Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022084.1 Corchorus olitorius cultivar O-4 contig22117, 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: 34440
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:11842 original size:437 final size:437
Alignment explanation
Indices: 11028--11904 Score: 1610
Period size: 437 Copynumber: 2.0 Consensus size: 437
11018 TCGAACCTTT
11028 CTTCCAAAAGCTCACTGTGGTTAACTTCTTTGCTTGTTTTAATGGGTTCGGGGCCATAAGTCGCC
1 CTTCCAAAAGCTCACTGTGGTTAACTTCTTTGCTTGTTTTAATGGGTTCGGGGCCATAAGTCGCC
*
11093 ATTTTTTTTTGGTTTGTACAAAGGTCTCAAAGTAGTTTTTGTGTAGTGTGAGATTCGGTTTTGAG
66 ATTTATTTTTGGTTTGTACAAAGGTCTCAAAGTAGTTTTTGTGTAGTGTGAGATTCGGTTTTGAG
*
11158 ATCTAGGTTTCGGGTTTCGAAGGAAAGGGGACCCTTTTGGTTGTTTTAGGGCTGATTGACGGAGG
131 ATCTAGGTTTCGGGTTTCGAAGGAAAGGGGACCCTTTTGGTTGTTTTAGGGCCGATTGACGGAGG
* * *
11223 AGGGAGGCGGTTCCGTCGTCGACAGTTGAGAGTTTACGTTAGAAAGAGAGGGATTAGGGTTGAGG
196 AGGGAGGCGGTTCCGCCGTCGACAATTGAGAGTTTACATTAGAAAGAGAGGGATTAGGGTTGAGG
*
11288 GGTCGAGCAAGGGGATAAAGAAGAAGAGAAGGGGTTGATTATAAACCCTACACCTCCAAACGGCG
261 GGTCGAGCAAGGAGATAAAGAAGAAGAGAAGGGGTTGATTATAAACCCTACACCTCCAAACGGCG
*
11353 TCGTTTGAGTAGGTAGTTTTCTTTTCTCTTCAATTTACTCCCATATAATATCAACTCATGCACTT
326 TCATTTGAGTAGGTAGTTTTCTTTTCTCTTCAATTTACTCCCATATAATATCAACTCATGCACTT
*
11418 TAGGGCTTGTTTGTTTTATTTTGTTTCTAATTTTATTATTGATGAAG
391 TAGGGCCTGTTTGTTTTATTTTGTTTCTAATTTTATTATTGATGAAG
* *
11465 CTTCCAAAAGCTCACTGTGGTTCATTTCTTTGCTTGTTTTAATGGGTTCGGGGCCATAAGTCGCC
1 CTTCCAAAAGCTCACTGTGGTTAACTTCTTTGCTTGTTTTAATGGGTTCGGGGCCATAAGTCGCC
*
11530 ATTTATTTTTGGTTTGTACAGAGGTCTCAAAGTAGTTTTTGTGTAGTGTGAGATTCGGTTTTGAG
66 ATTTATTTTTGGTTTGTACAAAGGTCTCAAAGTAGTTTTTGTGTAGTGTGAGATTCGGTTTTGAG
11595 ATCTAGGTTTCGGGTTTCGAAGGAAAGGGGACCCTTTTGGTTGTTTTAGGGCCGATTGACGGAGG
131 ATCTAGGTTTCGGGTTTCGAAGGAAAGGGGACCCTTTTGGTTGTTTTAGGGCCGATTGACGGAGG
* * *
11660 AGGGAGGCGGTTCTGCCGTTGACAATTGAGAGTTTGCATTAGAAAGAGAGGGATTAGGGTTGAGG
196 AGGGAGGCGGTTCCGCCGTCGACAATTGAGAGTTTACATTAGAAAGAGAGGGATTAGGGTTGAGG
11725 GGTCGAGCAAGGAGATAAAGAAGAAGAGAAGGGGTTGATTATAAACCCTACACCTCCAAACGGCG
261 GGTCGAGCAAGGAGATAAAGAAGAAGAGAAGGGGTTGATTATAAACCCTACACCTCCAAACGGCG
*
11790 TCATTTGAGTAGGTAGTTTTCTTTTCTCTTCAATTTACTCCCGTATAATATCAACTCATGCACTT
326 TCATTTGAGTAGGTAGTTTTCTTTTCTCTTCAATTTACTCCCATATAATATCAACTCATGCACTT
*
11855 TAGGGCCTGTTTGTTTTATTTTGTTTCTAATTTTATTATTGGTGAAG
391 TAGGGCCTGTTTGTTTTATTTTGTTTCTAATTTTATTATTGATGAAG
11902 CTT
1 CTT
11905 ACTTTAATTA
Statistics
Matches: 424, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
437 424 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.35
Consensus pattern (437 bp):
