Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002298.1 Hibiscus syriacus cultivar Beakdansim tig00004677_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: 79604
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4995 original size:17 final size:17
Alignment explanation
Indices: 4954--5007 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
4944 TTGCTTGAAG
*
4954 ATGAAAAAAAAAAGGAAA
1 ATGAAAAAAAAAA-AAAA
* * *
4972 TTTAAAAAAAAGAAAAA
1 ATGAAAAAAAAAAAAAA
4989 ATGAAAAAAAAAAAAAA
1 ATGAAAAAAAAAAAAAA
5006 AT
1 AT
5008 ATAAAAATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (17 bp):
ATGAAAAAAAAAAAAAA
Found at i:5013 original size:17 final size:17
Alignment explanation
Indices: 4957--5014 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
4947 CTTGAAGATG
* *
4957 AAAAAAAAAAGGAAATTT
1 AAAAAAAAAA-AAAATAT
4975 AAAAAAAAGAAAAAATGA-
1 AAAAAAAA-AAAAAAT-AT
4993 AAAAAAAAAAAAAATAT
1 AAAAAAAAAAAAAATAT
5010 AAAAA
1 AAAAA
5015 TATAAAATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 1 0.03
17 12 0.34
18 20 0.57
19 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (17 bp):
AAAAAAAAAAAAAATAT
Found at i:5028 original size:35 final size:35
Alignment explanation
Indices: 4951--5031 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
4941 GTTTTGCTTG
** *
4951 AAGATGAAAAAAAAAAGGAAATTTAAAAAAAAGAA
1 AAGATGAAAAAAAAAAAAAAATATAAAAAAAAGAA
* *
4986 AAAATGAAAAAAAAAAAAAAATATAAAAATATA-AA
1 AAGATGAAAAAAAAAAAAAAATATAAAAA-AAAGAA
*
5021 ATGATGAAAAA
1 AAGATGAAAAA
5032 GGAGGGTTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 36 0.95
36 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.14
Consensus pattern (35 bp):
AAGATGAAAAAAAAAAAAAAATATAAAAAAAAGAA
Found at i:6399 original size:53 final size:53
Alignment explanation
Indices: 6312--7466 Score: 1504
Period size: 53 Copynumber: 21.7 Consensus size: 53
6302 AGTGAAGCAA
*
6312 AAGAATATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCG-GACCCGTAGG
1 AAGATTATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGAG-CCCGTAGG
* * *
6366 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCAAGCCTGTAAG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
*
6419 AAGATTATTGTTTGAGTTCTTACTCCCTGAAGAAATAGAGAGCG-GACCCGTAGG
1 AAGATTATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGAG-CCCGTAGG
* * *
6473 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAA-AGAGAGC-AGACTCTTAAG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAG-CCCGTAGG
*
6525 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
* * *
6578 AAGATTATCGTTCGAGTGCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
* * * *
6631 CAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCAAGCCCGTAAG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
6684 AAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCG-GACCCGTAGG
1 AAGATTATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGAG-CCCGTAGG
* *
6738 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGATCCCGTAGG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
* * * * *
6791 AAGATTATCGTTTGAGTTCTACACCCTGAAGAAAGAGAGAGCGAGCCTGTAGG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
* * * *
6844 CAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCAAGCCCGTAAG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
*
6897 AAGATTATTGTTCGAGTTCTTACTCCCTTAAGAAATAGAGAGCGAGCCCGTAGG
1 AAGATTATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
* *
6951 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAA-AGAGAGCG-GACTCGTAAG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAG-CCCGTAGG
* * *
7003 AAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATTGAGAGAGAGCCCGTAGG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
* *
7056 AAGATTATCGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
* * *
7109 CAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
* * * * *
7162 CAGATTATTGTTCGAGTTCTTACTCCCTGAATAAAGAGAGAGTGAGCCCATAGG
1 AAGATTATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
** * * *
7216 CGGATGATTGTTCGAGTTCTACTCCTTGAAGAAATAGAGAGTGAGCCCGTAGG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
* * *
7269 AAGATTATCGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCG-GACCTGTAGG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAG-CCCGTAGG
** * * *
7322 AAGAAGATTGTTCGAGTTCTACTCCTTGAAGAAAGAGAGAGCGAACCCGTAGG
1 AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
* * * * *
7375 CAA-AATATTGCTCGAGTTTCTACTCCCTGAAGGAATATG-GAGCGAACCCATAGG
1 -AAGATTATTGTTCGAG-TTCTACTCCCTGAAGAAATA-GAGAGCGAGCCCGTAGG
** * *
7429 CAA-AAGATTGTTCGAGTTTTTACTCCCTGAAGGAATAG
1 -AAGATTATTGTTCGAG-TTCTACTCCCTGAAGAAATAG
7467 GGAGTGAACA
Statistics
Matches: 979, Mismatches: 103, Indels: 39
0.87 0.09 0.03
Matches are distributed among these distances:
51 1 0.00
52 95 0.10
53 600 0.61
54 282 0.29
55 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (53 bp):
AAGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGG
Found at i:6797 original size:213 final size:209
Alignment explanation
Indices: 6318--7466 Score: 1480
Period size: 213 Copynumber: 5.4 Consensus size: 209
6308 GCAAAAGAAT
6318 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGC-GACCCGTAGGAAGATTATTGTTCGAGT
* * * *
6383 TCTACTCCCTGAAGAAATAGAGAGCAAGCCTGTAAGAAGATTATTGTTTGAGTTCTTACTCCCTG
64 TCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTC-TACTCCCTG
*
6448 AAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAGAAA-AGAGA
128 AAGAAATAGAGAGCAG-CCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGA
* * *
6512 GCAGACTCTTAAGAAGATG
192 GC-GACCCGTAGGAAGATG
* *
6531 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATCGTTCGAGTG
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGA-CCCGTAGGAAGATTATTGTTCGAGTT
* * *
6596 CTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGCAGATGATTGTTCGAGTTCTACTCCCTGAA
65 CTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAA
* *
6661 GAAATAGAGAGCAAGCCCGTAAGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAG
130 GAAATAGAGAGC-AGCCCGTAGGAAGATTATTGTTCGAGTTC-TACTCCCTGAAGAAAGAGAGAG
6726 CGGACCCGTAGGAAGATG
193 C-GACCCGTAGGAAGATG
* *
6744 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGATCCCGTAGGAAGATTATCGTTTGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGA-CCCGTAGGAAGATTATTGTTCGAGTT
* * * * *
6809 CTACACCCTGAAGAAAGAGAGAGCGAGCCTGTAGGCAGATGATTGTTCGAGTTCTACTCCCTGAA
65 CTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAA
* * *
6874 GAAATAGAGAGCAAGCCCGTAAGAAGATTATTGTTCGAGTTCTTACTCCCTTAAGAAATAGAGAG
130 GAAATAGAGAGC-AGCCCGTAGGAAGATTATTGTTCGAGTTC-TACTCCCTGAAGAAAGAGAGAG
*
6939 CGAGCCCGTAGGAAGATT
193 CGA-CCCGTAGGAAGATG
* * *
6957 ATTGTTCGAGTTCTACTCCCTGAAGAAA-AGAGAGCGGACTCGTAAGAAGATGATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGC-GACCCGTAGGAAGATTATTGTTCGAGTT
* * *
7021 CTACTCCCTGAAGAAATTGAGAGAGAGCCCGTAGGAAGATTATCGTTCGAGTTCTACTCCCTGAA
65 CTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAA
* * *
7086 GAAAGAGAGAGCGAGCCCGTAGGCAGATGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGC
130 GAAATAGAGAGC-AGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGC
* *
7151 GAGCCCGTAGGCAGATT
194 GA-CCCGTAGGAAGATG
* * * * ** *
7168 ATTGTTCGAGTTCTTACTCCCTGAATAAAGAGAGAGTGAGCCCATAGGCGGATGATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGA-CCCGTAGGAAGATTATTGTTCGAGT
* * *
7233 TCTACTCCTTGAAGAAATAGAGAGTGAGCCCGTAGGAAGATTATCGTTCGAGTTCTACTCCCTGA
64 TCTACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGA
* * * ** *
7298 AGAAAGAGAGAGCGGACCTGTAGGAAGAAGATTGTTCGAGTTCTACTCCTTGAAGAAAGAGAGAG
129 AGAAATAGAGAGCAG-CCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAG
*
7363 CGAACCCGTAGGCAAAAT-
193 CG-ACCCGTAGG-AAGATG
* * * **
7381 ATTGCTCGAGTTTCTACTCCCTGAAGGAATATG-GAGCGAACCCATAGGCAA-AAGATTGTTCGA
1 ATTGTTCGAG-TTCTACTCCCTGAAGAAATA-GAGAGCG-ACCCGTAGG-AAGATTATTGTTCGA
* *
7444 GTTTTTACTCCCTGAAGGAATAG
62 G-TTCTACTCCCTGAAGAAATAG
7467 GGAGTGAACA
Statistics
Matches: 848, Mismatches: 71, Indels: 33
0.89 0.07 0.03
Matches are distributed among these distances:
211 101 0.12
212 251 0.30
213 469 0.55
214 27 0.03
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (209 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGACCCGTAGGAAGATTATTGTTCGAGTTC
TACTCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAG
AAATAGAGAGCAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGA
CCCGTAGGAAGATG
Found at i:7232 original size:478 final size:478
Alignment explanation
Indices: 6312--7460 Score: 1783
Period size: 478 Copynumber: 2.4 Consensus size: 478
6302 AGTGAAGCAA
* * * * *
6312 AAGAATATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGT
1 AAGATTATCGTTCGAGTTC-TACTCCCTGAAGAAAGAGAGAGCGGACCTGTAGGAAGATGATTGT
* *
6377 TCGAGTTCTACTCCCTGAAGAAATAGAGAGCAAGCCTGTAAGAAGATTATTGTTTGAGTTCTTAC
65 TCGAGTTCTACTCCCTGAAGAAATAGAGAGCAAGCCCGTAAGAAGATTATTGTTCGAGTTCTTAC
6442 TCCCTGAAGAAATAGAGAGCG-GACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAGAA
130 TCCCTGAAGAAATAGAGAGCGAG-CCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAGAA
* *
6506 AAGAGAGCAGACTCTTAAGAAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAGC
194 AAGAGAGCAGACTCGTAAGAAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGAGAGC
6571 CCGTAGGAAGATTATCGTTCGAGTGCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGCAGAT
259 CCGTAGGAAGATTATCGTTCGAGTGCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGCAGAT
*
6636 GATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCAAGCCCGTAAGAAGATTATTGTTCGAGT
324 GATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCAAGCCCGTAAGAAGATTATTGTTCGAGT
* *
6701 TCTTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATGATTGTTCGAGTTCTACTCCCTG
389 TCTTACTCCCTGAAGAAAGAGAGAGCGGACCCATAGGAAGATGATTGTTCGAGTTCTACTCCCTG
*
6766 AAGAAATAGAGAGCGATCCCGTAGG
454 AAGAAATAGAGAGCGAGCCCGTAGG
* * *
6791 AAGATTATCGTTTGAGTTCTACACCCTGAAGAAAGAGAGAGC-GAGCCTGTAGGCAGATGATTGT
1 AAGATTATCGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGGA-CCTGTAGGAAGATGATTGT
6855 TCGAGTTCTACTCCCTGAAGAAATAGAGAGCAAGCCCGTAAGAAGATTATTGTTCGAGTTCTTAC
65 TCGAGTTCTACTCCCTGAAGAAATAGAGAGCAAGCCCGTAAGAAGATTATTGTTCGAGTTCTTAC
*
6920 TCCCTTAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAGAAA
130 TCCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAGAAA
* *
6985 AGAGAGCGGACTCGTAAGAAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATTGAGAGAGAGCC
195 AGAGAGCAGACTCGTAAGAAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGAGAGCC
*
7050 CGTAGGAAGATTATCGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGCAGATG
260 CGTAGGAAGATTATCGTTCGAGTGCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGCAGATG
* * *
7115 ATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGCAGATTATTGTTCGAGTT
325 ATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCAAGCCCGTAAGAAGATTATTGTTCGAGTT
* * ** *
7180 CTTACTCCCTGAATAAAGAGAGAG-TGAGCCCATAGGCGGATGATTGTTCGAGTTCTACTCCTTG
390 CTTACTCCCTGAAGAAAGAGAGAGCGGA-CCCATAGGAAGATGATTGTTCGAGTTCTACTCCCTG
*
7244 AAGAAATAGAGAGTGAGCCCGTAGG
454 AAGAAATAGAGAGCGAGCCCGTAGG
*
7269 AAGATTATCGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGGACCTGTAGGAAGAAGATTGTT
1 AAGATTATCGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGGACCTGTAGGAAGATGATTGTT
* * * * *
7334 CGAGTTCTACTCCTTGAAGAAAGAGAGAGCGAA-CCCGTAGGCAA-AATATTGCTCGAGTT-TCT
