Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013823.1 Kokia drynarioides strain JFW-HI SEQ_128851, 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: 125980
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:609 original size:15 final size:15
Alignment explanation
Indices: 591--646 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
581 TTTTGGGTAG
591 TTTGTAATTGGGCTA
1 TTTGTAATTGGGCTA
*
606 TTTGTATTTGGG-TCA
1 TTTGTAATTGGGCT-A
* * *
621 TCTGTATTTGGGCCA
1 TTTGTAATTGGGCTA
636 TTTGTAATTGG
1 TTTGTAATTGG
647 ACTTTGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 1 0.03
15 33 0.97
ACGTcount: A:0.16, C:0.09, G:0.27, T:0.48
Consensus pattern (15 bp):
TTTGTAATTGGGCTA
Found at i:700 original size:17 final size:16
Alignment explanation
Indices: 678--756 Score: 68
Period size: 16 Copynumber: 4.8 Consensus size: 16
668 TTGGACTTTC
678 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
695 TAAATTTAAATTTCAAAA
1 TAAATTT-AATTT-TAAA
* * *
713 AAAATTAAATTTAAAA
1 TAAATTTAATTTTAAA
* *
729 TAAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
*
745 TAAATTCAATTT
1 TAAATTTAATTT
757 CGAATAAGTC
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
16 24 0.49
17 12 0.24
18 12 0.24
19 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:9933 original size:16 final size:17
Alignment explanation
Indices: 9912--9945 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9902 AGAAAATGGA
*
9912 AGCC-TTGTGGCGATCT
1 AGCCTTTGTGACGATCT
9928 AGCCTTTGTGACGATCT
1 AGCCTTTGTGACGATCT
9945 A
1 A
9946 TGCAATGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (17 bp):
AGCCTTTGTGACGATCT
Found at i:10135 original size:28 final size:27
Alignment explanation
Indices: 10093--10242 Score: 158
Period size: 28 Copynumber: 5.3 Consensus size: 27
10083 ATCAAGAGCT
*
10093 TTTGTGGCAAACTATGAAAATGGAAGCC
1 TTTGTGGCAATCTAT-AAAATGGAAGCC
* * *
10121 TTTGTGGTAATCTATAAAAATGGAAACA
1 TTTGTGGCAATCTAT-AAAATGGAAGCC
* *
10149 TTTCTGGCAATCTATAAAGATGAAAGCC
1 TTTGTGGCAATCTATAAA-ATGGAAGCC
10177 TTTGTGGCAATATCTATAAAGATGGAAGCC
1 TTTGTGGC-A-ATCTATAAA-ATGGAAGCC
*
10207 TTTGTGGCGATCTATGAAAA-GGAAAGCC
1 TTTGTGGCAATCTAT-AAAATGG-AAGCC
10235 TTTGTGGC
1 TTTGTGGC
10243 TAATAATGAA
Statistics
Matches: 104, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
27 5 0.05
28 69 0.66
29 4 0.04
30 26 0.25
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (27 bp):
TTTGTGGCAATCTATAAAATGGAAGCC
Found at i:10220 original size:58 final size:58
Alignment explanation
Indices: 10093--10247 Score: 190
Period size: 58 Copynumber: 2.7 Consensus size: 58
10083 ATCAAGAGCT
* * *
10093 TTTGTGGCAAACTATGAAAATGGAAGCCTTTGTGG-TA-ATCTATAAAAATGGAAACA
1 TTTGTGGCAATCTATGAAAATGAAAGCCTTTGTGGCAATATCTATAAAAATGGAAACA
* * * *
10149 TTTCTGGCAATCTAT-AAAGATGAAAGCCTTTGTGGCAATATCTATAAAGATGGAAGCC
1 TTTGTGGCAATCTATGAAA-ATGAAAGCCTTTGTGGCAATATCTATAAAAATGGAAACA
* *
10207 TTTGTGGCGATCTATGAAAAGGAAAGCCTTTGTGGCTAATA
1 TTTGTGGCAATCTATGAAAATGAAAGCCTTTGTGGC-AATA
10248 ATGAAAGGAA
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
55 3 0.04
56 28 0.33
57 1 0.01
58 45 0.54
59 7 0.08
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (58 bp):
TTTGTGGCAATCTATGAAAATGAAAGCCTTTGTGGCAATATCTATAAAAATGGAAACA
Found at i:10254 original size:27 final size:28
Alignment explanation
Indices: 10093--10270 Score: 109
Period size: 28 Copynumber: 6.3 Consensus size: 28
10083 ATCAAGAGCT
* *
10093 TTTGTGGCAAACTATGAAAATGG-AAGCC
1 TTTGTGGCAATCAATGAAAA-GGAAAGCC
* * * *
10121 TTTGTGGTAATCTATAAAAATGGAAA-CA
1 TTTGTGGCAATCAATGAAAA-GGAAAGCC
* * *
10149 TTTCTGGCAATCTAT-AAAGATGAAAGCC
1 TTTGTGGCAATCAATGAAA-AGGAAAGCC
*
10177 TTTGTGGCAATATCTAT-AAAGATGG-AAGCC
1 TTTGTGGC-A-ATCAATGAAA-A-GGAAAGCC
* *
10207 TTTGTGGCGATCTATGAAAAGGAAAGCC
1 TTTGTGGCAATCAATGAAAAGGAAAGCC
*
10235 TTTGTGGCTAAT-AATG-AAAGGAATGCC
1 TTTGTGGC-AATCAATGAAAAGGAAAGCC
*
10262 TTCGTGGCA
1 TTTGTGGCA
10271 CATTCTAAAG
Statistics
Matches: 126, Mismatches: 15, Indels: 20
0.78 0.09 0.12
Matches are distributed among these distances:
26 1 0.01
27 26 0.21
28 66 0.52
29 8 0.06
30 24 0.19
31 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (28 bp):
TTTGTGGCAATCAATGAAAAGGAAAGCC
Found at i:10403 original size:27 final size:27
Alignment explanation
Indices: 10309--10385 Score: 145
Period size: 27 Copynumber: 2.9 Consensus size: 27
10299 CACTCTGAAG
*
10309 GAATAATATGTAAGACGAACTCTACAA
1 GAATGATATGTAAGACGAACTCTACAA
10336 GAATGATATGTAAGACGAACTCTACAA
1 GAATGATATGTAAGACGAACTCTACAA
10363 GAATGATATGTAAGACGAACTCT
1 GAATGATATGTAAGACGAACTCT
10386 GAAGGAATCG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.23
Consensus pattern (27 bp):
GAATGATATGTAAGACGAACTCTACAA
Found at i:17300 original size:18 final size:19
Alignment explanation
Indices: 17263--17303 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
17253 TCTTAATTTT
*
17263 TTTA-AAATTTTGAATATA
1 TTTATAAATTTTAAATATA
17281 TTTATAAATTTTAAAT-TA
1 TTTATAAATTTTAAATATA
17299 TTTAT
1 TTTAT
17304 TTATATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTATAAATTTTAAATATA
Found at i:17315 original size:15 final size:15
Alignment explanation
Indices: 17295--17324 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17285 TAAATTTTAA
17295 ATTATTTATTTATAT
1 ATTATTTATTTATAT
17310 ATTATTTATTTATAT
1 ATTATTTATTTATAT
17325 GACATATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTATTTATTTATAT
Found at i:18468 original size:165 final size:162
Alignment explanation
Indices: 18193--18642 Score: 575
Period size: 165 Copynumber: 2.7 Consensus size: 162
18183 AAAAAAATAC
* * *
18193 AAGTGACATGGAATTAAATGATGAGTAGGATTAGATAAAAGTATTATAGAGGTCATTATACTAGA
1 AAGTGACATGGAATTAAAGGAT-AGTAGGATTAGATAAAAGTATCATATAGGTC-TTATACTAG-
* * * *
18258 AATCAGATTGCATTTTGCCTCTTTTACTAAAAAATAGAAAAATTAGTTCTTATAAGTTAGATCAA
63 AATCAGATTGCATTTT-TCTCTTTTACTAAAAAATAGACAAATTAGTCCCTATAAGTTAGATCAA
