Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018819.1 Corchorus olitorius cultivar O-4 contig18852, 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: 116480
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:384 original size:27 final size:28
Alignment explanation
Indices: 316--390 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
306 TTAAGATGTC
* *
316 AAAATTACTGCTTTACCCTTGGTCAGCT
1 AAAATTACAGTTTTACCCTTGGTCAGCT
*
344 AAAATTACCA-TTTTACCCTTGGT-TGACT
1 AAAATTA-CAGTTTTACCCTTGGTCAG-CT
*
372 -AAATTACAGTTTTGCCCTT
1 AAAATTACAGTTTTACCCTT
391 AAATGCCGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 2 0.05
27 16 0.40
28 21 0.52
29 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.39
Consensus pattern (28 bp):
AAAATTACAGTTTTACCCTTGGTCAGCT
Found at i:843 original size:25 final size:24
Alignment explanation
Indices: 793--845 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
783 TGAGGAACTA
* *
793 TTTTATTACTGTTTTATTAATATG
1 TTTTATTAATGTTTTATAAATATG
817 TTTTATTAATGGTTTTAATAAAT-TG
1 TTTTATTAAT-GTTTT-ATAAATATG
842 TTTT
1 TTTT
846 GGGTGCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 11 0.44
26 5 0.20
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.62
Consensus pattern (24 bp):
TTTTATTAATGTTTTATAAATATG
Found at i:844 original size:13 final size:12
Alignment explanation
Indices: 793--845 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
783 TGAGGAACTA
*
793 TTTTATT-ACTG
1 TTTTATTAATTG
804 TTTTATTAATATG
1 TTTTATTAAT-TG
*
817 TTTTATTAATGG
1 TTTTATTAATTG
*
829 TTTTAATAAATTG
1 TTTT-ATTAATTG
842 TTTT
1 TTTT
846 GGGTGCATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 7 0.20
12 6 0.17
13 22 0.63
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.62
Consensus pattern (12 bp):
TTTTATTAATTG
Found at i:4331 original size:14 final size:13
Alignment explanation
Indices: 4300--4345 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
4290 ATCGGGTTTT
4300 AGTCAGTTTGTTG
1 AGTCAGTTTGTTG
*
4313 AGTCAGTTTTTTCG
1 AGTCAGTTTGTT-G
4327 AGTCAGTTAGTGTTG
1 AGTCAGTT--TGTTG
4342 AGTC
1 AGTC
4346 TGAGTCTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.43
Consensus pattern (13 bp):
AGTCAGTTTGTTG
Found at i:4856 original size:28 final size:28
Alignment explanation
Indices: 4816--4874 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
4806 AGTTCAAAAC
4816 AAGCATAAATTAACCATCAATTTATATA
1 AAGCATAAATTAACCATCAATTTATATA
4844 AAGCATAAATTAACCATCAATTTATATA
1 AAGCATAAATTAACCATCAATTTATATA
4872 AAG
1 AAG
4875 TCTGTGTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (28 bp):
AAGCATAAATTAACCATCAATTTATATA
Found at i:13219 original size:32 final size:31
Alignment explanation
Indices: 13141--13220 Score: 78
Period size: 32 Copynumber: 2.6 Consensus size: 31
13131 AGAAAATACC
*
13141 ATAACTAGAATTGTTGTTTTTCTTTTTTGGCG
1 ATAACTAGAATTGTTG-TTTTCTTTTTGGGCG
* *
13173 ATAACAAGAA---TTGTTTT-TTTTTGGGCAAT
1 ATAACTAGAATTGTTGTTTTCTTTTTGGGC--G
13202 ATAACTAGAATTGTTGTTT
1 ATAACTAGAATTGTTGTTT
13221 ATCAAAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
27 8 0.21
28 4 0.10
29 12 0.31
32 15 0.38
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.49
Consensus pattern (31 bp):
ATAACTAGAATTGTTGTTTTCTTTTTGGGCG
Found at i:15962 original size:30 final size:30
Alignment explanation
