Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015138.1 Corchorus capsularis cultivar CVL-1 contig15159, 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: 97596
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:4586 original size:24 final size:23
Alignment explanation
Indices: 4464--4617 Score: 99
Period size: 22 Copynumber: 6.9 Consensus size: 23
4454 GTCTCTATGT
* *
4464 GGTTATCAAAATTTCATAAGAT-
1 GGTTATTAAAATTTCATAGGATA
* *
4486 GGTTATTATAATTCCATGAGG--A
1 GGTTATTAAAATTTCAT-AGGATA
* *
4508 GGTTATCAAAATTCCATAGTG-T-
1 GGTTATTAAAATTTCATAG-GATA
**
4530 GGTTACCAAAATTTCATAGTG-TA
1 GGTTATTAAAATTTCATAG-GATA
**
4553 -GTTACCAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGGAT-A
* *
4576 GGTTATTAAAATTTCTTA-GATT
1 GGTTATTAAAATTTCATAGGATA
*
4598 GGTTATTGAAATTTCATAGG
1 GGTTATTAAAATTTCATAGG
4618 GTGGTTAATT
Statistics
Matches: 109, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
21 3 0.03
22 85 0.78
23 7 0.06
24 14 0.13
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (23 bp):
GGTTATTAAAATTTCATAGGATA
Found at i:4770 original size:22 final size:22
Alignment explanation
Indices: 4744--4798 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4734 CTTCATCGAG
*
4744 AGGTTATAAAAATTTGATAGTG-
1 AGGTTATAAAAATTTCATA-TGA
* *
4766 TGGTTATCAAAATTTCATATGA
1 AGGTTATAAAAATTTCATATGA
4788 AGGTTATAAAA
1 AGGTTATAAAA
4799 GTCTCAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (22 bp):
AGGTTATAAAAATTTCATATGA
Found at i:4893 original size:25 final size:21
Alignment explanation
Indices: 4857--4917 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 21
4847 CTCATAGAGT
*
4857 GATTATCGAAATTTCATAAAGATA
1 GATTATCAAAATTT-AT-AAGA-A
*
4881 GGATTATCAAAATTTATATGAA
1 -GATTATCAAAATTTATAAGAA
4903 GATTATCAAAATTTA
1 GATTATCAAAATTTA
4918 GACACCACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.44
22 1 0.03
23 3 0.09
24 2 0.06
25 13 0.38
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (21 bp):
GATTATCAAAATTTATAAGAA
Found at i:5082 original size:28 final size:29
Alignment explanation
Indices: 5036--5091 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
5026 GACATTGCTC
*
5036 ACCAAGTAGAGATCAATGGTCACAAATTA
1 ACCAAGTAGAAATCAATGGTCACAAATTA
5065 ACCAAGTA-AAATCAATGGTCACAAATT
1 ACCAAGTAGAAATCAATGGTCACAAATT
5092 GATAATTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (29 bp):
ACCAAGTAGAAATCAATGGTCACAAATTA
Found at i:6944 original size:43 final size:43
Alignment explanation
Indices: 6883--6968 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
6873 CCTATTTTTT
6883 CCGAATTAATTTCTAATTGAATTGAAACATGATTTATATGCTC
1 CCGAATTAATTTCTAATTGAATTGAAACATGATTTATATGCTC
6926 CCGAATTAATTTCTAATTGAATTGAAACATGATTTATATGCTC
1 CCGAATTAATTTCTAATTGAATTGAAACATGATTTATATGCTC
6969 GTAAAAGCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (43 bp):
CCGAATTAATTTCTAATTGAATTGAAACATGATTTATATGCTC
Found at i:8440 original size:12 final size:13
Alignment explanation
Indices: 8416--8444 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
8406 TTGACAAACC
8416 TATAGACCTATAG
1 TATAGACCTATAG
8429 TATAGA-CTATAG
1 TATAGACCTATAG
8441 TATA
1 TATA
8445 TTTGAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (13 bp):
TATAGACCTATAG
Found at i:15271 original size:31 final size:31
Alignment explanation
Indices: 15236--15320 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
15226 TTAAGTCTCA
*
15236 AACGTTGCAAAATCGGCTCAAATTAGTCCAT
1 AACGTTGCAAAATCGGCTCAAATTAGTCCAC
* ** *
15267 AACGTTACAAAAGAGGCTCATATTAGTCCAC
1 AACGTTGCAAAATCGGCTCAAATTAGTCCAC
** * *
15298 AATATAGCAAAATCGGTTCAAAT
1 AACGTTGCAAAATCGGCTCAAAT
15321 AAGTTTTTAA
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (31 bp):
AACGTTGCAAAATCGGCTCAAATTAGTCCAC
Found at i:16584 original size:21 final size:21
Alignment explanation
Indices: 16555--16602 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
16545 CCATCCTTCC
16555 AAATAATCAAATACAAATTAT
1 AAATAATCAAATACAAATTAT
*
16576 AAATGATCAAATACAAATTAT
1 AAATAATCAAATACAAATTAT
16597 -AATAAT
1 AAATAAT
16603 GCTAGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (21 bp):
AAATAATCAAATACAAATTAT
Found at i:16737 original size:65 final size:65
Alignment explanation
Indices: 16633--16763 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
16623 TAATATCCAA
*
16633 TCATCATCTTCACTTTTCTAGTCTCACTGCAAGGCTTTCTCCGAAATGCCAGGGACAATCCTTGT
1 TCATCATCTTCACTTTTCTAGTCTCACTGCAAGGCTTTCTCCGAAATACCAGGGACAATCCTTGT
*
16698 TCATCATCTTCACTTTTCTAGTCTCATTGCAAGGCTTTCTCCGAAATACCAGGGACAATCCTTGT
1 TCATCATCTTCACTTTTCTAGTCTCACTGCAAGGCTTTCTCCGAAATACCAGGGACAATCCTTGT
16763 T
