Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016919.1 Corchorus olitorius cultivar O-4 contig16952, 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: 92484
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:140 original size:16 final size:16
Alignment explanation
Indices: 119--161 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
109 TATTTTTTAG
119 TTCAAAAAATAATTAT
1 TTCAAAAAATAATTAT
* * *
135 TTCAAATAATTATTTT
1 TTCAAAAAATAATTAT
*
151 TTGAAAAAATA
1 TTCAAAAAATA
162 TTTTCTTAAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (16 bp):
TTCAAAAAATAATTAT
Found at i:143 original size:13 final size:13
Alignment explanation
Indices: 125--149 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
115 TTAGTTCAAA
125 AAATAATTATTTC
1 AAATAATTATTTC
138 AAATAATTATTT
1 AAATAATTATTT
150 TTTGAAAAAA
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATAATTATTTC
Found at i:5681 original size:21 final size:21
Alignment explanation
Indices: 5657--5703 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
5647 TTCAAAGTGG
5657 GAAAGTTCCCAACAAGTTTTC
1 GAAAGTTCCCAACAAGTTTTC
*
5678 GAAAGTTCCCATCAAGTTTTC
1 GAAAGTTCCCAACAAGTTTTC
5699 -AAAGT
1 GAAAGT
5704 ATTCAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (21 bp):
GAAAGTTCCCAACAAGTTTTC
Found at i:5788 original size:36 final size:36
Alignment explanation
Indices: 5720--5882 Score: 208
Period size: 37 Copynumber: 4.5 Consensus size: 36
5710 TTTAGCTCTG
* *
5720 TTCAAATTGGGAAAGTTCCCATCATGTCTTCAAAGTT
1 TTCAAATTGGGAAAGTTCCCATCAAGTTTTC-AAGTT
5757 TTCAAATTGGGAAA-TTCCCATCAAGTTTTCAAGTT
1 TTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAGTT
* *
5792 TTCAAATTGGGAAAGTTGCCACCAAGTTTTTCAAGTT
1 TTCAAATTGGGAAAGTTCCCATCAAG-TTTTCAAGTT
5829 TTCAAATTGGGAAAGTTCCCATC-AGCTTTT--AGTT
1 TTCAAATTGGGAAAGTTCCCATCAAG-TTTTCAAGTT
* *
5863 TTCAATTTAAGGAAAGTTCC
1 TTCAAATT-GGGAAAGTTCC
5883 TGTCATTTTC
Statistics
Matches: 114, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
34 11 0.10
35 29 0.25
36 29 0.25
37 45 0.39
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (36 bp):
TTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAGTT
Found at i:5799 original size:72 final size:71
Alignment explanation
Indices: 5720--5882 Score: 206
Period size: 72 Copynumber: 2.3 Consensus size: 71
5710 TTTAGCTCTG
* *
5720 TTCAAATTGGGAAAGTTCCCATCATG-TCTTCAAAGTTTTCAAATTGGGAAA-TTCCCATCAAG-
1 TTCAAATTGGGAAAGTTCCCACCAAGTTCTTC-AAGTTTTCAAATTGGGAAAGTTCCCATC-AGC
5782 TTTTCAAGTT
64 TTTT--AGTT
* *
5792 TTCAAATTGGGAAAGTTGCCACCAAGTTTTTCAAGTTTTCAAATTGGGAAAGTTCCCATCAGCTT
1 TTCAAATTGGGAAAGTTCCCACCAAGTTCTTCAAGTTTTCAAATTGGGAAAGTTCCCATCAGCTT
5857 TTAGTT
66 TTAGTT
* *
5863 TTCAATTTAAGGAAAGTTCC
1 TTCAAATT-GGGAAAGTTCC
5883 TGTCATTTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
71 11 0.14
72 53 0.66
73 16 0.20
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (71 bp):
TTCAAATTGGGAAAGTTCCCACCAAGTTCTTCAAGTTTTCAAATTGGGAAAGTTCCCATCAGCTT
TTAGTT
Found at i:8527 original size:19 final size:19
Alignment explanation
Indices: 8503--8541 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
8493 CTGACGTGGC
*
8503 AATGCCACGTCGGACCAAA
1 AATGCCACGTCGCACCAAA
*
8522 AATGCCACGTTGCACCAAA
1 AATGCCACGTCGCACCAAA
8541 A
1 A
8542 TATCACGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (19 bp):
AATGCCACGTCGCACCAAA
Found at i:20260 original size:35 final size:35
Alignment explanation
Indices: 20219--20299 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
20209 TTATGTGCAG
*
20219 AACAATGGTTTGTAACCCTTAATTTCTATTCTCTA
1 AACAATGGTTTGTAACCCTTAATTTCTATTCTCGA
* *
20254 AACAATGGTTTGTAATCCTTAATTTCTATTCTCGG
1 AACAATGGTTTGTAACCCTTAATTTCTATTCTCGA
20289 AACAATGGTTT
1 AACAATGGTTT
20300 TATGATATGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (35 bp):
AACAATGGTTTGTAACCCTTAATTTCTATTCTCGA
Found at i:26356 original size:116 final size:116
Alignment explanation
Indices: 26152--26386 Score: 470
Period size: 116 Copynumber: 2.0 Consensus size: 116
26142 CCCTGATGGT
26152 GATTATTACCCGGCCACAGCTAGACTAGAATTCCCTGCGACCAGTAATGTGGCGAAGTATGAGGC
1 GATTATTACCCGGCCACAGCTAGACTAGAATTCCCTGCGACCAGTAATGTGGCGAAGTATGAGGC
26217 ATGCATTTTGGGAATCTAGTTAGCATTGGAAAGGAAAGTGAAGGAATTAGA
66 ATGCATTTTGGGAATCTAGTTAGCATTGGAAAGGAAAGTGAAGGAATTAGA
26268 GATTATTACCCGGCCACAGCTAGACTAGAATTCCCTGCGACCAGTAATGTGGCGAAGTATGAGGC
1 GATTATTACCCGGCCACAGCTAGACTAGAATTCCCTGCGACCAGTAATGTGGCGAAGTATGAGGC
26333 ATGCATTTTGGGAATCTAGTTAGCATTGGAAAGGAAAGTGAAGGAATTAGA
66 ATGCATTTTGGGAATCTAGTTAGCATTGGAAAGGAAAGTGAAGGAATTAGA
26384 GAT
1 GAT
26387 ACATGGAAAC
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 119 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (116 bp):
GATTATTACCCGGCCACAGCTAGACTAGAATTCCCTGCGACCAGTAATGTGGCGAAGTATGAGGC
ATGCATTTTGGGAATCTAGTTAGCATTGGAAAGGAAAGTGAAGGAATTAGA
Found at i:29080 original size:26 final size:27
Alignment explanation
Indices: 29050--29112 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
29040 TTACCAGGGT
29050 ATTTTGGTCATTTTCA-CCTCAGGGGC
1 ATTTTGGTCATTTTCAGCCTCAGGGGC
*
29076 ATTTTGGTCATTTTTAGCCTCAGGGGC
1 ATTTTGGTCATTTTCAGCCTCAGGGGC
29103 ATTTTGGTCA
1 ATTTTGGTCA
29113 AAATTACTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 15 0.43
27 20 0.57
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (27 bp):
ATTTTGGTCATTTTCAGCCTCAGGGGC
Found at i:31158 original size:2 final size:2
Alignment explanation
Indices: 31151--31180 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31141 TCAAAACAGC
31151 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
