Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 137 of 290
Found at i:46416578 original size:12 final size:12
Alignment explanation
Indices: 46416561--46416591 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
46416551 AGTACTACCT
46416561 CGGCCTCGACCA
1 CGGCCTCGACCA
46416573 CGGCCTCGACCA
1 CGGCCTCGACCA
46416585 CGGCCTC
1 CGGCCTC
46416592 TTCCTCGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.52, G:0.26, T:0.10
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:46418235 original size:25 final size:27
Alignment explanation
Indices: 46418198--46418250 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
46418188 TCAAACATGC
46418198 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
46418224 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
46418250 A
1 A
46418251 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:46420342 original size:39 final size:39
Alignment explanation
Indices: 46420146--46420342 Score: 279
Period size: 39 Copynumber: 5.1 Consensus size: 39
46420136 CGTTACACAT
* * *
46420146 CGGCACATAGCCTGCTAGGCACAAAGCCTGAATAATCAC
1 CGGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCAC
* *
46420185 CAGCACAAAGCCTACTAGGCACATAGCCCGAATAATC-C
1 CGGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCAC
* * * *
46420223 CTAGCACAAAGCTTGCTAGGAACTTAGCCCGAATAATCAC
1 C-GGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCAC
* *
46420263 TGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCAC
1 CGGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCAC
46420302 CGGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCAC
1 CGGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCAC
46420341 CG
1 CG
46420343 TATTTCTATT
Statistics
Matches: 141, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
38 2 0.01
39 138 0.98
40 1 0.01
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.16
Consensus pattern (39 bp):
CGGCACAAAGCCTGCTAGGCACATAGCCCGAATAATCAC
Found at i:46421312 original size:22 final size:22
Alignment explanation
Indices: 46421287--46421328 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
46421277 CAATTTAGCC
46421287 ATTTTTTCTTTAATTAACTACA
1 ATTTTTTCTTTAATTAACTACA
46421309 ATTTTTTCTTTAATTAACTA
1 ATTTTTTCTTTAATTAACTA
46421329 TCTAATCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTTCTTTAATTAACTACA
Found at i:46427581 original size:27 final size:28
Alignment explanation
Indices: 46427551--46427607 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
46427541 CATAAATAAT
*
46427551 TAAATAAAGTATT-AAATATTATAACAA
1 TAAATAAAGTATTAAAATAATATAACAA
46427578 TAAATAAAGTATTAAAATAATATAACAA
1 TAAATAAAGTATTAAAATAATATAACAA
46427606 TA
1 TA
46427608 TATTATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (28 bp):
TAAATAAAGTATTAAAATAATATAACAA
Found at i:46431943 original size:40 final size:40
Alignment explanation
Indices: 46431882--46431957 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
46431872 CAATACTTTA
*
46431882 TGGTGTGTAAGGTTGGATGGGTCGATTTTATCCCCATATT
1 TGGTGTGTAAGGATGGATGGGTCGATTTTATCCCCATATT
* * *
46431922 TGGTGTGTAGGGATGGGTGGGTCGTTTTTATCCCCA
1 TGGTGTGTAAGGATGGATGGGTCGATTTTATCCCCA
46431958 CATGGTGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.14, C:0.13, G:0.34, T:0.38
Consensus pattern (40 bp):
TGGTGTGTAAGGATGGATGGGTCGATTTTATCCCCATATT
Found at i:46432616 original size:22 final size:22
Alignment explanation
Indices: 46432590--46432634 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
46432580 ATTGAGGTCC
46432590 ATAGCTCACCTCCCTTTTCCTT
1 ATAGCTCACCTCCCTTTTCCTT
46432612 ATAGCTCACCTCCCTTTTCCTT
1 ATAGCTCACCTCCCTTTTCCTT
46432634 A
1 A
46432635 CATCTTTACA
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:0.16, C:0.40, G:0.04, T:0.40
Consensus pattern (22 bp):
ATAGCTCACCTCCCTTTTCCTT
Found at i:46433277 original size:45 final size:45
Alignment explanation
Indices: 46433213--46433303 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
46433203 TTATTTGAGT
46433213 TATTTCTTTTTATACTTCTAATAGAACCAATAAAAAACTTACATA
1 TATTTCTTTTTATACTTCTAATAGAACCAATAAAAAACTTACATA
46433258 TATTTCTTTTTATACTTCTAATAGAACCAATAAAAAACTTACATA
1 TATTTCTTTTTATACTTCTAATAGAACCAATAAAAAACTTACATA
46433303 T
1 T
46433304 GGTGAGGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.41
Consensus pattern (45 bp):
TATTTCTTTTTATACTTCTAATAGAACCAATAAAAAACTTACATA
Found at i:46438127 original size:20 final size:20
Alignment explanation
Indices: 46438102--46438146 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
46438092 AGGGACTAAA
*
46438102 ATGAAAAGTTATAAAATTTT
1 ATGAAAAATTATAAAATTTT
* *
46438122 ATGAAAAATTTTGAAATTTT
1 ATGAAAAATTATAAAATTTT
46438142 ATGAA
1 ATGAA
46438147 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGAAAAATTATAAAATTTT
Found at i:46465171 original size:44 final size:44
Alignment explanation
Indices: 46465106--46465189 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
46465096 TTGATATCTC
* * *
46465106 AAAGTCCATGGTTGTACCATGGCAATTAAGGAAGAATTGACGGA
1 AAAGTCCATGGTTATAACATGGCAATTAAAGAAGAATTGACGGA
* *
46465150 AAAGTCCAT-GTTCATAACATGGCATTTAAAGAGGAATTGA
1 AAAGTCCATGGTT-ATAACATGGCAATTAAAGAAGAATTGA
46465190 TTAAGACCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 3 0.09
44 31 0.91
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (44 bp):
AAAGTCCATGGTTATAACATGGCAATTAAAGAAGAATTGACGGA
Found at i:46465339 original size:47 final size:47
Alignment explanation
Indices: 46465283--46465388 Score: 176
Period size: 47 Copynumber: 2.3 Consensus size: 47
46465273 GCATTGGCAC
*
46465283 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGAAACATGGCATTTGG
* *
46465330 TATGACAAGGATACCATGTAAGACTATGTTTGAAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGAAACATGGCATTTGG
*
46465377 TAAGATAAGGAT
1 TAAGACAAGGAT
46465389 GTAACACCCC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGAAACATGGCATTTGG
Found at i:46478497 original size:47 final size:47
Alignment explanation
Indices: 46478438--46478653 Score: 396
Period size: 47 Copynumber: 4.6 Consensus size: 47
46478428 GCATTGGCAC
46478438 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
46478485 TAAGACAAGGATACCATGTAAGGCCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
46478532 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
46478579 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTAG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
46478626 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
46478654 CCAAGGCATG
Statistics
Matches: 164, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 164 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:46478773 original size:55 final size:55
Alignment explanation
Indices: 46478640--46478828 Score: 174
Period size: 55 Copynumber: 3.5 Consensus size: 55
46478630 ATAAGGATAT
* * * *
46478640 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAA-GAAAAGGAAAT
1 CATGTAAGACCATTCCAAGGCATGGCATTGATGAGTTCTATAAGGCAAAGGAAAC
* * * **
46478694 CATGTAAGACCGTGT-TAAGACATGGCATTGATGAGTTACTATAAGGCAAAGG-TCC
1 CATGTAAGACCAT-TCCAAGGCATGGCATTGATGAGTT-CTATAAGGCAAAGGAAAC
* * *
46478749 CATGTAATACCATTCCAAGGCATGGCATTGGTGAGTT-TATAAGGC-AAGGATAC
1 CATGTAAGACCATTCCAAGGCATGGCATTGATGAGTTCTATAAGGCAAAGGAAAC
** *
46478802 CACATAAGACCATGT-CAAGACATGGCA
1 CATGTAAGACCAT-TCCAAGGCATGGCA
46478829 ATGGTAAGTT
Statistics
Matches: 110, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
52 4 0.04
53 31 0.28
54 33 0.30
55 36 0.33
56 6 0.05
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (55 bp):
CATGTAAGACCATTCCAAGGCATGGCATTGATGAGTTCTATAAGGCAAAGGAAAC
Found at i:46478826 original size:53 final size:54
Alignment explanation
Indices: 46478632--46478839 Score: 197
Period size: 54 Copynumber: 3.9 Consensus size: 54
46478622 TTAGTAAGAT
* * * **
46478632 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGAA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGC
* * * * *
46478686 AAGGAAATCATGTAAGACCGTGTTAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTT-CTATAAGGC
* * * * *
46478741 AAAGG-TCCCATGTAATACCAT-TCCAAGGCATGGCATTGGTGAGTT-TATAAGGC
1 -AAGGATACCATGTAAGACCATGT-CAAGACATGGCATTGATAAGTTCTATAAGGC
** * *
46478794 AAGGATACCACATAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTC
46478840 AAAGGGAAAA
Statistics
Matches: 125, Mismatches: 23, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
52 4 0.03
53 39 0.31
54 41 0.33
55 37 0.30
56 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGC
Found at i:46484079 original size:44 final size:44
Alignment explanation
Indices: 46484030--46484133 Score: 199
Period size: 44 Copynumber: 2.4 Consensus size: 44
46484020 TGCTTTAACA
46484030 TCCGCACACTTAGTGCTTTAAGGATTAGCCGAAGCTAGAACGAT
1 TCCGCACACTTAGTGCTTTAAGGATTAGCCGAAGCTAGAACGAT
*
46484074 TCCGCACACTTAGTGCTTTAAGGGTTAGCCGAAGCTAGAACGAT
1 TCCGCACACTTAGTGCTTTAAGGATTAGCCGAAGCTAGAACGAT
46484118 TCCGCACACTTAGTGC
1 TCCGCACACTTAGTGC
46484134 CATTTCATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (44 bp):
TCCGCACACTTAGTGCTTTAAGGATTAGCCGAAGCTAGAACGAT
Found at i:46484228 original size:40 final size:40
Alignment explanation
Indices: 46484165--46484261 Score: 167
