Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015255.1 Corchorus olitorius cultivar O-4 contig15288, 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: 149554
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:948 original size:129 final size:134
Alignment explanation
Indices: 781--1032 Score: 302
Period size: 135 Copynumber: 1.9 Consensus size: 134
771 TTTAATCTTA
* * *
781 ATCTGAAATATATAAAACACCAATTTTAATATTTAACATTAGTTTTAACCTTT-G-GTT-GT-TA
1 ATCTGAAATATATAAAACACCAATTTTAATATTTAACATGAATTTTAACCTTTAGAGTTAATATA
* * *
842 -GTAGTTTAATATACCAATCTAAAATATATTAAATATAGCAAATA-TCTTTAAAATACCATATAA
66 TATAATTTAATATACCAATCTAAAATATATTAAATATAGCAAA-AGTATTTAAAATACCATATAA
905 ACTTG
130 ACTTG
* * * ** *
910 ATCTGAAATATCTAAAATATCTCTTTTAAT-TTTAAACATGAATTTTAAGCTTTAGTAGTTAATA
1 ATCTGAAATATATAAAACACCAATTTTAATATTT-AACATGAATTTTAACCTTTAG-AGTTAATA
* *
974 TATATAATTTAATATATCATTCTAAAATATATTAAATATAGCAAAAGTATTTAAAATAC
64 TATATAATTTAATATACCAATCTAAAATATATTAAATATAGCAAAAGTATTTAAAATAC
1033 GTGCAACACA
Statistics
Matches: 101, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
128 3 0.03
129 41 0.41
130 1 0.01
132 3 0.03
133 1 0.01
134 3 0.03
135 49 0.49
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (134 bp):
ATCTGAAATATATAAAACACCAATTTTAATATTTAACATGAATTTTAACCTTTAGAGTTAATATA
TATAATTTAATATACCAATCTAAAATATATTAAATATAGCAAAAGTATTTAAAATACCATATAAA
CTTG
Found at i:7583 original size:5 final size:5
Alignment explanation
Indices: 7575--7612 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
7565 ACCTCAACTC
*
7575 AACAA AACAG AACAG AACAG AACAG AACAG AACAG AAC
1 AACAG AACAG AACAG AACAG AACAG AACAG AACAG AAC
7613 TTTTCTGCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.63, C:0.21, G:0.16, T:0.00
Consensus pattern (5 bp):
AACAG
Found at i:8136 original size:7 final size:7
Alignment explanation
Indices: 8124--8162 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
8114 AAGAATACCA
8124 TGCTTCT
1 TGCTTCT
8131 TGCTTCT
1 TGCTTCT
8138 TGCTTCT
1 TGCTTCT
8145 TGCTTCT
1 TGCTTCT
8152 TGCTTC-
1 TGCTTCT
8158 TGCTT
1 TGCTT
8163 TTCCCACCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.00, C:0.28, G:0.15, T:0.56
Consensus pattern (7 bp):
TGCTTCT
Found at i:21170 original size:13 final size:13
Alignment explanation
Indices: 21152--21177 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21142 ACGTGCAGCA
21152 AGGAAACAATTTT
1 AGGAAACAATTTT
21165 AGGAAACAATTTT
1 AGGAAACAATTTT
21178 CGAGACTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AGGAAACAATTTT
Found at i:22415 original size:36 final size:36
Alignment explanation
Indices: 22375--22491 Score: 123
Period size: 36 Copynumber: 3.3 Consensus size: 36
22365 ATCCAGGATG
*
22375 ATTAAGTAAGATCAATAAAAGACTTAATTCAAGGTA
1 ATTAAGTAAGATCAGTAAAAGACTTAATTCAAGGTA
* * * *
22411 ATTAAGTAAAATCAGTAAAGGGCTTAATTCAGGGTA
1 ATTAAGTAAGATCAGTAAAAGACTTAATTCAAGGTA
* * *
22447 ATTAAGCAAG-TCAGTAAATA-ACTTAATT-TAGGATT
1 ATTAAGTAAGATCAGTAAA-AGACTTAATTCAAGG-TA
22482 ATTAAGTAAG
1 ATTAAGTAAG
22492 TAACTCAGTT
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
34 2 0.03
35 25 0.38
36 39 0.59
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (36 bp):
ATTAAGTAAGATCAGTAAAAGACTTAATTCAAGGTA
Found at i:22451 original size:72 final size:72
Alignment explanation
Indices: 22293--22474 Score: 174
Period size: 72 Copynumber: 2.5 Consensus size: 72
22283 AGTAATAAAC
* * *
22293 TCAGGGTAATTAAGTAA-ATCAGTAATAAGCAACTTAATTCGAGGTAACTAAGTAAAGTCAATTA
1 TCAGGGTAATTAAGTAAGATCAGTAA-AAG--ACTTAATTCAAGGTAACTAAGTAAAATCAATAA
**
22357 GTTATTCAAT
63 GGGATTCAAT
* * * * * *
22367 CCAGGATGATTAAGTAAGATCAATAAAAGACTTAATTCAAGGTAATTAAGTAAAATCAGTAAAGG
1 TCAGGGTAATTAAGTAAGATCAGTAAAAGACTTAATTCAAGGTAACTAAGTAAAATCAAT-AAGG
*
22432 GCTT-AAT
65 GATTCAAT
*
22439 TCAGGGTAATTAAGCAAG-TCAGTAAATA-ACTTAATT
1 TCAGGGTAATTAAGTAAGATCAGTAAA-AGACTTAATT
22475 TAGGATTATT
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
71 15 0.17
72 45 0.51
73 4 0.05
74 17 0.19
75 7 0.08
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.29
Consensus pattern (72 bp):
TCAGGGTAATTAAGTAAGATCAGTAAAAGACTTAATTCAAGGTAACTAAGTAAAATCAATAAGGG
ATTCAAT
Found at i:22472 original size:35 final size:35
Alignment explanation
Indices: 22392--22492 Score: 96
Period size: 35 Copynumber: 2.9 Consensus size: 35
22382 AAGATCAATA
* *
22392 AAAG-ACTTAATTCAAGGTAATTAAGTAAAATCAGT
1 AAAGAACTTAATTCAGGGTAATTAAG-AAAGTCAGT
** *
22427 AAAGGGCTTAATTCAGGGTAATTAAGCAAGTCAGT
1 AAAGAACTTAATTCAGGGTAATTAAGAAAGTCAGT
* * * * *
22462 AAATAACTTAATTTAGGATTATTAAGTAAGT
1 AAAGAACTTAATTCAGGGTAATTAAGAAAGT
22493 AACTCAGTTC
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
35 35 0.65
36 19 0.35
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.31
Consensus pattern (35 bp):
AAAGAACTTAATTCAGGGTAATTAAGAAAGTCAGT
Found at i:32397 original size:130 final size:128
Alignment explanation
Indices: 32119--32358 Score: 351
