Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008108.1 Corchorus capsularis cultivar CVL-1 contig08129, 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: 25613
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Found at i:3180 original size:26 final size:26
Alignment explanation
Indices: 3144--3196 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3134 TGAAAATAAA
3144 ATAATTATTATAAGGTAGTTTGTGGT
1 ATAATTATTATAAGGTAGTTTGTGGT
3170 ATAATTATTATAAGGTAGTTTGTGGT
1 ATAATTATTATAAGGTAGTTTGTGGT
3196 A
1 A
3197 GTTTTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (26 bp):
ATAATTATTATAAGGTAGTTTGTGGT
Found at i:3224 original size:17 final size:18
Alignment explanation
Indices: 3192--3226 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3182 AGGTAGTTTG
3192 TGGTAGTTTTTATTAAAT
1 TGGTAGTTTTTATTAAAT
3210 TGGTAGTTTTT-TTAAAT
1 TGGTAGTTTTTATTAAAT
3227 GATATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (18 bp):
TGGTAGTTTTTATTAAAT
Found at i:4852 original size:3 final size:3
Alignment explanation
Indices: 4844--4894 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
4834 GTATAGATAT
*
4844 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
4890 ATA AT
1 ATA AT
4895 TTATGCTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:5895 original size:20 final size:19
Alignment explanation
Indices: 5867--5907 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5857 CAAAATCCTC
*
5867 TGATTTCGTTATCATTTGTT
1 TGATATCGTTATCATTT-TT
*
5887 TGATATCGTTGTCATTTTT
1 TGATATCGTTATCATTTTT
5906 TG
1 TG
5908 TTTTTACCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.15, C:0.10, G:0.17, T:0.59
Consensus pattern (19 bp):
TGATATCGTTATCATTTTT
Found at i:8350 original size:3 final size:3
Alignment explanation
Indices: 8342--8368 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
8332 ACATAACACA
8342 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
8369 AAGTATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11167 original size:16 final size:17
Alignment explanation
Indices: 11146--11180 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11136 ATCACCAAAC
11146 AACAAA-TTATCACAGT
1 AACAAACTTATCACAGT
*
11162 AACAAACTTTTCACAGT
1 AACAAACTTATCACAGT
11179 AA
1 AA
11181 TACAGGCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.26
Consensus pattern (17 bp):
AACAAACTTATCACAGT
Found at i:13162 original size:74 final size:74
Alignment explanation
Indices: 13044--13450 Score: 539
Period size: 74 Copynumber: 5.5 Consensus size: 74
13034 AGAAAATTAG
13044 AAGACTGACTTAATTTC-AAGGAAATTAGGTAAA-AGAAGACTGACTTAATTTC-A-AA-GAAAT
1 AAGACTGACTTAATTTCGAAGGAAATTAGGTAAAGA-AAGACTGACTTAATTTCAAGAAGGAAAT
13104 TAGGTAAAGA
65 TAGGTAAAGA
* *
13114 AAGACTGGCTTAATTTCAAGGAAGGAAATTAGGCAAAGAAAGACTGACTTAATTTCAAGGAAGGA
1 AAGACTGACTTAATTTC---GAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAA-GAAGGA