CTTCCAAAAGCTCACTGTGGTTAACTTCTTTGCTTGTTTTAATGGGTTCGGGGCCATAAGTCGCC
ATTTATTTTTGGTTTGTACAAAGGTCTCAAAGTAGTTTTTGTGTAGTGTGAGATTCGGTTTTGAG
ATCTAGGTTTCGGGTTTCGAAGGAAAGGGGACCCTTTTGGTTGTTTTAGGGCCGATTGACGGAGG
AGGGAGGCGGTTCCGCCGTCGACAATTGAGAGTTTACATTAGAAAGAGAGGGATTAGGGTTGAGG
GGTCGAGCAAGGAGATAAAGAAGAAGAGAAGGGGTTGATTATAAACCCTACACCTCCAAACGGCG
TCATTTGAGTAGGTAGTTTTCTTTTCTCTTCAATTTACTCCCATATAATATCAACTCATGCACTT
TAGGGCCTGTTTGTTTTATTTTGTTTCTAATTTTATTATTGATGAAG
Found at i:13685 original size:40 final size:40
Alignment explanation
Indices: 13621--14119 Score: 401
Period size: 40 Copynumber: 11.8 Consensus size: 40
13611 GTCAGCTTTA
* * * *
13621 CCCAATTTGCTCTTCCCCACCGGAAGGTGCTGTTTAAGTT
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTT
* *
13661 CCCAGTTTGCCCTTACCCATCGGAAGATGTTGTTTAAGTATGCTTT
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-A--A-G--TT
* * * *
13707 ACCCAATTCGCCCTTCCCCACCTGAAGGTGTTGTTTAAGTT
1 -CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTT
*
13748 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTTT
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAA----G--TT
*
13794 ACCCAATTTGCCCTTCCCCA-CGGGAAGGTGTTGTTTAAGTT
1 -CCCAGTTTGCCCTTCCCCATC-GGAAGGTGTTGTTTAAGTT
* *
13835 CCCAGTATT-CTCTTCCCCATCGAAAGGTGTTGTTTAAGTCTGTTTT
1 CCCAGT-TTGCCCTTCCCCATCGGAAGGTGTTGTTTAA----G--TT
* * * *
13881 ATCCAATTTGCCCTTCTCCACCGGAAGGTGTTGTTTAAGTT
1 -CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTT
* *
13922 CTCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTGCGTT
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAA------GTT
* * *
13968 ACCCAGTTTGCCCTTCCCCACCAGAAGGTGTTGTTTAAATT
1 -CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTT
* * *
14009 CCTAGTTTGTCCTTCCCC-TCTGGAAGGTGTTGTTTAAATT
1 CCCAGTTTGCCCTTCCCCATC-GGAAGGTGTTGTTTAAGTT
* * * *
14049 CCTAGTTTGCCCTTCCCCACCGAAAGGTGTTGTTCAAGTT
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTT
* * *
14089 CCCAGTCTGCACTTCCTCATCGGAAGGTGTT
1 CCCAGTTTGCCCTTCCCCATCGGAAGGTGTT
14120 ATTCCTATTC
Statistics
Matches: 371, Mismatches: 54, Indels: 68
0.75 0.11 0.14
Matches are distributed among these distances:
39 1 0.00
40 213 0.57
41 13 0.04
43 4 0.01
44 4 0.01
46 13 0.04
47 123 0.33
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (40 bp):
CCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAGTT
Found at i:13694 original size:87 final size:87
Alignment explanation
Indices: 13571--14119 Score: 697
Period size: 87 Copynumber: 6.4 Consensus size: 87
13561 CTTGTCTGTA
* * *
13571 TTCCCGGTTTGCCCTTTCCTCATCGGAAGGCGTTGTTTAAGTCAGCTTTACCCAATTTGCTCTTC
1 TTCCCAGTTTGCCC-TTCCTCATCGGAAGGTGTTGTTTAAGTCAGCTTTACCCAATTTGCCCTTC
