Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005513.1 Hibiscus syriacus cultivar Beakdansim tig00012729_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: 61524
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:7353 original size:42 final size:42
Alignment explanation
Indices: 7305--7638 Score: 339
Period size: 43 Copynumber: 7.8 Consensus size: 42
7295 TTGTATAAAC
* * *
7305 AAACGCCGCTATAGATCTGACATTTTGCGGTGTTTGTTCCAA
1 AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAA
* *
7347 AAACGCCGCTATAGATCTGACCTTTTACGGCGTTTGTATCCAA
1 AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCTAA
** *
7390 AAACGCCGCTATAGATCAT-ACCTTTTGCGATGTTTGTTCAAA
1 AAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTTCTAA
** * * *
7432 AAATACCGCTATAGATCTGACTTTTTGCGACGTTTGTTCTGA
1 AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAA
* * * * *
7474 AAATGCCGTTATAGATATTGACCTTTTGCGGCGTTTGTTTTGA
1 AAACGCCGCTATAGAT-CTGACCTTTTGCGGCGTTTGTTCTAA
* * * * *
7517 AAACGCAGCTATAGATCTCGACGTTTTACGACGTTTGTTCAAA
1 AAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCTAA
** *
7560 AAACGATGCTATATATCTCGACCTTTTGCGGCGTTTGTTCTAA
1 AAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCTAA
* *
7603 AAACACCG-TGATAGATCTTGACCTATTGCGGCGTTT
1 AAACGCCGCT-ATAGATC-TGACCTTTTGCGGCGTTT
7639 TTTGTTCTCA
Statistics
Matches: 244, Mismatches: 41, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.00
42 88 0.36
43 153 0.63
44 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (42 bp):
AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAA
Found at i:7404 original size:85 final size:84
Alignment explanation
Indices: 7291--7626 Score: 345
Period size: 85 Copynumber: 3.9 Consensus size: 84
7281 ATATTTGGCA
* * * *
7291 ACGTTTGTAT-AAACAAACGCCGCTATAGATCTGACATTTTGCGGTGTTTGTTCCAAAAACGCCG
1 ACGTTTGT-TCAAA-AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACACCG
7355 CTATAGATCTGACCTTTTACG
64 CTATAGATCTGACCTTTTACG
* * ** * *
7376 GCGTTTGTATCCAAAAACGCCGCTATAGATCAT-ACCTTTTGCGATGTTTGTTCAAAAAATACCG
1 ACGTTTGT-TCAAAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTTCTAAAAACACCG
* *
7440 CTATAGATCTGACTTTTTGCG
64 CTATAGATCTGACCTTTTACG
** * * * * * * *
7461 ACGTTTGTTCTGAAAATGCCGTTATAGATATTGACCTTTTGCGGCGTTTGTTTTGAAAACGCAGC
1 ACGTTTGTTCAAAAAACGCCGCTATAGAT-CTGACCTTTTGCGGCGTTTGTTCTAAAAACACCGC
*
7526 TATAGATCTCGACGTTTTACG
65 TATAGATCT-GACCTTTTACG
** *
7547 ACGTTTGTTCAAAAAACGATGCTATATATCTCGACCTTTTGCGGCGTTTGTTCTAAAAACACCG-
1 ACGTTTGTTCAAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCTAAAAACACCGC
7611 TGATAGATCTTGACCT
65 T-ATAGATC-TGACCT
7627 ATTGCGGCGT
Statistics
Matches: 205, Mismatches: 38, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
84 18 0.09
85 113 0.55
86 73 0.36
87 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (84 bp):
ACGTTTGTTCAAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCTAAAAACACCGCT
ATAGATCTGACCTTTTACG
Found at i:8907 original size:21 final size:22
Alignment explanation
Indices: 8857--8907 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
8847 AAAAAAAGAT
*
8857 CTTCAACTATTTCTTTCTTTACA
1 CTTCAA-TATTTCTTTCTATACA
*
8880 CTT-AATATTTTTTTCTATA-A
1 CTTCAATATTTCTTTCTATACA
8900 CTTCAATA
1 CTTCAATA
8908 GGGTCAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 4 0.16
21 16 0.64
22 2 0.08
23 3 0.12
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (22 bp):
CTTCAATATTTCTTTCTATACA
Found at i:12322 original size:22 final size:23
Alignment explanation
Indices: 12280--12324 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
12270 AACTGCGTGC
*
12280 ACTTTCGGATATTTATTATATTT
1 ACTTTCGGATATTTATAATATTT
12303 ACTTT-GGATATTTCA-AATATTT
1 ACTTTCGGATATTT-ATAATATTT
12325 GGTATGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (23 bp):
ACTTTCGGATATTTATAATATTT
Found at i:12875 original size:39 final size:37
Alignment explanation
Indices: 12805--13081 Score: 217
Period size: 37 Copynumber: 7.4 Consensus size: 37
12795 ATATATATAT
* ** *
12805 ATATATTATATATAGTTTGCAAACGGT-TTTTGAAGATAC
1 ATATATAATATATAGTTTTTAAAC-ATATTTTGAA-A-AC
* *
12844 ATATATAATATATAGTTTCTAAACATATTTTGAAAAT
1 ATATATAATATATAGTTTTTAAACATATTTTGAAAAC
* *
12881 GTATATAATATAAAGTTTTTAAA-ATACTTTTGAAAA-
1 ATATATAATATATAGTTTTTAAACATA-TTTTGAAAAC
* * *
12917 TTATATAATATATAGTTTTTAAAACAT-TTTAGAAAAT
1 ATATATAATATATAGTTTTT-AAACATATTTTGAAAAC
*
