Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007894.1 Hibiscus syriacus cultivar Beakdansim tig00110279_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: 1425917
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1205390 original size:19 final size:20
Alignment explanation
Indices: 1205366--1205409 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1205356 AGTTTTATTT
*
1205366 ATTATTA-AAGAATAA-AAGA
1 ATTATTAGAA-AATAACAAAA
1205385 ATTATTAGAAAATAACAAAA
1 ATTATTAGAAAATAACAAAA
1205405 ATTAT
1 ATTAT
1205410 AGATAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (20 bp):
ATTATTAGAAAATAACAAAA
Found at i:1205708 original size:72 final size:72
Alignment explanation
Indices: 1205620--1205764 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
1205610 AATGCCTCTA
1205620 AATAAATATCAAATTAATTACAAATAAAAAATATTTTATAAAATGTCAATGAATTCTTTTTCCTC
1 AATAAATATCAAATTAATTACAAATAAAAAATATTTTATAAAATGTCAATGAATTCTTTTTCCTC
1205685 ACAAACG
66 ACAAACG
1205692 AATAAATATCAAATTAATTACAAATAAAAAATATTTTATAAAATGTCAATGAATTCTTTTTCCTC
1 AATAAATATCAAATTAATTACAAATAAAAAATATTTTATAAAATGTCAATGAATTCTTTTTCCTC
1205757 ACAAACG
66 ACAAACG
1205764 A
1 A
1205765 GATTTTAGTG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.34
Consensus pattern (72 bp):
AATAAATATCAAATTAATTACAAATAAAAAATATTTTATAAAATGTCAATGAATTCTTTTTCCTC
ACAAACG
Found at i:1215312 original size:16 final size:16
Alignment explanation
Indices: 1215291--1215324 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1215281 TTACTATTCA
*
1215291 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1215307 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1215323 CG
1 CG
1215325 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1216095 original size:15 final size:16
Alignment explanation
Indices: 1216075--1216106 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1216065 TGGCAGATCC
1216075 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
1216090 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
1216106 A
1 A
1216107 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:1222971 original size:21 final size:21
Alignment explanation
Indices: 1222945--1222989 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1222935 CCCTAAATTA
*
1222945 TAAATCATAATCCCAT-AATCC
1 TAAATCATAA-ACCATAAATCC
*
1222966 TAAATCTTAAACCATAAATCC
1 TAAATCATAAACCATAAATCC
1222987 TAA
1 TAA
1222990 GCCCTGACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAATCATAAACCATAAATCC
Found at i:1223590 original size:16 final size:16
Alignment explanation
Indices: 1223561--1223596 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1223551 AAATTAACAA
1223561 AAAT-TATTAAATATT
1 AAATATATTAAATATT
*
1223576 AAATATATTATATATT
1 AAATATATTAAATATT
1223592 AAATA
1 AAATA
1223597 CATATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATATTAAATATT
Found at i:1224080 original size:2 final size:2
Alignment explanation
Indices: 1224073--1224106 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1224063 CATGATGTGT
1224073 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
1224107 AGAGTTCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1224228 original size:29 final size:29
Alignment explanation
Indices: 1224195--1224255 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
1224185 ATTATTTTTG
1224195 TAGTTAATTTATAAATTTCAATTAAATCT
1 TAGTTAATTTATAAATTTCAATTAAATCT
1224224 TAGTTAATTTATAAATTTCAATTAAATCT
1 TAGTTAATTTATAAATTTCAATTAAATCT
1224253 TAG
1 TAG
1224256 ATGTATCATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (29 bp):
TAGTTAATTTATAAATTTCAATTAAATCT
Found at i:1224318 original size:2 final size:2
Alignment explanation
Indices: 1224311--1224336 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1224301 TATTGTATCA
1224311 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
1224337 TAAGAGAGAA
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:1225168 original size:22 final size:21
Alignment explanation
Indices: 1225143--1225183 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1225133 TATAAAAAAT
1225143 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
1225165 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
1225184 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:1226205 original size:22 final size:22
Alignment explanation
Indices: 1226162--1226208 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1226152 TGATAAAAAA
* *
1226162 TTATTTAAAATATTATTATTTT
1 TTATTTAAAACATAATTATTTT
1226184 TTATTTAAAACATCAATT-TTTT
1 TTATTTAAAACAT-AATTATTTT
1226206 TTA
1 TTA
1226209 ATATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTTAAAACATAATTATTTT
Found at i:1226777 original size:17 final size:17
Alignment explanation
Indices: 1226750--1226788 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1226740 AATTTACAAT
1226750 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
1226766 TAATTATAAATAATATC
1 TAATTATAAATAATATC
1226783 TAATTA
1 TAATTA
1226789 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:1228062 original size:82 final size:82
Alignment explanation
Indices: 1227930--1228080 Score: 248
Period size: 82 Copynumber: 1.8 Consensus size: 82
1227920 GCCCCCAATT
* *
1227930 TTTTTTATCATTAAATAATATTGGGATAATTACCTATTGATGCCTTTAAATTTTGATTTATTTTA
1 TTTTTTATCATTAAATAATATTGGGATAATTACCTATTGAGGCCTTTAAATTTTAATTTATTTTA
1227995 ATTTTTCCCACTCCCAA
66 ATTTTTCCCACTCCCAA
* * * *
1228012 TTTTTTATCATTAAATAATATTGGGATAATTATCTATTTAGGTCTTTAAATTTTAATTTATTTTG
1 TTTTTTATCATTAAATAATATTGGGATAATTACCTATTGAGGCCTTTAAATTTTAATTTATTTTA
1228077 ATTT
66 ATTT
1228081 AACCCCCTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (82 bp):
TTTTTTATCATTAAATAATATTGGGATAATTACCTATTGAGGCCTTTAAATTTTAATTTATTTTA
ATTTTTCCCACTCCCAA
Found at i:1229452 original size:31 final size:31
Alignment explanation
Indices: 1229360--1229470 Score: 102
Period size: 31 Copynumber: 3.5 Consensus size: 31
1229350 GTTACTAAAT
*
1229360 TCATTAAACTTAGT-GAACT-GTTACAAAATGAG
1 TCATTAAACTTA-TCAAACTAG-TACAAAATG-G
*
1229392 -CATTAAACTTTTGCAAACTAGTACAAAATGG
1 TCATTAAACTTAT-CAAACTAGTACAAAATGG
* * * *
1229423 TCATTGAACTTATCAAACTATTACGAAATGT
1 TCATTAAACTTATCAAACTAGTACAAAATGG
*
1229454 TCCTTAAACTTATCAAA
1 TCATTAAACTTATCAAA
1229471 TTTTATCACT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
30 1 0.02
31 41 0.62
32 23 0.35
33 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (31 bp):
TCATTAAACTTATCAAACTAGTACAAAATGG
Found at i:1229609 original size:23 final size:23
Alignment explanation
Indices: 1229579--1229626 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1229569 TCGTTTCAAC
1229579 ATAGTTTAATAATCATTTTGTAT
1 ATAGTTTAATAATCATTTTGTAT
1229602 ATAGTTTAATAATCATTTTGTAT
1 ATAGTTTAATAATCATTTTGTAT
1229625 AT
1 AT
1229627 TTACCCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.52
Consensus pattern (23 bp):
ATAGTTTAATAATCATTTTGTAT
Found at i:1230985 original size:21 final size:21
Alignment explanation
Indices: 1230955--1231100 Score: 133
Period size: 21 Copynumber: 7.0 Consensus size: 21
1230945 GATTTACATA
*
1230955 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* *
1230976 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCGAAG
1230999 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* *
1231018 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCGAAG
1231041 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
* *
1231060 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCGAAG
1231083 TT--CGTTGCGATAGTCGAA
1 TTCGCGTTGCGATAGTCGAA
1231101 CGAGACGAGA
Statistics
Matches: 102, Mismatches: 13, Indels: 22
0.74 0.09 0.16
Matches are distributed among these distances:
19 24 0.24
21 51 0.50
23 27 0.26
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:1231012 original size:42 final size:42
Alignment explanation
Indices: 1230961--1231100 Score: 280
Period size: 42 Copynumber: 3.3 Consensus size: 42
1230951 CATATTCGCA
1230961 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1231003 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1231045 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1231087 TTGCGATAGTCGAA
1 TTGCGATAGTCGAA
1231101 CGAGACGAGA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 98 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:1233333 original size:126 final size:126
Alignment explanation
Indices: 1233108--1233361 Score: 391
Period size: 126 Copynumber: 2.0 Consensus size: 126
1233098 AGAACGAGCT
* ** *
1233108 TTCAATCTAAGCTAACGTTGAATGAGTTTCTAAAGAACACCGATATTCACTGGTGCATAACCGAT
1 TTCAACCTAAGCTAAAATTGAATGAGTTTCTAAAGAACACCGATATTCACTAGTGCATAACCGAT
** *
1233173 CACCACGTGTGATAAAAAAGTTGTTAGATCTGTAAATAAGGCTTATATCACAAATAAGTAC
66 CACCACAAGTGATAAAAAAGTTGTTAGATCTGTAAATAAGGCTTATATAACAAATAAGTAC
* * * *
1233234 TTCAACCTAAGCTAAAATTGAATGGGTTTCTAATGAACATCGATATTCACTAGTGCATAACTGAT
1 TTCAACCTAAGCTAAAATTGAATGAGTTTCTAAAGAACACCGATATTCACTAGTGCATAACCGAT
* *
1233299 CACCACAAGTGATAAAAAAGTTGTTTGGTCTGTAAATAAGGCTTATATAACAAATAAGTAC
66 CACCACAAGTGATAAAAAAGTTGTTAGATCTGTAAATAAGGCTTATATAACAAATAAGTAC
1233360 TT
1 TT
1233362 AAAGTATGCC
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 115 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (126 bp):
TTCAACCTAAGCTAAAATTGAATGAGTTTCTAAAGAACACCGATATTCACTAGTGCATAACCGAT
CACCACAAGTGATAAAAAAGTTGTTAGATCTGTAAATAAGGCTTATATAACAAATAAGTAC
Found at i:1233448 original size:31 final size:29
Alignment explanation
Indices: 1233388--1233449 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 29
1233378 TTCATCTAAG
* *
1233388 TACCTAAAGTACTTTTTGGTCAAAGTAGA
