Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008577.1 Hibiscus syriacus cultivar Beakdansim tig00111506_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: 1329373
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:910621 original size:16 final size:17
Alignment explanation
Indices: 910589--910621 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
910579 ATCTATTTGT
*
910589 ATTTAAATACTAATAAA
1 ATTTAAAAACTAATAAA
910606 ATTTAAAAAC-AATAAA
1 ATTTAAAAACTAATAAA
910622 TTTTTCTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTTAAAAACTAATAAA
Found at i:912371 original size:21 final size:21
Alignment explanation
Indices: 912345--912394 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
912335 CACCGTCGGT
*
912345 GGTTGTTTCCGC-TCTTAACGG
1 GGTTGTTTCCACTTC-TAACGG
912366 GGTTGTTTCCACTTCTAACGG
1 GGTTGTTTCCACTTCTAACGG
*
912387 AGTTGTTT
1 GGTTGTTT
912395 TCCTTGTCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.12, C:0.20, G:0.26, T:0.42
Consensus pattern (21 bp):
GGTTGTTTCCACTTCTAACGG
Found at i:912803 original size:22 final size:21
Alignment explanation
Indices: 912756--912804 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
912746 AACTATATAA
*
912756 TATATAGTATATTTCAAAAAC
1 TATATAATATATTTCAAAAAC
* * *
912777 AATATAATATATTTTCAAAGAT
1 TATATAATATA-TTTCAAAAAC
912799 TATATA
1 TATATA
912805 TATTATATAC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (21 bp):
TATATAATATATTTCAAAAAC
Found at i:912861 original size:67 final size:65
Alignment explanation
Indices: 912771--912917 Score: 162
Period size: 65 Copynumber: 2.3 Consensus size: 65
912761 AGTATATTTC
* * * *
912771 AAAAAC-A-ATATA-ATATATTTTCAAAGATTATATATATTATATACT-TTTTCAAAAACTG-TT
1 AAAAACTATATATATATATATATTCAAAAACTATAT-TA-TATATA-TGTTTTCAAAAACCGTTT
912831 TTT
63 TTT
* *
912834 AAAAAGTTATATATATATATATATTCAAAAACTATATTATATATATGTTTTTAAAAACCGTTTTT
1 AAAAA-CTATATATATATATATATTCAAAAACTATATTATATATATGTTTTCAAAAACCGTTTTT
912899 T
65 T
912900 AAAAACTATATAT-TATAT
1 AAAAACTATATATATATAT
912918 GTTTTTAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
63 5 0.07
64 6 0.08
65 25 0.35
66 17 0.24
67 18 0.25
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (65 bp):
AAAAACTATATATATATATATATTCAAAAACTATATTATATATATGTTTTCAAAAACCGTTTTTT
Found at i:912889 original size:26 final size:26
Alignment explanation
Indices: 912827--912891 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
912817 TTTCAAAAAC
*
912827 TGTTTTTAAAAAGTTATATATATATA
1 TGTTTTTAAAAACTTATATATATATA
* * *
912853 TATATTCAAAAAC-TATATTATATATA
1 TGTTTTTAAAAACTTATA-TATATATA
912879 TGTTTTTAAAAAC
1 TGTTTTTAAAAAC
912892 CGTTTTTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
25 4 0.13
26 27 0.87
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (26 bp):
TGTTTTTAAAAACTTATATATATATA
Found at i:912951 original size:17 final size:16
Alignment explanation
Indices: 912913--912951 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
912903 AACTATATAT
*
912913 TATATGTTTTTAAAAA
1 TATATGTTTTCAAAAA
912929 TAATATGTTTTCAAAAA
1 T-ATATGTTTTCAAAAA
912946 CTATAT
1 -TATAT
912952 TATATATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.90
18 1 0.05
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
TATATGTTTTCAAAAA
Found at i:912990 original size:39 final size:39
Alignment explanation
Indices: 912860--913006 Score: 160
Period size: 39 Copynumber: 3.8 Consensus size: 39
912850 ATATATATTC
* *
912860 AAAAACTATAT-TATATATATGTTTTTAAAAACCGTTTTTT
1 AAAAACTATATAT-TATATATGTTTATAAAAATCG-TTTTT
* * * * *
912900 AAAAACTATATATTATATGTTTTTAAAAATAATATGTTTTC
1 AAAAACTATATATTATATATGTTTATAAA-AAT-CGTTTTT
912941 AAAAAC--TATATTATATATGTTTATAAAAATCGTTTTT
1 AAAAACTATATATTATATATGTTTATAAAAATCGTTTTT
912978 AAAAACTATATATTATATAT-TTT-TAAAAA
1 AAAAACTATATATTATATATGTTTATAAAAA
913007 CTATATTATA
Statistics
Matches: 90, Mismatches: 12, Indels: 13
0.78 0.10 0.11
Matches are distributed among these distances:
37 17 0.19
38 6 0.07
39 30 0.33
40 23 0.26
41 13 0.14
42 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (39 bp):
AAAAACTATATATTATATATGTTTATAAAAATCGTTTTT
Found at i:913001 original size:78 final size:81
Alignment explanation
Indices: 912857--913006 Score: 252
Period size: 78 Copynumber: 1.9 Consensus size: 81
912847 TATATATATA
* *
912857 TTCAAAAACTATATTATATATATGTTTTTAAAAACCGTTTTTTAAAAACTATATATTATATGTTT
1 TTCAAAAACTATATTATATATATGTTTATAAAAACCGTTTTTTAAAAACTATATATTATATATTT
912922 TTAAAAATAATATGTT
66 TTAAAAATAATATGTT
*
912938 TTCAAAAACTATA-T-TATATATGTTTATAAAAATCG-TTTTTAAAAACTATATATTATATATTT
1 TTCAAAAACTATATTATATATATGTTTATAAAAACCGTTTTTTAAAAACTATATATTATATATTT
913000 TTAAAAA
66 TTAAAAA
913007 CTATATTATA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
78 33 0.50
79 19 0.29
80 1 0.02
81 13 0.20
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (81 bp):
TTCAAAAACTATATTATATATATGTTTATAAAAACCGTTTTTTAAAAACTATATATTATATATTT
TTAAAAATAATATGTT
Found at i:913018 original size:24 final size:24
Alignment explanation
Indices: 912973--913030 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 24
912963 ATAAAAATCG
912973 TTTTTAAAAACTATATATTATATA
1 TTTTTAAAAACTATATATTATATA
912997 TTTTTAAAAAC--TATATTATATA
1 TTTTTAAAAACTATATATTATATA
913019 TGTTTTCAAAAA
1 T-TTTT-AAAAA
913031 ACCATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 12 0.38
23 4 0.12
24 16 0.50
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTTTAAAAACTATATATTATATA
Found at i:913068 original size:62 final size:61
Alignment explanation
Indices: 912931--913081 Score: 223
Period size: 61 Copynumber: 2.5 Consensus size: 61
912921 TTTAAAAATA
* **
912931 ATATGTTTTCAAAAACTATATTATATATGTTTATAAAAATCGTTTTTAAAAACTATATATT
1 ATATGTTTTCAAAAACTATATTATATATGTTTATAAAAAACCATTTTAAAAACTATATATT
* *
912992 ATATATTTTTAAAAACTATATTATATATGTTT-TCAAAAAACCATTTTAATAAACTATATATT
1 ATATGTTTTCAAAAACTATATTATATATGTTTAT-AAAAAACCATTTTAA-AAACTATATATT
*
913054 ATATGTTTTCAAAAACTATACTATATAT
1 ATATGTTTTCAAAAACTATATTATATAT
913082 CTTCAAAAAT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
60 1 0.01
61 42 0.52
62 37 0.46
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (61 bp):
ATATGTTTTCAAAAACTATATTATATATGTTTATAAAAAACCATTTTAAAAACTATATATT
Found at i:913078 original size:22 final size:21
Alignment explanation
Indices: 913042--913100 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 21
913032 CCATTTTAAT
*
913042 AAACTATATATTATATGTTTTCAA
1 AAACTATATA-TATA--TCTTCAA
913066 AAACTATACTATATATCTTCAA
1 AAACTATA-TATATATCTTCAA
*
913088 AAATTATATATAT
1 AAACTATATATAT
913101 TATATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 5 0.16
22 13 0.41
24 12 0.38
25 2 0.06
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (21 bp):
AAACTATATATATATCTTCAA
Found at i:913098 original size:140 final size:141
Alignment explanation
Indices: 912804--913068 Score: 339
Period size: 140 Copynumber: 1.9 Consensus size: 141
912794 AAGATTATAT
*
912804 ATATTATATACT-TTT-TCAAAAA-CTGTTTTTAAAAAGTTATATATATATATATATTCAAAAAC
1 ATATTATATA-TGTTTAT-AAAAATC-GTTTTTAAAAAGCTATATATATATATATATTCAAAAAC
* * *
912866 TATATTATATATATGTTTTTAAAAACCGTTTTTTAAAAACTATATATTATATGTTTTTAAAAATA
63 TATATTATATATATGTTTTAAAAAACCG-ATTTTAAAAACTATATATTATATGTTTTCAAAAATA
*
912931 ATATGTTTTCAAAAAC
127 ATATATTTTC-AAAAC
* *
912947 TATATTATATATGTTTATAAAAATCGTTTTTAAAAA-CTATATAT-TATATATTTTTAAAAACTA
1 -ATATTATATATGTTTATAAAAATCGTTTTTAAAAAGCTATATATATATATATATTCAAAAACTA
913010 TA-T-TATATATGTTTTCAAAAAACC-ATTTTAATAAACTATATATTATATGTTTTCAAAAA
65 TATTATATATATGTTTT-AAAAAACCGATTTTAA-AAACTATATATTATATGTTTTCAAAAA
913069 CTATACTATA
Statistics
Matches: 110, Mismatches: 6, Indels: 14
0.85 0.05 0.11
Matches are distributed among these distances:
139 6 0.05
140 38 0.35
141 8 0.07
142 19 0.17
143 8 0.07
144 29 0.26
145 2 0.02
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (141 bp):
ATATTATATATGTTTATAAAAATCGTTTTTAAAAAGCTATATATATATATATATTCAAAAACTAT
ATTATATATATGTTTTAAAAAACCGATTTTAAAAACTATATATTATATGTTTTCAAAAATAATAT
ATTTTCAAAAC
Found at i:913105 original size:26 final size:24
Alignment explanation
Indices: 913070--913134 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 24
913060 TTTCAAAAAC
*
913070 TATACTATATATCTTCAAAAATTAT
1 TATATTATATAT-TTCAAAAATTAT
**
913095 ATATATTATATATTTTTAAAATTAT
1 -TATATTATATATTTCAAAAATTAT
913120 TATTATATATATATT
1 TA-TAT-TATATATT
913135 ATCATATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.06
25 13 0.38
26 19 0.56
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (24 bp):
TATATTATATATTTCAAAAATTAT
Found at i:913997 original size:24 final size:24
Alignment explanation
Indices: 913965--914011 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
913955 ATTTTGATTT
913965 TTTTTTGTAATTTTAAAGATTTTA
1 TTTTTTGTAATTTTAAAGATTTTA
*
913989 TTTTTTGTAATTTTAAAGGTTTT
1 TTTTTTGTAATTTTAAAGATTTT
914012 TAAAAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.64
Consensus pattern (24 bp):
TTTTTTGTAATTTTAAAGATTTTA
Found at i:914198 original size:2 final size:2
Alignment explanation
Indices: 914191--914224 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
914181 AGGCCCAAAT
*
914191 TA TA TA TA CA 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
