Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001392.1 Hibiscus syriacus cultivar Beakdansim tig00002716_pilon, 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: 81724
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3987 original size:239 final size:239
Alignment explanation
Indices: 3565--4641 Score: 1268
Period size: 239 Copynumber: 4.5 Consensus size: 239
3555 TTTCTTGATG
* * *
3565 AGTAAGTCCTTCGGGACATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCAGGTCATCTAT
1 AGTAAGTCCTTC-GGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCAAGTCATCTAT
* * * * * * *
3630 AAATATTTCGACCAAAATGATAAGTCCTTCGAACCATCCATAAGACCTTCAGGCAGGA-TGTTTT
65 AAGTCTTTCGAGCAAGATGATAAGTCATTCGGACCATCCATAAGACCTTCGGGCAGGATTG-TTT
* * *
3694 CACTTGATTTTCAAAAATGAGAAAGCGATTTCCAAACTTTCTTATTTAAATCTTTTCTGAAAATT
129 CACATGATTTTCGAAAATGAGAAAGCGATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAAATT
3759 GATTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTT
194 GATTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTT
* * * * *
3805 ACTAAGTCCTTTGGACCATCAGTAAGTCTTTCGATCGTGATGTTTAAATCC-TCAAGCCATC-AG
1 AGTAAGTCCTTCGG-CCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCAAGTCATCTA-
* * * * * *
3868 TAAGTCTTTCGAGGAAGATGATAAGTAATTCGGGCCATCTATAAGTCCTTTGGGCAGGATTGTTT
64 TAAGTCTTTCGAGCAAGATGATAAGTCATTCGGACCATCCATAAGACCTTCGGGCAGGATTGTTT
* * * *
3933 CACATGATTTTTGAAAATGAGAAAGCTATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAAAT
129 CACATGATTTTCGAAAATGAGAAAGCGATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAAATT
* *
3998 GATTTTTCTTGAAAAGT-ATAAAATGATTTCCAAAGTTTCTTACTT
194 GATTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTT
* * ** * ***
4043 AATAAGTCCTTCGGCCAATCAATAAGGATTTCGAGCATGATGCTTAAATCCTTTGGGTCATCTAT
1 AGTAAGTCCTTCGGCC-ATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCAAGTCATCTAT
* * **
4108 AAGTCTTTCGAGTAAGATGATAAGTCATTTGGACCATCCATAAGACCTTCGGGCATAATAT-TTT
65 AAGTCTTTCGAGCAAGATGATAAGTCATTCGGACCATCCATAAGACCTTCGGGCAGGAT-TGTTT
* * *
4172 CACATGATATTCGAAAATGAGAAAGCGATTTCCAAAGTTTCTTATTTAAATATTTTTTGAAAATT
129 CACATGATTTTCGAAAATGAGAAAGCGATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAAATT
* *
4237 GAATTTTCTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTT
194 GATTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTT
* *
4283 AGTAAGT-CTT-----ATCAGTAAGTCTTTTGAGCATGATGTTTAAATCCTTCGAGTCATCTATA
1 AGTAAGTCCTTCGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCAAGTCATCTATA
* * *
4342 AGTCTTTCGAGCAAGATGATAAGTCTTTCGGGCCATCCATAAGACCTTCGGGCAGGATTATTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCATTCGGACCATCCATAAGACCTTCGGGCAGGATTGTTTCA
* * * * * * *
4407 CGTGATTTCCG--AATAAGAAAGCAATTTCCAAAGTTTTTTATTTAAATCTTTTATGAAAACTGA
131 CATGATTTTCGAAAATGAGAAAGCGATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAAATTGA
* *
4470 TTTTTC-TAAAAAGTAAGAAAATGA-TTCTCAAAGTTTCTTACTT
196 TTTTTCTTGAAAAGTAAGAAAACGATTTC-CAAAGTTTCTTACTT
* * ***
4513 AGTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTTGGGTCATCTAT
1 AGTAAGTCCTTC-GGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCAAGTCATCTAT
** * * * * * * ** *
4578 AAGTCCCTCGAGCATGATGTTTAAATCCTTCGGGCCTTCTGTAAGACCTTCGGGCATGA-TGTTT
65 AAGTCTTTCGAGCAAGATG-ATAAGTCATTCGGACCATCCATAAGACCTTCGGGCAGGATTGTTT
4642 TCATATGGTG
Statistics
Matches: 716, Mismatches: 103, Indels: 39
0.83 0.12 0.05
Matches are distributed among these distances:
229 3 0.00
230 37 0.05
231 54 0.08
232 1 0.00
233 107 0.15
237 67 0.09
238 99 0.14
239 271 0.38
240 77 0.11
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (239 bp):
AGTAAGTCCTTCGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCAAGTCATCTATA
AGTCTTTCGAGCAAGATGATAAGTCATTCGGACCATCCATAAGACCTTCGGGCAGGATTGTTTCA
CATGATTTTCGAAAATGAGAAAGCGATTTCCAAAGTTTCTTATTTAAATCTTTTCTGAAAATTGA
TTTTTCTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTT
Found at i:4635 original size:42 final size:42
Alignment explanation
Indices: 4519--4641 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 42
