Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 35
Found at i:11372 original size:15 final size:17
Alignment explanation
Indices: 11341--11374 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
11331 GCTAAACTAA
11341 TTTAATTTTTCAATAAT
1 TTTAATTTTTCAATAAT
11358 TTTAA-TTTT-AATAAT
1 TTTAATTTTTCAATAAT
11373 TT
1 TT
11375 ACTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATTTTTCAATAAT
Found at i:22087 original size:21 final size:21
Alignment explanation
Indices: 22061--22125 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
22051 AAGACAATCA
*
22061 AGAGTCGAAGATAAACTTAAT
1 AGAGTCGAAGATAAACTTAAG
* *
22082 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGATAAACTTAAG
* *
22103 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGATAAACTTAAG
22124 AG
1 AG
22126 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.43, C:0.11, G:0.28, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGATAAACTTAAG
Found at i:22196 original size:33 final size:33
Alignment explanation
Indices: 22159--22224 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
22149 AAATAGATGG
*
22159 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
22192 AGTGGTGAAATAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
22225 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:22426 original size:21 final size:21
Alignment explanation
Indices: 22400--22454 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
22390 GAAAAAATAT
22400 GAAGAAGAAAAGAGGGAGGAG
1 GAAGAAGAAAAGAGGGAGGAG
* *
22421 GAAGAACAAAAGAGGGGGGAG
1 GAAGAAGAAAAGAGGGAGGAG
22442 GAAGAAGAAAAGA
1 GAAGAAGAAAAGA
22455 TGGAAGAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.55, C:0.02, G:0.44, T:0.00
Consensus pattern (21 bp):
GAAGAAGAAAAGAGGGAGGAG
Found at i:24800 original size:181 final size:181
Alignment explanation
Indices: 24487--24857 Score: 634
Period size: 181 Copynumber: 2.0 Consensus size: 181
24477 CAAAAATTGT
* * * **
24487 GAATGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATTTCAGAAACATATGCATCCATAAGT
1 GAATGGATGAAGTGTCGATACATTTTCAAAAAATGTCGATCCCAGAAACATATGCATCCATAAGT
*
24552 ATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTTATAAGAGAATAGGT
66 ATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAATTTTATAAGAGAATAGGT
* * *
24617 CTACAACATGTATTGACACTTTTTTAATTTTGTGTTGATACTTTTGGTCCA
131 CTACAACATGTATCGACACATTTTTAATTTTGTGTCGATACTTTTGGTCCA
*
24668 TAATGGATGAAGTGTCGATACATTTTCAAAAAATGTCGATCCCAGAAACATATGCATCCATAAGT
1 GAATGGATGAAGTGTCGATACATTTTCAAAAAATGTCGATCCCAGAAACATATGCATCCATAAGT
* *
24733 ATAATGTAATAGGTAAATTTACAATGTAACTGGTATAAATATACCAATTTTATGAGAGAATAGGT
66 ATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAATTTTATAAGAGAATAGGT
24798 CTACAACATGTATCGACACATTTTTAATTTTGTGTCGATACTTTTGGTCCA
131 CTACAACATGTATCGACACATTTTTAATTTTGTGTCGATACTTTTGGTCCA
24849 GAATGGATG
1 GAATGGATG
24858 CCAAAAAGGG
Statistics
Matches: 177, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
181 177 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (181 bp):
GAATGGATGAAGTGTCGATACATTTTCAAAAAATGTCGATCCCAGAAACATATGCATCCATAAGT
ATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCAATTTTATAAGAGAATAGGT
CTACAACATGTATCGACACATTTTTAATTTTGTGTCGATACTTTTGGTCCA
Found at i:26234 original size:12 final size:12
Alignment explanation
Indices: 26219--26244 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
26209 GACGACGGCA
26219 ATGATGATGACG
1 ATGATGATGACG
26231 ATGATGATGACG
1 ATGATGATGACG
26243 AT
1 AT
26245 CCAAACAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (12 bp):
ATGATGATGACG
Found at i:27950 original size:200 final size:199
Alignment explanation
Indices: 27550--28056 Score: 694
Period size: 200 Copynumber: 2.5 Consensus size: 199
27540 GTAACACAAA
*
27550 AAAAACATCGAAACCCATAATTATAATGTAATGGGTAATTTTTCAATATAACCGGTATAAATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTT-AATATAACCGGTATAAATATA
* ** * * *
27615 CCGGTTTTATGA-AAAATATTTCTACAACATTTATCGACACTTATTAGTATTGTGTCGATACTAT
65 CCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTATTAATATTGTGTCGATAATAT
* *
27679 GTGTCCAGAATGGATGCCAAAAAGGGGGAACATACAAAGTGTCGATACATTTATTAAAAGTGTCG
130 GTGTCCAGAATGGATGCCAAAAAGGGGGAACACACAAAGTGTCGATACATTTATAAAAAGTGTCG
27744 ATCCC
195 ATCCC
* *
27749 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACTGGTATACATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTT-TAATATAACCGGTATAAATATA
* * * * *
27814 CCGGTTTTATGAGAGAATAGGTCTATAATATGTATCGACGCTTATTAATGTTGTGTCGATAATTT
65 CCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTATTAATATTGTGTCGATAATAT
* * ** * * *
27879 TTGTCCATAATTTATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTT-TCAAAAAGTGTC
130 GTGTCCAGAATGGATGCCAAAAAGGGGGAACACACAAAGTGTCGATACATTTAT-AAAAAGTGTC
*
27943 TATCCC
194 GATCCC
** *
27949 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGT-AATTTTTAATATAACCGGTATAAATATA
* * *
28014 CTGGTTTTATGAGAGAATAGGTATACAACATGTATCAACACTT
65 CCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTT
28057 TGTTGAAAAA
Statistics
Matches: 269, Mismatches: 35, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
199 73 0.27
200 191 0.71
201 5 0.02
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (199 bp):
AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTAATATAACCGGTATAAATATAC
CGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTATTAATATTGTGTCGATAATATG
TGTCCAGAATGGATGCCAAAAAGGGGGAACACACAAAGTGTCGATACATTTATAAAAAGTGTCGA
TCCC
Found at i:30400 original size:45 final size:43
Alignment explanation
Indices: 30349--30451 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 43
30339 GCACCAATCC
** *
30349 ATGCATCGATGCATCA-ATTAATTTCTTGAACATCGAATGCATTTT
1 ATGCATCGATGCATCAGATT--TTTC-AAAACATCGAATGCACTTT
*
30394 ATGCATCGATGCAATCAGGCTTTTTCAAAACATCGAATGCACTTT
1 ATGCATCGATGC-ATCA-GATTTTTCAAAACATCGAATGCACTTT
30439 ATGCATCGATGCA
1 ATGCATCGATGCA
30452 CTCTTAGTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
44 1 0.02
45 40 0.78
46 8 0.16
48 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (43 bp):
ATGCATCGATGCATCAGATTTTTCAAAACATCGAATGCACTTT
Found at i:30452 original size:17 final size:19
Alignment explanation
Indices: 30424--30472 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
30414 TTTTTCAAAA
30424 CATCGAATGCACT-TTA-TG
1 CATCG-ATGCACTCTTAGTG
30442 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTTAGTG
* *
30461 TACCGATGCACT
1 CATCGATGCACT
30473 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 8 0.30
19 12 0.44
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (19 bp):
CATCGATGCACTCTTAGTG
Found at i:32703 original size:6 final size:6
Alignment explanation
Indices: 32694--32761 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
32684 ATTATTCTCA
* * *
32694 TTTTAT TTTTA- TTTTAT ATTT-G TTTTAT TTTTAT TTTCT-T GTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT TTTTAT
*
32740 TCTTTTT ATTTTAT TTTTAT TT
1 T-TTTAT -TTTTAT TTTTAT TT
32762 ATTTTTCCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
5 9 0.19
6 29 0.60
7 9 0.19
8 1 0.02
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:32707 original size:11 final size:11
Alignment explanation
Indices: 32693--32767 Score: 84
Period size: 11 Copynumber: 7.0 Consensus size: 11
32683 TATTATTCTC
32693 ATTTTATTTTT
1 ATTTTATTTTT
*
32704 ATTTTATATTT
1 ATTTTATTTTT
*
32715 GTTTTATTTTT
1 ATTTTATTTTT
*
32726 ATTTTCTTGTTT
1 ATTTTATT-TTT
*
32738 A--TTCTTTTT
1 ATTTTATTTTT
32747 ATTTTATTTTT
1 ATTTTATTTTT
32758 A-TTTATTTTT
1 ATTTTATTTTT
32768 CCATTTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
9 4 0.07
10 14 0.25
11 33 0.60
12 4 0.07
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:32708 original size:5 final size:5
Alignment explanation
Indices: 32693--32766 Score: 53
Period size: 5 Copynumber: 14.0 Consensus size: 5
32683 TATTATTCTC
* * *
32693 ATTTT ATTTTT ATTTT ATATTT GTTTT ATTTTT ATTTT CTTGTTT ATTCT
1 ATTTT A-TTTT ATTTT AT-TTT ATTTT A-TTTT ATTTT -AT-TTT ATTTT
32743 -TTTT ATTTT ATTTT -TATTT ATTTT
1 ATTTT ATTTT ATTTT AT-TTT ATTTT
32767 TCCATTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
4 4 0.07
5 31 0.56
6 17 0.31
7 3 0.05
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:32723 original size:27 final size:25
Alignment explanation
Indices: 32693--32761 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 25
32683 TATTATTCTC
*
32693 ATTTTATTTTTATTTTATATTTGTTTT
1 ATTTTATTTTTATTTTAT-TCT-TTTT
32720 ATTTTTATTTTCT-TGTTTATTCTTTTT
1 A-TTTTATTTT-TAT-TTTATTCTTTTT
32747 ATTTTATTTTTATTT
1 ATTTTATTTTTATTT
32762 ATTTTTCCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
25 3 0.08
26 10 0.27
27 6 0.16
28 12 0.32
29 6 0.16
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (25 bp):
ATTTTATTTTTATTTTATTCTTTTT