13179 AATTAGGTAAAGA
62 AATTAGGTAAAGA
* *
13192 TAGACTGACTTAATTT-GGAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCGAAGAAGGAAAT
1 AAGACTGACTTAATTTCGAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTC-AAGAAGGAAAT
13256 TAGGTAAAGA
65 TAGGTAAAGA
* *
13266 TAGACTGACTTAATTTC-AACGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAGGAAAT
1 AAGACTGACTTAATTTCGAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAA-GAAGGAAAT
13330 TAGGTAAA-A
65 TAGGTAAAGA
*
13339 GAAGACTGACTTAATTTC-AAGGAAATTAGGTAAA-AGAAGACTGACTTAATTTTAAGAAAGGAA
1 -AAGACTGACTTAATTTCGAAGGAAATTAGGTAAAGA-AAGACTGACTTAATTTCAAG-AAGGAA
13402 ATTAGGTAAA-A
63 ATTAGGTAAAGA
*
13413 GAAGACTGACTTAATTTCAAGAAAGGAAATTAAGTAAA
1 -AAGACTGACTTAATTTC--G-AAGGAAATTAGGTAAA
13451 AGATGTGACA
Statistics
Matches: 306, Mismatches: 12, Indels: 30
0.88 0.03 0.09
Matches are distributed among these distances:
70 16 0.05
73 5 0.02
74 235 0.77
75 4 0.01
77 2 0.01
78 44 0.14
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (74 bp):
AAGACTGACTTAATTTCGAAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAGAAGGAAATT
AGGTAAAGA
Found at i:13453 original size:39 final size:37
Alignment explanation
Indices: 13042--13450 Score: 515
Period size: 39 Copynumber: 11.0 Consensus size: 37
13032 AAAGAAAATT
13042 AGAAGACTGACTTAATTTC---AAGGAAATTAGGTAAA
1 AGAAGACTGACTTAATTTCAAGAAGGAAATTAGGT-AA
13077 AGAAGACTGACTTAATTTC-A-AA-GAAATTAGGTAA
1 AGAAGACTGACTTAATTTCAAGAAGGAAATTAGGTAA
* *
13111 AGAAAGACTGGCTTAATTTCAAGGAAGGAAATTAGGCAA
1 AG-AAGACTGACTTAATTTCAA-GAAGGAAATTAGGTAA
13150 AGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AG-AAGACTGACTTAATTTCAA-GAAGGAAATTAGGTAA
*
13189 AGATAGACTGACTTAATTT---GGAGGAAATTAGGTAA
1 AGA-AGACTGACTTAATTTCAAGAAGGAAATTAGGTAA
13224 AGAAAGACTGACTTAATTTCGAAGAAGGAAATTAGGTAA
1 AG-AAGACTGACTTAATTTC-AAGAAGGAAATTAGGTAA
*
13263 AGATAGACTGACTTAATTTC---AACGAAATTAGGTAA
1 AGA-AGACTGACTTAATTTCAAGAAGGAAATTAGGTAA
13298 AGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAAA
1 AG-AAGACTGACTTAATTTCAA-GAAGGAAATTAGGT-AA
13338 AGAAGACTGACTTAATTTC---AAGGAAATTAGGTAAA
1 AGAAGACTGACTTAATTTCAAGAAGGAAATTAGGT-AA
*
13373 AGAAGACTGACTTAATTTTAAGAAAGGAAATTAGGTAAA
1 AGAAGACTGACTTAATTTCAAG-AAGGAAATTAGGT-AA
*
13412 AGAAGACTGACTTAATTTCAAGAAAGGAAATTAAGTAA
1 AGAAGACTGACTTAATTTCAAG-AAGGAAATTAGGTAA
13450 A
1 A
13451 AGATGTGACA
Statistics
Matches: 340, Mismatches: 11, Indels: 43
0.86 0.03 0.11
Matches are distributed among these distances:
34 4 0.01
35 143 0.42
36 5 0.01
38 7 0.02
39 177 0.52
40 4 0.01
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (37 bp):
AGAAGACTGACTTAATTTCAAGAAGGAAATTAGGTAA
Found at i:13453 original size:113 final size:106
Alignment explanation
Indices: 13042--13450 Score: 479
Period size: 113 Copynumber: 3.7 Consensus size: 106
13032 AAAGAAAATT