1 TACCTAAAGTACATTTTGATCAAAGTAGA
1233417 TACCTAAAGTTATCATTTTGATC-AAGATAGA
1 TACCTAAAG-TA-CATTTTGATCAAAG-TAGA
1233448 TA
1 TA
1233450 GTATTCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 9 0.32
30 5 0.18
31 14 0.50
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (29 bp):
TACCTAAAGTACATTTTGATCAAAGTAGA
Found at i:1235098 original size:2 final size:2
Alignment explanation
Indices: 1235091--1235118 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1235081 TGAGCCTGGC
1235091 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
1235119 TCATCATTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1241866 original size:15 final size:15
Alignment explanation
Indices: 1241846--1241882 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1241836 ATATTTAGCT
*
1241846 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
1241861 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
1241876 GGGCGGG
1 GGGCGGG
1241883 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:1243821 original size:21 final size:21
Alignment explanation
Indices: 1243721--1243814 Score: 179
Period size: 21 Copynumber: 4.5 Consensus size: 21
1243711 TTTTGTTTGT
1243721 TTCGCTGTTTAATCCTTTTCA
1 TTCGCTGTTTAATCCTTTTCA
1243742 TTCGCTGTTTAATCCTTTTCA
1 TTCGCTGTTTAATCCTTTTCA
1243763 TTCGCTGTTTAATCCTTTTCA
1 TTCGCTGTTTAATCCTTTTCA
1243784 TTCGCTGTTTAATCCTTTTCA
1 TTCGCTGTTTAATCCTTTTCA
*
1243805 TTCACTGTTT
1 TTCGCTGTTT
1243815 GGACCTTGCA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.14, C:0.23, G:0.10, T:0.53
Consensus pattern (21 bp):
TTCGCTGTTTAATCCTTTTCA
Found at i:1243972 original size:11 final size:11
Alignment explanation
Indices: 1243956--1243981 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1243946 ATGTAACCCC
1243956 TAGATTAAATT
1 TAGATTAAATT
1243967 TAGATTAAATT
1 TAGATTAAATT
1243978 TAGA
1 TAGA
1243982 CGGTCACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (11 bp):
TAGATTAAATT
Found at i:1244113 original size:2 final size:2
Alignment explanation
Indices: 1244106--1244136 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1244096 ACTATAGATA
1244106 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1244137 AAGACAATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1246373 original size:67 final size:67
Alignment explanation
Indices: 1246260--1246393 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
1246250 TCCTGTGGGG
*
1246260 GAGTTAATACGATATCATTTTGGTATGTCATCAGATCATCTGACATATCATTACATTGTTTGTTA
1 GAGTTAATACGATATCATTTTGGTATGTCATCAGATCATCTAACATATCATTACATTGTTTGTTA
1246325 TT
66 TT
1246327 GAGTTAATACGATATCATTTTGGTATGTCATCAGATCATCTAACATATCATTACATTGTTTGTTA
1 GAGTTAATACGATATCATTTTGGTATGTCATCAGATCATCTAACATATCATTACATTGTTTGTTA
1246392 TT
66 TT
1246394 TAACGATTGA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (67 bp):
GAGTTAATACGATATCATTTTGGTATGTCATCAGATCATCTAACATATCATTACATTGTTTGTTA
TT
Found at i:1246378 original size:33 final size:32
Alignment explanation
Indices: 1246271--1246378 Score: 87
Period size: 33 Copynumber: 3.2 Consensus size: 32
1246261 AGTTAATACG
1246271 ATATCATTTTGGTATGTCATCAGATCATCTGAC
1 ATATCATTTTGGTATGTCATCAGATCATCT-AC
* * * * *
1246304 ATATCATTACATT-GTTTGTTAT-TGAGTTA-ATAC
1 ATATCATT---TTGGTATGTCATCAGA-TCATCTAC
1246337 GATATCATTTTGGTATGTCATCAGATCATCTAAC
1 -ATATCATTTTGGTATGTCATCAGATCATCT-AC
1246371 ATATCATT
1 ATATCATT
1246379 ACATTGTTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
31 2 0.04
32 9 0.16
33 21 0.38
34 13 0.23
35 9 0.16
36 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (32 bp):
ATATCATTTTGGTATGTCATCAGATCATCTAC
Found at i:1247631 original size:16 final size:18
Alignment explanation
Indices: 1247610--1247647 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1247600 AACGTCTTTT
1247610 AAAACA-ATTTTAAGA-A
1 AAAACATATTTTAAGACA
*
1247626 AAAACATTTTTTAAGACA
1 AAAACATATTTTAAGACA
1247644 AAAA
1 AAAA
1247648 TGGTATGCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 8 0.42
18 5 0.26
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAACATATTTTAAGACA
Found at i:1251390 original size:70 final size:70
Alignment explanation
Indices: 1251307--1251472 Score: 314
Period size: 70 Copynumber: 2.4 Consensus size: 70
1251297 TTAAACAATC
**
1251307 TCACATGGCTAAGAAACATAGAAGAGTATTCCAAAAGTCTAAAGAGTAAAAATATGATAACAAAA
1 TCACATGATTAAGAAACATAGAAGAGTATTCCAAAAGTCTAAAGAGTAAAAATATGATAACAAAA
1251372 CATTA
66 CATTA
1251377 TCACATGATTAAGAAACATAGAAGAGTATTCCAAAAGTCTAAAGAGTAAAAATATGATAACAAAA
1 TCACATGATTAAGAAACATAGAAGAGTATTCCAAAAGTCTAAAGAGTAAAAATATGATAACAAAA
1251442 CATTA
66 CATTA
1251447 TCACATGATTAAGAAACATAGAAGAG
1 TCACATGATTAAGAAACATAGAAGAG
1251473 CATCCCAACT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 94 1.00
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (70 bp):
TCACATGATTAAGAAACATAGAAGAGTATTCCAAAAGTCTAAAGAGTAAAAATATGATAACAAAA
CATTA
Found at i:1256010 original size:2 final size:2
Alignment explanation
Indices: 1256005--1256054 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1255995 TAAGACAAAT
1256005 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
1256047 TA TA TA TA
1 TA TA TA TA
1256055 AAGATCATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1257948 original size:181 final size:183
Alignment explanation
Indices: 1257627--1258019 Score: 584
Period size: 181 Copynumber: 2.2 Consensus size: 183
1257617 TTTTCTAATT
* *
1257627 TATATAA-A-ATTAAATATTTTTTAATTTAAAAAAAGTTTATAATTAATTTAAATAATAAATAAT
1 TATATAATATATTTAATA-TTTTTAATTTAAAAAAAGTTTACAATTAATTTAAATAATAAATAAT
*
1257690 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTCATT
65 TATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTCATT
* *
1257755 GAATCTTAAATTATTAATTGGGTTTTAAAT-AGTTTGGGCTT-AGTTCATATGTTA
130 GAATCTTAAATTATTAATTGGGTTTTAAATGA-TTT-GGATTAAGCTCATATGTTA
* *
1257809 TATATAATATATTTAATATTTTTAA-TTAAAAACAGTTTACAATTAATTTAAATAATATATAATT
1 TATATAATATATTTAATATTTTTAATTTAAAAAAAGTTTACAATTAATTTAAATAATAAATAATT
* *
1257873 ATAAAATAAAAAATTTATG-T-AATTTTTTATTTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 ATAAAATAAAAAATTTA-GATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTCATT
* *
1257936 GGATCTTAAATTATTAATTGGGTTTTTAATGATTTGGATTAAGCTCATATGTTA
130 GAATCTTAAATTATTAATTGGGTTTTAAATGATTTGGATTAAGCTCATATGTTA
**
1257990 TATATAATATATTTAATATTTAAAATTTAA
1 TATATAATATATTTAATATTTTTAATTTAA
1258020 TTTCAGTTAA
Statistics
Matches: 192, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
180 4 0.02
181 107 0.56
182 65 0.34
183 9 0.05
184 7 0.04
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTAATTTAAAAAAAGTTTACAATTAATTTAAATAATAAATAATT
ATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTCATTG
AATCTTAAATTATTAATTGGGTTTTAAATGATTTGGATTAAGCTCATATGTTA
Found at i:1259978 original size:13 final size:13
Alignment explanation
Indices: 1259960--1259984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1259950 GTTCATGTAT
1259960 TCGGTAAGTTAAA
1 TCGGTAAGTTAAA
1259973 TCGGTAAGTTAA
1 TCGGTAAGTTAA
1259985 GTTAGATCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (13 bp):
TCGGTAAGTTAAA
Found at i:1262558 original size:12 final size:11
Alignment explanation
Indices: 1262515--1262556 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
1262505 TCAATTCAAC
1262515 TTAAATTTT-T
1 TTAAATTTTAT
*
1262525 TTATATTTTTAT
1 TTA-AATTTTAT
1262537 TTAAATTTTAT
1 TTAAATTTTAT
1262548 TTAAATTTT
1 TTAAATTTT
1262557 TAAATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 3 0.11
11 21 0.75
12 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTAAATTTTAT
Found at i:1266515 original size:14 final size:15
Alignment explanation
Indices: 1266496--1266533 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1266486 TCCCCATCTC
1266496 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1266510 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1266526 TAATTTTT
1 TAATTTTT
1266534 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1267107 original size:12 final size:12
Alignment explanation
Indices: 1267086--1267119 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1267076 ACCACATTTC
*
1267086 CAATACCAAACA
1 CAATATCAAACA
1267098 CAATATCAAACA
1 CAATATCAAACA
*
1267110 CAATCTCAAA
1 CAATATCAAA
1267120 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1267272 original size:24 final size:24
Alignment explanation
Indices: 1267245--1267298 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1267235 GTATTCGAAA
1267245 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1267269 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1267293 TTTGAT
1 TTTGAT
1267299 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1269583 original size:18 final size:18
Alignment explanation
Indices: 1269560--1269595 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1269550 AAGCAAAAGG
*
1269560 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1269578 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1269596 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1269939 original size:20 final size:20
Alignment explanation
Indices: 1269914--1269953 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1269904 CGAAATAAGG
1269914 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
1269934 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
1269954 AACGCTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:1270072 original size:25 final size:25
Alignment explanation
Indices: 1270044--1270093 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1270034 AAATCAATTA
*
1270044 AACATTATTGTGGGTACATTATTTG
1 AACATTATTATGGGTACATTATTTG
