTGGTTTAGGATCATTGCTTTATCAGTTTA-TTTCAATCCTGGTTTAGGATCATT-T
*
40251 TTATTTC---
64 TTTTTTCTTT
*
40258 --TCAATCCTGGTTTTAGGATCATTGCTTTATCAGTTTATTTTCAATCCTAGTTTAGGATCATTG
1 TTTCAATCCTGG-TTTAGGATCATTGCTTTATCAGTTTA-TTTCAATCCTGGTTTAGGATCATT-
*
40321 TTTATTTCT
63 TTTTTTTCT
40330 CGAATCCTGG
Statistics
Matches: 182, Mismatches: 13, Indels: 31
0.81 0.06 0.14
Matches are distributed among these distances:
64 29 0.16
65 2 0.01
66 1 0.01
67 5 0.03
69 1 0.01
70 30 0.16
71 59 0.32
72 19 0.10
74 5 0.03
75 1 0.01
77 30 0.16
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.50
Consensus pattern (73 bp):
TTTCAATCCTGGTTTAGGATCATTGCTTTATCAGTTTATTTCAATCCTGGTTTAGGATCATTTTT
TTTTCTTT
Found at i:40150 original size:30 final size:30
Alignment explanation
Indices: 40114--40656 Score: 500
Period size: 30 Copynumber: 17.2 Consensus size: 30
40104 ATTTCCTTTT
* *
40114 TTGCTTTATTTCGATCCTGGTTTAGGGTCA
1 TTGCTTTATTTCAATCCTGGTTTAGGATCA
*
40144 TTGCTTTATGAGTTCAATCCTGGTTTACGATCA
1 TTGCTTTAT---TTCAATCCTGGTTTAGGATCA
40177 TTG-TTTATTTTTCAATCCTGGTTTAGGATCA
1 TTGCTTTA--TTTCAATCCTGGTTTAGGATCA
40208 TTGCTTTATCAGTTTATTTTCAATCCTGGTTTAGGATCA
1 TTG------C--TTTA-TTTCAATCCTGGTTTAGGATCA
40247 TTG-TTTATTTCTCAATCCTGGTTTTAGGATCA
1 TTGCTTTA-TT-TCAATCCTGG-TTTAGGATCA
*
40279 TTGCTTTATCAGTTTATTTTCAATCCTAGTTTAGGATCA
1 TTG------C--TTTA-TTTCAATCCTGGTTTAGGATCA
*
40318 TTG-TTTATTTCTCGAATCCTGGTTTAGGATCC
1 TTGCTTTA-TT-TC-AATCCTGGTTTAGGATCA
*
40350 TTG-TTTATTTCTCAATCCTGGTTGAGGATCA
1 TTGCTTTA-TT-TCAATCCTGGTTTAGGATCA
* *
40381 TTGCTTTATTTTAATCCTGGTTTAGGATTA
1 TTGCTTTATTTCAATCCTGGTTTAGGATCA
*** *
40411 TTGCTTTATTTTGGTCCTAGTTTAGGATCA
1 TTGCTTTATTTCAATCCTGGTTTAGGATCA
* *
40441 TTGCTTTATTTTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTCAATCCTGGTTTAGGATCA
* *
40471 TTGCTTTATTTAAATCCTGATTTAGGATCA
1 TTGCTTTATTTCAATCCTGGTTTAGGATCA
* * * * *
40501 TTTCTTCATTTTAATCCTGATCTAGGATCA
1 TTGCTTTATTTCAATCCTGGTTTAGGATCA
* *
40531 TTGCTTTATTTAAATCCTGGTTGAGGATCA
1 TTGCTTTATTTCAATCCTGGTTTAGGATCA
* * *
40561 TTGCTTCATTTAAATCCTGGTTGAGGATCA
1 TTGCTTTATTTCAATCCTGGTTTAGGATCA
* * * *
40591 TTGCTTCATTTAAATCCTGATTTAGGATCG
1 TTGCTTTATTTCAATCCTGGTTTAGGATCA
*
40621 TTGCTTTATTTTAATCCTGGTTTAGGATCA
1 TTGCTTTATTTCAATCCTGGTTTAGGATCA
40651 TTGCTT
1 TTGCTT
40657 CATCAGTTAA
Statistics
Matches: 444, Mismatches: 41, Indels: 56
0.82 0.08 0.10
Matches are distributed among these distances:
30 257 0.58
31 56 0.13
32 50 0.11
33 21 0.05
34 1 0.00
39 39 0.09
40 13 0.03
41 7 0.02
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.47
