Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008838.1 Hibiscus syriacus cultivar Beakdansim tig00112042_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: 388168
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:201293 original size:39 final size:39
Alignment explanation
Indices: 201212--201300 Score: 126
Period size: 39 Copynumber: 2.3 Consensus size: 39
201202 TTTTTAAATA
*
201212 TTTTTGAAAAATGATATAATATATAGTTTTAAAAATCAT
1 TTTTTGAAAAATGATATAATATATAATTTTAAAAATCAT
* * *
201251 TTTTTGGAAAATTATATAATATATAATTTTAAAACAT-TT
1 TTTTTGAAAAATGATATAATATATAATTTTAAAA-ATCAT
201290 TTTTTGAAAAA
1 TTTTTGAAAAA
201301 AACATATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 42 0.95
40 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (39 bp):
TTTTTGAAAAATGATATAATATATAATTTTAAAAATCAT
Found at i:207901 original size:81 final size:80
Alignment explanation
Indices: 207645--208313 Score: 789
Period size: 81 Copynumber: 8.2 Consensus size: 80
207635 TAGACAAACT
*
207645 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
207710 GCTTCGAGGGCACATC
66 GC-TCGAGGGCACATC
* * * * * * * *** *
207726 ATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCCGAGTTCGATTACA
* *
207791 CTCAGCTCAACGGCACATC
62 CTCAGCTCGAGGGCACATC
207810 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
*
207875 GTTTCGAGGGCACATC
66 G-CTCGAGGGCACATC
* * * *** * *
207891 ATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTACA
* *
207956 CTCAGCTCCAAGGCACATC
62 CTCAGCTCGAGGGCACATC
*
207975 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
208040 GCTTCGAGGGCACATC
66 GC-TCGAGGGCACATC
* * *** * *
208056 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTACA
* *
208121 CTCAGCTCCAAGGCACATC
62 CTCAGCTCGAGGGCACATC
* *
208140 ATTTACAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * *
208205 GCTCAACGACACATC
66 GCTCGAGGGCACATC
* *
208220 ATTTGCAGCATAGCTTAATTCGAGAAGGGCTATCTGCCAAAGACCCCCCAAGTTCGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCCCCGAGTTCGATTACACTC
*
208285 AGCTTTGAGGGCACATC
65 AGC-TCGAGGGCACATC
*
208302 ATTTACAGCATA
1 ATTTGCAGCATA
208314 ACTCAAGGTT
Statistics
Matches: 491, Mismatches: 81, Indels: 31
0.81 0.13 0.05
Matches are distributed among these distances:
80 125 0.25
81 141 0.29
82 22 0.04
83 2 0.00
84 127 0.26
85 74 0.15
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (80 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTCGAGGGCACATC
Found at i:207921 original size:165 final size:165
Alignment explanation
Indices: 207645--208259 Score: 1011
Period size: 165 Copynumber: 3.7 Consensus size: 165
207635 TAGACAAACT
*
207645 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * * **
207710 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTATAAGGGTTATCTG-TGACCAAAAGAC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGAC
*
207774 CTTTGAGTTCGACTACACTCAGCT-CAACGGCACATC
130 CTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATC
207810 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* *
207875 GTTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
207940 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
207975 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
208040 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
208105 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* *
208140 ATTTACAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * * *
208205 GC-TCAACGACACATCATTTGCAGCATAGCTTAATTCGAGAAGGGCTATCTGCCAA
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
208260 AGACCCCCCA
Statistics
Matches: 426, Mismatches: 22, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
164 47 0.11
165 373 0.88
166 6 0.01
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (165 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:208466 original size:246 final size:243
Alignment explanation
Indices: 207667--208428 Score: 592
Period size: 246 Copynumber: 3.1 Consensus size: 243
207657 GCTTAAGTCG
* ** * * * * * *
207667 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTAC
1 AGAAGGGCCATCTGAAAAAAACCCCCGAGTTCGATTACACTCAGC-TCAACGACACATCATTTGC
* * * * * * **** *
207732 AGCATAACTCAAGGCTATAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACACTCAGC
65 AGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCCAAGTTCGATTACACTCAGC
* * * * * * **
207797 -TCAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCC
126 TTCGAGGGCACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTT
* ** * * * * * * * *
207857 CGAGTTCGATTACACTCAGTTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCA
191 CGAGTTCGACTACACTCA-ACTCCAAGGCAAATCACTTACA--ATAGCTCAAGGCA
** * *** * * *
207913 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
1 AGAAGGGCCATCTG--AA--AAAAACCCCCGAGTTCGATTACACTCAGCT-CAACGACACATCAT
* *
207977 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTTGATTACACTCAGC
61 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAGC
* *
208042 TTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTT
126 TTCGAGGGCACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTT
* * * * * * * *
208107 TGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGTATAGCTTAAGTCG
191 CGAGTTCGACTACACTCAACTCCAAGGCAAATCACTTACA--ATAGCTCAAGGCA
* ** *
208162 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTCAACGACACATCATTTGCA
1 AGAAGGGCCATCTGAAAAAAACCCCCGAGTTCGATTACACTCAGCTCAACGACACATCATTTGCA
* *
208227 GCATAGCTTAATTCGAGAAGGGCTATCTGCCAAAGACCCCCCAAGTTCGATTACACTCAGCTTTG
66 GCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCCCCAAGTTCGATTACACTCAGCTTCG
* **
208292 AGGGCACATCATTTACAGCATAACTCAAGGT-TAGAAGGGTTATCTTTC-ACCAAAAGACCTTCG
130 AGGGCACATCATTTACAGCATAACTCAA-GTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCG
* * *
208355 AGTTCGATTATACTCAACT-TAGAGGCAAATCAAGCTTAC-A-AGCTCAAGGCA
193 AGTTCGACTACACTCAACTCCA-AGGCAAATC-A-CTTACAATAGCTCAAGGCA
208406 AGAAGGGCCATCTGTAAATAAAA
1 AGAAGGGCCATCTG-AAA-AAAA
208429 TTGTCGAGTT
Statistics
Matches: 425, Mismatches: 72, Indels: 38
0.79 0.13 0.07
Matches are distributed among these distances:
244 24 0.06
245 104 0.24
246 161 0.38
247 5 0.01
248 4 0.01
249 78 0.18
250 49 0.12
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (243 bp):
AGAAGGGCCATCTGAAAAAAACCCCCGAGTTCGATTACACTCAGCTCAACGACACATCATTTGCA
GCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAGCTTCGA
GGGCACATCATTTACAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGT
TCGACTACACTCAACTCCAAGGCAAATCACTTACAATAGCTCAAGGCA
Found at i:209137 original size:11 final size:12
Alignment explanation
Indices: 209123--209148 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
209113 TAATATATAG
209123 TTTTGAAAACAT
1 TTTTGAAAACAT
209135 TTTTGAAAACAT
1 TTTTGAAAACAT
209147 TT
1 TT
209149 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:209163 original size:39 final size:37
Alignment explanation
Indices: 209038--209351 Score: 206
Period size: 39 Copynumber: 8.5 Consensus size: 37
209028 TTTTGACAAA
*
209038 ATATAATATATAATTTTCAGAAAACATTTTTTTTG-AAAATT
1 ATATAATATATAGTTTT-A-AAAACA---TTTTTGAAAAATT
* * * *
209079 -T-T-ATATA-ATTTTTGAAAATATTTTT-AAATA-T
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATT
*
209110 ATATAATATATAGTTTTGAAAACATTTTTGAAAACATTT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAA-A-TT
* * * * *
209149 ATATATTATATAGTTTTTAAAATA-ATTTGAAAACTT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATT
* ** * *
209185 ATATAGTATATAGTTTTTTAAATATTTTTGAAAAATG
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAATT
*
209222 ATATAATATATAGTTTTAAAAATCATTTTTTGGAAAATT
1 ATATAATATATAGTTTTAAAAA-CA-TTTTTGAAAAATT
* *
209261 ATATAATATATAATTTTAAAAACATTTTTTTTGAAAAA-A
1 ATATAATATATAGTTTTAAAAACA---TTTTTGAAAAATT
* *
209300 ACAT-ATATAATA-TTTTAAAATA-ATTTTTGAAATA-T
1 ATATAATAT-ATAGTTTTAAAA-ACATTTTTGAAAAATT
*
209335 ATATATTATATA-TTTTA
1 ATATAATATATAGTTTTA
209352 GAATATATAT
Statistics
Matches: 225, Mismatches: 31, Indels: 40
0.76 0.10 0.14
Matches are distributed among these distances:
31 1 0.00
32 9 0.04
33 1 0.00
34 5 0.02
35 42 0.19
36 30 0.13
37 34 0.15
38 29 0.13
39 62 0.28
40 12 0.05
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (37 bp):
ATATAATATATAGTTTTAAAAACATTTTTGAAAAATT
Found at i:211231 original size:36 final size:36
Alignment explanation
Indices: 211183--211267 Score: 152
Period size: 36 Copynumber: 2.3 Consensus size: 36
211173 AATAGAGGAT
211183 TTTGAAACTCTTGGTGATATGACCTACCTTGAGTGC
1 TTTGAAACTCTTGGTGATATGACCTACCTTGAGTGC
*
211219 TTTGAAATTCTTGGTGATATGACCTACCTTGAGTGC
1 TTTGAAACTCTTGGTGATATGACCTACCTTGAGTGC
211255 TTTCGAAACTCTT
1 TTT-GAAACTCTT
211268 CACTTGTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
36 38 0.83
37 8 0.17
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (36 bp):
TTTGAAACTCTTGGTGATATGACCTACCTTGAGTGC
Found at i:211249 original size:18 final size:18
Alignment explanation
Indices: 211192--211249 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
211182 TTTTGAAACT
211192 CTTGGTGATATGACCTAC
1 CTTGGTGATATGACCTAC
* * ** *
211210 CTTGAGTGCTTTGAAAT-T
1 CTTG-GTGATATGACCTAC
211228 CTTGGTGATATGACCTAC
1 CTTGGTGATATGACCTAC
211246 CTTG
1 CTTG
211250 AGTGCTTTCG
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
17 8 0.29
18 12 0.43
19 8 0.29
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (18 bp):
CTTGGTGATATGACCTAC