4509 ACTTAGTAAG
* * * *
4519 TCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCTGTAAGTCCTTCGAGCATGATGTTTAAA
* * * *
4561 TCCTTTGGGTCATCTATAAGTCCCTCGAGCATGATGTTTAAA
1 TCCTTCGGGCCATCTGTAAGTCCTTCGAGCATGATGTTTAAA
* * *
4603 TCCTTCGGGCCTTCTGTAAGACCTTCGGGCATGATGTTT
1 TCCTTCGGGCCATCTGTAAGTCCTTCGAGCATGATGTTT
4642 TCATATGGTG
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (42 bp):
TCCTTCGGGCCATCTGTAAGTCCTTCGAGCATGATGTTTAAA
Found at i:14191 original size:14 final size:14
Alignment explanation
Indices: 14162--14190 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
14152 ATACCTATTA
14162 TTAATATATATTTT
1 TTAATATATATTTT
14176 TTAAT-TATATTTT
1 TTAATATATATTTT
14189 TT
1 TT
14191 TGGTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTAATATATATTTT
Found at i:14236 original size:10 final size:11
Alignment explanation
Indices: 14216--14265 Score: 68
Period size: 10 Copynumber: 4.6 Consensus size: 11
14206 TTTTAAGTAC
*
14216 TATATTTTATA
1 TATATTATATA
14227 -ATATTATATA
1 TATATTATATA
14237 TATA-TATATA
1 TATATTATATA
14247 TATATATATATA
1 TATAT-TATATA
14259 TATATTA
1 TATATTA
14266 ATTTTCTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 19 0.54
11 5 0.14
12 11 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATATTATATA
Found at i:14238 original size:2 final size:2
Alignment explanation
Indices: 14223--14263 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
14213 TACTATATTT
14223 TA TA -A TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14263 T
1 T
14264 TAATTTTCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18847 original size:95 final size:95
Alignment explanation
Indices: 18659--18898 Score: 256
Period size: 95 Copynumber: 2.7 Consensus size: 95
18649 ATATTATATA
* * * *
18659 TATACAATAAATCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAAGCTCCGGCTTTATGGATAAT
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAAGCCCCGACTTTATGGATAAG
* *
18724 ATTCTGCTAGCCTGATAAAGGTGATTACAC
66 ATTCAGCTAACCTGATAAAGGTGATTACAC
* **
18754 TATATAATAAAGCTTGAGCTT-TCCCTCTA-AGGCAATTGGTTAAACTCCCCGACTTTATGGATA
1 TATACAATAAAGCTTGAG-TTGTCCCTCTAGA-GCAATTGGTTAAAAGCCCCGACTTTATGGATA
*
18817 AGATTCAGCTAACCTGATGAAGGT-A-T----
64 AGATTCAGCTAACCTGATAAAGGTGATTACAC
* *
18843 T-TAC-AT--A--TTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACATTATGGAT
1 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAAGCCCCGACTTTATGGAT
18899 TCAGCTAGCC
Statistics
Matches: 128, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
82 2 0.02
83 42 0.33
84 1 0.01
85 1 0.01
87 2 0.02
88 2 0.02
89 1 0.01
93 1 0.01
94 2 0.02
95 72 0.56
96 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAAAGCCCCGACTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTGATTACAC
Found at i:20226 original size:72 final size:72
Alignment explanation
Indices: 20109--20536 Score: 680
Period size: 72 Copynumber: 5.9 Consensus size: 72
20099 TACAGATGAT
* *
20109 TTGTCTCACTTGAGAAC-GTTTTACTTGAAAGAGGATTTATTTCCCTCGAGATTGTTTTTCTTAA
1 TTGTCTCACTTGAG-ACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAA
20173 AACAGACC
65 AACAGACC
* * **
20181 TTGTCTCACTTGAGACTGTTCTACTTGAAAGAAGATTTATTTCCCTCAAGAGTGTCATTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAA
20246 ACAGACC
66 ACAGACC
* *
20253 TTGTCTCACTTGAGATTGTTTTACTTGAAAGAGGATTTATTTCCCTCAAGATTGTTTTTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAA
20318 ACAGACC
66 ACAGACC
* * **
20325 TTGTCTCACTTGAGACTGTTCTACTTGAAAGAAGATGTATTTCCCTCAAGATTGTCATTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAA
20390 ACAGACC
66 ACAGACC
*
20397 TTGTCTCACTTGAGACTATTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAA
*
20462 ACAGACT
66 ACAGACC
* *
20469 TTGTCTCACTTGAGACTGTTTTACTCGAAAGAATATTTATTTCCCTCAAGATTGTTTTT-TATAA
1 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCT-TAA
20533 AACA
65 AACA
20537 ATATTTTATC
Statistics
Matches: 327, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
71 3 0.01
72 324 0.99
