Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003816.1 Hibiscus syriacus cultivar Beakdansim tig00008178_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: 86636
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4873 original size:2 final size:2
Alignment explanation
Indices: 4866--4920 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
4856 TACGAAAACA
4866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
4907 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
4921 TTGACACGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5389 original size:272 final size:272
Alignment explanation
Indices: 4899--5461 Score: 914
Period size: 272 Copynumber: 2.1 Consensus size: 272
4889 TATATAATAT
* *
4899 ATATATATATATATATATATATTTGACACGATTTTTTGAAATTTATAAAATATCTTGAAAATCCA
1 ATATATATATATATATATAAATTTGACACGATTTTTTGAAATATATAAAATATCTTGAAAATCCA
* * *
4964 TATTTTTAGACTCATCTACAGTCCGAGTGTTTAAAATCGAAGGCTCTGATACCACCAAATGTAAT
66 GATTTTGAGACTCATCCACAGTCCGAGTGTTTAAAATCGAAGGCTCTGATACCACCAAATGTAAT
* *
5029 CCCTAGTCCCGGTTTGGACGTTATGACCAAATCTAGGTGGTTACATGTAGTATTCAGAAATTATT
131 CCCTAGTCCCGGCTTGGACGTTATGACCAAATCTAGGTGGTTACATATAGTATTCAGAAATTATT
**
5094 TTCATATTTAAACAACAATAAAATCCATATAATAGTATAATATG-AATTAGTCATAAGAAAGATT
196 TTCATATTTAAACAACAATAAAATCCATATAATAGTATAATATGAAATTAACCATAAGAAAGATT
*
5158 AATATGAT-AAC
261 AATACGATAAAC
* * *
5169 ATATATATATATAAATATAAATTTGACCCGATTTTTTGAAAATATCTAAAATATCTTGAAAATCC
1 ATATATATATATATATATAAATTTGACACGATTTTTTG-AAATATATAAAATATCTTGAAAATCC
*
5234 AGATTTTGAGACTCATCCACAGTCCGAGTGTTTAAAATTGAAGGCTCTGATACCACCAAATGTAA
65 AGATTTTGAGACTCATCCACAGTCCGAGTGTTTAAAATCGAAGGCTCTGATACCACCAAATGTAA
* * * *
5299 CTCCCTAGTCTCGGCTTGGACGTTATGACCAAATCTATGTGGTTACATATCGTATTCAGAAATTC
130 -TCCCTAGTCCCGGCTTGGACGTTATGACCAAATCTAGGTGGTTACATATAGTATTCAGAAATTA
*
5364 TTTTCATATTTAAACAACGATAAAATCCATATAATAGTATAATATGAAATTAACCATAAGAAAGA
194 TTTTCATATTTAAACAACAATAAAATCCATATAATAGTATAATATGAAATTAACCATAAGAAAGA
*
5429 TTCATACGATAAAC
259 TTAATACGATAAAC
5443 ATATATATATATATATATA
1 ATATATATATATATATATA
5462 TATATATATC
Statistics
Matches: 268, Mismatches: 21, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
270 35 0.13
271 85 0.32
272 103 0.38
273 24 0.09
274 21 0.08
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (272 bp):
ATATATATATATATATATAAATTTGACACGATTTTTTGAAATATATAAAATATCTTGAAAATCCA
GATTTTGAGACTCATCCACAGTCCGAGTGTTTAAAATCGAAGGCTCTGATACCACCAAATGTAAT
CCCTAGTCCCGGCTTGGACGTTATGACCAAATCTAGGTGGTTACATATAGTATTCAGAAATTATT
TTCATATTTAAACAACAATAAAATCCATATAATAGTATAATATGAAATTAACCATAAGAAAGATT
AATACGATAAAC
Found at i:5450 original size:2 final size:2
Alignment explanation
Indices: 5443--5470 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5433 TACGATAAAC
5443 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
5471 CATAAAATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17766 original size:2 final size:2
Alignment explanation
Indices: 17759--17815 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
17749 TGATTAATTC
17759 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
17801 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
17816 GTTGTATCCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20147 original size:17 final size:19
Alignment explanation
Indices: 20110--20148 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
20100 CTCATCCAAA
*
20110 ATAAATATATAATTAGGAC
1 ATAAATATATAATTAGAAC
20129 ATAAATATA-AATTA-AAC
1 ATAAATATATAATTAGAAC
20146 ATA
1 ATA
20149 TAATTAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
ATAAATATATAATTAGAAC
Found at i:20903 original size:21 final size:20
Alignment explanation
Indices: 20817--20974 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
20807 AAATGACCAA
**
20817 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
20836 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
20856 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
20876 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
20897 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
20918 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
20938 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
20959 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
20975 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:21003 original size:20 final size:20
Alignment explanation
Indices: 20941--21094 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
20931 CGATTTTCCA
* ** *
20941 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
20961 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
20981 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
21001 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
21021 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * * *
21041 AAATCGGAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
21061 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
21082 AAATCGCAACGCG
1 AAATCGCAACGCG
21095 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.02
20 91 0.83
21 16 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:21515 original size:33 final size:33
Alignment explanation
Indices: 21476--21546 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
21466 TTCACTTAGA
*
21476 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
21509 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
21542 TTTCA
1 TTTCA
21547 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:21670 original size:20 final size:20
Alignment explanation
Indices: 21626--21735 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
21616 TGCAGAAGAG
*