* *
1270069 AACATTGTTATGGGTATATTATTTG
1 AACATTATTATGGGTACATTATTTG
1270094 GAAAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (25 bp):
AACATTATTATGGGTACATTATTTG
Found at i:1270500 original size:18 final size:18
Alignment explanation
Indices: 1270479--1270515 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1270469 GTAATTGGAG
1270479 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1270497 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1270515 T
1 T
1270516 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1270522 original size:24 final size:24
Alignment explanation
Indices: 1270471--1270523 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1270461 TTTCATATGT
* * *
1270471 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1270495 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1270519 AATTT
1 AATTT
1270524 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1270868 original size:39 final size:39
Alignment explanation
Indices: 1270825--1270911 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1270815 TCCGATGCTC
1270825 ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
* *
1270864 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
1270903 ATCAAAATC
1 ATCAAAATC
1270912 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
Found at i:1272706 original size:21 final size:21
Alignment explanation
Indices: 1272682--1272723 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1272672 TGAACAGTAG
*
1272682 GAGGAGCTTCTTCG-ATGATGA
1 GAGGAGCCTCTT-GAATGATGA
*
1272703 GAGGGGCCTCTTGAATGATGA
1 GAGGAGCCTCTTGAATGATGA
1272724 TAGGTGCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.24, C:0.14, G:0.36, T:0.26
Consensus pattern (21 bp):
GAGGAGCCTCTTGAATGATGA
Found at i:1275460 original size:25 final size:25
Alignment explanation
Indices: 1275431--1275482 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1275421 TTAAAAGGAT
1275431 TATTTT-TATAAATATATATTT-ATAA
1 TATTTTATATAAAT-TA-ATTTAATAA
*
1275456 TATTTTATTTAAATTAATTTAATAA
1 TATTTTATATAAATTAATTTAATAA
1275481 TA
1 TA
1275483 AATGAGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 4 0.17
25 14 0.58
26 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTTTATATAAATTAATTTAATAA
Found at i:1275620 original size:35 final size:35
Alignment explanation
Indices: 1275574--1275647 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
1275564 ATCAAAGTCT
1275574 GACAATGCTAGGTATGGCTCATATAGCAGTTGGAG
1 GACAATGCTAGGTATGGCTCATATAGCAGTTGGAG
1275609 GACAATGCTAGGTATGGCTCATATAGCAGTTGGAG
1 GACAATGCTAGGTATGGCTCATATAGCAGTTGGAG
1275644 GACA
1 GACA
1275648 GATGTTAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (35 bp):
GACAATGCTAGGTATGGCTCATATAGCAGTTGGAG
Found at i:1279773 original size:15 final size:15
Alignment explanation
Indices: 1279755--1279786 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1279745 TTTTGTGTAG
*
1279755 TATTCTTTTTAAGTT
1 TATTCTTTTTAAATT
1279770 TATTCTTTTTAAATT
1 TATTCTTTTTAAATT
1279785 TA
1 TA
1279787 GTCAGGTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (15 bp):
TATTCTTTTTAAATT
Found at i:1282474 original size:21 final size:24
Alignment explanation
Indices: 1282448--1282498 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
1282438 TAATTATTAA
1282448 AATATTTA-AAAT-ATATT-TATT
1 AATATTTATAAATAATATTATATT
*
1282469 AATATTTATTAATAATATTATATT
1 AATATTTATAAATAATATTATATT
1282493 -ATATTT
1 AATATTT
1282499 TTAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.31
22 3 0.12
23 11 0.42
24 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATATTTATAAATAATATTATATT
Found at i:1282475 original size:10 final size:10
Alignment explanation
Indices: 1282460--1282506 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
1282450 TATTTAAAAT
1282460 ATATTTATTA
1 ATATTTATTA
1282470 ATATTTATTA
1 ATATTTATTA
*
1282480 ATAATATTATATT
1 AT-AT-TTAT-TA
1282493 ATATTT-TTA
1 ATATTTATTA
1282502 ATATT
1 ATATT
1282507 ATAATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 6 0.19
10 13 0.41
11 4 0.12
12 6 0.19
13 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATATTTATTA
Found at i:1282489 original size:22 final size:24
Alignment explanation
Indices: 1282448--1282504 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 24
1282438 TAATTATTAA
*
1282448 AATATTTA-AAAT-ATATTTAT-T
1 AATATTTATTAATAATATTTATAT
1282469 AATATTTATTAATAATA-TTATAT
1 AATATTTATTAATAATATTTATAT
*
1282492 TATATTT-TTAATA
1 AATATTTATTAATA
1282505 TTATAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 8 0.26
22 13 0.42
23 10 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATATTTATTAATAATATTTATAT
Found at i:1282496 original size:33 final size:32
Alignment explanation
Indices: 1282440--1282513 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
1282430 CAAAATATTA
1282440 ATTATTAA-AATATTTAAAATATATTTATTAAT
1 ATTATTAATAATATTTAAAATATATTT-TTAAT
* *
1282472 ATTTATTAATAATA-TTATATTATATTTTTAAT
1 A-TTATTAATAATATTTAAAATATATTTTTAAT
1282504 ATTA-TAATAA
1 ATTATTAATAA
1282514 AATAATCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 6 0.16
31 3 0.08
32 7 0.18
33 18 0.47
34 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
ATTATTAATAATATTTAAAATATATTTTTAAT
Found at i:1282526 original size:32 final size:33
Alignment explanation
Indices: 1282459--1282539 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 33
1282449 ATATTTAAAA
* *
1282459 TATATTTATTAATATTTATTAATAATATTATAT
1 TATATTTATTAATATTTAATAATAATATCATAT
1282492 TATATTT-TTAATATTATAATAA-AATAATCA-AT
1 TATATTTATTAATATT-TAATAATAAT-ATCATAT
*
1282524 TATATTATAATAATAT
1 TATATT-TATTAATAT
1282540 AAGATATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
32 19 0.46
33 16 0.39
34 6 0.15
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (33 bp):
TATATTTATTAATATTTAATAATAATATCATAT
Found at i:1282635 original size:17 final size:17
Alignment explanation
Indices: 1282579--1282638 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
1282569 ATAATAAATT
*
1282579 ATTAATAA-ATTTATATT
1 ATTAATAATA-TTATATA
* *
1282596 ATTATTAAT-TTCATAGA
1 ATTAATAATATT-ATATA
*
1282613 AATAATAATATTATATA
1 ATTAATAATATTATATA
1282630 ATTAATAAT
1 ATTAATAAT
1282639 GAATAATATT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 2 0.06
17 29 0.88
18 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTAATAATATTATATA
Found at i:1282707 original size:23 final size:23
Alignment explanation
Indices: 1282681--1282734 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1282671 GATTAATATA
**
1282681 AAAATATTTTAATAAAGATATTT
1 AAAATATACTAATAAAGATATTT
* * *
1282704 AAAATATACTAATTAATATTTTT
1 AAAATATACTAATAAAGATATTT
1282727 AAAATATA
1 AAAATATA
1282735 ATATAACACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
AAAATATACTAATAAAGATATTT
Found at i:1289652 original size:23 final size:22
Alignment explanation
Indices: 1289618--1289662 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
1289608 CAGTTTTACA
*
1289618 TATATTTTTCTAT-TTTTTATT
1 TATATTTTTCTATAATTTTATT
1289639 TATATTGTTATCTATAATTTTATT
1 TATATT-TT-TCTATAATTTTATT
1289663 GAACAATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 2 0.10
23 5 0.25
24 7 0.35
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (22 bp):
TATATTTTTCTATAATTTTATT
Found at i:1294527 original size:17 final size:18
Alignment explanation
Indices: 1294507--1294551 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
1294497 TATTGATCAA
*
1294507 TATCTTTTAG-GGTAAAC
1 TATCATTTAGAGGTAAAC
1294524 TATCATTTAGTAGGTAAAC
1 TATCATTTAG-AGGTAAAC
1294543 TATCATTTA
1 TATCATTTA
1294552 ATACCTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.36
19 16 0.64
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.42
Consensus pattern (18 bp):
TATCATTTAGAGGTAAAC
Found at i:1294541 original size:19 final size:19
Alignment explanation
Indices: 1294517--1294572 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1294507 TATCTTTTAG
*
1294517 GGTAAACTATCATTTAGTA
1 GGTAAACTATCATTTAATA
1294536 GGTAAACTATCATTTAATA
1 GGTAAACTATCATTTAATA
**
1294555 CCTAAACTATCAGTTTAA
1 GGTAAACTATCA-TTTAA
1294573 GTTTGTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 28 0.85
20 5 0.15
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (19 bp):
GGTAAACTATCATTTAATA
Found at i:1295675 original size:21 final size:20
Alignment explanation
Indices: 1295646--1295689 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1295636 AATGTATTTT
*
1295646 ATATTTTTTAATAAT-TAAAGA
1 ATATATTTTAA-AATATAAA-A
1295667 ATATATTTTAAAATATAAAA
1 ATATATTTTAAAATATAAAA
1295687 ATA
1 ATA
1295690 AAAATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATATATTTTAAAATATAAAA
Found at i:1301068 original size:30 final size:29
Alignment explanation
Indices: 1301031--1301109 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 29
1301021 ATTTGATATT
*
1301031 AATAGAAACTTGAAGGACCAAAATAGCAAA
1 AATAGAAA-TTGAAGGACCAAAATAGAAAA
* *
1301061 GATAGAAATAT-AAAGATCCAAAATAGAAAA
1 AATAGAAAT-TGAAGGA-CCAAAATAGAAAA
1301091 AATAGAAATTTGAAGGACC
1 AATAGAAA-TTGAAGGACC
1301110 TAATAAACCA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
29 5 0.12
30 30 0.75
31 5 0.12
ACGTcount: A:0.57, C:0.10, G:0.16, T:0.16
Consensus pattern (29 bp):
AATAGAAATTGAAGGACCAAAATAGAAAA
Found at i:1306582 original size:13 final size:13
Alignment explanation
Indices: 1306542--1306586 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
1306532 AAACACTCAA
1306542 AATATTATTATTTT
1 AATA-TATTATTTT
*
1306556 -ATATATTTAATTT
1 AATATA-TTATTTT
1306569 AATATATTATTTT
1 AATATATTATTTT
1306582 AATAT