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (72 bp):
TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAA
ACAGACC
Found at i:20675 original size:36 final size:36
Alignment explanation
Indices: 20627--20713 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
20617 CATTGAAAAC
** *
20627 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATA
* * *
20663 GTTTCCCTTGAAACAAATCTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATA
* *
20699 ATTTCTCTTAAAACA
1 ATTTCCCTTGAAACA
20714 TAAACATTGA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATA
Found at i:20717 original size:101 final size:101
Alignment explanation
Indices: 20539--20813 Score: 426
Period size: 101 Copynumber: 2.7 Consensus size: 101
20529 ATAAAACAAT
* * *
20539 ATTTTATCTCGCTTGAGATAGTTT-CCTTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTC
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTT-GAAAC---AAATTTTGTCTCCCTTGAGACAATTTC
* *
20603 TCTTGAAGCATAAACATTGAAAACATTTCCCTTGAAATGA
62 TCTTAAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
20643 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATCTTGTCTCCCTTGAGACAATTTCTCTT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTT
*
20708 AAAACATAAACATTGAAAATATTTCCCTTGAAATGA
66 AAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
20744 AATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTT
20809 GAAAA
66 -AAAA
20814 AAACCTTTGA
Statistics
Matches: 160, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
101 125 0.78
102 4 0.03
104 27 0.17
105 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (101 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTT
AAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:20776 original size:36 final size:36
Alignment explanation
Indices: 20728--20812 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
20718 CATTGAAAAT
* * *
20728 ATTTCCCTTGAAATGAAA-TTTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAA-CAAATTTTGTCTCCCTTGAGACA
*
20764 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
20800 ATTTCTCTTGAAA
1 ATTTCCCTTGAAA
20813 AAAACCTTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 3 0.07
36 39 0.93
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:20854 original size:34 final size:37
Alignment explanation
Indices: 20813--20951 Score: 159
Period size: 37 Copynumber: 3.9 Consensus size: 37
20803 TCTCTTGAAA
*
20813 AAAACCTTTGAAATCAT-TTTCTCTTGAAAC-ACAA-
1 AAAACCTTTGAAATCATGTTTCTCTTGAAACAAAAAG
* *
20847 AAAACCTTTAAAATCGT-TTTCTCTTGGAACACAAAAAG
1 AAAACCTTTGAAATCATGTTTCTCTT-GAA-ACAAAAAG
20885 AAAACCTTTGAAAT--TGTTTCTCTTGAAACAAAAAAAG
1 AAAACCTTTGAAATCATGTTTCTCTTGAAAC--AAAAAG
20922 AAAACCTTTG-AA-CATGTTTCTCTTGAAACA
1 AAAACCTTTGAAATCATGTTTCTCTTGAAACA
20952 CCAAAGTTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
34 23 0.25
35 6 0.07
36 8 0.09
37 42 0.46
38 13 0.14
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (37 bp):
AAAACCTTTGAAATCATGTTTCTCTTGAAACAAAAAG
Found at i:22401 original size:2 final size:2
Alignment explanation
Indices: 22390--22435 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
22380 TTTTAAGTAC
22390 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22431 TA TA T
1 TA TA T
22436 TTCTATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26205 original size:2 final size:2
Alignment explanation
Indices: 26190--26224 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
26180 TACTATATTT
26190 TA TA -A TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26225 TTCTATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28149 original size:95 final size:95
Alignment explanation
Indices: 27986--28282 Score: 441
Period size: 95 Copynumber: 3.1 Consensus size: 95
27976 CATTACTTAT
* * *
27986 AGTATCGGTACTACTAATCTAAGTAGTATCGATATCATATATGGTATCGGTACCATTCTAGCGTT
1 AGTATCGGTACTACTACTCTAAGTAGTATCGATATCATATATGGTATCGGTACCATTTTAGCATT
* *
28051 CTGTTTTGACAATATTGGTATTGCCTCAGC
66 CTGTTTTGACAGTATCGGTATTGCCTCAGC
* *
