Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004631.1 Hibiscus syriacus cultivar Beakdansim tig00010364_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: 70811
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:2301 original size:23 final size:23
Alignment explanation
Indices: 2271--2318 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2261 TTTTAATTGC
2271 GGAGAATGTTGGAATGATGCAGT
1 GGAGAATGTTGGAATGATGCAGT
2294 GGAGAATGTTGGAATGATGCAGT
1 GGAGAATGTTGGAATGATGCAGT
2317 GG
1 GG
2319 GACCTCGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.42, T:0.25
Consensus pattern (23 bp):
GGAGAATGTTGGAATGATGCAGT
Found at i:6464 original size:19 final size:19
Alignment explanation
Indices: 6440--6489 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
6430 ATACAAAATG
*
6440 GGTATCGATACCCAGGCTT
1 GGTATCGATACCCAGGCCT
6459 GGTATCGATACCCAGGCCT
1 GGTATCGATACCCAGGCCT
*
6478 GGCATCGATACC
1 GGTATCGATACC
6490 ACAGCTAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (19 bp):
GGTATCGATACCCAGGCCT
Found at i:10012 original size:3 final size:3
Alignment explanation
Indices: 9999--10059 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
9989 ATATATATTT
9999 ATA AT- ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
10045 ATA ATA ATA AAA ATA
1 ATA ATA ATA ATA ATA
10060 TGGATAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10564 original size:117 final size:116
Alignment explanation
Indices: 10283--10668 Score: 528
Period size: 117 Copynumber: 3.3 Consensus size: 116
10273 TAGAATTATG
* * *
10283 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTT-CTTCTTCATATGAGGAGTTCTT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTT-TTTCCTTCTTCAGATGACGAGTTCTT
* * * * *
10347 CTCATTATGAACT-TTCTCTGGAA-GAAATAATCCATCCAGTGATGAATTCAGA-
65 CTCATTATGAACTCTTC-CTGGAATG--TTGATCCATCAAATGATGAATTCAAAC
* * * *
10399 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGACGAGTTCTTC
10464 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 TCATTATGAACTCTTCCTGG-AATGTTGATCCATCAAATGATGAATTCAAAC
* * *
10516 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTCTTCAGATGATGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGACGAGTTCTTC
*
10581 TCATTATGAACTCTACCTGGTAATGTTGATCCATCAAATGATGAATTCAAAC
66 TCATTATGAACTCTTCCTGG-AATGTTGATCCATCAAATGATGAATTCAAAC
*
10633 CAAAAAAATTGAACAAGTTCTTCTCATTATGAACTT
1 C-AAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
10669 TCCGCTGGGG
Statistics
Matches: 242, Mismatches: 22, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
115 2 0.01
116 92 0.38
117 116 0.48
118 32 0.13
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (116 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGACGAGTTCTTC
TCATTATGAACTCTTCCTGGAATGTTGATCCATCAAATGATGAATTCAAAC
Found at i:10824 original size:94 final size:95
Alignment explanation
Indices: 10648--10824 Score: 223
Period size: 94 Copynumber: 1.9 Consensus size: 95
10638 AAATTGAACA
** * * * ***
10648 AGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTCCATCAAGTAATGGATTCATGTAAAA
1 AGTTCTTCTCATTATGAACTTTCCGCTGGAAAAGATGATCCATCAAATAATGGATTCAACCAAAA
10713 GGTTTGAACAAATTCTTCCTTCTTTAGATG
66 GGTTTGAACAAATTCTTCCTTCTTTAGATG
* * *
10743 AGTTCTTCTCATTATGAACTTT-CTCTGGAAAAGCTGATCCATCAAATGATGGATTCAAACCAAA
1 AGTTCTTCTCATTATGAACTTTCCGCTGGAAAAGATGATCCATCAAATAATGGATTC-AACCAAA
*
10807 AGG-TTGAACAAGTTCTTC
65 AGGTTTGAACAAATTCTTC
10825 TTATTATGAA
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
94 40 0.58
95 29 0.42
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (95 bp):
AGTTCTTCTCATTATGAACTTTCCGCTGGAAAAGATGATCCATCAAATAATGGATTCAACCAAAA
GGTTTGAACAAATTCTTCCTTCTTTAGATG
Found at i:11899 original size:83 final size:83
Alignment explanation
Indices: 11760--12559 Score: 1414
Period size: 83 Copynumber: 9.7 Consensus size: 83
11750 CCTACTGAAT
*
11760 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCGAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
11825 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
*
11843 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
11908 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
11926 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
*
11991 TGATTGGTTCTGCGAAAC
66 TGATTGGTTCTGCCAAAC
12009 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
*
12074 TGATTGGTTCTGCGAAAC
66 TGATTGGTTCTGCCAAAC
*
12092 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
