Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012424.1 Corchorus olitorius cultivar O-4 contig12457, 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: 44516
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:350 original size:16 final size:16
Alignment explanation
Indices: 306--340 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
296 AGTTTTGGCC
*
306 TTTG-GTCACTCGGGT
1 TTTGAGTCATTCGGGT
321 TTTGAGTCATTCGGGT
1 TTTGAGTCATTCGGGT
337 TTTG
1 TTTG
341 GGTTTTTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.09, C:0.14, G:0.31, T:0.46
Consensus pattern (16 bp):
TTTGAGTCATTCGGGT
Found at i:2282 original size:132 final size:133
Alignment explanation
Indices: 2126--2425 Score: 532
Period size: 132 Copynumber: 2.3 Consensus size: 133
2116 TTGTTTAGAC
* *
2126 TTTTATAGGTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATATAATATATCCTTATAAC
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATCCTTATAAC
2191 TATTTAATTTTTACCATTTTACTATTTTAATTAGAAA-AATTATATATATTAGAATTTTTTAAAT
66 TATTTAATTTTTACCATTTTACTATTTTAATTA-AAAGAATTATATATATTAGAATTTTTTAAAT
2255 ATA-
130 ATAT
*
2258 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATATTATATCCTTATAAC
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATCCTTATAAC
*
2323 TATTTAATTTTTACCATTTTACTATTTTAATTAAAAGAATTTTATATATTAGAATTTTTTAAATA
66 TATTTAATTTTTACCATTTTACTATTTTAATTAAAAGAATTATATATATTAGAATTTTTTAAATA
2388 TAT
131 TAT
*
2391 TTTTATAGTTTTATTCAACTAAAAACTCTATTTTT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTT
2426 TGGCCAAAAA
Statistics
Matches: 161, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
131 3 0.02
132 124 0.77
133 34 0.21
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (133 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATCCTTATAAC
TATTTAATTTTTACCATTTTACTATTTTAATTAAAAGAATTATATATATTAGAATTTTTTAAATA
TAT
Found at i:5316 original size:24 final size:24
Alignment explanation
Indices: 5283--5338 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
5273 GTCAGCTTTG
* *
5283 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATATTTAATTATTA
* *
5306 AATTTATTTAATATTTTATTATTC
1 AATTTATTTAATATTTAATTATTA
5330 AATTTATTT
1 AATTTATTT
5339 TACAATCCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (24 bp):
AATTTATTTAATATTTAATTATTA
Found at i:7626 original size:20 final size:21
Alignment explanation
Indices: 7586--7627 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
7576 CTTTCAATAA
7586 ACATAAACCCTTAATTTTTTT
1 ACATAAACCCTTAATTTTTTT
7607 ACATAAACCCTTAATTTTTTT
1 ACATAAACCCTTAATTTTTTT
7628 CTTCTTGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (21 bp):
ACATAAACCCTTAATTTTTTT
Found at i:11638 original size:37 final size:37
Alignment explanation
Indices: 11560--11638 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 37
11550 AACTTAATTT
*
11560 TTCAAATTGGGAAAGTTCCCATCAAGTCTTAATAGTT
1 TTCAAATTGGGAAAGTTCCCATCAAGTCTTAATAGTA
*
11597 TTCAAATTGGGAAAGTTCCCATCAAGTTTTCAA-AGTA
1 TTCAAATTGGGAAAGTTCCCATCAAGTCTT-AATAGTA
11634 TTCAA
1 TTCAA
11639 TTTAGCTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 37 0.95
38 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (37 bp):
TTCAAATTGGGAAAGTTCCCATCAAGTCTTAATAGTA
Found at i:11699 original size:52 final size:52
Alignment explanation
Indices: 11595--11834 Score: 347
Period size: 52 Copynumber: 4.6 Consensus size: 52