Found at i:32747 original size:21 final size:20
Alignment explanation
Indices: 32699--32760 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
32689 TCTCATTTTA
* *
32699 TTTTTATTTTATATTTGTTTTA
1 TTTTTATTTTAT-TTT-TATTC
*
32721 TTTTTATTTTCTTGTTTATTC
1 TTTTTATTTTATT-TTTATTC
32742 TTTTTATTTTATTTTTATT
1 TTTTTATTTTATTTTTATT
32761 TATTTTTCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 6 0.17
21 16 0.46
22 13 0.37
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTTATTTTATTTTTATTC
Found at i:46585 original size:75 final size:76
Alignment explanation
Indices: 46435--46643 Score: 271
Period size: 75 Copynumber: 2.8 Consensus size: 76
46425 AAAGCCAAAA
* * **
46435 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
46499 TTTTGGCTCCGAG
64 TTTTGGCTCCGAG
* *
46512 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAGACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
*
46577 TT-GTTCCGAG
66 TTGGCTCCGAG
* * * *
46587 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
46644 TGTACAACGG
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
75 73 0.62
76 19 0.16
77 26 0.22
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TTGGCTCCGAG
Found at i:55144 original size:75 final size:75
Alignment explanation
Indices: 54994--55201 Score: 249
Period size: 75 Copynumber: 2.7 Consensus size: 75
54984 CAAAGCCAAA
* * **
54994 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCTAAACAGT
55059 TTTGGCTCCGAG
64 TTTGGCTCCGAG
* * *
55071 ATTTCCAGAATGCTCGGAGGGAACCAATTCCCCCATAGGAGGAACCGATTCCCCCCTAGACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGTT
*
55136 TT-GTTCCGAG
65 TTGGCTCCGAG
* * * * *
55146 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACTGATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCT
55202 TGTACAACGG
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
74 6 0.05
75 64 0.56
76 19 0.17
77 25 0.22
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
TGGCTCCGAG
Found at i:55961 original size:18 final size:19
Alignment explanation
Indices: 55935--55973 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
55925 TGTAACAATA
* *
55935 ATAATATTTTTTA-ATTTT
1 ATAAAATTTTATATATTTT
55953 ATAAAATTTTATATATTTT
1 ATAAAATTTTATATATTTT
55972 AT
1 AT
55974 CAATTTAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATAAAATTTTATATATTTT
Found at i:60752 original size:60 final size:60
Alignment explanation
Indices: 60645--60814 Score: 153
Period size: 60 Copynumber: 2.8 Consensus size: 60
60635 AGATAACCAA
* *
60645 TTTATAACTTTTAATAATCGAGAGACTCAAGAAAACAACACCCTATAGTCAGGT-GACTAT
1 TTTATAACTTTTAATAATCGAGAGACTCAACAAAACAACACCCTATAGTCA-GTAAACTAT
* * * ** ** * * *
60705 TTTATAATTTTTAATAATTGAGGGACTCAACAAAGTAACGTCTTATAGTTAGTAAATTAT
1 TTTATAACTTTTAATAATCGAGAGACTCAACAAAACAACACCCTATAGTCAGTAAACTAT
* * * * * * *
60765 TTTATAACTTTTAATAGTCGAAAGACTAAATAAAATAATATCCTATAGTC
1 TTTATAACTTTTAATAATCGAGAGACTCAACAAAACAACACCCTATAGTC
60815 GCGGGACCAT
Statistics
Matches: 85, Mismatches: 24, Indels: 2
0.77 0.22 0.02
Matches are distributed among these distances:
59 2 0.02
60 83 0.98
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (60 bp):
TTTATAACTTTTAATAATCGAGAGACTCAACAAAACAACACCCTATAGTCAGTAAACTAT
Found at i:61128 original size:2 final size:2
Alignment explanation
Indices: 61121--61155 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
61111 CTTTCTACAC
61121 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61156 TTGTAACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61240 original size:2 final size:2
Alignment explanation
Indices: 61235--61260 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61225 AGGATTCAAA
61235 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
61261 GCAACTTTTA
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:67526 original size:13 final size:13
Alignment explanation
Indices: 67510--67540 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
67500 GTCAACGGGT
*
67510 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
67523 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
67536 CGGGT
1 CGGGT
67541 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:67573 original size:10 final size:10
Alignment explanation
Indices: 67553--67607 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
67543 ACGGGTCGTG
67553 ACCGGTC-AA
1 ACCGGTCAAA
67562 ACCGGTCAAA
1 ACCGGTCAAA
67572 ACCGGTTCAAA
1 ACCGG-TCAAA
*
67583 ACCGGT-TAA
1 ACCGGTCAAA
67592 ACCGGTCAAA
1 ACCGGTCAAA
67602 ACCGGT
1 ACCGGT
67608 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:67608 original size:19 final size:19
Alignment explanation
Indices: 67553--67608 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
67543 ACGGGTCGTG
*
67553 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
67572 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
67592 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
67609 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:74795 original size:13 final size:13
Alignment explanation
Indices: 74779--74809 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
74769 GTCAACGGGT
*
74779 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
74792 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
74805 CGGGT
1 CGGGT
74810 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:74842 original size:10 final size:10
Alignment explanation
Indices: 74822--74876 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
74812 ACGGGTCGTG
74822 ACCGGTC-AA
1 ACCGGTCAAA
74831 ACCGGTCAAA
1 ACCGGTCAAA
74841 ACCGGTTCAAA
1 ACCGG-TCAAA
*
74852 ACCGGT-TAA
1 ACCGGTCAAA
74861 ACCGGTCAAA
1 ACCGGTCAAA
74871 ACCGGT
1 ACCGGT
74877 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:74877 original size:19 final size:19
Alignment explanation
Indices: 74822--74877 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
74812 ACGGGTCGTG
*
74822 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
74841 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
74861 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
74878 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:78203 original size:19 final size:19
Alignment explanation
Indices: 78179--78232 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
78169 AAAAACCGAA
*
78179 CCGAACCGAACCGAAAAAT
1 CCGAACCGAACCGAAAAAC
*
78198 CCGAACCGTTA---AAAAAC
1 CCGAACCG-AACCGAAAAAC
78215 CCGAACCGAACCGAAAAA
1 CCGAACCGAACCGAAAAA
78233 ACCGGTTTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
19 13 0.46
20 1 0.04
ACGTcount: A:0.48, C:0.31, G:0.15, T:0.06
Consensus pattern (19 bp):
CCGAACCGAACCGAAAAAC
Found at i:85594 original size:47 final size:47
Alignment explanation
Indices: 85525--85617 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 47
85515 AAAACTTTTG
*
85525 AAGTAATAGGAAAACATCATGCAAGCACCAAAAAGAAATTAACACTA
1 AAGTAATAGGAAAACATCATGCAAGCACCAAAAAGAAATGAACACTA
* *
85572 AAGTAATAGGAAAACATCATGCAGGCACCAAAAGGAAATGAACACT
1 AAGTAATAGGAAAACATCATGCAAGCACCAAAAAGAAATGAACACT
85618 TAAACTTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.53, C:0.17, G:0.16, T:0.14
Consensus pattern (47 bp):
AAGTAATAGGAAAACATCATGCAAGCACCAAAAAGAAATGAACACTA
Found at i:87967 original size:3 final size:3
Alignment explanation
Indices: 87959--87996 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
87949 TTGTAGTATC
87959 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
87997 CATTGTCAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:88529 original size:31 final size:31
Alignment explanation
Indices: 88489--88558 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
88479 AGTTTCAAAA
* * *
88489 ATAATAAATTAGTTACTAACGTTATCGACTT
1 ATAACAAATTAGTCACTAACATTATCGACTT
*
88520 ATAACAAATTAGTCACTAACATTATCGATTT
1 ATAACAAATTAGTCACTAACATTATCGACTT
88551 ATAACAAA
1 ATAACAAA
88559 CCAATCAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.34
Consensus pattern (31 bp):
ATAACAAATTAGTCACTAACATTATCGACTT
Found at i:92049 original size:24 final size:26
Alignment explanation
Indices: 91996--92063 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 26
91986 ATTATTTTAT
* *
91996 TATTTTTAAT-ATATATATATATATA
1 TATTTTTAATAAAATTTATATATATA
92021 TATTTTTTAATAAAATTTATATATA-A
1 TA-TTTTTAATAAAATTTATATATATA
*
92047 T-TTTTTTATAAAATTTA
1 TATTTTTAATAAAATTTA
92064 AAAGATAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 15 0.39
25 2 0.05
26 10 0.26
27 11 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TATTTTTAATAAAATTTATATATATA
Found at i:92071 original size:25 final size:24
Alignment explanation
Indices: 92022--92071 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
92012 ATATATATAT
* *
92022 ATTTTTTAATAAAATTTATATATA
1 ATTTTTTAATAAAATTTAAAGATA
*
92046 ATTTTTTTATAAAATTTAAAAGATA
