Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 170 of 186
Found at i:56535022 original size:34 final size:34
Alignment explanation
Indices: 56534984--56535050 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
56534974 TGCATTTGCA
56534984 TTACACCACATCATATGCATTCAAAGTTATAGAT
1 TTACACCACATCATATGCATTCAAAGTTATAGAT
* *
56535018 TTACATCATATCATATGCATTCAAAGTTATAGA
1 TTACACCACATCATATGCATTCAAAGTTATAGA
56535051 AAGACCCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (34 bp):
TTACACCACATCATATGCATTCAAAGTTATAGAT
Found at i:56543449 original size:205 final size:205
Alignment explanation
Indices: 56543096--56543606 Score: 860
Period size: 205 Copynumber: 2.5 Consensus size: 205
56543086 TAGGCCGCAG
* ** * * *
56543096 CATAGCAGATTTGGCCTTCAGATGTTTATACTGAAGTAAGATCCAAAATGATTTGGCATCCTTGT
1 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAG-GAGATCCAAGATGATTTGGCATTCTTGT
*
56543161 GTTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
65 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATC
* *
56543226 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTAGCATCTCCACTTTGACG
130 TAAGATGATTTGGCATCTCTATATTGTCAGAGAACAAATCAAAGTCTAGCATCTCCACTTCGACG
56543291 GGGAGCAGATA
195 GGGAGCAGATA
56543302 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGGAGATCCAAGATGATTTGGCATTCTTGTG
1 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGGAGATCCAAGATGATTTGGCATTCTTGTG
* *
56543367 CTTACAAGGAGCGAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCT
66 CTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCT
* * * *
56543432 AAGATGATTTGGCATCTCTATATTTTCAGAGTACAAATCGAAGTCTGGCATCTCCACTTCGACGG
131 AAGATGATTTGGCATCTCTATATTGTCAGAGAACAAATCAAAGTCTAGCATCTCCACTTCGACGG
56543497 GGAGCAGATA
196 GGAGCAGATA
56543507 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGGAGATCCAAGATGATTTGGCATTCTTGTG
1 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGGAGATCCAAGATGATTTGGCATTCTTGTG
* *
56543572 CTTACAAGGAACAAATCGAGGACATAGCAGATTTG
66 CTTACAAGGAACAAATCGAAGACATAGCTGATTTG
56543607 ACTCTCAGAT
Statistics
Matches: 286, Mismatches: 19, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
205 253 0.88
206 33 0.12
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (205 bp):
CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGGAGATCCAAGATGATTTGGCATTCTTGTG
CTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCT
AAGATGATTTGGCATCTCTATATTGTCAGAGAACAAATCAAAGTCTAGCATCTCCACTTCGACGG
GGAGCAGATA
Found at i:56543686 original size:288 final size:288
Alignment explanation
Indices: 56543339--56544051 Score: 1088
Period size: 289 Copynumber: 2.5 Consensus size: 288
56543329 ATACTGAAGG
* * *
56543339 AGATCCAAGATGATTTGGCATTCTTGTGCTTACAAGGAGCGAATCGAAGACATAGCTGATTTGGC
1 AGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAA-ACATAGCTGATTTGGC
* * *
56543404 TTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTTTCAGAGTACAAA
65 TTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAA
* * * * *
56543469 TCGAAGTCTGGCATCTCCA-CTTCGACGG-GGAGCAGATACATAGCAGATCTCACCTTCAGATGT
130 TCGAAGTCTGGCATCTCCATATTCGACGGAGG-GCAGACACATAGCAAATCTAACCTTCAGATAT
56543532 TTATACTGAAGGAGATCCAAGATGATTTGGCATTCTTGTGCTTACAAGGAACAAATCGAGGACAT
194 TTATACTGAAGGAGATCCAAGATGATTTGGCATTCTTGTGCTTACAAGGAACAAATCGAGGACAT
* *
56543597 AGCAGATTTGACTCTCAGATGTTCTCAAGC
259 AGAAGATTTGACTCTCAGATGTTCTCAAAC
* *
56543627 AGATCCAAGATGATTTGGTATCCTTGTGTTTACAAGGAACAAATCGAAACCATAGCTGATTTGGC
1 AGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAA-CATAGCTGATTTGGC
* * *
56543692 TTTCACGTGTTTACGTTGAAGTAAGTCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAA
65 TTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAA
* *
56543757 TCGAAGTTTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAAATCTAACCTTTAGATATT
130 TCGAAGTCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAAATCTAACCTTCAGATATT
* * *
56543822 TATACTGAAGTAGATCCAAGATGATTTGGCCTTCTTGTGTTTACAAGGAACAAATCGAGGACATA
195 TATACTGAAGGAGATCCAAGATGATTTGGCATTCTTGTGCTTACAAGGAACAAATCGAGGACATA
* *
56543887 GAAGATTTGACTCTCAGATGTTCTTAAAT
260 GAAGATTTGACTCTCAGATGTTCTCAAAC
* *
56543916 AGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCAAAAACATAGTTGATTTGGC
1 AGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATC-GAAACATAGCTGATTTGGC
* * * *
56543981 TTTCGCGTGCTTACGCTGAAGCAAATCTAAGATGATTTCGCATCTCTGTATTGTCAGAGAACAAA
65 TTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAA
*
56544046 TTGAAG
130 TCGAAG
56544052 AAGTAGATTT
Statistics
Matches: 385, Mismatches: 36, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
287 1 0.00
288 135 0.35
289 244 0.63
290 5 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (288 bp):
AGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAACATAGCTGATTTGGCT
TTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAAT
CGAAGTCTGGCATCTCCATATTCGACGGAGGGCAGACACATAGCAAATCTAACCTTCAGATATTT
ATACTGAAGGAGATCCAAGATGATTTGGCATTCTTGTGCTTACAAGGAACAAATCGAGGACATAG
AAGATTTGACTCTCAGATGTTCTCAAAC
Found at i:56547334 original size:31 final size:31
Alignment explanation
Indices: 56547296--56547358 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
56547286 CAACAAAAAG
56547296 TAAAAGTTTATTATTCATAGGAGGCAATAAC
1 TAAAAGTTTATTATTCATAGGAGGCAATAAC
56547327 TAAAAGTTTATTATTCATAGGAGGCAATAAC
1 TAAAAGTTTATTATTCATAGGAGGCAATAAC
56547358 T
1 T
56547359 CATTAACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (31 bp):
TAAAAGTTTATTATTCATAGGAGGCAATAAC
Found at i:56550809 original size:12 final size:12
Alignment explanation
Indices: 56550792--56550816 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56550782 AAAAAATATT
56550792 ATAATAATCCTA
1 ATAATAATCCTA
56550804 ATAATAATCCTA
1 ATAATAATCCTA
56550816 A
1 A
56550817 ATTTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATAATCCTA
Found at i:56556152 original size:42 final size:42
Alignment explanation
Indices: 56556090--56556252 Score: 168
Period size: 42 Copynumber: 3.9 Consensus size: 42
56556080 TACCATACCA
* * * **
56556090 ATGCCATATCCCAAATATGGTCTTAC-TGAAATCTTGTATCG
1 ATGCCATAGCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
56556131 ATGCCAATAGCCCAGCTATGGTCTTACACGAAGTCTCATATTG
1 ATGCC-ATAGCCCAGATATGGTCTTACACGAAATCTCATATCG
* **
56556174 ATGCCATATCCCAGATATGGTCTTACACGAAGCCTCATATCG
1 ATGCCATAGCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
56556216 ACT-TCATATCCCAGATATGGTCTTACACGTAATCTCA
1 A-TGCCATAGCCCAGATATGGTCTTACACGAAATCTCA
56556253 GTAACCCTAA
Statistics
Matches: 103, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
41 5 0.05
42 82 0.80
43 16 0.16
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:56562357 original size:27 final size:27
Alignment explanation
Indices: 56562310--56562377 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
56562300 TTTCCTTCGT
*
56562310 AGTTCACCATGTA-TACAATTCTTTTAA
1 AGTTCACCATG-AGTACAATTCGTTTAA
*
56562337 AGTTCACCATGAGTACCATTCGTTTAA
1 AGTTCACCATGAGTACAATTCGTTTAA
56562364 AGTTCACCATGAGT
1 AGTTCACCATGAGT
56562378 TAGAGTTCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (27 bp):
AGTTCACCATGAGTACAATTCGTTTAA
Found at i:56562528 original size:27 final size:27
Alignment explanation
Indices: 56562498--56562585 Score: 104
Period size: 27 Copynumber: 3.3 Consensus size: 27
56562488 CAAGATTTTT
56562498 CACAAAGATTTTCATTTAATGCTTTGC
1 CACAAAGATTTTCATTTAATGCTTTGC
** * * * **
56562525 CACAAAGGCTTTCTTTTCATGGTTCAC
1 CACAAAGATTTTCATTTAATGCTTTGC
*
56562552 CACAAAGATTTTCATTTAATACTTTGC
1 CACAAAGATTTTCATTTAATGCTTTGC
56562579 CACAAAG
1 CACAAAG
56562586 GCTTTCTTTT
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (27 bp):
CACAAAGATTTTCATTTAATGCTTTGC
Found at i:56562528 original size:54 final size:54
Alignment explanation
Indices: 56562470--56562591 Score: 156
Period size: 54 Copynumber: 2.3 Consensus size: 54
56562460 CTATTTTTTA
*** *
56562470 CCAC-AAGGCTATTCCTTCCAAGATTTTTCACAAAGATTTTCATTTAATGCTTTG
1 CCACAAAGGCT-TTCCTTCCAAGATTCACCACAAAGATTTTCATTTAATACTTTG
* * * *
56562524 CCACAAAGGCTTTCTTTTCATGGTTCACCACAAAGATTTTCATTTAATACTTTG
1 CCACAAAGGCTTTCCTTCCAAGATTCACCACAAAGATTTTCATTTAATACTTTG
56562578 CCACAAAGGCTTTC
1 CCACAAAGGCTTTC
56562592 TTTTTATGTC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
54 53 0.90
55 6 0.10
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (54 bp):
CCACAAAGGCTTTCCTTCCAAGATTCACCACAAAGATTTTCATTTAATACTTTG
Found at i:56569884 original size:31 final size:33
Alignment explanation
Indices: 56569819--56569889 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
56569809 ATGAAAAATT
*
56569819 ATTAAATTAATAATTTATTTTAATTATACTTAA
1 ATTAAATTAATAATTTATTCTAATTATACTTAA
* *
56569852 ATTAAATTATTAATTT-TTCTATTTA-ACTTAA
1 ATTAAATTAATAATTTATTCTAATTATACTTAA
56569883 ATTAAAT
1 ATTAAAT
56569890 ATTTTAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 13 0.37
32 7 0.20
33 15 0.43
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (33 bp):
ATTAAATTAATAATTTATTCTAATTATACTTAA
Found at i:56569924 original size:9 final size:9
Alignment explanation
Indices: 56569910--56569944 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
56569900 ATAATAAATT
56569910 CTAAATATA
1 CTAAATATA
*
56569919 CTAAAT-TT
1 CTAAATATA
56569927 CTAAATATA
1 CTAAATATA
56569936 CTAAATATA
1 CTAAATATA
56569945 ATATATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (9 bp):
CTAAATATA
Found at i:56569930 original size:17 final size:17
Alignment explanation
Indices: 56569904--56569941 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
56569894 TAATAAATAA
56569904 TAAA-TTCTAAATATAC
1 TAAATTTCTAAATATAC
56569920 TAAATTTCTAAATATAC
1 TAAATTTCTAAATATAC
56569937 TAAAT
1 TAAAT
56569942 ATAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTCTAAATATAC
Found at i:56569959 original size:26 final size:26