1 AATAT
1306587 CATTTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.07
13 20 0.74
14 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATATTATTTT
Found at i:1306837 original size:19 final size:19
Alignment explanation
Indices: 1306813--1306878 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
1306803 AAATATAATA
1306813 TAATATAATATTTTTATTT
1 TAATATAATATTTTTATTT
*
1306832 TAATATTATAATTTTTGATATT
1 TAATATAAT-ATTTTT-AT-TT
*
1306854 TTA-ATAATA-TTTTA-TT
1 TAATATAATATTTTTATTT
1306870 TAATA-AATA
1 TAATATAATA
1306879 ATTAATATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
16 8 0.21
17 1 0.03
18 1 0.03
19 12 0.31
20 7 0.18
21 6 0.15
22 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TAATATAATATTTTTATTT
Found at i:1306843 original size:22 final size:22
Alignment explanation
Indices: 1306816--1306859 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1306806 TATAATATAA
1306816 TATAATATTTT-TATTTTAATAT
1 TATAAT-TTTTATATTTTAATAT
1306838 TATAATTTTTGATATTTTAATA
1 TATAATTTTT-ATATTTTAATA
1306860 ATATTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 6 0.30
23 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TATAATTTTTATATTTTAATAT
Found at i:1306880 original size:37 final size:38
Alignment explanation
Indices: 1306851--1307013 Score: 137
Period size: 41 Copynumber: 4.3 Consensus size: 38
1306841 AATTTTTGAT
1306851 ATTT-TAATAATATTTTATTTAATAAATAATTAATATA
1 ATTTATAATAATATTTTATTTAATAAATAATTAATATA
* *
1306888 ATTTATAATATATTATTCTTTTTTAATAAATAATCAATATA
1 ATTTATAATA-A-TATT-TTATTTAATAAATAATTAATATA
* * *
1306929 ATTTATAAT-A-ATTTTATTTTAAGAAAAAATAAAT-TA
1 ATTTATAATAATATTTTA-TTTAATAAATAATTAATATA
*
1306965 A-TTATAAT-AT-TTTTATTT-ATAAA-ATTATAGATATA
1 ATTTATAATAATATTTTATTTAATAAATAAT-TA-ATATA
*
1307000 ATATTTTAATAATA
1 AT-TTATAATAATA
1307014 ATATTGAATG
Statistics
Matches: 103, Mismatches: 10, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
32 2 0.02
33 5 0.05
34 5 0.05
35 16 0.16
36 5 0.05
37 27 0.26
38 7 0.07
39 2 0.02
40 4 0.04
41 30 0.29
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (38 bp):
ATTTATAATAATATTTTATTTAATAAATAATTAATATA
Found at i:1306904 original size:35 final size:36
Alignment explanation
Indices: 1306804--1306982 Score: 125
Period size: 37 Copynumber: 4.8 Consensus size: 36
1306794 TATTCCTTGA
*
1306804 AATATAATATAA--TATAATATTTTTATTTTAATATTAT
1 AATA-AATATAATTTATAATA-TTTTATTTTAATA-AAT
*** *
1306841 AATTTTTGATATTTTAATAATATTTTA-TTTAATAAAT
1 AATAAAT-ATAATTT-ATAATATTTTATTTTAATAAAT
* *
1306878 AATTAATATAATTTATAATATATTATTCTTTTTTAATAAAT
1 AATAAATATAATTTAT-A-ATA-T-TT-TATTTTAATAAAT
* * *
1306919 AATCAATATAATTTATAATAATTTTATTTTAAGAAAA
1 AATAAATATAATTTATAAT-ATTTTATTTTAATAAAT
1306956 AATAAAT-TAA-TTATAATATTTTTATTT
1 AATAAATATAATTTATAATA-TTTTATTT
1306983 ATAAAATTAT
Statistics
Matches: 116, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
34 1 0.01
35 17 0.15
36 11 0.09
37 32 0.28
38 10 0.09
39 11 0.09
40 9 0.08
41 25 0.22
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (36 bp):
AATAAATATAATTTATAATATTTTATTTTAATAAAT
Found at i:1307944 original size:27 final size:27
Alignment explanation
Indices: 1307914--1307991 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
1307904 TATTACTTTT
1307914 AAAGATTGCGAGTTCAATATTGTAATC
1 AAAGATTGCGAGTTCAATATTGTAATC
* *
1307941 AAAGA-T--GA-TTGAA-CTT-T--T-
1 AAAGATTGCGAGTTCAATATTGTAATC
1307959 AAAGATTGCGAGTTCAATATTGTAATC
1 AAAGATTGCGAGTTCAATATTGTAATC
1307986 AAAGAT
1 AAAGAT
1307992 GATTGAACGT
Statistics
Matches: 38, Mismatches: 4, Indels: 18
0.63 0.07 0.30
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
21 3 0.08
22 6 0.16
23 6 0.16
24 3 0.08
26 2 0.05
27 11 0.29
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (27 bp):
AAAGATTGCGAGTTCAATATTGTAATC
Found at i:1307972 original size:45 final size:45
Alignment explanation
Indices: 1307908--1307999 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
1307898 AATTATTATT
1307908 ACTTTTAAAGATTGCGAGTTCAATATTGTAATCAAAGATGATTGA
1 ACTTTTAAAGATTGCGAGTTCAATATTGTAATCAAAGATGATTGA
1307953 ACTTTTAAAGATTGCGAGTTCAATATTGTAATCAAAGATGATTGA
1 ACTTTTAAAGATTGCGAGTTCAATATTGTAATCAAAGATGATTGA
1307998 AC
1 AC
1308000 GTTCATTATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (45 bp):
ACTTTTAAAGATTGCGAGTTCAATATTGTAATCAAAGATGATTGA
Found at i:1308288 original size:18 final size:17
Alignment explanation
Indices: 1308251--1308284 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1308241 CATGATTTTT
1308251 TTTAAAAAAACAACTTA
1 TTTAAAAAAACAACTTA
1308268 TTTAAAAAAACAA-TTA
1 TTTAAAAAAACAACTTA
1308284 T
1 T
1308285 ATTTTTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (17 bp):
TTTAAAAAAACAACTTA
Found at i:1308386 original size:32 final size:32
Alignment explanation
Indices: 1308344--1308407 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1308334 ACTTTTGTAT
*
1308344 TTATAATATTAAATTAAGATTACAATGTTATA
1 TTATAATATTAAATTAAGATTACAATATTATA
* * *
1308376 TTATAGTATTAAATTACGATTGCAATATTATA
1 TTATAATATTAAATTAAGATTACAATATTATA
1308408 GGTGCGGAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (32 bp):
TTATAATATTAAATTAAGATTACAATATTATA
Found at i:1312622 original size:2 final size:2
Alignment explanation
Indices: 1312615--1312641 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1312605 AATCAGAAGA
1312615 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1312642 AACAAACGGG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1315213 original size:27 final size:27
Alignment explanation
Indices: 1315183--1315261 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
1315173 TTTCGGTTAA
1315183 TTTTTTAATTAATCAAAAAAATTAATT
1 TTTTTTAATTAATCAAAAAAATTAATT
* * * * *
1315210 TTTTTAAATTTAT-ATAACAATTGAATA
1 TTTTTTAATTAATCAAAAAAATT-AATT
*
1315237 TTTTTTAA--ATTCAAAAAAA-TAATT
1 TTTTTTAATTAATCAAAAAAATTAATT
1315261 T
1 T
1315262 ACAATTAATT
Statistics
Matches: 39, Mismatches: 11, Indels: 7
0.68 0.19 0.12
Matches are distributed among these distances:
24 4 0.10
25 2 0.05
26 12 0.31
27 21 0.54
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (27 bp):
TTTTTTAATTAATCAAAAAAATTAATT
Found at i:1319166 original size:16 final size:15
Alignment explanation
Indices: 1319129--1319189 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 15
1319119 AACAAATAAT
*
1319129 ATAA-TAAATATAATA
1 ATAATTAAA-ATATTA
1319144 ATAATTAATAATATTA
1 ATAATTAA-AATATTA
*
1319160 ATTATTAAATATATTAA
1 ATAATTAAA-ATATT-A
1319177 ATAATTAAAATAT
1 ATAATTAAAATAT
1319190 CATAATAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
15 5 0.13
16 24 0.62
17 10 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATTAAAATATTA
Found at i:1319236 original size:27 final size:28
Alignment explanation
Indices: 1319129--1319238 Score: 96
Period size: 27 Copynumber: 3.8 Consensus size: 28
1319119 AACAAATAAT
*
1319129 ATAATAAATATAATAATAATTAATAATATTA
1 ATAATAAATA-AATAATAATTAA-AATA-TC
* *
1319160 ATTATTAAATATATTAAATAATTAAAATATC
1 A-TAATAAATA-AAT-AATAATTAAAATATC
*
1319191 ATAATAAATAAATAGTAATTAAAATAT-
1 ATAATAAATAAATAATAATTAAAATATC
* **
1319218 ATATTTTATAAATAATAATTA
1 ATAATAAATAAATAATAATTA
1319239 TAATCTATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
27 17 0.25
28 13 0.19
29 2 0.03
30 8 0.12
31 3 0.04
32 15 0.22
33 9 0.13
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (28 bp):
ATAATAAATAAATAATAATTAAAATATC
Found at i:1319304 original size:21 final size:21
Alignment explanation
Indices: 1319280--1319320 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1319270 AACTATACAC
1319280 ATAATA-TAGTAAATATAATAA
1 ATAATATTA-TAAATATAATAA
*
1319301 ATAATATTATAATTATAATA
1 ATAATATTATAAATATAATA
1319321 TATTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATATTATAAATATAATAA
Found at i:1325723 original size:18 final size:16
Alignment explanation
Indices: 1325702--1325760 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 16
1325692 TGTTTATAAA
1325702 ATATTTATTTTAATTACT
1 ATATTTA-TTT-ATTACT
*
1325720 ATATTTATTTATTATT
1 ATATTTATTTATTACT
* *
1325736 ATATTTTAATTATTTATT
1 ATA-TTTATTTA-TTACT
1325754 ATATTTA
1 ATATTTA
1325761 ATACTTAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
16 8 0.22
17 14 0.38
18 15 0.41
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
ATATTTATTTATTACT
Found at i:1325738 original size:16 final size:16
Alignment explanation
Indices: 1325702--1325820 Score: 79
Period size: 16 Copynumber: 7.4 Consensus size: 16
1325692 TGTTTATAAA
*
1325702 ATATTTATTTTAATTACT
1 ATATTTA-TTT-ATTATT
1325720 ATATTTATTTATTATT
1 ATATTTATTTATTATT
*
1325736 ATA-TT-TTAATTATT
1 ATATTTATTTATTATT
*
1325750 -TATTATATTTAATACTT
1 ATATT-TATTTATTA-TT
*
1325767 A-ATATTATTAATTATT
1 ATAT-TTATTTATTATT
*
1325783 -TATTATACTTATTTATT
1 ATATT-TATTTA-TTATT
*
1325800 ATATTTATTTGTTATT
1 ATATTTATTTATTATT
1325816 A-ATTT
1 ATATTT
1325821 CAATTTGAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
13 2 0.02
14 9 0.11
15 8 0.10
16 27 0.33
17 23 0.28
18 12 0.15
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (16 bp):
ATATTTATTTATTATT
Found at i:1325743 original size:30 final size:30
Alignment explanation
Indices: 1325703--1325805 Score: 120
Period size: 33 Copynumber: 3.3 Consensus size: 30
1325693 GTTTATAAAA
*
1325703 TATT-TATTTTAATTACTATATT-TATTTAT
1 TATTATATTTTAATTA-TTTATTATATTTAT
*
1325732 TATTATATTTTAATTATTTATTATATTTAA
1 TATTATATTTTAATTATTTATTATATTTAT
*
1325762 TACTTAATATTATTAATTATTTATTATACTTATT
1 TA-TT-ATATT-TTAATTATTTATTATATTTA-T
1325796 TATTATATTT
1 TATTATATTT
1325806 ATTTGTTATT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
29 9 0.14
30 19 0.30
