Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000919.1 Hibiscus syriacus cultivar Beakdansim tig00001832_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: 127907
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:3468 original size:3 final size:3
Alignment explanation
Indices: 3462--3521 Score: 75
Period size: 3 Copynumber: 19.0 Consensus size: 3
3452 TTTTTTCAGT
* *
3462 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
3508 TATA TATA TTA TTA
1 T-TA T-TA TTA TTA
3522 AACAAAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 41 0.79
4 11 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:4712 original size:10 final size:12
Alignment explanation
Indices: 4691--4723 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
4681 ATTTAATCAC
4691 TGTTTATATATA
1 TGTTTATATATA
4703 TGTTTATATATA
1 TGTTTATATATA
4715 TGTTTATAT
1 TGTTTATAT
4724 TTTAGGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (12 bp):
TGTTTATATATA
Found at i:4990 original size:2 final size:2
Alignment explanation
Indices: 4985--5045 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
4975 TTAGTTTATC
4985 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
5027 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
5046 TTGTTTAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5308 original size:141 final size:140
Alignment explanation
Indices: 5058--5316 Score: 337
Period size: 141 Copynumber: 1.8 Consensus size: 140
5048 GTTTAAATAA
* ** * *
5058 TAATGTTTATTTATTTCTAATATATAAGAAAAGGGCTGTCTTAAAGCACCTAGAAGTCTTTTTTT
1 TAATATTTATTTATTTCTAATATATAAGAAAAGAACTGTCTTAAAGCACCTAGAAGTCCTTTTCT
* *
5123 GATATTCTTAAATAAATAAATATACTATTTTTATATAAATTATATATATTAATTTATTTTAATAG
66 GATATTCTTAAATAAATAAATATACTATATTTATAT-AATTATATAAATTAATTTATTTTAATAG
5188 AAATGTTTTAT
130 AAATGTTTTAT
* *
5199 TAATATTTATTTATTTTTTAATAT-TAAGAAATGAACTGTCTTAAAGCACCTAGAAGTCCTTTTC
1 TAATATTTATTTA-TTTCTAATATATAAGAAAAGAACTGTCTTAAAGCACCTAGAAGTCCTTTTC
**
5263 TGATATT-TCTAAAGTAAATAAATATTTTATAAATTTATAT-A-TATATAAATTAAT
65 TGATATTCT-TAAA-TAAATAAATATACTAT--ATTTATATAATTATATAAATTAAT
5317 AGATTTTCTT
Statistics
Matches: 102, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
140 1 0.01
141 70 0.69
142 24 0.24
144 7 0.07
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (140 bp):
TAATATTTATTTATTTCTAATATATAAGAAAAGAACTGTCTTAAAGCACCTAGAAGTCCTTTTCT
GATATTCTTAAATAAATAAATATACTATATTTATATAATTATATAAATTAATTTATTTTAATAGA
AATGTTTTAT
Found at i:13864 original size:72 final size:74
Alignment explanation
Indices: 13708--13958 Score: 236
Period size: 75 Copynumber: 3.4 Consensus size: 74
13698 ATCAACAAGA
* * * * * * * * **
13708 AGCAAATATTGGGGTATGCTGAAAACCTATTTCAATCATAATCACGAACATTGATGCATTTTGAA
1 AGCAAATGTTGGGGCATACTGAAAGCCCATTTCAAT-AGAATCAAGAATATTGACACATTTTGAA
* *** *
13773 TGTTTACGTC
65 CGTTTGTATT
* * * ** *
13783 AACAAATGTTGGGGCATACTGCAAGCCCATTTCAAT-TAAT-TGGAATATTGGCACATTTTGAAC
1 AGCAAATGTTGGGGCATACTGAAAGCCCATTTCAATAGAATCAAGAATATTGACACATTTTGAAC
13846 GTTTGTATT
66 GTTTGTATT
* *
13855 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATGTTGACACATTTTGAA
1 AGCAAATGTTGGGGCATACTGAAAGCCCATTTCAAT-AGAATCAAGAATATTGACACATTTTGAA
13920 CGTTTGTATT
65 CGTTTGTATT
* * *
13930 AGCCAATGTTGGGGCATGCTGAAGGCCCA
1 AGCAAATGTTGGGGCATACTGAAAGCCCA
13959 CATCGTCATA
Statistics
Matches: 145, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
72 54 0.37
73 4 0.03
74 3 0.02
75 84 0.58
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (74 bp):
AGCAAATGTTGGGGCATACTGAAAGCCCATTTCAATAGAATCAAGAATATTGACACATTTTGAAC
GTTTGTATT
Found at i:13938 original size:75 final size:72
Alignment explanation
Indices: 13785--13958 Score: 240
Period size: 75 Copynumber: 2.4 Consensus size: 72
13775 TTTACGTCAA
* * * ** *
13785 CAAATGTTGGGGCATACTGCAAGCCCATTTCAATTAATTGGAATATTGGCACATTTTGAACGTTT
1 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATGAATAAGAATATTGACACATTTTGAACGTTT
13850 GTATTAG
66 GTATTAG
*
13857 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATGTTGACACATTTTGAACG
1 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAAT--GAAT-AAGAATATTGACACATTTTGAACG
13922 TTTGTATTAG
63 TTTGTATTAG
* *
13932 CCAATGTTGGGGCATGCTGAAGGCCCA
1 CAAATGTTGGGGCATGCTGAAAGCCCA
13959 CATCGTCATA
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
72 32 0.36
74 3 0.03
75 55 0.61
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (72 bp):
CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATGAATAAGAATATTGACACATTTTGAACGTTT
GTATTAG
Found at i:15140 original size:22 final size:22
Alignment explanation
Indices: 15115--15191 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
15105 ATCTACACTT
15115 TTCAAAGATGATAGAATCTTTC
1 TTCAAAGATGATAGAATCTTTC
** * *
15137 TTCAAAGATGATAGCCTATCTC
1 TTCAAAGATGATAGAATCTTTC
* * *
15159 TTTAAAGATAATAGATTCTCTT-
1 TTCAAAGATGATAGAATCT-TTC
15181 TTCAAAGATGA
1 TTCAAAGATGA
15192 AAGCTTTATT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
22 41 0.98
23 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGATAGAATCTTTC
Found at i:15913 original size:45 final size:45
Alignment explanation
Indices: 15849--16422 Score: 977
Period size: 45 Copynumber: 12.7 Consensus size: 45
15839 TTTCCCACAT
*
15849 TGTAAACCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
15894 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATC
*
15940 TGTAAGCCCTTCAGTGCATGATGTTTTAAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * *
15985 TGTATGCCCTTCAGTGCATGATGTTTTAAAAACCTTCAGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
16030 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
16075 TGTAAACCCTTCAGTGCATGATGTTTTCGAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATC
*
16121 TGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
16166 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* *
16211 TGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATA
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
16256 TGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
16301 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATC
* *
16347 TGTAAGCCCTTCAATGCTTGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * * *
16392 CGTAAGACCTACAGTGCAGGATGTTTTCAAA
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAA
16423 CAAGATTTTA
Statistics
Matches: 503, Mismatches: 23, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
45 373 0.74
46 130 0.26
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (45 bp):
TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
Found at i:16108 original size:136 final size:136
Alignment explanation
Indices: 15849--16422 Score: 981
Period size: 136 Copynumber: 4.2 Consensus size: 136
15839 TTTCCCACAT
*
15849 TGTAAACCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
15914 ATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTAAAAACCTTCGG
66 ATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
15979 GTCATC
131 GTCATC
* * *
15985 TGTATGCCCTTCAGTGCATGATGTTTTAAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATG
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
16050 ATGTTTTC-AAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATGATGTTTTCGAAAACCTTCG
66 ATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCG
16114 GGTCATC
130 GGTCATC
*
16121 TGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
16186 ATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGG
66 ATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
*
16250 GTCATA
131 GTCATC
*
16256 TGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
* *
16321 ATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAACCTTCGG
66 ATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
16386 GTCATC
131 GTCATC
* * * *
16392 CGTAAGACCTACAGTGCAGGATGTTTTCAAA
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAA
16423 CAAGATTTTA
Statistics
Matches: 414, Mismatches: 22, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
135 130 0.31
136 284 0.69
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (136 bp):
TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
ATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
GTCATC
Found at i:16159 original size:181 final size:180
Alignment explanation
Indices: 15849--16422 Score: 977
Period size: 181 Copynumber: 3.2 Consensus size: 180
15839 TTTCCCACAT
*
15849 TGTAAACCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
15914 ATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTAAAAACCTTCGG
66 ATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
* * *
15979 GTCATCTGTATGCCCTTCAGTGCATGATGTTTTAAAAACCTTCAGGTCATC
130 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
16030 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATG
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
16095 ATGTTTTCGAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAACCTTCGG
66 ATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
16160 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
130 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * *
16211 TGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATATGTAAGCCCTTCAGTGCTTG
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
16276 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGG
66 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGG
* *
16341 GTCATCTGTAAGCCCTTCAATGCTTGATGTTTTCAAAACCTTCGGGTCATC
130 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * * *
16392 CGTAAGACCTACAGTGCAGGATGTTTTCAAA
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAA
16423 CAAGATTTTA
Statistics
Matches: 372, Mismatches: 20, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
180 44 0.12
181 328 0.88
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (180 bp):
TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
Found at i:16687 original size:6 final size:6
Alignment explanation
Indices: 16676--16758 Score: 76