Alignment explanation
Indices: 56569937--56570037 Score: 89
Period size: 27 Copynumber: 3.8 Consensus size: 26
56569927 CTAAATATAC
*
56569937 TAAATATAATATATATAATAATAATA
1 TAAAAATAATATATATAATAATAATA
*
56569963 TATAAA-AATAGTATATAAATAGATAATA
1 TAAAAATAATA-TATAT-AATA-ATAATA
56569991 TAAAAATAGATA-ATATAATAATAGATA
1 TAAAAATA-ATATATATAATAATA-ATA
* * * *
56570018 GAATAATAAAATAAATAATA
1 TAAAAATAATATATATAATA
56570038 TAGAAATATA
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
25 4 0.07
26 14 0.23
27 24 0.39
28 15 0.25
29 1 0.02
30 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (26 bp):
TAAAAATAATATATATAATAATAATA
Found at i:56569962 original size:15 final size:14
Alignment explanation
Indices: 56569930--56570087 Score: 96
Period size: 15 Copynumber: 10.9 Consensus size: 14
56569920 TAAATTTCTA
56569930 AATATACTAAAT-AT
1 AATATA-TAAATAAT
56569944 AATATATATAATAAT
1 AATATATA-AATAAT
56569959 AATATATAAA-AAT
1 AATATATAAATAAT
*
56569972 AGTATATAAATAGAT
1 AATATATAAATA-AT
*
56569987 AATATAAAAATAGAT
1 AATATATAAATA-AT
56570002 AATATA-ATAATAGAT
1 AATATATA-AATA-AT
56570017 AGA-ATAATAAAATAAAT
1 A-ATAT-AT-AAAT-AAT
*
56570034 AATATAGAAAT-AT
1 AATATATAAATAAT
* *
56570047 AGATTTATAAATCGA-
1 A-ATATATAAAT-AAT
*
56570062 AATATATTAAT-AT
1 AATATATAAATAAT
56570075 AATAATATAAATA
1 AAT-ATATAAATA
56570088 TTATTAATTA
Statistics
Matches: 118, Mismatches: 9, Indels: 33
0.74 0.06 0.21
Matches are distributed among these distances:
12 1 0.01
13 20 0.17
14 36 0.31
15 46 0.39
16 5 0.04
17 8 0.07
18 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (14 bp):
AATATATAAATAAT
Found at i:56569978 original size:28 final size:28
Alignment explanation
Indices: 56569930--56570013 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 28
56569920 TAAATTTCTA
* *
56569930 AATATACTAAATATAATATATATAATAAT
1 AATATA-TAAAAATAGTATATATAATAAT
56569959 AATATATAAAAATAGTATATA-AATAGAT
1 AATATATAAAAATAGTATATATAATA-AT
56569987 -A-ATATAAAAATAG-ATAATATAATAAT
1 AATATATAAAAATAGTAT-ATATAATAAT
56570013 A
1 A
56570014 GATAGAATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
25 2 0.04
26 17 0.35
27 9 0.18
28 15 0.31
29 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (28 bp):
AATATATAAAAATAGTATATATAATAAT
Found at i:56570011 original size:8 final size:8
Alignment explanation
Indices: 56569930--56570084 Score: 60
Period size: 8 Copynumber: 18.9 Consensus size: 8
56569920 TAAATTTCTA
*
56569930 AATATACT
1 AATATAAT
56569938 AA-AT-AT
1 AATATAAT
56569944 AATATATAT
1 AATATA-AT
56569953 AATAATAAT
1 AAT-ATAAT
*
56569962 -ATATAAA
1 AATATAAT
56569969 AATAGTATAT
1 AATA-TA-AT
56569979 AA-ATAGAT
1 AATATA-AT
56569987 AATATAA-
1 AATATAAT
56569994 AA-ATAGAT
1 AATATA-AT
56570002 AATATAAT
1 AATATAAT
*
56570010 AATA-GAT
1 AATATAAT
56570017 AGA-ATAAT
1 A-ATATAAT
*
56570025 AAAATAAAT
1 AATAT-AAT
56570034 AATATAGA-
1 AATATA-AT
56570042 AATATAGAT
1 AATATA-AT
*
56570051 -TTATAAAT
1 AATAT-AAT
*
56570059 CGAAATATATT
1 ---AATATAAT
56570070 AATATAAT
1 AATATAAT
56570078 AATATAA
1 AATATAA
56570085 ATATTATTAA
Statistics
Matches: 114, Mismatches: 11, Indels: 44
0.67 0.07 0.26
Matches are distributed among these distances:
6 6 0.05
7 16 0.14
8 56 0.49
9 25 0.22
10 6 0.05
11 2 0.02
12 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (8 bp):
AATATAAT
Found at i:56571044 original size:457 final size:457
Alignment explanation
Indices: 56570190--56571094 Score: 1720
Period size: 457 Copynumber: 2.0 Consensus size: 457
56570180 TTGTTATATA
*
56570190 ATTTCGATTGTTAATTGGTTTAGTAGTGGAATTTGATAAAATTGCCTTGAACTGAAGAAAGTATC
1 ATTTCGATTGTTAATTGGTTTAGTAGTGGAATTTGATAAAATTGCCCTGAACTGAAGAAAGTATC
*
56570255 TGTCCTAGCTCTGACCAAATATTCTTTCGTATCAAGAATCAAGAACGAAAATGCGGATATAGTCG
66 TGTCCTAGCTCTGACCAAACATTCTTTCGTATCAAGAATCAAGAACGAAAATGCGGATATAGTCG
56570320 AATGGTAAAATTTCTCTTTGCCAAGGAGAAGACGCGGGTTCGATTCCCGCTATCCGCCCAGGGCA
131 AATGGTAAAATTTCTCTTTGCCAAGGAGAAGACGCGGGTTCGATTCCCGCTATCCGCCCAGGGCA
56570385 ATGTATTTAAGATAAGAGGATAAAAGATTCGTTATAGTTGACTGTAAATAGTTGACTGGAATTGG
196 ATGTATTTAAGATAAGAGGATAAAAGATTCGTTATAGTTGACTGTAAATAGTTGACTGGAATTGG
*
56570450 AATATAATACACCCCCCTAAAAGAAAAAATGACTAGTTAATAGGGTCAAGTCTAATTTTTTTTGT
261 AATATAATACACCCCCCTAAAAGAAAAAATGACTAGTTAATAGGGTCAAGTATAATTTTTTTTGT
*
56570515 CAAAAAAATGTAATGTTGCGGGAACGGGATTTGAACCCATGACCTCAAGGTTATGAGCCTTGCGA
326 CAAAAAAATGTAATGTTGAGGGAACGGGATTTGAACCCATGACCTCAAGGTTATGAGCCTTGCGA
56570580 GCTACCAAACTGCTCTATCCCGCGATGAAAAGAAACCAAACTAATGGACAAACAAAGACCTATCC
391 GCTACCAAACTGCTCTATCCCGCGATGAAAAGAAACCAAACTAATGGACAAACAAAGACCTATCC
56570645 GC
456 GC
56570647 ATTTCGATTGTTAATTGGTTTAGTAGTGGAATTTGATAAAATTGCCCTGAACTGAAGAAAGTATC
1 ATTTCGATTGTTAATTGGTTTAGTAGTGGAATTTGATAAAATTGCCCTGAACTGAAGAAAGTATC
*
56570712 TGTCCTAGCTCTGACCAAACATTCTTTCGTATCAAGAATCAAGAACGAAAATGTGGATATAGTCG
66 TGTCCTAGCTCTGACCAAACATTCTTTCGTATCAAGAATCAAGAACGAAAATGCGGATATAGTCG
* * *
56570777 AATGGTAAAATTTCTCTTTGCCAAGGAGAAGACGCGGGTTTGATTCCTGCTATGCGCCCAGGGCA
131 AATGGTAAAATTTCTCTTTGCCAAGGAGAAGACGCGGGTTCGATTCCCGCTATCCGCCCAGGGCA
56570842 ATGTATTTAAGATAAGAGGATAAAAGATTCGTTATAGTTGACTGTAAATAGTTGACTGGAATTGG
196 ATGTATTTAAGATAAGAGGATAAAAGATTCGTTATAGTTGACTGTAAATAGTTGACTGGAATTGG
56570907 AATATAATACACCCCCCTAAAAGAAAAAATGACTAGTTAATAGGGTCAAGTATAATTTTTTTTGT
261 AATATAATACACCCCCCTAAAAGAAAAAATGACTAGTTAATAGGGTCAAGTATAATTTTTTTTGT
*
56570972 CAAAAAAATGTAATGTTGAGGGAACGGTATTTGAACCCATGACCTCAAGGTTATGAGCCTTGCGA
326 CAAAAAAATGTAATGTTGAGGGAACGGGATTTGAACCCATGACCTCAAGGTTATGAGCCTTGCGA
*
56571037 GCTACCAAACTGCTCTATCCTGCGATGAAAAGAAACCAAACTAATGGACAAACAAAGA
391 GCTACCAAACTGCTCTATCCCGCGATGAAAAGAAACCAAACTAATGGACAAACAAAGA
56571095 TTGAATGCAC
Statistics
Matches: 438, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
457 438 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (457 bp):
ATTTCGATTGTTAATTGGTTTAGTAGTGGAATTTGATAAAATTGCCCTGAACTGAAGAAAGTATC
TGTCCTAGCTCTGACCAAACATTCTTTCGTATCAAGAATCAAGAACGAAAATGCGGATATAGTCG
AATGGTAAAATTTCTCTTTGCCAAGGAGAAGACGCGGGTTCGATTCCCGCTATCCGCCCAGGGCA
ATGTATTTAAGATAAGAGGATAAAAGATTCGTTATAGTTGACTGTAAATAGTTGACTGGAATTGG
AATATAATACACCCCCCTAAAAGAAAAAATGACTAGTTAATAGGGTCAAGTATAATTTTTTTTGT
CAAAAAAATGTAATGTTGAGGGAACGGGATTTGAACCCATGACCTCAAGGTTATGAGCCTTGCGA
GCTACCAAACTGCTCTATCCCGCGATGAAAAGAAACCAAACTAATGGACAAACAAAGACCTATCC
GC
Found at i:56574295 original size:149 final size:149
Alignment explanation
Indices: 56574025--56574316 Score: 575
Period size: 149 Copynumber: 2.0 Consensus size: 149
56574015 ATTTATTATG
*
56574025 AGCCCAAACGATGGATTCAATAAGTTCTTGCCAATAACCACGTCCGCTGAATAGAAACATTAAAC
1 AGCCCAAACAATGGATTCAATAAGTTCTTGCCAATAACCACGTCCGCTGAATAGAAACATTAAAC
56574090 TAAAAGCCCATACAAAATGAGCACCTAAGAAAAGAAGGCCATATGCAGATAATGAAGAACCATAA
66 TAAAAGCCCATACAAAATGAGCACCTAAGAAAAGAAGGCCATATGCAGATAATGAAGAACCATAA
56574155 GACTGAATTACCTGGGATA
131 GACTGAATTACCTGGGATA
56574174 AGCCCAAACAATGGATTCAATAAGTTCTTGCCAATAACCACGTCCGCTGAATAGAAACATTAAAC
1 AGCCCAAACAATGGATTCAATAAGTTCTTGCCAATAACCACGTCCGCTGAATAGAAACATTAAAC
56574239 TAAAAGCCCATACAAAATGAGCACCTAAGAAAAGAAGGCCATATGCAGATAATGAAGAACCATAA
66 TAAAAGCCCATACAAAATGAGCACCTAAGAAAAGAAGGCCATATGCAGATAATGAAGAACCATAA
56574304 GACTGAATTACCT
131 GACTGAATTACCT
56574317 ACAATGCTTG
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 142 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.19
Consensus pattern (149 bp):
AGCCCAAACAATGGATTCAATAAGTTCTTGCCAATAACCACGTCCGCTGAATAGAAACATTAAAC
TAAAAGCCCATACAAAATGAGCACCTAAGAAAAGAAGGCCATATGCAGATAATGAAGAACCATAA
GACTGAATTACCTGGGATA
Found at i:56576409 original size:15 final size:15
Alignment explanation
Indices: 56576391--56576421 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56576381 ATCTCTCATC
56576391 TATCTATCTATTTTT
1 TATCTATCTATTTTT
56576406 TATCTATCTATTTTT
1 TATCTATCTATTTTT
56576421 T
1 T
56576422 CTTTAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (15 bp):
TATCTATCTATTTTT
Found at i:56580868 original size:26 final size:25
Alignment explanation
Indices: 56580822--56580882 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
56580812 AATAAATTTT
*
56580822 ATTTTTATTTTTAAAAATATTTAAA-
1 ATTTATATTTTTAAAAATA-TTAAAC
* *
56580847 ATTTATATTTTTCAATATTATTAAAC
1 ATTTATATTTTT-AAAAATATTAAAC
*
56580873 ATATATATTT
1 ATTTATATTT
56580883 AATTATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 16 0.53
26 14 0.47
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTATATTTTTAAAAATATTAAAC
Found at i:56580931 original size:22 final size:22
Alignment explanation
Indices: 56580906--56580949 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
56580896 TTGTCATATA
56580906 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
56580928 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
56580950 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:56580985 original size:13 final size:14
Alignment explanation
Indices: 56580969--56581010 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
56580959 TTTCAATTTT
56580969 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
56580982 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
56580997 ATTTTAAATAATAT
1 ATTTT-AATAATAT
56581011 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:56580995 original size:16 final size:16
Alignment explanation
Indices: 56580973--56581009 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
56580963 AATTTTATTT
56580973 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
56580990 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
56581005 TAATA
1 TAATA
56581010 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:56581579 original size:14 final size:14
Alignment explanation
Indices: 56581557--56581594 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
56581547 CCAGAAAAGT
*
56581557 AAATTATTTTCCAG