11585 GTCTTAATAG
11595 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCATC-AGTTTTCAAAGTATTCAATTTAGCTCT
*
11648 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGCATTCAATTTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCT
* * * * *
11700 TTTTCAAGTCGGGAGAGTTCCCATC-GGTCTCAAAGTATTCAATTTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCT
* * ** *
11751 TTTTCAAGTCGGGAGGGTTCCCATCAGTCTTCAAAGTATTCAATTTAGCTCT
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCT
*
11803 TTTCCAAATTGGGAAAGTTCCCATCAGGTTTT
1 TTTTCAAATTGGGAAAGTTCCCATCA-GTTTT
11835 AGTTTTCAAT
Statistics
Matches: 168, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
51 47 0.28
52 92 0.55
53 29 0.17
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (52 bp):
TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCT
Found at i:11745 original size:103 final size:103
Alignment explanation
Indices: 11595--11827 Score: 324
Period size: 103 Copynumber: 2.3 Consensus size: 103
11585 GTCTTAATAG
* * * *
11595 TTTT-CAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATTG
1 TTTTCCAAATCGGGAAAGTTCCCATC--GGTCTCAAAGTATTCAATTTAGCTCTTTTTCAAATCG
*
11659 GGAAAGTTCCCATCAGTTTTCAAAGCATTCAATTTAGCTC
64 GGAAAGTTCCCATCAGTCTTCAAAGCATTCAATTTAGCTC
* * * *
11699 TTTTTCAAGTCGGGAGAGTTCCCATCGGTCTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGG
1 TTTTCCAAATCGGGAAAGTTCCCATCGGTCTCAAAGTATTCAATTTAGCTCTTTTTCAAATCGGG
** *
11764 AGGGTTCCCATCAGTCTTCAAAGTATTCAATTTAGCTC
66 AAAGTTCCCATCAGTCTTCAAAGCATTCAATTTAGCTC
*
11802 TTTTCCAAATTGGGAAAGTTCCCATC
1 TTTTCCAAATCGGGAAAGTTCCCATC
11828 AGGTTTTAGT
Statistics
Matches: 113, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
103 91 0.81
104 4 0.04
105 18 0.16
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (103 bp):
TTTTCCAAATCGGGAAAGTTCCCATCGGTCTCAAAGTATTCAATTTAGCTCTTTTTCAAATCGGG
AAAGTTCCCATCAGTCTTCAAAGCATTCAATTTAGCTC
Found at i:12125 original size:46 final size:46
Alignment explanation
Indices: 12073--12184 Score: 215
Period size: 46 Copynumber: 2.4 Consensus size: 46
12063 AATAAAATCT
*
12073 AAAAAATAGAAACAACCAATAATAGAAACTATTTTATTATTTGTTA
1 AAAAAATAGAAACAACCAATAATAGAAACTAGTTTATTATTTGTTA
12119 AAAAAATAGAAACAACCAATAATAGAAACTAGTTTATTATTTGTTA
1 AAAAAATAGAAACAACCAATAATAGAAACTAGTTTATTATTTGTTA
12165 AAAAAATAGAAACAACCAAT
1 AAAAAATAGAAACAACCAAT
12185 CTTTTAACGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (46 bp):
AAAAAATAGAAACAACCAATAATAGAAACTAGTTTATTATTTGTTA
Found at i:35828 original size:27 final size:26
Alignment explanation
Indices: 35797--35870 Score: 103
Period size: 27 Copynumber: 2.8 Consensus size: 26
35787 AGTGGACTTA
* *
35797 AAATGACCAAAATGTCCCTGAATGTGC
1 AAATGACCAAAATGCCCCTG-ATATGC
*
35824 GAATGACCAAAATGCCCCTTGATATGC
1 AAATGACCAAAATGCCCC-TGATATGC
35851 AAATGACCAAAATGCCCCTG
1 AAATGACCAAAATGCCCCTG
35871 GATGACCCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 2 0.05
27 38 0.90
28 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (26 bp):
AAATGACCAAAATGCCCCTGATATGC
Found at i:35887 original size:27 final size:27
Alignment explanation
Indices: 35797--35888 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
35787 AGTGGACTTA
* * ***
35797 AAATGACCAAAATGTCCCTGAATGTGC
1 AAATGACCAAAATGCCCCTGGATACCC
* * **
35824 GAATGACCAAAATGCCCCTTGATATGC
1 AAATGACCAAAATGCCCCTGGATACCC