914225 ATAAATTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:918825 original size:60 final size:60
Alignment explanation
Indices: 918720--918853 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
918710 ATAAAAGGGT
** * * * *
918720 AAAG-TACACAAATGGTCCTCTGACTATATGATGCTACTTTATTGAGTCC-CCTGACTATTA
1 AAAGTTACA-AAATGGTCCTCCAACTATAGGAAGCTACTTTATTGAGTCCATC-AACTATTA
* * *
918780 AAAGTTACAAAATGGTCCTCCAACTATAGGAAGTTGCTTTGTTGAGTCCATCAACTATTA
1 AAAGTTACAAAATGGTCCTCCAACTATAGGAAGCTACTTTATTGAGTCCATCAACTATTA
918840 AAAGTTACAAAATG
1 AAAGTTACAAAATG
918854 ATCACCCGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 58 0.92
61 5 0.08
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCTCCAACTATAGGAAGCTACTTTATTGAGTCCATCAACTATTA
Found at i:925528 original size:18 final size:17
Alignment explanation
Indices: 925505--925541 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
925495 ATCCAAGTAT
*
925505 AGTAGATAAGGTCAATGG
1 AGTAGACAAGGTCAA-GG
925523 AGTAGACAAGGTCAAGG
1 AGTAGACAAGGTCAAGG
925540 AG
1 AG
925542 GACAAGGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.41, C:0.08, G:0.35, T:0.16
Consensus pattern (17 bp):
AGTAGACAAGGTCAAGG
Found at i:934416 original size:80 final size:80
Alignment explanation
Indices: 934318--934477 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
934308 TATCCTTAAA
934318 GCAAGGGTGCCTTATCATCGTTTCAAATAGCTCCTCGTCTGCATCATCTTTTTTTGAAGTAGTGA
1 GCAAGGGTGCCTTATCATCGTTTCAAATAGCTCCTCGTCTGCATCATCTTTTTTTGAAGTAGTGA
934383 TCCACTGCCGCTGCT
66 TCCACTGCCGCTGCT
934398 GCAAGGGTGCCTTATCATCGTTTCAAATAGCTCCTCGTCTGCATCATCTTTTTTTGAAGTAGTGA
1 GCAAGGGTGCCTTATCATCGTTTCAAATAGCTCCTCGTCTGCATCATCTTTTTTTGAAGTAGTGA
934463 TCCACTGCCGCTGCT
66 TCCACTGCCGCTGCT
934478 ATCTGGTGCT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (80 bp):
GCAAGGGTGCCTTATCATCGTTTCAAATAGCTCCTCGTCTGCATCATCTTTTTTTGAAGTAGTGA
TCCACTGCCGCTGCT
Found at i:935380 original size:24 final size:24
Alignment explanation
Indices: 935353--935458 Score: 178
Period size: 24 Copynumber: 4.5 Consensus size: 24
935343 GAAACTGCTG
935353 CGTAGAATTTGCACCGAAGTGCCA
1 CGTAGAATTTGCACCGAAGTGCCA
935377 CGTAGAATTTGCACCGAAGTGCCA
1 CGTAGAATTTGCACCGAAGTGCCA
935401 CGTAGAATTTGCACCGAAGTGCCA
1 CGTAGAATTTGCACCGAAGTGCCA
* *
935425 CGTAGAATATGCACCGAAGTGTCA
1 CGTAGAATTTGCACCGAAGTGCCA
*
935449 CATAG-ATTTG
1 CGTAGAATTTG
935459 TCCCGAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
23 4 0.05
24 74 0.95
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (24 bp):
CGTAGAATTTGCACCGAAGTGCCA
Found at i:935475 original size:23 final size:23
Alignment explanation
Indices: 935449--935502 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
935439 CGAAGTGTCA
* *
935449 CATAGATTTGTCCCGAAAGACCG
1 CATAGAATTATCCCGAAAGACCG
*
935472 CATAGAATTATCCCGAAGGACCG
1 CATAGAATTATCCCGAAAGACCG
*
935495 CGTAGAAT
1 CATAGAAT
935503 CCTCAACTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (23 bp):
CATAGAATTATCCCGAAAGACCG
Found at i:939037 original size:35 final size:35
Alignment explanation
Indices: 938986--939063 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 35
938976 ATAAATTGCC
*
938986 ATTTTCATGATTTTGATTCTTCCATCTGCCATGCT
1 ATTTCCATGATTTTGATTCTTCCATCTGCCATGCT
*
939021 ATTTCCATGATTTTGATTCTTCCATCTGTCATGCT
1 ATTTCCATGATTTTGATTCTTCCATCTGCCATGCT
939056 ATTTCCAT
1 ATTTCCAT
939064 TAAATTCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.18, C:0.23, G:0.10, T:0.49
Consensus pattern (35 bp):
ATTTCCATGATTTTGATTCTTCCATCTGCCATGCT
Found at i:941279 original size:21 final size:21
Alignment explanation
Indices: 941250--941306 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
941240 CAGGATGCAA
* * *
941250 CCACTGCTCCACTTGATTCTT
1 CCACGGCTCCAATTGAATCTT
941271 CCACGGCTCCAATTGAATCTT
1 CCACGGCTCCAATTGAATCTT
* * *
941292 CAACTGCTCTAATTG
1 CCACGGCTCCAATTG
941307 CTCCTTCCAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.33
Consensus pattern (21 bp):
CCACGGCTCCAATTGAATCTT
Found at i:942424 original size:24 final size:25
Alignment explanation
Indices: 942397--942465 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
942387 AATATCAAAT
942397 ACAATAA-AATAATATTATTTATTA
1 ACAATAAGAATAATATTATTTATTA
*
942421 ACAA-AATAATAATATTATTT-TTA
1 ACAATAAGAATAATATTATTTATTA
942444 A-AATATTAGAATAAT-TTATTTA
1 ACAATA--AGAATAATATTATTTA
942466 ATATTATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 23 0.59
25 7 0.18
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (25 bp):
ACAATAAGAATAATATTATTTATTA
Found at i:942576 original size:40 final size:42
Alignment explanation
Indices: 942523--942614 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 42
942513 AATAAATAAA
* *
942523 AAATTATGA-TTATTATATT-TTATTAAAATAA-AAT-TATTAT
1 AAATTAT-ATTTATTAT-TTATTATTAAAAGAATAATATATCAT
*
942563 AAATTATATTTATTATTTATTATTATAAGAATAATATATCAT
1 AAATTATATTTATTATTTATTATTAAAAGAATAATATATCAT
*
942605 TAATTATATT
1 AAATTATATT
942615 ATAATGAGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
39 3 0.07
40 24 0.55
41 3 0.07
42 14 0.32
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (42 bp):
AAATTATATTTATTATTTATTATTAAAAGAATAATATATCAT
Found at i:942610 original size:26 final size:26
Alignment explanation
Indices: 942554--942611 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
942544 ATTAAAATAA
* * *
942554 AATTATTATAAATTATATTTATTATT
1 AATTATTATAAAATATATATATCATT
*
942580 TATTATTATAAGAATA-ATATATCATT
1 AATTATTATAA-AATATATATATCATT
942606 AATTAT
1 AATTAT
942612 ATTATAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
AATTATTATAAAATATATATATCATT
Found at i:943546 original size:18 final size:19
Alignment explanation
Indices: 943523--943566 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
943513 TATAATAAAT
943523 TAACGTAGC-TTTTTTTTA
1 TAACGTAGCTTTTTTTTTA
943541 TAACGTAGCTTTTTTTTTA
1 TAACGTAGCTTTTTTTTTA
943560 TAACGTA
1 TAACGTA
943567 CAAGTTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.52
Consensus pattern (19 bp):
TAACGTAGCTTTTTTTTTA
Found at i:943743 original size:23 final size:23
Alignment explanation
Indices: 943717--943776 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
943707 TAAGTAATTA
**
943717 ACTTATTTTATTATATAAGCG-C
1 ACTTATTACATTATATAAGCGTC
*
943739 TACTTATTACGTTATATAAGCGTC
1 -ACTTATTACATTATATAAGCGTC
*
943763 ACTTATTACGTTAT
1 ACTTATTACATTAT
943777 TGTGCTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (23 bp):
ACTTATTACATTATATAAGCGTC
Found at i:943839 original size:23 final size:23
Alignment explanation
Indices: 943804--943847 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
943794 CTTGTAATTA
**
943804 ACATATTTTATTATATAAGTGTT
1 ACATATTACATTATATAAGTGTT
943827 ACATATTACATTATATAAGTG
1 ACATATTACATTATATAAGTG
943848 GTACCTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (23 bp):
ACATATTACATTATATAAGTGTT
Found at i:943842 original size:87 final size:86
Alignment explanation
Indices: 943709--943915 Score: 254
Period size: 87 Copynumber: 2.4 Consensus size: 86
943699 TAACAAATTA
* * * * * *
943709 AGTAATTAACTTATTTTATTATATAAGCGCTACTTATTACGTTATATAAG-CGTCACTTATTACG
1 AGTAATTAAC-TATTTTATTATATAAGAGTTACATATTACATTATATAAGTCGT-ACCTAATACG
*
943773 TTATTGTGCTTAATAATGTTTCT
64 TTATTGTGCTTAATAATGTTTCC
* * * *
943796 TGTAATTAACATATTTTATTATATAAGTGTTACATATTACATTATATAAGTGGTACCTAATATGT
1 AGTAATTAAC-TATTTTATTATATAAGAGTTACATATTACATTATATAAGTCGTACCTAATACGT
*
943861 TATTGTGCTTGATAATGTTTCC
65 TATTGTGCTTAATAATGTTTCC
*
943883 AATAATTAATCTATTTTATTATATAAGAGTTAC
1 AGTAATTAA-CTATTTTATTATATAAGAGTTAC
943916 CTAATATGTT
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
87 100 0.97
88 3 0.03
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (86 bp):
AGTAATTAACTATTTTATTATATAAGAGTTACATATTACATTATATAAGTCGTACCTAATACGTT
ATTGTGCTTAATAATGTTTCC
Found at i:943863 original size:23 final size:23
Alignment explanation
Indices: 943813--943857 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
943803 AACATATTTT
* *
943813 ATTATATAAGTGTTACATATTAC
1 ATTATATAAGTGGTACATAATAC
*
943836 ATTATATAAGTGGTACCTAATA
1 ATTATATAAGTGGTACATAATA
943858 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (23 bp):
ATTATATAAGTGGTACATAATAC
Found at i:943917 original size:64 final size:64
Alignment explanation
Indices: 943836--943973 Score: 213
Period size: 64 Copynumber: 2.2 Consensus size: 64
943826 TACATATTAC
* * *
943836 ATTATATAAGTGGTACCTAATATGTTATTGTGCTTGATAATGTTTCCAATAATTAATCTATTTT
1 ATTATATAAGAGGTACCTAATATGTTATTGTGCTTGATAATGTTTCCAATAATTAACCGATTTT
* * * *
943900 ATTATATAAGAGTTACCTAATATGTTATTGTGTTTGATAATGTTTTCAGTAATTAACCGATTTT
1 ATTATATAAGAGGTACCTAATATGTTATTGTGCTTGATAATGTTTCCAATAATTAACCGATTTT
943964 ATTATATAAG
1 ATTATATAAG
943974 TGATACTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (64 bp):
ATTATATAAGAGGTACCTAATATGTTATTGTGCTTGATAATGTTTCCAATAATTAACCGATTTT
Found at i:943991 original size:87 final size:87
Alignment explanation
Indices: 943900--944114 Score: 290
Period size: 87 Copynumber: 2.5 Consensus size: 87
943890 AATCTATTTT
* *
943900 ATTATATAAGAGTTACCTAATATGTTATTGTGTTTGATAATGTTT-TCAGTAATTAACCGATTTT
1 ATTATATAAGAGGTACCTAATATGTTATTGTGCTTGATAATGTTTCT-AGTAATTAACCGATTTT
* *
943964 ATTATATAAGTGATACTTATTAC
65 ATTATATAAGCGATACCTATTAC
