Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021860.1 Corchorus olitorius cultivar O-4 contig21893, 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: 56200
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5275 original size:26 final size:26
Alignment explanation
Indices: 5226--5288 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
5216 TCATGGCGTC
*
5226 TCCTTTCTTTACCTTTCCTCCCCTTT
1 TCCTTTCTTTTCCTTTCCTCCCCTTT
* * *
5252 TCCTTTCTTTTCTTTTTCTTCCCTTT
1 TCCTTTCTTTTCCTTTCCTCCCCTTT
* *
5278 TTCTTTATTTT
1 TCCTTTCTTTT
5289 TCCTCTCTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (26 bp):
TCCTTTCTTTTCCTTTCCTCCCCTTT
Found at i:6645 original size:29 final size:30
Alignment explanation
Indices: 6592--6668 Score: 113
Period size: 29 Copynumber: 2.6 Consensus size: 30
6582 GCTAAATACC
**
6592 CAAAA-AATCCCTTACATTTTCTTTTGGGA
1 CAAAATAATCCCTTATGTTTTCTTTTGGGA
6621 CAAAATAATCCCTTATGTTTT-TTTTGGGA
1 CAAAATAATCCCTTATGTTTTCTTTTGGGA
*
6650 CAAATTAATCCCTTATGTT
1 CAAAATAATCCCTTATGTT
6669 GTAAAAATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 31 0.70
30 13 0.30
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTTGGGA
Found at i:7868 original size:12 final size:12
Alignment explanation
Indices: 7851--7884 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
7841 AGAAGAAAGG
7851 AAAAGAAAACAA
1 AAAAGAAAACAA
7863 AAAAGAAAA-AA
1 AAAAGAAAACAA
7874 ATAAAGAAAAC
1 A-AAAGAAAAC
7885 GGTATCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.15
12 17 0.85
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (12 bp):
AAAAGAAAACAA
Found at i:10661 original size:22 final size:21
Alignment explanation
Indices: 10609--10662 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
10599 TGCTTCTTGA
10609 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
10630 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
10649 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
10663 CATGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:19992 original size:21 final size:21
Alignment explanation
Indices: 19961--20009 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
19951 AGTAACAATA
*
19961 AAATAAA-TAAGCAACAAA-AT
1 AAATAAATTAAG-AAAAAAGAT
*
19981 AATTAAATTAAGAAAAAAGAT
1 AAATAAATTAAGAAAAAAGAT
20002 AAATAAAT
1 AAATAAAT
20010 ACTCCAATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.20
Consensus pattern (21 bp):
AAATAAATTAAGAAAAAAGAT
Found at i:21683 original size:53 final size:53
Alignment explanation
Indices: 21614--21715 Score: 132
Period size: 53 Copynumber: 1.9 Consensus size: 53
21604 TTCCAATTTT
* ** ** * *
21614 TTTTAGTTTAATCAAACCATGGAAAGTTTTTCTATCTTTTATTTTTCCACATG
1 TTTTAGTTTAACCAAACCATAAAAAGTGCTTCCATCATTTATTTTTCCACATG
*
21667 TTTTATTTTAACCAAACCATAAAAAGTGCTTCCATCATTTATTTTTCCA
1 TTTTAGTTTAACCAAACCATAAAAAGTGCTTCCATCATTTATTTTTCCA
21716 TGTTTAATTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 41 1.00
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (53 bp):
TTTTAGTTTAACCAAACCATAAAAAGTGCTTCCATCATTTATTTTTCCACATG
Found at i:24496 original size:389 final size:390
Alignment explanation