*
13636 CCCACCGGAAGGTGCTGTTTAAG
65 CCCACCGGAAGGTGTTGTTTAAG
* *
13659 TTCCCAGTTTGCCCTTACC-CATCGGAAGATGTTGTTTAAGT-ATGCTTTACCCAATTCGCCCTT
1 TTCCCAGTTTGCCCTT-CCTCATCGGAAGGTGTTGTTTAAGTCA-GCTTTACCCAATTTGCCCTT
*
13722 CCCCACCTGAAGGTGTTGTTTAAG
64 CCCCACCGGAAGGTGTTGTTTAAG
*
13746 TTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTGCTTTACCCAATTTGCCCTTCC
1 TTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCAGCTTTACCCAATTTGCCCTTCC
*
13811 CCACGGGAAGGTGTTGTTTAAG
66 CCACCGGAAGGTGTTGTTTAAG
* * * * * *
13833 TTCCCAGTATT-CTCTTCCCCATCGAAAGGTGTTGTTTAAGTCTGTTTTATCCAATTTGCCCTTC
1 TTCCCAGT-TTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCAGCTTTACCCAATTTGCCCTTC
*
13897 TCCACCGGAAGGTGTTGTTTAAG
65 CCCACCGGAAGGTGTTGTTTAAG
* * * *
13920 TTCTCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTGCGTTACCCAGTTTGCCCTTCC
1 TTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCAGCTTTACCCAATTTGCCCTTCC
* *
13985 CCACCAGAAGGTGTTGTTTAAA
66 CCACCGGAAGGTGTTGTTTAAG
* * * * *
14007 TTCCTAGTTTGTCCTTCC-CCTCTGGAAGGTGTTGTTTAA---A---TT-CCTAGTTTGCCCTTC
1 TTCCCAGTTTGCCCTTCCTCATC-GGAAGGTGTTGTTTAAGTCAGCTTTACCCAATTTGCCCTTC
* *
14064 CCCACCGAAAGGTGTTGTTCAAG
65 CCCACCGGAAGGTGTTGTTTAAG
* *
14087 TTCCCAGTCTGCACTTCCTCATCGGAAGGTGTT
1 TTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTT
14120 ATTCCTATTC
Statistics
Matches: 408, Mismatches: 45, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
80 57 0.14
81 5 0.01
86 8 0.02
87 321 0.79
88 17 0.04
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (87 bp):
TTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCAGCTTTACCCAATTTGCCCTTCC
CCACCGGAAGGTGTTGTTTAAG
Found at i:14856 original size:25 final size:25
Alignment explanation
Indices: 14810--14857 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
14800 AAGTAATTGC
* *
14810 TAATTAATATATATACTAATTATGG
1 TAATTAATATATAAAATAATTATGG
* *
14835 TAATTATTATATAAAATTATTAT
1 TAATTAATATATAAAATAATTAT
14858 TATTGCAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (25 bp):
TAATTAATATATAAAATAATTATGG
Found at i:17444 original size:22 final size:21
Alignment explanation
Indices: 17410--17474 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
17400 TTTCTAGAAC
* *
17410 CTCCATATGAAATTTTGTTAA
1 CTCCCTATAAAATTTTGTTAA
17431 CTTCCCTATAAAATTTTGTTACA
1 C-TCCCTATAAAATTTTGTTA-A
17454 CTCCCTATAAAATATTT-TTAA
1 CTCCCTATAAAAT-TTTGTTAA
17475 TAACCACCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.05
22 32 0.82
23 5 0.13
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (21 bp):
CTCCCTATAAAATTTTGTTAA
Found at i:17499 original size:22 final size:21