** * *
943987 ATTATATAA-ACGGTATATAATATATTATTGTGCTTGATAATGTTTCTAGTAATTAACCTATTTT
1 ATTATATAAGA-GGTACCTAATATGTTATTGTGCTTGATAATGTTTCTAGTAATTAACCGATTTT
*
944051 ATTATATAAGCGCTACCTATTAC
65 ATTATATAAGCGATACCTATTAC
* * *
944074 ATTATATAAGCGGTACCTAATATGTTATTGTACTTGGTAAT
1 ATTATATAAGAGGTACCTAATATGTTATTGTGCTTGATAAT
944115 ATTCTGGTTA
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
86 1 0.01
87 108 0.98
88 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (87 bp):
ATTATATAAGAGGTACCTAATATGTTATTGTGCTTGATAATGTTTCTAGTAATTAACCGATTTTA
TTATATAAGCGATACCTATTAC
Found at i:944024 original size:151 final size:151
Alignment explanation
Indices: 943772--944069 Score: 427
Period size: 151 Copynumber: 2.0 Consensus size: 151
943762 CACTTATTAC
* * *
943772 GTTATTGTGCTTAATAATGTTTCTTGTAATTAACATATTTTATTATATAAGTGTTACATATTACA
1 GTTATTGTGCTTAATAATGTTTCTAGTAATTAACAGATTTTATTATATAAGTGATACATATTACA
** * * *
943837 TTATATAAGTGGTACCTAATATGTTATTGTGCTTGATAATGTTTCCAATAATTAATCTATTTTAT
66 TTATATAAACGGTACATAATATATTATTGTGCTTGATAATGTTTCCAATAATTAACCTATTTTAT
*
943902 TATATAAGAGTTACCTAATAT
131 TATATAAGAGCTACCTAATAT
* * * *
943923 GTTATTGTGTTTGATAATGTTT-TCAGTAATTAACCGATTTTATTATATAAGTGATACTTATTAC
1 GTTATTGTGCTTAATAATGTTTCT-AGTAATTAACAGATTTTATTATATAAGTGATACATATTAC
* * *
943987 ATTATATAAACGGTATATAATATATTATTGTGCTTGATAATGTTTCTAGTAATTAACCTATTTTA
65 ATTATATAAACGGTACATAATATATTATTGTGCTTGATAATGTTTCCAATAATTAACCTATTTTA
*
944052 TTATATAAGCGCTACCTA
130 TTATATAAGAGCTACCTA
944070 TTACATTATA
Statistics
Matches: 129, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
150 1 0.01
151 128 0.99
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (151 bp):
GTTATTGTGCTTAATAATGTTTCTAGTAATTAACAGATTTTATTATATAAGTGATACATATTACA
TTATATAAACGGTACATAATATATTATTGTGCTTGATAATGTTTCCAATAATTAACCTATTTTAT
TATATAAGAGCTACCTAATAT
Found at i:944077 original size:23 final size:23
Alignment explanation
Indices: 944042--944092 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
944032 CTAGTAATTA
**
944042 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
944065 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
944088 ACCTA
1 ACCTA
944093 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:947446 original size:33 final size:31
Alignment explanation
Indices: 947375--947460 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 31
947365 GAAGAGTAGT
*
947375 CGACCTCAATTTAACTTTCTATTGTAGAGGAGT
1 CGACCTCAATTTAACTTT-T-TTGTAGAGGAGG
* *
947408 TGACCTCAATTTAACTTTTTTGTATGAAGGGGG
1 CGACCTCAATTTAACTTTTTTGTA-G-AGGAGG
* *
947441 CGACCTTAATTTGACTTTTT
1 CGACCTCAATTTAACTTTTT
947461 CTTATTAAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 5 0.11
32 2 0.04
33 38 0.84
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (31 bp):
CGACCTCAATTTAACTTTTTTGTAGAGGAGG
Found at i:952863 original size:25 final size:25
Alignment explanation
Indices: 952829--952877 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
952819 TTCGTGTTTT
952829 TCGCCAAATATTCAACGTATTTCTA
1 TCGCCAAATATTCAACGTATTTCTA
*
952854 TCGCCAAATATTCAATGTATTTCT
1 TCGCCAAATATTCAACGTATTTCT
952878 CATATTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (25 bp):
TCGCCAAATATTCAACGTATTTCTA
Found at i:955434 original size:22 final size:22
Alignment explanation
Indices: 955406--955447 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
955396 CCAGAGGATC
955406 CAATTATCGTAGTCAAAAACGT
1 CAATTATCGTAGTCAAAAACGT
*
955428 CAATTATCGTAGTCGAAAAC
1 CAATTATCGTAGTCAAAAAC
955448 AATAGAAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (22 bp):
CAATTATCGTAGTCAAAAACGT
Found at i:958628 original size:23 final size:23
Alignment explanation
Indices: 958536--958637 Score: 66
Period size: 23 Copynumber: 4.3 Consensus size: 23
958526 TAATTTTAAC
*
958536 TAAAATTTAAAAT-TCTTCTATTT
1 TAAAATTTAAAATAT-TTTTATTT
*
958559 T-ATATTGTAAAATAATTTATATATTT
1 TAAAATT-TAAAAT-ATTT-T-TATTT
** * *
958585 TCATTATTT-AAATAATATTATTT
1 T-AAAATTTAAAATATTTTTATTT
958608 TAAAATTTAAAATATTTTTATTT
1 TAAAATTTAAAATATTTTTATTT
*
958631 TAGAATT
1 TAAAATT
958638 AATTTATAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
22 9 0.15
23 31 0.51
24 3 0.05
25 3 0.05
26 10 0.16
27 1 0.02
28 4 0.07
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (23 bp):
TAAAATTTAAAATATTTTTATTT
Found at i:958977 original size:9 final size:9
Alignment explanation
Indices: 958967--958997 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
958957 CTTCTTCCTC
*
958967 TTCTCATTC
1 TTCTCATTA
958976 TTCTCATTA
1 TTCTCATTA
958985 TTCTCATTA
1 TTCTCATTA
958994 TTCT
1 TTCT
958998 TAACCAACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (9 bp):
TTCTCATTA
Found at i:959463 original size:3 final size:3
Alignment explanation
Indices: 959450--959502 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
959440 GAGGTGTGAG
* * *
959450 AGA AAA AGA AGA AGA AGA AGA AGA AGA AGT AGA AAA AGA AG- AGA AGGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA
959498 AGA AG
1 AGA AG
959503 GATAAGGGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:960224 original size:2 final size:2
Alignment explanation
Indices: 960217--960267 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
960207 GAAAAAGCAA
* *
960217 AG AG AG AG AG AG AG GG AG AG GG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
960259 AG AG AG AG A
1 AG AG AG AG A
960268 TGATATTGGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:965398 original size:3 final size:3
Alignment explanation
Indices: 965390--965414 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
965380 TTATCAACAG
965390 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
965415 TAGATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:981038 original size:7 final size:7
Alignment explanation
Indices: 981026--981063 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
981016 ATGAGTACTA
981026 TTTAAGG
1 TTTAAGG
981033 TTTAAGG
1 TTTAAGG
981040 TTTAAGG
1 TTTAAGG
981047 TTTAAGG
1 TTTAAGG
981054 TTTAAGG
1 TTTAAGG
981061 TTT
1 TTT
981064 TAAAACAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (7 bp):
TTTAAGG
Found at i:991383 original size:33 final size:34
Alignment explanation
Indices: 991346--991462 Score: 120
Period size: 33 Copynumber: 3.6 Consensus size: 34
991336 TTCAACCTCC
991346 TCGTCTGAAAATCC-TTCGCACTTTAGAGAGATT
1 TCGTCTGAAAATCCATTCGCACTTTAGAGAGATT
* * ** *
991379 TCGTCTGAAAAACCATTCGC-C-TT-CA-ACCTCC
1 TCGTCTGAAAATCCATTCGCACTTTAGAGAGAT-T
*
991410 TCGTCTGATAATCC-TTCGCACTTTAGAGAGATT
1 TCGTCTGAAAATCCATTCGCACTTTAGAGAGATT
*
991443 TCGTCTGAAAACCCATTCGC
1 TCGTCTGAAAATCCATTCGC
991463 CTTCATCACA
Statistics
Matches: 64, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
30 7 0.11
31 14 0.22
32 4 0.06
33 27 0.42
34 12 0.19
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (34 bp):
TCGTCTGAAAATCCATTCGCACTTTAGAGAGATT
Found at i:991400 original size:64 final size:64
Alignment explanation
Indices: 991321--991467 Score: 267
Period size: 64 Copynumber: 2.3 Consensus size: 64
991311 CTTCATCGCA
991321 AAAAACCCATTCGCCTTCAACCTCCTCGTCTGAAAATCCTTCGCACTTTAGAGAGATTTCGTCTG
1 AAAAA-CCATTCGCCTTCAACCTCCTCGTCTGAAAATCCTTCGCACTTTAGAGAGATTTCGTCTG
*
991386 AAAAACCATTCGCCTTCAACCTCCTCGTCTGATAATCCTTCGCACTTTAGAGAGATTTCGTCTG
1 AAAAACCATTCGCCTTCAACCTCCTCGTCTGAAAATCCTTCGCACTTTAGAGAGATTTCGTCTG
*
991450 AAAACCCATTCGCCTTCA
1 AAAAACCATTCGCCTTCA
991468 TCACAGAAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
64 75 0.94
65 5 0.06
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (64 bp):
AAAAACCATTCGCCTTCAACCTCCTCGTCTGAAAATCCTTCGCACTTTAGAGAGATTTCGTCTG
Found at i:991417 original size:31 final size:31
Alignment explanation
Indices: 991321--991417 Score: 90
Period size: 33 Copynumber: 3.0 Consensus size: 31
991311 CTTCATCGCA
991321 AAAAACCCATTCGCCTTCAACCTCCTCGTCTG
1 AAAAA-CCATTCGCCTTCAACCTCCTCGTCTG
* * ** *
991353 AAAATCC-TTCGCACTTTAGAGAGAT-TTCGTCTG
1 AAAAACCATTCGC-C-TT-CA-ACCTCCTCGTCTG
991386 AAAAACCATTCGCCTTCAACCTCCTCGTCTG
1 AAAAACCATTCGCCTTCAACCTCCTCGTCTG
991417 A
1 A
991418 TAATCCTTCG
Statistics
Matches: 49, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
30 7 0.14
31 12 0.24
32 8 0.16
33 15 0.31
34 7 0.14
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.28
Consensus pattern (31 bp):
AAAAACCATTCGCCTTCAACCTCCTCGTCTG
Found at i:991575 original size:24 final size:24
Alignment explanation
Indices: 991548--991613 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
991538 ATTTCGTCTG
*
991548 AAAACCCATTAGCCTTCATCGTAA
1 AAAACCCATTAGCCTTCATCGCAA
* * *
991572 AAAATCTATTAGCCTTCATCGCAG
1 AAAACCCATTAGCCTTCATCGCAA
*
991596 AAAACCCATTCGCCTTCA
1 AAAACCCATTAGCCTTCA
991614 ACCTCCCCGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (24 bp):
AAAACCCATTAGCCTTCATCGCAA
Found at i:992196 original size:17 final size:15
Alignment explanation
Indices: 992151--992192 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
992141 AATGTGAGTA
992151 CTGCATGTATATGTT
1 CTGCATGTATATGTT
992166 CTGCATGTATATGTT
1 CTGCATGTATATGTT
*
992181 CTGCATGAATAT
1 CTGCATGTATAT
992193 ATGTGTTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (15 bp):
CTGCATGTATATGTT
Found at i:992855 original size:45 final size:44
