Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008146.1 Hibiscus syriacus cultivar Beakdansim tig00110710_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 305896
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:727 original size:16 final size:16
Alignment explanation
Indices: 706--738 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
696 AGGGCCACAG
*
706 TTACTCTATTGAACTT
1 TTACTCCATTGAACTT
722 TTACTCCATTGAACTT
1 TTACTCCATTGAACTT
738 T
1 T
739 GACCATTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.48
Consensus pattern (16 bp):
TTACTCCATTGAACTT
Found at i:9455 original size:197 final size:191
Alignment explanation
Indices: 9119--9596 Score: 545
Period size: 197 Copynumber: 2.5 Consensus size: 191
9109 TTTTTTAAAT
* * ** * *
9119 TTTGTATTTTA-CGAGTCGATATATGTTTCTGATATGTGTTAGAA-CTAGAATTGAGGATTTTGA
1 TTTGTATTTTATAG-GTC-ATATATGTGTCTGAGGTGTATT-GAAGCTAAAATTGAGGATTTTGA
* *
9182 TGAAGTTTAGACACTTAA-AGATAAAAAAGACGAATGACATTCCTACTTATGTTAGAACTCTTAT
63 TGAAGTTT-GAAACTTAAGAGA-AAAAAAGACGAATGACATTCCTACTTATGTTAGAAATCTTAT
* * * * * *
9246 CATTATTTTTTAATAGGATTAGGATAACCCAAAATAATATACTTTTCAATTTAAACCCTTGTTAC
126 CATTACTTTTTAATAGGATTAGGATAAACCAAAAGAATATAATCTTCAATTTAAACCCTT-ATAC
9311 AC
190 AC
9313 TTTGTATTTTATAGGTCAATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGATTTTTGAT
1 TTTGTATTTTATAGGTC-ATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGA-TTTTGAT
9378 GAAGTTTGGAAACTTGAAGAGAAAAAAAGGAC-AGATGACATTCCTACTTCA-GTTAGAAATCTT
64 GAAGTTT-GAAACTT-AAGAGAAAAAAA-GACGA-ATGACATTCCTACTT-ATGTTAGAAATCTT
* * * *
9441 ATCTTTACTTTTTAATAGGATTAGGATAAACCAAAAGAATGTAATCTTCAATTTAAACTCTTATG
124 ATCATTACTTTTTAATAGGATTAGGATAAACCAAAAGAATATAATCTTCAATTTAAACCCTTATA
*
9506 GAC
189 CAC
* * * * * *
9509 TTTGTATTTTATAGATCA-GTATGTGTATGAGGTGTATTGGAGCTAAAATTGACGATTTTAATGA
1 TTTGTATTTTATAGGTCATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGATTTTGATGA
*
9573 AGTTTGAACAGTTAAAGAGAAAAA
66 AGTTTGAA-ACTT-AAGAGAAAAA
9597 GGAGGAATGG
Statistics
Matches: 246, Mismatches: 29, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
192 3 0.01
193 29 0.12
194 77 0.31
195 22 0.09
196 28 0.11
197 86 0.35
198 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (191 bp):
TTTGTATTTTATAGGTCATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGATTTTGATGA
AGTTTGAAACTTAAGAGAAAAAAAGACGAATGACATTCCTACTTATGTTAGAAATCTTATCATTA
CTTTTTAATAGGATTAGGATAAACCAAAAGAATATAATCTTCAATTTAAACCCTTATACAC
Found at i:13026 original size:17 final size:20
Alignment explanation
Indices: 13006--13055 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
12996 TTTTTTTAAA
13006 ATAAATAT-A-TTATTT-TT
1 ATAAATATCATTTATTTATT
13023 AT-AATATCATTTATTTAATT
1 ATAAATATCATTTATTT-ATT
*
13043 ATAAATATTATTT
1 ATAAATATCATTT
13056 TTGTTACATC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 3 0.11
18 6 0.22
20 4 0.15
21 9 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAAATATCATTTATTTATT
Found at i:15014 original size:22 final size:22
Alignment explanation
Indices: 14989--15030 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
14979 ATATCTATTA
14989 TATTGATTA-AAAATATAATTTG
1 TATT-ATTATAAAATATAATTTG
*
15011 TATTATTATAAATTATAATT
1 TATTATTATAAAATATAATT
15031 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TATTATTATAAAATATAATTTG
Found at i:15629 original size:96 final size:94
Alignment explanation
Indices: 15418--15700 Score: 361
Period size: 95 Copynumber: 3.0 Consensus size: 94
15408 TATCTGAGCC
* * * * *
15418 TAAACTAAAAGCAAAGAAACATAGTAAGAATCATTGATAAAGGCTTGAGAGGACCTTTGTCTTT-
1 TAAACTAAAA-CAAAGAAAGATAGTAAGAATAATTGATAAAGACTTGAGAGGTCCTTAGTCTTTC
* *
15482 TTTATTTATTTACACTTTTCAATTCTTTTAT
65 TTTCTTTATTTATACTTTTCAATT-TTTTAT
15513 TAAACTAAAACTAAAGAAAGATAGTAAGAATAATTGATAAAGACTTGAGAGGTCCTTGAGTCTTT
1 TAAACTAAAAC-AAAGAAAGATAGTAAGAATAATTGATAAAGACTTGAGAGGTCCTT-AGTCTTT
15578 CTTTCTTTATTTATACTTTTCAATTTTTTAT
64 CTTTCTTTATTTATACTTTTCAATTTTTTAT
* * * * * * *
15609 TAAATTAAAATCAAAGAAAGATAATAATAATAATTGATTAAGAGTGGAGAAGTCCTTAGTCTTTC
1 TAAACTAAAA-CAAAGAAAGATAGTAAGAATAATTGATAAAGACTTGAGAGGTCCTTAGTCTTTC
* **
15674 TTTCCTTATTTATTTTTTTCAATTTTT
65 TTTCTTTATTTATACTTTTCAATTTTT
15701 GATGATAATT
Statistics
Matches: 167, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
94 1 0.01
95 83 0.50
96 60 0.36
97 23 0.14
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (94 bp):
TAAACTAAAACAAAGAAAGATAGTAAGAATAATTGATAAAGACTTGAGAGGTCCTTAGTCTTTCT
TTCTTTATTTATACTTTTCAATTTTTTAT
Found at i:16988 original size:30 final size:29
Alignment explanation
Indices: 16953--17016 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
16943 CTAACAATAG
*
16953 AAAATGAAAGGGGTAAAATCAAACTAAACC
1 AAAATGAAAGGGG-AAAATCAAAATAAACC
** *
16983 AAAATGGGAGGGGCAAATCAAAATAAACC
1 AAAATGAAAGGGGAAAATCAAAATAAACC
17012 AAAAT
1 AAAAT
17017 TTGAAGGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.12
Consensus pattern (29 bp):
AAAATGAAAGGGGAAAATCAAAATAAACC
Found at i:28433 original size:32 final size:31
Alignment explanation
Indices: 28397--28473 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
28387 CGGGGCCACG
*
28397 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** ** *
28429 GGGCCTACCCGAGAATGATCTCAGGGCCGTA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
28460 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
28474 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:30068 original size:16 final size:16
Alignment explanation
Indices: 30047--30079 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
30037 AGGGCCACAG
*
30047 TTACTCTATTGAACTT
1 TTACTCCATTGAACTT
30063 TTACTCCATTGAACTT
1 TTACTCCATTGAACTT
30079 T
1 T
30080 GACCATTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.48
Consensus pattern (16 bp):
TTACTCCATTGAACTT
Found at i:38840 original size:197 final size:191
Alignment explanation
Indices: 38504--38981 Score: 545
Period size: 197 Copynumber: 2.5 Consensus size: 191
38494 TTTTTTAAAT
* * ** * *
38504 TTTGTATTTTA-CGAGTCGATATATGTTTCTGATATGTGTTAGAA-CTAGAATTGAGGATTTTGA
1 TTTGTATTTTATAG-GTC-ATATATGTGTCTGAGGTGTATT-GAAGCTAAAATTGAGGATTTTGA
* *
38567 TGAAGTTTAGACACTTAA-AGATAAAAAAGACGAATGACATTCCTACTTATGTTAGAACTCTTAT
63 TGAAGTTT-GAAACTTAAGAGA-AAAAAAGACGAATGACATTCCTACTTATGTTAGAAATCTTAT
* * * * * *
38631 CATTATTTTTTAATAGGATTAGGATAACCCAAAATAATATACTTTTCAATTTAAACCCTTGTTAC
126 CATTACTTTTTAATAGGATTAGGATAAACCAAAAGAATATAATCTTCAATTTAAACCCTT-ATAC
38696 AC
190 AC
38698 TTTGTATTTTATAGGTCAATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGATTTTTGAT
1 TTTGTATTTTATAGGTC-ATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGA-TTTTGAT
38763 GAAGTTTGGAAACTTGAAGAGAAAAAAAGGAC-AGATGACATTCCTACTTCA-GTTAGAAATCTT
64 GAAGTTT-GAAACTT-AAGAGAAAAAAA-GACGA-ATGACATTCCTACTT-ATGTTAGAAATCTT
* * * *
38826 ATCTTTACTTTTTAATAGGATTAGGATAAACCAAAAGAATGTAATCTTCAATTTAAACTCTTATG
124 ATCATTACTTTTTAATAGGATTAGGATAAACCAAAAGAATATAATCTTCAATTTAAACCCTTATA
*
38891 GAC
189 CAC
* * * * * *
38894 TTTGTATTTTATAGATCA-GTATGTGTATGAGGTGTATTGGAGCTAAAATTGACGATTTTAATGA
1 TTTGTATTTTATAGGTCATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGATTTTGATGA
*
38958 AGTTTGAACAGTTAAAGAGAAAAA
66 AGTTTGAA-ACTT-AAGAGAAAAA
38982 GGAGGAATGG
Statistics
Matches: 246, Mismatches: 29, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
192 3 0.01
193 29 0.12
194 77 0.31
195 22 0.09
196 28 0.11
197 86 0.35
198 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (191 bp):
TTTGTATTTTATAGGTCATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGATTTTGATGA
AGTTTGAAACTTAAGAGAAAAAAAGACGAATGACATTCCTACTTATGTTAGAAATCTTATCATTA
CTTTTTAATAGGATTAGGATAAACCAAAAGAATATAATCTTCAATTTAAACCCTTATACAC
Found at i:42412 original size:17 final size:20
Alignment explanation
Indices: 42392--42441 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
42382 TTTTTTTAAA
42392 ATAAATAT-A-TTATTT-TT
1 ATAAATATCATTTATTTATT
42409 AT-AATATCATTTATTTAATT
1 ATAAATATCATTTATTT-ATT
*
42429 ATAAATATTATTT
1 ATAAATATCATTT
42442 TTGTTACATC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 3 0.11
18 6 0.22
20 4 0.15
21 9 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAAATATCATTTATTTATT
Found at i:44407 original size:22 final size:22
Alignment explanation
Indices: 44382--44423 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
44372 ATATCTATGA
44382 TATTGATTA-AAAATATAATTTG
1 TATT-ATTATAAAATATAATTTG
*
44404 TATTATTATAAATTATAATT
1 TATTATTATAAAATATAATT
44424 ATATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TATTATTATAAAATATAATTTG
Found at i:45024 original size:96 final size:94
Alignment explanation
Indices: 44813--45095 Score: 361
Period size: 95 Copynumber: 3.0 Consensus size: 94
44803 TATCTGAGCC
* * * * *
44813 TAAACTAAAAGCAAAGAAACATAGTAAGAATCATTGATAAAGGCTTGAGAGGACCTTTGTCTTT-
1 TAAACTAAAA-CAAAGAAAGATAGTAAGAATAATTGATAAAGACTTGAGAGGTCCTTAGTCTTTC
* *
44877 TTTATTTATTTACACTTTTCAATTCTTTTAT