1 T
16764 TCATGTACCA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (65 bp):
TCATCATCTTCACTTTTCTAGTCTCACTGCAAGGCTTTCTCCGAAATACCAGGGACAATCCTTGT
Found at i:19635 original size:337 final size:332
Alignment explanation
Indices: 18899--21158 Score: 1790
Period size: 337 Copynumber: 6.9 Consensus size: 332
18889 GTTAGTCTCA
* * * * * * **
18899 GTTTTGCATAATTTTTCGCACCAAGACTCATTGAAATATCTATATTCATATAACGAAATCTCATA
1 GTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATTCATCTAACCAAATCTCACC
*** *
18964 CACATAT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCCGGTTTCGATTTAATAAGAAATT
66 CACAT-TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATATTTCGATTTAATTAGAAATT
** * * * * * *
19028 AATT--------T-GGAAAAAAAATATTTGAAGTGTGAGAAGTGC-TTCAA-ACTTTTTGTCGTT
130 AATTCAGAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAG-CCTTTCAATA-TTTTTGGCATT
* * * ** * * * *
19082 GAGTTATATATTTTTTGTGAGTATTGTGACCAAAAATTGGGGAGAAATT-TTTTGGATCAAAATT
193 GAATTATATATATTTTATGAGTATCATGGCCAAAAATTGAGGA-AAATTCTTTCGGGT--AAATT
* * * *
19146 TTT--AAAATTTTAGCCGAACTCGTG--T----ATCACGGTTTTTTACTATAAACGCGTTCCAGG
255 TTTGCAAAATTTTAGCTGAAATCGTGTATAACCATCACGGTTTTTTGCTAAAAACGCGTTCC-GG
* *
19203 AG-C-C-CAACTCT
319 GGCCTCTCGACTCT
* * *
19214 GTTTTACATGATTTTTGACACCAAGTCTCATTGAAATATCTATATTCATCTAACCAAATCTCACC
1 GTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATTCATCTAACCAAATCTCACC
* * * * *
19279 CACAATAGATTTAAGGATTTGCTTTTACGAGCGTTTGAATCATATTTCGATTTAATTAGAAATTA
66 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATATTTCGATTTAATTAGAAATTA
* * *
19344 ATTTAGAAAAATAGGAAAAACAATATTAGAAG-GATGAAAAACCTTTCAATATTTTTGGCATTGA
131 ATTCAGAAAAATAGGAAAAACGATATTAGAAGCG-TGAAAAGCCTTTCAATATTTTTGGCATTGA
* *
19408 ATTATATATATTTTATAAGTATCATGGCCAAAAATTGAGGAAATTTCTTTCGGGTAAATTTTTGC
195 ATTATATATATTTTATGAGTATCATGGCCAAAAATTGAGGAAAATTCTTTCGGGTAAATTTTTGC
*
19473 AAAGTTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGTCC
260 AAAATTTTAGCTGAAATCGTGTA-TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGG--C
19538 CGTCTCAGACTCT
322 C-TCTC-GACTCT
* * ** *
19551 CTTTTGCATGATTTTTGACGCCAAGTCTCATTGAAATATCTATATTCATCTAATGAAATCTCAGC
1 GTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATTCATCTAACCAAATCTCACC
* * * *
19616 CATATTGAATTTAAGGATTTGTTTTTACGAGTATCCT-AATC-TAGTTTTGATTTAATTAGAAAT
66 CACATTGGATTTAAGGATTTGTTTTTACGAGCAT-CTGAATCATA-TTTCGATTTAATTAGAAAT
* * * **
19679 TAATTCAGAAAAAAATAGGAAAAACGATCTTAGAAGCGTGAGAAGCCCTTCAA-ACTTTTTGGTG
129 TAATTCAG--AAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTCAATA-TTTTTGGCA
* * * * * **
19743 TTGAGTTATATATTTTTTATGAGTATTATGGCCAAAAATTGGGGAGAAATT-TTTCTAGCCAAAT
191 TTGAATTATATATATTTTATGAGTATCATGGCCAAAAATTGAGGA-AAATTCTTTC-GGGTAAAT
* ** * * * * * *
19807 TTTTGCAAAATTTTATCCAAAATC----AT----GT-ACGGTTTTAAT--TATAAATGCATTTCG
254 TTTTGCAAAATTTTAGCTGAAATCGTGTATAACCATCACGGTTTT-TTGCTAAAAACGCGTTCCG
19861 GGGCC-C-CGACTCT
318 GGGCCTCTCGACTCT
* * ** * *
19874 GTTTTACATGATTTTTTGGCGTCATTTCTCATTGAAATAT-TCATATTCAACTAAGCAAATCTCA
1 GTTTTGCATGA-TTTTTGGCGCCAAGTCTCATTGAAATATCT-ATATTCATCTAACCAAATCTCA
*
19938 CCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCGTATTTCGATTTAATTAGAAAT
64 CCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATATTTCGATTTAATTAGAAAT
* * **
20003 TAATTCAGAAAAATAGGAAAAACAATATTAGAAGCGTGAAAA-CCTTTCAATCTTTTTGGTGTTG
129 TAATTCAGAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTCAATATTTTTGGCATTG
* * * * *
20067 AATTATATAT-TTTT-T-A-TATCGTGGCTAAAAATTGAGGAAAATCCTTTTGGGTCAATTTTTG
194 AATTATATATATTTTATGAGTATCATGGCCAAAAATTGAGGAAAATTCTTTCGGGTAAATTTTTG
* * ** * *
20128 CATAATTTTA-TTAGAAATCGTGTACTAACCATCAC-G------G-TAAAAATACGTACCGGGGG
259 CAAAATTTTAGCT-GAAATCGTGTA-TAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGC
20184 C-C-C-A-TC-
322 CTCTCGACTCT
* * * **
20190 ---TT--A--ATTTTTGGCACCAAGACTCATTGAAATATCTATATTCATCTAACAAAATCTCATA
1 GTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATTCATCTAACCAAATCTCACC
* *** *
20248 GACATAT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCCGGTTTCGATTTAATAAGAAATT
66 CACAT-TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATATTTCGATTTAATTAGAAATT
* * * * ** * *
20312 AATTTTGGAAAAAAAAAATGGAAAAACGATATTTGAATTGTGAGAAGTCC-TTCAAACTTTTTTT
130 AA--TT--CAGAAAAATA-GGAAAAACGATATTAGAAGCGTGAAAAG-CCTTTC-AA-TATTTTT
* * ** * * **
20376 TGCA-TAAAGTTATATATATTTTATGATGTATTGTGTGCCAAAAATTGGGGAAAATTGTTTTTGG
187 GGCATTGAA-TTATATATATTTTATGA-GTATCATG-GCCAAAAATTGAGGAAAATTCTTTCGGG
* * * *
20440 TCAATTTTTGCAAAATCTTAGCCGAAATCGTG--T-ACCATCACAGTTTTTTGACTAAAAACGCG