Period size: 40 Copynumber: 2.4 Consensus size: 40
46484155 TCTCGATATT
*
46484165 GCACACTTAGTGCCTCAGTTAGCCGAAGCTATTTTGAATC
1 GCACACTTAGTGCCTCAGATAGCCGAAGCTATTTTGAATC
* *
46484205 TCATACTTAGTGCCTCAGATAGCCGAAGCTATTTTGAATC
1 GCACACTTAGTGCCTCAGATAGCCGAAGCTATTTTGAATC
46484245 GCACACTTAGTGCCTCA
1 GCACACTTAGTGCCTCA
46484262 TACCATTGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (40 bp):
GCACACTTAGTGCCTCAGATAGCCGAAGCTATTTTGAATC
Found at i:46491641 original size:40 final size:40
Alignment explanation
Indices: 46491586--46491683 Score: 153
Period size: 40 Copynumber: 2.5 Consensus size: 40
46491576 ATCTCAATAC
46491586 CGCACACTTAGTGCCTCAGATAGCCGAAGCTATTTTGAATT
1 CGCACACTTAGTGCCTCAGATAGCCGAAGCTATTTTG-ATT
* *
46491627 -GTACACTTAGTGCCTTAGATAGCCGAAGCTATTTTGATT
1 CGCACACTTAGTGCCTCAGATAGCCGAAGCTATTTTGATT
*
46491666 CGCACACTTAATGCCTCA
1 CGCACACTTAGTGCCTCA
46491684 TACCATTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
39 3 0.06
40 48 0.94
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (40 bp):
CGCACACTTAGTGCCTCAGATAGCCGAAGCTATTTTGATT
Found at i:46495654 original size:21 final size:21
Alignment explanation
Indices: 46495601--46495642 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
46495591 ACAGAGCAGG
*
46495601 CACGACCGTATGAGGGTATCA
1 CACGACCGTGTGAGGGTATCA
46495622 CACGACCGTGTGAGGGTATCA
1 CACGACCGTGTGAGGGTATCA
46495643 GGCGCTCGTG
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:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (21 bp):
CACGACCGTGTGAGGGTATCA
Found at i:46496345 original size:6 final size:6
Alignment explanation
Indices: 46496334--46496393 Score: 93
Period size: 6 Copynumber: 9.7 Consensus size: 6
46496324 TTTTCATATC
*
46496334 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAGAAAA AACAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT AA-AAAT
46496384 AAAAAT AAAA
1 AAAAAT AAAA
46496394 TCTAACCTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
6 40 0.80
7 10 0.20
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:46498344 original size:25 final size:25
Alignment explanation
Indices: 46498301--46498350 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
46498291 GTAATATATA
* *
46498301 ATTTATTAAAAACTTAAAATAAATT
1 ATTTATTAAAAACTAAAAAAAAATT
46498326 ATTTATGTAAAAA-TAAAAAAAAATT
1 ATTTAT-TAAAAACTAAAAAAAAATT
46498351 GATAAACCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
ATTTATTAAAAACTAAAAAAAAATT
Found at i:46499917 original size:16 final size:16
Alignment explanation
Indices: 46499880--46499918 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
46499870 ATTTAACATA
*
46499880 AATAATAATTAATTAT
1 AATAATTATTAATTAT
**
46499896 TTTAATTATTAATTAT
1 AATAATTATTAATTAT
46499912 AATAATT
1 AATAATT
46499919 TGTTTTTCTT
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATAATTATTAATTAT
Found at i:46508891 original size:5 final size:6
Alignment explanation
Indices: 46508845--46509035 Score: 67
Period size: 6 Copynumber: 33.0 Consensus size: 6
46508835 ATTGATTTAC
**
46508845 TATTAA T-TTAA TA-TAA TACTT-A TATTAA TAGTATTT TATTAA T-TTAA
1 TATTAA TATTAA TATTAA TA-TTAA TATTAA TA-T-TAA TATTAA TATTAA
* * * *
46508892 TATTAAA GTGATT-A TCTTAA TATTAA -ATTTAA T-TTAA CATTTA TATTGA
1 TATT-AA -T-ATTAA TATTAA TATTAA TA-TTAA TATTAA TATTAA TATTAA
*
46508941 TA--AA TATT-A TATTAA T-TTAA TATTAAA GTGATT-A TCTTAA TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATT-AA -T-ATTAA TATTAA TATTAA
* * *
46508987 -ATTTAA T-TTAA CATTTA TATTGA TA--AA TATT-A TATTAA T-TTAA
1 TA-TTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
46509030 TATTAA
1 TATTAA
46509036 AGTGATTAAG
Statistics
Matches: 138, Mismatches: 18, Indels: 58
0.64 0.08 0.27
Matches are distributed among these distances:
4 6 0.04
5 51 0.37
6 61 0.44
7 9 0.07
8 5 0.04
9 6 0.04
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (6 bp):
TATTAA
Found at i:46508911 original size:25 final size:26
Alignment explanation
Indices: 46508858--46508917 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
46508848 TAATTTAATA
*
46508858 TAATACTT-ATATTAATAGTATTTTAT
1 TAATA-TTAATATTAATAGTATTATAT
*
46508884 TAAT-TTAATATTAA-AGTGATTATCT
1 TAATATTAATATTAATAGT-ATTATAT
46508909 TAATATTAA
1 TAATATTAA
46508918 ATTTAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 5 0.17
25 16 0.55
26 8 0.28
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (26 bp):
TAATATTAATATTAATAGTATTATAT
Found at i:46508933 original size:12 final size:12
Alignment explanation
Indices: 46508908--46509036 Score: 50
Period size: 11 Copynumber: 10.9 Consensus size: 12
46508898 AGTGATTATC
46508908 TTAATATTAAAT
1 TTAATATTAAAT
46508920 TTAAT-TTAACAT
1 TTAATATTAA-AT
46508932 TT-ATATTGATAAAT
1 TTAATA-T--TAAAT
46508946 ATT-ATATT-AAT
1 -TTAATATTAAAT
46508957 TTAATATTAAA-
1 TTAATATTAAAT
* *
46508968 GT--GATT--AT
1 TTAATATTAAAT
46508976 CTTAATATTAAAT
1 -TTAATATTAAAT
46508989 TTAAT-TTAACAT
1 TTAATATTAA-AT
46509001 TT-ATATTGATAAAT
1 TTAATA-T--TAAAT
46509015 ATT-ATATT-AAT
1 -TTAATATTAAAT
46509026 TTAATATTAAA
1 TTAATATTAAA
46509037 GTGATTAAGT
Statistics
Matches: 91, Mismatches: 4, Indels: 44
0.65 0.03 0.32
Matches are distributed among these distances:
7 1 0.01
9 4 0.04
10 4 0.04
11 32 0.35
12 24 0.26
13 4 0.04
14 6 0.07
15 16 0.18
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (12 bp):
TTAATATTAAAT
Found at i:46508958 original size:32 final size:33
Alignment explanation
Indices: 46508910--46509029 Score: 129
Period size: 32 Copynumber: 3.6 Consensus size: 33
46508900 TGATTATCTT
46508910 AATATTAAATTTAATTTAACATTTATATTGATA
1 AATATTAAATTTAATTTAACATTTATATTGATA
* * * *
46508943 AATATTATA-TTAATTTAATATTAAAGTGATT-ATCTT
1 AATATTAAATTTAATTTAACATT-TA-T-ATTGA--TA
46508979 AATATTAAATTTAATTTAACATTTATATTGATA
1 AATATTAAATTTAATTTAACATTTATATTGATA
*
46509012 AATATTATA-TTAATTTAA
1 AATATTAAATTTAATTTAA
46509030 TATTAAAGTG
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
32 21 0.30
33 18 0.25
34 5 0.07
35 5 0.07
36 10 0.14
37 12 0.17
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (33 bp):
AATATTAAATTTAATTTAACATTTATATTGATA
Found at i:46508964 original size:69 final size:69
Alignment explanation
Indices: 46508845--46509043 Score: 330
Period size: 69 Copynumber: 2.9 Consensus size: 69
46508835 ATTGATTTAC
* * * * * *
46508845 TATT-AATTTAATATAATACTTATATTAAT-AGTATTTTATTAATTTAATATTAAAGTGATTATC
1 TATTAAATTTAATTTAACATTTATATTGATAAATATTATATTAATTTAATATTAAAGTGATTATC
46508908 TTAA
66 TTAA
46508912 TATTAAATTTAATTTAACATTTATATTGATAAATATTATATTAATTTAATATTAAAGTGATTATC
1 TATTAAATTTAATTTAACATTTATATTGATAAATATTATATTAATTTAATATTAAAGTGATTATC
46508977 TTAA
66 TTAA
46508981 TATTAAATTTAATTTAACATTTATATTGATAAATATTATATTAATTTAATATTAAAGTGATTA
1 TATTAAATTTAATTTAACATTTATATTGATAAATATTATATTAATTTAATATTAAAGTGATTA
46509044 AGTTTAATCA
Statistics
Matches: 124, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
67 4 0.03
68 21 0.17
69 99 0.80
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (69 bp):
TATTAAATTTAATTTAACATTTATATTGATAAATATTATATTAATTTAATATTAAAGTGATTATC
TTAA
Found at i:46510052 original size:34 final size:34
Alignment explanation
Indices: 46509966--46510054 Score: 124
Period size: 34 Copynumber: 2.6 Consensus size: 34
46509956 TTCTACTATC
* * *
46509966 TTGATTTGTTATAAGCATATCTATTCCTACCGTT
1 TTGATTTGTTATAAGCATGTCCATTACTACCGTT
* *
46510000 TTAATTCGTTATAAGCATGTCCATTACTACCGTT
1 TTGATTTGTTATAAGCATGTCCATTACTACCGTT
*
46510034 TTGATTTATTATAAGCATGTC
1 TTGATTTGTTATAAGCATGTC
46510055 ATATTGCATT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (34 bp):
TTGATTTGTTATAAGCATGTCCATTACTACCGTT
Found at i:46513077 original size:45 final size:44
Alignment explanation
Indices: 46513009--46513158 Score: 192
Period size: 45 Copynumber: 3.3 Consensus size: 44
46512999 TTATTTGCAC
* * * *
46513009 CGATGAGTGGTTTATCCATAATGTATTACCAGCTTTTATATACA
1 CGATGAGTGGTTTATCCACAATGTACTAGCAGCTTTTATCTACA
* *
46513053 CAGATGAATGGTTTATCCACAATGTACTAGTAGCTTTTATCTACA
1 C-GATGAGTGGTTTATCCACAATGTACTAGCAGCTTTTATCTACA
* * *
46513098 TCGATGAGTGGTTTATCTACAAGGTACTAGCAACTTTTATCTACA
1 -CGATGAGTGGTTTATCCACAATGTACTAGCAGCTTTTATCTACA
46513143 CCGATGAGTGGTTTAT
1 -CGATGAGTGGTTTAT
46513159 TGTAATACCC
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.01
45 90 0.98
46 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (44 bp):
CGATGAGTGGTTTATCCACAATGTACTAGCAGCTTTTATCTACA
Found at i:46519128 original size:27 final size:27
Alignment explanation
Indices: 46519091--46519142 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
46519081 AAGTGATACA
*
46519091 TTTAGAATTTGCCACAAAGGCTATTCT
1 TTTAGAATTTGCCACAAAGACTATTCT
* * *
46519118 TTTAGAGTTTGTCACTAAGACTATT
1 TTTAGAATTTGCCACAAAGACTATT
46519143 TTTAGCTGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (27 bp):
TTTAGAATTTGCCACAAAGACTATTCT
Found at i:46519890 original size:64 final size:64
Alignment explanation
Indices: 46519788--46519916 Score: 188
Period size: 64 Copynumber: 2.0 Consensus size: 64
46519778 TTCATATACA
* *
46519788 ATTTAATGCAAATCTTCATACTTATATCTTACTATTCATGCACCTCTTATAGAGTTATTCTTTC
1 ATTTAATGCAAACCTTCATACTTATATCTTACTATTCATGCACCTCTTACAGAGTTATTCTTTC
* * * *
46519852 ATTTAATGCAAAGCCTT-ATACTTATATCTTATTGTTCATGCATCTTTTACAGAGTTATTCTTTC