13042 AGAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACTTAATTTC-AAA-GAAATT
1 AGAAGACTGACTTAATTTCAAGGAAATTAGGT-AAAGAAGACTGACTTAATTTCGAAAGGAAATT
* *
13105 AGGTAAAGAAAGACTGGCTTAATTTCAAGGAAGGAAATTAGGCAA
65 AGGTAAAGAAAGACTGACTTAATTTC-A--AAGGAAATTAGGTAA
*
13150 AGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAAAGATAGACTGACTTAATTT-G-GAGG
1 AG-AAGACTGACTTAATTTC----AAGGAAATTAGGTAAAGA-AGACTGACTTAATTTCGAAAGG
13213 AAATTAGGTAAAGAAAGACTGACTTAATTTCGAAGAAGGAAATTAGGTAA
60 AAATTAGGTAAAGAAAGACTGACTTAATTTC--A-AAGGAAATTAGGTAA
* *
13263 AGATAGACTGACTTAATTTCAACGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAGGAA
1 AGA-AGACTGACTTAATTTCAAGGAAATTAGGTAAAG-AAGACTGACTTAATTTC--GAAAGGAA
13328 ATTAGGTAAA-AGAAGACTGACTTAATTTC-AAGGAAATTAGGTAAA
62 ATTAGGTAAAGA-AAGACTGACTTAATTTCAAAGGAAATTAGGT-AA
*
13373 AGAAGACTGACTTAATTTTAAGAAAGGAAATTAGGTAAAAGAAGACTGACTTAATTTCAAGAAAG
1 AGAAGACTGACTTAA-TTT---CAAGGAAATTAGGT-AAAGAAGACTGACTTAATTTC--GAAAG
*
13438 GAAATTAAGTAAA
59 GAAATTAGGTAAA
13451 AGATGTGACA
Statistics
Matches: 270, Mismatches: 9, Indels: 39
0.85 0.03 0.12
Matches are distributed among these distances:
108 2 0.01
109 73 0.27
110 9 0.03
112 9 0.03
113 171 0.63
114 6 0.02
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (106 bp):
AGAAGACTGACTTAATTTCAAGGAAATTAGGTAAAGAAGACTGACTTAATTTCGAAAGGAAATTA
GGTAAAGAAAGACTGACTTAATTTCAAAGGAAATTAGGTAA
Found at i:14596 original size:27 final size:27
Alignment explanation
Indices: 14566--14640 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 27
14556 CCCATTTTTT
*
14566 TAAATTACTGTTTTACCCTTGGTCAG-C
1 TAAATTACAGTTTTACCCTTGGT-AGAC
*
14593 TAAAATTACCA-TTTTACCCTTGGTTGAC
1 T-AAATTA-CAGTTTTACCCTTGGTAGAC
*
14621 TAAATTACAGTTTTGCCCTT
1 TAAATTACAGTTTTACCCTT
14641 AAATTCCGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
26 2 0.05
27 17 0.41
28 21 0.51
29 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (27 bp):
TAAATTACAGTTTTACCCTTGGTAGAC
Found at i:15553 original size:16 final size:15
Alignment explanation
Indices: 15512--15558 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
15502 ATTTGATTTA
15512 TTATTAATAA-TTGTT
1 TTATT-ATAACTTGTT
15527 TTATTATAACTTGTT
1 TTATTATAACTTGTT
*
15542 TTTTTATGAAC-TGTT
1 TTATTAT-AACTTGTT
15557 TT
1 TT
15559 GGTTGTGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
15 22 0.76
16 3 0.10
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (15 bp):
TTATTATAACTTGTT
Found at i:16049 original size:18 final size:18
Alignment explanation
Indices: 16026--16063 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
16016 GGCGGTTGTC
16026 CGTGCTCGACTTCCGGGT
1 CGTGCTCGACTTCCGGGT
16044 CGTGCTCGACTTCCGGGT
1 CGTGCTCGACTTCCGGGT
16062 CG
1 CG
16064 GGGCGTGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.34, G:0.34, T:0.26
Consensus pattern (18 bp):
CGTGCTCGACTTCCGGGT
Found at i:16119 original size:36 final size:36
Alignment explanation