Alignment explanation
Indices: 992803--992968 Score: 171
Period size: 45 Copynumber: 3.8 Consensus size: 44
992793 GGTCTGAACA
* * *
992803 TAATGAACCTGAAATTGATGAAGCATAACCAGTTCAACCAGAAAT
1 TAATGAACCTGAAATTGATGAAGCA-AACCAGCTGAGCCAGAAAT
* * * *
992848 TACTGAACCCGAAATT-A-G-TG--AACCAGCTGAGCCATAAAT
1 TAATGAACCTGAAATTGATGAAGCAAACCAGCTGAGCCAGAAAT
* *
992887 TAATGAACCTGAAATTAATGAACCAGAACCAGCTGAGCCAGAAAT
1 TAATGAACCTGAAATTGATGAAGCA-AACCAGCTGAGCCAGAAAT
* *
992932 TAATGAACCTGAAATTGATGAACCAGAACCTGCTGAG
1 TAATGAACCTGAAATTGATGAAGCA-AACCAGCTGAG
992969 GTGAGGATAG
Statistics
Matches: 101, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
39 29 0.29
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
45 67 0.66
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (44 bp):
TAATGAACCTGAAATTGATGAAGCAAACCAGCTGAGCCAGAAAT
Found at i:992861 original size:15 final size:15
Alignment explanation
Indices: 992838--992959 Score: 62
Period size: 15 Copynumber: 8.5 Consensus size: 15
992828 TAACCAGTTC
992838 AACCAGAAATTACTG
1 AACCAGAAATTACTG
* *
992853 AACCCGAAATTAGTG
1 AACCAGAAATTACTG
992868 AACCAG------CTG
1 AACCAGAAATTACTG
* * *
992877 AGCCATAAATTAATG
1 AACCAGAAATTACTG
* *
992892 AACCTGAAATTAATG
1 AACCAGAAATTACTG
**
992907 AACCAG-AACCAGCTG
1 AACCAGAAATTA-CTG
* *
992922 AGCCAGAAATTAATG
1 AACCAGAAATTACTG
*
992937 AACCTGAAATTGA-TG
1 AACCAGAAATT-ACTG
992952 AACCAGAA
1 AACCAGAA
992960 CCTGCTGAGG
Statistics
Matches: 77, Mismatches: 21, Indels: 18
0.66 0.18 0.16
Matches are distributed among these distances:
9 6 0.08
14 3 0.04
15 64 0.83
16 4 0.05
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (15 bp):
AACCAGAAATTACTG
Found at i:992872 original size:39 final size:39
Alignment explanation
Indices: 992829--992957 Score: 107
Period size: 39 Copynumber: 3.2 Consensus size: 39
992819 GATGAAGCAT
* * *
992829 AACCAGTTCAACCAGAAATTACTGAACCCGAAATTAGTG
1 AACCAGCTCAACCAGAAATTAATGAACCCGAAATTAATG
* * * *
992868 AACCAGCTGAGCCATAAATTAATGAACCTGAAATTAATG
1 AACCAGCTCAACCAGAAATTAATGAACCCGAAATTAATG
* *
992907 AACCAGAAC-CAGCTGAGCCAGAAATTAATGAACCTGAAATTGATG
1 AACCAG--CTCA----A-CCAGAAATTAATGAACCCGAAATTAATG
992952 AACCAG
1 AACCAG
992958 AACCTGCTGA
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
39 38 0.53
40 1 0.01
41 1 0.01
45 32 0.44
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (39 bp):
AACCAGCTCAACCAGAAATTAATGAACCCGAAATTAATG
Found at i:992877 original size:24 final size:24
Alignment explanation
Indices: 992850--992895 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
992840 CCAGAAATTA
* *
992850 CTGAACCCGAAATTAGTGAACCAG
1 CTGAACCAGAAATTAATGAACCAG
* *
992874 CTGAGCCATAAATTAATGAACC
1 CTGAACCAGAAATTAATGAACC
992896 TGAAATTAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (24 bp):
CTGAACCAGAAATTAATGAACCAG
Found at i:992946 original size:84 final size:84
Alignment explanation
Indices: 992803--992957 Score: 222
Period size: 84 Copynumber: 1.8 Consensus size: 84
992793 GGTCTGAACA
* * * * *
992803 TAATGAACCTGAAATTGATGAAGCATAACCAGTTCAACCAGAAATTACTGAACCCGAAATT-AGT
1 TAATGAACCTGAAATTAATGAACCAGAACCAGCTCAACCAGAAATTAATGAACCCGAAATTGA-T
992867 GAACCAGCTGAGCCATAAAT
65 GAACCAGCTGAGCCATAAAT
* * *
992887 TAATGAACCTGAAATTAATGAACCAGAACCAGCTGAGCCAGAAATTAATGAACCTGAAATTGATG
1 TAATGAACCTGAAATTAATGAACCAGAACCAGCTCAACCAGAAATTAATGAACCCGAAATTGATG
992952 AACCAG
66 AACCAG
992958 AACCTGCTGA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
84 61 0.98
85 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (84 bp):
TAATGAACCTGAAATTAATGAACCAGAACCAGCTCAACCAGAAATTAATGAACCCGAAATTGATG
AACCAGCTGAGCCATAAAT
Found at i:992958 original size:30 final size:30
Alignment explanation
Indices: 992883--992959 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 30
992873 GCTGAGCCAT
* *
992883 AAATTAATGAACCTGAAATTAATGAACCAG
1 AAATTGATGAACCAGAAATTAATGAACCAG
*** * * *
992913 AACCAGCTGAGCCAGAAATTAATGAACCTG
1 AAATTGATGAACCAGAAATTAATGAACCAG
992943 AAATTGATGAACCAGAA
1 AAATTGATGAACCAGAA
992960 CCTGCTGAGG
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (30 bp):
AAATTGATGAACCAGAAATTAATGAACCAG
Found at i:995319 original size:64 final size:64
Alignment explanation
Indices: 995251--995471 Score: 214
Period size: 64 Copynumber: 3.5 Consensus size: 64
995241 TTGAAGGTGT
** * ** * *
995251 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCATAAGTAATGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATGCAATTAGTG
995314 C
64 C
*
995315 ATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
** * * * * * * *
995379 ATCGATGCATAAGGCATGCATCGATGTATCCCAGTAATAATACAACATCAAATACATTTTA-TGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCA-ATTAGTGC
* * *
995443 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
995472 ACCTTCATTA
Statistics
Matches: 130, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
64 122 0.94
65 8 0.06
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGTGC
Found at i:996486 original size:29 final size:30
Alignment explanation
Indices: 996391--996483 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
996381 GTGGTCCTTA
996391 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
996421 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
996451 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
996480 TGGA
1 TGGA
996484 TAGGTCATTC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
29 18 0.30
30 42 0.70
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:999081 original size:23 final size:23
Alignment explanation
Indices: 999054--999116 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
999044 TTTAATTAAG
*
999054 GTGGCGTCCTGCATGTTGATGAT
1 GTGGCGTCCTGCATGTCGATGAT
999077 GTGGCGTCCTGCATGTCGATGAT
1 GTGGCGTCCTGCATGTCGATGAT
* *
999100 GTGGAGTTCTGCATGTC
1 GTGGCGTCCTGCATGTC
999117 AAACCTGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.13, C:0.19, G:0.35, T:0.33
Consensus pattern (23 bp):
GTGGCGTCCTGCATGTCGATGAT
Found at i:1002102 original size:29 final size:29
Alignment explanation
Indices: 1002056--1002133 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
1002046 ATTTGGTTTG
* * *
1002056 ATTAATCGAACCAAAATTTATTTGAAAATT
1 ATTAACCGAACC-GAATTAATTTGAAAATT
1002086 ATTAACCGAACCGAATTAATTTGAAAATT
1 ATTAACCGAACCGAATTAATTTGAAAATT
*
1002115 ATTAACTGAACCGAATTAA
1 ATTAACCGAACCGAATTAA
1002134 CCAAATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 33 0.75
30 11 0.25
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (29 bp):
ATTAACCGAACCGAATTAATTTGAAAATT
Found at i:1002185 original size:131 final size:129
Alignment explanation
Indices: 1002042--1002373 Score: 448
Period size: 131 Copynumber: 2.5 Consensus size: 129
1002032 GGTTAAAGAA
*
1002042 AAAAATTTGGTTTGATTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATT
1 AAAAATTAGGTTTGATTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATT
*
1002107 TGAAAATTATTAACTGAACCGAATTAACCAAATTTTTTGAAAATTATTAACCGAATTAATCGAAA
66 TGAAAATTATTAACCGAACCGAATTAACC-AATTTTTT-AAAATTATTAACCGAATTAATCGAAA
1002172 C
129 C
* * * *
1002173 AAAAATTCGGTTTGGTTAATCGAACCAAATTTTATTTGGAAATTATTAACCGAACCGAATTAATT
1 AAAAATTAGGTTTGATTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATT
* * * * *
1002238 TGGAAATTATTAACCGAACCGAATTAACCGATTTTTTTAAATTATTAACCTAATTAATCGAAGC
66 TGAAAATTATTAACCGAACCGAATTAACCAATTTTTTAAAATTATTAACCGAATTAATCGAAAC
* *
1002302 AAAAATTTAGTTAATTTGGTTTAGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGTACC
1 AAAAA-TTAG---GTTT-G---A-TTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACC
1002367 GAATTAA
57 GAATTAA
1002374 CTGTTTTTTT
Statistics
Matches: 176, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
129 29 0.16
130 10 0.06
131 88 0.50
133 3 0.02
134 1 0.01
138 45 0.26
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (129 bp):
AAAAATTAGGTTTGATTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATT
TGAAAATTATTAACCGAACCGAATTAACCAATTTTTTAAAATTATTAACCGAATTAATCGAAAC
Found at i:1002240 original size:29 final size:29
Alignment explanation
Indices: 1002188--1002264 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 29
1002178 TTCGGTTTGG
* * *
1002188 TTAATCGAACCAAATTTTATTTGGAAATTA
1 TTAACCGAACCGAA-TTAATTTGGAAATTA
1002218 TTAACCGAACCGAATTAATTTGGAAATTA
1 TTAACCGAACCGAATTAATTTGGAAATTA
1002247 TTAACCGAACCGAATTAA
1 TTAACCGAACCGAATTAA
1002265 CCGATTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 32 0.73
30 12 0.27
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (29 bp):
TTAACCGAACCGAATTAATTTGGAAATTA
Found at i:1002335 original size:108 final size:108
Alignment explanation
Indices: 1002230--1002481 Score: 364
Period size: 108 Copynumber: 2.3 Consensus size: 108
1002220 AACCGAACCG
* * *
1002230 AATTAATTTGGAAATTATTAACCGAACCGAATTAACCGATTTTTTTAAATTATTAACCT-AATTA
1 AATTTATTTGAAAATTATTAACCGAACCGAATTAACCG-TTTTTTTAAATTATTAA-CTGAATGA
*
1002294 ATCGAAGCAAAAATTTAGTTAATTTGGTT-TAGTTAATCGAACCAA
64 ATCGAAGCAAAAATTTAGTTAATTCGGTTCT-GTTAATCGAACCAA
* *
1002339 AATTTATTTGAAAATTATTAACCGTACCGAATTAACTGTTTTTTTAAATTATTAACTGAATGAAT
1 AATTTATTTGAAAATTATTAACCGAACCGAATTAACCGTTTTTTTAAATTATTAACTGAATGAAT
* * * *
1002404 CGAAGCAAAAGTTTGGTTAATTCGGTTCTGTTAATTGATCCAA
66 CGAAGCAAAAATTTAGTTAATTCGGTTCTGTTAATCGAACCAA
