Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019520.1 Corchorus olitorius cultivar O-4 contig19553, 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: 6424
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:1329 original size:12 final size:13
Alignment explanation
Indices: 1305--1334 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1295 GATTGCCATG
1305 TCATGCTACATTT
1 TCATGCTACATTT
1318 TCATGC-ACATTT
1 TCATGCTACATTT
1330 TCATG
1 TCATG
1335 ATTTGTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.43
Consensus pattern (13 bp):
TCATGCTACATTT
Found at i:2201 original size:75 final size:76
Alignment explanation
Indices: 2099--2247 Score: 228
Period size: 75 Copynumber: 2.0 Consensus size: 76
2089 TTATCTGGAC
* *
2099 TGTGAGCAAAGGAATGATGAGTTTTAATTAAAAGATGTTTC-AAAATCAGTTTCAGTCAAAGCAA
1 TGTGAGCAAAAGAATGATGAGTTTTAATCAAAAGATGTTTCAAAAATCAGTTTCAGTCAAAGCAA
2163 TGATTTCAAGG
66 TGATTTCAAGG
* * * * *
2174 TGTGAGCAAAAGATTGATGAGTTTTAATCAAAGGATGTTTCAAAAATTAGTTTTAGTCAAGGCAA
1 TGTGAGCAAAAGAATGATGAGTTTTAATCAAAAGATGTTTCAAAAATCAGTTTCAGTCAAAGCAA
2239 TGATTTCAA
66 TGATTTCAA
2248 TGTGACTGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
75 37 0.56
76 29 0.44
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (76 bp):
TGTGAGCAAAAGAATGATGAGTTTTAATCAAAAGATGTTTCAAAAATCAGTTTCAGTCAAAGCAA
TGATTTCAAGG
Found at i:3093 original size:7 final size:7
Alignment explanation
Indices: 3081--3126 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
3071 AAACAAAAGA
3081 AAAATTG
1 AAAATTG
3088 AAAATTG
1 AAAATTG
*
3095 -AAAGTG
1 AAAATTG
*
3101 -AAAGTG
1 AAAATTG
3107 AAAATTG
1 AAAATTG
3114 AAAATTG
1 AAAATTG
3121 AAAATT
1 AAAATT
3127 TTTGATGGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 11 0.31
7 25 0.69
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.26
Consensus pattern (7 bp):
AAAATTG
Found at i:3746 original size:50 final size:48
Alignment explanation
Indices: 3689--3831 Score: 190
Period size: 42 Copynumber: 3.0 Consensus size: 48
3679 GAAGTTTTAT
3689 AATAAGATTGCATTCCATTTGTGAGTCCAGGATCAAAATTCGCTTTTCAA
1 AATAAGATTG-ATTCCA-TTGTGAGTCCAGGATCAAAATTCGCTTTTCAA
3739 AATAAGATTG----CA-T-TGAGTCCAGGATCAAAATTCGCTTTTCAA
1 AATAAGATTGATTCCATTGTGAGTCCAGGATCAAAATTCGCTTTTCAA
* *
3781 AATAAGATTGTATTCCAATTGTGAGTCCAAGATCAAAATTTGCTTTTCAA
1 AATAAGATTG-ATTCC-ATTGTGAGTCCAGGATCAAAATTCGCTTTTCAA
3831 A
1 A
3832 GGGCATTTTA
Statistics
Matches: 83, Mismatches: 2, Indels: 16
0.82 0.02 0.16
Matches are distributed among these distances:
42 39 0.47
43 1 0.01
45 2 0.02
47 1 0.01
48 1 0.01
49 1 0.01
50 38 0.46
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (48 bp):
AATAAGATTGATTCCATTGTGAGTCCAGGATCAAAATTCGCTTTTCAA
Found at i:4725 original size:47 final size:47
Alignment explanation
Indices: 4634--4734 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 47
4624 AGTTCCGTCC
* *
4634 AAGTTGATCTTTTCTCGCTTCCATGCGAGTTTGCAATCTAGTGACCA
1 AAGTTGATCTTTTCTCGCTTCCATGCGAGTATACAATCTAGTGACCA
* * * * * *
4681 AAGTTGGTCTTTTCTCGCTTTCATGCGGGTATACGATTTGGTGACCA