Period size: 6 Copynumber: 12.5 Consensus size: 6
16666 TTTTTCCAGT
* *
16676 TTATTA TTATTA TTATTA TTATTA TTATAA ATATTA TTATTA TTATATA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTAT-TA
16725 TATATATA TATATATA TATATATA TATATTA TTA
1 T-TAT-TA T-TAT-TA T-TAT-TA T-TATTA TTA
16759 AACAAAATAT
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
6 38 0.54
7 6 0.08
8 27 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTATTA
Found at i:16697 original size:18 final size:20
Alignment explanation
Indices: 16676--16758 Score: 102
Period size: 18 Copynumber: 4.2 Consensus size: 20
16666 TTTTTCCAGT
16676 TTATTATTAT-TAT-TATTA
1 TTATTATTATATATATATTA
16694 TTATTATTATA-A-ATATTA
1 TTATTATTATATATATATTA
16712 TTATTATTATATATATATATA
1 TTATTATTATATATATAT-TA
16733 TATATATATATATATATATATTA
1 T-TAT-TAT-TATATATATATTA
16756 TTA
1 TTA
16759 AACAAAATAT
Statistics
Matches: 57, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
18 27 0.47
19 1 0.02
20 4 0.07
21 3 0.05
22 5 0.09
23 6 0.11
24 11 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATTATTATATATATATTA
Found at i:16726 original size:2 final size:2
Alignment explanation
Indices: 16719--16753 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16709 TTATTATTAT
16719 TA TA 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 TA TA T
16754 TATTAAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18231 original size:17 final size:16
Alignment explanation
Indices: 18182--18231 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
18172 AATACTATAT
*
18182 TTTTAAT-TTCTTTTA
1 TTTTAATATTATTTTA
18197 TTTTAATCATTA-TTTA
1 TTTTAAT-ATTATTTTA
18213 TTTTCAATATTATTTTA
1 TTTT-AATATTATTTTA
18230 TT
1 TT
18232 ATTACTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 7 0.23
16 12 0.40
17 11 0.37
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATATTATTTTA
Found at i:18269 original size:15 final size:14
Alignment explanation
Indices: 18220--18280 Score: 56
Period size: 14 Copynumber: 4.3 Consensus size: 14
18210 TTATTTTCAA
*
18220 TATTATTTTATTAT
1 TATTATTTCATTAT
18234 TACTT-TTAT-ATT-T
1 TA-TTATT-TCATTAT
18247 TGATTATTTCATTAAT
1 T-ATTATTTCATT-AT
18263 TATTATTTCATTAT
1 TATTATTTCATTAT
18277 TATT
1 TATT
18281 TTTTATCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.12
14 19 0.47
15 14 0.35
16 2 0.05
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (14 bp):
TATTATTTCATTAT
Found at i:18307 original size:2 final size:2
Alignment explanation
Indices: 18295--18361 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
18285 ATCTTAGTTT
*
18295 TA TA AA 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
18337 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 T
18362 TTGTTTAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19912 original size:36 final size:36
Alignment explanation
Indices: 19830--20024 Score: 241
Period size: 36 Copynumber: 5.4 Consensus size: 36
19820 AGAAACACTT
* * * *
19830 TCAAATGAGATAAAATCTATTTTAAGAAAAGCAA-C
1 TCAAGTGAGATAAAATATGTTTTAAGAAAAACAATC
*
19865 TCAAGTAAGATAAAATATGTTTTAAGAAAAACAATC
1 TCAAGTGAGATAAAATATGTTTTAAGAAAAACAATC
*
19901 TCAAGTGAGATAAAGTATGTTTTAAGAAAAACAATC
1 TCAAGTGAGATAAAATATGTTTTAAGAAAAACAATC
* * *
19937 TCAAGTGAGATAAAATATATTTTCAG-AAAATAATC
1 TCAAGTGAGATAAAATATGTTTTAAGAAAAACAATC
* * * **
19972 TCAAGTGAGATTAAGTCTGTTTTTTTGAAAAACAATC
1 TCAAGTGAGATAAAATATG-TTTTAAGAAAAACAATC
20009 TCAAGTGAGATAAAAT
1 TCAAGTGAGATAAAAT
20025 CTTTAGTGAA
Statistics
Matches: 137, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
35 52 0.38
36 63 0.46
37 22 0.16
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (36 bp):
TCAAGTGAGATAAAATATGTTTTAAGAAAAACAATC
Found at i:19972 original size:71 final size:72
Alignment explanation
Indices: 19812--20024 Score: 259
Period size: 71 Copynumber: 3.0 Consensus size: 72
19802 GAAAAAAATC
* * * * * * * * *
19812 ATTTCAAGAGAAACACTTTCAAATGAGATAAAATCTATTTTAAGAAAAGCAA-CTCAAGTAAGAT
1 ATTTTAAGAAAAACAATCTCAAGTGAGATAAAGTCTGTTTTAAGAAAAACAATCTCAAGTGAGAT
19876 AAAATAT
66 AAAATAT
* *
19883 GTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTATGTTTTAAGAAAAACAATCTCAAGTGAGAT
1 ATTTTAAGAAAAACAATCTCAAGTGAGATAAAGTCTGTTTTAAGAAAAACAATCTCAAGTGAGAT
19948 AAAATAT
66 AAAATAT
* * * **
19955 ATTTTCAG-AAAATAATCTCAAGTGAGATTAAGTCTGTTTTTTTGAAAAACAATCTCAAGTGAGA
1 ATTTTAAGAAAAACAATCTCAAGTGAGATAAAGTCTG-TTTTAAGAAAAACAATCTCAAGTGAGA
20019 TAAAAT
65 TAAAAT
20025 CTTTAGTGAA
Statistics
Matches: 122, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
71 67 0.55
72 55 0.45
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.30
Consensus pattern (72 bp):
ATTTTAAGAAAAACAATCTCAAGTGAGATAAAGTCTGTTTTAAGAAAAACAATCTCAAGTGAGAT
AAAATAT
Found at i:20331 original size:116 final size:116
Alignment explanation
Indices: 20173--20460 Score: 350
Period size: 116 Copynumber: 2.5 Consensus size: 116
20163 GTTAAATAAT
* *
20173 TTCTTCTCATTATGAATTTCTTCTCCCTCATCGAATGAGTTCTTCTTATTATGAACCCTTAC-AT
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTTATTATGAACCCTT-CTAT
* * * * *
20237 TGGAAATGTTGATTCACCTCCTTCTGTGATGGACAAATCAAGGTTGAACAAG
65 TGAAAATGTTGATCCACCTACTTCTGTGATAGACAAACCAAGGTTGAACAAG
* * *
20289 TTCTTCTCATTATGAACTTCTTC-CCCTTCATCGGATGGGTTCTT-TCCATTATGAACTCTTCTA
1 TTCTTCTCATTATGAACTTCTTCTCCC-TCATCGGATGAGTTCTTCT-TATTATGAACCCTTCTA
* ** **
20352 TTGAAAATGTTGATCCACCTATTTCTGTGATAGATGAACCAAGGTTGAACTTG
64 TTGAAAATGTTGATCCACCTACTTCTGTGATAGACAAACCAAGGTTGAACAAG
* * *
20405 TTCTTCTCGTTATGAACTTCTTCTCCCTCAGT-AGATGTGTTCTTCTTATTATGAAC
1 TTCTTCTCATTATGAACTTCTTCTCCCTCA-TCGGATGAGTTCTTCTTATTATGAAC
20461 ATTTCCATTA
Statistics
Matches: 147, Mismatches: 19, Indels: 12
0.83 0.11 0.07
Matches are distributed among these distances:
115 5 0.03
116 137 0.93
117 5 0.03
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (116 bp):
TTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTTATTATGAACCCTTCTATT
GAAAATGTTGATCCACCTACTTCTGTGATAGACAAACCAAGGTTGAACAAG
Found at i:20831 original size:14 final size:14
Alignment explanation
Indices: 20812--20847 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
20802 GTCATATAAA
20812 TCTTTGTTTCATTC
1 TCTTTGTTTCATTC
20826 TCTTTGTTTCATTC
1 TCTTTGTTTCATTC
20840 TCTTTGTT
1 TCTTTGTT
20848 GAGTTTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.06, C:0.19, G:0.08, T:0.67
Consensus pattern (14 bp):
TCTTTGTTTCATTC
Found at i:22673 original size:5 final size:5
Alignment explanation
Indices: 22663--22690 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
22653 AATTAATGTT
22663 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
22691 AGATATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:24109 original size:19 final size:19
Alignment explanation
Indices: 24085--24152 Score: 91
Period size: 19 Copynumber: 3.6 Consensus size: 19
24075 TTGGTTAAAA
*
24085 TCAAAGTCAACGAGTTGGG
1 TCAAAGTCAACGGGTTGGG
* *
24104 TCAAAGTCAACGGGTCGAG
1 TCAAAGTCAACGGGTTGGG
* *
24123 TCAAAGTCAATGGGTTGGA
1 TCAAAGTCAACGGGTTGGG
24142 TCAAAGTCAAC
1 TCAAAGTCAAC
24153 AGGTCAGGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.21
Consensus pattern (19 bp):
TCAAAGTCAACGGGTTGGG
Found at i:24140 original size:38 final size:38
Alignment explanation
Indices: 24085--24157 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
24075 TTGGTTAAAA
* *
24085 TCAAAGTCAACGAGTTGGGTCAAAGTCAACGGGTCGAG
1 TCAAAGTCAACGAGTTGGATCAAAGTCAACAGGTCGAG
* *
24123 TCAAAGTCAATGGGTTGGATCAAAGTCAACAGGTC
1 TCAAAGTCAACGAGTTGGATCAAAGTCAACAGGTC
24158 AGGTTGGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.21
Consensus pattern (38 bp):
TCAAAGTCAACGAGTTGGATCAAAGTCAACAGGTCGAG
Found at i:25337 original size:115 final size:115
Alignment explanation
Indices: 25132--25389 Score: 306
Period size: 115 Copynumber: 2.2 Consensus size: 115
25122 TTTCTCCTTA
* *
25132 ATCGAATGAGTTCTTCTTATTATGAACCCTTTCATTGGAAATATTGACCCACCTCATTATGTGAT
1 ATCGAATGAGTACTTCTCATTATGAACCCTTTCATTGGAAATATTGACCCACCTCATTATGTGAT
* * * *
25197 GGGCAAACCAAGGTTGAACAAGTTCTTCTTATTTTGAACTTCTTCCCCTC
66 GGGAAAACCAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCCCCTC
* * * ** *
25247 ATCGAATGGGTACTTCTCATTATTAACCCTTAT-ATTGGAAATGTTGATTCACCTTATTATGTGA
1 ATCGAATGAGTACTTCTCATTATGAACCCTT-TCATTGGAAATATTGACCCACCTCATTATGTGA
* * *
25311 T-GGAAGAACCAAGGTCGAACATGTTCTTCTCATTATGAACTTTTTTTCCCTC
65 TGGGAA-AACCAAGGTCGAACAAGTTCTTCTCATTATGAAC-TTCTTCCCCTC
* *
25363 AGTAG-ATGAGTTCTTCTCATTATGAAC
1 A-TCGAATGAGTACTTCTCATTATGAAC
25390 TCTTCAATTA
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
114 3 0.03
115 85 0.71
116 30 0.25
117 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (115 bp):
ATCGAATGAGTACTTCTCATTATGAACCCTTTCATTGGAAATATTGACCCACCTCATTATGTGAT
GGGAAAACCAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCCCCTC
Found at i:34131 original size:28 final size:28
Alignment explanation
Indices: 34090--34150 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
34080 CTTTGCTATT
*
34090 GATTCTTAAATACAAGAGATGAACATTA
1 GATTCTTAAATACAAGAAATGAACATTA
*
34118 TATTCTTAAATACAAGAAATGAACATTA
1 GATTCTTAAATACAAGAAATGAACATTA
34146 GATTC
1 GATTC
34151 AAAGATGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (28 bp):
GATTCTTAAATACAAGAAATGAACATTA
Found at i:40995 original size:15 final size:16
Alignment explanation
Indices: 40953--40995 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
40943 TGAATAATTA
*
40953 ATAAATTAT-TTAAAT
1 ATAAAATATATTAAAT
40968 ATAAAATATATTAAAT
1 ATAAAATATATTAAAT
*
40984 CTAAAA-ATATTA
1 ATAAAATATATTA
40996 TAAAATTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAAATATATTAAAT
Found at i:42062 original size:29 final size:28
Alignment explanation
Indices: 42023--42182 Score: 112
Period size: 29 Copynumber: 5.6 Consensus size: 28
42013 TTAACTTATT
*
42023 AAATATGTTTTATTCTTTTTGTAACCTAA
1 AAATATATTTTATTCTTTTT-TAACCTAA
*
42052 AAATATATTTTTATTCTTATTTTAA--TAT
1 AAATATA-TTTTATTCTT-TTTTAACCTAA
* * * * *
42080 AATTACTATTTT-TT-TATCTTAACTTATT