1 AAATCATTTTCCAG
56581571 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
56581585 AAGTCATTTT
1 AAATCATTTT
56581595 TAGTGAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:56581793 original size:18 final size:18
Alignment explanation
Indices: 56581770--56581805 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
56581760 TACGGAGTAA
56581770 GAAAAACTACACATGAAG
1 GAAAAACTACACATGAAG
56581788 GAAAAACTACACATGAAG
1 GAAAAACTACACATGAAG
56581806 ATTTAATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.17, G:0.17, T:0.11
Consensus pattern (18 bp):
GAAAAACTACACATGAAG
Found at i:56584242 original size:23 final size:21
Alignment explanation
Indices: 56584216--56584259 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
56584206 AATGGTTCGA
56584216 ATTTGT-ATTTGTAATTATATTAT
1 ATTTGTGA-TTGT-ATTAT-TTAT
56584239 ATTTGTGATTGTATTATTTAT
1 ATTTGTGATTGTATTATTTAT
56584260 GTAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 10 0.50
24 1 0.05
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.61
Consensus pattern (21 bp):
ATTTGTGATTGTATTATTTAT
Found at i:56584243 original size:17 final size:17
Alignment explanation
Indices: 56584221--56584264 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
56584211 TTCGAATTTG
56584221 TATTTGTAATTATATTA
1 TATTTGTAATTATATTA
* *
56584238 TATTTGTGATTGTATTA
1 TATTTGTAATTATATTA
56584255 T-TTATGTAAT
1 TATT-TGTAAT
56584265 AATAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (17 bp):
TATTTGTAATTATATTA
Found at i:56586594 original size:21 final size:20
Alignment explanation
Indices: 56586570--56586615 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
56586560 CTAAATTCAC
*
56586570 AAAAGAAAAAAATTAATACCT
1 AAAA-AAAAAAATTAATAACT
*
56586591 AAAACAAAAAATTAATAACT
1 AAAAAAAAAAATTAATAACT
56586611 AAAAA
1 AAAAA
56586616 TTAATATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (20 bp):
AAAAAAAAAAATTAATAACT
Found at i:56586601 original size:20 final size:20
Alignment explanation
Indices: 56586576--56586614 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
56586566 TCACAAAAGA
*
56586576 AAAAAATTAATACCTAAAAC
1 AAAAAATTAATAACTAAAAC
56586596 AAAAAATTAATAACTAAAA
1 AAAAAATTAATAACTAAAA
56586615 ATTAATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAATTAATAACTAAAAC
Found at i:56587353 original size:22 final size:22
Alignment explanation
Indices: 56587328--56587372 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
56587318 GAGTTACTAT
* *
56587328 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAAGGG
* *
56587350 TTTAGGGATTATGGTTTAAGGG
1 TTTAAGGATTATGGATTAAGGG
56587372 T
1 T
56587373 GGTTTAATGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (22 bp):
TTTAAGGATTATGGATTAAGGG
Found at i:56587371 original size:15 final size:15
Alignment explanation
Indices: 56587333--56587367 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
56587323 ACTATTTTAA
*
56587333 GGTTTATGGATTATG
1 GGTTTAGGGATTATG
56587348 GGTTTAGGGATTAT-
1 GGTTTAGGGATTATG
56587362 GGTTTA
1 GGTTTA
56587368 AGGGTGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:56587439 original size:14 final size:14
Alignment explanation
Indices: 56587429--56587485 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
56587419 TAGGGGTTCT
56587429 TGGTTTAGGGTTTA
1 TGGTTTAGGGTTTA
* *
56587443 TGTTTTAGGATTTA
1 TGGTTTAGGGTTTA
56587457 TGGTTTAGGGTTTA
1 TGGTTTAGGGTTTA
* *
56587471 GGGATTAGGAGTTTA
1 TGGTTTAGG-GTTTA
56587486 ATGATTAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
14 31 0.86
15 5 0.14
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.47
Consensus pattern (14 bp):
TGGTTTAGGGTTTA
Found at i:56587440 original size:7 final size:7
Alignment explanation
Indices: 56587386--56587485 Score: 62
Period size: 7 Copynumber: 14.0 Consensus size: 7
56587376 TTAATGGTTG
56587386 GGGTTTA
1 GGGTTTA
*
56587393 AGGTTTA
1 GGGTTTA
56587400 -GGTGTTA
1 GGGT-TTA
*
56587407 TGGGTTAA
1 -GGGTTTA
56587415 GGG-TTA
1 GGGTTTA
56587421 GGGGTTCT-
1 -GGGTT-TA
*
56587429 TGGTTTA
1 GGGTTTA
56587436 GGGTTTA
1 GGGTTTA
* *
56587443 TGTTTTA
1 GGGTTTA
*
56587450 GGATTTA
1 GGGTTTA
*
56587457 TGGTTTA
1 GGGTTTA
56587464 GGGTTTA
1 GGGTTTA
*
56587471 GGGATTA
1 GGGTTTA
56587478 GGAGTTTA
1 GG-GTTTA
56587486 ATGATTAGTT
Statistics
Matches: 71, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
6 6 0.08
7 54 0.76
8 7 0.10
9 4 0.06
ACGTcount: A:0.18, C:0.01, G:0.37, T:0.44
Consensus pattern (7 bp):
GGGTTTA
Found at i:56587478 original size:28 final size:29
Alignment explanation
Indices: 56587395--56587485 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 29
56587385 GGGGTTTAAG
* *
56587395 GTTTA-GGTGTTATGGGTTAAGGG-TTAGGG
1 GTTTATGGT-TTA-GGGTTTAGGGATTAGGA
* **
56587424 GTTCT-TGGTTTAGGGTTTATGTTTTAGGA
1 GTT-TATGGTTTAGGGTTTAGGGATTAGGA
56587453 -TTTATGGTTTAGGGTTTAGGGATTAGGA
1 GTTTATGGTTTAGGGTTTAGGGATTAGGA
56587481 GTTTA
1 GTTTA
56587486 ATGATTAGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
27 1 0.02
28 30 0.60
29 15 0.30
30 4 0.08
ACGTcount: A:0.18, C:0.01, G:0.36, T:0.45
Consensus pattern (29 bp):
GTTTATGGTTTAGGGTTTAGGGATTAGGA
Found at i:56587661 original size:15 final size:15
Alignment explanation
Indices: 56587641--56587688 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
56587631 ACTATTTTAA
56587641 GGTTTATGGATTATG
1 GGTTTATGGATTATG
56587656 GGTTTA-GAGATTAT-
1 GGTTTATG-GATTATG
* *
56587670 GGTTTATGGTTTAAG
1 GGTTTATGGATTATG
56587685 GGTT
1 GGTT
56587689 GGGGTTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:56587661 original size:22 final size:21
Alignment explanation
Indices: 56587636--56587685 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
56587626 GAGTTACTAT
*
56587636 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAT-GG
*
56587658 TTT-AGAGATTATGGTTTATGG
1 TTTAAG-GATTATGGATTATGG
56587679 TTTAAGG
1 TTTAAGG
56587686 GTTGGGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:56588498 original size:21 final size:20
Alignment explanation
Indices: 56588474--56588528 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 20
56588464 ATGTTAATTT
*
56588474 AAAAAATTTAAAAATCTTCAA
1 AAAAAATTTAAAAAT-TTAAA
56588495 AAAAAA-TT-AAAATTTAAA
1 AAAAAATTTAAAAATTTAAA
56588513 AATAAAATATTAAAAA
1 AA-AAAAT-TTAAAAA
56588529 ATAAAAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 9 0.31
20 2 0.07
21 8 0.28
22 4 0.14
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAAAATTTAAAAATTTAAA
Found at i:56588528 original size:15 final size:14
Alignment explanation
Indices: 56588495--56588534 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
56588485 AAATCTTCAA
56588495 AAAAAATTAAAATTT
1 AAAAAA-TAAAATTT
56588510 -AAAAATAAAATATT
1 AAAAAATAAAAT-TT
56588524 AAAAAATAAAA
1 AAAAAATAAAA
56588535 AACTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.26
14 7 0.30
15 10 0.43
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAAAATAAAATTT
Found at i:56588533 original size:21 final size:21
Alignment explanation
Indices: 56588495--56588535 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
56588485 AAATCTTCAA
**
56588495 AAAAAATTAAAATTTAAAAAT
1 AAAAAATTAAAAAATAAAAAT
*
56588516 AAAATATTAAAAAATAAAAA
1 AAAAAATTAAAAAATAAAAA
56588536 ACTTAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAAAAATAAAAAT
Found at i:56588541 original size:16 final size:15
Alignment explanation
Indices: 56588503--56588542 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
56588493 AAAAAAAATT
*
56588503 AAAATTTAAAAATAA
1 AAAATTAAAAAATAA
*
56588518 AATATTAAAAAATAA
1 AAAATTAAAAAATAA
56588533 AAAACTTAAA
1 AAAA-TTAAA
56588543 TATTTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATTAAAAAATAA
Found at i:56588560 original size:14 final size:14
Alignment explanation
Indices: 56588541--56588567 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56588531 AAAAAACTTA
56588541 AATATTTAATATTC
1 AATATTTAATATTC
56588555 AATATTTAATATT
1 AATATTTAATATT
56588568 TTAGTCCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
AATATTTAATATTC
Found at i:56588699 original size:22 final size:22
Alignment explanation
Indices: 56588656--56588700 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
56588646 TAGAAAGAAA
*
56588656 AAAATAGAAAAAAAATATATTG
1 AAAATAGAAAAAAAATAAATTG
56588678 AAAAT-GAAAAAAAATAAAATTG
1 AAAATAGAAAAAAAAT-AAATTG
56588700 A
1 A
56588701 GCAATAGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (22 bp):
AAAATAGAAAAAAAATAAATTG
Found at i:56591987 original size:46 final size:46
Alignment explanation
Indices: 56591935--56592294 Score: 533
Period size: 46 Copynumber: 7.8 Consensus size: 46
56591925 AGTGTGCTCT
*
56591935 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
56591981 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
56592027 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
56592073 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
56592119 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
56592165 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** **
56592211 ATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
56592258 ATGACA-GAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC
56592295 TATGACATCA
Statistics
Matches: 297, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
46 255 0.86
47 42 0.14
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:56596440 original size:321 final size:322
Alignment explanation
Indices: 56595848--56596502 Score: 1163
Period size: 321 Copynumber: 2.0 Consensus size: 322
56595838 TTGTACGAGG
* *
56595848 ATATA-ATTAATTTTTAGTGAAGAAGAGTCGAAACTGTTAGATAGCAGAACAGGAGTAACTTTAA
1 ATATATATGAATTTTTAGTGAAGAAGAGTCGAAACTGTTAGACAGCAGAACAGGAGTAACTTTAA
*
56595912 AGAATAAACTGTACTTATTGGAAAAAAACCAAAAATTCTGAAAATTTTATGGTGAGAATATATAT