65 TTTCTTTATTTATACTTTTCAATT-TTTTAT
44908 TAAACTAAAACTAAAGAAAGATAGTAAGAATAATTGATAAAGACTTGAGAGGTCCTTGAGTCTTT
1 TAAACTAAAAC-AAAGAAAGATAGTAAGAATAATTGATAAAGACTTGAGAGGTCCTT-AGTCTTT
44973 CTTTCTTTATTTATACTTTTCAATTTTTTAT
64 CTTTCTTTATTTATACTTTTCAATTTTTTAT
* * * * * * *
45004 TAAATTAAAATCAAAGAAAGATAATAATAATAATTGATTAAGAGTGGAGAAGTCCTTAGTCTTTC
1 TAAACTAAAA-CAAAGAAAGATAGTAAGAATAATTGATAAAGACTTGAGAGGTCCTTAGTCTTTC
* **
45069 TTTCCTTATTTATTTTTTTCAATTTTT
65 TTTCTTTATTTATACTTTTCAATTTTT
45096 GATGATAATT
Statistics
Matches: 167, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
94 1 0.01
95 83 0.50
96 60 0.36
97 23 0.14
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (94 bp):
TAAACTAAAACAAAGAAAGATAGTAAGAATAATTGATAAAGACTTGAGAGGTCCTTAGTCTTTCT
TTCTTTATTTATACTTTTCAATTTTTTAT
Found at i:46383 original size:30 final size:29
Alignment explanation
Indices: 46348--46411 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
46338 CTAACAATAG
*
46348 AAAATGAAAGGGGTAAAATCAAACTAAACC
1 AAAATGAAAGGGG-AAAATCAAAATAAACC
** *
46378 AAAATGGGAGGGGCAAATCAAAATAAACC
1 AAAATGAAAGGGGAAAATCAAAATAAACC
46407 AAAAT
1 AAAAT
46412 TTGAAGGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.12
Consensus pattern (29 bp):
AAAATGAAAGGGGAAAATCAAAATAAACC
Found at i:57816 original size:32 final size:31
Alignment explanation
Indices: 57780--57856 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
57770 CGGGGCCACG
*
57780 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** ** *
57812 GGGCCTACCCGAGAATGATCTCAGGGCCGTA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
57843 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
57857 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:59451 original size:16 final size:16
Alignment explanation
Indices: 59430--59462 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
59420 AGGGCCACAG
*
59430 TTACTCTATTGAACTT
1 TTACTCCATTGAACTT
59446 TTACTCCATTGAACTT
1 TTACTCCATTGAACTT
59462 T
1 T
59463 GACCATTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.48
Consensus pattern (16 bp):
TTACTCCATTGAACTT
Found at i:68358 original size:194 final size:193
Alignment explanation
Indices: 67946--68813 Score: 898
Period size: 194 Copynumber: 4.5 Consensus size: 193
67936 TTTTTTAAAT
* * * ** * *
67946 TTTGTATTTTA-CGAGTCGATATATGTTTCTGATATGTGTTAGAA-CTAGAATTGAGGATTTTGA
1 TTTGTATTTTATAGA-TCAATATATGTGTCTGAGGTGTATT-GAAGCTAAAATTGAGGATTTTGA
* *
68009 TGAAGTTTAGACACTTAA-AGATAAAAAA-GAC-GAATGACATTACTACTTATGTTAGAACTCTT
64 TGAAGTTT-GAAACTTAAGAGA-AAAAAAGGACGGAATGACATTCCTACTTA--TTAGAACTCTT
* * * * *
68071 ATCATTA-TTTTTAATAGGATTAGGATAACCCAAAATAA--TAATTTTCAATTTAAACCCTTGTT
125 ATCTTTACTTTTTAATAGGATTAGGATAAACCAAAAGAATGTAATCTTCAATTTAAACCCTTATT
*
68133 ACAC
190 AGAC
*
68137 TTTGTATTTTATAGGTCAATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGATTTTTGAT
1 TTTGTATTTTATAGATCAATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGA-TTTTGAT
* *
68202 GAAGTTTGGAAACTTGAAGAGAAAAAAAGGACAG-ATGACATTCCTACTTCAGTTAGAAATCTTA
65 GAAGTTT-GAAACTT-AAGAGAAAAAAAGGACGGAATGACATTCCTACTT-A-TTAGAACTCTTA
* *
68266 TCTTTACTTTTTAATAGGATTAGGATAAACCAAAAGAATGTAATCTTCAATTTAAACTCTTA-TG
126 TCTTTACTTTTTAATAGGATTAGGATAAACCAAAAGAATGTAATCTTCAATTTAAACCCTTATTA
68330 GAC
191 GAC
* * * * *
68333 TTTGTATTTTATAGATC-A-GTATGTGTATGAGGTGTATTGGAGCTAAAATTGACGATTTTAATG
1 TTTGTATTTTATAGATCAATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGATTTTGATG
* * * *
68396 AAGTTTGAACAGTTAA-AGAGAAAAAGGA-GGAATGGCATTTCTACCGTTATTAGAACTCTTATC
66 AAGTTTGAA-ACTTAAGAGAAAAAAAGGACGGAATGACATTCCTA-C-TTATTAGAACTCTTATC
* * * * * * *
68459 TTT-GTTTTT--TAGAATTAGGATAAACAAAAACAATATAATCTTCAATTTAAACTCTAATTAGA
128 TTTACTTTTTAATAGGATTAGGATAAACCAAAAGAATGTAATCTTCAATTTAAACCCTTATTAGA
68521 C
193 C
* * * * * * *
68522 TTTGTATTTTATAGGTCAATATACGTGTCTAAGGTGTATT-AGAGATAGAATTAAAGATTTTGAT
1 TTTGTATTTTATAGATCAATATATGTGTCTGAGGTGTATTGA-AGCTAAAATTGAGGATTTTGAT
* *
68586 GAAGTTTGGACACTTGAAGAG--AAAAAGGACGG-ATGACATTCCTACTTCCATTAGAACTTTTA
65 GAAGTTT-GAAACTT-AAGAGAAAAAAAGGACGGAATGACATTCCTACTT--ATTAGAACTCTTA
* ** * * *
68648 TCTCTACTTTTTAATAATACTAAGATAAACCAAACGAATGTAATCTTCAATTTAAACCCTTATTA
126 TCTTTACTTTTTAATAGGATTAGGATAAACCAAAAGAATGTAATCTTCAATTTAAACCCTTATTA
*
68713 AAC
191 GAC
* *
68716 TTTGTATTTTACAGATCAATATATGTGTCTGAGGTGTATTGGAGCTAAAATTGAGGATTTTGATG
1 TTTGTATTTTATAGATCAATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGATTTTGATG
*
68781 AAGTTTGAACACTTAA-AGATAAAAAAGTACGGA
66 AAGTTTGAA-ACTTAAGAGA-AAAAAAGGACGGA
68814 TAAGATTCAT
Statistics
Matches: 564, Mismatches: 79, Indels: 63
0.80 0.11 0.09
Matches are distributed among these distances:
188 43 0.08
189 22 0.04
190 11 0.02
191 157 0.28
192 41 0.07
193 32 0.06
194 178 0.32
195 42 0.07
196 19 0.03
197 19 0.03
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (193 bp):
TTTGTATTTTATAGATCAATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGATTTTGATG
AAGTTTGAAACTTAAGAGAAAAAAAGGACGGAATGACATTCCTACTTATTAGAACTCTTATCTTT
ACTTTTTAATAGGATTAGGATAAACCAAAAGAATGTAATCTTCAATTTAAACCCTTATTAGAC
Found at i:68743 original size:385 final size:384
Alignment explanation
Indices: 67940--68807 Score: 1108
Period size: 385 Copynumber: 2.3 Consensus size: 384
67930 TCTATTTTTT
* * ** * * * *
67940 TTAAATTTTGTATTTTAC-GAGTCGATATATGTTTCTGATATGTGTTAGAACTAGAATTGAGGAT
1 TTAAACTTTGTATTTTACAGA-TC-ATATATGTGTCTGAGGTGTATTGGAGCTAAAATTGAGGAT
68004 TTTGATGAAGTTT-AGACACTTAAAGATAAAAAAGACGAATGACATTACTACTTATGTTAGAACT
64 TTTGATGAAGTTTGA-ACACTTAAAGATAAAAAAGACGAATGACATTACTACTTA-GTTAGAACT
* * * * * **
68068 CTTATCATTATTTTTAATAGGATTAGGATAACCCAAAATAATAATTTTCAATTTAAACCCTTGTT
127 CTTATCATTATTTTT-ATAGAATTAGGATAAACAAAAAAAATAATCTTCAATTTAAACCCTAATT
* * * * *
68133 ACACTTTGTATTTTATAGGTCAATATATGTGTCTGAGGTGTATTGAAGCTAAAATTGAGGATTTT
191 ACACTTTGTATTTTATAGGTCAATATACGTGTCTAAGGTGTATTGAAGATAAAATTAAAGATTTT
68198 TGATGAAGTTTGGAAACTTGAAGAGAAAAAAAGGACAGATGACATTCCTACTTCAGTTAGAAATC
256 TGATGAAGTTTGGAAACTTGAAGAG-AAAAAAGGACAGATGACATTCCTACTTCAGTTAGAAATC
* * * * *
68263 TTATCTTTACTTTTTAATAGGATTAGGATAAACCAAAAGAATGTAATCTTCAATTTAAACTCTTA
320 TTATCTCTACTTTTTAATAAGACTAAGATAAACCAAAAGAATGTAATCTTCAATTTAAACCCTTA
** * * * *
68328 -TGGACTTTGTATTTTATAGATCA-GTATGTGTATGAGGTGTATTGGAGCTAAAATTGACGATTT
1 TTAAACTTTGTATTTTACAGATCATATATGTGTCTGAGGTGTATTGGAGCTAAAATTGAGGATTT
* * * * * * *
68391 TAATGAAGTTTGAACAGTTAAAGAGAAAAAGGAGGAATGGCATTTCTACCGTTA-TTAGAACTCT
66 TGATGAAGTTTGAACACTTAAAGATAAAAAAGACGAATGACATTACTA-C-TTAGTTAGAACTCT
* * *
68455 TATCTTTGTTTTT-TAGAATTAGGATAAACAAAAACAATATAATCTTCAATTTAAACTCTAATTA
129 TATCATTATTTTTATAGAATTAGGATAAACAAAAA-AA-ATAATCTTCAATTTAAACCCTAATTA
* *
68519 GACTTTGTATTTTATAGGTCAATATACGTGTCTAAGGTGTATT-AGAGATAGAATTAAAGA-TTT
192 CACTTTGTATTTTATAGGTCAATATACGTGTCTAAGGTGTATTGA-AGATAAAATTAAAGATTTT
* * * *
68582 TGATGAAGTTTGGACACTTGAAGAG-AAAAAGGACGGATGACATTCCTACTTCCA-TTAGAACTT
256 TGATGAAGTTTGGAAACTTGAAGAGAAAAAAGGACAGATGACATTCCTACTT-CAGTTAGAAATC
* *
68645 TTATCTCTACTTTTTAATAATACTAAGATAAACCAAACGAATGTAATCTTCAATTTAAACCCTTA
320 TTATCTCTACTTTTTAATAAGACTAAGATAAACCAAAAGAATGTAATCTTCAATTTAAACCCTTA
68710 TTAAACTTTGTATTTTACAGATCAATATATGTGTCTGAGGTGTATTGGAGCTAAAATTGAGGATT
1 TTAAACTTTGTATTTTACAGATC-ATATATGTGTCTGAGGTGTATTGGAGCTAAAATTGAGGATT
68775 TTGATGAAGTTTGAACACTTAAAGATAAAAAAG
65 TTGATGAAGTTTGAACACTTAAAGATAAAAAAG
68808 TACGGATAAG
Statistics
Matches: 410, Mismatches: 59, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
382 90 0.22
383 39 0.10
384 30 0.07
385 228 0.56
386 3 0.01
387 18 0.04
388 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (384 bp):
TTAAACTTTGTATTTTACAGATCATATATGTGTCTGAGGTGTATTGGAGCTAAAATTGAGGATTT
TGATGAAGTTTGAACACTTAAAGATAAAAAAGACGAATGACATTACTACTTAGTTAGAACTCTTA
TCATTATTTTTATAGAATTAGGATAAACAAAAAAAATAATCTTCAATTTAAACCCTAATTACACT
TTGTATTTTATAGGTCAATATACGTGTCTAAGGTGTATTGAAGATAAAATTAAAGATTTTTGATG
AAGTTTGGAAACTTGAAGAGAAAAAAGGACAGATGACATTCCTACTTCAGTTAGAAATCTTATCT
CTACTTTTTAATAAGACTAAGATAAACCAAAAGAATGTAATCTTCAATTTAAACCCTTA
Found at i:70841 original size:27 final size:21
Alignment explanation
Indices: 70789--70833 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
70779 GTCGTTAGTC
70789 TTTTTTATTATTATTTATACT
1 TTTTTTATTATTATTTATACT
70810 TTTTTTATTATTATTTATACT
1 TTTTTTATTATTATTTATACT
70831 TTT
1 TTT
70834 CAATTTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTATTATTATTTATACT
Found at i:70981 original size:83 final size:85
Alignment explanation
Indices: 70820--70974 Score: 224
Period size: 83 Copynumber: 1.8 Consensus size: 85
70810 TTTTTTATTA
* * *
70820 TTATTTATACTTTTCAATTTTTGATTAAACTAAAATTAAATAAAGATAATAATAATTGATAAATA
1 TTATTTATACTTTTCAATTTTTGATTAAACTAAAATTAAAGAAAGATAAAAATAATTGATAAAGA
*
70885 CTTGAGAGATCCTTGAGTCT
66 CTGGAGAGATCCTTGAGTCT
* * *
70905 TTATTTATAGTTTTCAATTTTT-ATTAAATTAAAA-TAAAGAAAGATAAAAATAATTGATTAAGA
1 TTATTTATACTTTTCAATTTTTGATTAAACTAAAATTAAAGAAAGATAAAAATAATTGATAAAGA
*
70968 GTGGAGA