28081 AGTATCGGTACTACTACTCTAAGTTGTATCGATATCATATATGGTATAGGTACCATTTTAGCATT
1 AGTATCGGTACTACTACTCTAAGTAGTATCGATATCATATATGGTATCGGTACCATTTTAGCATT
* *
28146 CTGTTTTGACAGTATCGGTACTGCCTCAGA
66 CTGTTTTGACAGTATCGGTATTGCCTCAGC
* * *
28176 AGTATTGGTACTACTACTCAAAGTAGTATCGATATCATATATGGTATCGGTACCAATTTAGCATT
1 AGTATCGGTACTACTACTCTAAGTAGTATCGATATCATATATGGTATCGGTACCATTTTAGCATT
* * * *
28241 ATGTTTTGATAGTATCGGTATTGCATCAAC
66 CTGTTTTGACAGTATCGGTATTGCCTCAGC
*
28271 AGTATCGATACT
1 AGTATCGGTACT
28283 TCTTTAACAA
Statistics
Matches: 180, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 180 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (95 bp):
AGTATCGGTACTACTACTCTAAGTAGTATCGATATCATATATGGTATCGGTACCATTTTAGCATT
CTGTTTTGACAGTATCGGTATTGCCTCAGC
Found at i:30595 original size:20 final size:21
Alignment explanation
Indices: 30545--30599 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
30535 ATCGGTATTG
*
30545 GATGAACAATATCGATACTAA
1 GATGAACAGTATCGATACTAA
* *
30566 GCAAGAACAGTATCGTTACT-A
1 G-ATGAACAGTATCGATACTAA
30587 GATGAACAGTATC
1 GATGAACAGTATC
30600 AGTACAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 11 0.38
21 3 0.10
22 15 0.52
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (21 bp):
GATGAACAGTATCGATACTAA
Found at i:34697 original size:3 final size:3
Alignment explanation
Indices: 34689--34773 Score: 79
Period size: 3 Copynumber: 29.0 Consensus size: 3
34679 TTTGGGCATG
* * *
34689 TAA TAA TAA TAA TAA TAA TAA TAA T-A TATA TAT TAA TAT TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* *
34734 TAA TAA TAG TAA T-A TAA TTAA -AA TAA TAA TAT TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
34774 AAAGGTACAA
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
2 8 0.12
3 52 0.79
4 6 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:35169 original size:123 final size:123
Alignment explanation
Indices: 34902--35523 Score: 878
Period size: 123 Copynumber: 5.1 Consensus size: 123
34892 AGACGGAAAT
* ** * * * * *
34902 GTTGAACAAGTTCTTCTTATTATGAACTTCCTCTTTCTCTTC-GAATAAGTTCTTCTCATTATGA
1 GTTGAATAAGTTCTTCAAATTATGAACTTCTTCTTCCTCTTCAG-ATGAGTTCTTCTTATTACGA
* * *
34966 ACTCC-TCTAGAAATGTTGATGATGCTCTATCTCCTTCTGCGATAAAGTCGAGCAAAAG
65 ACTCCTTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTTGAGCAAAAG
* * *
35024 GTTGAATAAGTTCTTCATATTATGAACTTCTTCTTCCTCTTC-GAATGAGTTCTTCTCATTATGA
1 GTTGAATAAGTTCTTCAAATTATGAACTTCTTCTTCCTCTTCAG-ATGAGTTCTTCTTATTACGA
* * * *
35088 ACTCATTCTGGAAATGTTGATGTTGCTATATCTCCTTCTGCGATAGAGTTGAGCAAAAT
65 ACTCCTTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTTGAGCAAAAG
* *
35147 GTTTAATAAGTTTTTCAAATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
1 GTTGAATAAGTTCTTCAAATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
* *
35212 CTCCTTATGGAAATGTTGATGATGCTCTATCTCCATCTGCGATAGAGTTGAGCAAAAG
66 CTCCTTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTTGAGCAAAAG
* *
35270 GTTGAATAAGTTCTTTAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
1 GTTGAATAAGTTCTTCAAATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
* * * * *
35335 CTCCTTCTGAAAATGTTAATGCTGCTCTATCTCCTTCTGTGACAGAGTTGAGCAAAAG
66 CTCCTTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTTGAGCAAAAG
*
35393 GTTGAATAAGTTCTTCAAATTATGAACTTCTTCTTCCTCTTCAGATGAG-TC--CTTATTACAAA
1 GTTGAATAAGTTCTTCAAATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
* * * *
35455 CTCCTTCTGGAAATGTTGATGCTACTCTATCTCCTTATGCGATAGAGTCGAGCAAAAG
66 CTCCTTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTTGAGCAAAAG
35513 GTTGAATAAGT
1 GTTGAATAAGT
35524 GATCTCAGAT
Statistics
Matches: 454, Mismatches: 44, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
120 72 0.16
122 65 0.14
123 316 0.70
124 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (123 bp):
GTTGAATAAGTTCTTCAAATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAA
CTCCTTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGCGATAGAGTTGAGCAAAAG
Found at i:37174 original size:63 final size:63
Alignment explanation
Indices: 37092--37268 Score: 169