12954 ATATATAATATATAGGTTTTAAA-ATCATTTTGAAAAAC
1 ATATATAATATATAGTTTTTAAACAT-ATTTTG-AAAAC
* * *
12992 TTATATAATATATAGTTTTTGAAAACATTTTTTAAATAAAC
1 ATATATAATATATAGTTTTT--AAACATATTTT-GA-AAAC
* * * * *
13033 TTATATAATATACAGTTTTT-TA-ATTTTTTTAAAAC
1 ATATATAATATATAGTTTTTAAACATATTTTGAAAAC
*
13068 TTATATAATATATA
1 ATATATAATATATA
13082 ATTAAAAAAA
Statistics
Matches: 202, Mismatches: 23, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
35 19 0.09
36 33 0.16
37 62 0.31
38 27 0.13
39 28 0.14
40 8 0.04
41 25 0.12
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTAAACATATTTTGAAAAC
Found at i:12886 original size:37 final size:35
Alignment explanation
Indices: 12845--13110 Score: 246
Period size: 37 Copynumber: 7.2 Consensus size: 35
12835 TGAAGATACA
*
12845 TATATAATATATAGTTTCTAAACATATTTTGAAAAT
1 TATATAATATATAGTTTTTAAA-ATATTTTGAAAAT
*
12881 GTATATAATATAAAGTTTTTAAAATACTTTTGAAAAT
1 -TATATAATATATAGTTTTTAAAATA-TTTTGAAAAT
*
12918 TATATAATATATAGTTTTTAAAACATTTTAGAAAAT
1 TATATAATATATAGTTTTTAAAATATTTT-GAAAAT
*
12954 ATATATAATATATAGGTTTTAAAATCATTTTGAAAAACT
1 -TATATAATATATAGTTTTTAAAAT-ATTTTG-AAAA-T
* *
12993 TATATAATATATAGTTTTTGAAAACATTTTTTAAATAAACT
1 TATATAATATATAGTTTTT--AAA-ATATTTT-GA-AAA-T
* * * *
13034 TATATAATATACAGTTTTT-TAATTTTTTTAAAACT
1 TATATAATATATAGTTTTTAAAATATTTTGAAAA-T
* *** *
13069 TATATAATATATAATTAAAAAAACATTTTGGAAAAT
1 TATATAATATATAGTTTTTAAAATATTTT-GAAAAT
13105 TATATA
1 TATATA
13111 GTTTTCAAAA
Statistics
Matches: 195, Mismatches: 21, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
35 23 0.12
36 46 0.24
37 64 0.33
38 28 0.14
39 1 0.01
40 8 0.04
41 25 0.13
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (35 bp):
TATATAATATATAGTTTTTAAAATATTTTGAAAAT
Found at i:12952 original size:73 final size:72
Alignment explanation
Indices: 12845--13110 Score: 286
Period size: 73 Copynumber: 3.6 Consensus size: 72
12835 TGAAGATACA
* *
12845 TATATAATATATAGTTTCT-AAACATATTTTGAAAATGTATATAATATAAAGTTTTTAAAATACT
1 TATATAATATATAGTTTTTAAAACAT-TTTAGAAAAT-TATATAATATAAAGTTTTTAAAAT-CT
12909 TTTGAAAA-T
63 TTTGAAAACT
* *
12918 TATATAATATATAGTTTTTAAAACATTTTAGAAAATATATATAATATATAGGTTTTAAAATCATT
1 TATATAATATATAGTTTTTAAAACATTTTAGAAAAT-TATATAATATAAAGTTTTTAAAATC-TT
12983 TTGAAAAACT
64 TTG-AAAACT
* * *
12993 TATATAATATATAGTTTTTGAAAACATTTTTTAAATAAACTTATATAATATACAGTTTTT-TAAT
1 TATATAATATATAGTTTTT-AAAACA--TTTTAGA-AAA-TTATATAATATAAAGTTTTTAAAAT
* *
13057 TTTTTTAAAACT
61 CTTTTGAAAACT
* *** *
13069 TATATAATATATAATTAAAAAAACATTTTGGAAAATTATATA
1 TATATAATATATAGTTTTTAAAACATTTTAGAAAATTATATA
13111 GTTTTCAAAA
Statistics
Matches: 167, Mismatches: 17, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
71 7 0.04
72 4 0.02
73 59 0.35
74 10 0.06
75 26 0.16
76 27 0.16
77 4 0.02
78 9 0.05
79 20 0.12
80 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (72 bp):
TATATAATATATAGTTTTTAAAACATTTTAGAAAATTATATAATATAAAGTTTTTAAAATCTTTT
GAAAACT
Found at i:13136 original size:33 final size:30
Alignment explanation
Indices: 13083--13173 Score: 121
Period size: 33 Copynumber: 2.9 Consensus size: 30
13073 TAATATATAA
*
13083 TTAAAAAAACATTTTGGAAAATTATATAGTT
1 TTAAAAAAACATTTTTGAAAATTATATAG-T
*
13114 TTCAAAAAAATATTTTTTGAAAATTATATAGT
1 TT-AAAAAAACA-TTTTTGAAAATTATATAGT
13146 TT-AAAAAACATTTTTGAAAATGTATATA
1 TTAAAAAAACATTTTTGAAAAT-TATATA
13174 TAATATTGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
29 11 0.20
30 13 0.24
31 2 0.04
32 11 0.20
33 17 0.31
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (30 bp):
TTAAAAAAACATTTTTGAAAATTATATAGT
Found at i:13197 original size:37 final size:37
Alignment explanation
Indices: 13139--13217 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
13129 TTTGAAAATT
* *
13139 ATATAGTTTAAAAAACATTTTTGAAAATGTATATATA
1 ATATAGTTTAAAAAACATTTTTAAAAAAGTATATATA
* * * * *
13176 ATATTGTTTATAAAACGTTTTTAAAAAAGTTTATATT
1 ATATAGTTTAAAAAACATTTTTAAAAAAGTATATATA
13213 ATATA
1 ATATA
13218 AAAAATATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATAGTTTAAAAAACATTTTTAAAAAAGTATATATA
Found at i:13261 original size:2 final size:2
Alignment explanation
Indices: 13256--13286 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13246 TTTTATTACT
13256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13287 TCTTCAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14270 original size:16 final size:17
Alignment explanation