* *
18323 ATAA-CAAACTCACCTTTTTTGTT-AAAAAAATTATGT
127 A-AAGCAAACTAACC-CTTTTGTTAAAAAAAATTATGT
* *
18359 AAGTGACATGGAATTTAAGGATAGTAGGATTAGATAAAAGTACCATATAGGTTCTTATACTAAGA
1 AAGTGACATGGAATTAAAGGATAGTAGGATTAGATAAAAGTATCATATAGG-TCTTATACT-AGA
* * *
18424 ATCGGATTGCATTTTATCTCTTTTACTAAAAAATAGGCAAATTAGTCCCTGTAAGTTAGATCAAA
64 ATCAGATTGCATTTT-TCTCTTTTACTAAAAAATAGACAAATTAGTCCCTATAAGTTAGATCAAA
18489 AAGCAAACTAACCCTTTTGTTAAAAAAAATTATGT
128 AAGCAAACTAACCCTTTTGTTAAAAAAAATTATGT
** *
18524 AAGTGACATGGAA-TAAAGGATAGTAGGATTAGATAAAAGTATCATATAAGCCCTTATACTGCGA
1 AAGTGACATGGAATTAAAGGATAGTAGGATTAGATAAAAGTATCATAT-AGGTCTTATACT-AGA
* * * *
18588 ATCAGATTG-AATTTTCATCTTTTACTAAAAAATAGCCAACTTAGTCCCTTTAAGT
64 ATCAGATTGCATTTTTC-TCTTTTACTAAAAAATAGACAAATTAGTCCCTATAAGT
18643 CTCATCTATT
Statistics
Matches: 252, Mismatches: 26, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
162 2 0.01
163 39 0.15
164 59 0.23
165 128 0.51
166 24 0.10
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (162 bp):
AAGTGACATGGAATTAAAGGATAGTAGGATTAGATAAAAGTATCATATAGGTCTTATACTAGAAT
CAGATTGCATTTTTCTCTTTTACTAAAAAATAGACAAATTAGTCCCTATAAGTTAGATCAAAAAG
CAAACTAACCCTTTTGTTAAAAAAAATTATGT
Found at i:20182 original size:2 final size:2
Alignment explanation
Indices: 20175--20199 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20165 TTTGATGTGA
20175 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20200 AACACATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21349 original size:30 final size:31
Alignment explanation
Indices: 21287--21357 Score: 117
Period size: 30 Copynumber: 2.3 Consensus size: 31
21277 AACATTTGAC
* *
21287 ACTTGAACTTGACACTTTTTCTTAATTTGGT
1 ACTTAAACTTGACACTTTTTCTTAAGTTGGT
21318 ACTTAAACTTGACACTTTTT-TTAAGTTGGT
1 ACTTAAACTTGACACTTTTTCTTAAGTTGGT
21348 ACTTAAACTT
1 ACTTAAACTT
21358 TTTGGGGTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 19 0.50
31 19 0.50
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.46
Consensus pattern (31 bp):
ACTTAAACTTGACACTTTTTCTTAAGTTGGT
Found at i:21627 original size:31 final size:30
Alignment explanation
Indices: 21589--21663 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
21579 CTAAAAAAGC
* *
21589 TTAGGTACCAAATTAGGAAAAAATGCCAAGT
1 TTAGGTACCAAATTAAG-AAAAATGCCAAAT
* *
21620 TTAGGTACCAAATTAAGAAAAGTGTCAAAT
1 TTAGGTACCAAATTAAGAAAAATGCCAAAT
*
21650 TCAGGTACCAAATT
1 TTAGGTACCAAATT
21664 GGGTTCAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 23 0.59
31 16 0.41
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.25
Consensus pattern (30 bp):
TTAGGTACCAAATTAAGAAAAATGCCAAAT
Found at i:23801 original size:19 final size:20
Alignment explanation
Indices: 23758--23806 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
23748 TTCGGTGAAC
*
23758 TAATTATTTAATTTGGTATTTG
1 TAATTA-TTAATTT-GTAATTG
23780 TAATTATTAATTT-TAATTG
1 TAATTATTAATTTGTAATTG
23799 TAATTATT
1 TAATTATT
23807 GTAAGTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.50
21 7 0.27
22 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
TAATTATTAATTTGTAATTG
Found at i:26173 original size:23 final size:24
Alignment explanation
Indices: 26143--26187 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
26133 TTTTATGTTA
26143 ACAATTTAAA-ACTATTTTTTCCC
1 ACAATTTAAATACTATTTTTTCCC
*
26166 ACAATTTAAATATTATTTTTTC
1 ACAATTTAAATACTATTTTTTC
26188 ATGATGTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.49
Consensus pattern (24 bp):
ACAATTTAAATACTATTTTTTCCC
Found at i:26949 original size:122 final size:123
Alignment explanation
Indices: 26797--27227 Score: 407
Period size: 122 Copynumber: 3.5 Consensus size: 123
26787 ATAAACACTG
** ** **
26797 CAAAAGGTAAAG-CGCAATAGCAGCGTTTATGATAAAACGATGCAAAAGGTAAAGCAATAGTAAC
1 CAAAAGGTAAAGAC-CAATAGCAGCGTTTATGGGAAAACGCCGCAAAAGGTAAAGCAATAGTGGC
* ** *
26861 GCTTTCCCATAAACGCCGCAAAAGGTAAAGAGCAATAGTGGTGTTTATGGGAAAACGCCA
65 GCTTTCCCATAAACGCTGCAAAAGGTAAAGA-CAATAACGGTGTTTATGGAAAAACGCCA
* * * * *
26921 TAAAAGGT-AA-TCCAATAGC-GACGTTTATGGGAAAACGCCGTAAAAGATAAAACAATAGTGGC
1 CAAAAGGTAAAGACCAATAGCAG-CGTTTATGGGAAAACGCCGCAAAAGGTAAAGCAATAGTGGC
* * * * *
26983 GCTTACCCATAAATGCTGCAAAAGATAAA-ACAATAACGGAGTTTATAGGAAAAACGCCG
65 GCTTTCCCATAAACGCTGCAAAAGGTAAAGACAATAACGGTGTTTAT-GGAAAAACGCCA
* *
27042 CAAAAGGTAAAGAGCAATAGCAGCG-TTATGGGAAAACGCCGCAAAAGGTAAAGCAATAGCGGCG
1 CAAAAGGTAAAGACCAATAGCAGCGTTTATGGGAAAACGCCGCAAAAGGTAAAGCAATAGTGGCG
* ** *
27106 CTTTACCATAAACATTGCAAAAGGTAAAGCACAATAACGGTGTTTAT-GATAAAATG-CA
66 CTTTCCCATAAACGCTGCAAAAGGTAAAG-ACAATAACGGTGTTTATGGA-AAAACGCCA
** * ***
27164 GCAAAAGGTAAA-A-CAATAGTGGCGCTT-TCCCATAAACGCCGCAAAAGGTAAAGAGCAATAGT
1 -CAAAAGGTAAAGACCAATAGCAGCGTTTATGGGA-AAACGCCGCAAAAGGT-AA-AGCAATAGT
27226 GG
62 GG
27228 TGTTTGTGGG
Statistics
Matches: 252, Mismatches: 41, Indels: 28
0.79 0.13 0.09
Matches are distributed among these distances:
120 13 0.05
121 30 0.12
122 145 0.58
123 30 0.12
124 34 0.13
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (123 bp):
CAAAAGGTAAAGACCAATAGCAGCGTTTATGGGAAAACGCCGCAAAAGGTAAAGCAATAGTGGCG
CTTTCCCATAAACGCTGCAAAAGGTAAAGACAATAACGGTGTTTATGGAAAAACGCCA
Found at i:26977 original size:40 final size:40
Alignment explanation
Indices: 26667--27329 Score: 254
Period size: 40 Copynumber: 16.2 Consensus size: 40
26657 ACTTACCCAT
** * * *
26667 AAACGCCGCAAAAGGTAAAACAATAATGTCATTTATAGGAA
1 AAACGCCGCAAAAGGTAAAACAATAGCGACGTTTAT-GGGA
* * *
26708 AAACGCCGCAAAAGATAAAGAGCAATAGTGACG-TTATGAGA
1 AAACGCCGCAAAAGGTAAA-A-CAATAGCGACGTTTATGGGA
* * * * **
26749 AAATGCCACAAATGGTAAAGCAATAGC-AGCGCTTTA--CCA
1 AAACGCCGCAAAAGGTAAAACAATAGCGA-CG-TTTATGGGA
* * * **
26788 TAAACACTGCAAAAGGTAAAGCGCAATAGC-AGCGTTTATGATA
1 -AAACGCCGCAAAAGGTAAA--ACAATAGCGA-CGTTTATGGGA
** * ** * ***
26831 AAACGATGCAAAAGGTAAAGCAATAGTAACGCTT-TCCCA
1 AAACGCCGCAAAAGGTAAAACAATAGCGACGTTTATGGGA
* **
26870 TAAACGCCGCAAAAGGTAAAGAGCAATAGTGGTGTTTATGGGA