12157 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
12175 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
12240 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
12258 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
12323 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
* * *
12341 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCA
12405 ATGATT-GTTCTGTCC-AAC
65 ATGATTGGTTCTG-CCAAAC
* * * *
12423 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCA
12487 ATGATT-GTTCTGTCC-AAC
65 ATGATTGGTTCTG-CCAAAC
12505 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTT
12560 TCATTTAATT
Statistics
Matches: 701, Mismatches: 13, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
81 2 0.00
82 140 0.20
83 557 0.79
84 2 0.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
TGATTGGTTCTGCCAAAC
Found at i:20983 original size:14 final size:15
Alignment explanation
Indices: 20966--20998 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20956 TATTATTTTC
20966 AAATTTTA-ATTAAT
1 AAATTTTATATTAAT
*
20980 AAATTTTATCTTAAT
1 AAATTTTATATTAAT
20995 AAAT
1 AAAT
20999 AAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTTATATTAAT
Found at i:24438 original size:6 final size:7
Alignment explanation
Indices: 24419--24443 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
24409 TAAATATATA
24419 AATTTTT
1 AATTTTT
24426 AATTTTT
1 AATTTTT
24433 AATTTTT
1 AATTTTT
24440 AATT
1 AATT
24444 AATGGAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:26545 original size:17 final size:15
Alignment explanation
Indices: 26502--26542 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
26492 GGTCTGTAAT
26502 TATTTATTT-ATATA
1 TATTTATTTAATATA
26516 TATTTATTTAATATA
1 TATTTATTTAATATA
26531 TATTTA-TTAATA
1 TATTTATTTAATA
26543 ATAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTTAATATA
Found at i:26546 original size:3 final size:3
Alignment explanation
Indices: 26538--26599 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
26528 ATATATTTAT
* *
26538 TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
26586 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
26600 TGGATAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:33895 original size:19 final size:19
Alignment explanation
Indices: 33871--33920 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
33861 ATACAAAATG
*
33871 GGTATCGATACCCAGGCTT
1 GGTATCGATACCCAGGCCT
33890 GGTATCGATACCCAGGCCT
1 GGTATCGATACCCAGGCCT
*
33909 GGCATCGATACC
1 GGTATCGATACC
33921 ACAGCTAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (19 bp):
GGTATCGATACCCAGGCCT
Found at i:36831 original size:42 final size:42
Alignment explanation
Indices: 36731--36837 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
36721 ACCCGAAGGT
* * *
36731 CTTACGGATGGCCAGAAGGACTTATCATCTTGCTCGAAAGAG
1 CTTACTGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAG
* * * *
36773 C-TA-TAAATGACTCGAAGGATTTAATCATCATGCTCGAAAGA-
1 CTTACT-GATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGAG
36814 CTTACTGATGGCCCGAAGGACTTA
1 CTTACTGATGGCCCGAAGGACTTA
36838 CCAACTTGGG
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
41 16 0.32
42 33 0.66
43 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (42 bp):
CTTACTGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAG
Found at i:37208 original size:42 final size:42
Alignment explanation
Indices: 37103--37209 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 42
37093 GCCTGAAGGT
* * *
37103 CTTATAGATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAAGATTTAATCATCATGCTCGAAAGA
* **
37144 CTTATAGATGACCTAAAAGATTTAATCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAAGATTTAATCATCATGCTCGAAAGA
* *
37186 CTTACAGATGGCCCGAATGATTTA
1 CTTATAGATGGCCCGAAAGATTTA
37210 CTAATTTTGA
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
41 18 0.33
42 36 0.67
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (42 bp):
CTTATAGATGGCCCGAAAGATTTAATCATCATGCTCGAAAGA
Found at i:37441 original size:257 final size:258
Alignment explanation
Indices: 36926--37577 Score: 913
Period size: 258 Copynumber: 2.5 Consensus size: 258
36916 CTGCCTGAAG
* *
36926 GACTTACTGATGGCCCGAAAGACTTTCCAATTTGGGAAATAGTTTACTGGGTAAGAAATTTTGGA
1 GACTTACTGATGGCCCGAAAGACTTTACAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGA
* * *
36991 AATCACTTTCTTACTTTTCAAAAATTTCATTTTTTG-AAAATAGTAAATGAGAAACTTTGGAAAT
66 AATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAATA-TAAATGAGAAACTTTGAAAAT