1 AAATA-TATTTTATTCTTTTTTAACCTA-A
* *
42108 AAATATGTTTTATTCTTTTCATAACCTAA
1 AAATATATTTTATTCTTTT-TTAACCTAA
* **
42137 AAATATATTTTATTCGTATTTTAATTTAA
1 AAATATATTTTATTC-TTTTTTAACCTAA
*
42166 AAATATATTTTAATCTT
1 AAATATATTTTATTCTT
42183 AACATATATT
Statistics
Matches: 102, Mismatches: 19, Indels: 21
0.72 0.13 0.15
Matches are distributed among these distances:
25 5 0.05
26 1 0.01
27 9 0.09
28 18 0.18
29 44 0.43
30 22 0.22
31 3 0.03
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (28 bp):
AAATATATTTTATTCTTTTTTAACCTAA
Found at i:42102 original size:85 final size:85
Alignment explanation
Indices: 42003--42161 Score: 275
Period size: 85 Copynumber: 1.9 Consensus size: 85
41993 ATTAAAAATA
**
42003 TTTTTTATCTTTAACTTATTAAATATGTTTTATTCTTTTTGTAACCTAAAAATATATTTTTATTC
1 TTTTTTATCTTTAACTTATTAAATATGTTTTATTCTTTTCATAACCTAAAAATATA-TTTTATTC
*
42068 TTATTTTAATATAATTACTAT
65 GTATTTTAATATAATTACTAT
42089 TTTTTTATC-TTAACTTATTAAATATGTTTTATTCTTTTCATAACCTAAAAATATATTTTATTCG
1 TTTTTTATCTTTAACTTATTAAATATGTTTTATTCTTTTCATAACCTAAAAATATATTTTATTCG
42153 TATTTTAAT
66 TATTTTAAT
42162 TTAAAAATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
84 17 0.24
85 44 0.63
86 9 0.13
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (85 bp):
TTTTTTATCTTTAACTTATTAAATATGTTTTATTCTTTTCATAACCTAAAAATATATTTTATTCG
TATTTTAATATAATTACTAT
Found at i:42201 original size:85 final size:85
Alignment explanation
Indices: 41998--42185 Score: 265
Period size: 85 Copynumber: 2.2 Consensus size: 85
41988 CCAAAATTAA
* **
41998 AAATAT-TTTTTATCTTTAACTTATTAAATATGTTTTATTCTTTTTGTAACCTAAAAATATATTT
1 AAATATATTTTAATC-TTAACTTATTAAATATGTTTTATTCTTTTCATAACCTAAAAATATATTT
*
42062 TTATTCTTATTTTAATATAAT
65 TTATTCGTATTTTAATATAAT
* * * *
42083 TACTATTTTTTTATCTTAACTTATTAAATATGTTTTATTCTTTTCATAACCTAAAAATATA-TTT
1 AAATATATTTTAATCTTAACTTATTAAATATGTTTTATTCTTTTCATAACCTAAAAATATATTTT
*
42147 TATTCGTATTTTAATTTAA-
66 TATTCGTATTTTAATATAAT
42166 AAATATATTTTAATCTTAAC
1 AAATATATTTTAATCTTAAC
42186 ATATATTTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
83 16 0.17
84 20 0.22
85 48 0.52
86 8 0.09
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.55
Consensus pattern (85 bp):
AAATATATTTTAATCTTAACTTATTAAATATGTTTTATTCTTTTCATAACCTAAAAATATATTTT
TATTCGTATTTTAATATAAT
Found at i:42203 original size:19 final size:18
Alignment explanation
Indices: 42153--42194 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
42143 ATTTTATTCG
42153 TATTTTAATTTAAAAATA
1 TATTTTAATTTAAAAATA
*
42171 TATTTTAATCTT-AACATA
1 TATTTTAAT-TTAAAAATA
42189 TATTTT
1 TATTTT
42195 TAATGTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTTAATTTAAAAATA
Found at i:42226 original size:18 final size:18
Alignment explanation
Indices: 42194--42242 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
42184 ACATATATTT
42194 TTAATGTTAAGATGTAAAA
1 TTAAT-TTAAGATGTAAAA
* * *
42213 TTAATTTAATATGTGAAT
1 TTAATTTAAGATGTAAAA
42231 TTAATTTAAGAT
1 TTAATTTAAGAT
42243 ATATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (18 bp):
TTAATTTAAGATGTAAAA
Found at i:42474 original size:16 final size:16
Alignment explanation
Indices: 42453--42486 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42443 GATTGATGAG
* *
42453 AAAATATATTAAATTA
1 AAAATAAATTAAAATA
42469 AAAATAAATTAAAATA
1 AAAATAAATTAAAATA
42485 AA
1 AA
42487 TTTAATCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAAATTAAAATA
Found at i:44299 original size:2 final size:2
Alignment explanation
Indices: 44292--44338 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
44282 AAGAATCAAT
44292 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
44334 TA TA T
1 TA TA T
44339 TAATGATAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48920 original size:14 final size:14
Alignment explanation
Indices: 48901--48930 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
48891 ATTTTGATTT
*
48901 ATATTTATTTAATA
1 ATATTTATATAATA
48915 ATATTTATATAATA
1 ATATTTATATAATA
48929 AT
1 AT
48931 TGTATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATTTATATAATA
Found at i:49763 original size:3 final size:3
Alignment explanation
Indices: 49755--49785 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
49745 CCATTTTAAA
49755 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
49786 AACAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:51792 original size:21 final size:21
Alignment explanation
Indices: 51767--51821 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
51757 ATTTCTAAGT
51767 AAATAAATATATTATTTATAA
1 AAATAAATATATTATTTATAA
*
51788 AAATAAA-AAATATATTTATAA
1 AAATAAATATAT-TATTTATAA
*
51809 AAATCAATATATT
1 AAATAAATATATT
51822 TTATTGGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 3 0.10
21 23 0.79
22 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAAATATATTATTTATAA
Found at i:62742 original size:11 final size:11
Alignment explanation
Indices: 62726--62788 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
62716 TTATTCCCTC
62726 TTTTTTTCA-T
1 TTTTTTTCATT
62736 TTTTTTT-ATT
1 TTTTTTTCATT
*
62746 TATTTTTCATT
1 TTTTTTTCATT
62757 TTTTATTT-ATT
1 TTTT-TTTCATT
*
62768 TTTCTTTTCTTCT
1 TTT-TTTTCAT-T
62781 TTTTTTTC
1 TTTTTTTC
62789 TTCAATTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
9 1 0.02
10 14 0.32
11 15 0.34
12 10 0.23
13 4 0.09
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTTCATT
Found at i:62775 original size:17 final size:17
Alignment explanation
Indices: 62737--62790 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 17
62727 TTTTTTCATT
62737 TTTTTTATTTATTTTTC
1 TTTTTTATTTATTTTTC
62754 ATTTTTTATTTATTTTTC
1 -TTTTTTATTTATTTTTC
*
62772 TTTTCTTCTTT-TTTTTC
1 TTTT-TTATTTATTTTTC
62789 TT
1 TT
62791 CAATTTTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 12 0.35
18 22 0.65
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTATTTATTTTTC
Found at i:62785 original size:27 final size:26
Alignment explanation
Indices: 62724--62844 Score: 68
Period size: 27 Copynumber: 4.4 Consensus size: 26
62714 TTTTATTCCC
* *
62724 TCTTTTTTTCATTT-TTTTTATTTATT
1 TCTTTTTTTTATTTATTTTTCTTT-TT
62750 T-TTCATTTTTTATTTATTTTTCTTTTCT
1 TCTT--TTTTTTATTTATTTTTCTTTT-T
* * * *
62778 TCTTTTTTTTCTTCAATTTTGTTTTT
1 TCTTTTTTTTATTTATTTTTCTTTTT
62804 ATCTTTTTCACTTTATTT-TTTATTCTTTTAT
1 -TCTTTTT---TTTATTTATTT-TTCTTTT-T
*
62835 TCTTTGTTTT
1 TCTTTTTTTT
62845 CTACAGGTGT
Statistics
Matches: 73, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
25 2 0.03
26 2 0.03
27 37 0.51
28 10 0.14
29 4 0.05
30 17 0.23
31 1 0.01
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.77
Consensus pattern (26 bp):
TCTTTTTTTTATTTATTTTTCTTTTT
Found at i:62805 original size:57 final size:57
Alignment explanation
Indices: 62726--62846 Score: 133
Period size: 57 Copynumber: 2.1 Consensus size: 57
62716 TTATTCCCTC
* * * *
62726 TTTTT-TTCATTTTTTTTATTTA-TTTTTCATTTTTTATTTATTT-TTCTTTTCTTCTTT
1 TTTTTCTTCAATTTTGTTATTTACTTTTTCA--CTTTATTT-TTTATTCTTTTATTCTTT
62783 TTTTTCTTCAATTTTGTT-TTTATCTTTTTCACTTTATTTTTTATTCTTTTATTCTTT
1 TTTTTCTTCAATTTTGTTATTTA-CTTTTTCACTTTATTTTTTATTCTTTTATTCTTT
*
62840 GTTTTCT
1 TTTTTCT
62847 ACAGGTGTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
56 3 0.05
57 35 0.64
58 10 0.18
59 7 0.13
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.77
Consensus pattern (57 bp):
TTTTTCTTCAATTTTGTTATTTACTTTTTCACTTTATTTTTTATTCTTTTATTCTTT
Found at i:68519 original size:3 final size:3
Alignment explanation
Indices: 68513--68550 Score: 58
Period size: 3 Copynumber: 12.0 Consensus size: 3
68503 TTATTTATTT
68513 ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA A-TA ATA
68551 TTTGAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:68961 original size:3 final size:3
Alignment explanation
Indices: 68955--68987 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
68945 TTATTTGTTG
68955 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
68988 TGAAAAATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:79339 original size:15 final size:15
Alignment explanation
Indices: 79319--79352 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
79309 AAAAGGTCAA
79319 TAATAGTGTTGTAAT
1 TAATAGTGTTGTAAT
79334 TAATAGTGTTGTAAT
1 TAATAGTGTTGTAAT
79349 TAAT
1 TAAT
79353 TGGATAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (15 bp):
TAATAGTGTTGTAAT
Found at i:80339 original size:2 final size:2
Alignment explanation
Indices: 80332--80366 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
80322 TCTAACCATC
80332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80367 TCTTTTCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:81948 original size:21 final size:20
Alignment explanation
Indices: 81924--81969 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
81914 TCTTGAAAGT
81924 AAAAAAAATTC-GAAAATTTA
1 AAAAAAAATTCTGAAAA-TTA
81944 AAAAAAAATTCTGAAAATTA
1 AAAAAAAATTCTGAAAATTA
81964 AAAAAA
1 AAAAAA
81970 GAAAAGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAAAAAATTCTGAAAATTA
Found at i:88427 original size:20 final size:19
Alignment explanation
Indices: 88386--88425 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
88376 TATATAAAAC
88386 TTAAACAAAAATAATCAAT
1 TTAAACAAAAATAATCAAT
*
88405 TTAAACAAAAATGATCAAT
1 TTAAACAAAAATAATCAAT
88424 TT
1 TT
88426 TATTTTAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.30
Consensus pattern (19 bp):
TTAAACAAAAATAATCAAT
Found at i:89651 original size:29 final size:29
Alignment explanation
Indices: 89561--89773 Score: 133
Period size: 30 Copynumber: 7.2 Consensus size: 29
89551 ATTACAGACC
* * * *
89561 AAAATAGCAAACACATAAACTAAAAGGACC
1 AAAATAGTAAA-ACAGAAACTTAAAGGACT
*
89591 AAAATAGTACAAACAGAAATTTAAAGGACT
1 AAAATAGTA-AAACAGAAACTTAAAGGACT
* *
89621 AAAATGGTAAAATAGAAACTTAAATGG-CT
1 AAAATAGTAAAACAGAAACTTAAA-GGACT
* * *
89650 AAAATAGTAAAAACACAAACTTAAGGGTCT
1 AAAATAGT-AAAACAGAAACTTAAAGGACT
** * * * *
89680 -ATTTAGCAAATAAAGATATTTAAAGGACT
1 AAAATAGTAAA-ACAGAAACTTAAAGGACT