Alignment explanation
Indices: 17469--17829 Score: 133
Period size: 22 Copynumber: 16.4 Consensus size: 21
17459 TATAAAATAT
*
17469 TTTTAATAACCACCTAATGAAA
1 TTTTGATAACCACCT-ATGAAA
17491 TTTTGATAACCACCCTATGAAA
1 TTTTGATAACCA-CCTATGAAA
* *
17513 TTTTGATAACCTCCCAATGAAA
1 TTTTGATAACC-ACCTATGAAA
* * * *
17535 TGTTGGTAAGAACACATTATGAAA
1 TTTTGAT-A-ACCAC-CTATGAAA
** *
17559 TTTTGATAACCTTCTGATAAAA
1 TTTTGATAACCACCT-ATGAAA
* * *
17581 TATTGGTACGTAATCACATTATGAAA
1 T-TTTG-A--TAACCAC-CTATGAAA
* **
17607 TTTTTATAACCATATCATGAAA
1 TTTTGATAACCACCT-ATGAAA
* *
17629 TTGTGAT-ACCTCACTATGAAA
1 TTTTGATAACCAC-CTATGAAA
* * *
17650 TTTTTATAAACCTCCCTATAAAA
1 TTTTGAT-AACC-ACCTATGAAA
* *
17673 TTTTGATAACCTCCATTTGAAA
1 TTTTGATAACCACC-TATGAAA
*
17695 TTTTGATAACC-TC-ATGAAA
1 TTTTGATAACCACCTATGAAA
* *
17714 TTTTGAAAATCACCTCATG-AA
1 TTTTGATAACCACCT-ATGAAA
*
17735 -TTTGATAACCATCTTATGAAA
1 TTTTGATAACCA-CCTATGAAA
* *
17756 ATTTCATAA-CATCCTTAT-AAA
1 TTTTGATAACCA-CC-TATGAAA
* * *
17777 TTTTTTATAACCTCCTTATAAAA
1 -TTTTGATAACCACC-TATGAAA
** ** *
17800 TTTTTTTAACCTGCTACGAAA
1 TTTTGATAACCACCTATGAAA
17821 TTTTGATAA
1 TTTTGATAA
17830 GAAAACTATT
Statistics
Matches: 253, Mismatches: 59, Indels: 55
0.69 0.16 0.15
Matches are distributed among these distances:
19 14 0.06
20 13 0.05
21 44 0.17
22 124 0.49
23 29 0.11
24 16 0.06
25 2 0.01
26 10 0.04
27 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCACCTATGAAA
Found at i:17527 original size:69 final size:68
Alignment explanation
Indices: 17416--17569 Score: 166
Period size: 69 Copynumber: 2.2 Consensus size: 68
17406 GAACCTCCAT
* ** * * ** *
17416 ATGAAATTTTGTTAACTTCCCTATAAAATTTTGTTACACTCCCTATAAAATATTTTTAATAACCA
1 ATGAAATTTTGATAACCACCCTATAAAATTTTGTAACACTCCCAATAAAATATTGGTAAGAA-CA
*
17481 CCTA
65 CATA
* * *
17485 ATGAAATTTTGATAACCACCCTATGAAATTTTGATAAC-CTCCCAATGAAATGTTGGTAAGAACA
1 ATGAAATTTTGATAACCACCCTATAAAATTTTG-TAACACTCCCAATAAAATATTGGTAAGAACA
*
17549 CATT
65 CATA
17553 ATGAAATTTTGATAACC
1 ATGAAATTTTGATAACC
17570 TTCTGATAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
68 21 0.30
69 47 0.66
70 3 0.04
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (68 bp):
ATGAAATTTTGATAACCACCCTATAAAATTTTGTAACACTCCCAATAAAATATTGGTAAGAACAC
ATA
Found at i:17565 original size:46 final size:48
Alignment explanation
Indices: 17506--17617 Score: 147
Period size: 46 Copynumber: 2.4 Consensus size: 48
17496 ATAACCACCC
* *
17506 TATGAAATTTTGATAACCTCCCAATGAAATGTTGGTAAG-AA-CACAT
1 TATGAAATTTTGATAACCTCCCAATAAAATATTGGTAAGTAATCACAT
* ** *
17552 TATGAAATTTTGATAACCTTCTGATAAAATATTGGTACGTAATCACAT