66 CTGGAGA
70975 AGTCCTTAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 30 0.48
84 11 0.18
85 21 0.34
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (85 bp):
TTATTTATACTTTTCAATTTTTGATTAAACTAAAATTAAAGAAAGATAAAAATAATTGATAAAGA
CTGGAGAGATCCTTGAGTCT
Found at i:76825 original size:2 final size:2
Alignment explanation
Indices: 76818--76859 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
76808 GAATATGAAG
76818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76860 GGTTAGAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76953 original size:15 final size:15
Alignment explanation
Indices: 76933--76964 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
76923 AATTTGTATA
*
76933 GAACTCGAATAACTC
1 GAACTCGAACAACTC
76948 GAACTCGAACAACTC
1 GAACTCGAACAACTC
76963 GA
1 GA
76965 CTCAAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.28, G:0.16, T:0.16
Consensus pattern (15 bp):
GAACTCGAACAACTC
Found at i:77459 original size:3 final size:3
Alignment explanation
Indices: 77451--77539 Score: 151
Period size: 3 Copynumber: 29.7 Consensus size: 3
77441 ATATTATAAA
* *
77451 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
77499 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
77540 AATATATTAA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:77547 original size:9 final size:10
Alignment explanation
Indices: 77535--77573 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
77525 TTATTATTAT
77535 TATTAAAT-A
1 TATTAAATAA
77544 TATTAAATACA
1 TATTAAATA-A
77555 TATATAAATAA
1 TAT-TAAATAA
77566 TATTAAAT
1 TATTAAAT
77574 TACAAAGCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.30
10 5 0.19
11 8 0.30
12 6 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:79702 original size:28 final size:27
Alignment explanation
Indices: 79619--79704 Score: 70
Period size: 28 Copynumber: 3.0 Consensus size: 27
79609 AAATTAAAAA
79619 TTCAT-ATATTTA-ATTTTTAATTTTATCTT
1 TTCATAATATTTATA-TTTT-ATTTTA--TT
* *
79648 TTCAAAATTTTTATA-TTTACTTATTATT
1 TTCATAATATTTATATTTTA-TT-TTATT
79676 TTCATAATATTTATAGTTTTATTTTATT
1 TTCATAATATTTATA-TTTTATTTTATT
79704 T
1 T
79705 GCAATTATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
28 22 0.47
29 11 0.23
30 13 0.28
31 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (27 bp):
TTCATAATATTTATATTTTATTTTATT
Found at i:79714 original size:15 final size:13
Alignment explanation
Indices: 79694--79731 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
79684 ATTTATAGTT
79694 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
79709 TTATTTTATTTCA
1 TTATTTTATTTCA
79722 TTA-TTTATTT
1 TTATTTTATTT
79732 TGCTGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:91572 original size:83 final size:83
Alignment explanation
Indices: 91433--91887 Score: 822
Period size: 83 Copynumber: 5.5 Consensus size: 83
91423 CAATGGGCTC
*
91433 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
* * *
91498 TGGAAGATGAATTTGCTA
66 TAGAAGATGAATGTGTTA
*
91516 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
* *
91581 TGGAAGATGAAAT-TGCTA
66 TAGAAGATG-AATGTGTTA
91599 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
91664 TAGAAGATGAATGTGTTA
66 TAGAAGATGAATGTGTTA
91682 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
91747 TAGAAGATGAATGTGTTA
66 TAGAAGATGAATGTGTTA
91765 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
*
91830 TAGAAGATGAATGTGTTC
66 TAGAAGATGAATGTGTTA
91848 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
91888 ATTCGGTAGG
Statistics
Matches: 366, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
82 3 0.01
83 360 0.98
84 3 0.01
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
TAGAAGATGAATGTGTTA
Found at i:92831 original size:114 final size:114
Alignment explanation
Indices: 92631--93524 Score: 1305
Period size: 114 Copynumber: 7.8 Consensus size: 114
92621 AATATATCAT
* *
92631 TTGATAGATTAGCTTTTCCAAAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAAAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
92696 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
92745 TTGATGGATTATCTTTTCCAAAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAAAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
92810 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
* * *
92859 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGA
1 TTGATGGATTATCTTTTCCAAAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
92924 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
* *
92973 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAAAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
93038 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
* *
93087 TTGATGGATTATCTTTTTCAGAGAAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATTATCTTTTCCA-AAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* *
93151 AAGTTCATAATGAGAATAATTTGTTCAACCTTTTACCTGAATTCATTAAA
65 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
*
93201 TTGATGGATTATCTTTTCCAGAGAAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATTATCTTTTCCA-AAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * * * *
93265 AAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATC-AT
65 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
* * * * ***
93314 TTGATGGATCAACATTGCC-AGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAG
1 TTGATGGATTATCTTTTCCAAAAAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAG
* *** *
93378 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTCATC-AT
62 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
* * * * * ** *
93430 TTGATGTATCAACATTGCC-AAGTAGAGTTCATAATGAAAAGAACTCGTCATCTGAAGAAGGAAG
1 TTGATGGATTATCTTTTCCAAAAAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAG
* *
93494 AAGAAGTTCATAATAAGAAGAACTTGTTCAA
62 AAGAAGTTCATAATGAGAAGAATTTGTTCAA
93525 TAATTCTATC
Statistics
Matches: 742, Mismatches: 32, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
111 3 0.00
113 33 0.04
114 545 0.73
115 3 0.00
116 158 0.21
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (114 bp):
TTGATGGATTATCTTTTCCAAAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
Found at i:93858 original size:3 final size:3
Alignment explanation
Indices: 93850--93938 Score: 103
Period size: 3 Copynumber: 30.7 Consensus size: 3
93840 ATATTATAAA
* * * *
93850 TAT TAT TAT TAT TGT TAT TA- TAA TAA TAA TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
93897 TAT TAT CA- TAT TAT TAT TAT TAT TAT TA- TAT CAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
93939 AATATATATT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
2 5 0.07
3 71 0.93
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:93908 original size:23 final size:22
Alignment explanation
Indices: 93841--93938 Score: 108
Period size: 23 Copynumber: 4.4 Consensus size: 22
93831 TTTTTACCCA
* *
93841 TATTATAAATATTATTAT-TAT
1 TATTATTATTATTATTATATAT
* * * *
93862 TGTTATTATAATAATAATATTAT
1 TATTATTATTATTATTATA-TAT
93885 TATTATTATTATTATTATCATAT
1 TATTATTATTATTATTAT-ATAT
93908 TATTATTATTATTATTATATCAT
1 TATTATTATTATTATTATAT-AT
93931 TATTATTA
1 TATTATTA
93939 AATATATATT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
21 12 0.19
22 2 0.03
23 48 0.76
24 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATTATATAT
Found at i:93923 original size:26 final size:26
Alignment explanation
Indices: 93853--93938 Score: 120
Period size: 26 Copynumber: 3.3 Consensus size: 26
93843 TTATAAATAT
* * * *
93853 TATTATTATTGTTATTATAATAATAA
1 TATTATTATTATTATTATTATTATCA
93879 TATTATTATTATTATTATTATTATCA
1 TATTATTATTATTATTATTATTATCA
93905 TATTATTATTATTATTATTA-TATCA
1 TATTATTATTATTATTATTATTATCA
93930 TTATTATTA
1 -TATTATTA
93939 AATATATATT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
25 5 0.09
26 50 0.91
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.59
Consensus pattern (26 bp):
TATTATTATTATTATTATTATTATCA
Found at i:93947 original size:20 final size:19
Alignment explanation
Indices: 93849--93938 Score: 78
Period size: 20 Copynumber: 4.8 Consensus size: 19
93839 CATATTATAA
* *
93849 ATATTATTATTATTGTTAT
1 ATATCATTATTATTATTAT
* * *
93868 -TAT-AATAATAATATTAT
1 ATATCATTATTATTATTAT
*
93885 -TATTATTATTATTATTAT
1 ATATCATTATTATTATTAT
*
93903 CATATTATTATTATTATTATT
1 -ATATCATTATTATTATTA-T
93924 ATATCATTATTATTA
1 ATATCATTATTATTA
93939 AATATATATT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
17 13 0.22
18 14 0.24
20 31 0.53
21 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (19 bp):
ATATCATTATTATTATTAT
Found at i:93963 original size:10 final size:10
Alignment explanation
Indices: 93934--93972 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
93924 ATATCATTAT
93934 TATTAAATATA
1 TATTAAATA-A
93945 TATTAAATACA
1 TATTAAATA-A
93956 TA-TAAATAA
1 TATTAAATAA
93965 TATTAAAT
1 TATTAAAT