Indices: 16073--16645 Score: 538
Period size: 40 Copynumber: 15.4 Consensus size: 36
16063 GGGGCGTGAC
*
16073 AAAAGAAGACTGACTTAATTTC-AAGGAAATTAGGT
1 AAAAAAAGACTGACTTAATTTCAAAGGAAATTAGGT
16108 AAAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
1 -AAAAAAAGACTGACTTAATTTC---AAAGGAAATTAGGT
16148 AAAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
1 -AAAAAAAGACTGACTTAATTTC---AAAGGAAATTAGGT
* *
16188 -AAAAAAGACTGGCTTAATCTCAAGAAAGGAAATTAGGT
1 AAAAAAAGACTGACTTAATTTC---AAAGGAAATTAGGT
* ** *
16226 AAAGAGAAGACTGGTTTAATTTC-AATGAAATTAGGT
1 AAA-AAAAGACTGACTTAATTTCAAAGGAAATTAGGT
* *
16262 AAAAAGAAGACTGGCTTAATTTC-AAGGAAATTAAGT
1 AAAAA-AAGACTGACTTAATTTCAAAGGAAATTAGGT
* *
16298 -AAAAAAGACTGGCTTAATTTC-AAGGAAATTAAGT
1 AAAAAAAGACTGACTTAATTTCAAAGGAAATTAGGT
* *
16332 -AAAAAAGACTGGCTTAATTTCAAGAAAGGAAATTAGTT
1 AAAAAAAGACTGACTTAATTTC---AAAGGAAATTAGGT
*
16370 AAAAAGAAGACTGTCTTAATTTC-AAGGAAATTAGGT
1 AAAAA-AAGACTGACTTAATTTCAAAGGAAATTAGGT
* * *
16406 AAAGATAGACTGGCTTAATTTCAAGAAAGGAAATTAGGT
1 AAAAAAAGACTGACTTAATTTC---AAAGGAAATTAGGT
* *
16445 -AAAAAAGACTGGCTTAATTTTAAGAAAGGAAATTAGGT
1 AAAAAAAGACTGACTTAA-TTT--CAAAGGAAATTAGGT
* *
16483 -AAAGAAGACTGACTTAATTTC-AAGGAAATTAGAT
1 AAAAAAAGACTGACTTAATTTCAAAGGAAATTAGGT
* *
16517 AAAATGAAGACTGACTTAATTTCAAGGAAGGAAATTAGGC
1 AAAA-AAAGACTGACTTAATTTC-A--AAGGAAATTAGGT
* *
16557 AAATAAAGACTAACTTAATTTCAAAAGGAAATTAGGT
1 AAAAAAAGACTGACTTAATTTC-AAAGGAAATTAGGT
* *
16594 AAAGAAAGACTGAATTAATTTCAAGAAAGGAAATTAGGT
1 AAAAAAAGACTGACTTAATTTC---AAAGGAAATTAGGT
*
16633 AAAGAAAGACTGA
1 AAAAAAAGACTGA
16646 GGCACAGGCT
Statistics
Matches: 474, Mismatches: 35, Indels: 53
0.84 0.06 0.09
Matches are distributed among these distances:
34 63 0.13
35 23 0.05
36 97 0.20
37 34 0.07
38 91 0.19
39 67 0.14
40 99 0.21
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.25
Consensus pattern (36 bp):
AAAAAAAGACTGACTTAATTTCAAAGGAAATTAGGT
Found at i:16150 original size:40 final size:39
Alignment explanation
Indices: 16073--16645 Score: 614
Period size: 38 Copynumber: 15.3 Consensus size: 39
16063 GGGGCGTGAC
*
16073 AAAAGAAGACTGACTTAATTTC----AAGGAAATTAGGT
1 AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
16108 AAAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
1 -AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
16148 AAAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
1 -AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
* *
16188 -AAAAAAGACTGGCTTAATCTCAAGAAAGGAAATTAGGT
1 AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
* ** *
16226 AAAGAGAAGACTGGTTTAATTTC----AATGAAATTAGGT
1 AAA-AAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
* *
16262 AAAAAGAAGACTGGCTTAATTTC----AAGGAAATTAAGT
1 AAAAA-AAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
* *
16298 -AAAAAAGACTGGCTTAATTTC----AAGGAAATTAAGT
1 AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