* * *
37055 CGCTTTCTCATTTTTCGAAAATCATGAGGAAACATCCTGCCTGAAGGTCTTATAGATGGCCCGAA
130 CTCTTTCTCATTTTTCGAAAATCATGAGGAAACATCCTACCAGAAGGTCTTATAGATGGCCCGAA
* * * * *
37120 GGACTTATCATCTTGCTCGAAAGACTTATAGATGACCTAAAAGATTTAATCATCATGCTCGAAA
195 AGACTTATCATATTGCTCGAAAGACTTACAGATGACATAAAAGATTTAATCATAATGCTCGAAA
* * * * * *
37184 GACTTACAGATGGCCCGAATGA-TTTACTAATTT-TGAAATAATTTACTGGGAAAGATACTTTGG
1 GACTTACTGATGGCCCGAAAGACTTTAC-AATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGG
37247 AAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAATACTTAAATGAGAAACTTTGAAA
65 AAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAATA--TAAATGAGAAACTTTGAAA
* * *
37312 ATCTCTTTCTCATTTTTTGAAAATCATGTGGAAACATCCTACCAGAATGTCTTATAGATGGCCCG
128 ATCTCTTTCTCATTTTTCGAAAATCATGAGGAAACATCCTACCAGAAGGTCTTATAGATGGCCCG
* * * *
37377 AAAGACTTA-CATATTTCTCGAAAGACTTACAG-TGATATGAAGGATTTAATCATAATGCTCGAA
193 AAAGACTTATCATATTGCTCGAAAGACTTACAGATGACATAAAAGATTTAATCATAATGCTCGAA
37440 A
258 A
* * *
37441 GACTTACTGATGGCCCGAAGGACTTAACAATTTGGGAAATAGTTTACTGGGTAATAAACTTTGGA
1 GACTTACTGATGGCCCGAAAGACTTTACAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGA
* * *
37506 AATCGCTTTATTACTTTTCAAAAATTCCATTTTCTGAAAACA-ATAAATGAAAAACTTTGAAAAT
66 AATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAA-ATATAAATGAGAAACTTTGAAAAT
37570 -TGCTTTCT
130 CT-CTTTCT
37578 TGTTTCCAAA
Statistics
Matches: 349, Mismatches: 38, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
255 1 0.00
256 26 0.07
257 116 0.33
258 120 0.34
259 86 0.25
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (258 bp):
GACTTACTGATGGCCCGAAAGACTTTACAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGA
AATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAATATAAATGAGAAACTTTGAAAATC
TCTTTCTCATTTTTCGAAAATCATGAGGAAACATCCTACCAGAAGGTCTTATAGATGGCCCGAAA
GACTTATCATATTGCTCGAAAGACTTACAGATGACATAAAAGATTTAATCATAATGCTCGAAA
Found at i:38528 original size:18 final size:19
Alignment explanation
Indices: 38502--38540 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
38492 ACTATTTGCT
*
38502 TTCAATATTGTGGAAT-GC
1 TTCAATATTCTGGAATCGC
*
38520 TTCATTATTCTGGAATCGC
1 TTCAATATTCTGGAATCGC
38539 TT
1 TT
38541 ATTTTGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (19 bp):
TTCAATATTCTGGAATCGC
Found at i:47156 original size:11 final size:10
Alignment explanation
Indices: 47135--47176 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
47125 TTGGAACTAC
47135 ATAAAATAAT
1 ATAAAATAAT
47145 ATAAATATAAT
1 ATAAA-ATAAT
47156 ATAATAATAAT
1 ATAA-AATAAT
*
47167 A-ATAATAAT
1 ATAAAATAAT
47176 A
1 A
47177 AATATTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 7 0.24
10 6 0.21
11 15 0.52
12 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
ATAAAATAAT
Found at i:47162 original size:3 final size:3
Alignment explanation
Indices: 47135--47189 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
47125 TTGGAACTAC
47135 ATA A-A ATA AT- ATA A-A TATA AT- ATA ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
47178 ATA TTA ATA ATA
1 ATA ATA ATA ATA
47190 CCCCGGACAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
2 7 0.16
3 33 0.75
4 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:47170 original size:19 final size:18
Alignment explanation
Indices: 47138--47189 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
47128 GAACTACATA
47138 AAATAAT-ATAAATATAAT
1 AAATAATAAT-AATATAAT
47156 ATAATAATAATAATAATAAT
1 A-AATAATAATAAT-ATAAT
*
47176 AAATATTAATAATA
1 AAATAATAATAATA
47190 CCCCGGACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.07
19 20 0.67
20 8 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATAATAATAATATAAT
Found at i:47599 original size:22 final size:24
Alignment explanation
Indices: 47554--47605 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 24
47544 GAAAATATGC
*
47554 CACAAAGGCATAGACAAAACGTGT
1 CACAAAGGCATAGACAAAAAGTGT
47578 CACAAAGGCATA-A-AAAAAGTGT
1 CACAAAGGCATAGACAAAAAGTGT
47600 CACAAA
1 CACAAA
47606 TGTATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 14 0.52
23 1 0.04
24 12 0.44
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.12
Consensus pattern (24 bp):
CACAAAGGCATAGACAAAAAGTGT
Found at i:48784 original size:31 final size:31
Alignment explanation
Indices: 48735--48801 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
48725 ACGGCTAAGG
* *
48735 GACTAGAATCGAAGAGATCGATAACATTAGA
1 GACTAAAATCGAACAGATCGATAACATTAGA
* * *
48766 GACTAAAATTGAACAGATCGATAACGTTAGG