Indices: 23728--24506 Score: 1472
Period size: 389 Copynumber: 2.0 Consensus size: 390
23718 CTCTTATAAA
*
23728 ACTTTTGAATCGCCCATTATATCCTTATTTTTCGAATATATTTCTTAAATACCATTGTTTAGATT
1 ACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATATATTTCTTAAATACCATTGTTTAGATT
23793 TTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTAT
66 TTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTAT
*
23858 TTAATTTTTACCATTTTACTATTTTAATTAAAAAATTATATATATTAGAATTTTTTAAATATATT
131 TTAATTTTTACCATTTTACTATTTTAATTAAAAAATTATATATATTAGAATTTTTTAAATATAAT
23923 TTTATAGTTTTACTCAACAAAAAACTCTATTTTTTGGCAAAAAAAAACTAAAAAATCTATGTTTA
196 TTTATAGTTTTACTCAACAAAAAACTCTATTTTTTGGCAAAAAAAAACTAAAAAATCTATGTTTA
23988 TTTAATTGAATCTAATATCCATATACCTATTTTATTTTTATCAATTTACTAATTTAATTAAAAAA
261 TTTAATTGAATCTAATATCCATATACCTATTTTATTTTTATCAATTTACTAATTTAATTAAAAAA
24053 CTTAGATAGATTATAATTTTTAAAATATATTTCTTAAATGATATTGATTAAATTTTACAGTTTTT
326 CTTAGATAGATTATAATTTTTAAAATATATTTCTTAAATGATATTGATTAAATTTTACAGTTTTT
*
24118 ACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATATATTTCTTAAATGCCATTGTTTAGATT
1 ACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATATATTTCTTAAATACCATTGTTTAGATT
24183 TTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTAT
66 TTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTAT
24248 TTAATTTTTACCATTTTACTATTTTAATTAAAAAATTATATATATTAGAA-TTTTTAAATATAAT
131 TTAATTTTTACCATTTTACTATTTTAATTAAAAAATTATATATATTAGAATTTTTTAAATATAAT
* *
24312 TTTATAGTTTTACTCAACTAAAAACTCTATTTTTTGGCAAAAAAAAACTAAAAAATCTATTTTTA
196 TTTATAGTTTTACTCAACAAAAAACTCTATTTTTTGGCAAAAAAAAACTAAAAAATCTATGTTTA
*
24377 TTTAATT-AATTCTAATATCCTTATACCTATTTTATTTTTATCAATTTACTAATTTAATTAAAAA
261 TTTAATTGAA-TCTAATATCCATATACCTATTTTATTTTTATCAATTTACTAATTTAATTAAAAA
*
24441 ACTTAGATATATTATAATTTTTAAAATATATTTCTTAAATGATATTGATTAAATTTTACAGTTTT
325 ACTTAGATAGATTATAATTTTTAAAATATATTTCTTAAATGATATTGATTAAATTTTACAGTTTT
24506 T
390 T
24507 TAAGAAATAA
Statistics
Matches: 381, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
388 2 0.01
389 201 0.53
390 178 0.47
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (390 bp):
ACTTTTGAATCGCCCATTATACCCTTATTTTTCGAATATATTTCTTAAATACCATTGTTTAGATT
TTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTAT
TTAATTTTTACCATTTTACTATTTTAATTAAAAAATTATATATATTAGAATTTTTTAAATATAAT
TTTATAGTTTTACTCAACAAAAAACTCTATTTTTTGGCAAAAAAAAACTAAAAAATCTATGTTTA
TTTAATTGAATCTAATATCCATATACCTATTTTATTTTTATCAATTTACTAATTTAATTAAAAAA
CTTAGATAGATTATAATTTTTAAAATATATTTCTTAAATGATATTGATTAAATTTTACAGTTTTT
Found at i:24519 original size:159 final size:157
Alignment explanation
Indices: 24198--24484 Score: 396
Period size: 159 Copynumber: 1.8 Consensus size: 157
24188 AGTTTTACTC
* *
24198 AACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCATT
1 AACTAAAAAATCTATTTTTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCAAT
* * * **
24263 TTACTATTTTAATTAAAAAATTATATATATTAGAATTTTTAAATATAATTTTATAGTTTTACTCA
66 TTACTAATTTAATTAAAAAATTAGATATATTAGAATTTTTAAATATAATTTTATAATGATACTCA
24328 ACTAAAAACTCTATTTTTTGGCAAAAAAA
131 ACTAAAAACTCTATTTTTT-G-AAAAAAA
* * * * *
24357 AACTAAAAAATCTATTTTTATTTAATTAATTCTAATATCCTTATACCTATTTTATTTTTATCAAT
1 AACTAAAAAATCTATTTTTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCAAT
* *
24422 TTACTAATTTAATTAAAAAACTTAGATATATTATAATTTTTAAAATATATTTCTTA-AATGATA
66 TTACTAATTTAATTAAAAAA-TTAGATATATTAGAATTTTT-AAATATAATT-TTATAATGATA
24485 TTGATTAAAT
Statistics
Matches: 111, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
159 77 0.69
160 18 0.16
161 13 0.12
162 3 0.03
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (157 bp):
AACTAAAAAATCTATTTTTATTTAATTAAATATAATATCCTTATAACTATTTAATTTTTACCAAT
TTACTAATTTAATTAAAAAATTAGATATATTAGAATTTTTAAATATAATTTTATAATGATACTCA
ACTAAAAACTCTATTTTTTGAAAAAAA
Found at i:25316 original size:21 final size:22
Alignment explanation
Indices: 25292--25332 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
25282 GTTTATAATA
*
25292 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
25313 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
25333 CAAGTCTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:35283 original size:31 final size:31
Alignment explanation
Indices: 35212--35283 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
35202 GTCTATCAGC
*
35212 TTTTAATTTGTTTAATTTAAAGCTTTCATTT
1 TTTTAATTTGTTTAATTTAAAGCTTTAATTT
* *
35243 TCATT-ATTTGTTTAATTTAATGC-TTAATTT
1 T-TTTAATTTGTTTAATTTAAAGCTTTAATTT
35273 GTTTTAATTTG
1 -TTTTAATTTG
35284 CAATAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 8 0.24
31 24 0.71
32 2 0.06
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAAGCTTTAATTT
Found at i:35759 original size:32 final size:32
Alignment explanation
Indices: 35718--35805 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
35708 AGCCCGAGTC
* *
35718 CGAA-CCGAAAATACCCGAACTCGATACAAC-
1 CGAACCCGAAAATACCCGAACCCGACACAACT
* *
35748 CGGAACCCGAAAATATCCGAACCCGACAGAACT
1 C-GAACCCGAAAATACCCGAACCCGACACAACT
* *
35781 CGAACCCGAAAAAACCCAAACCCGA
1 CGAACCCGAAAATACCCGAACCCGA
35806 AAAAACCGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 1 0.02
31 3 0.06
32 43 0.90
33 1 0.02
ACGTcount: A:0.43, C:0.35, G:0.15, T:0.07
Consensus pattern (32 bp):
CGAACCCGAAAATACCCGAACCCGACACAACT
Found at i:35769 original size:16 final size:14
Alignment explanation
Indices: 35717--35821 Score: 59
Period size: 16 Copynumber: 6.8 Consensus size: 14
35707 GAGCCCGAGT
35717 CCGAA-CCGAAAATA
1 CCGAACCCGAAAA-A
* *
35731 CCCGAACTCGATACAA
1 -CCGAACCCGA-AAAA
35747 CCGGAACCCGAAAATA
1 CC-GAACCCGAAAA-A
*
35763 TCCGAACCCGACAGAA
1 -CCGAACCCGA-AAAA
35779 CTCGAACCCGAAAAAA
1 C-CGAACCCG-AAAAA
*
35795 CCCAAACCCGAAAAAA
1 -CCGAACCCG-AAAAA
*
35811 CCGAACTCGAA
1 CCGAACCCGAA
35822 GTACCCGATC
Statistics
Matches: 72, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
14 2 0.03
15 17 0.24
16 45 0.62
17 8 0.11
ACGTcount: A:0.45, C:0.34, G:0.14, T:0.07
Consensus pattern (14 bp):
CCGAACCCGAAAAA
Found at i:36892 original size:27 final size:27
Alignment explanation
Indices: 36862--36930 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
36852 CTATTATTTG
*
36862 CCTAGTAGGAATTTGAGGTCACCATCT
1 CCTAGCAGGAATTTGAGGTCACCATCT
36889 CCTAGCAGGAATTTGAGGTCACCATCT
1 CCTAGCAGGAATTTGAGGTCACCATCT
*
36916 CCAAGCAGGAGATTT
