Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003600.1 Hibiscus syriacus cultivar Beakdansim tig00007615_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: 80147
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4912 original size:20 final size:20
Alignment explanation
Indices: 4875--4913 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
4865 CGGTAAACAT
4875 AATTTATCGATACTTTTTTA
1 AATTTATCGATACTTTTTTA
4895 AATTGTATCGATACTTTTT
1 AATT-TATCGATACTTTTT
4914 GTCCAGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (20 bp):
AATTTATCGATACTTTTTTA
Found at i:5091 original size:396 final size:396
Alignment explanation
Indices: 4364--5903 Score: 2372
Period size: 396 Copynumber: 3.9 Consensus size: 396
4354 ACTTGAGGTA
*
4364 TCGATACAAGTATTATAAGTATCG-TCCCAAAAACATCGAAACCGATAATTATAAAGTAACAGGT
1 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
* * * **
4428 AAATTT--AATGTAACCGAAAAAATATACCTGTTTCATGAGAGAAT-GGTAAACATAATGTATTA
66 AAATTTACAATGTAACCGATAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATCG
*
4490 ATACTTTTTTAAATTGTATCGATACGTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATAA
131 ATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATAA
4555 AGTGTCGATACAA-TATATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATA
196 AGTGTCGATACAAGTATATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATA
* * * *
4619 GGTAAATTTGCAATGTTACCGGTAAAAATATACTGATTTAATGAGAGAATATGTAAACATAATGT
261 GGTAAATTTACAATGTAACCGATAAAAATATACTAATTTAATGAGAGAATATGTAAACATAATGT
* * *
4684 ATCGCTACTTTTTTAAATTGTATCAATACGTTTTGTCCAGAATGAATGACAAACGATATGCACAT
326 ATCGATACTTTTTTAAATTGTATCAATACTTTTTGTCCAGAATGAATGACAAACGAGATGCACAT
4749 AAAGTG
391 AAAGTG
*
4755 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATTGAAA-CGATAATTATAAAGTAATAGGT
1 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
* * * *
4819 AAATTTACAATGTAACTGATAAAATATACCAGTTTAATGAGAGAATCGGTAAACATAATTTATCG
66 AAATTTACAATGTAACCGATAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATCG
4884 ATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATAA
131 ATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATAA
4949 AGTGTCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAAT
196 AGTGTCGATACAAGTA-TATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAAT
* *
5014 AGGTTAATTTACAATGTTAA-CGATAAAAATCTACTAATTTAATGAGAGAATATGTAAACATAAT
260 AGGTAAATTTACAATG-TAACCGATAAAAATATACTAATTTAATGAGAGAATATGTAAACATAAT
*
5078 GTATCGATAC-TTTTTAAATTGTATCAATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCAC
324 GTATCGATACTTTTTTAAATTGTATCAATACTTTTTGTCCAGAATGAATGACAAACGAGATGCAC
5142 AT-AAGTG
389 ATAAAGTG
* *
5149 TCGATACAAGTATTATATGTATCGATCCCAAAAACATTGAAACCGATAATTATAAAGTAATAGGT
1 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
*
5214 AAATTTACAATGTAACCGATAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATTTATC
66 AAATTTACAATGTAACCGAT-AAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
* * *
5279 GATACTTTTTTAAATTGTATCGATACATTTTGTCTAGAATGAATGCCAAACGAGATGCACGCATA
130 GATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATA
* *
5344 AATTGTCGATACAAGTATTATAAGTATCGATCCCAAAAA-ATCAAAACCGATAATTATAAAGTAA
195 AAGTGTCGATACAAGTA-TATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAA
* * * * *
5408 TAGGTAAATTTACAATGTAATCGGTAAAAATATACCAGTTTAATGAGAGAATAGGTAAACATAAT
259 TAGGTAAATTTACAATGTAACCGATAAAAATATACTAATTTAATGAGAGAATATGTAAACATAAT
* * *
5473 GTATCGATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGTCAAATGAGATGCAC
324 GTATCGATACTTTTTTAAATTGTATCAATACTTTTTGTCCAGAATGAATGACAAACGAGATGCA-
*
5538 GCATAAACTG
388 -CATAAAGTG
** * * *
5548 TCGATACATTTATTATAAATATCAATCCTC-AAAACATCGAAACCAATAATTATAAAGTAATAGG
1 TCGATACAAGTATTATAAGTATCGATCC-CAAAAACATCGAAACCGATAATTATAAAGTAATAGG
* * **
5612 TAAATTTACAATGTAA-TGGTAAAA-ATATTGGTTTAATGAGAGAATAGGTAAACATAATGTATC
65 TAAATTTACAATGTAACCGATAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATC
*
5675 GATACTTTTTTAAATTATATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATA
130 GATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATA
** *
5740 AAGTGTCGATACATTTATATTAAGTATCAATCCC-AAAACATCGAAACCGATAATTATAAAGTAA
195 AAGTGTCGATACAAGTATA-TAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAA
* * * *
5804 TAGGTAAATTTACAATGTAACCAATAAAAATATATTAGTTTATTGAGAGAATATGTAAACATAAT
259 TAGGTAAATTTACAATGTAACCGATAAAAATATACTAATTTAATGAGAGAATATGTAAACATAAT
* *
5869 GTATCGATACTTTATTAAATTTTAT-AGATACTTTT
324 GTATCGATACTTTTTTAAATTGTATCA-ATACTTTT
5904 GTTAAATTAC
Statistics
Matches: 1061, Mismatches: 70, Indels: 31
0.91 0.06 0.03
Matches are distributed among these distances:
391 51 0.05
392 16 0.02
393 34 0.03
394 141 0.13
395 191 0.18
396 541 0.51
397 6 0.01
398 5 0.00
399 75 0.07
400 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (396 bp):
TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
AAATTTACAATGTAACCGATAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATGTATCG
ATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATAA
AGTGTCGATACAAGTATATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATA
GGTAAATTTACAATGTAACCGATAAAAATATACTAATTTAATGAGAGAATATGTAAACATAATGT
ATCGATACTTTTTTAAATTGTATCAATACTTTTTGTCCAGAATGAATGACAAACGAGATGCACAT
AAAGTG
Found at i:5097 original size:199 final size:200
Alignment explanation
Indices: 4364--5903 Score: 2320
Period size: 199 Copynumber: 7.8 Consensus size: 200
4354 ACTTGAGGTA
*
4364 TCGATACAAGTATTATAAGTATCG-TCCCAAAAACATCGAAACCGATAATTATAAAGTAACAGGT
1 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
*
4428 AAATTT--AATGTAACCGA-AAAAATATACCT-GTTTCATGAGAGAAT-GGTAAACATAATGTAT
66 AAATTTACAATGTAACCGATAAAAATATA-CTAGTTTAATGAGAGAATAGGTAAACATAATGTAT
** *
4488 TAATACTTTTTTAAATTGTATCGATACGTTTTGTCCAGAATGAATGCCAAACGAGATGCACACAT
130 CGATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACAT
4553 AAAGTG
195 AAAGTG
4559 TCGATACAA-TA-TATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
1 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
* * * *
4622 AAATTTGCAATGTTACCGGTAAAAATATACT-GATTTAATGAGAGAATATGTAAACATAATGTAT
66 AAATTTACAATGTAACCGATAAAAATATACTAG-TTTAATGAGAGAATAGGTAAACATAATGTAT
* * * * *
4686 CGCTACTTTTTTAAATTGTATCAATACGTTTTGTCCAGAATGAATGACAAACGATATG--CACAT
130 CGATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACAT
4749 AAAGTG
195 AAAGTG
*
4755 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATTGAAA-CGATAATTATAAAGTAATAGGT
1 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
* * * *
4819 AAATTTACAATGTAACTGAT-AAAATATACCAGTTTAATGAGAGAATCGGTAAACATAATTTATC
66 AAATTTACAATGTAACCGATAAAAATATACTAGTTTAATGAGAGAATAGGTAAACATAATGTATC
4883 GATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATA
131 GATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATA
4948 AAGTG
196 AAGTG
4953 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
1 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
* * * *
5018 TAATTTACAATGTTAA-CGATAAAAATCTACTAATTTAATGAGAGAATATGTAAACATAATGTAT
66 AAATTTACAATG-TAACCGATAAAAATATACTAGTTTAATGAGAGAATAGGTAAACATAATGTAT
*
5082 CGATAC-TTTTTAAATTGTATCAATACTTTTTGTCCAGAATGAATGCCAAACGAGATG--CACAT
130 CGATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACAT
5144 -AAGTG
195 AAAGTG
* *
5149 TCGATACAAGTATTATATGTATCGATCCCAAAAACATTGAAACCGATAATTATAAAGTAATAGGT
1 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
** *
5214 AAATTTACAATGTAACCGATAAAAATATACCGGTTTAATGAGAGAATAGGTAAACATAATTTATC
66 AAATTTACAATGTAACCGATAAAAATATACTAGTTTAATGAGAGAATAGGTAAACATAATGTATC
* * *
5279 GATACTTTTTTAAATTGTATCGATACATTTTGTCTAGAATGAATGCCAAACGAGATGCACGCATA
131 GATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATA
*
5344 AATTG
196 AAGTG
*
5349 TCGATACAAGTATTATAAGTATCGATCCCAAAAA-ATCAAAACCGATAATTATAAAGTAATAGGT
1 TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
* * *
5413 AAATTTACAATGTAATCGGTAAAAATATACCAGTTTAATGAGAGAATAGGTAAACATAATGTATC
66 AAATTTACAATGTAACCGATAAAAATATACTAGTTTAATGAGAGAATAGGTAAACATAATGTATC
* * *
5478 GATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGTCAAATGAGATGCACGCATA
131 GATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATA
*
5543 AACTG
196 AAGTG
** * * *
5548 TCGATACATTTATTATAAATATCAATCCTC-AAAACATCGAAACCAATAATTATAAAGTAATAGG
1 TCGATACAAGTATTATAAGTATCGATCC-CAAAAACATCGAAACCGATAATTATAAAGTAATAGG
* * *
5612 TAAATTTACAATGTAA-TGGTAAAAATAT--TGGTTTAATGAGAGAATAGGTAAACATAATGTAT
65 TAAATTTACAATGTAACCGATAAAAATATACTAGTTTAATGAGAGAATAGGTAAACATAATGTAT
*
5674 CGATACTTTTTTAAATTATATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACAT
130 CGATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACAT
5739 AAAGTG
195 AAAGTG
** *
5745 TCGATACATTTA-TATTAAGTATCAATCCC-AAAACATCGAAACCGATAATTATAAAGTAATAGG
1 TCGATACAAGTATTA-TAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGG
* * * *
5808 TAAATTTACAATGTAACCAATAAAAATATATTAGTTTATTGAGAGAATATGTAAACATAATGTAT
65 TAAATTTACAATGTAACCGATAAAAATATACTAGTTTAATGAGAGAATAGGTAAACATAATGTAT
* * *
5873 CGATACTTTATTAAATTTTATAGATACTTTT
130 CGATACTTTTTTAAATTGTATCGATACTTTT
5904 GTTAAATTAC
Statistics
Matches: 1234, Mismatches: 86, Indels: 46
0.90 0.06 0.03
Matches are distributed among these distances:
193 11 0.01
194 47 0.04
195 12 0.01
196 301 0.24
197 247 0.20
198 147 0.12
199 342 0.28