31181 GGCATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32917 original size:36 final size:36
Alignment explanation
Indices: 32870--33210 Score: 282
Period size: 36 Copynumber: 10.4 Consensus size: 36
32860 GTGCATCCAA
*
32870 GAAATTAAGTAAAAACAGTTAAGGATTTAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGGACTTAATTCAGG
32906 GAAATTAAGT---AA-A---AA-GACTTAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGGACTTAATTCAGG
* **
32934 GAAATTAAGTAAAAGCAGTTAAAAACTTAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGGACTTAATTCAGG
32970 GAAATTAAGT----A-A---AA-GACTTAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGGACTTAATTCAGG
* * *
32997 GAAATTAAGGAAAAACAGTTAAGAACTTAATTCAGT
1 GAAATTAAGTAAAAACAGTTAAGGACTTAATTCAGG
33033 GAAATTAAGT----A-A---AA-GACTTAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGGACTTAATTCAGG
* * *
33060 GAAATTAAGTAAAAATAGTTAAGGATTTAATTTCAAG
1 GAAATTAAGTAAAAACAGTTAAGGACTTAA-TTCAGG
33097 GAAATTAAGT---AA-AG---A-GACTTAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGGACTTAATTCAGG
* * *
33125 GAAATTAAGTAAAAGCAGTTAAGAACATAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGGACTTAATTCAGG
* *
33161 GAAATTAAGTAAAAACAATTAAGGATTTAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGGACTTAATTCAGG
* *
33197 GAAGTTAAATAAAA
1 GAAATTAAGTAAAA
33211 GTCTTAATCC
Statistics
Matches: 245, Mismatches: 25, Indels: 70
0.72 0.07 0.21
Matches are distributed among these distances:
27 42 0.17
28 41 0.17
29 8 0.03
30 1 0.00
31 6 0.02
32 7 0.03
33 4 0.02
34 2 0.01
35 7 0.03
36 112 0.46
37 15 0.06
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (36 bp):
GAAATTAAGTAAAAACAGTTAAGGACTTAATTCAGG
Found at i:32991 original size:27 final size:27
Alignment explanation
Indices: 32953--33139 Score: 151
Period size: 27 Copynumber: 6.2 Consensus size: 27
32943 TAAAAGCAGT
32953 TAAAA-ACTTAATTCAGGGAAATTAAG
1 TAAAAGACTTAATTCAGGGAAATTAAG
32979 TAAAAGACTTAATTCAGGGAAATTAAGG
1 TAAAAGACTTAATTCAGGGAAATTAA-G
* *
33007 AAAAACAGTTAAGAACTTAATTCAGTGAAATTAAG
1 ---TA-A---AAG-ACTTAATTCAGGGAAATTAAG
33042 TAAAAGACTTAATTCAGGGAAATTAAG
1 TAAAAGACTTAATTCAGGGAAATTAAG
* *
33069 TAAAAATAGTTAAGGATTTAATTTCAAGGAAATTAAG
1 T----A-A---AA-GACTTAA-TTCAGGGAAATTAAG
33106 TAAAGAGACTTAATTCAGGGAAATTAAG
1 TAAA-AGACTTAATTCAGGGAAATTAAG
33134 TAAAAG
1 TAAAAG
33140 CAGTTAAGAA
Statistics
Matches: 132, Mismatches: 8, Indels: 41
0.73 0.04 0.23
Matches are distributed among these distances:
26 5 0.04
27 43 0.33
28 22 0.17
29 7 0.05
30 1 0.01
31 3 0.02
32 4 0.03
33 1 0.01
35 6 0.05
36 25 0.19
37 15 0.11
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (27 bp):
TAAAAGACTTAATTCAGGGAAATTAAG
Found at i:33016 original size:63 final size:63
Alignment explanation
Indices: 32870--33174 Score: 475
Period size: 63 Copynumber: 4.8 Consensus size: 63
32860 GTGCATCCAA
* *
32870 GAAATTAAGTAAAAACAGTTAAGGATTTAATTCAGGGAAATTAAGTAAAAAGACTTAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGAACTTAATTCAGGGAAATTAAGT-AAAAGACTTAATTCAGG
* *
32934 GAAATTAAGTAAAAGCAGTTAAAAACTTAATTCAGGGAAATTAAGTAAAAGACTTAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGAACTTAATTCAGGGAAATTAAGTAAAAGACTTAATTCAGG
* *
32997 GAAATTAAGGAAAAACAGTTAAGAACTTAATTCAGTGAAATTAAGTAAAAGACTTAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGAACTTAATTCAGGGAAATTAAGTAAAAGACTTAATTCAGG
* * * *
33060 GAAATTAAGTAAAAATAGTTAAGGATTTAATTTCAAGGAAATTAAGTAAAGAGACTTAATTCAGG
1 GAAATTAAGTAAAAACAGTTAAGAACTTAA-TTCAGGGAAATTAAGTAAA-AGACTTAATTCAGG
* *
33125 GAAATTAAGTAAAAGCAGTTAAGAACATAATTCAGGGAAATTAAGTAAAA
1 GAAATTAAGTAAAAACAGTTAAGAACTTAATTCAGGGAAATTAAGTAAAA
33175 ACAATTAAGG
Statistics
Matches: 219, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
63 103 0.47
64 77 0.35
65 39 0.18
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.26
Consensus pattern (63 bp):
GAAATTAAGTAAAAACAGTTAAGAACTTAATTCAGGGAAATTAAGTAAAAGACTTAATTCAGG
Found at i:33218 original size:128 final size:127
Alignment explanation
Indices: 32870--33185 Score: 367
Period size: 127 Copynumber: 2.5 Consensus size: 127
32860 GTGCATCCAA
* * ** *
32870 GAAATTAAGTAAAAACAGTTAAGGATTTAATTCAGGGAAATTAAGTAAAAAGACTTAATTCAGGG
1 GAAATTAAGGAAAAACAGTTAAGAACATAATTCAGGGAAATTAAGT-AAAAGAC-TAATTCAAGG
* ** * *
32935 AAATTAAGTAAAAGCAGTTAAAA-A-CTTAA-TTCAGGGAAATTAAGTAAAAGACTTAATTCAGG
64 AAATTAAGGAAAAATA-ATAAAAGATCTTAATTTCAAGGAAATTAAGTAAAAGACTTAATTCAGG
* * *
32997 GAAATTAAGGAAAAACAGTTAAGAACTTAATTCAGTGAAATTAAGTAAAAGACTTAATTCAGGGA
1 GAAATTAAGGAAAAACAGTTAAGAACATAATTCAGGGAAATTAAGTAAAAGAC-TAATTCAAGGA
* * * *
33062 AATTAAGTAAAAATAGTTAAGGAT-TTAATTTCAAGGAAATTAAGTAAAGAGACTTAATTCAGG
65 AATTAAGGAAAAATAATAAAAGATCTTAATTTCAAGGAAATTAAGTAAA-AGACTTAATTCAGG
* *
33125 GAAATTAAGTAAAAGCAGTTAAGAACATAATTCAGGGAAATTAAGTAAAA-AC-AATT-AAGGA
1 GAAATTAAGGAAAAACAGTTAAGAACATAATTCAGGGAAATTAAGTAAAAGACTAATTCAAGGA
33186 TTTAATTCAG
Statistics
Matches: 170, Mismatches: 15, Indels: 11
0.87 0.08 0.06
Matches are distributed among these distances:
124 4 0.02
125 7 0.04
126 37 0.22
127 62 0.36
128 60 0.35
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.26
Consensus pattern (127 bp):
GAAATTAAGGAAAAACAGTTAAGAACATAATTCAGGGAAATTAAGTAAAAGACTAATTCAAGGAA
ATTAAGGAAAAATAATAAAAGATCTTAATTTCAAGGAAATTAAGTAAAAGACTTAATTCAGG
Found at i:33225 original size:128 final size:126
Alignment explanation
Indices: 32870--33237 Score: 352
Period size: 128 Copynumber: 2.9 Consensus size: 126
32860 GTGCATCCAA
* * ** *
32870 GAAATTAAGTAAAAACAGTTAAGGATTTAATTCAGGGAAATTAAGTAAAAAGACTTAATTCAGGG