1 AAGTTGATCTTTTCTCGCTTCCATGCGAGTATACAATCTAGTGACCA
*
4728 CAGTTGA
1 AAGTTGA
4735 CAGTTGGTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (47 bp):
AAGTTGATCTTTTCTCGCTTCCATGCGAGTATACAATCTAGTGACCA
Found at i:4773 original size:22 final size:21
Alignment explanation
Indices: 4747--4798 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
4737 GTTGGTCAAT
*
4747 TTCAATTCTTCAAATTCAATCC
1 TTCAATT-TTCAAATTCAATCA
* *
4769 TTCAATGTTTCAATTTCAATTA
1 TTCAAT-TTTCAAATTCAATCA
4791 TTCAATTT
1 TTCAATTT
4799 CAGTTCTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.08
22 23 0.88
23 1 0.04
ACGTcount: A:0.31, C:0.19, G:0.02, T:0.48
Consensus pattern (21 bp):
TTCAATTTTCAAATTCAATCA
Found at i:4789 original size:36 final size:35
Alignment explanation
Indices: 4742--4860 Score: 166
Period size: 36 Copynumber: 3.3 Consensus size: 35
4732 TGACAGTTGG
4742 TCAATTTCAATTCTTCAAATTCAATCCTTCAATGTT
1 TCAATTTCAATTCTTCAAATTCAAT-CTTCAATGTT
* * *
4778 TCAATTTCAATTATTCAATTTCAGTTCTTCAATGTT
1 TCAATTTCAATTCTTCAAATTCA-ATCTTCAATGTT
**
4814 TCAATTTCAATTCTTCAAAACCAAATCTTCAATGTT
1 TCAATTTCAATTCTTCAAATTC-AATCTTCAATGTT
4850 TCAATTTCAAT
1 TCAATTTCAAT
4861 ATGTTAATGT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
36 71 0.97
37 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (35 bp):
TCAATTTCAATTCTTCAAATTCAATCTTCAATGTT
Found at i:4830 original size:14 final size:14
Alignment explanation
Indices: 4742--4906 Score: 58
Period size: 14 Copynumber: 11.4 Consensus size: 14
4732 TGACAGTTGG
4742 TCAATTTCAATTCT
1 TCAATTTCAATTCT
* *
4756 TCAAATTCAATCCT
1 TCAATTTCAATTCT
4770 TCAATGTTTCAA-T-T
1 TCAA--TTTCAATTCT
4784 TCAATTATTCAA-T-T
1 TCAA-T-TTCAATTCT
*
4798 TCAGTTCTTCAATGT-T
1 TCA-AT-TTCAAT-TCT
4814 TCAATTTCAATTCT
1 TCAATTTCAATTCT
*** *
4828 TCAAAACCAAATCT
1 TCAATTTCAATTCT
4842 TCAATGTTTCAA-T-T
1 TCAA--TTTCAATTCT
*
4856 TCAATATGTTAATGT-T
1 TCAAT-T-TCAAT-TCT
*
4872 TCAATTCCAATTCT
1 TCAATTTCAATTCT
*
4886 TTAATGCTTCAATTCT
1 TCAAT--TTCAATTCT
4902 TCAAT
1 TCAAT
4907 GCATCAAATC
Statistics
Matches: 114, Mismatches: 21, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
12 1 0.01
13 4 0.04
14 74 0.65
15 3 0.03
16 32 0.28
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.45
Consensus pattern (14 bp):
TCAATTTCAATTCT
Found at i:4869 original size:22 final size:22
Alignment explanation
Indices: 4844--4900 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
4834 CCAAATCTTC
*
4844 AATGTTTCAATTTCAATAT-GTT
1 AATGTTTCAATTCCAAT-TCGTT
*
4866 AATGTTTCAATTCCAATTCTTT
1 AATGTTTCAATTCCAATTCGTT
*
4888 AATGCTTCAATTC
1 AATGTTTCAATTC
4901 TTCAATGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (22 bp):
AATGTTTCAATTCCAATTCGTT
Found at i:4900 original size:16 final size:16
Alignment explanation
Indices: 4879--4923 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
4869 GTTTCAATTC
* *
4879 CAATTCTTTAATGCTT
1 CAATTCTTCAATGCAT
4895 CAATTCTTCAATGCAT
1 CAATTCTTCAATGCAT
*
4911 CAAATCTTCAATG
1 CAATTCTTCAATG
4924 ATCCAGGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (16 bp):
