Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016124.1 Corchorus olitorius cultivar O-4 contig16157, 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: 50664
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1362 original size:15 final size:15
Alignment explanation
Indices: 1332--1373 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
1322 TTACTTTGTT
1332 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
1348 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
1363 TTGCTTTCTGT
1 TTGTTTTCTGT
1374 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:2892 original size:54 final size:54
Alignment explanation
Indices: 2834--3907 Score: 1456
Period size: 54 Copynumber: 20.0 Consensus size: 54
2824 TAGCCTAATT
* *
2834 ACTAATTACTGCTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAAAATTAA
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
*
2888 ACTAACTT-CTGTTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAA
1 ACTAA-TTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
2942 ACTAACTT-CTGTTTACTCTTTCTTCTACTATTTAGTTTAATTACCCAGAATTAA
1 ACTAA-TTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
*
2996 ACTAACTT-CTGTTTACTCTTTC-TTTACTATTTAGTTTAATTACCCAGAATTAA
1 ACTAA-TTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * *
3049 ACTAATTACTGTTTACTCCTTCTTTATACTCTTTAGCTTAATTACCCGGAATTAA
1 ACTAATTACTGTTTACTCTTTCTTT-TACTCTTTAGTTTAATTACCCAGAATTAA
* *
3104 ACTAATTACTGTTCAC-CTCTTCTTTTACTCTTTAGTTTAATTACCAAGAATTAA
1 ACTAATTACTGTTTACTCT-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
*
3158 ACTAATTACTGTTTAATC-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
3211 ACTAA-TACTGCTCACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
*
3264 ACTAACTT-CTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCTAGAATTAA
1 ACTAA-TTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
3318 ACTAATTACTGTTCA-TCTCTTCTTTTACTCTTTAGTTTAATTACCAAGAATTAA
1 ACTAATTACTGTTTACTCT-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
3372 ACTAATTACTGTTTAATC-TTCTTTTACTCTTTAGTTTAATTACCAAGAATTAA
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * *
3425 ACTAACTACTGCTCACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * *
3479 ACTAATTACTGTTTACTC---CTTATACTGTTTAGCTTAATTACCCAGAATTAA
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
3530 ACTAATTACTGTTTACTCCTTGTTTTACTCTTTAGTTTAATTACCCCA-AATTAA
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTA-CCCAGAATTAA
* * *
3584 ACTAATTATTGTTCAC-CTCTTCTTTTACTCTTTAGTTTAATTACCAAGAATTAA
1 ACTAATTACTGTTTACTCT-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
*
3638 ACTAATTACTGTTTAATC-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * * *
3691 ACTAACTACTGCTCACTCTTTCTTTTACTCTTTAGTTTAGTTACCCAGAATTAA
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * *
3745 ACTAACTT-CTGTTTACTTTTTATTTTACTATTTTTTAGTTTAATTACCCAGAATTAA
1 ACTAA-TTACTGTTTACTCTTTCTTTTAC---TCTTTAGTTTAATTACCCAGAATTAA
* *
3802 ACTAATTACTGTTTACTCCTTT-TTTTACTTTTTAGTTTAATTACCCCGAATTAA
1 ACTAATTACTGTTTACT-CTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * * *
3856 ACTAATTATTGATTAC-C-TT-TTTT-CT-TCTTAGTTTAATTACTCAGAACTAA
1 ACTAATTACTGTTTACTCTTTCTTTTACTCT-TTAGTTTAATTACCCAGAATTAA
3906 AC
1 AC
3908 CTACTACTGA
Statistics
Matches: 923, Mismatches: 69, Indels: 60
0.88 0.07 0.06
Matches are distributed among these distances:
49 1 0.00
50 24 0.03
51 54 0.06
52 12 0.01
53 233 0.25
54 491 0.53
55 59 0.06
56 2 0.00
57 44 0.05
58 3 0.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (54 bp):
ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
Found at i:3037 original size:161 final size:162
Alignment explanation