66 AGAATAAACTGTACTTATTGG-AAAAAACCAAAAATTCTGAAAATTTTATGGTAAGAATATATAT
*
56595977 GAGTCTAGTTTCAGGGAAAATTATCGGATCTTAATTTGGAGTTATATAGCTCCAGATATAAATAA
130 GAGTCTAGTTTCAGGAAAAATTATCGGATCTTAATTTGGAGTTATATAGCTCCAGATATAAATAA
56596042 TTTAGTGACTATGACACAGATGGACAGCTTGAATATTCATAAAAGTAAATAATAAAGATTATAGA
195 TTTAGTGACTATGACACAGATGGACAGCTTGAATATTCATAAAAGTAAATAATAAAGATTATAGA
*
56596107 TAATGTTACTTATAAGTGTGTTATATACATTAAGGATGTGGAATGGAGAGGAGGAGGAGAAAA
260 TAATGTTACTTATAAGTGTATTATATACATTAAGGATGTGGAATGGAGAGGAGGAGGAGAAAA
* * *
56596170 ATATGTATGAATTTTTAGTGAAGAAGAGTC-AGAATTGTTAGACAGCAGAACAGGGGTAACTTTA
1 ATATATATGAATTTTTAGTGAAGAAGAGTCGA-AACTGTTAGACAGCAGAACAGGAGTAACTTTA
**
56596234 AAGAATAAACTGTACTTATTGG-CTAAACCAAAAATTCTGAAAATTTTATGGTAAGAATATATAT
65 AAGAATAAACTGTACTTATTGGAAAAAACCAAAAATTCTGAAAATTTTATGGTAAGAATATATAT
*
56596298 GAGTCTAGTTTTAGGAAAAATTATCGGATCTTAATTTGGAGTTATATAGCTCCAGATATAAATAA
130 GAGTCTAGTTTCAGGAAAAATTATCGGATCTTAATTTGGAGTTATATAGCTCCAGATATAAATAA
56596363 TTTAGTGACTATGACACAGATGGACAGCTTGAATATTCATAAAAGTAAATAATAAAGATTATAGA
195 TTTAGTGACTATGACACAGATGGACAGCTTGAATATTCATAAAAGTAAATAATAAAGATTATAGA
*
56596428 TAATGTTACTTATAAGTGTATTATATACATTAAGGATGTGGAATGGAGAGGAGGAGGAGGAAA
260 TAATGTTACTTATAAGTGTATTATATACATTAAGGATGTGGAATGGAGAGGAGGAGGAGAAAA
56596491 ATATATATGAAT
1 ATATATATGAAT
56596503 ATCCAGCTAG
Statistics
Matches: 318, Mismatches: 13, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
321 239 0.75
322 5 0.02
323 74 0.23
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (322 bp):
ATATATATGAATTTTTAGTGAAGAAGAGTCGAAACTGTTAGACAGCAGAACAGGAGTAACTTTAA
AGAATAAACTGTACTTATTGGAAAAAACCAAAAATTCTGAAAATTTTATGGTAAGAATATATATG
AGTCTAGTTTCAGGAAAAATTATCGGATCTTAATTTGGAGTTATATAGCTCCAGATATAAATAAT
TTAGTGACTATGACACAGATGGACAGCTTGAATATTCATAAAAGTAAATAATAAAGATTATAGAT
AATGTTACTTATAAGTGTATTATATACATTAAGGATGTGGAATGGAGAGGAGGAGGAGAAAA
Found at i:56599764 original size:6 final size:6
Alignment explanation
Indices: 56599755--56599783 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
56599745 TTCTGCTTCT
56599755 GAAAGG GAAAGG GAAAGG GAAAGG GAAAG
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAG
56599784 AAATTTCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:56603473 original size:21 final size:21
Alignment explanation
Indices: 56603441--56603481 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
56603431 GAACATTTGG
56603441 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
56603462 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
56603482 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:56607148 original size:43 final size:43
Alignment explanation
Indices: 56607017--56607148 Score: 169
Period size: 43 Copynumber: 3.1 Consensus size: 43
56607007 TTTAGTGGCA
* *
56607017 TTTGTAAGAAAAGCGACGCTAAAAATCATGATTTTTAACGGCA
1 TTTGTAAGAAAAGCGACGCTAAAAGTCATGATTTTTAACGGCG
* **
56607060 TTTGTAA-AAAGAGCGACGCTAAAAGTCATGATTTTTAGCAACG
1 TTTGTAAGAAA-AGCGACGCTAAAAGTCATGATTTTTAACGGCG
* *
56607103 TTTGTAAGAAAAGCGCCGCTAAAGGTCATG-TTCTTTAACGGCG
1 TTTGTAAGAAAAGCGACGCTAAAAGTCATGATT-TTTAACGGCG
56607146 TTT
1 TTT
56607149 TTTATAAACG
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
42 5 0.07
43 68 0.89
44 3 0.04
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (43 bp):
TTTGTAAGAAAAGCGACGCTAAAAGTCATGATTTTTAACGGCG
Found at i:56608499 original size:25 final size:25
Alignment explanation
Indices: 56608461--56608511 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
56608451 TGCTCTGAAC
*
56608461 AAAGTTAATGGATTATTACTGGTAT
1 AAAGTTAATAGATTATTACTGGTAT
56608486 AAAGTTAATAGATTATTACTGGTAT
1 AAAGTTAATAGATTATTACTGGTAT
56608511 A
1 A
56608512 CCTGAGTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (25 bp):
AAAGTTAATAGATTATTACTGGTAT
Found at i:56612548 original size:21 final size:21
Alignment explanation
Indices: 56612522--56612562 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
56612512 AGACGAGCAA
* *
56612522 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
56612543 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
56612563 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:56620914 original size:34 final size:34
Alignment explanation
Indices: 56620844--56620922 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 34
56620834 CATGGTATCC
* * * **
56620844 ATAGAGATAAGTCTATTGGGACAGTAAACATGGA
1 ATAGAGATAAGTCTACTAGGACAATAAACACAGA
56620878 ATAGAGATAAGTCCT-CTAGGACAATAAACACAGA
1 ATAGAGATAAGT-CTACTAGGACAATAAACACAGA
*
56620912 ATAAAG-TAAGT
1 ATAGAGATAAGT
56620923 TCGTCGAGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 5 0.13
34 31 0.82
35 2 0.05
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (34 bp):
ATAGAGATAAGTCTACTAGGACAATAAACACAGA
Found at i:56622433 original size:86 final size:86
Alignment explanation
Indices: 56622262--56622432 Score: 272
Period size: 86 Copynumber: 2.0 Consensus size: 86
56622252 ATAAAAGGGA
* *
56622262 ATCATAAAAACCCTAAGGTGAGAGAGTGTTACCAACATTAACCACGAAAATAAAAAAAAAACCTA
1 ATCACAAAAACCCTAAGGTGAGAGAGTGTTACCAACATTAACCAAGAAAATAAAAAAAAAACCTA
56622327 GGTCTAGCAGCCACATTTTTT
66 GGTCTAGCAGCCACATTTTTT
** *
56622348 ATCACAAAAACCCTAAGGTGAGAGAGTGTTACCAACATTAACCAAGAAAA-CGAAAAGAAACCTA
1 ATCACAAAAACCCTAAGGTGAGAGAGTGTTACCAACATTAACCAAGAAAATAAAAAAAAAACCTA
**
56622412 GGTCTAGCAGCTGCATTTTTT
66 GGTCTAGCAGCCACATTTTTT
56622433 TGAAAAAAAC
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 30 0.38
86 48 0.62
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (86 bp):
ATCACAAAAACCCTAAGGTGAGAGAGTGTTACCAACATTAACCAAGAAAATAAAAAAAAAACCTA
GGTCTAGCAGCCACATTTTTT
Found at i:56644689 original size:40 final size:40
Alignment explanation
Indices: 56644606--56644712 Score: 133
Period size: 40 Copynumber: 2.6 Consensus size: 40
56644596 ACTCAAATTC
** * * *
56644606 TCGCACACTAAGTGTTAATACATAGACGAAGTTATCTCAAA
1 TCGCACACTAAGTG-CCATACTTAGCCGAAGCTATCTCAAA
**
56644647 TCGCACACTAAGTGCCATACTTAGCCGAAGCTATCTTGAA
1 TCGCACACTAAGTGCCATACTTAGCCGAAGCTATCTCAAA
*
56644687 TCGCACACTAAGTGCCACACTTAGCC
1 TCGCACACTAAGTGCCATACTTAGCC
56644713 AAATTGTCGT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 44 0.76
41 14 0.24
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATACTTAGCCGAAGCTATCTCAAA
Found at i:56647481 original size:14 final size:16
Alignment explanation
Indices: 56647462--56647499 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
56647452 AAGGAAATGA
*
56647462 TGATATATGACA-A-G
1 TGATATATGAAATAGG
56647476 TGATATATGAAATAGG
1 TGATATATGAAATAGG
56647492 TGATATAT
1 TGATATAT
56647500 ATTATGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.52
15 1 0.05
16 9 0.43
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (16 bp):
TGATATATGAAATAGG
Found at i:56647804 original size:43 final size:43
Alignment explanation
Indices: 56647756--56647841 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
56647746 GATATATGTG
*
56647756 GCATCCGAGCTCGTTAAGTGGTCCGAGTTCATTATGGATGCAA
1 GCATCCGAGCTCGTTAAGTGGTCCGAGTTCATAATGGATGCAA
* * *
56647799 GCATCCGAGCTTGTTGAGTGGTCTGAGTTCATAATGGATGCAA
1 GCATCCGAGCTCGTTAAGTGGTCCGAGTTCATAATGGATGCAA
56647842 TACATGTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (43 bp):
GCATCCGAGCTCGTTAAGTGGTCCGAGTTCATAATGGATGCAA
Found at i:56647875 original size:26 final size:26
Alignment explanation
Indices: 56647846--56647908 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
56647836 ATGCAATACA
*
56647846 TGTGATTGAGTTCCGGGAGATGGTCT
1 TGTGATTGAGTTCCGGGAAATGGTCT
*
56647872 TGTGATTGAGTTTCGGGAAATGGTCT
1 TGTGATTGAGTTCCGGGAAATGGTCT
*
56647898 TTTGATTGAGT
1 TGTGATTGAGT
56647909 GGTCAGATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.17, C:0.08, G:0.35, T:0.40
Consensus pattern (26 bp):
TGTGATTGAGTTCCGGGAAATGGTCT
Found at i:56652394 original size:17 final size:17
Alignment explanation
Indices: 56652372--56652405 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56652362 AGTCTAAGAA
56652372 GGAAGGTTTGTCCTAAG
1 GGAAGGTTTGTCCTAAG
56652389 GGAAGGTTTGTCCTAAG
1 GGAAGGTTTGTCCTAAG
56652406 AATCCTTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.35, T:0.29
Consensus pattern (17 bp):
GGAAGGTTTGTCCTAAG
Found at i:56653557 original size:38 final size:38
Alignment explanation
Indices: 56653514--56653627 Score: 228
Period size: 38 Copynumber: 3.0 Consensus size: 38
56653504 TTCATCCTTT
56653514 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
56653552 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
56653590 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
56653628 GGAGTTCTTG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:56654910 original size:40 final size:40
Alignment explanation
Indices: 56654816--56654960 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
56654806 TACTCGAATG
*
56654816 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
56654857 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
56654897 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
56654937 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
56654961 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:56656792 original size:13 final size:13
Alignment explanation
Indices: 56656774--56656802 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
56656764 AGTACCAACG
56656774 CCATTGTTAAGTA
1 CCATTGTTAAGTA
56656787 CCATTGTTAAGTA
1 CCATTGTTAAGTA
56656800 CCA
1 CCA
56656803 GCTCACTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (13 bp):
CCATTGTTAAGTA
Found at i:56661218 original size:16 final size:16
Alignment explanation
Indices: 56661197--56661228 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56661187 GGTATGAAAG
56661197 TAGAATTTATCAAACC
1 TAGAATTTATCAAACC
56661213 TAGAATTTATCAAACC
1 TAGAATTTATCAAACC