31 3 0.05
32 10 0.16
33 21 0.33
34 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (30 bp):
TATTATATTTTAATTATTTATTATATTTAT
Found at i:1325807 original size:13 final size:13
Alignment explanation
Indices: 1325721--1325814 Score: 67
Period size: 13 Copynumber: 7.5 Consensus size: 13
1325711 TTAATTACTA
1325721 TATT-TATTTA-T
1 TATTATATTTATT
*
1325732 TATTATATTTTAAT
1 TATTATA-TTTATT
1325746 TATT-TATTATATT
1 TATTATATT-TATT
*
1325759 TA--ATACTTAATAT
1 TATTATA-TTTAT-T
1325772 TATTA-A-TTATT
1 TATTATATTTATT
*
1325783 TATTATACTTATT
1 TATTATATTTATT
1325796 TATTATATTTATT
1 TATTATATTTATT
*
1325809 TGTTAT
1 TATTAT
1325815 TAATTTCAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
11 10 0.15
12 12 0.18
13 38 0.57
14 6 0.09
15 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (13 bp):
TATTATATTTATT
Found at i:1331753 original size:2 final size:2
Alignment explanation
Indices: 1331748--1331784 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1331738 GCATCAAAGC
1331748 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1331785 GTTTTGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1339002 original size:15 final size:16
Alignment explanation
Indices: 1338964--1339004 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1338954 ACAGAGCCTC
*
1338964 TGAATCATTTAGCATT
1 TGAATCATTCAGCATT
*
1338980 TGAATCATTCAGCGTT
1 TGAATCATTCAGCATT
1338996 T-AATCATTC
1 TGAATCATTC
1339005 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:1339757 original size:28 final size:28
Alignment explanation
Indices: 1339700--1339759 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
1339690 GAAAAAATTT
1339700 AAATAATTTATGTACCTATTTTAATAAA
1 AAATAATTTATGTACCTATTTTAATAAA
** *
1339728 AAATAACTTTATGTATTTATTTTGATAAA
1 AAATAA-TTTATGTACCTATTTTAATAAA
1339757 AAA
1 AAA
1339760 AACATTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (28 bp):
AAATAATTTATGTACCTATTTTAATAAA
Found at i:1345806 original size:2 final size:2
Alignment explanation
Indices: 1345799--1345832 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1345789 CCCAGAGTAG
1345799 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1345833 AAACATAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1350175 original size:60 final size:60
Alignment explanation
Indices: 1350032--1350211 Score: 179
Period size: 60 Copynumber: 3.0 Consensus size: 60
1350022 AATATACATT
* * * * *
1350032 TAGTTTGGGATGAAATTGGAATGTTCAAAAGCTTTGGGGATTAATTTAGAATGAAGATCAA
1 TAGTTTGGGATGAAATTGAAATATTCAAAAG-TTTGAGGACTAATTTAAAATGAAGATCAA
* *
1350093 TA-TTCGGGGATGAAATTGAAATATTCAAAAGTTTGAGGACTAGTTTAAAATGATA-ATC-A
1 TAGTT-TGGGATGAAATTGAAATATTCAAAAGTTTGAGGACTAATTTAAAATGA-AGATCAA
* * * * *
1350152 TAGTTTAGGGATGAAATTAAAATATTTAAAAGTTTAAGGA-TCAATCTAAAATAAAGATCA
1 TAGTTT-GGGATGAAATTGAAATATTCAAAAGTTTGAGGACT-AATTTAAAATGAAGATCA
1350212 TACTTTGAGG
Statistics
Matches: 98, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
59 5 0.05
60 67 0.68
61 26 0.27
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.32
Consensus pattern (60 bp):
TAGTTTGGGATGAAATTGAAATATTCAAAAGTTTGAGGACTAATTTAAAATGAAGATCAA
Found at i:1350192 original size:29 final size:29
Alignment explanation
Indices: 1350100--1350192 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
1350090 CAATATTCGG
* * *
1350100 GGATGAAATTGAAATATTCAAAAGTTTGA
1 GGATGAAATTAAAATATTTAAAAGTTTAA
** * * * *
1350129 GGACT-AGTTTAAAATGATAATCATAGTTTAG
1 GGA-TGAAATTAAAAT-AT-TTAAAAGTTTAA
1350160 GGATGAAATTAAAATATTTAAAAGTTTAA
1 GGATGAAATTAAAATATTTAAAAGTTTAA
1350189 GGAT
1 GGAT
1350193 CAATCTAAAA
Statistics
Matches: 45, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
29 22 0.49
30 6 0.13
31 17 0.38
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.33
Consensus pattern (29 bp):
GGATGAAATTAAAATATTTAAAAGTTTAA
Found at i:1350673 original size:2 final size:2
Alignment explanation
Indices: 1350666--1350712 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1350656 TACATTTAGA
1350666 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
1350708 AT AT A
1 AT AT A
1350713 AGAATCAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1352080 original size:31 final size:31
Alignment explanation
Indices: 1352044--1352109 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1352034 AAACTATGCA
1352044 TTTAATACTTAAACTATCAATTTTAATCCAT
1 TTTAATACTTAAACTATCAATTTTAATCCAT
* *
1352075 TTTAATACTTAAACTATCAATTTTATTTCAT
1 TTTAATACTTAAACTATCAATTTTAATCCAT
1352106 TTTA
1 TTTA
1352110 GTATTCAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (31 bp):
TTTAATACTTAAACTATCAATTTTAATCCAT
Found at i:1354177 original size:14 final size:14
Alignment explanation
Indices: 1354160--1354189 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1354150 TCTTTTCCCT
*
1354160 TTTAAATTTTGCTA
1 TTTAAATTTAGCTA
1354174 TTTAAATTTAGCTA
1 TTTAAATTTAGCTA
1354188 TT
1 TT
1354190 ATCAATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTAAATTTAGCTA
Found at i:1362550 original size:52 final size:51
Alignment explanation
Indices: 1362404--1362596 Score: 210
Period size: 52 Copynumber: 3.8 Consensus size: 51
1362394 TTCATATTAC
* ** * * *
1362404 AAAAAAATATAACACTTAACACATACTTACAAAGATGTGACTGAATAAAAT
1 AAAAAAATGTAACACTTAACACATACTTACATCGGTGTAAGTGAATAAAAT
* * * *
1362455 AAATAAGTG-AAGCACTTAACACATACTTACACCGGTGTGAGTGAATAAAAT
1 AAAAAAATGTAA-CACTTAACACATACTTACATCGGTGTAAGTGAATAAAAT
* * *
1362506 AAAAAAAATGTAGCATTTAATACATACTTACATCGGTGTAAGTGAATAAAAT
1 -AAAAAAATGTAACACTTAACACATACTTACATCGGTGTAAGTGAATAAAAT
* * *
1362558 -AAAAAGTGTAACACTTAACACCTACTTATATCGGTGTAA
1 AAAAAAATGTAACACTTAACACATACTTACATCGGTGTAA
1362597 ATATGTACAT
Statistics
Matches: 119, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
50 35 0.29
51 41 0.34
52 42 0.35
53 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (51 bp):
AAAAAAATGTAACACTTAACACATACTTACATCGGTGTAAGTGAATAAAAT
Found at i:1364466 original size:5 final size:5
Alignment explanation
Indices: 1364456--1364490 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
1364446 AAATCAAAGG
1364456 AAATA AAAT- -AATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
1364491 TAATGGTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
5 25 0.89
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:1364472 original size:23 final size:22
Alignment explanation
Indices: 1364432--1364489 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
1364422 TAGATTGTAA
* *
1364432 AAAATATATATAATAAATCAAAG
1 AAAATA-AAATAATAAATAAAAG
* *
1364455 GAAATAAAATAATAAAATAAAAT
1 AAAATAAAATAAT-AAATAAAAG
1364478 AAAATAAAATAA
1 AAAATAAAATAA
1364490 ATAATGGTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (22 bp):
AAAATAAAATAATAAATAAAAG
Found at i:1365129 original size:21 final size:21
Alignment explanation
Indices: 1365090--1365142 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1365080 TTGGGTCCCC
* * * *
1365090 CCGTAACTTCCATGTCCACCT
1 CCGTAGCTTCCACGACCACCA
1365111 CCGTAGCTTCCACGACCACCA
1 CCGTAGCTTCCACGACCACCA
*
1365132 CCATAGCTTCC
1 CCGTAGCTTCC
1365143 GCGGTTACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.45, G:0.11, T:0.23
Consensus pattern (21 bp):
CCGTAGCTTCCACGACCACCA
Found at i:1366159 original size:81 final size:80
Alignment explanation
Indices: 1366056--1366299 Score: 281
Period size: 84 Copynumber: 3.0 Consensus size: 80
1366046 CTTTGGTTGG
* * * *
1366056 CAGATAGCCCTTCTCGACTTAAGTTATGCTTTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTAG-AGCTGAGCGTAATCGA
* *
1366121 ACTTGAGGGTCTTTGA
65 ACTCGAAGGTCTTTGA
* * * *
1366137 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTAGAGCTGAGCGTAATCGAA
*
1366202 CTCAAAGGTCTTTTGGTGA
66 CTCGAAGGTC--TT--TGA
* * * * * * *
1366221 CATATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAATCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTAGAGCTGAGCGTAATCGAA
1366286 CTCGAAGGTCTTTG
66 CTCGAAGGTCTTTG
1366300 TTGACAAATA
Statistics
Matches: 138, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
80 24 0.17
81 42 0.30
82 4 0.03
84 68 0.49
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (80 bp):
CAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCCTAGAGCTGAGCGTAATCGAA
CTCGAAGGTCTTTGA
Found at i:1366257 original size:84 final size:83
Alignment explanation
Indices: 1366042--1366317 Score: 261
Period size: 84 Copynumber: 3.3 Consensus size: 83
1366032 CGAACTCGTC
* * * * * * ** * *
1366042 AGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTTTAAATGATGTGCCCTCGAAG
1 AGGTCTTTGG-TGACAAATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTTAG-AG
* **
1366107 CTGAGTGTAATCGAACTTGA
64 CTGAGCGTAATCGAACTCAA
* * * *
1366127 GGGTC-TT--TGACAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCT
1 AGGTCTTTGGTGACAAATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCT
*
1366189 GAGCGTAGTCGAACTCAA
66 GAGCGTAATCGAACTCAA
* * * * * *
1366207 AGGTCTTTTGGTGACATATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGC
1 AGGTC-TTTGGTGACAAATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGC
*
1366272 TGAGCGTAATCGAACTCGA
65 TGAGCGTAATCGAACTCAA
* *
1366291 AGGTCTTTGTTGACAAATAATCCTTCT
1 AGGTCTTTGGTGACAAATAACCCTTCT
1366318 TTGAGTTGGA
Statistics
Matches: 161, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
80 22 0.14
81 44 0.27
82 2 0.01
83 19 0.12
84 70 0.43
85 4 0.02
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (83 bp):
AGGTCTTTGGTGACAAATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCT
GAGCGTAATCGAACTCAA
Found at i:1366665 original size:106 final size:106
Alignment explanation
Indices: 1366480--1368200 Score: 2697