1 ATTTAATGCAAA-CCTTCATACTTATATCTTACTATTCATGCACCTCTTACAGAGTTATTCTTTC
46519916 A
1 A
46519917 GAATTTAACA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 55 0.95
65 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.46
Consensus pattern (64 bp):
ATTTAATGCAAACCTTCATACTTATATCTTACTATTCATGCACCTCTTACAGAGTTATTCTTTC
Found at i:46522813 original size:45 final size:44
Alignment explanation
Indices: 46522764--46522931 Score: 147
Period size: 45 Copynumber: 3.7 Consensus size: 44
46522754 ATCCATACCA
* * *
46522764 ATGAGTGGTTTATCTGTAACATACTAGCAGCTTTTATTTTCACCG
1 ATGAGTGGTTTATC-ATAACATACTAGCAGCTTTTATATGCACCG
* ** * **
46522809 ATGAGTGATTTATCCATAATTTACTAGCAGATTTTATATGCATTG
1 ATGAGTGGTTTAT-CATAACATACTAGCAGCTTTTATATGCACCG
* * * * *
46522854 ATGAATGGTTTATGCATAACGTACTAGCAACTTTTATCTGCACCA
1 ATGAGTGGTTTAT-CATAACATACTAGCAGCTTTTATATGCACCG
***
46522899 ATGAGTGGTTTATCAATATTGTACTAGCAGCTT
1 ATGAGTGGTTTATC-ATAACATACTAGCAGCTT
46522932 GTCTTCAAAA
Statistics
Matches: 97, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
44 1 0.01
45 95 0.98
46 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (44 bp):
ATGAGTGGTTTATCATAACATACTAGCAGCTTTTATATGCACCG
Found at i:46523215 original size:67 final size:67
Alignment explanation
Indices: 46523090--46523215 Score: 173
Period size: 67 Copynumber: 1.9 Consensus size: 67
46523080 TGGAGTTAGG
*
46523090 ATTAGGATATTAAAAATAGGGCATAATATGTAAAACCATAGCTCAACTATGGTCACATAGAGAGA
1 ATTAGGATATTAAAAATAGGGCATAATATGTAAAACCATAGCTCAACTATGGACACATAGAGAGA
46523155 TT
66 TT
* * * * * *
46523157 ATTAGGATATTAAACATGGGGCATTATGTGTAAGACCATAGCTCGACTAT-GACAACATA
1 ATTAGGATATTAAAAATAGGGCATAATATGTAAAACCATAGCTCAACTATGGAC-ACATA
46523216 TGGAGTTTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 2 0.04
67 49 0.96
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (67 bp):
ATTAGGATATTAAAAATAGGGCATAATATGTAAAACCATAGCTCAACTATGGACACATAGAGAGA
TT
Found at i:46527756 original size:16 final size:16
Alignment explanation
Indices: 46527735--46527765 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46527725 GATATTTTAA
46527735 TATATTATATTAATAT
1 TATATTATATTAATAT
*
46527751 TATATTATGTTAATA
1 TATATTATATTAATA
46527766 AAATAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:46527862 original size:12 final size:12
Alignment explanation
Indices: 46527845--46527875 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
46527835 GAAGCAGGGG
46527845 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
46527857 AGAAAAAGGGAA
1 AGAAAAAGAGAA
46527869 AGAAAAA
1 AGAAAAA
46527876 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:46540206 original size:67 final size:67
Alignment explanation
Indices: 46540092--46540413 Score: 378
Period size: 67 Copynumber: 4.8 Consensus size: 67
46540082 GGTTGTATTA
* *
46540092 GGTATAATGTGTAATACCATAGCTCGACTAT-AGCAACATAGAGAGTCTGCCAGGACATTAAACA
1 GGTATGATGTGTAAGACCATAGCTCGACTATGA-CAACATAGAGAGTCTGCCAGGACATTAAACA
46540156 TGG
65 TGG
* * * * *
46540159 GGTGTGATGTGTAAGACCATAGCTCAACTATGGCAACATAGGGAGTCTGCCAGGCCATTAAACAT
1 GGTATGATGTGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCTGCCAGGACATTAAACAT
46540224 GG
66 GG
* * * * *
46540226 AGTATGATGTGTAAAACCATAGCTCGATTATGACAACATCGAGAGTCTGCTAGGACATTAAACAT
1 GGTATGATGTGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCTGCCAGGACATTAAACAT
46540291 GG
66 GG
* * * * *** * *
46540293 TGTATGATGTGTAAGACCATAGCTCG-GTATGACCATATAGAGAGTCCATCAGAATATTAAACAT
1 GGTATGATGTGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCTGCCAGGACATTAAACAT
46540357 GG
66 GG
* * * * * *
46540359 GGTATGATGTGTAAGACCATAGTTCGATTATGACAGCACATAGAGTCTACCAGGA
1 GGTATGATGTGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCTGCCAGGA
46540414 AAATAAATGC
Statistics
Matches: 213, Mismatches: 40, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
66 54 0.25
67 159 0.75
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (67 bp):
GGTATGATGTGTAAGACCATAGCTCGACTATGACAACATAGAGAGTCTGCCAGGACATTAAACAT
GG
Found at i:46542435 original size:27 final size:27
Alignment explanation
Indices: 46542405--46542654 Score: 356
Period size: 27 Copynumber: 9.3 Consensus size: 27
46542395 GGGGCAAAAT
* * *
46542405 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
46542432 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
46542459 GGCATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
46542486 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
46542513 GGCATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
46542540 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
46542567 GGCATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
46542594 GGTAATTCTACCCTACATGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
46542621 GATAATTCTACCCTACATGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
46542648 GATAATT
1 GGTAATT
46542655 TCACAAATCA
Statistics
Matches: 200, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 200 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:46542670 original size:81 final size:81
Alignment explanation
Indices: 46542406--46542683 Score: 339
Period size: 81 Copynumber: 3.4 Consensus size: 81
46542396 GGGCAAAATG
* * * * * *
46542406 GTAATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGCATTTCTAC
1 GTAATTTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTAC
46542470 CCTACAAGGGTATTTC
66 CCTACAAGGGTATTTC
* *
46542486 GGTAA-TTCTACCCTACAGGGGTATTTCGGCATTTCTACCCTACAAGGGTATTTCGGTAATTCTA
1 -GTAATTTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTA
*
46542550 CCCTACAGGGGTATTTC
65 CCCTACAAGGGTATTTC
** * * *
46542567 GGCATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACATGGGTATTTCGATAATTCTAC
1 GTAATTTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTAC
*
46542632 CCTACATGGGTATTTC
66 CCTACAAGGGTATTTC
** *
46542648 GATAATTTC-A-CAAATCAGGGGTATTTTGGTAATTCT
1 G-TAATTTCTACCCTA-CAGGGGTATTTCGGTAATTCT
46542684 GTAAACCAAG
Statistics
Matches: 170, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
80 6 0.04
81 159 0.94
82 5 0.03
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (81 bp):
GTAATTTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTAC
CCTACAAGGGTATTTC
Found at i:46542683 original size:54 final size:54
Alignment explanation
Indices: 46542409--46542654 Score: 413
Period size: 54 Copynumber: 4.6 Consensus size: 54
46542399 CAAAATGGTA
* *
46542409 ATTT-TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGC
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGC
46542462 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGC
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGC
46542516 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGC
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGC
* **
46542570 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACATGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGC
* * *
46542624 AATTCTACCCTACATGGGTATTTCGATAATT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATT
46542655 TCACAAATCA
Statistics
Matches: 184, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 4 0.02
54 180 0.98
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (54 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGC
Found at i:46542717 original size:54 final size:54
Alignment explanation
Indices: 46542639--46542751 Score: 127
Period size: 54 Copynumber: 2.1 Consensus size: 54
46542629 TACCCTACAT
* * *** *
46542639 GGGTATTTCGATAATTTCACAAATCAGGGGTATTTTGGTAATTCTGTAAACCAA
1 GGGTATTTCAATAATTTCACAAATCAAGGGTAAAATGGTAATTCTATAAACCAA
*** * *
46542693 GGGTATTTCAATAATTTTGTAAATCAAGGGTAAAATGGTAATTCTATAAATCGA
1 GGGTATTTCAATAATTTCACAAATCAAGGGTAAAATGGTAATTCTATAAACCAA
46542747 GGGTA
1 GGGTA
46542752 AAATGGTAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.35
Consensus pattern (54 bp):
GGGTATTTCAATAATTTCACAAATCAAGGGTAAAATGGTAATTCTATAAACCAA
Found at i:46542734 original size:27 final size:27
Alignment explanation
Indices: 46542712--46542820 Score: 157
Period size: 27 Copynumber: 4.0 Consensus size: 27
46542702 AATAATTTTG
46542712 TAAATCAAGGGTAAAATGGTAATTCTA
1 TAAATCAAGGGTAAAATGGTAATTCTA
*
46542739 TAAATCGAGGGTAAAATGGTAATTCTA
1 TAAATCAAGGGTAAAATGGTAATTCTA
* * * *
46542766 TAAATCGAGAGTAAAACGGTAATTCTG
1 TAAATCAAGGGTAAAATGGTAATTCTA
46542793 TAAAT-AGAGGGTAAAATGGTAATTCTA
1 TAAATCA-AGGGTAAAATGGTAATTCTA
46542820 T
1 T
46542821 CTTACAGGAG
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.29
Consensus pattern (27 bp):
TAAATCAAGGGTAAAATGGTAATTCTA
Found at i:46542832 original size:54 final size:54
Alignment explanation
Indices: 46542712--46542820 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
46542702 AATAATTTTG
* * * *
46542712 TAAATCAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGAGTAAAACGGTAATTCTATAAATAGAGGGTAAAATGGTAATTCTA
*
46542766 TAAATCGAGAGTAAAACGGTAATTCTGTAAATAGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGAGTAAAACGGTAATTCTATAAATAGAGGGTAAAATGGTAATTCTA
46542820 T
1 T
46542821 CTTACAGGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.29
Consensus pattern (54 bp):
TAAATCGAGAGTAAAACGGTAATTCTATAAATAGAGGGTAAAATGGTAATTCTA