249 TAAATTTTTGCAAAATTTTAGCTGAAATCGTGTATAACCATCACGGTTTTTTG-CTAAAAACGCG
* * *
20502 TTCTGGAGCCT-TAG-CTCT
313 TTCCGGGGCCTCTCGACTCT
* * * * *
20520 GTTTTGCATTATTTTTGGTGCCAAGTCTCATTGAAATATCTATATCCGTCTAACCAAATCTTACC
1 GTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATTCATCTAACCAAATCTCACC
* ** * * *
20585 CATATTGGATTTAATTATTTATTTTTACGAGCATCTGAATCATGTTTCAATTTAATTAGAAATTA
66 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATATTTCGATTTAATTAGAAATTA
* * * * *
20650 ATTCGGAAAAAAGAGGAAAACCGATATTAGAAGCGTGAATAGCGTTTCAATATTTTTGTG--TTG
131 ATTCAG-AAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTCAATATTTTTG-GCATTG
* * * * *
20713 AATTATAT-TTTTTTATGAGCATCATGGCCAAAAATTGAGGAAAATTTTTTCGGGTCAGTTTTTG
194 AATTATATATATTTTATGAGTATCATGGCCAAAAATTGAGGAAAATTCTTTCGGGTAAATTTTTG
* * ** * * * * *
20777 CAAAAGTGTAG-TCGAAATCAAGTAATAACCATCACAGTTTTTGGCTAAAAAAGCGTGCCGGAGC
259 CAAAATTTTAGCT-GAAATCGTGT-ATAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGC
* **
20841 ATCT--ACTAA
322 CTCTCGACTCT
* ** * * *
20850 GGTTTGCATGATTTTTGGCGCCAAGAGTCATTGAATTATCTATATCCATCTAATCAAATCTCACC
1 GTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATTCATCTAACCAAATCTCACC
*
20915 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTA
66 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATATTTCGATTTAATTAGAAATTA
* * * * *
20980 ATTCGGAAAAATAGGAAAACCGATATTAGAAGAGTGAAAAGCTTTTCAATCTTTTTGGCATTGAT
131 ATTCAGAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTCAATATTTTTGGCATTG--
* * * *
21045 TTATATATATATATATATATTTATGAGTATCATTGCAAAAAATTTAGGAAAATGCTTTCGGGTAA
194 ----A-AT-TATATATAT-TTTATGAGTATCATGGCCAAAAATTGAGGAAAATTCTTTCGGGTAA
* *
21110 ACTTTTGCAAAATTTTAGAC-GAAATCGTGTGTTAACCATCACGGTTTTT
252 ATTTTTGCAAAATTTTAG-CTGAAATCGTGT-ATAACCATCACGGTTTTT
21159 GGCAACAAAG
Statistics
Matches: 1562, Mismatches: 260, Indels: 221
0.76 0.13 0.11
Matches are distributed among these distances:
308 101 0.06
309 3 0.00
310 2 0.00
311 1 0.00
312 7 0.00
313 24 0.02
314 4 0.00
315 121 0.08
316 42 0.03
317 27 0.02
318 11 0.01
319 20 0.01
320 5 0.00
321 35 0.02
322 89 0.06
323 25 0.02
324 201 0.13
325 7 0.00
326 2 0.00
327 65 0.04
328 6 0.00
329 71 0.05
330 163 0.10
331 55 0.04
332 4 0.00
333 28 0.02
334 6 0.00
335 5 0.00
336 6 0.00
337 223 0.14
338 7 0.00
339 89 0.06
340 107 0.07
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (332 bp):
GTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATTCATCTAACCAAATCTCACC
CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATATTTCGATTTAATTAGAAATTA
ATTCAGAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTCAATATTTTTGGCATTGAA
TTATATATATTTTATGAGTATCATGGCCAAAAATTGAGGAAAATTCTTTCGGGTAAATTTTTGCA
AAATTTTAGCTGAAATCGTGTATAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGGGCCTCT
CGACTCT
Found at i:22299 original size:29 final size:29
Alignment explanation
Indices: 22260--22315 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
22250 AAATATTTTA
22260 TTTTTACCATTTAAATATTTTAATTAATT
1 TTTTTACCATTTAAATATTTTAATTAATT
* *
22289 TTTTTACCATTTTACTATTTTAATTAA
1 TTTTTACCATTTAAATATTTTAATTAA
22316 AAGACTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTTACCATTTAAATATTTTAATTAATT
Found at i:23518 original size:84 final size:84
Alignment explanation
Indices: 23414--23587 Score: 248
Period size: 84 Copynumber: 2.1 Consensus size: 84
23404 TCTATTTTTA
23414 TTTT-ATTAAATCTAATTCTTTATAACTATTTTATTTTTAACA-TTTTACTATTTTAATTAAAAA
1 TTTTAATTAAATCTAATTCTTTATAACTATTTTATTTTTAACATTTTTACTATTTTAATT--AAA
23477 AAACTTAG-ATATATTAGAAT
64 AAACTTAGAATATATTAGAAT
* * *
23497 TTTTAATTAAATC-AATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTACAT
1 TTTTAATTAAATCTAAT-TCTTTATAACTATTTTATTTTTAACATTTTTACTATTTTAATTAAAA
*
23561 AACTTAGATATATATTATAAT
65 AACTTAGA-ATATATTAGAAT
23582 TTTTAA
1 TTTTAA
23588 AATATATTTC
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
83 16 0.20
84 33 0.40
85 33 0.40
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (84 bp):
TTTTAATTAAATCTAATTCTTTATAACTATTTTATTTTTAACATTTTTACTATTTTAATTAAAAA
ACTTAGAATATATTAGAAT
Found at i:26893 original size:31 final size:31
Alignment explanation
Indices: 26858--26923 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
26848 AACTTTATGT
* *
26858 TTTCCAATTGTACCCTTATTTT-TAAAATATA
1 TTTCCAATTGTACCCTT-TTTTAAAAAACATA
26889 TTTCCAATTGTACCCTTTTTTAAAAAACATA
1 TTTCCAATTGTACCCTTTTTTAAAAAACATA
26920 TTTC
1 TTTC
26924 TAAATTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTTTAAAAAACATA
Found at i:27152 original size:19 final size:20
Alignment explanation
Indices: 27125--27162 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