Indices: 2834--3907 Score: 1472
Period size: 161 Copynumber: 6.7 Consensus size: 162
2824 TAGCCTAATT
* *
2834 ACTAATTACTGCTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAAAATTAAACTAACTT-CT
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAA-TTACT
* *
2898 GTTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACTTCTGTTTACTCTTT
65 GTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGTTCACTCTTT
* *
2963 CTTCTACTATTTAGTTTAATTACCCAGAATTAA
130 CTTTTACTCTTTAGTTTAATTACCCAGAATTAA
*
2996 ACTAACTT-CTGTTTACTCTTTC-TTTACTATTTAGTTTAATTACCCAGAATTAAACTAATTACT
1 ACTAA-TTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACT
* * *
3059 GTTTACTCCTTCTTTATACTCTTTAGCTTAATTACCCGGAATTAAACTAA-TTACTGTTCAC-CT
65 GTTTACTCTTTCTTT-TACTCTTTAGTTTAATTACCCAGAATTAAACTAACTT-CTGTTCACTCT
*
3122 CTTCTTTTACTCTTTAGTTTAATTACCAAGAATTAA
128 -TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
*
3158 ACTAATTACTGTTTAATC-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAA-TACTG
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTG
* * *
3221 CTCACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGTTTACTCTTTC
66 TTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGTTCACTCTTTC
*
3286 TTTTACTCTTTAGTTTAATTACCTAGAATTAA
131 TTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
3318 ACTAATTACTGTTCA-TCTCTTCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTAATTACT
1 ACTAATTACTGTTTACTCT-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACT
* * * *
3382 GTTTAATC-TTCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTAACTACTGCTCACTCTTT
65 GTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGTTCACTCTTT
3446 CTTTTACTCTTTAGTTTAATTACCCAGAATTAA
130 CTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * *
3479 ACTAATTACTGTTTACTC---CTTATACTGTTTAGCTTAATTACCCAGAATTAAACTAATTACTG
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTG
* * *
3541 TTTACTCCTTGTTTTACTCTTTAGTTTAATTACCCCA-AATTAAACTAA-TTATTGTTCAC-CTC
66 TTTACTCTTTCTTTTACTCTTTAGTTTAATTA-CCCAGAATTAAACTAACTT-CTGTTCACTCT-
*
3603 TTCTTTTACTCTTTAGTTTAATTACCAAGAATTAA
128 TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
3638 ACTAATTACTGTTTAATC-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACTG
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTG
* * * * * *
3702 CTCACTCTTTCTTTTACTCTTTAGTTTAGTTACCCAGAATTAAACTAACTTCTGTTTACTTTTTA
66 TTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGTTCACTCTTTC
*
3767 TTTTACTATTTTTTAGTTTAATTACCCAGAATTAA
131 TTTTAC---TCTTTAGTTTAATTACCCAGAATTAA
* * *
3802 ACTAATTACTGTTTACTCCTTT-TTTTACTTTTTAGTTTAATTACCCCGAATTAAACTAATTATT
1 ACTAATTACTGTTTACT-CTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACT
* * *
3866 GATTAC-C-TT-TTTT-CT-TCTTAGTTTAATTACTCAGAACTAAAC
65 GTTTACTCTTTCTTTTACTCT-TTAGTTTAATTACCCAGAATTAAAC
3908 CTACTACTGA
Statistics
Matches: 816, Mismatches: 68, Indels: 57
0.87 0.07 0.06
Matches are distributed among these distances:
158 49 0.06
159 93 0.11
160 97 0.12
161 332 0.41
162 155 0.19
163 4 0.00
164 41 0.05
165 43 0.05
166 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (162 bp):
ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTACTG
TTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTTCTGTTCACTCTTTC
TTTTACTCTTTAGTTTAATTACCCAGAATTAA
Found at i:3291 original size:107 final size:108
Alignment explanation
Indices: 2834--3907 Score: 1441
Period size: 107 Copynumber: 10.0 Consensus size: 108
2824 TAGCCTAATT
* * *
2834 ACTAATTACTGCTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAAAATTAAACTAACTTCTG
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACTG
*
2899 TTTACTCTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAA
66 TTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * *
2942 ACTAACTT-CTGTTTACTCTTTCTTCTACTATTTAGTTTAATTACCCAGAATTAAACTAACTTCT
1 ACTAA-TTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACT
*
3006 GTTTACTCTTTC-TTTACTATTTAGTTTAATTACCCAGAATTAA
65 GTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * * *
3049 ACTAATTACTGTTTACTCCTTCTTTATACTCTTTAGCTTAATTACCCGGAATTAAACTAATTACT
1 ACTAATTACTGTTTACTCTTTCTTT-TACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACT
* *
3114 GTTCAC-CTCTTCTTTTACTCTTTAGTTTAATTACCAAGAATTAA
65 GTTTACTCT-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
*
3158 ACTAATTACTGTTTAATC-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAA-TACTG
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACTG
* *
3221 CTCACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
66 TTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
3264 ACTAACTT-CTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCTAGAATTAAACTAATTACT
1 ACTAA-TTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACT
* *
3328 GTTCA-TCTCTTCTTTTACTCTTTAGTTTAATTACCAAGAATTAA
65 GTTTACTCT-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* *
3372 ACTAATTACTGTTTAATC-TTCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTAACTACTG
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACTG
* *
3436 CTCACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
66 TTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * * *
3479 ACTAATTACTGTTTACTC---CTTATACTGTTTAGCTTAATTACCCAGAATTAAACTAATTACTG
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACTG
* *
3541 TTTACTCCTTGTTTTACTCTTTAGTTTAATTACCCCA-AATTAA
66 TTTACTCTTTCTTTTACTCTTTAGTTTAATTA-CCCAGAATTAA
* * * *
3584 ACTAATTATTGTTCAC-CTCTTCTTTTACTCTTTAGTTTAATTACCAAGAATTAAACTAATTACT
1 ACTAATTACTGTTTACTCT-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACT
*
3648 GTTTAATC-TTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
65 GTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
* * * * *
3691 ACTAACTACTGCTCACTCTTTCTTTTACTCTTTAGTTTAGTTACCCAGAATTAAACTAACTTCTG
1 ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACTG
* * *
3756 TTTACTTTTTATTTTACTATTTTTTAGTTTAATTACCCAGAATTAA
66 TTTACTCTTTCTTTTAC---TCTTTAGTTTAATTACCCAGAATTAA
* * * *
3802 ACTAATTACTGTTTACTCCTTT-TTTTACTTTTTAGTTTAATTACCCCGAATTAAACTAATTATT
1 ACTAATTACTGTTTACT-CTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACT
* * *
3866 GATTAC-C-TT-TTTT-CT-TCTTAGTTTAATTACTCAGAACTAA
65 GTTTACTCTTTCTTTTACTCT-TTAGTTTAATTACCCAGAATTAA
3906 AC
1 AC
3908 CTACTACTGA
Statistics
Matches: 871, Mismatches: 70, Indels: 54
0.88 0.07 0.05
Matches are distributed among these distances:
103 1 0.00
104 25 0.03
105 87 0.10
106 67 0.08
107 321 0.37
108 236 0.27
109 50 0.06
111 80 0.09
112 4 0.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (108 bp):
ACTAATTACTGTTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACTACTG
TTTACTCTTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAA
Found at i:15045 original size:44 final size:41
Alignment explanation
Indices: 14980--15100 Score: 152
Period size: 44 Copynumber: 2.9 Consensus size: 41
14970 CTTACCAAAT
* *
14980 AACTAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCT
1 AACTAAAGTCCCCAAACACATTTATAACACAGAGGC-A-TCT-A
** *
15024 TTCTAAAGTCCTCAAACACATTTATAACACAGAGGCATCTA
1 AACTAAAGTCCCCAAACACATTTATAACACAGAGGCATCTA
* *
15065 AACAAAAGTCCCCAAACACATTTATAACACAAAGGC
1 AACTAAAGTCCCCAAACACATTTATAACACAGAGGC
15101 GCCAGCCAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 31 0.46
42 3 0.04
43 1 0.01
44 32 0.48
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.21
Consensus pattern (41 bp):