Consensus pattern (30 bp):
TTGCTTTATTTCAATCCTGGTTTAGGATCA
Found at i:40236 original size:103 final size:100
Alignment explanation
Indices: 40050--40656 Score: 391
Period size: 90 Copynumber: 6.2 Consensus size: 100
40040 TTTTATTTCG
* *
40050 ATCCTGGTTTAGGATCATTGCTTTATTAGTTTATTTCGATCCTAGTTTAGGATCATTTCCTTTTT
1 ATCCTGGTTTAGGATCATTGC--T-TTA--TT-TTTCAATCCTAGTTTAGGATCA-TTGC-TTTT
* * * *
40115 TGCTTTA-TTTCGATCCTGGTTTAGGGTCATTGCTTTATGAGT-TCA
58 AG-TTTATTTTCAATCCTGGTTTAGGATCATTG-TTTAT--TTCTCA
* *
40160 ATCCTGGTTTACGATCATTG-TTTATTTTTCAATCCTGGTTTAGGATCATTGCTTTATCAGTTTA
1 ATCCTGGTTTAGGATCATTGCTTTATTTTTCAATCCTAGTTTAGGATCATTGCTTT-T-AGTTTA
40224 TTTTCAATCCTGGTTTAGGATCATTGTTTATTTCTCA
64 TTTTCAATCCTGGTTTAGGATCATTGTTTATTTCTCA
40261 ATCCTGGTTTTAGGATCATTGCTTTATCAGTTTATTTTCAATCCTAGTTTAGGATCATTG--TTT
1 ATCCTGG-TTTAGGATCATTGC-TT-T-A---T-TTTTCAATCCTAGTTTAGGATCATTGCTTTT
* *
40324 A---T-TTCTCGAATCCTGGTTTAGGATCCTTGTTTATTTCTCA
58 AGTTTATTTTC-AATCCTGGTTTAGGATCATTGTTTATTTCTCA
* * *
40364 ATCCTGGTTGAGGATCATTGCTTTA-TTTT-AATCCTGGTTTAGGATTATTGC------TTTATT
1 ATCCTGGTTTAGGATCATTGCTTTATTTTTCAATCCTAGTTTAGGATCATTGCTTTTAGTTTATT
** *
40421 TT-GGTCCTAGTTTAGGATCATTGCTTTATTT-T-A
66 TTCAATCCTGGTTTAGGATCATTG-TTTATTTCTCA
* * * *
40454 ATCCTGGTTGAGGATCATTGCTTTA--TTTAAATCCT-GATTTAGGATCA-----TTT-CTTCAT
1 ATCCTGGTTTAGGATCATTGCTTTATTTTTCAATCCTAG-TTTAGGATCATTGCTTTTAGTTTAT
* * *
40510 TTT-AATCCTGATCTAGGATCATTGCTTTA-TT-TAA
65 TTTCAATCCTGGTTTAGGATCATTG-TTTATTTCTCA
* * * * * *
40544 ATCCTGGTTGAGGATCATTGCTTCA--TTTAAATCCTGGTTGAGGATCATTGC-TTCA-TTTA--
1 ATCCTGGTTTAGGATCATTGCTTTATTTTTCAATCCTAGTTTAGGATCATTGCTTTTAGTTTATT
* *
40603 ---AATCCTGATTTAGGATCGTTGCTTTATTT-T-A
66 TTCAATCCTGGTTTAGGATCATTG-TTTATTTCTCA
40634 ATCCTGGTTTAGGATCATTGCTT
1 ATCCTGGTTTAGGATCATTGCTT
40657 CATCAGTTAA
Statistics
Matches: 430, Mismatches: 34, Indels: 86
0.78 0.06 0.16
Matches are distributed among these distances:
89 7 0.02
90 160 0.37
91 22 0.05
92 8 0.02
93 22 0.05
94 9 0.02
99 1 0.00
100 2 0.00
101 15 0.03
102 42 0.10
103 83 0.19
104 4 0.01
105 1 0.00
106 5 0.01
107 2 0.00
108 2 0.00
109 1 0.00
110 44 0.10
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (100 bp):
ATCCTGGTTTAGGATCATTGCTTTATTTTTCAATCCTAGTTTAGGATCATTGCTTTTAGTTTATT
TTCAATCCTGGTTTAGGATCATTGTTTATTTCTCA
Found at i:40380 original size:173 final size:176
Alignment explanation
Indices: 40015--40389 Score: 453
Period size: 173 Copynumber: 2.1 Consensus size: 176
40005 ATTTCGATCA
* *
40015 TGGTTTAGGATCATTGCTTTGTCAGTTTTATTTCGATCCTGGTTTAGGATCATTGCTTTATTAGT