1 GAAATTAAGGAAAAACAGTTAAGAACATAATTCAGGGAAATTAAGT-AAAAGAC-TAATTCAAGG
* ** * * * *
32935 AAATTAAGTAAAAGCAGTTAAAA-ACTTAAT-TCAGGGAAATTAAGTAAAAGACTTAATTCAGG
64 AAATTAAGGAAAAATA-ATAAAAGATTTAATCCCAAGGAAATTAAGTAAAAGACTTAATTCAGG
* * *
32997 GAAATTAAGGAAAAACAGTTAAGAACTTAATTCAGTGAAATTAAGTAAAAGACTTAATTCAGGGA
1 GAAATTAAGGAAAAACAGTTAAGAACATAATTCAGGGAAATTAAGTAAAAGAC-TAATTCAAGGA
* * * * **
33062 AATTAAGTAAAAATAGTTAAGGATTTAATTTCAAGGAAATTAAGTAAAGAGACTTAATTCAGG
65 AATTAAGGAAAAATAATAAAAGATTTAATCCCAAGGAAATTAAGTAAA-AGACTTAATTCAGG
* *
33125 GAAATTAAGTAAAAGCAGTTAAGAACATAATTCAGGGAAATTAAGTAAAA-AC-AATT-AAGGAT
1 GAAATTAAGGAAAAACAGTTAAGAACATAATTCAGGGAAATTAAGTAAAAGACTAATTCAAGGA-
* * ** *
33187 TTAATTCAGGGAAGTTAAATAAAAG-TCTTAATCCCAAGGAAATTAGGTAAA
65 --AATTAAGGAAAAAT-AATAAAAGAT-TTAATCCCAAGGAAATTAAGTAAA
33238 TCAAGCAAAG
Statistics
Matches: 206, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
124 4 0.02
125 7 0.03
126 38 0.18
127 71 0.34
128 86 0.42
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (126 bp):
GAAATTAAGGAAAAACAGTTAAGAACATAATTCAGGGAAATTAAGTAAAAGACTAATTCAAGGAA
ATTAAGGAAAAATAATAAAAGATTTAATCCCAAGGAAATTAAGTAAAAGACTTAATTCAGG
Found at i:33332 original size:72 final size:71
Alignment explanation
Indices: 33221--33698 Score: 476
Period size: 72 Copynumber: 6.7 Consensus size: 71
33211 GTCTTAATCC
* * *
33221 CAAGGAAATTAGGTAAATCAAGCAAAGACTTAATTCAGGGTAATTAAGTAAATCAGGCAAAGACT
1 CAAGGAAATTAAGTAAATCAAGCAAAGACTTAATTCAGGGTAATTAAGTAAATCAAGCACAGACT
33286 TAATTT
66 TAATTT
* * *
33292 CAAGGAAATTAGGTAAAATCAAGCACAA-ACTTAATTCAGGGTAATTAAGTAAGTCAATCACAGA
1 CAAGGAAATTAAGT-AAATCAAGCA-AAGACTTAATTCAGGGTAATTAAGTAAATCAAGCACAGA
33356 CTTAA-TT
64 CTTAATTT
* * * *
33363 CAGGGTAATTAAGTAAATC-AGTCAAAGACTTAATTTCAAGGAAATT-AGATAAAATCAAGCACA
1 CAAGGAAATTAAGTAAATCAAG-CAAAGACTTAA-TTCAGGGTAATTAAG-T-AAATCAAGCACA
*
33426 TACTTAA-TT
62 GACTTAATTT
* * * * *
33435 C-AGGATGATTAAGTAAATC-AGTCAAAGACTTATTTTCAAGGAAATTGAGTAAAATCAAGCACA
1 CAAGGA-AATTAAGTAAATCAAG-CAAAGACTTA-ATTCAGGGTAATTAAGT-AAATCAAGCACA
33498 GACTTAATTT
62 GACTTAATTT
* * * *
33508 CAAGGAAATTAAGTAAAATCAAGCACAGACTTAATTCAGGGTAGTTAAGTAAATCAAGCAAAAAC
1 CAAGGAAATTAAGT-AAATCAAGCAAAGACTTAATTCAGGGTAATTAAGTAAATCAAGCACAGAC
33573 TTAATTT
65 TTAATTT
* * * * *
33580 CAAGGAAATTAGGTAAAATCAAGCACATACTTAATTCAGGGTAATTAAGTAGAGTCAA-TA-A-A
1 CAAGGAAATTAAGT-AAATCAAGCAAAGACTTAATTCAGGGTAATTAAGTA-AATCAAGCACAGA
33642 CTTAA-TT
64 CTTAATTT
** * *
33649 CGGGGTAATTAAGTAAAGTCAA-TAAAGAACTTAATTCAGGGTAATTAAGT
1 CAAGGAAATTAAGTAAA-TCAAGCAAAG-ACTTAATTCAGGGTAATTAAGT
33699 GGGGACATTA
Statistics
Matches: 352, Mismatches: 38, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
68 5 0.01
69 42 0.12
70 21 0.06
71 41 0.12
72 192 0.55
73 31 0.09
74 18 0.05
75 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (71 bp):
CAAGGAAATTAAGTAAATCAAGCAAAGACTTAATTCAGGGTAATTAAGTAAATCAAGCACAGACT
TAATTT
Found at i:33416 original size:107 final size:108
Alignment explanation
Indices: 33227--33698 Score: 557
Period size: 107 Copynumber: 4.4 Consensus size: 108
33217 ATCCCAAGGA
* * *
33227 AATTAGGTAAATCAAGCAAAGACTTAATTCAGGGTAATTAAGT-AAATCAGGCAAAGACTTAATT
1 AATTAAGTAAATCAATCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAAGCAAAGACTTAATT
*
33291 TCAAGGAAATTAGGTAAAATCAAGCACAAACTTAATTCAGGGT
66 TCAAGGAAATTAAGTAAAATCAAGCACAAACTTAATTCAGGGT
* *
33334 AATTAAGTAAGTCAATCACAGACTTAATTCAGGGTAATTAAGT-AAATC-AGTCAAAGACTTAAT
1 AATTAAGTAAATCAATCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAAG-CAAAGACTTAAT
* *
33397 TTCAAGGAAATT-AGATAAAATCAAGCACATACTTAATTCAGGAT
65 TTCAAGGAAATTAAG-TAAAATCAAGCACAAACTTAATTCAGGGT
* * * * * * *
33441 GATTAAGTAAATCAGTCAAAGACTTATTTTCAAGGAAATTGAGTAAAATCAAGCACAGACTTAAT
1 AATTAAGTAAATCAATCAAAGACTTA-ATTCAGGGTAATTAAGTAAAATCAAGCAAAGACTTAAT
*
33506 TTCAAGGAAATTAAGTAAAATCAAGCACAGACTTAATTCAGGGT
65 TTCAAGGAAATTAAGTAAAATCAAGCACAAACTTAATTCAGGGT
* * * * * * * *
33550 AGTTAAGTAAATCAAGCAAAAACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACATACTTAA-
1 AATTAAGTAAATCAATCAAAGACTTAA-TTCAGGGTAATTAAGTAAAATCAAGCAAAGACTTAAT
* * * * * *
33614 TTCAGGGTAATTAAGTAGAGTC-A--ATAAACTTAATTCGGGGT
65 TTCAAGGAAATTAAGTAAAATCAAGCACAAACTTAATTCAGGGT
33655 AATTAAGTAAAGTCAAT-AAAGAACTTAATTCAGGGTAATTAAGT
1 AATTAAGTAAA-TCAATCAAAG-ACTTAATTCAGGGTAATTAAGT
33699 GGGGACATTA
Statistics
Matches: 315, Mismatches: 41, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
105 41 0.13
106 12 0.04
107 118 0.37
108 31 0.10
109 109 0.35
110 4 0.01
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (108 bp):
AATTAAGTAAATCAATCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAAGCAAAGACTTAATT
TCAAGGAAATTAAGTAAAATCAAGCACAAACTTAATTCAGGGT
Found at i:33648 original size:33 final size:35
Alignment explanation
Indices: 33248--33698 Score: 232
Period size: 36 Copynumber: 12.6 Consensus size: 35
33238 TCAAGCAAAG
33248 ACTTAATTCAGGGTAATTAAGTAAA-TCAGGCA-AAG-
1 ACTTAATTCAGGGTAATTAAGTAAAGTCA---ATAAGA
* * * * *
33283 ACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACA-A
1 ACTTAA-TTCAGGGTAATTAAGTAAAGTCAA-TA-AGA
33320 ACTTAATTCAGGGTAATTAAGT-AAGTCAATCACAG-
1 ACTTAATTCAGGGTAATTAAGTAAAGTCAAT-A-AGA
*
33355 ACTTAATTCAGGGTAATTAAGTAAA-TCAGTCAA-A
1 ACTTAATTCAGGGTAATTAAGTAAAGTCAAT-AAGA
* * * ** *
33389 GACTTAATTTCAAGGAAATT-AGATAAAATCAAGCACA
1 -ACTTAA-TTCAGGGTAATTAAG-TAAAGTCAATAAGA
* * *
33426 TACTTAATTCAGGATGATTAAGTAAA-TCAGTCAA-A
1 -ACTTAATTCAGGGTAATTAAGTAAAGTCAAT-AAGA
* * * * * *
33461 GACTTATTTTCAAGGAAATTGAGTAAAATCAAGCACAG-
1 -ACTTA-ATTCAGGGTAATTAAGTAAAGTCAA-TA-AGA
* * * *
33499 ACTTAATTTCAAGGAAATTAAGTAAAATCAAGCACAG-