200 127 0.10
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (200 bp):
TCGATACAAGTATTATAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGT
AAATTTACAATGTAACCGATAAAAATATACTAGTTTAATGAGAGAATAGGTAAACATAATGTATC
GATACTTTTTTAAATTGTATCGATACTTTTTGTCCAGAATGAATGCCAAACGAGATGCACACATA
AAGTG
Found at i:5299 original size:21 final size:20
Alignment explanation
Indices: 5271--5309 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5261 AGGTAAACAT
*
5271 AATTTATCGATACTTTTTTA
1 AATTTATCGATACATTTTTA
5291 AATTGTATCGATACATTTT
1 AATT-TATCGATACATTTT
5310 GTCTAGAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (20 bp):
AATTTATCGATACATTTTTA
Found at i:6225 original size:36 final size:36
Alignment explanation
Indices: 6185--6253 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
6175 CAGTCCTTCT
*
6185 AACGACAACCTTCTTTTCAACCAAGCTCTTCTTTTC
1 AACGACAACCTTCTTCTCAACCAAGCTCTTCTTTTC
6221 AACGACAACCTTCTTCTCAACCAAGCTCTTCTT
1 AACGACAACCTTCTTCTCAACCAAGCTCTTCTT
6254 CTAACCAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.35, G:0.06, T:0.33
Consensus pattern (36 bp):
AACGACAACCTTCTTCTCAACCAAGCTCTTCTTTTC
Found at i:6254 original size:18 final size:18
Alignment explanation
Indices: 6194--6261 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
6184 TAACGACAAC
*
6194 CTTCTTTTCAACCAAGCT
1 CTTCTTCTCAACCAAGCT
*
6212 CTTCTTTTCAACGACAA-C-
1 CTTCTTCTCAAC--CAAGCT
6230 CTTCTTCTCAACCAAGCT
1 CTTCTTCTCAACCAAGCT
6248 CTTCTTCT-AACCAA
1 CTTCTTCTCAACCAA
6262 ATCAGGTCGT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
16 3 0.07
17 7 0.16
18 31 0.69
19 1 0.02
20 3 0.07
ACGTcount: A:0.25, C:0.35, G:0.04, T:0.35
Consensus pattern (18 bp):
CTTCTTCTCAACCAAGCT
Found at i:10738 original size:20 final size:20
Alignment explanation
Indices: 10693--10738 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
10683 GTTTATATAA
*
10693 AGTATCGATACTTTTTGTAT
1 AGTATCGATACTTTTTGTAC
*
10713 ATGTATCGATACTTTTTGTCC
1 A-GTATCGATACTTTTTGTAC
10734 AGTAT
1 AGTAT
10739 GCTTCTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (20 bp):
AGTATCGATACTTTTTGTAC
Found at i:10742 original size:202 final size:202
Alignment explanation
Indices: 10468--10871 Score: 666
Period size: 202 Copynumber: 2.0 Consensus size: 202
10458 TAACTGTATT
10468 ATGGTAACATAAGTTTATATAAAGTATCAATACGCTATTTTATATGTATCGATACTTTTTGTCCA
1 ATGGTAACATAAGTTTATATAAAGTATCAATAC-CTATTTTATATGTATCGATACTTTTTGTCCA
*
10533 ATATGCTTCTCAAAACTACATACACGTAAGAAGTATCGATACCTATAAATATATATCGATACATA
65 ATATGCTTCTCAAAACTACATACACGTAAGAAGTATCGATACCTATAAAAATATATCGATACATA
* * * *
10598 ATGATATAAAAGGTTAAAAATTGATAAAACCAGTTTCAATATACAATGTAACCGGTCATTAGATA
130 ATGATATAAAAAGTTAAAAATTGATAAAACCAATTTCAATATACAATATAACCGGTCAATAGATA
10663 CCGGTTTA
195 CCGGTTTA
* *
10671 ATGGTAACATAAGTTTATATAAAGTATCGATA-CTTTTTGTATATGTATCGATACTTTTTGTCCA
1 ATGGTAACATAAGTTTATATAAAGTATCAATACCTATTT-TATATGTATCGATACTTTTTGTCCA
* * * * *
10735 GTATGCTTCTCAAAACTACATGCACGTAAGAAGTATCGATACTTATAAAAATGTATCGATACATT
65 ATATGCTTCTCAAAACTACATACACGTAAGAAGTATCGATACCTATAAAAATATATCGATACATA
10800 ATGATATAAAAAGTTAAAAATTGATAAAACCAATTTCAATATACAATATAACCGGTCAATAGATA
130 ATGATATAAAAAGTTAAAAATTGATAAAACCAATTTCAATATACAATATAACCGGTCAATAGATA
*
10865 CTGGTTT
195 CCGGTTT
10872 TGAAAAAACG
Statistics
Matches: 187, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
201 5 0.03
202 151 0.81
203 31 0.17
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (202 bp):
ATGGTAACATAAGTTTATATAAAGTATCAATACCTATTTTATATGTATCGATACTTTTTGTCCAA
TATGCTTCTCAAAACTACATACACGTAAGAAGTATCGATACCTATAAAAATATATCGATACATAA
TGATATAAAAAGTTAAAAATTGATAAAACCAATTTCAATATACAATATAACCGGTCAATAGATAC
CGGTTTA
Found at i:23669 original size:975 final size:975
Alignment explanation
Indices: 21779--23728 Score: 3118
Period size: 975 Copynumber: 2.0 Consensus size: 975
21769 TATACCCAAG
* *
21779 GAATGACACCTCCCGAAGCCAAAACTCACATTTTCTCAAATTAGCATACAACCGATGCTCTCTCA
1 GAATGACACCTCCCGAAGCCAAAACTCACATTTGCTCAAATTAACATACAACCGATGCTCTCTCA
*
21844 GAGTCTGTAGAACAATCTTCAAATGATCATCCAACTCTGCCTCGATTCAGGAATAAACTAGAATA
66 GAGTCTGTAGAACAATCTTCAAATGATCATCCAACTCTGCCTCGATTCAGGAATAAACCAGAATA
* * ** *
21909 TCATCAATGAATACTACTACAAATTGATCCAAATACGTTCGGAACACATGATACATCAAATGCAT
131 TCATCAATGAATACAACTACAAATTGATCCAAATACGGTCGGAACACACAATACATCAAATCCAT
* *
21974 AAAAGCTACGGGAGCGTTCGTCAGACCAAAAAACATCACCAAGAACTCATAATGCCTATATCTAG
196 AAAAACTACGGGAGCGTTCGTCAGACCAAAAAACATCACCAAGAACTCATAATGCCCATATCTAG
* * *
22039 TGCGAATGACAGTTTTCGCAACATCTGAACCTTTCACTTTTAATTGATAATACCCCGAACGAAGA
261 TGCGAATGACAGTCTTCGCAACATCAGAACCTTTAACTTTTAATTGATAATACCCCGAACGAAGA
*
22104 TCAATCTTAGAGAATACAATAGCACATCAAAATTGATCAAATAAGTCATTAATCCTGGGTAGTGG