56661229 AAACCATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (16 bp):
TAGAATTTATCAAACC
Found at i:56665396 original size:17 final size:17
Alignment explanation
Indices: 56665374--56665410 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
56665364 TCATACATAG
56665374 TCATGAATTCAATACTT
1 TCATGAATTCAATACTT
56665391 TCATGAATTCAATACTT
1 TCATGAATTCAATACTT
56665408 TCA
1 TCA
56665411 CATTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (17 bp):
TCATGAATTCAATACTT
Found at i:56670588 original size:13 final size:13
Alignment explanation
Indices: 56670570--56670597 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56670560 ACTATGACCG
56670570 TAGTTACAAGCAC
1 TAGTTACAAGCAC
56670583 TAGTTACAAGCAC
1 TAGTTACAAGCAC
56670596 TA
1 TA
56670598 ATGCAGCCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (13 bp):
TAGTTACAAGCAC
Found at i:56675452 original size:24 final size:24
Alignment explanation
Indices: 56675424--56675474 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
56675414 TCGTAACATA
*
56675424 GAAAGACGACTTATATTAATAGAT
1 GAAAGACAACTTATATTAATAGAT
56675448 GAAAGACAACTTATATTAATAGAT
1 GAAAGACAACTTATATTAATAGAT
56675472 GAA
1 GAA
56675475 CTTAAACACG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (24 bp):
GAAAGACAACTTATATTAATAGAT
Found at i:56699928 original size:24 final size:24
Alignment explanation
Indices: 56699901--56699969 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 24
56699891 TGAGTTATGG
56699901 TCTGAGTTCATGATATATGTGACA
1 TCTGAGTTCATGATATATGTGACA
* * *
56699925 TCTGAGCTCAT-CTAGT-TGTG--G
1 TCTGAGTTCATGATA-TATGTGACA
*
56699946 TCTGAGTTCATGATGTATGTGACA
1 TCTGAGTTCATGATATATGTGACA
56699970 CATGTTTTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
21 11 0.33
22 5 0.15
23 6 0.18
24 11 0.33
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (24 bp):
TCTGAGTTCATGATATATGTGACA
Found at i:56699947 original size:45 final size:45
Alignment explanation
Indices: 56699879--56699969 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
56699869 GAACAATGTG
56699879 ATCTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGAC
1 ATCTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGAC
* * *
56699924 ATCTGAGCTCATCT-AGTTGTGGTCTGAGTTCATGATGTATGTGAC
1 ATCTGAACTCAT-TGAGTTATGGTCTGAGTTCATGATATATGTGAC
56699969 A
1 A
56699970 CATGTTTTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (45 bp):
ATCTGAACTCATTGAGTTATGGTCTGAGTTCATGATATATGTGAC
Found at i:56706850 original size:3 final size:3
Alignment explanation
Indices: 56706842--56706887 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
56706832 ACTTGTTCTA
* * *
56706842 AAT AAT AAT GAT AAT AAT AAT AAT GAT AAT AAC AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
56706888 CAATACATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:56706862 original size:15 final size:15
Alignment explanation
Indices: 56706842--56706887 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
56706832 ACTTGTTCTA
56706842 AATAATAATGATAAT
1 AATAATAATGATAAT
56706857 AATAATAATGATAAT
1 AATAATAATGATAAT
* *
56706872 AACAATAATAATAAT
1 AATAATAATGATAAT
56706887 A
1 A
56706888 CAATACATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (15 bp):
AATAATAATGATAAT
Found at i:56709445 original size:19 final size:20
Alignment explanation
Indices: 56709421--56709458 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
56709411 TTAAAGCAGT
56709421 AATTT-AGTAAATAAAAGAA
1 AATTTAAGTAAATAAAAGAA
56709440 AATTTAAGTAAATAAAAGA
1 AATTTAAGTAAATAAAAGA
56709459 TAAAAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (20 bp):
AATTTAAGTAAATAAAAGAA
Found at i:56710641 original size:12 final size:13
Alignment explanation
Indices: 56710604--56710641 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
56710594 AAATATTTGA
56710604 CTTGTCCTTAATT
1 CTTGTCCTTAATT
*
56710617 ATGTGTCCTTAATT
1 CT-TGTCCTTAATT
56710631 CTTGT-CTTAAT
1 CTTGTCCTTAAT
56710642 ATTCCAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.53
Consensus pattern (13 bp):
CTTGTCCTTAATT
Found at i:56712266 original size:20 final size:21
Alignment explanation
Indices: 56712231--56712273 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
56712221 TTAAAGCAAT
*
56712231 AATTTAGTAAATAAAAGA-AA
1 AATTAAGTAAATAAAAGATAA
56712251 AATTAAGTAAATAAAAGATAA
1 AATTAAGTAAATAAAAGATAA
56712272 AA
1 AA
56712274 GAAACCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (21 bp):
AATTAAGTAAATAAAAGATAA
Found at i:56713490 original size:20 final size:21
Alignment explanation
Indices: 56713455--56713497 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
56713445 TTAAAGCAAT
*
56713455 AATTTAGTAAATAAAAGA-AA
1 AATTAAGTAAATAAAAGATAA
56713475 AATTAAGTAAATAAAAGATAA
1 AATTAAGTAAATAAAAGATAA
56713496 AA
1 AA
56713498 GAAACCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (21 bp):
AATTAAGTAAATAAAAGATAA
Found at i:56727004 original size:23 final size:24
Alignment explanation
Indices: 56726978--56727054 Score: 115
Period size: 23 Copynumber: 3.3 Consensus size: 24
56726968 GTGTTAGAAC
* *
56726978 TTAATATGATTTATGTTTAAAAT-
1 TTAATGTGATTTATGCTTAAAATA
56727001 TTAATGTGATTTATGCTT-AAATA
1 TTAATGTGATTTATGCTTAAAATA
56727024 TTAATGTGATTTATGCTT-AAATA
1 TTAATGTGATTTATGCTTAAAATA
56727047 TTAATGTG
1 TTAATGTG
56727055 TAAATGGACC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.08
23 47 0.92
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (24 bp):
TTAATGTGATTTATGCTTAAAATA
Found at i:56730339 original size:16 final size:17
Alignment explanation
Indices: 56730312--56730346 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
56730302 TAGAATTAGG
56730312 TTGAGAAAATTAATTAA
1 TTGAGAAAATTAATTAA
56730329 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
56730345 TT
1 TT
56730347 TAAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:56733060 original size:25 final size:25
Alignment explanation
Indices: 56733032--56733082 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
56733022 ATATTATTGA
*
56733032 TCACTTTGATAATAAAAAATTTAAG
1 TCACTTTGATAACAAAAAATTTAAG
*
56733057 TCACTTTTATAACAAAAAATTTAAG
1 TCACTTTGATAACAAAAAATTTAAG
56733082 T
1 T
56733083 GAATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (25 bp):
TCACTTTGATAACAAAAAATTTAAG
Found at i:56733097 original size:24 final size:25
Alignment explanation
Indices: 56733040--56733097 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
56733030 GATCACTTTG
* *
56733040 ATAATAAAAAATTTAAGTCACTTTT
1 ATAAAAAAAAATTTAAGTCAATTTT
* *
56733065 ATAACAAAAAATTTAAGTGAATTTT
1 ATAAAAAAAAATTTAAGTCAATTTT
56733090 -TAAAAAAA
1 ATAAAAAAA
56733098 TTCTAACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (25 bp):
ATAAAAAAAAATTTAAGTCAATTTT
Found at i:56733926 original size:20 final size:18
Alignment explanation
Indices: 56733883--56733918 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
56733873 CCAAAATTTT
56733883 ATTTTAATATTTTTATAC
1 ATTTTAATATTTTTATAC
56733901 ATTTTAAT-TTTATTATAC
1 ATTTTAATATTT-TTATAC
56733919 GCATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTAATATTTTTATAC
Found at i:56735976 original size:143 final size:137
Alignment explanation
Indices: 56735779--56736065 Score: 344
Period size: 143 Copynumber: 2.1 Consensus size: 137
56735769 TTGTTAATTG
* * * * **
56735779 TGTTGGAGACTGCAGCTCTTCACCTACAAGCTTTAATATGACAACTGGGAGCTTTGTTCTCGCTA
1 TGTTGGAGACTACAGCTCTTCACCTACAAGCCTAAATATAACAACTGGGAGCTTTACTCTCGCTA
56735844 A-TTGTGTTGGAGGCTGAGGCTGCGACTCTTCACCTGCGAGCC-TAATATGACAGTTAGGAGCTT
66 ACTT-T-TT---GG--G-GGCTGCGACTCTTCACCTGCGAGCCTTAATATGACAGTTAGGAGCTT
*
56735907 TGCTCTCGCTAACTA
123 CGCTCTCGCTAACTA
* * **
56735922 TGTTGGAGACTACGGCTCTTCACCTGCAAGCCTAAATATAACAGTTGGGAGCTTTACTCTCGCTA
1 TGTTGGAGACTACAGCTCTTCACCTACAAGCCTAAATATAACAACTGGGAGCTTTACTCTCGCTA
* * * *
56735987 ACTTTTTGGGGGCTGCGGCTCTTCACCTGCGAGCCTTAATATGACAGTTGGGAGCTTCGTTCTTG
66 ACTTTTTGGGGGCTGCGACTCTTCACCTGCGAGCCTTAATATGACAGTTAGGAGCTTCGCTCTCG
*
56736052 CTAACTG
131 CTAACTA
56736059 TGTTGGA
1 TGTTGGA
56736066 CATAGAAGGT
Statistics
Matches: 126, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
136 24 0.19
137 39 0.31
139 2 0.02
142 2 0.02
143 57 0.45
144 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (137 bp):
TGTTGGAGACTACAGCTCTTCACCTACAAGCCTAAATATAACAACTGGGAGCTTTACTCTCGCTA
ACTTTTTGGGGGCTGCGACTCTTCACCTGCGAGCCTTAATATGACAGTTAGGAGCTTCGCTCTCG
CTAACTA
Found at i:56736055 original size:68 final size:69
Alignment explanation
Indices: 56735779--56736065 Score: 299
Period size: 68 Copynumber: 4.1 Consensus size: 69
56735769 TTGTTAATTG
* * * * * ** *
56735779 TGTTGGAGACTGCAGCTCTTCACCTACAAGCTTTAATATGACAACTGGGAGCTTTGTTCTCGCTA
1 TGTTGGAGGCTGCGGCTCTTCACCTGCGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTA
* *
56735844 ATTG
66 ACTA
*
56735848 TGTTGGAGGCTGAGGCTGCGACTCTTCACCTGCGAGCC-TAATATGACAGTTAGGAGCTTTGCTC
1 TGTTGGAGGCT---GC-G-G-CTCTTCACCTGCGAGCCTTAATATGACAGTTGGGAGCTTTGCTC
56735912 TCGCTAACTA
60 TCGCTAACTA
* * * * * *
56735922 TGTTGGAGACTACGGCTCTTCACCTGCAAGCCTAAATATAACAGTTGGGAGCTTTACTCTCGCTA
1 TGTTGGAGGCTGCGGCTCTTCACCTGCGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTA
56735987 ACT-
66 ACTA
* * * * *
56735990 TTTTGGGGGCTGCGGCTCTTCACCTGCGAGCCTTAATATGACAGTTGGGAGCTTCGTTCTTGCTA
1 TGTTGGAGGCTGCGGCTCTTCACCTGCGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTA
*
56736055 ACTG
66 ACTA
56736059 TGTTGGA
1 TGTTGGA
56736066 CATAGAAGGT
Statistics
Matches: 179, Mismatches: 31, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
68 73 0.41
69 47 0.26
70 1 0.01
71 1 0.01
72 2 0.01
74 41 0.23
75 14 0.08
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (69 bp):
TGTTGGAGGCTGCGGCTCTTCACCTGCGAGCCTTAATATGACAGTTGGGAGCTTTGCTCTCGCTA
ACTA
Found at i:56737665 original size:21 final size:21