1 ATTTTTTAATAAAATTT-AAAGATA
92071 A
1 A
92072 ATGGTAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTTTTAATAAAATTTAAAGATA
Found at i:92185 original size:35 final size:31
Alignment explanation
Indices: 92122--92186 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
92112 ATTTTAATTA
**
92122 ATATTAAATTTTACATAATTTATCTAAATAT
1 ATATTAAATTTTACATAATTTAAATAAATAT
92153 ATATTAAAATTTTACATCAACATTTAAATAAATA
1 ATATT-AAATTTTACAT--A-ATTTAAATAAATA
92187 AGCATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 5 0.18
32 11 0.39
34 1 0.04
35 11 0.39
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (31 bp):
ATATTAAATTTTACATAATTTAAATAAATAT
Found at i:98880 original size:23 final size:21
Alignment explanation
Indices: 98828--98889 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
98818 TTTTGGTGCA
*
98828 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
98848 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
98869 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
98890 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:102906 original size:24 final size:20
Alignment explanation
Indices: 102853--102910 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
102843 TTCCCCTTGA
*
102853 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
102873 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
102896 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
102911 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:105780 original size:18 final size:18
Alignment explanation
Indices: 105757--105792 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
105747 ATACAACACA
105757 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
105775 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
105793 GTAGACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:106601 original size:24 final size:24
Alignment explanation
Indices: 106549--106629 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
106539 TCCCCTTGAA
*
106549 GTGCATCGATACATTC--T-ACA-
1 GTGCATCGATGCATTCTTTAACAT
106569 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
106593 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
106617 GTGCATCGATGCA
1 GTGCATCGATGCA
106630 CTACCCTTGC
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
20 15 0.27
22 1 0.02
23 3 0.05
24 37 0.66
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (24 bp):
GTGCATCGATGCATTCTTTAACAT
Found at i:107788 original size:120 final size:122
Alignment explanation
Indices: 107569--107807 Score: 374
Period size: 120 Copynumber: 1.9 Consensus size: 122
107559 AAGAATAACA
*
107569 ATAAAAGCTGAGGTTACTCTTATAAAAGATAAGAAACACTTAAGAAGATCAATGATGCACATCAA
1 ATAAAAGCTGAGGCTACTCTTATAAAAGAT-A-AAACACTT-A-AAGATCAATGATGCACATCAA
* *
107634 TGTTATAACATTTATCATTCCACAAATCTAAACATCCAGTTTAGGCCAGGAGAAGTAAAAT
62 TGTTAGAACATTTATCATTCCACAAATCCAAACATCCAGTTTAGGCCAGGAGAAGTAAAAT
*
107695 ATAAAAGCTGAGGCTACTCTTATAAAAGAT-AAACACTT-AAGATTAATGATGCACATCAATGTT
1 ATAAAAGCTGAGGCTACTCTTATAAAAGATAAAACACTTAAAGATCAATGATGCACATCAATGTT
* *
107758 AGAACATTTATCATTCCGCAAATCCAAACATTCAGTTTAGGCCAGGAGAA
66 AGAACATTTATCATTCCACAAATCCAAACATCCAGTTTAGGCCAGGAGAA
107808 CTTTATTTTA
Statistics
Matches: 107, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
120 70 0.65
123 8 0.07
126 29 0.27
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (122 bp):
ATAAAAGCTGAGGCTACTCTTATAAAAGATAAAACACTTAAAGATCAATGATGCACATCAATGTT
AGAACATTTATCATTCCACAAATCCAAACATCCAGTTTAGGCCAGGAGAAGTAAAAT
Found at i:115034 original size:61 final size:62
Alignment explanation
Indices: 114928--115051 Score: 205
Period size: 61 Copynumber: 2.0 Consensus size: 62
114918 TAGAATATTA
*
114928 CTCTTATCACAAAAGACATGTCTAATAGAATATATAATGTCACCATTTTTAAATTTTGGGATT
1 CTCTCATCACAAAAGACA-GTCTAATAGAATATATAATGTCACCATTTTTAAATTTTGGGATT
* *
114991 CTCTCATCTCAAAAGAC-GTCTCATAGAATATATAATGTCACCATTTTTAAATTTTGGGATT
1 CTCTCATCACAAAAGACAGTCTAATAGAATATATAATGTCACCATTTTTAAATTTTGGGATT
115052 TTTTCCCTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 43 0.74
63 15 0.26
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (62 bp):
CTCTCATCACAAAAGACAGTCTAATAGAATATATAATGTCACCATTTTTAAATTTTGGGATT
Found at i:120733 original size:15 final size:17
Alignment explanation
Indices: 120714--120754 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
120704 TGAAAAAGTC
120714 CAAACCTGAAAAAAA-T
1 CAAACCTGAAAAAAATT
120730 -AAA-CTCGAAAAAAATT
1 CAAACCT-GAAAAAAATT
120746 CAAACCTGA
1 CAAACCTGA
120755 GATAGTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
14 2 0.10
15 11 0.52
16 1 0.05
17 5 0.24
18 2 0.10
ACGTcount: A:0.59, C:0.20, G:0.07, T:0.15
Consensus pattern (17 bp):
CAAACCTGAAAAAAATT
Found at i:122348 original size:24 final size:24
Alignment explanation
Indices: 122330--122376 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
122320 AGTCAGTATT
122330 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
* *
122354 CGGACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
122377 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:122381 original size:24 final size:24
Alignment explanation
Indices: 122335--122388 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
122325 GTATTCGAAA
122335 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
122359 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
122383 TTTGAT
1 TTTGAT
122389 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:124701 original size:12 final size:12
Alignment explanation
Indices: 124684--124735 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
124674 AGTAAAGGGA
*
124684 AATCAAAATCGC
1 AATCAAAATCAC
*
124696 AATCAAAATCAA
1 AATCAAAATCAC
124708 AATCAAAATCAC
1 AATCAAAATCAC
*
124720 AATCACAATCAC
1 AATCAAAATCAC
124732 AATC
1 AATC
124736 GCCTTCACCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.56, C:0.25, G:0.02, T:0.17
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:124705 original size:6 final size:6
Alignment explanation
Indices: 124683--124735 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
124673 AAGTAAAGGG
* * * *
124683 AAATCA AAATCG CAATCA AAATCA AAATCA AAATCA CAATCA CAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
*
124731 CAATC
1 AAATC
124736 GCCTTCACCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.57, C:0.25, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:124706 original size:18 final size:18
Alignment explanation
Indices: 124683--124735 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
124673 AAGTAAAGGG
*
124683 AAATCAAAATCGCAATCA
1 AAATCAAAATCACAATCA
*
124701 AAATCAAAATCAAAATCA
1 AAATCAAAATCACAATCA
* *
124719 CAATCACAATCACAATC
1 AAATCAAAATCACAATC
124736 GCCTTCACCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.57, C:0.25, G:0.02, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:124992 original size:20 final size:20
Alignment explanation
Indices: 124965--125096 Score: 134
Period size: 20 Copynumber: 6.9 Consensus size: 20
124955 ATATCGCAAC
124965 TCAAATTCGCAACTCGAAAA
1 TCAAATTCGCAACTCGAAAA
* *
124985 TAAAATTCACAACTCGAAAA
1 TCAAATTCGCAACTCGAAAA
* * *
125005 TCGAATTCGCAATTCGAAAC
1 TCAAATTCGCAACTCGAAAA
*
125025 TCAAATTCGCAACTCGAAAC
1 TCAAATTCGCAACTCGAAAA
*
125045 TCAAATTCACAACGT-GAAAA
1 TCAAATTCGCAAC-TCGAAAA
125065 TC--A-T---AACTCGAAAA
1 TCAAATTCGCAACTCGAAAA
*
125079 TAAAATTCGCAACTCGAA
1 TCAAATTCGCAACTCGAA
125097 TTTTGAATTC
Statistics
Matches: 92, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.01
14 9 0.10
16 1 0.01
17 2 0.02
18 1 0.01
20 77 0.84
21 1 0.01
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.21
Consensus pattern (20 bp):
TCAAATTCGCAACTCGAAAA
Found at i:125105 original size:20 final size:20
Alignment explanation
Indices: 125082--125119 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
125072 TCGAAAATAA
*
125082 AATTCGCAACTCGAATTTTG
1 AATTCGCAACTCAAATTTTG
125102 AATTCGCAACTCAAATTT
1 AATTCGCAACTCAAATTT
125120 CATTTTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
AATTCGCAACTCAAATTTTG
Found at i:125145 original size:20 final size:20
Alignment explanation
Indices: 125115--125260 Score: 128
Period size: 20 Copynumber: 7.6 Consensus size: 20
125105 TCGCAACTCA
*
125115 AATTTCATTTTTGAGTTGCG
1 AATTTCATTTTCGAGTTGCG
* *
125135 ATTTTCGTTTTCGAGTTGCG
1 AATTTCATTTTCGAGTTGCG
*
125155 AATTTCGTTTTCGAGTTGCG
1 AATTTCATTTTCGAGTTGCG
*
125175 AATTTCATTTTCGAGTTACG
1 AATTTCATTTTCGAGTTGCG
*
125195 ATTTTCA---T---GTTGC-
1 AATTTCATTTTCGAGTTGCG
* * *
125208 AAATTCAAGTTTCGAATTGCG
1 AATTTC-ATTTTCGAGTTGCG
125229 AA-TTCGATTTTCGAGTTGCG
1 AATTTC-ATTTTCGAGTTGCG
*
125249 AATTTGATTTTC
1 AATTTCATTTTC
125261 TTGAATAAAT
Statistics
Matches: 102, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
13 4 0.04
14 5 0.05
17 2 0.02