326 TCAATCTTAGAGAATACAATAGCACATCAAAATTGATCAAATAAGTCATCAATCCTGGGTAGTGG
*
22169 GTACTTATTCTTAACTATCATCTAATTCAACTTCCGGTAGTCAATACATAGCCTTAGTGATCCAT
391 GTACTTATTCTTAACTATCATCTAATTCAACTTCCGGTAGTCAATACATAGCCTTAGTGATACAT
* * *
22234 CCTTCTTTTTTCACAAACAGAACTGGAGCTCTACAGGGTGAGGTACTATGCCTGATAAATCCTCG
456 CCTTCTTTTTTCACAAACAGAACTAGAGCTCCACAGGGTGAGGTACTATGCCTGATAAATCCTCA
* *
22299 ATCGAATAATTCTTGTAACTGAACCTTCAACTCCTTATGTTCATTTGGAGCCATGCGATAGGGGT
521 ATCGAATAATTCTTGTAACTGAACCTTCAACTCCTTAAGTTCATTTGGAGCCATGCGATAGGGAT
* * *
22364 GCCATGGAAATAAGTGCAGATCCTGGATAAGTCCCAATCTAAAACTCTATCTCTCTATCAGGAGG
586 GCCATGGAAATAAGTGCAGATCCTGGATAAGTCCCAATCTAAAACTCTACCTCTCTAACAAGAGG
* ** *
22429 TAACCCTGACAACTCCTCCGGAAAGACATCAGGAAACTCGCTAACTGTATGAATCTTCTTAATCG
651 TAACCCTGACAACTCCTCCGGAAAGACATCAGGAAACTCGCTAACTGTACGAATCCCCTCAATCG
* *
22494 CGGACAAGGAACCTTTAATGTTCAAAATAAAATCAATGAAAGACTCATATCCCTTCTAGGCCATA
716 CGGACAAGGAACCTTTAATGTTCAAAATAAAATCAATGAAAGACTCAAAACCCTTCTAGGCCATA
*
22559 TGATCAATTTCCCAAGCTAAAACTATATTGGAGAGATAGCTGCGACGTTCACCAATTAACACAAC
781 TGATCAATTTCCAAAGCTAAAACTATATTGGAGAGATAGCTGCGACGTTCACCAATTAACACAAC
*
22624 AATCCGACCATCAGAAGTCTTCAGAGTATCTGTCTTGTATTCAATATCCAAATTGACCTTATGTT
846 AATCCGACCATCAGAAGTCTTCAGAGTATCTGTCTTGTATTCAAAATCCAAATTGACCTTATGTT
* *
22689 TATTCAACTAATCCATCCCCAGAATTAAATTCAACTCCTCTAAAGGAAGCTCCATAAGGTCTGCA
911 TATTCAACCAATCCATCCCCAGAATTAAATTCAACTCCTCTAAAGGAAGCTCCATAAGGTATGCA
* * *
22754 GAATGACACCTCCCGAATCCAAAACTCACATTTGCTCAACTTAACATACAACTGATGCTCTCTCA
1 GAATGACACCTCCCGAAGCCAAAACTCACATTTGCTCAAATTAACATACAACCGATGCTCTCTCA
* * * *
22819 GAGTCTGTAGAACAATCTTCAAATGATCAT-CATGCTCTCTGCCTCGGTTCGGGAATATACCAGA
66 GAGTCTGTAGAACAATCTTCAAATGATCATCCA---ACTCTGCCTCGATTCAGGAATAAACCAGA
* * * *
22883 ATATCATCAATGAATACAACTCCAAATTGATCCAAATATGGTCGGAACATACAATTCATCAAATC
128 ATATCATCAATGAATACAACTACAAATTGATCCAAATACGGTCGGAACACACAATACATCAAATC
* ** *
22948 CATAAAAACTACGGGAGTGTTCGTCAGACCAAAAGGCATCACCAAGAACTCATAATTCCCATATC
193 CATAAAAACTACGGGAGCGTTCGTCAGACCAAAAAACATCACCAAGAACTCATAATGCCCATATC
* *
23013 TAGTGCGAATGACAGTCTTCGCAACATCAGAACCTTTAATTTTTAATTGATAATACCTCGAACGA
258 TAGTGCGAATGACAGTCTTCGCAACATCAGAACCTTTAACTTTTAATTGATAATACCCCGAACGA
* **
23078 AGATTAATCTTAGAGAATACAATAGCACATCGCAATTGATCAAATAAGTCATCAATCCTGGGTAG
323 AGATCAATCTTAGAGAATACAATAGCACATCAAAATTGATCAAATAAGTCATCAATCCTGGGTAG
* * *
23143 TGGGTAGTTATTCTTAACTATCATCTTATTCAACTTTCGGTAGTCAATACATAGCCTTAGTGATA
388 TGGGTACTTATTCTTAACTATCATCTAATTCAACTTCCGGTAGTCAATACATAGCCTTAGTGATA
*
23208 CATCCTTC-TTTTTCACAAACAGAACTAGAGCTCCCCAGGGTGAGGTACTATGCCTGATAAATCC
453 CATCCTTCTTTTTTCACAAACAGAACTAGAGCTCCACAGGGTGAGGTACTATGCCTGATAAATCC
* * *
23272 TCAATCGAATAATTCTTGTAACTGAACCTTTAACTCCTTAAGTTCATTTGGAGCCTTGTGATA-G
518 TCAATCGAATAATTCTTGTAACTGAACCTTCAACTCCTTAAGTTCATTTGGAGCCATGCGATAGG
* * * *
23336 GATGCCATGGAAATATGTGCAGATCCTTGATAAGTCTCAATCTAAAACTCTACCTCTTTAACAAG
583 GATGCCATGGAAATAAGTGCAGATCCTGGATAAGTCCCAATCTAAAACTCTACCTCTCTAACAAG
* * ** *
23401 AGGTAACCTTGGCAACTCCTTTGGAAAGACATCAGGAAACTCGCTAATTGTACGAATCCCCTCAA
648 AGGTAACCCTGACAACTCCTCCGGAAAGACATCAGGAAACTCGCTAACTGTACGAATCCCCTCAA
* * * * *
23466 TCGTGGACAAGGAACCTTTAATGTTCACAATACAAGT-AATGAAAGACTTAAAACCCTTCTGGGC
713 TCGCGGACAAGGAACCTTTAATGTTCAAAATA-AAATCAATGAAAGACTCAAAACCCTTCTAGGC
*
23530 CATATGATTAATTTCCAAAGCTAAAACTATATTGGAGAGATAGCTGCGACGTTCACCAATTAACA
777 CATATGATCAATTTCCAAAGCTAAAACTATATTGGAGAGATAGCTGCGACGTTCACCAATTAACA
23595 CAACAATCCGACCATCAGAAGTCTTCAGAGTAGT-TGTCTTGTATTCAAAATCCAAATTGACCTT
842 CAACAATCCGACCATCAGAAGTCTTCAGAGTA-TCTGTCTTGTATTCAAAATCCAAATTGACCTT
* * *
23659 ATGTTTATTCAACCAATCTATCCCCAGAATTAAATTGAACTCCTCTAAATGAAGCTCCATAAGGT
906 ATGTTTATTCAACCAATCCATCCCCAGAATTAAATTCAACTCCTCTAAAGGAAGCTCCATAAGGT
23724 ATGCA
971 ATGCA
23729 AGAAATATTT
Statistics
Matches: 892, Mismatches: 78, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
974 2 0.00
975 446 0.50
976 115 0.13
977 329 0.37
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (975 bp):
GAATGACACCTCCCGAAGCCAAAACTCACATTTGCTCAAATTAACATACAACCGATGCTCTCTCA
GAGTCTGTAGAACAATCTTCAAATGATCATCCAACTCTGCCTCGATTCAGGAATAAACCAGAATA
TCATCAATGAATACAACTACAAATTGATCCAAATACGGTCGGAACACACAATACATCAAATCCAT
AAAAACTACGGGAGCGTTCGTCAGACCAAAAAACATCACCAAGAACTCATAATGCCCATATCTAG
TGCGAATGACAGTCTTCGCAACATCAGAACCTTTAACTTTTAATTGATAATACCCCGAACGAAGA
TCAATCTTAGAGAATACAATAGCACATCAAAATTGATCAAATAAGTCATCAATCCTGGGTAGTGG
GTACTTATTCTTAACTATCATCTAATTCAACTTCCGGTAGTCAATACATAGCCTTAGTGATACAT
CCTTCTTTTTTCACAAACAGAACTAGAGCTCCACAGGGTGAGGTACTATGCCTGATAAATCCTCA
ATCGAATAATTCTTGTAACTGAACCTTCAACTCCTTAAGTTCATTTGGAGCCATGCGATAGGGAT