21626 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
21647 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
21667 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
21688 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
21702 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
21721 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
21736 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:21683 original size:41 final size:38
Alignment explanation
Indices: 21619--21735 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
21609 TTCAATTTGC
* *
21619 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
21657 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
21698 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
21731 AGAAT
1 AGAAT
21736 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:21705 original size:14 final size:14
Alignment explanation
Indices: 21686--21742 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
21676 GAGAAATGAA
21686 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
21700 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
21719 AATCGCAACGAGAG
1 AATCGCAACGAGAG
21733 AATCGCAACG
1 AATCGCAACG
21743 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:21718 original size:33 final size:33
Alignment explanation
Indices: 21678--21758 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
21668 CGCAACGAGA
21678 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
21711 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
21744 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
21759 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:21776 original size:19 final size:19
Alignment explanation
Indices: 21754--21851 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
21744 GAAACCAAAA
*
21754 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21773 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
21787 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21806 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
21820 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21839 TCGCGTTGCGATT
1 TCGCGTTGCGATT
21852 CTCTCATTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
16 6 0.10
17 6 0.10
19 31 0.50
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:21795 original size:14 final size:14
Alignment explanation
Indices: 21776--21865 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
21766 TTTCATTTCG
21776 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
21790 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
21809 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
21823 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
21842 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
21856 CATTGCGATT
1 CGTTGCGATT
21866 TTCATTTCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 28 0.47
16 6 0.10
17 6 0.10
19 19 0.32
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:21801 original size:33 final size:33
Alignment explanation
Indices: 21759--21873 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
21749 CAAAATCGCA
21759 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
21792 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
21825 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
21858 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
21874 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:24082 original size:93 final size:93
Alignment explanation
Indices: 23565--24215 Score: 1258
Period size: 92 Copynumber: 7.1 Consensus size: 93
23555 TAGATTGCTT
*
23565 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
23630 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
23657 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
23722 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
23749 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
23814 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
23842 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
23906 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
23933 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
23998 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24026 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24091 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24119 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
24184 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
24211 AGTAA
1 AGTAA
24216 TGCAATCCAT
Statistics
Matches: 554, Mismatches: 1, Indels: 8
0.98 0.00 0.01
Matches are distributed among these distances:
91 16 0.03
92 318 0.57
93 220 0.40
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:24303 original size:19 final size:19
Alignment explanation
Indices: 24263--24391 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
24253 TAGTTTACTT
* *
24263 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
24283 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
24302 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
24321 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
24335 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
24354 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
24368 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
24387 TCGCA
1 TCGCA
24392 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:24342 original size:33 final size:32
Alignment explanation
Indices: 24299--24391 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
24289 CGCGAAACCA
**
24299 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