1 TATGAAATTTTGATAACCTCCCAATAAAATATTGGTAAGTAATCACAT
*
17600 TATGAAATTTTTATAACC
1 TATGAAATTTTGATAACC
17618 ATATCATGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 33 0.58
47 2 0.04
48 22 0.39
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.36
Consensus pattern (48 bp):
TATGAAATTTTGATAACCTCCCAATAAAATATTGGTAAGTAATCACAT
Found at i:17980 original size:21 final size:22
Alignment explanation
Indices: 17905--18003 Score: 92
Period size: 22 Copynumber: 4.5 Consensus size: 22
17895 AAAAACTTGC
* * *
17905 CTATGAAATTTTGTTCATCTCC
1 CTATGAAATTTTGATAATCTCA
* * * *
17927 CTATAAAATTTTGAGAACCACA
1 CTATGAAATTTTGATAATCTCA
* *
17949 CTATCAAATTTTGTTAATCTCA
1 CTATGAAATTTTGATAATCTCA
*
17971 CTAT-AAATTTTGATAAACTCA
1 CTATGAAATTTTGATAATCTCA
*
17992 TTATGAAATTTT
1 CTATGAAATTTT
18004 AATTACCACA
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
21 18 0.30
22 43 0.70
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCTCA
Found at i:18083 original size:22 final size:22
Alignment explanation
Indices: 18049--18198 Score: 83
Period size: 22 Copynumber: 7.0 Consensus size: 22
18039 TCTGAAATAC
* *
18049 CACATTATAAAATTTTGATAAT
1 CACACTATGAAATTTTGATAAT
*
18071 CACACTATGAAATTTTGGTAAT
1 CACACTATGAAATTTTGATAAT
* * * * ** *
18093 CTCCCTCTAAAATTTCAATAAC
1 CACACTATGAAATTTTGATAAT
* * * * *
18115 CTCCCAATTAAATTTTGTTAA-
1 CACACTATGAAATTTTGATAAT
* * *
18136 C-CTCTATGAAATTATGATTAT
1 CACACTATGAAATTTTGATAAT
* *
18157 TACACTATGAAATTTTGGTAA-
1 CACACTATGAAATTTTGATAAT
18178 CGACACT-TGAAATTTTGATAA
1 C-ACACTATGAAATTTTGATAA
18199 GCTCACTCTA
Statistics
Matches: 95, Mismatches: 30, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
20 13 0.14
21 14 0.15
22 68 0.72
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
CACACTATGAAATTTTGATAAT
Found at i:18128 original size:104 final size:105
Alignment explanation
Indices: 17943--18140 Score: 229
Period size: 105 Copynumber: 1.9 Consensus size: 105
17933 AATTTTGAGA
* * * * * * *
17943 ACCACACTATCAAATTTTGTTAATCTCACTATAAATTTTGATAAACTCATTATGAAATTTTAATT
1 ACCACACTATAAAATTTTGATAATCACACTATAAATTTTGATAAACTCACTATAAAATTTCAATA
18008 ACCACACAATGCAAATTTAG-TAACCTCTCCCTCTGAAAT
66 ACCACACAATGCAAATTTAGTTAACCTCTCCCTCTGAAAT
* * * * *
18047 ACCACATTATAAAATTTTGATAATCACACTATGAAATTTTGGTAATCTCCCTCTAAAATTTCAAT
1 ACCACACTATAAAATTTTGATAATCACACTAT-AAATTTTGATAAACTCACTATAAAATTTCAAT
* * * *
18112 AACCTCCCAAT-TAAATTTTGTTAACCTCT
65 AACCACACAATGCAAATTTAGTTAACCTCT
18141 ATGAAATTAT
Statistics
Matches: 76, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
104 35 0.46
105 41 0.54
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (105 bp):