*
1002447 AATTTATTTGAAAATTATTAACCGAACCAAATTAA
1 AATTTATTTGAAAATTATTAACCGAACCGAATTAA
1002482 TTTAAAAATT
Statistics
Matches: 129, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
107 2 0.02
108 92 0.71
109 35 0.27
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (108 bp):
AATTTATTTGAAAATTATTAACCGAACCGAATTAACCGTTTTTTTAAATTATTAACTGAATGAAT
CGAAGCAAAAATTTAGTTAATTCGGTTCTGTTAATCGAACCAA
Found at i:1002489 original size:29 final size:29
Alignment explanation
Indices: 1002446--1002510 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
1002436 AATTGATCCA
* *
1002446 AAATTTATTTGAAAATTATTAACCGAACC
1 AAATTAATTTAAAAATTATTAACCGAACC
*
1002475 AAATTAATTTAAAAATTATTAACTGAACC
1 AAATTAATTTAAAAATTATTAACCGAACC
*
1002504 GAATTAA
1 AAATTAA
1002511 CCGCTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (29 bp):
AAATTAATTTAAAAATTATTAACCGAACC
Found at i:1002597 original size:29 final size:29
Alignment explanation
Indices: 1002565--1002628 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1002555 TGGTTCAGTT
*
1002565 AATTTATTTAAAAATTATTAACCGAACCG
1 AATTAATTTAAAAATTATTAACCGAACCG
* * *
1002594 AATTAATTTGAAAATTATTAACTGGACCG
1 AATTAATTTAAAAATTATTAACCGAACCG
1002623 AATTAA
1 AATTAA
1002629 CCGATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (29 bp):
AATTAATTTAAAAATTATTAACCGAACCG
Found at i:1008760 original size:2 final size:2
Alignment explanation
Indices: 1008753--1008808 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
1008743 TGCTTTTGAC
1008753 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1008794 TA TA T- TA TA AA TA TA
1 TA TA TA TA TA TA TA TA
1008809 GAGTGAATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1010901 original size:2 final size:2
Alignment explanation
Indices: 1010894--1010928 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1010884 CAAACATTCT
1010894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1010929 GAAAGAGGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1014793 original size:70 final size:70
Alignment explanation
Indices: 1014677--1014828 Score: 168
Period size: 70 Copynumber: 2.2 Consensus size: 70
1014667 ACACTGTTCG
*
1014677 TTTTCAAA-TTAATGAAATTAAACCATAACTCCATATTTGTACGGTTTAATTATTTTTTAAGACA
1 TTTT-AAAGTTAATGAAATTAAACCATAACTCCATATTTGTACGGTTTAATTACTTTTT-AGACA
1014741 TT-TGGA
64 TTATGGA
* ** * *
1014747 TTTTAAAGTTAATGAAATTAAACCCTTAA-TCTGTTATTT-TATGGTTTAATTACTTTTTAGACC
1 TTTTAAAGTTAATGAAATTAAA-CCATAACTC-CATATTTGTACGGTTTAATTACTTTTTAGACA
**
1014810 TTATTTA
64 TTATGGA
1014817 TTTTAAAGTTAA
1 TTTTAAAGTTAA
1014829 ACAACTTACC
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
69 9 0.13
70 51 0.73
71 10 0.14
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (70 bp):
TTTTAAAGTTAATGAAATTAAACCATAACTCCATATTTGTACGGTTTAATTACTTTTTAGACATT
ATGGA
Found at i:1017938 original size:25 final size:23
Alignment explanation
Indices: 1017902--1017947 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
1017892 TTTTCACAAA
*
1017902 TACTTTTTTTAAATGAAATAATC
1 TACTTTTTTTAAATAAAATAATC
*
1017925 TACTGTTTTATTAATTAAAATAA
1 TACT-TTTT-TTAAATAAAATAA
1017948 GAGACAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 4 0.21
25 11 0.58
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (23 bp):
TACTTTTTTTAAATAAAATAATC
Found at i:1020082 original size:14 final size:14
Alignment explanation
Indices: 1020062--1020102 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1020052 TTGACTTTTT
1020062 GGTCAAAGTCAACA
1 GGTCAAAGTCAACA
* *
1020076 TGTCAAAGTCAATA
1 GGTCAAAGTCAACA
*
1020090 GGTCAAATTCAAC
1 GGTCAAAGTCAAC
1020103 TGGTTGACTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (14 bp):
GGTCAAAGTCAACA
Found at i:1020124 original size:14 final size:14
Alignment explanation
Indices: 1020105--1020140 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1020095 AATTCAACTG
1020105 GTTGACTCGGACGA
1 GTTGACTCGGACGA
1020119 GTTGACTCGGACGA
1 GTTGACTCGGACGA
1020133 GTTGACTC
1 GTTGACTC
1020141 AATATGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.25
Consensus pattern (14 bp):
GTTGACTCGGACGA
Found at i:1020168 original size:14 final size:14
Alignment explanation
Indices: 1020105--1020183 Score: 63
Period size: 14 Copynumber: 5.6 Consensus size: 14
1020095 AATTCAACTG
*
1020105 GTTGACTCGGACGA
1 GTTGACTCAGACGA
*
1020119 GTTGACTCGGACGA
1 GTTGACTCAGACGA
* *
1020133 GTTGACTCAATATG-
1 GTTGACTC-AGACGA
*
1020147 GTTTGACTCAGATGA
1 G-TTGACTCAGACGA
*
1020162 GTTGACTCA-ACCAA
1 GTTGACTCAGA-CGA
1020176 GTTGACTC
1 GTTGACTC
1020184 GGTTCAAACC
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
13 1 0.02
14 44 0.80
15 10 0.18
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:1020220 original size:19 final size:19
Alignment explanation
Indices: 1020193--1020231 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1020183 CGGTTCAAAC
* * *
1020193 CGGTTTGACTGGACCTGTT
1 CGGTCTGACTAGACCAGTT
1020212 CGGTCTGACTAGACCAGTT
1 CGGTCTGACTAGACCAGTT
1020231 C
1 C
1020232 CAGAAACCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (19 bp):
CGGTCTGACTAGACCAGTT
Found at i:1021369 original size:2 final size:2
Alignment explanation
Indices: 1021362--1021393 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1021352 ATGCAAACAA
1021362 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
1021394 TGTCACGGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1033124 original size:2 final size:2
Alignment explanation
Indices: 1033119--1033158 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1033109 TTTTTATCCA
1033119 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
1033159 GAAATTGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1042212 original size:82 final size:82
Alignment explanation
Indices: 1042056--1042219 Score: 310
Period size: 82 Copynumber: 2.0 Consensus size: 82
1042046 ACATTTATTA
*
1042056 ATTATACTTAAAAGGATATTTTAAAATTTTCTTAATAATTACATTACATTACAAAAATATATAGT
1 ATTATACTTAAAAGGATATTTTAAAATTTTCTTAATAATTACATTACATTAAAAAAATATATAGT
1042121 TAATAAAAAAGAAAGAT
66 TAATAAAAAAGAAAGAT
1042138 ATTATACTTAAAAGGATATTTTAAAATTTTCTTAATAATTACATTACATTAAAAAATATATATAG
1 ATTATACTTAAAAGGATATTTTAAAATTTTCTTAATAATTACATTACATTAAAAAA-ATATATAG
1042203 TTAATAAAAAAGAAAGA
65 TTAATAAAAAAGAAAGA
1042220 ATCTAAAATT
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 55 0.69
83 25 0.31
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (82 bp):
ATTATACTTAAAAGGATATTTTAAAATTTTCTTAATAATTACATTACATTAAAAAAATATATAGT
TAATAAAAAAGAAAGAT
Found at i:1042557 original size:17 final size:18
Alignment explanation
Indices: 1042521--1042571 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1042511 AGAGCAGTGG
* *
1042521 TTTTTTTAAATCTTTTAA-
1 TTTTTTTATAT-TTTAAAT
1042539 TTTTTTTATATTTTAAAT
1 TTTTTTTATATTTTAAAT
1042557 TTATTTTTATATTTT
1 TT-TTTTTATATTTT
1042572 CTATTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 5 0.17
18 12 0.41
19 12 0.41
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTTATATTTTAAAT
Found at i:1044388 original size:18 final size:17
Alignment explanation
Indices: 1044356--1044389 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1044346 TCAGCCGGTC
1044356 CGGTTTGAACGGTTCAA
1 CGGTTTGAACGGTTCAA
*
1044373 CGGTTCTGACCGGTTCA
1 CGGTT-TGAACGGTTCA
1044390 CTAATAGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (17 bp):
CGGTTTGAACGGTTCAA
Found at i:1046236 original size:2 final size:2
Alignment explanation
Indices: 1046229--1046268 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1046219 TGCATCATTA
1046229 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
1046269 TAAAATTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1046314 original size:21 final size:20
Alignment explanation
Indices: 1046288--1046327 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1046278 CGTAATCTAT
1046288 ATATTAAATAATTTGTTTATG
1 ATATTAAATAATTT-TTTATG
**
1046309 ATATTATTTAATTTTTTAT
1 ATATTAAATAATTTTTTAT
1046328 TATTACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
ATATTAAATAATTTTTTATG
Found at i:1048709 original size:28 final size:28
Alignment explanation
Indices: 1048655--1048711 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1048645 TTCTCCATTT
*
1048655 ACATTATGTAATCGAGCTAGTGTTTGAA
1 ACATTATGTAATCGAGCCAGTGTTTGAA
*
1048683 ACATTATGTAGTCGAGCCAGT-TCTTGAA
1 ACATTATGTAATCGAGCCAGTGT-TTGAA
1048711 A
1 A
1048712 GCAACGCCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (28 bp):
ACATTATGTAATCGAGCCAGTGTTTGAA
Found at i:1048930 original size:60 final size:60
Alignment explanation
Indices: 1048834--1048952 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
1048824 AGAACATATG
** **
1048834 AATAGTCGTGGTACTCAACAAAACAACACCACATAGTTGGGGGACCATTTTGTA-ACTTTT
1 AATAGTCGTGAAACTCAACAAAACAACACCACATAGTAAGGGGACCA-TTTGTATACTTTT
* * **
1048894 AATAGTCGTGAAACTTAACAAAACAACGCCTTATAGTAAGGGGACCATTTGTATACTTT
1 AATAGTCGTGAAACTCAACAAAACAACACCACATAGTAAGGGGACCATTTGTATACTTT
1048953 ATCCTTTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
59 6 0.12
60 44 0.88
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (60 bp):
AATAGTCGTGAAACTCAACAAAACAACACCACATAGTAAGGGGACCATTTGTATACTTTT
Found at i:1061406 original size:2 final size:2