20 87 0.85
21 4 0.04
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.46
Consensus pattern (20 bp):
AATTTCATTTTCGAGTTGCG
Found at i:127067 original size:21 final size:21
Alignment explanation
Indices: 127012--127070 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
127002 AGTATGGAAT
*
127012 GTGGATCCTGAACAATGCGGG
1 GTGGATCCTGAACGATGCGGG
* *
127033 GTAGATCCTAAACGATGCGGG
1 GTGGATCCTGAACGATGCGGG
127054 GTGGATCCTGAACGATG
1 GTGGATCCTGAACGATG
127071 GGAGGGGCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.20
Consensus pattern (21 bp):
GTGGATCCTGAACGATGCGGG
Found at i:127107 original size:21 final size:21
Alignment explanation
Indices: 127016--127118 Score: 77
Period size: 21 Copynumber: 4.9 Consensus size: 21
127006 TGGAATGTGG
*
127016 ATCCTGAACAATGCGG-GGT-A
1 ATCCTGAACGATG-GGAGGTGA
* *
127036 GATCCTAAACGATGCGG-GGTGG
1 -ATCCTGAACGATG-GGAGGTGA
* *
127058 ATCCTGAACGATGGGAGGGGC
1 ATCCTGAACGATGGGAGGTGA
* *
127079 CTCTTGAACGATGGGAGGTGA
1 ATCCTGAACGATGGGAGGTGA
**
127100 ATCCTGAATAATGGGAGGT
1 ATCCTGAACGATGGGAGGT
127119 AGACCCTGAA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
20 2 0.03
21 64 0.97
ACGTcount: A:0.26, C:0.17, G:0.37, T:0.20
Consensus pattern (21 bp):
ATCCTGAACGATGGGAGGTGA
Found at i:127126 original size:21 final size:21
Alignment explanation
Indices: 127089--127129 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
127079 CTCTTGAACG
*
127089 ATGGGAGGTGAATCCTGAATA
1 ATGGGAGGTGAACCCTGAATA
127110 ATGGGAGGT-AGACCCTGAAT
1 ATGGGAGGTGA-ACCCTGAAT
127130 TTCATTTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.22
Consensus pattern (21 bp):
ATGGGAGGTGAACCCTGAATA
Found at i:127154 original size:20 final size:20
Alignment explanation
Indices: 127129--127194 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
127119 AGACCCTGAA
*
127129 TTTCATTTTCGAGTTGCGAT
1 TTTCATTTTTGAGTTGCGAT
*
127149 TTTCATTTTTGAGTTGCGAA
1 TTTCATTTTTGAGTTGCGAT
*
127169 ATTCATTTTTGAGTTGCGAT
1 TTTCATTTTTGAGTTGCGAT
127189 TTTCAT
1 TTTCAT
127195 GTTGCGATGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCATTTTTGAGTTGCGAT
Found at i:127770 original size:40 final size:39
Alignment explanation
Indices: 127721--127877 Score: 109
Period size: 40 Copynumber: 3.9 Consensus size: 39
127711 GCGATATTTT
127721 AATTCGTGTTACGAATTCT-AAAATCGAGTTGCGAAAACAA
1 AATTCGTGTTACGAATT-TAAAAATCGAGTTGCGAAAA-AA
* * * * * * * **
127761 AATTTGTGTTACTAAATTGAAACTCGTGTTGCTTAAAGGA
1 AATTCGTGTTACGAATTTAAAAATCGAGTTGC-GAAAAAA
* * * *
127801 AACTAGAGTGACGAATTTAAAAATCGAGTTGCGAAAAAGA
1 AATTCGTGTTACGAATTTAAAAATCGAGTTGCGAAAAA-A
* * *
127841 AATTCGTGTTGCGAAATTGTCAAATTCGAGTTGCGAA
1 AATTCGTGTTACG-AATT-TAAAAATCGAGTTGCGAA
127878 TTCGACTTAT
Statistics
Matches: 85, Mismatches: 27, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
39 4 0.05
40 58 0.68
41 7 0.08
42 16 0.19
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (39 bp):
AATTCGTGTTACGAATTTAAAAATCGAGTTGCGAAAAAA
Found at i:127835 original size:20 final size:20
Alignment explanation
Indices: 127812--127879 Score: 50
Period size: 20 Copynumber: 3.3 Consensus size: 20
127802 ACTAGAGTGA
127812 CGAATTTAAAAATCGAGTTG
1 CGAATTTAAAAATCGAGTTG
* *
127832 CGAA--AAAGAAATTCGTGTTG
1 CGAATTTAA-AAA-TCGAGTTG
* *
127852 CGAAATTGTCAAATTCGAGTTG
1 CG-AATT-TAAAAATCGAGTTG
127874 CGAATT
1 CGAATT
127880 CGACTTATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 11
0.68 0.11 0.21
Matches are distributed among these distances:
18 2 0.06
19 3 0.08
20 13 0.36
21 6 0.17
22 9 0.25
23 2 0.06
24 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (20 bp):
CGAATTTAAAAATCGAGTTG
Found at i:127941 original size:20 final size:20
Alignment explanation
Indices: 127840--127961 Score: 104
Period size: 20 Copynumber: 6.0 Consensus size: 20
127830 TGCGAAAAAG
* *
127840 AAATTCGTGTTGCGAAATTGTC
1 AAATTCGAGTTGCG-AATT-CC
127862 AAATTCGAGTTGCGAATT-C
1 AAATTCGAGTTGCGAATTCC
* * * * *
127881 GACTTATGTGTTGTGAATTCC
1 AAATT-CGAGTTGCGAATTCC
127902 AAATTCTGTA-TTGCGAATTCC
1 AAATTC-G-AGTTGCGAATTCC
* *
127923 AAATTCGAGTTGTGAATTCT
1 AAATTCGAGTTGCGAATTCC
127943 AAATTCGAGTTGCGAATTC
1 AAATTCGAGTTGCGAATTC
127962 GGAAACTGTG
Statistics
Matches: 81, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.06
20 38 0.47
21 25 0.31
22 13 0.16
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (20 bp):
AAATTCGAGTTGCGAATTCC
Found at i:128487 original size:15 final size:17
Alignment explanation
Indices: 128468--128508 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
128458 TGAAAAAGTC
128468 CAAACCTGAAAAAAA-T
1 CAAACCTGAAAAAAATT
128484 -AAA-CTCGAAAAAAATT
1 CAAACCT-GAAAAAAATT
128500 CAAACCTGA
1 CAAACCTGA
128509 GATAGTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
14 2 0.10
15 11 0.52
16 1 0.05
17 5 0.24
18 2 0.10
ACGTcount: A:0.59, C:0.20, G:0.07, T:0.15
Consensus pattern (17 bp):
CAAACCTGAAAAAAATT
Found at i:137629 original size:21 final size:21
Alignment explanation
Indices: 137604--137644 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
137594 TGGTGGCAAC
137604 AAAAGGAGGGAAAATAGCAGA
1 AAAAGGAGGGAAAATAGCAGA
137625 AAAAGGAGGGAAAATAGCAG
1 AAAAGGAGGGAAAATAGCAG
137645 CAAATTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.34, T:0.05
Consensus pattern (21 bp):
AAAAGGAGGGAAAATAGCAGA
Found at i:138234 original size:35 final size:36
Alignment explanation
Indices: 138194--138274 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 36
138184 AACATAGTCA
138194 TCAATTACATTCTAAAACCT-AAATTCC-AAAATACT
1 TCAATTACATTCT-AAACCTCAAATTCCAAAAATACT
*
138229 TCAATTAAATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
*
138265 TCAAATACAT
1 TCAATTACAT
138275 GACCAACCCC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
34 6 0.15
35 19 0.46
36 16 0.39
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (36 bp):
TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
Found at i:138959 original size:20 final size:20
Alignment explanation
Indices: 138926--139000 Score: 55
Period size: 20 Copynumber: 3.7 Consensus size: 20
138916 CAACGCGAAC
* *
138926 TCCAATTTCACAACTCAGTT
1 TCCAAATTCGCAACTCAGTT
* *
138946 TCCAAATTCGCAACACTGAATT
1 TCCAAATTCGC-A-ACTCAGTT
138968 T-CAAATTCGCAACTC-GATT
1 TCCAAATTCGCAACTCAG-TT
**
138987 TCTGAATTCGCAAC
1 TCCAAATTCGCAAC
139001 GCGGATTTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 6 0.14
20 20 0.47
21 10 0.23
22 7 0.16
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (20 bp):
TCCAAATTCGCAACTCAGTT
Found at i:139034 original size:40 final size:40
Alignment explanation
Indices: 138910--139060 Score: 133
Period size: 40 Copynumber: 3.8 Consensus size: 40
138900 ATGACCAACA
* * ** * * **
138910 AATTCGCAACGCGAACTCCAATTTCACAACTCAGTTTCCA
1 AATTCGCAACACGAATTTTAATTTCGCAACTCAATTTCTG
* * *
138950 AATTCGCAACACTGAATTTCAAATTCGCAACTCGATTTCTG
1 AATTCGCAACAC-GAATTTTAATTTCGCAACTCAATTTCTG
* * **
138991 AATTCGCAACGCGGATTTTGTTTTCGCAACTCAATTT-TCG
1 AATTCGCAACACGAATTTTAATTTCGCAACTCAATTTCT-G
*
139031 AATTCGTAACACGAATTTTAATTTCGCAAC
1 AATTCGCAACACGAATTTTAATTTCGCAAC
139061 AGGTTTTAGT
Statistics
Matches: 88, Mismatches: 21, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
39 1 0.01
40 56 0.64
41 31 0.35
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (40 bp):
AATTCGCAACACGAATTTTAATTTCGCAACTCAATTTCTG
Found at i:139061 original size:20 final size:20
Alignment explanation
Indices: 138952--139080 Score: 72
Period size: 20 Copynumber: 6.5 Consensus size: 20
138942 AGTTTCCAAA
* *
138952 TTCGCAACACTGAATTTCAAA
1 TTCGCAACAC-GAATTTTAAT
*
138973 TTCGCAACTCG-ATTTCTGAA-
1 TTCGCAACACGAATTT-T-AAT
* * **
138993 TTCGCAACGCGGATTTTGTT
1 TTCGCAACACGAATTTTAAT
*
139013 TTCGCAACTC-AATTTTCGAA-
1 TTCGCAACACGAATTTT--AAT
*
139033 TTCGTAACACGAATTTTAAT
1 TTCGCAACACGAATTTTAAT
* *
139053 TTCGCAACA-G-GTTTTAGT
1 TTCGCAACACGAATTTTAAT
139071 TTCGCAACAC
1 TTCGCAACAC
139081 AAATGTTTTG
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
18 15 0.18
19 12 0.14
20 37 0.44
21 21 0.25
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (20 bp):
TTCGCAACACGAATTTTAAT
Found at i:142641 original size:33 final size:33
Alignment explanation
Indices: 142560--142641 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
142550 AATTCGCAAC
* **
142560 GCGAAAGTCAAATTCACGTTACGATTTTTTGTT
1 GCGAAAGTCAAATTCGCGTTACGATTTTGCGTT
142593 GCGAAAGTCAAATTCGCGTT-CGATTTTCGCGTT
1 GCGAAAGTCAAATTCGCGTTACGATTTT-GCGTT
142626 GCGAAAGTCAAATTCG
1 GCGAAAGTCAAATTCG
142642 AAACGCGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 7 0.16
33 38 0.84
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (33 bp):
GCGAAAGTCAAATTCGCGTTACGATTTTGCGTT
Found at i:142812 original size:64 final size:64
Alignment explanation
Indices: 142742--142909 Score: 291
Period size: 64 Copynumber: 2.6 Consensus size: 64