93973 TACAAAGCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 3 0.12
10 11 0.42
11 12 0.46
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:111297 original size:2 final size:2
Alignment explanation
Indices: 111290--111314 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
111280 TGATAAAAAT
111290 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
111315 GTTTTAGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:112245 original size:3 final size:3
Alignment explanation
Indices: 112237--112262 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
112227 ACCTACTCAG
112237 GAC GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GA
112263 TGGTGATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:114156 original size:15 final size:15
Alignment explanation
Indices: 114136--114172 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
114126 TAGAATTGGC
114136 ATCGATCGCGGAGAA
1 ATCGATCGCGGAGAA
114151 ATCGATCGCGGAGAA
1 ATCGATCGCGGAGAA
*
114166 CTCGATC
1 ATCGATC
114173 ATTATGGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.30, C:0.24, G:0.30, T:0.16
Consensus pattern (15 bp):
ATCGATCGCGGAGAA
Found at i:122542 original size:3 final size:3
Alignment explanation
Indices: 122536--122588 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
122526 ATTATTATTT
* * *
122536 TAA TAA T-A TATA TAA AAA TAA TAA T-T TAA TAA TCA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
122580 TAA TAA TAA
1 TAA TAA TAA
122589 GAGAAAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:122573 original size:23 final size:23
Alignment explanation
Indices: 122539--122583 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
122529 ATTATTTTAA
122539 TAATATATATAAAAATAATAATT
1 TAATATATATAAAAATAATAATT
*
122562 TAATA-ATCATAATAATAATAAT
1 TAATATAT-ATAAAAATAATAAT
122584 AATAAGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TAATATATATAAAAATAATAATT
Found at i:122576 original size:26 final size:26
Alignment explanation
Indices: 122534--122586 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
122524 TTATTATTAT
122534 TTTAATAATATATATAAAAATAATAA
1 TTTAATAATATATATAAAAATAATAA
*
122560 TTTAATAATCATA-ATAATAATAATAA
1 TTTAATAAT-ATATATAAAAATAATAA
122586 T
1 T
122587 AAGAGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
TTTAATAATATATATAAAAATAATAA
Found at i:122749 original size:21 final size:21
Alignment explanation
Indices: 122725--122903 Score: 73
Period size: 21 Copynumber: 8.7 Consensus size: 21
122715 CGCAAATTCG
*
122725 AGTTGCATTTCGCGTTGCAAT
1 AGTTGCATTTCGCGTTGCGAT
* **
122746 AGTTGAAAATCGCGTTGCGAT
1 AGTTGCATTTCGCGTTGCGAT
* *
122767 -TTTCCATTTCGCGTTGCGAT
1 AGTTGCATTTCGCGTTGCGAT
* ** ***
122787 AGTTGAAAATCGCAACGCGAT
1 AGTTGCATTTCGCGTTGCGAT
*
122808 --TTTCTATTTCGCGTTGCGAT
1 AGTTGC-ATTTCGCGTTGCGAT
* ** ***
122828 AGTTGAAAATCGCAACGCGAT
1 AGTTGCATTTCGCGTTGCGAT
* *
122849 -TTTCCATTTCGCGTTGCGAT
1 AGTTGCATTTCGCGTTGCGAT
* *
122869 AGTCTACA-GTCGCGTTGCGAT
1 AGT-TGCATTTCGCGTTGCGAT
* *
122890 -TTTCCATTTCGCGT
1 AGTTGCATTTCGCGT
122904 ATTACCACGA
Statistics
Matches: 106, Mismatches: 45, Indels: 15
0.64 0.27 0.09
Matches are distributed among these distances:
19 5 0.05
20 44 0.42
21 52 0.49
22 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
AGTTGCATTTCGCGTTGCGAT
Found at i:122758 original size:41 final size:40
Alignment explanation
Indices: 122713--122871 Score: 185
Period size: 41 Copynumber: 3.9 Consensus size: 40
122703 GATCTCCACT
* * *
122713 ATCGCAAATTCGAGTTGCATTTCGCGTTGCAATAGTTGAAA
1 ATCGC-AATTCGATTTCCATTTCGCGTTGCGATAGTTGAAA
*
122754 ATCGC-GTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 ATCGCAATT-CGA-TTTCCATTTCGCGTTGCGATAGTTGAAA
** *
122795 ATCGCAACGCGATTTTCTATTTCGCGTTGCGATAGTTGAAA
1 ATCGCAATTCGA-TTTCCATTTCGCGTTGCGATAGTTGAAA
**
122836 ATCGCAACGCGATTTTCCATTTCGCGTTGCGATAGT
1 ATCGCAATTCGA-TTTCCATTTCGCGTTGCGATAGT
122872 CTACAGTCGC
Statistics
Matches: 106, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 101 0.95
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (40 bp):
ATCGCAATTCGATTTCCATTTCGCGTTGCGATAGTTGAAA
Found at i:122889 original size:41 final size:41
Alignment explanation
Indices: 122730--122903 Score: 242
Period size: 41 Copynumber: 4.2 Consensus size: 41
122720 ATTCGAGTTG
* ***
122730 CATTTCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
122771 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
*
122812 TATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
* * ***
122853 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCAACGCGATTTTC
122894 CATTTCGCGT
1 CATTTCGCGT
122904 ATTACCACGA
Statistics
Matches: 121, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
41 120 0.99
42 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
Found at i:122916 original size:6 final size:6
Alignment explanation
Indices: 122907--122933 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
122897 TTCGCGTATT
122907 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
122934 CGAGACGAGA
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:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:123463 original size:6 final size:6
Alignment explanation
Indices: 123426--123471 Score: 57
Period size: 5 Copynumber: 8.5 Consensus size: 6
123416 GTCCGTCTCG
123426 GGTCG- GGTCG- GGTCG- GGTCGT -GTCGT -GTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
123469 GGT
1 GGT
123472 AATGGTAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 25 0.64
6 14 0.36
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:146260 original size:28 final size:28
Alignment explanation
Indices: 146205--146260 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
146195 CCGAAAAGGG
* * *
146205 ACATCAAAAAGGCCTGTTTTCCGACATT
1 ACATCAAAAAGACCTGTTGTACGACATT
*
146233 ACATCAAAAAGACCTGTTGTACGGCATT
1 ACATCAAAAAGACCTGTTGTACGACATT
146261 CTTTCTAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (28 bp):
ACATCAAAAAGACCTGTTGTACGACATT
Found at i:156562 original size:21 final size:21
Alignment explanation
Indices: 156520--156564 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
156510 CGGTAAAAAA
*
156520 TTACTTAAAACATTATTATTT
1 TTACTTAAAACATAATTATTT
156541 TTACTTAAAACATCAATT-TTT
1 TTACTTAAAACAT-AATTATTT
156562 TTA
1 TTA
156565 ACATATCTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (21 bp):
TTACTTAAAACATAATTATTT
Found at i:156967 original size:26 final size:27
Alignment explanation
Indices: 156938--157001 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
156928 GACGTTATCG
*
156938 TTTTATAATAAATTGG-TATTAGATTA
1 TTTTATAATAAATTGGTTATTAGATCA
* *
156964 TTTTATAACAAATTGGTTATTCGATCA
1 TTTTATAATAAATTGGTTATTAGATCA
156991 TTTTATAATAA
1 TTTTATAATAA
157002 TCCGAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 15 0.45
27 18 0.55
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (27 bp):
TTTTATAATAAATTGGTTATTAGATCA
Found at i:158317 original size:14 final size:14
Alignment explanation
Indices: 158297--158335 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
158287 TGGTTTTCTG
158297 AAAAACCAATTCCA
1 AAAAACCAATTCCA
*
158311 GAAAACCAATTCCA
1 AAAAACCAATTCCA
158325 AAAAACCAATT
1 AAAAACCAATT
158336 ACAATGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.56, C:0.26, G:0.03, T:0.15
Consensus pattern (14 bp):
AAAAACCAATTCCA
Found at i:158497 original size:15 final size:14
Alignment explanation
Indices: 158473--158506 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
158463 TTTATTTTTT
158473 AATTTATTTTATAA
1 AATTTATTTTATAA
158487 AATTGTATTTTATAA
1 AATT-TATTTTATAA
158502 AATTT
1 AATTT
158507 TGAAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
AATTTATTTTATAA
Found at i:159871 original size:36 final size:36
Alignment explanation
Indices: 159826--159911 Score: 138
Period size: 36 Copynumber: 2.4 Consensus size: 36
159816 AATTTAGTTA
*
159826 ACCTAAAGCTAAAGTTCATATTAAGTTTTAGCTTTT
1 ACCTAAAGCTAAAGTTCATATTAAGTTTAAGCTTTT
*
159862 ACCTAAAGCTAAAGTTCATATTACGTTTAAGCTTTT
1 ACCTAAAGCTAAAGTTCATATTAAGTTTAAGCTTTT
*
159898 ACCT-AAGTTAAAGT
1 ACCTAAAGCTAAAGT
159912 GGATGTAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.19
36 38 0.81
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (36 bp):
ACCTAAAGCTAAAGTTCATATTAAGTTTAAGCTTTT
Found at i:165919 original size:2 final size:2
Alignment explanation
Indices: 165912--165959 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
165902 CAATATACAG
165912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
165954 AT AT AT
1 AT AT AT
165960 GAAGTTTCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:179152 original size:31 final size:31
Alignment explanation
Indices: 179086--179152 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
179076 TATGTAATAT
* *
179086 ATATCATGTGTTAAAAGAGATTACGTGATAT
1 ATATCATGTGTTAAAAGAGATCACGTGATAC
* * *
179117 ATATCATGTGTTAAAAGTGATCACTTGGTAC