24331 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
24364 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
24392 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:24389 original size:52 final size:52
Alignment explanation
Indices: 24263--24391 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
24253 TAGTTTACTT
**
24263 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
24315 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
24368 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
24392 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:24409 original size:19 final size:19
Alignment explanation
Indices: 24387--24521 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
24377 GAAACCAAAA
*
24387 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
24406 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
24422 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
24439 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
24455 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
24472 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
24491 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
24511 TCGTGTTGCGA
1 TCGCGTTGCGA
24522 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:24428 original size:14 final size:14
Alignment explanation
Indices: 24409--24465 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
24399 TTTCATTTCG
24409 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
24423 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
24440 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
24456 CGTTGCGATT
1 CGTTGCGATT
24466 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:24434 original size:33 final size:33
Alignment explanation
Indices: 24392--24484 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
24382 CAAAATCGCA
*
24392 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
24425 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
24458 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
24485 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:26732 original size:24 final size:24
Alignment explanation
Indices: 26698--26744 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26688 CTGAAACATC
26698 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
26722 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
26745 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:27453 original size:20 final size:20
Alignment explanation
Indices: 27425--27694 Score: 290
Period size: 20 Copynumber: 13.5 Consensus size: 20
27415 AAATTTCAGT
* * *
27425 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27445 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
27465 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27485 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
27505 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
27525 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
27545 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27565 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
27585 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
27605 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
27625 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
27645 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
27665 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
27685 GTTGCGATTT
1 GTTGCGATTT
27695 TGGAAAATCG
Statistics
Matches: 220, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 219 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:27711 original size:21 final size:21
Alignment explanation
Indices: 27661--27780 Score: 102
Period size: 21 Copynumber: 5.8 Consensus size: 21
27651 ATTTATGTGT
* * *
27661 TCGCGTTGCGATTTT-CATAT
1 TCGCATTGCGATTTTGCAAAA
* *
27681 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGCAAAA
* * * **
27702 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGCAAAA
27723 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGCAA-AA
27744 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGCAA-AA
*
27765 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
27781 GAAACTGATT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.20
21 66 0.80
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTGCAAAA
Found at i:27734 original size:42 final size:42
Alignment explanation
Indices: 27681--27784 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
27671 ATTTTCATAT
** *
27681 TCGCGTTGCGATTTTGGAAAATCGCAATGCGAATTTGTACTA
1 TCGCGTTGCGATTTTGGAAAATCGCAATGCGAATTTCAACAA
* * * * *
27723 TCGCATTGCGATTTT-CAAGAATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTGGAA-AATCGCAATGCGAATTTCAACAA
27765 TCGCGTTGCGATTTTGGAAA
1 TCGCGTTGCGATTTTGGAAA
27785 CTGATTTGCG
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 2 0.04
42 46 0.92
43 2 0.04
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (42 bp):
TCGCGTTGCGATTTTGGAAAATCGCAATGCGAATTTCAACAA
Found at i:28534 original size:19 final size:19
Alignment explanation
Indices: 28497--28537 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
28487 AATTAATTAA
* **
28497 AAACCCTAAATTATCCCCT
1 AAACCCAAAATTAGACCCT
28516 AAACCCAAAATTAGACCCT
1 AAACCCAAAATTAGACCCT
28535 AAA
1 AAA
28538 ATCATATACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.20
Consensus pattern (19 bp):
AAACCCAAAATTAGACCCT
Found at i:34048 original size:41 final size:41
Alignment explanation
Indices: 33991--34072 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
33981 ATCAAATCAG
33991 ATGCTTATATCTTCTTCATTAGATTTGAAAAATAAAGAAAT