Indices: 14251--14283 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14241 GTATTTTTAA
14251 TTTTGACT-TTTAATTT
1 TTTTGACTGTTTAATTT
*
14267 TTTTGCCTGTTTAATTT
1 TTTTGACTGTTTAATTT
14284 AATCACACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.15, C:0.09, G:0.09, T:0.67
Consensus pattern (17 bp):
TTTTGACTGTTTAATTT
Found at i:14319 original size:18 final size:18
Alignment explanation
Indices: 14296--14352 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
14286 TCACACTTTG
**
14296 TTTATTTATTTTGGTTAT
1 TTTATTTATTTTACTTAT
14314 TTTATTTATTTTACTTAT
1 TTTATTTATTTTACTTAT
14332 TTTATTTTATTTTACTT-T
1 TTTA-TTTATTTTACTTAT
14350 TTT
1 TTT
14353 TTCGAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 24 0.67
19 12 0.33
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTATTTATTTTACTTAT
Found at i:14320 original size:5 final size:5
Alignment explanation
Indices: 14310--14354 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
14300 TTTATTTTGG
*
14310 TTATT TTA-T TTATT TTA-C TTATT TTATT TTATT TTACTT TT-TT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTA-TT TTATT TT
14355 CGAATTTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
4 11 0.31
5 20 0.57
6 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:14322 original size:9 final size:9
Alignment explanation
Indices: 14296--14345 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
14286 TCACACTTTG
14296 TTTATTTAT
1 TTTATTTAT
**
14305 TTTGGTTAT
1 TTTATTTAT
14314 TTTATTTAT
1 TTTATTTAT
*
14323 TTTACTTAT
1 TTTATTTAT
14332 TTTATTTTAT
1 TTTA-TTTAT
14342 TTTA
1 TTTA
14346 CTTTTTTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
9 26 0.76
10 8 0.24
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:14353 original size:9 final size:10
Alignment explanation
Indices: 14310--14353 Score: 58
Period size: 9 Copynumber: 4.7 Consensus size: 10
14300 TTTATTTTGG
14310 TTATTTTA-T
1 TTATTTTACT
14319 TTATTTTAC-
1 TTATTTTACT
*
14328 TTATTTTATT
1 TTATTTTACT
14338 TTATTTTACT
1 TTATTTTACT
14348 TT-TTTT
1 TTATTTT
14354 TCGAATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 20 0.65
10 11 0.35
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (10 bp):
TTATTTTACT
Found at i:14435 original size:15 final size:14
Alignment explanation
Indices: 14382--14433 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
14372 AGAATCTAAC
14382 ATTTTTTTCTTTTT
1 ATTTTTTTCTTTTT
*
14396 AGTTTTTTCTTCTTTT
1 ATTTTTTTC-T-TTTT
*
14412 ATCTTTTATCTTTTT
1 AT-TTTTTTCTTTTT
14427 ATTTTTT
1 ATTTTTT
14434 ATTTATTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 12 0.39
15 7 0.23
16 6 0.19
17 6 0.19
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.79
Consensus pattern (14 bp):
ATTTTTTTCTTTTT
Found at i:14436 original size:7 final size:7
Alignment explanation
Indices: 14382--14437 Score: 51
Period size: 7 Copynumber: 7.6 Consensus size: 7
14372 AGAATCTAAC
14382 ATTTTTT
1 ATTTTTT
14389 -TCTTTTT
1 AT-TTTTT
14396 AGTTTTTT
1 A-TTTTTT
*
14404 CTTCTTTT
1 ATT-TTTT
*
14412 ATCTTTT
1 ATTTTTT
14419 ATCTTTTT
1 AT-TTTTT
14427 ATTTTTT
1 ATTTTTT
14434 ATTT
1 ATTT
14438 ATTGATTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
6 1 0.03
7 22 0.55
8 16 0.40
9 1 0.03
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:18173 original size:95 final size:95
Alignment explanation
Indices: 18004--18190 Score: 261
Period size: 95 Copynumber: 2.0 Consensus size: 95
17994 TATAATATTA
* * *
18004 TATATATACAATAAAGCTTGAGTTATCCCTCCTAGAGCAATTGGTTAAACGCCCTAACTTTATAG
1 TATATATACAATAAAGCTTGAGCTATCCCTCCTAGAGCAATTGATTAAACGCCCCAACTTTATAG
* * *
18069 ATAATATTCAGCTAGCTTGATAAAGGTAAT
66 ATAAGATTCAGCTAACCTGATAAAGGTAAT
* *
18099 TATACTATACAATAAAGCTTGAGCTGTCCCT-CTA-AGGCAATTGATTAAACGCCCCGACTTTAT
1 TATA-TATACAATAAAGCTTGAGCTATCCCTCCTAGA-GCAATTGATTAAACGCCCCAACTTTAT
*
18162 GGATAAGATTCAGCTAACCTGATAAAGGT
64 AGATAAGATTCAGCTAACCTGATAAAGGT
18191 GTTTATGTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
94 1 0.01
95 56 0.69
96 24 0.30
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (95 bp):
TATATATACAATAAAGCTTGAGCTATCCCTCCTAGAGCAATTGATTAAACGCCCCAACTTTATAG
ATAAGATTCAGCTAACCTGATAAAGGTAAT
Found at i:19661 original size:164 final size:160
Alignment explanation
Indices: 19403--20396 Score: 943
Period size: 164 Copynumber: 6.0 Consensus size: 160
19393 TGCAACTTAG
* ** *
19403 CTCAAGGCCAGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGGTTAGCTCCAAGGCA
1 CTCAAGGCGAGAAGGGCTATCTGCCA--AAGACCTTCGAGTTC-ACTACACTCAGCTCCAAGGCA
* * *
19468 CATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAGACCTCCGAGTTTGATTAC
63 CATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTTGACTAC
* * * *
19533 ACTCAGCTTCGAGGGCACATCATTTGCAGAATAA
128 GCTCAGC-TCCAAGGCACATCATTTGCAGCATAA
* * * *
19567 CTCAAGGCTATAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT-ACTACGCTCAGCTCCAAGGC
1 CTCAAGGCGAGAAGGGCTATCTG----CCAAAGACCTTCGAGTTCACTACACTCAGCTCCAAGGC
* * *
19631 ACATCATTTGCAGCATAGCATAAGTCGAGAAGGGCTATCTGCC-AAAGACCCTCGAGTTTGACTA
62 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTTGACTA
* * *
19695 CGCTCAGCTTCTAGGGCACATCATTTACAGCATAA
127 CGCTCAGC-TCCAAGGCACATCATTTGCAGCATAA
* * * * * *
19730 CTCAAGGCTAGAAGAGTTATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGC-CCTTAG
1 CTCAAGGCGAGAAGGGCTATC--T-GCC-AAAGACCTTCGAGTTC-ACTACACTCAGCTCC-AAG
* * * * *
19794 GCATATCATTTGCAGTATAACTTAAGTCGAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTC
60 GCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC-A--AAAGACCTTCGAGTTT
* * *
19859 GACTATGCTCAGCTCCAAGGAACATCATTTGCAGCATAG
122 GACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAA
* * * * ***
19898 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTGGAGAGCAC
1 CTCAAGGCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTC-ACTACACTCAGCTCCAAG-GCAC
* * * * * * * *
19963 ATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTAGACTA
64 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C-CAAAAGACCTTCGAGTTTGACTA
* * * *
20028 AGCTCAGCTCTAAGGCACACCATTTGCAGAATAA
127 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAA
* * * *
20062 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACC
1 CTCAAGGCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTC-ACTACACTCAGCTCCAAGGCA-C
* * * *
20127 AACATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGATT
64 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC-A--AAAGACCTTCGAGTTTGACT
* *
20192 ATGCTCAGCTCCAAGGCACATCATTTGCAGCATAG
126 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAA
* * * * * * * *
20227 CTTAAGTCGAGAAGGGATATCTGCCAAAGACCTTCGATTTCGATTATACCCAGCTCAAAGGCACC
1 CTCAAGGCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTC-ACTACACTCAGCTCCAAGGCA-C
* * * *
20292 ATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGTCTTC-AAAGACCTTTGAGTTCGACT
64 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--CAAAAGACCTTCGAGTTTGACT
* * * *
20356 ACGCTCAACTCCTAGGCACTATCATTTGTAGCATAG
126 ACGCTCAGCTCCAAGGCAC-ATCATTTGCAGCATAA
20392 CTCAA
1 CTCAA
20397 AGCAAGAGGG
Statistics
Matches: 710, Mismatches: 93, Indels: 53
0.83 0.11 0.06
Matches are distributed among these distances:
162 3 0.00
163 87 0.12
164 282 0.40
165 253 0.36
166 17 0.02
167 1 0.00
168 41 0.06
169 26 0.04
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (160 bp):
CTCAAGGCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCACTACACTCAGCTCCAAGGCACAT
CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAAGACCTTCGAGTTTGACTACGCT
CAGCTCCAAGGCACATCATTTGCAGCATAA
Found at i:20135 original size:329 final size:326
Alignment explanation
Indices: 19403--20362 Score: 1108
Period size: 329 Copynumber: 2.9 Consensus size: 326
19393 TGCAACTTAG
* * * *
19403 CTCAAGGCCAGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGGTTAGCTCCAAGGCA
1 CTCAAGGCGAGAAGGGCTATCTGCCA--AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCA
* * *
19468 CATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-A--AAAGACCTCCGAGTTTGAT
64 CATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGAT
** * * * * * * * * *
19530 TACACTCAGCTTCGAGGGCACATCATTTGCAGAATAACTCAAGGCTATAAGGGTTATCTGCCAAC
129 TATGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTG----C
* * * *
19595 CAAAGACCTTCGAGTT--ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCATAAGTCG
189 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGC-TAAGTCA
* * * *
19658 AGAAGGGCTATCTG--CCAAAGACCCTCGAGTTTGACTACGCTCAGCTTCTAGGGCACATCATTT
253 AGAAGGGCTATCTGTCCCAAAGACCTTCGAGTTAGACTACGCTCAGCTTCTAAGGCACACCATTT
*
19721 ACAGCATAA
318 ACAGAATAA
* * * * * **
19730 CTCAAGGCTAGAAGAGTTATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCCCTTAGG
1 CTCAAGGCGAGAAGGGCTATC--T-GCC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGG
* * * *
