Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012531.1 Corchorus capsularis cultivar CVL-1 contig12552, 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: 57569
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:1883 original size:28 final size:27
Alignment explanation
Indices: 1826--1899 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
1816 TAGCCAAAGA
* * **
1826 TGCCGCAACAACCAAAAATTTCAAAAT
1 TGCCGCAACTACCCAAAATCCCAAAAT
1853 TGCCGCAACTACCCAAAATCCCAAAATT
1 TGCCGCAACTACCCAAAATCCCAAAA-T
* *
1881 TGCCGTAACTAGCCAAAAT
1 TGCCGCAACTACCCAAAAT
1900 TACAAAAACC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.19
Consensus pattern (27 bp):
TGCCGCAACTACCCAAAATCCCAAAAT
Found at i:1905 original size:28 final size:27
Alignment explanation
Indices: 1826--1906 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 27
1816 TAGCCAAAGA
* * *
1826 TGCCGCAACAACCAAAAATTTCAAAAT
1 TGCCGCAACTACCCAAAATTACAAAAT
**
1853 TGCCGCAACTACCCAAAATCCCAAAATT
1 TGCCGCAACTACCCAAAATTACAAAA-T
* *
1881 TGCCGTAACTAGCCAAAATTACAAAA
1 TGCCGCAACTACCCAAAATTACAAAA
1907 ACCCTGTAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 22 0.49
28 23 0.51
ACGTcount: A:0.44, C:0.28, G:0.09, T:0.19
Consensus pattern (27 bp):
TGCCGCAACTACCCAAAATTACAAAAT
Found at i:2000 original size:27 final size:28
Alignment explanation
Indices: 1970--2036 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
1960 TAGCAACCTA
*
1970 AAAATTGCAAAA-TTGCCGCAAGTACCC
1 AAAATTACAAAATTTGCCGCAAGTACCC
* * **
1997 AAAATTCCAAAATTTGCCGCAATTGGCC
1 AAAATTACAAAATTTGCCGCAAGTACCC
2025 AAAATTACAAAA
1 AAAATTACAAAA
2037 ACCGCGTAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 11 0.32
28 23 0.68
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.21
Consensus pattern (28 bp):
AAAATTACAAAATTTGCCGCAAGTACCC
Found at i:2011 original size:130 final size:129
Alignment explanation
Indices: 1787--2073 Score: 407
Period size: 130 Copynumber: 2.2 Consensus size: 129
1777 AACGGTGCAC
* * *
1787 CTAGCCAAAATTGCCACAATTGCCGTAACTAGCCAAAGATGCCGCAACAACCAAAAATTTCAAAA
1 CTAGCCAAAATTGCCACAATTTCCGCAACTAGCCAAAGATGCCGCAACAACCAAAAATTGCAAAA
*
1852 TTGCCGCAACTACCCAAAATCCCAAAATTTGCCGTAACTAGCCAAAATTACAAAAACC-CTGTAA
66 TTGCCGCAACTACCCAAAATCCCAAAATTTGCCGCAACTAGCCAAAATTACAAAAACCGC-GTAA
* * * * *
1916 CTAGCCGAAATTGCCACAATTTCCGCAACTTGCCAAAGATGTCGTAGCAACCTAAAAATTGCAAA
1 CTAGCCAAAATTGCCACAATTTCCGCAACTAGCCAAAGATGCCGCAACAACC-AAAAATTGCAAA
* * * *
1981 ATTGCCGCAAGTACCCAAAATTCCAAAATTTGCCGCAATTGGCCAAAATTACAAAAACCGCGTAA
65 ATTGCCGCAACTACCCAAAATCCCAAAATTTGCCGCAACTAGCCAAAATTACAAAAACCGCGTAA
* *
2046 CTAGCCAAAATTGCAAGAA-TTCCGCAAC
1 CTAGCCAAAATTGCCACAATTTCCGCAAC
2074 AAGACAAAAT
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
129 54 0.39
130 85 0.61
131 1 0.01
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.20
Consensus pattern (129 bp):
CTAGCCAAAATTGCCACAATTTCCGCAACTAGCCAAAGATGCCGCAACAACCAAAAATTGCAAAA
TTGCCGCAACTACCCAAAATCCCAAAATTTGCCGCAACTAGCCAAAATTACAAAAACCGCGTAA
