Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014287.1 Kokia drynarioides strain JFW-HI SEQ_129320, 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: 43722
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:7981 original size:215 final size:216
Alignment explanation
Indices: 7305--8718 Score: 1554
Period size: 215 Copynumber: 6.6 Consensus size: 216
7295 GCTTGCATCA
* * * * *
7305 CAAGAGAGAATCAATTCTCATGTAAATAAGTTTGTAATTCAAAGACAAAAAGTTATTTACAAAAT
1 CAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAAT
* ** * * * * *
7370 GACAAACTTTTTAGACCAAATGATGAAATTTCTCAACCACGGAATGTTCAAAAAATTGGTCGAAG
66 GACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTAAAAAATTGGTCAAAG
* * * *
7435 GAATGGATCATCTTCAATACTCTCAGGAACTAAAGTTATAAAAGAACTCATAAATGTTTGACAAG
131 GAATGGATCGTCTTGAATACTCTAAGGAACCAAAGTTATAAAAGAACTCATAAATGTTTGACAAG
* *
7500 TTCGGAAGTTCGTCTC-ATATC
196 TTCGGAAGTTCGTC-CAAGAAC
* * * *
7521 CAAGAGAGAAACAATTCTTACATAAATTAGTTTTTAATTCAAAAACAAAAAGTTGTTTACAAAAT
1 CAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAAT
* * * * * * *
7586 G-CAAACTATTTAGACCTAATGATGAGATTTCTTGAGCATGAAATATTTGAAAAATTGCTCAAAG
66 GACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTAAAAAATTGGTCAAAG
* * * * *
7650 GAATGGATCGTCTTAAAATACT-TAAAGGAACCGAAGTTATAAAAGAACTCATAAAAGTTTAACT
131 GAATGGATCGTCTT-GAATACTCT-AAGGAACCAAAGTTATAAAAGAACTCATAAATGTTTGACA
* *
7714 AGTCCGTAAGTTCGTCCAAGAAC
194 AGTTCGGAAGTTCGTCCAAGAAC
* * * * *
7737 CAAGGGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGCCCAAAAGTTATTTACAAAAT
1 CAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAAT
* * * * ** *
7802 GACAAACAATTT-CACCAAATGATGCGATTTTTCGAGCGTGGAATGTTTGGAAAATTTGTCAAAG
66 GACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTAAAAAATTGGTCAAAG
* * * * *
7866 GAATGAATTGTCTTGAATACTTTAAGGAACAAAAGTTATAAAAGAACTCACTGAA-GTTTGACAA
131 GAATGGATCGTCTTGAATACTCTAAGGAACCAAAGTTATAAAAGAACTCA-TAAATGTTTGACAA
* *
7930 GTTTGGAAGTTCATCCAAGAAC
195 GTTCGGAAGTTCGTCCAAGAAC
* * ** * * * *
7952 CAAGATATAAACAATTCTAACAAAAATAAGTTTTTAATTCATAGACCAATAGTTGTTAACAAAAT
1 CAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAAT
* * * * *
8017 TACAAACAATTT-GACCAAATGATGCGATTTCCCGAGCATGGAATTTTTAAAAAATTGGTTAAAG
66 GACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTAAAAAATTGGTCAAAG
* * *
8081 GAATGGATCGTCCTGAATACTCTCAGGAACCAAAGTTATAAAAGAACTCATAAATGTTTGACAAT
131 GAATGGATCGTCTTGAATACTCTAAGGAACCAAAGTTATAAAAGAACTCATAAATGTTTGACAAG
*
8146 TTCGAAAGTTCGTCCAAGAAC
196 TTCGGAAGTTCGTCCAAGAAC
* * *
8167 CAAGAGTGAAACAATTCTAACGTAAACAAGTTTTTAATTCAAAGACTAAAAGTTGTTTACAAAAT
1 CAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAAT
* * * * *** *
8232 AACAAACTTTTTAGACCAAATGATTCGATTTCTCGAGCATGGATTG-TTCGGAAATTGGTCGAAG
66 GACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTAAAAAATTGGTCAAAG
* * * * * *
8296 GAATGGATTGTATTGAATAAC-CTCATGAACCAAAGCTATAAAAGAACTCGTAAATGTTTGACAA
131 GAATGGATCGTCTTGAAT-ACTCTAAGGAACCAAAGTTATAAAAGAACTCATAAATGTTTGACAA
* * * **
8360 GTTCAGAAATTCGTCTAAGATT
195 GTTCGGAAGTTCGTCCAAGAAC
* * * * * *
8382 CAGGAGAGAAACAATTCTCATGTAAAAAAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAAT
1 CAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAAT
* * ** *
8447 GACAAACTTTTTAGACCAAATGATGTGATTTC-CCCGCATGGAAT-TTTCAAAAAATTGGTCGAA
66 GACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTT-AAAAAATTGGTCAAA
* * * * *
8510 GGCATGGATCGTCTTAAATACTTTAAGGAACCAAAGTTATAAATGAACTCGTAAATGTTTGACAA
130 GGAATGGATCGTCTTGAATACTCTAAGGAACCAAAGTTATAAAAGAACTCATAAATGTTTGACAA
* * * *
8575 GTTTGAAAGTTTGTCCATGAA-
195 GTTCGGAAGTTCGTCCAAGAAC
* ** * * * *
8596 CTAGAGAGAAACAATTCTCTCGTAATTAAATTTTTAATTCAAAGATAAAAAGTTGTTTACAGAAT
1 CAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAAT
** * * *
8661 GACAAACTATTTAGACCAAATGATATGATTTCTCGAGTATGGAATGATAAAAAAATTG
66 GACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTAAAAAATTG
8719 CTGATGTGAG
Statistics
Matches: 1001, Mismatches: 183, Indels: 29
0.83 0.15 0.02
Matches are distributed among these distances:
214 100 0.10
215 630 0.63
216 262 0.26
217 9 0.01
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (216 bp):
CAAGAGAGAAACAATTCTAACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAAT
GACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTAAAAAATTGGTCAAAG
GAATGGATCGTCTTGAATACTCTAAGGAACCAAAGTTATAAAAGAACTCATAAATGTTTGACAAG
TTCGGAAGTTCGTCCAAGAAC
Found at i:9072 original size:48 final size:48
Alignment explanation
Indices: 9020--9142 Score: 201
Period size: 48 Copynumber: 2.5 Consensus size: 48
9010 TAATTATGCT
*
9020 TCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAATCTGCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATATTTGTTTAATAATCTGCA
*
9068 TCATTAAGTGTTTTGTTTGTTAAATGCATATTTGTTTAGTAATCTGCA
1 TCATTAAGTGTTTTGTTTGTTAAATGCATATTTGTTTAATAATCTGCA
* *
9116 TTATTAAATGTTTTGTTTTGTTAAATG
1 TCATTAAGTGTTTTG-TTTGTTAAATG
9143 TCTTGCATTA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
48 59 0.84
49 11 0.16
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.52
Consensus pattern (48 bp):
TCATTAAGTGTTTTGTTTGTTAAATGCATATTTGTTTAATAATCTGCA
Found at i:9684 original size:80 final size:79
Alignment explanation
Indices: 9589--9738 Score: 237
Period size: 80 Copynumber: 1.9 Consensus size: 79
9579 TGTCATGTCT
* *
9589 TTTCAGCTACATCAGATCCTAATGAAGAGACATGACTCACTGGCTTCCCTACAAGAGCTAAAAAT
1 TTTCAACTACATCAGATCCTAACGAAGAGACATGACTCACTGGCTTCCCTACAAGAG-TAAAAAT
9654 GAAATTGTAATGCCC
65 GAAATTGTAATGCCC
* * * *
9669 TTTCAACTACATCAGATCCTAACGAAGAGATATGACTCACTGGCTTCCTTACAAGAGTTAAAGTG
1 TTTCAACTACATCAGATCCTAACGAAGAGACATGACTCACTGGCTTCCCTACAAGAGTAAAAATG
9734 AAATT
66 AAATT
9739 AGTGCTTGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
79 11 0.17
80 53 0.83
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (79 bp):
TTTCAACTACATCAGATCCTAACGAAGAGACATGACTCACTGGCTTCCCTACAAGAGTAAAAATG
AAATTGTAATGCCC
Found at i:11711 original size:215 final size:217
Alignment explanation
Indices: 10194--14170 Score: 3928
Period size: 215 Copynumber: 18.5 Consensus size: 217
10184 AACTCACATC
* * *
10194 AATTGCT-ACAAGGAATGGATCGTCTTTAAATACTTTAAGGAATCGAAGTTATGAAAGAACTCAT
1 AATTGCTCA-AAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCAT
** *
10258 AAAAAGTTTGACTAGTTCGTAACATCATCCAAGAACCAAGAGAGAAACAATTCTCAGGTAAATAA