** * *
89709 AAAATAACAAAAATAGAAAATTAAAGGACT
1 AAAAT-AGTAAAACAGAAACTTAAAGGACT
* * **
89739 AAAATAGCTAAAACAAAAAGTTAAATAACT
1 AAAATAG-TAAAACAGAAACTTAAAGGACT
89769 AAAAT
1 AAAAT
89774 GAAATAAACA
Statistics
Matches: 140, Mismatches: 35, Indels: 16
0.73 0.18 0.08
Matches are distributed among these distances:
28 3 0.02
29 41 0.29
30 90 0.64
31 6 0.04
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.20
Consensus pattern (29 bp):
AAAATAGTAAAACAGAAACTTAAAGGACT
Found at i:91283 original size:3 final size:3
Alignment explanation
Indices: 91275--91322 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
91265 AATATAACAT
91275 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T-A TAAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
91318 TAA TA
1 TAA TA
91323 TATTTTTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.15
3 33 0.80
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:91762 original size:133 final size:132
Alignment explanation
Indices: 91523--91969 Score: 576
Period size: 133 Copynumber: 3.4 Consensus size: 132
91513 GGTCGTCTAA
* * *
91523 GGGTAACACGACTCCTACATGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACATGATGA
1 GGGTGACA-GACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGA
* * **
91588 AGAGTTCTGGCCATCTTTAGGAAGGGTGATAACACGATTCCTACACGATGAGGACGACTGGTTAT
65 AGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTAT
91653 CTAG
130 C-AG
* * * * * *
91657 GGTTGA-AGTGCTCCTACGCGATGAGGAGATCTGGTCAGGGGATGACACGACTCAAATGTGATGA
1 GGGTGACAG-ACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGA
* * * *
91721 AGAGTTCTGGCTATTTTTAGGAAGGGTGATAACTCGGTTCCTACGTTATGAGGACGGCTGGTTAT
65 AGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTAT
91786 CAG
130 CAG
* * *
91789 GGGTGACACGACTCCTACGTGAT-ATGGAGGTCTGGTCGGGGGATGACACAACTCATACGTGACG
1 GGGTGACA-GACTCCTACGTGATGA-GGAGATCTGGTCGGGGGATGACACGACTCATACGTGATG
* * **
91853 AAGAGTTCTAGCCATCTTTAGGAAGAGTGATAACTCGGTTCCTACGTGAAAAGGACGACTGGTTA
64 AAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTA
91918 TCAG
129 TCAG
* * *
91922 GGGTGACACAACTCCTATGTGATGAGGAGGTCTGGTC-GGGGATGACAC
1 GGGTGACA-GACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACAC
91970 AGTTCCTACG
Statistics
Matches: 272, Mismatches: 36, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
132 20 0.07
133 246 0.90
134 6 0.02
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.24
Consensus pattern (132 bp):
GGGTGACAGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATACGTGATGAA
GAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTATC
AG
Found at i:92040 original size:82 final size:82
Alignment explanation
Indices: 91890--92052 Score: 229
Period size: 82 Copynumber: 2.0 Consensus size: 82
91880 TGATAACTCG
* * * *
91890 GTTCCTACGTGAAAAGGACGACTGGTTATCAGGGGTGACACAACTCCTATGTGATGAGGAGGTCT
1 GTTCCTACGCGAAAAGGACGACTGGTTATCAGGGGTGACACAACTCCTACGTGATAAGGAGGTAT
91955 GGTCG-GGGATGACACA
66 GGTCGAGGGATGACACA
** ** *
91971 GTTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACACGGCTTCTACGTGATAAGGAGGTA
1 GTTCCTACGCGAAAAGGACGACTGGTTATC-AGGGGTGACACAACTCCTACGTGATAAGGAGGTA
92036 TGGTCGAGGGATGACAC
65 TGGTCGAGGGATGACAC
92053 GACTCATACA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 27 0.38
82 34 0.48
83 10 0.14
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (82 bp):
GTTCCTACGCGAAAAGGACGACTGGTTATCAGGGGTGACACAACTCCTACGTGATAAGGAGGTAT
GGTCGAGGGATGACACA
Found at i:92333 original size:130 final size:127
Alignment explanation
Indices: 92180--92455 Score: 378
Period size: 133 Copynumber: 2.1 Consensus size: 127
92170 TGCCTCTAGG
* *
92180 GAGACAAAATTTGTTTCAATGGAAACGATATCAAAGG-TTGGTTT-T-AAGAGAAATTTTCTCAA
1 GAGACAAAATTTGTTTCAATGGAAACGATATCAAAGGTTTGGTTTCTCAAAAGAAATTATCTCAA
* * *
92242 GAGAGAAAAAACTTTGTTTTCATAGGAAACAGACTCAAAGATTTTTATTCAATAGAAACTGTCTC
66 GAGAGAAAAAACTTTGTTTCCA-AAGAAACAGACTC--AGA-TTTT-TTCAAAAGAAACTGTCTC
92307 AA
126 AA
* **
92309 GAGACAAAATTTTGTTTCAATGGAAACGATCTCAAAGGTTTTTTTTCTCAAAAGAAATTATCTCA
1 GAGACAAAA-TTTGTTTCAATGGAAACGATATCAAAGGTTTGGTTTCTCAAAAGAAATTATCTCA
* * *
92374 AGAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAGATTTTTTCAAAATAAACTGTCTCGA
65 AGAGAGAAAAAACTTTGTTTCCAAAGAAACAGACTCAGATTTTTTCAAAAGAAACTGTCTCAA
92437 GAGACAAAATTTGTTTCAA
1 GAGACAAAATTTGTTTCAA
92456 GAGACACAAC
Statistics
Matches: 132, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
127 10 0.08
128 26 0.20
129 13 0.10
130 30 0.23
131 5 0.04
132 13 0.10
133 35 0.27
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (127 bp):
GAGACAAAATTTGTTTCAATGGAAACGATATCAAAGGTTTGGTTTCTCAAAAGAAATTATCTCAA
GAGAGAAAAAACTTTGTTTCCAAAGAAACAGACTCAGATTTTTTCAAAAGAAACTGTCTCAA
Found at i:92343 original size:64 final size:64
Alignment explanation
Indices: 92118--92455 Score: 241
Period size: 66 Copynumber: 5.2 Consensus size: 64
92108 AACCGACTCA
* * * * * * * * * *
92118 AAAATGTGTTTTAATAGAAACATACTCAAATATTTTGTGTTTCCAAATAAACTGCCTCTAGGGAG
1 AAAATTTGTTTCAATGGAAACAGACTCAAAGA-TTT-T-TTTCAAAAGAAACTGTCTCAAGAGAG
92183 AC
63 AC
* * * * * *
92185 AAAATTTGTTTCAATGGAAAC-GATATCAAAGGTTGGTTTT-AAGAGAAATTTTCTCAAGAGAGA
1 AAAATTTGTTTCAATGGAAACAGA-CTCAAAGATT-TTTTTCAAAAGAAACTGTCTCAAGAGAGA
*
92248 A
64 C
*
92249 AAAACTTTGTTTTC-ATAGGAAACAGACTCAAAGATTTTTATTCAATAGAAACTGTCTC-A-AGA
1 AAAA-TTTG-TTTCAAT-GGAAACAGACTCAAAGATTTTT-TTCAAAAGAAACTGTCTCAAGAGA
92311 GAC
62 GAC
* * *
92314 AAAATTTTGTTTCAATGGAAAC-GATCTCAAAGGTTTTTTTTCTCAAAAGAAATTATCTCAAGAG
1 AAAA-TTTGTTTCAATGGAAACAGA-CTCAAA-G-ATTTTTT-TCAAAAGAAACTGTCTCAAGAG
92378 AGAC
61 AGAC
* *
92382 AAAACTTTGTTTCCAA-AGAAACAGACTC--AGA-TTTTTTCAAAATAAACTGTCTC--GAGAGA
1 AAAA-TTTGTTT-CAATGGAAACAGACTCAAAGATTTTTTTCAAAAGAAACTGTCTCAAGAGAGA
92441 C
64 C
92442 AAAATTTGTTTCAA
1 AAAATTTGTTTCAA
92456 GAGACACAAC
Statistics
Matches: 219, Mismatches: 35, Indels: 43
0.74 0.12 0.14
Matches are distributed among these distances:
58 3 0.01
59 7 0.03
60 11 0.05
62 14 0.06
63 7 0.03
64 35 0.16
65 29 0.13
66 45 0.21
67 38 0.17
68 25 0.11
69 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (64 bp):
AAAATTTGTTTCAATGGAAACAGACTCAAAGATTTTTTTCAAAAGAAACTGTCTCAAGAGAGAC
Found at i:93620 original size:16 final size:16
Alignment explanation
Indices: 93601--93751 Score: 77
Period size: 16 Copynumber: 9.6 Consensus size: 16
93591 TTTTCTTCGC
*
93601 TTTTTCTTTTGTTGTT
1 TTTTTCTTTTGTTCTT
93617 TTTTTC-TTTG--CTT
1 TTTTTCTTTTGTTCTT
* *
93630 TTTTTC--TT-TACTC
1 TTTTTCTTTTGTTCTT
*
93643 TTTTTCTTCTTCTTCTT
1 TTTTTCTT-TTGTTCTT
*
93660 TTTTTCTCTTTGTTTTT
1 TTTTTCT-TTTGTTCTT
93677 TTCTTTCTCTTTGTT-TT
1 TT-TTTCT-TTTGTTCTT
*
93694 TTTTTCTTTTCTT-TT
1 TTTTTCTTTTGTTCTT
* *
93709 CTCTTTGTTTT-TTCTT
1 -TTTTTCTTTTGTTCTT
* *
93725 TTATTTTTTCTTTTTCTT
1 TT-TTTCTT-TTGTTCTT
*
93743 TTTCTCTTT
1 TTTTTCTTT
93752 GCTTTTTCTC
Statistics
Matches: 109, Mismatches: 13, Indels: 26
0.74 0.09 0.18
Matches are distributed among these distances:
12 2 0.02
13 16 0.15
15 14 0.13
16 29 0.27
17 28 0.26
18 20 0.18
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.79
Consensus pattern (16 bp):
TTTTTCTTTTGTTCTT
Found at i:93631 original size:13 final size:13
Alignment explanation
Indices: 93590--93769 Score: 87
Period size: 13 Copynumber: 14.1 Consensus size: 13
93580 TCTTGTCTTC
*
93590 TTTTTCTTCGCTT
1 TTTTTCTTTGCTT
*
93603 TTTCTTTTGTTG-TT
1 TTT-TTCT-TTGCTT
93617 TTTTTCTTTGCTT
1 TTTTTCTTTGCTT
* *
93630 TTTTTCTTTACTC
1 TTTTTCTTTGCTT
*
93643 TTTTTCTTCTTCTT
1 TTTTTCTT-TGCTT
93657 CTTTTT-TTCT-CTT
1 -TTTTTCTT-TGCTT
93670 TGTTTT-TTT-C--
1 T-TTTTCTTTGCTT
* *
93680 TTTCTCTTTGTTTT
1 TTTTTCTTTG-CTT
*
93694 TTTTTCTTTTC-T
1 TTTTTCTTTGCTT
*
93706 TTTCTCTTTG--T
1 TTTTTCTTTGCTT
93717 TTTTTCTTT--TAT
1 TTTTTCTTTGCT-T
*
93729 TTTTTCTTTTTCTT
1 TTTTTC-TTTGCTT
*
93743 TTTCTCTTTGCTT
1 TTTTTCTTTGCTT
*
93756 TTTCTCTTTGCTT
1 TTTTTCTTTGCTT
93769 T
1 T
93770 GATTTGATCT
Statistics
Matches: 134, Mismatches: 17, Indels: 32
0.73 0.09 0.17
Matches are distributed among these distances:
9 3 0.02
10 4 0.03
11 9 0.07
12 22 0.16
13 59 0.44
14 29 0.22
15 8 0.06
ACGTcount: A:0.01, C:0.17, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTTTCTTTGCTT
Found at i:93664 original size:32 final size:28
Alignment explanation
Indices: 93601--93745 Score: 113
Period size: 29 Copynumber: 5.0 Consensus size: 28
93591 TTTTCTTCGC
*
93601 TTTTTCTTTTGTTGTTT-TTTTCT-TTGCTT
1 TTTTTCTTTTCTT-TTTCTTTTCTCTT--TT
93630 TTTTTCTTTACTCTTTTTCTTCTTCTTCTTTT
1 TTTTTCTTT--TCTTTTTCTT-TTC-TCTTTT
* * *
93662 TTTCTCTTTGTTTTTTTC-TTTCTCTTTG
1 TTTTTCTTT-TCTTTTTCTTTTCTCTTTT
93690 TTTTT-TTTTC-TTTTCTTTTCTCTTTGT
1 TTTTTCTTTTCTTTTTCTTTTCTCTTT-T
*
93717 TTTTTCTTTTATTTTTTCTTTT-TCTTTT
1 TTTTTCTTTT-CTTTTTCTTTTCTCTTTT
93745 T
1 T
93746 CTCTTTGCTT
Statistics
Matches: 96, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
25 5 0.05
26 10 0.10
27 8 0.08
28 15 0.16
29 17 0.18
30 13 0.14
31 12 0.12
32 13 0.14
33 1 0.01
34 2 0.02
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.79
Consensus pattern (28 bp):
TTTTTCTTTTCTTTTTCTTTTCTCTTTT
Found at i:93678 original size:44 final size:43
Alignment explanation
Indices: 93600--93764 Score: 163
Period size: 44 Copynumber: 3.9 Consensus size: 43
93590 TTTTTCTTCG
*
93600 CTTTTTCTTTTGTT-GTTTTTT-TCTTTGCTTTTTTTCTTTACT
1 CTTTTTCTTTT-TTCTTTTTTTCTCTTTGCTTTTTTTCTTTACT
93642 CTTTTTCTTCTTCTTCTTTTTTTCTCTTTG-TTTTTTTCTTT-CT
1 CTTTTTCTT-TT-TTCTTTTTTTCTCTTTGCTTTTTTTCTTTACT
*
93685 CTTTGTTTTTTTTTCTTTTCTTTTCTCTTTG--TTTTTTCTTTTA-T
1 CTTT-TTCTTTTTTC-TTT-TTTTCTCTTTGCTTTTTTTC-TTTACT
*
93729 -TTTTTC-TTTTTC--TTTTTCTCTTTGCTTTTTCTCTTT
1 CTTTTTCTTTTTTCTTTTTTTCTCTTTGCTTTTTTTCTTT
93765 GCTTTGATTT
Statistics
Matches: 108, Mismatches: 5, Indels: 24
0.79 0.04 0.18
Matches are distributed among these distances:
37 11 0.10
38 4 0.04
39 6 0.06
41 6 0.06
42 14 0.13
43 25 0.23
44 36 0.33
45 6 0.06
ACGTcount: A:0.01, C:0.17, G:0.04, T:0.78
Consensus pattern (43 bp):
CTTTTTCTTTTTTCTTTTTTTCTCTTTGCTTTTTTTCTTTACT
Found at i:93683 original size:18 final size:17