1 ATGCTTATATCTTCTTCATTAGATTTGAAAAATAAAGAAAT
34032 ATGCTTATATCTTCTTCATTAGATTTGAAAAATAAAGAAAT
1 ATGCTTATATCTTCTTCATTAGATTTGAAAAATAAAGAAAT
34073 CTGAATAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (41 bp):
ATGCTTATATCTTCTTCATTAGATTTGAAAAATAAAGAAAT
Found at i:35194 original size:25 final size:25
Alignment explanation
Indices: 35144--35193 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
35134 TGCATTTTAT
35144 TTAAAAAATAAATTTATAAAAAAAA
1 TTAAAAAATAAATTTATAAAAAAAA
35169 TTAAAAACTATAAA-TTATAAAAAAA
1 TTAAAAA--ATAAATTTATAAAAAAA
35194 TAACTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.30
26 11 0.48
27 5 0.22
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (25 bp):
TTAAAAAATAAATTTATAAAAAAAA
Found at i:35454 original size:15 final size:16
Alignment explanation
Indices: 35423--35455 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35413 TTCAATTAAT
35423 TTTTAAATATATTTTA
1 TTTTAAATATATTTTA
*
35439 TTTTGAATAT-TTTTA
1 TTTTAAATATATTTTA
35454 TT
1 TT
35456 GTTTCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTTAAATATATTTTA
Found at i:36946 original size:26 final size:26
Alignment explanation
Indices: 36889--36939 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
36879 ATGTTAGAAA
* * *
36889 ACAAATTTTTAAAGTTTTAATAGGAG
1 ACAAATTTATAAAATTTTAATAAGAG
36915 ACAAATTTATAAAATTTTAATAAGA
1 ACAAATTTATAAAATTTTAATAAGA
36940 TGAAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (26 bp):
ACAAATTTATAAAATTTTAATAAGAG
Found at i:37944 original size:26 final size:22
Alignment explanation
Indices: 37891--37935 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
37881 ATTAAGAAAA
37891 AGTCCTCCAATCATATCAATAT
1 AGTCCTCCAATCATATCAATAT
*
37913 AGTCCTTCAATCATATCAATAT
1 AGTCCTCCAATCATATCAATAT
37935 A
1 A
37936 CTTAGTCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.33
Consensus pattern (22 bp):
AGTCCTCCAATCATATCAATAT
Found at i:38916 original size:61 final size:60
Alignment explanation
Indices: 38750--38917 Score: 176
Period size: 60 Copynumber: 2.8 Consensus size: 60
38740 ATTATGACCC
* * ** * * **
38750 TCATTTTAAATTAGTCCCTGAACTTTTAAGTATTCCAATTTTATCCTTAAACTATGACTA
1 TCATTCTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGACTA
* * * * * *
38810 TCATTCTAAATTAGTTCTTAAAATTTTGAACATTTCAGTTTCATCCCCAAAGTATGATCT-
1 TCATTCTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGA-CTA
*
38870 TCATTCTAAATTGGTCCCTAAACTTTTTAAACATTTCAATTTCATCCC
1 TCATTCTAAATTAGTCCCTAAAC-TTTTAAACATTTCAATTTCATCCC
38918 AAATTACGTA
Statistics
Matches: 86, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
60 62 0.72
61 24 0.28
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTCATCCCCAAACTATGACTA
Found at i:42740 original size:21 final size:22
Alignment explanation
Indices: 42707--42747 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
42697 AAAAATATCA
42707 AAATAATTTATTAAATATATAT
1 AAATAATTTATTAAATATATAT
*
42729 AAATAA-TTATTATATATAT
1 AAATAATTTATTAAATATAT
42748 TTATAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATAATTTATTAAATATATAT
Found at i:42745 original size:19 final size:21
Alignment explanation
Indices: 42707--42747 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
42697 AAAAATATCA
42707 AAATAATTTATTAAATATATAT
1 AAATAATTTATT-AATATATAT
42729 AAATAA-TTATT-ATATATAT
1 AAATAATTTATTAATATATAT
42748 TTATAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATAATTTATTAATATATAT
Found at i:44088 original size:3 final size:3
Alignment explanation
Indices: 44080--44173 Score: 100
Period size: 3 Copynumber: 30.7 Consensus size: 3
44070 GGCCCGTTTG
* * *
44080 TAA TAA TAA TTAA TAA TAA TAT TAG TAA TAAA TAA TAA -AA TTAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA
* * *
44127 TTA TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
44174 TTTAATTGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.03
3 67 0.88
4 7 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:44850 original size:113 final size:113
Alignment explanation
Indices: 44721--45812 Score: 1543
Period size: 112 Copynumber: 9.7 Consensus size: 113
44711 TTCTTCTTCC
* * * * *
44721 TTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTTAAGCAAAAAGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATCCATCAAGTGATGAATTCAAGCAAAAGGT
44786 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * **
44834 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAA-TGATGGATTTGAGCAAAAGG
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATCCATC-AAGTGATGAATTCAAGCAAAAGG
* *
44898 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
65 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * * *
44947 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATCCATCAAGTGATGAATTCAAGCAAAAGGT
* *
45012 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* *
45060 TTCTTCTCATTATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGCAAAAGGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATCCATCAAGTGATGAATTCAAGCAAAAGGT
* *
45125 TAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * * * * *
45172 TTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGAATTTAAGCAAAAAGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATCCATCAAGTGATGAATTCAAGCAAAAGGT
45237 TGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * **
45284 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCGAA-TGATGGATTTGAGCAAAAGG
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATCCATC-AAGTGATGAATTCAAGCAAAAGG
* *
45348 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
65 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * *
45397 TTCTTCTCATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATCCATCAAGTGATGAATTCAAGCAAAAGGT
* *
45462 TAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* *
45509 TTCTTCTCATTATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTCGAGCAAAAGGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATCCATCAAGTGATGAATTCAAGCAAAAGGT
* *
45574 TAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* *** * * * *
45621 TTCTTCTCATTATGAACTTCCTCTGGAAAAAATAATTCATCAAGTAATGAATTCAGGGAAAAGGT
1 TTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATCCATCAAGTGATGAATTCAAGCAAAAGGT
* *
45686 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAG
66 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* ** * * * ** * *
45733 TTCTTCTCATTATGAACTCTAACT-GACACTGCTGATCCACCGGGTGATGAATTTAAGCAAAAAG
1 TTCTTCTCATTATGAACTTTCTCTGGA-AATGCTAATCCATCAAGTGATGAATTCAAGCAAAAGG
45797 TTGAACAAGTTCTTCT
65 TTGAACAAGTTCTTCT
45813 TCTTCAAATG
Statistics
Matches: 885, Mismatches: 87, Indels: 15
0.90 0.09 0.02
Matches are distributed among these distances:
111 3 0.00
112 479 0.54
113 401 0.45
114 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTTCTCTGGAAATGCTAATCCATCAAGTGATGAATTCAAGCAAAAGGT
TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:45392 original size:337 final size:337
Alignment explanation
Indices: 44561--45812 Score: 1755
Period size: 337 Copynumber: 3.7 Consensus size: 337
44551 ATAGAATTAT
*
44561 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAAGAGTTCTT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGAT---GAGTTCTT
* * * * *
44626 CTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAA
62 CTCATTATGAACT-TTCTCTGGAAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAA
44690 CAAATTCTTCTCATTATGAA---CTTCTT-CTTC--C-------TTCTTCTCATTATGAACTTTC
126 CAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC
* * * * * * *
44742 TCTGGAAAAGCTGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTAT
191 TCTGGAAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTAT
*
44807 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCC
256 GAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCC
* *
44872 ATCGAATGATGGATTTGA
320 ATCAAATGATGAATTTGA
* * *
44890 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTC
* * *
44955 ATTATGAACCTTCTCTGGCAATGATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAA
65 ATTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAA
45020 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
130 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
45085 GAAATGTTAATCCATCAAGTGATGAATTCGAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
195 GAAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
* *
45150 TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAA
260 TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCAA
*
45215 ATGATGAATTTAA
325 ATGATGAATTTGA
45228 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCA
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCA
* * * **
45293 TTATGAACTTTCTCTGGAAATGCTGATCCATCGAA-TGATGGATTTGAGCAAAAGGTTGAACAAA
66 TTATGAACTTTCTCTGGAAATGATAATCCATC-AAGTGATGAATTCAAGCAAAAGGTTGAACAAA
*
45357 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
130 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
45422 GCAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
195 GAAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
* *
45487 TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTAATCCATCAA
260 TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCAA
* *
45552 GTGATGAATTCGA
325 ATGATGAATTTGA
* * * *
45565 GCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCA
* ** * * * *
45630 TTATGAACTTCCTCTGGAAAAAATAATTCATCAAGTAATGAATTCAGGGAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAAT
* **
45695 TCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT-G
131 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * * * ** * * *
45758 ACACTGCTGATCCACCGGGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCT
196 A-AATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCT
45813 TCTTCAAATG
Statistics
Matches: 829, Mismatches: 76, Indels: 29
0.89 0.08 0.03
Matches are distributed among these distances:
325 2 0.00
326 83 0.10
328 2 0.00
329 53 0.06
330 4 0.00
332 1 0.00
335 1 0.00
336 78 0.09
337 410 0.49
338 103 0.12
339 92 0.11
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (337 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAAT
TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAATGATAATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACT
TCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCAAA
TGATGAATTTGA
Found at i:46304 original size:22 final size:22
Alignment explanation
Indices: 46279--46333 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
46269 CATAAAGTTT
*
46279 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
46301 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
46323 TCATCTTTGAA
1 TCATCTTTGAA
46334 GAGTGTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:49093 original size:83 final size:82
Alignment explanation
Indices: 48891--49360 Score: 712
Period size: 83 Copynumber: 5.7 Consensus size: 82
48881 GTTCCTACCA
* * * * *
48891 AACCAGATCAAATAACTCAAAGAATACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
48956 CAATGATTGG---TGCC
66 CAATGATTGGTTCTGCC
*
48970 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAAT
1 -AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAAT
*
49035 TCAATGATTGATTCTGTCC
65 TCAATGATTGGTTCTG-CC
*
49054 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