1 -AAACGCCGCAAAAGGTAAA-A-CAATAGCGACGTTTATGGGA
** **
26913 AAACGCCATAAAAGGTAATCCAATAGCGACGTTTATGGGA
1 AAACGCCGCAAAAGGTAAAACAATAGCGACGTTTATGGGA
* * * * * ***
26953 AAACGCCGTAAAAGATAAAACAATAGTGGCGCTTA-CCCA
1 AAACGCCGCAAAAGGTAAAACAATAGCGACGTTTATGGGA
* * * * *
26992 TAAATGCTGCAAAAGATAAAACAATAACGGA-GTTTATAGGAA
1 -AAACGCCGCAAAAGGTAAAACAATAGC-GACGTTTAT-GGGA
27034 AAACGCCGCAAAAGGTAAAGAGCAATAGC-AGCG-TTATGGGA
1 AAACGCCGCAAAAGGTAAA-A-CAATAGCGA-CGTTTATGGGA
* * **
27075 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGCTTTA--CCA
1 AAACGCCGCAAAAGGTAAAACAATAGCGACG-TTTATGGGA
*** * ** **
27114 TAAACATTGCAAAAGGTAAAGCACAATAACGGTGTTTATGATA
1 -AAACGCCGCAAAAGGTAAA--ACAATAGCGACGTTTATGGGA
* * * * * ***
27157 AAATGCAGCAAAAGGTAAAACAATAGTGGCGCTT-TCCCA
1 AAACGCCGCAAAAGGTAAAACAATAGCGACGTTTATGGGA
* ** *
27196 TAAACGCCGCAAAAGGTAAAGAGCAATAGTGGTGTTTGTGGGA
1 -AAACGCCGCAAAAGGTAAA-A-CAATAGCGACGTTTATGGGA
* * * * *
27239 AAATGCCACAAAAGGTAAACCAATAGTGGCGTTTATGGGA
1 AAACGCCGCAAAAGGTAAAACAATAGCGACGTTTATGGGA
* * * * *
27279 AAACGCTGCAAAAGATAAAGAGCATTAGCGACATTTATGAGA
1 AAACGCCGCAAAAGGTAAA-A-CAATAGCGACGTTTATGGGA
27321 AAACGCCGC
1 AAACGCCGC
27330 TAATGCTCTT
Statistics
Matches: 469, Mismatches: 116, Indels: 73
0.71 0.18 0.11
Matches are distributed among these distances:
38 1 0.00
39 24 0.05
40 190 0.41
41 91 0.19
42 142 0.30
43 21 0.04
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.18
Consensus pattern (40 bp):
AAACGCCGCAAAAGGTAAAACAATAGCGACGTTTATGGGA
Found at i:27200 original size:326 final size:326
Alignment explanation
Indices: 26627--27297 Score: 1006
Period size: 326 Copynumber: 2.1 Consensus size: 326
26617 GTTTTTCAAT
* * *
26627 AAACCCCGCAAAAGATAAAGCAATAGTGGCACTTACCCATAAACGCCGCAAAAGGTAAAACAATA
1 AAACGCCGCAAAAGATAAAACAATAGTGGCACTTACCCATAAACGCCGCAAAAGATAAAACAATA
* * *
26692 ATGTCATTTATAGGAAAAACGCCGCAAAAGATAAAGAGCAATAGTGACGTTATGAGAAAATGCCA
66 ACGTCATTTATAGGAAAAACGCCGCAAAAGATAAAGAGCAATAGAGACGTTATGAGAAAACGCCA
* * *
26757 CAAATGGTAAAGCAATAGCAGCGCTTTACCATAAACACTGCAAAAGGTAAAGCGCAATAGCAGCG
131 CAAAAGGTAAAGCAATAGCAGCGCTTTACCATAAACACTGCAAAAGGTAAAGCACAATAACAGCG
*
26822 TTTATGATAAAACGATGCAAAAGGTAAAGCAATAGTAACGCTTTCCCATAAACGCCGCAAAAGGT
196 TTTATGATAAAACGATGCAAAAGGTAAAACAATAGTAACGCTTTCCCATAAACGCCGCAAAAGGT
* *
26887 AAAGAGCAATAGTGGTGTTTATGGGAAAACGCCATAAAAGGTAATCCAATAGCGACGTTTATGGG
261 AAAGAGCAATAGTGGTGTTTATGGGAAAACGCCACAAAAGGTAAACCAATAGCGACGTTTATGGG
26952 A
326 A
* * * *
26953 AAACGCCGTAAAAGATAAAACAATAGTGGCGCTTACCCATAAATGCTGCAAAAGATAAAACAATA
1 AAACGCCGCAAAAGATAAAACAATAGTGGCACTTACCCATAAACGCCGCAAAAGATAAAACAATA
* * *
27018 ACG-GAGTTTATAGGAAAAACGCCGCAAAAGGTAAAGAGCAATAGCAG-CGTTATGGGAAAACGC
66 ACGTCA-TTTATAGGAAAAACGCCGCAAAAGATAAAGAGCAATAG-AGACGTTATGAGAAAACGC
* * * *
27081 CGCAAAAGGTAAAGCAATAGCGGCGCTTTACCATAAACATTGCAAAAGGTAAAGCACAATAACGG
129 CACAAAAGGTAAAGCAATAGCAGCGCTTTACCATAAACACTGCAAAAGGTAAAGCACAATAACAG
* * **
27146 TGTTTATGATAAAATGCA-GCAAAAGGTAAAACAATAGTGGCGCTTTCCCATAAACGCCGCAAAA
194 CGTTTATGATAAAACG-ATGCAAAAGGTAAAACAATAGTAACGCTTTCCCATAAACGCCGCAAAA
* * * *
27210 GGTAAAGAGCAATAGTGGTGTTTGTGGGAAAATGCCACAAAAGGTAAACCAATAGTGGCGTTTAT
258 GGTAAAGAGCAATAGTGGTGTTTATGGGAAAACGCCACAAAAGGTAAACCAATAGCGACGTTTAT
27275 GGGA
323 GGGA
*
27279 AAACGCTGCAAAAGATAAA
1 AAACGCCGCAAAAGATAAA
27298 GAGCATTAGC
Statistics
Matches: 309, Mismatches: 33, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
325 1 0.00
326 306 0.99
327 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (326 bp):
AAACGCCGCAAAAGATAAAACAATAGTGGCACTTACCCATAAACGCCGCAAAAGATAAAACAATA
ACGTCATTTATAGGAAAAACGCCGCAAAAGATAAAGAGCAATAGAGACGTTATGAGAAAACGCCA
CAAAAGGTAAAGCAATAGCAGCGCTTTACCATAAACACTGCAAAAGGTAAAGCACAATAACAGCG
TTTATGATAAAACGATGCAAAAGGTAAAACAATAGTAACGCTTTCCCATAAACGCCGCAAAAGGT
AAAGAGCAATAGTGGTGTTTATGGGAAAACGCCACAAAAGGTAAACCAATAGCGACGTTTATGGG
A
Found at i:27230 original size:82 final size:82
Alignment explanation
Indices: 26708--27323 Score: 432
Period size: 82 Copynumber: 7.5 Consensus size: 82
26698 TTTATAGGAA
* * *
26708 AAACGCCGCAAAAGATAAAGAGCAATAGTGACG-TTATGAGAAAATGCCA-CAAATGGTAAAGCA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGTGGCGTTTATGAGAAAATG-CAGCAAAAGGTAAAGCA
*
26771 ATAGCAGCGCTTTACCAT
65 ATAGCGGCGCTTTACCAT
* * * ** * *
26789 AAACACTGCAAAAGGTAAAGCGCAATAGCAGCGTTTATGATAAAACG-ATGCAAAAGGTAAAGCA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGTGGCGTTTATGAGAAAATGCA-GCAAAAGGTAAAGCA
*** *
26853 ATAGTAACGCTTTCCCAT
65 ATAGCGGCGCTTTACCAT
* * * * **
26871 AAACGCCGCAAAAGGTAAAGAGCAATAGTGGTGTTTATGGGAAAACGCCA-TAAAAGGTAATCCA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGTGGCGTTTATGAGAAAATG-CAGCAAAAGGTAAAGCA
* **
26935 ATAGCGACG-TTTATGGGA-
65 ATAGCGGCGCTTTA--CCAT
* * * ** * * * *
26953 AAACGCCGTAAAAGATAAA-A-CAATAGTGGCGCTTACCCA-TAAATGCTGCAAAAGATAAAACA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGTGGCGTTTA-TGAGAAAATGCAGCAAAAGGTAAAGCA
* * * ** *
27015 ATAACGGAGTTTATAGGAA
65 ATAGCGGCGCTT-TACCAT
** * * *
27034 AAACGCCGCAAAAGGTAAAGAGCAATAGCAGCG-TTATGGGAAAACGCCGCAAAAGGTAAAGCAA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGTGGCGTTTATGAGAAAATGCAGCAAAAGGTAAAGCAA
27098 TAGCGGCGCTTTACCAT
66 TAGCGGCGCTTTACCAT
*** ** * * *
27115 AAACATTGCAAAAGGTAAAGCA-CAATAACGGTGTTTATGATAAAATGCAGCAAAAGGTAAAACA
1 AAACGCCGCAAAAGGTAAAG-AGCAATAGTGGCGTTTATGAGAAAATGCAGCAAAAGGTAAAGCA
* *
27179 ATAGTGGCGCTTTCCCAT
65 ATAGCGGCGCTTTACCAT
* * * *
27197 AAACGCCGCAAAAGGTAAAGAGCAATAGTGGTGTTTGTGGGAAAATGCCA-CAAAAGGTAAACCA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGTGGCGTTTATGAGAAAATG-CAGCAAAAGGTAAAGCA
* **
27261 ATAGTGGCG-TTTATGGGA-
65 ATAGCGGCGCTTTA--CCAT
* * * * * *
27279 AAACGCTGCAAAAGATAAAGAGCATTAGCGACATTTATGAGAAAA
1 AAACGCCGCAAAAGGTAAAGAGCAATAGTGGCGTTTATGAGAAAA
27324 CGCCGCTAAT
Statistics
Matches: 416, Mismatches: 98, Indels: 41
0.75 0.18 0.07
Matches are distributed among these distances:
79 1 0.00