Found at i:215255 original size:27 final size:27
Alignment explanation
Indices: 215217--215272 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
215207 TAATGATACG
215217 TGAAAACCCTGAAATTTACTAGCCTTA
1 TGAAAACCCTGAAATTTACTAGCCTTA
*
215244 TGAAAACCCTGAAATTTACTCGCCTTA
1 TGAAAACCCTGAAATTTACTAGCCTTA
215271 TG
1 TG
215273 CTTTCTTCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.30
Consensus pattern (27 bp):
TGAAAACCCTGAAATTTACTAGCCTTA
Found at i:215905 original size:30 final size:30
Alignment explanation
Indices: 215871--215927 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
215861 AATTCTCACG
*
215871 TAGTTTACTAACATTAATTATTTCTTAACA
1 TAGTTTACTAAAATTAATTATTTCTTAACA
215901 TAGTTTACTAAAATTAATTATTTCTTA
1 TAGTTTACTAAAATTAATTATTTCTTA
215928 GATTAAGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (30 bp):
TAGTTTACTAAAATTAATTATTTCTTAACA
Found at i:216130 original size:69 final size:69
Alignment explanation
Indices: 216019--216157 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
216009 ACTGTAATAC
216019 GTCTTCGGTTTTTCCAGACAAAACGCATGGAAATGTAAAACAAAAGAAAATTTGATTGGTCCTGG
1 GTCTTCGGTTTTTCCAGACAAAACGCATGGAAATGTAAAACAAAAGAAAATTTGATTGGTCCTGG
216084 AGAA
66 AGAA
216088 GTCTTCGGTTTTTCCAGACAAAACGCATGGAAATGTAAAACAAAAGAAAATTTGATTGGTCCTGG
1 GTCTTCGGTTTTTCCAGACAAAACGCATGGAAATGTAAAACAAAAGAAAATTTGATTGGTCCTGG
216153 AGAA
66 AGAA
216157 G
1 G
216158 ATGCACTGTG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.26
Consensus pattern (69 bp):
GTCTTCGGTTTTTCCAGACAAAACGCATGGAAATGTAAAACAAAAGAAAATTTGATTGGTCCTGG
AGAA
Found at i:219668 original size:63 final size:59
Alignment explanation
Indices: 219595--219752 Score: 165
Period size: 63 Copynumber: 2.5 Consensus size: 59
219585 AATTGTTCAG
* * *
219595 TGTGTATCGATGCACAGGAAGTGCATTGATGCACCCATTAAAAATGGAAACATCGAA-TTAAT
1 TGTGCATCGATGCA-AGG-AGTGCATCGATGCACCCATT-AAAAT-GAAACATCGAAGGTAAT
* *
219657 TAGTGCATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAAATGAAACATCGAAGGTGAT
1 T-GTGCATCGATGC--AAGGAGTGCATCGATGCA-CCCATTAAAATGAAACATCGAAGGTAAT
* *
219720 TGTGTATCGATGCATGGTAGTGCATCGATGCAC
1 TGTGCATCGATGCAAGG-AGTGCATCGATGCAC
219753 TTCAAGGGAA
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
60 4 0.05
61 14 0.17
62 23 0.28
63 33 0.40
64 8 0.10
65 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (59 bp):
TGTGCATCGATGCAAGGAGTGCATCGATGCACCCATTAAAATGAAACATCGAAGGTAAT
Found at i:220120 original size:170 final size:170
Alignment explanation
Indices: 219822--220157 Score: 656
Period size: 170 Copynumber: 2.0 Consensus size: 170
219812 TCAATTGGAT
219822 ATTAATATGTATCAATGTATGATTATATAGAAATCGAGCACGAACAAGTCCCGGAACGATTATCA
1 ATTAATATGTATCAATGTATGATTATATAGAAATCGAGCACGAACAAGTCCCGGAACGATTATCA
219887 AGTTATGATTCGATCGCAAGAGAGGAAATTATAAAAAGGATTGGAACTTAGTGAGGCCCAAGGTG
66 AGTTATGATTCGATCGCAAGAGAGGAAATTATAAAAAGGATTGGAACTTAGTGAGGCCCAAGGTG
219952 AGTGCGCATTATTTTATATATGATGCTTAATGGGAACTAA
131 AGTGCGCATTATTTTATATATGATGCTTAATGGGAACTAA
219992 ATTAATATGTATCAATGTATGATTATATAGAAATCGAGCACGAACAAGTCCCGGAACGATTATCA
1 ATTAATATGTATCAATGTATGATTATATAGAAATCGAGCACGAACAAGTCCCGGAACGATTATCA
220057 AGTTATGATTCGATCGCAAGAGAGGAAATTATAAAAATGGATTGGAACTTAGTGAGG-CCAAGGT
66 AGTTATGATTCGATCGCAAGAGAGGAAATTATAAAAA-GGATTGGAACTTAGTGAGGCCCAAGGT
220121 GAGTGCGCATTATTTTATATATGATGCTTAATGGGAA
130 GAGTGCGCATTATTTTATATATGATGCTTAATGGGAA
220158 ATAAGACTTG
Statistics
Matches: 165, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
170 146 0.88
171 19 0.12
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.29
Consensus pattern (170 bp):
ATTAATATGTATCAATGTATGATTATATAGAAATCGAGCACGAACAAGTCCCGGAACGATTATCA
AGTTATGATTCGATCGCAAGAGAGGAAATTATAAAAAGGATTGGAACTTAGTGAGGCCCAAGGTG
AGTGCGCATTATTTTATATATGATGCTTAATGGGAACTAA
Found at i:220352 original size:20 final size:21
Alignment explanation
Indices: 220327--220377 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
220317 TGATATAAAC
*
220327 TATATGATATGATAAGA-AA-T
1 TATATGATAT-AAAAGAGAAGT
220347 TATATGAATATAAAAGAGAAGT
1 TATATG-ATATAAAAGAGAAGT
220369 TATATGATA
1 TATATGATA
220378 AGACATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.41
21 9 0.33
22 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (21 bp):
TATATGATATAAAAGAGAAGT
Found at i:224222 original size:64 final size:64
Alignment explanation
Indices: 224148--224308 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 64
224138 ATTGTTCAGT
* * * * *
224148 GTGTATCGATGCA-CAGGAAGTGCATTAATGTA-CCCATTAAAAATGGAAACATCGAATGTAATT
1 GTGTATCGATGCATAAGG-AGTGCATCAATGCACCCCATT-AAAATGAAAACATCGAAGGTAATT
224211 A
64 A
* * * *
224212 GTGTATCGATGCATAAGGAGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTT
1 GTGTATCGATGCATAAGGAGTGCATCAATGCACCCCATTAAAATGAAAACATCGAAGGTAATTA
* *
224276 GTGTATCGATGCAT-GGGTAGTGCATCGATGCAC
1 GTGTATCGATGCATAAGG-AGTGCATCAATGCAC
224309 TTCAAGGGAA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 2 0.02
64 74 0.88
65 8 0.10
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCATAAGGAGTGCATCAATGCACCCCATTAAAATGAAAACATCGAAGGTAATTA
Found at i:225195 original size:24 final size:23
Alignment explanation
Indices: 225143--225202 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
225133 ACAACTTTAT
*
225143 ATGGCACTTCGGTGCATTTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
* *
225166 ACGGCACTACGGTGCAAATTCTAC
1 ATGGCACTTCGGTGC-AATTCTAC
*
225190 GTGGCACTTCGGT
1 ATGGCACTTCGGT
225203 TCATTTATAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTCTAC
Found at i:231560 original size:18 final size:18
Alignment explanation
Indices: 231537--231577 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
231527 GGTTGAGATA
231537 TGGGTGTTTAAGCATGTT
1 TGGGTGTTTAAGCATGTT
231555 TGGGTGTTTAAGCATGTT
1 TGGGTGTTTAAGCATGTT
231573 TGGGT
1 TGGGT
231578 TCTTGCTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.15, C:0.05, G:0.37, T:0.44
Consensus pattern (18 bp):
TGGGTGTTTAAGCATGTT
Found at i:231951 original size:18 final size:19
Alignment explanation
Indices: 231925--231974 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
231915 GCTAGTTTTG
*
231925 GTATAGATACT-CAAGAGA
1 GTATTGATACTCCAAGAGA
*
231943 GTATTGATACTTGCCAAGGGA
1 GTATTGATAC-T-CCAAGAGA
231964 GTATTGATACT
1 GTATTGATACT
231975 ACATGTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.33
19 1 0.04
20 1 0.04
21 16 0.59
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (19 bp):
GTATTGATACTCCAAGAGA
Found at i:233469 original size:65 final size:65
Alignment explanation
Indices: 233313--233471 Score: 155
Period size: 65 Copynumber: 2.4 Consensus size: 65
233303 TTTTAATTAC
* * * * * *
233313 ACATCTAATGC-ATTATGTGTATCGATGCACATACCATGCATAGATGCACTCCAGGTTTTATTGA
1 ACATCGAATGCTATTA-GTGTATCGATGCACAGACCATGCATAGATACACTACAGGTCTTATTAA
233377 A
65 A
* * * * *
233378 ACATCGAATGCT-TTTGATGTACCGATGCACAGACCATGTATCGATACACTACTGGCTCTT-TTA
1 ACATCGAATGCTATTAG-TGTATCGATGCACAGACCATGCATAGATACACTACAGG-TCTTATTA
233441 AA
64 AA
233443 ACATCGAATG-TAATTAGTGTATCGATGCA
1 ACATCGAATGCT-ATTAGTGTATCGATGCA
233472 TCCCAAGTGT
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
64 2 0.03
65 68 0.89
66 6 0.08
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (65 bp):
ACATCGAATGCTATTAGTGTATCGATGCACAGACCATGCATAGATACACTACAGGTCTTATTAAA
Found at i:233559 original size:54 final size:54
Alignment explanation
Indices: 233477--233599 Score: 246
Period size: 54 Copynumber: 2.3 Consensus size: 54
233467 ATGCATCCCA
233477 AGTGTACCGATGCACTAAGTCTTATAACGGTCGAAATATTTGAATTTTACACAC
1 AGTGTACCGATGCACTAAGTCTTATAACGGTCGAAATATTTGAATTTTACACAC
233531 AGTGTACCGATGCACTAAGTCTTATAACGGTCGAAATATTTGAATTTTACACAC
1 AGTGTACCGATGCACTAAGTCTTATAACGGTCGAAATATTTGAATTTTACACAC
233585 AGTGTACCGATGCAC
1 AGTGTACCGATGCAC
233600 CTTGATGGTG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (54 bp):
AGTGTACCGATGCACTAAGTCTTATAACGGTCGAAATATTTGAATTTTACACAC
Found at i:239904 original size:41 final size:41
Alignment explanation
Indices: 239866--240124 Score: 295
Period size: 41 Copynumber: 6.3 Consensus size: 41
239856 CGTTTTTTCA
* *
239866 ACAAACGCCGCAAAAGAGTAGTACTTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
* * *
239907 ACAAACGCCGCTAAAGACTCGTAATTTAGTGGTATTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
* * * *
239948 ACAAACGCCGCTATAGAATTGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
*
239989 ACAAACGCCGCTAAAGACTCA-TACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACT-AGTACTTTAGTGGCATTTTTAT
* **
240030 ACAAACTCCGCTAAAGACGCGTACTTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
* * * * * * * *
240071 TCAAACGCCGTTATACACTTGTACTATAGTGGCGTTTGTGTTT
1 ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTT-T-TAT
240114 ACAAACGCCGC
1 ACAAACGCCGC
240125 AAGTTTACAA
Statistics
Matches: 184, Mismatches: 30, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
41 172 0.93
42 1 0.01
43 11 0.06
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (41 bp):
ACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
Found at i:239913 original size:82 final size:82
Alignment explanation
Indices: 239818--240124 Score: 279
Period size: 82 Copynumber: 3.7 Consensus size: 82
239808 TTTAGCAGCG
* ** * *
239818 TTTTTATAAAAACGCCGC-AATAGGTTCATCGATAGTGGCGTTTTTTCA-ACAAACGCCGCAAAA
1 TTTTTATACAAACGCCGCTAA-AGACTCATCAATAGTGGCGTTTTTT-ATACAAACGCCGCTAAA
239881 GAGTAGTACTTTAGTGGCA