49119 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTG-CC
* * * *
49137 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
*
49202 CAATGATTGGTTCTGCTA
66 CAATGATTGGTTCTGC-C
* * *
49220 AACCAGGTCAGATAACTCAAAGAACACTTTCAGAAGATGCTATTAACAAATTCATCTTCCCAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
*
49285 CAATGATTGGTTCTGCTA
66 CAATGATTGGTTCTGC-C
*
49303 AACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
49361 TCAGTTAATG
Statistics
Matches: 365, Mismatches: 20, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
80 70 0.19
82 1 0.00
83 292 0.80
84 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (82 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
CAATGATTGGTTCTGCC
Found at i:51504 original size:11 final size:11
Alignment explanation
Indices: 51488--51513 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
51478 TCAATTTTCC
51488 TTTTTCTTTTT
1 TTTTTCTTTTT
51499 TTTTTCTTTTT
1 TTTTTCTTTTT
51510 TTTT
1 TTTT
51514 CTTCTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:51507 original size:17 final size:17
Alignment explanation
Indices: 51482--51523 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
51472 CTTGATTCAA
*
51482 TTTTCCTTTTTCTTTT-T
1 TTTTTCTTTTT-TTTTCT
51499 TTTTTCTTTTTTTTTCT
1 TTTTTCTTTTTTTTTCT
*
51516 TCTTTCTT
1 TTTTTCTT
51524 GCTGGATGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTCT
Found at i:53498 original size:26 final size:26
Alignment explanation
Indices: 53469--53525 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
53459 ATGTAATTAT
*
53469 GTAAAAATGAAAATGTAAATACAAAC
1 GTAAAAATGAAAATGCAAATACAAAC
* * *
53495 GTAAAAATGCAAATGCAAATTCAAAT
1 GTAAAAATGAAAATGCAAATACAAAC
53521 GTAAA
1 GTAAA
53526 TATGTGAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (26 bp):
GTAAAAATGAAAATGCAAATACAAAC
Found at i:53619 original size:7 final size:7
Alignment explanation
Indices: 53585--53626 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
53575 ATAAAAGTAT
53585 AAATGCA
1 AAATGCA
* *
53592 CAATGAA
1 AAATGCA
53599 AAATGCA
1 AAATGCA
53606 AAGATGCA
1 AA-ATGCA
53614 AAATGC-
1 AAATGCA
53620 AAATGCA
1 AAATGCA
53627 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:55870 original size:21 final size:22
Alignment explanation
Indices: 55837--55881 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
55827 AAAAATATCA
55837 AAATAATTTATTAAATATATAT
1 AAATAATTTATTAAATATATAT
* *
55859 AAATAA-TTATTATATATTTAT
1 AAATAATTTATTAAATATATAT
55880 AA
1 AA
55882 CTATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATAATTTATTAAATATATAT
Found at i:57216 original size:3 final size:3
Alignment explanation
Indices: 57208--57301 Score: 100
Period size: 3 Copynumber: 30.7 Consensus size: 3
57198 GGCCCGTTTG
* * * *
57208 TAA TAA TAA TTAA TAA TAT TAG TAA TAAA TAA TAA -AA TTAG TAA TTA
1 TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA TAA
* *
57255 TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
57302 TTTAAATGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.03
3 67 0.88
4 7 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:57942 original size:235 final size:235
Alignment explanation
Indices: 57519--57950 Score: 785
Period size: 235 Copynumber: 1.8 Consensus size: 235
57509 TGGATTGCGG
*
57519 AAAAAATAATGATGTGGGAAATATTGTTTTGAAAAATGCACCTAAAAATAATCAAATGATTGTAC
1 AAAAAATAATGATGTGGGAAATATTGTTTTGAAAAATGCACCTAAAAATAATCAAATGATTGCAC
* * *
57584 CTTCAATTCAAAAAGATCTTGTCAATTGTTGTGCAGAAGAAACTACTAAGGAAATTATGAAAGAT
66 CTTCAATTCAAAAAGAGCTTATCAATTGTTGTGCAGAAGAAACTACAAAGGAAATTATGAAAGAT
57649 CTTGGTAAGGATTATTTTGGAGTGCTAGTATATGAGTCTAGTGACGTGTCTCAAAAAGAACAAAT
131 CTTGGTAAGGATTATTTTGGAGTGCTAGTATATGAGTCTAGTGACGTGTCTCAAAAAGAACAAAT
57714 GAAAAGCTCTTTTTGAATTGAAGGTGCAATATTGTTTTGA
196 GAAAAGCTCTTTTTGAATTGAAGGTGCAATATTGTTTTGA
57754 AAAAAATAATGATGTGGGAAATATTGTTTTGAAAAATGCACCTAAAAATAATCAAATGATTGCAC
1 AAAAAATAATGATGTGGGAAATATTGTTTTGAAAAATGCACCTAAAAATAATCAAATGATTGCAC
*
57819 CTTCAATTCAAAAAGAGCTTATCAATTGTTGTG-AGAAAGAAACTACAAAGGAAATTGTGAAAGA
66 CTTCAATTCAAAAAGAGCTTATCAATTGTTGTGCAG-AAGAAACTACAAAGGAAATTATGAAAGA
* *
57883 TCTTGGTAAGGATTATTTTGGAGTGCTAGTATATGAGTCTAGTGATGTGTCTTAAAAAGAACAAA
130 TCTTGGTAAGGATTATTTTGGAGTGCTAGTATATGAGTCTAGTGACGTGTCTCAAAAAGAACAAA
57948 TGA
195 TGA
57951 CTTTTTGTGT
Statistics
Matches: 189, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
234 2 0.01
235 187 0.99
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (235 bp):
AAAAAATAATGATGTGGGAAATATTGTTTTGAAAAATGCACCTAAAAATAATCAAATGATTGCAC
CTTCAATTCAAAAAGAGCTTATCAATTGTTGTGCAGAAGAAACTACAAAGGAAATTATGAAAGAT
CTTGGTAAGGATTATTTTGGAGTGCTAGTATATGAGTCTAGTGACGTGTCTCAAAAAGAACAAAT
GAAAAGCTCTTTTTGAATTGAAGGTGCAATATTGTTTTGA
Found at i:58518 original size:18 final size:18
Alignment explanation
Indices: 58492--58527 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
58482 TTGATTTGAT
58492 TGATAATGATACTCGAAA
1 TGATAATGATACTCGAAA
* *
58510 TGATGATGATGCTCGAAA
1 TGATAATGATACTCGAAA
58528 AGCCGATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (18 bp):
TGATAATGATACTCGAAA
Found at i:61681 original size:3 final size:3
Alignment explanation
Indices: 61673--61698 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61663 CTAGTTGTTA
61673 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
61699 AATAATAATT
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):
TAT
Found at i:70645 original size:12 final size:12
Alignment explanation
Indices: 70628--70676 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
70618 ATTATTATAT
70628 TTAATAATATTA
1 TTAATAATATTA
**
70640 TTAATAATAAAA
1 TTAATAATATTA
*
70652 ATAATAAT-TTA