27115 AACTATTAGT
27125 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
27145 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
27163 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:27355 original size:22 final size:22
Alignment explanation
Indices: 27323--27466 Score: 123
Period size: 22 Copynumber: 6.5 Consensus size: 22
27313 TTCTTGTCCC
27323 TAGG-TGGTTATCAAAATTTCA
1 TAGGATGGTTATCAAAATTTCA
* * *
27344 TAAGATGGTTATTATAATTTCA
1 TAGGATGGTTATCAAAATTTCA
*
27366 TGAGGA-GGTTATCAAAATTCCA
1 T-AGGATGGTTATCAAAATTTCA
*
27388 TAGTG-TGGTTACCAAAATTTCA
1 TAG-GATGGTTATCAAAATTTCA
* * *
27410 TAGGATCAAGTTATTAAAATTTCT
1 TAGGAT--GGTTATCAAAATTTCA
* **
27434 TAGGTTGGTTATTGAAATTTCA
1 TAGGATGGTTATCAAAATTTCA
*
27456 TAGGGTGGTTA
1 TAGGATGGTTA
27467 ATTTTCACAA
Statistics
Matches: 98, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
21 6 0.06
22 72 0.73
23 3 0.03
24 17 0.17
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (22 bp):
TAGGATGGTTATCAAAATTTCA
Found at i:27445 original size:68 final size:66
Alignment explanation
Indices: 27325--27466 Score: 160
Period size: 68 Copynumber: 2.1 Consensus size: 66
27315 CTTGTCCCTA
* * *
27325 GGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCATA
1 GGTGGTTACCAAAATTTCATAAGATAGTTATTAAAATTTCATGAGGAGGTTATCAAAATTCCATA
27390 G
66 G
* * * * ** *
27391 TGTGGTTACCAAAATTTCATAGGATCAAGTTATTAAAATTTC-TTAGGTTGGTTATTGAAATTTC
1 GGTGGTTACCAAAATTTCATAAGAT--AGTTATTAAAATTTCATGAGG-AGGTTATCAAAATTCC
27455 ATAG
63 ATAG
27459 GGTGGTTA
1 GGTGGTTA
27467 ATTTTCACAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
66 22 0.35
67 4 0.06
68 36 0.58
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (66 bp):
GGTGGTTACCAAAATTTCATAAGATAGTTATTAAAATTTCATGAGGAGGTTATCAAAATTCCATA
G
Found at i:27624 original size:44 final size:44
Alignment explanation
Indices: 27328--28340 Score: 219
Period size: 44 Copynumber: 23.3 Consensus size: 44
27318 GTCCCTAGGT
* * *
27328 GGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCAT-GAGGA
1 GGTTATCAAAATTTCAT-AGCGTGGTTATCAAAATTTCATAG-GGA
* * * *
27372 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGG--GA
* * * ** *
27418 AGTTATTAAAATTTCTTAG-GTTGGTTATTGAAATTTCATAGGGT
1 GGTTATCAAAATTTCATAGCG-TGGTTATCAAAATTTCATAGGGA
* * * * *
27462 GG-T-T--AATTTTCACA--AT-TTTAT-AGAAAGGTTATCA-A-AGA
1 GGTTATCAAAATTTCATAGCGTGGTTATCA-AAA--TT-TCATAGGGA
* * * * * *
27500 GATTATCAAAATGTCATAGCGAGATTAT-AAGAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGCGTGGTTATCAA-AATTTCATAGGGA
* * * *
27544 GGTTAACAAAATTTCATTA-TGTGGTTA-CTAATATTTCATGGGGA
1 GGTTATCAAAATTTCA-TAGCGTGGTTATC-AAAATTTCATAGGGA
* *
27588 GGTTATCAAAATTTTATAGCGTGGTTATCAAAATTTCATA-TGA
1 GGTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGA
* * * * *
27631 GGGTTATAAAAGTCTCAATTTCATAAG-G-AGTT-CCAAAATTTGATA-GAA
1 -GGTTAT-CAA-----AATTTCAT-AGCGTGGTTATCAAAATTTCATAGGGA
* * * * * *
27679 GGTTA-CCAAATCTCATAGAGTGATTATCGAAATTTCATAGAGATCA
1 GGTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAG-G--GA
* * * * ** *
27725 GATTATCAAAATTT-ATAG-GAAGATTATCAAAATTTTATAATGT
1 GGTTATCAAAATTTCATAGCG-TGGTTATCAAAATTTCATAGGGA
* * * * * ** *
27768 TGTTATCAAAATTCCAAAGCGAGGTTATCAAAATTACATAATGT
1 GGTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGA
* * * * * * * **
27812 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GGTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGA
** * *
27856 GGTTATCAAAATTTCATAGTATGGTTA-CCAAA--T--TAGGAA
1 GGTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGA
* *** * *
27895 GGTTATTATTTTTATCAT-G-G-AGTAATCAAAATTTC--AGGGA
1 GGTTATCAAAATT-TCATAGCGTGGTTATCAAAATTTCATAGGGA
* ** *** *
27935 GGATATCAAAATTTCATAGTATGCAGATCAAAATTTCATAGTGA
1 GGTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGA
* * * ** * ** *
27979 GATTAACAAAATTTTATAATGAGGTTATCAAAAAATCATAGGTA
1 GGTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGA
* * * *
28023 GGTTATCAAAA-TT--T---GTAGTTATCAAGATTTCATAAGAA
1 GGTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGA
* * * * *
28061 AGTTATCAAAATTTTATAG-GAAGGTTTATCAAAATTTTATAGGAA
1 GGTTATCAAAATTTCATAGCG-TGG-TTATCAAAATTTCATAGGGA
* * * * *
28106 GATTTATCAAAATTTCATAGCGAGGTTATCAAAATTCCATAGTGT
1 G-GTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGA
* * * * *
28151 GATTATCAAAATTTCAAAGTGTGATTA-CTAACAA-TTCATATGGA
1 GGTTATCAAAATTTCATAGCGTGGTTATC-AA-AATTTCATAGGGA
* * * * ** * ** * *
28195 GGTTTTTAAATTTTTATAATGTGGTTATCAATATACCATATGAA
1 GGTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGA
* * * * *
28239 GGTTATCAACATCTCATAGTGCTGGTTATCAAAATATCATTGGGA