1 ATATCATGTGTTAAAAGAGATCACGTGATAC
179148 ATATC
1 ATATC
179153 GAAAGTGGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (31 bp):
ATATCATGTGTTAAAAGAGATCACGTGATAC
Found at i:179217 original size:29 final size:29
Alignment explanation
Indices: 179172--179233 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
179162 GACATGCTAA
*
179172 ATATCATATGTCAAAAGTAATGAGGTGAC
1 ATATCATATGTCAAAAGTAATGAGATGAC
** * *
179201 ATATCATATGTTGAAAGTGATGATATGAC
1 ATATCATATGTCAAAAGTAATGAGATGAC
179230 ATAT
1 ATAT
179234 GTTACTAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.32
Consensus pattern (29 bp):
ATATCATATGTCAAAAGTAATGAGATGAC
Found at i:179343 original size:31 final size:31
Alignment explanation
Indices: 179256--179343 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
179246 AAAATGATAG
* * * * *
179256 TGTGGTACATATCACGTGTCGAAAATTATGA
1 TGTGGTATATATCACATGTAGAAAGTAATGA
* * * *
179287 CGTGGTATATACCACATATAAAAAGTAATGA
1 TGTGGTATATATCACATGTAGAAAGTAATGA
*
179318 TGTGGTATATATCACATGTTGAAAGT
1 TGTGGTATATATCACATGTAGAAAGT
179344 GATAACATGT
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (31 bp):
TGTGGTATATATCACATGTAGAAAGTAATGA
Found at i:179382 original size:31 final size:31
Alignment explanation
Indices: 179323--179383 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
179313 AATGATGTGG
* *
179323 TATATATCACATGTTGAAAGTGATAACATGT
1 TATATACCACATGTTGAAAATGATAACATGT
*
179354 TATATACCATATGTTGAAAATGGA-AACATG
1 TATATACCACATGTTGAAAAT-GATAACATG
179384 ACAATCTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (31 bp):
TATATACCACATGTTGAAAATGATAACATGT
Found at i:180648 original size:20 final size:20
Alignment explanation
Indices: 180625--180662 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
180615 TTTTAAAAGT
180625 TAATTAAAATTATATTATAC
1 TAATTAAAATTATATTATAC
*
180645 TAATTAAAATTATTTTAT
1 TAATTAAAATTATATTAT
180663 GTTTCTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTAAAATTATATTATAC
Found at i:180929 original size:29 final size:29
Alignment explanation
Indices: 180887--180946 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
180877 ATTCTACAGT
180887 GATCTCGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
* *
180916 GATCTTGTAGGACGTCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
180945 GA
1 GA
180947 CATACGGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.28, T:0.20
Consensus pattern (29 bp):
GATCTCGTAGGACGCCATGCAATCCAGGC
Found at i:180972 original size:9 final size:9
Alignment explanation
Indices: 180958--181006 Score: 71
Period size: 9 Copynumber: 5.2 Consensus size: 9
180948 ATACGGGAGA
180958 CATACGAGC
1 CATACGAGC
180967 CATACGAGC
1 CATACGAGC
*
180976 CATACAAGC
1 CATACGAGC
180985 CATATACGAGC
1 C--ATACGAGC
180996 CATACGAGC
1 CATACGAGC
181005 CA
1 CA
181007 ATGGAGAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
9 28 0.78
11 8 0.22
ACGTcount: A:0.37, C:0.33, G:0.18, T:0.12
Consensus pattern (9 bp):
CATACGAGC
Found at i:180991 original size:20 final size:20
Alignment explanation
Indices: 180968--181006 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
180958 CATACGAGCC
180968 ATACGAGCCATACAAGCCAT
1 ATACGAGCCATACAAGCCAT
*
180988 ATACGAGCCATACGAGCCA
1 ATACGAGCCATACAAGCCA
181007 ATGGAGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
ATACGAGCCATACAAGCCAT
Found at i:181123 original size:29 final size:29
Alignment explanation
Indices: 181073--181138 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
181063 GCCAATGGAG
**
181073 AGGTCGCCATGCAATCTGGGCGACCTTGT
1 AGGTCGCCATGCAATCCCGGCGACCTTGT
* *
181102 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGCAATCCCGGCGACCTTGT
*
181131 AGGACGCC
1 AGGTCGCC
181139 GGGCGTGCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.17, C:0.30, G:0.32, T:0.21
Consensus pattern (29 bp):
AGGTCGCCATGCAATCCCGGCGACCTTGT
Found at i:185026 original size:23 final size:23
Alignment explanation
Indices: 184986--185046 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
184976 AGAAATATAT
* **
184986 ATAAAAAAGATTCTATATAAATA
1 ATAAAAAATATTAAATATAAATA
* *
185009 ATAATAAAAT-TTAAATATGAATC
1 ATAA-AAAATATTAAATATAAATA
185032 ATAAAAAATATTAAA
1 ATAAAAAATATTAAA
185047 AAGAAGAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 5 0.16
23 22 0.71
24 4 0.13
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (23 bp):
ATAAAAAATATTAAATATAAATA
Found at i:201441 original size:20 final size:21
Alignment explanation
Indices: 201404--201443 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
201394 AAATTAAGTT
201404 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
201425 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
201444 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:201729 original size:65 final size:63
Alignment explanation
Indices: 201613--201819 Score: 229
Period size: 65 Copynumber: 3.2 Consensus size: 63
201603 ATTTGAGGTG
* * * * *
201613 ATGCACCGATGCATCAACCATGCATCGATGCAATAGTGAAT-TAATTGAAACATCGAATGCATTC
1 ATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
201677 C
63 C
* *
201678 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* * **
201743 ATGCATCGATGCA-CAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATC-A-CCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
*
201807 ATGCATCGATGCA
1 ATGCACCGATGCA
201820 CACTTGGTGC
Statistics
Matches: 124, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 37 0.30
65 84 0.68
66 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:201838 original size:64 final size:65
Alignment explanation
Indices: 201660--201823 Score: 231
Period size: 65 Copynumber: 2.5 Consensus size: 65
201650 GAATTAATTG
* * ** *
201660 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
* ** **
201725 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
201789 AAACATCGAATGCATTTCATGCATCGATGCACACT
1 AAACATCGAATGCATTTCATGCATCGATGCACACT
201824 TGGTGCACCG
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:210128 original size:25 final size:25
Alignment explanation
Indices: 210079--210125 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
210069 ATTTTATATT
*
210079 GGGAGAGTTAATTTCTAAAATTTAA
1 GGGAGAGTAAATTTCTAAAATTTAA
210104 GGGAGA-TAAATTTCTAAAATTT
1 GGGAGAGTAAATTTCTAAAATTT
210126 TAAAGGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.36
Consensus pattern (25 bp):
GGGAGAGTAAATTTCTAAAATTTAA
Found at i:211505 original size:20 final size:20
Alignment explanation
Indices: 211480--211580 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
211470 AATTGGGAAA
211480 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
211500 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
211520 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
211541 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
211561 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
211581 TTCGTAACGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 51 0.75
21 13 0.19
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:211581 original size:20 final size:20
Alignment explanation
Indices: 211542--211594 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
211532 TAATACAAAA
* *
211542 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
211562 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
211582 TCGTAACGCGATT
1 TCGCAACGCGATT
211595 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:211593 original size:61 final size:61
Alignment explanation
Indices: 211477--211593 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
211467 ACGAATTGGG
* * * * *
211477 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
211538 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGTAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
211594 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:212234 original size:20 final size:19
Alignment explanation
Indices: 212188--212367 Score: 120
Period size: 20 Copynumber: 10.1 Consensus size: 19
212178 GAAACAAAAA
*
212188 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
212207 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
212226 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
212246 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
212262 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
212279 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
212293 TCTCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
212307 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
212326 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
212346 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
212366 TC
1 TC
212368 AACCAAAAGA
Statistics
Matches: 133, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 34 0.26
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 41 0.31
20 49 0.37
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:212269 original size:39 final size:39