35851 AAATGACCAAAATGCCCCTGGATGACCC
1 AAATGACCAAAATGCCCCTGGAT-ACCC
*
35879 TAATG-CCAAA
1 AAATGACCAAA
35889 TAAGAAATAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 48 0.89
28 6 0.11
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATACCC
Found at i:36486 original size:90 final size:90
Alignment explanation
Indices: 36141--36577 Score: 557
Period size: 90 Copynumber: 4.9 Consensus size: 90
36131 CTTCAACTTG
* * * ** * *
36141 TTTGAAAATGTGCTGCACCGAGCTCACCGAATTCCAATCTTTG---AAGGGATGCACAGTATTAA
1 TTTGAAGATTTGCTGCACCGAGCTCACC-AAGTCCAATC-TTGAAAAAGTAATGCACCGCATTAA
*
36203 CTTGATTCACTGAATCACCCTGATCTA
64 CTTGATTCACCGAATCACCCTGATCTA
*
36230 TTTGAAGA-TTGCTGCACCGAGCTCACCGAGTCCAATCTTGAAAAAGTAATGCACCGCATTAACT
1 TTTGAAGATTTGCTGCACCGAGCTCACCAAGTCCAATCTTGAAAAAGTAATGCACCGCATTAACT
* * * *
36294 TGATTCACCGAATCATCCTCAACTG
66 TGATTCACCGAATCACCCTGATCTA
* * * * * *
36319 TTTGAAAATGTGTTGCACCGAGCTCACAGAATTCCAATCTTTG---AAGAAATGCACCGCATTAA
1 TTTGAAGATTTGCTGCACCGAGCTCAC-CAAGTCCAATC-TTGAAAAAGTAATGCACCGCATTAA
36381 CTTGATTCACCGAATCACCCTGATCTA
64 CTTGATTCACCGAATCACCCTGATCTA
*
36408 TTTGAAGATTTGCTGCACCGAGCTCACCAAGTCCAATCTTGAAAAAGTAATGCACCCCATTAACT
1 TTTGAAGATTTGCTGCACCGAGCTCACCAAGTCCAATCTTGAAAAAGTAATGCACCGCATTAACT
*
36473 TGATTCACCGAATCACCGTGATCTA
66 TGATTCACCGAATCACCCTGATCTA
* * *
36498 TTTGAAGATTTGTTGCACCGAGCTCACCGAGTCGAATCTT-AAAAATGTAATGCACCGCATTAAC
1 TTTGAAGATTTGCTGCACCGAGCTCACCAAGTCCAATCTTGAAAAA-GTAATGCACCGCATTAAC
36562 TTGATTCACCGAATCA
65 TTGATTCACCGAATCA
36578 TCCTTTGAAG
Statistics
Matches: 302, Mismatches: 36, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
86 3 0.01
87 11 0.04
88 27 0.09
89 121 0.40
90 129 0.43
91 8 0.03
92 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (90 bp):
TTTGAAGATTTGCTGCACCGAGCTCACCAAGTCCAATCTTGAAAAAGTAATGCACCGCATTAACT
TGATTCACCGAATCACCCTGATCTA
Found at i:36683 original size:34 final size:33
Alignment explanation
Indices: 36596--36683 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 33
36586 AGATTTGCCG
* *
36596 CACCGAGTCATCTGAATTCAATTTGAAGATGCC
1 CACCGAGTCATCTGAATTCAATATGAAGATGCA
*
36629 CGACTGAGTCATCTGAATTCAACTATGAAGATGCTA
1 C-ACCGAGTCATCTGAATTCAA-TATGAAGATGC-A
*
36665 CACCAAGTCATCTG-ATTCA
1 CACCGAGTCATCTGAATTCA
36684 CTGAATCCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 1 0.02
34 24 0.51
35 21 0.45
36 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (33 bp):
CACCGAGTCATCTGAATTCAATATGAAGATGCA
Found at i:36701 original size:42 final size:42
Alignment explanation
Indices: 36654--36774 Score: 170
Period size: 42 Copynumber: 2.9 Consensus size: 42
36644 AATTCAACTA
*
36654 TGAAGATGCTACACCAAGTCATCTGATTCACTGAATCCCACT
1 TGAAGATGCTACACCGAGTCATCTGATTCACTGAATCCCACT
* *
36696 TGAAGATGCTACACCGAGCCATGTGATTCACTGAATCCCACT
1 TGAAGATGCTACACCGAGTCATCTGATTCACTGAATCCCACT
* * ** *
36738 TGAAAATGCTGCAATGAGTCATCCGATTCACTGAATC
1 TGAAGATGCTACACCGAGTCATCTGATTCACTGAATC
36775 ATCCTGAACT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
TGAAGATGCTACACCGAGTCATCTGATTCACTGAATCCCACT
Found at i:36865 original size:90 final size:90
Alignment explanation
Indices: 36762--37413 Score: 920
Period size: 90 Copynumber: 7.3 Consensus size: 90
36752 TGAGTCATCC
* *
36762 GATTCACTGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCAAATCTTG
1 GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCCAATCTTG
*