Found at i:7015 original size:667 final size:658
Alignment explanation
Indices: 5727--7272 Score: 1692
Period size: 667 Copynumber: 2.3 Consensus size: 658
5717 GGCTCCCCAC
* * *
5727 AGACTCCTTGAAATATCTTTATTCATCTAATCAAAGCTTAAG-CACATTGGATTTAAGGATTTGT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATC-TAAGCCACATTAGATTTAAGGATTTGT
* * *
5791 TTTTATGTGCATCTGAATCTTGTTTCGATTTAATTATAAATTAATTTAGAAAAATATGAAAAGCG
65 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA-AAATTAATTT-GAAAAATA-GAAAAAC-
* ** * * * ** ** * *
5856 ATATATT-GAAATCGTGAAAAGTTCTCCAAATTTTTTTTACATTAAATTATATATATATTATGAG
126 A-ATATTAGAAA-CGTTAAAAGCCCTTC-AATCTTTTTGATGTCGAATTATATATTTTTTATGAG
** * *
5920 TATTTTAGGAAAAAATGATGAAAAAATCTTTCAGGTCAATTTTTACAAAATTTTAGCCGAAATCG
188 TATTTTACCAAAAAATGA-GGAAATATCTTTC-GGTCAATTTTTACAAAATTTTAGCCGAAATCG
* * ** * *
5985 TGTACTAACCATCACAATTTTCGGCTAAAAATGCATTCTGGGGCCCGACTCAGTTTTGCATGATT
251 TGTACTAACCATAACAATTTTCGGCTAAAAAGGCATTCCAGGGCACGACACAGTTTTGCATGATT
* * *
6050 TTTGGTGCCGAGAGTCCTTAAAATATCTATATTCATATAATCAAAATCTCAGCCACATTGAATTT
316 TTTAGCGCCGAGACTCCTTAAAATATCTATATTCATATAATCAAAATCTCAGCCACATTGAATTT
*** * * *
6115 AGTGATTTGTTTTTATGAGTTTCTGAATCTTGTTTCGATTTAATCATAAAATAATTCATAAAAAT
381 AGTGATTTGTTTTTATGACAATCCGAATCTTGTTTAGATTTAATCATAAAATAATTCAAAAAAAT
* ** ** *
6180 ATGAAAAAAAAATATTAAAAGCGTGAAAAAGGCTTTCAATTTTTTTTTGGTGTTGAATTATATAT
446 ACGAAAAAAAAATATTAAAAGCGTGAAAAAGGCTTTCAA-TTCCTTTTGACGTTGAAATATATAT
* * * *
6245 TTTTTATGAATGTTATCATGAGAAATCAAGGAAAAATCTTTCGAGTCAATTTTTGCAAAAGTTTA
510 ATTTTATGAATATTATCATGAGAAATCAAGGAAAAACCATTCGAGTCAATTTTTGCAAAAGTTTA
* * * *
6310 GCCGAAATCATGTACTAACCATCACGTTTTCTGCTAAAACCGCGTTTCAGAGTCTAG-CTCAGTT
575 GCCGAAATCATGTACTAACCATCACGTTTTCGGCTAAAACCGCGTTCCAG-GGCCAGACTCAGTT
*
6374 TTGCATGATTTTTGGTGTCA
639 TTGCATGATTTTTGGTGCCA
* * *
6394 AGACTTCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACGTTAGATTTAAGGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTAAGCCACATTAGATTTAAGGATTTGTT
* **
6459 TTTACGAGCAACTGAATCTTGTTTAAATTTAATTAGAAATTAATTTGAAAAATAGCAAAAACAAT
66 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTA-AAATTAATTTGAAAAATAG-AAAAACAAT
6524 ATTAGAAACGTTAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTTTATGAGTATTT
129 ATTAGAAACGTTAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATA-TTTTTTATGAGTATTT
* *
6589 TATCCAAAAATTGAGGAAATATCTTTCGGATCAATTTTTGA-AAAATTTTGGCCGAAATCGTGTA
193 TA-CCAAAAAATGAGGAAATATCTTTCGG-TCAATTTTT-ACAAAATTTTAGCCGAAATCGTGTA
* * * * *
6653 CTAACAATATATAACAGTTTTTGGCTAAAAAGGCGTTCCAGGGCGACGACACTA-TTTTGCTTGA
255 CTAAC----CATAACAATTTTCGGCTAAAAAGGCATTCCAGGGC-ACGACAC-AGTTTTGCATGA
* * * * *
6717 -TTTTAGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATC-AAATCTTAGGCACATT-AGA
314 TTTTTAGCGCCGAGACTCCTTAAAATATCTATATTCATATAATCAAAATCTCAGCCACATTGA-A
* * * * *
6779 TTTAAG-GATTTTTTTTTAATGTCAATCCGAATCTTGTTTAGATTTAATTA-AAAATTTATTTAG
378 TTT-AGTGATTTGTTTTT-ATGACAATCCGAATCTTGTTTAGATTTAATCATAAAA--TAATT-C
**
6842 AAAAAAATACG-AAAAACGATATTAAAAGCGT-AAAAA-G-TTCTCCAA-TCCTTTTGACGTTGA