Alignment explanation
Indices: 56737636--56737679 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
56737626 ATAACTTAAC
* *
56737636 TTCTCAAAGTAAA-AAATCAAA
1 TTCTAAAAGGAAATAAAT-AAA
56737657 TTCTAAAAGGAAATAAATAAA
1 TTCTAAAAGGAAATAAATAAA
56737678 TT
1 TT
56737680 AGATTAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.27
Consensus pattern (21 bp):
TTCTAAAAGGAAATAAATAAA
Found at i:56740962 original size:22 final size:22
Alignment explanation
Indices: 56740934--56740978 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
56740924 ATCCATAGTT
56740934 AATAGTTTTCTTTAAGTAACTA
1 AATAGTTTTCTTTAAGTAACTA
56740956 AATAGTTTTCTTTAAGTAACTA
1 AATAGTTTTCTTTAAGTAACTA
56740978 A
1 A
56740979 GTACTCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (22 bp):
AATAGTTTTCTTTAAGTAACTA
Found at i:56742762 original size:15 final size:16
Alignment explanation
Indices: 56742738--56742771 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
56742728 ACTGAAGTTC
56742738 AACTTCAAATTTAT-A
1 AACTTCAAATTTATCA
*
56742753 AACTTTAAATTTATCA
1 AACTTCAAATTTATCA
56742769 AAC
1 AAC
56742772 GCTTCATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (16 bp):
AACTTCAAATTTATCA
Found at i:56745375 original size:16 final size:18
Alignment explanation
Indices: 56745347--56745382 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
56745337 ATTTTTAAGG
56745347 AAATTATTTTATTT-ATA
1 AAATTATTTTATTTGATA
56745364 AAATTA-TTTATTTGATA
1 AAATTATTTTATTTGATA
56745381 AA
1 AA
56745383 TAAACTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AAATTATTTTATTTGATA
Found at i:56747013 original size:26 final size:26
Alignment explanation
Indices: 56746983--56747035 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
56746973 CTTAACAATA
56746983 ATGGTAAAAGAATTTAAAAAAATCTT
1 ATGGTAAAAGAATTTAAAAAAATCTT
56747009 ATGGTAAAAGAATTTAAAAAAATCTT
1 ATGGTAAAAGAATTTAAAAAAATCTT
56747035 A
1 A
56747036 GACTAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (26 bp):
ATGGTAAAAGAATTTAAAAAAATCTT
Found at i:56747050 original size:27 final size:26
Alignment explanation
Indices: 56746987--56747043 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
56746977 ACAATAATGG
*
56746987 TAAAAGAATTTAAAAAAATCTTATGG
1 TAAAAGAATTTAAAAAAATCTTATGC
56747013 TAAAAGAATTTAAAAAAATCTTA-GAC
1 TAAAAGAATTTAAAAAAATCTTATG-C
56747039 TAAAA
1 TAAAA
56747044 ATTATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (26 bp):
TAAAAGAATTTAAAAAAATCTTATGC
Found at i:56751216 original size:22 final size:23
Alignment explanation
Indices: 56751172--56751216 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
56751162 AATTAATTAC
*
56751172 AATCTTCTATTATTAATAAATTT
1 AATCTTCTAATATTAATAAATTT
* *
56751195 AATCTT-TAATATTTATATATTT
1 AATCTTCTAATATTAATAAATTT
56751217 TTTGTCATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (23 bp):
AATCTTCTAATATTAATAAATTT
Found at i:56754848 original size:68 final size:68
Alignment explanation
Indices: 56754776--56754951 Score: 175
Period size: 68 Copynumber: 2.6 Consensus size: 68
56754766 CATCATGTGT
** * * *
56754776 ACAAGAGAGCTACGAGATACTATGTAGTAGCTAGGTCACATGTGTGA-T-ACGGGATGTATC-CC
1 ACAAGAGAGCTACGAGATA-TAAAT-GTAGCTAGGTCACATGTGTGATTCAAGGGAAGGA-CACC
56754838 ATGTAG
63 ATGTAG
* * *
56754844 ACAAGAGAGCTACGGGAGAGATAAATGTAGCTAGGTCGCATGTGTGATTCCAAGTGAAGGACACC
1 ACAAGAGAGCTAC--GAGATATAAATGTAGCTAGGTCACATGTGTGATT-CAAGGGAAGGACACC
56754909 ATGTAG
63 ATGTAG
*
56754915 ACAAGAGAGCTACGAG--ATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATG
56754952 GGTGGTACTA
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
66 13 0.14
67 6 0.07
68 33 0.36
69 7 0.08
70 6 0.07
71 27 0.29
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.22
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATGTGTGATTCAAGGGAAGGACACCATG
TAG
Found at i:56755594 original size:119 final size:119
Alignment explanation
Indices: 56755379--56755615 Score: 420
Period size: 119 Copynumber: 2.0 Consensus size: 119
56755369 TGACTCGCTC
*
56755379 AGAATGACTATGTGATCCCCTGTTCTAACTTTGAAAAATCATTAAAAATTGTACAAAACAAATTA
1 AGAATGACTATGTGATCCCCTATTCTAACTTTGAAAAATCATTAAAAATTGTACAAAACAAATTA
* *
56755444 AGAAATATAGTTTATATTTCTAGATTCCTTATTGAGTCTAGTTTTAAATGAAAA
66 AGAAATATAGTTTATATGTCTAGATTACTTATTGAGTCTAGTTTTAAATGAAAA
* *
56755498 AGAATGACTATGTGATCCCCTATTCTAACTTTGAAAAATCATTAAAAATTGTATAAAATAAATTA
1 AGAATGACTATGTGATCCCCTATTCTAACTTTGAAAAATCATTAAAAATTGTACAAAACAAATTA
*
56755563 AGAAATATAGTTTATATGTCTAGATTACTTATTGAGTTTAGTTTTAAATGAAA
66 AGAAATATAGTTTATATGTCTAGATTACTTATTGAGTCTAGTTTTAAATGAAA
56755616 CAAATTTAAT
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 112 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (119 bp):
AGAATGACTATGTGATCCCCTATTCTAACTTTGAAAAATCATTAAAAATTGTACAAAACAAATTA
AGAAATATAGTTTATATGTCTAGATTACTTATTGAGTCTAGTTTTAAATGAAAA
Found at i:56769274 original size:6 final size:6
Alignment explanation
Indices: 56769250--56769296 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
56769240 GGCAATACAA
*
56769250 TTTTAT TTATAT ATTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
56769297 TTGCATGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:56772705 original size:18 final size:18
Alignment explanation
Indices: 56772682--56772720 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
56772672 CACACAAATA
56772682 TTTATTAT-TTCTTCTCTT
1 TTTATTATATTCTT-TCTT
*
56772700 TTTATTTTATTCTTTCTT
1 TTTATTATATTCTTTCTT
56772718 TTT
1 TTT
56772721 CTAACTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTATATTCTTTCTT
Found at i:56775126 original size:36 final size:38
Alignment explanation
Indices: 56775064--56775143 Score: 119
Period size: 36 Copynumber: 2.1 Consensus size: 38
56775054 AAAAGAAAAA
*
56775064 AAAAGTTAAAAGAACATAAAAGAAAAAAATTAAATTGCTT
1 AAAAGTTAAAAGAACAT--AAGAAAAAAATTAAATAGCTT
56775104 AAAAGTTAAAAGAACAT-A-AAAAAAATTAAATAGCTT
1 AAAAGTTAAAAGAACATAAGAAAAAAATTAAATAGCTT
56775140 AAAA
1 AAAA
56775144 TAAAAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 21 0.54
37 1 0.03
40 17 0.44
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (38 bp):
AAAAGTTAAAAGAACATAAGAAAAAAATTAAATAGCTT
Found at i:56776380 original size:60 final size:60
Alignment explanation
Indices: 56776315--56776437 Score: 212
Period size: 60 Copynumber: 2.0 Consensus size: 60
56776305 TCCGAACTTG
56776315 GGGTGGTGGTGGAAATACTTGGGAGGAATCTTAGGG-AGAGGAGGCAGCTTAGGAAGAGGA
1 GGGTGGTGGTGGAAATACTTGGGAGGAATCTT-GGGAAGAGGAGGCAGCTTAGGAAGAGGA
* *
56776375 GGGTGGTGGTGGAAATACTTGGGAGGAATCTTGGGAAGAGGAGGTAGCTTAGGAAGGGGA
1 GGGTGGTGGTGGAAATACTTGGGAGGAATCTTGGGAAGAGGAGGCAGCTTAGGAAGAGGA
56776435 GGG
1 GGG
56776438 CATGGCTTCT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 3 0.05
60 57 0.95
ACGTcount: A:0.27, C:0.06, G:0.49, T:0.19
Consensus pattern (60 bp):
GGGTGGTGGTGGAAATACTTGGGAGGAATCTTGGGAAGAGGAGGCAGCTTAGGAAGAGGA
Found at i:56776476 original size:18 final size:18
Alignment explanation
Indices: 56776445--56776480 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
56776435 GGGCATGGCT
56776445 TCTTAGGGAATGGAGGGA
1 TCTTAGGGAATGGAGGGA
56776463 TCTT-GGGAAGTGGAGGGA
1 TCTTAGGGAA-TGGAGGGA
56776481 GTGGCTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.25, C:0.06, G:0.47, T:0.22
Consensus pattern (18 bp):
TCTTAGGGAATGGAGGGA
Found at i:56776628 original size:57 final size:57
Alignment explanation
Indices: 56776557--56776664 Score: 146
Period size: 57 Copynumber: 1.9 Consensus size: 57
56776547 TCGTATACAC
* * * * *
56776557 TGGAACCCGGGGAGGTAGTGGTTTGTTGTATACAGGAACTGGAGGGGGCTTGTAGAT
1 TGGAACCCGGGGAGGGACTCGTTTCTTGTATACAGGAACTGGAGGAGGCTTGTAGAT
*
56776614 TGGAA-CCGGAGGAGGGACTCGTTTCTTGTATACCGGAACTGGAGGAGGCTT
1 TGGAACCCGG-GGAGGGACTCGTTTCTTGTATACAGGAACTGGAGGAGGCTT
56776665 ATGGACTGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 4 0.09
57 40 0.91
ACGTcount: A:0.21, C:0.14, G:0.40, T:0.25
Consensus pattern (57 bp):
TGGAACCCGGGGAGGGACTCGTTTCTTGTATACAGGAACTGGAGGAGGCTTGTAGAT
Found at i:56776675 original size:57 final size:56
Alignment explanation
Indices: 56776575--56776914 Score: 275
Period size: 57 Copynumber: 6.0 Consensus size: 56
56776565 GGGGAGGTAG
* * * * * *
56776575 TGGTTTGTTGTATACAGGAACTGGAGGGGGCTTGTAGATTGGAACCGGAGGAGGGAC
1 TGGTTTCTTGTATACTGGAACTGGAGGAGGCTTATAGACTGGAACTGGAGGA-GGAC
* * * *
56776632 TCGTTTCTTGTATACCGGAACTGGAGGAGGCTTATGGACTGGAACTGGCGGAGGA-
1 TGGTTTCTTGTATACTGGAACTGGAGGAGGCTTATAGACTGGAACTGGAGGAGGAC
* * ** *
56776687 T-G----TGGT-T-CCGGAACTGGAGGAGATTTATAGACTGGAACTGGGGGAGGAC
1 TGGTTTCTTGTATACTGGAACTGGAGGAGGCTTATAGACTGGAACTGGAGGAGGAC
56776736 ATGGTTTCTTGTATACTGGAACTGGAGGTGGATGTGGTTTCTTATAGACTGGAACTGGAGGAGGA
1 -TGGTTTCTTGTATACTGGAACTGGA---GGA---GG---CTTATAGACTGGAACTGGAGGAGGA
56776801 -
56 C
* ** *
56776801 TGCGGTTTCTTGTATACTGGAACCGGAGGAGATTTATAGACTGGAACTGGTGGAGGAC
1 T--GGTTTCTTGTATACTGGAACTGGAGGAGGCTTATAGACTGGAACTGGAGGAGGAC
* * * * *
56776859 ATGGTTTCTTATATACTGGAACTGGTGGAGGTTTATAGACTGGAACAGGTGGAGGA
1 -TGGTTTCTTGTATACTGGAACTGGAGGAGGCTTATAGACTGGAACTGGAGGAGGA
56776915 TGTGGTTTTT
Statistics
Matches: 233, Mismatches: 28, Indels: 44
0.76 0.09 0.14
Matches are distributed among these distances:
48 37 0.16
49 1 0.00
50 4 0.02
51 1 0.00
54 1 0.00
55 4 0.02
56 4 0.02
57 125 0.54
59 1 0.00
60 4 0.02
63 4 0.02
64 1 0.00
66 46 0.20
ACGTcount: A:0.24, C:0.12, G:0.37, T:0.27
Consensus pattern (56 bp):
TGGTTTCTTGTATACTGGAACTGGAGGAGGCTTATAGACTGGAACTGGAGGAGGAC
Found at i:56776741 original size:48 final size:48
Alignment explanation
Indices: 56776646--56776741 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
56776636 TTCTTGTATA
* * **
56776646 CCGGAACTGGAGGAGGCTTATGGACTGGAACTGGCGGAGGATGTGGTT
1 CCGGAACTGGAGGAGACTTATAGACTGGAACTGGCGGAGGACATGGTT
* *