Period size: 130 Copynumber: 1.9 Consensus size: 128
32109 GTTTTACTCA
* **
32119 ACTAAAAGCTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTTATTTTTACCATTT
1 ACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCCCATAACTATTTTATTTTTACCATTT
* * * *
32184 TACTATTTTAATTAAAAAAACTTAGGTATGTTATAAATTTTTAAATACTTTTACAGTTTTACTT
66 TACTATATTAATTAAAAAAACTTAGATATATTATAAATTTTTAAATACTTTTACA-TTTAACTT
32248 AACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCCCATAACTATTTTATTTTTACCATT
1 -ACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCCCATAACTATTTTATTTTTACCATT
* *
32313 TTACTA-ATTAATT-CAAAAACTTAGATATATTA-GAATCTTTTAAATA
65 TTACTATATTAATTAAAAAAACTTAGATATATTATAAAT-TTTTAAATA
32359 TATTTCTTAA
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
127 3 0.03
128 25 0.25
129 6 0.06
130 67 0.66
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (128 bp):
ACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCCCATAACTATTTTATTTTTACCATTT
TACTATATTAATTAAAAAAACTTAGATATATTATAAATTTTTAAATACTTTTACATTTAACTT
Found at i:33104 original size:14 final size:14
Alignment explanation
Indices: 33081--33116 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
33071 TGGCACCTTT
33081 TTCA-TATTAGTAA
1 TTCAGTATTAGTAA
*
33094 TTTAGTATTAGTAA
1 TTCAGTATTAGTAA
33108 TTCAGTATT
1 TTCAGTATT
33117 TTGGATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 3 0.15
14 17 0.85
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (14 bp):
TTCAGTATTAGTAA
Found at i:33172 original size:21 final size:21
Alignment explanation
Indices: 33146--33187 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
33136 AGGTGGGTTC
33146 GTAGTTACCCAAATTAAACAT
1 GTAGTTACCCAAATTAAACAT
*
33167 GTAGTTACCCAAATTGAACAT
1 GTAGTTACCCAAATTAAACAT
33188 AACACTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (21 bp):
GTAGTTACCCAAATTAAACAT
Found at i:37528 original size:36 final size:36
Alignment explanation
Indices: 37488--37821 Score: 440
Period size: 36 Copynumber: 9.2 Consensus size: 36
37478 AAACAGCCCC
* *
37488 TAAGTGAAAGCAATCAAAGACTTAATTCAGGGTAAT
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAAT
** * * *
37524 TAAGTAAAATTAGT-AAGGACTTAATTCGGGGAAAT
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAAT
*
37559 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGAAAT
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAAT
*
37595 TAAGTAAACA-TAGTCAAAGACTTAATTCAGGGTAAT
1 TAAGTAAA-AGCAGTCAAAGACTTAATTCAGGGTAAT
*
37631 TAAGTAAAATCAGT-AAAGACTTAATTCAGGGTAAT
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAAT
* *
37666 TAAGTGAAAGCAGTCAAAGACTTAATTCAGGATAAT
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAAT
*
37702 TAAGTAAAAGCAGTCGAAGACTTAATTCAGGGTAAT
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAAT
* * *
37738 TAAGTAAAATCAGTCAAGCAAAGACTTAATTTAGGGAAAT
1 TAAGTAAAAGCAGT----CAAAGACTTAATTCAGGGTAAT
* *
37778 TAGGTAAAAGCAGTCAAAGACTTAATTCAGGGAAAT
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAAT
37814 TAAGTAAA
1 TAAGTAAA
37822 TATAGCCAAA
Statistics
Matches: 262, Mismatches: 28, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
35 64 0.24
36 166 0.63
37 1 0.00
40 31 0.12
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.25
Consensus pattern (36 bp):
TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAAT
Found at i:37578 original size:71 final size:72
Alignment explanation
Indices: 37488--37837 Score: 467
Period size: 71 Copynumber: 4.8 Consensus size: 72
37478 AAACAGCCCC
* * * * *
37488 TAAGTGAAAGCAATCAAAGACTTAATTCAGGGTAATTAAGTAAAATTAGT-AAGGACTTAATTCG
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCA
37552 GGGAAAT
66 GGGAAAT
*
37559 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAACAT-AGTCAAAGACTTAATTC
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAA-ATCAGTCAAAGACTTAATTC
*
37623 AGGGTAAT
65 AGGGAAAT
* * *
37631 TAAGTAAAATCAGT-AAAGACTTAATTCAGGGTAATTAAGTGAAAGCAGTCAAAGACTTAATTCA
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCA
37695 -GGATAAT
66 GGGA-AAT
*
37702 TAAGTAAAAGCAGTCGAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAGCAAAGACTTAA
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT----CAAAGACTTAA
*
37767 TTTAGGGAAAT
62 TTCAGGGAAAT
* * *
37778 TAGGTAAAAGCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAATAT-AGCCAAAGACTTA
1 TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAA-ATCAGTCAAAGACTTA
37838 GGTCCTGTTT
Statistics
Matches: 248, Mismatches: 20, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
70 3 0.01
71 105 0.42
72 75 0.30
76 60 0.24
77 5 0.02
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.25
Consensus pattern (72 bp):
TAAGTAAAAGCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCA
GGGAAAT
Found at i:37676 original size:107 final size:106
Alignment explanation
Indices: 37501--37837 Score: 496
Period size: 107 Copynumber: 3.1 Consensus size: 106
37491 GTGAAAGCAA
* * *