80 37 0.09
81 81 0.19
82 283 0.68
83 13 0.03
84 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.19
Consensus pattern (82 bp):
AAACGCCGCAAAAGGTAAAGAGCAATAGTGGCGTTTATGAGAAAATGCAGCAAAAGGTAAAGCAA
TAGCGGCGCTTTACCAT
Found at i:30700 original size:23 final size:25
Alignment explanation
Indices: 30661--30706 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
30651 TTATAATACT
30661 AATTCAATAAAAATTTAAAAATAAA
1 AATTCAATAAAAATTTAAAAATAAA
30686 AATT-AAT-AAAATTTAAAAATA
1 AATTCAATAAAAATTTAAAAATA
30707 TCAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.67
24 3 0.14
25 4 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (25 bp):
AATTCAATAAAAATTTAAAAATAAA
Found at i:30714 original size:19 final size:17
Alignment explanation
Indices: 30682--30716 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
30672 AATTTAAAAA
30682 TAAAAATTAATAAAATT
1 TAAAAATTAATAAAATT
30699 TAAAAATATCAATAAAAT
1 TAAAAAT-T-AATAAAAT
30717 CATCATAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAATTAATAAAATT
Found at i:30887 original size:21 final size:21
Alignment explanation
Indices: 30861--30900 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30851 TTTTAGAATG
30861 TTAATT-CTACAAAATAATTAT
1 TTAATTACTA-AAAATAATTAT
*
30882 TTAATTATTAAAAATAATT
1 TTAATTACTAAAAATAATT
30901 TAAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAATTACTAAAAATAATTAT
Found at i:30888 original size:8 final size:8
Alignment explanation
Indices: 30875--30924 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
30865 TTCTACAAAA
30875 TAATTATT
1 TAATTATT
30883 TAATTATT
1 TAATTATT
* *
30891 AAAAATAATT
1 --TAATTATT
*
30901 TAAATATT
1 TAATTATT
30909 TAATTATT
1 TAATTATT
30917 TAATTATT
1 TAATTATT
30925 AAAAACAACC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
8 28 0.82
10 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TAATTATT
Found at i:30913 original size:34 final size:34
Alignment explanation
Indices: 30875--30950 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
30865 TTCTACAAAA
* **
30875 TAATTATTTAATTATTAAAAATAATTTAAATATT
1 TAATTATTTAATTATTAAAAACAACCTAAATATT
30909 TAATTATTTAATTATTAAAAACAACCTAAATATT
1 TAATTATTTAATTATTAAAAACAACCTAAATATT
30943 TAATTATT
1 TAATTATT
30951 AAAAACAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (34 bp):
TAATTATTTAATTATTAAAAACAACCTAAATATT
Found at i:30943 original size:26 final size:26
Alignment explanation
Indices: 30913--30968 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
30903 AATATTTAAT
30913 TATTTAATTATTAAAAACAAC-CTAAA
1 TATTTAATTATTAAAAACAACTC-AAA
30939 TATTTAATTATTAAAAACAACTCAAA
1 TATTTAATTATTAAAAACAACTCAAA
30965 TATT
1 TATT
30969 CGGTTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.38
Consensus pattern (26 bp):
TATTTAATTATTAAAAACAACTCAAA
Found at i:31188 original size:6 final size:6
Alignment explanation
Indices: 31177--31203 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31167 TAGGAAGATA
31177 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
31204 CATATAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:31578 original size:17 final size:17
Alignment explanation
Indices: 31556--31650 Score: 127
Period size: 17 Copynumber: 5.5 Consensus size: 17
31546 ATTTTTAAAA
*
31556 AAATTTATTTTAAGGTT
1 AAATTTATTTTAAGTTT
31573 AAATTTATTTTAAGTTT
1 AAATTTATTTTAAGTTT
* *
31590 AAATTTGTTTTAAATTT
1 AAATTTATTTTAAGTTT
*
31607 AAATTTAATTTAAGTTT
1 AAATTTATTTTAAGTTT
*
31624 AAATTTATTTATAAATTT
1 AAATTTATTT-TAAGTTT
*
31642 AAAATTATT
1 AAATTTATT
31651 CCAAATTTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
17 54 0.79
18 14 0.21
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
AAATTTATTTTAAGTTT
Found at i:31590 original size:6 final size:6
Alignment explanation
Indices: 31571--31644 Score: 57
Period size: 6 Copynumber: 12.8 Consensus size: 6
31561 TATTTTAAGG
* * **
31571 TTAAAT TT-ATT TTAAGT TTAAAT TT-GTT TTAAAT TTAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
31616 TTAAGT TTAAAT TT-ATT TATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT T-TAAAT TTAAA
31645 ATTATTCCAA
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
5 15 0.29
6 34 0.65
7 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
TTAAAT
Found at i:32287 original size:11 final size:11
Alignment explanation
Indices: 32268--32312 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
32258 TATATAATAG
32268 TATATATTTAT
1 TATATATTTAT
32279 T-TGATATTTAT
1 TAT-ATATTTAT
32290 TATATATTTA-
1 TATATATTTAT
*
32300 -ATACATTTAT
1 TATATATTTAT
32310 TAT
1 TAT
32313 TTCCTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
9 8 0.28
10 1 0.03
11 19 0.66
12 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (11 bp):
TATATATTTAT
Found at i:33354 original size:224 final size:224
Alignment explanation
Indices: 32958--33405 Score: 860
Period size: 224 Copynumber: 2.0 Consensus size: 224
32948 GGGAGGGAAA
*
32958 AATAATTTTTTTTGAAGTTTTAATAGTATTTATAGCCCTCCAAAACGGCGCCGTTTTGGGTGTGG
1 AATAAATTTTTTTGAAGTTTTAATAGTATTTATAGCCCTCCAAAACGGCGCCGTTTTGGGTGTGG
33023 CTAAAACACCACAAAATGAAGTTGTTTTGGCCAAATCGATTTGACCCGTCCCGACCCGCCTGATA
66 CTAAAACACCACAAAATGAAGTTGTTTTGGCCAAATCGATTTGACCCGTCCCGACCCGCCTGATA
33088 GGATCCGCGTGTTTTATAAAAATGGTTTATTTATGCGCACAGTCCTTCCACTTTTTTTATATTTT
131 GGATCCGCGTGTTTTATAAAAATGGTTTATTTATGCGCACAGTCCTTCCACTTTTTTTATATTTT
*
33153 TACAATCAGGTCATTTTTATATTTTTAAT
196 TACAATCAGGTCATTTTTATAATTTTAAT
33182 AATAAATTTTTTTGAAGTTTTAATAGTATTTATAGCCCTCCAAAACGGCGCCGTTTTGGGTGTGG
1 AATAAATTTTTTTGAAGTTTTAATAGTATTTATAGCCCTCCAAAACGGCGCCGTTTTGGGTGTGG
*
33247 CTAAAACACCACAAAATGAAGTTGTTTTGGCCAAATTGATTTGACCCGTCCCGACCCGCCTGATA
66 CTAAAACACCACAAAATGAAGTTGTTTTGGCCAAATCGATTTGACCCGTCCCGACCCGCCTGATA
*
33312 GGATCCGCGTGTTTTATAAAAATGGTTTATTTATGTGCACAGTCCTTCCACTTTTTTTATATTTT
131 GGATCCGCGTGTTTTATAAAAATGGTTTATTTATGCGCACAGTCCTTCCACTTTTTTTATATTTT