Alignment explanation
Indices: 93658--93698 Score: 73
Period size: 18 Copynumber: 2.4 Consensus size: 17
93648 CTTCTTCTTC
93658 TTTTTTTCTCTTTGTTT
1 TTTTTTTCTCTTTGTTT
93675 TTTTCTTTCTCTTTGTTT
1 TTTT-TTTCTCTTTGTTT
93693 TTTTTT
1 TTTTTT
93699 CTTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (17 bp):
TTTTTTTCTCTTTGTTT
Found at i:93702 original size:57 final size:55
Alignment explanation
Indices: 93612--93760 Score: 153
Period size: 55 Copynumber: 2.7 Consensus size: 55
93602 TTTTCTTTTG
**
93612 TTGTTTTTTTCTTTGCT-TTTTTTCTTTACTCTTTTTCTTCTTCTTCTTT-TTTTCTCT
1 TTGTTTTTTTCTTT-CTCTTTTTT-TTTTTTCTTTTTCTT-TTC-TCTTTGTTTTCTCT
*
93669 TTGTTTTTTTCTTTCTCTTTGTTTTTTTTTC-TTTTCTTTTCTCTTTGTTTTTTCT
1 TTGTTTTTTTCTTTCTCTTT-TTTTTTTTTCTTTTTCTTTTCTCTTTGTTTTCTCT
* * * *
93724 TT-TATTTTTTCTTTTTCTTTTTCTCTTTGCTTTTTCT
1 TTGT-TTTTTTCTTTCTCTTTTTTTTTTTTCTTTTTCT
93761 CTTTGCTTTG
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
54 13 0.16
55 33 0.41
56 9 0.11
57 22 0.28
58 3 0.04
ACGTcount: A:0.01, C:0.17, G:0.04, T:0.78
Consensus pattern (55 bp):
TTGTTTTTTTCTTTCTCTTTTTTTTTTTTCTTTTTCTTTTCTCTTTGTTTTCTCT
Found at i:93725 original size:37 final size:37
Alignment explanation
Indices: 93587--93765 Score: 109
Period size: 38 Copynumber: 4.7 Consensus size: 37
93577 GTTTCTTGTC
* *
93587 TTCTTTT-TCTTCGCTTTTTCTTTTGTTGTTTTTTTCTT
1 TTCTTTTCTCTTTGTTTTTTC-TTTGTT-TTTTTTTCTT
* * * * * *
93625 TGCTTTTTTTCTTTACTCTTTTTC-TTCTTCTTCTTT-TT
1 TTC-TTTTCTCTTT-GT-TTTTTCTTTGTTTTTTTTTCTT
* *
93663 TTCTCTTTGT-TTTTTTCTTTCTCTTTGTTTTTTTTTCTT
1 TTCT-TTTCTCTTTGTT-TTT-TCTTTGTTTTTTTTTCTT
*
93702 TTCTTTTCTCTTTGTTTTTTC-TT-TTATTTTTTCTTT
1 TTCTTTTCTCTTTGTTTTTTCTTTGTTTTTTTTTC-TT
93738 TTCTTTTTCTCTTTGCTTTTTCTCTTTG
1 TTC-TTTTCTCTTTG-TTTTT-TCTTTG
93766 CTTTGATTTG
Statistics
Matches: 109, Mismatches: 16, Indels: 29
0.71 0.10 0.19
Matches are distributed among these distances:
35 10 0.09
36 11 0.10
37 19 0.17
38 31 0.28
39 22 0.20
40 10 0.09
42 6 0.06
ACGTcount: A:0.01, C:0.17, G:0.05, T:0.77
Consensus pattern (37 bp):
TTCTTTTCTCTTTGTTTTTTCTTTGTTTTTTTTTCTT
Found at i:93764 original size:57 final size:53
Alignment explanation
Indices: 93616--93747 Score: 74
Period size: 57 Copynumber: 2.4 Consensus size: 53
93606 CTTTTGTTGT
* *
93616 TTTTTTCTTTGCTTTTTTTCTTTACTCTTT-TTCTTCTTCTTCTTTTTTTCTCTTTGT-
1 TTTTTTCTTT-C-TTTTTTCTTTTCTCTTTGTT-TT-TTCTT-TTTTTTT-TCTTTTTC
* * * *
93673 TTTTTTCTTTCTCTTTGTTTTTTTTTCTTT-TCTTTTCTCTTTGTTTTTTC-TTTTA
1 TTTTTTCTTTCT-TTT-TTCTTTTCTCTTTGT-TTTT-TCTTTTTTTTTTCTTTTTC
*
93728 TTTTTTCTTTTTCTTTTTCT
1 TTTTTTCTTTCT-TTTTTCT
93748 CTTTGCTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
54 6 0.10
55 18 0.29
56 11 0.17
57 27 0.43
58 1 0.02
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.79
Consensus pattern (53 bp):
TTTTTTCTTTCTTTTTTCTTTTCTCTTTGTTTTTTCTTTTTTTTTTCTTTTTC
Found at i:93769 original size:26 final size:26
Alignment explanation
Indices: 93680--93769 Score: 87
Period size: 25 Copynumber: 3.5 Consensus size: 26
93670 TGTTTTTTTC
* * *
93680 TTTCTCTTTGTTTTTTTTTCTTTTC-T
1 TTTCTCTTTG-CTTTTTCTCTTTACTT
* *
93706 TTTCTCTTTGTTTTTTCT-TTTATTT
1 TTTCTCTTTGCTTTTTCTCTTTACTT
* *
93731 TTTCT-TTTTCTTTTTCTCTTTGCTT
1 TTTCTCTTTGCTTTTTCTCTTTACTT
93756 TTTCTCTTTGCTTT
1 TTTCTCTTTGCTTT
93770 GATTTGATCT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
24 13 0.25
25 23 0.43
26 17 0.32
ACGTcount: A:0.01, C:0.17, G:0.04, T:0.78
Consensus pattern (26 bp):
TTTCTCTTTGCTTTTTCTCTTTACTT
Found at i:94380 original size:20 final size:20
Alignment explanation
Indices: 94357--94397 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
94347 GGATAAATGC
94357 AATGTTTCAAGGTCTCAAAG
1 AATGTTTCAAGGTCTCAAAG
*
94377 AATGTTTCAAGGTCTTAAAG
1 AATGTTTCAAGGTCTCAAAG
94397 A
1 A
94398 GAGGGAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
AATGTTTCAAGGTCTCAAAG
Found at i:97515 original size:18 final size:18
Alignment explanation
Indices: 97492--97529 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
97482 TTGTTCTTAA
*
97492 AATATTTGGATAATATTT
1 AATATTCGGATAATATTT
97510 AATATTCGGATAATATTT
1 AATATTCGGATAATATTT
97528 AA
1 AA
97530 ATAAAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (18 bp):
AATATTCGGATAATATTT
Found at i:97560 original size:15 final size:15
Alignment explanation
Indices: 97542--97581 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
97532 AAAGAAATGC
97542 AATGGAAATAAATCA
1 AATGGAAATAAATCA
97557 AATGGAAATAAATCA
1 AATGGAAATAAATCA
*
97572 AATAGAAATA
1 AATGGAAATA
97582 TACAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (15 bp):
AATGGAAATAAATCA
Found at i:97921 original size:30 final size:30
Alignment explanation
Indices: 97748--97931 Score: 128
Period size: 30 Copynumber: 6.2 Consensus size: 30
97738 ATTACAGACC
* *
97748 AAAATAGC-AAACACATAAACTTAAAAGACC
1 AAAATAGCTAAA-ACATAAACTTAAAGGACT
* * *
97778 AAAATAG-TACAAATAAAAATTTAAAGGACT
1 AAAATAGCTA-AAACATAAACTTAAAGGACT
* * * *
97808 AAAATGGCAAAAATAAAAACTTAAATGG-CT
1 AAAATAGCTAAAACATAAACTTAAA-GGACT
* * * *
97838 AAAATA-ATAAAAACACAAACTTAAGGGTCT
1 AAAATAGCT-AAAACATAAACTTAAAGGACT
* *
97868 -AAATAGC-AAATACATACATTTAAAGGACT
1 AAAATAGCTAAA-ACATAAACTTAAAGGACT
* *
97897 AAAATAGCTAAAACATAAAGTTAAAGAACT
1 AAAATAGCTAAAACATAAACTTAAAGGACT
97927 AAAAT
1 AAAAT
97932 GAAATAAAAA
Statistics
Matches: 121, Mismatches: 23, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
28 3 0.02
29 20 0.17
30 90 0.74
31 8 0.07
ACGTcount: A:0.58, C:0.12, G:0.10, T:0.20
Consensus pattern (30 bp):
AAAATAGCTAAAACATAAACTTAAAGGACT
Found at i:98397 original size:14 final size:14
Alignment explanation
Indices: 98378--98412 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
98368 TGGCCCAAAG
98378 CTTTCTCTTCTCAT
1 CTTTCTCTTCTCAT
98392 CTTTCTCTTCTCAT
1 CTTTCTCTTCTCAT
*
98406 ATTTCTC
1 CTTTCTC
98413 ATTTGCTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.09, C:0.34, G:0.00, T:0.57
Consensus pattern (14 bp):
CTTTCTCTTCTCAT
Found at i:99510 original size:45 final size:45
Alignment explanation
Indices: 99455--99699 Score: 366
Period size: 45 Copynumber: 5.5 Consensus size: 45
99445 GAATACCATG
*
99455 AGTGGCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
*
99500 AGTGGAACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
* * * *
99545 AGTAGCACCTTTTATGCCAATAATGCACCATTATGCATTTCCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
*
99590 ATTGGCA-CTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
* * * * *
99634 TGTGGAACATTTTATGCCGATAATGCACCATTATTCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
*
99679 AGTGGCACCTTTTATGTCGAT
1 AGTGGCACCTTTTATGCCGAT
99700 TCATAGATTT
Statistics
Matches: 177, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
44 38 0.21
45 139 0.79
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
Found at i:99633 original size:89 final size:90
Alignment explanation
Indices: 99459--99699 Score: 367
Period size: 89 Copynumber: 2.7 Consensus size: 90
99449 ACCATGAGTG
* * *
99459 GCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATTAGTGGAACCTTTTATGCCGATAAT
1 GCACCTTTTATGCCGATAATGCACCATTATGCATTTTCATTAGTGGCACCTTTTATGCCGATAAT
99524 GCACCGTTATGCATTTTCATTAGTA
66 GCACCGTTATGCATTTTCATTAGTA
* * *
99549 GCACCTTTTATGCCAATAATGCACCATTATGCATTTCCATTATTGGCA-CTTTTATGCCGATAAT
1 GCACCTTTTATGCCGATAATGCACCATTATGCATTTTCATTAGTGGCACCTTTTATGCCGATAAT
* *
99613 GCACCGTTATGCATTTTCATTTGTG
66 GCACCGTTATGCATTTTCATTAGTA
* * * *
99638 GAACATTTTATGCCGATAATGCACCATTATTCATTTTCATTAGTGGCACCTTTTATGTCGAT
1 GCACCTTTTATGCCGATAATGCACCATTATGCATTTTCATTAGTGGCACCTTTTATGCCGAT
99700 TCATAGATTT
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
89 81 0.60
90 54 0.40
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (90 bp):
GCACCTTTTATGCCGATAATGCACCATTATGCATTTTCATTAGTGGCACCTTTTATGCCGATAAT
GCACCGTTATGCATTTTCATTAGTA
Found at i:103498 original size:10 final size:10
Alignment explanation
Indices: 103483--103513 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
103473 AAAAGCTATG
103483 TATGTATATA
1 TATGTATATA
103493 TATGTATATA
1 TATGTATATA
*
103503 TATATATATA
1 TATGTATATA
103513 T
1 T
103514 TTCTGACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (10 bp):
TATGTATATA
Found at i:103498 original size:14 final size:14
Alignment explanation
Indices: 103479--103509 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
103469 CCAGAAAAGC
*
103479 TATGTATGTATATA
1 TATGTATATATATA
103493 TATGTATATATATA
1 TATGTATATATATA
103507 TAT
1 TAT
103510 ATATTTCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:106159 original size:23 final size:23
Alignment explanation
Indices: 106113--106250 Score: 129
Period size: 23 Copynumber: 6.1 Consensus size: 23
106103 CACTGAAGTG
* * *
106113 CCACATAG-AATGTCTCGGATGA
1 CCACATAGAAATGTCCCGAAGGA
* **
106135 CCACAAAGGTATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* *
106158 CCACGTAGAAATGTCCCGAAAGA
1 CCACATAGAAATGTCCCGAAGGA
*
106181 CCACATAGAAATGTCTCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* *
106204 CCACATAG--ATGTCTCGAAGAA
1 CCACATAGAAATGTCCCGAAGGA
* **
106225 CCACATAGAAATCTCCTTAAGGA
1 CCACATAGAAATGTCCCGAAGGA
106248 CCA
1 CCA
106251 TATATATATT
Statistics
Matches: 94, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
21 20 0.21
22 7 0.07
23 67 0.71
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.17
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAAGGA
Found at i:106239 original size:21 final size:21
Alignment explanation
Indices: 106180--106239 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
106170 GTCCCGAAAG
*
106180 ACCACATAGAAATGTCTCGAAGG
1 ACCACATAGAAA--TCTCGAAGA
**
106203 ACCACATAGATGTCTCGAAGA
1 ACCACATAGAAATCTCGAAGA
106224 ACCACATAGAAATCTC
1 ACCACATAGAAATCTC
106240 CTTAAGGACC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 22 0.69
23 10 0.31
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (21 bp):
ACCACATAGAAATCTCGAAGA
Found at i:106270 original size:21 final size:20