64 GAGTAGTACTTTAGTGGCA
* *
239900 TTTTTATACAAACGCCGCTAAAGACTCGT-AATTTAGT-G-GTATTTTTATACAAACGCCGCTAT
1 TTTTTATACAAACGCCGCTAAAGACTCATCAA--TAGTGGCGT-TTTTTATACAAACGCCGCTAA
* * *
239962 AGAATTGTACTTTAGTGGCG
63 AGAGTAGTACTTTAGTGGCA
** *
239982 TTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCG-TTTTTATACAAACTCCGCTAAAG
1 TTTTTATACAAACGCCGCTAAAGACTCAT-CAATAGTGGCGTTTTTTATACAAACGCCGCTAAAG
*
240046 ACG-CGTACTTTAGTGGCA
65 A-GTAGTACTTTAGTGGCA
* * * * ** *
240064 TTTTTATTCAAACGCCGTTATACACTTGTACTATAGTGGCGTTTGTGTT-TACAAACGCCGC
1 TTTTTATACAAACGCCGCTAAAGACTCAT-CAATAGTGGCGTTT-T-TTATACAAACGCCGC
240125 AAGTTTACAA
Statistics
Matches: 186, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
81 4 0.02
82 158 0.85
83 9 0.05
84 13 0.07
85 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (82 bp):
TTTTTATACAAACGCCGCTAAAGACTCATCAATAGTGGCGTTTTTTATACAAACGCCGCTAAAGA
GTAGTACTTTAGTGGCA
Found at i:239986 original size:123 final size:122
Alignment explanation
Indices: 239849--240126 Score: 369
Period size: 123 Copynumber: 2.2 Consensus size: 122
239839 AGGTTCATCG
*
239849 ATAGTGGCGTTTTTTCAACAAACGCCGCAAAAGAGT-AGTACTTTAGTGGCATTTTTATACAAAC
1 ATAGTGGCG-TTTTT-AACAAACGCCGCAAAAGACTCA-TACTTTAGTGGCATTTTTATACAAAC
* * *
239913 GCCGCTAAAGACTCGTAATTTAGTGGTATTTTTATACAAACGCCGCTATAGAATTGTACT
63 GCCGCTAAAGACGCGTAATTTAGTGGCATTTTTATACAAACGCCGCTATACAATTGTACT
* * * *
239973 TTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACTC
1 ATAGTGGCGTTTTTA-ACAAACGCCGCAAAAGACTCATACTTTAGTGGCATTTTTATACAAACGC
* * * *
240038 CGCTAAAGACGCGTACTTTAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACT
65 CGCTAAAGACGCGTAATTTAGTGGCATTTTTATACAAACGCCGCTATACAATTGTACT
*
240096 ATAGTGGCGTTTGTGTTTACAAACGCCGCAA
1 ATAGTGGCG-TT-T-TTAACAAACGCCGCAA
240127 GTTTACAAAT
Statistics
Matches: 134, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
122 1 0.01
123 107 0.80
124 11 0.08
125 13 0.10
126 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (122 bp):
ATAGTGGCGTTTTTAACAAACGCCGCAAAAGACTCATACTTTAGTGGCATTTTTATACAAACGCC
GCTAAAGACGCGTAATTTAGTGGCATTTTTATACAAACGCCGCTATACAATTGTACT
Found at i:243464 original size:43 final size:43
Alignment explanation
Indices: 243403--243797 Score: 342
Period size: 43 Copynumber: 9.2 Consensus size: 43
243393 AAGGTAATTA
*
243403 GCGGCGTTTGTATCCAAAAACGCCGCTATAAATATGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACTTTTT
243446 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACTTTTT
* * * * * * * * *
243489 GTGGTGTTTG-AGTTCATAAATGCCGTTATAGGTTTGACCTTTT
1 GCGGCGTTTGTA-TCCAAAAACGCCGCTATAGATATGACTTTTT
* * * * *
243532 GCGGCGTTTGTGTCCAAAAACACCGCTATAGGTCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACTTTTT
* * *
243575 GCGGCGTTTGT-TCTAAAAACGCCAG-TATATG-TCT-TCTCTTTT
1 GCGGCGTTTGTATCCAAAAACGCC-GCTATA-GATATGACT-TTTT
* * * *
243617 GCGACGTTTTTATCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACTTTTT
* * * * *
243660 GCGGCGTTT-TTTCTAGAAACGCCGCTATATATCATAACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGAT-ATGACTTTTT
* *
243703 GCGGCGTTTAT-TCCAAAAACGCCGATATAGATATCGA-TCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATAT-GACT-TTTT
* * *
243746 GCGGCGTTTGT-TCAAAAAACGCCG-TAATAGATATTGACCTATT
1 GCGGCGTTTGTATCCAAAAACGCCGCT-ATAGATA-TGACTTTTT
*
243789 GTGGCGTTT
1 GCGGCGTTT
243798 TTTGTTCTCA
Statistics
Matches: 290, Mismatches: 46, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
41 1 0.00
42 56 0.19
43 230 0.79
44 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACTTTTT
Found at i:251236 original size:21 final size:21
Alignment explanation
Indices: 251206--251262 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
251196 GCATGCTTGC
251206 ATTCCTAGCCCACAGTGGTAT
1 ATTCCTAGCCCACAGTGGTAT
* * *
251227 ATATCC-AGCCCGCAATGTTAT
1 AT-TCCTAGCCCACAGTGGTAT
251248 ATTCCTAGCCCACAG
1 ATTCCTAGCCCACAG
251263 GGTTTTATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 3 0.10
21 23 0.79
22 3 0.10
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (21 bp):
ATTCCTAGCCCACAGTGGTAT
Found at i:252082 original size:21 final size:21
Alignment explanation
Indices: 252031--252104 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
252021 CCTTAAATAA
* *
252031 TAATTAATATATTTGAAAGAA
1 TAATTAATATATTTGAATGAC
252052 TAATTAATATATTTGAATGAC
1 TAATTAATATATTTGAATGAC
* *
252073 TGATT--CATATTTGAATGAC
1 TAATTAATATATTTGAATGAC
252092 TAAATTGAATATA
1 T-AATT-AATATA
252105 ATCTTAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 14 0.33
20 3 0.07
21 23 0.53
23 3 0.07
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.41
Consensus pattern (21 bp):
TAATTAATATATTTGAATGAC
Found at i:255608 original size:25 final size:25
Alignment explanation
Indices: 255579--255656 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
255569 ATCGAACCTT
*
255579 ACCCTAAACCACTTTAACCTACACA
1 ACCCTAAACCACTTTAACCTACAAA
** * * *
255604 ACCCTTGACCACTCTCACCTTAAAAAA
1 ACCCTAAACCACTTTAACC-T-ACAAA
*
255631 ACCCTAAACTACTTTAACCTACAAA
1 ACCCTAAACCACTTTAACCTACAAA
255656 A
1 A
255657 TCCTTCACCA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
25 20 0.51
26 2 0.05
27 17 0.44
ACGTcount: A:0.41, C:0.36, G:0.01, T:0.22
Consensus pattern (25 bp):
ACCCTAAACCACTTTAACCTACAAA
Found at i:255656 original size:27 final size:27
Alignment explanation
Indices: 255579--255656 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 27
255569 ATCGAACCTT
*
255579 ACCCTAAACCACTTTAACCTAC--ACA
1 ACCCTAAACCACTTTAACCTACAAAAA
** * *
255604 ACCCTTGACCACTCTCACCTTA-AAAAA
1 ACCCTAAACCACTTTAACC-TACAAAAA
*
255631 ACCCTAAACTACTTTAACCTACAAAA
1 ACCCTAAACCACTTTAACCTACAAAA
255657 TCCTTCACCA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
25 15 0.38
26 4 0.10
27 20 0.51
ACGTcount: A:0.41, C:0.36, G:0.01, T:0.22
Consensus pattern (27 bp):
ACCCTAAACCACTTTAACCTACAAAAA
Found at i:255674 original size:52 final size:52
Alignment explanation
Indices: 255579--255677 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 52
255569 ATCGAACCTT
* *
255579 ACCCTAAACCACTTTAACCTACACAACCCTTGACCACTCTCACCTTAAAAAA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAAAAAA
* * * *
255631 ACCCTAAACTACTTTAACCTACAAAATCCTTCACCATTTTCACCTTA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTA
255678 TCGAACCCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.36, C:0.36, G:0.01, T:0.26
Consensus pattern (52 bp):
ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAAAAAA
Found at i:255847 original size:13 final size:13
Alignment explanation
Indices: 255829--255858 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
255819 TTTAACCTTT
255829 AACCCTAAATCAA
1 AACCCTAAATCAA
*
255842 AACCCTAATTCAA
1 AACCCTAAATCAA
255855 AACC
1 AACC
255859 AGGTGAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (13 bp):
AACCCTAAATCAA
Found at i:258253 original size:7 final size:7
Alignment explanation
Indices: 258241--258278 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
258231 TTTAAAACCC
258241 TAAATCT
1 TAAATCT
258248 TAAATCT
1 TAAATCT
258255 TAAATCT
1 TAAATCT
258262 TAAA-CT
1 TAAATCT
*
258268 ATAACTCT
1 -TAAATCT
258276 TAA
1 TAA
258279 TTCTAAACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 2 0.07
7 24 0.86
8 2 0.07
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (7 bp):
TAAATCT
Found at i:262869 original size:113 final size:113
Alignment explanation
Indices: 262666--262869 Score: 363
Period size: 113 Copynumber: 1.8 Consensus size: 113
262656 TTTTGATGCC
* * * *
262666 AAATCTCAGCCACTTAAACGTGGAATCAATGGTTACCTTCTTACACGTTTTGTATCTGCAGGACT
1 AAATATCAGCAACTTAAACGTGGAATCAAGGGTTACCTTCTTACACGTTTTGCATCTGCAGGACT
262731 CATGTTCTCCATTGTTCCGTTTTCGCAACTTAAACATGGAAGTAAGTA
66 CATGTTCTCCATTGTTCCGTTTTCGCAACTTAAACATGGAAGTAAGTA
*
262779 AAATATCAGCAACTTAAACGTGGAATCAAGGGTTACCTTCTTACACGTTTTGCATCTGCAGGATT
1 AAATATCAGCAACTTAAACGTGGAATCAAGGGTTACCTTCTTACACGTTTTGCATCTGCAGGACT
262844 CATGTTCTCCATTGTTCCGTTTTCGC
66 CATGTTCTCCATTGTTCCGTTTTCGC
262870 CTTCAACTTC
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 86 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (113 bp):
AAATATCAGCAACTTAAACGTGGAATCAAGGGTTACCTTCTTACACGTTTTGCATCTGCAGGACT
CATGTTCTCCATTGTTCCGTTTTCGCAACTTAAACATGGAAGTAAGTA
Found at i:263471 original size:26 final size:26
Alignment explanation
Indices: 263432--263484 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
263422 CATGCATGCA
*
263432 TCGGCTTTCTGTTCACCGGATAAAAC
1 TCGGCTTTCGGTTCACCGGATAAAAC
*
263458 TCGGCTTTCGGTTCATCGGATAAAAC
1 TCGGCTTTCGGTTCACCGGATAAAAC
263484 T
1 T
263485 ATTTCGATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (26 bp):
TCGGCTTTCGGTTCACCGGATAAAAC
Found at i:266717 original size:3 final size:3
Alignment explanation
Indices: 266705--266759 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
266695 TTATATTTAA
266705 ATT A-T ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
266750 ATT ATT ATT A
1 ATT ATT ATT A
266760 ATGTTACATA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.12
3 43 0.88
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:266722 original size:14 final size:14
Alignment explanation
Indices: 266712--266759 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
266702 TAAATTATAT
266712 TATTATTATTATTA
1 TATTATTATTATTA
266726 TATTATTATTATTA
1 TATTATTATTATTA
266740 TATTATTATTATTA
1 TATTATTATTATTA