33377 TACAATCAGGTCATTTTTATAATTTTAAT
196 TACAATCAGGTCATTTTTATAATTTTAAT
33406 TAATTTTTAA
Statistics
Matches: 220, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
224 220 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (224 bp):
AATAAATTTTTTTGAAGTTTTAATAGTATTTATAGCCCTCCAAAACGGCGCCGTTTTGGGTGTGG
CTAAAACACCACAAAATGAAGTTGTTTTGGCCAAATCGATTTGACCCGTCCCGACCCGCCTGATA
GGATCCGCGTGTTTTATAAAAATGGTTTATTTATGCGCACAGTCCTTCCACTTTTTTTATATTTT
TACAATCAGGTCATTTTTATAATTTTAAT
Found at i:33764 original size:29 final size:28
Alignment explanation
Indices: 33734--34178 Score: 213
Period size: 29 Copynumber: 15.3 Consensus size: 28
33724 AAAAATAAAT
*
33734 TTTTACCCCAAACATCCAAAATTTACCA
1 TTTTACCCCAAACATCCAAAAATTACCA
* *** *
33762 TTTTACCCCCGAGTGTTCAAAAATTACCA
1 TTTTA-CCCCAAACATCCAAAAATTACCA
**
33791 TTTTACCCTCAAATGTCCAAAAATTA-CA
1 TTTTACCC-CAAACATCCAAAAATTACCA
** ***
33819 TTATTGACCTTGAATTTTCCAAAAATTACCA
1 TT-TT-ACC-CCAAACATCCAAAAATTACCA
* *
33850 TTTTATCCCTAAACATCCAAAAATTATCA
1 TTTTA-CCCCAAACATCCAAAAATTACCA
* **
33879 TTTTATCCTCAAATGTCCAAAAATTA-CA
1 TTTTA-CCCCAAACATCCAAAAATTACCA
* * * *
33907 TTTTTGACCCCGAACTTTTC-AAAATTACTA
1 -TTTT-ACCCCAAAC-ATCCAAAAATTACCA
*
33937 TTTTACCCTCGAACATCCAAAAATTA-CA
1 TTTTACCC-CAAACATCCAAAAATTACCA
* * * *
33965 TTTTTGATCTCAAACTTTCTAAAAATTACCA
1 -TTTT-ACCCCAAAC-ATCCAAAAATTACCA
* *
33996 TTTTACCCTCAAACATTCAAAAATTAGCA
1 TTTTACCC-CAAACATCCAAAAATTACCA
* **
34025 -TTTACCCCTGAATGTCCAAAAATTA-CA
1 TTTTACCCC-AAACATCCAAAAATTACCA
* * **
34052 TTTTTGACCTCAAACCTTTAAAAAATTACCA
1 -TTTT-ACCCCAAA-CATCCAAAAATTACCA
** **
34083 TTTTACCCTCGGATGTCCAAAAATTA-CA
1 TTTTACCC-CAAACATCCAAAAATTACCA
* * *
34111 TTTTTGACCCCGAACTTTCC-AAAATTACTA
1 -TTTT-ACCCCAAAC-ATCCAAAAATTACCA
* *
34141 TTTTACCCTCTAATATCCAAAAATTACCA
1 TTTTACCC-CAAACATCCAAAAATTACCA
34170 TTTTACCCC
1 TTTTACCCC
34179 TGAACATATA
Statistics
Matches: 318, Mismatches: 68, Indels: 62
0.71 0.15 0.14
Matches are distributed among these distances:
27 3 0.01
28 50 0.16
29 184 0.58
30 73 0.23
31 8 0.03
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.34
Consensus pattern (28 bp):
TTTTACCCCAAACATCCAAAAATTACCA
Found at i:33842 original size:88 final size:88
Alignment explanation
Indices: 33748--33968 Score: 268
Period size: 88 Copynumber: 2.5 Consensus size: 88
33738 ACCCCAAACA
* *** *
33748 TCCAAAATTTACCATTTTACCCCCGAGTGTTCAAAAATTACCATTTTACCCTCAAATGTCCAAAA
1 TCCAAAA-TTACCATTTTACCCCCAAACATCCAAAAATTACCATTTTACCCTCAAATGTCCAAAA
**
33813 ATTACATTATTGACCTTGAA-TTT
65 ATTACATTATTGACCCCGAACTTT
* * * *
33836 TCCAAAAATTACCATTTTATCCCTAAACATCCAAAAATTATCATTTTATCCTCAAATGTCCAAAA
1 TCC-AAAATTACCATTTTACCCCCAAACATCCAAAAATTACCATTTTACCCTCAAATGTCCAAAA
*
33901 ATTACATTTTTGACCCCGAACTTT
65 ATTACATTATTGACCCCGAACTTT
* * *
33925 T-CAAAATTACTATTTTACCCTCGAACATCCAAAAATTA-CATTTT
1 TCCAAAATTACCATTTTACCCCCAAACATCCAAAAATTACCATTTT
33969 TGATCTCAAA
Statistics
Matches: 114, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
86 6 0.05
87 31 0.27
88 69 0.61
89 8 0.07
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (88 bp):
TCCAAAATTACCATTTTACCCCCAAACATCCAAAAATTACCATTTTACCCTCAAATGTCCAAAAA
TTACATTATTGACCCCGAACTTT
Found at i:33956 original size:146 final size:147
Alignment explanation
Indices: 33780--34179 Score: 531
Period size: 146 Copynumber: 2.7 Consensus size: 147
33770 CCGAGTGTTC
* * * *
33780 AAAAATTACCATTTTACCCTCAAATGTCCAAAAATTACATTATTGACCTTGAATTTTCCAAAAAT
1 AAAAATTACCATTTTACCCTCGAATGTCCAAAAATTACATTTTTGACCTCGAACTTTCCAAAAAT
* *
33845 TACCATTTTATCCCT-AAACATCCAAAAATTATCATTTTA-TCCTCAAATGTCCAAAAATTACAT
66 TACCATTTTA-CCCTCAAACATCCAAAAATTACCATTTTACCCCT-AAATGTCCAAAAATTACAT
* *
33908 TTTTGACCCCGAA-CTTTT
129 TTTTGACCCCAAACCTTTA
* * ** * * *
33926 CAAAATTACTATTTTACCCTCGAACATCCAAAAATTACATTTTTGATCTCAAACTTTCTAAAAAT
1 AAAAATTACCATTTTACCCTCGAATGTCCAAAAATTACATTTTTGACCTCGAACTTTCCAAAAAT
* * *
33991 TACCATTTTACCCTCAAACATTCAAAAATTAGCA-TTTACCCCTGAATGTCCAAAAATTACATTT
66 TACCATTTTACCCTCAAACATCCAAAAATTACCATTTTACCCCTAAATGTCCAAAAATTACATTT
*
34055 TTGACCTCAAACCTTTA
131 TTGACCCCAAACCTTTA
* *
34072 AAAAATTACCATTTTACCCTCGGATGTCCAAAAATTACATTTTTGACCCCGAACTTTCC-AAAAT
1 AAAAATTACCATTTTACCCTCGAATGTCCAAAAATTACATTTTTGACCTCGAACTTTCCAAAAAT
* * *
34136 TACTATTTTACCCTCTAATATCCAAAAATTACCATTTTACCCCT
66 TACCATTTTACCCTCAAACATCCAAAAATTACCATTTTACCCCT
34180 GAACATATAA
Statistics
Matches: 218, Mismatches: 32, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
145 71 0.33
146 147 0.67
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (147 bp):
AAAAATTACCATTTTACCCTCGAATGTCCAAAAATTACATTTTTGACCTCGAACTTTCCAAAAAT
TACCATTTTACCCTCAAACATCCAAAAATTACCATTTTACCCCTAAATGTCCAAAAATTACATTT
TTGACCCCAAACCTTTA
Found at i:34066 original size:87 final size:87
Alignment explanation
Indices: 33690--34224 Score: 345
Period size: 87 Copynumber: 6.1 Consensus size: 87
33680 CCCTAAATTT
* * * * *
33690 TCCAAAAATCACATTTTGATTCTCAAACTTTCCAAAAAATAAATTTTTACCC-CAAACATCCAAA
1 TCCAAAAATTACATTTTGATCCTCAAACTTTCCAAAAATTACA-TTTTACCCTCAAACATTCAAA
* * ***
33754 ATTTACCATTTTACCCCCGAGTG
65 AATTACCATTTTACCCCTGAACA
* * * ** **
33777 TTCAAAAATTACCATTTT-ACCCTCAAA-TGTCCAAAAATTACATTATTGA-CCTTGAATTTTCC
1 TCCAAAAATTA-CATTTTGATCCTCAAACTTTCCAAAAATTACATT-TT-ACCCTCAAACATT-C
* *
33839 AAAAATTACCATTTTATCCCTAAACA
62 AAAAATTACCATTTTACCCCTGAACA
* * *
33865 TCCAAAAATTATCATTTT-ATCCTCAAA-TGTCCAAAAATTACATTTTTGACCC-CGAACTTTTC
1 TCCAAAAATTA-CATTTTGATCCTCAAACTTTCCAAAAATTACA-TTTT-ACCCTCAAAC-ATTC
*
33927 -AAAATTACTATTTTA-CCCTCGAACA
62 AAAAATTACCATTTTACCCCT-GAACA
*
33952 TCCAAAAATTACATTTTTGAT-CTCAAACTTTCTAAAAATTACCATTTTACCCTCAAACATTCAA
1 TCCAAAAATTACA-TTTTGATCCTCAAACTTTCCAAAAATTA-CATTTTACCCTCAAACATTCAA
* **
34016 AAATTAGCA-TTTACCCCTGAATG
64 AAATTACCATTTTACCCCTGAACA
* ** ** *
34039 TCCAAAAATTACATTTTTGA-CCTCAAACCTTT-AAAAAATTACCATTTTACCCTCGGATGTCCA
1 TCCAAAAATTACA-TTTTGATCCTCAAA-CTTTCCAAAAATTA-CATTTTACCCTCAAACATTCA