36827 AA-AAAGTAATGCACCGCATTAACTT
66 AAGAAA-CAATGCACCGCATTAACTT
* * * *
36852 GATTCACCGAATCATCCTGAACTGCTTGAAAATATGTTGCACCGAGCTCACCGAATCCAATCTTG
1 GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCCAATCTTG
*
36917 AAGAAACAATGCACCACATTAACTT
66 AAGAAACAATGCACCGCATTAACTT
* *
36942 GATTCACCGAATCATCCTGAACTGTTTGATGATTTGCTGCACCGAGCTCACCGAATCAAATCTTG
1 GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCCAATCTTG
*
37007 AAGAAACAATGCACCGCATTGACTT
66 AAGAAACAATGCACCGCATTAACTT
** * *
37032 GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACTAAGCTCACTGAATCAAATCTTG
1 GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCCAATCTTG
37097 AAGAAACAATGCACCGCA--AACTT
66 AAGAAACAATGCACCGCATTAACTT
* * * * *
37120 GATTCACCGAATCATCCTGAACTGTTTAAAAATATGTTGCACCGAGCTCGCCGAATCCAATCTTG
1 GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCCAATCTTG
* * *
37185 AGGAAACAATGCATCACATTAACTT
66 AAGAAACAATGCACCGCATTAACTT
* * * *
37210 GATTCACCGAATCACCCTGAACTGTTTGAAAATGTGCTGCACTGAGCTCACCGAATCCAATCTTG
1 GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCCAATCTTG
*
37275 AAGAAACAATGCACCACATTAACTT
66 AAGAAACAATGCACCGCATTAACTT
* * *
37300 GATTCACCGAATCATCCTGAACAG---GAAGATAAGTGTGTTGTACCGAGCTCACCGAATCCAAT
1 GATTCACCGAATCATCCTGAACTGTTTGAAGAT---T-TGCTGCACCGAGCTCACCGAATCCAAT
*
37362 CTTGTAGAAACAATGCACCGCATTAACTT
62 CTTGAAGAAACAATGCACCGCATTAACTT
*
37391 GATTCACTGAATCATCCTGAACT
1 GATTCACCGAATCATCCTGAACT
37414 AGAAGATAAA
Statistics
Matches: 503, Mismatches: 52, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
87 5 0.01
88 75 0.15
90 348 0.69
91 75 0.15
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (90 bp):
GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCCAATCTTG
AAGAAACAATGCACCGCATTAACTT
Found at i:37250 original size:268 final size:269
Alignment explanation
Indices: 36762--37413 Score: 990
Period size: 268 Copynumber: 2.4 Consensus size: 269
36752 TGAGTCATCC
*
36762 GATTCACTGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCAAATCTTG
1 GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCAAATCTTG
* *
36827 AA-AAAGTAATGCACCGCATTAACTTGATTCACCGAATCATCCTGAACTGCTTGAAAATATGTTG
66 AAGAAA-CAATGCACCGCA-TAACTTGATTCACCGAATCATCCTGAACTGCTTAAAAATATGTTG
36891 CACCGAGCTCACCGAATCCAATCTTGAAGAAACAATGCACCACATTAACTTGATTCACCGAATCA
129 CACCGAGCTCACCGAATCCAATCTTGAAGAAACAATGCACCACATTAACTTGATTCACCGAATCA
* ** *
36956 TCCTGAACTGTTTGATGATTTGCTGCACCGAGCTCACCGAATCAAATCTTGAAGAAACAATGCAC
194 CCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAATCAAATCTTGAAGAAACAATGCAC
* *
37021 CGCATTGACTT
259 CACATTAACTT
** *
37032 GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACTAAGCTCACTGAATCAAATCTTG
1 GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCAAATCTTG
*
37097 AAGAAACAATGCACCGCA-AACTTGATTCACCGAATCATCCTGAACTGTTTAAAAATATGTTGCA
66 AAGAAACAATGCACCGCATAACTTGATTCACCGAATCATCCTGAACTGCTTAAAAATATGTTGCA
* * *
37161 CCGAGCTCGCCGAATCCAATCTTGAGGAAACAATGCATCACATTAACTTGATTCACCGAATCACC
131 CCGAGCTCACCGAATCCAATCTTGAAGAAACAATGCACCACATTAACTTGATTCACCGAATCACC
* *
37226 CTGAACTGTTTGAAAATGTGCTGCACTGAGCTCACCGAATCCAATCTTGAAGAAACAATGCACCA
196 CTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAATCAAATCTTGAAGAAACAATGCACCA
37291 CATTAACTT
261 CATTAACTT
* * * *
37300 GATTCACCGAATCATCCTGAACAG---GAAGATAAGTGTGTTGTACCGAGCTCACCGAATCCAAT
1 GATTCACCGAATCATCCTGAACTGTTTGAAGAT---T-TGCTGCACCGAGCTCACCGAATCAAAT