Indices: 15928--15989 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
15918 ATTTTTATCT
15928 TGACTTTCCTCTTATACTCTCAAATTTTAA
1 TGACTTTCCTCTTATACTCTCAAATTTTAA
* *
15958 TGACTTTTCTCTTATATTCTCAAATTTTAA
1 TGACTTTCCTCTTATACTCTCAAATTTTAA
15988 TG
1 TG
15990 GCTTATTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.50
Consensus pattern (30 bp):
TGACTTTCCTCTTATACTCTCAAATTTTAA
Found at i:17852 original size:27 final size:26
Alignment explanation
Indices: 17813--17864 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
17803 TTTAGGTCGG
* *
17813 TTTTTCTTTTTATATATATACTATAA
1 TTTTTCTTATTATATATAGACTATAA
*
17839 TTTTTCCTTATTATGTATAGACTATA
1 TTTTT-CTTATTATATATAGACTATA
17865 GAGGAGTCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTTTCTTATTATATATAGACTATAA
Found at i:22208 original size:17 final size:18
Alignment explanation
Indices: 22165--22212 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
22155 CTCCCAAAAG
22165 CAGAGCAAAACAGAGGAAA
1 CAGAG-AAAACAGAGGAAA
* *
22184 TAGA-AAAACAGA-GAAC
1 CAGAGAAAACAGAGGAAA
22200 CAGAGAAAACAGA
1 CAGAGAAAACAGA
22213 TTCCACCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 6 0.24
17 16 0.64
19 3 0.12
ACGTcount: A:0.60, C:0.15, G:0.23, T:0.02
Consensus pattern (18 bp):
CAGAGAAAACAGAGGAAA
Found at i:25028 original size:21 final size:20
Alignment explanation
Indices: 24985--25028 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
24975 GAACAACTGA
* *
24985 TTTCTTTGTTTTGGGTCTTT
1 TTTCTTTGTTTTGCGTCTGT
*
25005 TTTCATTTGTTTTGCTTCTGT
1 TTTC-TTTGTTTTGCGTCTGT
25026 TTT
1 TTT
25029 GGCCTTGGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.02, C:0.11, G:0.16, T:0.70
Consensus pattern (20 bp):
TTTCTTTGTTTTGCGTCTGT
Found at i:28337 original size:16 final size:16
Alignment explanation
Indices: 28312--28343 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28302 GGCAAATCAA
*
28312 ATAAATTAAATACCAT
1 ATAAAGTAAATACCAT
28328 ATAAAGTAAATACCAT
1 ATAAAGTAAATACCAT
28344 CATTAGAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.28
Consensus pattern (16 bp):
ATAAAGTAAATACCAT
Found at i:35295 original size:7 final size:7
Alignment explanation
Indices: 35277--35305 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
35267 AATGACATTA
35277 TTTATA-
1 TTTATAT
35283 TTTATAT
1 TTTATAT
35290 TTTATAT
1 TTTATAT
35297 TTTATAT
1 TTTATAT
35304 TT
1 TT
35306 GTCATTAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATAT
Found at i:36025 original size:13 final size:13
Alignment explanation
Indices: 36007--36036 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35997 AGAGAACCGA
*
36007 TTTTCATTCAGTG
1 TTTTCATTCAATG
36020 TTTTCATTCAATG
1 TTTTCATTCAATG
36033 TTTT
1 TTTT
36037 AAAATTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (13 bp):
TTTTCATTCAATG
Found at i:46315 original size:57 final size:55
Alignment explanation
Indices: 46204--46316 Score: 190
Period size: 57 Copynumber: 2.0 Consensus size: 55
46194 ATCCGTTTCT
*
46204 TTTCACACAATAAATGTTAAATAAATCCTATCCTCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTAAATAAATCCTATCCCCCTATCTCTACTTAATTATTC
*
46259 TTTCACACAATAAATGTTATAATAAATTCTATCCCCCTTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTA-AATAAATCCTATCCCCC-TATCTCTACTTAATTATTC
46316 T
1 T
46317 ACAGAATAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 19 0.35
56 15 0.28
57 20 0.37