66 CGAGTTCTACTCCCTGAAGAAATAGAGAGC-AAGCCCGTAAG-AAGATTATTGTTCGAGTTCT-T
* * * ** *
7396 ACTCCCTGAAGGAATATG-GAGCGAACCCATAGGCAA-AAGATTGTTCGAGTTTTTACTCCCTGA
128 ACTCCCTGAAGAAATA-GAGAGCGAGCCCGTAGG-AAGATTATTGTTCGAG-TTCTACTCCCTGA
7459 AG
190 AG
7461 GAATAGGGAG
Statistics
Matches: 615, Mismatches: 45, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
477 5 0.01
478 570 0.93
479 40 0.07
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (478 bp):
AAGATTATCGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGGACCTGTAGGAAGATGATTGTT
CGAGTTCTACTCCCTGAAGAAATAGAGAGCAAGCCCGTAAGAAGATTATTGTTCGAGTTCTTACT
CCCTGAAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAAGAAAA
GAGAGCAGACTCGTAAGAAGATGATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGAGAGCCC
GTAGGAAGATTATCGTTCGAGTGCTACTCCCTGAAGAAAGAGAGAGCGAGCCCGTAGGCAGATGA
TTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCAAGCCCGTAAGAAGATTATTGTTCGAGTTC
TTACTCCCTGAAGAAAGAGAGAGCGGACCCATAGGAAGATGATTGTTCGAGTTCTACTCCCTGAA
GAAATAGAGAGCGAGCCCGTAGG
Found at i:7679 original size:3 final size:3
Alignment explanation
Indices: 7663--7768 Score: 180
Period size: 3 Copynumber: 35.7 Consensus size: 3
7653 AAAATATATA
*
7663 TAT TAT TAAA TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
7708 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
7755 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
7769 CCCAAGCACT
Statistics
Matches: 98, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
2 4 0.04
3 92 0.94
4 2 0.02
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:7824 original size:12 final size:12
Alignment explanation
Indices: 7809--7833 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7799 TTTCCACCAC
7809 TCCATGTTTTAT
1 TCCATGTTTTAT
7821 TCCATGTTTTAT
1 TCCATGTTTTAT
7833 T
1 T
7834 ATTCCACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TCCATGTTTTAT
Found at i:8265 original size:146 final size:145
Alignment explanation
Indices: 8003--8269 Score: 365
Period size: 146 Copynumber: 1.8 Consensus size: 145
7993 CCAGAGATAA
* * * *
8003 GGATCTCCGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAATATATTGAA
1 GGATATCCGATCAACATTCCGAACGGTCAAAAGTTGAGGAAGACCATCACGAACAACATATTGAA
* **
8068 AAATCAGGACGATCGGACGGTGGACGGTAATGGATCGGAGAAAACAAATCCGGACGGTTTTTAGC
66 AAATCAGGACGATCGGACGGTGGACGGGAA-GGATCAAAGAAAACAAATCCGGACGGTTTTTAGC
8133 CTCTTGCCGGAGATCG
130 CTCTTGCCGGAGATCG
* * * **
8149 GGATATCCGATCAATATTCCTAACGTTCAAAAGTTGAGGAAGACCATCACGAATGACATATTGAA
1 GGATATCCGATCAACATTCCGAACGGTCAAAAGTTGAGGAAGACCATCACGAACAACATATTGAA
* * *
8214 AAATCAGGACGATCGGACGGTGGACGACGGCA-GATCAAAGAAAATACATCCGGACG
66 AAATCAGGACGATCGGACGGTGGACG--GGAAGGATCAAAGAAAACAAATCCGGACG
8270 ATTATCTTTG
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
146 102 0.98
148 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (145 bp):
GGATATCCGATCAACATTCCGAACGGTCAAAAGTTGAGGAAGACCATCACGAACAACATATTGAA
AAATCAGGACGATCGGACGGTGGACGGGAAGGATCAAAGAAAACAAATCCGGACGGTTTTTAGCC
TCTTGCCGGAGATCG
Found at i:9911 original size:17 final size:18
Alignment explanation
Indices: 9889--9922 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9879 AAGGGATGGA
9889 AGAGTGTAGAGC-TTCTT
1 AGAGTGTAGAGCATTCTT
*
9906 AGAGTGTGGAGCATTCT
1 AGAGTGTAGAGCATTCT
9923 AGATAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.32
Consensus pattern (18 bp):
AGAGTGTAGAGCATTCTT
Found at i:10703 original size:16 final size:16
Alignment explanation
Indices: 10682--10716 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10672 AATATATATT
*
10682 TAAGTTATGATAAGAA
1 TAAGTTAAGATAAGAA
*
10698 TAAGTTAAGTTAAGAA
1 TAAGTTAAGATAAGAA
10714 TAA
1 TAA
10717 AATATATGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
TAAGTTAAGATAAGAA
Found at i:10720 original size:21 final size:21
Alignment explanation
Indices: 10681--10720 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10671 TAATATATAT
*
10681 TTAAGTTATGATAAGAATAAG
1 TTAAGTTAAGATAAGAATAAG
10702 TTAAGTTAAGAATAA-AATA
1 TTAAGTTAAG-ATAAGAATA
10721 TATGTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (21 bp):
TTAAGTTAAGATAAGAATAAG
Found at i:10799 original size:28 final size:29
Alignment explanation
Indices: 10698--10997 Score: 123
Period size: 30 Copynumber: 10.3 Consensus size: 29
10688 ATGATAAGAA
** *
10698 TAAGTTAAGTTAAGAATAAAATATATGTTT
1 TAAGTTAAAATAAAAATAAAATATAT-TTT
*
10728 TGAGTTAAAATAAAAATAAAATATACATTTT
1 TAAGTTAAAATAAAAATAAAATAT--ATTTT
** * *
10759 TAAGTTATGATAAGAATAAGATAT-TTTT
1 TAAGTTAAAATAAAAATAAAATATATTTT
* * *
10787 TAAATTAAAAT-AATATTAAA-ATATTTT
1 TAAGTTAAAATAAAAATAAAATATATTTT
* ** **
10814 TAAGTTAAGATAAAAATAAAATAGGTTAAA
1 TAAGTTAAAATAAAAATAAAATATATT-TT
* * * * *
10844 TAATTTAAAATAATAATATAATCTA--TA
1 TAAGTTAAAATAAAAATAAAATATATTTT
* * *
10871 TAA--T-AAATTAAGATAAACTATATACTTTCA
1 TAAGTTAAAATAAAAATAAA--ATATA-TTT-T
* *
10901 AAAGTTAAAATAATAATAAAATATATTTT
1 TAAGTTAAAATAAAAATAAAATATATTTT
* * * **
10930 TAAAATTTTACATACGAATAAAATATATTTAT
1 T--AAGTTAAAATAAAAATAAAATATATTT-T
* * * *
10962 AAAATTAAAATAATAATAAAATAGATTTT
1 TAAGTTAAAATAAAAATAAAATATATTTT
10991 TAA-TTAA
1 TAAGTTAA
10998 GTTATTGTCA
Statistics
Matches: 196, Mismatches: 56, Indels: 38
0.68 0.19 0.13
Matches are distributed among these distances:
24 9 0.05
25 1 0.01
26 6 0.03
27 22 0.11
28 23 0.12
29 7 0.04
30 65 0.33
31 49 0.25
32 4 0.02
33 10 0.05
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (29 bp):
TAAGTTAAAATAAAAATAAAATATATTTT
Found at i:10821 original size:27 final size:27
Alignment explanation
Indices: 10698--10836 Score: 107
Period size: 27 Copynumber: 4.9 Consensus size: 27
10688 ATGATAAGAA
* *
10698 TAAGTTAAGTTAAGAATAAAATATATGTTT
1 TAAGTTAAGATAAAAAT-AAA-ATAT-TTT
* *