1 GACTAAAATCGAACAGATCGATAACATTAGA
48797 GACTA
1 GACTA
48802 TTTTCCCTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.21
Consensus pattern (31 bp):
GACTAAAATCGAACAGATCGATAACATTAGA
Found at i:49500 original size:5 final size:5
Alignment explanation
Indices: 49484--49545 Score: 56
Period size: 5 Copynumber: 11.8 Consensus size: 5
49474 AAGAATATAA
*
49484 AAAAT AATAT AAAAT --AAT AAAAT AAAAT AAAAAGT GGGAAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAA-T ---AAAAT AAAAT
49532 AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
49546 AAGTGTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
3 3 0.06
5 35 0.73
6 4 0.08
7 1 0.02
8 1 0.02
9 4 0.08
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:49502 original size:13 final size:13
Alignment explanation
Indices: 49477--49513 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
49467 GTTAAAAAAG
49477 AATATAAAA-AAT
1 AATATAAAATAAT
49489 AATATAAAATAAT
1 AATATAAAATAAT
*
49502 AAAATAAAATAA
1 AATATAAAATAA
49514 AAAGTGGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATATAAAATAAT
Found at i:49514 original size:30 final size:30
Alignment explanation
Indices: 49480--49547 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
49470 AAAAAAGAAT
* *
49480 ATAAAAAATAATATAAA-ATAATAAAATAAA
1 ATAAAAAATAAGA-AAATAAAATAAAATAAA
* **
49510 ATAAAAAGTGGGAAAATAAAATAAAATAAA
1 ATAAAAAATAAGAAAATAAAATAAAATAAA
49540 ATAAAAAA
1 ATAAAAAA
49548 GTGTTGAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (30 bp):
ATAAAAAATAAGAAAATAAAATAAAATAAA
Found at i:50813 original size:40 final size:38
Alignment explanation
Indices: 50756--51122 Score: 299
Period size: 38 Copynumber: 9.9 Consensus size: 38
50746 TTTCAAAACA
**
50756 TTTTCAAAACTATATATTATATATAT-TTAAAAAAATG
1 TTTTCAAAACTATATATTATATATATGTTTTAAAAATG
*
50793 TTTTCAAAAAAGCTATATATTATATATAT-TTTTCAAAATG
1 TTTTC--AAAA-CTATATATTATATATATGTTTTAAAAATG
* * * * *
50833 TTTTCAAAAACTATA-ATATATATATAT-ATATATATATA
1 TTTTC-AAAACTATATAT-TATATATATGTTTTAAAAATG
* * *
50871 TATTCAAAACTATATATTATAGATATGTTTTTAAAATG
1 TTTTCAAAACTATATATTATATATATGTTTTAAAAATG
* *
50909 TATTCAAAACTATATATTATATATATATATGTTTTTAAAATG
1 TTTTCAAAAC--TATA-TAT-TATATATATGTTTTAAAAATG
* *
50951 TTTTCAAAACTATATGTTATATATATGTTTTCAAAATG
1 TTTTCAAAACTATATATTATATATATGTTTTAAAAATG
*
50989 TTTTCAAAACTATATA-T-TATATATGTTTT---CA--
1 TTTTCAAAACTATATATTATATATATGTTTTAAAAATG
* *
51020 -----AAAACTATATATTATATATAT-ATTCAAAATAT-
1 TTTTCAAAACTATATATTATATATATGTTTTAAAA-ATG
* *
51052 TTTTAAAAACTATATATTATATATA--TTTTCAAAATG
1 TTTTCAAAACTATATATTATATATATGTTTTAAAAATG
* *
51088 TTTTCAAAACTATATAATATATATAT-TTTCAAAAA
1 TTTTCAAAACTATATATTATATATATGTTTTAAAAA
51123 CTATATAATA
Statistics
Matches: 273, Mismatches: 33, Indels: 48
0.77 0.09 0.14
Matches are distributed among these distances:
26 11 0.04
27 3 0.01
28 7 0.03
31 1 0.00
33 1 0.00
35 2 0.01
36 40 0.15
37 52 0.19
38 75 0.27
39 11 0.04
40 38 0.14
41 3 0.01
42 29 0.11
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (38 bp):
TTTTCAAAACTATATATTATATATATGTTTTAAAAATG
Found at i:50887 original size:2 final size:2
Alignment explanation
Indices: 50844--50873 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
50834 TTTCAAAAAC
50844 TA TA -A 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 T
50874 TCAAAACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50972 original size:36 final size:36
Alignment explanation
Indices: 50926--51121 Score: 216
Period size: 36 Copynumber: 5.7 Consensus size: 36
50916 AACTATATAT
* *
50926 TATATA-TATATATGTTTTTAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCAAAATGTTTTCAAAAC
*
50961 TATATGTTATATATATGTTTTCAAAATGTTTTCAAAAC
1 TATATATTATATATA--TTTTCAAAATGTTTTCAAAAC
*
50999 TATATATTATATATGTTTTC---A-------AAAAC
1 TATATATTATATATATTTTCAAAATGTTTTCAAAAC
* * *
51025 TATATATTATATATATATTCAAAATATTTTTAAAAAC
1 TATATATTATATATATTTTCAAAAT-GTTTTCAAAAC
51062 TATATATTATATATATTTTCAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCAAAATGTTTTCAAAAC
*
51098 TATATAATATATATATTTTCAAAA
1 TATATATTATATATATTTTCAAAA
51122 ACTATATAAT
Statistics
Matches: 136, Mismatches: 11, Indels: 27
0.78 0.06 0.16
Matches are distributed among these distances:
26 23 0.17
29 1 0.01
33 1 0.01
35 5 0.04
36 44 0.32
37 29 0.21
38 33 0.24
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.47
Consensus pattern (36 bp):
TATATATTATATATATTTTCAAAATGTTTTCAAAAC
Found at i:51030 original size:26 final size:26
Alignment explanation