1 TTAATAATATTA
*
70663 TTAATATTATTA
1 TTAATAATATTA
70675 TT
1 TT
70677 TTACAGATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
11 7 0.24
12 22 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TTAATAATATTA
Found at i:73824 original size:46 final size:48
Alignment explanation
Indices: 73733--73826 Score: 122
Period size: 46 Copynumber: 2.0 Consensus size: 48
73723 TTAGTGTAAT
* *
73733 TTTAATTTCTTGAATAAATGTATGCGAACTAAAGATCATACGGTTAGG
1 TTTAATTTCTTGAATAAATGCATGCGAACTAAAGAGCATACGGTTAGG
* *
73781 TTTAATTTCTTGAAT-AA-GCATGCGAACTAGATAGCATGA-GGTTAGG
1 TTTAATTTCTTGAATAAATGCATGCGAACTAAAGAGCAT-ACGGTTAGG
73827 ATGCTCTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
46 23 0.56
47 3 0.07
48 15 0.37
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (48 bp):
TTTAATTTCTTGAATAAATGCATGCGAACTAAAGAGCATACGGTTAGG
Found at i:74601 original size:16 final size:18
Alignment explanation
Indices: 74580--74612 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
74570 ATTAGCTTAT
74580 CAATTTG-TT-TATTCTG
1 CAATTTGCTTCTATTCTG
74596 CAATTTGCTTCTATTCT
1 CAATTTGCTTCTATTCT
74613 TATCATCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (18 bp):
CAATTTGCTTCTATTCTG
Found at i:80439 original size:22 final size:22
Alignment explanation
Indices: 80414--80525 Score: 67
Period size: 22 Copynumber: 5.3 Consensus size: 22
80404 TCCAAAATTT
80414 ATAAGTCTTTCGAGCATGATGC
1 ATAAGTCTTTCGAGCATGATGC
* * * *
80436 ATAAATCCTTCG-G-GTCAT-C
1 ATAAGTCTTTCGAGCATGATGC
*
80455 AGTAAGTCTTTTGAGCATGATGC
1 A-TAAGTCTTTCGAGCATGATGC
* * * *
80478 ATAAATCCTTCGGGTCAT-CTG-
1 ATAAGTCTTTCGAG-CATGATGC
*
80499 -TAAGTCTTTCGAGCAAGATG-
1 ATAAGTCTTTCGAGCATGATGC
80519 ATAAGTC
1 ATAAGTC
80526 CTTTGGGCTA
Statistics
Matches: 64, Mismatches: 19, Indels: 15
0.65 0.19 0.15
Matches are distributed among these distances:
19 4 0.06
20 23 0.36
21 8 0.12
22 24 0.38
23 5 0.08
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (22 bp):
ATAAGTCTTTCGAGCATGATGC
Found at i:80474 original size:42 final size:42
Alignment explanation
Indices: 80415--80528 Score: 185
Period size: 42 Copynumber: 2.7 Consensus size: 42
80405 CCAAAATTTA
80415 TAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTCATCAG
1 TAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTCATCAG
* *
80457 TAAGTCTTTTGAGCATGATGCATAAATCCTTCGGGTCATCTG
1 TAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTCATCAG
* *
80499 TAAGTCTTTCGAGCAAGATG-ATAAGTCCTT
1 TAAGTCTTTCGAGCATGATGCATAAATCCTT
80529 TGGGCTATCC
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 9 0.13
42 58 0.87
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTCATCAG
Found at i:80730 original size:42 final size:42
Alignment explanation
Indices: 80667--80777 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
80657 TCCAAAATTT
* * *
80667 ATAAGTCTTCTGAGCATGATGCATAAATCATTTGGGTCATCA
1 ATAAGTCTTCTGAGCAAGATGCATAAATCATTCGAGTCATCA
* * *
80709 ATAAGTCTTCTGAGCACGATGCATAAATCCTTCGAGTCATCT
1 ATAAGTCTTCTGAGCAAGATGCATAAATCATTCGAGTCATCA
*
80751 GTAAGTCTT-TCGAGCAAGATG-ATAAAT
1 ATAAGTCTTCT-GAGCAAGATGCATAAAT
80778 TCTTTGGACC
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 7 0.11
42 54 0.89
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (42 bp):
ATAAGTCTTCTGAGCAAGATGCATAAATCATTCGAGTCATCA
Found at i:80794 original size:253 final size:253
Alignment explanation
Indices: 80324--80993 Score: 1175
Period size: 253 Copynumber: 2.7 Consensus size: 253
80314 ATGTAAAAAA
80324 ATGAAAT--GAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTC
1 ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTC
80387 TTACCTAGTAAACTATTTCCAAAATTTATAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTC
66 TTACCTAGTAAACTATTTCCAAAATTTATAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTC
* * *
80452 ATCAGTAAGTCTTTTGAGCATGATGCATAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGA
131 ATCAATAAGTCTTCTGAGCATGATGCATAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGA
* * *
80517 TGATAAGTCCTTTGGGCTATCCATAAGACCTTTGGCAGGATGTTTTCAAATGTCTATC
196 TGATAAATCCTTTGGACCATCCATAAGACCTTTGGCAGGATGTTTTCAAATGTCTATC
*
80575 ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAAAAAGGTTTC
1 ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTC
* *
80640 TTACCTAGTAAACTATTTCCAAAATTTATAAGTC-TTCTGAGCATGATGCATAAATCATTTGGGT
66 TTACCTAGTAAACTATTTCCAAAATTTATAAGTCTTTC-GAGCATGATGCATAAATCCTTCGGGT
*
80704 CATCAATAAGTCTTCTGAGCACGATGCATAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAG
130 CATCAATAAGTCTTCTGAGCATGATGCATAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAG
*
80769 ATGATAAATTCTTTGGACCATCCATAAGACCTTTGGCAGGATGTTTTCAAATGTCTATC
195 ATGATAAATCCTTTGGACCATCCATAAGACCTTTGGCAGGATGTTTTCAAATGTCTATC
* *
80828 ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAATGTTTT
1 ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTC
*
80893 TTACCTAGTAAAATATTTCCAAAATTTATAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTC
66 TTACCTAGTAAACTATTTCCAAAATTTATAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTC
*
80958 ATCAATAAGTCTTCAGAGCATGATGCATAAATCCTT
131 ATCAATAAGTCTTCTGAGCATGATGCATAAATCCTT
80994 TAGATCTGAT
Statistics
Matches: 396, Mismatches: 19, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
251 7 0.02
252 3 0.01
253 383 0.97
254 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (253 bp):
ATGAAATGAGAAAGGTTTCTCATTTAAATCTGAAATTGAAATTGTTGAAAAGTAAGAAAGGTTTC
TTACCTAGTAAACTATTTCCAAAATTTATAAGTCTTTCGAGCATGATGCATAAATCCTTCGGGTC
ATCAATAAGTCTTCTGAGCATGATGCATAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGA
TGATAAATCCTTTGGACCATCCATAAGACCTTTGGCAGGATGTTTTCAAATGTCTATC