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.42
Consensus pattern (55 bp):
TTTCACACAATAAATGTTAAATAAATCCTATCCCCCTATCTCTACTTAATTATTC
Found at i:46443 original size:42 final size:42
Alignment explanation
Indices: 46381--46461 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
46371 TAAGGATCAG
*
46381 GATTTGAGTTGAGTAGTTCTTAATTTATAAAGAATTTTCTAT
1 GATTTGAGTTGAGTAGTTCTTAATTTACAAAGAATTTTCTAT
* *
46423 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTAGTTCTTAATTTACAAAGAATTTTC
46462 AATACTTAGC
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:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTAGTTCTTAATTTACAAAGAATTTTCTAT
Found at i:47378 original size:6 final size:6
Alignment explanation
Indices: 47367--47398 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
47357 TTGCCTTAGA
47367 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
47399 GAAAAGAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:52353 original size:11 final size:12
Alignment explanation
Indices: 52333--52358 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52323 TCTTCAATTG
52333 TTTTGTTTTTTT
1 TTTTGTTTTTTT
52345 TTTTGTTTTTTT
1 TTTTGTTTTTTT
52357 TT
1 TT
52359 CAAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:54944 original size:55 final size:55
Alignment explanation
Indices: 54860--54972 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
54850 TTAAGTCACG
*
54860 TAAATTTGAAGTGGAGATTTAGTTATAAGGAGTATCTGTAGAGAGATTAATAACT
1 TAAATTTGAAGTGGAGATTGAGTTATAAGGAGTATCTGTAGAGAGATTAATAACT
54915 TAAATTTGAAGTGGAGATTGAGTTATAAGGAGTATCTGTAGAGAGATTAATAACT
1 TAAATTTGAAGTGGAGATTGAGTTATAAGGAGTATCTGTAGAGAGATTAATAACT
54970 TAA
1 TAA
54973 GCAGATAGAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.34
Consensus pattern (55 bp):
TAAATTTGAAGTGGAGATTGAGTTATAAGGAGTATCTGTAGAGAGATTAATAACT
Found at i:56033 original size:41 final size:41
Alignment explanation
Indices: 55976--56055 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
55966 AGCAATCATG
55976 AATAAGAGCACTGTAAGTTTGGTTACTATAACAAGTTGCCT
1 AATAAGAGCACTGTAAGTTTGGTTACTATAACAAGTTGCCT
56017 AATAAGAGCACTGTAAGTTTGGTTACTATAACAAGTTGC
1 AATAAGAGCACTGTAAGTTTGGTTACTATAACAAGTTGC
56056 AAGGCAACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (41 bp):
AATAAGAGCACTGTAAGTTTGGTTACTATAACAAGTTGCCT
Found at i:56115 original size:25 final size:25
Alignment explanation
Indices: 56081--56132 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
56071 TCGCATTCAA
56081 CCACAATTTTGCTATGTAAATTGAG
1 CCACAATTTTGCTATGTAAATTGAG
56106 CCACAATTTTGCTATGTAAATTGAG
1 CCACAATTTTGCTATGTAAATTGAG
56131 CC
1 CC
56133 TCTCGGCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (25 bp):
CCACAATTTTGCTATGTAAATTGAG
Found at i:64108 original size:42 final size:43
Alignment explanation
Indices: 64057--64150 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 43
64047 AGTTCATTAC
*
64057 CTAA-ATTCTACT-CCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAA
* * * *
64098 CTAATATTCTACTCCACCATTTCTAGATAATTCATCAATATAGAG
1 CTAATATTCTACT-C-CCATCTCTAGATAATTCATCAAAATAAAA
64143 CTAATATT
1 CTAATATT
64151 AATTGTTGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.18
45 32 0.73
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACTCCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:72424 original size:12 final size:12