56776694 CCGGAACTGGAGGAGATTTATAGACTGGAACTGGGGGAGGACATGGTT
1 CCGGAACTGGAGGAGACTTATAGACTGGAACTGGCGGAGGACATGGTT
56776742 TCTTGTATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.24, C:0.14, G:0.42, T:0.21
Consensus pattern (48 bp):
CCGGAACTGGAGGAGACTTATAGACTGGAACTGGCGGAGGACATGGTT
Found at i:56776759 original size:33 final size:33
Alignment explanation
Indices: 56776711--56776889 Score: 160
Period size: 33 Copynumber: 5.7 Consensus size: 33
56776701 TGGAGGAGAT
* *
56776711 TTATAGACTGGAACTGGGGGAGGACATGGTTTC
1 TTATATACTGGAACTGGAGGAGGACATGGTTTC
* * **
56776744 TTGTATACTGGAACTGGAGGTGGATGTGGTTTC
1 TTATATACTGGAACTGGAGGAGGACATGGTTTC
* ***
56776777 TTATAGACTGGAACTGGAGGAGGATGCGGTTTC
1 TTATATACTGGAACTGGAGGAGGACATGGTTTC
* *
56776810 TTGTATACTGGAACCGGAGGA-G--A-----T-
1 TTATATACTGGAACTGGAGGAGGACATGGTTTC
* *
56776834 TTATAGACTGGAACTGGTGGAGGACATGGTTTC
1 TTATATACTGGAACTGGAGGAGGACATGGTTTC
*
56776867 TTATATACTGGAACTGGTGGAGG
1 TTATATACTGGAACTGGAGGAGG
56776890 TTTATAGACT
Statistics
Matches: 118, Mismatches: 19, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
24 17 0.14
25 2 0.02
27 1 0.01
32 2 0.02
33 96 0.81
ACGTcount: A:0.24, C:0.11, G:0.35, T:0.30
Consensus pattern (33 bp):
TTATATACTGGAACTGGAGGAGGACATGGTTTC
Found at i:56776894 original size:24 final size:24
Alignment explanation
Indices: 56776867--56776961 Score: 77
Period size: 24 Copynumber: 4.0 Consensus size: 24
56776857 ACATGGTTTC
*
56776867 TTATATACTGGAACTGGTGGAGGT
1 TTATATACTGGAACAGGTGGAGGT
*
56776891 TTATAGACTGGAACAGGTGGAGGAT
1 TTATATACTGGAACAGGTGGAGG-T
** * ** *
56776916 GTGGT-T-TTTCAACTGGTGGAGGT
1 -TTATATACTGGAACAGGTGGAGGT
*
56776939 TTATAAACTGGAACAGGTGGAGG
1 TTATATACTGGAACAGGTGGAGG
56776962 ATGTGGTTTT
Statistics
Matches: 51, Mismatches: 16, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
22 2 0.04
23 1 0.02
24 45 0.88
25 1 0.02
26 2 0.04
ACGTcount: A:0.26, C:0.08, G:0.36, T:0.29
Consensus pattern (24 bp):
TTATATACTGGAACAGGTGGAGGT
Found at i:56776934 original size:48 final size:48
Alignment explanation
Indices: 56776878--56777252 Score: 615
Period size: 48 Copynumber: 7.8 Consensus size: 48
56776868 TATATACTGG
* *
56776878 AACTGGTGGAGGTTTATAGACTGGAACAGGTGGAGGATGTGGTTTTTC
1 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTC
* * *
56776926 AACTGGTGGAGGTTTATAAACTGGAACAGGTGGAGGATGTGGTTTTTC
1 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTC
56776974 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTC
1 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTC
56777022 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTC
1 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTC
56777070 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTC
1 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTC
*
56777118 AACTGGTGGAGGTTTGTAGATCGGAACAGGTGGAGGATGTGGTTTTTC
1 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTC
* *
56777166 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGAAGTGGTTTTACTGG
1 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTT--T-C
* * * *
56777217 AACTGGAGGAGGTTTATAGACTGGAACTGGTGGAGG
1 AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGG
56777253 TTTATAGATT
Statistics
Matches: 312, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
48 279 0.89
50 1 0.00
51 32 0.10
ACGTcount: A:0.23, C:0.07, G:0.39, T:0.31
Consensus pattern (48 bp):
AACTGGTGGAGGTTTGTAGATTGGAACAGGTGGAGGATGTGGTTTTTC
Found at i:56777250 original size:27 final size:26
Alignment explanation
Indices: 56777224--56777274 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
56777214 TGGAACTGGA
*
56777224 GGAGGTTTATAGACTGGAACTGGT--
1 GGAGGTTTATAGACTGGAACAGGTGG
*
56777248 GGAGGTTTATAGATTGGAACAGGTGG
1 GGAGGTTTATAGACTGGAACAGGTGG
56777274 G
1 G
56777275 TTTACGGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
26 1 0.04
ACGTcount: A:0.25, C:0.06, G:0.41, T:0.27
Consensus pattern (26 bp):
GGAGGTTTATAGACTGGAACAGGTGG
Found at i:56779265 original size:22 final size:21
Alignment explanation
Indices: 56779224--56779266 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
56779214 TTTAGATTTT
* *
56779224 ATTTAAATATATTTATCACGA
1 ATTTAAATATATTAAGCACGA
56779245 ATTTAAATATTATTAAGCACGA
1 ATTTAAATA-TATTAAGCACGA
56779267 CTAACTATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (21 bp):
ATTTAAATATATTAAGCACGA
Found at i:56780142 original size:20 final size:19
Alignment explanation
Indices: 56780110--56780148 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
56780100 AATTTTAATG
*
56780110 ATTTTTTATTTTTAAAAAT
1 ATTTTTTAATTTTAAAAAT
*
56780129 ATTTTTTGAATTTTTAAAAT
1 ATTTTTT-AATTTTAAAAAT
56780149 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTTTTAATTTTAAAAAT
Found at i:56780151 original size:29 final size:30
Alignment explanation
Indices: 56780081--56780156 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 30
56780071 TTTAATTAAT
56780081 TTTTTAAAAATTTT-AAAATAATTTTAATGA
1 TTTTT-AAAATTTTAAAAATAATTTTAATGA
* * *
56780111 TTTTT-TATTTTTAAAAAT-ATTTT-TTGAA
1 TTTTTAAAATTTTAAAAATAATTTTAATG-A
56780139 TTTTTAAAATTTTAAAAA
1 TTTTTAAAATTTTAAAAA
56780157 ATTAATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.05
28 16 0.42
29 15 0.39
30 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTTTAAAATTTTAAAAATAATTTTAATGA
Found at i:56788421 original size:41 final size:41
Alignment explanation
Indices: 56788359--56788609 Score: 288
Period size: 41 Copynumber: 6.1 Consensus size: 41
56788349 AGATATTCTG
* * *
56788359 TCAGGCCTTGAGCCTAACAGGCTTCGTGCCGGAGTATTGTA
1 TCAGGCCTTGAGCCTAGCAGGCTTCGTGCCAGTGTATTGTA
* *
56788400 TCAGGACTTGAGCCTAGCAGGCTTTGTGCCAGTGTATTGTA
1 TCAGGCCTTGAGCCTAGCAGGCTTCGTGCCAGTGTATTGTA
* *
56788441 TCAGGCCTTGAGCCTAGCAGGCTTTGTGCTAGTGTATTGTA
1 TCAGGCCTTGAGCCTAGCAGGCTTCGTGCCAGTGTATTGTA
* * * **
56788482 TCAGGCTTTGAGCCTAGCAAGCTTCATGCTGGTGTATTGTA
1 TCAGGCCTTGAGCCTAGCAGGCTTCGTGCCAGTGTATTGTA
* * * * *
56788523 TTAGG-CTGTAAGCCTCGTAGGCTTCGTGTCAGTGTATTGTA
1 TCAGGCCT-TGAGCCTAGCAGGCTTCGTGCCAGTGTATTGTA
* * * * *
56788564 TCAGGCCTTGAGCTTAGCAGGCTTTGTGGCGGTGTATTGTG
1 TCAGGCCTTGAGCCTAGCAGGCTTCGTGCCAGTGTATTGTA
56788605 TCAGG
1 TCAGG
56788610 TAATTTGTAT
Statistics
Matches: 177, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
40 1 0.01
41 174 0.98
42 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.33
Consensus pattern (41 bp):
TCAGGCCTTGAGCCTAGCAGGCTTCGTGCCAGTGTATTGTA
Found at i:56788582 original size:123 final size:123
Alignment explanation
Indices: 56788359--56788609 Score: 335
Period size: 123 Copynumber: 2.0 Consensus size: 123
56788349 AGATATTCTG
* * *
56788359 TCAGGCCTTGAGCCTAACAGGCTTCGTGCCGGAGTATTGTATCAGGACTTGAGCCTAGCAGGCTT
1 TCAGGCCTTGAGCCTAACAAGCTTCATGCCGGAGTATTGTATCAGGACTTAAGCCTAGCAGGCTT
*
56788424 TGTGCCAGTGTATTGTATCAGGCCTTGAGCCTAGCAGGCTTTGT-GCTAGTGTATTGTA
66 CGTGCCAGTGTATTGTATCAGGCCTTGAGCCTAGCAGGCTTTGTGGC-AGTGTATTGTA
* * * * * * *
56788482 TCAGGCTTTGAGCCTAGCAAGCTTCATGCTGGTGTATTGTATTAGG-CTGTAAGCCTCGTAGGCT
1 TCAGGCCTTGAGCCTAACAAGCTTCATGCCGGAGTATTGTATCAGGACT-TAAGCCTAGCAGGCT
* * * *
56788546 TCGTGTCAGTGTATTGTATCAGGCCTTGAGCTTAGCAGGCTTTGTGGCGGTGTATTGTG
65 TCGTGCCAGTGTATTGTATCAGGCCTTGAGCCTAGCAGGCTTTGTGGCAGTGTATTGTA
56788605 TCAGG
1 TCAGG
56788610 TAATTTGTAT
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
122 2 0.02
123 107 0.96
124 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.33
Consensus pattern (123 bp):
TCAGGCCTTGAGCCTAACAAGCTTCATGCCGGAGTATTGTATCAGGACTTAAGCCTAGCAGGCTT
CGTGCCAGTGTATTGTATCAGGCCTTGAGCCTAGCAGGCTTTGTGGCAGTGTATTGTA
Found at i:56790109 original size:19 final size:21
Alignment explanation
Indices: 56790060--56790110 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
56790050 GTGTGACCCG
*
56790060 TGTTTTCAAATTTTTTAACTT
1 TGTTTTCAAATTTTCTAACTT
* *
56790081 T-TTTTGAAATTTTCTGA-TT
1 TGTTTTCAAATTTTCTAACTT
56790100 TGTTTT-AAATT
1 TGTTTTCAAATT
56790111 AGTCCTGGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.31
20 17 0.65
21 1 0.04
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.63
Consensus pattern (21 bp):
TGTTTTCAAATTTTCTAACTT
Found at i:56792119 original size:88 final size:88
Alignment explanation
Indices: 56791953--56792124 Score: 211
Period size: 88 Copynumber: 2.0 Consensus size: 88
56791943 GAATGATCGC
* * * *
56791953 TTTGATTGACATTGAAAACACAATGAATAGAAATGATAGATCATTGAGGAAACTTAAAAATATGT
1 TTTGATTGACATTAAAAACACAATGAATAGAAATGATAGACCATAGAAGAAACTTAAAAATATGT
** * *
56792018 TTTTTTTTAAAATATGATATCAG
66 TCCTCTTCAAAATATGATATCAG
* * * *
56792041 TTTGATTGATATTAAAAAGACAATGAATAGAAAT-AGTATACCATAGAAGAAATTTAAAAATATG
1 TTTGATTGACATTAAAAACACAATGAATAGAAATGA-TAGACCATAGAAGAAACTTAAAAATATG
*
56792105 TTCCTCTTCCAAATATGATA
65 TTCCTCTTCAAAATATGATA
56792125 CGTATTCAAT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
87 1 0.01
88 69 0.99
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (88 bp):
TTTGATTGACATTAAAAACACAATGAATAGAAATGATAGACCATAGAAGAAACTTAAAAATATGT
TCCTCTTCAAAATATGATATCAG
Found at i:56792818 original size:17 final size:18
Alignment explanation
Indices: 56792803--56792846 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
56792793 AACTAAAATT
56792803 TATTTTATAATAAAATAA
1 TATTTTATAATAAAATAA
* *
56792821 TATTTTGTAAT-AATTAA
1 TATTTTATAATAAAATAA
*
56792838 TATCTTATA
1 TATTTTATA
56792847 TAGTTTTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
TATTTTATAATAAAATAA
Found at i:56793813 original size:17 final size:17
Alignment explanation
Indices: 56793793--56793891 Score: 144
Period size: 17 Copynumber: 5.6 Consensus size: 17
56793783 CTATGATATG
56793793 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
56793810 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
56793828 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