Period size: 63 Copynumber: 2.8 Consensus size: 63
37082 TTTTTATCTC
* * * *
37092 ATTTATTTCGATTTTGATATTCTGTGTTTGTTTTTTTAGATTTTGGTCACTTATCTACATTCT
1 ATTTATTTCAATTTCGATATGCTGTGTTTGTTTATTTAGATTTTGGTCACTTATCTACATTCT
* * ** * *
37155 ATTTATTTTAATTTCGATATGCTGTTTTTGTTTATTTATTTTTTGGTCACTTATTTACATTTT
1 ATTTATTTCAATTTCGATATGCTGTGTTTGTTTATTTAGATTTTGGTCACTTATCTACATTCT
** * * * * *
37218 ACATATTGT-AATTTTGATATGATACT-TGTGTTTATTTATATTTTGGTCACT
1 ATTTATT-TCAATTTCGATATGCT-GTGTTTGTTTATTTAGATTTTGGTCACT
37269 CTAATTCTGT
Statistics
Matches: 95, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
63 93 0.98
64 2 0.02
ACGTcount: A:0.20, C:0.09, G:0.12, T:0.59
Consensus pattern (63 bp):
ATTTATTTCAATTTCGATATGCTGTGTTTGTTTATTTAGATTTTGGTCACTTATCTACATTCT
Found at i:41509 original size:3 final size:3
Alignment explanation
Indices: 41501--41599 Score: 182
Period size: 3 Copynumber: 33.3 Consensus size: 3
41491 TTTTTTATCC
41501 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
41548 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41596 TTA T
1 TTA T
41600 ATATATTAAA
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 91 0.98
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54452 original size:14 final size:13
Alignment explanation
Indices: 54422--54479 Score: 79
Period size: 12 Copynumber: 4.7 Consensus size: 13
54412 ATTATGCTTG
54422 AAGAAAAAAATG-
1 AAGAAAAAAATGA
54434 AAGAAAAAAATGA
1 AAGAAAAAAATGA
54447 AGAGAAAAAAA-GA
1 A-AGAAAAAAATGA
54460 AAGAAAAAAA--A
1 AAGAAAAAAATGA
54471 AAGAAAAAA
1 AAGAAAAAA
54480 GGGGGGTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.23
12 21 0.48
13 4 0.09
14 9 0.20
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (13 bp):
AAGAAAAAAATGA
Found at i:55768 original size:84 final size:84
Alignment explanation
Indices: 55624--56388 Score: 1265
Period size: 83 Copynumber: 9.2 Consensus size: 84
55614 ACTGGAACAA
* *
55624 ATGAATGTGCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
55689 CAATCATTGAATTTGGAAG
66 CAATCATTGAATTTGGAAG
* *
55708 AAT-AATGTGCTCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA
1 -ATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
55772 CCAATCATTGAATTTGGAAG
65 CCAATCATTGAATTTGGAAG
* *
55792 AAT-AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACATAA
1 -ATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
55856 CCAATCATTGAATTTGGAAG
65 CCAATCATTGAATTTGGAAG
* * *
55876 ATGAATGTGCTCAATAGCATCTTTTAGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGACAGAAC
1 ATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
55941 CAATCATTGAATTTGGAAG
66 CAATCATTGAATTTGGAAG
*
55960 AAT-AATGTGTTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 -ATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
56024 CCAATCATTGAATTTAGAAG
65 CCAATCATTGAATTTGGAAG
*
56044 ATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
56108 CAATCATTGAATTTAGAAG
66 CAATCATTGAATTTGGAAG
*
56127 ATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
56191 CAATCATTGAATTTAGAAG
66 CAATCATTGAATTTGGAAG
*
56210 ATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
56274 CAATCATTGAATTTAGAAG
66 CAATCATTGAATTTGGAAG
* *
56293 ATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
56357 CAATCATTGAATTTGAAAG
66 CAATCATTGAATTTGGAAG
*
56376 ATGAATTTGCTCA
1 ATGAATGTGCTCA
56389 TAATAGAAAT
Statistics
Matches: 657, Mismatches: 19, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
83 333 0.51
84 320 0.49
85 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35
Consensus pattern (84 bp):
ATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
CAATCATTGAATTTGGAAG
Found at i:57375 original size:114 final size:113
Alignment explanation
Indices: 57192--57848 Score: 904
Period size: 114 Copynumber: 5.7 Consensus size: 113
57182 ATTAGCTTTT
* *
57192 CCAGAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAGGAAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
* *** * * *** *
57257 ATTTGTTCAACCTTTT-ACCTGAATTCATCAAATTGATGGATTATTTTTT