Alignment explanation
Indices: 212193--212269 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
212183 AAAAATCGCA
* **
212193 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
212232 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
212270 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:212299 original size:14 final size:14
Alignment explanation
Indices: 212282--212318 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
212272 AGTCATTTCG
212282 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
212296 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
212310 CGTTGCGAT
1 CGTTGCGAT
212319 AGTCATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.08, C:0.27, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:212304 original size:33 final size:33
Alignment explanation
Indices: 212231--212304 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
212221 TTATTTCGCG
** * *
212231 GTTGCGATTTTCATTTCGCGTTGCGATTGTCTG
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
*
212264 GTCGCGATAGTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
212297 GTTGCGAT
1 GTTGCGAT
212305 TCTCTCGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.41
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
Found at i:212318 original size:47 final size:48
Alignment explanation
Indices: 212249--212342 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 48
212239 TTTCATTTCG
* *
212249 CGTTGCGATTGTCTGGTCGCGATAGTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGATTCTCT
*
212296 CGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGATTCTC
212343 ATTATCTCGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
47 28 0.65
48 15 0.35
ACGTcount: A:0.11, C:0.26, G:0.26, T:0.38
Consensus pattern (48 bp):
CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:214417 original size:21 final size:21
Alignment explanation
Indices: 214393--214459 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
214383 TCTTTCCTCG
214393 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
214414 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
214435 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
214456 AGAG
1 AGAG
214460 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:215834 original size:14 final size:14
Alignment explanation
Indices: 215815--215850 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
215805 ATTGTTTAAT
215815 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
215829 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
215843 TGATTTGT
1 TGATTTGT
215851 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:216051 original size:19 final size:19
Alignment explanation
Indices: 216029--216146 Score: 67
Period size: 19 Copynumber: 6.7 Consensus size: 19
216019 CGAAATTAAA
216029 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
216048 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
216063 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
216081 TTAGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
216096 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
216114 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
216133 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
216147 AGACATTAAG
Statistics
Matches: 71, Mismatches: 17, Indels: 21
0.65 0.16 0.19
Matches are distributed among these distances:
14 16 0.23
16 6 0.08
17 6 0.08
19 33 0.46
20 10 0.14
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:216075 original size:33 final size:33
Alignment explanation
Indices: 216033--216126 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
216023 ATTAAATTCG
216033 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
216066 CGTTGCGATTTTCATTTAGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
216099 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
216127 AGTAATTTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:218431 original size:12 final size:12
Alignment explanation
Indices: 218416--218440 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
218406 TTTTCGGGGA
218416 CTTTTTCTTCTT
1 CTTTTTCTTCTT
218428 CTTTTTCTTCTT
1 CTTTTTCTTCTT
218440 C
1 C
218441 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:219750 original size:20 final size:20
Alignment explanation
Indices: 219725--219762 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
219715 ATTCATTTGA
219725 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
219745 CTATCGCAACGCGAAAAT
1 CTATCGCAACGCGAAAAT
219763 TGCAATGCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:219822 original size:19 final size:19
Alignment explanation
Indices: 219781--219848 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
219771 GAAATGAAAA
219781 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
219797 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
219814 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
219833 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
219849 TCGTTGCTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:219984 original size:14 final size:14
Alignment explanation
Indices: 219965--220001 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
219955 TATCAATTAA
219965 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
219979 ACAAATCATCTTTT
1 ACAAATCAACATTT
219993 ACAAATCAA
1 ACAAATCAA
220002 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:221889 original size:20 final size:19
Alignment explanation
Indices: 221866--221933 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
221856 GAAACTTAAA
221866 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
221886 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
221906 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
221925 ATCGCAACG
1 ATCGCAACG
221934 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:222004 original size:14 final size:14
Alignment explanation
Indices: 221981--222038 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
221971 TTTCATTTCG
*
221981 CGTTGTGATTTTGT
1 CGTTGCGATTTTGT
*
221995 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
222011 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
222027 CGTTGCGATTTT
1 CGTTGCGATTTT
222039 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 21 0.60
16 4 0.11
18 10 0.29
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:222050 original size:33 final size:33
Alignment explanation
Indices: 221964--222054 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
221954 ACAAATCGCA
* *
221964 TTGCGATTTTCATTTCGCGTTGTGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
221997 TTGCGA-TTTCATTTCACATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
222029 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
222055 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.55
33 24 0.45
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:222073 original size:20 final size:19
Alignment explanation
Indices: 222039--222093 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
222029 TTGCGATTTT
*
222039 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
222058 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
222078 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
222094 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:222594 original size:18 final size:18
Alignment explanation
Indices: 222568--222612 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
222558 GTCGATCAGA
*
222568 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
222586 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
222604 TGATGGCTC
1 TGATGGCTC
222613 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:223957 original size:20 final size:20
Alignment explanation
Indices: 223932--223969 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
223922 AATAGTTTCT
223932 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
223952 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
223970 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:224260 original size:22 final size:22
Alignment explanation
Indices: 224233--224276 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
224223 GATGGAGATA
*
224233 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
224255 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
224277 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:224570 original size:20 final size:20
Alignment explanation
Indices: 224464--224574 Score: 107
Period size: 20 Copynumber: 5.5 Consensus size: 20
224454 GATTATGTAT
*
224464 TATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGAAAGTCAG
*
224484 AATCGCATTGCGAAAGTCAG
1 TATCGCATTGCGAAAGTCAG
* *
224504 TATCGCGTTGCGAAAGTAAG
1 TATCGCATTGCGAAAGTCAG
* * ** *
224524 TATCTCGTTGCGATTTTGT-AT
1 TATCGCATTGCGA--AAGTCAG
*