19795 CATATCATTTGCAGTATAACTTAAGTCGAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCG
62 CACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTG
* * *
19860 ACTATGCTCAGCTCCAAGGAACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
127 ATTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAA
* *** * * * * *
19925 AGACCCTCGAGTTCGATTACACTCAGCTTGGAGAGCACATCATTTACAACATAACTCAAGGCTAG
192 AGACCTTCGAGTTCGATTACACTCAGCTCAAAG-GCACATCATTTGCAGCATAGCT-AAGTCAAG
* * *
19990 AAGGGTTATCTGTCACCAAAGACCTTCGAGTTAGACTAAGCTCAGC-TCTAAGGCACACCATTTG
255 AAGGGCTATCTGTC-CCAAAGACCTTCGAGTTAGACTACGCTCAGCTTCTAAGGCACACCATTTA
20054 CAGAATAA
319 CAGAATAA
* * * *
20062 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACC
1 CTCAAGGCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCA-C
* *
20127 AACATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGATT
65 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGATT
20192 ATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGA
130 ATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGA
* * *
20257 CCTTCGATTTCGATTATACCCAGCTCAAAGGCACCATCATTTGCAGCATAGCTTAAGTCAAGAAG
195 CCTTCGAGTTCGATTACACTCAGCTCAAAGGCA-CATCATTTGCAGCATAGC-TAAGTCAAGAAG
* * *
20322 GGCTATCTGTCTTCAAAGACCTTTGAGTTCGACTACGCTCA
258 GGCTATCTGTC-CCAAAGACCTTCGAGTTAGACTACGCTCA
20363 ACTCCTAGGC
Statistics
Matches: 530, Mismatches: 86, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
327 34 0.06
328 36 0.07
329 290 0.55
330 40 0.08
331 40 0.08
332 62 0.12
333 28 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (326 bp):
CTCAAGGCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACA
TCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGATTA
TGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGAC
CTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTAAGTCAAGAAGGGC
TATCTGTCCCAAAGACCTTCGAGTTAGACTACGCTCAGCTTCTAAGGCACACCATTTACAGAATA
A
Found at i:20200 original size:413 final size:411
Alignment explanation
Indices: 19420--20362 Score: 1240
Period size: 413 Copynumber: 2.3 Consensus size: 411
19410 CCAGAAGGGC
* * * *
19420 TATCTGCCACC-AAGACCTTCGAGTTCGACTACGGTTAGCTCCAAGGCACATCATTTGCAGCATA
1 TATCTGCCACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGAACATCATTTGCAGCATA
* *
19484 GCTTAAGTCGAGAAGGGCTATCTGCCAAAAGA-CCTCCGAGTTTGATTACACTCAGCTTCGAGGG
66 GCTTAAGTCGAGAAGGGCTATCTGCC-AAAGACCCT-CGAGTTCGATTACACTCAGCTTCGAGAG
* *
19548 CACATCATTTGCAGAATAACTCAAGGCTATAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTAC
129 CACATCATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTAC
* * * *
19613 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCATAAGTCGAGAAGGGCTATCTGCCAAAG
194 TAAGCTCAGCTCCAAGGCACACCATTTGCAGAATAACATAAGTCGAGAAGGGCTATCTGCCAAAG
* * * * * * *
19678 ACCCTCGAGTTTGACTACGCTCAGCTTCTAGGGCACATCATTTACAGCATAACTCAAGGCTAGAA
259 ACCCTCGAGTTCGACTACACTCAGCTTCAAAGGCACAACATTTACAACATAACTCAAGGCGAGAA
* * *
19743 GAGTTATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGC-CCTTAGGCATATCATTTGC
324 GAGTTATCTACCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCC-AAGGCACATCATTTGC
* *
19807 AGTATAACTTAAGTCGAGAAAGGT
388 AGCATAACTTAAGTCGAGAAAGGA
19831 TATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGAACATCATTTGCAGCAT
1 TATCTGCC-ACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGAACATCATTTGCAGCAT
*
19896 AGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTGGAGAGC
65 AGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGAGC
*
19961 ACATCATTTACA-ACATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTAG
130 ACATCATTTACAGA-ATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT--
* *
20024 ACTAAGCTCAGCTCTAAGGCACACCATTTGCAGAATAACTTAAGTCGAGAAGGGCTATCTGCCAA
192 ACTAAGCTCAGCTCCAAGGCACACCATTTGCAGAATAACATAAGTCGAGAAGGGCTATCTGCCAA
* * * * *
20089 AGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACCAACATTTGCAACATAACTTAAGTCGA
257 AGACCCTCGAGTTCGACTACACTCAGCTTCAAAGGCA-CAACATTTACAACATAACTCAAGGCGA
* * * * *
20153 GAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTTGATTATGCTCAGCTCCAAGGCACATCATT
321 GAAGAGTTATCTACC-ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
20217 TGCAGCATAGCTTAAGTCGAGAAGGGA
385 TGCAGCATAACTTAAGTCGAGAAAGGA
* * * * * *
20244 TATCTG---CCAAAGACCTTCGATTTCGATTATACCCAGCTCAAAGGCACCATCATTTGCAGCAT
1 TATCTGCCACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGG-AACATCATTTGCAGCAT