56793845 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
56793863 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
56793882 CAATCTTAGA
1 CAATCTTAGA
56793892 AGATATGATT
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
17 31 0.42
18 31 0.42
19 11 0.15
20 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:56793831 original size:35 final size:35
Alignment explanation
Indices: 56793784--56793891 Score: 189
Period size: 35 Copynumber: 3.0 Consensus size: 35
56793774 TATAATCTTC
56793784 TATGATATGCAATCTTAGATATGATACAATCTTAGA
1 TATGAT-TGCAATCTTAGATATGATACAATCTTAGA
56793820 TATGATTGCAATCTTAGATATGATACAATCTTAGA
1 TATGATTGCAATCTTAGATATGATACAATCTTAGA
56793855 TATGATTGCAATCTTAGATATGATATACAATCTTAGA
1 TATGATTGCAATCTTAGATATG--ATACAATCTTAGA
56793892 AGATATGATT
Statistics
Matches: 70, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
35 51 0.73
36 6 0.09
37 13 0.19
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (35 bp):
TATGATTGCAATCTTAGATATGATACAATCTTAGA
Found at i:56793833 original size:18 final size:18
Alignment explanation
Indices: 56793793--56793891 Score: 157
Period size: 18 Copynumber: 5.6 Consensus size: 18
56793783 CTATGATATG
56793793 CAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTA
*
56793810 CAATCTTAGATATGATTG
1 CAATCTTAGATATGATTA
56793828 CAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTA
*
56793845 CAATCTTAGATATGATTG
1 CAATCTTAGATATGATTA
56793863 CAATCTTAGATATGATATA
1 CAATCTTAGATATGAT-TA
56793882 CAATCTTAGA
1 CAATCTTAGA
56793892 AGATATGATT
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
17 31 0.41
18 33 0.44
19 11 0.15
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (18 bp):
CAATCTTAGATATGATTA
Found at i:56797880 original size:47 final size:47
Alignment explanation
Indices: 56797811--56797904 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
56797801 AGGGAGTCAA
*
56797811 GACTTATGGGGCATGTATGTTATGGGCCCGAGCTCGTCAAAAGTTTC
1 GACTTATGGGGCATGTATGTTATGGGCCCGAGCTCATCAAAAGTTTC
56797858 GACTTATGGGGCATGTATGTTATGGGCCCGAGCTCATCAAAAGTTTC
1 GACTTATGGGGCATGTATGTTATGGGCCCGAGCTCATCAAAAGTTTC
56797905 AAGCTGACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (47 bp):
GACTTATGGGGCATGTATGTTATGGGCCCGAGCTCATCAAAAGTTTC
Found at i:56799524 original size:1 final size:1
Alignment explanation
Indices: 56799518--56799599 Score: 65
Period size: 1 Copynumber: 82.0 Consensus size: 1
56799508 CTTCTATTTC
* * * * * * * * *
56799518 AAAAAAAAAAAGAAAAGAAAAAGAGAAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
56799583 AAAGAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAA
56799600 TGGAGAGGCC
Statistics
Matches: 59, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:56799544 original size:8 final size:7
Alignment explanation
Indices: 56799518--56799599 Score: 107
Period size: 7 Copynumber: 11.6 Consensus size: 7
56799508 CTTCTATTTC
56799518 AAAAA-A
1 AAAAAGA
56799524 AAAAAG-
1 AAAAAGA
56799530 -AAAAGA
1 AAAAAGA
56799536 AAAAGAGAA
1 AAAA-AG-A
56799545 AAAAAGA
1 AAAAAGA
56799552 AAAAAGA
1 AAAAAGA
56799559 AAAAAGA
1 AAAAAGA
56799566 AAAAAGA
1 AAAAAGA
56799573 AAAAAGAA
1 AAAAAG-A
56799581 AAAAAGAA
1 AAAAAG-A
56799589 AAAAAGA
1 AAAAAGA
56799596 AAAA
1 AAAA
56799600 TGGAGAGGCC
Statistics
Matches: 70, Mismatches: 0, Indels: 11
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.07
6 5 0.07
7 36 0.51
8 19 0.27
9 5 0.07
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:56799548 original size:21 final size:20
Alignment explanation
Indices: 56799518--56799598 Score: 101
Period size: 22 Copynumber: 3.9 Consensus size: 20
56799508 CTTCTATTTC
56799518 AAAA-AAAAAAAGAAAAGAA
1 AAAAGAAAAAAAGAAAAGAA
56799537 AAAGAGAAAAAAAGAAAAAAGAA
1 AAA-AGAAAAAAAG--AAAAGAA
*
56799560 AAAAGAAAAAAGAAAAAAGAAA
1 AAAAGAAAAAA-AGAAAAG-AA
56799582 AAAAGAAAAAAAGAAAA
1 AAAAGAAAAAAAGAAAA
56799599 ATGGAGAGGC
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.06
20 1 0.02
21 18 0.33
22 21 0.39
23 11 0.20
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAGAAAAGAA
Found at i:56799578 original size:44 final size:41
Alignment explanation
Indices: 56799519--56799599 Score: 126
Period size: 44 Copynumber: 1.9 Consensus size: 41
56799509 TTCTATTTCA
*
56799519 AAAAAAAAAAGAAAAGAAAAAGAGAAAAAAAGAAAAAAGAA
1 AAAAAAAAAAGAAAAGAAAAAAAGAAAAAAAGAAAAAAGAA
56799560 AAAAGAAAAAAGAAAAAAGAAAAAAAGAAAAAAAGAAAAA
1 AAAA-AAAAAAG--AAAAGAAAAAAAGAAAAAAAGAAAAA
56799600 TGGAGAGGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
41 4 0.11
42 7 0.19
44 25 0.69
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (41 bp):
AAAAAAAAAAGAAAAGAAAAAAAGAAAAAAAGAAAAAAGAA
Found at i:56800682 original size:84 final size:84
Alignment explanation
Indices: 56800541--56800699 Score: 239
Period size: 84 Copynumber: 1.9 Consensus size: 84
56800531 AAATTCAGCG
* * *
56800541 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTGCAGATCTTATCTCCCTAAGCAGTAGT
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAGT
*
56800606 GGAGCAGATCGAAGACTTA
66 GGAACAGATCGAAGACTTA
** *
56800625 CCTTAA-CCCTCTAAGCAGTAGGGTAATGGGCTAAAATTACAGATCTTATCTCCCTAAGTAGTAG
1 CCTTAATCCC-CTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAG
56800689 TGGAACAGATC
65 TGGAACAGATC
56800700 AACGACGACT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
83 3 0.04
84 64 0.96
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (84 bp):
CCTTAATCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAGT
GGAACAGATCGAAGACTTA
Found at i:56801195 original size:87 final size:88
Alignment explanation
Indices: 56801026--56801200 Score: 210
Period size: 87 Copynumber: 2.0 Consensus size: 88
56801016 GAGGGCAGAC
* * * *
56801026 ACATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATTTTTG
1 ACATAGCAGATCTGGCCTTCAGATGTTTACACTGAAGCAAGATCCAAGATGATTTGGCATCTCTG
* *
56801091 TGCTTACAAGGAACAAATCGAAG
66 TACTTACAAAGAACAAATCGAAG
* * * * *
56801114 ACATAGCTGATTTGGCTTTCACG-TGTTTACATTGAAGCAAG-TCTAAGATGATTTGGCATCTCT
1 ACATAGCAGATCTGGCCTTCA-GATGTTTACACTGAAGCAAGATCCAAGATGATTTGGCATCTCT
* *
56801177 GTATTTTCAAAGAACAAATCGAAG
65 GTACTTACAAAGAACAAATCGAAG
56801201 TTTGGCGTCT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
87 38 0.52
88 34 0.47
89 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (88 bp):
ACATAGCAGATCTGGCCTTCAGATGTTTACACTGAAGCAAGATCCAAGATGATTTGGCATCTCTG
TACTTACAAAGAACAAATCGAAG
Found at i:56801373 original size:206 final size:207
Alignment explanation
Indices: 56800820--56801406 Score: 942
Period size: 207 Copynumber: 2.8 Consensus size: 207
56800810 CAGGTTAAAG
56800820 CATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
1 CATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
* *
56800885 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGTTGAGGCAAGTC
66 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTC
* *
56800950 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAACTTTGGCGTCTCCATATTCGAT
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
*
56801015 GGAGGGCAGACA
196 GGAGGACAGACA
** **
56801027 CATAGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATTTTTGT
1 CATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
*
56801092 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACATTGAAGCAAGTC
66 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTC
* *
56801157 TAAGATGATTTGGCATCTCTGTATTTTCAAAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
56801222 GGAGGACAGACA
196 GGAGGACAGACA
* * * * * *
56801234 TATAGCAGATCTAACCTTCAGATGATTAGACTAAAGC-AGATCTAAGATGGTTTGGTATCCTTGT
1 CATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
* * * **
56801298 GCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCGCGTGTTTACGCTGAAGCAAACC
66 GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTC
* *
56801363 TAAGATGATTTGGCATCTCTGTATTGTCAGGGAACAAATTGAAG
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG
56801407 AAGCAGATTT
Statistics
Matches: 348, Mismatches: 32, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
206 122 0.35
207 226 0.65
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (207 bp):
CATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGT
GCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTC
TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
GGAGGACAGACA
Found at i:56811178 original size:24 final size:25
Alignment explanation
Indices: 56811147--56811257 Score: 90
Period size: 24 Copynumber: 4.6 Consensus size: 25
56811137 TTCGGGCTAT
56811147 ATAA-CGGGAAGCTCA-TAAGAGCC
1 ATAATCGGGAAGCTCACTAAGAGCC
* * *
56811170 ATAATCGGGAAGTTCACAAAGAACC
1 ATAATCGGGAAGCTCACTAAGAGCC
* **
56811195 AT-ATCAGGAAGCTCAGGAAGAGCC
1 ATAATCGGGAAGCTCACTAAGAGCC
* *
56811219 -T-ATCAGGAAGCTCAATAAGAGCC
1 ATAATCGGGAAGCTCACTAAGAGCC
56811242 ATTTAAT-GGGAAGCTC
1 A--TAATCGGGAAGCTC
56811258 CCGATAGCCA
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
23 25 0.35
24 27 0.38
25 8 0.11
26 9 0.13
27 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (25 bp):
ATAATCGGGAAGCTCACTAAGAGCC
Found at i:56818288 original size:43 final size:42
Alignment explanation
Indices: 56818133--56818280 Score: 161
Period size: 43 Copynumber: 3.5 Consensus size: 42
56818123 CAACGCCATA
* ** * *
56818133 TCCCAGATATGGTCTTACATGTTATCATATATCGATGCCACTG
1 TCCCAGACATGGTCTTACACATAATCATATA-CGATGCCAATG
* * * * *
56818176 TCCTAGACAGGGTCTTATACAAAATCATATAACGGTGCCAATG
1 TCCCAGACATGGTCTTACACATAATCATAT-ACGATGCCAATG
*
56818219 TCCCAGACATGGTCTTACACATAATCATAATACAATGCCAATG
1 TCCCAGACATGGTCTTACACATAATCAT-ATACGATGCCAATG
*
56818262 CCCCAGACATGGTCTTACA
1 TCCCAGACATGGTCTTACA
56818281 TGTAATCACA
Statistics
Matches: 86, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
43 83 0.97
44 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACATAATCATATACGATGCCAATG
Done.