438 AAAAAAATACGAAAAAAAAATATTAAAAGCGTGAAAAAGGCTT-T-CAATTCCTTTTGACGTTGA
* * * *
6902 AATATATATATTTTATGAGTATTTTCACT-AGAAATCGAGGAGAAACCATTCGCA-TCAATTTTT
501 AATATATATATTTTATGAATATTATCA-TGAGAAATCAAGGAAAAACCATTCG-AGTCAATTTTT
* *
6965 GCAAAATTTTAGCCGAAATCATGTACTAACCATCACTGTTTTCGGCTAAAATCGCGTTCCAGGGC
564 GCAAAAGTTTAGCCGAAATCATGTACTAACCATCAC-GTTTTCGGCTAAAACCGCGTTCCAGGGC
* **
7030 CCGACTCAGTTTTGTTTGATTTTTGGTGCCA
628 CAGACTCAGTTTTGCATGATTTTTGGTGCCA
* * * *
7061 AGACTCCTTGAAATATCTATTTTCATCTAACCAAATCTTAGCCACATTAAATTTAA-GATTTTGT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTAAGCCACATTAGATTTAAGGA-TTTGT
7125 TTTTACGAGCATCTGAATCTTGTTTCGA--T--TT--AATTAA----AAAAATAGGAAAAACAAT
65 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAATTAATTTGAAAAATA-GAAAAACAAT
* * *
7180 ATTAGAAGA-ATTAAAAGCCCTTCAATCTTTTTGATGTCGGATTATATACTTTTTATGAGTATTT
129 ATTAGAA-ACGTTAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTTATGAGTATTT
*
7244 TAGCCAAAAAATGAGGAATTATCTTTCGG
193 TA-CCAAAAAATGAGGAAATATCTTTCGG
7273 GTTAGCCAAA
Statistics
Matches: 749, Mismatches: 102, Indels: 68
0.82 0.11 0.07
Matches are distributed among these distances:
655 41 0.05
656 60 0.08
657 2 0.00
660 6 0.01
663 23 0.03
664 79 0.11
665 16 0.02
666 120 0.16
667 257 0.34
668 99 0.13
669 36 0.05
670 10 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (658 bp):
AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTAAGCCACATTAGATTTAAGGATTTGTT
TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAATTAATTTGAAAAATAGAAAAACAATAT
TAGAAACGTTAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTTATGAGTATTTTAC
CAAAAAATGAGGAAATATCTTTCGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACC
ATAACAATTTTCGGCTAAAAAGGCATTCCAGGGCACGACACAGTTTTGCATGATTTTTAGCGCCG
AGACTCCTTAAAATATCTATATTCATATAATCAAAATCTCAGCCACATTGAATTTAGTGATTTGT
TTTTATGACAATCCGAATCTTGTTTAGATTTAATCATAAAATAATTCAAAAAAATACGAAAAAAA
AATATTAAAAGCGTGAAAAAGGCTTTCAATTCCTTTTGACGTTGAAATATATATATTTTATGAAT
ATTATCATGAGAAATCAAGGAAAAACCATTCGAGTCAATTTTTGCAAAAGTTTAGCCGAAATCAT
GTACTAACCATCACGTTTTCGGCTAAAACCGCGTTCCAGGGCCAGACTCAGTTTTGCATGATTTT
TGGTGCCA
Found at i:7098 original size:333 final size:328
Alignment explanation
Indices: 5727--7164 Score: 1330
Period size: 334 Copynumber: 4.3 Consensus size: 328
5717 GGCTCCCCAC
* *
5727 AGACTCCTTGAAATATCT-TTATTCATCTAATCAAAGCTTAAG-CACATTGGATTTAAGGATTTG
1 AGACTCCTTGAAATATCTATT-TTCATCTAATCAAATCTT-AGCCACATTAGATTTAAGGATTTG
* * *
5790 TTTTTATGTGCATCTGAATCTTGTTTCGATTTAATTATAAATTAATTTAGAAAAATATG-AAAAG
64 TTTTTA-ATGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTT-GAAAAATATGAAAAAA
* * * * * * *
5854 CGATATATTGAAATCGTGAAAAGTTCTCCAAATTTTTTTTACATT-AAATTATATATATATTATG
127 C-A-ATATTAAAAGCGTAAAAAGTTCTCC-AATCTTTTTGACGTTGAAA-TATATATATTTTATG
** * * *
5918 AGTATTTTAGGAAAAAAT-GATGAAAAAATCTTTCAGGTCAATTTTTACAAAATTTTAGCCGAAA
188 AGTATTTTAGCTAAAAATCGA-GGAAAAATCTTTC-GATCAATTTTTGCAAAATTTTAGCCGAAA
* * * **
5982 TCGTGTACTAACCATCACAATTTTCGGCTAAAAAT-GCATTCTGGGGCCCGACTCAGTTTTGCAT