Indices: 50986--51048 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
50976 TGTTTTCAAA
50986 ATGTTTTC-AAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATATTATAT
51011 ATGTTTTCAAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATATTATAT
* *
51037 ATATATTCAAAA
1 ATGTTTTCAAAA
51049 TATTTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 8 0.23
26 27 0.77
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (26 bp):
ATGTTTTCAAAAACTATATATTATAT
Found at i:51035 original size:24 final size:25
Alignment explanation
Indices: 50986--51137 Score: 100
Period size: 26 Copynumber: 6.1 Consensus size: 25
50976 TGTTTTCAAA
50986 ATGTTTTCAAAACTATATATTATAT
1 ATGTTTTCAAAACTATATATTATAT
51011 ATGTTTTCAAAAACTATATATTATAT
1 ATGTTTTC-AAAACTATATATTATAT
* * * *
51037 ATATATTCAAAA-TAT-TTTTAAAAACT
1 ATGTTTTCAAAACTATATATT--ATA-T
* * * * *
51063 ATATATT--ATA-TATATTTTCA-AA
1 ATGTTTTCAAAACTATATATT-ATAT
*
51085 ATGTTTTCAAAACTATATAATATAT
1 ATGTTTTCAAAACTATATATTATAT
* *
51110 ATATTTTCAAAAACTATATAATATAT
1 ATGTTTTC-AAAACTATATATTATAT
51136 AT
1 AT
51138 AAATTTTAAA
Statistics
Matches: 103, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
22 5 0.05
23 4 0.04
24 12 0.12
25 32 0.31
26 50 0.49
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (25 bp):
ATGTTTTCAAAACTATATATTATAT
Found at i:51064 original size:63 final size:63
Alignment explanation
Indices: 50948--51085 Score: 199
Period size: 63 Copynumber: 2.2 Consensus size: 63
50938 TGTTTTTAAA
* * *
50948 ATGTTTTC-AAAACTATATGTTATATATATGTTTTCAAAATGTTTTCAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATATTATATATA-GTATTCAAAATGTTTTAAAAACTATATATTATAT
*
51011 ATGTTTTCAAAAACTATATATTATATATA-TATTCAAAATATTTTTAAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATATTATATATAGTATTCAAAAT-GTTTTAAAAACTATATATTATAT
*
51074 ATATTTTCAAAA
1 ATGTTTTCAAAA
51086 TGTTTTCAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
62 9 0.13
63 40 0.59
64 19 0.28
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (63 bp):
ATGTTTTCAAAAACTATATATTATATATAGTATTCAAAATGTTTTAAAAACTATATATTATAT
Found at i:51088 original size:99 final size:98
Alignment explanation
Indices: 50926--51138 Score: 313
Period size: 99 Copynumber: 2.2 Consensus size: 98
50916 AACTATATAT
* * * * *
50926 TATATATATATATGTTTTTAAAATGTTTTCAAAACTATATGTTATATATATGTTTTCAAAATGTT
1 TATATATATATATATATTCAAAATGTTTTAAAAACTATATATTATATATA-GTTTTCAAAATGTT
* *
50991 TTCAAAACTATATATTATATATGTTTTCAAAAAC
65 TTCAAAACTATATAATATATATATTTTCAAAAAC
*
51025 TATATATTATATATATATTCAAAATATTTTTAAAAACTATATATTATATATA-TTTTCAAAATGT
1 TATATA-TATATATATATTCAAAAT-GTTTTAAAAACTATATATTATATATAGTTTTCAAAATGT
51089 TTTCAAAACTATATAATATATATATTTTCAAAAAC
64 TTTCAAAACTATATAATATATATATTTTCAAAAAC
51124 TATATA-ATATATATA
1 TATATATATATATATA
51139 AATTTTAAAA
Statistics
Matches: 104, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
97 9 0.09
99 57 0.55
100 15 0.14
101 23 0.22
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (98 bp):
TATATATATATATATATTCAAAATGTTTTAAAAACTATATATTATATATAGTTTTCAAAATGTTT
TCAAAACTATATAATATATATATTTTCAAAAAC
Found at i:51127 original size:26 final size:27
Alignment explanation
Indices: 51088--51152 Score: 98
Period size: 26 Copynumber: 2.4 Consensus size: 27
51078 TTTCAAAATG
51088 TTTTC-AAAACTATATAATATATAT-A
1 TTTTCAAAAACTATATAATATATATAA
51113 TTTTCAAAAACTATATAATATATATAAA
1 TTTTCAAAAACTATATAATATATAT-AA
*
51141 TTTTAAAAAACT
1 TTTTCAAAAACT
51153 GATTTTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
25 5 0.14
26 19 0.53
28 12 0.33
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (27 bp):
TTTTCAAAAACTATATAATATATATAA
Found at i:51138 original size:28 final size:26
Alignment explanation
Indices: 51088--51152 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 26
51078 TTTCAAAATG
*
51088 TTTTC-AAAACTATATAATATATATA
1 TTTTCAAAAACTATATAATATATAAA
51113 TTTTCAAAAACTATATAATATATATAAA
1 TTTTCAAAAACTATAT-A-ATATATAAA
*
51141 TTTTAAAAAACT
1 TTTTCAAAAACT
51153 GATTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 5 0.14
26 10 0.29
27 1 0.03
28 19 0.54
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (26 bp):
TTTTCAAAAACTATATAATATATAAA
Found at i:51792 original size:21 final size:21
Alignment explanation
Indices: 51768--51820 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
51758 ATTCTGACTA
51768 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
51789 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
51810 TCGCAATGCGA