GCCATGGAAATAAGTGCAGATCCTGGATAAGTCCCAATCTAAAACTCTACCTCTCTAACAAGAGG
TAACCCTGACAACTCCTCCGGAAAGACATCAGGAAACTCGCTAACTGTACGAATCCCCTCAATCG
CGGACAAGGAACCTTTAATGTTCAAAATAAAATCAATGAAAGACTCAAAACCCTTCTAGGCCATA
TGATCAATTTCCAAAGCTAAAACTATATTGGAGAGATAGCTGCGACGTTCACCAATTAACACAAC
AATCCGACCATCAGAAGTCTTCAGAGTATCTGTCTTGTATTCAAAATCCAAATTGACCTTATGTT
TATTCAACCAATCCATCCCCAGAATTAAATTCAACTCCTCTAAAGGAAGCTCCATAAGGTATGCA
Found at i:26732 original size:14 final size:14
Alignment explanation
Indices: 26708--26746 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
26698 TGAATTTTTT
26708 GTCAA-AGTCAACG
1 GTCAACAGTCAACG
*
26721 GTCAACAGTCAATG
1 GTCAACAGTCAACG
26735 GTCAACGAGTCA
1 GTCAAC-AGTCA
26747 GATCGGGCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.22
14 13 0.57
15 5 0.22
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (14 bp):
GTCAACAGTCAACG
Found at i:27506 original size:2 final size:2
Alignment explanation
Indices: 27499--27523 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27489 CCAAATTGCT
27499 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
27524 TGGTTATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45083 original size:24 final size:24
Alignment explanation
Indices: 45038--45083 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
45028 TCTCTTGTTC
*
45038 GAATCTCCCCTTTTTCTTCTATTT
1 GAATCTCCCCTTTTTCTGCTATTT
*
45062 GAATCTCTCTCTTTTT-TGCTAT
1 GAATCTC-CCCTTTTTCTGCTAT
45084 CTCTTCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.13, C:0.26, G:0.07, T:0.54
Consensus pattern (24 bp):
GAATCTCCCCTTTTTCTGCTATTT
Found at i:45534 original size:3 final size:3
Alignment explanation
Indices: 45517--45567 Score: 59
Period size: 3 Copynumber: 16.3 Consensus size: 3
45507 GTAAAAAATG
*
45517 ATA ATA AAA ATTA ATA ATA ATA AT- ATAA ATA ATA ATA ATA ATAA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA AT-A ATA ATA ATA ATA AT-A ATA
45564 ATA A
1 ATA A
45568 CCCAGACAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 2 0.05
3 33 0.79
4 7 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:45547 original size:9 final size:9
Alignment explanation
Indices: 45517--45567 Score: 59
Period size: 10 Copynumber: 5.4 Consensus size: 9
45507 GTAAAAAATG
*
45517 ATAATAAAA
1 ATAATAATA
45526 ATTAATAATA
1 A-TAATAATA
45536 ATAAT-ATAA
1 ATAATAAT-A
45545 ATAATAATA
1 ATAATAATA
45554 ATAATAAATA
1 ATAAT-AATA
45564 ATAA
1 ATAA
45568 CCCAGACAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
8 2 0.05
9 17 0.46
10 18 0.49
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
ATAATAATA
Found at i:45552 original size:21 final size:20
Alignment explanation
Indices: 45519--45564 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
45509 AAAAAATGAT
45519 AATAAAAATTAATAATAATA
1 AATAAAAATTAATAATAATA
45539 ATATAAATAA-TAATAATAATA
1 A-ATAAA-AATTAATAATAATA
45560 AATAA
1 AATAA
45565 TAACCCAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.21
21 17 0.71
22 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AATAAAAATTAATAATAATA
Found at i:47112 original size:30 final size:30
Alignment explanation
Indices: 47072--47130 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
47062 TTGACTTACC
* *
47072 ATTTTGTAACAAACGATAACATTAGTGACT
1 ATTTTATAACAAACGATAACATTAATGACT
* *
47102 ATTTTATAACAAATGGTAACATTAATGAC
1 ATTTTATAACAAACGATAACATTAATGAC
47131 CAATTCGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (30 bp):
ATTTTATAACAAACGATAACATTAATGACT
Found at i:47532 original size:43 final size:43
Alignment explanation
Indices: 47469--47739 Score: 255
Period size: 43 Copynumber: 6.3 Consensus size: 43
47459 TTAGCGAAAG
* **
47469 ACAAACGCCGCAATAGGTGTTGATG-TTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAATAAGTGTTGA-GATTTAGCGGCGTTTTTATC
* *
47512 ACAAACGCCGCAAAAAGTGTTGAGATTTTAG-GACGTTTTTATC
1 ACAAACGCCGCAATAAGTGTTGAGA-TTTAGCGGCGTTTTTATC
* * * *
47555 ACAAGCGCCGCAATAAGTGTTGATATTTTGCGGAGTTTTTATC
1 ACAAACGCCGCAATAAGTGTTGAGATTTAGCGGCGTTTTTATC
* * * *
47598 ACAAACGACACAATAAGTGTTGAGATTTAGCGGTGTTTTTTCTC
1 ACAAACGCCGCAATAAGTGTTGAGATTTAGCGGCG-TTTTTATC
* * ** *
47642 AAAAACGCCGCAATCAGTGTTGAGATTTAGAAGTGTTTTTATC
1 ACAAACGCCGCAATAAGTGTTGAGATTTAGCGGCGTTTTTATC
* * *
47685 GA-AAATGCCGCAATAGGTGTTG-GCATTTAGCGTCGTTTTTTGAT-
1 -ACAAACGCCGCAATAAGTGTTGAG-ATTTAGCGGCG-TTTTT-ATC
47729 ACAAACGCCGC
1 ACAAACGCCGC
47740 TAAAGTTGTA
Statistics
Matches: 186, Mismatches: 33, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
42 6 0.03
43 123 0.66
44 55 0.30
45 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (43 bp):
ACAAACGCCGCAATAAGTGTTGAGATTTAGCGGCGTTTTTATC
Found at i:47683 original size:130 final size:129