10728 TGAGTTAAAATAAAAATAAAATATACATTTT
1 TAAGTTAAGATAAAAAT-AAA-AT--ATTTT
* * *
10759 TAAGTTATGATAAGAATAAGATATTTTT
1 TAAGTTAAGATAAAAATAAAATA-TTTT
* * * *
10787 TAAATTAAAATAATATTAAAATATTTT
1 TAAGTTAAGATAAAAATAAAATATTTT
10814 TAAGTTAAGATAAAAATAAAATA
1 TAAGTTAAGATAAAAATAAAATA
10837 GGTTAAATAA
Statistics
Matches: 87, Mismatches: 19, Indels: 9
0.76 0.17 0.08
Matches are distributed among these distances:
27 24 0.28
28 21 0.24
29 2 0.02
30 22 0.25
31 16 0.18
32 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.38
Consensus pattern (27 bp):
TAAGTTAAGATAAAAATAAAATATTTT
Found at i:10826 original size:55 final size:60
Alignment explanation
Indices: 10698--10998 Score: 163
Period size: 61 Copynumber: 5.2 Consensus size: 60
10688 ATGATAAGAA
* * *
10698 TAAGTTAAGTTAAGAATAAAATATATGTTTTGAGTTAAAATAAAAATAAAATATACATTTT
1 TAAGTTAAGATAAGAATAAAATATATGTTTTAAATTAAAATAAAAATAAAATATA-ATTTT
* * * *
10759 TAAGTTATGATAAGAATAAGATAT-T-TTTTAAATTAAAAT-AATATTAAA-AT-ATTTT
1 TAAGTTAAGATAAGAATAAAATATATGTTTTAAATTAAAATAAAAATAAAATATAATTTT
* * * * *
10814 TAAGTTAAGATAAAAAT-AAA-ATA-G-GTTAAA-T-AATTTAAAATAATAATATAATCTATA
1 TAAGTTAAGATAAGAATAAAATATATGTTTTAAATTAAAATAAAAATAA-AATATAAT-T-TT
* * * *
10871 TAA--TAA-ATTAAG-ATAAACTATATACTTTCAAAAGTTAAAATAATAATAAAATAT-ATTTT
1 TAAGTTAAGA-TAAGAATAAAATATAT-GTTT-TAAA-TTAAAATAAAAATAAAATATAATTTT
* * * * * * *
10930 TAAAATTTTACATACGAATAAAATATAT-TTATAAAATTAAAATAATAATAAAATA-GATTTT
1 T--AAGTTAAGATAAGAATAAAATATATGTT-TTAAATTAAAATAAAAATAAAATATAATTTT
10991 TAA-TTAAG
1 TAAGTTAAG
10999 TTATTGTCAA
Statistics
Matches: 185, Mismatches: 29, Indels: 55
0.69 0.11 0.20
Matches are distributed among these distances:
51 3 0.02
52 6 0.03
53 9 0.05
54 7 0.04
55 30 0.16
56 4 0.02
57 6 0.03
58 10 0.05
59 17 0.09
60 5 0.03
61 50 0.27
62 12 0.06
63 15 0.08
64 11 0.06
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.38
Consensus pattern (60 bp):
TAAGTTAAGATAAGAATAAAATATATGTTTTAAATTAAAATAAAAATAAAATATAATTTT
Found at i:10982 original size:30 final size:30
Alignment explanation
Indices: 10732--10989 Score: 112
Period size: 31 Copynumber: 8.8 Consensus size: 30
10722 ATGTTTTGAG
* * *
10732 TTAAAATAAAAATAAAATATACATTT-TTAAG
1 TTAAAATAATAATAAAATAT--ATTTATAAAA
** * * *
10763 TTATGATAAGAATAAGATAT-TTT-TTAAA
1 TTAAAATAATAATAAAATATATTTATAAAA
* *
10791 TTAAAATAATATTAAAATAT-TTT-T-AAG
1 TTAAAATAATAATAAAATATATTTATAAAA
* * **
10818 TTAAGATAAAAATAAAATA-GGTTA-AATAA
1 TTAAAATAATAATAAAATATATTTATAA-AA
* * *
10847 TTTAAAATAATAATATAATCTATATA-ATAAA
1 -TTAAAATAATAATAAAATATATTTATA-AAA
* * *
10878 TTAAGATAA-ACT---ATATACTTTCA-AAAG
1 TTAAAATAATAATAAAATATA-TTT-ATAAAA
*
10905 TTAAAATAATAATAAAATATATTTTTAAAA
1 TTAAAATAATAATAAAATATATTTATAAAA
* * **
10935 TTTTACATACGAATAAAATATATTTATAAAA
1 -TTAAAATAATAATAAAATATATTTATAAAA
*
10966 TTAAAATAATAATAAAATAGATTT
1 TTAAAATAATAATAAAATATATTT
10990 TTAATTAAGT
Statistics
Matches: 170, Mismatches: 42, Indels: 31
0.70 0.17 0.13
Matches are distributed among these distances:
26 4 0.02
27 32 0.19
28 31 0.18
29 3 0.02
30 48 0.28
31 51 0.30
32 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (30 bp):
TTAAAATAATAATAAAATATATTTATAAAA
Found at i:11525 original size:21 final size:21
Alignment explanation
Indices: 11477--11528 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
11467 TTTTCAACCG
11477 TTTTGTAACTCATATAATTAC
1 TTTTGTAACTCATATAATTAC
* *
11498 TTATGTAACTCATTTAATTA-
1 TTTTGTAACTCATATAATTAC
11518 TATTTGTAACT
1 T-TTTGTAACT
11529 AGTTCAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.50
Consensus pattern (21 bp):
TTTTGTAACTCATATAATTAC
Found at i:16865 original size:15 final size:16
Alignment explanation
Indices: 16845--16874 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16835 AATTCAAGAA
16845 AAATAAAAAC-AAAAT
1 AAATAAAAACGAAAAT
16860 AAATAAAAACGAAAA
1 AAATAAAAACGAAAA
16875 CAAAAATGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (16 bp):
AAATAAAAACGAAAAT
Found at i:21697 original size:29 final size:29
Alignment explanation
Indices: 21641--21697 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
21631 AATTAAATAT
* *** *
21641 AATAGTTTAAATACCTAATTGAACAAAAA
1 AATAGATTAAATACCTAAAACAAAAAAAA
21670 AATAGATTAAATACCTAAAACAAAAAAA
1 AATAGATTAAATACCTAAAACAAAAAAA
21698 GGAGCATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (29 bp):
AATAGATTAAATACCTAAAACAAAAAAAA
Found at i:30022 original size:33 final size:34
Alignment explanation
Indices: 29964--30048 Score: 163
Period size: 33 Copynumber: 2.5 Consensus size: 34
29954 TATATATATA
29964 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
29998 TATATATATAATATTTTATA-TTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
30031 TATATATATAATATTTTA
1 TATATATATAATATTTTA
30049 GGGTTTGGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 31 0.61
34 20 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:30034 original size:42 final size:46
Alignment explanation
Indices: 29950--30035 Score: 117
Period size: 42 Copynumber: 2.0 Consensus size: 46
29940 TCCCGTCTCG
**
29950 ATTATATATATATATATATATATAATATTTTATATTTTTTATATTA
1 ATTATATATATATATATATATATAATATTTTATATTAATTATATTA
*
29996 ATTATATATATA-ATAT-TTTAT-AT-TTTTATATTAATTATAT
1 ATTATATATATATATATATATATAATATTTTATATTAATTATAT
30036 ATATAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 15 0.41
43 2 0.05
44 4 0.11
45 4 0.11
46 12 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (46 bp):
ATTATATATATATATATATATATAATATTTTATATTAATTATATTA
Found at i:32954 original size:24 final size:25
Alignment explanation
Indices: 32927--32974 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
32917 AATCGTCCTC
32927 AGAGAG-TATTTTTTAATCTAGCCA
1 AGAGAGTTATTTTTTAATCTAGCCA
*