* *
37362 CTTGTAGAAACAATGCACCGCATTAACTTGATTCACTGAATCATCCTGAACT
62 CTTGAAGAAACAATGCACCGCA-TAACTTGATTCACCGAATCATCCTGAACT
37414 AGAAGATAAA
Statistics
Matches: 348, Mismatches: 27, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
265 6 0.02
268 196 0.56
269 42 0.12
270 74 0.21
271 30 0.09
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (269 bp):
GATTCACCGAATCATCCTGAACTGTTTGAAGATTTGCTGCACCGAGCTCACCGAATCAAATCTTG
AAGAAACAATGCACCGCATAACTTGATTCACCGAATCATCCTGAACTGCTTAAAAATATGTTGCA
CCGAGCTCACCGAATCCAATCTTGAAGAAACAATGCACCACATTAACTTGATTCACCGAATCACC
CTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGAATCAAATCTTGAAGAAACAATGCACCA
CATTAACTT
Found at i:37475 original size:54 final size:54
Alignment explanation
Indices: 37415--37686 Score: 280
Period size: 54 Copynumber: 5.1 Consensus size: 54
37405 TCCTGAACTA
* * * * * *
37415 GAAGATAAACCCAAATCACTAAAAACTTCCTTGATTGACTGCACTAGATCACTT
1 GAAGATAAACCTAAACCACTAGAAACTTTCTTGATTGACCGCACTGGATCACTT
** * ** *
37469 GAAGATAAATTTAAACCACTGGAAACTTTC-TGAACGATCGC-CTTGGATCACTT
1 GAAGATAAACCTAAACCACTAGAAACTTTCTTGATTGACCGCAC-TGGATCACTT
* *
37522 AAAGATAAACCTAAACCACTATAAACTTTCTTGATTGACCGCACTGGATCACTT
1 GAAGATAAACCTAAACCACTAGAAACTTTCTTGATTGACCGCACTGGATCACTT
* * * * **
37576 GATGATAAACTTTAACCACTGGAAACTTTCTTGATTGACCGCACTGGATTGCTT
1 GAAGATAAACCTAAACCACTAGAAACTTTCTTGATTGACCGCACTGGATCACTT
* * * * *
37630 GAAGCTAAACTTAACCCACT-GTAGACTTTCTTGATTGGCCGCACTGGATCACTT
1 GAAGATAAACCTAAACCACTAG-AAACTTTCTTGATTGACCGCACTGGATCACTT
37684 GAA
1 GAA
37687 ATTCTGCTAA
Statistics
Matches: 178, Mismatches: 36, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
52 1 0.01
53 42 0.24
54 134 0.75
55 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (54 bp):
GAAGATAAACCTAAACCACTAGAAACTTTCTTGATTGACCGCACTGGATCACTT
Found at i:37602 original size:107 final size:108
Alignment explanation
Indices: 37416--37686 Score: 332
Period size: 107 Copynumber: 2.5 Consensus size: 108
37406 CCTGAACTAG
* * * * * *
37416 AAGATAAACCCAAATCACTAAAAACTTCCTTGATTGACTGCACTAGATCACTTGAAGATAAATTT
1 AAGATAAACCTAAACCACTATAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAATTT
*
37481 AAACCACTGGAAACTTTC-TGAACGATCGC-CTTGGATCACTTA
66 AAACCACTGGAAACTTTCTTGAACGACCGCAC-TGGATCACTTA
*
37523 AAGATAAACCTAAACCACTATAAACTTTCTTGATTGACCGCACTGGATCACTTGATGATAAACTT
1 AAGATAAACCTAAACCACTATAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAA-TT
** ** *
37588 T-AACCACTGGAAACTTTCTTGATTGACCGCACTGGATTGCTTG
65 TAAACCACTGGAAACTTTCTTGAACGACCGCACTGGATCACTTA
* * * * * *
37631 AAGCTAAACTTAACCCACTGTAGACTTTCTTGATTGGCCGCACTGGATCACTTGAA
1 AAGATAAACCTAAACCACTATAAACTTTCTTGATTGACCGCACTGGATCACTTGAA
37687 ATTCTGCTAA
Statistics
Matches: 141, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
107 72 0.51
108 68 0.48
109 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (108 bp):
AAGATAAACCTAAACCACTATAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAATTT
AAACCACTGGAAACTTTCTTGAACGACCGCACTGGATCACTTA
Found at i:42983 original size:19 final size:18
Alignment explanation
Indices: 42959--42994 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42949 TGAAGACTTA
42959 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
42978 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
42995 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.