1 GGTTATCAAAATTTCATAGCG-TGGTTATCAAAATTTCATAGGGA
** ** * *
28284 --TTATCAAAATTTCATATTGAAGTCT-TCAAAATTCCTTAGGGA
1 GGTTATCAAAATTTCATAGCGTGGT-TATCAAAATTTCATAGGGA
*
28326 GGTTAACAAAATTTC
1 GGTTATCAAAATTTC
28341 GTAAGAAGGT
Statistics
Matches: 694, Mismatches: 205, Indels: 140
0.67 0.20 0.13
Matches are distributed among these distances:
37 10 0.01
38 34 0.05
39 25 0.04
40 37 0.05
41 5 0.01
42 47 0.07
43 47 0.07
44 301 0.43
45 73 0.11
46 78 0.11
47 12 0.02
48 12 0.02
49 3 0.00
50 8 0.01
51 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGCGTGGTTATCAAAATTTCATAGGGA
Found at i:27748 original size:21 final size:24
Alignment explanation
Indices: 27700--27759 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 24
27690 CTCATAGAGT
*
27700 GATTATCGAAATTTCATAGAGATCA
1 GATTATCAAAATTTCATAGAGA-CA
27725 GATTATCAAAATTT-ATAG-GA-A
1 GATTATCAAAATTTCATAGAGACA
27746 GATTATCAAAATTT
1 GATTATCAAAATTT
27760 TATAATGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 15 0.44
23 2 0.06
24 4 0.12
25 13 0.38
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.35
Consensus pattern (24 bp):
GATTATCAAAATTTCATAGAGACA
Found at i:28093 original size:23 final size:22
Alignment explanation
Indices: 27502--28431 Score: 187
Period size: 22 Copynumber: 42.7 Consensus size: 22
27492 ATCAAAGAGA
* *
27502 TTATCAAAATGTCATAGCG-AGA
1 TTATCAAAATTTCATAG-GAAGG
*
27524 TTAT-AAGAATTTCATAGTG-TGG
1 TTATCAA-AATTTCATAG-GAAGG
* * *
27546 TTAACAAAATTTCATTATG-TGG
1 TTATCAAAATTTCA-TAGGAAGG
* * *
27568 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGGAAGG
* *
27590 TTATCAAAATTTTATAGCG-TGG
1 TTATCAAAATTTCATAG-GAAGG
* *
27612 TTATCAAAATTTCATATGAGGG
1 TTATCAAAATTTCATAGGAAGG
* * *
27634 TTATAAAAGTCTCAATTTCATAAGGA-G
1 TTAT-CAA-----AATTTCATAGGAAGG
* *
27661 TT-CCAAAATTTGATA-GAAGG
1 TTATCAAAATTTCATAGGAAGG
* *
27681 TTA-CCAAATCTCATA-G-AGTG
1 TTATCAAAATTTCATAGGAAG-G
* *
27701 ATTATCGAAATTTCATAGAGATCAGA
1 -TTATCAAAATTTCATAG-GA--AGG
*
27727 TTATCAAAATTT-ATAGGAAGA
1 TTATCAAAATTTCATAGGAAGG
* *
27748 TTATCAAAATTTTATA--ATGTTG
1 TTATCAAAATTTCATAGGAAG--G
* *
27770 TTATCAAAATTCCAAAGCG-AGG
1 TTATCAAAATTTCATAG-GAAGG
* *
27792 TTATCAAAATTACATA--ATGTG
1 TTATCAAAATTTCATAGGAAG-G
* *
27813 ATTATCAGAATTTCATA-GAGGGG
1 -TTATCAAAATTTCATAGGA-AGG
* * * *
27836 TCAACAAAATTTTATA-AAGAGG
1 TTATCAAAATTTCATAGGA-AGG
* *
27858 TTATCAAAATTTCATAGTATGG
1 TTATCAAAATTTCATAGGAAGG
*
27880 TTA-CCAAA--T--TAGGAAGG
1 TTATCAAAATTTCATAGGAAGG
* ***
27897 TTATTATTTTTATCAT-GG-A-G
1 TTATCAAAATT-TCATAGGAAGG
* *
27917 TAATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATAGGAAGG
* * * *
27937 ATATCAAAATTTCATAGTATGC
1 TTATCAAAATTTCATAGGAAGG
** *
27959 AGATCAAAATTTCATAGTG-AGA
1 TTATCAAAATTTCATAG-GAAGG
* * *
27981 TTAACAAAATTTTATAATG-AGG
1 TTATCAAAATTTCAT-AGGAAGG
** *
28003 TTATCAAAAAATCATAGGTAGG
1 TTATCAAAATTTCATAGGAAGG
*
28025 TTATCAAAA-TT--T--GTA-G
1 TTATCAAAATTTCATAGGAAGG
* * *
28041 TTATCAAGATTTCATAAGAAAG
1 TTATCAAAATTTCATAGGAAGG
*
28063 TTATCAAAATTTTATAGGAAGG
1 TTATCAAAATTTCATAGGAAGG
* *
28085 TTTATCAAAATTTTATAGGAAGAT
1 -TTATCAAAATTTCATAGGAAG-G
28109 TTATCAAAATTTCATAGCG-AGG
1 TTATCAAAATTTCATAG-GAAGG
* * *
28131 TTATCAAAATTCCATAGTG-TGA
1 TTATCAAAATTTCATAG-GAAGG
* * *
28153 TTATCAAAATTTCAAAGTG-TGA
1 TTATCAAAATTTCATAG-GAAGG
28175 TTA-CTAACAA-TTCATATGG-AGG
1 TTATC-AA-AATTTCATA-GGAAGG
* * * * * *
28197 TTTTTAAATTTTTATAATG-TGG
1 TTATCAAAATTTCAT-AGGAAGG
* ** *
28219 TTATCAATATACCATATGAAGG
1 TTATCAAAATTTCATAGGAAGG
* * **
28241 TTATCAACATCTCATAGTGCTGG
1 TTATCAAAATTTCATAG-GAAGG
* * *
28264 TTATCAAAATATCATTGG--GA
1 TTATCAAAATTTCATAGGAAGG
*
28284 TTATCAAAATTTCATATTGAA-G
1 TTATCAAAATTTCATA-GGAAGG
* * *
28306 TCT-TCAAAATTCCTTAGGGAGG
1 T-TATCAAAATTTCATAGGAAGG
* * *
28328 TTAACAAAATTTCGTAAGAAGG
1 TTATCAAAATTTCATAGGAAGG
** **
28350 TTAAAAAAAATTT-ATAAAAAGG
1 TT-ATCAAAATTTCATAGGAAGG
* * * * ***
28372 TTCTCGAAATTCCATAGTATCA
1 TTATCAAAATTTCATAGGAAGG
* *
28394 TTATTAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAGGAAGG
28416 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
28432 ATGGGATCAT
Statistics
Matches: 665, Mismatches: 168, Indels: 150
0.68 0.17 0.15
Matches are distributed among these distances:
16 9 0.01
17 14 0.02
18 2 0.00
19 10 0.02
20 59 0.09
21 50 0.08
22 400 0.60
23 85 0.13
24 8 0.01
25 13 0.02
27 5 0.01
28 10 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGAAGG
Found at i:30602 original size:10 final size:11
Alignment explanation
Indices: 30576--30607 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
30566 GAGAGTTAAT
30576 TATAGAAAGAA
1 TATAGAAAGAA
30587 TA-AGAAA-AA