Alignment explanation
Indices: 47469--47706 Score: 302
Period size: 130 Copynumber: 1.8 Consensus size: 129
47459 TTAGCGAAAG
* * * *
47469 ACAAACGCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTTCCCACAAACGCCGCAAAAAGTGTTG
1 ACAAACGACACAATAAGTGTTGATGTTTAGCGGCGTTTTTCCCAAAAACGCCGCAAAAAGTGTTG
* *
47534 AGATTTTAGGACGTTTTTATC-ACAAGCGCCGCAATAAGTGTTGATATTTTGCGGAGTTTTTATC
66 AGATTTTAGAACGTTTTTATCGA-AAACGCCGCAATAAGTGTTGATATTTTGCGGAGTTTTTATC
* * **
47598 ACAAACGACACAATAAGTGTTGA-GATTTAGCGGTGTTTTTTCTCAAAAACGCCGCAATCAGTGT
1 ACAAACGACACAATAAGTGTTGATG-TTTAGCGGCG-TTTTTCCCAAAAACGCCGCAAAAAGTGT
* * *
47662 TGAGA-TTTAGAAGTGTTTTTATCGAAAATGCCGCAATAGGTGTTG
64 TGAGATTTTAGAA-CGTTTTTATCGAAAACGCCGCAATAAGTGTTG
47707 GCATTTAGCG
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
128 1 0.01
129 35 0.38
130 55 0.60
131 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (129 bp):
ACAAACGACACAATAAGTGTTGATGTTTAGCGGCGTTTTTCCCAAAAACGCCGCAAAAAGTGTTG
AGATTTTAGAACGTTTTTATCGAAAACGCCGCAATAAGTGTTGATATTTTGCGGAGTTTTTATC
Found at i:47699 original size:87 final size:87
Alignment explanation
Indices: 47471--47739 Score: 228
Period size: 87 Copynumber: 3.1 Consensus size: 87
47461 AGCGAAAGAC
* ** * ** *
47471 AAACGCCGCAATAGGTGTTGATG-TTTAGCGGCGTTTTTCCCACAAACGCCGCAAAAAGTGTTGA
1 AAACGCCGCAATAAGTGTTGA-GATTTAGAAGAGTTTTTATCACAAACGCCGCAATAAGTGTTGA
** *
47535 GATTTTAG-GACG-TTTTTATCAC
65 GA-TTTAGCGGTGTTTTTTATCAA
* * * ** * *
47557 AAGCGCCGCAATAAGTGTTGATATTTTGCGGAGTTTTTATCACAAACGACACAATAAGTGTTGAG
1 AAACGCCGCAATAAGTGTTGAGATTTAGAAGAGTTTTTATCACAAACGCCGCAATAAGTGTTGAG
*
47622 ATTTAGCGGTGTTTTTTCTCAA
66 ATTTAGCGGTGTTTTTTATCAA
* * * *
47644 AAACGCCGCAATCAGTGTTGAGATTTAGAAGTGTTTTTATCGA-AAATGCCGCAATAGGTGTTG-
1 AAACGCCGCAATAAGTGTTGAGATTTAGAAGAGTTTTTATC-ACAAACGCCGCAATAAGTGTTGA
*
47707 GCATTTAGC-GTCGTTTTTTGAT-AC
65 G-ATTTAGCGGT-GTTTTTT-ATCAA
47731 AAACGCCGC
1 AAACGCCGC
47740 TAAAGTTGTA
Statistics
Matches: 149, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
85 5 0.03
86 60 0.40
87 82 0.55
88 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (87 bp):
AAACGCCGCAATAAGTGTTGAGATTTAGAAGAGTTTTTATCACAAACGCCGCAATAAGTGTTGAG
ATTTAGCGGTGTTTTTTATCAA
Found at i:47880 original size:44 final size:43
Alignment explanation
Indices: 47720--47917 Score: 182
Period size: 44 Copynumber: 4.6 Consensus size: 43
47710 TTTAGCGTCG
* **
47720 TTTTTTGATACAAACGCCGCTAAA-GTTGTAGTAGATAAAGGCA
1 TTTTTGGATACAAACGCCGCTAAAGGTT-TAGTAGATAGCGGCA
** * *
47763 TTTTTTTATACAAACGCCGCTAAAGGTCTAGTAGATAGCGGCG
1 TTTTTGGATACAAACGCCGCTAAAGGTTTAGTAGATAGCGGCA
* * * *
47806 TTTTTAGGATACAAACGTCGCTAAAGGTTTGGTATATTGCGGCA
1 TTTTT-GGATACAAACGCCGCTAAAGGTTTAGTAGATAGCGGCA
* * * * * **
47850 TTTTTAGGATACAAACGCCGCTAAATGTTTGGTATATTGTGGTG
1 TTTTT-GGATACAAACGCCGCTAAAGGTTTAGTAGATAGCGGCA
* *
47894 TTTTTTGTTACAAACGCCGCTAAA
1 TTTTTGGATACAAACGCCGCTAAA
47918 AAACACAGAA
Statistics
Matches: 133, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
43 57 0.43
44 76 0.57
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (43 bp):
TTTTTGGATACAAACGCCGCTAAAGGTTTAGTAGATAGCGGCA
Found at i:56848 original size:42 final size:42
Alignment explanation
Indices: 56801--56949 Score: 192
Period size: 42 Copynumber: 3.5 Consensus size: 42
56791 TACTAAGGCA
* * * *
56801 TTTATTACGAAAATGCCACTAACGGAGAAAACAAATGCAGCG
1 TTTATTACGAAAACGCCACTAAAGGAGAAAACAATTACAGCG
* * *
56843 TTTATTACAAAAACGCCACTAATGGAGAAAACAATTACAGTG
1 TTTATTACGAAAACGCCACTAAAGGAGAAAACAATTACAGCG
* *
56885 TTTATTATGAAAACGCCACTAAAGGAGAAAACAATTACGGCG
1 TTTATTACGAAAACGCCACTAAAGGAGAAAACAATTACAGCG
*
56927 TTTATTTC-AAAAGCGCCACTAAA
1 TTTATTACGAAAA-CGCCACTAAA
56950 TTACAACTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
41 4 0.04
42 89 0.96
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (42 bp):
TTTATTACGAAAACGCCACTAAAGGAGAAAACAATTACAGCG
Found at i:56968 original size:42 final size:41
Alignment explanation
Indices: 56922--57053 Score: 135
Period size: 41 Copynumber: 3.2 Consensus size: 41
56912 AAAACAATTA
* *
56922 CGGCGTTTATTTCAAAAGCGCCACTAAATTACAACTTTTTAG
1 CGGCGTTTATGTCAAAAACGCCACTAAA-TACAACTTTTTAG
* * *
56964 CGGCGTTT-GGT-AACAAATGCCACTAAATACAACTCTATT-G
1 CGGCGTTTATGTCAA-AAACGCCACTAAATACAACT-TTTTAG
* *
57004 CGACGTTTATGTCAAAAACGCCATTAAAGTACAACTTTTTAG
1 CGGCGTTTATGTCAAAAACGCCACTAAA-TACAACTTTTTAG
*
57046 CGGTGTTT
1 CGGCGTTT
57054 GGGGTTTAGA
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
40 17 0.24
41 31 0.43
42 24 0.33
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (41 bp):
CGGCGTTTATGTCAAAAACGCCACTAAATACAACTTTTTAG
Found at i:58544 original size:57 final size:57