1 TCGCATTGCGA
51821 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:51835 original size:20 final size:20
Alignment explanation
Indices: 51810--51943 Score: 196
Period size: 20 Copynumber: 6.7 Consensus size: 20
51800 TTTTCCTAAT
51810 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
51830 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
51851 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
51871 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
51891 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
51911 TAGCAAAGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
51931 TCGCAACGCGAAT
1 TCGCAATGCGAAT
51944 CTGACTATCG
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 85 0.84
21 16 0.16
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:52157 original size:22 final size:22
Alignment explanation
Indices: 52132--52207 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
52122 CACTCTCTAA
* *
52132 GACGACATCCGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
52154 GACGAAATCAGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
* *
52176 GACGATATCAGTCTCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
*
52198 GGCGAAATCA
1 GACGAAATCA
52208 TTCACGGTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (22 bp):
GACGAAATCAGTCCCCATCTCC
Found at i:52391 original size:20 final size:20
Alignment explanation
Indices: 52303--52393 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
52293 GCGATTCTGT
52303 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
52322 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
* **
52342 CATTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
52362 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
52382 TGTTGCGATTTT
1 CGTTGCGATTTT
52394 AAGTTTCAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 12 0.20
20 49 0.80
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:52400 original size:20 final size:20
Alignment explanation
Indices: 52357--52400 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
52347 CGATAGTCAT
* *
52357 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
52377 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
52397 TTTC
1 TTTC
52401 AGAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:53592 original size:20 final size:20
Alignment explanation
Indices: 53567--53609 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
53557 TCAGTATTGT
*
53567 GATAGTCAGAATCTCGTTGC
1 GATAGTCAGAATCGCGTTGC
*
53587 GATAGTCAGATTCGCGTTGC
1 GATAGTCAGAATCGCGTTGC
53607 GAT
1 GAT
53610 TTATAGATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (20 bp):
GATAGTCAGAATCGCGTTGC
Found at i:53617 original size:20 final size:20
Alignment explanation
Indices: 53596--53749 Score: 193
Period size: 20 Copynumber: 7.7 Consensus size: 20
53586 CGATAGTCAG
* *
53596 ATTCGCGTTGCGATTTATAG-
1 ATTCGCATTGCGATTTA-CGT
*
53616 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
53636 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
53656 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
53676 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * * **
53696 AATAGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* *
53717 ATTTGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
53737 ATTCGCATTGCGA
1 ATTCGCATTGCGA
53750 ATTAGGAAAA
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.01
20 102 0.87
21 14 0.12
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:53772 original size:21 final size:21
Alignment explanation
Indices: 53746--53791 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
53736 TATTCGCATT
*
53746 GCGAATTAGGAAAATCTCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
53767 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
53788 GCGA
1 GCGA
53792 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:54014 original size:3 final size:3
Alignment explanation
Indices: 54006--54031 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53996 AAAGGGATCC
54006 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
54032 ATTGAGGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:56320 original size:16 final size:15
Alignment explanation
Indices: 56298--56340 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
56288 TATGTTTTTT
56298 TTTTAATATTTTTAA
1 TTTTAATATTTTTAA
*
56313 TTTATAATAGTTTATAA
1 TTT-TAATA-TTTTTAA
56330 TTTT-ATATTTT
1 TTTTAATATTTT