37501 TCAAAGACTTAATTCAGGGTAATTAAGTAAAATTAGTAAGGACTTAATTCGGGGAAATTAAGTAA
1 TCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTAAAGACTTAATTCAGGGAAATTAAGTAA
37566 AAGCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAACATAG
66 AAGCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAA-ATAG
* *
37608 TCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTAAAGACTTAATTCAGGGTAATTAAGTGA
1 TCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTAAAGACTTAATTCAGGGAAATTAAGTAA
*
37673 AAGCAGTCAAAGACTTAATTCA-GGATAATTAAGTAAAAGCAG
66 AAGCAGTCAAAGACTTAATTCAGGGA-AATTAAGTAAAA-TAG
* *
37715 TCGAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAGCAAAGACTTAATTTAGGGAAATTA
1 TCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT-----AAAGACTTAATTCAGGGAAATTA
*
37780 GGTAAAAGCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAATATAG
61 AGTAAAAGCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAA-ATAG
*
37827 CCAAAGACTTA
1 TCAAAGACTTA
37838 GGTCCTGTTT
Statistics
Matches: 207, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
106 4 0.02
107 131 0.63
112 68 0.33
113 4 0.02
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (106 bp):
TCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTAAAGACTTAATTCAGGGAAATTAAGTAA
AAGCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAAATAG
Found at i:38335 original size:36 final size:36
Alignment explanation
Indices: 38262--38690 Score: 447
Period size: 36 Copynumber: 12.2 Consensus size: 36
38252 CAAACAGCCC
* * * *
38262 CTTAATTGAGGGTAATTAAGTAAAACCAGT-AAGGA
1 CTTAATTCAGGGAAATTAAGTAAAATCAGTCAAAGA
*
38297 CTTAATTCAGGGAAATTAAGTAAAAACAGTCAAAGA
1 CTTAATTCAGGGAAATTAAGTAAAATCAGTCAAAGA
* *
38333 CTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAAAA
1 CTTAATTCAGGGAAATTAAGTAAAATCAGTC-AAAGA
38370 CTTAATTCGAGGTG--ATTAAGTAAAATCAGT----GA
1 CTTAATTC-AGG-GAAATTAAGTAAAATCAGTCAAAGA
* * *
38402 ---AA-GCAGAGAAATTGAGTAAAATCAGTCAAAGA
1 CTTAATTCAGGGAAATTAAGTAAAATCAGTCAAAGA
*
38434 CTTAATTTAGGGAAATTAAGTAAAATCAGTCAAAGA
1 CTTAATTCAGGGAAATTAAGTAAAATCAGTCAAAGA
* *
38470 CTTAATTCAGGGAAATTAAGTAAAATCAGTCACATA
1 CTTAATTCAGGGAAATTAAGTAAAATCAGTCAAAGA
* * * *
38506 CTTAATTCAAGGAAATTAAAT-AACTCGGTCAAAGA
1 CTTAATTCAGGGAAATTAAGTAAAATCAGTCAAAGA
* *
38541 CTTAATTCAGGGTAATTAAGTAAAATCGGTCAAAGA
1 CTTAATTCAGGGAAATTAAGTAAAATCAGTCAAAGA
*
38577 CTTAATTCAGGTAAATTAAGTAAAAT-AGTCAAAGA
1 CTTAATTCAGGGAAATTAAGTAAAATCAGTCAAAGA
* * * *
38612 CTTAATTCAGGGTAATTAAGTATAGTCAAT-AAAGAA
1 CTTAATTCAGGGAAATTAAGTAAAATCAGTCAAAG-A
* * * * *
38648 CTTAATTCGGGGTAATTGAGTAAAGTCAAT-AAAGAA
1 CTTAATTCAGGGAAATTAAGTAAAATCAGTCAAAG-A
38684 CTTAATT
1 CTTAATT
38691 TAAGGTAACT
Statistics
Matches: 338, Mismatches: 39, Indels: 33
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.00
27 2 0.01
28 16 0.05
29 2 0.01
32 3 0.01
35 91 0.27
36 191 0.57
37 28 0.08
38 3 0.01
39 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.27
Consensus pattern (36 bp):
CTTAATTCAGGGAAATTAAGTAAAATCAGTCAAAGA
Found at i:38354 original size:71 final size:72
Alignment explanation
Indices: 38262--38704 Score: 466
Period size: 71 Copynumber: 6.3 Consensus size: 72
38252 CAAACAGCCC
* * * *
38262 CTTAATTGAGGGTAATTAAGTAAAACCAGT-AAGGACTTAATTCAGGGAAATTAAGTAAAAACAG
1 CTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAAATCAG
38326 TCAAAGA
66 TCAAAGA
*
38333 CTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAAAACTTAATTCGAGGTG--ATTAAGTAAAAT
1 CTTAATTCAGGGTAATTAAGTAAAATCAGTC-AAAGACTTAATTC-AGG-GAAATTAAGTAAAAT
38396 CAGT----GA
63 CAGTCAAAGA
* * * * *
38402 ---AA-GCAGAGAAATTGAGTAAAATCAGTCAAAGACTTAATTTAGGGAAATTAAGTAAAATCAG
1 CTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAAATCAG
38463 TCAAAGA
66 TCAAAGA
* * * * * * *
38470 CTTAATTCAGGGAAATTAAGTAAAATCAGTCACATACTTAATTCAAGGAAATTAAAT-AACTCGG
1 CTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAAATCAG
38534 TCAAAGA
66 TCAAAGA
* *
38541 CTTAATTCAGGGTAATTAAGTAAAATCGGTCAAAGACTTAATTCAGGTAAATTAAGTAAAAT-AG
1 CTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAAATCAG
38605 TCAAAGA
66 TCAAAGA
* * * * * * *
38612 CTTAATTCAGGGTAATTAAGTATAGTCAAT-AAAGAACTTAATTCGGGGTAATTGAGTAAAGTCA
1 CTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAG-ACTTAATTCAGGGAAATTAAGTAAAATCA
*
38676 AT-AAAGAA
65 GTCAAAG-A
* * *
38684 CTTAATTTAAGGTAACTAAGT
1 CTTAATTCAGGGTAATTAAGT
38705 GGGGAACATT
Statistics
Matches: 311, Mismatches: 43, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.00
63 3 0.01
64 27 0.09
65 21 0.07
66 2 0.01
68 2 0.01
69 2 0.01
70 4 0.01
71 152 0.49
72 67 0.22
73 26 0.08
74 3 0.01
75 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (72 bp):
CTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGAAATTAAGTAAAATCAG
TCAAAGA
Found at i:38455 original size:64 final size:65
Alignment explanation
Indices: 38346--38468 Score: 171
Period size: 64 Copynumber: 1.9 Consensus size: 65
38336 AATTCAGGGT
*
38346 AATTAAGTAAAATCAGTCAAAAAACTTAATTCGAGGTGATTAAGTAAAATCAGTGAAAGCAGAGA