Alignment explanation
Indices: 58480--58594 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 57
58470 AAAAAATGCC
* * ** *
58480 ACTATTGATTAACACTATTGTGGTGTTTGTTTAAAAGCGTCACGATTGATTAACACT
1 ACTATTGATTAACACTATTGCGGTGTTTGTCTAAAAGCACCACGATTGATTAAAACT
*
58537 ACTATTGATTAACACTATTGCGGTGTTTGTCTAAAAGCACCACTATTGATTAAAACT
1 ACTATTGATTAACACTATTGCGGTGTTTGTCTAAAAGCACCACGATTGATTAAAACT
58594 A
1 A
58595 TTACGGCGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (57 bp):
ACTATTGATTAACACTATTGCGGTGTTTGTCTAAAAGCACCACGATTGATTAAAACT
Found at i:59181 original size:3 final size:3
Alignment explanation
Indices: 59173--59204 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
59163 AGAAGATTTT
59173 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
59205 CTATCACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:59467 original size:15 final size:15
Alignment explanation
Indices: 59431--59468 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
59421 ACGTCCTCTG
59431 CCACCACCCCCACGT
1 CCACCACCCCCACGT
*
59446 CTACCACCCCCAC-T
1 CCACCACCCCCACGT
59460 CCATCCACC
1 CCA-CCACC
59469 ACTAACATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.21, C:0.66, G:0.03, T:0.11
Consensus pattern (15 bp):
CCACCACCCCCACGT
Found at i:59500 original size:30 final size:30
Alignment explanation
Indices: 59455--59531 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
59445 TCTACCACCC
59455 CCACTCC-ATCCACCACTAACATCTCTTCCT
1 CCACTCCTA-CCACCACTAACATCTCTTCCT
* * * *
59485 CCATTCCTACCACCACCACCGTCTCTTCCT
1 CCACTCCTACCACCACTAACATCTCTTCCT
59515 CCACTCCTACCACCACT
1 CCACTCCTACCACCACT
59532 CTTCCGCCAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
30 39 0.98
31 1 0.03
ACGTcount: A:0.21, C:0.53, G:0.01, T:0.25
Consensus pattern (30 bp):
CCACTCCTACCACCACTAACATCTCTTCCT
Found at i:63267 original size:13 final size:13
Alignment explanation
Indices: 63249--63275 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
63239 TTACAGAAGC
63249 GCATATGAAGACT
1 GCATATGAAGACT
63262 GCATATGAAGACT
1 GCATATGAAGACT
63275 G
1 G
63276 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:67684 original size:21 final size:20
Alignment explanation
Indices: 67653--67697 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
67643 TAACCACTTA
67653 ATTATATAATCTTTTTAGTTTT
1 ATTATATAATC-TTTTA-TTTT
67675 ATTAT-TAATCTTTTATTTT
1 ATTATATAATCTTTTATTTT
67694 ATTA
1 ATTA
67698 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 5 0.22
21 5 0.22
22 5 0.22
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTATATAATCTTTTATTTT
Found at i:67718 original size:23 final size:22
Alignment explanation
Indices: 67692--67740 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
67682 ATCTTTTATT
* *
67692 TTATTAATTAGATTATTTAATTA
1 TTATTAATTAAATCA-TTAATTA
67715 TTATTAATTAAATCATTAATTA
1 TTATTAATTAAATCATTAATTA
67737 TTAT
1 TTAT
67741 CAGTTGACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATTAATTAAATCATTAATTA
Found at i:67823 original size:15 final size:15
Alignment explanation
Indices: 67763--67824 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
67753 ATACTGATAT
67763 TTTTTATATTTTAAA
1 TTTTTATATTTTAAA
* **
67778 ATTAAATATTTTATAA
1 TTTTTATATTTTA-AA
*
67794 TATTATTAAATTTTAAA
1 T-TT-TTATATTTTAAA
67811 TTTTTATATTTTAA
1 TTTTTATATTTTAA
67825 TACTAATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
15 20 0.56
16 4 0.11
17 5 0.14
18 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTATATTTTAAA
Found at i:67911 original size:28 final size:27
Alignment explanation
Indices: 67851--67904 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
67841 ATATGTGTAA
*
67851 GTTTTAAAATATAAAATATTAACTTTT
1 GTTTTAAAATATAAAATATTAAATTTT
*
67878 GTTTTAAAATATAAAAATCTTAAATTT
1 GTTTTAAAATAT-AAAATATTAAATTT
67905 ATTTTTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (27 bp):
GTTTTAAAATATAAAATATTAAATTTT
Found at i:70119 original size:13 final size:13
Alignment explanation
Indices: 70101--70145 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
70091 CATTGCCATT
*
70101 TCATCATCATCCA
1 TCATCAACATCCA
*
70114 TCATCAACATCCT
1 TCATCAACATCCA
*
70127 TCATCAAGA-CCA
1 TCATCAACATCCA
70139 TCATCAA
1 TCATCAA
70146 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:70496 original size:21 final size:22
Alignment explanation
Indices: 70465--70523 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
70455 AAATTGGAGT
70465 GAAAA-AAGAAAGAAAAATAT-A
1 GAAAAGAAGAAAGAAAAAT-TCA
70486 -AAAAGAAGAAA-AAAAATTCA
1 GAAAAGAAGAAAGAAAAATTCA
70506 GAAAAGAAGAAAAGAAAA
1 GAAAAGAAG-AAAGAAAA
70524 GAAAAAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 1 0.03