32951 AGAGAGTTTTTTTTTAATCTAGCC
1 AGAGAGTTATTTTTTAATCTAGCC
32975 GAGAAAGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (25 bp):
AGAGAGTTATTTTTTAATCTAGCCA
Found at i:32987 original size:25 final size:25
Alignment explanation
Indices: 32935--32988 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
32925 TCAGAGAGTA
* **
32935 TTTTTTAATCTAGCCAAGAGAGTTT
1 TTTTTTAATCTAGCCAAGAAAGACT
*
32960 TTTTTTAATCTAGCCGAGAAAGACT
1 TTTTTTAATCTAGCCAAGAAAGACT
32985 TTTT
1 TTTT
32989 ACAGTGATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (25 bp):
TTTTTTAATCTAGCCAAGAAAGACT
Found at i:33950 original size:2 final size:2
Alignment explanation
Indices: 33943--33988 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
33933 TGTATGTCTG
33943 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
33985 TA TA
1 TA TA
33989 AGAGCCCGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34651 original size:82 final size:75
Alignment explanation
Indices: 34547--34711 Score: 204
Period size: 76 Copynumber: 2.1 Consensus size: 75
34537 ATATTTAAAA
**
34547 TAAAATAAAATAAATATTTTTATATCTCTAGACTAAATTCAATATTTTTTTTCATACTTATTTTT
1 TAAAATAAAATAAATATTTTTATATCTCTA-A--AAA-TCAATA--AATTTTCATACTTATTTTT
* *
34612 ATAAATATGAAAATTT
60 AGAAATATGAAAATAT
* * *
34628 TAGAAATAAATTTAATATTTTTATATCTTTAAAAATCAATAAATTTTCATACTTATTTTTAGAAA
1 TA-AAATAAAATAAATATTTTTATATCTCTAAAAATCAATAAATTTTCATACTTATTTTTAGAAA
34693 TATGAAAATAT
65 TATGAAAATAT
34704 TAAAATAA
1 TAAAATAA
34712 GTTCAATAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
75 6 0.08
76 33 0.43
78 6 0.08
79 3 0.04
81 3 0.04
82 25 0.33
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (75 bp):
TAAAATAAAATAAATATTTTTATATCTCTAAAAATCAATAAATTTTCATACTTATTTTTAGAAAT
ATGAAAATAT
Found at i:39425 original size:7 final size:7
Alignment explanation
Indices: 39413--39446 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
39403 TCCCTTTCTA
39413 CAAGTTG
1 CAAGTTG
39420 CAAGTTG
1 CAAGTTG
39427 CAAGTTG
1 CAAGTTG
*
39434 CGAGTTG
1 CAAGTTG
*
39441 CGAGTT
1 CAAGTT
39447 ACAACTGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (7 bp):
CAAGTTG
Found at i:40463 original size:47 final size:48
Alignment explanation
Indices: 40394--40488 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
40384 CGAATACGTA
* * * *
40394 CCAACAAGCGTGTGGATTGCAT-GAAATCCATTTGTTCATATTTGGGT
1 CCAACAAGCATGTGGATTGCATGGAAATCCATATATTCAGATTTGGGT
40441 CCAACAAGCATG-GGTATTGCATGGAAATCCATATATTCAGATTTGGGT
1 CCAACAAGCATGTGG-ATTGCATGGAAATCCATATATTCAGATTTGGGT
40489 TGCACTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
46 2 0.05
47 18 0.43
48 22 0.52
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (48 bp):
CCAACAAGCATGTGGATTGCATGGAAATCCATATATTCAGATTTGGGT
Found at i:42043 original size:17 final size:17
Alignment explanation
Indices: 42018--42051 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42008 TTTCCTAATT
*
42018 TTTTAATTTATGTTTTA
1 TTTTAATTTATCTTTTA
*
42035 TTTTCATTTATCTTTTA
1 TTTTAATTTATCTTTTA
42052 AATTCATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTAATTTATCTTTTA
Found at i:46463 original size:22 final size:21
Alignment explanation
Indices: 46422--46488 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
46412 ATAAAGTGAG
*
46422 AAAAGAAAGAAAGAAAAGAGAA
1 AAAAGAAAGAAA-AAGAGAGAA
46444 AAAAGAAAGAACAAAGAGAGATA
1 AAAAGAAAGAA-AAAGAGAGA-A
46467 TAAAA-AAAGAAAAAGAG-GAA
1 -AAAAGAAAGAAAAAGAGAGAA
46487 AA
1 AA
46489 GAGGAAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 2 0.05
20 1 0.02
21 2 0.05
22 24 0.59
23 8 0.20
24 4 0.10
ACGTcount: A:0.75, C:0.01, G:0.21, T:0.03
Consensus pattern (21 bp):
AAAAGAAAGAAAAAGAGAGAA
Found at i:46501 original size:29 final size:29
Alignment explanation
Indices: 46469--46527 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
46459 GAGAGATATA
* * *
46469 AAAAAAGAAAAAGAGGAAAAGAGGAAAAT
1 AAAAAAGAAAAAAAGGAAAAAAGAAAAAT
*
46498 AAAAAATAAAAAAAGGAAAAAAGAAAAAT
1 AAAAAAGAAAAAAAGGAAAAAAGAAAAAT
46527 A
1 A
46528 CTTCAAGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (29 bp):
AAAAAAGAAAAAAAGGAAAAAAGAAAAAT
Found at i:49051 original size:37 final size:37
Alignment explanation
Indices: 48965--49056 Score: 96
Period size: 37 Copynumber: 2.5 Consensus size: 37
48955 AAACTATTTT
** *
48965 GTCCTTATTAGGATCATTTTTCTAGAAAATTCATTTGA
1 GTCCTTATTAGGATTGTTTATCTAG-AAATTCATTTGA
** * *
49003 GTTATTCTTAGGATTGTTTATCTAG-AATGTCGTTTGA
1 GTCCTTATTAGGATTGTTTATCTAGAAAT-TCATTTGA
49040 GTCCTTATTAGGATTGT
1 GTCCTTATTAGGATTGT
49057 CTCCCTAGAA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
36 3 0.07
37 21 0.49
38 19 0.44
ACGTcount: A:0.24, C:0.11, G:0.18, T:0.47
Consensus pattern (37 bp):
GTCCTTATTAGGATTGTTTATCTAGAAATTCATTTGA
Found at i:50086 original size:203 final size:203
Alignment explanation
Indices: 49720--50263 Score: 788
Period size: 203 Copynumber: 2.7 Consensus size: 203
49710 TTGTTCAAAC
* * * *
49720 ACTTTGCTCATCTATCGCATATAGAGTTGGATCAACATCATCACTTTGTTCGATTCCATCACAGA
1 ACTTGGCTCATCTATCACATATGGAGTTGGATCAACATCATCACTTTGTTCGATTCCATCACAAA
*
49785 AGGAGGTGGATCAACATTTCCAA-TGGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAG
66 AGGAGGTGTATCAACATTT-CAAGT-GGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAG
* * * *
49849 AAAAAGTTCATAATGAGAAGAACTTATCCAACCTTAGCTCATTTCCATCACATAAGGAGTTGGAA
129 AAGAAGTTCATAACGAGAAGAACTTATCCAACCTTAGCTCATTTCCATAACATAAGAAGTTGGAA
*
49914 CAGCACCAAT
194 CAACACCAAT
* * * * *
49924 ACTTGGCTCATCCATCACATATGGAGTTGGATCAACATCATCACTTTATTCAATCCCATCATAAA
1 ACTTGGCTCATCTATCACATATGGAGTTGGATCAACATCATCACTTTGTTCGATTCCATCACAAA
* * * * * *
49989 AGGAGGTGTATCAATATTTCTAGTGGAAAGTTCATAATGA-AACAAACTCATCAGATAAGGGAGA
66 AGGAGGTGTATCAACATTTCAAGTGGAGAGTTCATAATGAGAA-GAACTCATCCGATGAGGGAGA