65 -AAAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
* * *
10323 GTTTTT-ATTCAAAGACCAAAAGTTGTTTAAAAAATGACTACCTATTTAGACCAAATGATGCGAT
129 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * ** *
10387 TTCCCGAGCAAGCAA-TGATCGAAA
194 TTCTCGAGCATGGAATTTTTAG-AA
* *
10411 AATTGCTCAAAGGAATGGATCGTCATTGAATACTTTAAGGAAACGAAGTTATAAAAGAACTCATA
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
* * *
10476 AAAG-TT--C-A-----AAAGTTCGTCCAAGAACC-A-AGAGAAACAAATCTCACG----TAAGT
66 AAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* * * * * *
10526 TTTTAGTTCAAAAACAAAAAAGTTGTTCACAAAATGACAAAACTATTTATACCTAATGATGCGAT
131 TTTTAATTCAAAGAC-CAAAAGTTGTTTACAAAATGAC-AAACTATTTAGACCAAATGATGCGAT
* * * * * * *
10591 CTCTCAAGTATCGAATATTCAAAA
194 TTCTCGAGCATGGAATTTTTAGAA
* * * * * *
10615 AATTGCTCTAAGGAATGAATCATCTTTGAATACTTAAAGGAACCGATGTTATAAAAGAATTCATA
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
* * * * ** *
10680 AAATTTTGACAAGTTTGTAAGTTCATCCAAGAAGCAAGAGAGAATGAATTCTCATGTAAATAAGT
66 AAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* * * *
10745 TTTTAATACAAAGACTAAAAGTTGCTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTT
131 TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
** * *
10810 CTCGAGCATGGAATGATCAAAA
196 CTCGAGCATGGAATTTTTAGAA
* * ** * * *
10832 AATAGCTAAAAGGAATGGATTATCTTTAAATACTTTAAGGAACTGAAGTTATGAAAGAACTCATA
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCAT-
* * * * *
10897 AAAAGTTTGACTAGTTTGTAACTTCGTCCAAAAACCAAGAGAGAAACAATTCTCAGGTAAATAAG
65 AAAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * * * * *
10962 TTTTTTTATTCAGAGACCAAAAGTTGTTTA-AAAGATCACAACCTATTTAGACCAAATTATGTGA
130 -TTTTTAATTCAAAGACCAAAAGTTGTTTACAAA-ATGACAAACTATTTAGACCAAATGATGCGA
* * ** *
11026 TTTCCCGAGCATGAAATGATCAGAA
193 TTTCTCGAGCATGGAATTTTTAGAA
* * * * * * * *
11051 ATTTGGTCAAAGGAATGGATCATCCTTGAATACTTTCAGGAAACAAAGTTATAAAAGAACTCTTA
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
* ** *
11116 AAAGTTTGACAAGTTCAAAAGTTCATCCAAGAACCAAGAGAGAAACAAATCTCACGTAAATAAGT
66 AAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
** * *
11181 TTTTAATT-AAA-AAAAAATTAGTTGTTTACAAAATGACAAACTATTTATACCTAATGATGCGAT
131 TTTTAATTCAAAGACCAAA--AGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * * * *
11244 CTCTTGAGTATGGAATATTTGGAA
194 TTCTCGAGCATGGAATTTTTAGAA
* **
11268 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTAAAGGAAATGAAGTTATAAAAGAACTCATA
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
** ** * *
11333 AAAGTTTGACTAGTTTATAAGTTCATCCAAGAGGCAAGAGAGAATCAATTCTCACGAAAATAAGT
66 AAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* * ** * * *
11398 TTTTAATACAAAGA-AAAAAACTG-TTACAAAATGATAAACTTTTTAGACCAAAAGATGCGATTT
131 TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * * *
11461 CTCGAGCACGAAATGTTCAGTA
196 CTCGAGCATGGAATTTTTAGAA
* * * *
11483 AATTGGC-CGAAGGAATGGATCATC-TTGAATACTCTCAA-GAACCGAAGTTATTAAA-AACTCA
1 AATT-GCTCAAAGGAATGGATCGTCTTTGAATACT-TTAAGGAACCGAAGTTATAAAAGAACTCA
* * * *
11544 TAAAAGTTTGACTGGTTCGTATGTTCATCCAAGAATCAAGAGAGAAACAATTCTCATGTAAATAA
64 TAAAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
* *
11609 GTTTTTAATTCAAACACCAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGAT
129 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* *
11674 TTCCCGAGCATGGAATTTTTTGAA
194 TTCTCGAGCATGGAATTTTTAGAA
* * * * * *
11698 AATTGGTCGAAGGATTGGATCGTC-TTGAATACTTTAAGGAACCAAAGTTGTAAAAG-ACTCGTA
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
* * * * * * * * * **
11761 AATGTTTGACAAGTTCGAAAGTTCGTCCATGAA-CTAGAGAGAAACAATTCTTACATAATTAAAA
66 AAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
**
11825 TTTTAATTCAAAGAGAAAAAGTTGTTTACTAAAA-GACAAACTATTTAGACCAAATGATGCGATT
131 TTTTAATTCAAAGACCAAAAGTTGTTTAC-AAAATGACAAACTATTTAGACCAAATGATGCGATT
*
11889 TCTCGAGCATGGAATGATCTT--AA
195 TCTCGAGCATGGAAT--TTTTAGAA
* * * * * *
11912 AATTGCTAAAAGGAATGGATCTTCTTTAAATACTTTAAGGAACCCAAGTTATGAAAGAACTCATT
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
* * * *
11977 AAAGTTTGACTAGTTCATAACTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAGGTAAATAAGT
66 AAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* * *** * * *
12042 TTTTTATTCAAAGGCCAAAA-TTAACTAAAAAATGACAACCTATTTAGACCAAATGATGCAATTT
131 TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * ** *
12106 CCCGAGCATGCAA-TGATCGAAA
196 CTCGAGCATGGAATTTTTAG-AA
* * * * ** *
12128 AATTGCTCAAAGTAATGGATTGTCCTTGAATACTTTAACGAAATGAAGTTATAAAATAACTCATA
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
* * * * ** * *
12193 AAAGTTTGACAAATTCGAAAGTTCGTCCAAGAAATAAAAGAGAAACAAATCTCACGTAAATAAGT
66 AAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* ** * * * * * * *
12258 TTTTAATTCAAAAATAAAAATGTTGTTTATAAAATGACAAACTGTTTATACCTAAGGATGGGATC
131 TTTTAATTCAAAGACCAAAA-GTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
* *
12323 TCTCGAGTATGGAATATTT-GAAA
195 TCTCGAGCATGGAATTTTTAG-AA
* *
12346 AATTACTCAAAGGAATGGATCGTCTTTGAATACTTAAAGGAACCGAAGTTATAAAAGAACTC--A
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
* * * * *
12409 AAAGTTTGACTAGTTCGTAAGTTCGTCTAAGAAGCAAGAGAGAATCAATTCTCTCGT-AATAAGT
66 AAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* * * * **
12473 TTTTAATACAAAGACAAAAAGTTGTTTACAAAATGACAAACTTTTTAGACCAAATGTTATGATTT
131 TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* *
12538 CTCGAGCATGGAATGTTCAGAA
196 CTCGAGCATGGAATTTTTAGAA
* * * * * *
12560 AATTGGT-AGAAGGAATGGTTCGTC-TTGAATACTCTCAGGAA-AGAAAGTTATGAAAGAACTCA
1 AATTGCTCA-AAGGAATGGATCGTCTTTGAATACTTTAAGGAACCG-AAGTTATAAAAGAACTCA
* * *
12622 TAAAATTTTGACTAGTTCATAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAA
64 TAAAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
* * * ** * *
12687 GTTTTTAATTAAAACACCAAAAGTTGTTTACAAAATGACAAACAATTT-CTCCAAGTGATACGAT
129 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* *
12751 TTC-CAAAGCGTGGAATATTTTTA-AA
194 TTCTC-GAGCATGG-A-ATTTTTAGAA
* * * * ** *
12776 ATTTG-TCGAAA-GAATGGACCATC-TTGAATACTTTAAGTAATTGAAGATATAAAAGAACTCAT
1 AATTGCTC-AAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCAT
* * * ** *
12838 TAATGTTTGACAAGTTCAG-AAGTTTGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAA
65 AAAAGTTTGACTAGTTC-GTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
* * * *