Alignment explanation
Indices: 1061399--1061424 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1061389 TTCTTTCAAA
1061399 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
1061425 TATCATATTA
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:1061726 original size:32 final size:32
Alignment explanation
Indices: 1061665--1061729 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1061655 TCTTTTGAGC
*
1061665 ATATATAATCTTATATTCACTCCATATTAATA
1 ATATATAATCTTATATTCACTCCAGATTAATA
* **
1061697 ATATATGATCTTATATTCACTTTAGATTAATA
1 ATATATAATCTTATATTCACTCCAGATTAATA
1061729 A
1 A
1061730 AAAAATAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (32 bp):
ATATATAATCTTATATTCACTCCAGATTAATA
Found at i:1064730 original size:2 final size:2
Alignment explanation
Indices: 1064723--1064766 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1064713 GTTTAGCCAC
1064723 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
1064765 AT
1 AT
1064767 CATACTATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1065741 original size:21 final size:21
Alignment explanation
Indices: 1065716--1065764 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1065706 GCCAACGCCA
*
1065716 CGAACAATAGCTTCTGGATTT
1 CGAACAATAACTTCTGGATTT
1065737 CGAACAATAACTTCTGGATTT
1 CGAACAATAACTTCTGGATTT
1065758 CGAACAA
1 CGAACAA
1065765 AATCAGTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (21 bp):
CGAACAATAACTTCTGGATTT
Found at i:1067178 original size:19 final size:22
Alignment explanation
Indices: 1067154--1067197 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 22
1067144 TACCACTTAA
1067154 TTTCATA-AAG-TTATAT-AAC
1 TTTCATACAAGATTATATAAAC
1067173 TTTCATACAAGATTATATAAAC
1 TTTCATACAAGATTATATAAAC
1067195 TTT
1 TTT
1067198 TAGTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
20 3 0.14
21 6 0.27
22 6 0.27
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (22 bp):
TTTCATACAAGATTATATAAAC
Found at i:1080923 original size:3 final size:3
Alignment explanation
Indices: 1080915--1080963 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1080905 TTAATAAAAT
1080915 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1080963 G
1 G
1080964 GTGTTTACCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1083719 original size:18 final size:20
Alignment explanation
Indices: 1083696--1083734 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1083686 TTTATTGATG
1083696 GTGTTCA-CT-TAAAAAATT
1 GTGTTCATCTATAAAAAATT
1083714 GTGTTCATCTCATAAAAAATT
1 GTGTTCATCT-ATAAAAAATT
1083735 TATATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
21 9 0.50
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (20 bp):
GTGTTCATCTATAAAAAATT
Found at i:1092517 original size:15 final size:15
Alignment explanation
Indices: 1092497--1092526 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1092487 AGTTTAATCA
1092497 GATTATAAAATAATT
1 GATTATAAAATAATT
1092512 GATTATAAAATAATT
1 GATTATAAAATAATT
1092527 AGAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (15 bp):
GATTATAAAATAATT
Found at i:1099256 original size:37 final size:38
Alignment explanation
Indices: 1099176--1099256 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
1099166 AACAAGTTGG
* * *
1099176 AAAATATTTATATATTTTCTTTAAAAATTTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTGAAAATCAT
1099215 -AAAATTTATATAATTTT-TTTAAAAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAATTGAAAATCAT
1099251 AAAAAT
1 AAAAAT
1099257 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 2 0.05
37 27 0.73
38 8 0.22
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:1107524 original size:216 final size:216
Alignment explanation
Indices: 1107050--1107628 Score: 870
Period size: 217 Copynumber: 2.7 Consensus size: 216
1107040 TTTTATTATT
* * *
1107050 TCGGGTCGAGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCG
1 TCGGGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTT-GT----TAG
1107115 GATCGGGTTTTTTTAAGTGTGATA-T----TCGGGTCGGG-TCGGGTTTAGGGTGAAAAAAA-CG
61 GATCGGG-TTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCG
* * *
1107173 GACCGACCCTAAAATATATATAATTCAGATCGGGTCAGATTAAGTCACTGTTTTTATTAAATTAA
125 GACCGACCCGAAAATATATATAATTCAGATCGGGTCAGATTAAGTCAATGTTTTTATTAAATAAA
*
1107238 AATAATTTTTTATTATTTCGGGTCGGG
190 AATAATTTTTTATTATTTCAGGTCGGG
*
1107265 TCGGGTTGAATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTAGGATCG
1 TCGGGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTAGGATCG
1107330 GGTTTTTTAAGTGTGATATTCGGGTCGGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCG
66 GGTTTTTTAAGTGTGATATTCGGGTC-GGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCG
* * * *
1107395 ACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCAATGTTTTTATTAAATAAAAATAT
130 ACCCGAAAATATATATAATTCAGATCGGGTCAGATTAAGTCAATGTTTTTATTAAATAAAAATAA
1107460 TTTTTTATTATTTCAGGTCGGG
195 TTTTTTATTATTTCAGGTCGGG
* * * *
1107482 TC-TGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTTGGGTC-
1 TCGGGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTAGGATCG
* *
1107545 AGTTTTTTAAGTGTGCTATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGA
66 GGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGA
1107610 CCCGAAAATATATATAATT
131 CCCGAAAATATATATAATT
1107629 TTACCTTATA
Statistics
Matches: 337, Mismatches: 19, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
209 16 0.05
210 10 0.03
214 62 0.18
215 84 0.25
216 77 0.23
217 88 0.26
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.36
Consensus pattern (216 bp):
TCGGGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTAGGATCG
GGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGA
CCCGAAAATATATATAATTCAGATCGGGTCAGATTAAGTCAATGTTTTTATTAAATAAAAATAAT
TTTTTATTATTTCAGGTCGGG
Found at i:1113188 original size:15 final size:15
Alignment explanation
Indices: 1113170--1113221 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1113160 TCCGCTTCCC
1113170 TCCCTCCTCTCCTCT
1 TCCCTCCTCTCCTCT
1113185 TCCCTCC-CAGTCCTCT
1 TCCCTCCTC--TCCTCT
** *
1113201 TCGTTCCTCTCCCCT
1 TCCCTCCTCTCCTCT
1113216 TCCCTC
1 TCCCTC
1113222 GCTGGAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.55
16 11 0.38
17 1 0.03
ACGTcount: A:0.02, C:0.58, G:0.04, T:0.37
Consensus pattern (15 bp):
TCCCTCCTCTCCTCT
Found at i:1115395 original size:40 final size:41
Alignment explanation
Indices: 1115350--1115438 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
1115340 TCGAGCGATC
* *
1115350 ATTTTATAATTTTTAATAATT-AAA-TATTTAATAAAATAAT
1 ATTTTATAATTTTTAAT-ATTAAAAGAATTTAATAAAATAAA
1115390 ATTTTATAATTTTTAATATTAAAAGAATTTAATAAAATAAA
1 ATTTTATAATTTTTAATATTAAAAGAATTTAATAAAATAAA
*
1115431 ACTTTATA
1 ATTTTATA
1115439 GTCGATGTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 3 0.07
40 20 0.45
41 21 0.48
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (41 bp):
ATTTTATAATTTTTAATATTAAAAGAATTTAATAAAATAAA
Found at i:1115766 original size:19 final size:19
Alignment explanation
Indices: 1115742--1115801 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
1115732 AAAAACCGAT
1115742 AAATCGAACCAAACCGAAA
1 AAATCGAACCAAACCGAAA
**
1115761 AAATCGAACCGTTA---AAA
1 AAATCGAACC-AAACCGAAA
*
1115778 AAATCGAACCGAACCGAAA
1 AAATCGAACCAAACCGAAA
1115797 AAATC
1 AAATC
1115802 TATTTCGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 1 0.03
17 13 0.39
19 18 0.55
20 1 0.03
ACGTcount: A:0.55, C:0.23, G:0.12, T:0.10
Consensus pattern (19 bp):
AAATCGAACCAAACCGAAA
Found at i:1122171 original size:11 final size:11
Alignment explanation
Indices: 1122150--1122182 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1122140 ATATTTTATC
1122150 ATTT-AAATAA
1 ATTTGAAATAA
*
1122160 ATTTGGAATAA
1 ATTTGAAATAA
1122171 ATTTGAAATAA
1 ATTTGAAATAA
1122182 A
1 A
1122183 GAGAATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (11 bp):
ATTTGAAATAA
Found at i:1125543 original size:37 final size:38
Alignment explanation
Indices: 1125462--1125553 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 38
1125452 CGTCCTATTA
* * *
1125462 AGATTAAAATTCTTAAAAATAAAGATAGAATTTTGCTT
1 AGATTTAAACTCTTAAAAATAAAGATAGAATTTTACTT
*
1125500 AGATTTAAACTCTTAAAAATAGA-ATAG-ATTTCTACTAT
1 AGATTTAAACTCTTAAAAATAAAGATAGAATTT-TACT-T
*
1125538 A-ATTTAAACTCCTAAA
1 AGATTTAAACTCTTAAA
1125554 GATATGATCC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 4 0.09
37 21 0.45
38 22 0.47
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.36
Consensus pattern (38 bp):
AGATTTAAACTCTTAAAAATAAAGATAGAATTTTACTT
Found at i:1126129 original size:24 final size:23
Alignment explanation
Indices: 1126102--1126209 Score: 95
Period size: 24 Copynumber: 4.9 Consensus size: 23
1126092 CTTTACATTT
1126102 TTATTATTACTATTATATTTATTA
1 TTATTATTACTATTATATTTA-TA
* * *
1126126 TTATTTTTACTATTATATTTTTC
1 TTATTATTACTATTATATTTATA
*
1126149 TT-TTATT-CTACT-TATTTATA
1 TTATTATTACTATTATATTTATA
1126169 TTATATATGTA-TATT-T-TTTATA
1 TTAT-TAT-TACTATTATATTTATA
*
1126191 TT-TTATTATTATTATATTT
1 TTATTATTACTATTATATTT
1126210 TTTACTTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.03
20 15 0.22
21 7 0.10
22 18 0.26
23 8 0.12
24 19 0.28
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.67
Consensus pattern (23 bp):