1 AATTAAGTAAAATCAGTCAAAAAACTTAATTCGAGGTGATTAAGTAAAATCAGTCAAAGCAGAGA
* * *
38411 AATTGAGTAAAATCAGTC-AAAGACTTAATT-TAGG-GAAATTAAGTAAAATCAGTCAAAG
1 AATTAAGTAAAATCAGTCAAAAAACTTAATTCGAGGTG--ATTAAGTAAAATCAGTCAAAG
38469 ACTTAATTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
62 1 0.02
63 3 0.06
64 31 0.60
65 17 0.33
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (65 bp):
AATTAAGTAAAATCAGTCAAAAAACTTAATTCGAGGTGATTAAGTAAAATCAGTCAAAGCAGAGA
Found at i:38563 original size:107 final size:107
Alignment explanation
Indices: 38262--38690 Score: 400
Period size: 107 Copynumber: 4.1 Consensus size: 107
38252 CAAACAGCCC
* * * * * * * **
38262 CTTAATTGAGGGTAATTAAGTAAAACCAGT-AAGGACTTAATTCAGGGAAATTAAGTAAAAACAG
1 CTTAATTCAGGGAAATTAAGTAAAA-TAGTCAAAGACTTAATTCAAGGAAATTAAATATACTCAG
*
38326 TCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAAAA
65 TCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTC-AAAGA
* * * * * *
38370 CTTAATTCGAGGTG--ATTAAGTAAAATCAGTGAAAG-C---A---GA-GAAATTGAGTAAAATC
1 CTTAATTC-AGG-GAAATTAAGTAAAAT-AGTCAAAGACTTAATTCAAGGAAATTAAATATACTC
* *
38425 AGTCAAAGACTTAATTTAGGGAAATTAAGTAAAATCAGTCAAAGA
63 AGTCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGA
* * *
38470 CTTAATTCAGGGAAATTAAGTAAAATCAGTCACATACTTAATTCAAGGAAATTAAATA-ACTCGG
1 CTTAATTCAGGGAAATTAAGTAAAAT-AGTCAAAGACTTAATTCAAGGAAATTAAATATACTCAG
*
38534 TCAAAGACTTAATTCAGGGTAATTAAGTAAAATCGGTCAAAGA
65 TCAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGA
* * * * * *
38577 CTTAATTCAGGTAAATTAAGTAAAATAGTCAAAGACTTAATTCAGGGTAATTAAGTATAGTCAAT
1 CTTAATTCAGGGAAATTAAGTAAAATAGTCAAAGACTTAATTCAAGGAAATTAAATATACTCAGT
* * * *
38642 -AAAGAACTTAATTCGGGGTAATTGAGTAAAGTCAAT-AAAGAA
66 CAAAG-ACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAG-A
38684 CTTAATT
1 CTTAATT
38691 TAAGGTAACT
Statistics
Matches: 269, Mismatches: 35, Indels: 35
0.79 0.10 0.10
Matches are distributed among these distances:
98 1 0.00
99 3 0.01
100 30 0.11
101 53 0.20
104 1 0.00
105 1 0.00
106 34 0.13
107 108 0.40
108 31 0.12
109 6 0.02
110 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.27
Consensus pattern (107 bp):
CTTAATTCAGGGAAATTAAGTAAAATAGTCAAAGACTTAATTCAAGGAAATTAAATATACTCAGT
CAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGA
Found at i:39891 original size:19 final size:19
Alignment explanation
Indices: 39847--39892 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
39837 TAATGAAGTT
*
39847 TAGT-AATTTTAATCATAA
1 TAGTAAATTTTAATAATAA
39865 TATGTAAATTTATAATAATAA
1 TA-GTAAATTT-TAATAATAA
39886 TA-TAAAT
1 TAGTAAAT
39893 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.08
19 7 0.29
20 5 0.21
21 10 0.42
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (19 bp):
TAGTAAATTTTAATAATAA
Found at i:43646 original size:3 final size:3
Alignment explanation
Indices: 43638--43674 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
43628 CTAGATCAAT
*
43638 TTC TTC TTC TTC TTC TTC TTC TAC TTTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC
43675 ACCTTCTACC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:43668 original size:22 final size:22
Alignment explanation
Indices: 43641--43683 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
43631 GATCAATTTC
**
43641 TTCTTCTTCTTCTTCTTCTACT
1 TTCTTCTTCTTCACCTTCTACT
43663 TTCTTCTTCTTCACCTTCTAC
1 TTCTTCTTCTTCACCTTCTAC
43684 CTCGGACTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.35, G:0.00, T:0.58
Consensus pattern (22 bp):
TTCTTCTTCTTCACCTTCTACT
Found at i:43728 original size:3 final size:3
Alignment explanation
Indices: 43720--43768 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
43710 CTAGATCAAT
43720 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
43768 T
1 T
43769 ACCTCGGACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:52520 original size:13 final size:13
Alignment explanation
Indices: 52504--52530 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52494 AATTTGAAAT
52504 CTGCAATTGAAGG
1 CTGCAATTGAAGG
52517 CTGCAATTGAAGG
1 CTGCAATTGAAGG
52530 C
1 C
52531 ATTGGCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (13 bp):
CTGCAATTGAAGG
Found at i:54657 original size:87 final size:85
Alignment explanation
Indices: 54539--54724 Score: 198
Period size: 87 Copynumber: 2.1 Consensus size: 85
54529 TGAATATTTT
* * * * * *
54539 TATGAAATTTTGATAACTATCCTATTAAATTTTGATAATCAC-GCTATGAAATTTTGATAA-TTA
1 TATGAAACTTTGATAACTATACTATGAAATTTTAATAAAC-CTCCTATGAAATTTTG-TAACTT-
*
54602 TCTATGAAATTGTGATAAACTCCA
63 TCTATG-AATTCTGATAAACTCCA
54626 TATGAAACTTTGATAACCTA-ACTATGAAATTTTAATAAACCTTCCTATGAAATTTTGTAACCTT
1 TATGAAACTTTGATAA-CTATACTATGAAATTTTAATAAACC-TCCTATGAAATTTTGTAA-CTT
* *
54690 TCTATGAATTCTGATAACCTCCC
63 TCTATGAATTCTGATAAACTCCA
*
54713 TATGAGACTTTG
1 TATGAAACTTTG
54725 TTAATCTCCC
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
86 1 0.01
87 59 0.70
88 22 0.26
89 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (85 bp):