224545 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGAAAGTCAG
224565 TATCGCATTG
1 TATCGCATTG
224575 TGATTTTCCC
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.04
20 58 0.77
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCATTGCGAAAGTCAG
Found at i:224581 original size:41 final size:41
Alignment explanation
Indices: 224444--224579 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
224434 CGCTTTGAAA
*
224444 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * *
224485 ATCGCATTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
224525 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
*
224566 ATCGCATTGTGATT
1 ATCGCATTGCGATT
224580 TTCCCAATTC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.39
41 42 0.55
42 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:224597 original size:41 final size:41
Alignment explanation
Indices: 224567--224659 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
224557 ATAGTCAGTA
* * *
224567 TCGCATTGTGATTTTCCCAATTCACGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTCACGTAT
* * *
224608 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTCACGTAT
224649 TCGCATTGCGA
1 TCGCATTGCGA
224660 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCACGTTGCGATTCACGTAT
Found at i:224616 original size:20 final size:20
Alignment explanation
Indices: 224593--224659 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
224583 CCAATTCACG
224593 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
* ** *
224613 TTGCGATTTTCCCAATTCGCG
1 TTGCGA-TTTACTTATTCGCA
224634 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
224654 TTGCGA
1 TTGCGA
224660 ATTGGGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:224632 original size:21 final size:20
Alignment explanation
Indices: 224567--224659 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
224557 ATAGTCAGTA
* *
224567 TCGCATTGTGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* * **
224588 TCACGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
224608 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
224629 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
224649 TCGCATTGCGA
1 TCGCATTGCGA
224660 ATTGGGAAAA
Statistics
Matches: 55, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 31 0.56
21 24 0.44
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:227347 original size:2 final size:2
Alignment explanation
Indices: 227342--227377 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
227332 TTTAAAAATA
227342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
227378 TAAATGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:229263 original size:2 final size:2
Alignment explanation
Indices: 229256--229289 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
229246 CAAATACATA
* *
229256 AT AT AT AT AT AT AT AT AT AT GT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
229290 GTATGTACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:232402 original size:5 final size:5
Alignment explanation
Indices: 232392--232417 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
232382 TTATTGTTGG
232392 ATTTA ATTTA ATTTA ATTTA ATTTA A
1 ATTTA ATTTA ATTTA ATTTA ATTTA A
232418 ACACTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:236070 original size:32 final size:29
Alignment explanation
Indices: 236025--236085 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 29
236015 ATAATAATTT
*
236025 ATATATAATAAAATCCATATATA-ATTATATA
1 ATATAAAATAAAAT--ATATATATA-TATATA
236056 ATATAAAATTAAAATATATATATATATATA
1 ATATAAAA-TAAAATATATATATATATATA
236086 CGATACATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 13 0.48
31 8 0.30
32 6 0.22
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (29 bp):
ATATAAAATAAAATATATATATATATATA
Found at i:236139 original size:2 final size:2
Alignment explanation
Indices: 236132--236168 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
236122 TACAATACAA
236132 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
236169 ATGACAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:236569 original size:3 final size:3
Alignment explanation
Indices: 236561--236597 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
236551 CTTTTAAAAG
236561 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
236598 GGAAGTGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:237620 original size:15 final size:15
Alignment explanation
Indices: 237603--237631 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
237593 TTAATTTTAA
237603 AAAATT-AATCATAT
1 AAAATTAAATCATAT
237617 AAAATTAAATCATAT
1 AAAATTAAATCATAT
237632 CAGAGCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAATTAAATCATAT
Found at i:239072 original size:21 final size:21
Alignment explanation
Indices: 239048--239118 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 21
239038 CACAAGTCAC
239048 AACATTAAGATTTAAACTTTT
1 AACATTAAGATTTAAACTTTT
* **
239069 AACATTAATATTTATTCTATTT
1 AACATTAAGATTTAAACT-TTT
*
239091 ACAACATTAAGATTCAAACTTTT
1 --AACATTAAGATTTAAACTTTT
239114 AACAT
1 AACAT
239119 ATATTTATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
21 20 0.50
22 3 0.08
23 3 0.08
24 14 0.35
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (21 bp):
AACATTAAGATTTAAACTTTT
Found at i:247883 original size:20 final size:20
Alignment explanation
Indices: 247858--247898 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
247848 TGTACGGGTT
247858 TTAAATTATTATTATTATTA
1 TTAAATTATTATTATTATTA
*
247878 TTAAATTGTTATTATTATTA
1 TTAAATTATTATTATTATTA
247898 T
1 T
247899 GAAAAATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTAAATTATTATTATTATTA
Found at i:253199 original size:478 final size:472
Alignment explanation
Indices: 252303--253253 Score: 1731
Period size: 478 Copynumber: 2.0 Consensus size: 472
252293 TCTAATTTCT
252303 TTTTGTATGAATATTTTTCACACCGATAAAATTGAAATCACTTGAAGTTATTTTCGATATCCACA
1 TTTTGTATGAATATTTTTCACACCGATAAAATTGAAATCACTTGAAGTTATTTTCGATATCCACA
252368 AATAAAATATATATTTATATATATAATTTTAAAAAATTAATTAACGATTTAAAAACACATGGATA
66 AATAAAATATATATTTATATATATAATTTTAAAAAATTAATTAACGATTTAAAAACACATGGATA
*
252433 TATGATATCCATGTTGGAATTTGAATTTGAATTTGAGTAATGATGGAATAAAGGACCTGATAAAT
131 TATGATATCCATGTTGGAATTTGAATTTGAATTTGAGTAATGATGCAATAAAGGACCTGATAAAT
252498 TTGATGGGTACATTTTTCTGTGACTAAATCGACTATGAACAATGACATCTTATCCATGTGTAGAA
196 TTGATGGGTACATTTTTCTGTGACTAAATCGACTATGAACAATGACATCTTATCCATGTGTAGAA
* *
252563 CTAGTGGCGGATACACATCTACATTAAGATGGGCACGCACTGACTTTAAAATCTGAATTTTCTTT
261 CTAGTGGCGGATACACATCTACAGTAAGATGGGCACGCACCGACTTTAAAATCTGAATTTTCTTT
252628 GATTAATTATCTATTTTATTAATAGATGTTCACCCTAAAATTTTAGTTGTACTCATCCCATTTAC
326 GATTAATTATCTATTTTATTAATAGATGTTCACCCTAAAATTTTAGTTGTACTCATCCCATTTAC
*
252693 AAATTTACGTTATAAACCCATATGTGTTCATCCAAAAAAATATTTCTAGATCCATCATCGGTATA
391 AAATTTACGTTATAAACACATATGTGTTCATCCAAAAAAATATTTCTAGATCCATCATCGGTATA
*
252758 ACATTTGATATAGCAGC
456 ACATGTGATATAGCAGC
252775 TTTTGTATGAATATTTTTCACACCGATAAAATTGAAATCACTTGAAGTTATTTTCGATATCCACA
1 TTTTGTATGAATATTTTTCACACCGATAAAATTGAAATCACTTGAAGTTATTTTCGATATCCACA
252840 AATAAAATATATATTTATATATATAATTTTAAAAAATTAATTAACGATTTAAAAACACATGGATA
66 AATAAAATATATATTTATATATATAATTTTAAAAAATTAATTAACGATTTAAAAACACATGGATA
252905 TATGATATCCATGTTGGAATTTGAATTTGAATTTTAATTTGAGTAATGATGCAATAAAGGACCTG
131 TATGATATCCATGTTGGAATTTGAATTTG------AATTTGAGTAATGATGCAATAAAGGACCTG
252970 ATAAATTTGATGGGTACATTTTTCTGTGACTAAATCGACTATGAACAATGACATCTTATCCATGT
190 ATAAATTTGATGGGTACATTTTTCTGTGACTAAATCGACTATGAACAATGACATCTTATCCATGT
**
253035 GTAGAACTAGTGGCGGATACACATCTACAGTAAGATGGGCACGTGCCGACTTTAAAATCTGAATT
255 GTAGAACTAGTGGCGGATACACATCTACAGTAAGATGGGCACGCACCGACTTTAAAATCTGAATT
* * * * *
253100 TTCTTTGGTTAATTATCTATTTTATTAATAGGTGTTCATCCTAAAATTTTAGTTGTACTTATCCT
320 TTCTTTGATTAATTATCTATTTTATTAATAGATGTTCACCCTAAAATTTTAGTTGTACTCATCCC
*
253165 ATTTACAAATTTACGTTATAAACACATGTGTGTTCATCCAAAAAAATATTTCTAGATCCATCATC
385 ATTTACAAATTTACGTTATAAACACATATGTGTTCATCCAAAAAAATATTTCTAGATCCATCATC
253230 GGTATAACATGTGATATAGCAGC
450 GGTATAACATGTGATATAGCAGC
253253 T
1 T
253254 AAAACATGAT
Statistics
Matches: 460, Mismatches: 13, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
472 159 0.35
478 301 0.65
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (472 bp):
TTTTGTATGAATATTTTTCACACCGATAAAATTGAAATCACTTGAAGTTATTTTCGATATCCACA
AATAAAATATATATTTATATATATAATTTTAAAAAATTAATTAACGATTTAAAAACACATGGATA
TATGATATCCATGTTGGAATTTGAATTTGAATTTGAGTAATGATGCAATAAAGGACCTGATAAAT
TTGATGGGTACATTTTTCTGTGACTAAATCGACTATGAACAATGACATCTTATCCATGTGTAGAA
CTAGTGGCGGATACACATCTACAGTAAGATGGGCACGCACCGACTTTAAAATCTGAATTTTCTTT
GATTAATTATCTATTTTATTAATAGATGTTCACCCTAAAATTTTAGTTGTACTCATCCCATTTAC
AAATTTACGTTATAAACACATATGTGTTCATCCAAAAAAATATTTCTAGATCCATCATCGGTATA
ACATGTGATATAGCAGC
Found at i:253591 original size:31 final size:31
Alignment explanation
Indices: 253556--253652 Score: 103