1 ACTTAA-TTCAGGGTAATTAAGTAAAGTCAA-TA-AGA
* * *
33536 ACTTAATTCAGGGTAGTTAAGTAAA-TCAAGCAAAA
1 ACTTAATTCAGGGTAATTAAGTAAAGTCAA-TAAGA
* * * * ** *
33571 ACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACA
1 ACTTAA-TTCAGGGTAATTAAGTAAAGTCAATAAGA
*
33607 TACTTAATTCAGGGTAATTAAGTAGAGTCAAT-A-A
1 -ACTTAATTCAGGGTAATTAAGTAAAGTCAATAAGA
*
33641 ACTTAATTCGGGGTAATTAAGTAAAGTCAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAAAGTCAAT-AAGA
33677 ACTTAATTCAGGGTAATTAAGT
1 ACTTAATTCAGGGTAATTAAGT
33699 GGGGACATTA
Statistics
Matches: 333, Mismatches: 53, Indels: 59
0.75 0.12 0.13
Matches are distributed among these distances:
33 29 0.09
34 4 0.01
35 75 0.23
36 148 0.44
37 76 0.23
38 1 0.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (35 bp):
ACTTAATTCAGGGTAATTAAGTAAAGTCAATAAGA
Found at i:33713 original size:36 final size:35
Alignment explanation
Indices: 33608--33698 Score: 132
Period size: 33 Copynumber: 2.6 Consensus size: 35
33598 TCAAGCACAT
*
33608 ACTTAATTCAGGGTAATTAAGTAGAGTCA-ATA-A
1 ACTTAATTCAGGGTAATTAAGTAGAGTCATAAAGA
* *
33641 ACTTAATTCGGGGTAATTAAGTAAAGTCAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAGAGTC-ATAAAGA
33677 ACTTAATTCAGGGTAATTAAGT
1 ACTTAATTCAGGGTAATTAAGT
33699 GGGGACATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
33 26 0.51
34 1 0.02
35 2 0.04
36 22 0.43
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.31
Consensus pattern (35 bp):
ACTTAATTCAGGGTAATTAAGTAGAGTCATAAAGA
Found at i:38229 original size:76 final size:76
Alignment explanation
Indices: 38092--38243 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
38082 ACAAGGGCCC
* * * *
38092 CGACTCCACCTGGGCGCCCACATGGTTGCCATGAGTACCCATGTGGTTTGCTTGAGGACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCATAAGTACCCATGTGGTTTGCCTGAGCACCCAGAT
38157 GGGCGGTGTCA
66 GGGCGGTGTCA
* * * *
38168 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TAAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCAT-AAGTACCCATGTGGTTT-GCCTGAGCACCCA
*
38230 GATGGGCTGTGTCA
63 GATGGGCGGTGTCA
38244 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.17, C:0.29, G:0.30, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCATAAGTACCCATGTGGTTTGCCTGAGCACCCAGAT
GGGCGGTGTCA
Found at i:43911 original size:91 final size:91
Alignment explanation
Indices: 43756--44005 Score: 482
Period size: 91 Copynumber: 2.7 Consensus size: 91
43746 TGATCAAATA
*
43756 ATTTCTTCCTTGATGTTTGCATCATCATTAAATTAATTAATTAATTAATACAAACTTAATGAAAT
1 ATTTCTTCCTTGATGTTTGCATCATCATTAAATTAATTAATTAATAAATACAAACTTAATGAAAT
43821 CGAGTATATAATTTACCAGTTATTTG
66 CGAGTATATAATTTACCAGTTATTTG
43847 ATTTCTTCCTTGATGTTTGCATCATCATTAAATTAATTAATTAATAAATACAAACTTAATGAAAT
1 ATTTCTTCCTTGATGTTTGCATCATCATTAAATTAATTAATTAATAAATACAAACTTAATGAAAT
43912 CGAGTATATAATTTACCAGTTATTTG
66 CGAGTATATAATTTACCAGTTATTTG
*
43938 ATTTCTTCCTTGATGTTTGCATCATCATTAAATTAATTAATTAATAAATACAAACTTAATGATAT
1 ATTTCTTCCTTGATGTTTGCATCATCATTAAATTAATTAATTAATAAATACAAACTTAATGAAAT
44003 CGA
66 CGA
44006 CTATCGAGTA
Statistics
Matches: 157, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 157 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.42
Consensus pattern (91 bp):
ATTTCTTCCTTGATGTTTGCATCATCATTAAATTAATTAATTAATAAATACAAACTTAATGAAAT
CGAGTATATAATTTACCAGTTATTTG
Found at i:44470 original size:21 final size:21
Alignment explanation
Indices: 44432--44472 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
44422 CTCGGAATCA
44432 AACTAACTGACTCAAAAAAAG
1 AACTAACTGACTCAAAAAAAG
44453 AACTGAACTGACTCAAAAAA
1 AACT-AACTGACTCAAAAAA
44473 CTGACTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.56, C:0.20, G:0.10, T:0.15
Consensus pattern (21 bp):
AACTAACTGACTCAAAAAAAG
Found at i:48407 original size:29 final size:30
Alignment explanation
Indices: 48354--48427 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
48344 TACCCAGAAA
*
48354 AATCCCTTATGTTTTGTTTTTGGGACAAAAT
1 AATCCCTTATG-TTTGTTTTCGGGACAAAAT
*
48385 AATCCCTTATGTTT-TTTTCGGGACAAATT
1 AATCCCTTATGTTTGTTTTCGGGACAAAAT
*
48414 AATCCCTTACGTTT
1 AATCCCTTATGTTT
48428 CAAAAATGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 26 0.65
30 3 0.08
31 11 0.28
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.45
Consensus pattern (30 bp):
AATCCCTTATGTTTGTTTTCGGGACAAAAT
Found at i:48618 original size:30 final size:30
Alignment explanation
Indices: 48571--48660 Score: 150
Period size: 29 Copynumber: 3.1 Consensus size: 30
48561 AAGGGACTAA
48571 TTTGT-CCAAAA-AAAAACATAAGGGATTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTT
48599 TTTGTCCCAAAAGAAAAACATAAGGGA-TT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTT
*
48628 TTTGTCCCAAAAGAAAAACATTAGGGATTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTT
48658 TTT
1 TTT
48661 AGTATTTAGT
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
28 5 0.09
29 34 0.59
30 19 0.33
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (30 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTT
Found at i:48722 original size:15 final size:15
Alignment explanation
Indices: 48702--48743 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
48692 AAAAATTTGA
48702 TTTTTTCCTTTTTCC
1 TTTTTTCCTTTTTCC
*
48717 TTTTTTCTTTTTTCC
1 TTTTTTCCTTTTTCC
*
48732 TTATTCTCCTTT
1 TT-TTTTCCTTT
48744 CCAAAAACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTCCTTTTTCC
Found at i:49032 original size:127 final size:124
Alignment explanation
Indices: 48819--49058 Score: 317
Period size: 126 Copynumber: 1.9 Consensus size: 124
48809 ATTCCCTAAA
* * *