TATGAAACTTTGATAACTATACTATGAAATTTTAATAAACCTCCTATGAAATTTTGTAACTTTCT
ATGAATTCTGATAAACTCCA
Found at i:54673 original size:23 final size:22
Alignment explanation
Indices: 54539--54717 Score: 147
Period size: 22 Copynumber: 8.2 Consensus size: 22
54529 TGAATATTTT
54539 TATGAAATTTTGATAA-CTATCC
1 TATGAAATTTTGATAACCT-TCC
* * *
54561 TATTAAATTTTGATAATC-ACGC
1 TATGAAATTTTGATAACCTTC-C
*
54583 TATGAAATTTTGATAA--TTATC
1 TATGAAATTTTGATAACCTT-CC
* *
54604 TATGAAATTGTGATAAAC-TCC
1 TATGAAATTTTGATAACCTTCC
* **
54625 ATATGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAACCTTCC
*
54648 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
54671 TATGAAATTTTG-TAACCTTTC
1 TATGAAATTTTGATAACCTTCC
* *
54692 TATG-AATTCTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
54713 TATGA
1 TATGA
54718 GACTTTGTTA
Statistics
Matches: 125, Mismatches: 21, Indels: 22
0.74 0.12 0.13
Matches are distributed among these distances:
20 6 0.05
21 40 0.32
22 60 0.48
23 19 0.15
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:57403 original size:32 final size:32
Alignment explanation
Indices: 57366--57426 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
57356 TGGCATTTAA
57366 GAAATATATT-AGAAAAATAAGGGTATAATGAT
1 GAAATATATTCA-AAAAATAAGGGTATAATGAT
57398 GAAATATATTCAAAAAATAAGGGTATAAT
1 GAAATATATTCAAAAAATAAGGGTATAAT
57427 AGTCGATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.16, T:0.28
Consensus pattern (32 bp):
GAAATATATTCAAAAAATAAGGGTATAATGAT
Found at i:57820 original size:128 final size:130
Alignment explanation
Indices: 57580--57841 Score: 341
Period size: 128 Copynumber: 2.0 Consensus size: 130
57570 CGATGTTTAA
57580 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATT-AA-CTAATATCCTTATAAC
** * * * * * *
57645 TATTTAATTTTTACCATTTTACTGTTTTAATTTAAAAACTTA-TATATATTAGACTTTTTTAAAT
64 TATTTAATTTTTACCATTTTACTAATATAATTAAAAAACTAAGAATATATTAGAATTTTTAAAAT
57709 AT
129 AT
* *
57711 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATT-A-TAATATCCTTTTACCT
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTA-TTTTTATTTAATTAACTAATATCCTTATAACT
* * * *
57774 ATTTTATTTTTATCATTTTTCTAATATGATTAAAAAACTAAGATATATATTAGAATTTTTAAAAT
65 ATTTAATTTTTACCATTTTACTAATATAATTAAAAAACTAAGA-ATATATTAGAATTTTTAAAAT
57839 AT
129 AT
57841 A
1 A
57842 TTTGTTAAAT
Statistics
Matches: 114, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
128 46 0.40
130 23 0.20
131 32 0.28
132 13 0.11
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.50
Consensus pattern (130 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAACTAATATCCTTATAACTA
TTTAATTTTTACCATTTTACTAATATAATTAAAAAACTAAGAATATATTAGAATTTTTAAAATAT
Found at i:58114 original size:15 final size:16
Alignment explanation
Indices: 58094--58123 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
58084 TTCATATTTT
58094 TTAAAAA-TTATTAAG
1 TTAAAAATTTATTAAG
58109 TTAAAAATTTATTAA
1 TTAAAAATTTATTAA
58124 AAATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TTAAAAATTTATTAAG
Found at i:69478 original size:16 final size:16
Alignment explanation
Indices: 69457--69503 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
69447 AATGTAACAA
69457 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
**
69473 AAACAAAAAAAAAAC-
1 AAACAAAACGAAAACG
*
69488 AGA-AAAACGAAAACG
1 AAACAAAACGAAAACG
69503 A
1 A
69504 TGCCAAACGA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 9 0.36
15 3 0.12
16 13 0.52
ACGTcount: A:0.74, C:0.15, G:0.11, T:0.00
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:70013 original size:58 final size:56
Alignment explanation
Indices: 69951--70070 Score: 152
Period size: 58 Copynumber: 2.1 Consensus size: 56
69941 GGAAAATTAA
69951 AAAAAAGAAGA-AAAACTTGAAGGATTTAAATAAAAGAGAGTTAATATGTTAAAATATT
1 AAAAAAGAAGACAAAA--TGAAGGATTTAAATAAAAGAGAGTTAATATGTT-AAATATT
*** * *
70009 AAAAATTTAGATCTAAATGAAGGATTTAAATAAAAGATAGTTAATATGTTAAATATT
1 AAAAAAGAAGA-CAAAATGAAGGATTTAAATAAAAGAGAGTTAATATGTTAAATATT
70066 AAAAA
1 AAAAA
70071 TTTATAACTA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
57 12 0.22
58 40 0.73
60 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.29
Consensus pattern (56 bp):
AAAAAAGAAGACAAAATGAAGGATTTAAATAAAAGAGAGTTAATATGTTAAATATT
Found at i:78443 original size:16 final size:16
Alignment explanation
Indices: 78422--78460 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
78412 AGCAATAACT
78422 TGAGTGAATCAAAATA
1 TGAGTGAATCAAAATA
78438 TGAGTGAATCAAAATA
1 TGAGTGAATCAAAATA
*
78454 AGAGTGA
1 TGAGTGA
78461 TCTTTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.23, T:0.23
Consensus pattern (16 bp):
TGAGTGAATCAAAATA
Found at i:79805 original size:21 final size:21
Alignment explanation
Indices: 79781--79822 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
79771 TCCTTTGCAT
*
79781 ATGATCTCTAATGCCCTTCAA
1 ATGAACTCTAATGCCCTTCAA
* *
79802 ATGAACTCTGATGGCCTTCAA
1 ATGAACTCTAATGCCCTTCAA