*
34102 AAAATTA-CATTTTTGACCCC-GAACTT
63 AAAATTACCA-TTTT-ACCCCTGAAC-A
* * * *
34128 TCC-AAAATTACTATTTT-ACCCTCTAA-TATCCAAAAATTACCATTTTACCC-CTGAACATAT-
1 TCCAAAAATTAC-ATTTTGATCCTCAAACTTTCCAAAAATTA-CATTTTACCCTC-AAACAT-TC
*** * *
34188 AAAAATTATTGTTTTACCCTTGAACG
62 AAAAATTACCATTTTACCCCTGAACA
34214 TCCAAAAATTA
1 TCCAAAAATTA
34225 TCGTTTTGCC
Statistics
Matches: 365, Mismatches: 53, Indels: 60
0.76 0.11 0.13
Matches are distributed among these distances:
85 2 0.01
86 34 0.09
87 177 0.48
88 134 0.37
89 18 0.05
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (87 bp):
TCCAAAAATTACATTTTGATCCTCAAACTTTCCAAAAATTACATTTTACCCTCAAACATTCAAAA
ATTACCATTTTACCCCTGAACA
Found at i:34193 original size:58 final size:60
Alignment explanation
Indices: 33985--34224 Score: 227
Period size: 58 Copynumber: 4.1 Consensus size: 60
33975 CAAACTTTCT
33985 AAAAATTACCA-TTTT-ACCCTCAAACA-TTCAAAAATTAGC-A-TTTACCC-CTGAATGTCC
1 AAAAATTA-CATTTTTGACCC-CAAACATTTCAAAAATTA-CTATTTTACCCTCTGAATGTCC
* * * * *
34042 AAAAATTACATTTTTGACCTCAAACCTTTAAAAAATTACCATTTTACCCTC-GGATGTCC
1 AAAAATTACATTTTTGACCCCAAACATTTCAAAAATTACTATTTTACCCTCTGAATGTCC
* * *
34101 AAAAATTACATTTTTGACCCCGAAC-TTTCCAAAATTACTATTTTACCCTCT-AATATCC
1 AAAAATTACATTTTTGACCCCAAACATTTCAAAAATTACTATTTTACCCTCTGAATGTCC
* * * * *
34159 AAAAATTACCA-TTTT-ACCCCTGAACATAT-AAAAATTATTGTTTTACCCT-TGAACGTCC
1 AAAAATTA-CATTTTTGACCCC-AAACATTTCAAAAATTACTATTTTACCCTCTGAATGTCC
34217 AAAAATTA
1 AAAAATTA
34225 TCGTTTTGCC
Statistics
Matches: 155, Mismatches: 17, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
56 2 0.01
57 24 0.15
58 87 0.56
59 41 0.26
60 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (60 bp):
AAAAATTACATTTTTGACCCCAAACATTTCAAAAATTACTATTTTACCCTCTGAATGTCC
Found at i:34202 original size:29 final size:29
Alignment explanation
Indices: 34141--34236 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
34131 AAAATTACTA
* * * *
34141 TTTTACCCTCT-AATATCCAAAAATTACCA
1 TTTTACCC-CTGAACATACAAAAATTATCG
* *
34170 TTTTACCCCTGAACATATAAAAATTATTG
1 TTTTACCCCTGAACATACAAAAATTATCG
* * *
34199 TTTTACCCTTGAACGTCCAAAAATTATCG
1 TTTTACCCCTGAACATACAAAAATTATCG
*
34228 TTTTGCCCC
1 TTTTACCCC
34237 CCGACATCCA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 2 0.04
29 51 0.96
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.36
Consensus pattern (29 bp):
TTTTACCCCTGAACATACAAAAATTATCG
Found at i:34641 original size:97 final size:96
Alignment explanation
Indices: 34475--34758 Score: 391
Period size: 97 Copynumber: 3.0 Consensus size: 96
34465 TAAACCTTTA
* * *
34475 AAATCGAGGCAATATTCCTTTATCTCGGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
1 AAATCGAGGCAATGTTTCTTTATCTCTGG-TTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
* *
34540 TTTTCTTCAAACCGGGATGATGGAATACCCTT
65 TTTTCTTCAAACCGGGATAATCGAATACCCTT
* * *
34572 AAATCGAGGCAATGTTTCTTTATCTCTGGTTCTGAAAATTTGTGTCTTAACTTACTAGGCACAAT
1 AAATCGAGGCAATGTTTCTTTATCTCTGGTT-TGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
* *
34637 TTTTCTTCAAACCGGGATAATCAAATACCTTT
65 TTTTCTTCAAACCGGGATAATCGAATACCCTT
* *
34669 AAATCGAGGCAATGATTCTTTATCTCTGG-TT-----TTTGTGCCTTAACTTACTAGGCGCGACT
1 AAATCGAGGCAATGTTTCTTTATCTCTGGTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGATT
*
34728 TTTCTTCAAATCGGGATAATCGAATACCCTT
66 TTTCTTCAAACCGGGATAATCGAATACCCTT
34759 TTCTAAGGTT
Statistics
Matches: 168, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
90 52 0.31
95 1 0.01
96 3 0.02
97 112 0.67
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (96 bp):
AAATCGAGGCAATGTTTCTTTATCTCTGGTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGATT
TTTCTTCAAACCGGGATAATCGAATACCCTT
Found at i:40739 original size:66 final size:66
Alignment explanation
Indices: 40632--40765 Score: 180
Period size: 66 Copynumber: 2.0 Consensus size: 66
40622 GCAAATTGCT
* * *
40632 CAACTTAAAGCGAAGCCAGTAGCGAGAGAAGCAGAGGCTCAAAGAAAATATGATGAACT-TCAGC
1 CAACTTAAAGCCAAGCCAGCAGCGAGAGAAGCAGAGGCTCAAAGAAAATATGACGAACTGT-AGC
40696 TA
65 TA
** * * *
40698 CAACTTAAAGCCAAGGTAGCAGCGAGGGAAGCAGAGTCTCAAAGAAAGTATGACGAACTGTAGCT
1 CAACTTAAAGCCAAGCCAGCAGCGAGAGAAGCAGAGGCTCAAAGAAAATATGACGAACTGTAGCT
40763 A
66 A
40764 CA
1 CA
40766 GCTTCAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
66 58 0.98
67 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (66 bp):
CAACTTAAAGCCAAGCCAGCAGCGAGAGAAGCAGAGGCTCAAAGAAAATATGACGAACTGTAGCT
A
Found at i:41174 original size:43 final size:42
Alignment explanation
Indices: 41039--41180 Score: 176
Period size: 43 Copynumber: 3.3 Consensus size: 42
41029 ATGTTAATGG
* * * *
41039 CGTTTGTGGGAAAAATGCCGCCAAAGAACATGTTCTATAGCGG
1 CGTTTGTGGGAAAAATGCCGCTAAAG-ACATGTTTTATAGTGA
*
41082 CGCTTGTGGGAAAAATGCCGCTAAAGGACATGTTTTATAGTGA
1 CGTTTGTGGGAAAAATGCCGCTAAA-GACATGTTTTATAGTGA
* *
41125 CATTTGTGGTAAAAATGCCGCTAAAGACCATGTTTTATAGTGA
1 CGTTTGTGGGAAAAATGCCGCTAAAGA-CATGTTTTATAGTGA
* *
41168 TGTTTGTCGGAAA
1 CGTTTGTGGGAAA
41181 GCGCTGCTAA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 2 0.02
43 82 0.96
44 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (42 bp):
CGTTTGTGGGAAAAATGCCGCTAAAGACATGTTTTATAGTGA
Found at i:42302 original size:30 final size:29
Alignment explanation
Indices: 42268--42479 Score: 181
Period size: 29 Copynumber: 7.5 Consensus size: 29
42258 AGGCTGCAGA
42268 AAACAGAATAATTTATTCAATTTTAAATTC
1 AAACAGAATAATTTATTCAA-TTTAAATTC
*
42298 AAACAAAATAATTTATTTCAATTTAAAATT-
1 AAACAGAATAATTTA-TTCAATTT-AAATTC
* * *
42328 TATCAGAATAATTTATTCAA--TCAATT-
1 AAACAGAATAATTTATTCAATTTAAATTC
* *
42354 ----AGAATAATTTATTGAATTTAAAATC
1 AAACAGAATAATTTATTCAATTTAAATTC
* *
42379 AATCAGAACAATTTATTCAATTTAAATTC
1 AAACAGAATAATTTATTCAATTTAAATTC
* * *
42408 AAACGGAATAATTTATTCAAATTAAAATC
1 AAACAGAATAATTTATTCAATTTAAATTC
* * * *
42437 AATCAAAATAATTTATTCAAATTAAAATC
1 AAACAGAATAATTTATTCAATTTAAATTC
*
42466 AGTA-AGAATAATTT
1 A-AACAGAATAATTT