48819 AAAATGGTAAAGATAAAATAGTTGTAAAAATATTGAATTTAATTGAATAAAAATAGAAGTTTTGG
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAAGTTTT-G
*
48884 TAAAATAAAACTGTAAAAGTTTAAATAAT-GTCATTTAAGAAATATATTTAATTAAAATAGT
65 TAAAATAAAACTGTAAAAGTTTAAA-AATGGT-ATTTAAAAAATATATTTAATTAAAATAGT
*
48945 AAAATGGTAAAAATAAAATAGTTATAAAATATATT-AGATTTGATTAAATAAAAATAG-AGTTTT
1 AAAATGGTAAAAATAAAATAGTTATAAAA-ATATTGA-ATTTAATTAAATAAAAATAGAAGTTTT
* *
49008 -TAATTGAGTAAAATTGTAAAAGTTTAAAAATGGTATTTAAAAAATATATTT
64 GTAA---AATAAAACTGTAAAAGTTTAAAAATGGTATTTAAAAAATATATTT
49059 GAAAAATAAG
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
124 3 0.03
126 53 0.52
127 45 0.45
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35
Consensus pattern (124 bp):
AAAATGGTAAAAATAAAATAGTTATAAAAATATTGAATTTAATTAAATAAAAATAGAAGTTTTGT
AAAATAAAACTGTAAAAGTTTAAAAATGGTATTTAAAAAATATATTTAATTAAAATAGT
Found at i:49708 original size:32 final size:31
Alignment explanation
Indices: 49672--49731 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
49662 ACTAAATACT
49672 AAAAAAATTCTCTTATATTTTTCTTTTGGGAC
1 AAAAAAATTC-CTTATATTTTTCTTTTGGGAC
*
49704 AAAAAAATTCCTTATGTTTTTCTTTTGG
1 AAAAAAATTCCTTATATTTTTCTTTTGG
49732 AGCAAATCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (31 bp):
AAAAAAATTCCTTATATTTTTCTTTTGGGAC
Found at i:49941 original size:31 final size:30
Alignment explanation
Indices: 49861--49941 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
49851 CTCATTTTTG
* *
49861 AAACGTAAGGGATTAATTTGTCCCGAAAAA
1 AAACATAAGGGATTATTTTGTCCCGAAAAA
49891 AAACATAAGGGATTATTTTGTCCC-AAAAGCA
1 AAACATAAGGGATTATTTTGTCCCGAAAA--A
* * *
49922 AAATATAATGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
49942 GGTATTTAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 4 0.09
30 22 0.50
31 18 0.41
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (30 bp):
AAACATAAGGGATTATTTTGTCCCGAAAAA
Found at i:55217 original size:228 final size:228
Alignment explanation
Indices: 54320--55230 Score: 975
Period size: 228 Copynumber: 4.0 Consensus size: 228
54310 GACCTTGTAG
* * * * * * * *
54320 ATGCAAATCTTTGTGAAGACCCTAACAGGCAAGACCATCACCCTT-GAGGTCGAAAGTTCTGACA
1 ATGCAAATCTTTGTGAAGACTCTCACAGGAAAGACAATCA-CTTTGGAGGTAGAAAGCTCCGACA
* * * * * *
54384 CCATCGACAATGTCAAGGCTAAGATACAAGATAAAGAAGGAATTCCACCAGATCAGCAAAGACTC
65 CCATCGACAATGTAAAGGCTAAGATTCAAGATAAAGAGGGAATCCCACCAGACCAGCAAAGGCTC
* * * ** * * * * *
54449 ATCTTTGCTGGCAAACAGCTTGAAGATGGTCGCACACTAGCAGACTATAATATCCAAAAAGAGTC
130 ATCTTTGCTGGTAAGCAACTTGAAGATGGGAGGACACTTGCAGATTATAACATCCAAAAGGAGTC
* * *
54514 CACCCTTCACTTAGTGCTCCGTCTTCGTGGTGGC
195 CACTCTTCACTTGGTGCTCCGTCTTCGTGGTGGA
* * *
54548 ATGCAAATTTTTGTTAAGACTCTCACAGGAAAGACAATCACTTTGGAGGTAGAGAGCTCCGACAC
1 ATGCAAATCTTTGTGAAGACTCTCACAGGAAAGACAATCACTTTGGAGGTAGAAAGCTCCGACAC
* * * * * * * *
54613 TATTGACAATGTAAAGGCTAAGATTCAGGACAAAGAGGGTATTCCACCAGACCAGCAAAGGTTGA
66 CATCGACAATGTAAAGGCTAAGATTCAAGATAAAGAGGGAATCCCACCAGACCAGCAAAGGCTCA
* * * * * *
54678 TTTTTGCTGGAAAGCAACTTGAAGATGGAAGGACACTTGCTGATTATAACATTCAAAAGGAGTCT
131 TCTTTGCTGGTAAGCAACTTGAAGATGGGAGGACACTTGCAGATTATAACATCCAAAAGGAGTCC
* *
54743 ACTCTTCACTTGGTGCTTCGTCTTCGTGGTGGT
196 ACTCTTCACTTGGTGCTCCGTCTTCGTGGTGGA
* * * *
54776 ATGCAGATCTTTGTCAAGACTCTCACAGGAAAGACAATCACTTTGGAGGTGGAGAGCTCCGACAC
1 ATGCAAATCTTTGTGAAGACTCTCACAGGAAAGACAATCACTTTGGAGGTAGAAAGCTCCGACAC
* * * * * * *
54841 CATTGACAATGTCAAGGCTAAGATTCAAGATAAGGAGGGAATCCCACCAGATCAGCAGAGGTTGA
66 CATCGACAATGTAAAGGCTAAGATTCAAGATAAAGAGGGAATCCCACCAGACCAGCAAAGGCTCA
* * * * *
54906 TCTTTGCTGGTAAGCAACTTGAGGATGGGAGGACACTCGCTGATTATAACATTCAAAAGGAGTCA
131 TCTTTGCTGGTAAGCAACTTGAAGATGGGAGGACACTTGCAGATTATAACATCCAAAAGGAGTCC
* *
54971 ACTCTTCATTTGGTTCTCCGTCTTCGTGGTGGA
196 ACTCTTCACTTGGTGCTCCGTCTTCGTGGTGGA
* * * * * * * * *
55004 ATGCAGATCTTTGTGAAGACTCTTACTGGAAAGACTATCACATTGGAGGTTGAAAGTTCAGATAC
1 ATGCAAATCTTTGTGAAGACTCTCACAGGAAAGACAATCACTTTGGAGGTAGAAAGCTCCGACAC
* * * * * *
55069 CATCGATAATGTAAAGGCAAAGATCCAAGATAAGGAGGGTATCCCACCTGACCAGCAAAGGCTCA
66 CATCGACAATGTAAAGGCTAAGATTCAAGATAAAGAGGGAATCCCACCAGACCAGCAAAGGCTCA
* * * * * *
55134 TTTTTGCTGGTAAGCAGCTTGAAGATGGGAGAACCCTTGCAGATTACAACATCCAGAAA-GAATC
131 TCTTTGCTGGTAAGCAACTTGAAGATGGGAGGACACTTGCAGATTATAACATCCA-AAAGGAGTC
* *
55198 CAC-CTTGCATCTT-GTTCTCCGCCTTCGTGGTGG
195 CACTCTT-CA-CTTGGTGCTCCGTCTTCGTGGTGG
55231 CTTTTAAGTT
Statistics
Matches: 581, Mismatches: 98, Indels: 8
0.85 0.14 0.01
Matches are distributed among these distances:
227 6 0.01
228 570 0.98
229 5 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (228 bp):
ATGCAAATCTTTGTGAAGACTCTCACAGGAAAGACAATCACTTTGGAGGTAGAAAGCTCCGACAC
CATCGACAATGTAAAGGCTAAGATTCAAGATAAAGAGGGAATCCCACCAGACCAGCAAAGGCTCA
TCTTTGCTGGTAAGCAACTTGAAGATGGGAGGACACTTGCAGATTATAACATCCAAAAGGAGTCC
ACTCTTCACTTGGTGCTCCGTCTTCGTGGTGGA
Found at i:55226 original size:456 final size:456
Alignment explanation
Indices: 54320--55230 Score: 1074
Period size: 456 Copynumber: 2.0 Consensus size: 456
54310 GACCTTGTAG
* * * * *
54320 ATGCAAATCTTTGTGAAGACCCTAACAGGCAAGACCATCACCCTTGAGGTCGAAAGTTCTGACAC
1 ATGCAAATCTTTGTCAAGACCCTAACAGGAAAGACAATCACCCTTGAGGTCGAAAGCTCCGACAC
*
54385 CATCGACAATGTCAAGGCTAAGATACAAGATAAAGAAGGAATTCCACCAGATCAGCAAAGACTCA
66 CATCGACAATGTCAAGGCTAAGATACAAGATAAAGAAGGAATCCCACCAGATCAGCAAAGACTCA
* ** * *
54450 TCTTTGCTGGCAAACAGCTTGAAGATGGTCGCACACTAGCAGACTATAATATCCAAAAAGAGTCC
131 TCTTTGCTGGCAAACAACTTGAAGATGGGAGCACACTAGCAGACTATAACATCCAAAAAGAGTCA
* * *
54515 ACCCTTCACTTAGTGCTCCGTCTTCGTGGTGGCATGCAAATTTTTGTTAAGACTCTCACAGGAAA
196 ACCCTTCACTTAGTGCTCCGTCTTCGTGGTGGAATGCAAATCTTTGTGAAGACTCTCACAGGAAA