266754 TTATTA
1 -TATTA
266760 ATGTTACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 28 0.85
15 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:266725 original size:17 final size:17
Alignment explanation
Indices: 266705--266759 Score: 94
Period size: 17 Copynumber: 3.2 Consensus size: 17
266695 TTATATTTAA
266705 ATTATATTATTATTATT
1 ATTATATTATTATTATT
266722 ATTATATTATTATTATT
1 ATTATATTATTATTATT
266739 A-TATTATTATTATTATT
1 ATTA-TATTATTATTATT
266756 ATTA
1 ATTA
266760 ATGTTACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
16 2 0.06
17 32 0.89
18 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATATTATTATTATT
Found at i:267373 original size:146 final size:146
Alignment explanation
Indices: 267116--267506 Score: 568
Period size: 146 Copynumber: 2.7 Consensus size: 146
267106 GGAGATCGGG
* * * *
267116 ATCTCCGATCAACATTCCGAAAGGTCAAAAGTTGCGTAAGGCCATCACGAACAACATATTGAAAA
1 ATCTGCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
* * * *
267181 ATCAAGACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGCTTTTAGCCT
66 ATCAGGACGATCAGACGGTGGATGGTGACAGATCGGAGAAAACAAATCCGGACGGCTTTTAGCCT
*
267246 CTTTCCGGTGATCGAA
131 CTTGCCGGTGATCGAA
**
267262 ATCTTTGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
1 ATCTGCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
*
267327 ATCAGGACGATCAGACGGTGGATGGTGACAGATCGGAGAAAACAAATCCGGACGGTTTTTAGCCT
66 ATCAGGACGATCAGACGGTGGATGGTGACAGATCGGAGAAAACAAATCCGGACGGCTTTTAGCCT
*
267392 CTTGCCGGTGATCGGA
131 CTTGCCGGTGATCGAA
* * * * *
267408 ATCTGCGATCAATATTCCGAACGGTGAAAAGTTGCGCG-ATGCCAACACAAACAACCTATTGAAA
1 ATCTGCGATCAATATTCCGAACGGTCAAAAGTTGCG-GAAGGCCATCACGAACAACATATTGAAA
* * **
267472 AATCAGGACAATCGGACGGTGGATGACGACAGATC
65 AATCAGGACGATCAGACGGTGGATGGTGACAGATC
267507 AAAGAAAATA
Statistics
Matches: 221, Mismatches: 23, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
146 220 1.00
147 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (146 bp):
ATCTGCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
ATCAGGACGATCAGACGGTGGATGGTGACAGATCGGAGAAAACAAATCCGGACGGCTTTTAGCCT
CTTGCCGGTGATCGAA
Found at i:270631 original size:6 final size:6
Alignment explanation
Indices: 270620--270666 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
270610 ATTAACACCT
*
270620 TTTGCA TTTGCA TTTGGCA TTTGCA TCTGCA -TTGCA TGTATGCA TTT
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA TTTGCA T-T-TGCA TTT
270667 AAGCCTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
5 4 0.11
6 18 0.51
7 8 0.23
8 5 0.14
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (6 bp):
TTTGCA
Found at i:273551 original size:125 final size:125
Alignment explanation
Indices: 273329--273836 Score: 835
Period size: 125 Copynumber: 4.1 Consensus size: 125
273319 AAGTTGTGAT
273329 ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGAAAAGACTCAGACCAAGGAGGCATGAA
1 ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGAAAAGACTCAGACCAAGGAGGCATGAA
*
273394 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCATACCAGTATAAGATA
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
273454 ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGAAAAGACTCAGACCAAGGAGGCATGAA
1 ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGAAAAGACTCAGACCAAGGAGGCATGAA
* *
273519 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTGTAAGATG
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
* *
273579 AGGTTGGGGCATGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGGAGGCATGAA
1 ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGAAAAGACTCAGACCAAGGAGGCATGAA
273644 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
* * *
273704 ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGA---AGACCAAGAAGGAATTG-
1 ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGAAAAGACTCAGACCAAGGAGGCA-TGA
* * *** * *
273765 AGAATGAGCCTTACAAGTTGAGGTGTTGGAATATTTTGAAGGCCCGTATCAATATAAGATA
65 AGAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
*
273826 ATGTTGTGGCA
1 ATGTTGGGGCA
273837 CAAGTGACGA
Statistics
Matches: 363, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
122 76 0.21
123 2 0.01
125 285 0.79
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (125 bp):
ATGTTGGGGCATGACTGAACCCACATCATGTTGAGATGAAAAGACTCAGACCAAGGAGGCATGAA
GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
Found at i:275051 original size:36 final size:36
Alignment explanation
Indices: 275009--275085 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
274999 AGCAAAGTCA
* * * * *
275009 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
*
275045 GTCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
1 ATCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
275081 ATCTT
1 ATCTT
275086 GTGTCTTCAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (36 bp):
ATCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
Found at i:275650 original size:54 final size:54
Alignment explanation
Indices: 275513--276083 Score: 739
Period size: 54 Copynumber: 10.7 Consensus size: 54
275503 AAGATTTTCA
* * **
275513 AGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTTTGAAG-A-TTGTTTG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
* * * * *
275565 AGTTTCATGCTCCCT-GAAGAAAGAGGGAGCGAACACGTTTGAAGAAGAGGTACG
1 AGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
* *
275619 AGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTTGAAGAAGATGTCCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
*
275673 AGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
*
275727 AGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
* *
275781 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTTCTG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
* * *
275835 AGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCG--TG-TGAAGATATCCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
* * * * **
275886 AGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCATTTGAAG-AGATGTTTG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
* *
275939 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTTTCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
* * * *
275993 AGTTCCATACTTCCTAGAGAAAGAGGGAGTGAACCCCG--T-AAGAAGATTATTCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAA-CCCGTTTGAAGAAGA-TGTCCG
* * *
276046 AGTTCTATACTGCCTGAAAGAAAGAGGGAGCGAACCCG
1 AGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCG
276084 ATTGTTGAAG
Statistics
Matches: 463, Mismatches: 45, Indels: 21
0.88 0.09 0.04
Matches are distributed among these distances:
51 42 0.09
52 47 0.10
53 72 0.16
54 297 0.64
55 5 0.01
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.21
Consensus pattern (54 bp):
AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
Found at i:276203 original size:55 final size:55
Alignment explanation
Indices: 276034--276626 Score: 638
Period size: 55 Copynumber: 10.8 Consensus size: 55
276024 AACCCCGTAA
* * *
276034 GAAGATTATTCGAGT-TCTATACTGC-CTGAAAGAAAGAGGGAGC-GAACCCGATTGTT
1 GAAGATTGTTCGAGTCT-TATACT-CTCTG-AAGAAATAGGGAGCAG-ACACGATTGTT
* *
276090 GAAGATTGTTCGAGTCTTATACTCTCTCTGAAGAAATAGGGAGTAGACACGACTGTT
1 GAAGATTGTTCGAGTCTTATA--CTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
*
276147 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * *
276202 GAAGATTGTTCGAGTCTTATACTCTTTGAAGGAATAGGGAGCGGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
*
276257 GAAGATTGTTCGAGTCTTATACTCTCTGAATG-AATAGAGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAA-GAAATAGGGAGCAGACACGATTGTT
* * * * * *
276312 GAAGATTGTTTGAGTCTTATACTTTCTGAAGGAATAGGGAGAAAACACGGTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * *
276367 GAAGGTTGTTCGAGTCTTATACTTTCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* *
276422 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGATACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
* * * *
276477 GAAGA-TGTTCGAGT-TCTATACT-TCCTAAAGAAAGAGGGAGC-GAACCCGATT-TCA
1 GAAGATTGTTCGAGTCT-TATACTCT-CTGAAGAAATAGGGAGCAG-ACACGATTGT-T
* ** * * * **
276531 GAAGATT-TACGAGT-TCCTACTCCCTAAAGAAATAGGGAGC-GA-ACCCATTGGCA
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA-CGATT-GTT
* * *
276584 GAAGATTATTCGAGT-TTCATACTCTCTGAAGCAAGAGGGAGCA
1 GAAGATTGTTCGAGTCTT-ATACTCTCTGAAGAAATAGGGAGCA
276627 AACCCGTAGG
Statistics
Matches: 468, Mismatches: 50, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
52 5 0.01
53 33 0.07
54 55 0.12
55 306 0.65
56 19 0.04
57 44 0.09
58 6 0.01
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
Found at i:276515 original size:54 final size:52
Alignment explanation
Indices: 275502--276574 Score: 484
Period size: 54 Copynumber: 19.9 Consensus size: 52
275492 TGAAGCAAAA
* * * * * * ***
275502 GAAGATTTTCAAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGT-TT
1 GAAGATGTTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAACGATTGTT
* * * * * **
275553 GAAGATTGTTTGAGTT-TCATGCTCCCTGAAGAAAGAGGGAGCGAACACGTTTGAA
1 GAAGA-TGTTCGAGTTCT-ATACTTCCTAAAGAAAGAGGGAGCG-A-ACGATTGTT
* * * * * * **
275608 GAAGAGGTACGAGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTTGAA
1 GAAGATGTTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAA--CGATTGTT
* * * * **
275662 GAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
1 GAAGATGTTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAA--CGATTGTT