Found at i:46542860 original size:27 final size:27
Alignment explanation
Indices: 46542830--46542979 Score: 178
Period size: 27 Copynumber: 5.6 Consensus size: 27
46542820 TCTTACAGGA
46542830 GTATTTCAGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * *
46542857 GTATTTTAGTAATTTTGCAAATTGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
46542884 GTATTTC-GATAATTTTACAAATCGAGG
1 GTATTTCAG-TAATTTTACAAATCGAGG
* ** *
46542911 ATATTTGGGTAATTTTATAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * *
46542938 GTCCTTT-GGTAATTTTACAAGTCGAGG
1 GT-ATTTCAGTAATTTTACAAATCGAGG
46542965 GTATTTCAGTAATTT
1 GTATTTCAGTAATTT
46542980 GGTAAACTAA
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.04
27 96 0.92
28 4 0.04
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.41
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAATCGAGG
Found at i:46549411 original size:19 final size:20
Alignment explanation
Indices: 46549373--46549411 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
46549363 TTTTCTTTTA
**
46549373 CTAAAAAATTAAAATTAATT
1 CTAAAAAATTAAAAGAAATT
46549393 CTAAAAAA-TAAAAGAAATT
1 CTAAAAAATTAAAAGAAATT
46549412 AAAAAGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
CTAAAAAATTAAAAGAAATT
Found at i:46553212 original size:21 final size:19
Alignment explanation
Indices: 46553178--46553239 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 19
46553168 TAAGTTATAT
46553178 ATAATAATATAATATGAATAAA
1 ATAATAA-A-AATAT-AATAAA
46553200 AT-ATAAGGAAATATAATATAAA
1 ATAATAA--AAATAT-A-ATAAA
46553222 ATAATAAAAATATAATAA
1 ATAATAAAAATATAATAA
46553240 GTAATTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 16 0.46
22 10 0.29
23 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATATAATAAA
Found at i:46553289 original size:21 final size:22
Alignment explanation
Indices: 46553263--46553304 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
46553253 AAAATATAGT
*
46553263 AAAATAAATAGTATA-AAAAAC
1 AAAATAAATAATATATAAAAAC
46553284 AAAATAAATAATATATAAAAA
1 AAAATAAATAATATATAAAAA
46553305 TATAAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAATAAATAATATATAAAAAC
Found at i:46553654 original size:14 final size:14
Alignment explanation
Indices: 46553624--46553688 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
46553614 CAATTTTATA
46553624 AAAATATAT-AAA-
1 AAAATATATAAAAT
*
46553636 GAAATATATAAAAT
1 AAAATATATAAAAT
*
46553650 AAAATATATAATAT
1 AAAATATATAAAAT
* * *
46553664 AATATAATTTATAGAT
1 AAAAT-ATATA-AAAT
46553680 AAAATATAT
1 AAAATATAT
46553689 GATAAAATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
12 8 0.20
13 3 0.07
14 16 0.39
15 7 0.17
16 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
AAAATATATAAAAT
Found at i:46576111 original size:21 final size:19
Alignment explanation
Indices: 46576077--46576138 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 19
46576067 TAAGTTATAT
46576077 ATAATAATATAATATGAATAAA
1 ATAATAA-A-AATAT-AATAAA
46576099 AT-ATAAGGAAATATAATATAAA
1 ATAATAA--AAATAT-A-ATAAA
46576121 ATAATAAAAATATAATAA
1 ATAATAAAAATATAATAA
46576139 GTAATTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 16 0.46
22 10 0.29
23 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATATAATAAA
Found at i:46576192 original size:23 final size:23
Alignment explanation
Indices: 46576162--46576205 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
46576152 AAAATATAGT
46576162 AAAATAAATAATATAAAAAAAAC
1 AAAATAAATAATATAAAAAAAAC
*
46576185 AAAATAAATAATATATAAAAA
1 AAAATAAATAATATAAAAAAA
46576206 TATAAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (23 bp):
AAAATAAATAATATAAAAAAAAC
Found at i:46580279 original size:13 final size:14
Alignment explanation
Indices: 46580255--46580283 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
46580245 AGTAGAAAAC
46580255 GAAAATAAAAGAAA
1 GAAAATAAAAGAAA
46580269 GAAAA-AAAAGAAA
1 GAAAATAAAAGAAA
46580282 GA
1 GA
46580284 GGAATGAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (14 bp):
GAAAATAAAAGAAA
Found at i:46582516 original size:56 final size:55
Alignment explanation
Indices: 46582453--46582620 Score: 178
Period size: 56 Copynumber: 3.0 Consensus size: 55
46582443 GACCATGGCA
*
46582453 TCGATATATGTGTTCGAGTAAGACCACATTTAATACATTGGGATCGATATGTGAT
1 TCGATATATGTGTTCGAGTAAGACCACATTTAATACATTGGCATCGATATGTGAT
* **
46582508 TCTGATATATGTGTGT-GAGTATGACCACATTTAATATGTTGGCATCGATATGTGAT
1 TC-GATATATGTGT-TCGAGTAAGACCACATTTAATACATTGGCATCGATATGTGAT
* * * * *** *
46582564 TCCATTATATGTGTGCGAGTAATACC-CTATCTGGGACAGTGGCATCGATATGTGAT
1 TCGA-TATATGTGTTCGAGTAAGACCAC-ATTTAATACATTGGCATCGATATGTGAT
46582620 T
1 T
46582621 ACATGTAAGA
Statistics
Matches: 93, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
55 4 0.04
56 88 0.95
57 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (55 bp):
TCGATATATGTGTTCGAGTAAGACCACATTTAATACATTGGCATCGATATGTGAT
Found at i:46591371 original size:56 final size:56
Alignment explanation
Indices: 46591285--46591416 Score: 201
Period size: 56 Copynumber: 2.4 Consensus size: 56
46591275 ACCATGGCAT
* * *
46591285 CAATATATGTGTACGAGTAAGACCACGTTTAATACGTTGGGATCGATGTGTGATTC
1 CAATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
* * *
46591341 CAATATATGTGTGCGAGTATGTCCACGTTTAATATGTTGGCATCGATATGTGATTC
1 CAATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
*
46591397 CAATATATGTGTGCAAGTAA
1 CAATATATGTGTGCGAGTAA
46591417 TACCCTATCT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (56 bp):
CAATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
Found at i:46592743 original size:2 final size:2
Alignment explanation
Indices: 46592732--46592769 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
46592722 CTTACTTATG
* *
46592732 TA TA -A TA TA TA TG TA TA TA TA TA TA TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46592770 GAATGCTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:46595120 original size:23 final size:22
Alignment explanation
Indices: 46595082--46595137 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
46595072 TAACTATATA
* *
46595082 TTTTTATTTCTGTTTTT-TTCTAC
1 TTTTTATTTTTATTTTTATT-T-C
46595105 TTTTTATTTTTATTTTTATTTC
1 TTTTTATTTTTATTTTTATTTC
*
46595127 ATTTTATTTTT
1 TTTTTATTTTT
46595138 TCTTTGCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.38
23 16 0.55
24 2 0.07
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTATTTTTATTTTTATTTC
Found at i:46597695 original size:18 final size:17
Alignment explanation
Indices: 46597665--46597699 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
46597655 GAGAAAGGAG
*
46597665 TTTTAGCTCAAAAATCT
1 TTTTAGCTAAAAAATCT
46597682 TTTTCAGCTAAAAAATCT
1 TTTT-AGCTAAAAAATCT
46597700 GACTTAATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (17 bp):
TTTTAGCTAAAAAATCT
Found at i:46598933 original size:16 final size:16
Alignment explanation
Indices: 46598912--46598943 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46598902 AGTTAATTAA
46598912 ATTAGTTAATTTTAGT
1 ATTAGTTAATTTTAGT
46598928 ATTAGTTAATTTTAGT
1 ATTAGTTAATTTTAGT
46598944 TTCAATCAAT
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:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (16 bp):
ATTAGTTAATTTTAGT
Found at i:46605487 original size:20 final size:20
Alignment explanation
Indices: 46605462--46605514 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 20
46605452 TATTATCAAA
*
46605462 TCAATATTTTATTCTAAATT
1 TCAATATTTTATTCTAAATC
46605482 TCAATAATTTTTTATTCTAAATC
1 TCAAT-A--TTTTATTCTAAATC
46605505 TCAATATTTT
1 TCAATATTTT
46605515 CATCTTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 9 0.31
21 1 0.03
22 1 0.03
23 18 0.62
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (20 bp):
TCAATATTTTATTCTAAATC
Found at i:46605513 original size:22 final size:23
Alignment explanation
Indices: 46605468--46605514 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
46605458 CAAATCAATA
*
46605468 TTTTATTCTAAATTTCAATAATT
1 TTTTATTCTAAATCTCAATAATT
46605491 TTTTATTCTAAATCTCAAT-ATT
1 TTTTATTCTAAATCTCAATAATT
46605513 TT
1 TT
46605515 CATCTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTATTCTAAATCTCAATAATT
Found at i:46609329 original size:18 final size:18
Alignment explanation
Indices: 46609306--46609371 Score: 123
Period size: 18 Copynumber: 3.7 Consensus size: 18
46609296 AAAATGTGAG
*
46609306 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
46609324 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
46609342 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
46609360 AAATGATGTTCA
1 AAATGATGTTCA
46609372 AATTGATGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:46611581 original size:13 final size:13
Alignment explanation
Indices: 46611560--46611621 Score: 88
Period size: 13 Copynumber: 4.8 Consensus size: 13
46611550 ACACCTAAAA
46611560 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
46611573 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
46611586 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
*
46611599 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
46611612 TTTTCAAAAG
1 TTTTCAAAAG
46611622 TTTGCCAAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:46614177 original size:27 final size:27