1 TATAGAAAGAA
30596 TATAGAAAGAA
1 TATAGAAAGAA
30607 T
1 T
30608 CTTACCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.21
10 10 0.53
11 5 0.26
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (11 bp):
TATAGAAAGAA
Found at i:32606 original size:27 final size:27
Alignment explanation
Indices: 32568--32621 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
32558 TTTCACAACA
32568 AAATTTCATTTCTTAACTGAATTTTCT
1 AAATTTCATTTCTTAACTGAATTTTCT
32595 AAATTTCATTTCTTAACTGAATTTTCT
1 AAATTTCATTTCTTAACTGAATTTTCT
32622 TAAAATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.52
Consensus pattern (27 bp):
AAATTTCATTTCTTAACTGAATTTTCT
Found at i:32620 original size:14 final size:14
Alignment explanation
Indices: 32576--32624 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
32566 CAAAATTTCA
32576 TTTCTTAACTGAAT
1 TTTCTTAACTGAAT
* * **
32590 TTTCTAAATTTCA-
1 TTTCTTAACTGAAT
32603 TTTCTTAACTGAAT
1 TTTCTTAACTGAAT
32617 TTTCTTAA
1 TTTCTTAA
32625 AATAATTTAT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (14 bp):
TTTCTTAACTGAAT
Found at i:32632 original size:27 final size:27
Alignment explanation
Indices: 32575--32632 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
32565 ACAAAATTTC
* *
32575 ATTTCTTAACTGAATTTTCTAAATTTC
1 ATTTCTTAACTGAATTTTCTAAATATA
32602 ATTTCTTAACTGAATTTTCTTAAA-ATA
1 ATTTCTTAACTGAATTTTC-TAAATATA
32629 ATTT
1 ATTT
32633 ATAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (27 bp):
ATTTCTTAACTGAATTTTCTAAATATA
Found at i:35624 original size:4 final size:4
Alignment explanation
Indices: 35617--35648 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
35607 ATACATCTAT
35617 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
35649 CATTCCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:36097 original size:31 final size:34
Alignment explanation
Indices: 35986--36090 Score: 147
Period size: 34 Copynumber: 3.1 Consensus size: 34
35976 CGTCCTCCAG
* * * *
35986 TTATTACAACTCATTGGGCAGGGTCTTCCACTTA
1 TTATCACAACCCACTGGGCAGGGTCTTCCAGTTA
*
36020 TTATCACAACCCACTGGGTAGGGTCTTCCAGTTA
1 TTATCACAACCCACTGGGCAGGGTCTTCCAGTTA
* *
36054 TTATCACAACCCACAGGGCAAGGTCTTCCAGTTA
1 TTATCACAACCCACTGGGCAGGGTCTTCCAGTTA
36088 TTA
1 TTA
36091 CAACCCATTA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (34 bp):
TTATCACAACCCACTGGGCAGGGTCTTCCAGTTA
Found at i:40525 original size:24 final size:24
Alignment explanation
Indices: 40498--40547 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
40488 GAAGATGTTA
40498 AGGCTGAGGAGATCGAAAATGATG
1 AGGCTGAGGAGATCGAAAATGATG
40522 AGGCTGAGGAGATCGAAAATGATG
1 AGGCTGAGGAGATCGAAAATGATG
40546 AG
1 AG
40548 TGTTGGAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.38, T:0.16
Consensus pattern (24 bp):
AGGCTGAGGAGATCGAAAATGATG
Found at i:41470 original size:31 final size:31
Alignment explanation
Indices: 41420--41636 Score: 155
Period size: 31 Copynumber: 7.0 Consensus size: 31
41410 TCCTTTTGTG
41420 TGCCACGTGTCA-TTTTTGGTACATGTGGCA
1 TGCCACGTGTCACTTTTTGGTACATGTGGCA
*
41450 TGCCACGTGTCACTTTTTGGTACATGTGGCG
1 TGCCACGTGTCACTTTTTGGTACATGTGGCA
* * *
41481 TGACACGTGT--C---TT-GTGCACGTGGCATA
1 TGCCACGTGTCACTTTTTGGTACATGTGGC--A
41508 TTGCCACGTGTCA--TTTTGGTACATGTGGCA
1 -TGCCACGTGTCACTTTTTGGTACATGTGGCA
*
41538 TGCCACGTGTCACGTGTCACTTTTTGGTACATGTGGCG
1 TG---C----CACGTGTCACTTTTTGGTACATGTGGCA
* * * * * *
41576 TGACACGTGTCACCTTTTGATACACGTGACG
1 TGCCACGTGTCACTTTTTGGTACATGTGGCA
* * *
41607 TGCCACATGTCACTTTTTTGTACACGTGGC
1 TGCCACGTGTCACTTTTTGGTACATGTGGC
41637 CACGTTGGAC
Statistics
Matches: 149, Mismatches: 20, Indels: 35
0.73 0.10 0.17
Matches are distributed among these distances:
25 9 0.06
26 2 0.01
28 9 0.06
29 3 0.02
30 13 0.09
31 76 0.51
32 10 0.07
36 9 0.06
38 18 0.12
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (31 bp):
TGCCACGTGTCACTTTTTGGTACATGTGGCA
Found at i:41567 original size:38 final size:36
Alignment explanation
Indices: 41512--41588 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 36
41502 GGCATATTGC
*
41512 CACGTGTCATTTTGGTACATGTGGCATGCCACGTGT
1 CACGTGTCATTTTGGTACATGTGGCATGACACGTGT
*
41548 CACGTGTCACTTTTTGGTACATGTGGCGTGACACGTGT
1 CACGTGTCA--TTTTGGTACATGTGGCATGACACGTGT
41586 CAC
1 CAC
41589 CTTTTGATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 9 0.24
38 28 0.76
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.32
Consensus pattern (36 bp):
CACGTGTCATTTTGGTACATGTGGCATGACACGTGT
Found at i:47931 original size:30 final size:29
Alignment explanation
Indices: 47895--47966 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
47885 ACCGTTTGAA
* *