* * * * *
20306 AGCTTAAGTCAAGAAGGGCTATCTGTCTTCAAAGACCTTTGAGTTCGACTACGCTCA
65 AGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCGATTACACTCA
20363 ACTCCTAGGC
Statistics
Matches: 468, Mismatches: 51, Indels: 24
0.86 0.09 0.04
Matches are distributed among these distances:
409 33 0.07
410 40 0.09
411 28 0.06
412 79 0.17
413 283 0.60
414 5 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (411 bp):
TATCTGCCACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGAACATCATTTGCAGCATA
GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGAGCA
CATCATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTACTA
AGCTCAGCTCCAAGGCACACCATTTGCAGAATAACATAAGTCGAGAAGGGCTATCTGCCAAAGAC
CCTCGAGTTCGACTACACTCAGCTTCAAAGGCACAACATTTACAACATAACTCAAGGCGAGAAGA
GTTATCTACCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGC
ATAACTTAAGTCGAGAAAGGA
Found at i:20972 original size:2 final size:2
Alignment explanation
Indices: 20965--20996 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20955 TTTCGTCCAC
20965 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
20997 TTGCAAACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21060 original size:35 final size:34
Alignment explanation
Indices: 21019--21282 Score: 167
Period size: 35 Copynumber: 7.2 Consensus size: 34
21009 TTTGAAGATA
21019 TATATATAATATAGTTTCTAAAAACATTTTAAAAAT
1 TATATAT-ATATAGTTT-TAAAAACATTTTAAAAAT
* *
21055 GTATATAATATATAGTTTTTAAAAA-ACTTTTGAAAAC
1 -TATAT-ATATATAG-TTTTAAAAACA-TTTTAAAAAT
*
21092 TATATAATATATAGTTTTTAAAACATTTTAGAAAA-
1 TATAT-ATATATAGTTTTAAAAACATTTTA-AAAAT
*
21127 TATATAATATATAGTTTTAAAATCATTTTGAAAAACT
1 TATAT-ATATATAGTTTTAAAAACATTTT-AAAAA-T
***
21164 TATATA-ATATAGTTTTTGAAAATTTTTTTTAAATAAACT
1 TATATATATATAG-TTTT-AAAA-ACATTTT-AA-AAA-T
** *
21203 TATATATATATAGTTTTTGAAAATATTTTTTTAAAACT
1 TATATATATATAG-TTTT-AAAA-A-CATTTTAAAAAT
* * *
21241 TATATA-ATATAATTTAAAAAAAACATTTTGGAAAAT
1 TATATATATATAGTTT--TAAAAACATTTT-AAAAAT
21277 TATATA
1 TATATA
21283 GTTTTCAAAA
Statistics
Matches: 193, Mismatches: 17, Indels: 35
0.79 0.07 0.14
Matches are distributed among these distances:
35 53 0.27
36 40 0.21
37 43 0.22
38 19 0.10
39 13 0.07
40 19 0.10
41 6 0.03
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (34 bp):
TATATATATATAGTTTTAAAAACATTTTAAAAAT
Found at i:21186 original size:37 final size:36
Alignment explanation
Indices: 21021--21282 Score: 186
Period size: 37 Copynumber: 7.2 Consensus size: 36
21011 TGAAGATATA
*
21021 TATATAATATAGTTTCTAAAAACATTTT-AAAAA-T
1 TATATAATATAGTTTTTAAAAACATTTTGAAAAACT
21055 GTATATAATATATAGTTTTTAAAAA-ACTTTTG-AAAAC-
1 -TATAT-A-ATATAGTTTTTAAAAACA-TTTTGAAAAACT
21092 TATATAATATATAGTTTTT-AAAACATTTT-AGAAAA--
1 TATAT-A-ATATAGTTTTTAAAAACATTTTGA-AAAACT
*
21127 TATATAATATA-TAGTTTTAAAATCATTTTGAAAAACT
1 TATATAATATAGT--TTTTAAAAACATTTTGAAAAACT
*** *
21164 TATATAATATAGTTTTTGAAAATTTTTTTTAAATAAACT
1 TATATAATATAGTTTTT-AAAA-ACATTTTGAA-AAACT
* * **
21203 TATATATATATAGTTTTTGAAAATATTTTTTTAAAACT
1 TATATA-ATATAGTTTTTAAAAACA-TTTTGAAAAACT
* ** *
21241 TATATAATATAATTTAAAAAAAACATTTTGGAAAA-T
1 TATATAATATAGTTT-TTAAAAACATTTTGAAAAACT
21277 TATATA
1 TATATA
21283 GTTTTCAAAA
Statistics
Matches: 189, Mismatches: 17, Indels: 41
0.77 0.07 0.17
Matches are distributed among these distances:
32 1 0.01
33 5 0.03
34 5 0.03
35 31 0.16
36 38 0.20
37 54 0.29
38 25 0.13
39 19 0.10
40 11 0.06
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (36 bp):
TATATAATATAGTTTTTAAAAACATTTTGAAAAACT
Found at i:21202 original size:39 final size:37
Alignment explanation
Indices: 21158--21251 Score: 145
Period size: 40 Copynumber: 2.5 Consensus size: 37
21148 ATCATTTTGA
21158 AAAACTTATATAATATAGTTTTTGAAAAT-TTTTTTT
1 AAAACTTATATAATATAGTTTTTGAAAATATTTTTTT
21194 AAATAAACTTATATATATATAGTTTTTGAAAATATTTTTTT
1 --A-AAACTTATATA-ATATAGTTTTTGAAAATATTTTTTT
21235 AAAACTTATATAATATA
1 AAAACTTATATAATATA
21252 ATTTAAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
37 5 0.09
38 12 0.23
39 12 0.23
40 17 0.32
41 7 0.13
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (37 bp):
AAAACTTATATAATATAGTTTTTGAAAATATTTTTTT
Found at i:21302 original size:33 final size:32
Alignment explanation
Indices: 21247--21349 Score: 136
Period size: 33 Copynumber: 3.2 Consensus size: 32
21237 AACTTATATA
* *
21247 ATATAATTT-AAAAAAAACATTTTGGAAAATT
1 ATATAGTTTAAAAAAAAACATTTTTGAAAATT
* *