* * * *
50053 AGAAGTTCATAACGTA-AAGTACTTGTTCAACCTTAGCTCGTTTCCATAACATAAGAAGTTGGAA
130 AGAAGTTCATAACG-AGAAGAACTTATCCAACCTTAGCTCATTTCCATAACATAAGAAGTTGGAA
50117 CAACACCAAT
194 CAACACCAAT
*
50127 ACTTGGCTCATCTATCACATATGGAGTTGGATCAACATCATCACTTTGTTCGATTACATCACAAA
1 ACTTGGCTCATCTATCACATATGGAGTTGGATCAACATCATCACTTTGTTCGATTCCATCACAAA
50192 AGGAGGTGTATCAACATTTCCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGA
66 AGGAGGTGTATCAACATTT-CAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGA
50257 AGAAGTT
130 AGAAGTT
50264 TATACATGAG
Statistics
Matches: 298, Mismatches: 37, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
202 2 0.01
203 175 0.59
204 119 0.40
205 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (203 bp):
ACTTGGCTCATCTATCACATATGGAGTTGGATCAACATCATCACTTTGTTCGATTCCATCACAAA
AGGAGGTGTATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAA
GAAGTTCATAACGAGAAGAACTTATCCAACCTTAGCTCATTTCCATAACATAAGAAGTTGGAACA
ACACCAAT
Found at i:50337 original size:203 final size:206
Alignment explanation
Indices: 49720--50368 Score: 722
Period size: 203 Copynumber: 3.2 Consensus size: 206
49710 TTGTTCAAAC
* * * * *
49720 ACTTTGCTCATCTATCGCATATAGAGTTGGATCAACATCATCACTTTGTTCGATTCCATCACAGA
1 ACTTGGCTCATCCATCACATATGGAGTTGGATCAACATCATCACTTTGTTCGATTCCATCACAAA
*
49785 AGGAGGTGGATCAACATTTCCAA-TGGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAG
66 AGGAGGTGTATCAACATTTCCAAGT-GGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAG
* ** *
49849 AAAAAGTTCATA-ATGA---GAAGAAC-TTATCCAACCTTAGCTCATTTCCATCACATAAGGAGT
130 AAGAAGTTCATACATGAGTTGATCAACATCAT-CAA--TTAGCTCATTTCCATCACATAAGGAGT
*
49909 TGGAACAGCACCAAT
192 TGGAACAACACCAAT
* * * *
49924 ACTTGGCTCATCCATCACATATGGAGTTGGATCAACATCATCACTTTATTCAATCCCATCATAAA
1 ACTTGGCTCATCCATCACATATGGAGTTGGATCAACATCATCACTTTGTTCGATTCCATCACAAA
* * * * * *
49989 AGGAGGTGTATCAATATTT-CTAGTGGAAAGTTCATAATGA-AACAAACTCATCAGATAAGGGAG
66 AGGAGGTGTATCAACATTTCCAAGTGGAGAGTTCATAATGAGAA-GAACTCATCCGATGAGGGAG
* ** * ** * * *
50052 AAGAAGTTCATA-A--CGTAAAGT--ACTTGTTCAACCTTAGCTCGTTTCCATAACATAAGAAGT
130 AAGAAGTTCATACATGAGTTGA-TCAACATCATCAA--TTAGCTCATTTCCATCACATAAGGAGT
50112 TGGAACAACACCAAT
192 TGGAACAACACCAAT
* *
50127 ACTTGGCTCATCTATCACATATGGAGTTGGATCAACATCATCACTTTGTTCGATTACATCACAAA
1 ACTTGGCTCATCCATCACATATGGAGTTGGATCAACATCATCACTTTGTTCGATTCCATCACAAA
50192 AGGAGGTGTATCAACATTTCCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGA
66 AGGAGGTGTATCAACATTTCCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGA
* **
50257 AGAAGTTTATACATGAGTTGGATCAACATCATCAATTTTCTC-TTT-CATCACATAAGGAGTTGG
131 AGAAGTTCATACATGAGTT-GATCAACATCATCAATTAGCTCATTTCCATCACATAAGGAGTTGG
* *
50320 ATCAACATC-A-
195 AACAACACCAAT
* ** *
50330 CCTTGGCTCGCCCATCACATAAGGAGTTGGATC-ACATCA
1 ACTTGGCTCATCCATCACATATGGAGTTGGATCAACATCA
50369 CCTTGAGTCA
Statistics
Matches: 374, Mismatches: 56, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
202 8 0.02
203 196 0.52
204 125 0.33
205 26 0.07
206 3 0.01
207 8 0.02
208 1 0.00
209 7 0.02
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (206 bp):
ACTTGGCTCATCCATCACATATGGAGTTGGATCAACATCATCACTTTGTTCGATTCCATCACAAA
AGGAGGTGTATCAACATTTCCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGA
AGAAGTTCATACATGAGTTGATCAACATCATCAATTAGCTCATTTCCATCACATAAGGAGTTGGA
ACAACACCAAT
Found at i:52786 original size:28 final size:29
Alignment explanation
Indices: 52687--52903 Score: 264
Period size: 29 Copynumber: 7.6 Consensus size: 29
52677 ACCCGACCCG
*
52687 GTGACATTTTGGGAATTATTTTG-AAAAT
1 GTGACATTCTGGGAATTATTTTGAAAAAT
* *
52715 GGTGACATTCTGGGAATTATCTT-ATAAA-
1 -GTGACATTCTGGGAATTATTTTGAAAAAT
* *
52743 GTGACATTTTGGGAATTTTTTTGAAAAA-
1 GTGACATTCTGGGAATTATTTTGAAAAAT
* * * *
52771 GTGATATTATGTGAATTATTTTGAAAAAG
1 GTGACATTCTGGGAATTATTTTGAAAAAT
* *
52800 GTGACATTCTAGGAAATATTTTGAAAAAT
1 GTGACATTCTGGGAATTATTTTGAAAAAT
52829 GTGACATTCTGGGAATTATTTTGAAAAAT
1 GTGACATTCTGGGAATTATTTTGAAAAAT
* *
52858 GTGACATTCTGAGAATTATTTTGAAAAAAA
1 GTGACATTCTGGGAATTATTTTG-AAAAAT
52888 GTGACATT-TGGGAATT
1 GTGACATTCTGGGAATT
52904 TTCGAATGTG
Statistics
Matches: 162, Mismatches: 22, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
27 19 0.12
28 28 0.17
29 102 0.63
30 13 0.08
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (29 bp):
GTGACATTCTGGGAATTATTTTGAAAAAT
Found at i:52905 original size:113 final size:112
Alignment explanation
Indices: 52686--52895 Score: 278
Period size: 113 Copynumber: 1.8 Consensus size: 112
52676 AACCCGACCC
* * * *
52686 GGTGACATTTTGGGAATTATTTTGAAAATGGTGACATTCTGGGAATTATCTTATAAAGTGACATT
1 GGTGACATTCTAGGAAATATTTTGAAAATGGTGACATTCTGGGAATTATCTTAAAAAGTGACATT
* * * *
52751 TTGGGAATTTTTTTGAAAAAGTGATATTATGTGAATTATTTTGAAAAA
66 CTGAGAATTATTTTGAAAAAGTGACATTATGTGAA-TATTTTGAAAAA
*
52799 GGTGACATTCTAGGAAATATTTTGAAAAAT-GTGACATTCTGGGAATTATTTTGAAAAATGTGAC
1 GGTGACATTCTAGGAAATATTTTG-AAAATGGTGACATTCTGGGAATTATCTT-AAAAA-GTGAC
52863 ATTCTGAGAATTATTTTGAAAAAAAGTGACATT
63 ATTCTGAGAATTATTTTG--AAAAAGTGACATT
52896 TGGGAATTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
113 42 0.51
114 9 0.11
115 20 0.24
117 12 0.14
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (112 bp):
GGTGACATTCTAGGAAATATTTTGAAAATGGTGACATTCTGGGAATTATCTTAAAAAGTGACATT
CTGAGAATTATTTTGAAAAAGTGACATTATGTGAATATTTTGAAAAA
Found at i:53980 original size:25 final size:25
Alignment explanation
Indices: 53928--53980 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
53918 AGGGCAACTC
* *
53928 TTTTATGGGATTTACTGCAGTATAA
1 TTTTATGAGATTTACTGCACTATAA
* *
53953 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATAA
53978 TTT
1 TTT
53981 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATAA
Found at i:60144 original size:29 final size:29
Alignment explanation
Indices: 60102--60159 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
60092 TGATGTTATG
60102 ACCGGTTTGACCAGTCC-AAATCGGTCTGA
1 ACCGGTTTGACCAGTCCGAAA-CGGTCTGA
60131 ACCGGTTTGACCAGTCCGAAACGGTCTGA
1 ACCGGTTTGACCAGTCCGAAACGGTCTGA
60160 CCCGACCCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (29 bp):
ACCGGTTTGACCAGTCCGAAACGGTCTGA
Found at i:60213 original size:29 final size:29
Alignment explanation
Indices: 60168--60300 Score: 178
Period size: 29 Copynumber: 4.6 Consensus size: 29
60158 GACCCGACCC
*
60168 GGTGACATTTTGAGAATTATTTTGAAAAT
1 GGTGACATTTTGAGAATTATTTTGAAAAA
*
60197 GGTGACATTTTGGGAATTATTTTGAAAAA
1 GGTGACATTTTGAGAATTATTTTGAAAAA
* * *
60226 AGTGACATTTTCAGAATT-TTTTTAAAAA
1 GGTGACATTTTGAGAATTATTTTGAAAAA
* *
60254 AGTGACATTGTGAGAATTATTTTGAAAAA
1 GGTGACATTTTGAGAATTATTTTGAAAAA
* *
60283 GGTGACATTATGGGAATT
1 GGTGACATTTTGAGAATT
60301 TTCGAATGTG
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
28 25 0.27
29 66 0.73
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (29 bp):
GGTGACATTTTGAGAATTATTTTGAAAAA
Found at i:60300 original size:57 final size:57
Alignment explanation
Indices: 60168--60302 Score: 180
Period size: 57 Copynumber: 2.4 Consensus size: 57
60158 GACCCGACCC
** * *
60168 GGTGACATTTTGAGAATTATTTTGAAAATGGTGACATTTTGGGAATTATTTTGAAAAA
1 GGTGACATTTTGAGAATT-TTTTGAAAAAAGTGACATTGTGAGAATTATTTTGAAAAA
* * *
60226 AGTGACATTTTCAGAATTTTTTTAAAAAAGTGACATTGTGAGAATTATTTTGAAAAA
1 GGTGACATTTTGAGAATTTTTTGAAAAAAGTGACATTGTGAGAATTATTTTGAAAAA
* *
60283 GGTGACATTATGGGAATTTT
1 GGTGACATTTTGAGAATTTT
60303 CGAATGTGGA
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
57 50 0.76
58 16 0.24
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (57 bp):
GGTGACATTTTGAGAATTTTTTGAAAAAAGTGACATTGTGAGAATTATTTTGAAAAA
Found at i:61214 original size:32 final size:31
Alignment explanation
Indices: 61178--61253 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 31
61168 TAGGCCCTGT
*
61178 GGCCCCAAGATGTGTTCTTAGGTAGGCTC-CA
1 GGCCCCAAGATGT-ATCTTAGGTAGGCTCTCA
* *
61209 CGGCCCCGAA-ATCTATCTTGGGTAGGCTCTCA
1 -GGCCCC-AAGATGTATCTTAGGTAGGCTCTCA
*
61241 GGCCCTAAGATGT
1 GGCCCCAAGATGT
61254 TCCCTTAGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
30 2 0.06
31 21 0.58
32 11 0.31
33 2 0.06
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.25
Consensus pattern (31 bp):
GGCCCCAAGATGTATCTTAGGTAGGCTCTCA
Found at i:61232 original size:63 final size:63
Alignment explanation
Indices: 61130--61253 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
61120 CTAATGTGAC
* * * **
61130 TCTTAGGTAGGCTCTGAGGCCCTGAGATCATTCTCGGGTAGGCCCTGTGGCCCCAAGATGTGT
1 TCTTAGGTAGGCTCTCAGGCCCCGAAATCATTCTCGGGTAGGCCCTCAGGCCCCAAGATGTGT
* * *
61193 TCTTAGGTAGGCTC-CACGGCCCCGAAATC-TATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCA-GGCCCCGAAATCAT-TCTCGGGTAGGCCCTCAGGCCCCAAGATGT
61254 TCCCTTAGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCTCTCAGGCCCCGAAATCATTCTCGGGTAGGCCCTCAGGCCCCAAGATGTGT
Found at i:61322 original size:25 final size:25
Alignment explanation
Indices: 61270--61322 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
61260 AGGGTAACTC
* *
61270 TTTTATGGGATTTAATGCAGTATAA
1 TTTTATGAGATTTAATGCACTATAA
* * *
61295 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTAATGCACTATAA
61320 TTT
1 TTT
61323 GTTTAGTGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (25 bp):
TTTTATGAGATTTAATGCACTATAA
Found at i:65032 original size:2 final size:2
Alignment explanation
Indices: 65025--65050 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65015 CGCGTACAGA
65025 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
65051 GAATCCAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66312 original size:17 final size:16
Alignment explanation
Indices: 66290--66321 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
66280 AATAATATAT
66290 AAATTATATTGAAAATA
1 AAATTATATT-AAAATA
66307 AAATTATATTAAAAT
1 AAATTATATTAAAAT
66322 TATTTAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAATTATATTAAAATA
Found at i:66325 original size:26 final size:26
Alignment explanation
Indices: 66275--66325 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
66265 CAGTTATTTT
*
66275 AAAATAATAATATATAAATTATATTG
1 AAAATAATAATATATAAAATATATTG
66301 AAAATAA-AATTATATTAAAAT-TATT
1 AAAATAATAA-TATA-TAAAATATATT
66326 TAGAGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.09
26 15 0.68
27 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAATAATAATATATAAAATATATTG
Found at i:66508 original size:16 final size:15
Alignment explanation
Indices: 66483--66512 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
66473 CTTTAAATAA
66483 TTTTAATATAATTTT
1 TTTTAATATAATTTT
66498 TTTTCAATATAATTT
1 TTTT-AATATAATTT
66513 ATATATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTAATATAATTTT
Found at i:66534 original size:25 final size:25
Alignment explanation
Indices: 66474--66535 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
66464 ATTTGGATTC
*
66474 TTTAAATAATTTTAATATAATTTTT
1 TTTAAATAATTTTAATATAATTATT
*
66499 TTTCAATATAA-TTTATATATTATTATT
1 TTT-AA-ATAATTTTA-ATATAATTATT
66526 TTTAAATAAT
1 TTTAAATAAT
66536 CGTAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
25 7 0.23
26 8 0.26
27 16 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTAAATAATTTTAATATAATTATT
Found at i:66647 original size:2 final size:2
Alignment explanation
Indices: 66640--66737 Score: 189
Period size: 2 Copynumber: 49.5 Consensus size: 2
66630 ATTTGTTTTA
66640 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66723 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