42480 TGGGATTGAC
Statistics
Matches: 150, Mismatches: 22, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
22 15 0.10
24 4 0.03
26 4 0.03
27 1 0.01
29 87 0.58
30 29 0.19
31 10 0.07
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (29 bp):
AAACAGAATAATTTATTCAATTTAAATTC
Found at i:42419 original size:80 final size:82
Alignment explanation
Indices: 42272--42427 Score: 210
Period size: 80 Copynumber: 1.9 Consensus size: 82
42262 TGCAGAAAAC
* * * *
42272 AGAATAATTTATTCAATTTTAAATTCAAACAAAATAATTTATTTCAATTTAAAATTTATCAGAAT
1 AGAATAATTTATTCAATTTTAAAATCAAACAAAACAATTTATTTCAATTTAAAATTAAACAGAAT
42337 AATTTATTCAATCAATT
66 AATTTATTCAATCAATT
* * * *
42354 AGAATAATTTATTGAA-TTTAAAATCAATCAGAACAATTTA-TTCAATTT-AAATTCAAACGGAA
1 AGAATAATTTATTCAATTTTAAAATCAAACAAAACAATTTATTTCAATTTAAAATT-AAACAGAA
42416 TAATTTATTCAA
65 TAATTTATTCAA
42428 ATTAAAATCA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
79 5 0.08
80 25 0.38
81 20 0.31
82 15 0.23
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (82 bp):
AGAATAATTTATTCAATTTTAAAATCAAACAAAACAATTTATTTCAATTTAAAATTAAACAGAAT
AATTTATTCAATCAATT
Found at i:44186 original size:13 final size:13
Alignment explanation
Indices: 44170--44197 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
44160 TTATCAACTT
44170 AAGTAAGAGTAGA
1 AAGTAAGAGTAGA
44183 AAGTAAGAGTAGA
1 AAGTAAGAGTAGA
44196 AA
1 AA
44198 TGTCATTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (13 bp):
AAGTAAGAGTAGA
Found at i:45129 original size:28 final size:28
Alignment explanation
Indices: 45088--45141 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
45078 GTTATTCGAT
* * *
45088 TTACTCCTTGTTGACCCAATGGTCATGC
1 TTACTCCCTATTGACCCAAAGGTCATGC
45116 TTACTCCCTATTGACCCAAAGGTCAT
1 TTACTCCCTATTGACCCAAAGGTCAT
45142 ACCTATTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (28 bp):
TTACTCCCTATTGACCCAAAGGTCATGC
Found at i:51158 original size:22 final size:22
Alignment explanation
Indices: 51133--51201 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
51123 TACAGTTTAA
*
51133 AATCAATCATAATAATTTATTC
1 AATCAATCAGAATAATTTATTC
* *
51155 AATCAA-CTAGAATAAATTATTT
1 AATCAATC-AGAATAATTTATTC
*
51177 AATCAATTAGAATAATTTATTC
1 AATCAATCAGAATAATTTATTC
51199 AAT
1 AAT
51202 TTAAATTCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (22 bp):
AATCAATCAGAATAATTTATTC
Found at i:51219 original size:29 final size:29
Alignment explanation
Indices: 51177--51282 Score: 167
Period size: 29 Copynumber: 3.7 Consensus size: 29
51167 TAAATTATTT
*
51177 AATCAATTAGAATAATTTATTCAATTTAA
1 AATCAATCAGAATAATTTATTCAATTTAA
* * *
51206 ATTCAAACAAAATAATTTATTCAATTTAA
1 AATCAATCAGAATAATTTATTCAATTTAA
*
51235 AATCAATTAGAATAATTTATTCAATTTAA
1 AATCAATCAGAATAATTTATTCAATTTAA
51264 AATCAATCAGAATAATTTA
1 AATCAATCAGAATAATTTA
51283 AGGATTAACA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (29 bp):
AATCAATCAGAATAATTTATTCAATTTAA
Found at i:51971 original size:37 final size:37
Alignment explanation
Indices: 51921--51994 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
51911 ATCCATATTA
*
51921 ACTTGATACAGACCTGAATGGATACACGAATTCCAAC
1 ACTTGATACAGACCTGAACGGATACACGAATTCCAAC
51958 ACTTGATACAGACCTGAACGGATACACGAATTCCAAC
1 ACTTGATACAGACCTGAACGGATACACGAATTCCAAC
51995 TAACACACCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (37 bp):
ACTTGATACAGACCTGAACGGATACACGAATTCCAAC
Found at i:63497 original size:23 final size:23
Alignment explanation
Indices: 63471--63515 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
63461 AATTTCGAAT
**
63471 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
63494 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
63516 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:71373 original size:17 final size:17
Alignment explanation
Indices: 71329--71373 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
71319 CGACAAATTA
71329 TTTCTTTTTTTCATTCT
1 TTTCTTTTTTTCATTCT
* *
71346 TTTCTCTTTTTC-TTTT
1 TTTCTTTTTTTCATTCT
71362 CTTTCTTTTTTT
1 -TTTCTTTTTTT
71374 ATAGGTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTCTTTTTTTCATTCT
Found at i:71990 original size:18 final size:18
Alignment explanation
Indices: 71954--71999 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
71944 AGATAAACTA
*
71954 ACAAATAAA-ATGCAGTG
1 ACAAATAAATATGCAATG
71971 ACAAATAAATATGCAATG
1 ACAAATAAATATGCAATG
*
71989 ACAACTAAATA
1 ACAAATAAATA
72000 AAATGCATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.20
Consensus pattern (18 bp):
ACAAATAAATATGCAATG
Found at i:94261 original size:18 final size:18
Alignment explanation
Indices: 94234--94276 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
94224 TTAAAAAACC
* *
94234 CCTTTACTCAACTCTATT
1 CCTTTTCTCAACTCCATT
94252 CCTTTTCTCAACTCCATT
1 CCTTTTCTCAACTCCATT
*
94270 TCTTTTC
1 CCTTTTC
94277 ACAATTGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.49
Consensus pattern (18 bp):
CCTTTTCTCAACTCCATT
Found at i:95091 original size:3 final size:3
Alignment explanation
Indices: 95085--95168 Score: 91
Period size: 3 Copynumber: 28.7 Consensus size: 3
95075 GAGCTAAAAA
*
95085 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG TAG -AG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * * * * *
95131 GAG AAG GAG AAG GAG AAG GAG AAG GAG AAG GAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
95169 AGGGAAAGAG
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
2 4 0.06
3 64 0.94
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:95485 original size:147 final size:147
Alignment explanation
Indices: 95192--95709 Score: 565
Period size: 147 Copynumber: 3.6 Consensus size: 147
95182 TGATTTTTTT
* * * * * **
95192 TTTTGTTGTTTTTAATTTATTTTAAAATTATTTTGTTTGT--TT-TTA-ATTATTATAAAGTTTA
1 TTTTGTTGCTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATA-AATTAT-TTGTTTA
* * * * *