Found at i:80945 original size:22 final size:21
Alignment explanation
Indices: 80920--80987 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
80910 TCCAAAATTT
80920 ATAAGTCTTTCGAGCATGATGC
1 ATAAGTC-TTCGAGCATGATGC
* * *
80942 ATAAATCCTTCG-G-GTCAT-C
1 ATAAGT-CTTCGAGCATGATGC
80961 AATAAGTCTTCAGAGCATGATGC
1 -ATAAGTCTTC-GAGCATGATGC
80984 ATAA
1 ATAA
80988 ATCCTTTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
19 5 0.15
20 9 0.26
21 2 0.06
22 16 0.47
23 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (21 bp):
ATAAGTCTTCGAGCATGATGC
Found at i:81420 original size:11 final size:11
Alignment explanation
Indices: 81395--81428 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
81385 CTCATTTTTG
81395 ATATTATTGATA
1 ATATTATT-ATA
*
81407 ATATTGTTATA
1 ATATTATTATA
81418 ATATTATTATA
1 ATATTATTATA
81429 TTTAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (11 bp):
ATATTATTATA
Found at i:84739 original size:80 final size:80
Alignment explanation
Indices: 84605--84757 Score: 222
Period size: 80 Copynumber: 1.9 Consensus size: 80
84595 CTGGAGCAAG
* *
84605 AAATGATAAATGTTGGGGCACTTTTCAAGGCCCTTATCATCCAGAAGTAATAAATTTTAGGG-CA
1 AAATGATAAATGGTGGGGCACTTTTCAAGGCCCTTATCATCCAGAAGTAATAAATGTT-GGGTCA
84669 TTTTTGAAGGGTCGTTT
65 -TTTTGAAGGGTCGTTT
* *
84686 AAATGATAAATGGTGGGGCA-TTTTCAAGG-CCTCTGTCATTCAGAAGTAATAAATGTTGGGTCA
1 AAATGATAAATGGTGGGGCACTTTTCAAGGCCCT-TATCATCCAGAAGTAATAAATGTTGGGTCA
84749 TTTTGAAGG
65 TTTTGAAGG
84758 CATGTTTCAG
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
79 15 0.23
80 32 0.48
81 19 0.29
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.33
Consensus pattern (80 bp):
AAATGATAAATGGTGGGGCACTTTTCAAGGCCCTTATCATCCAGAAGTAATAAATGTTGGGTCAT
TTTGAAGGGTCGTTT
Found at i:85900 original size:60 final size:62
Alignment explanation
Indices: 85741--86224 Score: 682
Period size: 62 Copynumber: 8.0 Consensus size: 62
85731 TCTTGTTTGC
* * *
85741 TAGAGTCAACCCTTGAATTCTTCGTGAAGAGAATTCAACCTTTGTTATTTCTGACTCCCCAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAG
* *
85803 TAGAGTCAACCCTTGACTTTCTCGTGAAGAGAA-TCAACCTTTGTTA-TTCTGACTCCCCAA
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAG
** *
85863 TAGAGTCAA-CCTTGACTTCCTTATGACGAGAAGTCAA-CTTTGTTATTTCTGACT-CCCAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAG
* *
85922 TAGAGTCAACCCTTGACTTTCTCATGAAGA-AAGTCAACCTTTGTTATTTCTGACTCCCCAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAG
* * *
85983 TAGAGTCAACCCTTGACTTCATCGTGAAGAGAAGTCAACCTTTGTTATTTATAACTCCCCAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAG
* * * * * *
86045 TAGAGTCAACCATTGACTTTCTCGTGAAGAGAAGTTAACTTTTGTTATTTCTGACTCCCTAA
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAG
* *
86107 TAGAGT-AACCCTTGACTTCCTCATGAAGAGAACTCAACCTTTGTTATTTCTGACTCCCCA-
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAG
* * *
86167 -ATAGTCAACCATTGACTTCCTCGTGAAGAGAAGTCAACC-TTGTTATTTTTGACTCCCC
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCC
86225 GGTAAATCAA
Statistics
Matches: 377, Mismatches: 38, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
59 69 0.18
60 98 0.26
61 92 0.24
62 118 0.31
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (62 bp):
TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCCAG
Found at i:85990 original size:33 final size:32
Alignment explanation
Indices: 85775--86055 Score: 92
Period size: 28 Copynumber: 9.2 Consensus size: 32
85765 TGAAGAGAAT
85775 TCAACCTTTGTTATTTCTGACTCCCCAGTAGAG
1 TCAACCTTTGTTATTTCT-ACTCCCCAGTAGAG
* ** *
85808 TCAACCCTTG--ACTTTCT-CGT--GAAG-AGAA
1 TCAACCTTTGTTA-TTTCTAC-TCCCCAGTAGAG
*
85836 TCAACCTTTGTTA-TTCTGACTCCCCAATAGAG
1 TCAACCTTTGTTATTTCT-ACTCCCCAGTAGAG
* ** *
85868 TCAACC-TTG--ACTTCCTTA-TGACGAG-A-AG
1 TCAACCTTTGTTA-TTTC-TACTCCCCAGTAGAG
85896 TCAA-CTTTGTTATTTCTGACT-CCCAGTAGAG
1 TCAACCTTTGTTATTTCT-ACTCCCCAGTAGAG
* ** *
85927 TCAACCCTTG--ACTTTCT-CAT--GAAG-AAAG
1 TCAACCTTTGTTA-TTTCTAC-TCCCCAGTAGAG
85955 TCAACCTTTGTTATTTCTGACTCCCCAGTAGAG
1 TCAACCTTTGTTATTTCT-ACTCCCCAGTAGAG
* * ***
85988 TCAACCCTTG--ACTTC-A-TCGTGAAG-AGAAG
1 TCAACCTTTGTTATTTCTACTC-CCCAGTAG-AG
*
86017 TCAACCTTTGTTATTTATAACTCCCCAGTAGAG
1 TCAACCTTTGTTATTTCT-ACTCCCCAGTAGAG
86050 TCAACC
1 TCAACC
86056 ATTGACTTTC
Statistics
Matches: 175, Mismatches: 36, Indels: 74
0.61 0.13 0.26
Matches are distributed among these distances:
27 1 0.01
28 42 0.24
29 34 0.19
30 13 0.07
31 28 0.16
32 21 0.12
33 32 0.18
34 4 0.02
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (32 bp):
TCAACCTTTGTTATTTCTACTCCCCAGTAGAG
Found at i:86377 original size:88 final size:88
Alignment explanation
Indices: 86225--86467 Score: 283
Period size: 88 Copynumber: 2.8 Consensus size: 88
86215 TTGACTCCCC
* * *
86225 GGTAAATCAATCTCGAGTATGATCTCCACGAAAGAGTAGTGGAACAGATTCTTC-TATTTTAGAT
1 GGTAAATCAATCTCGAGTCTGATCTCCACGGAAGAGTAGTGGAA-AGATTCTTCTTATTTCAGAT
* * * *
86289 TTGGTC-TCCATGGAAGATTAGTGA
65 TTGGTCTTCC-CGAAAGAGTAGCGA
** *
86313 GGTAAATCAATCTCGAGTCTGATCTCCACGGAAGAACAGTGGAAAAATTCTTCTTATTTCAGATT
1 GGTAAATCAATCTCGAGTCTGATCTCCACGGAAGAGTAGTGGAAAGATTCTTCTTATTTCAGATT
*
86378 TGGTCTTCCCGAAAGGGTAGCGA
66 TGGTCTTCCCGAAAGAGTAGCGA
* * * * * * *
86401 AGCAAATCAATCTCAAGTCTGATCTCCCCAGAAGAGTAGAGGAGAAGATTCTTCTTATTTCTGAT
1 GGTAAATCAATCTCGAGTCTGATCTCCACGGAAGAGTAGTGGA-AAGATTCTTCTTATTTCAGAT
86466 TT
65 TT
86468 AATATTTATA
Statistics
Matches: 131, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
87 8 0.06
88 99 0.76
89 24 0.18
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (88 bp):
GGTAAATCAATCTCGAGTCTGATCTCCACGGAAGAGTAGTGGAAAGATTCTTCTTATTTCAGATT
TGGTCTTCCCGAAAGAGTAGCGA
Done.