AACTAAAGTCCCCAAACACATTTATAACACAGAGGCATCTA
Found at i:15085 original size:41 final size:44
Alignment explanation
Indices: 14984--15100 Score: 150
Period size: 41 Copynumber: 2.7 Consensus size: 44
14974 CCAAATAACT
* *** *
14984 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTTTCT
1 AAAGTCCCCAAACACATTTATAACACAGAGGCAATTCTCAAACA
*
15028 AAAGTCCTCAAACACATTTATAACACAGAGGC-A-TCT-AAACA
1 AAAGTCCCCAAACACATTTATAACACAGAGGCAATTCTCAAACA
*
15069 AAAGTCCCCAAACACATTTATAACACAAAGGC
1 AAAGTCCCCAAACACATTTATAACACAGAGGC
15101 GCCAGCCAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
41 31 0.48
42 3 0.05
43 1 0.02
44 30 0.46
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.21
Consensus pattern (44 bp):
AAAGTCCCCAAACACATTTATAACACAGAGGCAATTCTCAAACA
Found at i:18015 original size:9 final size:9
Alignment explanation
Indices: 18001--18031 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
17991 ACATAAATCA
18001 AAAATTATC
1 AAAATTATC
18010 AAAATTATC
1 AAAATTATC
18019 AAAATTAT-
1 AAAATTATC
18027 AAAAT
1 AAAAT
18032 AAAATAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTATC
Found at i:19237 original size:48 final size:48
Alignment explanation
Indices: 19166--19281 Score: 223
Period size: 48 Copynumber: 2.4 Consensus size: 48
19156 TTTAGATAAT
*
19166 ATTACCCGTCAAGACTTAAATTACCCCCTTTTACTTCCTAACAAATCA
1 ATTACCCGTCAAGGCTTAAATTACCCCCTTTTACTTCCTAACAAATCA
19214 ATTACCCGTCAAGGCTTAAATTACCCCCTTTTACTTCCTAACAAATCA
1 ATTACCCGTCAAGGCTTAAATTACCCCCTTTTACTTCCTAACAAATCA
19262 ATTACCCGTCAAGGCTTAAA
1 ATTACCCGTCAAGGCTTAAA
19282 GATTTGCTAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (48 bp):
ATTACCCGTCAAGGCTTAAATTACCCCCTTTTACTTCCTAACAAATCA
Found at i:31786 original size:5 final size:5
Alignment explanation
Indices: 31776--31810 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
31766 TCAAATCATT
* *
31776 AAAGG AAAGG AAAGG AAATG AAAGG AAAGG GAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG
31811 GAAGTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (5 bp):
AAAGG
Found at i:37686 original size:43 final size:41
Alignment explanation
Indices: 37618--37702 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 41
37608 TCTCTTAGTG
* * *
37618 TCTGCGTTTTTTATCTAAAAAAAAAATTTTGTGTTGTCCGTTT
1 TCTGCGTTTTTTATCAAAAAAAAAAAATTTCT-TT-TCCGTTT
* *
37661 TCTGCGTTTTTTCTGAAAAAAAAAAAATTTCTTTTCCGTTT
1 TCTGCGTTTTTTATCAAAAAAAAAAAATTTCTTTTCCGTTT
37702 T
1 T
37703 TAATTTTTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 8 0.22
42 2 0.05
43 27 0.73
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (41 bp):
TCTGCGTTTTTTATCAAAAAAAAAAAATTTCTTTTCCGTTT
Found at i:37827 original size:50 final size:52
Alignment explanation
Indices: 37729--37828 Score: 127
Period size: 50 Copynumber: 2.0 Consensus size: 52
37719 TTTTTTCTAA
* * *
37729 AAAAAAAAATATTTTTGCGTCATAAAAAAAAATTGTTTTGTGTTTTGCGTCG
1 AAAAAAAAATATTTCTGCGTCATAAAAAAAAATTGTCTTGTGTCTTGCGTCG
37781 AAAAAAAAA-A-TTCTGCGTCATAAATAAAAATATT-TCTTGT-TCTTGCGT
1 AAAAAAAAATATTTCTGCGTCATAAA-AAAAA-ATTGTCTTGTGTCTTGCGT
37829 TTTTAGATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
50 20 0.47
51 11 0.26
52 12 0.28
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (52 bp):
AAAAAAAAATATTTCTGCGTCATAAAAAAAAATTGTCTTGTGTCTTGCGTCG
Found at i:40933 original size:42 final size:42
Alignment explanation
Indices: 40847--40934 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
40837 CGAGTATCAC
* * * **
40847 GCCCGGCCATGCCCGGCACCACAAGCCTCAGCTGCGCCTTAT
1 GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT
* * *
40889 GCCCGGCCATGCCCGCCATCTCAAGCCTCATCCGAGCCACAT
1 GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT
40931 GCCC