65 ACTTGTTCAACCTTTTGGTTTGAATTCATC-ATTTGATGGATCAACATTG
*
57306 TCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
1 CCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
*
57371 ATTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
65 ACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
*
57420 CCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
1 CCAGG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
57485 AGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
62 AGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
*
57537 CCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 CCAGGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
* * * * * * *** *
57602 AGAATTTGTTCAACCTTTT-ATCTGAATTCATCACTGGATGGATTATTTTTT
62 AGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
*
57653 CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 CCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
*
57718 ACTTGTTCAACTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
65 ACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
* *
57767 CCAGGAAGAGTTCATAAGGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGA
1 CCAGGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
*
57832 ACTTGTTCAACTTTTTG
65 ACTTGTTCAACCTTTTG
57849 CATAATTCTA
Statistics
Matches: 491, Mismatches: 42, Indels: 20
0.89 0.08 0.04
Matches are distributed among these distances:
113 56 0.11
114 208 0.42
115 13 0.03
116 47 0.10
117 167 0.34
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (113 bp):
CCAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAA
CTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTG
Found at i:58171 original size:3 final size:3
Alignment explanation
Indices: 58163--58240 Score: 133
Period size: 3 Copynumber: 26.7 Consensus size: 3
58153 TTTTTATCCA
58163 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
58210 TAT TAT TAT TAT CA- TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
58241 AATATATATT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 3 0.04
3 68 0.96
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:58250 original size:11 final size:11
Alignment explanation
Indices: 58236--58265 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
58226 TTATTATTAT
58236 TATTAAATATA
1 TATTAAATATA
58247 TATTAAATATA
1 TATTAAATATA
58258 TA-TAAATA
1 TATTAAATA
58266 ATTAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:58749 original size:25 final size:29
Alignment explanation
Indices: 58701--58758 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 29
58691 ACCCCAACCT
*
58701 GAAAAGAAAAAAGACAGAGAGAAA-TACA
1 GAAAAGAAAAAAGACAGAGAGAAACAACA
*
58729 GAAAA-AAAAGAGAC-GAG-GAAACAACA
1 GAAAAGAAAAAAGACAGAGAGAAACAACA
58755 GAAA
1 GAAA
58759 CAGAGAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 4 0.15
26 10 0.37
27 8 0.30
28 5 0.19
ACGTcount: A:0.67, C:0.09, G:0.22, T:0.02
Consensus pattern (29 bp):
GAAAAGAAAAAAGACAGAGAGAAACAACA
Found at i:64925 original size:22 final size:23
Alignment explanation
Indices: 64899--64943 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
64889 TTATAAATTT
64899 TTAAAACTA-TATT-TTAAAAAAA
1 TTAAAA-TATTATTATTAAAAAAA
*
64921 TTAAAATATTATTATTTAAAAAA
1 TTAAAATATTATTATTAAAAAAA
64944 CCCCAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 10 0.50
23 8 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAAAATATTATTATTAAAAAAA
Found at i:71308 original size:19 final size:20
Alignment explanation
Indices: 71271--71308 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
71261 GAAATCCCTT
*
71271 TAAAAATACATGAATTTTAC
1 TAAAAATACATGAACTTTAC
71291 TAAAAATACATG-ACTTTA
1 TAAAAATACATGAACTTTA
71309 ATGAAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (20 bp):
TAAAAATACATGAACTTTAC
Found at i:71315 original size:20 final size:20
Alignment explanation
Indices: 71271--71316 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
71261 GAAATCCCTT
* *
71271 TAAAAATACATGAATTTTAC