79823 CTCTTCAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (21 bp):
ATGAACTCTAATGCCCTTCAA
Found at i:79960 original size:21 final size:21
Alignment explanation
Indices: 79934--79975 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
79924 GCATCTTAGG
*
79934 CAACTCCGATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
79955 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
79976 TTCTTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (21 bp):
CAACTCCAATGAGCTTGAAAC
Found at i:84621 original size:9 final size:9
Alignment explanation
Indices: 84607--84637 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
84597 GAAAGTAGTT
84607 GAGGAGGTG
1 GAGGAGGTG
*
84616 GAGGAGGAG
1 GAGGAGGTG
84625 GAGGAGGTG
1 GAGGAGGTG
84634 GAGG
1 GAGG
84638 TGGAGGCGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.68, T:0.06
Consensus pattern (9 bp):
GAGGAGGTG
Found at i:90500 original size:11 final size:12
Alignment explanation
Indices: 90483--90519 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
90473 CGTCGTGTTT
90483 TAATTAAATTAA
1 TAATTAAATTAA
90495 -AATTAAATTAA
1 TAATTAAATTAA
90506 TAATTGAAATTAA
1 TAATT-AAATTAA
90519 T
1 T
90520 TATAAGTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 4 0.17
13 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
TAATTAAATTAA
Found at i:90763 original size:22 final size:22
Alignment explanation
Indices: 90738--90784 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
90728 TTTTAAGAAT
*
90738 TAAATTAT-ATTAATTAATTATA
1 TAAATTATAATT-ATTAAATATA
90760 TAAA-TATAATTATTAAATATA
1 TAAATTATAATTATTAAATATA
90781 -AAAT
1 TAAAT
90785 ATGATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 3 0.14
21 12 0.55
22 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTATAATTATTAAATATA
Found at i:90776 original size:13 final size:14
Alignment explanation
Indices: 90740--90781 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
90730 TTAAGAATTA
*
90740 AATTATATTAAT-T
1 AATTATATAAATAT
90753 AATTATATAAATAT
1 AATTATATAAATAT
90767 AATTAT-TAAATAT
1 AATTATATAAATAT
90780 AA
1 AA
90782 AATATGATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 20 0.74
14 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTATATAAATAT
Found at i:92916 original size:8 final size:8
Alignment explanation
Indices: 92903--92933 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
92893 TTTTAGTTAA
92903 GTAAAATG
1 GTAAAATG
92911 GTAAAATG
1 GTAAAATG
92919 GTAAAATG
1 GTAAAATG
*
92927 ATAAAAT
1 GTAAAAT
92934 TGAATAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (8 bp):
GTAAAATG
Found at i:92916 original size:85 final size:85
Alignment explanation
Indices: 92827--92982 Score: 210
Period size: 85 Copynumber: 1.8 Consensus size: 85
92817 TTTTTTAAAT
* * *
92827 TAAAATATTAAAATGGT-AAATAT-AATAGTTATAAGGATATT-GTACTTAGTTAAATAAAAATA
1 TAAAATAGTAAAATGATAAAAT-TGAATAGTTATAAAGATATTAG-ACTTA-TTAAATAAAAATA
92889 GAGTTTTTAGTTAAGTAAAATGG
63 GAGTTTTTAGTTAAGTAAAATGG
* * *
92912 TAAAATGGTAAAATGATAAAATTGAATAGTTATAAATATATTAGATTTATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGATAAAATTGAATAGTTATAAAGATATTAGACTTATTAAATAAAAATAGAG
92977 TTTTTA
66 TTTTTA
92983 TAAGAATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
85 37 0.60
86 24 0.39
87 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37
Consensus pattern (85 bp):
TAAAATAGTAAAATGATAAAATTGAATAGTTATAAAGATATTAGACTTATTAAATAAAAATAGAG
TTTTTAGTTAAGTAAAATGG
Found at i:93614 original size:2 final size:2
Alignment explanation
Indices: 93607--93632 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
93597 TATAAGTTCA
93607 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
93633 CATGAATATG
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:105280 original size:29 final size:29
Alignment explanation
Indices: 105261--105330 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
105251 CAGGGTCAAG
*
105261 AGGTCAAACAGGTAGAAAACGGGACCGAA
1 AGGTCAAACAGGCAGAAAACGGGACCGAA
*
105290 AGGTCAAACATGCAGAAAACGGGACCGAA
1 AGGTCAAACAGGCAGAAAACGGGACCGAA
105319 AGGTCAAACAGG
1 AGGTCAAACAGG
105331 ACCAATAGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.44, C:0.19, G:0.30, T:0.07
Consensus pattern (29 bp):
AGGTCAAACAGGCAGAAAACGGGACCGAA
Found at i:105319 original size:76 final size:76
Alignment explanation
Indices: 105227--105375 Score: 217
Period size: 76 Copynumber: 2.0 Consensus size: 76
105217 ATCAACAGAA
* * ** *
105227 AGAAAACGGGATCGAAAGTTCAAACAGGGTCAAGAGGTCAAACAGGTAGAAAACGGGACCGAAAG
1 AGAAAACGGGACCGAAAGGTCAAACAGGACCAAGAGGTCAAACAGGCAGAAAACGGGACCGAAAG
105292 GTCAAACATGC
66 GTCAAACATGC
* * * *
105303 AGAAAACGGGACCGAAAGGTCAAACAGGACCAATAGGTCAAATATGCAGAAAACGGGACTGAAAG
1 AGAAAACGGGACCGAAAGGTCAAACAGGACCAAGAGGTCAAACAGGCAGAAAACGGGACCGAAAG
105368 GTCAAACA
66 GTCAAACA
105376 AGACCAAGAG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.45, C:0.17, G:0.28, T:0.10
Consensus pattern (76 bp):