95253 GTTTAATGTTTA--TGATATGTTATAGA-GTTTTTGTTTAGTAGAGTAGATTAATA-GAAAAAAC
64 GTTTAATGTTTATGTGATTTGTTATAAATTTTTTTGTTTAGTAGAGTAGATTAA-AGGGAAGAA-
** * *
95314 AGCCAAAAGAGA-GATAACTT-
127 AGATAAAAGAAATG-TAAATTG
95334 TTTTGTTGCTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATAAATTATTTGTTTAGT
1 TTTTGTTGCTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATAAATTATTTGTTTAGT
*
95399 TTAATGTTTATGTGATTTATTATAAATTTTTTTGTTTAGTAGAGTAGATTAAAGGGAAGAAAGAT
66 TTAATGTTTATGTGATTTGTTATAAATTTTTTTGTTTAGTAGAGTAGATTAAAGGGAAGAAAGAT
95464 AAAAGAAATGTAAATTG
131 AAAAGAAATGTAAATTG
* *
95481 TTTTGTTGCTTTTAATTTAATTTAAAGTTATTTTATTAGTAATTATTATAAATTATTTCTTTAGT
1 TTTTGTTGCTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATAAATTATTTGTTTAGT
* * * *
95546 TTAATTTTTCTGTGATTTGTTATTAATTTTTTTTATTTAGTAGAGTAGATTAAAGGGAAAGAAAG
66 TTAATGTTTATGTGATTTGTTA-TAAATTTTTTTGTTTAGTAGAGTAGATTAAAGGG-AAGAAAG
* *
95611 AT---A-AATTGTTAA--G
129 ATAAAAGAAATGTAAATTG
* *
95624 --TT-TT-CTTTTAATTTAATTTAAATTTATTTT-TTAGTAATTATTATAAATTATTTATTTAGT
1 TTTTGTTGCTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATAAATTATTTGTTTAGT
* *
95684 TTCATGTTTATATGATTTGTTATAAA
66 TTAATGTTTATGTGATTTGTTATAAA
95710 AAATTGTTTA
Statistics
Matches: 331, Mismatches: 33, Indels: 29
0.84 0.08 0.07
Matches are distributed among these distances:
137 3 0.01
138 47 0.14
139 25 0.08
140 2 0.01
141 2 0.01
142 36 0.11
143 1 0.00
144 19 0.06
145 15 0.05
146 28 0.08
147 112 0.34
148 32 0.10
149 9 0.03
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (147 bp):
TTTTGTTGCTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATAAATTATTTGTTTAGT
TTAATGTTTATGTGATTTGTTATAAATTTTTTTGTTTAGTAGAGTAGATTAAAGGGAAGAAAGAT
AAAAGAAATGTAAATTG
Found at i:95778 original size:25 final size:25
Alignment explanation
Indices: 95749--95808 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
95739 TTTTTTTGTT
* *
95749 TTTTTTTTTAAATTATTTTAAAGTTA
1 TTTTGTTTTAAATTATTATAAA-TTA
*
95775 TTTTGTTTTTAATTATTATAAATTA
1 TTTTGTTTTAAATTATTATAAATTA
95800 TTTTGTTTT
1 TTTTGTTTT
95809 GTTTAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 12 0.39
26 19 0.61
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (25 bp):
TTTTGTTTTAAATTATTATAAATTA
Found at i:95788 original size:26 final size:26
Alignment explanation
Indices: 95748--95808 Score: 88
Period size: 25 Copynumber: 2.3 Consensus size: 26
95738 ATTTTTTTGT
* *
95748 TTTTTTTTTTAAATTATTTTAAAGTTA
1 TTTTGTTTTTAAATTATTATAAA-TTA
95775 TTTTGTTTTT-AATTATTATAAATTA
1 TTTTGTTTTTAAATTATTATAAATTA
95800 TTTTGTTTT
1 TTTTGTTTT
95809 GTTTAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 12 0.38
26 11 0.34
27 9 0.28
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (26 bp):
TTTTGTTTTTAAATTATTATAAATTA
Found at i:97673 original size:32 final size:33
Alignment explanation
Indices: 97629--97709 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
97619 TCGAGCCACT
* * * *
97629 GCAGTACTCCACTCCTTCCGACCCTTTATCACC
1 GCAGTACACCACTCCTTCCGACCCATTACCAAC
*
97662 GCAGT-CACCACTCCTTCCGGCCCATTACCAAC
1 GCAGTACACCACTCCTTCCGACCCATTACCAAC
*
97694 GCAGTACTCCACTCCT
1 GCAGTACACCACTCCT
97710 CCCAAACAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 27 0.66
33 14 0.34
ACGTcount: A:0.20, C:0.46, G:0.11, T:0.23
Consensus pattern (33 bp):
GCAGTACACCACTCCTTCCGACCCATTACCAAC
Found at i:102940 original size:17 final size:18
Alignment explanation
Indices: 102905--102942 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
102895 AGCGAGCCAA
* *
102905 TTATATTTGTGTACTATG
1 TTATATTTGTGAACCATG
102923 TTATA-TTGTGAACCATG
1 TTATATTTGTGAACCATG
102940 TTA
1 TTA
102943 ACTTAGCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (18 bp):
TTATATTTGTGAACCATG
Found at i:110266 original size:21 final size:21
Alignment explanation
Indices: 110242--110293 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
110232 TGAGACAATA
110242 CTACCGATACGA-GT-ATGACTT
1 CTACCGATAC-ATGTAATG-CTT
*
110263 CTACCGAAACATGTAATGCTT
1 CTACCGATACATGTAATGCTT
110284 CTACCGATAC
1 CTACCGATAC
110294 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.85
22 3 0.11
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (21 bp):
CTACCGATACATGTAATGCTT
Found at i:114478 original size:33 final size:35
Alignment explanation
Indices: 114432--114496 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 35
114422 ATTCAATAAA
114432 AGAAAAAATTATAAATT-T-TAAA-GTAAAATGAT
1 AGAAAAAATTATAAATTATATAAAGGTAAAATGAT
*
114464 AGAAAATATTTATAAATTATATAAAGGTAAAAT
1 AGAAAA-AATTATAAATTATATAAAGGTAAAAT
114497 ATTTATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 6 0.21
33 10 0.36
34 1 0.04
35 4 0.14
36 7 0.25
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.32
Consensus pattern (35 bp):
AGAAAAAATTATAAATTATATAAAGGTAAAATGAT
Found at i:114495 original size:26 final size:25
Alignment explanation
Indices: 114466--114514 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
114456 AAAATGATAG
*
114466 AAAATATTTATAAATTATATAAAGGT
1 AAAATATTTATAAA-AATATAAAGGT
114492 AAAATATTTATAAAAATATAAAG
1 AAAATATTTATAAAAATATAAAG
114515 TATTTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (25 bp):
AAAATATTTATAAAAATATAAAGGT
Found at i:114772 original size:13 final size:13
Alignment explanation
Indices: 114754--114788 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
114744 GTATTTAATA
114754 TTTAATTAGTATT
1 TTTAATTAGTATT
*
114767 TTTAATATTGTATT
1 TTTAAT-TAGTATT
114781 TTTAATTA
1 TTTAATTA
114789 CAATAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (13 bp):
TTTAATTAGTATT
Found at i:122392 original size:17 final size:18
Alignment explanation
Indices: 122370--122403 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
122360 ATTATTGTAA
122370 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
122387 TTTAAATGTGTAATTAT
1 TTTAAATGTCTAATTAT
122404 CAAAACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Done.