1 TAAAAATACATGAACTTTAA
71291 TAAAAATACATG-ACTTTAA
1 TAAAAATACATGAACTTTAA
*
71310 TGAAAAT
1 TAAAAAT
71317 CCGTGGTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (20 bp):
TAAAAATACATGAACTTTAA
Found at i:72815 original size:43 final size:43
Alignment explanation
Indices: 72724--72821 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
72714 TGTGGTAGAC
* * * *
72724 CAAGTTCTAACACCCAAAACTTACCTCATGACTTTGAGTGGAG
1 CAAGCTCTAACACCCAAAACTTACCTCATAACTTCGAGGGGAG
* * * * *
72767 TAAGCTCTAACACCCCAACCTTGCCTCGTAACTTCGAGGGGAG
1 CAAGCTCTAACACCCAAAACTTACCTCATAACTTCGAGGGGAG
*
72810 CAAGCTTTAACA
1 CAAGCTCTAACA
72822 TTGTCTTGTC
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (43 bp):
CAAGCTCTAACACCCAAAACTTACCTCATAACTTCGAGGGGAG
Found at i:73779 original size:20 final size:20
Alignment explanation
Indices: 73754--73798 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
73744 TGATGGCTTC
*
73754 TTAAAAA-TCATAAAGATTCA
1 TTAAAAACT-ATAAAGAATCA
73774 TTAAAAACTATAAAGAATCA
1 TTAAAAACTATAAAGAATCA
73794 TTAAA
1 TTAAA
73799 GATATAGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (20 bp):
TTAAAAACTATAAAGAATCA
Found at i:76408 original size:32 final size:32
Alignment explanation
Indices: 76372--76437 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
76362 ATGGGATTCG
76372 GTGGCACAGTGAAGGTGACATGGAGTGTTGGT
1 GTGGCACAGTGAAGGTGACATGGAGTGTTGGT
*
76404 GTGGCATAGTGAAGGTGACATGGAGTGTTGGT
1 GTGGCACAGTGAAGGTGACATGGAGTGTTGGT
76436 GT
1 GT
76438 AGAAGTAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.21, C:0.08, G:0.44, T:0.27
Consensus pattern (32 bp):
GTGGCACAGTGAAGGTGACATGGAGTGTTGGT
Found at i:76459 original size:34 final size:32
Alignment explanation
Indices: 76379--76468 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
76369 TCGGTGGCAC
* *
76379 AGTGAAGGTGACATGGAGTGTTGGTGTGGCAT
1 AGTGAAGGTGACATGGAGTGTTGGTGTAGAAT
76411 AGTGAAGGTGACATGGAGTGTTGGTGTAGAAGT
1 AGTGAAGGTGACATGGAGTGTTGGTGTAGAA-T
* *
76444 AGTTGGAGGTGACATGGAGTATTGG
1 AG-TGAAGGTGACATGGAGTGTTGG
76469 CAATGAACTG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.56
33 3 0.06
34 20 0.38
ACGTcount: A:0.24, C:0.04, G:0.43, T:0.28
Consensus pattern (32 bp):
AGTGAAGGTGACATGGAGTGTTGGTGTAGAAT
Found at i:77300 original size:135 final size:134
Alignment explanation
Indices: 76888--77731 Score: 919
Period size: 135 Copynumber: 6.3 Consensus size: 134
76878 AGAGATATGA
* * * * * *
76888 AAATATTGATTCGTTCCACTATTATT-AGGGAAGATTGAATCGAGGCAGACTTGTTCAACTTTTC
1 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTC
*
76952 CTC----A-ATCAAATCTA-AAAAAAGAGGGATTTG-TTCTGCTGCTTCTTGAGGGAAAATCAGA
66 CTCAGGAAGATCAAATCTAGAAAAAAGAGGGATCTGTTTC-GCTGCTTCTTGAGGGAAAATCAGA
*
77010 TCTAG
130 TCTGG
* * * *
77015 AAATGTTGATTCATTCCACTATTCTTTAGGGATGATTGAATCGA-GCATACTTGTTCCACTGTTC
1 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTC
* * * * * * * *
77079 CTCAAGAAAGATCAATTCTGGAAAAAA-AGGGATTTGTTCCGCTACTTATTGAGGGAAAATCATA
66 CTC-AGGAAGATCAAATCTAGAAAAAAGAGGGATCTGTTTCGCTGCTTCTTGAGGGAAAATCAGA
*
77143 TCTAG
130 TCTGG
* *
77148 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTATT-
1 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTC
* * * * *
77212 CTACAAGGAAGATCAAATATAGAAAAAAGAGGGATCTGTTTCACTGATTCTTGAGAGAAAATTAG
66 CT-C-AGGAAGATCAAATCTAGAAAAAAGAGGGATCTGTTTCGCTGCTTCTTGAGGGAAAATCAG
77277 ATCTGG
129 ATCTGG
* * * *
77283 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTAAATCTAGGTAGACTTGTTCCACTATTC
1 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTC
* * * *
77348 CTCAGGTAAGATCAAATTTAGAACAAAGAGGGATCTGTTAT-GTTGCTTGTTGAGGGAAAATCAG
66 CTCAGG-AAGATCAAATCTAGAAAAAAGAGGGATCTGTT-TCGCTGCTTCTTGAGGGAAAATCAG
77412 ATCTGG
129 ATCTGG
* * * * *
77418 AAATGTTGATTTATTCCATTGTTCTTCAGAGAAGATTGAATCAAGGCAGACTTGTTCCATTGTTC
1 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTC
* * ** * *
77483 CTCAGGAAAGATCAAATCT-GTAAAAAAGAGGGATCTATTTCACTTTTTCTTGAGGGGATATCAG
66 CTCAGG-AAGATCAAATCTAG-AAAAAAGAGGGATCTGTTTCGCTGCTTCTTGAGGGAAAATCAG
*
77547 ATCTAGA