* * * * * * * *
54580 GACAATCACTTTGGAGGTAGAGAGCTCCGACACTATTGACAATGTAAAGGCTAAGATTCAGGACA
261 GACAATCACATTGGAGGTAGAAAGCTCAGACACCATCGACAATGTAAAGGCAAAGATCCAAGACA
* * * *
54645 AAGAGGGTATTCCACCAGACCAGCAAAGGTTGATTTTTGCTGGAAAGCAACTTGAAGATGGAAGG
326 AAGAGGGTATCCCACCAGACCAGCAAAGGCTCATTTTTGCTGGAAAGCAACTTGAAGATGGAAGA
* * * * * * *
54710 ACACTTGCTGATTATAACATTCAAAAGGAGTCTACTCTTCACTTGGTGCTTCGTCTTCGTGGTGG
391 ACACTTGCAGATTACAACATCCAAAAGGAATCCACTCTTCACTTGGTGCTCCGCCTTCGTGGTGG
54775 T
456 T
* * * * * *
54776 ATGCAGATCTTTGTCAAGACTCTCACAGGAAAGACAATCA-CTTTGGAGGTGGAGAGCTCCGACA
1 ATGCAAATCTTTGTCAAGACCCTAACAGGAAAGACAATCACCCTT-GAGGTCGAAAGCTCCGACA
* * * * * ** *
54840 CCATTGACAATGTCAAGGCTAAGATTCAAGATAAGGAGGGAATCCCACCAGATCAGCAGAGGTTG
65 CCATCGACAATGTCAAGGCTAAGATACAAGATAAAGAAGGAATCCCACCAGATCAGCAAAGACTC
* * * * * * * * *
54905 ATCTTTGCTGGTAAGCAACTTGAGGATGGGAGGACACTCGCTGATTATAACATTCAAAAGGAGTC
130 ATCTTTGCTGGCAAACAACTTGAAGATGGGAGCACACTAGCAGACTATAACATCCAAAAAGAGTC
* * * * * * *
54970 AACTCTTCATTTGGTTCTCCGTCTTCGTGGTGGAATGCAGATCTTTGTGAAGACTCTTACTGGAA
195 AACCCTTCACTTAGTGCTCCGTCTTCGTGGTGGAATGCAAATCTTTGTGAAGACTCTCACAGGAA
* * * * * *
55035 AGACTATCACATTGGAGGTTGAAAGTTCAGATACCATCGATAATGTAAAGGCAAAGATCCAAGAT
260 AGACAATCACATTGGAGGTAGAAAGCTCAGACACCATCGACAATGTAAAGGCAAAGATCCAAGAC
* * * * *
55100 AAGGAGGGTATCCCACCTGACCAGCAAAGGCTCATTTTTGCTGGTAAGCAGCTTGAAGATGGGAG
325 AAAGAGGGTATCCCACCAGACCAGCAAAGGCTCATTTTTGCTGGAAAGCAACTTGAAGATGGAAG
* *
55165 AACCCTTGCAGATTACAACATCCAGAAA-GAATCCAC-CTTGCATCTT-GTTCTCCGCCTTCGTG
390 AACACTTGCAGATTACAACATCCA-AAAGGAATCCACTCTT-CA-CTTGGTGCTCCGCCTTCGTG
55227 GTGG
452 GTGG
55231 CTTTTAAGTT
Statistics
Matches: 375, Mismatches: 76, Indels: 8
0.82 0.17 0.02
Matches are distributed among these distances:
455 6 0.02
456 363 0.97
457 6 0.02
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (456 bp):
ATGCAAATCTTTGTCAAGACCCTAACAGGAAAGACAATCACCCTTGAGGTCGAAAGCTCCGACAC
CATCGACAATGTCAAGGCTAAGATACAAGATAAAGAAGGAATCCCACCAGATCAGCAAAGACTCA
TCTTTGCTGGCAAACAACTTGAAGATGGGAGCACACTAGCAGACTATAACATCCAAAAAGAGTCA
ACCCTTCACTTAGTGCTCCGTCTTCGTGGTGGAATGCAAATCTTTGTGAAGACTCTCACAGGAAA
GACAATCACATTGGAGGTAGAAAGCTCAGACACCATCGACAATGTAAAGGCAAAGATCCAAGACA
AAGAGGGTATCCCACCAGACCAGCAAAGGCTCATTTTTGCTGGAAAGCAACTTGAAGATGGAAGA
ACACTTGCAGATTACAACATCCAAAAGGAATCCACTCTTCACTTGGTGCTCCGCCTTCGTGGTGG
T
Found at i:57289 original size:22 final size:22
Alignment explanation
Indices: 57264--57926 Score: 307
Period size: 22 Copynumber: 30.3 Consensus size: 22
57254 ATTTTTTATG
57264 ACCTCCTTATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
*
57286 ACCTTCC-TATGAAATTTTAATA
1 ACC-TCCTTATGAAATTTTGATA
* * * * *
57308 ACGATAC-TATGGAATTTCGAGA
1 AC-CTCCTTATGAAATTTTGATA
* ** **
57330 ATCTTTTTAT-AAATTTTTTTTA
1 ACCTCCTTATGAAA-TTTTGATA
* **
57352 ACCTTCTTATGAAATTTTTTTA
1 ACCTCCTTATGAAATTTTGATA
*
57374 ACCT-CTCTAAGAAATTTTGA-A
1 ACCTCCT-TATGAAATTTTGATA
*
57395 GACCTCATTATGAAATTTTGATA
1 -ACCTCCTTATGAAATTTTGATA
* **
57418 ACTTCCCAATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
* * *
57440 ACCAACAC-TATGAGATATTGATA
1 ACC-TC-CTTATGAAATTTTGATA
* * *
57463 ACCTCCATATGATATATTGATA
1 ACCTCCTTATGAAATTTTGATA
* * * * *
57485 ACCACGTTATGAAAATTTAAAA
1 ACCTCCTTATGAAATTTTGATA
*
57507 ACCTCCATATG-AATTGTT-AGTA
1 ACCTCCTTATGAAATT-TTGA-TA
* * * *
57529 ATCACAC-TCTGAAATGTTGATA
1 ACCTC-CTTATGAAATTTTGATA
* * *
57551 ATCACAC-TATGAAATTGTGATA
1 ACCTC-CTTATGAAATTTTGATA
57573 ACCT-CTCTATGAAATTTTGATAA
1 ACCTCCT-TATGAAATTTTGAT-A
*
57596 ACCTTCC-TATAAAATTTTGATAA
1 ACC-TCCTTATGAAATTTTGAT-A
* * *
57619 ACCTCCCTATAAAATTTTTATA
1 ACCTCCTTATGAAATTTTGATA
*
57641 ACCTCCTTATGAAATCTTGATA
1 ACCTCCTTATGAAATTTTGATA
* *
57663 A-----TTA-CAAATTTTTATA
1 ACCTCCTTATGAAATTTTGATA
* ** *
57679 ACCTCCCTATGATTTTTTTATA
1 ACCTCCTTATGAAATTTTGATA
* * *
57701 ACCTCATTATGAAATTTCGTTA
1 ACCTCCTTATGAAATTTTGATA
* * *
57723 ATCTCCCTATGAAATTTTGATCT
1 ACCTCCTTATGAAATTTTGAT-A
* *
57746 ACATAC-TATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
57767 ATCCT-CTTATGAAATTTTGA-A
1 A-CCTCCTTATGAAATTTTGATA
* *
57788 AACTAAGC-TATGAAATTTTGATA
1 ACCT--CCTTATGAAATTTTGATA
* * *
57811 ACCTTCATATGAAATTTTGATCT
1 ACCTCCTTATGAAATTTTGAT-A
* * *
57834 ACATAC-TATAAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
57855 ACC-CTCTTATGAAATTTTGA-A
1 ACCTC-CTTATGAAATTTTGATA
* *
57876 AACTAAAC-TATGAAATTTTGATA
1 ACCT--CCTTATGAAATTTTGATA
* *
57899 ACCTTCATATGAAATTTTGATA
1 ACCTCCTTATGAAATTTTGATA
*
57921 TCCTCC
1 ACCTCC
57927 GTGAAATTTT
Statistics
Matches: 491, Mismatches: 105, Indels: 90
0.72 0.15 0.13
Matches are distributed among these distances:
16 10 0.02
17 3 0.01
20 3 0.01
21 25 0.05
22 366 0.75
23 81 0.16
24 2 0.00
25 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
ACCTCCTTATGAAATTTTGATA
Found at i:57803 original size:88 final size:88
Alignment explanation
Indices: 57730--57919 Score: 353
Period size: 88 Copynumber: 2.2 Consensus size: 88
57720 TTAATCTCCC
* * *
57730 TATGAAATTTTGATCTACATACTATGAAATTTTGATAATCCTCTTATGAAATTTTGAAAACTAAG
1 TATGAAATTTTGATCTACATACTATAAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAA
57795 CTATGAAATTTTGATAACCTTCA
66 CTATGAAATTTTGATAACCTTCA
57818 TATGAAATTTTGATCTACATACTATAAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAA
1 TATGAAATTTTGATCTACATACTATAAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAA
57883 CTATGAAATTTTGATAACCTTCA
66 CTATGAAATTTTGATAACCTTCA
57906 TATGAAATTTTGAT
1 TATGAAATTTTGAT
57920 ATCCTCCGTG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 99 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (88 bp):
TATGAAATTTTGATCTACATACTATAAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAA
CTATGAAATTTTGATAACCTTCA
Found at i:58074 original size:22 final size:22
Alignment explanation
Indices: 58049--58263 Score: 109
Period size: 22 Copynumber: 9.8 Consensus size: 22
58039 AATGACATTT
*
58049 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTCTA
*
58071 TGAAATTTTGATAACCTCTCTA
1 TGAAAATTTGATAACCTCTCTA
* * *
58093 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTCTA
* * *
58115 TTAAAATTTTGATAATCACAT-TA
1 TGAAAA-TTTGATAACCTC-TCTA
* * * *
58138 TGTAATTTTGATAACCTCGCTT
1 TGAAAATTTGATAACCTCTCTA
* * ** *
58160 TGAAATTTTCATAACAACACTA
1 TGAAAATTTGATAACCTCTCTA
* *
58182 TGAAATTTTGATAATCT-TCCTA
1 TGAAAATTTGATAACCTCT-CTA
* * *
58204 T-AAATTTTGAGAATCCGCTCTA
1 TGAAAATTTGATAA-CCTCTCTA
* *
58226 TG-AAATTTCGATAATCACTCTA
1 TGAAAATTT-GATAACCTCTCTA
*
58248 TG-AGATTTGATAACCT
1 TGAAAATTTGATAACCT
58264 TATATCAAAT
Statistics
Matches: 146, Mismatches: 38, Indels: 19
0.72 0.19 0.09
Matches are distributed among these distances:
21 20 0.14
22 102 0.70
23 23 0.16
24 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTCTA
Found at i:58188 original size:89 final size:89
Alignment explanation
Indices: 58029--58191 Score: 211
Period size: 89 Copynumber: 1.8 Consensus size: 89
58019 TACCACTATG
* * * * * ** *
58029 AAATTTTGGTAATGACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTCTAT
1 AAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTCATAACAACACTAT
58094 AAAATTTTGTTGACCCCTCTATTA
66 AAAATTTTGTTGACCCCTCTATTA
* *
58118 AAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTCATAACAACACTA
1 AAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTCATAACAACACTA
*
58182 TGAAATTTTG
65 TAAAATTTTG
58192 ATAATCTTCC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
89 60 0.97
90 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (89 bp):
AAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTCATAACAACACTAT
AAAATTTTGTTGACCCCTCTATTA
Found at i:58189 original size:44 final size:42
Alignment explanation
Indices: 58049--58213 Score: 125
Period size: 44 Copynumber: 3.8 Consensus size: 42
58039 AATGACATTT
* * * *
58049 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCCTT-TGAAATTTTGATAA-CACACTA
* * * * * *
58093 TAAAATTTTGTTGACCCCTCTATTAAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTC-CT-TTGAAATTTTGATAA-CACACTA
* *
58138 TGTAATTTTGATAACCTCGCTTTGAAATTTTCATAACAACACTA
1 TGAAATTTTGATAACCTC-CTTTGAAATTTTGATAAC-ACACTA
* *
58182 TGAAATTTTGATAATCTTCCTAT-AAATTTTGA
1 TGAAATTTTGATAA-CCTCCTTTGAAATTTTGA
58214 GAATCCGCTC
Statistics
Matches: 93, Mismatches: 24, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
43 9 0.10
44 47 0.51
45 36 0.39
46 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (42 bp):
TGAAATTTTGATAACCTCCTTTGAAATTTTGATAACACACTA
Found at i:58396 original size:22 final size:22
Alignment explanation
Indices: 58358--58417 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
58348 GTAATCTCCT
*
58358 TATGAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
58380 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCACAC
*
58402 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
58418 TCCCTTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:58534 original size:22 final size:22
Alignment explanation
Indices: 58447--58658 Score: 159
Period size: 22 Copynumber: 9.5 Consensus size: 22
58437 ATAAAGTTTG
58447 TGATAACCACACTATGAAATTT
1 TGATAACCACACTATGAAATTT
** * *
58469 CAATAACCTTC-CTAAGAAATTT
1 TGATAACC-ACACTATGAAATTT
* *
58491 TAATAACCTGATC-CTATTAAATTT
1 TGATAACC--A-CACTATGAAATTT
*
58515 TGGTAACCACACTATGAAATTT
1 TGATAACCACACTATGAAATTT
* *
58537 TGATAACCTTC-CCATGAAATTT
1 TGATAACC-ACACTATGAAATTT
58559 TGATAACTTC-CA-TATGAAATTT
1 TGATAAC--CACACTATGAAATTT
* *
58581 TGGTAACCACACTATGGAATTT
1 TGATAACCACACTATGAAATTT
* *
58603 TGATAACCTC-CTCATGAAATTA
1 TGATAACCACACT-ATGAAATTT
* *
58625 TAATAACCATC-TTATGAAATTT
1 TGATAACCA-CACTATGAAATTT
58647 TGATAACCACAC
1 TGATAACCACAC
58659 AGAGACAAGA
Statistics
Matches: 149, Mismatches: 28, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
20 1 0.01
21 6 0.04
22 121 0.81
23 4 0.03
24 17 0.11
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (22 bp):
TGATAACCACACTATGAAATTT
Found at i:58604 original size:66 final size:66
Alignment explanation
Indices: 58426--58658 Score: 274
Period size: 66 Copynumber: 3.5 Consensus size: 66
58416 AATCCCTTTG
* * ** * *
58426 ATAACCTTTCTAT-AAAGTTTGTGATAACCACACTATGAAATTTCAATAACCTTCCTAAGAAATT
1 ATAACCTTCCTATGAAA-TTT-TGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
58490 TTA
64 TTA
*
58493 ATAACCTGATCCTATTAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
1 ATAACCT--TCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
*
58558 TTG
64 TTA
*
58561 ATAA-CTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-TCCTCATGAAATT
1 ATAACCTTCC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-CATGAAATT
*
58624 ATA
64 TTA
* * *
58627 ATAACCATCTTATGAAATTTTGATAACCACAC
1 ATAACCTTCCTATGAAATTTTGGTAACCACAC
58659 AGAGACAAGA
Statistics
Matches: 146, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
65 6 0.04
66 73 0.50
67 12 0.08
68 44 0.30
69 8 0.05
70 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (66 bp):
ATAACCTTCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTT
A
Found at i:58654 original size:44 final size:43
Alignment explanation
Indices: 58422--58654 Score: 193
Period size: 44 Copynumber: 5.2 Consensus size: 43