21278 ATATAGTTTTCAAAAAAAATATTTTTTGAAAATT
1 ATATAG-TTTAAAAAAAAACA-TTTTTGAAAATT
21312 ATATAGTTTAAAAAAAAACATTTTTGAAAATTT
1 ATATAGTTTAAAAAAAAACATTTTTGAAAA-TT
21345 ATATA
1 ATATA
21350 TAATATTGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
31 5 0.08
32 13 0.21
33 28 0.44
34 17 0.27
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (32 bp):
ATATAGTTTAAAAAAAAACATTTTTGAAAATT
Found at i:21309 original size:34 final size:34
Alignment explanation
Indices: 21229--21349 Score: 122
Period size: 33 Copynumber: 3.5 Consensus size: 34
21219 TTGAAAATAT
* * *
21229 TTTTTTAAAACTTATATAATATAATTTAAAAAAAACA
1 TTTTTGAAAACTTATATAGT-T--TTAAAAAAAAACA
* * *
21266 TTTTGGAAAA-TTATATAGTTTTCAAAAAAAATA
1 TTTTTGAAAACTTATATAGTTTTAAAAAAAAACA
21299 TTTTTTGAAAA-TTATATAG-TTTAAAAAAAAACA
1 -TTTTTGAAAACTTATATAGTTTTAAAAAAAAACA
*
21332 TTTTTGAAAATTTATATA
1 TTTTTGAAAACTTATATA
21350 TAATATTGTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
32 10 0.14
33 30 0.41
34 17 0.23
35 1 0.01
36 8 0.11
37 8 0.11
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (34 bp):
TTTTTGAAAACTTATATAGTTTTAAAAAAAAACA
Found at i:21393 original size:9 final size:9
Alignment explanation
Indices: 21376--21412 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
21366 AAAGTTTATA
*
21376 TTATATTTT
1 TTATTTTTT
21385 TTATTTTTT
1 TTATTTTTT
*
21394 TTATTTTTA
1 TTATTTTTT
21403 TTATTTTTT
1 TTATTTTTT
21412 T
1 T
21413 ATTATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTATTTTTT
Found at i:21402 original size:15 final size:16
Alignment explanation
Indices: 21382--21411 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21372 TATATTATAT
21382 TTTTTATT-TTTTTTA
1 TTTTTATTATTTTTTA
21397 TTTTTATTATTTTTT
1 TTTTTATTATTTTTT
21412 TATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTATTATTTTTTA
Found at i:21420 original size:2 final size:2
Alignment explanation
Indices: 21415--21457 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
21405 ATTTTTTTAT
21415 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21457 T
1 T
21458 TCTTCAGGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22484 original size:18 final size:18
Alignment explanation
Indices: 22461--22517 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
22451 CACACTTTTG
**
22461 TTTATTTATTTTGGTTAT
1 TTTATTTATTTTACTTAT
22479 TTTATTTATTTTACTTAT
1 TTTATTTATTTTACTTAT
22497 TTTATTTTATTTTACTT-T
1 TTTA-TTTATTTTACTTAT
22515 TTT
1 TTT
22518 TTTCTGAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 24 0.67
19 12 0.33
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (18 bp):
TTTATTTATTTTACTTAT
Found at i:22485 original size:5 final size:5
Alignment explanation
Indices: 22475--22519 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
22465 TTTATTTTGG
*
22475 TTATT TTA-T TTATT TTA-C TTATT TTATT TTATT TTACTT TT-TT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTA-TT TTATT TT
22520 TCTGAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
4 11 0.31
5 20 0.57
6 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:22487 original size:9 final size:9
Alignment explanation
Indices: 22461--22510 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
22451 CACACTTTTG
22461 TTTATTTAT
1 TTTATTTAT
**
22470 TTTGGTTAT
1 TTTATTTAT
22479 TTTATTTAT
1 TTTATTTAT
*
22488 TTTACTTAT
1 TTTATTTAT
22497 TTTATTTTAT
1 TTTA-TTTAT
22507 TTTA
1 TTTA
22511 CTTTTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
9 26 0.76
10 8 0.24
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:22518 original size:9 final size:10
Alignment explanation
Indices: 22475--22518 Score: 58
Period size: 9 Copynumber: 4.7 Consensus size: 10
22465 TTTATTTTGG
22475 TTATTTTA-T
1 TTATTTTACT
22484 TTATTTTAC-
1 TTATTTTACT
*
22493 TTATTTTATT
1 TTATTTTACT
22503 TTATTTTACT
1 TTATTTTACT
22513 TT-TTTT
1 TTATTTT
22519 TTCTGAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 20 0.65
10 11 0.35
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (10 bp):
TTATTTTACT
Found at i:22603 original size:15 final size:14
Alignment explanation
Indices: 22550--22601 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
22540 AGAATCTAAC
22550 ATTTTTTTCTTTTT
1 ATTTTTTTCTTTTT
*
22564 AGTTTTTTCTTATTTT
1 ATTTTTTTC-T-TTTT
*
22580 ATCTTTTATCTTTTT
1 AT-TTTTTTCTTTTT
22595 ATTTTTT
1 ATTTTTT
22602 ATTTATTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 12 0.39