12902 GTTTTTAATTCATAGACCAATAGTTGTTTACAAAATGACAAACAATTT-GACCAAATGATTCGAT
129 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* *
12966 TTCTCGAGCTCAT--AA-TGTTCGAAA
194 TTCTCGAG--CATGGAATTTTTAG-AA
* * * * * * *
12990 AATTGGTCGAAGGGATGGATCGTC-TTGAATACTCTCAGGAACCGAATTTATAAAAGAACTCGTA
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
** * * * *
13054 AGTGTTTGAC-AGGTTTGAAAGTTCAACCAAGAACCAAGAGAGAAACAATTTTCACGTAAATAAG
66 AAAGTTTGACTA-GTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * * * *
13118 TTTTTAATTTTAAA-A--AAAAGTTGTTTACAAAATCAAAAACTATTTAGACCTAATGAAGCGAT
130 TTTTTAA-TTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
**
13180 TTCTCGAGCATGGAAGATTTAGAA
194 TTCTCGAGCATGGAATTTTTAGAA
* * * * * *
13204 AGTTGCTCAAAGGAATGGATCATCTTTGAATACTTAAACGAACCAAAATTATAAAAGAACTCATA
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
* * * *
13269 AAAGTTTGACTAGTTCGTAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCTCATAAATAAGT
66 AAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* * * *
13334 TTTTAATTCATAGAACAATAGTTGTTTACAAAA-GAACAAACAATTT-GACCAAATGATGCGATT
131 TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATG-ACAAACTATTTAGACCAAATGATGCGATT
* *
13397 TCCCGAGCATGGAA-TTTTCGAAA
195 TCTCGAGCATGGAATTTTTAG-AA
* ** * * * * *
13420 AATTGGTTGAAGGAATGGATCATC-TTGAATTCTTTAAGGAATCAAAGTTATAAAAGAACTCATT
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
* * * * *
13484 AAAGTTTGACTAGTTCGAAAATTCGA-CCAAGAACCAAAAGAGAAACAATTCTCTCATAAATAAG
66 AAAGTTTGACTAGTTCGTAAGTTC-ATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * * *
13548 -TTTTAATTCATAGACCAATACTTGTTTACAAAATGACAAACAATTT-GACCAAATGATGCGATT
130 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATT
* *
13611 TTTCGAGCATGGAATTTTTTGAA
195 TCTCGAGCATGGAATTTTTAGAA
* * * *
13634 AATTGGTCAAAGGAATGGATCGTC-CTAAATACTCTCT-A-GAACCGAAGTTATAAAAGAACTCG
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACT-T-TAAGGAACCGAAGTTATAAAAGAACTCA
* * * * *
13696 TAAAAGTTTGACAAGTTTGAAAGTT-AGTCCAAGAACAAAGAGAGAAACAATTCTCACATAAATA
64 TAAAAGTTTGACTAGTTCGTAAGTTCA-TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * *
13760 AGTTTTTAATTCAAAAACAAAAAAGTTGTTTACAAAATGACAAACTATTTAGACCTAATGATGCG
128 AGTTTTTAATTCAAAGAC-CAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
* * * *
13825 ATTTCTCGAGCA-CGAAATATTCGAAA
192 ATTTCTCGAGCATGGAATTTTTAG-AA
13851 AATTGCTCAAAGGAATGGATCGTCTTTGAATA-TTTAGAGGAACCGAAGTTATAAAAGAACTCAT
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTA-AGGAACCGAAGTTATAAAAGAACTCAT
* ** * * * *
13915 AAAAGTTTGATTAGTTTATAAGTTCATCCAAAAACTAAGAGTGAAACAATTCACACGGT-AATAA
65 AAAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCAC-GTAAATAA
* * * * *
13979 ATTTTTAATTCAAAGATCAAAAGTTGTTTACAAAATGACAAACAATTT-CACCAAATGATGCAAT
129 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* *
14043 TTCTCGAGCAT-GAAATGTTATGAA
194 TTCTCGAGCATGGAATTTTTA-GAA
** * * * * *
14067 AATTTATCGAAGGAATGAATCATCTTTGAATAC-TTAATGGAATCGAAGTTATAAAAGAACTAAT
1 AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAA-GGAACCGAAGTTATAAAAGAACTCAT
* *
14131 AAAAGTTTGACTAGTTTGTAAGTTCGTCCAAGAACCAAGA