1 TGGTTTAGGATCATTGCTTTATCAGTTTTATTTCAATCCTGGTTTAGGATCATTG--TTATTAG-
* * ** * * *
40080 TTATTTCGATCCTAGTTTAGGATCATTTCCTTTTTTGCTTTATTTCGATCCTGGTTTAGGGTCAT
63 TTATCTCAATCCTAGTTTAGGATCATTTCCTTTTCAGCTTTATTTCAATCCTAGTTTAGGATCAT
*
40145 TGCTTTATGAGTTCAATCCTGGTTTACGATCATTGTTTATTTTTCAATCC
128 TGCTTTAT-AGTTCAATCCTGGTTTACGATCATTGTTTATTTCTCAATCC
40195 TGGTTTAGGATCATTGCTTTATCAG-TTTATTTTCAATCCTGGTTTAGGATCATTG-T-TTA-TT
1 TGGTTTAGGATCATTGCTTTATCAGTTTTA-TTTCAATCCTGGTTTAGGATCATTGTTATTAGTT
* *
40256 -TCTCAATCCTGGTTTTAGGATCA-TTGCTTTATCAG-TTTATTTTCAATCCTAGTTTAGGATCA
65 ATCTCAATCCTAG-TTTAGGATCATTTCCTTT-TCAGCTTTA-TTTCAATCCTAGTTTAGGATCA
* * *
40318 TTG-TTTAT-TTCTCGAATCCTGGTTTAGGATCCTTGTTTATTTCTCAATCC
127 TTGCTTTATAGT-TC-AATCCTGGTTTACGATCATTGTTTATTTCTCAATCC
*
40368 TGGTTGAGGATCATTGCTTTAT
1 TGGTTTAGGATCATTGCTTTAT
40390 TTTAATCCTG
Statistics
Matches: 173, Mismatches: 16, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
171 1 0.01
172 2 0.01
173 78 0.45
174 36 0.21
176 3 0.02
177 1 0.01
179 4 0.02
180 48 0.28
ACGTcount: A:0.18, C:0.15, G:0.17, T:0.49
Consensus pattern (176 bp):
TGGTTTAGGATCATTGCTTTATCAGTTTTATTTCAATCCTGGTTTAGGATCATTGTTATTAGTTA
TCTCAATCCTAGTTTAGGATCATTTCCTTTTCAGCTTTATTTCAATCCTAGTTTAGGATCATTGC
TTTATAGTTCAATCCTGGTTTACGATCATTGTTTATTTCTCAATCC
Found at i:40829 original size:39 final size:39
Alignment explanation
Indices: 40743--40831 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
40733 TTTGAATCTT
*
40743 GATCATTGCTTTATCAGTTTTATTTTAGTCATGATTTAG
1 GATCATTGCTTTATCAGTTTTATTTTAGTCATGATTCAG
* * * *
40782 CAGT-ATTGCTTTGTCAGTTTTATTTT-GATCTTGGTTCAG
1 GA-TCATTGCTTTATCAGTTTTATTTTAG-TCATGATTCAG
40821 GATCATTGCTT
1 GATCATTGCTT
40832 GTCGGTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
38 2 0.05
39 38 0.93
40 1 0.02
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.51
Consensus pattern (39 bp):
GATCATTGCTTTATCAGTTTTATTTTAGTCATGATTCAG
Found at i:41229 original size:26 final size:26
Alignment explanation
Indices: 41166--41260 Score: 120
Period size: 26 Copynumber: 3.6 Consensus size: 26
41156 TAAAGTCATC
* *
41166 CAGGGGCATTTTAGTCATTTGCA-TGT
1 CAGGGGCATTTTGGTCATTTGTACT-T
41192 CCAGGGGCATTTTGGTCATTTGTACTT
1 -CAGGGGCATTTTGGTCATTTGTACTT
*
41219 CAGGGGCATTTTGGTTATTTGTACTT
1 CAGGGGCATTTTGGTCATTTGTACTT
* *
41245 CAGGGGGATTTCGGTC
1 CAGGGGCATTTTGGTC
41261 TTTTTTTTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
26 38 0.62
27 22 0.36
28 1 0.02
ACGTcount: A:0.16, C:0.16, G:0.29, T:0.39
Consensus pattern (26 bp):