Alignment explanation
Indices: 46614146--46614221 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
46614136 AATAAGTATA
*
46614146 AAATTAACTGAATTAACCGAATTAATC
1 AAATTAACTGAATTAACCGAATTAACC
* * *
46614173 GAATTAACTGAATTACCCGAATTACCC
1 AAATTAACTGAATTAACCGAATTAACC
* *
46614200 AAATTAACCGAATTAGCCGAAT
1 AAATTAACTGAATTAACCGAAT
46614222 CATTTGTATA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (27 bp):
AAATTAACTGAATTAACCGAATTAACC
Found at i:46614194 original size:9 final size:9
Alignment explanation
Indices: 46614147--46614221 Score: 87
Period size: 9 Copynumber: 8.3 Consensus size: 9
46614137 ATAAGTATAA
*
46614147 AATTAACTG
1 AATTAACCG
46614156 AATTAACCG
1 AATTAACCG
*
46614165 AATTAATCG
1 AATTAACCG
*
46614174 AATTAACTG
1 AATTAACCG
*
46614183 AATTACCCG
1 AATTAACCG
* *
46614192 AATTACCCA
1 AATTAACCG
46614201 AATTAACCG
1 AATTAACCG
*
46614210 AATTAGCCG
1 AATTAACCG
46614219 AAT
1 AAT
46614222 CATTTGTATA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 56 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:46614258 original size:5 final size:6
Alignment explanation
Indices: 46614243--46614283 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
46614233 AATTATATGT
46614243 TTTTTA TTTTTA TTTTTA TTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTT--A TTTTTA TTTTTA TTT
46614284 ATTAAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 27 0.82
8 6 0.18
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:46614271 original size:14 final size:13
Alignment explanation
Indices: 46614243--46614280 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
46614233 AATTATATGT
46614243 TTTTTATTTTT-A
1 TTTTTATTTTTAA
46614255 TTTTTATTTTTAGA
1 TTTTTATTTTTA-A
46614269 TTTTTATTTTTA
1 TTTTTATTTTTA
46614281 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.46
14 13 0.54
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTTATTTTTAA
Found at i:46634728 original size:29 final size:29
Alignment explanation
Indices: 46634693--46634831 Score: 147
Period size: 29 Copynumber: 4.8 Consensus size: 29
46634683 TGAATATAAG
* *
46634693 GTGATTTGGGCCTAATGGGCCATATAAAG
1 GTGAATTGGGCCTAATGGGCCATATAAAT
* *
46634722 GTGATTTGGGCCTAATGGGCCATATGAAT
1 GTGAATTGGGCCTAATGGGCCATATAAAT
* * * * *
46634751 ATGAATTGGGCCTGATGGGCTATGTGAAT
1 GTGAATTGGGCCTAATGGGCCATATAAAT
* *
46634780 GTGAATTGGGCCTGATGAGCCATATAAAT
1 GTGAATTGGGCCTAATGGGCCATATAAAT
*
46634809 GAG-ATTGGG-CTAAGTGGGCCATA
1 GTGAATTGGGCCTAA-TGGGCCATA
46634832 CGCATGTATG
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
27 3 0.03
28 14 0.15
29 77 0.82
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (29 bp):
GTGAATTGGGCCTAATGGGCCATATAAAT
Found at i:46646725 original size:24 final size:25
Alignment explanation
Indices: 46646593--46646749 Score: 87
Period size: 24 Copynumber: 6.4 Consensus size: 25
46646583 TCTAGGCTGT
*
46646593 ATAA-CAGGAAGCTTATA-AGAGCC-
1 ATAATCAGGAAGCTCA-AGAGAGCCA
* * *
46646616 ACAATCAGGAAGCTCATGCGAGCCA
1 ATAATCAGGAAGCTCAAGAGAGCCA
*
46646641 ATAAT-AGGTAA-CTTCGA-AGAGCCA
1 ATAATCAGG-AAGC-TCAAGAGAGCCA
* ** * *
46646665 TTAATCAGGAAGCTCCGGATAGTC-
1 ATAATCAGGAAGCTCAAGAGAGCCA
* * *
46646689 ATATATCGGGAAGTTCAAGCGAGCCA
1 ATA-ATCAGGAAGCTCAAGAGAGCCA
*
46646715 ATAA-CAGGAAGCTCCAGAGAGCCA
1 ATAATCAGGAAGCTCAAGAGAGCCA
*
46646739 TTAATCAGGAA
1 ATAATCAGGAA
46646750 AATCACAAAG
Statistics
Matches: 97, Mismatches: 26, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
23 3 0.03
24 54 0.56
25 37 0.38
26 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (25 bp):
ATAATCAGGAAGCTCAAGAGAGCCA
Found at i:46646749 original size:25 final size:25
Alignment explanation
Indices: 46646658--46646749 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 25
46646648 GTAACTTCGA
*
46646658 AGAGCCATTAATCAGGAAGCTCCGG
1 AGAGCCATTAATCAGGAAGCTCCAG
* * * * *
46646683 ATAGTCA-TATATCGGGAAGTTCAAG
1 AGAGCCATTA-ATCAGGAAGCTCCAG
* *
46646708 CGAGCCAATAA-CAGGAAGCTCCAG
1 AGAGCCATTAATCAGGAAGCTCCAG
46646732 AGAGCCATTAATCAGGAA
1 AGAGCCATTAATCAGGAA
46646750 AATCACAAAG
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
24 21 0.42
25 27 0.54
26 2 0.04
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (25 bp):
AGAGCCATTAATCAGGAAGCTCCAG
Found at i:46646763 original size:26 final size:26
Alignment explanation
Indices: 46646732--46646791 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
46646722 GAAGCTCCAG
46646732 AGAGCCATTAATCAGGAAA-ATCACAA
1 AGAGCCATTAAT-AGGAAAGATCACAA
* * * *
46646758 AGAGCCTTTAATTGGAAAGCTCACGA
1 AGAGCCATTAATAGGAAAGATCACAA
46646784 AGAGCCAT
1 AGAGCCAT
46646792 ATATCGAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATAGGAAAGATCACAA
Found at i:46647756 original size:12 final size:12
Alignment explanation
Indices: 46647739--46647764 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46647729 TAATTAAAAT
46647739 AAATTAAAAGCC
1 AAATTAAAAGCC
46647751 AAATTAAAAGCC
1 AAATTAAAAGCC
46647763 AA
1 AA
46647765 TTTTTGTCCA
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:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (12 bp):
AAATTAAAAGCC
Found at i:46648483 original size:22 final size:22
Alignment explanation
Indices: 46648457--46648530 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
46648447 AATGCTATAT
46648457 TATTGAAATGAAATGTGAATGC
1 TATTGAAATGAAATGTGAATGC
**
46648479 TATTGATTGTGTTAAATGCT-ATAT--
1 TATTGA-AATG--AAATG-TGA-ATGC
46648503 TATTGAAATGAAATGTGAATGC
1 TATTGAAATGAAATGTGAATGC
46648525 TATTGA
1 TATTGA
46648531 GTACAATACT
Statistics
Matches: 40, Mismatches: 4, Indels: 16
0.67 0.07 0.27
Matches are distributed among these distances:
20 3 0.08
21 6 0.15
22 12 0.30
23 4 0.10
24 6 0.15
25 6 0.15
26 3 0.08
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.39
Consensus pattern (22 bp):
TATTGAAATGAAATGTGAATGC
Found at i:46648486 original size:46 final size:46
Alignment explanation
Indices: 46648436--46648530 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
46648426 TTAATTGATA
46648436 TGATTGTGGTAAATGCTATATTATTGAAATGAAATGTGAATGCTAT
1 TGATTGTGGTAAATGCTATATTATTGAAATGAAATGTGAATGCTAT
*
46648482 TGATTGTGTTAAATGCTATATTATTGAAATGAAATGTGAATGCTAT
1 TGATTGTGGTAAATGCTATATTATTGAAATGAAATGTGAATGCTAT
46648528 TGA
1 TGA
46648531 GTACAATACT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (46 bp):
TGATTGTGGTAAATGCTATATTATTGAAATGAAATGTGAATGCTAT
Found at i:46648742 original size:42 final size:42
Alignment explanation
Indices: 46648632--46648753 Score: 156
Period size: 41 Copynumber: 2.9 Consensus size: 42
46648622 TTAGGGTTAC
** *
46648632 TGAGATTTCGTGTAAGACCATATTTGGGATATGGCATCGAGA
1 TGAGATTTCGTGTAAGACCATAACTGGGATATAGCATCGAGA
* *
46648674 TGAAATTTC-TGTAAGACCATAACTGGGATATAGCATCGATA
1 TGAGATTTCGTGTAAGACCATAACTGGGATATAGCATCGAGA
* * *
46648715 TGAGACTTCGTGTAAGACCATAGCTGGGCTATTAGCATC
1 TGAGATTTCGTGTAAGACCATAACTGGGATA-TAGCATC
46648754 AATACACGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
41 35 0.51
42 27 0.39
43 7 0.10
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (42 bp):
TGAGATTTCGTGTAAGACCATAACTGGGATATAGCATCGAGA
Found at i:46650671 original size:28 final size:28
Alignment explanation
Indices: 46650639--46650695 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
46650629 TAAATTTGAG
* *
46650639 TAGAAATTTATGTCTCGGTTTTTAATGT
1 TAGAAATTTATGTCTCGATTTTGAATGT
46650667 TAGAAATTTATGTCTCGATTTTGAATGT
1 TAGAAATTTATGTCTCGATTTTGAATGT
46650695 T
1 T
46650696 TGCTGAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.07, G:0.18, T:0.49
Consensus pattern (28 bp):
TAGAAATTTATGTCTCGATTTTGAATGT
Found at i:46653964 original size:42 final size:44
Alignment explanation
Indices: 46653917--46654014 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
46653907 TCCCAGACAA
* * *
46653917 GGTCTTACAC-AAAATCA-AA-TGCGATGGCAATGTCCCAAATGT
1 GGTCTTACACGAAAATCATAAGT-CGATGCCAACGCCCCAAATGT
* *
46653959 GGTCTTACACGTAAATCATAAGTCGATGCCAACGCCCCAGATGT
1 GGTCTTACACGAAAATCATAAGTCGATGCCAACGCCCCAAATGT
46654003 GGTCTTACACGA
1 GGTCTTACACGA
46654015 GAACACTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 10 0.21
43 6 0.13
44 30 0.64
45 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (44 bp):
GGTCTTACACGAAAATCATAAGTCGATGCCAACGCCCCAAATGT
Found at i:46662807 original size:21 final size:23
Alignment explanation
Indices: 46662781--46662830 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
46662771 TGAATTTTTT
46662781 ACACATTA-TTGCTTCAGTCG-A
1 ACACATTAGTTGCTTCAGTCGAA
*
46662802 ACACA-TAGTTGCTTTAGTCGAA
1 ACACATTAGTTGCTTCAGTCGAA
46662824 ACACATT
1 ACACATT
46662831 CTCGTACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 16 0.64
22 6 0.24
23 1 0.04
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (23 bp):
ACACATTAGTTGCTTCAGTCGAA
Found at i:46666156 original size:16 final size:17
Alignment explanation
Indices: 46666128--46666159 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
46666118 GATTCAATGA
46666128 GTCTTTATGGGGTTTAG
1 GTCTTTATGGGGTTTAG
46666145 GTCTTT-TGGGGTTTA
1 GTCTTTATGGGGTTTA
46666160 TGTAATGGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.09, C:0.06, G:0.34, T:0.50
Consensus pattern (17 bp):
GTCTTTATGGGGTTTAG