Alignment explanation
Indices: 72407--72432 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
72397 AACAAAGATC
72407 TTAGGGTAATTA
1 TTAGGGTAATTA
72419 TTAGGGTAATTA
1 TTAGGGTAATTA
72431 TT
1 TT
72433 TGATATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (12 bp):
TTAGGGTAATTA
Found at i:73649 original size:60 final size:60
Alignment explanation
Indices: 73505--73632 Score: 238
Period size: 60 Copynumber: 2.1 Consensus size: 60
73495 AAATTGGTCA
* *
73505 CTAATGTTTGTAAAAATGCTCAAATAAGGGATTAATCTTTTAATTTGAATAATTAAGTTC
1 CTAATGTTTGTAAAAATGCTCAAATAAGGGACTAACCTTTTAATTTGAATAATTAAGTTC
73565 CTAATGTTTGTAAAAATGCTCAAATAAGGGACTAACCTTTTAATTTGAATAATTAAGTTC
1 CTAATGTTTGTAAAAATGCTCAAATAAGGGACTAACCTTTTAATTTGAATAATTAAGTTC
73625 CTAATGTT
1 CTAATGTT
73633 GCAAAATCGG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (60 bp):
CTAATGTTTGTAAAAATGCTCAAATAAGGGACTAACCTTTTAATTTGAATAATTAAGTTC
Found at i:75740 original size:25 final size:25
Alignment explanation
Indices: 75705--75778 Score: 130
Period size: 25 Copynumber: 3.0 Consensus size: 25
75695 TGTTAGTTTG
75705 TAGAGATCGAGCGAGGGTGCTCAAT
1 TAGAGATCGAGCGAGGGTGCTCAAT
*
75730 TAGAGACCGAGCGAGGGTGCTCAAT
1 TAGAGATCGAGCGAGGGTGCTCAAT
*
75755 TAGAGATCGAGCGAGAGTGCTCAA
1 TAGAGATCGAGCGAGGGTGCTCAA
75779 GATTGTTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.30, C:0.18, G:0.35, T:0.18
Consensus pattern (25 bp):
TAGAGATCGAGCGAGGGTGCTCAAT
Found at i:76681 original size:25 final size:25
Alignment explanation
Indices: 76647--76695 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
76637 TGTTAGTTTG
*
76647 TAGAGACCGAGCGAGGGTGCTCAAT
1 TAGAGACCGAGCGAGAGTGCTCAAT
76672 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
76696 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.20, G:0.35, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAT
Found at i:78182 original size:81 final size:81
Alignment explanation
Indices: 78047--78289 Score: 486
Period size: 81 Copynumber: 3.0 Consensus size: 81
78037 AAATTTTATT
78047 AAGATGATCTACATAGCTCAAGGATCATCATGGTACGCTCCTTGGTAGAAATCGCAACCTCTAGC
1 AAGATGATCTACATAGCTCAAGGATCATCATGGTACGCTCCTTGGTAGAAATCGCAACCTCTAGC
78112 CCTCTCAATTGGCTAA
66 CCTCTCAATTGGCTAA
78128 AAGATGATCTACATAGCTCAAGGATCATCATGGTACGCTCCTTGGTAGAAATCGCAACCTCTAGC
1 AAGATGATCTACATAGCTCAAGGATCATCATGGTACGCTCCTTGGTAGAAATCGCAACCTCTAGC
78193 CCTCTCAATTGGCTAA
66 CCTCTCAATTGGCTAA
78209 AAGATGATCTACATAGCTCAAGGATCATCATGGTACGCTCCTTGGTAGAAATCGCAACCTCTAGC
1 AAGATGATCTACATAGCTCAAGGATCATCATGGTACGCTCCTTGGTAGAAATCGCAACCTCTAGC
78274 CCTCTCAATTGGCTAA
66 CCTCTCAATTGGCTAA
78290 TTTTACCATT
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 162 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (81 bp):
AAGATGATCTACATAGCTCAAGGATCATCATGGTACGCTCCTTGGTAGAAATCGCAACCTCTAGC
CCTCTCAATTGGCTAA
Found at i:78751 original size:18 final size:18
Alignment explanation
Indices: 78709--78753 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
78699 GGGGTGACAT
78709 TTTAATAATAATTATTCA
1 TTTAATAATAATTATTCA
*** *
78727 GAAAATAATAATTATTTA
1 TTTAATAATAATTATTCA
78745 TTTAATAAT
1 TTTAATAAT
78754 TAATAAATTT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
TTTAATAATAATTATTCA
Found at i:84691 original size:17 final size:18
Alignment explanation
Indices: 84642--84691 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