66738 AACACAACAT
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 94 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67735 original size:15 final size:15
Alignment explanation
Indices: 67717--67790 Score: 78
Period size: 15 Copynumber: 4.9 Consensus size: 15
67707 TTATTATCCA
67717 AGTCATTGTTATTAG
1 AGTCATTGTTATTAG
* *
67732 AGTCATTGTTAATGG
1 AGTCATTGTTATTAG
*
67747 AGTCGA-TGTTATTGG
1 AGTC-ATTGTTATTAG
* *
67762 AGTCGTTGTTAATAG
1 AGTCATTGTTATTAG
*
67777 AGTCGTTGTTATTA
1 AGTCATTGTTATTA
67791 AAAATGTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 49 0.98
16 1 0.02
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (15 bp):
AGTCATTGTTATTAG
Found at i:67759 original size:30 final size:30
Alignment explanation
Indices: 67723--67790 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
67713 TCCAAGTCAT
*
67723 TGTTATTAGAGTCATTGTTAATGGAGTCGA
1 TGTTATTAGAGTCATTGTTAATAGAGTCGA
* * *
67753 TGTTATTGGAGTCGTTGTTAATAGAGTCGT
1 TGTTATTAGAGTCATTGTTAATAGAGTCGA
67783 TGTTATTA
1 TGTTATTA
67791 AAAATGTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.24, C:0.06, G:0.26, T:0.44
Consensus pattern (30 bp):
TGTTATTAGAGTCATTGTTAATAGAGTCGA
Found at i:68567 original size:30 final size:30
Alignment explanation
Indices: 68531--68601 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
68521 CACTCGAGGA
68531 CGTGGACGAGGACAAGGTCATAGGACCAAT
1 CGTGGACGAGGACAAGGTCATAGGACCAAT
68561 CGTGGACGAGGACAAGGTCATAGGACCAAT
1 CGTGGACGAGGACAAGGTCATAGGACCAAT
*
68591 CGTGGCCGAGG
1 CGTGGACGAGG
68602 TGGTCGATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.21, G:0.37, T:0.13
Consensus pattern (30 bp):
CGTGGACGAGGACAAGGTCATAGGACCAAT
Found at i:72258 original size:129 final size:129
Alignment explanation
Indices: 72028--72288 Score: 414
Period size: 129 Copynumber: 2.0 Consensus size: 129
72018 GTGGTCTGGT
72028 ATGAAGAAGGATGTAACATGATTTGTATCTAAATGCCTAACATGCCATCAGGTTAAAGCGGAGCA
1 ATGAAGAAGGATGTAACATGATTTGTATCTAAATGCCTAACATGCCATCAGGTTAAAGCGGAGCA
* * * *
72093 CCATGTTCCTTTAGGATTATTGCAACCGATTCAAATACCGCAATGGAAGTGATAGAGAGTAACC
66 CCAGGTTCCTTCAGGATTATTGCAACCGACTCAAATACCGCAATGGAAGTGAGAGAGAGTAACC
* *
72157 ATGAAGAAGGATGTAACATGATTTGTATCTAAATGCCTAACATGCCATTAGGTTAAAGCGGAGTA
1 ATGAAGAAGGATGTAACATGATTTGTATCTAAATGCCTAACATGCCATCAGGTTAAAGCGGAGCA
* *** * *
72222 CTAGGTTCCTTCAGGATTATTGCAGTTGACTCAAATACCGCAATGGAAGTGGGAGAGAGTCACC
66 CCAGGTTCCTTCAGGATTATTGCAACCGACTCAAATACCGCAATGGAAGTGAGAGAGAGTAACC
72286 ATG
1 ATG
72289 GATTTTGTAT
Statistics
Matches: 120, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 120 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (129 bp):
ATGAAGAAGGATGTAACATGATTTGTATCTAAATGCCTAACATGCCATCAGGTTAAAGCGGAGCA
CCAGGTTCCTTCAGGATTATTGCAACCGACTCAAATACCGCAATGGAAGTGAGAGAGAGTAACC
Found at i:74153 original size:2 final size:2
Alignment explanation
Indices: 74146--74229 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
74136 CGCTTACAGA
74146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74188 -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74229 A
1 A
74230 AATTCAACGC
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 80 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74979 original size:27 final size:25
Alignment explanation
Indices: 74949--75020 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
74939 TTATTATCAC
*
74949 ATTTGTATATATAATATATGTTATAGT
1 ATTT-TAT-TATAATATATATTATAGT
* *
74976 ATTTTATTATATTATATATTATAAT
1 ATTTTATTATAATATATATTATAGT
*
75001 AATTTTTTTATAATATATAT
1 -ATTTTATTATAATATATAT
75021 ATTTATATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 15 0.38
26 20 0.51
27 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
ATTTTATTATAATATATATTATAGT
Found at i:75017 original size:19 final size:18
Alignment explanation
Indices: 74987--75042 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
74977 TTTTATTATA
*
74987 TTATATATTATAATAATTT
1 TTATATAATAT-ATAATTT
* *
75006 TTTTATAATATAT-ATAT
1 TTATATAATATATAATTT
75023 TTATAT-ATATTATAATTT
1 TTATATAATA-TATAATTT
75041 TT
1 TT
75043 GAAAATATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.10
17 11 0.37
18 7 0.23
19 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATAATATATAATTT
Found at i:75036 original size:17 final size:17
Alignment explanation
Indices: 74962--75040 Score: 59
Period size: 16 Copynumber: 5.0 Consensus size: 17
74952 TGTATATATA
*
74962 ATATATGTTATAGTATTT
1 ATATATATTATA-TATTT
74980 -TATTATATTATATA-TT
1 ATA-TATATTATATATTT
74996 ATA-ATAATT-T-T-TTT
1 ATATAT-ATTATATATTT
75010 ATA-ATA-TATATATTT
1 ATATATATTATATATTT
75025 ATATATATTATA-ATTT
1 ATATATATTATATATTT
75041 TTGAAAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 20
0.71 0.01 0.28
Matches are distributed among these distances:
12 1 0.02
13 2 0.04
14 9 0.18
15 9 0.18
16 12 0.24
17 10 0.20
18 8 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATATATATTATATATTT
Found at i:75654 original size:3 final size:3
Alignment explanation
Indices: 75646--75681 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
75636 TTTAAAAGCA
75646 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
75682 TTTTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:76976 original size:19 final size:20
Alignment explanation
Indices: 76933--76979 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
76923 TATAGTGTTC
*
76933 TGATTTTTTATTTATATATA
1 TGATTTTTTATTTATACATA
76953 T-ATTTTTTATCTTA-ACAT-
1 TGATTTTTTAT-TTATACATA
76971 TGATTTTTT
1 TGATTTTTT
76980 CTTTTAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 19 0.79
20 4 0.17
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (20 bp):
TGATTTTTTATTTATACATA
Done.