Found at i:46668799 original size:29 final size:30
Alignment explanation
Indices: 46668766--46668824 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
46668756 AATTTCGAGC
* * *
46668766 TTAA-GGGTAAAATGGTCAGTTTGCCAAAG
1 TTAAGGGGCAAAATAGTCAGTTTACCAAAG
*
46668795 TTAAGGGGCAAAATAGTCATTTTACCAAAG
1 TTAAGGGGCAAAATAGTCAGTTTACCAAAG
46668825 ATGTAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (30 bp):
TTAAGGGGCAAAATAGTCAGTTTACCAAAG
Found at i:46669295 original size:46 final size:45
Alignment explanation
Indices: 46669151--46669321 Score: 157
Period size: 46 Copynumber: 3.7 Consensus size: 45
46669141 TGTGTGAGCT
* **
46669151 AGTGTAAGACATGTCTGGGACATGTATCGGCCAT-A-TTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CATGAGACAT-A-AGCC
* * **** *
46669197 AGTGTAAGAACATGTCTGGGAAATGGCATTGGCATTGAGACGGGTGCT
1 AGTGTAAG-ACATGTCTGGGACAT-GCATCGGCA-TGAGACATAAGCC
*
46669245 AGTGTAAGACATGTTTGGGACATGCATCGGCATCGAGACATAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCAT-GAGACATAAGCC
*
46669291 AGTGTAAGACATGTTTGGGACATGCATCGGC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC
46669322 TAAACATTGT
Statistics
Matches: 101, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
45 1 0.01
46 54 0.53
47 29 0.29
48 16 0.16
49 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATGAGACATAAGCC
Found at i:46671947 original size:49 final size:48
Alignment explanation
Indices: 46671886--46672059 Score: 213
Period size: 49 Copynumber: 3.5 Consensus size: 48
46671876 TGAGGTCACG
*
46671886 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATTATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCG-ATAATTGGTCGCA
* * * * * *
46671935 TGTGTAGTACTAAGTGCAAGCTACTATGCGTACCCGATAACTTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCGATAA-TTGGTCGCA
**
46671985 TGTACAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GATAATTGGTCGCA
**
46672034 TGTGTAGTACTAAGTATAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
46672060 TGCATATCAG
Statistics
Matches: 103, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
49 62 0.60
50 41 0.40
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (48 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGATAATTGGTCGCA
Found at i:46672057 original size:99 final size:99
Alignment explanation
Indices: 46671881--46672062 Score: 301
Period size: 99 Copynumber: 1.8 Consensus size: 99
46671871 TATTGTGAGG
** *
46671881 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGAATTATTGGTCGCATGTGTAGTACT
1 TCACGTGTACAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACT
*
46671946 AAGTGCAAGCTACTATGCGTACCCGATAACTTGA
66 AAGTACAAGCTACTATGCGTACCCGATAACTTGA
*
46671980 TCACGTGTACAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTACAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACT
* *
46672045 AAGTATAGGCTACTATGC
66 AAGTACAAGCTACTATGC
46672063 ATATCAGATA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 76 1.00
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (99 bp):
TCACGTGTACAGTACTAAGTGCAGGCTACTACGTGTACCGAATAATTGGTCGCATGTGTAGTACT
AAGTACAAGCTACTATGCGTACCCGATAACTTGA
Found at i:46691242 original size:46 final size:45
Alignment explanation
Indices: 46691189--46691361 Score: 147
Period size: 46 Copynumber: 3.8 Consensus size: 45
46691179 TATTTGGGCA
*
46691189 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACG
* * * *
46691235 TCCGAACTCATTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAC---G
* * * *
46691280 CATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATATGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-GGAACG
* *
46691328 -CCCAAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
46691362 GGGGCGGGTT
Statistics
Matches: 100, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
45 5 0.05
46 54 0.54
47 26 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACG
Found at i:46691344 original size:93 final size:93
Alignment explanation
Indices: 46691185--46691356 Score: 247
Period size: 93 Copynumber: 1.8 Consensus size: 93
46691175 TGGATATTTG
* * *
46691185 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGTCCCAACTCATTGAG
46691250 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * * * *
46691278 GGCATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATATGAATG-CCCAAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGTCCCAA-CTCATTGA
*
46691342 GTTGAGTCTGAGTTC
65 GTTGAGTCCGAGTTC
46691357 ACTTAGGGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
92 4 0.06
93 65 0.94
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGTCCCAACTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:46695809 original size:49 final size:50
Alignment explanation
Indices: 46695736--46695874 Score: 183
Period size: 49 Copynumber: 2.8 Consensus size: 50
46695726 AGATGAAGCT
* * *
46695736 ATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCG-GC-CAAC
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTCAAC
* *
46695784 AGTCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTCACC
1 A-TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTCAAC
** *
46695835 ATCTAATACACGTAGTAGCCTGCACTTAGTACTACACACG
1 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACG
46695875 TGATCACAGT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
48 1 0.01
49 38 0.47
50 37 0.46
51 4 0.05
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (50 bp):
ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTCAAC
Found at i:46695866 original size:50 final size:50
Alignment explanation
Indices: 46695746--46695877 Score: 178
Period size: 50 Copynumber: 2.7 Consensus size: 50
46695736 ATCTGGTACG
* * * **
46695746 CATAGTAGCCTGCACTTAGTACTACACATGCG-GCCAACAGTCTGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGACCCAACAGTCTAATACA
*
46695795 CATAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCA-TCTAATACA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGACC-CAACAGTCTAATACA
*
46695845 CGTAGTAGCCTGCACTTAGTACTACACACGTGA
1 CATAGTAGCCTGCACTTAGTACTACACACGTGA
46695878 TCACAGTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
49 30 0.41
50 40 0.54
51 4 0.05
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACACGTGACCCAACAGTCTAATACA
Found at i:46697888 original size:42 final size:43
Alignment explanation
Indices: 46697786--46697899 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 43
46697776 TATAATGCCA
* * * *
46697786 ATGTCCCAGACGTGGTCTTACATGTAATTCAGTATCGATGCCT
1 ATGTCCCAGACATGGTCTTACATGTAAATCAGTATCGATACCG
* * * * *
46697829 TTTTCCCAGATAGGGTCTTATATG-AAATCAG-ATACGATACCG
1 ATGTCCCAGACATGGTCTTACATGTAAATCAGTAT-CGATACCG
*
46697871 ATGTCCCAGACATGGTCTTACACGTAAAT
1 ATGTCCCAGACATGGTCTTACATGTAAAT
46697900 TTCAAATCGA
Statistics
Matches: 54, Mismatches: 15, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
41 2 0.04
42 30 0.56
43 22 0.41
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
ATGTCCCAGACATGGTCTTACATGTAAATCAGTATCGATACCG
Found at i:46700368 original size:7 final size:7
Alignment explanation
Indices: 46700356--46700381 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
46700346 TTCATTTCAT
46700356 TTTACAG
1 TTTACAG
46700363 TTTACAG
1 TTTACAG
46700370 TTTACAG
1 TTTACAG
46700377 TTTAC
1 TTTAC
46700382 TACAACATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (7 bp):
TTTACAG
Found at i:46708464 original size:46 final size:46
Alignment explanation
Indices: 46708406--46708527 Score: 147
Period size: 48 Copynumber: 2.6 Consensus size: 46
46708396 TTAACATGTA
*
46708406 TAACCGTAGCATATCCACTTAGCACCACGTTAACA-ATCAATATATG
1 TAACCGTGGCATATCCACTTAGCACCACG-TAACATATCAATATATG
* *
46708452 TAACCGTGGCATATCCACTTAGCGCCACGTAACATGTATCAATATGTG
1 TAACCGTGGCATATCCACTTAGCACCACGTAACA--TATCAATATATG
* * **
46708500 TAATCATGGTGTATCCACTTAGCACCAC
1 TAACCGTGGCATATCCACTTAGCACCAC
46708528 ATTTTTCTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
45 5 0.08
46 27 0.42
48 33 0.51
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (46 bp):
TAACCGTGGCATATCCACTTAGCACCACGTAACATATCAATATATG
Found at i:46711121 original size:30 final size:30
Alignment explanation
Indices: 46711086--46711142 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
46711076 GAAAACTGAG
*
46711086 TAAAGAAATTCAAG-ATAGAGAAACCCAGAA
1 TAAAGAAA-TCAAGAATAAAGAAACCCAGAA
*
46711116 TAAAGAAATCCAGAATAAAGAAACCCA
1 TAAAGAAATCAAGAATAAAGAAACCCA
46711143 AGATACGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.58, C:0.16, G:0.14, T:0.12
Consensus pattern (30 bp):
TAAAGAAATCAAGAATAAAGAAACCCAGAA
Found at i:46711122 original size:15 final size:15
Alignment explanation
Indices: 46711104--46711142 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
46711094 TTCAAGATAG
46711104 AGAAACCCAGAATAA
1 AGAAACCCAGAATAA
*
46711119 AGAAATCCAGAATAA
1 AGAAACCCAGAATAA
46711134 AGAAACCCA
1 AGAAACCCA
46711143 AGATACGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.59, C:0.21, G:0.13, T:0.08
Consensus pattern (15 bp):
AGAAACCCAGAATAA
Found at i:46711830 original size:268 final size:268
Alignment explanation
Indices: 46711353--46711890 Score: 1049
Period size: 268 Copynumber: 2.0 Consensus size: 268
46711343 ATATTCTCTC
*