56341 ATATTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 3 0.12
15 6 0.25
16 6 0.25
17 9 0.38
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTTAATATTTTTAA
Found at i:56341 original size:15 final size:16
Alignment explanation
Indices: 56298--56347 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
56288 TATGTTTTTT
56298 TTTTAATATTTT-TAA
1 TTTTAATATTTTATAA
*
56313 TTTATAATAGTTTATAA
1 TTT-TAATATTTTATAA
56330 TTTT-ATATTTTAT-A
1 TTTTAATATTTTATAA
56344 TTTT
1 TTTT
56348 TTGTAATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 5 0.16
15 11 0.35
16 9 0.29
17 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTTAATATTTTATAA
Found at i:56401 original size:23 final size:23
Alignment explanation
Indices: 56368--56466 Score: 75
Period size: 21 Copynumber: 4.3 Consensus size: 23
56358 TTTTTATTTA
*
56368 ATTTTT-A-ATATTGTTTTTAGT
1 ATTTTTAATATATTATTTTTAGT
56389 ATTTTTAATATATTTACATTTTTAGT
1 ATTTTTAATATA-TT--ATTTTTAGT
* *
56415 A-ATTTAAT-TTTTATTTTTAGT
1 ATTTTTAATATATTATTTTTAGT
*
56436 ATTTTT-ATAT-TTAATTTTTTAAT
1 ATTTTTAATATATT-A-TTTTTAGT
56459 ATTTTTAA
1 ATTTTTAA
56467 ATTTTAAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
21 20 0.32
22 6 0.10
23 18 0.29
24 4 0.06
25 6 0.10
26 9 0.14
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (23 bp):
ATTTTTAATATATTATTTTTAGT
Found at i:56419 original size:16 final size:16
Alignment explanation
Indices: 56389--56494 Score: 66
Period size: 15 Copynumber: 6.9 Consensus size: 16
56379 TGTTTTTAGT
56389 ATTTTTAATATATTTA
1 ATTTTTAATATATTTA
*
56405 CATTTTTAGTA-ATTTA
1 -ATTTTTAATATATTTA
56421 ATTTTT-AT-T-TTTA
1 ATTTTTAATATATTTA
*
56434 GTATTTT--TATATTTA
1 AT-TTTTAATATATTTA
*
56449 ATTTTTTAATATTTTTA
1 A-TTTTTAATATATTTA
*
56466 AATTTTAA-AT-TTTA
1 ATTTTTAATATATTTA
* * *
56480 AATTCTAAAATATTT
1 ATTTTTAATATATTT
56495 TTAGTTTTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
13 6 0.08
14 17 0.23
15 18 0.25
16 15 0.21
17 17 0.23
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
ATTTTTAATATATTTA
Found at i:56426 original size:15 final size:17
Alignment explanation
Indices: 56389--56427 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
56379 TGTTTTTAGT
56389 ATTTTTAATATATTTAC
1 ATTTTTAATATATTTAC
*
56406 ATTTTTAGTA-ATTTA-
1 ATTTTTAATATATTTAC
56421 ATTTTTA
1 ATTTTTA
56428 TTTTTAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 5 0.24
17 9 0.43
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTTTAATATATTTAC
Found at i:56446 original size:8 final size:8
Alignment explanation
Indices: 56381--56471 Score: 50
Period size: 9 Copynumber: 11.5 Consensus size: 8
56371 TTTAATATTG
56381 TTTTTAGTA
1 TTTTTA-TA
56390 TTTTTAATA
1 TTTTT-ATA
* *
56399 TATTTACA
1 TTTTTATA
56407 TTTTTAGTA
1 TTTTTA-TA
*
56416 -ATTTA-A
1 TTTTTATA
56422 -TTTT-TA
1 TTTTTATA
56428 TTTTTAGTA
1 TTTTTA-TA
56437 TTTTTATA
1 TTTTTATA
*
56445 -TTTAAT-
1 TTTTTATA
56451 TTTTTAATA
1 TTTTT-ATA
*
56460 TTTTTAAA
1 TTTTTATA
56468 TTTT
1 TTTT
56472 AAATTTTAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 19
0.70 0.10 0.21
Matches are distributed among these distances:
6 5 0.08
7 12 0.19
8 21 0.33
9 25 0.39
10 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (8 bp):
TTTTTATA
Found at i:56478 original size:23 final size:23
Alignment explanation
Indices: 56381--56480 Score: 80
Period size: 23 Copynumber: 4.3 Consensus size: 23
56371 TTTAATATTG
*
56381 TTTTTAGTATTTTTAATATATTTACA
1 TTTTTAATATTTTTAA-AT-TTTA-A
* * *
56407 TTTTTAGTA-ATTT-AATTTTTA
1 TTTTTAATATTTTTAAATTTTAA
* *
56428 TTTTTAGTATTTTTATA-TTTAA
1 TTTTTAATATTTTTAAATTTTAA
56450 TTTTTTAATATTTTTAAATTTTAA
1 -TTTTTAATATTTTTAAATTTTAA
*
56474 ATTTTAA
1 TTTTTAA
56481 ATTCTAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
21 10 0.16
22 10 0.16
23 24 0.39
24 6 0.10
25 3 0.05
26 9 0.15
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (23 bp):
TTTTTAATATTTTTAAATTTTAA
Found at i:56565 original size:29 final size:27
Alignment explanation
Indices: 56519--56573 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
56509 ATTTAAAAAA
*
56519 ACCCTTGAACTTAAAAAAAATTAATTTG
1 ACCCTTGAACTGAAAAAAAA-TAATTTG
*
56547 ACCCTTGAACTCGACAAAAAATAATTT
1 ACCCTTGAACT-GAAAAAAAATAATTT
56574 AGTCCATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.29
Consensus pattern (27 bp):
ACCCTTGAACTGAAAAAAAATAATTTG
Found at i:57063 original size:46 final size:45
Alignment explanation
Indices: 56970--57081 Score: 165
Period size: 46 Copynumber: 2.5 Consensus size: 45
56960 TATAATTGCA