ACCACACTATAAAATTTTGATAATCACACTATAAATTTTGATAAACTCACTATAAAATTTCAATA
ACCACACAATGCAAATTTAGTTAACCTCTCCCTCTGAAAT
Found at i:18264 original size:22 final size:22
Alignment explanation
Indices: 18236--18563 Score: 142
Period size: 22 Copynumber: 14.8 Consensus size: 22
18226 TATAAGCACA
18236 CTATGAAATTTTGATAATCTTC
1 CTATGAAATTTTGATAATCTTC
* *
18258 CTGTGAAATTTTGATAA-CCTC
1 CTATGAAATTTTGATAATCTTC
* **
18279 CATATCG-AATTTCGATAATCGCC
1 C-TAT-GAAATTTTGATAATCTTC
* ** *
18302 CTATGAAATTTTGTTAGCCTCC
1 CTATGAAATTTTGATAATCTTC
***
18324 CTATGAAATTTTGATAATCAGA
1 CTATGAAATTTTGATAATCTTC
*
18346 GTATGAAATTTT-AGTAATC-TC
1 CTATGAAATTTTGA-TAATCTTC
*
18367 CATGTGAAATTTTGATAATCTTC
1 C-TATGAAATTTTGATAATCTTC
* * * *
18390 CCAAG-AATTTCGATAA-CCTC
1 CTATGAAATTTTGATAATCTTC
* *
18410 CATATAAAATTTTGATAA-CATC
1 C-TATGAAATTTTGATAATCTTC
*
18432 CTTATGAAATTTT-ATTTTAATAACCTC
1 C-TATGAAATTTTGA---TAAT--CTTC
*
18459 CTCATGAAATTTTGATAA-CAT-
1 CT-ATGAAATTTTGATAATCTTC
* *
18480 CTCATGAAATTGTGATAA-CTAC
1 CT-ATGAAATTTTGATAATCTTC
* * *
18502 ACTATAAAATTTTAAT-ATCCTAC
1 -CTATGAAATTTTGATAAT-CTTC
* *
18525 CTATGAAATTTTGGTAA-CCTC
1 CTATGAAATTTTGATAATCTTC
* *
18546 ACAATAAAATTTTGATAA
1 -CTATGAAATTTTGATAA
18564 CCACACTGTA
Statistics
Matches: 232, Mismatches: 50, Indels: 48
0.70 0.15 0.15
Matches are distributed among these distances:
20 4 0.02
21 39 0.17
22 152 0.66
23 15 0.06
24 3 0.01
25 3 0.01
26 1 0.00
27 14 0.06
28 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCTTC
Found at i:18296 original size:44 final size:44
Alignment explanation
Indices: 18237--18563 Score: 185
Period size: 44 Copynumber: 7.4 Consensus size: 44
18227 ATAAGCACAC
** *
18237 TATGAAATTTTGATAATCTTCCTGTGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAATCGCCCTATGAAATTTTGATAACCTCCA
* * * *
18281 TATCG-AATTTCGATAATCGCCCTATGAAATTTTGTTAGCCTCCC
1 TAT-GAAATTTTGATAATCGCCCTATGAAATTTTGATAACCTCCA
** *
18325 TATGAAATTTTGATAATCAG-AGTATGAAATTTT-AGTAATCTCCA
1 TATGAAATTTTGATAATC-GCCCTATGAAATTTTGA-TAACCTCCA
* * * *
18369 TGTGAAATTTTGATAATCTTCCC-AAG-AATTTCGATAACCTCCA
1 TATGAAATTTTGATAATC-GCCCTATGAAATTTTGATAACCTCCA
* * * *
18412 TATAAAATTTTGATAA-CATCCTTATGAAATTTTATTTTAATAACCTCC-
1 TATGAAATTTTGATAATC-GCCCTATG-AA----ATTTTGATAACCTCCA
** * *
18460 TCATGAAATTTTGATAA-C-ATCTCATGAAATTGTGATAA-CTACA
1 T-ATGAAATTTTGATAATCGCCCT-ATGAAATTTTGATAACCTCCA
* * *
18503 CTATAAAATTTTAAT-ATC-CTACCTATGAAATTTTGGTAACCTCACA
1 -TATGAAATTTTGATAATCGC--CCTATGAAATTTTGATAACCTC-CA
*
18549 -ATAAAATTTTGATAA
1 TATGAAATTTTGATAA
18564 CCACACTGTA
Statistics
Matches: 216, Mismatches: 44, Indels: 45
0.71 0.14 0.15
Matches are distributed among these distances:
42 8 0.04
43 50 0.23
44 113 0.52
45 8 0.04
46 2 0.01
47 3 0.01
48 4 0.02
49 28 0.13
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAATCGCCCTATGAAATTTTGATAACCTCCA
Found at i:18460 original size:27 final size:27
Alignment explanation
Indices: 18418--18471 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
18408 TCCATATAAA
* *
18418 ATTTTGATAACATCCTTATGAAATTTT
1 ATTTTAATAACATCCTCATGAAATTTT
*
18445 ATTTTAATAACCTCCTCATGAAATTTT
1 ATTTTAATAACATCCTCATGAAATTTT
18472 GATAACATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (27 bp):
ATTTTAATAACATCCTCATGAAATTTT
Found at i:18537 original size:65 final size:66
Alignment explanation
Indices: 18445--18607 Score: 190
Period size: 65 Copynumber: 2.5 Consensus size: 66
18435 ATGAAATTTT
* * *
18445 ATTTTAATAACCT-CCTCATGAAATTTTGATAACATCTC-ATGAAATTGTGATAACTACACTATA
1 ATTTTAATAACCTACCT-ATGAAATTTTGATAACATCACAATAAAATTGTGATAACCACACTATA
18508 AA
65 AA
* * * * *
18510 ATTTTAATATCCTACCTATGAAATTTTGGTAACCTCACAATAAAATTTTGATAACCACACTGTAA
1 ATTTTAATAACCTACCTATGAAATTTTGATAACATCACAATAAAATTGTGATAACCACACTATAA
18575 A
66 A
* *
18576 ATTTTAGTAACC-ACACAATG-AATTTTGATAAC
1 ATTTTAATAACCTAC-CTATGAAATTTTGATAAC
18608 TTCCAAAATT
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
65 43 0.52
66 40 0.48
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (66 bp):
ATTTTAATAACCTACCTATGAAATTTTGATAACATCACAATAAAATTGTGATAACCACACTATAA
A
Found at i:18564 original size:22 final size:22
Alignment explanation
Indices: 18210--18607 Score: 113
Period size: 22 Copynumber: 18.0 Consensus size: 22
18200 CTCACTCTAT
** * *
18210 CTCACTATGTAATTTTTATAAG
1 CTCACTATAAAATTTTGATAAC
* *
18232 CACACTATGAAATTTTGATAATC
1 CTCACTATAAAATTTTGATAA-C
* * *
18255 TTC-CTGTGAAATTTTGATAAC
1 CTCACTATAAAATTTTGATAAC
** * *
18276 CTC-CATATCGAATTTCGATAAT
1 CTCAC-TATAAAATTTTGATAAC
* * * * *
18298 CGCCCTATGAAATTTTGTTAGC
1 CTCACTATAAAATTTTGATAAC
* * *
18320 CTCCCTATGAAATTTTGATAAT
1 CTCACTATAAAATTTTGATAAC
** * * *
18342 CAGAGTATGAAATTTT-AGTAAT
1 CTCACTATAAAATTTTGA-TAAC
* *
18364 CTC-CATGTGAAATTTTGATAATC
1 CTCAC-TATAAAATTTTGATAA-C
* * * *
18387 TTC-CCA-AGAATTTCGATAAC
1 CTCACTATAAAATTTTGATAAC
18407 CTC-CATATAAAATTTTGATAAC
1 CTCAC-TATAAAATTTTGATAAC
* *
18429 ATC-CTTATGAAATTTTATTTTAATAAC
1 CTCAC-TAT-AAA----ATTTTGATAAC
*
18456 CTC-CTCATGAAATTTTGATAAC
1 CTCACT-ATAAAATTTTGATAAC
* * * *
18478 ATCTC-ATGAAATTGTGATAA-
1 CTCACTATAAAATTTTGATAAC
* *
18498 CTACACTATAAAATTTTAATATC
1 CT-CACTATAAAATTTTGATAAC
* *
18521 CT-ACCTATGAAATTTTGGTAAC
1 CTCA-CTATAAAATTTTGATAAC
*
18543 CTCACAATAAAATTTTGATAAC
1 CTCACTATAAAATTTTGATAAC
* *
18565 CACACTGTAAAATTTT-AGTAAC