251 TCATGTACTAACCATCACAGTTTTCGGCT-AAAATCGCGTTCCAGGGCCCGACTCAGTTTTGCAT
*
6046 GATTTTTGGTGCCG
315 GATTTTTGGTGCCA
* * * * *
6060 AGAGTCCTTAAAATATCTATATTCATATAATCAAAATCTCAGCCACATT-GAATTT-AGTGATTT
1 AGACTCCTTGAAATATCTATTTTCATCTAATC-AAATCTTAGCCACATTAG-ATTTAAG-GATTT
*
6123 GTTTTT-ATG-AGTTTCTGAATCTTGTTTCGATTTAATCATAAAA-TAATTCAT-AAAAATATGA
63 GTTTTTAATGCA---TCTGAATCTTGTTTCGATTTAATTA-AAAATTAATT--TGAAAAATATGA
* * ** * *
6184 AAAAAAAATATTAAAAGCGTGAAAAAGGCTT-T-CAATTTTTTTTTGGTGTTGAATTATATATTT
122 AAAAACAATATTAAAAGCGT-AAAAA-G-TTCTCCAA--TCTTTTTGACGTTGAAATATATATAT
* * * * *
6247 TTTATGA--ATGTTATCATGAGAAATCAAGGAAAAATCTTTCGAGTCAATTTTTGCAAAAGTTTA
182 TTTATGAGTATTTTAGC-T-AAAAATCGAGGAAAAATCTTTCGA-TCAATTTTTGCAAAATTTTA
* * * * * *
6310 GCCGAAATCATGTACTAACCATCAC-GTTTTCTGCTAAAACCGCGTTTCAGAG-TCTAGCTCAGT
244 GCCGAAATCATGTACTAACCATCACAGTTTTCGGCTAAAATCGCGTTCCAGGGCCCGA-CTCAGT
*
6373 TTTGCATGATTTTTGGTGTCA
308 TTTGCATGATTTTTGGTGCCA
* * * *
6394 AGACTTCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACGTTAGATTTAAGGATTTGTT
1 AGACTCCTTGAAATATCTATTTTCATCTAATCAAATCTTAGCCACATTAGATTTAAGGATTTGTT
* ** * *
6459 TTTACGA-GCAACTGAATCTTGTTTAAATTTAATTAGAAATTAATTTGAAAAATA-GCAAAAACA
66 TTTA--ATGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTGAAAAATATGAAAAAACA
* ** * * * * *
6522 ATATTAGAAA-CGTTAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTTTATGAGTA
129 ATATTA-AAAGCGTAAAAAGTTCTCCAATCTTTTTGACGTTGAAATATATA-TATTTTATGAGTA
* * * * * * *
6586 TTTTATCCAAAAATTGAGGAAATATCTTTCGGATCAATTTTTGAAAAATTTTGGCCGAAATCGTG
192 TTTTAGCTAAAAATCGAGGAAAAATCTTTC-GATCAATTTTTGCAAAATTTTAGCCGAAATCATG
* * * ** * * *
6651 TACTAACAATATATAACAGTTTTTGGCTAAAAAGGCGTTCCAGGGCGACGACACTA-TTTTGCTT
256 TACTAAC----CATCACAGTTTTCGGCTAAAATCGCGTTCCAGGGC-CCGACTC-AGTTTTGCAT
* * *
6715 GA-TTTTAGCGCCG
315 GATTTTTGGTGCCA
* *
6728 AGACTCCTTGAAATATCT-TTATTCATCTAATCAAATCTTAGGCACATTAGATTTAAGGATTTTT
1 AGACTCCTTGAAATATCTATT-TTCATCTAATCAAATCTTAGCCACATTAGATTTAAGGATTTGT
* * * *
6792 TTTTAATGTCAATCCGAATCTTGTTTAGATTTAATTAAAAATTTATTTAGAAAAAAAT-ACGAAA
65 TTTTAATG-C-ATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTT-GAAAAATATGA--AAA
* *
6856 AACGATATTAAAAGCGTAAAAAGTTCTCCAATCCTTTTGACGTTGAAATATATATATTTTATGAG
125 AACAATATTAAAAGCGTAAAAAGTTCTCCAATCTTTTTGACGTTGAAATATATATATTTTATGAG
* * * *
6921 TATTTTCA-CTAGAAATCGAGGAGAAACCATTCGCATCAATTTTTGCAAAATTTTAGCCGAAATC
190 TATTTT-AGCTAAAAATCGAGGAAAAATCTTTCG-ATCAATTTTTGCAAAATTTTAGCCGAAATC
* **
6985 ATGTACTAACCATCACTGTTTTCGGCTAAAATCGCGTTCCAGGGCCCGACTCAGTTTTGTTTGAT
253 ATGTACTAACCATCACAGTTTTCGGCTAAAATCGCGTTCCAGGGCCCGACTCAGTTTTGCATGAT
7050 TTTTGGTGCCA
318 TTTTGGTGCCA
* *
7061 AGACTCCTTGAAATATCTATTTTCATCTAACCAAATCTTAGCCACATTAAATTTAA-GATTTTGT
1 AGACTCCTTGAAATATCTATTTTCATCTAATCAAATCTTAGCCACATTAGATTTAAGGA-TTTGT
7125 TTTTACGA-GCATCTGAATCTTGTTTCGATTTAATTAAAAA
65 TTTTA--ATGCATCTGAATCTTGTTTCGATTTAATTAAAAA
7165 AATAGGAAAA
Statistics
Matches: 902, Mismatches: 139, Indels: 129
0.77 0.12 0.11
Matches are distributed among these distances:
328 20 0.02