46711353 ATCAATTCTTATCAGACGAAATGTAATAGAATGCCCGAGGGAATAGAGCGCTACGAATTATACAC
1 ATCAATTCTTATCAGACGAAATGTAATAGAATGCCCGAGGGAATAGAGCGCTACGAATTATAAAC
46711418 CAGTCAGGCTACCAATGTTTTCATTTAGCATCAGGATTAGAAAACATCCCTATATAACAAGAAGT
66 CAGTCAGGCTACCAATGTTTTCATTTAGCATCAGGATTAGAAAACATCCCTATATAACAAGAAGT
*
46711483 TCTTCAGAAAATCAACAACCATAGAAATATTTCTGAGAACGGATAAACACATAGACCATCTTTGA
131 TCTTCAGAAAATCAACAACCATAGAAATATTTCTGAGAACGGATAAACACATAGAACATCTTTGA
46711548 AGAGACTGTTAAAATTTGTCCAGCCGTAACTGTCACACTCAGATATTACACATTTCAAATATCAT
196 AGAGACTGTTAAAATTTGTCCAGCCGTAACTGTCACACTCAGATATTACACATTTCAAATATCAT
46711613 TCCTCCAA
261 TCCTCCAA
46711621 ATCAATTCTTATCAGACGAAATGTAATAGAATGCCCGAGGGAATAGAGCGCTACGAATTATAAAC
1 ATCAATTCTTATCAGACGAAATGTAATAGAATGCCCGAGGGAATAGAGCGCTACGAATTATAAAC
46711686 CAGTCAGGCTACCAATGTTTTCATTTAGCATCAGGATTAGAAAACATCCCTATATAACAAGAAGT
66 CAGTCAGGCTACCAATGTTTTCATTTAGCATCAGGATTAGAAAACATCCCTATATAACAAGAAGT
*
46711751 TCTTCAGAAAATCAACAACCATAGAAATATTTCTGAGAATGGATAAACACATAGAACATCTTTGA
131 TCTTCAGAAAATCAACAACCATAGAAATATTTCTGAGAACGGATAAACACATAGAACATCTTTGA
46711816 AGAGACTGTTAAAATTTGTCCAGCCGTAACTGTCACACTCAGATATTACACATTTCAAATATCAT
196 AGAGACTGTTAAAATTTGTCCAGCCGTAACTGTCACACTCAGATATTACACATTTCAAATATCAT
46711881 TCCTCCAA
261 TCCTCCAA
46711889 AT
1 AT
46711891 AGTTCTAACT
Statistics
Matches: 267, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
268 267 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.27
Consensus pattern (268 bp):
ATCAATTCTTATCAGACGAAATGTAATAGAATGCCCGAGGGAATAGAGCGCTACGAATTATAAAC
CAGTCAGGCTACCAATGTTTTCATTTAGCATCAGGATTAGAAAACATCCCTATATAACAAGAAGT
TCTTCAGAAAATCAACAACCATAGAAATATTTCTGAGAACGGATAAACACATAGAACATCTTTGA
AGAGACTGTTAAAATTTGTCCAGCCGTAACTGTCACACTCAGATATTACACATTTCAAATATCAT
TCCTCCAA
Found at i:46713867 original size:43 final size:43
Alignment explanation
Indices: 46713764--46713895 Score: 131
Period size: 43 Copynumber: 3.0 Consensus size: 43
46713754 TGAAAAGATA
* * * * * *
46713764 CCGCTAAAAGGTCATAACTTTTAGCAGCGCTTTTCCCACAAATG
1 CCGCT-AAAGCTCATGACTTTTAGCGGCGCTTTTCCTAAAAACG
* *
46713808 CCGCTAAAGGTCATGACTTTTAGCGGCGCTTTTCCTGAAAACG
1 CCGCTAAAGCTCATGACTTTTAGCGGCGCTTTTCCTAAAAACG
* * * *
46713851 CCGCTAAAGACT-ATGACCTTTAGCGACACTTTTTCTAAAAACG
1 CCGCTAAAG-CTCATGACTTTTAGCGGCGCTTTTCCTAAAAACG
46713894 CC
1 CC
46713896 ACTATATAAC
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
43 69 0.92
44 6 0.08
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (43 bp):
CCGCTAAAGCTCATGACTTTTAGCGGCGCTTTTCCTAAAAACG
Found at i:46719845 original size:15 final size:15
Alignment explanation
Indices: 46719822--46719872 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
46719812 ATACCCATGG
*
46719822 CCATTAAACCTTAAA
1 CCATAAAACCTTAAA
*
46719837 CCATAAAACCCTAAA
1 CCATAAAACCTTAAA
* *
46719852 TCAT-AGACCTTAAA
1 CCATAAAACCTTAAA
*
46719866 CCTTAAA
1 CCATAAA
46719873 TATTAAACCG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24
Consensus pattern (15 bp):
CCATAAAACCTTAAA
Found at i:46720177 original size:41 final size:41
Alignment explanation
Indices: 46720119--46720320 Score: 203
Period size: 41 Copynumber: 5.0 Consensus size: 41
46720109 GGGTTATATA
* * * *
46720119 ACTTTTAACGGCGTTTTATCAAAAGCACCGCTAATGCTCCG
1 ACTTTTAGCGGCATTTTACCAAAAGCGCCGCTAATGCTCCG
*
46720160 ACTTTTAGCGGCATTTTACCAAAAGTGCCGCTAATGCTCCG
1 ACTTTTAGCGGCATTTTACCAAAAGCGCCGCTAATGCTCCG
* *
46720201 ACTTTTAGCGGCATTTTACCAAAAGCGCCGCTATTGCTCTG
1 ACTTTTAGCGGCATTTTACCAAAAGCGCCGCTAATGCTCCG
* * * * * *
46720242 -TTTTTAGCGGCGTTTTAACAAAAAACGCCGCTATTGCTCTG
1 ACTTTTAGCGGCATTTT-ACCAAAAGCGCCGCTAATGCTCCG
* * ** *
46720283 -TTTTTAGCGGCGTTTTTAGTAAAA-CGCCGCTACTGCTC
1 ACTTTTAGCGGC-ATTTTACCAAAAGCGCCGCTAATGCTC
46720321 TGTGTTTTAC
Statistics
Matches: 143, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
40 27 0.19
41 112 0.78
42 4 0.03
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.32
Consensus pattern (41 bp):
ACTTTTAGCGGCATTTTACCAAAAGCGCCGCTAATGCTCCG
Found at i:46721126 original size:47 final size:48
Alignment explanation
Indices: 46721068--46721196 Score: 197
Period size: 48 Copynumber: 2.7 Consensus size: 48
46721058 TTAACATGTA
46721068 TAACCGTGGCATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGAATCAATATATG
* * *
46721115 TAACCGTGGCATATTCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGAATCAATATATG
* * *
46721163 TAATCATGGTATATCCACTTAGCACCACGTTACA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACA
46721197 CGTATAACCG
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
47 31 0.42
48 43 0.58
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (48 bp):
TAACCGTGGCATATCCACTTAGCACCACGTTACATGAATCAATATATG
Found at i:46731962 original size:21 final size:24
Alignment explanation
Indices: 46731933--46731978 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
46731923 TGCTTTTAAC
46731933 TAATAA-TTTTAAAT-TA-AATTA
1 TAATAATTTTTAAATGTATAATTA
*
46731954 TAATTATTTTTAAATGTATAATTA
1 TAATAATTTTTAAATGTATAATTA
46731978 T
1 T
46731979 CACAATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 8 0.38
23 2 0.10
24 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TAATAATTTTTAAATGTATAATTA
Found at i:46733144 original size:20 final size:20
Alignment explanation
Indices: 46733083--46733147 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
46733073 ATAACGGTAA
46733083 ATTAAATTATAATTATTTTT
1 ATTAAATTATAATTATTTTT
* * **
46733103 AAATATGTAATTATCACAATTTTT
1 --AT-T-AAATTATAATTATTTTT
46733127 ATTAAATTATAATTATTTTT
1 ATTAAATTATAATTATTTTT
46733147 A
1 A
46733148 AATGTATAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
20 14 0.42
21 1 0.03
22 4 0.12
23 1 0.03
24 13 0.39
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTAAATTATAATTATTTTT
Found at i:46748867 original size:11 final size:11
Alignment explanation
Indices: 46748851--46748882 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
46748841 AAGTATGGGT
46748851 AGGTATGGGAA
1 AGGTATGGGAA
*
46748862 AGGTATGGGCA
1 AGGTATGGGAA
46748873 AGGTATGGGA
1 AGGTATGGGA
46748883 TATATTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.47, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:46752696 original size:18 final size:18
Alignment explanation
Indices: 46752669--46752739 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
46752659 TCCAACTACT
*
46752669 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* * *
46752687 GTATATGTGAATAGTTCT
1 GTATACGTGAATAGTACC
*
46752705 GTATACGTGAATAGTATC
1 GTATACGTGAATAGTACC
46752723 GTATACGTGAATAGTAC
1 GTATACGTGAATAGTAC
46752740 TATAAACGGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:46752714 original size:36 final size:36
Alignment explanation
Indices: 46752667--46752737 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
46752657 ATTCCAACTA
*
46752667 CTGTATACGTGAACAGTACCGTATATGTGAATAGTT
1 CTGTATACGTGAACAGTACCGTATACGTGAATAGTT
* *
46752703 CTGTATACGTGAATAGTATCGTATACGTGAATAGT
1 CTGTATACGTGAACAGTACCGTATACGTGAATAGT
46752738 ACTATAAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.34
Consensus pattern (36 bp):
CTGTATACGTGAACAGTACCGTATACGTGAATAGTT
Found at i:46753302 original size:21 final size:22
Alignment explanation
Indices: 46753276--46753317 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
46753266 TGACCTTTCC
*
46753276 AAGGTATGGG-TAGGTATGGGA
1 AAGGTATGGGCAAGGTATGGGA
46753297 AAGGTATGGGCAAGGTATGGG
1 AAGGTATGGGCAAGGTATGGG
46753318 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (22 bp):
AAGGTATGGGCAAGGTATGGGA
Found at i:46753303 original size:11 final size:10
Alignment explanation
Indices: 46753276--46753317 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
46753266 TGACCTTTCC
46753276 AAGGTATGGG
1 AAGGTATGGG
*
46753286 TAGGTATGGG
1 AAGGTATGGG
46753296 AAAGGTATGGG
1 -AAGGTATGGG
46753307 CAAGGTATGGG
1 -AAGGTATGGG
46753318 GTATATTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.29, C:0.02, G:0.48, T:0.21
Consensus pattern (10 bp):
AAGGTATGGG
Found at i:46759308 original size:23 final size:23
Alignment explanation
Indices: 46759282--46759334 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
46759272 TCATTTCATA
*
46759282 ATGGATGATTTCTTGAAATAAGT
1 ATGGATGATTTCATGAAATAAGT
46759305 ATGGATGATTTCATGAAATAAGT
1 ATGGATGATTTCATGAAATAAGT
46759328 ATGGATG
1 ATGGATG
46759335 TTTGCTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (23 bp):
ATGGATGATTTCATGAAATAAGT
Found at i:46769247 original size:24 final size:24
Alignment explanation
Indices: 46769205--46769264 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
46769195 GGAAACTCAT
*
46769205 AAGAGCCATAATCAGAAAGTTCACA
1 AAGAGCCAT-ATCAGAAAGCTCACA
*
46769230 AAGAACCATATCAGAAAGCTCACA
1 AAGAGCCATATCAGAAAGCTCACA
46769254 AAGAGCCATAT
1 AAGAGCCATAT
46769265 AACAGGAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 24 0.75
25 8 0.25
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (24 bp):
AAGAGCCATATCAGAAAGCTCACA
Found at i:46769394 original size:25 final size:25
Alignment explanation
Indices: 46769343--46769404 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
46769333 TAATTTAACA
*
46769343 AGAAGCTCATGAAAGAGCCCTTAATCG
1 AGAAGCTC-TG-AAGAGCCATTAATCG
46769370 AGAAGCTCTGAAGAGCCA-TATATCG