58412 TGATAATCCC
* *
58422 TTTGATAACCTTTCTAT-AAAGTTTGTGATAACCA-CACTATGAAAT
1 TTTGATAACC-TCCTATGAAA-TTT-TAATAACCATC-CTATGAAAT
** * *
58467 TTCAATAACCTTCCTAAGAAATTTTAATAACCTGATCCTATTAAAT
1 TTTGATAACC-TCCTATGAAATTTTAATAACC--ATCCTATGAAAT
* * * * *
58513 TTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTC-CTATGAAATTTTAATAACCATCCTATGAAAT
* ** *
58557 TTTGATAACTTCCATATGAAATTTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCTCC-TATGAAATTTTAATAACCATC-CTATGAAAT
* *
58601 TTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAAT
1 TTTGATAACCTCCT-ATGAAATTTTAATAACCATCCTATGAAAT
58645 TTTGATAACC
1 TTTGATAACC
58655 ACACAGAGAC
Statistics
Matches: 151, Mismatches: 28, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
43 3 0.02
44 93 0.62
45 18 0.12
46 36 0.24
47 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (43 bp):
TTTGATAACCTCCTATGAAATTTTAATAACCATCCTATGAAAT
Found at i:68479 original size:19 final size:19
Alignment explanation
Indices: 68439--68475 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
68429 AATTTTTAAG
68439 TAAAAATTTAATATATAAA
1 TAAAAATTTAATATATAAA
68458 TAAAAATTTAATAT-TAAA
1 TAAAAATTTAATATATAAA
68476 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATTTAATATATAAA
Found at i:71585 original size:19 final size:19
Alignment explanation
Indices: 71561--71599 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
71551 TGGACTAAAC
71561 AGGCCAAAACTTGGAAAGT
1 AGGCCAAAACTTGGAAAGT
71580 AGGCCAAAACTTGGAAAGT
1 AGGCCAAAACTTGGAAAGT
71599 A
1 A
71600 ATATAAACGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (19 bp):
AGGCCAAAACTTGGAAAGT
Found at i:71895 original size:15 final size:15
Alignment explanation
Indices: 71875--71905 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
71865 AGTTCGAGTC
71875 TCTATATAACCTTAT
1 TCTATATAACCTTAT
71890 TCTATATAACCTTAT
1 TCTATATAACCTTAT
71905 T
1 T
71906 GGTAAGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (15 bp):
TCTATATAACCTTAT
Found at i:75746 original size:21 final size:21
Alignment explanation
Indices: 75722--75762 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
75712 GCACCAGCCC
75722 AGCCCACCAAAACATATTCCA
1 AGCCCACCAAAACATATTCCA
* *
75743 AGCCCACCAAAGCATGTTCC
1 AGCCCACCAAAACATATTCC
75763 GGGCCAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.39, G:0.10, T:0.15
Consensus pattern (21 bp):
AGCCCACCAAAACATATTCCA
Found at i:76598 original size:19 final size:19
Alignment explanation
Indices: 76574--76610 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
76564 GGGGTTTAAT
*
76574 AGTGAAGTGAATTATAGCC
1 AGTGAAGTGAATCATAGCC
76593 AGTGAAGTGAATCATAGC
1 AGTGAAGTGAATCATAGC
76611 ATTGTGGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.24
Consensus pattern (19 bp):
AGTGAAGTGAATCATAGCC
Found at i:86629 original size:33 final size:33
Alignment explanation
Indices: 86592--86674 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
86582 ACCTAAGCCT
*
86592 CCCGTCGTGAAGCCTCCTCATGTGCCCAAACCA
1 CCCGTCGTAAAGCCTCCTCATGTGCCCAAACCA
* *
86625 CCCGTTGTAAAGCCTCCTCATGTTCCCAAACCA
1 CCCGTCGTAAAGCCTCCTCATGTGCCCAAACCA
86658 CCCGTCGTAAAGCCTCC
1 CCCGTCGTAAAGCCTCC
86675 ACACATTCCG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.22, C:0.42, G:0.16, T:0.20
Consensus pattern (33 bp):
CCCGTCGTAAAGCCTCCTCATGTGCCCAAACCA
Found at i:86701 original size:33 final size:33
Alignment explanation
Indices: 86616--86707 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
86606 TCCTCATGTG
* **
86616 CCCAAACCACCCGTTGTAAAGCCTCCTCATGTT
1 CCCAAACCACCCGTTGTAAAGCCTCCACACATT
*
86649 CCCAAACCACCCGTCGTAAAGCCTCCACACATT
1 CCCAAACCACCCGTTGTAAAGCCTCCACACATT
* *
86682 CCGAAGCC-CCCAGTTGTAAAGCCTCC
1 CCCAAACCACCC-GTTGTAAAGCCTCC
86708 GCCGGCGCCT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 3 0.06
33 48 0.94
ACGTcount: A:0.26, C:0.42, G:0.13, T:0.18
Consensus pattern (33 bp):
CCCAAACCACCCGTTGTAAAGCCTCCACACATT
Found at i:86832 original size:63 final size:63
Alignment explanation
Indices: 86754--86876 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 63
86744 ACCACCAATT
* *
86754 CTGCCTCCCAAGCCTCCTGTTTACCCAAGTCCGCCGATTGTGAAGCCACCAACGCCGCCAACC
1 CTGCCTCCCAAGCCTCCTGTCTACCCAACTCCGCCGATTGTGAAGCCACCAACGCCGCCAACC
* * * * *
86817 CTGCCT-CCAACGCCTCCTGTCTATCCATCTCCTCCTATTGTGAAGCCTCCAACGCCGCCA
1 CTGCCTCCCAA-GCCTCCTGTCTACCCAACTCCGCCGATTGTGAAGCCACCAACGCCGCCA
86877 GTCTTGCCTC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
62 4 0.08
63 48 0.92
ACGTcount: A:0.19, C:0.45, G:0.15, T:0.21
Consensus pattern (63 bp):
CTGCCTCCCAAGCCTCCTGTCTACCCAACTCCGCCGATTGTGAAGCCACCAACGCCGCCAACC
Found at i:87940 original size:30 final size:30
Alignment explanation
Indices: 87906--87966 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
87896 ATAATCATGA
87906 TTTAGTCCTGATAGACATAGTCTGAATTAT
1 TTTAGTCCTGATAGACATAGTCTGAATTAT
87936 TTTAGTCCTGATAGACATAGTCTGAATTAT
1 TTTAGTCCTGATAGACATAGTCTGAATTAT
87966 T
1 T
87967 AAAAAAGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (30 bp):
TTTAGTCCTGATAGACATAGTCTGAATTAT
Found at i:92330 original size:21 final size:22
Alignment explanation
Indices: 92288--92330 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
92278 TAATGTGCAT
*
92288 TTTATTTTTATTTGACTTATAA
1 TTTAATTTTATTTGACTTATAA
92310 TTTAATTTT-TTTG-CTTGATAA
1 TTTAATTTTATTTGACTT-ATAA
92331 AAACTTGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 8 0.42
22 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.63
Consensus pattern (22 bp):
TTTAATTTTATTTGACTTATAA
Done.