329 65 0.07
330 9 0.01
331 26 0.03
332 60 0.07
333 214 0.24
334 235 0.26
335 136 0.15
336 19 0.02
337 73 0.08
338 45 0.05
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (328 bp):
AGACTCCTTGAAATATCTATTTTCATCTAATCAAATCTTAGCCACATTAGATTTAAGGATTTGTT
TTTAATGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTTGAAAAATATGAAAAAACAAT
ATTAAAAGCGTAAAAAGTTCTCCAATCTTTTTGACGTTGAAATATATATATTTTATGAGTATTTT
AGCTAAAAATCGAGGAAAAATCTTTCGATCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTA
ACCATCACAGTTTTCGGCTAAAATCGCGTTCCAGGGCCCGACTCAGTTTTGCATGATTTTTGGTG
CCA
Found at i:7281 original size:31 final size:31
Alignment explanation
Indices: 7243--7305 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
7233 TATGAGTATT
7243 TTAGCCAAAAAATGAGGAATTATCTTTCGGG
1 TTAGCCAAAAAATGAGGAATTATCTTTCGGG
*
7274 TTAGCCAAAAACTGAGGAATTATCTTTCGGG
1 TTAGCCAAAAAATGAGGAATTATCTTTCGGG
7305 T
1 T
7306 CAATTTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (31 bp):
TTAGCCAAAAAATGAGGAATTATCTTTCGGG
Found at i:7851 original size:38 final size:40
Alignment explanation
Indices: 7803--7884 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
7793 TTGTTTCGAT
7803 TTAATTAGAAATGAA-TTAAAATTAATT-TCTAGCAATAA
1 TTAATTAGAAATGAATTTAAAATTAATTATCTAGCAATAA
* * *
7841 TTAATTAGAAATTAATTTCAATTTAATTATCTAGCAATAA
1 TTAATTAGAAATGAATTTAAAATTAATTATCTAGCAATAA
7881 TTAA
1 TTAA
7885 AATTAATTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
38 14 0.36
39 10 0.26
40 15 0.38
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (40 bp):
TTAATTAGAAATGAATTTAAAATTAATTATCTAGCAATAA
Found at i:8167 original size:27 final size:27
Alignment explanation
Indices: 8120--8172 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
8110 TAAAAAATAG
*
8120 TAAAATGGTAAAAATAAAATTTTAAAT
1 TAAAATGGTAAAAATAAAATTATAAAT
8147 TAAAATGGTAAAAA-AATAATTATAAA
1 TAAAATGGTAAAAATAA-AATTATAAA
8173 ATATTGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (27 bp):
TAAAATGGTAAAAATAAAATTATAAAT
Found at i:8279 original size:146 final size:150
Alignment explanation
Indices: 7988--8283 Score: 406
Period size: 147 Copynumber: 2.0 Consensus size: 150
7978 CACAATAAGG
*
7988 TTTTAAATTAAAATGGGAAAAATAAAACAATTATAAAAAAATTGAATTTAATTAAATAAAAATAG
1 TTTTAAATTAAAATGGGAAAAATAAAACAATTATAAAAAAATTGAATTTAATTAAATAAAAATAA
** * *
8053 AGTTTTTAGTAGAATAAAAATGTATCTTAAAAAATTTTAATGTATCCAAGTTTTTAATAAAAAAT
66 AGCCTTTAGTAGAATAAAAATGTATCTTAAAAAATTTTAATATATCCAAGTTTTTAATAAAAAAG
8118 AGTAAAATGGTAAAAATAAAA
131 AGTAAAATGGTAAAAA-AAAA
* * * *
8139 TTTTAAATTAAAAT-GG-TAAA-AAAATAATTAT-AAAATATTGAATTTAATTAAATGAAAATAA
1 TTTTAAATTAAAATGGGAAAAATAAAACAATTATAAAAAAATTGAATTTAATTAAATAAAAATAA
* ** * *
8200 AGCCTTTAGTAGAATAAAACTGTA-CATT-AAATTTTTTAATATATCCTAGTTTTTAATGAAAAA
66 AGCCTTTAGTAGAATAAAAATGTATC-TTAAAAAATTTTAATATATCCAAGTTTTTAATAAAAAA
8263 GAGTAAAATGGTAAAAAAAAA
130 GAGTAAAATGGTAAAAAAAAA
8284 GGTAATTATA
Statistics
Matches: 130, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
145 4 0.03
146 47 0.36
147 50 0.38
148 10 0.08
149 3 0.02