1 CCTAGCAGGA-ATTT
36931 AATCCTGCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 35 0.90
28 4 0.10
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (27 bp):
CCTAGCAGGAATTTGAGGTCACCATCT
Found at i:41171 original size:2 final size:2
Alignment explanation
Indices: 41159--41190 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
41149 GGTTTAGACT
41159 TA TA TA T- TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41191 GGTTTAACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:42852 original size:20 final size:20
Alignment explanation
Indices: 42810--42850 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42800 TATGTTTAGG
**
42810 ATTCAAACTAATGTGTACAA
1 ATTCAAACTAATGTAAACAA
42830 ATTCAAACTAATGATAAACAA
1 ATTCAAACTAATG-TAAACAA
42851 TTTTTAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (20 bp):
ATTCAAACTAATGTAAACAA
Found at i:43660 original size:60 final size:60
Alignment explanation
Indices: 43578--43696 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
43568 ATTGATAGAT
43578 ACTGAGGTCTTTATATTACACTAGTACTCACTTTCACGTGGCGTTGCACGTGATTCAATA
1 ACTGAGGTCTTTATATTACACTAGTACTCACTTTCACGTGGCGTTGCACGTGATTCAATA
*
43638 ACTGGGGTCTTTATATTACACTAGTACTCACTTTCACGTGGCGTTGCACGTGATTCAAT
1 ACTGAGGTCTTTATATTACACTAGTACTCACTTTCACGTGGCGTTGCACGTGATTCAAT
43697 CTGTTTTAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (60 bp):
ACTGAGGTCTTTATATTACACTAGTACTCACTTTCACGTGGCGTTGCACGTGATTCAATA
Found at i:46719 original size:15 final size:15
Alignment explanation
Indices: 46695--46727 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
46685 TATGGAACCG
*
46695 GATCAGGGAAGAACT
1 GATCAAGGAAGAACT
46710 GATCAAGGAAGAACT
1 GATCAAGGAAGAACT
46725 GAT
1 GAT
46728 GTTGCGGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.30, T:0.15
Consensus pattern (15 bp):
GATCAAGGAAGAACT
Found at i:48127 original size:150 final size:144
Alignment explanation
Indices: 47853--48219 Score: 477
Period size: 150 Copynumber: 2.5 Consensus size: 144
47843 TTTTGACAGA
* * * *
47853 AAAACGCCGCCATATTAATATATGGAGGGAGAGATTTTTTTTCTCCTTTTTTTGGAGGGAAAAAT
1 AAAACGCCGCAATTTTAATATATGGAGGGAGA-ACTTTTTTTC-CCTTATTTTGGAGGGAAAAAT
*
47918 TCCCTCCCCACTAAAACAAAGAAAGCTTCCAACTCTACACCTATAATATATAGCGGCGTTTTGTC
64 TCCCTCCCCACTAAAACAAAGAAAGCTTCCAACTCTACACCTATAATATATAGCGGCGTTTTATC
47983 ACCAGACGCTGCTAATTGAAAAG
129 ACCAGACGC--C-----GAAAAG
*
48006 AAAACGCCGCTATTTTAATATATGGAGGGAGATA-TTTTTTTCCCTTATTTTGGAGGGAAAAATT
1 AAAACGCCGCAATTTTAATATATGGAGGGAGA-ACTTTTTTTCCCTTATTTTGGAGGGAAAAATT
** *
48070 CCCTCCCC-CTAAAACAAAGAAATTTTCCAACTCTACGCCTATAATATATAGCGGCGTTTTATCA
65 CCCTCCCCACTAAAACAAAGAAAGCTTCCAACTCTACACCTATAATATATAGCGGCGTTTTATCA
*
48134 CCAGACGCCGCAAAG
130 CCAGACGCCGAAAAG
* * * * *
48149 AAAACGCCGCAATTGTAATATATGGAGTGAGAGAACTTTTTTTTCTTTGTTTTGGAGGGAAAAGT
1 AAAACGCCGCAATTTTAATATATGGAG-G-GAGAACTTTTTTTCCCTTATTTTGGAGGGAAAAAT
48214 TCCCTC
64 TCCCTC
48220 GCCTATAATA
Statistics
Matches: 196, Mismatches: 15, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
143 30 0.15
144 2 0.01
145 35 0.18
148 1 0.01
150 60 0.31
151 29 0.15
152 8 0.04
153 31 0.16