AGAAAACGGGACCGAAAGGTCAAACAGGACCAAGAGGTCAAACAGGCAGAAAACGGGACCGAAAG
GTCAAACATGC
Found at i:105332 original size:18 final size:18
Alignment explanation
Indices: 105306--105344 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
105296 AACATGCAGA
*
105306 AAACGGGACCGAA-AGGTC
1 AAACAGGACC-AATAGGTC
105324 AAACAGGACCAATAGGTC
1 AAACAGGACCAATAGGTC
105342 AAA
1 AAA
105345 TATGCAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.46, C:0.21, G:0.26, T:0.08
Consensus pattern (18 bp):
AAACAGGACCAATAGGTC
Found at i:105333 original size:47 final size:47
Alignment explanation
Indices: 105277--105419 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
105267 AACAGGTAGA
*
105277 AAACGGGACCGAA-AGGTCAAACATGCAGAAAACGGGACCGAAAGGTC
1 AAACAGGACC-AAGAGGTCAAACATGCAGAAAACGGGACCGAAAGGTC
* * *
105324 AAACAGGACCAATAGGTCAAATATGCAGAAAACGGGACTGAAAGGTC
1 AAACAGGACCAAGAGGTCAAACATGCAGAAAACGGGACCGAAAGGTC
* * *
105371 AAACAAGACCAAGAGGTCAAACAGGCAGAAAACGGGACCGAGAGGTC
1 AAACAGGACCAAGAGGTCAAACATGCAGAAAACGGGACCGAAAGGTC
105418 AA
1 AA
105420 CAGAGCGGAA
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
46 2 0.02
47 84 0.98
ACGTcount: A:0.45, C:0.20, G:0.28, T:0.08
Consensus pattern (47 bp):
AAACAGGACCAAGAGGTCAAACATGCAGAAAACGGGACCGAAAGGTC
Found at i:108032 original size:16 final size:16
Alignment explanation
Indices: 108011--108042 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
108001 TTCCTATTAA
108011 AATTAAATTAATACAT
1 AATTAAATTAATACAT
108027 AATTAAATTAATACAT
1 AATTAAATTAATACAT
108043 GTAGATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTAAATTAATACAT
Found at i:108674 original size:20 final size:20
Alignment explanation
Indices: 108646--108699 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
108636 GCCAAAAATA
108646 TGATAATAAA-TAATACATAT
1 TGATAATAAATTAATAC-TAT
*
108666 TGATTATAAATTAATACTAT
1 TGATAATAAATTAATACTAT
*
108686 T-ATAGTAATATTAA
1 TGATAATAA-ATTAA
108700 ATATAGGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 5 0.17
20 18 0.62
21 6 0.21
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.41
Consensus pattern (20 bp):
TGATAATAAATTAATACTAT
Found at i:110739 original size:21 final size:21
Alignment explanation
Indices: 110687--110739 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
110677 GTTTAACATG
* * *
110687 TTGACTATCAAACTTTGTGGT
1 TTGACCATCAAAATTTGGGGT
*
110708 TTAACTC-TCAAAATTTGGGGT
1 TTGAC-CATCAAAATTTGGGGT
110729 TTGACCATCAA
1 TTGACCATCAA
110740 TGAGGTTTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TTGACCATCAAAATTTGGGGT
Found at i:110889 original size:21 final size:21
Alignment explanation
Indices: 110837--111024 Score: 177
Period size: 21 Copynumber: 9.1 Consensus size: 21
110827 TCAATCACCA
*
110837 AAATTTTGATAGTCAAACCGC
1 AAATTTTGATAGTCAAACCCC
* **
110858 --A--TTGATGGTCAAACCTT
1 AAATTTTGATAGTCAAACCCC
*
110875 AAATTTTGATAGTCAAACCTC
1 AAATTTTGATAGTCAAACCCC
* * *
110896 AAAGTTTGATGGTCAACCCCC
1 AAATTTTGATAGTCAAACCCC
110917 AAATTTTGATAGTCAAACCCC
1 AAATTTTGATAGTCAAACCCC
* * *
110938 AAAGTTTGATGGTCAACCCCC
1 AAATTTTGATAGTCAAACCCC
** *
110959 AAATTTTGATAACCAAACCCT
1 AAATTTTGATAGTCAAACCCC
* * * *
110980 AGAGTTTGATGGTCAACCCCC
1 AAATTTTGATAGTCAAACCCC
*
111001 GAATTTTGATAGTCAAACCCC
1 AAATTTTGATAGTCAAACCCC
111022 AAA
1 AAA
111025 GTTTCATATA
Statistics
Matches: 129, Mismatches: 34, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
17 13 0.10
19 2 0.02
21 114 0.88
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (21 bp):
AAATTTTGATAGTCAAACCCC
Found at i:110921 original size:42 final size:42
Alignment explanation
Indices: 110859--111028 Score: 259
Period size: 42 Copynumber: 4.0 Consensus size: 42
110849 TCAAACCGCA
* ** *
110859 TTGATGGTCAAACCTTAAATTTTGATAGTCAAACCTCAAAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
110901 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
** * *
110943 TTGATGGTCAACCCCCAAATTTTGATAACCAAACCCTAGAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
*
110985 TTGATGGTCAACCCCCGAATTTTGATAGTCAAACCCCAAAGT
1 TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
111027 TT
1 TT
111029 CATATATTTC
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 115 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.29
Consensus pattern (42 bp):
TTGATGGTCAACCCCCAAATTTTGATAGTCAAACCCCAAAGT
Found at i:112229 original size:2 final size:2
Alignment explanation
Indices: 112224--112250 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
112214 GGTGTGTGTG
112224 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 T
112251 GGACTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:112664 original size:24 final size:24
Alignment explanation
Indices: 112628--112677 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
112618 GTTAAATTGT
*
112628 AATAACTAGTGAAATGACTCTAGA
1 AATAACTAATGAAATGACTCTAGA
112652 AATAACTAATGAAATGACTCTAGA
1 AATAACTAATGAAATGACTCTAGA
112676 AA
1 AA