1 CTCACTATAAAATTTTGA-TAAC
* * *
18587 CACACAAT-GAATTTTGATAAC
1 CTCACTATAAAATTTTGATAAC
18608 TTCCAAAATT
Statistics
Matches: 283, Mismatches: 70, Indels: 47
0.71 0.17 0.12
Matches are distributed among these distances:
20 5 0.02
21 44 0.16
22 203 0.72
23 13 0.05
26 3 0.01
27 15 0.05
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
CTCACTATAAAATTTTGATAAC
Found at i:18576 original size:66 final size:65
Alignment explanation
Indices: 18445--18587 Score: 180
Period size: 66 Copynumber: 2.2 Consensus size: 65
18435 ATGAAATTTT
* * *
18445 ATTTTAATAACCTCCTCATGAAATTTTGATAACATCTCATGAAATTGTGATAACTACACTATAAA
1 ATTTTAATAACCTCCTCATGAAATTTTGATAACATCACATAAAATTGTGATAACCACACTATAAA
* * * * *
18510 ATTTTAATATCCTACCT-ATGAAATTTTGGTAACCTCACAATAAAATTTTGATAACCACACTGTA
1 ATTTTAATAACCT-CCTCATGAAATTTTGATAACATCAC-ATAAAATTGTGATAACCACACTATA
18574 AA
64 AA
*
18576 ATTTTAGTAACC
1 ATTTTAATAACC
18588 ACACAATGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
65 30 0.45
66 36 0.55
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (65 bp):
ATTTTAATAACCTCCTCATGAAATTTTGATAACATCACATAAAATTGTGATAACCACACTATAAA
Found at i:19014 original size:22 final size:21
Alignment explanation
Indices: 18978--19142 Score: 111
Period size: 22 Copynumber: 7.6 Consensus size: 21
18968 TGAATATTTT
*
18978 TATGAAATTTCGATAACTATCC
1 TATGAAATTTTGATAACTA-CC
* * *
19000 TATTAAATTTTGATAACCACGT
1 TATGAAATTTTGATAACTAC-C
*
19022 TATGAAATTTTGATAATTACC
1 TATGAAATTTTGATAACTACC
*
19043 TATGAAATTGTGATAAACT-CC
1 TATGAAATTTTGAT-AACTACC
* **
19064 ATATGAAACTTTGATAACCTAAA
1 -TATGAAATTTTGATAA-CTACC
*
19087 TATGAAATTTTAATAAACCT-CTC
1 TATGAAATTTTGAT-AA-CTAC-C
* *
19110 TATG-AGTTTTGATAACATCCC
1 TATGAAATTTTGATAAC-TACC
*
19131 TATGAGATTTTG
1 TATGAAATTTTG
19143 TTAATCTCCT
Statistics
Matches: 111, Mismatches: 22, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
20 1 0.01
21 26 0.23
22 75 0.68
23 9 0.08
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:19069 original size:43 final size:44
Alignment explanation
Indices: 18978--19081 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 44
18968 TGAATATTTT
* * * * **
18978 TATGAAATTTCGATAACTATCCTATTAAATTTTGATAACCACGT
1 TATGAAATTTTGATAACTATCCTATGAAATTGTGATAAACACCA
* *
19022 TATGAAATTTTGATAATTA-CCTATGAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAACTATCCTATGAAATTGTGATAAACACCA
*
19065 TATGAAACTTTGATAAC
1 TATGAAATTTTGATAAC
19082 CTAAATATGA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 33 0.66
44 17 0.34
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (44 bp):
TATGAAATTTTGATAACTATCCTATGAAATTGTGATAAACACCA
Done.