Period size: 106 Copynumber: 16.3 Consensus size: 106
1366470 GCATTGTTCC
* * * * * * * *
1366480 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTATTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1366545 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1366586 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAAAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1366651 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1366692 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
*
1366757 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1366798 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
*
1366863 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1366904 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
* *
1366969 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1367010 GAGTCCAATATCCTTCG-TGGTGAAGTTAAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
*
1367073 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTG-A---AC-TTGCGTTGTCTG
*
1367120 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
* *
1367185 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1367226 GAGTCCAATATCCTTCG-TGGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
*
1367289 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1367331 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
* * *
1367396 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGTGTTGTCAG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* **
1367437 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-ATGAAATTATTGGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATTGTTTATTGACA
1367501 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1367543 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-AGGAGATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATTGTTTATTGACA
1367607 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1367649 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT------TTTTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
* *
1367708 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1367749 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATTGTTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
* * *
1367814 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGTGTTGTCAG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* **
1367855 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-ATGAAATTATTGGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATTGTTTATTGACA
1367919 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1367961 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-AGGAGATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGA-GAAATTGTTTATTGACA
1368025 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1368067 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-----TTTTTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
*
1368127 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1368168 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1368201 TACTCTCGAG
Statistics
Matches: 1514, Mismatches: 82, Indels: 43
0.92 0.05 0.03
Matches are distributed among these distances:
100 93 0.06
101 85 0.06
105 138 0.09
106 1096 0.72
107 2 0.00
109 2 0.00
110 60 0.04
111 38 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1371846 original size:5 final size:5
Alignment explanation
Indices: 1371836--1371870 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
1371826 AAATCAAAGG
1371836 AAATA AAAT- -AATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
1371871 TAATGGTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
5 25 0.89
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:1371852 original size:23 final size:22
Alignment explanation
Indices: 1371812--1371869 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
1371802 TAGATTGTAA
* *
1371812 AAAATATATATAATAAATCAAAG
1 AAAATA-AAATAATAAATAAAAG
* *
1371835 GAAATAAAATAATAAAATAAAAT
1 AAAATAAAATAAT-AAATAAAAG
1371858 AAAATAAAATAA
1 AAAATAAAATAA
1371870 ATAATGGTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (22 bp):
AAAATAAAATAATAAATAAAAG
Found at i:1372509 original size:21 final size:21
Alignment explanation
Indices: 1372470--1372522 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1372460 TTGGGTCCCC
* * * *
1372470 CCGTAACTTCCATGTCCACCT
1 CCGTAGCTTCCACGACCACCA
1372491 CCGTAGCTTCCACGACCACCA
1 CCGTAGCTTCCACGACCACCA
*
1372512 CCATAGCTTCC
1 CCGTAGCTTCC
1372523 GCGGTTACCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.45, G:0.11, T:0.23
Consensus pattern (21 bp):
CCGTAGCTTCCACGACCACCA
Found at i:1375036 original size:21 final size:22
Alignment explanation
Indices: 1375005--1375052 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1374995 CCGCCACATT
* *
1375005 ATCAACCACAGTGGACTGCCAC
1 ATCAACCACAGTAGACCGCCAC
*
1375027 GTCAA-CACAGTAGACCGCCAC
1 ATCAACCACAGTAGACCGCCAC
1375048 ATCAA
1 ATCAA
1375053 TACAATGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.35, C:0.35, G:0.17, T:0.12
Consensus pattern (22 bp):
ATCAACCACAGTAGACCGCCAC
Found at i:1379600 original size:60 final size:60
Alignment explanation
Indices: 1379513--1379661 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 60
1379503 ATGGAATGGG
* *
1379513 AATGTTTAAAAAGTTTGGAGACCAATTTAGAAAGAGGGTCATAGTTTAGGAATGAAATTGA
1 AATGTTT-AAAAGTTTAGAGACCAATTTAGAAAGAGAGTCATAGTTTAGGAATGAAATTGA
* * * *
1379574 AATGTTTAAAAGTTTA-AGGACTAATTTAGAATGAGAGTCATAGTTTAGGGATGGAATTGA
1 AATGTTTAAAAGTTTAGA-GACCAATTTAGAAAGAGAGTCATAGTTTAGGAATGAAATTGA
* * * * *
1379634 AATATTAAAAAGTGTAAAAACCAATTTA
1 AATGTTTAAAAGTTTAGAGACCAATTTA
1379662 AAATGAAGAC
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
59 1 0.01
60 66 0.88
61 8 0.11
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (60 bp):
AATGTTTAAAAGTTTAGAGACCAATTTAGAAAGAGAGTCATAGTTTAGGAATGAAATTGA
Found at i:1382498 original size:20 final size:20
Alignment explanation
Indices: 1382454--1382721 Score: 248
Period size: 20 Copynumber: 13.2 Consensus size: 20
1382444 AATGACCAAC
*
1382454 AAAATCGCAACGCGAAAT-A-
1 AAAATCGCAACGCG-ATTCAG
*
1382473 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
1382493 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
1382513 AAAATCGCAACG-G--TCAAAAG
1 AAAATCGCAACGCGATTC---AG
1382533 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
1382555 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
1382575 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
1382597 AGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTCAG
1382617 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
1382637 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
1382657 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
1382677 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
1382697 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
1382717 AAAAT
1 AAAAT
1382722 GAGTAAATTT
Statistics
Matches: 212, Mismatches: 18, Indels: 37
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.01
19 20 0.09
20 152 0.72
21 5 0.02
22 28 0.13
23 2 0.01
25 1 0.00
26 1 0.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:1382868 original size:6 final size:6
Alignment explanation
Indices: 1382816--1382867 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
1382806 AGACACGTAT
*
1382816 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCCC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1382864 GACC
1 GACC
1382868 CGAGACGAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:1383377 original size:6 final size:6
Alignment explanation
Indices: 1383366--1383440 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
1383356 TCTCGTCTCG
1383366 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1383414 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1383441 AATACGTGTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1383591 original size:40 final size:40
Alignment explanation
Indices: 1383536--1383826 Score: 254
Period size: 40 Copynumber: 7.1 Consensus size: 40
1383526 GAATTTACTC
*
1383536 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1383576 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
* *
1383616 ATTTTCTGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* * *
1383658 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCATTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*** *
1383700 ATTCTTGGAATATCGCGTTGCGATTTTCTTTTG-A-C-CGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCGA--TTC-TTGGAATCGCGTTGCG
* * ** *
1383742 ATTTTCTT-TTCAACGTTGCGATT-TTCTAAATCACGGTTGCG
1 ATTTTCTTAATC-GCGTTGCGATTCTT-GGAATCGC-GTTGCG
* * *
1383783 ATTTTCTAAATCGCGTTGCGATT-TT-TATTTCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
1383822 ATTTT
1 ATTTT
1383827 GTTGGTCATT
Statistics
Matches: 210, Mismatches: 26, Indels: 31
0.79 0.10 0.12
Matches are distributed among these distances:
36 2 0.01
37 1 0.00
38 3 0.01
39 15 0.07
40 77 0.37
41 28 0.13
42 63 0.30
43 3 0.01
44 12 0.06
46 3 0.01
47 3 0.01
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.41
Consensus pattern (40 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:1383656 original size:22 final size:20
Alignment explanation
Indices: 1383543--1383724 Score: 201
Period size: 20 Copynumber: 8.8 Consensus size: 20
1383533 CTCATTTTCT
1383543 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1383563 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
1383584 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