47895 AAGGGTTGATTTGGC-TAAAATTGGTAGTTC
1 AAGGGTT-ATTTGGCACAAAATT-GAAGTTC
47925 AAGGGTTTATTT-GCACAAAATTGAAGTTC
1 AAGGG-TTATTTGGCACAAAATTGAAGTTC
47954 AAGGGCTTATTTG
1 AAGGG-TTATTTG
47967 ACTGTTGACG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 19 0.53
30 15 0.42
31 2 0.06
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.36
Consensus pattern (29 bp):
AAGGGTTATTTGGCACAAAATTGAAGTTC
Found at i:48637 original size:22 final size:22
Alignment explanation
Indices: 48581--48708 Score: 80
Period size: 22 Copynumber: 5.8 Consensus size: 22
48571 AATTACATGG
48581 GAAGATTATCAAAATTTCATA-
1 GAAGATTATCAAAATTTCATAT
* * *
48602 CAATGGTTACCAAAATTTCATAT
1 GAA-GATTATCAAAATTTCATAT
*
48625 GAAGATTATCAAAATATCATAGT
1 GAAGATTATCAAAATTTCATA-T
* * * *
48648 GTA-CTTATCAAAACTTCATAC
1 GAAGATTATCAAAATTTCATAT
* ** * *
48669 AAATCTTACCAAAATTTCATAA
1 GAAGATTATCAAAATTTCATAT
* * *
48691 AAAGTTTATCAGAATTTC
1 GAAGATTATCAAAATTTC
48709 TTAGGGAGGT
Statistics
Matches: 82, Mismatches: 21, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
21 3 0.04
22 74 0.90
23 5 0.06
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (22 bp):
GAAGATTATCAAAATTTCATAT
Found at i:48749 original size:22 final size:22
Alignment explanation
Indices: 48723--48797 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
48713 GGAGGTCAAA
48723 AAAATTTCATACG-AAAGTTATC
1 AAAATTTCATA-GTAAAGTTATC
* * **
48745 GAAATTTTATAGTATGGTTATC
1 AAAATTTCATAGTAAAGTTATC
* *
48767 AAAATTTC--A-TAAGGTTAAC
1 AAAATTTCATAGTAAAGTTATC
48786 AAAATTTCATAG
1 AAAATTTCATAG
48798 GGACTAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 16 0.39
20 1 0.02
21 2 0.05
22 22 0.54
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGTAAAGTTATC
Found at i:48788 original size:19 final size:19
Alignment explanation
Indices: 48760--48796 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
48750 TTTATAGTAT
*
48760 GGTTATCAAAATTTCATAA
1 GGTTAACAAAATTTCATAA
48779 GGTTAACAAAATTTCATA
1 GGTTAACAAAATTTCATA
48797 GGGACTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (19 bp):
GGTTAACAAAATTTCATAA
Found at i:49694 original size:30 final size:30
Alignment explanation
Indices: 49654--49715 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
49644 TACTAAATAT
49654 ACAAACAAATAAATTACAAAGAAAACTCAC
1 ACAAACAAATAAATTACAAAGAAAACTCAC
*
49684 ACAAATAAATAAATTACAAAGAAAACTCAC
1 ACAAACAAATAAATTACAAAGAAAACTCAC
49714 AC
1 AC
49716 TTCGTGAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.63, C:0.19, G:0.03, T:0.15
Consensus pattern (30 bp):
ACAAACAAATAAATTACAAAGAAAACTCAC
Found at i:50191 original size:28 final size:31
Alignment explanation
Indices: 50141--50201 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
50131 AGAGACATGC
50141 TAAAACCAACTATAAAGAGAAA-TAACTGAAT
1 TAAAACCAACTATAAAGAGAAATTAACT-AAT
*
50172 TAAAA-CAACTA-AATGA-AAATTAACTAAT
1 TAAAACCAACTATAAAGAGAAATTAACTAAT
50200 TA
1 TA
50202 TAAGAGTCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 8 0.29
29 9 0.32
30 6 0.21
31 5 0.18
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.23
Consensus pattern (31 bp):
TAAAACCAACTATAAAGAGAAATTAACTAAT
Found at i:50236 original size:149 final size:149
Alignment explanation
Indices: 49966--50254 Score: 533
Period size: 149 Copynumber: 1.9 Consensus size: 149
49956 TACTTCCTAA
* *
49966 AATTAAGCTACTACTAAGAGACATGCTAAAACCAACTCCAAAGAGAAATAACTGAATTAAAACAA
1 AATTAAGCCACTACTAAGAGACATGCTAAAACCAACTACAAAGAGAAATAACTGAATTAAAACAA
* *
50031 CTAAATGGAAATTAACTAGTTATAAGAGTCTGAATGGAAATTAACTTCTTATCCAGCAGTTGAGT
66 CTAAATGAAAATTAACTAATTATAAGAGTCTGAATGGAAATTAACTTCTTATCCAGCAGTTGAGT
50096 TTGTATCATTCTTAAAATT
131 TTGTATCATTCTTAAAATT
*
50115 AATTAAGCCACTACTAAGAGACATGCTAAAACCAACTATAAAGAGAAATAACTGAATTAAAACAA
1 AATTAAGCCACTACTAAGAGACATGCTAAAACCAACTACAAAGAGAAATAACTGAATTAAAACAA
50180 CTAAATGAAAATTAACTAATTATAAGAGTCTGAATGGAAATTAACTTCTTATCCAGCAGTTGAGT
66 CTAAATGAAAATTAACTAATTATAAGAGTCTGAATGGAAATTAACTTCTTATCCAGCAGTTGAGT
50245 TTGTATCATT
131 TTGTATCATT
50255 AAGCATCCCA
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 135 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (149 bp):
AATTAAGCCACTACTAAGAGACATGCTAAAACCAACTACAAAGAGAAATAACTGAATTAAAACAA
CTAAATGAAAATTAACTAATTATAAGAGTCTGAATGGAAATTAACTTCTTATCCAGCAGTTGAGT
TTGTATCATTCTTAAAATT
Found at i:51774 original size:27 final size:26
Alignment explanation
Indices: 51736--51787 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
51726 AATGTTATTT
51736 CCTTTCTCTTCCTCTCTATTTTCTTTA
1 CCTTTCTCTTCCTCTCTA-TTTCTTTA
* *
51763 CCTTTCTTTTCCTTTCTATTTCTTT
1 CCTTTCTCTTCCTCTCTATTTCTTT