84632 CTAAACCCAG
*
84642 GTAATCAAAGATCA-CAT
1 GTAATCTAAGATCACCAT
*
84659 GTGATCTAAGATCACCA-
1 GTAATCTAAGATCACCAT
84676 GTAATCTAAGATCACC
1 GTAATCTAAGATCACC
84692 CCTCATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 27 0.93
18 2 0.07
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (18 bp):
GTAATCTAAGATCACCAT
Found at i:85434 original size:38 final size:40
Alignment explanation
Indices: 85391--85476 Score: 99
Period size: 38 Copynumber: 2.2 Consensus size: 40
85381 GCCTTTTTAA
* * *
85391 CTAATTTTGAG-CACTATCGATCGTGATGGTTAGCATTGG
1 CTAATTTTGAGCCACTATCAATCATGATGGTTAACATTGG
* *
85430 -TAATTTTG-GCCATTGTCAATCATGATGGTTAACATTGG
1 CTAATTTTGAGCCACTATCAATCATGATGGTTAACATTGG
85468 CT-ATTTTGA
1 CTAATTTTGA
85477 TCATCTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
37 1 0.03
38 37 0.95
39 1 0.03
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (40 bp):
CTAATTTTGAGCCACTATCAATCATGATGGTTAACATTGG
Found at i:93562 original size:145 final size:150
Alignment explanation
Indices: 93337--93618 Score: 421
Period size: 145 Copynumber: 1.9 Consensus size: 150
93327 TCTATATATA
* * *
93337 GTATATATAATCGATTATGAGACGATCTTAGTTAATTATTAAATCGAGAGTAAGATTAAGATTAA
1 GTATAGATAATCGATTATGAGACAATCTTAGTTAA-TATTAAATCGAGAGTAAGACT-A-A-TAA
* *
93402 ATTAAATTAAAAGAAAATAAAAGAAGAATATATAGATCACATGACATCTATTATTAAGCTAAAAA
62 ATTAAATTAAAAGAAAATAAAAGAAGAATATATAGATCACATGACATCCATCATTAAGCTAAAAA
93467 AAAATAATAAAAAGTCAATCTCTT
127 AAAATAATAAAAAGTCAATCTCTT
*
93491 GTATAGATAATCGATTATGAGACAATTTTAGTTAA-A-TAAATCGAGAGT-AGACT-A-AAATTA
1 GTATAGATAATCGATTATGAGACAATCTTAGTTAATATTAAATCGAGAGTAAGACTAATAAATTA
* *
93551 AATTAAAAGAAAATAAAAGAAGAATATATAGATCACATGACATCCATCATTAAGCTATAAAAAGA
66 AATTAAAAGAAAATAAAAGAAGAATATATAGATCACATGACATCCATCATTAAGCTAAAAAAAAA
93616 TAA
131 TAA
93619 AAATTCATTC
Statistics
Matches: 120, Mismatches: 8, Indels: 9
0.88 0.06 0.07
Matches are distributed among these distances:
145 70 0.58
147 1 0.01
150 4 0.03
151 12 0.10
152 1 0.01
154 32 0.27
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (150 bp):
GTATAGATAATCGATTATGAGACAATCTTAGTTAATATTAAATCGAGAGTAAGACTAATAAATTA
AATTAAAAGAAAATAAAAGAAGAATATATAGATCACATGACATCCATCATTAAGCTAAAAAAAAA
TAATAAAAAGTCAATCTCTT
Found at i:97437 original size:39 final size:38
Alignment explanation
Indices: 97371--97454 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 38
97361 AAATTCTGAT
* *
97371 CACCTTGACTCATGATAATTAGCCTTGGTTATTTTGAC
1 CACCTTGACTCATGATAATTAGCCTTGGTCACTTTGAC
**
97409 CACCATTGA-TCATGATGGTTAGGCCTTGGTCACTTTGAC
1 CACC-TTGACTCATGATAATTA-GCCTTGGTCACTTTGAC
97448 CACCTTG
1 CACCTTG
97455 GGGCTTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
38 17 0.43
39 23 0.57
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (38 bp):
CACCTTGACTCATGATAATTAGCCTTGGTCACTTTGAC
Found at i:97604 original size:47 final size:46
Alignment explanation
Indices: 97550--97670 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 46
97540 GACTATGATA
*
97550 GTTAACCTTGGTCATTTTGTCAAATTTGGCCACCATCAGTTGTTATG
1 GTTAACCTTGG-CATTTTGTCAAATTTAGCCACCATCAGTTGTTATG
97597 GTTAACCTTGGCCATTTTGTCAAATTTAGCCACCATCAGTTGTTATG
1 GTTAACCTTGG-CATTTTGTCAAATTTAGCCACCATCAGTTGTTATG
*
97644 GTTAACCTTGAGCATTTTGGCAAATTT
1 GTTAACCTTG-GCATTTTGTCAAATTT
97671 TGACCACTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
47 69 0.99