CAATTCTTCAATGCAT
Found at i:4905 original size:8 final size:8
Alignment explanation
Indices: 4747--4922 Score: 57
Period size: 8 Copynumber: 23.8 Consensus size: 8
4737 GTTGGTCAAT
4747 TTCAATTC
1 TTCAATTC
*
4755 TTCAA--A
1 TTCAATTC
*
4761 TTCAATCC
1 TTCAATTC
4769 TTCAATGT-
1 TTCAAT-TC
4777 TTCAA-T-
1 TTCAATTC
*
4783 TTCAATTA
1 TTCAATTC
4791 TTCAA-T-
1 TTCAATTC
*
4797 TTCAGTTC
1 TTCAATTC
4805 TTCAATGT-
1 TTCAAT-TC
4813 TTCAA-T-
1 TTCAATTC
4819 TTCAATTC
1 TTCAATTC
**
4827 TTCAAAAC
1 TTCAATTC
*
4835 --CAAATC
1 TTCAATTC
4841 TTCAATGT-
1 TTCAAT-TC
4849 TTCAA-T-
1 TTCAATTC
*
4855 TTCAATATG
1 TTCAAT-TC
4864 TT-AATGT-
1 TTCAAT-TC
4871 TTCAATTC
1 TTCAATTC
4879 --CAATTC
1 TTCAATTC
* *
4885 TTTAATGC
1 TTCAATTC
4893 TTCAATTC
1 TTCAATTC
*
4901 TTCAATGC
1 TTCAATTC
* *
4909 ATCAAATC
1 TTCAATTC
4917 TTCAAT
1 TTCAAT
4923 GATCCAGGGT
Statistics
Matches: 128, Mismatches: 20, Indels: 40
0.68 0.11 0.21
Matches are distributed among these distances:
6 38 0.30
7 7 0.05
8 79 0.62
9 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (8 bp):
TTCAATTC
Found at i:4961 original size:38 final size:38
Alignment explanation
Indices: 4910--4999 Score: 171
Period size: 38 Copynumber: 2.4 Consensus size: 38
4900 CTTCAATGCA
*
4910 TCAAATCTTCAATGATCCAGGGTGGTCTTTCTTCAATT
1 TCAATTCTTCAATGATCCAGGGTGGTCTTTCTTCAATT
4948 TCAATTCTTCAATGATCCAGGGTGGTCTTTCTTCAATT
1 TCAATTCTTCAATGATCCAGGGTGGTCTTTCTTCAATT
4986 TCAATTCTTCAATG
1 TCAATTCTTCAATG
5000 CATCAATTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.41
Consensus pattern (38 bp):
TCAATTCTTCAATGATCCAGGGTGGTCTTTCTTCAATT
Found at i:4989 original size:92 final size:92
Alignment explanation
Indices: 4893--5075 Score: 248
Period size: 93 Copynumber: 2.0 Consensus size: 92
4883 TCTTTAATGC
* *
4893 TTCAATTCTTCAATGCATCAA-AT-CTTCAATGATCCAGGGTGGTC-TTTCTTCAATTTCAATTC
1 TTCAATTCTTCAATGCATCAATATACTTCAATGACCCAGGGTGATCTTTTCTTCAATTT--A-T-
* *
4955 TTCAA-TGATCCAGGGTGGTCTTTCTTCAAT
62 TTCAAGTGACCCAGGGTGGTCTCTCTTCAAT
*
4985 TTCAATTCTTCAATGCATCAATTTACTTCAATGACCCAGGGTGATCTTTTCTTCAATTTATTTCA
1 TTCAATTCTTCAATGCATCAATATACTTCAATGACCCAGGGTGATCTTTTCTTCAATTTATTTCA
5050 AGTTGACCCAGGGTGGTCTCTCTTCA
66 AG-TGACCCAGGGTGGTCTCTCTTCA
5076 GTTTATTTCA
Statistics
Matches: 81, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
91 5 0.06
92 22 0.27
93 23 0.28
94 19 0.23
95 12 0.15
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.40
Consensus pattern (92 bp):
TTCAATTCTTCAATGCATCAATATACTTCAATGACCCAGGGTGATCTTTTCTTCAATTTATTTCA
AGTGACCCAGGGTGGTCTCTCTTCAAT
Found at i:5274 original size:71 final size:71
Alignment explanation
Indices: 5016--5539 Score: 657
Period size: 71 Copynumber: 7.3 Consensus size: 71
5006 TTTACTTCAA
* * * *
5016 TGACCCAGGGTGATCTTTTCTTCAATTTATTTCAAGTTGACCCAGGGTGGTC-TCTCTTCAGTTT
1 TGACCCAGGGCGGTC-TTTCTTCAGTTTATTTC-AGTTGACCCAGGGTGGTCTTTTCTTCAGTTT
5080 ATTTCAGT
64 ATTTCAGT
*
5088 TGACCTAGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTA
1 TGACCCAGGGCGGTC-TTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTA
5153 TTTCAAGT
65 TTTC-AGT
*
5161 TGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTAT
1 TGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTAT
5226 TTCAGT
66 TTCAGT
* *
5232 TGACCTAAGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTAT
1 TGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTAT
5297 TTCAAGT
66 TTC-AGT
*
5304 TGA-CCAGGGCAGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTAT
1 TGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTAT
5368 TTCAGT
66 TTCAGT
* * *
5374 TGACCCAGGGTGGTCTTT-TCTCTAGTTTATTTCAGTTGACCCAGGGTGGTC-TTTCTTTAGTTG
1 TGACCCAGGGCGGTCTTTCT-TC-AGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTT
*** * *
5437 GCGTCGGAA
64 ATTTCAG-T
* * * * * * **
5446 TGATCGAGGGTGGTCATTT-TTCAGTTTATTTTAAG-TGACCTAGGGTGGTC-TTGCTTCAACTT
1 TGACCCAGGGCGGTC-TTTCTTCAGTTTA-TTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTT
*
5508 ATTTCAGAA
64 ATTTCAG-T
*
5517 TGACCCAGGGTGGTCTTTCTTCA
1 TGACCCAGGGCGGTCTTTCTTCA
5540 ATTCTTCAAG
Statistics
Matches: 405, Mismatches: 37, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
70 10 0.02
71 223 0.55
72 152 0.38
73 20 0.05
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (71 bp):
TGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTAT
TTCAGT
Found at i:5521 original size:143 final size:142
Alignment explanation
Indices: 5006--5539 Score: 665
Period size: 143 Copynumber: 3.7 Consensus size: 142
4996 AATGCATCAA
* * *
5006 TTTACTTCAA-TGACCCAGGGTGATCTTTTCTTCAATTTATTTCAAGTTGACCCAGGGTGGTC-T
1 TTTATTTCAAGTGA-CCAGGGTGGTC-TTTCTTCAGTTTATTT-AAGTTGACCCAGGGTGGTCTT
* *
5069 CTCTTCAGTTTATTTCAGTTGACCTAGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGACCCAGGG
63 TTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGACCCAGGG
5134 TGGTCTTTTCTTCAG
128 TGGTCTTTTCTTCAG
*
5149 TTTATTTCAAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTT
1 TTTATTTCAAG-TGA-CCAGGGTGGTCTTTCTTCAGTTTATTTAAGTTGACCCAGGGTGGTCTTT
* *
5214 TCTTCAGTTTATTTCAGTTGACCTAAGGCGGTC-TTTCTTCAGTTTATTTCAGTTGACCCAGGGT
64 TCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGT
5278 GGTCTTTTCTTCAG
129 GGTCTTTTCTTCAG
** *
5292 TTTATTTCAAGTTGACCAGGGCAGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTT
1 TTTATTTCAAG-TGACCAGGGTGGTCTTTCTTCAGTTTATTTAAGTTGACCCAGGGTGGTCTTTT
*
5357 CTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTC-TCTAGTTTATTTCAGTTGACCCAGGGT
65 CTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTTCTTC-AGTTTATTTCAGTTGACCCAGGGT
*
5421 GGTC-TTTCTTTAG
129 GGTCTTTTCTTCAG
**** * *
5434 TTGGCGTCGGAA-TGATCGAGGGTGGTCATTT-TTCAGTTTATTTTAAG-TGACCTAGGGTGGTC
1 TTTATTTC--AAGTGA-CCAGGGTGGTC-TTTCTTCAGTTTA-TTTAAGTTGACCCAGGGTGGTC
* ** * *
5496 -TTGCTTCAACTTATTTCAGAATGACCCAGGGTGGTC-TTTCTTCA
61 TTTTCTTCAGTTTATTTCAG-TTGACCCAGGGCGGTCTTTTCTTCA
5540 ATTCTTCAAG
Statistics
Matches: 354, Mismatches: 25, Indels: 25
0.88 0.06 0.06
Matches are distributed among these distances:
142 115 0.32
143 167 0.47
144 58 0.16
145 14 0.04
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.42