1383603 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
1383623 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1383643 GAAGATCGCGTTGCGATTCTCT-
1 G-A-ATCGCGTTGCGATTCT-TG
* *
1383665 TAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
1383685 GAATATCGCATTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTCTTG
1383707 GAATATCGCGTTGCGATT
1 G-A-ATCGCGTTGCGATT
1383725 TTCTTTTGAC
Statistics
Matches: 142, Mismatches: 8, Indels: 22
0.83 0.05 0.13
Matches are distributed among these distances:
18 5 0.04
19 3 0.02
20 73 0.51
21 5 0.04
22 55 0.39
23 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:1383744 original size:64 final size:64
Alignment explanation
Indices: 1383544--1383729 Score: 208
Period size: 64 Copynumber: 3.0 Consensus size: 64
1383534 TCATTTTCTG
* * *** *
1383544 AATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATT-TTCTTA-ATCGCGTTGCGATTCT-TGG
1 AATCGCATTGCGATTCTTGGAATATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTCTCT-T
* *
1383604 AATCGCGTTGCGATT-TTCTG-A-ATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTCTCTT
1 AATCGCATTGCGATTCTT-GGAATATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTCTCTT
* *
1383666 AATCGCATTGCGATTCTTGGAATATCGCATTGCGATTCTTGGAATATCGCGTTGCGATTTTCTT
1 AATCGCATTGCGATTCTTGGAATATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTCTCTT
1383730 TTGACCGTTG
Statistics
Matches: 109, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
59 2 0.02
60 30 0.28
61 3 0.03
62 31 0.28
63 4 0.04
64 39 0.36
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (64 bp):
AATCGCATTGCGATTCTTGGAATATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATTCTCTT
Found at i:1383802 original size:20 final size:20
Alignment explanation
Indices: 1383536--1383826 Score: 198
Period size: 20 Copynumber: 14.2 Consensus size: 20
1383526 GAATTTACTC
*
1383536 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1383556 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
1383576 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1383596 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
* *
1383616 ATTTTCTGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1383636 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
1383658 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
** *
1383678 ATTCTTGGAATATCGCATTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
**
1383700 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
1383722 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
1383742 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
1383762 ATTTTCTAAATCACGGTTGCG
1 ATTTTCTAAATCGC-GTTGCG
1383783 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1383803 ATTTT-TATTTCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
1383822 ATTTT
1 ATTTT
1383827 GTTGGTCATT
Statistics
Matches: 225, Mismatches: 32, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
18 2 0.01
19 21 0.09
20 118 0.52
21 36 0.16
22 48 0.21
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:1384809 original size:31 final size:30
Alignment explanation
Indices: 1384758--1384816 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
1384748 TCAGCTAATT
1384758 AATTATAATATAATAATAATAATAAATATC
1 AATTATAATATAATAATAATAATAAATATC
* * *
1384788 AATTTTAATAATAATAGTAATAATTAATA
1 AATTATAAT-ATAATAATAATAATAAATA
1384817 CTGGCCGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (30 bp):
AATTATAATATAATAATAATAATAAATATC
Found at i:1385943 original size:14 final size:14
Alignment explanation
Indices: 1385920--1385951 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1385910 GCACTACTCT
*
1385920 CTCTCTCTCTCTCC
1 CTCTCCCTCTCTCC
1385934 CTCTCCCTCTCTCC
1 CTCTCCCTCTCTCC
1385948 CTCT
1 CTCT
1385952 GCCCATTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (14 bp):
CTCTCCCTCTCTCC
Found at i:1397640 original size:24 final size:24
Alignment explanation
Indices: 1397611--1397667 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
1397601 AGATTTTGTG
1397611 TAAAAAAATTATGAATTATTTTTT
1 TAAAAAAATTATGAATTATTTTTT
1397635 TAAAAAAATTATGAATTATTTTTT
1 TAAAAAAATTATGAATTATTTTTT
1397659 TAAAAAAAT
1 TAAAAAAAT
1397668 ATCAAAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
TAAAAAAATTATGAATTATTTTTT
Found at i:1399556 original size:17 final size:17
Alignment explanation
Indices: 1399529--1399567 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1399519 AATTTACAAT
1399529 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
1399545 TAATTATAAATAATATC
1 TAATTATAAATAATATC
1399562 TAATTA
1 TAATTA
1399568 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:1402472 original size:23 final size:21
Alignment explanation
Indices: 1402434--1402476 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1402424 ATAATTATTT
1402434 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
1402455 AAAAATATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
1402476 A
1 A
1402477 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:1409117 original size:15 final size:16
Alignment explanation
Indices: 1409097--1409126 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1409087 AAATTTTAAA
1409097 AATATAT-TTTTAAGT
1 AATATATCTTTTAAGT
1409112 AATATATCTTTTAAG
1 AATATATCTTTTAAG
1409127 ATAAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (16 bp):
AATATATCTTTTAAGT
Found at i:1410669 original size:60 final size:59
Alignment explanation
Indices: 1410605--1410756 Score: 144
Period size: 60 Copynumber: 2.5 Consensus size: 59
1410595 GCATATAATG
* ** *
1410605 ATAGTTTATGAACGAAATTGAAATGTTCAAAAGTTAGGGGACCAATTTAAAATTAGAATC
1 ATAGTTTATG-ACGGAATTGAAATGTTCAAAAGTTAGGAAACCAATTTAAAATGAGAATC
* * * * * * *
1410665 ATAGTTTGATGATGGAATTGGAATATTCACAAGTTTGGAAACCAATTTATAATGAGATTC
1 ATAGTTT-ATGACGGAATTGAAATGTTCAAAAGTTAGGAAACCAATTTAAAATGAGAATC
* *
1410725 GTAGTTTGTGGACGGAATT-AGAATGTTCAAAA
1 ATAGTTTAT-GACGGAATTGA-AATGTTCAAAA
1410757 ATTTAAAGAT
Statistics
Matches: 72, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
59 1 0.01
60 68 0.94
61 3 0.04
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (59 bp):
ATAGTTTATGACGGAATTGAAATGTTCAAAAGTTAGGAAACCAATTTAAAATGAGAATC
Found at i:1410807 original size:58 final size:59
Alignment explanation
Indices: 1410740--1410888 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 59
1410730 TTGTGGACGG
* * * * *
1410740 AATTAGAATGTTCAAAAATTTAAAGATCAATATA-AA-ATAATTTATAGTTTTAGGATAA
1 AATTGGAATGTTCAAAAATTTAAAGAT-AATATAGAATAAAAATTATAATTTAAGGATAA
* * *
1410798 AATTGGAATGTTCAGAAGTTTGAGAA-ATAATTTAGAATAAAAATTATAATTTAAGGATAA
1 AATTGGAATGTTCAAAAATTT-A-AAGATAATATAGAATAAAAATTATAATTTAAGGATAA
*
1410858 AATTGGAATGTTCAAACATTTAAAGACTAAT
1 AATTGGAATGTTCAAAAATTTAAAGA-TAAT
1410889 TTAAAATGAT
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
58 25 0.34
59 7 0.09
60 42 0.57
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.34
Consensus pattern (59 bp):
AATTGGAATGTTCAAAAATTTAAAGATAATATAGAATAAAAATTATAATTTAAGGATAA
Found at i:1411208 original size:31 final size:30
Alignment explanation
Indices: 1411126--1411216 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 30
1411116 TATAGTGTAC
1411126 TACTTTATTAAGTCCATCGACTATTAAAAGT
1 TACTTTATTAAGTCCATCGACTA-TAAAAGT
* * * * *
1411157 TAC--AAATAA-TCCTTCAACTATAGAATGT
1 TACTTTATTAAGTCCATCGACTATA-AAAGT
1411185 TACTTTATTAAGTCCATCGACTATTAAAAGT
1 TACTTTATTAAGTCCATCGACTA-TAAAAGT
1411216 T
1 T
1411217 CCAAAATGGT
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
27 2 0.04
28 16 0.36
29 4 0.09
30 4 0.09
31 17 0.38
32 2 0.04
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (30 bp):
TACTTTATTAAGTCCATCGACTATAAAAGT
Found at i:1412382 original size:39 final size:39
Alignment explanation
Indices: 1412339--1412521 Score: 262
Period size: 39 Copynumber: 4.7 Consensus size: 39
1412329 ATACCTACAA
*
1412339 TTTAGTTTTTGTTTCATTTTAGTACCCAATGTTAAAAAT
1 TTTAGTTTTTGTTTCATTTTAGTACCCAATGTTAAAAAC
1412378 TTTAGTTTTTGTTTCATTTTAGTACCC-ATCGTTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGTACCCAAT-GTTAAAAAC
* *
1412417 TTTAGTTTTTGTTTCATTTTAGTACCCGCA-GTTAAAAAT
1 TTTAGTTTTTGTTTCATTTTAGTACCC-AATGTTAAAAAC
* * **
1412456 TTTAGTTTTTGTTTCATTTTAATGCCCACCGTTAAAAAC
1 TTTAGTTTTTGTTTCATTTTAGTACCCAATGTTAAAAAC
*
1412495 TTTAGCTTTTGTTTCATTTTAGTACCC
1 TTTAGTTTTTGTTTCATTTTAGTACCC
1412522 CTTTCAAAAT
Statistics
Matches: 130, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
38 2 0.02
39 127 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.50
Consensus pattern (39 bp):
TTTAGTTTTTGTTTCATTTTAGTACCCAATGTTAAAAAC
Found at i:1412424 original size:78 final size:78
Alignment explanation
Indices: 1412339--1412521 Score: 305
Period size: 78 Copynumber: 2.3 Consensus size: 78
1412329 ATACCTACAA
*
1412339 TTTAGTTTTTGTTTCATTTTAGTACCC-AATGTTAAAAATTTTAGTTTTTGTTTCATTTTAGTAC
1 TTTAGTTTTTGTTTCATTTTAGTACCCGAA-GTTAAAAATTTTAGTTTTTGTTTCATTTTAATAC
*
1412403 CCATCGTTAAAAAC
65 CCACCGTTAAAAAC
* *
1412417 TTTAGTTTTTGTTTCATTTTAGTACCCGCAGTTAAAAATTTTAGTTTTTGTTTCATTTTAATGCC
1 TTTAGTTTTTGTTTCATTTTAGTACCCGAAGTTAAAAATTTTAGTTTTTGTTTCATTTTAATACC
1412482 CACCGTTAAAAAC
66 CACCGTTAAAAAC
*
1412495 TTTAGCTTTTGTTTCATTTTAGTACCC
1 TTTAGTTTTTGTTTCATTTTAGTACCC
1412522 CTTTCAAAAT
Statistics
Matches: 99, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
78 98 0.99
79 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.50
Consensus pattern (78 bp):
TTTAGTTTTTGTTTCATTTTAGTACCCGAAGTTAAAAATTTTAGTTTTTGTTTCATTTTAATACC
CACCGTTAAAAAC
Found at i:1413252 original size:23 final size:21
Alignment explanation