* * * * **
275716 GAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
1 GAAGATGTTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAA--CGATTGTT
* * * * * **
275770 GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
1 GAAGATGTTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAA--CGATTGTT
* * ***
275824 GAAGAT-TTCTGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTG-T
1 GAAGATGTTC-GAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAACGATTGTT
* * * * *
275875 GAAGATATCCGAGTTCCATAC-TCCTTAAAGAAAGAAGGAGCGAACCCA-T-TT
1 GAAGATGTTCGAGTTCTATACTTCC-TAAAGAAAGAGGGAGCGAA-CGATTGTT
* * * * * **
275926 GAAGAGATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
1 G-A-AGATGTTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAA--CGATTGTT
* * * * *** *
275982 GAAGATTTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGTGAAC-CCCGTAA
1 GAAGATGTTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAACGATTGT-T
* *
276034 GAAGATTATTCGAGTTCTATACTGCCTGAAAGAAAGAGGGAGCGAACCCGATTGTT
1 GAAGA-TGTTCGAGTTCTATACTTCCT-AAAGAAAGAGGGAGCGAA--CGATTGTT
* * * *
276090 GAAGATTGTTCGAG-TCTTATACTCTCTCTGAAGAAATAGGGAGTAGACACGACTGTT
1 GAAGA-TGTTCGAGTTC-TATACT-TC-CTAAAGAAAGAGGGAG-CGA-ACGATTGTT
* * *
276147 GAAGATTGTTCGAG-TCTTATAC-TCTCTGAAGAAATAGGGAGCAGACACGATCGTT
1 GAAGA-TGTTCGAGTTC-TATACTTC-CTAAAGAAAGAGGGAGC-GA-ACGATTGTT
* * * *
276202 GAAGATTGTTCGAG-TCTTATAC-TCTTTGAAGGAATAGGGAGCGGACACGATTGTT
1 GAAGA-TGTTCGAGTTC-TATACTTC-CTAAAGAAAGAGGGAGC-GA-ACGATTGTT
*
276257 GAAGATTGTTCGAG-TCTTATAC-TCTCTGAATGAATAGA--GAGCAGACACGATTGTT
1 GAAGA-TGTTCGAGTTC-TATACTTC-CT-AAAGAA-AGAGGGAGC-GA-ACGATTGTT
* * * * * ** *
276312 GAAGATTGTTTGAG-TCTTATACTTTCTGAAGGAATAGGGAGAAAACACGGTTGTT
1 GAAGA-TGTTCGAGTTC-TATACTTCCTAAAGAAAGAGGGAG-CGA-ACGATTGTT
* * * * *
276367 GAAGGTTGTTCGAG-TCTTATACTTTCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAA-GATGTTCGAGTTC-TATACTTCCTAAAGAAAGAGGGAGC-GA-ACGATTGTT
* * *
276422 GAAGATTGTTCGAG-TCTTATAC-TCTCTGAAGGAATAGGGAGCAGATACGATTGTT
1 GAAGA-TGTTCGAGTTC-TATACTTC-CTAAAGAAAGAGGGAGC-GA-ACGATTGTT
*
276477 GAAGATGTTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAACCCGATT-TCA
1 GAAGATGTTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAA--CGATTGT-T
* * *
276531 GAAGAT-TTACGAGTTC-CTACTCCCTAAAGAAATAGGGAGCGAAC
1 GAAGATGTT-CGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAAC
276575 CCATTGGCAG
Statistics
Matches: 871, Mismatches: 104, Indels: 94
0.81 0.10 0.09
Matches are distributed among these distances:
50 3 0.00
51 44 0.05
52 45 0.05
53 86 0.10
54 344 0.39
55 272 0.31
56 26 0.03
57 46 0.05
58 4 0.00
59 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (52 bp):
GAAGATGTTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAACGATTGTT
Found at i:276571 original size:53 final size:53
Alignment explanation
Indices: 276477--276646 Score: 184
Period size: 55 Copynumber: 3.2 Consensus size: 53
276467 TACGATTGTT
* *
276477 GAAGATGTTCGAGTTCTATACTTCCTAAAGAAAGAGGGAGCGAACCCGATT-TCA
1 GAAGAT-TTCGAGTTC-ATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTGGCA
* *
276531 GAAGATTTACGAGTTCCTACTCCCTAAAGAAATAGGGAGCGAACCC-ATTGGCA
1 GAAGATTT-CGAGTTCATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTGGCA
* * * * *
276584 GAAGATTATTCGAGTTTCATACTCTCTGAAGCAAGAGGGAGCAAACCCG-TAGGCA
1 GAAGA-T-TTCGAG-TTCATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTGGCA
276639 GAAGATTT
1 GAAGATTT
276647 GTTCAAAGAA
Statistics
Matches: 99, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
52 3 0.03
53 38 0.38
54 19 0.19
55 39 0.39
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (53 bp):
GAAGATTTCGAGTTCATACTCCCTAAAGAAAGAGGGAGCGAACCCGATTGGCA
Found at i:276830 original size:3 final size:3
Alignment explanation
Indices: 276818--276869 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
276808 TTATATTTAA
276818 ATT A-T ATT ATT ATT ATT A-T ATT ATT ATT ATT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
276863 ATT ATT A
1 ATT ATT A
276870 ATGTTACATA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.13
3 40 0.87
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:276835 original size:14 final size:14
Alignment explanation
Indices: 276818--276869 Score: 95
Period size: 14 Copynumber: 3.6 Consensus size: 14
276808 TTATATTTAA
276818 ATTATATTATTATT
1 ATTATATTATTATT
276832 ATTATATTATTATT
1 ATTATATTATTATT
276846 ATTATATTATTATT
1 ATTATATTATTATT
276860 ATTATTATTA
1 ATTA-TATTA
276870 ATGTTACATA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 32 0.86
15 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATATTATTATT
Found at i:277484 original size:146 final size:146
Alignment explanation
Indices: 277232--277507 Score: 473
Period size: 146 Copynumber: 1.9 Consensus size: 146
277222 CGGGATCTCC
* *
277232 GATCAACATTCCGAACGGTCAAAAGTTGCGTAAGGCCATCATGAACAACATATTGAAAAATCAGG
1 GATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCAGGAACAACATATTGAAAAATCAGG
* *
277297 ACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCC-GAGCGGTTTTTAGCCTCTTGC
66 ACGATCAGACGGTGGACGGTGACGGATCAGAGAAAACAAATCCGGA-CGATTTTTAGCCTCTTGC
277361 CAGTGATCGGAATCTTT
130 CAGTGATCGGAATCTTT
*
277378 GATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCAGGAACAACATATTGAAAAATCAGG
1 GATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCAGGAACAACATATTGAAAAATCAGG
* *
277443 ACGATCAGACGGTGGATGGTGACGGATTAGAGAAAACAAATCCGGACGATTTTTAGCCTCTTGCC
66 ACGATCAGACGGTGGACGGTGACGGATCAGAGAAAACAAATCCGGACGATTTTTAGCCTCTTGCC
277508 GGTTTTTAGT
Statistics
Matches: 122, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
146 120 0.98
147 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.21
Consensus pattern (146 bp):
GATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCAGGAACAACATATTGAAAAATCAGG
ACGATCAGACGGTGGACGGTGACGGATCAGAGAAAACAAATCCGGACGATTTTTAGCCTCTTGCC
AGTGATCGGAATCTTT
Found at i:278674 original size:21 final size:23
Alignment explanation
Indices: 278635--278677 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
278625 TGCAGACCTA
278635 AATTTGTTGTTTTAATTAAAATT
1 AATTTGTTGTTTTAATTAAAATT
*
278658 AATTT-TT-TTTTATTTAAAAT
1 AATTTGTTGTTTTAATTAAAAT
278678 GGCAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (23 bp):
AATTTGTTGTTTTAATTAAAATT
Found at i:282088 original size:24 final size:24
Alignment explanation
Indices: 282067--282135 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
282057 GAACGTTCAG
* *
282067 TTATATTCGTTTGGTTATGTTCGT
1 TTATATTCGTTCGATTATGTTCGT
*
282091 TTATGTTCGTTCGATTATGTTCGT
1 TTATATTCGTTCGATTATGTTCGT
* *
282115 TTATGTTCATTC-ATTTATGTT
1 TTATATTCGTTCGA-TTATGTT
282136 TAACCCAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.03
24 39 0.98
ACGTcount: A:0.14, C:0.10, G:0.17, T:0.58
Consensus pattern (24 bp):
TTATATTCGTTCGATTATGTTCGT
Found at i:282102 original size:14 final size:14
Alignment explanation
Indices: 282085--282115 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
282075 GTTTGGTTAT
*
282085 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
282099 GTTCGATTATGTTC
1 GTTCGATTATGTTC
282113 GTT
1 GTT
282116 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:282893 original size:16 final size:16
Alignment explanation
Indices: 282868--282926 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
282858 CCAACGTTTA
282868 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
282884 TGTTCATTTATATTCG
1 TGTTCGTTTATGTTCG
*
282900 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
282916 TGTTCGTTTAT
1 TGTTCGTTTAT
282927 TTATTAAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.59
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:283013 original size:16 final size:16
Alignment explanation
Indices: 282992--283022 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
282982 AAAAAAAATT
282992 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
283008 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
283023 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:283752 original size:59 final size:57
Alignment explanation
Indices: 283640--283774 Score: 146
Period size: 59 Copynumber: 2.3 Consensus size: 57
283630 GGGGATATTA
* ** *
283640 TTGGAATGTTCAAAAGTTTGGGTAATTTAGACTAAGGGTCATAACTTGAGGATGAAT
1 TTGGAATGTTCAAAAGTTTGGGTAATTTAGAATAAGAATCATAACTTAAGGATGAAT
* ** *
283697 TTGGAATGGTT-AAAAGTTTGGGATCAATTTAGAATGAGAATCATAGTTTAAGGATGAAA
1 TTGGAAT-GTTCAAAAGTTTGGG-T-AATTTAGAATAAGAATCATAACTTAAGGATGAAT
**
283756 TTAAAATGTTCAAAAGTTT
1 TTGGAATGTTCAAAAGTTT
283775 AGTGATGCAT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
57 18 0.28
58 7 0.11
59 39 0.61
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (57 bp):
TTGGAATGTTCAAAAGTTTGGGTAATTTAGAATAAGAATCATAACTTAAGGATGAAT
Found at i:285655 original size:27 final size:27
Alignment explanation
Indices: 285604--285656 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
285594 GTTGTACAAG
* *
285604 TAATATGATAGAATGTATAATTATGAC
1 TAATATGATAGAATATATAAATATGAC
*
285631 TAATATGATAGAATATGTAAATATGA
1 TAATATGATAGAATATATAAATATGA
285657 GGATCAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.15, T:0.36
Consensus pattern (27 bp):
TAATATGATAGAATATATAAATATGAC
Found at i:286322 original size:23 final size:22
Alignment explanation
Indices: 286263--286330 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