Alignment explanation
Indices: 106246--106308 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
106236 TCTCCTTAAG
* *
106246 GACCATATATATATTCCAAA
1 GACCAAATATATGTTCCAAA
* *
106266 TGACCAAATATGTGTTTCAAA
1 -GACCAAATATATGTTCCAAA
*
106287 GAACCACATATATGTTCCAAA
1 G-ACCAAATATATGTTCCAAA
106308 G
1 G
106309 GATTACATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (20 bp):
GACCAAATATATGTTCCAAA
Found at i:106316 original size:21 final size:21
Alignment explanation
Indices: 106292--106331 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
106282 TCAAAGAACC
106292 ACATATATGTTCC-AAAGGATT
1 ACATATATG-TCCTAAAGGATT
106313 ACATATATGTCCTAAAGGA
1 ACATATATGTCCTAAAGGA
106332 CCACGTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
ACATATATGTCCTAAAGGATT
Found at i:107611 original size:24 final size:24
Alignment explanation
Indices: 107584--107650 Score: 111
Period size: 23 Copynumber: 2.9 Consensus size: 24
107574 ATGGATCGCG
107584 TAGAATTTGTCCCGAAGGACCACA
1 TAGAATTTGTCCCGAAGGACCACA
107608 TAGAA-TTGTCCCGAAGGACCACA
1 TAGAATTTGTCCCGAAGGACCACA
*
107631 TAG-ATTTGTCCCAAAGGACC
1 TAGAATTTGTCCCGAAGGACC
107651 GCGTGGAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 1 0.02
23 35 0.85
24 5 0.12
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (24 bp):
TAGAATTTGTCCCGAAGGACCACA
Found at i:107845 original size:15 final size:15
Alignment explanation
Indices: 107827--107859 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
107817 ACATTTTAAC
*
107827 ATAAAACATAATCTT
1 ATAAAACATAATCAT
107842 ATAAAACATAATCAT
1 ATAAAACATAATCAT
107857 ATA
1 ATA
107860 CATATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAAACATAATCAT
Found at i:112998 original size:24 final size:24
Alignment explanation
Indices: 112977--113050 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
112967 CAAAGAAGTG
*
112977 CCATGTAGAATTTGTCTCGAAGGA
1 CCATGTAGAATTTGTCCCGAAGGA
* *
113001 CCGCT-TAGAATTTGTCCCGAAGGT
1 CC-ATGTAGAATTTGTCCCGAAGGA
* *
113025 CCACGTAGAA-TTGTCCTGAAGGA
1 CCATGTAGAATTTGTCCCGAAGGA
113048 CCA
1 CCA
113051 CATAGATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
23 14 0.34
24 26 0.63
25 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (24 bp):
CCATGTAGAATTTGTCCCGAAGGA
Found at i:113045 original size:23 final size:24
Alignment explanation
Indices: 112982--113080 Score: 94
Period size: 23 Copynumber: 4.2 Consensus size: 24
112972 AAGTGCCATG
* * *
112982 TAGAATTTGTCTCGAAGGACCGCT
1 TAGAATTTGTCCCGAAGGACCACA
* *
113006 TAGAATTTGTCCCGAAGGTCCACG
1 TAGAATTTGTCCCGAAGGACCACA
*
113030 TAGAA-TTGTCCTGAAGGACCACA
1 TAGAATTTGTCCCGAAGGACCACA
* * * *
113053 TAG-ATTTATCCCAAAGTACCACG
1 TAGAATTTGTCCCGAAGGACCACA
113076 TAGAA
1 TAGAA
113081 CCCTTGACTC
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
22 1 0.02
23 34 0.56
24 26 0.43
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (24 bp):
TAGAATTTGTCCCGAAGGACCACA
Found at i:113341 original size:22 final size:21
Alignment explanation
Indices: 113316--113356 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
113306 AAAAATACAC
*
113316 ATTATATAAAACATAATAAAAT
1 ATTACATAAAACA-AATAAAAT
*
113338 ATTACATAAAATAAATAAA
1 ATTACATAAAACAAATAAA
113357 CAAATCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (21 bp):
ATTACATAAAACAAATAAAAT
Found at i:115260 original size:226 final size:226
Alignment explanation
Indices: 114842--115679 Score: 1081
Period size: 226 Copynumber: 3.7 Consensus size: 226
114832 ATGTAAACGG
* * * * *
114842 TAATATATTGATAATTTTGAAAACAAATAAAGTAATTAACCTATTTTGTTATCGTCGTATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTATCGTCGTATTTCTA
* * * *
114907 AGGCTCCATCAACTTTAAACAGGCG-TTACCTATTGCATTAAATAAGCGCTACTTGTTATGTTAT
66 AGGCCCCATCAGCTTTAAA-AGGCGACTACCTATTACATTAAATAAGCGCTACTTGTTATGTTAT
* * * * * *
114971 TATGGTTGATAATATTTCCAATAACTAACTTATTTTTTTATCGTCGGATTTTTAAGGCTCCATCA
130 TATGGTTGATAATATTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTATAAGACTCCATCA
115036 GCTTAAACTTTGGTAACATTTTAGGCGCTACC
195 GCTTAAACTTTGGTAACATTTTAGGCGCTACC
* *
115068 TAATATGTTGATAATATTCATAACATATCAAGTAATTAACATATTTTGTTATCGTCAG-ATTTCT
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTATCGTC-GTATTTCT
* * * * *
115132 AAGACCCCATCAGCTTTAAACATGCGTC-ACCTATTACATTAAATAAACGCTATTTGTTATGTTA
65 AAGGCCCCATCAGCTTTAAA-AGGCGACTACCTATTACATTAAATAAGCGCTACTTGTTATGTTA
* * *
115196 TTATGGTTGATAATGTTTCTAGTAATTAACCTATTTTGTTATCGTCGAATTTATAAGACTCCATC
129 TTATGGTTGATAATATTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTATAAGACTCCATC
* * *
115261 AGCTTAAATTTTGGTAACATTTTAGGCGTTACA
194 AGCTTAAACTTTGGTAACATTTTAGGCGCTACC
* * *
115294 TAATATGTTGATAATATTGATAACAAATCAATTAATTAACCAATTTTTTTGTTATCGTCGGATTT
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAA-C-A-TATTTTGTTATCGTCGTATTT
* * * * * * * *
115359 ATAAGGTCCCATCATCTTTTAAAAGGC-ACTACCTATTACGTCACATAAGTGCTACTTGTTATAT
63 CTAAGGCCCCATCAGC-TTTAAAAGGCGACTACCTATTACATTAAATAAGCGCTACTTGTTATGT
* * * * *
115423 TATTATGGTTGATAATGTTTCCCGTAATTAACCTATTTTGTTATCGTTGGATTTCTAAGTCTCCA
127 TATTATGGTTGATAATATTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTATAAGACTCCA
*
115488 TCAGCTTAAACTTTGGTAACATCTTAGGCGCTACC
192 TCAGCTTAAACTTTGGTAACATTTTAGGCGCTACC
* *
115523 AAATATGTTGTTAATATTGATAACAAATCAAGTAATTAACATATTTTGTTATCGTCGTATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTATCGTCGTATTTCTA
* ** * * * * *
115588 AGGCCCCATCAGCTTTAAAAAGAAACTACCTATTACGTTACATAAGCACTACCTATTATGTTATT
66 AGGCCCCATCAGCTTTAAAAGGCGACTACCTATTACATTAAATAAGCGCTACTTGTTATGTTATT
*
115653 ATGGTTGATAATATTTTCAGTAATTAA
131 ATGGTTGATAATATTTCCAGTAATTAA
115680 TCAGTTATGT
Statistics
Matches: 530, Mismatches: 73, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
225 8 0.02
226 323 0.61
227 3 0.01
228 4 0.01
229 186 0.35
230 6 0.01
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (226 bp):
TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTATCGTCGTATTTCTA
AGGCCCCATCAGCTTTAAAAGGCGACTACCTATTACATTAAATAAGCGCTACTTGTTATGTTATT
ATGGTTGATAATATTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTATAAGACTCCATCAG
CTTAAACTTTGGTAACATTTTAGGCGCTACC
Found at i:115796 original size:22 final size:22
Alignment explanation
Indices: 115768--115825 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
115758 ACCAACACAA
115768 ATAACATTTCTGGTGAAAACAT
1 ATAACATTTCTGGTGAAAACAT
115790 ATAACATTTCTGGTGAAAACAT
1 ATAACATTTCTGGTGAAAACAT
115812 ATAACATTTCTGGT
1 ATAACATTTCTGGT
115826 AGCGCTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (22 bp):
ATAACATTTCTGGTGAAAACAT
Found at i:121592 original size:5 final size:5
Alignment explanation
Indices: 121582--121804 Score: 231
Period size: 5 Copynumber: 45.0 Consensus size: 5
121572 TATTTATTTA
121582 ATATT ATATT ATATT ATATAT ATATT ATATT ATA-T ATATT ATTTATT
1 ATATT ATATT ATATT ATAT-T ATATT ATATT ATATT ATATT A--TATT
121629 ATATT ATATT ATATT ATA-T ATTATAT ATATT ATATT ATATT ATATTAT
1 ATATT ATATT ATATT ATATT A-TAT-T ATATT ATATT ATATT ATA-T-T
121677 ATATT ATATT ATATT ATA-T -TATT ATATT ATA-T -TATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
121723 ATATT ATA-T ATATT ATA-T ATTATAT ATATAT ATTATT ATATT ATA-T
1 ATATT ATATT ATATT ATATT A-TAT-T ATAT-T A-TATT ATATT ATATT
*
121769 AT-TT ATTATT -TCTT ATA-T ATATT ATATT -T-TT ATATT
1 ATATT A-TATT ATATT ATATT ATATT ATATT ATATT ATATT
121805 TTTTTTTCTT
Statistics
Matches: 191, Mismatches: 2, Indels: 50
0.79 0.01 0.21
Matches are distributed among these distances:
3 6 0.03
4 30 0.16
5 119 0.62
6 20 0.10
7 16 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:121601 original size:7 final size:7
Alignment explanation
Indices: 121586--121804 Score: 161
Period size: 7 Copynumber: 29.9 Consensus size: 7
121576 TATTTAATAT
121586 TATATTA
1 TATATTA
121593 TATTATATA
1 TA-TAT-TA
121602 TATATTA
1 TATATTA
121609 TAT-TATA
1 TATAT-TA
121616 TATATTA
1 TATATTA
*
121623 TTTATTA
1 TATATTA
121630 TAT-TATA
1 TATAT-TA
121637 TTATATTA
1 -TATATTA
121645 TATATTA
1 TATATTA
121652 TATA-TA
1 TATATTA
121658 TTATATTATA
1 -TATA-T-TA
121668 TTATATTA
1 -TATATTA
121676 TATATTA
1 TATATTA
121683 TAT-TATA
1 TATAT-TA
121690 TTATATTA
1 -TATATTA
121698 TTATATTA
1 -TATATTA
121706 TATTATTA
1 TA-TATTA
121714 TAT-TATA
1 TATAT-TA
121721 TTATATTATA
1 -TATA-T-TA
121731 TATATTA
1 TATATTA
121738 TATATTA
1 TATATTA
121745 TATA-TA
1 TATATTA
121751 TATATTA
1 TATATTA
121758 TTATATTA
1 -TATATTA
121766 TATATT-
1 TATATTA
121772 TATTATT-
1 TA-TATTA
*
121779 TCT-TATA
1 TATAT-TA
121786 TATATTA
1 TATATTA
*
121793 TAT-TTT
1 TATATTA
121799 TATATT
1 TATATT
121805 TTTTTTTCTT
Statistics
Matches: 181, Mismatches: 5, Indels: 52
0.76 0.02 0.22
Matches are distributed among these distances:
5 1 0.01
6 21 0.12
7 91 0.50
8 46 0.25
9 11 0.06
10 11 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TATATTA
Found at i:121611 original size:26 final size:26
Alignment explanation
Indices: 121582--121804 Score: 259
Period size: 26 Copynumber: 8.6 Consensus size: 26
121572 TATTTATTTA
121582 ATATTATATTATATTATATATATATT
1 ATATTATATTATATTATATATATATT
*
121608 ATATTATA-TATATTATTTATTATATT
1 ATATTATATTATATTATATA-TATATT
121634 ATATTATATTATA-TATTATATATATT
1 ATATTATATTATATTA-TATATATATT
121660 ATATTATATTATATTATATATTATATT
1 ATATTATATTATATTATATA-TATATT
121687 ATATTATA-T-TATTATATTATATTATT
1 ATATTATATTATATTATA-TATA-TATT
121713 ATATTATATTATATTATATATAT-TAT
1 ATATTATATTATATTATATATATAT-T
121739 ATATTATA-TATA-TATATTATTATATT
1 ATATTATATTATATTATA-TA-TATATT
* *
121765 ATATATTTATTAT-TTCTTATATATATT
1 ATAT-TATATTATATT-ATATATATATT
121792 ATATT-T-TTATATT
1 ATATTATATTATATT
121805 TTTTTTTCTT
Statistics
Matches: 175, Mismatches: 4, Indels: 37
0.81 0.02 0.17
Matches are distributed among these distances:
24 8 0.05
25 29 0.17
26 81 0.46
27 42 0.24
28 13 0.07
29 2 0.01
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATATTATATTATATTATATATATATT
Found at i:121680 original size:48 final size:48
Alignment explanation
Indices: 121571--121852 Score: 274