* *
16332 -AAAAAAGACTGGCTTAATTTCAAGAAAGGAAATTAGTT
1 AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
*
16370 AAAAAGAAGACTGTCTTAATTTC----AAGGAAATTAGGT
1 AAAAA-AAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
* * *
16406 AAAGATAGACTGGCTTAATTTCAAGAAAGGAAATTAGGT
1 AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
* *
16445 -AAAAAAGACTGGCTTAATTTTAAGAAAGGAAATTAGGT
1 AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
* *
16483 -AAAGAAGACTGACTTAATTTC----AAGGAAATTAGAT
1 AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
* * *
16517 AAAATGAAGACTGACTTAATTTCAAGGAAGGAAATTAGGC
1 AAAA-AAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
* *
16557 AAATAAAGACTAACTTAATTTC-A-AAAGGAAATTAGGT
1 AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
* *
16594 AAAGAAAGACTGAATTAATTTCAAGAAAGGAAATTAGGT
1 AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
*
16633 AAAGAAAGACTGA
1 AAAAAAAGACTGA
16646 GGCACAGGCT
Statistics
Matches: 477, Mismatches: 35, Indels: 47
0.85 0.06 0.08
Matches are distributed among these distances:
34 63 0.13
35 23 0.05
36 97 0.20
37 31 0.06
38 102 0.21
39 62 0.13
40 99 0.21
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.25
Consensus pattern (39 bp):
AAAAAAAGACTGACTTAATTTCAAGAAAGGAAATTAGGT
Found at i:16639 original size:18 final size:18
Alignment explanation
Indices: 16580--16640 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
16570 CTTAATTTCA
16580 AAAGGAAATTAGGTAAAG
1 AAAGGAAATTAGGTAAAG
** *
16598 AAA-GACTGAATTAATTTCAAG
1 AAAGGA---AATT-AGGTAAAG
16619 AAAGGAAATTAGGTAAAG
1 AAAGGAAATTAGGTAAAG
16637 AAAG
1 AAAG
16641 ACTGAGGCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
17 2 0.06
18 12 0.38
19 4 0.12
20 4 0.12
21 8 0.25
22 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (18 bp):
AAAGGAAATTAGGTAAAG
Found at i:16762 original size:36 final size:32
Alignment explanation
Indices: 16668--16809 Score: 189
Period size: 32 Copynumber: 4.3 Consensus size: 32
16658 ATTTCGGGGA
*
16668 AGGG-AATTAAGTAGAATAAAAGGCTTAATTC
1 AGGGTAATTAAGTAGAATAAAAGACTTAATTC
*
16699 AGGGTAATTAAGTAGAATAAAAAACTTAATTC
1 AGGGTAATTAAGTAGAATAAAAGACTTAATTC
*
16731 AGGGTAATTAAGTGGAGCTAATAAAAGACTTAATTT
1 AGGGTAATTAAGT--AG--AATAAAAGACTTAATTC
*
16767 AGGGTAATTAAGTAGAAT-AAAGAACTTGATTC
1 AGGGTAATTAAGTAGAATAAAAG-ACTTAATTC
16799 AGGGTAATTAA
1 AGGGTAATTAA
16810 ATGGAGTCAA
Statistics
Matches: 99, Mismatches: 6, Indels: 11
0.85 0.05 0.09
Matches are distributed among these distances:
31 8 0.08
32 59 0.60
34 4 0.04
36 28 0.28
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (32 bp):
AGGGTAATTAAGTAGAATAAAAGACTTAATTC
Found at i:16763 original size:68 final size:68
Alignment explanation
Indices: 16682--16832 Score: 225
Period size: 68 Copynumber: 2.2 Consensus size: 68
16672 AATTAAGTAG
* *
16682 AATAAAAGGCTTAATTCAGGGTAATTAAGTAGAATAAAAAACTTAATTCAGGGTAATTAAGTGGA