150 2 0.02
151 14 0.11
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.34
Consensus pattern (150 bp):
TTTTAAATTAAAATGGGAAAAATAAAACAATTATAAAAAAATTGAATTTAATTAAATAAAAATAA
AGCCTTTAGTAGAATAAAAATGTATCTTAAAAAATTTTAATATATCCAAGTTTTTAATAAAAAAG
AGTAAAATGGTAAAAAAAAA
Found at i:19925 original size:2 final size:2
Alignment explanation
Indices: 19918--19957 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
19908 ATTATACTAC
19918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19958 TAGTAGTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21325 original size:57 final size:61
Alignment explanation
Indices: 21213--21334 Score: 171
Period size: 57 Copynumber: 2.0 Consensus size: 61
21203 CTGTTGGAAG
*
21213 GCCTTTGCCCCATAAATCATCATCCTTAATAATTACCCTTTTCTTCTTCTTTCCTTGATGATT
1 GCCTCTGCCCCATAAA-CATCATCCTTAATAATTACCC-TTTCTTCTTCTTTCCTTGATGATT
* *
21276 GCCTCTGCCCCAT-AA-ATCATCCTTAATAATTACCC-TT-TTCTTCTTTCCTTTATGCTT
1 GCCTCTGCCCCATAAACATCATCCTTAATAATTACCCTTTCTTCTTCTTTCCTTGATGATT
21333 GC
1 GC
21335 TCGGATCTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
57 20 0.36
58 2 0.04
60 20 0.36
62 2 0.04
63 12 0.21
ACGTcount: A:0.20, C:0.30, G:0.07, T:0.43
Consensus pattern (61 bp):
GCCTCTGCCCCATAAACATCATCCTTAATAATTACCCTTTCTTCTTCTTTCCTTGATGATT
Found at i:26998 original size:78 final size:70
Alignment explanation
Indices: 26916--27070 Score: 222
Period size: 70 Copynumber: 2.2 Consensus size: 70
26906 TAATTAAAAT
* * * * ** *
26916 AGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTGTATAAAAATTGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
26981 AGTTG
66 AGTTG
*
26986 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
27051 AGTTG
66 AGTTG
27056 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
27071 ACCTAAACAA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
70 74 0.97
71 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.37
Consensus pattern (70 bp):
AGTAAAATAGTAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTG
Found at i:30921 original size:43 final size:43
Alignment explanation
Indices: 30872--30959 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
30862 GATGATTGCC
30872 CAAATCTTGGTTAATTTTCGACATACAAAAAATCAAATCGAAG
1 CAAATCTTGGTTAATTTTCGACATACAAAAAATCAAATCGAAG
30915 CAAATCTTGGTTAATTTTCGACATACAAAAAATCAAATCGAAG
1 CAAATCTTGGTTAATTTTCGACATACAAAAAATCAAATCGAAG
30958 CA
1 CA
30960 GTAAGGGTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.27
Consensus pattern (43 bp):
CAAATCTTGGTTAATTTTCGACATACAAAAAATCAAATCGAAG
Found at i:31264 original size:19 final size:20
Alignment explanation
Indices: 31219--31276 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
31209 GCTACTCTAA
31219 TAATCTCATATGTACAGTACC
1 TAATCTCATATGTACAGTA-C
* *
31240 TAATCTAATATGTACAGT-G
1 TAATCTCATATGTACAGTAC
*
31259 TAATCTCATCTGTACAGT
1 TAATCTCATATGTACAGT
31277 TGCTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TAATCTCATATGTACAGTAC
Found at i:36904 original size:21 final size:20