Period size: 48 Copynumber: 6.0 Consensus size: 48
121561 TAATTTCTTT
121571 TTAT-TTAT-TTA-ATATTATATTATATTATATA-TATATTATATTATA
1 TTATATTATATTATATATTATATTATATTATATATTATA-TATATTATA
121616 -TATATTAT-TTATTATATTATATTATATTATATATTATATATATTATA
1 TTATATTATATTA-TATATTATATTATATTATATATTATATATATTATA
121663 TTATATTATATTATATATTATATTATATTATATTATTATAT-TA-TATTA
1 TTATATTATATTATATATTATATTATATTATA-TATTATATATATTA-TA
121711 TTATATTATA-T-TATATTATA-TATATTATATATTATATATATATATTA
1 TTATATTATATTATATATTATATTATATTATATATTATATATAT-TA-TA
* * *
121758 TTATATTATA-TATTTATTAT-TTCT-TATATATATTATAT-TTTTATA
1 TTATATTATATTATATATTATATTATAT-TATATATTATATATATTATA
* * * * * * *
121803 TTTTTTTTTCTTTTCT-TTATTATTATTATTAT-TATTATATATTTTATA
1 TTATATTATATTATATATTA-TATTA-TATTATATATTATATATATTATA
121851 TT
1 TT
121853 CATTTTACTT
Statistics
Matches: 207, Mismatches: 10, Indels: 37
0.81 0.04 0.15
Matches are distributed among these distances:
44 11 0.05
45 29 0.14
46 15 0.07
47 61 0.29
48 79 0.38
49 12 0.06
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (48 bp):
TTATATTATATTATATATTATATTATATTATATATTATATATATTATA
Found at i:121806 original size:7 final size:7
Alignment explanation
Indices: 121590--121852 Score: 79
Period size: 7 Copynumber: 35.0 Consensus size: 7
121580 TAATATTATA
121590 TTATATT
1 TTATATT
*
121597 ATATATATA
1 -T-TATATT
121606 TTATATT
1 TTATATT
121613 ATATATATT
1 -T-TATATT
121622 ATT-TATT
1 -TTATATT
* *
121629 ATATTATA
1 TTA-TATT
121637 TTATATT
1 TTATATT
*
121644 ATATATT
1 TTATATT
121651 ATATATATT
1 -T-TATATT
* *
121660 ATATTATA
1 TTA-TATT
121668 TTATATT
1 TTATATT
*
121675 ATATATT
1 TTATATT
* *
121682 ATATTATA
1 TTA-TATT
121690 TTATATT
1 TTATATT
121697 ATTATATT
1 -TTATATT
*
121705 ATATTATT
1 TTA-TATT
* *
121713 ATATTATA
1 TTA-TATT
121721 TTATATT
1 TTATATT
* *
121728 ATATATA
1 TTATATT
*
121735 TTATATA
1 TTATATT
121742 TTATATAT
1 TTATAT-T
*
121750 ATATATT
1 TTATATT
121757 ATTATATT
1 -TTATATT
*
121765 ATATA-T
1 TTATATT
121771 TTATTATTT
1 TTA-TA-TT
121780 CTTATATAT
1 -TTATAT-T
121789 ATTATATTT
1 -TTATA-TT
121798 TTATATT
1 TTATATT
121805 TT-T-TT
1 TTATATT
*
121810 TTCT-TT
1 TTATATT
*
121816 TCTTTATT
1 T-TATATT
*
121824 ATTAT-TA
1 -TTATATT
121831 TTATTATT
1 TTA-TATT
*
121839 ATATATT
1 TTATATT
121846 TTATATT
1 TTATATT
121853 CATTTTACTT
Statistics
Matches: 195, Mismatches: 35, Indels: 51
0.69 0.12 0.18
Matches are distributed among these distances:
5 4 0.02
6 12 0.06
7 82 0.42
8 63 0.32
9 30 0.15
10 4 0.02
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (7 bp):
TTATATT
Found at i:121824 original size:32 final size:33
Alignment explanation
Indices: 121602--121852 Score: 87
Period size: 36 Copynumber: 7.4 Consensus size: 33
121592 ATATTATATA
* *
121602 TATATTATATTATATATATTATTTATTATATTATAT
1 TATATT-T-TTATATTTATTATTTCTTATATT-TAT
* *
121638 TATA-TTATATATTATATATATTATATTATATTATAT
1 TATATTTTTATATT-TAT-TATT-TCTTATATT-TAT
* *
121674 TATA-TATTATATTATATTATATTATTATATTATAT
1 TATATTTTTATATT-TATTAT-TTCTTATATT-TAT
* *
121709 TAT-TATATTATATTATATTATATATATTATA--TAT
1 TATAT-TTTTATATT-TATTAT-T-TCTTATATTTAT
* * *
121743 TATATATATATA-TTATTATATT-ATATATTTAT
1 TATATTTTTATATTTATTAT-TTCTTATATTTAT
* * *
121775 TAT-TTCTTATATATATTATATTTTTATATTT-T
1 TATATTTTTATATTTATTAT-TTCTTATATTTAT
* * *
121807 T-T-TTTCTTTTCTTTATTA-TTATTAT-TATTAT
1 TATATTT-TTATATTTATTATTTCTTATAT-TTAT
121838 TATATATTTTATATT
1 TATAT-TTTTATATT
121853 CATTTTACTT
Statistics
Matches: 177, Mismatches: 20, Indels: 39
0.75 0.08 0.17
Matches are distributed among these distances:
29 1 0.01
30 12 0.07
31 11 0.06
32 35 0.20
33 19 0.11
34 16 0.09
35 25 0.14
36 51 0.29
37 7 0.04
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (33 bp):
TATATTTTTATATTTATTATTTCTTATATTTAT
Found at i:122007 original size:2 final size:2
Alignment explanation
Indices: 122000--122032 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
121990 TATTAAATAC
122000 TA 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 TA T
122033 TACCTAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:122258 original size:17 final size:16
Alignment explanation
Indices: 122236--122360 Score: 83
Period size: 17 Copynumber: 7.2 Consensus size: 16
122226 ATTAATTTTC
122236 TTTTTTATTTTTCTTAT
1 TTTTTTATTTTT-TTAT
122253 TTTTTTATTCTTTATTTAT
1 TTTTTTA-T-TTT-TTTAT
*
122272 TTTTTTCTTTTGATTTAT
1 TTTTTTATTTT--TTTAT
*
122290 TCTTTTATTATTTTTAT
1 TTTTTTATT-TTTTTAT
*
122307 TATTTTA--TTTTTAT
1 TTTTTTATTTTTTTAT
*
122321 TTTTTTCTTTCTTTTGAT
1 TTTTTTATTT-TTTT-AT
*
122339 TTATTTAATATATTTTTAT
1 TT-TTT--TATTTTTTTAT
122358 TTT
1 TTT
122361 ATTTTCCCTT
Statistics
Matches: 88, Mismatches: 8, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
14 12 0.14
16 1 0.01
17 25 0.28
18 20 0.23
19 22 0.25
20 5 0.06
21 3 0.03
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTTTATTTTTTTAT
Found at i:122275 original size:57 final size:54
Alignment explanation
Indices: 122214--122391 Score: 152
Period size: 55 Copynumber: 3.2 Consensus size: 54
122204 TTTATTTCGC
* *
122214 TTTTTTCCTTTGATTAATTTTCTTTT-TTATTTTTCTTATTTTTTTATTCTTTATTTAT
1 TTTTTTCTTTTGATT-ATTTTCTTTTATTA--TTT-TTATTATTTTATT-TTTATTTAT
*
122272 TTTTTTCTTTTGATT-TATTCTTTTATTATTTTTATTATTTTATTTTTATTT-T
1 TTTTTTCTTTTGATTATTTTCTTTTATTATTTTTATTATTTTATTTTTATTTAT
* *** *
122324 TTTCTTTCTTTTGATTTATTTAATATATTT-TTA-TTTTATT-TTCCCTTTTGATTTAT
1 TTT-TTTCTTTTGA-TTATTT--TCT-TTTATTATTTTTATTATTTTATTTTTATTTAT
122380 TTTTTTCTTTTG
1 TTTTTTCTTTTG
122392 GTTTTTATTT
Statistics
Matches: 103, Mismatches: 9, Indels: 19
0.79 0.07 0.15
Matches are distributed among these distances:
52 4 0.04
53 17 0.17
54 14 0.14
55 24 0.23
56 19 0.18
57 8 0.08
58 17 0.17
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (54 bp):
TTTTTTCTTTTGATTATTTTCTTTTATTATTTTTATTATTTTATTTTTATTTAT
Found at i:122319 original size:14 final size:13
Alignment explanation
Indices: 122231--122335 Score: 90
Period size: 14 Copynumber: 7.7 Consensus size: 13
122221 CTTTGATTAA
122231 TTTTCTTTTTTAT
1 TTTTCTTTTTTAT
122244 TTTTCTTATTTT-T
1 TTTTCTT-TTTTAT
122257 TTATTCTTTATTTAT
1 TT-TTCTTT-TTTAT
122272 TTTT-TTCTTTTGAT
1 TTTTCTT-TTTT-AT
122286 TTATTCTTTTATTAT
1 TT-TTCTTTT-TTAT
*
122301 TTTTATTATTTTAT
1 TTTTCTT-TTTTAT
*
122315 TTTTATTTTTT-T
1 TTTTCTTTTTTAT
*
122327 CTTTCTTTT
1 TTTTCTTTT
122336 GATTTATTTA
Statistics
Matches: 79, Mismatches: 3, Indels: 21
0.77 0.03 0.20
Matches are distributed among these distances:
12 8 0.10
13 20 0.25
14 34 0.43
15 13 0.16
16 4 0.05
ACGTcount: A:0.12, C:0.07, G:0.01, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTTAT
Found at i:122340 original size:53 final size:54
Alignment explanation
Indices: 122238--122391 Score: 167
Period size: 53 Copynumber: 2.9 Consensus size: 54
122228 TAATTTTCTT
*
122238 TTTTATTTTTCTTATTTTTTTATTCTTTATTTATTTTTTTCTTTTGATTTATTC
1 TTTTATTTTTCTTATTATTTTATTCTTTATTTATTTTTTTCTTTTGATTTATTC
122292 TTTTATTATTT-TTATTATTTTATT-TTTATTT-TTTTCTTTCTTTTGATTTATT-
1 TTTTATT-TTTCTTATTATTTTATTCTTTATTTATTTT-TTTCTTTTGATTTATTC
* * * *
122344 TAATATATTTTTATT-TTATTTTCCCTT-TTGATTTATTTTTTTCTTTTG
1 T--TTTATTTTTCTTATTATTTT--ATTCTTTATTTATTTTTTTCTTTTG
122392 GTTTTTATTT
Statistics
Matches: 88, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
52 5 0.06
53 33 0.38
54 26 0.30
55 20 0.23
56 4 0.05
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (54 bp):
TTTTATTTTTCTTATTATTTTATTCTTTATTTATTTTTTTCTTTTGATTTATTC
Found at i:122343 original size:42 final size:42
Alignment explanation
Indices: 122238--122402 Score: 111
Period size: 37 Copynumber: 4.1 Consensus size: 42
122228 TAATTTTCTT
** *
122238 TTTTA-TTTTTCTTATTTTTTTATTCTTTATTTATTTT-TTTCT-
1 TTTTATTTTTTCTT-TTGATTTATT-TTTA-TTATTTTATTTTTA
* *
122280 TTTGATTTATTCTTTT-A-TTATTTTTATTATTTTATTTTTA
1 TTTTATTTTTTCTTTTGATTTATTTTTATTATTTTATTTTTA
*
122320 TTTT-TTTCTTTCTTTTGATTTA--TTTA--A-TATATTTTTA
1 TTTTATTT-TTTCTTTTGATTTATTTTTATTATTTTATTTTTA
** * *
122357 TTTTATTTTCCCTTTTGATTTATTTTT-TTCTTTTGGTTTTTA
1 TTTTATTTTTTCTTTTGATTTATTTTTATTATTTT-ATTTTTA
122399 TTTT
1 TTTT
122403 CATTCTTATG
Statistics
Matches: 98, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
37 25 0.26
38 11 0.11
39 14 0.14
40 19 0.19
41 3 0.03
42 19 0.19
43 7 0.07
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (42 bp):
TTTTATTTTTTCTTTTGATTTATTTTTATTATTTTATTTTTA
Found at i:122402 original size:18 final size:19
Alignment explanation
Indices: 122357--122403 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
122347 TATATTTTTA
122357 TTTTATTTTCCCTTTTGAT
1 TTTTATTTTCCCTTTTGAT
* *
122376 TTATT-TTTT-TCTTTTGGT
1 TT-TTATTTTCCCTTTTGAT
122394 TTTTATTTTC
1 TTTTATTTTC
122404 ATTCTTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
17 2 0.09
18 13 0.57
19 6 0.26
20 2 0.09
ACGTcount: A:0.09, C:0.11, G:0.06, T:0.74
Consensus pattern (19 bp):
TTTTATTTTCCCTTTTGAT
Found at i:122418 original size:21 final size:20
Alignment explanation
Indices: 122375--122417 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
122365 TCCCTTTTGA
* *
122375 TTTATTTTTTTCTTTTGGTT
1 TTTATTTTATTCTTATGGTT
122395 TTTATTTTCATTCTTAT-GTT
1 TTTATTTT-ATTCTTATGGTT
122415 TTT
1 TTT
122418 TCTTTGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.77
Consensus pattern (20 bp):
TTTATTTTATTCTTATGGTT
Found at i:123045 original size:43 final size:43
Alignment explanation
Indices: 122981--123583 Score: 324
Period size: 43 Copynumber: 14.2 Consensus size: 43
122971 ATCCCACATA
* * *
122981 TTTATAATTGAGTCCTCTAATTTTTTTAATATCACTTTTTACT
1 TTTATAATTGAGGCCTTTAATTTTTTTAATCTCACTTTTTACT
* * **
123024 TTTATAATTGAGGCCTTTAATTTTTCTAATCTCGCTTCATAGC-
1 TTTATAATTGAGGCCTTTAATTTTTTTAATCTCACTTTTTA-CT
** * *
123067 TTTATAATTGAAACGTCTAA-TTTTTTAATCTCACTTTTTA-T
1 TTTATAATTGAGGCCTTTAATTTTTTTAATCTCACTTTTTACT
* * *
123108 CTTTATAATTGAGG--TTCTAATTTTTTCAATTTCACTTTTTACA
1 -TTTATAATTGAGGCCTT-TAATTTTTTTAATCTCACTTTTTACT
* * *
123151 TTTATAATTGA-GACTTGTAATTTTTTCAAT-TCACTTTCTAGC-
1 TTTATAATTGAGGCCTT-TAATTTTTTTAATCTCACTTTTTA-CT