286253 TCAAACGACT
* *
286263 GAAAATATGTCATAAAGACAAA
1 GAAAATGTGTCATAAAAACAAA
*
286285 GAAAAACGTGTCATAAAAACAGAA
1 G-AAAATGTGTCATAAAAACA-AA
* *
286309 GAAAATGTGACATAAAATCAAA
1 GAAAATGTGTCATAAAAACAAA
286331 ATGATTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 3 0.08
23 32 0.84
24 3 0.08
ACGTcount: A:0.59, C:0.10, G:0.15, T:0.16
Consensus pattern (22 bp):
GAAAATGTGTCATAAAAACAAA
Found at i:292033 original size:29 final size:31
Alignment explanation
Indices: 291965--292030 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
291955 TGTTCAAAGT
* *
291965 TTGGCCACCAACCAAGATGAAATTTCTAATAAG
1 TTGGCCACCAACCAAGATGAAATTTC--ACAAC
291998 TTGGCCACCAACCAAGATGAAATTTC-CAAC
1 TTGGCCACCAACCAAGATGAAATTTCACAAC
292028 TTG
1 TTG
292031 CCAACTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.16
33 26 0.84
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCACAAC
Found at i:297932 original size:28 final size:29
Alignment explanation
Indices: 297898--297958 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
297888 GGTGATAAAG
*
297898 TTTAGGG-GTAATTTAAAAATTTTAAAAA
1 TTTAGGGAGTAACTTAAAAATTTTAAAAA
*
297926 TTTAGGGAGTAACTTAAAAGTTTTAAAAA
1 TTTAGGGAGTAACTTAAAAATTTTAAAAA
297955 TTTA
1 TTTA
297959 TAGATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.39
Consensus pattern (29 bp):
TTTAGGGAGTAACTTAAAAATTTTAAAAA
Found at i:297980 original size:30 final size:29
Alignment explanation
Indices: 297905--297983 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
297895 AAGTTTAGGG
* *
297905 GTAATTTAAAAATTTTAAAAATTTAGGGA
1 GTAAATTAAAAATTTTAAAAATTTAGAGA
* * *
297934 GTAACTTAAAAGTTTTAAAAATTTATAGA
1 GTAAATTAAAAATTTTAAAAATTTAGAGA
* *
297963 TTTAAATTAAAATTTTTAAAA
1 -GTAAATTAAAAATTTTAAAA
297984 TTTTTGAAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 25 0.60
30 17 0.40
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (29 bp):
GTAAATTAAAAATTTTAAAAATTTAGAGA
Found at i:303134 original size:30 final size:30
Alignment explanation
Indices: 302985--303117 Score: 257
Period size: 30 Copynumber: 4.4 Consensus size: 30
302975 TCCGAATGAC
302985 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
303015 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
303045 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
303075 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
303105 CTATCCATAGGTC
1 CTATCCAGAGGTC
303118 CCGAAGAACC
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 102 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:303134 original size:60 final size:60
Alignment explanation
Indices: 302985--303142 Score: 244
Period size: 60 Copynumber: 2.6 Consensus size: 60
302975 TCCGAATGAC
*
302985 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
*
303045 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * *
303105 CTATCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AACTATCCA
303143 TATGTTCCTT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
60 82 0.90
61 9 0.10
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:303157 original size:31 final size:31
Alignment explanation
Indices: 303103--303184 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
303093 GATCCTCGGT
* *
303103 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
303134 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
303165 TACTGTCCATATGTCTCGAA
1 AACTATCCATATGTCCCGAA
303185 AGATATAGGT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:303385 original size:4 final size:4
Alignment explanation
Indices: 303369--303405 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
303359 ATATAACCAT
*
303369 TACA TATA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
303406 GTCATCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (4 bp):
TACA
Found at i:307955 original size:30 final size:30
Alignment explanation
Indices: 307806--307938 Score: 257
Period size: 30 Copynumber: 4.4 Consensus size: 30
307796 TCCGAAGGAC
307806 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
307836 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
307866 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
307896 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
307926 CTATCCATAGGTC
1 CTATCCAGAGGTC
307939 CCGAAGAACC
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 102 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:307955 original size:60 final size:60
Alignment explanation
Indices: 307806--307963 Score: 244
Period size: 60 Copynumber: 2.6 Consensus size: 60
307796 TCCGAAGGAC
*
307806 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
*
307866 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * *
307926 CTATCCATAGGTCCCGAAGAACCTAGGTAAACTATCCA
1 CTATCCAGAGGTCACAAAGATCCTCGGT-AACTATCCA
307964 TATATTCCTT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
60 82 0.90
61 9 0.10
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (60 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:308200 original size:4 final size:4
Alignment explanation
Indices: 308191--308599 Score: 781
Period size: 4 Copynumber: 103.2 Consensus size: 4
308181 ATATAACCAT
308191 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
308239 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA GACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
308287 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
308335 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
308383 TACA TACA TACA TACA TACA TACA TACA TAC- -ACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
308429 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
308477 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
308525 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- -ACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
308571 TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA T
308600 GTCATCATTT
Statistics
Matches: 399, Mismatches: 2, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
2 4 0.01
4 395 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:314945 original size:18 final size:20
Alignment explanation
Indices: 314906--314948 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
314896 ACTAAATGGT
*
314906 AGTTAGTTTGTTAAACGAGC
1 AGTTAGCTTGTTAAACGAGC
314926 AGTTAGCTTGTT-AA-GAGC
1 AGTTAGCTTGTTAAACGAGC
314944 AGTTA
1 AGTTA
314949 TGTGCTGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 11 0.50
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (20 bp):
AGTTAGCTTGTTAAACGAGC
Found at i:319510 original size:18 final size:20
Alignment explanation
Indices: 319471--319513 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
319461 ACTAAATGGT
*
319471 AGTTAGTTTGTTAAACGAGC
1 AGTTAGCTTGTTAAACGAGC
319491 AGTTAGCTTGTT-AA-GAGC
1 AGTTAGCTTGTTAAACGAGC
319509 AGTTA
1 AGTTA
319514 TGTGCTGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 11 0.50
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (20 bp):
AGTTAGCTTGTTAAACGAGC
Found at i:322683 original size:16 final size:17
Alignment explanation
Indices: 322657--322689 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
322647 CCATTTATAT
322657 CGACGCTAGTGAGAAAA
1 CGACGCTAGTGAGAAAA
*
322674 CGAC-CTAGTGATAAAA
1 CGACGCTAGTGAGAAAA
322690 AAACTCAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (17 bp):
CGACGCTAGTGAGAAAA
Found at i:326473 original size:42 final size:43
Alignment explanation
Indices: 326427--326510 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 43
326417 ACAAATTTTG
326427 CTAAAGGTAATGATATTTAACGG-TGTGTTTTTACAAACGCCA
1 CTAAAGGTAATGATATTTAACGGCTGTGTTTTTACAAACGCCA
* * * * * * *
326469 CTAAATGTTATGGTATTTAGCGGCTTTTTTTTTTCAAACGCC
1 CTAAAGGTAATGATATTTAACGGCTGTGTTTTTACAAACGCC
326511 GCTATTTATC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 19 0.56
43 15 0.44
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (43 bp):
CTAAAGGTAATGATATTTAACGGCTGTGTTTTTACAAACGCCA
Found at i:326908 original size:21 final size:21
Alignment explanation
Indices: 326838--326908 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
326828 TAGCATTATC
*
326838 CAATAAACTTGACATCCATAA
1 CAATAAACTTGAAATCCATAA
*
326859 CAACAAACTTGAAATCCATAA
1 CAATAAACTTGAAATCCATAA
*
326880 CAAGAAACTTGAAATCCATAA
1 CAATAAACTTGAAATCCATAA
*
326901 TAATAAAC
1 CAATAAAC
326909 CAAAGTTTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.52, C:0.21, G:0.06, T:0.21
Consensus pattern (21 bp):
CAATAAACTTGAAATCCATAA
Found at i:331000 original size:24 final size:25
Alignment explanation
Indices: 330949--331000 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
330939 CAATGCATTC
*
330949 TACA-GTGTATCGATGCATCCCATA
1 TACATGTGCATCGATGCATCCCATA
*
330973 -ACATGTGCATCGATGCA-CCCTTA
1 TACATGTGCATCGATGCATCCCATA
330996 TACAT
1 TACAT
331001 CGATGCACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (25 bp):
TACATGTGCATCGATGCATCCCATA
Found at i:335536 original size:74 final size:72
Alignment explanation
Indices: 335448--335610 Score: 188
Period size: 71 Copynumber: 2.2 Consensus size: 72
335438 TACCCCCTTG
* *
335448 GGGGGGATCGGTTCCCTCCGAGCATACTAGAATTCTCGGA-ACAAAAATGTTTAAAG-GGGAATC
1 GGGGGAATCGGTTCCCTCCGAGCATAC-AGAAATCTCGGAGACAAAAA---TT-AAGTGGGAATC
335511 GGTTCCTCCTAT
61 GGTTCCTCCTAT
* * * ** *
335523 GGGGGAATC-GTTCCCTCCGAGCATTCGGAAATCTCGGAGCCAACCATTCAGTGGGAATCGGTTC