142732 AAATTAAAAC
*
142742 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTGCACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTCCACATCAATTA
*** *
142806 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTCCACATCAATTA
142870 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAA
142910 AGTGTACCCC
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 99 1.00
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.27
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTCCACATCAATTA
Found at i:144704 original size:63 final size:63
Alignment explanation
Indices: 144649--144771 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
144639 ACGTAGAGCG
*
144649 GCTACCTCATCACGTAAAG-TAGATACCTCACCACG-TAAAGCACCATTGTCATCACGTAAAACC
1 GCTACCTCACCACGTAAAGATAG-TACCTCACCACGCT-AAGCACCATTGTCATCACGTAAAACC
* * * * * *
144712 TCTACCTCACCACGTAAAGATCGTACCTCATCACGCTATGCACTATTGTCGTCACGTAAA
1 GCTACCTCACCACGTAAAGATAGTACCTCACCACGCTAAGCACCATTGTCATCACGTAAA
144772 GTACCGACCT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
63 48 0.94
64 3 0.06
ACGTcount: A:0.32, C:0.32, G:0.13, T:0.24
Consensus pattern (63 bp):
GCTACCTCACCACGTAAAGATAGTACCTCACCACGCTAAGCACCATTGTCATCACGTAAAACC
Found at i:144787 original size:21 final size:21
Alignment explanation
Indices: 144763--144812 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
144753 ACTATTGTCG
* *
144763 TCACGTAAAGTACCGACCTCC
1 TCACGTAAAGCACCGACCTCA
* **
144784 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCACCGACCTCA
144805 TCACGTAA
1 TCACGTAA
144813 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:146530 original size:19 final size:19
Alignment explanation
Indices: 146479--146532 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
146469 GATAGTTTCT
**
146479 GAAACTTAAAATCGTAACGC
1 GAAAC-TAAAATCACAACGC
*
146499 GAAAATGAAAATCACAACGC
1 GAAACT-AAAATCACAACGC
146519 GAAACTAAAATCAC
1 GAAACTAAAATCAC
146533 GTTACGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.52, C:0.20, G:0.13, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCACAACGC
Found at i:147617 original size:64 final size:63
Alignment explanation
Indices: 147520--147660 Score: 153
Period size: 64 Copynumber: 2.2 Consensus size: 63
147510 CATATTCAAT
* * *
147520 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATA-AGG-A
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGAT--ATATAGGTA
* * * * *
147583 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATATATGGGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTGGTGCATCGATATATAGGTA
147647 GTGCATCGATGCAC
1 GTGCATCGATGCAC
147661 ATGTTAAAGA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
62 3 0.05
63 18 0.27
64 45 0.68
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATATATAGGTA
Found at i:147693 original size:20 final size:22
Alignment explanation
Indices: 147648--147705 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
147638 ATATGGGTAG
147648 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
147672 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
147692 TGCATCGATGCACT
1 TGCATCGATGCACT
147706 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:148040 original size:18 final size:18
Alignment explanation
Indices: 147998--148036 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
147988 TGATTATATG
147998 TATATGTATGACATGAAT
1 TATATGTATGACATGAAT
148016 TATATGTATG-CATG-AT
1 TATATGTATGACATGAAT
148032 TATAT
1 TATAT
148037 ATGTTAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 4 0.19
18 10 0.48
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (18 bp):
TATATGTATGACATGAAT
Found at i:151658 original size:64 final size:63
Alignment explanation
Indices: 151559--151699 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 63
151549 CATATTCAAT
* * * *
151559 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGTATCAATGCATAAGGA
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGTATCAATACATAAGGA
* * * * * * *
151622 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATATATGAGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTGGTGTATCAATACATAAGGA
151686 GTGCATCGATGCAC
1 GTGCATCGATGCAC
151700 ATGTTAAAGA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 16 0.25
64 49 0.75
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGTATCAATACATAAGGA
Found at i:151732 original size:20 final size:22
Alignment explanation
Indices: 151687--151744 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
151677 ATATGAGTAG
151687 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
151711 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
151731 TGCATCGATGCACT
1 TGCATCGATGCACT
151745 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:152080 original size:18 final size:18
Alignment explanation
Indices: 152038--152076 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
152028 TGATTATATG
152038 TATATGTATGACATGAAT
1 TATATGTATGACATGAAT
152056 TATATGTATG-CATG-AT
1 TATATGTATGACATGAAT
152072 TATAT
1 TATAT
152077 ATGTTAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 4 0.19
18 10 0.48
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (18 bp):
TATATGTATGACATGAAT
Found at i:153193 original size:22 final size:22
Alignment explanation
Indices: 153166--153219 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
153156 GGAGATAGAC
153166 GGATTTCGCCGGAGATGGGGAT
1 GGATTTCGCCGGAGATGGGGAT
**
153188 GGATTTCATCGGAGATGGGGAT
1 GGATTTCGCCGGAGATGGGGAT
*
153210 GGATGTCGCC
1 GGATTTCGCC
153220 TTAGAGAGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.43, T:0.24
Consensus pattern (22 bp):
GGATTTCGCCGGAGATGGGGAT
Found at i:155249 original size:37 final size:37
Alignment explanation
Indices: 155208--155282 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
155198 TCTGATCTTG
*
155208 GATTTGCTTCACTACTCTTTGGAGAAGGCTTAAGATT
1 GATTTGCTTCACTACTCTTCGGAGAAGGCTTAAGATT
* *
155245 GATTTTCTTCACTACTCTTCGGTGAAGGCTTAAGATT
1 GATTTGCTTCACTACTCTTCGGAGAAGGCTTAAGATT
155282 G
1 G
155283 CCCGGGGGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (37 bp):
GATTTGCTTCACTACTCTTCGGAGAAGGCTTAAGATT
Found at i:155726 original size:43 final size:43
Alignment explanation
Indices: 155679--155789 Score: 150
Period size: 43 Copynumber: 2.6 Consensus size: 43
155669 CGATTCCCTT
* * ** *
155679 CGTCGTGAAGTTAAAATCGTGGATGTGTGGGCACGATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGCATGAGCACGATATCCTC
* * *
155722 CGTCGTGGAGTTGAAATCGTGGATCCATTAGTACGATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGCATGAGCACGATATCCTC
155765 CGTCGTGGAGTTGAAATCGTGGATG
1 CGTCGTGGAGTTGAAATCGTGGATG
155790 GTGCCTTCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (43 bp):
CGTCGTGGAGTTGAAATCGTGGATGCATGAGCACGATATCCTC
Found at i:156016 original size:335 final size:335
Alignment explanation
Indices: 155389--156909 Score: 2380
Period size: 335 Copynumber: 4.5 Consensus size: 335
155379 ATTCCCTTCA
* * * * *
155389 TCGTGAAGTTAAAACCGTGGATCCGTGGGTACAATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
1 TCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
* * * * * *
155454 GAC-CCATTCGTCGTAAAGTCGAGCCTTGACTTGAATATCCTTCATCGTGAAGTTGAATTACAAG
66 GGCGCC-TTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAG
* * * * * * *
155518 CTTATGATGTTTCGGGTCCAATATCCTTCGCCGTGAAGTTGAAATTAACTCTGGAACTGGAAAAT
130 CTTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGAAACTGGAAAGT
* * *
155583 TTATTGACATACACTCTTTCTTCGAGTTGGATATCCTTCGTCGTGAAATTGAAATCCAATCTAGA
195 TTATTGACATACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGA
* * * *
155648 GATGGATTTTGCTTGTGTGTACGATTCCCTTCGTCGTGAAGTTAAAATCGTGGATGTGTGGGCAC
260 GATAGATGTTGCTTGTGTGTACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCAC
155713 GATATCCTCCG
325 GATATCCTCCG
* *
155724 TCGTGGAGTTGAAATCGTGGATCCATTAGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
1 TCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
* * *
155789 GGTGCCTTCATCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTAAAATCCAAGC
66 GGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGC
* *
155854 TTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTAAAATTGGCTCTGAAACTGGAAAGTT
131 TTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGAAACTGGAAAGTT
* * *
155919 TATTGACATACACTCTTTCTTTGAGTTGGATATCATTCATCGTGAAGTTGAAATCCAATCTAGAG
196 TATTGACATACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAG
* *
155984 AT-GAATGCTGCTTGTGTGTACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCAC
261 ATAG-ATGTTGCTTGTGTGTACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCAC
156048 GATATCCTCCG
325 GATATCCTCCG
* * *
156059 TTGTGGAGTTAAAATCGTGGATCCATTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