Indices: 1413224--1413278 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 21
1413214 GGGTTTTATA
1413224 TTTTTATTTTCATTATT-ATAAT
1 TTTTTATTTT-ATTATTAAT-AT
1413246 TTATTTATTATTATTATTAATAT
1 TT-TTTATT-TTATTATTAATAT
1413269 TTTTTATTTT
1 TTTTTATTTT
1413279 TGCAGGTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.07
22 8 0.27
23 16 0.53
24 4 0.13
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATTTTATTATTAATAT
Found at i:1414466 original size:6 final size:6
Alignment explanation
Indices: 1414455--1414495 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
1414445 CAAATCGAAT
*
1414455 AATTTA AATTTA AATTTA AATTTA AATATA AATTTA AATTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT
1414496 TCGCAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
AATTTA
Found at i:1418558 original size:84 final size:82
Alignment explanation
Indices: 1418322--1419006 Score: 707
Period size: 84 Copynumber: 8.3 Consensus size: 82
1418312 CTATTTGCCA
* * *
1418322 ACCAAAGACCTTCGAGTTCGACTATGCTCAACTCCAAGGCACATCATTTGCAGTATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
*
1418387 CGAGAAGGGATATCTG-
66 CGAGAAGGGCTATCTGC
* * * * * ** * *
1418403 -CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTATAGCATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAG
* * *
1418467 GCTAGAAGGGTTATCTGTC
65 TCGAGAAGGGCTATCTG-C
*
1418486 ACCAAAAGACCTTCGAGTTCGACTGCGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
1418551 TCGAGAAGGGCTATCTG-
65 TCGAGAAGGGCTATCTGC
** * * ** * * * * *
1418568 -CCAAAGACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAACATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAG
* * * *
1418632 GCTAGAAGGGTTATATGTC
65 TCGAGAAGGGCTATCTG-C
* * * *
1418651 ACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTTGCAGTATAGCTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
1418716 TCGAGAAGGGCTATCTG-
65 TCGAGAAGGGCTATCTGC
* * * * * *
1418733 -CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAG
*
1418797 TCGAGAAGGGTTATCTGCC
65 TCGAGAAGGGCTATCTG-C
* * * *
1418816 AACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAACATAGCTCAAG
1 -ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
*** *
1418881 GAAAGAAGGGCTATTTGCC
65 TCGAGAAGGGCTATCTG-C
* * *
1418900 AACTAAAGACCTTCGAGTTTGACTACGCTCAGCTCCGAGGCACATCATTTGCAGCATAGCTTAAG
1 -ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
1418965 TCGAGAAGGGCTATCTGCC
65 TCGAGAAGGGCTATCTG-C
*
1418984 AACCAAAGACCTGACGAGTTCGA
1 -ACCAAAGACCT-TCGAGTTCGA
1419007 TTTCATTCAG
Statistics
Matches: 487, Mismatches: 101, Indels: 28
0.79 0.16 0.05
Matches are distributed among these distances:
80 75 0.15
81 124 0.25
84 204 0.42
85 84 0.17
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (82 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
CGAGAAGGGCTATCTGC
Found at i:1418597 original size:165 final size:165
Alignment explanation
Indices: 1418317--1419006 Score: 936
Period size: 165 Copynumber: 4.2 Consensus size: 165
1418307 AAGGACTATT
* * *
1418317 TGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAACTCCAAGGCACATCATTTGCAGTATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCT
*
1418382 TAAGTCGAGAAGGGATATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
66 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* *
1418447 CATTTATAGCATAACTCAAGGCTAGAAGGGTTATC
131 CATTTACAGCATAACTCAAGGCGAGAAGGGTTATC
* *
1418482 TGTC-ACCAAAAGACCTTCGAGTTCGACTGCGCTCAGCTCCAAGGCACATCATTTGCAGCATAGC
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGC
* *
1418546 TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCACA
65 TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
* * *
1418611 TCATTTACAACATAACTCAAGGCTAGAAGGGTTATA
130 TCATTTACAGCATAACTCAAGGCGAGAAGGGTTATC
* * * * *
1418647 TGTC-ACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTTGCAGTATAGC
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGC
1418711 TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
65 TTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
* * *
1418776 TCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
130 TCATTTACAGCATAACTCAAGGCGAGAAGGGTTATC
* * *
1418812 TGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAACATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCT
* *** * * * * * *
1418877 CAAGGAAAGAAGGGCTATTTGCCAACTAAAGACCTTCGAGTTTGACTACGCTCAGCTCCGA-GGC
66 TAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
* * * * *
1418941 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC
127 ACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATC
*
1418980 TGCCAACCAAAGACCTGACGAGTTCGA
1 TGCCAACCAAAGACCT-TCGAGTTCGA
1419007 TTTCATTCAG
Statistics
Matches: 474, Mismatches: 44, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
164 3 0.01
165 373 0.79
166 4 0.01
168 57 0.12
169 37 0.08
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCT
TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
CATTTACAGCATAACTCAAGGCGAGAAGGGTTATC
Found at i:1418725 original size:249 final size:248
Alignment explanation
Indices: 1418322--1419006 Score: 684
Period size: 249 Copynumber: 2.8 Consensus size: 248
1418312 CTATTTGCCA
** ** * * ** * * *
1418322 ACCAAAGACCTTCGAGTTCGACTATGCTCAACTCCAAGGCACATCATTTGCAGTATAGCTTAAGT
1 ACCAAAGACCCCCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGG
** * * * * * * *
1418387 CGAGAAGGGATATCTG-C--C-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
66 AAAGAAGGGCTATATGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATC
** * * * * * * *
1418448 ATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTGCG
130 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CACC-AAAGACCTTCGAGTTCGACTACA
*
1418513 CTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
193 CTCAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG
* ** *
1418568 -CCAAAGACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAACATAACTCAAG
1 ACCAAAGACCCCCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAACATAACTCAAG
** * * * * * *
1418632 GCTAGAAGGGTTATATGTCACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCATATC
65 GAAAGAAGGGCTATATGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * *
1418697 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG--CCAAAGACCCTCGAGTTCGATTACACT
130 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCACCAAAGACCTTCGAGTTCGACTACACT
* * *
1418760 CAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
195 CAGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG
*** * * * *
1418814 CCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAACATAGCTCA
1 ---ACCAAAGACCCCCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTCA
* * * *
1418879 AGGAAAGAAGGGCTATTTGCCAACTAAAGACCTTCGAGTTTGACTACGCTCAGCTCCGAGGCACA
63 AGGAAAGAAGGGCTATATGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
*
1418944 TCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTGACGAGTTCGA
128 TCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-ACCAAAGACCT-TCGAGTTCGA
1419007 TTTCATTCAG
Statistics
Matches: 357, Mismatches: 67, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
245 50 0.14
246 84 0.24
247 1 0.00
249 153 0.43
250 51 0.14
253 9 0.03
254 9 0.03
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (248 bp):
ACCAAAGACCCCCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAACATAACTCAAGG
AAAGAAGGGCTATATGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCACCAAAGACCTTCGAGTTCGACTACACTC
AGCTTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG
Found at i:1424500 original size:84 final size:82
Alignment explanation
Indices: 1424264--1424937 Score: 732
Period size: 84 Copynumber: 8.1 Consensus size: 82
1424254 ACTATTGCCA
* * * *
1424264 ACCAAAGACCTTCGAGTTCGACTATGCTCAACTCCAAGGCACATCATTTGCAGTATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
*
1424329 CGAGAAGGGATATCTG-
66 CGAGAAGGGCTATCTGC
* * * * * ** *
1424345 -CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTATAGCATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAG
* * *
1424409 GCTAGAAGGGTTATCTGTC
65 TCGAGAAGGGCTATCTG-C
*
1424428 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
1424493 TCGAGAAGGGCTATCTG-
65 TCGAGAAGGGCTATCTGC
** * * * * * *
1424510 -CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC-GACATAACTCAA
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAG-CATAACTTAA
* * *
1424573 GGCTAGAAGGGTTATCTGTC
64 GTCGAGAAGGGCTATCTG-C
* * * *
1424593 ACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTTGCAGTATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
1424658 TCGAGAAGGGCTATCTG-
65 TCGAGAAGGGCTATCTGC
* * * * * *
1424675 -CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGGAGCATAACTTAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAG
*
1424739 TCGAGAAGGGTTATCTGCC
65 TCGAGAAGGGCTATCTG-C
* * * *
1424758 AACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAACATAACTCAAG
1 -ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
* * *
1424823 GCAAGAAGGGCTATTTGCC
65 TCGAGAAGGGCTATCTG-C
* * *
1424842 AACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCGAGGCACATCATTTGCAGCATAGCTTAAG
1 -ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
1424907 TCGAGAAGGGCTATCTGCC
65 TCGAGAAGGGCTATCTG-C
1424926 AACCAAAGACCT
1 -ACCAAAGACCT
1424938 GACGATTTGA
Statistics
Matches: 489, Mismatches: 87, Indels: 31
0.81 0.14 0.05
Matches are distributed among these distances:
80 77 0.16
81 125 0.26
84 209 0.43
85 78 0.16
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (82 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
CGAGAAGGGCTATCTGC
Done.