1 GGGGGAATCGGTTCCCTCCGAGCATACAGAAATCTCGGAGACAAAAATTAAGTGGGAATCGGTTC
335587 CTCCTAT
66 CTCCTAT
335594 GGGGGAATCGGTTCCCT
1 GGGGGAATCGGTTCCCT
335611 GAGCAATCTG
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
70 2 0.03
71 30 0.39
72 7 0.09
73 10 0.13
74 20 0.26
75 8 0.10
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (72 bp):
GGGGGAATCGGTTCCCTCCGAGCATACAGAAATCTCGGAGACAAAAATTAAGTGGGAATCGGTTC
CTCCTAT
Found at i:338468 original size:21 final size:23
Alignment explanation
Indices: 338418--338468 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
338408 ATTCCCCTGT
338418 GGGGGGAATCGGTTCCTCTTCAA
1 GGGGGGAATCGGTTCCTCTTCAA
* *
338441 AGGGGGAATCGGTTCC-C-TCAG
1 GGGGGGAATCGGTTCCTCTTCAA
338462 GGGGGGA
1 GGGGGGA
338469 TCGATCCCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
22 1 0.04
23 15 0.60
ACGTcount: A:0.18, C:0.20, G:0.43, T:0.20
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCTCTTCAA
Found at i:344279 original size:75 final size:76
Alignment explanation
Indices: 344193--344391 Score: 267
Period size: 75 Copynumber: 2.6 Consensus size: 76
344183 GACCGTTGAA
* * * *
344193 CAGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
**
344257 ACAAAAATGTT
66 ACAAAAACATT
* *
344268 TAGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
* * *
344332 GCCAAACCATT
66 ACAAAAACATT
* *
344343 CAGGTGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCA
344392 ATCTGTAATT
Statistics
Matches: 108, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
75 84 0.78
76 24 0.22
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.23
Consensus pattern (76 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
ACAAAAACATT
Found at i:346723 original size:82 final size:82
Alignment explanation
Indices: 346558--346783 Score: 264
Period size: 82 Copynumber: 2.7 Consensus size: 82
346548 CTGTAAACTT
* * * * * *
346558 GCGGCGTTTGTAAATACAAACGTCACTAAAGTATGAGTATTTAGTGGT-TTTTTCTTAAAATGCC
1 GCGGCGTTTGTCAA-ACAAATGCCACTAAAGTATGAGT-TTTAGCGGTGTTTGTCTAAAAATGCC
*
346622 ACTAAAGTGCTAGGTTTTA
64 ACTAAAGTGATAGGTTTTA
*
346641 GCGGCGTTTGTCAAA-AAATGCCACTAAAGTATTAGGTTTTAGCGGTGTTTGTCTAAAAATGCCA
1 GCGGCGTTTGTCAAACAAATGCCACTAAAGTATGA-GTTTTAGCGGTGTTTGTCTAAAAATGCCA
346705 CTAAAGT-AT-GAGTATTTA
65 CTAAAGTGATAG-GT-TTTA
* * *
346723 GCGGCGTTTGTCAAATAAATGCAACTAAAGTATGAGTTTTAGCGATGTTTGT-TGAAAAATG
1 GCGGCGTTTGTCAAACAAATGCCACTAAAGTATGAGTTTTAGCGGTGTTTGTCT-AAAAATG
346784 TCGTTAATGT
Statistics
Matches: 126, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
80 1 0.01
81 28 0.22
82 67 0.53
83 30 0.24
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (82 bp):
GCGGCGTTTGTCAAACAAATGCCACTAAAGTATGAGTTTTAGCGGTGTTTGTCTAAAAATGCCAC
TAAAGTGATAGGTTTTA
Found at i:346774 original size:41 final size:40
Alignment explanation
Indices: 346558--346766 Score: 215
Period size: 41 Copynumber: 5.1 Consensus size: 40
346548 CTGTAAACTT
* * *
346558 GCGGCGTTTGTAAATACAAACGTCACTAAAGTATGAGTATTTA
1 GCGGCGTTTGTCAA-A-AAATGCCACTAAAGTATGAGT-TTTA
* * * ** *
346601 GTGG-TTTTTTCTTAAAATGCCACTAAAGTGCT-AGGTTTTA
1 GCGGCGTTTGTCAAAAAATGCCACTAAAGT-ATGA-GTTTTA
*
346641 GCGGCGTTTGTCAAAAAATGCCACTAAAGTATTAGGTTTTA
1 GCGGCGTTTGTCAAAAAATGCCACTAAAGTATGA-GTTTTA
* *
346682 GCGGTGTTTGTCTAAAAATGCCACTAAAGTATGAGTATTTA
1 GCGGCGTTTGTCAAAAAATGCCACTAAAGTATGAGT-TTTA
*
346723 GCGGCGTTTGTCAAATAAATGCAACTAAAGTATGAGTTTTA
1 GCGGCGTTTGTCAAA-AAATGCCACTAAAGTATGAGTTTTA
346764 GCG
1 GCG
346767 ATGTTTGTTG
Statistics
Matches: 139, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
40 24 0.17
41 88 0.63
42 24 0.17
43 3 0.02
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (40 bp):
GCGGCGTTTGTCAAAAAATGCCACTAAAGTATGAGTTTTA
Found at i:350072 original size:40 final size:41
Alignment explanation
Indices: 350028--350116 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 41
350018 GATTTGCAAC
* *
350028 GCGATTTTGACTATCGCAAGGCGA-ATATA-TAAATCACAAT
1 GCGATTTTGACTATCGCAACGCGATA-ATACAAAATCACAAT
* *
350068 GCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAAT
1 GCGATTTTGACTATCGCAACGCGATAATACAAAATCACAAT
350109 GCGATTTT
1 GCGATTTT
350117 CCAAATTTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 25 0.60
41 17 0.40
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (41 bp):
GCGATTTTGACTATCGCAACGCGATAATACAAAATCACAAT
Found at i:350153 original size:19 final size:19
Alignment explanation
Indices: 350129--350192 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
350119 AAATTTACGT
350129 TAGTCCAAATTCGTTGCGA
1 TAGTCCAAATTCGTTGCGA
*
350148 TAGTCCAAGTTCCCGTTGCGA
1 TAGTCCAAATT--CGTTGCGA
**
350169 TTTTCCAAATTCGTTGCGA
1 TAGTCCAAATTCGTTGCGA
350188 TAGTC
1 TAGTC
350193 TAAGTTCGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 21 0.57
21 16 0.43
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (19 bp):
TAGTCCAAATTCGTTGCGA
Found at i:350166 original size:21 final size:20
Alignment explanation
Indices: 350129--350209 Score: 76
Period size: 19 Copynumber: 4.0 Consensus size: 20
350119 AAATTTACGT
*
350129 TAGTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
350148 TAGTCCAAGTTCCCGTTGCGA
1 TAGTCCAAGTT-CCGTTGCGA
** *
350169 TTTTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
* *
350188 TAGTCTAAGTTCGCGCTGCGA
1 TAGTCCAAGTTC-CGTTGCGA
350209 T
1 T
350210 TTTCCAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 25 0.51
21 24 0.49
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.33
Consensus pattern (20 bp):
TAGTCCAAGTTCCGTTGCGA
Found at i:350187 original size:40 final size:40
Alignment explanation
Indices: 350132--350217 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
350122 TTTACGTTAG
*
350132 TCCAAATTCGTTGCGATAGTCCAAGTTCCCGTTGCGATTT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCCCGCTGCGATTT
* *
350172 TCCAAATTCGTTGCGATAGTCTAAGTTCGCGCTGCGATTT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCCCGCTGCGATTT
350212 TCCAAA
1 TCCAAA
350218 ATCGCAACGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (40 bp):
TCCAAATTCGTTGCGATAGTCCAAGTTCCCGCTGCGATTT
Found at i:350200 original size:19 final size:19
Alignment explanation
Indices: 350129--350200 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
350119 AAATTTACGT
*
350129 TAGTCCAAATTCGTTGCGA
1 TAGTCCAAGTTCGTTGCGA
350148 TAGTCCAAGTTCCCGTTGCGA
1 TAGTCCAAGTT--CGTTGCGA
** *
350169 TTTTCCAAATTCGTTGCGA
1 TAGTCCAAGTTCGTTGCGA
*
350188 TAGTCTAAGTTCG
1 TAGTCCAAGTTCG
350201 CGCTGCGATT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 27 0.63
21 16 0.37
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (19 bp):
TAGTCCAAGTTCGTTGCGA
Found at i:350646 original size:19 final size:19
Alignment explanation
Indices: 350622--350728 Score: 92
Period size: 19 Copynumber: 5.4 Consensus size: 19
350612 TTATTTTGGA
350622 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
350641 TTTTTCACTATCGCAACAAC
1 TTTTTCACTATCGCAAC-AC
*
350661 AAGTTTTTCAAACTCTCGCAACA-
1 ---TTTTTC--ACTATCGCAACAC
*
350684 -TTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
* * *
350702 ATTTTAACTATCGTAACAC
1 TTTTTCACTATCGCAACAC
350721 ATTTTTCA
1 -TTTTTCA
350729 AAATCGCGTT
Statistics
Matches: 73, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
17 11 0.15
19 38 0.52
20 7 0.10
23 6 0.08
24 1 0.01
25 10 0.14
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:350964 original size:4 final size:4
Alignment explanation
Indices: 350957--350986 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
350947 TATATATATA
350957 TATT TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TA
350987 ATATTTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:353152 original size:3 final size:3
Alignment explanation
Indices: 353144--353177 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
353134 TAATCAACAT
353144 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
353178 TCTCTGCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:353421 original size:2 final size:2
Alignment explanation
Indices: 353414--353439 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
353404 AAACGTGTGC
353414 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
353440 TCTCCGTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:355650 original size:19 final size:18
Alignment explanation
Indices: 355626--355681 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
355616 CTGTTTGACC
355626 GTTTGATCGGTCTGAACCA
1 GTTTGAT-GGTCTGAACCA
*
355645 GTTTGAATGGTTTGAACCA
1 GTTTG-ATGGTCTGAACCA
*
355664 GTTTGAATGGTTTGAACC
1 GTTTG-ATGGTCTGAACC
355682 GGTTCGACCC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 33 0.94
20 2 0.06
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (18 bp):
GTTTGATGGTCTGAACCA
Found at i:360184 original size:136 final size:135
Alignment explanation
Indices: 359943--360188 Score: 357
Period size: 136 Copynumber: 1.8 Consensus size: 135
359933 CCGTTAACCG
* *
359943 TTGACTTTGACCAAAAAGTCAAATTTTTCGAAAAGTCATATTTTATATTTTTTGACGTCCTGAGT
1 TTGACTTTGACCAAAAAGTCAAATTTTTCGAAAAGTCATATTTTATACTTTTCGACGTCCTGAGT
* * * * * *
360008 CTGATTCCGAAGTTCGTTTTTCCAAATTCGAACCCTAAAGCCTCCAAATTATCAGTCAAACCCAT
66 CTAATTCCAAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCCAAATTATCAGTCAAACCCAT
360073 TGACT
131 TGACT
* * * * * *
360078 TTGACTTTGACCAAAAATTCAAATTTTTTTGAAAAGTTATATTTTATGCTTTTCGATGTCTTGAG