* * * * * *
123193 TTTATAATTAAAGTCC-CTAATTTTTGTAATCTCGCTTTTTACA
1 TTTATAATT-GAGGCCTTTAATTTTTTTAATCTCACTTTTTACT
* * *
123236 TTTGTAAATGAGCGTCC--TAATTTTTTCAATCTCACTTTTTAC-
1 TTTATAATTGAG-G-CCTTTAATTTTTTTAATCTCACTTTTTACT
** * * * *
123278 -------CCGAGGTCCATTATTATTTTTTAATCTCACTTTCTATT
1 TTTATAATTGAGG-CCTTTAAT-TTTTTTAATCTCACTTTTTACT
* * * * *
123316 TTTATATTTGAAGCCTTTAGTTTTTTTAATCTCACATTTTAAT
1 TTTATAATTGAGGCCTTTAATTTTTTTAATCTCACTTTTTACT
* * * *
123359 TTTATAA-TGA-GACTCTTAATTTTTTCAATCTCACCTTTTACC
1 TTTATAATTGAGGCCT-TTAATTTTTTTAATCTCACTTTTTACT
** * *
123401 TTTATAATTGAAACAC--TAAATTTTTTAATCT-AGCTTTTTTTACA
1 TTTATAATTGAGGC-CTTTAATTTTTTTAATCTCA-C--TTTTTACT
* * * *
123445 TTTATAATTGAGGCCCTTAGTTTTTTTCAATATCACTTTTTTACC
1 TTTATAATTGAGGCCTTTAATTTTTTT-AATCTCAC-TTTTTACT
** * *
123490 TTTATAATTGAAACGC-TTAA-TTTTTTAATTTCACTTTTTACC
1 TTTATAATTGAGGC-CTTTAATTTTTTTAATCTCACTTTTTACT
* * * * *
123532 TTTATAATTGA-GACTCCTAATTTTTTCAATCTAATTTTTTACT
1 TTTATAATTGAGGCCT-TTAATTTTTTTAATCTCACTTTTTACT
123575 TTTATAATT
1 TTTATAATT
123584 TAAGACCTAC
Statistics
Matches: 436, Mismatches: 83, Indels: 82
0.73 0.14 0.14
Matches are distributed among these distances:
34 4 0.01
35 3 0.01
36 3 0.01
37 18 0.04
40 2 0.00
41 8 0.02
42 156 0.36
43 166 0.38
44 34 0.08
45 35 0.08
46 6 0.01
47 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.51
Consensus pattern (43 bp):
TTTATAATTGAGGCCTTTAATTTTTTTAATCTCACTTTTTACT
Found at i:123113 original size:85 final size:84
Alignment explanation
Indices: 122981--123583 Score: 372
Period size: 85 Copynumber: 7.1 Consensus size: 84
122971 ATCCCACATA
** * *
122981 TTTATAATTGAGTCCTCTAATTTTTTTAATATCACTTTTTA-CTTTTATAATTGAGGCCTTTAA-
1 TTTATAATTGAAACGTCTAA-TTTTTTAATCTCACTTTTTATC-TTTATAATTGAGGCCTTTAAT
* **
123044 TTTTTCTAATCTCGCTTCATAGC
64 TTTTTC-AATCTCACTTTTTA-C
123067 TTTATAATTGAAACGTCTAATTTTTTAATCTCACTTTTTATCTTTATAATTGAGG--TTCTAATT
1 TTTATAATTGAAACGTCTAATTTTTTAATCTCACTTTTTATCTTTATAATTGAGGCCTT-TAATT
*
123130 TTTTCAATTTCACTTTTTAC
65 TTTTCAATCTCACTTTTTAC
* * * * * * * *
123150 ATTTATAATTGAGACTTGTAATTTTTTCAAT-TCACTTTCTAGCTTTATAATTAAAGTCC-CTAA
1 -TTTATAATTGAAACGTCTAATTTTTT-AATCTCACTTTTTATCTTTATAATT-GAGGCCTTTAA
*
123213 TTTTTGT-AATCTCGCTTTTTAC
63 TTTTT-TCAATCTCACTTTTTAC
* * * **
123235 ATTTGTAAATG-AGCGTCCTAATTTTTTCAATCTCACTTTTTA-C-------CCGAGGTCCATTA
1 -TTTATAATTGAAACGT-CTAATTTTTT-AATCTCACTTTTTATCTTTATAATTGAGG-CC-TT-
* * *
123291 TTATTTTTT-AATCTCACTTTCTATT
60 TAATTTTTTCAATCTCACTTTTTA-C
* * * * * * *
123316 TTTATATTTGAAGCCTTTAGTTTTTTTAATCTCACATTTTAAT-TTTATAA-TGA-GACTCTTAA
1 TTTATAATTGAAACGTCTA-ATTTTTTAATCTCAC-TTTTTATCTTTATAATTGAGGCCT-TTAA
*
123378 TTTTTTCAATCTCACCTTTTACC
63 TTTTTTCAATCTCACTTTTTA-C
* * *
123401 TTTATAATTGAAAC-ACTAAATTTTTTAATCT-AGCTTTTTTTACATTTATAATTGAGGCCCTTA
1 TTTATAATTGAAACGTCT-AATTTTTTAATCTCA-CTTTTTAT-C-TTTATAATTGAGGCCTTTA
* *
123464 GTTTTTTTCAATATCACTTTTTTACC
62 -ATTTTTTCAATCTCAC-TTTTTA-C
* * * *
123490 TTTATAATTGAAACG-CTTAATTTTTTAATTTCACTTTTTACCTTTATAATTGA-GACTCCTAAT
1 TTTATAATTGAAACGTC-TAATTTTTTAATCTCACTTTTTATCTTTATAATTGAGGCCT-TTAAT
* *
123553 TTTTTCAATCTAATTTTTTAC
64 TTTTTCAATCTCACTTTTTAC
123574 TTTTATAATT
1 -TTTATAATT
123584 TAAGACCTAC
Statistics
Matches: 404, Mismatches: 70, Indels: 87
0.72 0.12 0.16
Matches are distributed among these distances:
77 2 0.00
78 2 0.00
80 30 0.07
81 22 0.05
83 9 0.02
84 80 0.20
85 129 0.32
86 50 0.12
87 21 0.05
88 17 0.04
89 40 0.10
90 2 0.00
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.51
Consensus pattern (84 bp):
TTTATAATTGAAACGTCTAATTTTTTAATCTCACTTTTTATCTTTATAATTGAGGCCTTTAATTT
TTTCAATCTCACTTTTTAC
Found at i:123340 original size:123 final size:122
Alignment explanation
Indices: 123170--123400 Score: 290
Period size: 123 Copynumber: 1.9 Consensus size: 122
123160 GAGACTTGTA
* *
123170 ATTTTTTCAATTCACTTTCTAGCTTTATAATTAAAGTCCCTAATTTTTGTAATCTCGCTTTTTAC
1 ATTTTTTCAATTCACTTTCTAGCTTTATAATTAAAGTCCCTAATTTTTGTAATCTCACATTTTA-
*
123235 ATTTGTA-AATGAG-CGTCCTAATTTTTTCAATCTCACTTTTTACCCGAGGTCCATTATT
65 ATTT-TATAATGAGAC-TCCTAATTTTTTCAATCTCACCTTTTACCCGAGGTCCATTATT
** * * * * *
123293 ATTTTTT-AATCTCACTTTCTATTTTTATATTTGAAG-CCTTTAGTTTTTTTAATCTCACATTTT
1 ATTTTTTCAAT-TCACTTTCTAGCTTTATAATTAAAGTCC-CTAATTTTTGTAATCTCACATTTT
*
123356 AATTTTATAATGAGACTCTTAATTTTTTCAATCTCACCTTTTACC
64 AATTTTATAATGAGACTCCTAATTTTTTCAATCTCACCTTTTACC
123401 TTTATAATTG
Statistics
Matches: 93, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
121 2 0.02
122 42 0.45
123 49 0.53
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (122 bp):
ATTTTTTCAATTCACTTTCTAGCTTTATAATTAAAGTCCCTAATTTTTGTAATCTCACATTTTAA
TTTTATAATGAGACTCCTAATTTTTTCAATCTCACCTTTTACCCGAGGTCCATTATT
Found at i:124641 original size:24 final size:24
Alignment explanation
Indices: 124601--124651 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
124591 GGAATTCTTA
* * *
124601 AAAAGAAAGTAAAAAATGTTAGAT
1 AAAAGAAACTAAAAAATATTAAAT
124625 AAAA-AAACTAAATAAATATTAAAT
1 AAAAGAAACTAAA-AAATATTAAAT
124649 AAA
1 AAA
124652 TCCAAGAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (24 bp):
AAAAGAAACTAAAAAATATTAAAT
Found at i:124694 original size:56 final size:56
Alignment explanation
Indices: 124633--124756 Score: 130
Period size: 56 Copynumber: 2.2 Consensus size: 56
124623 ATAAAAAAAC
* * * *
124633 TAAATAAATATTAAATAAATCCAA-GAACAAAACAAAATAATAAATA-ATAA-ATAAA
1 TAAATAAATAAT-AATAAATCAAAGGAAAAAAACAAAAT-ATAAATATAAAATATAAA
*
124688 TGAAATACTAA-AATAATAAATCAAAGGAAAAAAAGAAAATATAAATATAAAATATAAA
1 T-AAATA--AATAATAATAAATCAAAGGAAAAAAACAAAATATAAATATAAAATATAAA
124746 TAAATAAATAA
1 TAAATAAATAA
124757 GTCAAAAGGA
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
55 3 0.05
56 24 0.42
57 22 0.39
58 8 0.14
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.22
Consensus pattern (56 bp):
TAAATAAATAATAATAAATCAAAGGAAAAAAACAAAATATAAATATAAAATATAAA
Found at i:124741 original size:13 final size:13
Alignment explanation
Indices: 124723--124747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
124713 GGAAAAAAAG
124723 AAAATATAAATAT
1 AAAATATAAATAT
124736 AAAATATAAATA
1 AAAATATAAATA
124748 AATAAATAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATATAAATAT
Found at i:124805 original size:24 final size:22
Alignment explanation
Indices: 124778--124839 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 22
124768 AAAAGAATTG
124778 AATAAAAATTAAAAAAGAGGAAAA
1 AATAAAAA-TAAAAAA-AGGAAAA
* *
124802 AATAAAAAAATAAAAAAATGAGAA
1 AAT--AAAAATAAAAAAAGGAAAA
124826 AATAAAAATAAAAA
1 AATAAAAATAAAAA
124840 TAACAAGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 11 0.32
24 11 0.32
25 7 0.21
26 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (22 bp):
AATAAAAATAAAAAAAGGAAAA
Found at i:124808 original size:7 final size:7
Alignment explanation
Indices: 124798--124885 Score: 56
Period size: 8 Copynumber: 12.3 Consensus size: 7
124788 AAAAAAGAGG
124798 AAAAAAT
1 AAAAAAT
124805 AAAAAAAT
1 -AAAAAAT
124813 AAAAAAAT
1 -AAAAAAT
*
124821 GAGAAAAT
1 -AAAAAAT
124829 -AAAAAT
1 AAAAAAT
124835 -AAAAAT
1 AAAAAAT
* *
124841 AACAAGT
1 AAAAAAT
*
124848 CAAAAGAAG
1 -AAAA-AAT
* *
124857 AATAGA-
1 AAAAAAT
124863 AAAAAAT
1 AAAAAAT
124870 AAAAAAT
1 AAAAAAT
124877 AAAAAAT
1 AAAAAAT
124884 AA
1 AA
124886 TATAATAATA
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
6 15 0.23
7 21 0.33
8 27 0.42
9 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:124910 original size:23 final size:22
Alignment explanation
Indices: 124879--125001 Score: 78
Period size: 23 Copynumber: 5.5 Consensus size: 22
124869 TAAAAAATAA
*
124879 AAAATAATATAATAATAGTAAT
1 AAAATAAAATAATAATAGTAAT
124901 AAAAT-AAATAA-AATAGGTGAAT
1 AAAATAAAATAATAATA-GT-AAT
* *
124923 AGAGAT-AAATAA-AATTTAGTAAG
1 A-AAATAAAATAATAA--TAGTAAT
* *
124946 AAAAAACAAATAATAATAATAAT
1 AAAATA-AAATAATAATAGTAAT
* *
124969 AATAATGAAATAA-AATA-AAAT
1 AA-AATAAAATAATAATAGTAAT
124990 AAAATAAAATAA
1 AAAATAAAATAA
125002 AGAATAAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
20 13 0.16
21 12 0.15
22 15 0.19
23 27 0.33
24 10 0.12
25 4 0.05
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.24
Consensus pattern (22 bp):
AAAATAAAATAATAATAGTAAT
Found at i:124962 original size:3 final size:3
Alignment explanation
Indices: 124954--125001 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
124944 AGAAAAAACA
*
124954 AAT AAT AAT AAT AAT AAT AAT GA- AAT AA- AAT AA- AAT AA- AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
124997 AAT AA
1 AAT AA
125002 AGAATAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 9 0.24
3 29 0.76
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:124986 original size:5 final size:5
Alignment explanation
Indices: 124953--125002 Score: 64
Period size: 5 Copynumber: 9.4 Consensus size: 5
124943 AAGAAAAAAC
*
124953 AAATA ATAATA ATAATA ATAATG AAATA AAATA AAATA AAATA AAATA
1 AAATA A-AATA A-AATA A-AATA AAATA AAATA AAATA AAATA AAATA
125001 AA
1 AA
125003 GAATAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 26 0.62
6 16 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (5 bp):
AAATA
Found at i:127083 original size:22 final size:21
Alignment explanation
Indices: 127057--127097 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
127047 AACGAACTTT
127057 TTGAAAAATTACTCCCCCTTAC
1 TTGAAAAATT-CTCCCCCTTAC
* *
127079 TTGAACACTTCTCCCCCTT
1 TTGAAAAATTCTCCCCCTT
127098 TAAAACACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.24, C:0.37, G:0.05, T:0.34
Consensus pattern (21 bp):
TTGAAAAATTCTCCCCCTTAC
Found at i:127406 original size:18 final size:18
Alignment explanation
Indices: 127383--127420 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
127373 TCCAAAGTCT
127383 AACAATCCACAAA-ATCAA
1 AACAATCCA-AAATATCAA
127401 AACAATCCAAAATATCAA
1 AACAATCCAAAATATCAA
127419 AA
1 AA
127421 TGTTGAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.63, C:0.24, G:0.00, T:0.13
Consensus pattern (18 bp):
AACAATCCAAAATATCAA
Done.