15 7 0.23
16 6 0.19
17 6 0.19
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.79
Consensus pattern (14 bp):
ATTTTTTTCTTTTT
Found at i:22604 original size:7 final size:7
Alignment explanation
Indices: 22550--22605 Score: 51
Period size: 7 Copynumber: 7.6 Consensus size: 7
22540 AGAATCTAAC
22550 ATTTTTT
1 ATTTTTT
22557 -TCTTTTT
1 AT-TTTTT
22564 AGTTTTTT
1 A-TTTTTT
*
22572 CTTATTTT
1 ATT-TTTT
*
22580 ATCTTTT
1 ATTTTTT
22587 ATCTTTTT
1 AT-TTTTT
22595 ATTTTTT
1 ATTTTTT
22602 ATTT
1 ATTT
22606 ATTGATTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
6 1 0.03
7 22 0.55
8 16 0.40
9 1 0.03
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:23518 original size:30 final size:30
Alignment explanation
Indices: 23482--23545 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
23472 GATGAGCATT
23482 AACGATGAATATTATTAAATTAATTTATAA
1 AACGATGAATATTATTAAATTAATTTATAA
23512 AACGATGAATATTATTAAATTAATTTATAA
1 AACGATGAATATTATTAAATTAATTTATAA
23542 AACG
1 AACG
23546 TTAAAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.38
Consensus pattern (30 bp):
AACGATGAATATTATTAAATTAATTTATAA
Found at i:23742 original size:15 final size:15
Alignment explanation
Indices: 23722--23759 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
23712 CTTGAAGCTC
* *
23722 TCGTCGTCGTCGCTG
1 TCGTCGCCGTCACTG
23737 TCGTCGCCGTCACTG
1 TCGTCGCCGTCACTG
23752 TCGTCGCC
1 TCGTCGCC
23760 ATCGAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.03, C:0.39, G:0.29, T:0.29
Consensus pattern (15 bp):
TCGTCGCCGTCACTG
Found at i:32328 original size:20 final size:20
Alignment explanation
Indices: 32305--32364 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
32295 TAAAGGTATG
*
32305 GGTCAACGGTCAAAGTCAAT
1 GGTCAATGGTCAAAGTCAAT
* *
32325 GGTCAATGGTCAGAGTTAAT
1 GGTCAATGGTCAAAGTCAAT
* *
32345 AGTCAATGATCAATAGTCAA
1 GGTCAATGGTCAA-AGTCAA
32365 CAATCCGATT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (20 bp):
GGTCAATGGTCAAAGTCAAT
Found at i:49288 original size:31 final size:31
Alignment explanation
Indices: 49206--49290 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
49196 GGACTAGTGG
* * *
49206 CTAAAAA-GTAAAATTTGAAAA-TTTAGGGC
1 CTAAAAATGTAAATTTTAAAAAGTTTAGGGA
* *
49235 CT-AAAGTGTAAACTTATAAAAAGTTTAGGGA
1 CTAAAAATGTAAA-TTTTAAAAAGTTTAGGGA
*
49266 CTAAAAATGTAAATTTTCAAAAGTT
1 CTAAAAATGTAAATTTTAAAAAGTT
49291 ATGTATTGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 3 0.07
29 7 0.16
30 6 0.14
31 19 0.43
32 9 0.20
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (31 bp):
CTAAAAATGTAAATTTTAAAAAGTTTAGGGA
Found at i:49679 original size:29 final size:30
Alignment explanation
Indices: 49628--49689 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
49618 AAATTTTGTC
* **
49628 TAGTGACTAAAGTGTAAGTTTTG-AAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
*
49657 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
49687 TAG
1 TAG
49690 GGACCAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (30 bp):
TAGTGACTAAAGTATAAACTTTGAAAAGTT
Found at i:49780 original size:17 final size:18
Alignment explanation
Indices: 49758--49791 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
49748 ATTACAACAG
49758 AGATTTTAGT-GGGAATC
1 AGATTTTAGTAGGGAATC
*
49775 AGATTTTGGTAGGGAAT
1 AGATTTTAGTAGGGAAT
49792 TTTGTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.03, G:0.32, T:0.35
Consensus pattern (18 bp):
AGATTTTAGTAGGGAATC
Found at i:59746 original size:25 final size:24
Alignment explanation
Indices: 59708--59764 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
59698 ATTGTTAAAA
59708 TATTAAAA--ATATTAATATTAT-T
1 TATTAAAATTATATTAA-ATTATAT
*
59730 TATGTAAAATTATATTAAATTTTAT
1 TAT-TAAAATTATATTAAATTATAT
59755 TATTAAAATT
1 TATTAAAATT
59765 TTATAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 3 0.10
23 5 0.17
24 11 0.37
25 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TATTAAAATTATATTAAATTATAT
Found at i:60299 original size:31 final size:31
Alignment explanation
Indices: 60229--60306 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
60219 ACTTTTAAAC
** *
60229 TTGCAATACAGTCCCCTAACATTTAGTATGT
1 TTGCAATATGGTCCCCCAACATTTAGTATGT
*
60260 TTGCAATATGGTCCCCCAACATTTAGTTTGT
1 TTGCAATATGGTCCCCCAACATTTAGTATGT
*
60291 TTGCAATATGATCCCC
1 TTGCAATATGGTCCCC
60307 GACCTTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTATGT
Done.