1 TCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
*
156124 GGCGCCTTCATCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGC
66 GGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGC
* ** * *
156189 TTGTGCTGTTTCGAGTCTAATATCCTTCACCGTGAAGTTAAAATTGGCTCTGAAACTGGAAAGTT
131 TTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGAAACTGGAAAGTT
* *
156254 TATTAACATACACTCCTTCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAG
196 TATTGACATACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAG
* * *
156319 ATAGATGTTGTTTGTGTGTATGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCATG
261 ATAGATGTTGCTTGTGTGTACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCACG
*
156384 ATATCCTCTG
326 ATATCCTCCG
*
156394 TTGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
1 TCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
* * *
156459 GACCCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTAAAGTTGAAATCCAAGC
66 GGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGC
* *
156524 TTTTGTTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGAAACTGGAAAGTT
131 TTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGAAACTGGAAAGTT
* * *
156589 TATTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAAAG
196 TATTGACATACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAG
* *
156654 ATAGATGTTGTTTGTGTGTACGATTCCCTTCGTCGTGAAGTTGAAACCGTGAATGTGTGGGCACG
261 ATAGATGTTGCTTGTGTGTACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCACG
156719 ATATCCTCCG
326 ATATCCTCCG
* *
156729 TCGTTGAGTTGAAATCGTGGATCTGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
1 TCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
*
156794 GGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCATGAAGTTGAAATCCAAGC
66 GGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGC
* * * *
156859 TTGTGCTATTTTGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCT
131 TTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCT
156910 AAAAGCTGCA
Statistics
Matches: 1097, Mismatches: 86, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
334 1 0.00
335 1093 1.00
336 3 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (335 bp):
TCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
GGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGC
TTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGAAACTGGAAAGTT
TATTGACATACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAG
ATAGATGTTGCTTGTGTGTACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCACG
ATATCCTCCG
Found at i:156078 original size:43 final size:43
Alignment explanation
Indices: 156003--156124 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 43
155993 GCTTGTGTGT
* * * * **
156003 ACGATTTCCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGC
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGCATGGGC
* * * * *
156046 ACGATATCCTCCGTTGTGGAGTTAAAATCGTGGATCCATTGGT
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGCATGGGC
156089 ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
1 ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
156125 GCGCCTTCAT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (43 bp):
ACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGCATGGGC
Found at i:156404 original size:43 final size:43
Alignment explanation
Indices: 156349--156459 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
156339 TGATTCCCTT
* * * *
156349 CGTCGTGAAGTTGAAACCGTGGATGTGTGGGCATGATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGCGTGGGCACGATATCCTC
* * * * *
156392 TGTTGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGCGTGGGCACGATATCCTC
156435 CGTCGTGGAGTTGAAATCGTGGATG
1 CGTCGTGGAGTTGAAATCGTGGATG
156460 ACCCCTTCGT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (43 bp):
CGTCGTGGAGTTGAAATCGTGGATGCGTGGGCACGATATCCTC
Found at i:156791 original size:43 final size:43
Alignment explanation
Indices: 156666--156793 Score: 159
Period size: 43 Copynumber: 3.0 Consensus size: 43
156656 AGATGTTGTT
* * * * * *
156666 TGTGTGTACGAT-TCCCTTCGTCGTGAAGTTGAAACCGTGAATG
1 TGTGGGTACGATAT-CCTCCGTCGTGGAGTTGAAATCGTGGATC
* *
156709 TGTGGGCACGATATCCTCCGTCGTTGAGTTGAAATCGTGGATC
1 TGTGGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATC
*
156752 TGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
1 TGTGGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
156794 GGCGCCTTCG
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
43 72 0.99
44 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.32
Consensus pattern (43 bp):
TGTGGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATC
Found at i:157143 original size:32 final size:32
Alignment explanation
Indices: 157069--157143 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
157059 TTGCATCAGG
* *
157069 ATGTTGAATCCCCAAATATGCCCCAATATTCA
1 ATGTTGAATCTCCAAATATGCCCCAACATTCA
*
157101 ATGTTAAATCTCCAAATAT-CCCCTAACATAT-A
1 ATGTTGAATCTCCAAATATGCCCC-AACAT-TCA
*
157133 TTGTTGAATCT
1 ATGTTGAATCT
157144 TTGACGATGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 4 0.11
32 31 0.86
33 1 0.03
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (32 bp):
ATGTTGAATCTCCAAATATGCCCCAACATTCA
Found at i:158187 original size:10 final size:10
Alignment explanation
Indices: 158172--158240 Score: 59
Period size: 10 Copynumber: 6.9 Consensus size: 10
158162 ATTATCATCC
158172 CTTTTTTTTT
1 CTTTTTTTTT
158182 C-TTTTTTTT
1 CTTTTTTTTT
* *
158191 CTCTTTGTTT
1 CTTTTTTTTT
*
158201 CTCTTTTTTT
1 CTTTTTTTTT
* *
158211 CTTTTCTTTA
1 CTTTTTTTTT
*
158221 ATTTCTTTTTT
1 CTTT-TTTTTT
*
158232 ATTTTTTTT
1 CTTTTTTTT
158241 ATTTTTTTGC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
9 9 0.19
10 31 0.65
11 8 0.17
ACGTcount: A:0.04, C:0.13, G:0.01, T:0.81
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:158188 original size:9 final size:9
Alignment explanation
Indices: 158174--158248 Score: 62
Period size: 9 Copynumber: 7.8 Consensus size: 9
158164 TATCATCCCT
158174 TTTTTTTTC
1 TTTTTTTTC
158183 TTTTTTTTC
1 TTTTTTTTC
*
158192 TCTTTGTTTC
1 T-TTTTTTTC
158202 TCTTTTTTTC
1 T-TTTTTTTC
158212 TTTTCTTTAAT-
1 TTTT-TTT--TC
*
158223 TTCTTTTTTA
1 TT-TTTTTTC
*
158233 TTTTTTTTA
1 TTTTTTTTC
158242 TTTTTTT
1 TTTTTTT
158249 GCTCTGTGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
9 28 0.48
10 22 0.38
11 5 0.09
12 3 0.05
ACGTcount: A:0.05, C:0.11, G:0.01, T:0.83
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:158207 original size:19 final size:18
Alignment explanation
Indices: 158179--158214 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
158169 TCCCTTTTTT
*
158179 TTTCTTTTTTTTCTCTTTG
1 TTTCTCTTTTTT-TCTTTG
158198 TTTCTCTTTTTTTCTTT
1 TTTCTCTTTTTTTCTTT
158215 TCTTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTCTCTTTTTTTCTTTG
Found at i:158272 original size:49 final size:50
Alignment explanation
Indices: 158176--158272 Score: 110
Period size: 49 Copynumber: 2.0 Consensus size: 50
158166 TCATCCCTTT
* * * *
158176 TTTTTTCTTTTTTTTCTCTTTGTTTCTCTTTTTTTCTTTTCTTTAATTTC
1 TTTTTTATTTTTTTTATCTTTGTTTCTCTGTGTTTCTTTTCTTTAATTTC
*
158226 TTTTTTATTTTTTTTAT-TTT-TTTGCTCTGTGTTT-TTTTGTTCTAATT
1 TTTTTTATTTTTTTTATCTTTGTTT-CTCTGTGTTTCTTTTCTT-TAATT
158273 GGATCTTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
48 9 0.22
49 16 0.40
50 15 0.38
ACGTcount: A:0.06, C:0.11, G:0.05, T:0.77
Consensus pattern (50 bp):
TTTTTTATTTTTTTTATCTTTGTTTCTCTGTGTTTCTTTTCTTTAATTTC
Found at i:158451 original size:2 final size:2
Alignment explanation
Indices: 158444--158490 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
158434 GACAACAATG
158444 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
158486 TA TA T
1 TA TA T
158491 GGATAAATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:164401 original size:20 final size:20
Alignment explanation
Indices: 164378--164427 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
164368 TGACTTATGT
164378 GTTGCGAATTACAAATTCGA
1 GTTGCGAATTACAAATTCGA
* * * *
164398 GTTGCGATTTATAGATTCGC
1 GTTGCGAATTACAAATTCGA
*
164418 GTTGTGAATT
1 GTTGCGAATT
164428 TGGAAACTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGA
Found at i:165013 original size:35 final size:35
Alignment explanation
Indices: 164974--165053 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
164964 GGGGTTGAGT
*
164974 ATGTAATTGAAGTATTTTAGAATCTGAAGTTTAGA
1 ATGTAATTGAAGCATTTTAGAATCTGAAGTTTAGA
* * * * **
165009 ATGTAACTGAAGCATTTTGGATTTTGGGGTTTAGA
1 ATGTAATTGAAGCATTTTAGAATCTGAAGTTTAGA
165044 ATGTAATTGA
1 ATGTAATTGA
165054 TGAATGTGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.40
Consensus pattern (35 bp):
ATGTAATTGAAGCATTTTAGAATCTGAAGTTTAGA
Found at i:166649 original size:22 final size:23
Alignment explanation