1 TTGACTTTGACCAAAAAGTCAAA-TTTTTCGAAAAGTCATATTTTATACTTTTCGACGTCCTGAG
360143 TCTAATTCCAAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCC
65 TCTAATTCCAAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCC
360189 GAATCAACCC
Statistics
Matches: 96, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
135 22 0.23
136 74 0.77
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (135 bp):
TTGACTTTGACCAAAAAGTCAAATTTTTCGAAAAGTCATATTTTATACTTTTCGACGTCCTGAGT
CTAATTCCAAAGTCCGTTTTGCCAAATTCAAACCCGAAAGCCTCCAAATTATCAGTCAAACCCAT
TGACT
Found at i:361416 original size:32 final size:32
Alignment explanation
Indices: 361348--361416 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
361338 TTTGCTACTA
*
361348 ATATTTTATTTTCGATGCTTCGGATTTATTTC
1 ATATTTTATTTTCGATGCTTCGCATTTATTTC
* *
361380 ATATTTTATTTTACG-TGC-TCGCTTTTAGTTTT
1 ATATTTTATTTT-CGATGCTTCGCATTTA-TTTC
361412 ATATT
1 ATATT
361417 CAAGAGTTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 7 0.22
32 23 0.72
33 2 0.06
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.58
Consensus pattern (32 bp):
ATATTTTATTTTCGATGCTTCGCATTTATTTC
Found at i:362036 original size:45 final size:42
Alignment explanation
Indices: 361949--362036 Score: 104
Period size: 45 Copynumber: 2.0 Consensus size: 42
361939 TAGTATTTAC
* **
361949 ATTATGCATGATTTATAAATTTAATTTAATATTTTTGTTCTT
1 ATTATGCATGATTTATAAATTAAATTTAATATTTTTAATCTT
* *
361991 ATTATGTATGAATTTATAAATTCAAATTTTAGTATTTTTAATCTT
1 ATTATGCATG-ATTTATAAATT-AAA-TTTAATATTTTTAATCTT
362036 A
1 A
362037 CTTTAATAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
42 9 0.24
43 11 0.29
44 2 0.05
45 16 0.42
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (42 bp):
ATTATGCATGATTTATAAATTAAATTTAATATTTTTAATCTT
Found at i:362244 original size:31 final size:31
Alignment explanation
Indices: 362203--362278 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
362193 AATCATCCCG
362203 AATATTAATTTAACCCCTAAAC-TTAAGATAA
1 AATATTAATTTAACCCCTAAACTTTAA-ATAA
* *
362234 AATATCAATTTAACCCTTAAACTTTAAATAA
1 AATATTAATTTAACCCCTAAACTTTAAATAA
*
362265 AAGATTAATTTAAC
1 AATATTAATTTAAC
362279 TCAATTCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 36 0.90
32 4 0.10
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (31 bp):
AATATTAATTTAACCCCTAAACTTTAAATAA
Found at i:366029 original size:17 final size:17
Alignment explanation
Indices: 366009--366043 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
365999 CAGCTTCGAA
366009 CTCTTCCTTTGCAATCT
1 CTCTTCCTTTGCAATCT
366026 CTCTTCCTTTGCAATCT
1 CTCTTCCTTTGCAATCT
366043 C
1 C
366044 AAGTTCGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.37, G:0.06, T:0.46
Consensus pattern (17 bp):
CTCTTCCTTTGCAATCT
Found at i:369390 original size:27 final size:28
Alignment explanation
Indices: 369326--369594 Score: 105
Period size: 27 Copynumber: 9.7 Consensus size: 28
369316 CAGAATTTAG
*
369326 ATTGAAGCACAGAGGTGCTCAGTCAT-A
1 ATTGAAGCACAGAGGTGCTCAGTCCTCA
* **
369353 GTTGGCTGCACAGAGGTG-TCAGTCCTCA
1 ATT-GAAGCACAGAGGTGCTCAGTCCTCA
* *
369381 ATTGAAGCACAGAGGTGCTCAATCATC-
1 ATTGAAGCACAGAGGTGCTCAGTCCTCA
* *
369408 -TTAGCTA-CACAGAGGTG-TCAACTCC-CA
1 ATT-G-AAGCACAGAGGTGCTC-AGTCCTCA
** * **
369435 GCTGAAGCACAGAGGTGCTCAGTCATTTT
1 ATTGAAGCACAGAGGTGCTCAGTC-CTCA
* * * *
369464 TTTTAACTGCACAGAGGTG-TCAGTTCTCG
1 ATTGAA--GCACAGAGGTGCTCAGTCCTCA
*
369493 ATTGAAGCACAGAGGTGCTCAATCACT--
1 ATTGAAGCACAGAGGTGCTCAGTC-CTCA
* * *
369520 TTTGGCTA-CACAGAGGTG-TCAG-CTCTCG
1 ATT-G-AAGCACAGAGGTGCTCAGTC-CTCA
* * * *
369548 ATTGAAGCATAGAGGTGCTCAATCGTTA
1 ATTGAAGCACAGAGGTGCTCAGTCCTCA
**
369576 ATTCTAGCACAGAGGTGCT
1 ATTGAAGCACAGAGGTGCT
369595 ATGGATTCAG
Statistics
Matches: 176, Mismatches: 43, Indels: 45
0.67 0.16 0.17
Matches are distributed among these distances:
26 10 0.06
27 75 0.43
28 63 0.36
29 12 0.07
30 5 0.03
31 11 0.06
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (28 bp):
ATTGAAGCACAGAGGTGCTCAGTCCTCA
Found at i:369396 original size:55 final size:55
Alignment explanation
Indices: 369326--369571 Score: 264
Period size: 55 Copynumber: 4.4 Consensus size: 55
369316 CAGAATTTAG
* ** * *
369326 ATTGAAGCACAGAGGTGCTCAGTCATAGTTGGCTGCACAGAGGTGTCAGTCCTCA
1 ATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTCA
* *
369381 ATTGAAGCACAGAGGTGCTCAATCA-TCTTAGCTACACAGAGGTGTCAACTCC-CA
1 ATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTC-AGTCCTCA
** * * * * *
369435 GCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTCG
1 ATTGAAGCACAGAGGTGCTCAATCA---TTTTTAGCTACACAGAGGTGTCAGTCCTCA
* * *
369493 ATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAG-CTCTCG
1 ATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTC-CTCA
*
369548 ATTGAAGCATAGAGGTGCTCAATC
1 ATTGAAGCACAGAGGTGCTCAATC
369572 GTTAATTCTA
Statistics
Matches: 160, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
54 41 0.26
55 75 0.47
57 3 0.02
58 41 0.26
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (55 bp):
ATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTCA
Found at i:369587 original size:55 final size:55
Alignment explanation
Indices: 369271--369592 Score: 247
Period size: 55 Copynumber: 5.8 Consensus size: 55
369261 CTTGATTTTA
* * * * *
369271 GATTGTAGCACAGAGGTGCTCAATCATTCCAA---T-GCACAGAGGTGCCAGAATTTA
1 GATTGAAGCACAGAGGTGCTCAATCATT--AATTCTAGCACAGAGGTGTCAG-CTCTC
* *
369325 GATTGAAGCACAGAGGTGCTCAGTCA-TAGTTGGCT-GCACAGAGGTGTCAG-TCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTAATT--CTAGCACAGAGGTGTCAGCT-CTC
* * * *
369380 AATTGAAGCACAGAGGTGCTCAATCATCTTA-GCTA-CACAGAGGTGTCAACTC-C
1 GATTGAAGCACAGAGGTGCTCAATCAT-TAATTCTAGCACAGAGGTGTCAGCTCTC
* * * ** * *
369433 CAGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GA-TTGAAGCACAGAGGTGCTCAATCATTAATTCT-A--GCACAGAGGTGTCAGCTCTC
369492 GATTGAAGCACAGAGGTGCTCAATCACTT--TTGGCTA-CACAGAGGTGTCAGCTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA-TTAATT--CTAGCACAGAGGTGTCAGCTCTC
* *
369547 GATTGAAGCATAGAGGTGCTCAATCGTTAATTCTAGCACAGAGGTG
1 GATTGAAGCACAGAGGTGCTCAATCATTAATTCTAGCACAGAGGTG
369593 CTATGGATTC
Statistics
Matches: 218, Mismatches: 27, Indels: 45
0.75 0.09 0.16
Matches are distributed among these distances:
51 1 0.00
53 5 0.02
54 70 0.32
55 79 0.36
56 17 0.08
57 3 0.01
58 38 0.17
59 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTAATTCTAGCACAGAGGTGTCAGCTCTC
Found at i:369822 original size:81 final size:81
Alignment explanation
Indices: 369687--369844 Score: 271
Period size: 81 Copynumber: 2.0 Consensus size: 81
369677 GCGAGTTACA
*
369687 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGTTA
1 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
* *
369752 CTGAGCCGGTTGCACC
66 CCGAGCCAGTTGCACC
* *
369768 AAGAATGGTTCGCACACGAAATGGCGGATCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
1 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
369833 CCGAGCCAGTTG
66 CCGAGCCAGTTG
369845 TGCAAGAGAC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (81 bp):
AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
CCGAGCCAGTTGCACC
Found at i:375248 original size:3 final size:3
Alignment explanation
Indices: 375229--375296 Score: 50
Period size: 3 Copynumber: 23.0 Consensus size: 3
375219 AAATAAACAG
* * * * *
375229 AAT ATT AAT ACT AAT AAT AAT AATT TAT AAT AAT TAT AAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
* *
375275 -AT AAT AAT TAT TAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
375297 TTTTATTTCT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 4 0.08
3 44 0.88
4 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (3 bp):
AAT
Found at i:377777 original size:3 final size:3
Alignment explanation
Indices: 377769--377796 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
377759 GTAAAAATTT
377769 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
377797 AACAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:377812 original size:14 final size:14
Alignment explanation
Indices: 377771--377815 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
377761 AAAAATTTAT
*
377771 AATAATAATAATAAT
1 AATAATAATAA-AAC
377786 AATAATAATAAAAC
1 AATAATAATAAAAC
377800 AATATATAA-AAAAC
1 AATA-ATAATAAAAC
377814 AA
1 AA
377816 AACTATGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAATAATAAAAC
Found at i:378822 original size:3 final size:3
Alignment explanation
Indices: 378814--378918 Score: 144
Period size: 3 Copynumber: 35.3 Consensus size: 3
378804 ACCCTGCAAA
*
378814 AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT AAT AAT AAAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
*
378859 ATT AAT AAT AAT -AT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
*
378906 AAT TAT AAT AAT A
1 AAT AAT AAT AAT A
378919 TATATATTAA
Statistics
Matches: 91, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
2 6 0.07
3 79 0.87
4 6 0.07
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:383039 original size:35 final size:35
Alignment explanation
Indices: 382993--383063 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
382983 ACTTGAAATG
*
382993 TATATATTTGGTATATATAGACCTGGAATTGTTAT
1 TATATATTTGGTATATATAGACCTGGAATTATTAT
383028 TATATATTTGGTATATATAGACCTGGAATTATTAT
1 TATATATTTGGTATATATAGACCTGGAATTATTAT
383063 T
1 T
383064 CTTTCAATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (35 bp):
TATATATTTGGTATATATAGACCTGGAATTATTAT
Done.