Alignment explanation
Indices: 36866--36904 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
36856 TGTAATTAAT
*
36866 TAATTCATGAACCCAATAAC
1 TAATTCATGAACCAAATAAC
*
36886 TAATTCATTGAACTAAATA
1 TAATTCA-TGAACCAAATA
36905 TTTGTTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (20 bp):
TAATTCATGAACCAAATAAC
Found at i:38458 original size:2 final size:2
Alignment explanation
Indices: 38451--38478 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38441 TTTCCATCAA
38451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38479 CTTTATACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41996 original size:465 final size:460
Alignment explanation
Indices: 41123--42386 Score: 1843
Period size: 465 Copynumber: 2.7 Consensus size: 460
41113 TAAAAACGAG
* * * * ** * *
41123 AGCTTCATCATTCTCTACAAAACGAGAATGCGAGGGATGAGAGAATTTAGAAGCAGACCCTTTAG
1 AGCTTCATCCTTCTCTATAAAACGAGAATGAGAGGGATGAAAGGGTTCAGAAGTAGACCCTTTAG
* * * * *
41188 GAGTTTCAAACTCATACTTTATCTCTTCATTCAAAAGAGAGCTCAAGAACTCAACCGCTTGGAGA
66 GACTTTCAAACT-A-ACTTTATCTCTTCATTAAAAAGAGAGCTCAAGAACTCAATCTCTTGGAAA
* * * ***
41253 GAAACAAGCTCTTGATCTCCTTCTTTTATAACACCTATTGTAAGGTCAAGAAGGGTTGCCATGTG
129 GAAACAAGCTCTTGATCTCCTTTTTTTATAGCAGCTATTGTAAGGTCAAGAATAATTGCCATGTG
* *
41318 AGGCTCAAGCACATCATAGTTTGTTGATTGATGTTATCGCAATAAGACCCTTAAAGGCAGTTTCC
194 AGGCTCAAGCACATCATAG--T-TTG-TCGATGTTATCACAATAAGACCCTTAAAGGCAGTTTCC
* * *
41383 CTGATTTTTCACATCTCTGGAGGTCGTTGTATCATATACAACCTTAATGAGGTCTTGCATCTCAA
255 CTTATTTTTCACATCTTTGGAGGTCGTTGTATCATATACAACCTTAATGAGGTCCTGCATCTCAA
* * *
41448 GGTTAAAGTTCGTCAGAGCTTTATAAAAAGCCCTAGTTGCTGCAAGTGAAATTTCCTGATTGTAT
320 GGTTAAAGTTCGTCAGAGCTTCATAAAAAGCCCTAGTTGCTGCAAGTGAAATTTCCCGACTGTAT
*
41513 TCACCGTTCATCTTATCAACAAGATAAAAAAGAATATCATTGATTCATCCTTCATAAACCTGGTC
385 TCACCGTTCATCTTATCAACAAGATAAAAAA-AATAGCATTGATTCATCCTTCATAAACCTGGTC
41578 AGACATCTCCTC
449 AGACATCTCCTC
*
41590 AGCTTCATCCTTCTCTATAAAATGAGAATGAGAGGGATGAAAGGGTTCAGAAGTAGACCCTTTAG
1 AGCTTCATCCTTCTCTATAAAACGAGAATGAGAGGGATGAAAGGGTTCAGAAGTAGACCCTTTAG
*
41655 GACTTTCAAACTAAGACTTTATCTCTTCATTAAAAAGAGAGCTCAAGAACTCAATCTTTTGGAAA
66 GACTTTCAAACT-A-ACTTTATCTCTTCATTAAAAAGAGAGCTCAAGAACTCAATCTCTTGGAAA
* *
41720 GAAAAAAGCTCTTGATCTCCTTTTTTTTTATAGCAGCTATTGTAAGGTCAAGAATAATTGTCATG
129 GAAACAAGCTCTTGATCTCC--TTTTTTTATAGCAGCTATTGTAAGGTCAAGAATAATTGCCATG
* * *
41785 TGAGGCTCAAGCACATCATAGTTTGTCGATGTTATCACAATAAAACCCTCAAAGGTAGTTTCCCT
192 TGAGGCTCAAGCACATCATAGTTTGTCGATGTTATCACAATAAGACCCTTAAAGGCAGTTTCCCT
*
41850 TATTTTTCACATCTTTGGAGGTTGTTGTATCATATACAACCTTAATGAGGTCCTGCATCTCAAGG
257 TATTTTTCACATCTTTGGAGGTCGTTGTATCATATACAACCTTAATGAGGTCCTGCATCTCAAGG
*
41915 TTAAAGTTCGTCAGATCTTCATAAAAAGCCCTAGTTGCTGCAAGTGAAATTTCCCGACTGTATTC
322 TTAAAGTTCGTCAGAGCTTCATAAAAAGCCCTAGTTGCTGCAAGTGAAATTTCCCGACTGTATTC
* * * *
41980 ACCGTTCATCTTATCAATAAGATAAAAGAAATAGCATTGATTCGTCCTTCATGAACCTGGTCAGA
387 ACCGTTCATCTTATCAACAAGATAAAAAAAATAGCATTGATTCATCCTTCATAAACCTGGTCAGA
*
42045 TATCTCCTC
452 CATCTCCTC
* ** * ** * * * *