TTATTATTACTATTATATTTATA
Found at i:1126219 original size:25 final size:27
Alignment explanation
Indices: 1126161--1126213 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 27
1126151 TTATTCTACT
1126161 TATTTATATTATATATGTATATTTTTTA
1 TATTT-TATTATATATGTATATTTTTTA
1126189 TATTTTATTAT-TAT-TATATTTTTTA
1 TATTTTATTATATATGTATATTTTTTA
1126214 CTTTTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 11 0.44
26 3 0.12
27 6 0.24
28 5 0.20
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (27 bp):
TATTTTATTATATATGTATATTTTTTA
Found at i:1126231 original size:64 final size:59
Alignment explanation
Indices: 1126088--1126231 Score: 130
Period size: 63 Copynumber: 2.3 Consensus size: 59
1126078 TATATATTTA
*
1126088 TTTTCTTTACATTTTTATTATTACTATTATATTTATTATTATTTTTACTATTATATTTTTCT
1 TTTTCTTT-C-TTTTTA-TATTAATATTATATTTATTATTATTTTTACTATTATATTTTTCT
* * *
1126150 TTTAT-TCTACTTATTTATATTATATATGTATATTTTTTA-TATTTTATTATTATTATATTTTTT
1 TTT-TCT-TTCTT-TTTATATTA-ATAT-TATATTTATTATTA-TTT-TTACTATTATA-TTTTT
1126213 ACT
58 -CT
1126216 TTTTCTTTCTTTTTAT
1 TTTTCTTTCTTTTTAT
1126232 TATTCTTTTA
Statistics
Matches: 67, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
61 7 0.10
62 14 0.21
63 15 0.22
64 15 0.22
65 10 0.15
66 6 0.09
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.69
Consensus pattern (59 bp):
TTTTCTTTCTTTTTATATTAATATTATATTTATTATTATTTTTACTATTATATTTTTCT
Found at i:1126270 original size:11 final size:10
Alignment explanation
Indices: 1126180--1126270 Score: 60
Period size: 11 Copynumber: 8.5 Consensus size: 10
1126170 TATATATGTA
1126180 TATTTTTTA-
1 TATTTTTTAT
1126189 TATTTTATTAT
1 TATTTT-TTAT
*
1126200 TATTATATTTTT
1 TATT-T-TTTAT
* *
1126212 TACTTTTTCT
1 TATTTTTTAT
1126222 T-TCTTTTTAT
1 TAT-TTTTTAT
1126232 TATTCTTTTAT
1 TATT-TTTTAT
*
1126243 TATTACTTGTAT
1 TATT--TTTTAT
1126255 TATTTTTGTAT
1 TATTTTT-TAT
1126266 TATTT
1 TATTT
1126271 ATTTTGTTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
9 6 0.09
10 18 0.27
11 24 0.36
12 17 0.26
13 1 0.02
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:1126410 original size:25 final size:24
Alignment explanation
Indices: 1126377--1126449 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 24
1126367 AAGTGCTATA
1126377 TTTTA-TAATATTATACATATATT
1 TTTTATTAATATTATACATATATT
1126400 TTTCTATTAAT-TT-T-C-TATATT
1 TTT-TATTAATATTATACATATATT
*
1126421 TTTTATT-ATCATTATATTATATATT
1 TTTTATTAAT-ATTATA-CATATATT
1126446 TTTT
1 TTTT
1126450 CTTTTTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
19 2 0.05
20 4 0.10
21 11 0.27
22 2 0.05
23 4 0.10
24 4 0.10
25 14 0.34
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATTAATATTATACATATATT
Found at i:1126774 original size:9 final size:9
Alignment explanation
Indices: 1126729--1126883 Score: 51
Period size: 9 Copynumber: 17.1 Consensus size: 9
1126719 TCTTTTCGTC
*
1126729 ATTTAATTT
1 ATTTATTTT
*
1126738 A-TTAATTT
1 ATTTATTTT
*
1126746 ATATATATTT
1 ATTTAT-TTT
*
1126756 ACTT-TTTT
1 ATTTATTTT
1126764 ATTTATTTT
1 ATTTATTTT
1126773 ATATATATATATT
1 AT-T-TAT-T-TT
*
1126786 ATTCGTACTTT
1 ATT--TATTTT
*
1126797 GT-TATTATT
1 ATTTATT-TT
1126806 ATTT-TGTTT
1 ATTTAT-TTT
1126815 ATTT-TGTTT
1 ATTTAT-TTT
1126824 ATTTATTTT
1 ATTTATTTT
1126833 ATTTATTTT
1 ATTTATTTT
*
1126842 CTTT-TTCTT
1 ATTTATT-TT
* *
1126851 TTTTA-TAT
1 ATTTATTTT
*
1126859 ATATATTTT
1 ATTTATTTT
1126868 A-TTA-TTT
1 ATTTATTTT
1126875 ATTT-TTTT
1 ATTTATTTT
1126883 A
1 A
1126884 CTTACTATTT
Statistics
Matches: 112, Mismatches: 17, Indels: 35
0.68 0.10 0.21
Matches are distributed among these distances:
7 4 0.04
8 31 0.28
9 53 0.47
10 9 0.08
11 6 0.05
12 3 0.03
13 6 0.05
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (9 bp):
ATTTATTTT
Found at i:1126830 original size:13 final size:13
Alignment explanation
Indices: 1126729--1126883 Score: 63
Period size: 13 Copynumber: 11.8 Consensus size: 13
1126719 TCTTTTCGTC
* *
1126729 ATTTAATTTATTA
1 ATTTTATTTATTT
*
1126742 ATTTATATATATTT
1 ATTT-TATTTATTT
*
1126756 ACTTT-TTTATTT
1 ATTTTATTTATTT
* *
1126768 ATTTTATATATAT
1 ATTTTATTTATTT
*
1126781 ATATTATTCGTACTTT
1 ATTTTATT--TA-TTT
*
1126797 GTTATTA-TTATTT
1 ATT-TTATTTATTT
*
1126810 -TGTTTATTTTGTTT
1 AT-TTTA-TTTATTT
1126824 A-TTTATTTTATTT
1 ATTTTA-TTTATTT
*
1126837 ATTTTCTTT-TTCT
1 ATTTTATTTATT-T
* * *
1126850 TTTTTATATATAT
1 ATTTTATTTATTT
1126863 ATTTTA-TTATTT
1 ATTTTATTTATTT
1126875 ATTTT-TTTA
1 ATTTTATTTA
1126884 CTTACTATTT
Statistics
Matches: 105, Mismatches: 23, Indels: 29
0.67 0.15 0.18
Matches are distributed among these distances:
12 28 0.27
13 48 0.46
14 20 0.19
15 2 0.02
16 4 0.04
17 3 0.03
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (13 bp):
ATTTTATTTATTT
Found at i:1126854 original size:22 final size:22
Alignment explanation
Indices: 1126804--1126883 Score: 67
Period size: 22 Copynumber: 3.5 Consensus size: 22
1126794 TTTGTTATTA
* *
1126804 TTATTTTGTTTATTTTGTTTAT
1 TTATTTTATTTATTTTCTTTAT
1126826 TTATTTTATTTATTTTCTTT-T
1 TTATTTTATTTATTTTCTTTAT
*
1126847 TCTTTTTTATATATATATTT-TATTAT
1 T-TATTTTAT-T-TAT-TTTCT-TTAT
1126873 TTATTTT-TTTA
1 TTATTTTATTTA
1126884 CTTACTATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
21 2 0.04
22 27 0.56
23 2 0.04
24 5 0.10
25 10 0.21
26 2 0.04
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (22 bp):
TTATTTTATTTATTTTCTTTAT
Found at i:1126879 original size:27 final size:27
Alignment explanation
Indices: 1126745--1126881 Score: 70
Period size: 27 Copynumber: 5.0 Consensus size: 27
1126735 TTTATTAATT
*
1126745 TATATATA-TTTACTTTTTTATTTATTT-
1 TATATATATTTTA-TTATTTATTT-TTTA
* *
1126772 TATATATA-TATATTATTCGTACTTTGTTA
1 TATATATATTTTATTATT--TA-TTTTTTA
* *
1126801 T-TAT-TATTTTGTTTATTTTGTTTATTTA
1 TATATATATTTT-ATTA-TTTATTT-TTTA
* * * *
1126829 TTTTATTTATTTTCTT-TTTCTTTTTTA
1 -TATATATATTTTATTATTTATTTTTTA
1126856 TATATATATTTTATTATTTATTTTTT
1 TATATATATTTTATTATTTATTTTTT
1126882 TACTTACTAT
Statistics
Matches: 85, Mismatches: 13, Indels: 24
0.70 0.11 0.20
Matches are distributed among these distances:
26 16 0.19
27 29 0.34
28 19 0.22
29 8 0.09
30 7 0.08
31 6 0.07
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.71
Consensus pattern (27 bp):
TATATATATTTTATTATTTATTTTTTA
Found at i:1128871 original size:2 final size:2
Alignment explanation
Indices: 1128864--1128906 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1128854 TTTTATTCTT
1128864 TA TA TA TA TA TA 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
1128906 T
1 T
1128907 TAGAACTCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1144002 original size:277 final size:278
Alignment explanation
Indices: 1143527--1144049 Score: 863
Period size: 277 Copynumber: 1.9 Consensus size: 278
1143517 TAATGTCATG
*
1143527 ATTACTATTATTCATGTTATATGACTTCATATTCTTCAATGACACAGATTTAGATACCATTTGAT
1 ATTACTATTATTCATGTTATATGACTTCATATTCTTCAATGACACAGATTTAGATACCATTTGAC
*
1143592 CTCTCCCCCTACTCTCACTTGCAACAGTTTCTTTAACCAATCCTTCATTGCGGCATGTACCTTTC
66 CTCTCCCCCTACTCT-ACTTGCAACAGTTTCTTTAACCAATCCTTCATTGCGGCATGTACCTTTA
* *
1143657 TTGAGCTGTTTGACATCCTCTTTTAGGGTCGTAGTGGAGAATGATTTTGATTTAAAATGAAGTCC
130 TTGAGCTGTTGGACATCCTCTTTTAGGGTCGTAGCGGAGAATGATTTTGATTTAAAATGAAGTCC
* *
1143722 TGCAACGCCAGAAATAAGAACTTTTTAAGTTAGTCGATGAGAACTACATGTAACACTACGACGTA
195 TGCAACGCCAGAAATAAGAACTTTTTAAATTAGTCAATGAGAACTACATGTAACACTACGACGTA
1143787 ATTTAACGTCATGATTACT
260 ATTTAACGTCATGATTACT
*
1143806 ATTAGTATTATTCATGTTATATGACTTCATATTCTTCAATGACACAGATTTAGATACCATTTGAC
1 ATTACTATTATTCATGTTATATGACTTCATATTCTTCAATGACACAGATTTAGATACCATTTGAC
* * *
1143871 CTCTCCCCTTACTCT-CTTGCAGCAGTTTCTTTAACCAATCCTTCATTGCGGCATTTACCTTTAT
66 CTCTCCCCCTACTCTACTTGCAACAGTTTCTTTAACCAATCCTTCATTGCGGCATGTACCTTTAT
* *
1143935 TGAGCTGTTGGACATCCTCTTTTAGGGTTGTCA-CGGAGAATGATTTTGATTTAAAAAT-AATTC
131 TGAGCTGTTGGACATCCTCTTTTAGGGTCGT-AGCGGAGAATGATTTTGATTT-AAAATGAAGTC
* * *
1143998 CTGCAATGCCAGAAATGAGAACTTTTTAAATTAGTCAATGAGAACTATATGT
194 CTGCAACGCCAGAAATAAGAACTTTTTAAATTAGTCAATGAGAACTACATGT
1144050 TTAACATTCT
Statistics
Matches: 227, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
277 144 0.63
278 6 0.03
279 77 0.34
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (278 bp):
ATTACTATTATTCATGTTATATGACTTCATATTCTTCAATGACACAGATTTAGATACCATTTGAC
CTCTCCCCCTACTCTACTTGCAACAGTTTCTTTAACCAATCCTTCATTGCGGCATGTACCTTTAT
TGAGCTGTTGGACATCCTCTTTTAGGGTCGTAGCGGAGAATGATTTTGATTTAAAATGAAGTCCT
GCAACGCCAGAAATAAGAACTTTTTAAATTAGTCAATGAGAACTACATGTAACACTACGACGTAA
TTTAACGTCATGATTACT
Found at i:1148797 original size:22 final size:20
Alignment explanation
Indices: 1148748--1148788 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1148738 TTTTTTCTGA
1148748 AAATATAA-TTTTAACTAAT
1 AAATATAATTTTTAACTAAT
1148767 AAATATAATTGTTTAA-TAAT
1 AAATATAATT-TTTAACTAAT
1148787 AA
1 AA
1148789 CAATATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATATAATTTTTAACTAAT
Found at i:1149446 original size:2 final size:2
Alignment explanation
Indices: 1149435--1149471 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1149425 ACGTTAACTC
1149435 TA TA -A TA 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
1149472 ACTAAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1151716 original size:21 final size:22