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (144 bp):
AAAACGCCGCAATTTTAATATATGGAGGGAGAACTTTTTTTCCCTTATTTTGGAGGGAAAAATTC
CCTCCCCACTAAAACAAAGAAAGCTTCCAACTCTACACCTATAATATATAGCGGCGTTTTATCAC
CAGACGCCGAAAAG
Found at i:50953 original size:14 final size:14
Alignment explanation
Indices: 50931--50966 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
50921 CACTTTCATG
50931 TTTTCATTTTTTCCC
1 TTTT-ATTTTTTCCC
50946 TTTTA-TTTTTCCC
1 TTTTATTTTTTCCC
50959 TTTTATTT
1 TTTTATTT
50967 CCAAATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.65
14 3 0.15
15 4 0.20
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTATTTTTTCCC
Found at i:50956 original size:13 final size:13
Alignment explanation
Indices: 50938--50966 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
50928 ATGTTTTCAT
50938 TTTTTCCCTTTTA
1 TTTTTCCCTTTTA
50951 TTTTTCCCTTTTA
1 TTTTTCCCTTTTA
50964 TTT
1 TTT
50967 CCAAATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTCCCTTTTA
Found at i:53715 original size:27 final size:27
Alignment explanation
Indices: 53679--53780 Score: 143
Period size: 27 Copynumber: 3.8 Consensus size: 27
53669 GACTGTTACC
* *
53679 GCAGTGGATCCTTCCGCTTTGACCCCA
1 GCAGTGGATCCTTCCACTTCGACCCCA
* *
53706 GTAGTGGATCCTCCCACTTCGACCCCA
1 GCAGTGGATCCTTCCACTTCGACCCCA
53733 GCAGTGGATCC-TCACACTTCGACCCCA
1 GCAGTGGATCCTTC-CACTTCGACCCCA
*
53760 GCAGTGGATCCTCCCACTTCG
1 GCAGTGGATCCTTCCACTTCG
53781 CCTCGGGTCG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.02
27 64 0.97
28 1 0.02
ACGTcount: A:0.18, C:0.39, G:0.21, T:0.23
Consensus pattern (27 bp):
GCAGTGGATCCTTCCACTTCGACCCCA
Found at i:55861 original size:32 final size:32
Alignment explanation
Indices: 55825--55928 Score: 181
Period size: 32 Copynumber: 3.2 Consensus size: 32
55815 GTGTGAAACG
55825 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
55857 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
* * *
55889 AAAACGCTCTTATTTAGCGGCGTCTAAAAAAC
1 AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
55921 AAAACGCC
1 AAAACGCC
55929 GCGGCGTCTA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTATAGAAC
Found at i:55933 original size:24 final size:24
Alignment explanation
Indices: 55905--55952 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
55895 CTCTTATTTA
55905 GCGGCGTCTAAAAAACAAAACGCC
1 GCGGCGTCTAAAAAACAAAACGCC
*
55929 GCGGCGTCTAGAAAACAAAACGCC
1 GCGGCGTCTAAAAAACAAAACGCC
55953 CTTATTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.29, G:0.23, T:0.08
Consensus pattern (24 bp):
GCGGCGTCTAAAAAACAAAACGCC
Found at i:55946 original size:56 final size:56
Alignment explanation
Indices: 55873--55986 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
55863 CCCTTATTTA
* * * **
55873 GCGGCGTCTATAGAACAAAACGCTCTTATTTAGCGGCGTCTAAAAAACAAAACGCC
1 GCGGCGTCTAGAAAACAAAACGCCCTTATTTAGCAACGTCTAAAAAACAAAACGCC
* *
55929 GCGGCGTCTAGAAAACAAAACGCCCTTATTTAGTAACGTCTAAATAACAAAACGCC
1 GCGGCGTCTAGAAAACAAAACGCCCTTATTTAGCAACGTCTAAAAAACAAAACGCC
55985 GC
1 GC
55987 TATATTTAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (56 bp):
GCGGCGTCTAGAAAACAAAACGCCCTTATTTAGCAACGTCTAAAAAACAAAACGCC
Done.