129 ATCT-GG
** * * * *
77554 AAAT-TTGATTCATTTTACTATTCTTCAGGGAAGATTGAATCGAGGTAAAGTTGTTCCACTGTTC
1 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTC
* * * * * * *
77618 CTCAACGAAGATCAAATATTG-ACAAAGAGGGATTTATTAT-GCTGCTTATTGAGGGAAAATCAG
66 CTC-AGGAAGATCAAATCTAGAAAAAAGAGGGATCTGTT-TCGCTGCTTCTTGAGGGAAAATCAG
77681 ATCTGG
129 ATCTGG
*
77687 AAATGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCGAG
1 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG
77732 TTCGATTCGC
Statistics
Matches: 606, Mismatches: 89, Indels: 37
0.83 0.12 0.05
Matches are distributed among these distances:
127 43 0.07
128 16 0.03
132 1 0.00
133 91 0.15
134 122 0.20
135 322 0.53
136 11 0.02
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (134 bp):
AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTC
CTCAGGAAGATCAAATCTAGAAAAAAGAGGGATCTGTTTCGCTGCTTCTTGAGGGAAAATCAGAT
CTGG
Found at i:77454 original size:270 final size:268
Alignment explanation
Indices: 76888--77731 Score: 1011
Period size: 270 Copynumber: 3.2 Consensus size: 268
76878 AGAGATATGA
* * * * * *
76888 AAATATTGATTCGTTCCACTATTATT-AGGGAAGATTGAATCGAGGCAGACTTGTTCAACTTTTC
1 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTC
* * *
76952 CTC-----A-ATCAAATCTA-AAAAAAGAGGGATTTG-TTCTGCTGCTTCTTGAGGGAAAATCAG
66 CTCAGGAAAGATCAAATCTAGAAAAAAGAGGGATCTGTTTC-ACTGATTCTTGAGGGAAAATCAG
* * * * *
77009 ATCTAGAAATGTTGATTCATTCCACTATTCTTTAGGGATGATTGAATCGA-GCATACTTGTTCCA
130 ATCTGGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAAACTTGTTCCA
* ** *
77073 CTGTTCCTCAAGAAAGATC-AATTCTGGAA-AAAAAGGGATTTGTTCCGCTACTTATTGAGGGAA
195 CTGTTCCTCAAG-AAGATCAAATT-T-GAACAAAGAGGGATTTGTTATGCTGCTTATTGAGGGAA
* *
77136 AATCATATCTAG
257 AATCAGATCTGG
*
77148 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTATT-
1 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTC
* * *
77212 CTACAAGG-AAGATCAAATATAGAAAAAAGAGGGATCTGTTTCACTGATTCTTGAGAGAAAATTA
66 CT-C-AGGAAAGATCAAATCTAGAAAAAAGAGGGATCTGTTTCACTGATTCTTGAGGGAAAATCA
* * * *
77276 GATCTGGAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTAAATCTAGGTAGACTTGTTCC
129 GATCTGGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAAACTTGTTCC
* * * * *
77341 ACTATTCCTCAGGTAAGATCAAATTTAGAACAAAGAGGGATCTGTTATGTTGCTTGTTGAGGGAA
194 ACTGTTCCTCAAG-AAGATCAAATTT-GAACAAAGAGGGATTTGTTATGCTGCTTATTGAGGGAA
77406 AATCAGATCTGG
257 AATCAGATCTGG
* * * * * *
77418 AAATGTTGATTTATTCCATTGTTCTTCAGAGAAGATTGAATCAAGGCAGACTTGTTCCATTGTTC
1 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTC
* ** * *
77483 CTCAGGAAAGATCAAATCT-GTAAAAAAGAGGGATCTATTTCACTTTTTCTTGAGGGGATATCAG
66 CTCAGGAAAGATCAAATCTAG-AAAAAAGAGGGATCTGTTTCACTGATTCTTGAGGGAAAATCAG
* ** *
77547 ATCTAGAAAAT-TTGATTCATTTTACTATTCTTCAGGGAAGATTGAATCGAGGTAAAGTTGTTCC
130 ATCT-GGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAAACTTGTTCC
*
77611 ACTGTTCCTCAACGAAGATCAAATATTG-ACAAAGAGGGATTTATTATGCTGCTTATTGAGGGAA
194 ACTGTTCCTCAA-GAAGATCAAAT-TTGAACAAAGAGGGATTTGTTATGCTGCTTATTGAGGGAA
77675 AATCAGATCTGG
257 AATCAGATCTGG
*
77687 AAATGTTGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCGAG
1 AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG
77732 TTCGATTCGC
Statistics
Matches: 497, Mismatches: 68, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
260 24 0.05
261 35 0.07
266 1 0.00
267 9 0.02
268 78 0.16
269 123 0.25
270 217 0.44
271 10 0.02
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (268 bp):
AAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTC
CTCAGGAAAGATCAAATCTAGAAAAAAGAGGGATCTGTTTCACTGATTCTTGAGGGAAAATCAGA
TCTGGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGTAAACTTGTTCCAC
TGTTCCTCAAGAAGATCAAATTTGAACAAAGAGGGATTTGTTATGCTGCTTATTGAGGGAAAATC
AGATCTGG
Found at i:79586 original size:3 final size:3
Alignment explanation
Indices: 79578--79606 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
79568 TGTATAGTCT
79578 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
79607 TTATTAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.