Period size: 30 Copynumber: 3.2 Consensus size: 31
253546 TTTTTAAATG
253556 TTCTAATTTCATCCCTAAACTATGACCATGA
1 TTCTAATTTCATCCCTAAACTATGACCATGA
* * *
253587 TTCTAAATT-ATCCCTCAAACTTTTGAGCATG-
1 TTCTAATTTCATCCCT-AAAC-TATGACCATGA
* *
253618 -TC-AATTTCATCCCTAAACTATGACCTTCA
1 TTCTAATTTCATCCCTAAACTATGACCATGA
253647 TTCTAA
1 TTCTAA
253653 ATTGGTCCCC
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
28 6 0.12
29 8 0.15
30 16 0.31
31 14 0.27
32 8 0.15
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (31 bp):
TTCTAATTTCATCCCTAAACTATGACCATGA
Found at i:253633 original size:60 final size:61
Alignment explanation
Indices: 253560--253698 Score: 187
Period size: 60 Copynumber: 2.3 Consensus size: 61
253550 TAAATGTTCT
*
253560 AATTTCATCCCTAAACTATGACCATGATTCTAAATT-ATCCCTCAAAC-TTTTGAGCATGT-C
1 AATTTCATCCCTAAACTATGACCATCATTCTAAATTGATCCC-CAAACTTTTTGAGCAT-TCC
* * *
253620 AATTTCATCCCTAAACTATGACCTTCATTCTAAATTGGTCCCCAAACTTTTTTAGCATTCC
1 AATTTCATCCCTAAACTATGACCATCATTCTAAATTGATCCCCAAACTTTTTGAGCATTCC
*
253681 AATTTCATTCC-AAACTAT
1 AATTTCATCCCTAAACTAT
253699 ATGTATACAC
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
60 47 0.66
61 24 0.34
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (61 bp):
AATTTCATCCCTAAACTATGACCATCATTCTAAATTGATCCCCAAACTTTTTGAGCATTCC
Found at i:253923 original size:60 final size:60
Alignment explanation
Indices: 253838--254004 Score: 178
Period size: 60 Copynumber: 2.8 Consensus size: 60
253828 AAATTGTAAT
** * *
253838 ATTCAAAAGTTTGGGGACCAATTTAGAAAGAGAGTCATAGTTT-AGGGATAAAATTAGAAT
1 ATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCATAGTTTGA-GGATAAAATTAAAAC
* * * * * * *
253898 GTTCAAAAGTTTAATGACTAGTTTAGAATGAGATTCATAGTTTGAGGATGAAATTAAAAC
1 ATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCATAGTTTGAGGATAAAATTAAAAC
* *
253958 ATTCAAAAGTTTAGGGACCAATTTA-AAATGAGAGTCATA-ATTGAGGA
1 ATTCAAAAGTTTAAGGACCAATTTAGAAA-GAGAGTCATAGTTTGAGGA
254005 AATATAATGA
Statistics
Matches: 86, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
59 9 0.10
60 76 0.88
61 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (60 bp):
ATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCATAGTTTGAGGATAAAATTAAAAC
Found at i:256839 original size:23 final size:24
Alignment explanation
Indices: 256815--256862 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
256805 GAAAACTTTT
256815 CATAATCTATTCTAAAAATCGTTCA
1 CATAATCTATTCTAAAAATCGTT-A
**
256840 CATCCTCTATTCTAAAAATCGTT
1 CATAATCTATTCTAAAAATCGTT
256863 GATATACGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (24 bp):
CATAATCTATTCTAAAAATCGTTA
Found at i:257034 original size:46 final size:46
Alignment explanation
Indices: 256967--257057 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
256957 CATATCACCT
*
256967 TAAATATAAATTAATATATGACTCAATGGTACTTTAGGTAACGAAC
1 TAAATATAAATTAATATATGACTCAATGGTAATTTAGGTAACGAAC
257013 TAAATATAAATTAATATATGACTCAATGGTAATTTAGGTAACGAA
1 TAAATATAAATTAATATATGACTCAATGGTAATTTAGGTAACGAA
257058 GTAGCAGGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (46 bp):
TAAATATAAATTAATATATGACTCAATGGTAATTTAGGTAACGAAC
Found at i:259564 original size:34 final size:34
Alignment explanation
Indices: 259521--259592 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
259511 TGTATTGAGT
*
259521 TTTTTATTATTAAGT-GACTAGTTCTCTTCGATGA
1 TTTTTATTATTAAGTAG-CTAGTTCTCTTAGATGA
* *
259555 TTTTTATTATTAAGTAGTTAGTTCTTTTAGATGA
1 TTTTTATTATTAAGTAGCTAGTTCTCTTAGATGA
259589 TTTT
1 TTTT
259593 AAGAAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.56
Consensus pattern (34 bp):
TTTTTATTATTAAGTAGCTAGTTCTCTTAGATGA
Found at i:261243 original size:21 final size:21
Alignment explanation
Indices: 261203--261244 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
261193 TCAACCCTTG
*
261203 AATACATTTTTTAAACAAAAC
1 AATACATTTTCTAAACAAAAC
*
261224 AATACATTCTTCTAAAAAAAA
1 AATACATT-TTCTAAACAAAA
261245 AAAAAAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (21 bp):
AATACATTTTCTAAACAAAAC
Found at i:267389 original size:2 final size:2
Alignment explanation
Indices: 267373--267415 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
267363 TTATAAAGGG
* *
267373 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
267415 T
1 T
267416 TATTTCAGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:287172 original size:26 final size:27
Alignment explanation
Indices: 287129--287183 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
287119 TTAAATTCGC
*
287129 ATCTTAACTTAAAAAATTTCATTT-TT
1 ATCTTAACTTAAAAAATTTAATTTATT
***
287155 ATCTTAACTTATTTAATTTAATTTATT
1 ATCTTAACTTAAAAAATTTAATTTATT
287182 AT
1 AT
287184 TATTTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (27 bp):
ATCTTAACTTAAAAAATTTAATTTATT
Found at i:287196 original size:21 final size:20
Alignment explanation
Indices: 287170--287209 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
287160 AACTTATTTA
287170 ATTT-AATTTATTATTATTTTT
1 ATTTAAATTT-TTA-TATTTTT
287191 ATTTAAATTTTTATATTTT
1 ATTTAAATTTTTATATTTT
287210 ATTCTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTAAATTTTTATATTTTT
Found at i:287243 original size:29 final size:29
Alignment explanation
Indices: 287205--287270 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
287195 AAATTTTTAT
287205 ATTTTATTCTTATATGAACTTAAAAATAC
1 ATTTTATTCTTATATGAACTTAAAAATAC
* * *
287234 ATTTTATTCTTATTTTAACTTAAAAATAT
1 ATTTTATTCTTATATGAACTTAAAAATAC
287263 ATTTTATT
1 ATTTTATT
287271 TTGTCTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.53
Consensus pattern (29 bp):
ATTTTATTCTTATATGAACTTAAAAATAC
Found at i:287305 original size:28 final size:29
Alignment explanation
Indices: 287257--287313 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
287247 TTTAACTTAA
* *
287257 AAATATATTTTATTTTGTCTT-AAATTTT
1 AAATATATTATATTTTATCTTAAAATTTT
287285 AAATATA-TATATTTTAATCTTAAAATTTT
1 AAATATATTATATTTT-ATCTTAAAATTTT
287314 TGGACTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.28
28 11 0.44
29 7 0.28
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (29 bp):
AAATATATTATATTTTATCTTAAAATTTT
Found at i:292038 original size:43 final size:43
Alignment explanation
Indices: 291977--292062 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
291967 CATACTTTTA
291977 ACCTTCATCCTCAATATTGATACACACTCTCAAACAGAAAATT
1 ACCTTCATCCTCAATATTGATACACACTCTCAAACAGAAAATT
292020 ACCTTCATCCTCAATATTGATACACACTCTCAAACAGAAAATT
1 ACCTTCATCCTCAATATTGATACACACTCTCAAACAGAAAATT
292063 GGTCGTGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.28, G:0.05, T:0.28
Consensus pattern (43 bp):
ACCTTCATCCTCAATATTGATACACACTCTCAAACAGAAAATT
Found at i:295603 original size:44 final size:44
Alignment explanation
Indices: 295536--295641 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 44
295526 TAGTGAATTT
*
295536 GACGTTGTCCTTTAAAATGTAATACCTAGCGTGGGTTCAAATCTC
1 GACGTT-TCCTTTAAAATATAATACCTAGCGTGGGTTCAAATCTC
* * * *
295581 GACGTTTGCTTTAAACTATAATACCTAGTGTGGGTTCGAATCTC
1 GACGTTTCCTTTAAAATATAATACCTAGCGTGGGTTCAAATCTC
* * *
295625 AACATTTTCTTTAAAAT
1 GACGTTTCCTTTAAAAT
295642 TTTAATACAT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
44 46 0.88
45 6 0.12
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (44 bp):
GACGTTTCCTTTAAAATATAATACCTAGCGTGGGTTCAAATCTC
Found at i:300151 original size:21 final size:21
Alignment explanation
Indices: 300096--300151 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
300086 AGATTAGATT
*
300096 TTTAATCAAAAGGATAAGTCC
1 TTTAATCAAAAGGTTAAGTCC
300117 TTTAATCAAAAGGTTAAGTCC
1 TTTAATCAAAAGGTTAAGTCC
*
300138 TTTCATCAAAAGGT
1 TTTAATCAAAAGGT
300152 CTTAACCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (21 bp):
TTTAATCAAAAGGTTAAGTCC
Found at i:305621 original size:29 final size:29
Alignment explanation
Indices: 305558--305628 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
305548 CTGCTGGAAA
*
305558 CGGTTTAACCGGTTTTCAACAGGTTCTGAC
1 CGGTTTGACCGG-TTTCAACAGGTTCTGAC
* *
305588 TGGTTTGACCGGTTTCAACCGGTTC-GAAC
1 CGGTTTGACCGGTTTCAACAGGTTCTG-AC
305617 CGG-TTGACCGGT
1 CGGTTTGACCGGT
305629 CGAACCGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 10 0.28
29 16 0.44
30 10 0.28
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (29 bp):
CGGTTTGACCGGTTTCAACAGGTTCTGAC
Found at i:305633 original size:17 final size:18
Alignment explanation
Indices: 305595--305664 Score: 81
Period size: 18 Copynumber: 3.8 Consensus size: 18
305585 GACTGGTTTG
*
305595 ACCGGTTTCAACCGGTTCGA
1 ACCGGTTT-GACCGG-TCGA
305615 ACCGG-TTGACCGGTCGA
1 ACCGGTTTGACCGGTCGA
*
305632 ACCGGTTTGA-CGGTCTAA
1 ACCGGTTTGACCGGTC-GA
305650 ACCGGTTTGACCGGT
1 ACCGGTTTGACCGGT
305665 TGACCCGACT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
17 14 0.31
18 20 0.44
19 6 0.13
20 5 0.11
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.24
Consensus pattern (18 bp):
ACCGGTTTGACCGGTCGA
Done.