48 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (46 bp):
GTTAACCTTGGCATTTTGTCAAATTTAGCCACCATCAGTTGTTATG
Found at i:98787 original size:84 final size:85
Alignment explanation
Indices: 98646--98819 Score: 264
Period size: 84 Copynumber: 2.1 Consensus size: 85
98636 AGAAATATAT
98646 TTAAAAATTATAATATATATCTAAGTTATGTAATTAAAATAGTAAAAATAATAAAAATAAAATAG
1 TTAAAAATTATAATATATATCTAAGTTATGTAATTAAAATAGTAAAAATAATAAAAATAAAATAG
98711 TTATAAAAAGATTAGATTTAA
66 TTATAAAAA-ATTAGATTTAA
* * **
98732 TTAAAAATTAT-A-ATATATCTAAGTTTTTTTAATTAAAATAGT-AAAATGGTAAAAATAAAATA
1 TTAAAAATTATAATATATATCTAAG-TTATGTAATTAAAATAGTAAAAATAATAAAAATAAAATA
*
98794 GTTATAAAGAATTAGATTTAA
65 GTTATAAAAAATTAGATTTAA
98815 TTAAA
1 TTAAA
98820 TAAAAATAGA
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
83 16 0.20
84 38 0.46
85 17 0.21
86 11 0.13
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (85 bp):
TTAAAAATTATAATATATATCTAAGTTATGTAATTAAAATAGTAAAAATAATAAAAATAAAATAG
TTATAAAAAATTAGATTTAA
Found at i:99401 original size:88 final size:86
Alignment explanation
Indices: 99302--99460 Score: 203
Period size: 88 Copynumber: 1.8 Consensus size: 86
99292 AGTTGTAATA
* **
99302 GTTAGCTTTGGCCAGTTTGGCAAATTTTGGTCACCTTGAGT-TATGATGGTTAGCCTTGGCCCAA
1 GTTAGCCTTGGCCAGTTTGGCAAATTTTGACCACCTTGAGTCT-TGATGGTTAGCCTTGG-CC-A
99366 TTTTGGCCATCATTGGCCGTGAAT
63 TTTTGGCCATCATTGGCCGTGAAT
* * * * * *
99390 GTTAGCCTTGGCCATTTTTGCGAGTTTTGACCACCTTGAGTCTTGATGGTTATCCTTGGTCATTT
1 GTTAGCCTTGGCCAGTTTGGCAAATTTTGACCACCTTGAGTCTTGATGGTTAGCCTTGGCCATTT
99455 TGGCCA
66 TGGCCA
99461 ATTTTGGTCT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
86 10 0.16
87 1 0.02
88 49 0.80
89 1 0.02
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.38
Consensus pattern (86 bp):
GTTAGCCTTGGCCAGTTTGGCAAATTTTGACCACCTTGAGTCTTGATGGTTAGCCTTGGCCATTT
TGGCCATCATTGGCCGTGAAT
Found at i:100061 original size:16 final size:16
Alignment explanation
Indices: 100042--100084 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
100032 AATTAGGTCA
*
100042 TTTTCGAGTTTAAATT
1 TTTTCGAATTTAAATT
* *
100058 TTTTCAAATTTAACTT
1 TTTTCGAATTTAAATT
*
100074 TTTTCGGATTT
1 TTTTCGAATTT
100085 GGATCATATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.58
Consensus pattern (16 bp):
TTTTCGAATTTAAATT
Found at i:101770 original size:22 final size:22
Alignment explanation
Indices: 101742--101783 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
101732 CAAACAAAGG
101742 CTAAAGAATCAAGGAGGCTTTT
1 CTAAAGAATCAAGGAGGCTTTT
*
101764 CTAAAGAATCAATGAGGCTT
1 CTAAAGAATCAAGGAGGCTT
101784 CTCACTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (22 bp):
CTAAAGAATCAAGGAGGCTTTT
Found at i:115904 original size:2 final size:2
Alignment explanation
Indices: 115891--115998 Score: 64
Period size: 2 Copynumber: 55.5 Consensus size: 2
115881 TTACTATGTA
* * *
115891 AT AT AT AC AT AT AT TT AT AT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
115933 AT -T AT GT A- AT AC AT AT CT AT AT -T ACT -T CT AA AT A- AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
115971 AT AT AT AT TT AT AT AT AGT AT AG AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT A
115999 ACATCACAAT
Statistics
Matches: 78, Mismatches: 21, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
1 5 0.06
2 70 0.90
3 3 0.04
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Done.