* * *
56970 CTTAAATAGAAAAAGT-AATT-TATAAATTTTATTATGATGAAGC
1 CTTAAATAGAGAAAGTCATTTATATAAATATTATTATGATGAAGC
*
57013 CTTAAATAGAGAAAGTCATTTATAATAAATATTATTATGATGAAGT
1 CTTAAATAGAGAAAGTCATTTAT-ATAAATATTATTATGATGAAGC
57059 CTTAAATAGAGAAAGTCATTTAT
1 CTTAAATAGAGAAAGTCATTTAT
57082 TATGTATGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
43 15 0.24
44 3 0.05
45 1 0.02
46 43 0.69
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (45 bp):
CTTAAATAGAGAAAGTCATTTATATAAATATTATTATGATGAAGC
Found at i:60947 original size:2 final size:2
Alignment explanation
Indices: 60935--61006 Score: 119
Period size: 2 Copynumber: 36.5 Consensus size: 2
60925 AATAAAAATA
* *
60935 AT AT AT CT AT AT AT AT AT AA 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
60977 AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61007 AACTACTGGG
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65587 original size:179 final size:177
Alignment explanation
Indices: 65269--65625 Score: 630
Period size: 179 Copynumber: 2.0 Consensus size: 177
65259 ATTGAAATAA
65269 AACGAAAGTGATTGTATTATGTTTTTTTGAATCTAGTGACCATAAGTTATAAACAAATAAAGTGA
1 AACGAAAGTGATTGTATTATGTTTTTTTGAATCTAGTGACCATAAGTTATAAACAAATAAAGTGA
65334 CCAAATCTGTAGTTTACCCTATTTTTTCATCCCACTCTTTTCTCTCCCGACGTCGACAACGGCCA
66 CCAAATCTGTAGTTTACCCTATTTTTTCATCCCACTCTTTTCTCTCCCGACGTCGACAACGGCCA
*
65399 TAATGTTGTCCATCGAGGCATGCCTCCATCGGGCCTCCCTCCTATTT
131 TAATGTTGTCCATCGAGGCATGCCGCCATCGGGCCTCCCTCCTATTT
65446 AACGAAAGTGATTGTATTATG-TTTTTTGAATCTAGTGACCATAAGTTATAAAACTCAAATAAAA
1 AACGAAAGTGATTGTATTATGTTTTTTTGAATCTAGTGACCATAAGTTAT-AAA--CAAAT-AAA
65510 GTGACCAAATCTGTAGTTTACCCTATTTTTTCATCCCCACTC-TTT-TCTCCCGACGTCGACAAC
62 GTGACCAAATCTGTAGTTTACCCTATTTTTTCAT-CCCACTCTTTTCTCTCCCGACGTCGACAAC
*
65573 GGCCTTAATGTTGTCCATCGAGGCATGCCGCCATCGGGCCTCCCTCCTATTT
126 GGCCATAATGTTGTCCATCGAGGCATGCCGCCATCGGGCCTCCCTCCTATTT
65625 A
1 A
65626 GCTTCTCTAT
Statistics
Matches: 173, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
176 28 0.16
177 24 0.14
179 74 0.43
180 40 0.23
181 7 0.04
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (177 bp):
AACGAAAGTGATTGTATTATGTTTTTTTGAATCTAGTGACCATAAGTTATAAACAAATAAAGTGA
CCAAATCTGTAGTTTACCCTATTTTTTCATCCCACTCTTTTCTCTCCCGACGTCGACAACGGCCA
TAATGTTGTCCATCGAGGCATGCCGCCATCGGGCCTCCCTCCTATTT
Found at i:66487 original size:44 final size:45
Alignment explanation
Indices: 66438--66532 Score: 133
Period size: 44 Copynumber: 2.1 Consensus size: 45
66428 AGAATATGCA
66438 CCGAAGTG-CACGTAGAAATTGTCCCGAAGGACCACATAG-A-TGTC
1 CCGAAG-GACACGTAGAAA-TGTCCCGAAGGACCACATAGAATTGTC
*
66482 CCGAAGGATCACGTAGAAATGTCCCGAAGGACCACGTAGAATTGTC
1 CCGAAGGA-CACGTAGAAATGTCCCGAAGGACCACATAGAATTGTC
66528 CCGAA
1 CCGAA
66533 AGACCGCGTA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
43 1 0.02
44 25 0.54
45 11 0.24
46 9 0.20
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (45 bp):
CCGAAGGACACGTAGAAATGTCCCGAAGGACCACATAGAATTGTC
Found at i:66537 original size:23 final size:23
Alignment explanation
Indices: 66446--66545 Score: 132
Period size: 23 Copynumber: 4.4 Consensus size: 23
66436 CACCGAAGTG
66446 CACGTAGAAATTGTCCCGAAGGAC
1 CACGTAG-AATTGTCCCGAAGGAC
* *
66470 CACATAG-A-TGTCCCGAAGGAT
1 CACGTAGAATTGTCCCGAAGGAC
*
66491 CACGTAGAAATGTCCCGAAGGAC
1 CACGTAGAATTGTCCCGAAGGAC
*
66514 CACGTAGAATTGTCCCGAAAGAC
1 CACGTAGAATTGTCCCGAAGGAC
*
66537 CGCGTAGAA
1 CACGTAGAA
66546 CCCTCGACTC
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.27
22 2 0.03
23 41 0.61
24 6 0.09
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (23 bp):
CACGTAGAATTGTCCCGAAGGAC
Found at i:67199 original size:16 final size:17
Alignment explanation
Indices: 67151--67199 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
67141 ATATTATCCG
**
67151 ATCCGAAAAAATCGGAT
1 ATCCGAAAATTTCGGAT
67168 ATCCGAAAATTT-GGAT
1 ATCCGAAAATTTCGGAT
67184 ATCCG-AAATTTCGGAT
1 ATCCGAAAATTTCGGAT
67200 CGGATATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 6 0.21
16 13 0.45
17 10 0.34
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (17 bp):
ATCCGAAAATTTCGGAT
Found at i:67206 original size:21 final size:21
Alignment explanation
Indices: 67180--67230 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
67170 CCGAAAATTT
*
67180 GGATATCCGAAAT-TTCGGATC
1 GGATATCC-AAATATCCGGATC
67201 GGATATCCAAATATCCGGATC
1 GGATATCCAAATATCCGGATC
*
67222 CGA-ATCCAA
1 GGATATCCAA
67231 TTTTTTTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
GGATATCCAAATATCCGGATC
Done.