Indices: 166621--166669 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
166611 TATTGAAATA
166621 TAAAAAA-AATT-CATAATTAACT
1 TAAAAAATAATTCCA-AATTAACT
*
166643 TAAAAAATTATTCCAAATTAACT
1 TAAAAAATAATTCCAAATTAACT
166666 TAAA
1 TAAA
166670 CATTTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 15 0.62
24 2 0.08
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAAAAATAATTCCAAATTAACT
Found at i:171646 original size:23 final size:23
Alignment explanation
Indices: 171558--171638 Score: 119
Period size: 23 Copynumber: 3.5 Consensus size: 23
171548 TATTATATGA
*
171558 CACTTCGGTGCATTTCTACGTGG
1 CACTTCGGTGCAATTCTACGTGG
* *
171581 CACTACGGTGCAATTCTATGTGG
1 CACTTCGGTGCAATTCTACGTGG
171604 CACTAT-GGTGCAATTCTACGTGG
1 CACT-TCGGTGCAATTCTACGTGG
171627 CACTTCGGTGCA
1 CACTTCGGTGCA
171639 TTTATACGAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
22 1 0.02
23 50 0.98
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGTGG
Found at i:176131 original size:55 final size:56
Alignment explanation
Indices: 176061--176166 Score: 171
Period size: 55 Copynumber: 1.9 Consensus size: 56
176051 AAACATATAA
*
176061 ATAGTCAAGTGATCATTTTATAACTTTTAATAGTTTG-GACTCAACAAAGCAACTT
1 ATAGTCAAGTGATCATTTTATAACTTTTAATAGTTGGAGACTCAACAAAGCAACTT
176116 ATAGTCGAAGT-ATCATTTTATAACTTTTAATAGTTGGATGACTCAACAAAG
1 ATAGTC-AAGTGATCATTTTATAACTTTTAATAGTTGGA-GACTCAACAAAG
176167 TAGCACCCTA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
55 31 0.66
56 4 0.09
57 12 0.26
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (56 bp):
ATAGTCAAGTGATCATTTTATAACTTTTAATAGTTGGAGACTCAACAAAGCAACTT
Found at i:184378 original size:18 final size:18
Alignment explanation
Indices: 184352--184387 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
184342 CCGTTTGATT
* *
184352 TAGGTGGGTCGGGTCGAG
1 TAGGCGGGTCGGATCGAG
184370 TAGGCGGGTCGGATCGAG
1 TAGGCGGGTCGGATCGAG
184388 CAACTTCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.53, T:0.19
Consensus pattern (18 bp):
TAGGCGGGTCGGATCGAG
Found at i:189768 original size:28 final size:28
Alignment explanation
Indices: 189713--189768 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
189703 CCGTCATTGC
*
189713 TTTTAAGCACTGACTTGACGATATAATG
1 TTTTAAGCACTGACTTGACAATATAATG
189741 TTTTAAGCAC-GAGCTTGACTAATA-AATG
1 TTTTAAGCACTGA-CTTGAC-AATATAATG
189769 GAGACTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 2 0.08
28 20 0.80
29 3 0.12
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (28 bp):
TTTTAAGCACTGACTTGACAATATAATG
Found at i:193072 original size:37 final size:36
Alignment explanation
Indices: 193001--193072 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
192991 TATATTTTTT
*
193001 ATTTTGTAAAAAAATTATATAAATATTATGAATTTA
1 ATTTTGTAAAAAAATTATATAAATATTATCAATTTA
* *
193037 ATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
193073 GTAATATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 22 0.71
37 9 0.29
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (36 bp):
ATTTTGTAAAAAAATTATATAAATATTATCAATTTA
Found at i:193248 original size:20 final size:20
Alignment explanation
Indices: 193212--193249 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
193202 ATCCTATTCT
**
193212 CTGATAATCTTTTATTCCTA
1 CTGATAATCTTACATTCCTA
193232 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
193250 GTGAACCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (20 bp):
CTGATAATCTTACATTCCTA
Found at i:204435 original size:31 final size:32
Alignment explanation
Indices: 204399--204490 Score: 123
Period size: 34 Copynumber: 2.8 Consensus size: 32
204389 TTGTCCCTTT
* *
204399 ATTTTCTATGGTTAATTATATTTTACCC-CTC
1 ATTTTCCATGATTAATTATATTTTACCCTCTC
**
204430 ATTTTCCATGATTAATTATACTTTGCCCCCTCTC
1 ATTTTCCATGATTAATTATA-TTT-TACCCTCTC
204464 ATTTTCCATGATTAATTATATTTTACC
1 ATTTTCCATGATTAATTATATTTTACC
204491 TAGAGGACGG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
31 18 0.35
32 5 0.10
33 6 0.12
34 23 0.44
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (32 bp):
ATTTTCCATGATTAATTATATTTTACCCTCTC
Found at i:206940 original size:30 final size:30
Alignment explanation
Indices: 206899--206970 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
206889 AAAATCGAAT
*
206899 TAAACGGGGACGGGGAAAAATCGTTTATGC
1 TAAACGGGGACGGGAAAAAATCGTTTATGC
*
206929 TAAATGGGGACGGGAAAAAATCGTTTATGC
1 TAAACGGGGACGGGAAAAAATCGTTTATGC
206959 TAAACGGGGACG
1 TAAACGGGGACG
206971 AGGACGGGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.19
Consensus pattern (30 bp):
TAAACGGGGACGGGAAAAAATCGTTTATGC
Found at i:207139 original size:32 final size:32
Alignment explanation
Indices: 207067--207143 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 32
207057 TAATTATTAT
207067 ATATATAATATTAATAAATTTAAATTAAATTAAA
1 ATATAT-ATA-TAATAAATTTAAATTAAATTAAA
* * * *
207101 AAATATATATAAT-AATTATATATTTAATTTAA
1 ATATATATATAATAAATT-TAAATTAAATTAAA
207133 ATATATATATA
1 ATATATATATA
207144 TACCCGGCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 4 0.11
32 25 0.68
33 3 0.08
34 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATATATATAATAAATTTAAATTAAATTAAA
Found at i:208601 original size:2 final size:2
Alignment explanation
Indices: 208594--208621 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
208584 TGAAGTTTTA
208594 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
208622 TATCTTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:213132 original size:145 final size:145
Alignment explanation
Indices: 212940--213232 Score: 455
Period size: 145 Copynumber: 2.0 Consensus size: 145
212930 TACATGTATA
* * *
212940 GGATGTGTAGATTTCCAGGAACAAATTCATTAGAATTTGATAATAAAATATAAGAACTGCTTTTT
1 GGATATGTAGATTTCCAGGAACAAATTCATTAGAATATGAGAATAAAATATAAGAACTGCTTTTT
*
213005 GATTTCTT-GCTCGATGGTTTCTTATTAAGAGTAGTGGCATGGTGCAATATATCACATCATCTAC
66 GATTTCTTAG-TCGATGGTTTCTTATTAAGAGTAGTGGCATGGCGCAATATATCACATCATCTAC
*
213069 ATTTTAGCTATTTCAT
130 AGTTTAGCTATTTCAT
* * *
213085 GGATATGTAGGTTTCCAGGAACAAATTCATTAGAAATAT-AGAATAAAATATAAGAATTGTTTTT
1 GGATATGTAGATTTCCAGGAACAAATTCATTAG-AATATGAGAATAAAATATAAGAACTGCTTTT
* *
213149 TGATTTCTTAGTCGATGGTTTCTTGTTAAGAGTAGTGGCATGGCGCACTATATCACATCATCTAC
65 TGATTTCTTAGTCGATGGTTTCTTATTAAGAGTAGTGGCATGGCGCAATATATCACATCATCTAC
*
213214 AGTTTATCTATTTCAT
130 AGTTTAGCTATTTCAT
213230 GGA
1 GGA
213233 CTGTGACTGC
Statistics
Matches: 135, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
145 130 0.96
146 5 0.04
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (145 bp):
GGATATGTAGATTTCCAGGAACAAATTCATTAGAATATGAGAATAAAATATAAGAACTGCTTTTT
GATTTCTTAGTCGATGGTTTCTTATTAAGAGTAGTGGCATGGCGCAATATATCACATCATCTACA
GTTTAGCTATTTCAT
Found at i:214695 original size:2 final size:2
Alignment explanation
Indices: 214688--214735 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
214678 ATCATGAAGA
214688 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
214730 AT AT AT
1 AT AT AT
214736 TTGATAGAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:232577 original size:22 final size:22
Alignment explanation
Indices: 232552--232599 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
232542 ATTAAAACAA
232552 AGCAAACCCAATTCCTAAATGC
1 AGCAAACCCAATTCCTAAATGC
**
232574 AGCATTCCCAATTCCTAAATGC
1 AGCAAACCCAATTCCTAAATGC
232596 AGCA
1 AGCA
232600 TTCAATCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.21
Consensus pattern (22 bp):
AGCAAACCCAATTCCTAAATGC
Found at i:232600 original size:22 final size:22
Alignment explanation
Indices: 232558--232602 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
232548 ACAAAGCAAA
232558 CCCAATTCCTAAATGCAGCATT
1 CCCAATTCCTAAATGCAGCATT
232580 CCCAATTCCTAAATGCAGCATT
1 CCCAATTCCTAAATGCAGCATT
232602 C
1 C
232603 AATCCATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.33, G:0.09, T:0.27
Consensus pattern (22 bp):
CCCAATTCCTAAATGCAGCATT
Found at i:235687 original size:22 final size:21
Alignment explanation
Indices: 235624--235680 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 21
235614 AGTCGAGGGT
*
235624 TTCATAGGTCCTTTGGGACATA
1 TTCACAGGTCCTTT-GGACATA
*
235646 TTCACAAGTCCTTATGGACATA
1 TTCACAGGTCCTT-TGGACATA
235668 TTCACAGGTCCTT
1 TTCACAGGTCCTT
235681 CGAGACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (21 bp):
TTCACAGGTCCTTTGGACATA
Found at i:236782 original size:24 final size:24
Alignment explanation
Indices: 236755--236800 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
236745 TATATCAAAA
*
236755 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* **
236779 ATCATATTAGAAATCAGGTCAA
1 ATCAAAACAGAAATCAGGTCAA
236801 ATAACATATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:236825 original size:48 final size:49
Alignment explanation
Indices: 236772--236885 Score: 153
Period size: 48 Copynumber: 2.4 Consensus size: 49
236762 CATAAATCAG