1 AGAAGCTCTGAAGAGCCATTA-ATCG
46769395 AGAAGC-CTGA
1 AGAAGCTCTGA
46769405 GAGGGCTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 6 0.18
25 17 0.52
26 2 0.06
27 8 0.24
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (25 bp):
AGAAGCTCTGAAGAGCCATTAATCG
Found at i:46769922 original size:5 final size:5
Alignment explanation
Indices: 46769906--46769935 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
46769896 ATAGAAGATA
*
46769906 TTATT TTGTT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT
46769936 AATTTAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:46772558 original size:18 final size:18
Alignment explanation
Indices: 46772531--46772576 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
46772521 GCCCGTACTT
* *
46772531 GACACAAGTCGCGGCCAC
1 GACACTAGTCGCGCCCAC
*
46772549 GACACTAGTCGCGCCCAT
1 GACACTAGTCGCGCCCAC
46772567 GACACTAGTC
1 GACACTAGTC
46772577 AAGATAGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.37, G:0.24, T:0.13
Consensus pattern (18 bp):
GACACTAGTCGCGCCCAC
Found at i:46776959 original size:12 final size:12
Alignment explanation
Indices: 46776937--46776983 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
46776927 TAATTGACCC
46776937 AAAGA-AAAAAA
1 AAAGAGAAAAAA
46776948 AAAGAGAAAAAA
1 AAAGAGAAAAAA
46776960 AAAGAGAGAAAAA
1 AAAGAGA-AAAAA
*
46776973 GAAAAAGAAAA
1 -AAAGAGAAAA
46776984 TTAAACACCC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 5 0.16
12 13 0.41
13 8 0.25
14 6 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAGAGAAAAAA
Found at i:46776960 original size:14 final size:14
Alignment explanation
Indices: 46776941--46776980 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
46776931 TGACCCAAAG
46776941 AAAAAAAAAAGAGA
1 AAAAAAAAAAGAGA
*
46776955 AAAAAAAAGAGAGA
1 AAAAAAAAAAGAGA
*
46776969 AAAAGAAAAAGA
1 AAAAAAAAAAGA
46776981 AAATTAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGAGA
Found at i:46779905 original size:5 final size:5
Alignment explanation
Indices: 46779889--46779918 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
46779879 ATAGAAGATA
*
46779889 TTATT TTGTT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT
46779919 AATTTAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:46783234 original size:22 final size:23
Alignment explanation
Indices: 46783209--46783251 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
46783199 GAATTCAATT
46783209 TTAAATTT-AAATAATTCAAACA
1 TTAAATTTGAAATAATTCAAACA
*
46783231 TTAAATTTGAATTAATTCAAA
1 TTAAATTTGAAATAATTCAAA
46783252 ATTTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAAATTTGAAATAATTCAAACA
Found at i:46783257 original size:23 final size:22
Alignment explanation
Indices: 46783200--46783279 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 22
46783190 AAACCGATTG
*
46783200 AATTC-AATTTTAAATTTAAAT
1 AATTCAAAATTTAAATTTAAAT
*
46783221 AATTCAAACA-TTAAATTTGAATT
1 AATTCAAA-ATTTAAATTT-AAAT
46783244 AATTCAAAATTTAAAAATTTAAA-
1 AATTCAAAATTT--AAATTTAAAT
46783267 AA-TCATAAATTTA
1 AATTCA-AAATTTA
46783280 TAAATGATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
21 6 0.12
22 14 0.29
23 21 0.43
24 2 0.04
25 6 0.12
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (22 bp):
AATTCAAAATTTAAATTTAAAT
Found at i:46783276 original size:40 final size:40
Alignment explanation
Indices: 46783197--46783278 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 40
46783187 TTAAAACCGA
** *
46783197 TTGAATTCAATTTTAAATTTAAATAATTCAAACATTAAAT
1 TTGAATTCAATTCAAAATTTAAATAATTCAAAAATTAAAT
*
46783237 TTGAATT-AATTCAAAATTTAAA-AATTTAAAAATCATAAAT
1 TTGAATTCAATTCAAAATTTAAATAATTCAAAAAT--TAAAT
46783277 TT
1 TT
46783279 ATAAATGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 9 0.25
39 13 0.36
40 14 0.39
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.41
Consensus pattern (40 bp):
TTGAATTCAATTCAAAATTTAAATAATTCAAAAATTAAAT
Found at i:46784071 original size:19 final size:19
Alignment explanation
Indices: 46784032--46784072 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
46784022 TTCTTACTAT
*
46784032 AAAATTCATTTTTATTAAA
1 AAAATTCATTTTTAATAAA
46784051 AAAATTCATTTTTGAATAAA
1 AAAATTCATTTTT-AATAAA
46784071 AA
1 AA
46784073 TTATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATTCATTTTTAATAAA
Found at i:46784297 original size:60 final size:60
Alignment explanation
Indices: 46784189--46784366 Score: 189
Period size: 60 Copynumber: 3.0 Consensus size: 60
46784179 TCTTTTCAAC
* * * ** *
46784189 TTTTAGAATTAGAATTAAATTGATCAATTTTGTAAATGTTTCAGGCTAAATTTATTGAATT
1 TTTTAGAATTAGAACTAAATTGATAAATTTTGTAAATATTAAAGGCTAAATTTATT-AAAT
* * * *
46784250 TTTTAAAATTAGAACTAAA-TGATAAATTTTGTAAACATTGAAGGCTAAATTTGTTAAAT
1 TTTTAGAATTAGAACTAAATTGATAAATTTTGTAAATATTAAAGGCTAAATTTATTAAAT
* * * *
46784309 TTTTAGATTTAAGATC-AAATTGATAAAATTTGTAAATATTAAAGGGATAAATTTATTA
1 TTTTAGAATT-AGAACTAAATTGATAAATTTTGTAAATATTAAA-GGCTAAATTTATTA
46784367 TTAGGCCAAT
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
59 14 0.14
60 54 0.56
61 29 0.30
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (60 bp):
TTTTAGAATTAGAACTAAATTGATAAATTTTGTAAATATTAAAGGCTAAATTTATTAAAT
Found at i:46797378 original size:21 final size:21
Alignment explanation
Indices: 46797352--46797400 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
46797342 ATCTGATTTG
*
46797352 TAACTAACTATAACAGAGTAC
1 TAACTAACTATAACAAAGTAC
46797373 TAACTAACTATAACAAAGTAC
1 TAACTAACTATAACAAAGTAC
46797394 TAACTAA
1 TAACTAA
46797401 TATTGTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.18, G:0.06, T:0.24
Consensus pattern (21 bp):
TAACTAACTATAACAAAGTAC
Found at i:46805116 original size:15 final size:15
Alignment explanation
Indices: 46805096--46805130 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
46805086 CTGACTAGTT
46805096 AAGAAAAAAAAAAAG
1 AAGAAAAAAAAAAAG
* *
46805111 AAGAAAAAGAAAAGG
1 AAGAAAAAAAAAAAG
46805126 AAGAA
1 AAGAA
46805131 GAGAAGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAAAG
Found at i:46807756 original size:24 final size:24
Alignment explanation
Indices: 46807724--46807772 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
46807714 TAGCATCTAG
46807724 TAAGCATAAAAATAAAGTAGAACC
1 TAAGCATAAAAATAAAGTAGAACC
46807748 TAAGCATAAAAATAAAGTAGAACC
1 TAAGCATAAAAATAAAGTAGAACC
46807772 T
1 T
46807773 TACTTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.18
Consensus pattern (24 bp):
TAAGCATAAAAATAAAGTAGAACC
Found at i:46816399 original size:27 final size:27
Alignment explanation
Indices: 46816310--46816401 Score: 66
Period size: 27 Copynumber: 3.4 Consensus size: 27
46816300 TTATCTTAAT
*
46816310 ATTA-AAAT-TTGATAATAATAATTTTAA
1 ATTATAAATATTGATATTAAT-ATTTT-A
* * * *
46816337 ATTTTAAATAAT-ATTCTTAATATATT-
1 ATTATAAATATTGA-TATTAATATTTTA
*
46816363 ATTGAAAAATATTGATATTAATATTTTA
1 ATT-ATAAATATTGATATTAATATTTTA
46816391 ATTATAAATAT
1 ATTATAAATAT
46816402 ATTATTAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
26 3 0.06
27 26 0.54
28 13 0.27
29 6 0.12
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (27 bp):
ATTATAAATATTGATATTAATATTTTA
Found at i:46820774 original size:14 final size:14
Alignment explanation
Indices: 46820751--46820783 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
46820741 AGTGAGGGAA
*
46820751 ATTTTGGGAAATAT
1 ATTTTAGGAAATAT
46820765 ATTTTAGGAAATAT
1 ATTTTAGGAAATAT
46820779 ATTTT
1 ATTTT
46820784 GATCTCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
ATTTTAGGAAATAT
Found at i:46823238 original size:43 final size:44
Alignment explanation
Indices: 46823190--46823339 Score: 171
Period size: 43 Copynumber: 3.5 Consensus size: 44
46823180 ATCCCATATC
* *
46823190 TGGTCTTACATGTTATCACATAT-CGATGCCACTGTCCCAGACA
1 TGGTCTTACATGTAATCACATATACGATGCCAATGTCCCAGACA
* * * * * *
46823233 AGGTCTTATATGAAATC-GATTTACGAGGCCAATGTCCCAGACA
1 TGGTCTTACATGTAATCACATATACGATGCCAATGTCCCAGACA
* * *
46823276 TGGTCTTACACGTAATCTCA-ATACAATGCCAATGTCCCAGACA
1 TGGTCTTACATGTAATCACATATACGATGCCAATGTCCCAGACA
*
46823319 TGGTCTTACATCTAATCACAT
1 TGGTCTTACATGTAATCACAT
46823340 CTCGGTAACC
Statistics
Matches: 85, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
42 3 0.04
43 81 0.95
44 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (44 bp):
TGGTCTTACATGTAATCACATATACGATGCCAATGTCCCAGACA
Found at i:46838014 original size:68 final size:64
Alignment explanation
Indices: 46837897--46838047 Score: 162
Period size: 68 Copynumber: 2.3 Consensus size: 64
46837887 ATACAGATAG
* * * *
46837897 TATGTAGCTAGGTCACATGTATGATGCTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACAT
1 TATGTAGCTAGGTCGCATGGATGATACTGAGTGCACACCATGTGTACAAGAGAGCTAC--GACA-
46837962 TA
63 TA
* * **
46837964 TGATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAG-ACAAGAGAGCTACGGGA
1 T-ATGTAGCTAGGTCGCATGGATGATACTGA-GTGCACACCATGT-GTACAAGAGAGCTACGACA
46838027 TA
63 TA
46838029 TATGTAGCTAGGTCGCATG
1 TATGTAGCTAGGTCGCATG
46838048 CGCGGTTCCA
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
64 18 0.25
65 3 0.04
66 2 0.03
67 2 0.03
68 47 0.64
69 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (64 bp):
TATGTAGCTAGGTCGCATGGATGATACTGAGTGCACACCATGTGTACAAGAGAGCTACGACATA
Done.