20 11 0.33
21 14 0.42
22 3 0.09
23 4 0.12
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (22 bp):
GAAAAGAAGAAAGAAAAATTCA
Found at i:70531 original size:21 final size:21
Alignment explanation
Indices: 70466--70531 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
70456 AATTGGAGTG
*
70466 AAAA-AAGAAAGAAAAAT-ATA
1 AAAAGAAGAAA-AAAAATGAAA
** *
70486 AAAAGAAGAAAAAAAATTCAG
1 AAAAGAAGAAAAAAAATGAAA
70507 AAAAGAAGAAAAGAAAA-GAAA
1 AAAAGAAGAAAA-AAAATGAAA
70528 AAAA
1 AAAA
70532 TCAAAAAGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
20 10 0.27
21 23 0.62
22 4 0.11
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.06
Consensus pattern (21 bp):
AAAAGAAGAAAAAAAATGAAA
Found at i:74391 original size:3 final size:3
Alignment explanation
Indices: 74383--74410 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
74373 TAAAAAGGAA
74383 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
74411 TCATATAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:74441 original size:9 final size:9
Alignment explanation
Indices: 74422--74637 Score: 144
Period size: 9 Copynumber: 22.9 Consensus size: 9
74412 CATATAACAC
74422 ATAATACTAT
1 ATAATA-TAT
74432 A-AATGATAT
1 ATAAT-ATAT
74441 ATAATATAT
1 ATAATATAT
**
74450 AT--GCTAT
1 ATAATATAT
74457 ATAATATAT
1 ATAATATAT
74466 AT-ATATAT
1 ATAATATAT
74474 ACTAATACATAT
1 A-TAAT--ATAT
*
74486 GTAATATAT
1 ATAATATAT
*
74495 AAAATATAT
1 ATAATATAT
74504 ATAATATAAT
1 ATAATAT-AT
**
74514 ATACCATAT
1 ATAATATAT
74523 A-AATATAT
1 ATAATATAT
74531 A-ATATATAAT
1 ATA-ATAT-AT
74541 ATAATATAAT
1 ATAATAT-AT
74551 ATAAATATACT
1 AT-AATATA-T
74562 ATAATATAT
1 ATAATATAT
74571 AATATATACTACT
1 -ATA-ATA-TA-T
74584 ATAATATAT
1 ATAATATAT
74593 AT-ATATAT
1 ATAATATAT
74601 AATATATACTAT
1 -ATA-ATA-TAT
74613 ATAATATAT
1 ATAATATAT
74622 A-ACATATAT
1 ATA-ATATAT
74631 AT-ATATA
1 ATAATATA
74638 ATATGTTATC
Statistics
Matches: 170, Mismatches: 12, Indels: 50
0.73 0.05 0.22
Matches are distributed among these distances:
7 5 0.03
8 26 0.15
9 60 0.35
10 41 0.24
11 25 0.15
12 12 0.07
13 1 0.01
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (9 bp):
ATAATATAT
Found at i:74449 original size:2 final size:2
Alignment explanation
Indices: 74437--74641 Score: 149
Period size: 2 Copynumber: 108.0 Consensus size: 2
74427 ACTATAAATG
*
74437 AT AT AT A- AT AT AT AT GCT AT AT A- AT AT AT AT AT AT AT ACT A-
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
74478 AT AC AT AT GT A- AT AT AT A- AA AT AT AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
74516 ACC AT AT AA AT AT AT A- AT AT AT A- AT AT A- AT AT A- AT AT AA
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74555 AT AT ACT AT A- AT AT AT A- AT AT AT ACT ACT AT A- AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT A-T A-T AT AT AT AT AT AT
*
74595 AT AT AT A- AT AT AT ACT AT AT A- AT AT AT A- AC AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
74635 AT A- AT AT
1 AT AT AT AT
74642 GTTATCCGAA
Statistics
Matches: 165, Mismatches: 14, Indels: 48
0.73 0.06 0.21
Matches are distributed among these distances:
1 18 0.11
2 134 0.81
3 13 0.08
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:74449 original size:7 final size:7
Alignment explanation
Indices: 74384--74641 Score: 185
Period size: 7 Copynumber: 36.0 Consensus size: 7
74374 AAAAAGGAAA
74384 ATAATA-
1 ATAATAT
74390 ATAATA-
1 ATAATAT
74396 ATAATA-
1 ATAATAT
74402 ATAATA-
1 ATAATAT
74408 AT-ATCAT
1 ATAAT-AT
* *
74415 ATAACAC
1 ATAATAT
74422 ATAATACT
1 ATAATA-T
74430 ATAA-AT
1 ATAATAT
74436 GAT-ATAT
1 -ATAATAT
74443 A-ATATAT
1 ATA-ATAT
**
74450 ATGCTAT
1 ATAATAT
74457 ATAATAT
1 ATAATAT
74464 ATATATAT
1 ATA-ATAT
*
74472 ATACTA-
1 ATAATAT
74478 ATACATAT
1 ATA-ATAT
*
74486 GTAATAT
1 ATAATAT
*
74493 ATAAAAT
1 ATAATAT
74500 ATATATAAT
1 ATA-AT-AT
74509 ATAATAT
1 ATAATAT
**
74516 ACCATAT
1 ATAATAT
74523 A-AATAT
1 ATAATAT
74529 ATAATAT
1 ATAATAT
74536 ATAATATAAT
1 AT-A-AT-AT
74546 ATAATAT
1 ATAATAT
*
74553 AAATATACT
1 ATA-ATA-T
74562 ATAATAT
1 ATAATAT
74569 ATAATAT
1 ATAATAT
*
74576 ATACTACT
1 ATAATA-T
74584 ATAATAT
1 ATAATAT
74591 ATATATAT
1 ATA-ATAT
74599 ATAATAT
1 ATAATAT
*
74606 ATACTAT
1 ATAATAT
74613 ATAATAT
1 ATAATAT
*
74620 ATAACAT
1 ATAATAT
74627 ATATATAT
1 ATA-ATAT
74635 ATAATAT
1 ATAATAT
74642 GTTATCCGAA
Statistics
Matches: 204, Mismatches: 25, Indels: 45
0.74 0.09 0.16
Matches are distributed among these distances:
5 2 0.01
6 32 0.16
7 110 0.54
8 45 0.22
9 11 0.05
10 4 0.02
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.39
Consensus pattern (7 bp):
ATAATAT
Done.