1 GCCC
40935 TGCTAGGACC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.17, C:0.48, G:0.22, T:0.14
Consensus pattern (42 bp):
GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT
Found at i:41168 original size:21 final size:21
Alignment explanation
Indices: 41124--41178 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
41114 CGCCCATTCA
**
41124 CCGTGCCACCACCGGTTAAAC
1 CCGTGCCACCACCGGCCAAAC
**
41145 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAAC
*
41166 CCGTGCCATCACC
1 CCGTGCCACCACC
41179 ATTCCAAGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.49, G:0.20, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAAC
Found at i:43087 original size:8 final size:8
Alignment explanation
Indices: 43074--43098 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43064 ATTTCAAGAG
43074 GAAGAATT
1 GAAGAATT
43082 GAAGAATT
1 GAAGAATT
43090 GAAGAATT
1 GAAGAATT
43098 G
1 G
43099 GAGTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (8 bp):
GAAGAATT
Found at i:46822 original size:30 final size:29
Alignment explanation
Indices: 46786--46858 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
46776 ACATACAGCA
* *
46786 AACAAACAGCAATTACAAAATCTGAAATCT
1 AACAAACAGCAATTAC-AAATATGAAATAT
* **
46816 AACAAACAACAATT-CAAATATGATTTAT
1 AACAAACAGCAATTACAAATATGAAATAT
46844 AACAAACAGCAATTA
1 AACAAACAGCAATTA
46859 ACTCTGTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 22 0.61
29 1 0.03
30 13 0.36
ACGTcount: A:0.55, C:0.18, G:0.05, T:0.22
Consensus pattern (29 bp):
AACAAACAGCAATTACAAATATGAAATAT
Found at i:49584 original size:23 final size:23
Alignment explanation
Indices: 49553--49682 Score: 95
Period size: 23 Copynumber: 5.5 Consensus size: 23
49543 CTCTTGTTTG
* *
49553 ATCAACCTTATCTTTTACTTTTC
1 ATCACCCTTGTCTTTTACTTTTC
* *
49576 ATCACCCTTGT-TTTTACAAGTTGTG
1 ATCACCCTTGTCTTTTAC---TTTTC
*
49601 ATCAACCC-TATCTTTTACTTTTC
1 ATC-ACCCTTGTCTTTTACTTTTC
* *
49624 ATCACCCTTGT-TTTTACAAGTTGTG
1 ATCACCCTTGTCTTTTAC---TTTTC
* *
49649 ATCAACCTTGTCATTTACTTTTC
1 ATCACCCTTGTCTTTTACTTTTC
49672 ATCACCCTTGT
1 ATCACCCTTGT
49683 TGTTACAAGG
Statistics
Matches: 82, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
22 16 0.20
23 30 0.37
25 21 0.26
26 15 0.18
ACGTcount: A:0.21, C:0.25, G:0.08, T:0.46
Consensus pattern (23 bp):
ATCACCCTTGTCTTTTACTTTTC
Found at i:49606 original size:48 final size:48
Alignment explanation
Indices: 49551--49691 Score: 246
Period size: 48 Copynumber: 2.9 Consensus size: 48
49541 AACTCTTGTT
49551 TGATCAACCTTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
1 TGATCAACCTTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
*
49599 TGATCAACCCTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
1 TGATCAACCTTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
* * *
49647 TGATCAACCTTGTCATTTACTTTTCATCACCCTTGTTGTTACAAG
1 TGATCAACCTTATCTTTTACTTTTCATCACCCTTGTTTTTACAAG
49692 GTGTAATCTT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.21, C:0.24, G:0.09, T:0.45
Consensus pattern (48 bp):
TGATCAACCTTATCTTTTACTTTTCATCACCCTTGTTTTTACAAGTTG
Found at i:49657 original size:25 final size:25
Alignment explanation
Indices: 49576--49659 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
49566 TTTACTTTTC
*
49576 ATCACCCTTGTTTTTACAAGTTGTG
1 ATCAACCTTGTTTTTACAAGTTGTG
* * * *
49601 ATCAACCCTATCTTTTAC---TTTTC
1 ATCAACCTTGT-TTTTACAAGTTGTG
*
49624 ATCACCCTTGTTTTTACAAGTTGTG
1 ATCAACCTTGTTTTTACAAGTTGTG
49649 ATCAACCTTGT
1 ATCAACCTTGT
49660 CATTTACTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
22 6 0.14
23 11 0.25
25 21 0.48
26 6 0.14
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (25 bp):
ATCAACCTTGTTTTTACAAGTTGTG
Done.