Consensus pattern (142 bp):
TTTATTTCAAGTGACCAGGGTGGTCTTTCTTCAGTTTATTTAAGTTGACCCAGGGTGGTCTTTTC
TTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGG
TCTTTTCTTCAG
Found at i:5540 original size:36 final size:35
Alignment explanation
Indices: 5016--5539 Score: 660
Period size: 36 Copynumber: 14.7 Consensus size: 35
5006 TTTACTTCAA
* *
5016 TGACCCAGGGTGATCTTTTCTTCAATTTATTTCAAGT
1 TGACCCAGGGTGGTC-TTTCTTCAGTTTATTTC-AGT
*
5053 TGACCCAGGGTGGTCTCTCTTCAGTTTATTTCAGT
1 TGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGT
* *
5088 TGACCTAGGGCGGTCTTTTCTTCAGTTTATTTCAGT
1 TGACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAGT
5124 TGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAAGT
1 TGACCCAGGGTGGTC-TTTCTTCAGTTTATTTC-AGT
5161 TGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGT
1 TGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGT
5196 TGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGT
1 TGACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAGT
* * *
5232 TGACCTAAGGCGGTCTTTCTTCAGTTTATTTCAGT
1 TGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGT
5267 TGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAAGT
1 TGACCCAGGGTGGTC-TTTCTTCAGTTTATTTC-AGT
**
5304 TGA-CCAGGGCAGTCTTTCTTCAGTTTATTTCAGT
1 TGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGT
5338 TGACCCAGGGTGGTCTTTTCTTCAGTTTATTTCAGT
1 TGACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAGT
5374 TGACCCAGGGTGGTCTTT-TCTCTAGTTTATTTCAGT
1 TGACCCAGGGTGGTCTTTCT-TC-AGTTTATTTCAGT
* **** * *
5410 TGACCCAGGGTGGTCTTTCTTTAGTTGGCGTCGGAA
1 TGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAG-T
* * *
5446 TGATCGAGGGTGGTCATTT-TTCAGTTTATTTTAAG-
1 TGACCCAGGGTGGTC-TTTCTTCAGTTTA-TTTCAGT
* * ** *
5481 TGACCTAGGGTGGTCTTGCTTCAACTTATTTCAGAA
1 TGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAG-T
5517 TGACCCAGGGTGGTCTTTCTTCA
1 TGACCCAGGGTGGTCTTTCTTCA
5540 ATTCTTCAAG
Statistics
Matches: 429, Mismatches: 42, Indels: 33
0.85 0.08 0.07
Matches are distributed among these distances:
34 14 0.03
35 124 0.29
36 247 0.58
37 44 0.10
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (35 bp):
TGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGT
Found at i:5546 original size:8 final size:8
Alignment explanation
Indices: 5533--5581 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
5523 AGGGTGGTCT
5533 TTCTTCAA
1 TTCTTCAA
5541 TTCTTCAA
1 TTCTTCAA
* *
5549 GTTATTCGA
1 -TTCTTCAA
*
5558 TGCTTCAA
1 TTCTTCAA
5566 TTCTTCAA
1 TTCTTCAA
*
5574 TTATTCAA
1 TTCTTCAA
5582 GGCCTCAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
8 27 0.82
9 6 0.18
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (8 bp):
TTCTTCAA
Found at i:6064 original size:13 final size:13
Alignment explanation
Indices: 6029--6064 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
6019 TCTTCTCTTT
*
6029 ATTTCATTTCTCA
1 ATTTCATTTTTCA
6042 ATTTCATTTTTCA
1 ATTTCATTTTTCA
6055 ATTTCATTTT
1 ATTTCATTTT
6065 AGTGGTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTTCATTTTTCA
Done.