65 AAAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGA
14171 TCGTATCATT
Statistics
Matches: 3102, Mismatches: 555, Indels: 207
0.80 0.14 0.05
Matches are distributed among these distances:
201 9 0.00
202 8 0.00
203 19 0.01
204 92 0.03
205 18 0.01
206 1 0.00
207 15 0.00
208 1 0.00
212 9 0.00
213 152 0.05
214 457 0.15
215 824 0.27
216 533 0.17
217 483 0.16
218 338 0.11
219 143 0.05
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (217 bp):
AATTGCTCAAAGGAATGGATCGTCTTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
AAAGTTTGACTAGTTCGTAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
CTCGAGCATGGAATTTTTAGAA
Found at i:30188 original size:17 final size:17
Alignment explanation
Indices: 30168--30200 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30158 TTTAAGGACT
30168 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
30185 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
30201 TAAGTGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:30475 original size:50 final size:51
Alignment explanation
Indices: 30402--30549 Score: 137
Period size: 50 Copynumber: 2.9 Consensus size: 51
30392 CATTAACTCT
* * *
30402 CATGATTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAGTAATTTA-
1 CATG-TTAGTTAAATATGCATCATAAATAATGACATGCATTAAGTAATTGAC
** * *
30453 CATGTTAGTTAAATATGCATCATAAATCCT-ATCATGCATTATGTAA-CGAC
1 CATGTTAGTTAAATATGCATCATAAATAATGA-CATGCATTAAGTAATTGAC
* *
30503 CATGTTAGTT-AA-ATGCATCATTAAATCAA-GTCATGCATTTAGTAATT
1 CATGTTAGTTAAATATGCATCA-TAAAT-AATGACATGCATTAAGTAATT
30550 CATTAGTTAA
Statistics
Matches: 78, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
48 8 0.10
49 21 0.27
50 45 0.58
51 4 0.05
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (51 bp):
CATGTTAGTTAAATATGCATCATAAATAATGACATGCATTAAGTAATTGAC
Found at i:39254 original size:18 final size:19
Alignment explanation
Indices: 39231--39267 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39221 ATATTTTTTT
39231 TATTTTT-TATTTTTCTCG
1 TATTTTTCTATTTTTCTCG
*
39249 TATTTTTCTTTTTTTCTCG
1 TATTTTTCTATTTTTCTCG
39268 ACTTTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.08, C:0.14, G:0.05, T:0.73
Consensus pattern (19 bp):
TATTTTTCTATTTTTCTCG
Found at i:41017 original size:46 final size:46
Alignment explanation
Indices: 40946--41046 Score: 175
Period size: 46 Copynumber: 2.2 Consensus size: 46
40936 GACCTCGTTA
* *
40946 TTGGGCGTTGACAAACTTTGTTCCCATCACATTTATAAGCTTGAAT
1 TTGGGCCTTGACAAACTTTGATCCCATCACATTTATAAGCTTGAAT
*
40992 TTGGGCCTTGAGAAACTTTGATCCCATCACATTTATAAGCTTGAAT
1 TTGGGCCTTGACAAACTTTGATCCCATCACATTTATAAGCTTGAAT
41038 TTGGGCCTT
1 TTGGGCCTT
41047 ACGACTCGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (46 bp):
TTGGGCCTTGACAAACTTTGATCCCATCACATTTATAAGCTTGAAT
Found at i:42922 original size:18 final size:19
Alignment explanation
Indices: 42891--42927 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
42881 ATAATTTTTT
*
42891 TATTTTTTTATTTTTCTCG
1 TATTTTTCTATTTTTCTCG
42910 TATTTTTCT-TTTTTCTCG
1 TATTTTTCTATTTTTCTCG
42928 ACTTTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.08, C:0.14, G:0.05, T:0.73
Consensus pattern (19 bp):
TATTTTTCTATTTTTCTCG
Done.