51788 CCTCTCTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.06, C:0.31, G:0.00, T:0.63
Consensus pattern (26 bp):
CCTTTCTCTTCCTCTCTATTTCTTTA
Found at i:51985 original size:2 final size:2
Alignment explanation
Indices: 51978--52022 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
51968 CTATTATTCA
51978 AT 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 AT
52020 AT A
1 AT A
52023 GTAAGTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55661 original size:31 final size:32
Alignment explanation
Indices: 55602--55678 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
55592 ATTGTTAATG
55602 TGGCAATGCCACATAGAACCAAAAATGCCACA
1 TGGCAATGCCACATAGAACCAAAAATGCCACA
* * *
55634 TGGCAATGCCACATTGGACC-AAAATGCCACG
1 TGGCAATGCCACATAGAACCAAAAATGCCACA
**
55665 TGATAATGCCACAT
1 TGGCAATGCCACAT
55679 CAGCAATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 22 0.55
32 18 0.45
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.17
Consensus pattern (32 bp):
TGGCAATGCCACATAGAACCAAAAATGCCACA
Found at i:55797 original size:31 final size:29
Alignment explanation
Indices: 55729--55797 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
55719 GCTAGTTCAA
*
55729 GGGACAAAATGTCCAAAATTAAAGTTTAT
1 GGGACAAAATGTCCAAAATTAAAGTTTAG
55758 GGGACAAAATGT-CAAAATCATACAAGTTTAG
1 GGGACAAAATGTCCAAAAT--TA-AAGTTTAG
*
55789 GGGGCAAAA
1 GGGACAAAA
55798 AGGACATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 6 0.17
29 12 0.34
30 2 0.06
31 15 0.43
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (29 bp):
GGGACAAAATGTCCAAAATTAAAGTTTAG
Found at i:58248 original size:30 final size:29
Alignment explanation
Indices: 58212--58287 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
58202 ACTTGTAGTG
*
58212 TTTGGACGTTTTGCCCTCTAAAATTCAATT
1 TTTGGACATTTTGCCC-CTAAAATTCAATT
* *
58242 TTTGGACATTTTGCCCCTGAACTTCAATT
1 TTTGGACATTTTGCCCCTAAAATTCAATT
*
58271 TTGGGACATTTTGCCCC
1 TTTGGACATTTTGCCCC
58288 CTCAGCCTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 27 0.64
30 15 0.36
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.41
Consensus pattern (29 bp):
TTTGGACATTTTGCCCCTAAAATTCAATT
Found at i:58459 original size:29 final size:29
Alignment explanation
Indices: 58391--58467 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
58381 ACTAGGCTGA
*
58391 GGGGG-CAAAATGACCCAAAATTGAAGTTC
1 GGGGGACAAAAT-ATCCAAAATTGAAGTTC
** * *
58420 ATGAGATAAAATATCCAAAATTGAAGTTC
1 GGGGGACAAAATATCCAAAATTGAAGTTC
58449 GGGGGACAAAACT-TCCAAA
1 GGGGGACAAAA-TATCCAAA
58468 CCCTACAAGT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
29 31 0.84
30 6 0.16
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (29 bp):
GGGGGACAAAATATCCAAAATTGAAGTTC
Found at i:73321 original size:11 final size:11
Alignment explanation
Indices: 73305--73329 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
73295 AATCAATTTC
73305 TTGATTTTGTT
1 TTGATTTTGTT
73316 TTGATTTTGTT
1 TTGATTTTGTT
73327 TTG
1 TTG
73330 GGATAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.20, T:0.72
Consensus pattern (11 bp):
TTGATTTTGTT
Found at i:75255 original size:2 final size:2
Alignment explanation
Indices: 75242--75277 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
75232 ATGACTTTAT
75242 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
75278 CTTACCTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76288 original size:4 final size:4
Alignment explanation
Indices: 76279--76316 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
76269 TATCCATGAA
76279 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-T TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
76317 GGTTTTGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:77963 original size:14 final size:14
Alignment explanation
Indices: 77944--77973 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
77934 GAATTATAAA
77944 ATTTGATAAATATG
1 ATTTGATAAATATG
77958 ATTTGATAAATATG
1 ATTTGATAAATATG
77972 AT
1 AT
77974 ATTGTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
ATTTGATAAATATG
Found at i:96297 original size:45 final size:45
Alignment explanation
Indices: 96236--96335 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
96226 AAGAGGTGTA
* * * *
96236 AATGGTCCTGTACCACCAATGCCGAATCTACCTTCCCCACGGATG
1 AATGGTCCTGTACCACCAATGCCCAATCTACCATCACCAAGGATG
* *
96281 AATGGTCCTGTTCCACCAATGCCCAATCTTCCATCACCAAGGATG
1 AATGGTCCTGTACCACCAATGCCCAATCTACCATCACCAAGGATG
*
96326 AATGGGCCTG
1 AATGGTCCTG
96336 CACTTTTACC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (45 bp):
AATGGTCCTGTACCACCAATGCCCAATCTACCATCACCAAGGATG
Done.