1 AATAAAAGACTTAATTCAGGGTAATTAAGTAGAATAAAAAACTTAATTCAGGGTAATTAAATGGA
16747 G-C
66 GTC
* * *
16749 TAATAAAAGACTTAATTTAGGGTAATTAAGTAGAATAAAGAACTTGATTCAGGGTAATTAAATGG
1 -AATAAAAGACTTAATTCAGGGTAATTAAGTAGAATAAAAAACTTAATTCAGGGTAATTAAATGG
16814 AGTC
65 AGTC
16818 AAT-AAAGAACTTAAT
1 AATAAAAG-ACTTAAT
16833 CTAAAAAGAG
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
67 4 0.05
68 71 0.93
69 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (68 bp):
AATAAAAGACTTAATTCAGGGTAATTAAGTAGAATAAAAAACTTAATTCAGGGTAATTAAATGGA
GTC
Found at i:16828 original size:36 final size:32
Alignment explanation
Indices: 16668--16832 Score: 156
Period size: 32 Copynumber: 4.9 Consensus size: 32
16658 ATTTCGGGGA
* *
16668 AGGG-AATTAAGTAGAATAAA-AGGCTTAATTC
1 AGGGTAATTAAGGAGAATAAAGA-ACTTAATTC
* *
16699 AGGGTAATTAAGTAGAATAAAAAACTTAATTC
1 AGGGTAATTAAGGAGAATAAAGAACTTAATTC
*
16731 AGGGTAATTAAGTGGAGCTAATAAA-AGACTTAATTT
1 AGGGTAATTAA--GGAG--AATAAAGA-ACTTAATTC
* *
16767 AGGGTAATTAAGTAGAATAAAGAACTTGATTC
1 AGGGTAATTAAGGAGAATAAAGAACTTAATTC
16799 AGGGTAATTAAATGGAGTCAATAAAGAACTTAAT
1 AGGGTAATT-AA-GGAG--AATAAAGAACTTAAT
16833 CTAAAAAGAG
Statistics
Matches: 114, Mismatches: 8, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
31 4 0.04
32 57 0.50
33 4 0.04
34 9 0.08
35 1 0.01
36 39 0.34
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (32 bp):
AGGGTAATTAAGGAGAATAAAGAACTTAATTC
Found at i:18381 original size:76 final size:76
Alignment explanation
Indices: 18294--18446 Score: 243
Period size: 76 Copynumber: 2.0 Consensus size: 76
18284 ATCTAGGAAC
*
18294 ACAACCAAAATGCAATTTTAGGTATATATAGATTTATATTTCCATAAATTTAATCAAATCCAAAT
1 ACAACCAAAATGCAATTTGAGGTATATATAGATTTATATTTCCATAAATTTAATCAAATCCAAAT
* *
18359 TACGAGAATTA
66 TAAGAAAATTA
* * * *
18370 ACAACCGAAATGCACTTTGAGGTATATATAGATTTATATTTCCATAAATTTGATCGAATCCAAAT
1 ACAACCAAAATGCAATTTGAGGTATATATAGATTTATATTTCCATAAATTTAATCAAATCCAAAT
18435 TAAGAAAATTA
66 TAAGAAAATTA
18446 A
1 A
18447 AGATTAATTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (76 bp):
ACAACCAAAATGCAATTTGAGGTATATATAGATTTATATTTCCATAAATTTAATCAAATCCAAAT
TAAGAAAATTA
Found at i:23792 original size:36 final size:36
Alignment explanation
Indices: 23745--23876 Score: 167
Period size: 36 Copynumber: 3.7 Consensus size: 36
23735 TTAAGCGTGA
* *
23745 TAGGGTACGCCTTACTTCCTCCTCTCCAAGGGATGG
1 TAGGGTGCGCCTTACTTCTTCCTCTCCAAGGGATGG
* *
23781 TAGGGTGCGCCTTACTTCTTCCTCCCCACAAGG-TGG
1 TAGGGTGCGCCTTACTTCTTCCTCTCCA-AGGGATGG
** * *
23817 TAGCATGCGCCTTACCTCTTCCTCTCCAAGGGATAG
1 TAGGGTGCGCCTTACTTCTTCCTCTCCAAGGGATGG
*
23853 TAGGGTGCGCCCTACTTCTTCCTC
1 TAGGGTGCGCCTTACTTCTTCCTC
23877 CCCAGGAGCA
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
35 3 0.04
36 74 0.93
37 3 0.04
ACGTcount: A:0.15, C:0.33, G:0.23, T:0.29
Consensus pattern (36 bp):
TAGGGTGCGCCTTACTTCTTCCTCTCCAAGGGATGG
Done.