* *
236772 GTCAAGTATCATATTAGAAAT-CAGGTCAAATAACATATCAGAATCCAA
1 GTCAAGTATCATATCAGAAATCCAGGTCAAATAACAGATCAGAATCCAA
* * * *
236820 GTCAAGTATCATATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAAATCCAGGTCAAATAACAGATCAGAATCCAA
236868 GTCAAGTAT-ATATCAGAA
1 GTCAAGTATCATATCAGAA
236886 TTCAAATCGA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 10 0.17
48 48 0.83
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (49 bp):
GTCAAGTATCATATCAGAAATCCAGGTCAAATAACAGATCAGAATCCAA
Found at i:236839 original size:24 final size:24
Alignment explanation
Indices: 236772--236886 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
236762 CATAAATCAG
* *
236772 GTCAAGTATCATATTAGAAAT-CAG
1 GTCAAGTATCATATCAG-AATCCAT
* * *
236796 GTCAAATAACATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
236820 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
*
236844 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
236868 GTCAAGTAT-ATATCAGAAT
1 GTCAAGTATCATATCAGAAT
236887 TCAAATCGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
23 14 0.18
24 63 0.80
25 2 0.03
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:239321 original size:13 final size:13
Alignment explanation
Indices: 239303--239327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
239293 ATCAACGGTC
239303 AACGGGTCGGGTA
1 AACGGGTCGGGTA
239316 AACGGGTCGGGT
1 AACGGGTCGGGT
239328 CGGGTCGGGT
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:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:240797 original size:18 final size:18
Alignment explanation
Indices: 240770--240816 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
240760 AGGCATTTGA
*
240770 TCCTCTTGTTGTGATTGT
1 TCCTCGTGTTGTGATTGT
240788 TCCTCGTGTTGTGATTGT
1 TCCTCGTGTTGTGATTGT
240806 TCCTCGTGTTG
1 TCCTCGTGTTG
240817 CTCCGGCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.04, C:0.19, G:0.26, T:0.51
Consensus pattern (18 bp):
TCCTCGTGTTGTGATTGT
Found at i:242475 original size:23 final size:24
Alignment explanation
Indices: 242418--242475 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
242408 ACCCCGTAGG
242418 GGTATCGGTACCCACTCAAAGGGA
1 GGTATCGGTACCCACTCAAAGGGA
* * *
242442 GG-ATTGGTACCCATTC-AAGGGT
1 GGTATCGGTACCCACTCAAAGGGA
*
242464 GGTATCGATACC
1 GGTATCGGTACC
242476 TCCTGCACCC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 7 0.25
23 19 0.68
24 2 0.07
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.22
Consensus pattern (24 bp):
GGTATCGGTACCCACTCAAAGGGA
Found at i:255927 original size:18 final size:18
Alignment explanation
Indices: 255899--255941 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
255889 TATTCTTATT
*
255899 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
*
255918 TTTATTTAATCGCTTTTA
1 TTTATTTAATCACTTTTA
255936 -TTATTT
1 TTTATTT
255942 TAATATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:260025 original size:18 final size:18
Alignment explanation
Indices: 260002--260039 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
259992 GAGAGTCCCC
260002 AGCCTGCTGAAC-CTGAAG
1 AGCCTGCTG-ACGCTGAAG
260020 AGCCTGCTGACGCTGAAG
1 AGCCTGCTGACGCTGAAG
260038 AG
1 AG
260040 ACTGATAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.16
Consensus pattern (18 bp):
AGCCTGCTGACGCTGAAG
Found at i:274039 original size:54 final size:54
Alignment explanation
Indices: 273976--274085 Score: 195
Period size: 54 Copynumber: 2.0 Consensus size: 54
273966 GGGGTCAACA
273976 TAGTAACATGAATGCACAGC-AAGTTAGCCTACTCCTCTTGAGTATTAAGATAAG
1 TAGTAACATGAATGCACA-CAAAGTTAGCCTACTCCTCTTGAGTATTAAGATAAG
*
274030 TAGTAACATGAATGTACACAAAGTTAGCCTACTCCTCTTGAGTATTAAGATAAG
1 TAGTAACATGAATGCACACAAAGTTAGCCTACTCCTCTTGAGTATTAAGATAAG
274084 TA
1 TA
274086 TAGGTCATAT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
53 1 0.02
54 53 0.98
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (54 bp):
TAGTAACATGAATGCACACAAAGTTAGCCTACTCCTCTTGAGTATTAAGATAAG
Found at i:289337 original size:82 final size:82
Alignment explanation
Indices: 289229--289393 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
289219 TCAAGTAATT
*
289229 GCTTTTGGATGCATGTTGGGATATTGAGTGAGGCAAAGCCCTATGCAATGGTTATGATGAGACAA
1 GCTTTTGGATGCATGTTGGGAGATTGAGTGAGGCAAAGCCCTATGCAATGGTTATGATGAGACAA
289294 GGGAGGAAGGAATGCAA
66 GGGAGGAAGGAATGCAA
289311 GCTTTTGGATGCATGTTGGGAGATTGAGTGAGGCAAAGCCCTATGCAATGGTTATGATGAGACAA
1 GCTTTTGGATGCATGTTGGGAGATTGAGTGAGGCAAAGCCCTATGCAATGGTTATGATGAGACAA
289376 GGGAGGAAGGAATGCAA
66 GGGAGGAAGGAATGCAA
289393 G
1 G
289394 TGTTTTTTGC
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.30, C:0.11, G:0.35, T:0.24
Consensus pattern (82 bp):
GCTTTTGGATGCATGTTGGGAGATTGAGTGAGGCAAAGCCCTATGCAATGGTTATGATGAGACAA
GGGAGGAAGGAATGCAA
Found at i:289723 original size:2 final size:2
Alignment explanation
Indices: 289716--289748 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
289706 GGAGTGAAAG
289716 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
289749 TCTTGTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:292795 original size:3 final size:3
Alignment explanation
Indices: 292787--292816 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
292777 TAAATATAAA
292787 TAT TAT TAT TAT TAT TACT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
292817 CATATTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:292810 original size:13 final size:13
Alignment explanation
Indices: 292787--292822 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
292777 TAAATATAAA
292787 TATTA-TTATTAT
1 TATTACTTATTAT
292799 TATTACTTATTAT
1 TATTACTTATTAT
*
292812 TATTACATATT
1 TATTACTTATT
292823 TTGCAGCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTACTTATTAT
Found at i:305641 original size:24 final size:24
Alignment explanation
Indices: 305614--305665 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
305604 GACAAAAATG
*
305614 AAAAATGAAAGAAAAAGGAAAGAAA
1 AAAAATGAAA-AAAAAGAAAAGAAA
* *
305639 AAAAATGAGAAAAAATAAAAGAAA
1 AAAAATGAAAAAAAAGAAAAGAAA
305663 AAA
1 AAA
305666 TAAAAGGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (24 bp):
AAAAATGAAAAAAAAGAAAAGAAA
Found at i:305661 original size:12 final size:12
Alignment explanation
Indices: 305614--305671 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
305604 GACAAAAATG
*
305614 AAAAATGAAAG-
1 AAAAATAAAAGA
**
305625 AAAAAGGAAAGA
1 AAAAATAAAAGA
*
305637 AAAAA-AATGAGA
1 AAAAATAA-AAGA
305649 AAAAATAAAAGA
1 AAAAATAAAAGA
305661 AAAAATAAAAG
1 AAAAATAAAAG
305672 GAGGGTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
11 11 0.28
12 27 0.68
13 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (12 bp):
AAAAATAAAAGA
Found at i:306791 original size:48 final size:48
Alignment explanation
Indices: 306669--306797 Score: 213
Period size: 48 Copynumber: 2.7 Consensus size: 48
306659 CCTCCTGATC
*
306669 TGATATTCCCTTCAGAGTAAGAAGAACATGTCTCTCTTATCCAAGATT
1 TGATATTCCCTTCAGAGTAAGAGGAACATGTCTCTCTTATCCAAGATT
* *
306717 TGATATTCCTTTCAGAGTAAGCGGAACATGTCTCTCTTATCCAAGATT
1 TGATATTCCCTTCAGAGTAAGAGGAACATGTCTCTCTTATCCAAGATT
* *
306765 TGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 TGATATTCCCTTCAGAGTAAGAGGAACATGTCT
306798 ACCCTGATTC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (48 bp):
TGATATTCCCTTCAGAGTAAGAGGAACATGTCTCTCTTATCCAAGATT
Found at i:306864 original size:113 final size:112
Alignment explanation
Indices: 306712--307092 Score: 636
Period size: 113 Copynumber: 3.4 Consensus size: 112
306702 CTCTTATCCA
* * * *
306712 AGATTTGATATTCCTTTCAGAGTAAGCGGAACATGTCTCTCTTATCCAAGATTTGATATTCCCTT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCTAAGATTTGATATTCCCTT
306777 CAGAGTAAGTGGAACAAGTCTACCCTGATTCAATGGATTAACTCCCCC
66 CAGAGTAAGTGGAACAAGTCTA-CCTGATTCAATGGATTAACTCCCCC
*
306825 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTTTTTTCTAAGATTTGATATTCCCTT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCTAAGATTTGATATTCCCTT
*
306890 CAGAGTAAGTGGAACAAGTCTATCCTGATTCAATGGATCAACTCCCCC
66 CAGAGTAAGTGGAACAAGTCTA-CCTGATTCAATGGATTAACTCCCCC
* *
306938 AGACATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTTTTTTCTAAGATTTGATATTCCCTT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCTAAGATTTGATATTCCCTT
* *
307003 CAGAGTAAGTGGAATAAGTCTACTTCGATTCAATGGATTAACTCCCCC
66 CAGAGTAAGTGGAACAAGTCTACCT-GATTCAATGGATTAACTCCCCC
*
307051 ATATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
1 AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCT
307093 GACAACTGTC
Statistics
Matches: 253, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
112 2 0.01
113 251 0.99
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (112 bp):
AGATATGATATTCCCTTCAGAGTAAGCGGAACATGTCTCTCTTTTCTAAGATTTGATATTCCCTT
CAGAGTAAGTGGAACAAGTCTACCTGATTCAATGGATTAACTCCCCC
Done.