CAGGGGCATTTTGGTCATTTGTACTT
Found at i:41637 original size:18 final size:18
Alignment explanation
Indices: 41614--41663 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
41604 TTATATTAGA
*
41614 TGCACTTAGCTTTGGGCT
1 TGCACTTAGCATTGGGCT
**
41632 TGCACTGGGCATTGGGCT
1 TGCACTTAGCATTGGGCT
*
41650 TGCATTTAGGCATT
1 TGCACTTA-GCATT
41664 TTAGCTTTAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.36
Consensus pattern (18 bp):
TGCACTTAGCATTGGGCT
Found at i:51025 original size:199 final size:197
Alignment explanation
Indices: 50480--51031 Score: 773
Period size: 189 Copynumber: 2.8 Consensus size: 197
50470 CATTACCACT
50480 CCTCATTTCATCATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAAC
1 CCTCATTTCATCA-TAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAA-
* * *
50545 CCTTAAACCCCACACGTGCAGTCTGCTAAAATCCATTGACGGTGTATTA-TATAATTTTTCTTAT
64 CCTTAAACCCTACACGTGCAGTCTGCTAAACTCCACTGACGGTGTA-TAGTATAATTTTTCTTAT
* * * ** *
50609 AGGATTATTATACAATACGCTGTCAGTGTAAATTTTGGACTCTATAAGCAGGTTAAGAAGTTAGC
128 AAGATTATTATACAATACACTGTTAGTGTAAATTTTAAACTCCATAAGCAGGTTAAGAAGTTAGC
50674 ACATA
193 ACATA
50679 CCTCATTTCATCAT--TTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGT----C
1 CCTCATTTCATCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACC
* * * *
50738 --AAACCCTGCACGTGTAGTCTGTTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATATG
66 TTAAACCCTACACGTGCAGTCTGCTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATAAG
*
50801 ATTATTATACAATACACTGTTAGTGTAAATTTTAAACTCCATAAGCGGGTTAAGAAGTT-GACAC
131 ATTATTATACAATACACTGTTAGTGTAAATTTTAAACTCCATAAGCAGGTTAAGAAGTTAG-CAC
50865 ATA
195 ATA
* * *
50868 CCTCATTTCATAATAAATTAAATATTTAATATTAATATATATTCCTTAAGGGGACACATGTCAAC
1 CCTCATTTCATCAT-AATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAAC
* * * * *
50933 CATTAAACCCTACACGTGCAGTCTGCTAAACTCGACTGACAGTGTATAGCATAAATTTTCCTATA
65 C-TTAAACCCTACACGTGCAGTCTGCTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATA
*
50998 AGATTATTATACAATACACTTTTAGTGTAAATTT
129 AGATTATTATACAATACACTGTTAGTGTAAATTT
51032 GTTTGTGTAT
Statistics
Matches: 315, Mismatches: 26, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
188 3 0.01
189 125 0.40
191 1 0.00
192 42 0.13
196 45 0.14
198 1 0.00
199 98 0.31
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (197 bp):
CCTCATTTCATCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACC
TTAAACCCTACACGTGCAGTCTGCTAAACTCCACTGACGGTGTATAGTATAATTTTTCTTATAAG
ATTATTATACAATACACTGTTAGTGTAAATTTTAAACTCCATAAGCAGGTTAAGAAGTTAGCACA
TA
Done.