42054 GGGATGAAGCTGCTCTATAAAACAAGAATGAGATGGATGAAAAGGTTCAGAAGTAGACCCTTTAG
1 AGCTTCATCCTTCTCTATAAAACGAGAATGAGAGGGATGAAAGGGTTCAGAAGTAGACCCTTTAG
* * *
42119 GACTTTCAAACT--C-ATA-CTTTTCATTAAAAAGAGAGCTCAAGTACTCAATCTCTTGGAAAGA
66 GACTTTCAAACTAACTTTATCTCTTCATTAAAAAGAGAGCTCAAGAACTCAATCTCTTGGAAAGA
* *
42180 AACAAGCTCTTGATCTCCTTTTTTTATAGCAGCTATTGTAAGGTCAATAATTATTGCCATGTGAG
131 AACAAGCTCTTGATCTCCTTTTTTTATAGCAGCTATTGTAAGGTCAAGAATAATTGCCATGTGAG
* ** * *
42245 GCTTAAGCACATCATAGTTTACCGATGCTATCACAATAAGACCCTTAAAAGCAGTTTCCCTTATT
196 GCTCAAGCACATCATAGTTTGTCGATGTTATCACAATAAGACCCTTAAAGGCAGTTTCCCTTATT
42310 TTTCACATCTTTGGAGGTCGTTGTATCATATACAACCTTAATGAGGTCCTGCATCTCAAGGTTAA
261 TTTCACATCTTTGGAGGTCGTTGTATCATATACAACCTTAATGAGGTCCTGCATCTCAAGGTTAA
42375 AGTTCGTCAGAG
326 AGTTCGTCAGAG
42387 TAAATCTAAA
Statistics
Matches: 722, Mismatches: 73, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
456 176 0.24
458 59 0.08
459 2 0.00
460 1 0.00
464 107 0.15
465 184 0.25
466 3 0.00
467 133 0.18
469 57 0.08
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (460 bp):
AGCTTCATCCTTCTCTATAAAACGAGAATGAGAGGGATGAAAGGGTTCAGAAGTAGACCCTTTAG
GACTTTCAAACTAACTTTATCTCTTCATTAAAAAGAGAGCTCAAGAACTCAATCTCTTGGAAAGA
AACAAGCTCTTGATCTCCTTTTTTTATAGCAGCTATTGTAAGGTCAAGAATAATTGCCATGTGAG
GCTCAAGCACATCATAGTTTGTCGATGTTATCACAATAAGACCCTTAAAGGCAGTTTCCCTTATT
TTTCACATCTTTGGAGGTCGTTGTATCATATACAACCTTAATGAGGTCCTGCATCTCAAGGTTAA
AGTTCGTCAGAGCTTCATAAAAAGCCCTAGTTGCTGCAAGTGAAATTTCCCGACTGTATTCACCG
TTCATCTTATCAACAAGATAAAAAAAATAGCATTGATTCATCCTTCATAAACCTGGTCAGACATC
TCCTC
Found at i:43335 original size:21 final size:22
Alignment explanation
Indices: 43309--43353 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
43299 TTTATCTGAA
43309 TTGCTAAAT-ACCGTCCC-CTTT
1 TTGCT-AATCACCGTCCCACTTT
*
43330 TTGCTATTCACCGTCCCACTTT
1 TTGCTAATCACCGTCCCACTTT
43352 TT
1 TT
43354 AGATAGCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 13 0.62
22 6 0.29
ACGTcount: A:0.16, C:0.33, G:0.09, T:0.42
Consensus pattern (22 bp):
TTGCTAATCACCGTCCCACTTT
Found at i:44452 original size:39 final size:39
Alignment explanation
Indices: 44409--44506 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 39
44399 TTGATGGGTG
* *
44409 AGTCTACCAACGGGGCAGTTGCGCTGATTTTGGT-GGATA
1 AGTCTACCAACGGGACAGTTCCGCTGATTTTGGTAGG-TA
** * *
44448 AGTCTACCAACAAGACAGCTCCGCTGATTTTGGTAGGTG
1 AGTCTACCAACGGGACAGTTCCGCTGATTTTGGTAGGTA
*
44487 AGTCTACCAATGGGACAGTT
1 AGTCTACCAACGGGACAGTT
44507 ACGTACGCAA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 46 0.96
40 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (39 bp):
AGTCTACCAACGGGACAGTTCCGCTGATTTTGGTAGGTA
Found at i:56742 original size:22 final size:23
Alignment explanation
Indices: 56717--56763 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
56707 CATTTTTACG
56717 TTAAT-TGACATCTTCACGTAAA
1 TTAATCTGACATCTTCACGTAAA
*
56739 TTAATCTGACATCTTCACGTTAA
1 TTAATCTGACATCTTCACGTAAA
56762 TT
1 TT
56764 GGTATATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (23 bp):
TTAATCTGACATCTTCACGTAAA
Done.