Alignment explanation
Indices: 1151692--1151740 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1151682 GGTGGTATAG
1151692 GTACTCCT-CCAAGTAGTACAA
1 GTACTCCTACCAAGTAGTACAA
**
1151713 GTACT-CTAGTAAGTAGTACAA
1 GTACTCCTACCAAGTAGTACAA
*
1151734 ATACTCC
1 GTACTCC
1151741 AAGAATGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 20 0.87
22 1 0.04
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (22 bp):
GTACTCCTACCAAGTAGTACAA
Found at i:1158904 original size:41 final size:41
Alignment explanation
Indices: 1158754--1159116 Score: 410
Period size: 41 Copynumber: 8.9 Consensus size: 41
1158744 TTTTTAGAAT
* * * * * *
1158754 AAACGCCGCTAAAGA-TTGTACATTAGCGGCATTTGTATAAA
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT-AC
* * * *
1158795 AAACGCCG-TCAAAGAAT-GTACTTTAGTGGAGTTTGTATAA
1 AAACGCCGCT-AAAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
1158835 AAACGCCGCTAAAGACT-ATACTTTAGTGGCGTTTTTAGAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
** * *
1158875 AAACGCTACTATAGACTCGTACTTTAGTGGCGTTTTTAGAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
1158916 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTGTAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
1158957 AAACGCCGCTATAGACTCATACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
1158998 AAACGCCGCTACAGACTCGTACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* * * *
1159039 AAACGTCGCTAAAGACTCATACTTTAATGGCGTTTGTGTTTAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTT-T-TATAC
* *
1159082 AAACGCCGCTAAAGACTTGTATTTTAGTGGCGTTT
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTT
1159117 GTAAAAGACT
Statistics
Matches: 282, Mismatches: 34, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
40 49 0.17
41 197 0.70
42 2 0.01
43 34 0.12
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (41 bp):
AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:1162005 original size:13 final size:13
Alignment explanation
Indices: 1161973--1162012 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1161963 ACAAGCTGAG
1161973 GTTTTCTATCTCC
1 GTTTTCTATCTCC
*
1161986 G--TT-TATCTCT
1 GTTTTCTATCTCC
1161996 GTTTTCTATCTCC
1 GTTTTCTATCTCC
1162009 GTTT
1 GTTT
1162013 ACCTTTTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 7 0.32
11 2 0.09
12 2 0.09
13 11 0.50
ACGTcount: A:0.07, C:0.25, G:0.10, T:0.57
Consensus pattern (13 bp):
GTTTTCTATCTCC
Found at i:1162954 original size:128 final size:129
Alignment explanation
Indices: 1162734--1163046 Score: 352
Period size: 128 Copynumber: 2.4 Consensus size: 129
1162724 TAATGAGCTT
* ** *
1162734 TTTTGCGGCGTTTGTATCA-AAAAACGCCGCTATAGATATGAGATTTTGCGGCGTTTGTATCCAA
1 TTTTGCGGCGTTTGT-TCACAAAAACGCCGCTATAGATCTGACCTATTGCGGCGTTTGTATCCAA
* * **
1162798 AAACGCCGCTATAGATATGACCATTTGCGGTGTTTATTCCAAAAACGCCGCTATAGATC-TGACC
65 AAACGCCGCTATAGATATAACCATTTGCGGTGTTTATTCCAAAAACGCCGCTAAAGATCAACACC
* *
1162862 TTTTGCGGCGTTTGTTCACAAAAACGCCACTATAGATCTGACCTGTTGCGGCGTTTGT-TCCAAA
1 TTTTGCGGCGTTTGTTCACAAAAACGCCGCTATAGATCTGACCTATTGCGGCGTTTGTATCCAAA
* * ** * *
1162926 AACGCCGCTA-A-ATATCAACACCTATTGCGGTGTTTGTTGGACAAACGCCGCTAAATATCAACA
66 AACGCCGCTATAGATAT-AAC-CAT-TTGCGGTGTTTATTCCAAAAACGCCGCTAAAGATCAACA
1162989 CC
128 CC
* * *
1162991 TATTGCGGCGTTTG-TC-CAACAAACGCCGCTATATATCGTTACCTATTGCGGCGTTT
1 TTTTGCGGCGTTTGTTCACAA-AAACGCCGCTATAGATC-TGACCTATTGCGGCGTTT
1163047 TTTGTTACCA
Statistics
Matches: 158, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
125 4 0.03
126 3 0.02
127 24 0.15
128 95 0.60
129 32 0.20
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (129 bp):
TTTTGCGGCGTTTGTTCACAAAAACGCCGCTATAGATCTGACCTATTGCGGCGTTTGTATCCAAA
AACGCCGCTATAGATATAACCATTTGCGGTGTTTATTCCAAAAACGCCGCTAAAGATCAACACC
Found at i:1162972 original size:85 final size:83
Alignment explanation
Indices: 1162735--1163046 Score: 288
Period size: 85 Copynumber: 3.7 Consensus size: 83
1162725 AATGAGCTTT
* * * * ** *
1162735 TTTGCGGCGTTTGTATCAAAAAACGCCGCTATAGATATGAGATTTTGCGGCGTTTGTATC-CAAA
1 TTTGCGGCGTTTGT-TCCAAAAACGCCGCTATATATCTCACCTATTGCGGCGTTTGT-TCAC-AA
*
1162799 AACGCCGCTATAGATATGACC
63 AACGCCGCTATAGATCTGACC
* * * * *
1162820 ATTTGCGGTGTTTATTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCACAAAA
1 -TTTGCGGCGTTTGTTCCAAAAACGCCGCTATATATCTCACCTATTGCGGCGTTTGTTCAC-AAA
*
1162885 ACGCCACTATAGATCTGACC
64 ACGCCGCTATAGATCTGACC
* * * *
1162905 TGTTGCGGCGTTTGTTCCAAAAACGCCGCTAAATATCAACACCTATTGCGGTGTTTGTTGGAC-A
1 T-TTGCGGCGTTTGTTCCAAAAACGCCGCTATATATC-TCACCTATTGCGGCGTTTGTT-CACAA
* * **
1162969 AACGCCGCTAAATATCAACACC
63 AACGCCGCTATAGATC-TGACC
*
1162991 TATTGCGGCGTTTG-TCCAACAAACGCCGCTATATATCGTTACCTATTGCGGCGTTT
1 T-TTGCGGCGTTTGTTCCAA-AAACGCCGCTATATATC-TCACCTATTGCGGCGTTT
1163047 TTTGTTACCA
Statistics
Matches: 192, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
84 3 0.02
85 111 0.58
86 76 0.40
87 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (83 bp):
TTTGCGGCGTTTGTTCCAAAAACGCCGCTATATATCTCACCTATTGCGGCGTTTGTTCACAAAAC
GCCGCTATAGATCTGACC
Found at i:1163003 original size:86 final size:88
Alignment explanation
Indices: 1162902--1163064 Score: 224
Period size: 86 Copynumber: 1.9 Consensus size: 88
1162892 TATAGATCTG
* *
1162902 ACCTGTTGCGGCGTTTGTTCCAA-AAACGCCGCTAAATATCAACACCTATTGCGGTGTTTGTTG-
1 ACCTATTGCGGCGTTTG-TCCAACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGT
1162965 GA-CAAACGCCGCTAAATATCAAC
65 GACCAAACGCCGCTAAATATCAAC
* *** * *
1162988 ACCTATTGCGGCGTTTGTCCAACAAACGCCGCTATATATCGTTACCTATTGCGGCGTTTTTTGTT
1 ACCTATTGCGGCGTTTGTCCAACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGTG
1163053 ACCAAACGCCGC
66 ACCAAACGCCGC
1163065 GAACTTTAGC
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
85 5 0.08
86 50 0.76
87 1 0.02
88 10 0.15
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (88 bp):
ACCTATTGCGGCGTTTGTCCAACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTTGTG
ACCAAACGCCGCTAAATATCAAC
Found at i:1163027 original size:43 final size:43
Alignment explanation
Indices: 1162736--1163046 Score: 319
Period size: 43 Copynumber: 7.3 Consensus size: 43
1162726 ATGAGCTTTT
* ** *
1162736 TTGCGGCGTTTGTATCAAAAAACGCCGCTATAGAT-ATGAGATT
1 TTGCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCATGACCTA
1162779 TTGCGGCGTTTGTATCCAAAAACGCCGCTATAGAT-ATGACC-A
1 TTGCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCATGACCTA
* * *
1162821 TTTGCGGTGTTTATTCCAAAAACGCCGCTATAGATC-TGACCTT
1 -TTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCATGACCTA
* *
1162864 TTGCGGCGTTTGTTCACAAAAACGCCACTATAGATC-TGACCTG
1 TTGCGGCGTTTGTTC-CAAAAACGCCGCTATAGATCATGACCTA
* * **
1162907 TTGCGGCGTTTGTTCCAAAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCATGACCTA
* ** * * * **
1162950 TTGCGGTGTTTGTTGGACAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCATGACCTA
* * *
1162993 TTGCGGCGTTTG-TCCAACAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTTCCAA-AAACGCCGCTATAGATCATGACCTA
1163036 TTGCGGCGTTT
1 TTGCGGCGTTT
1163047 TTTGTTACCA
Statistics
Matches: 233, Mismatches: 29, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
42 58 0.25
43 175 0.75
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (43 bp):
TTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCATGACCTA
Found at i:1163535 original size:9 final size:8
Alignment explanation
Indices: 1163512--1163538 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1163502 CTTTAAAATA
1163512 TAATTTTT
1 TAATTTTT
1163520 TAATTTTT
1 TAATTTTT
1163528 TAATTTTT
1 TAATTTTT
1163536 TAA
1 TAA
1163539 CTAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TAATTTTT
Found at i:1168344 original size:2 final size:2
Alignment explanation
Indices: 1168337--1168363 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1168327 AGTAGGCGTT
1168337 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1168364 GTTTGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1175554 original size:2 final size:2
Alignment explanation
Indices: 1175547--1175584 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1175537 GCCGATAATG
1175547 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
1175585 TCAAGCTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1179365 original size:20 final size:20
Alignment explanation
Indices: 1179332--1179380 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1179322 TACACTTCAT
* *
1179332 TTCCACCATGAATTACATGAA
1 TTCCACCTTTAATTACAT-AA
*
1179353 TT-CACCTTTAATTCCATAA
1 TTCCACCTTTAATTACATAA
1179372 TTCCACCTT
1 TTCCACCTT
1179381 AAACCCTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 18 0.75
21 2 0.08
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.37
Consensus pattern (20 bp):
TTCCACCTTTAATTACATAA
Found at i:1185030 original size:15 final size:16
Alignment explanation
Indices: 1185000--1185049 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
1184990 AATATTAAAA
1185000 ATAATTATTATATATAT
1 ATAA-TATTATATATAT
1185017 ATAATATT-TATATAT
1 ATAATATTATATATAT
* *
1185032 TTAAT-TTAAATATAT
1 ATAATATTATATATAT
1185047 ATA
1 ATA
1185050 TCCGGCCCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 19 0.66
16 4 0.14
17 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATAATATTATATATAT
Done.