112678 ATTAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (24 bp):
AATAACTAATGAAATGACTCTAGA
Found at i:113032 original size:19 final size:19
Alignment explanation
Indices: 113008--113047 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
112998 TGCTACACAC
113008 TTTAGAGGAAGAAACAAAA
1 TTTAGAGGAAGAAACAAAA
*
113027 TTTAGAGGAGGAAACAAAA
1 TTTAGAGGAAGAAACAAAA
113046 TT
1 TT
113048 GAAGCTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.20
Consensus pattern (19 bp):
TTTAGAGGAAGAAACAAAA
Found at i:113315 original size:14 final size:14
Alignment explanation
Indices: 113296--113322 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
113286 ATTAGTTATT
113296 AGAAAGAGAGAGAG
1 AGAAAGAGAGAGAG
113310 AGAAAGAGAGAGA
1 AGAAAGAGAGAGA
113323 TGAGTGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AGAAAGAGAGAGAG
Found at i:120681 original size:22 final size:23
Alignment explanation
Indices: 120630--120689 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
120620 GTGTGATAAA
* *
120630 TTCCATATGAAACTTTGATAACC
1 TTCCCTATGAAATTTTGATAACC
**
120653 -TAACTATGAAATTTTG-TAACC
1 TTCCCTATGAAATTTTGATAACC
*
120674 TTCCCTATGAGATTTT
1 TTCCCTATGAAATTTT
120690 ATTAATCTCC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (23 bp):
TTCCCTATGAAATTTTGATAACC
Found at i:120804 original size:16 final size:16
Alignment explanation
Indices: 120783--120818 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
120773 TAAGTGTCTG
120783 TTGCGCCAAAAATCTC
1 TTGCGCCAAAAATCTC
120799 TTGCGCCAAAAATCTC
1 TTGCGCCAAAAATCTC
120815 TTGC
1 TTGC
120819 TAGAGTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.28
Consensus pattern (16 bp):
TTGCGCCAAAAATCTC
Found at i:122955 original size:13 final size:13
Alignment explanation
Indices: 122937--122962 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
122927 GATCAAGGTA
122937 AAAAAATCATCAC
1 AAAAAATCATCAC
122950 AAAAAATCATCAC
1 AAAAAATCATCAC
122963 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATCATCAC
Found at i:123565 original size:27 final size:28
Alignment explanation
Indices: 123499--123573 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
123489 AGGATCACCT
*
123499 AGGGGCATTTTGGTCATTTTCAAACATCC
1 AGGGGCATTTTGGTCATTTGC-AACATCC
* * *
123528 AGGGGCATTTTGGCCATTTGC-ACGTTC
1 AGGGGCATTTTGGTCATTTGCAACATCC
123555 AGGGGCATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
123574 TAAGTTCACT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 22 0.54
29 19 0.46
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.36
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTGCAACATCC
Found at i:135764 original size:16 final size:15
Alignment explanation
Indices: 135726--135767 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
135716 ACAGAGATTG
*
135726 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
135741 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
135756 ACTAGAAAACAA
1 AC-AGAAAACAA
135768 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:141873 original size:15 final size:15
Alignment explanation
Indices: 141855--141887 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
141845 ACTCAAAAGA
141855 AAATATGTTAGTAGT
1 AAATATGTTAGTAGT
*
141870 AAATATGTTAGTATT
1 AAATATGTTAGTAGT
141885 AAA
1 AAA
141888 GACAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (15 bp):
AAATATGTTAGTAGT
Found at i:142051 original size:22 final size:22
Alignment explanation
Indices: 141992--142057 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
141982 TTTTGAAAAA
*
141992 ACGCAAAAACT-TTTTTTTTATG
1 ACGCAAAAAATATTTTTTTT-TG
*
142014 ATGCATAAACAA-ATTTTTTTTTG
1 ACGCA-AAA-AATATTTTTTTTTG
142037 ACGCAAAAAATATTTTTTTTT
1 ACGCAAAAAATATTTTTTTTT
142058 TTCGACGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 2 0.05
22 17 0.46
23 9 0.24
24 9 0.24
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.47
Consensus pattern (22 bp):
ACGCAAAAAATATTTTTTTTTG
Found at i:142057 original size:23 final size:23
Alignment explanation
Indices: 141992--142069 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 23
141982 TTTTGAAAAA
* *
141992 ACGCAAAAACT-TTTTTTTTATG
1 ACGCAAAAAATATTTTTTTTTTG
*
142014 ATGCATAAACAA-A-TTTTTTTTTG
1 ACGCA-AAA-AATATTTTTTTTTTG
142037 ACGCAAAAAATATTTTTTTTTTTCG
1 ACGCAAAAAATA-TTTTTTTTTT-G
142062 ACGCAAAA
1 ACGCAAAA
142070 CACAAAACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
21 2 0.04
22 8 0.18
23 16 0.36
24 10 0.22
25 9 0.20
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (23 bp):
ACGCAAAAAATATTTTTTTTTTG
Found at i:142405 original size:16 final size:15
Alignment explanation
Indices: 142367--142408 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
142357 ACAAAGATTG
*
142367 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
142382 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
142397 ACTAGAAAACAA
1 AC-AGAAAACAA
142409 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.