Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000121.1 Hibiscus syriacus cultivar Beakdansim tig00000218_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: 2099483
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 10
Found at i:906982 original size:113 final size:113
Alignment explanation
Indices: 906772--907149 Score: 589
Period size: 113 Copynumber: 3.4 Consensus size: 113
906762 ATAAAGTCAT
* * *
906772 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCC-TCTTCAGAT-AAGTTCTTCT
1 GCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAA-TTCTTCT
* * * * *
906835 CATTATGAACTTTCTCTGGAAAAGTTGATACATCGAGCGATGAATTCGA
65 CATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCAA
*
906884 GCAAAAGGTTAAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
1 GCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
*
906949 ATTATGAACTTCCTCTGGAATAGTTAATCCATCGAGTGATGAATTCAA
66 ATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCAA
* * * *
906997 GCAAAAGGTTAAACAAGTTCTTATTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
907062 ATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCAA
66 ATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCAA
* *
907110 GCAAAATGTTAAACAAGTTCTTCTTATTATGAACTTCTTC
1 GCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTC
907150 AGATGAGTTC
Statistics
Matches: 246, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
112 40 0.16
113 204 0.83
114 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
ATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCAA
Found at i:907085 original size:226 final size:215
Alignment explanation
Indices: 906772--907210 Score: 608
Period size: 226 Copynumber: 2.0 Consensus size: 215
906762 ATAAAGTCAT
* * *
906772 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTCTTCAGATAAGTTCTTCTCA
1 GCAAAAGGTTAAACAAGCTCTTATCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
* * *
906837 TTATGAACTTTCTCTGGAAAAGTTGATACATCGAGCGATGAATTCGAGCAAAAGGTTAAACAAGT
66 TTATGAACTTCCTCTGGAAAAGTTAATACATCGAGCGATGAATTCAAGCAAAAGGTTAAACAAGT
906902 TCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTTCCTCTGG
131 TCTTCTCATTATAAA----------CTTCTTCAGATGAATTCTTCTCATTATGAACTTCCTCTGG
*
906967 AATAGTTAATCCATCGAGTGATGAATTCAA
186 AAAAGTTAATCCATCGAGTGATGAATTCAA
* * * *
906997 GCAAAAGGTTAAACAAGTTCTTATTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTAAACAAGCTCTTATCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
* * *
907062 ATTATGAACTTCCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCAAGCAAAATGTTAAACAAG
65 ATTATGAACTTCCTCTGGAAAAGTTAATACATCGAGCGATGAATTCAAGCAAAAGGTTAAACAAG
* * * *
907127 TTCTTCTTATTATGAACTTCTTCAGATGAGTTCTTCTTATTATGAACTTCCTCTGGAAAAGTTAA
130 TTCTTCTCATTATAAACTTCTTCAGATGAATTCTTCTCATTATGAACTTCCTCTGGAAAAGTTAA
*
907192 TCCATCGAGTGATGGATTC
195 TCCATCGAGTGATGAATTC
907211 GAATCTTTGC
Statistics
Matches: 194, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
216 64 0.33
225 39 0.20
226 91 0.47
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (215 bp):
GCAAAAGGTTAAACAAGCTCTTATCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
TTATGAACTTCCTCTGGAAAAGTTAATACATCGAGCGATGAATTCAAGCAAAAGGTTAAACAAGT
TCTTCTCATTATAAACTTCTTCAGATGAATTCTTCTCATTATGAACTTCCTCTGGAAAAGTTAAT
CCATCGAGTGATGAATTCAA
Found at i:910559 original size:2 final size:2
Alignment explanation
Indices: 910554--910586 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
910544 TTAAAAAATA
910554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
910587 ATTTTGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:911110 original size:28 final size:29
Alignment explanation
Indices: 911070--911134 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
911060 GTTATTTCAA
* *
911070 ATTTATTAGTATAATTTTA-AGAA-AATAT
1 ATTTATTTGTATAATTTTATA-AATAAAAT
* *
911098 ATTTATTTTTATATTTTTATAAATAAAAT
1 ATTTATTTGTATAATTTTATAAATAAAAT
911127 ATTTATTT
1 ATTTATTT
911135 ACTTAGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 18 0.58
29 13 0.42
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTATTTGTATAATTTTATAAATAAAAT
Found at i:912906 original size:3 final size:3
Alignment explanation
Indices: 912882--912989 Score: 96
Period size: 3 Copynumber: 36.0 Consensus size: 3
912872 GACATGTTTG
* * *
912882 TAA TAA TAC TAA TAT TAT TAA TAA TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
* * * *
912928 TAA AAA T-A TAA TAA AAA TAA TAG T-A TAAA TAAA TAA TAC TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TAA TAA
*
912972 TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
912990 AAACAACTGG
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
2 5 0.06
3 72 0.84
4 9 0.10
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:912947 original size:36 final size:37
Alignment explanation
Indices: 912900--912989 Score: 121
Period size: 36 Copynumber: 2.5 Consensus size: 37
912890 CTAATATTAT
912900 TAATAATAATAATAATAATAAAT-AATAATAAAAATA
1 TAATAATAATAATAATAATAAATAAATAATAAAAATA
* * **
912936 TAATAAAAATAATAGT-ATAAATAAATAATACTAATA
1 TAATAATAATAATAATAATAAATAAATAATAAAAATA
*
912972 TAATATTAATAATAATAA
1 TAATAATAATAATAATAA
912990 AAACAACTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
35 6 0.13
36 38 0.84
37 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (37 bp):
TAATAATAATAATAATAATAAATAAATAATAAAAATA
Found at i:914418 original size:23 final size:23
Alignment explanation
Indices: 914376--914431 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
914366 TATTATATTA
*
914376 AATAAGAATATAATATAATTTAT
1 AATAATAATATAATATAATTTAT
* *
914399 TATTATAATATAA-ATGAATTTAT
1 AATAATAATATAATAT-AATTTAT
914422 AATAATAATA
1 AATAATAATA
914432 ATATAAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
AATAATAATATAATATAATTTAT
Found at i:914427 original size:33 final size:30
Alignment explanation
Indices: 914353--914427 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 30
914343 AGATATTAGT
914353 TTTATTAATAATTTATTATATTAAATAAGAA
1 TTTA-TAATAATTTATTATATTAAATAAGAA
*
914384 TATA-ATATAATTTATTAT-TATAATATAAATGAA
1 TTTATA-ATAATTTATTATAT-TAA-AT-AA-GAA
914417 TTTATAATAAT
1 TTTATAATAAT
914428 AATAATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
29 2 0.06
30 15 0.42
31 5 0.14
32 2 0.06
33 11 0.31
34 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTATAATAATTTATTATATTAAATAAGAA
Found at i:914474 original size:21 final size:20
Alignment explanation
Indices: 914397--914477 Score: 65
Period size: 21 Copynumber: 4.0 Consensus size: 20
914387 AATATAATTT
*
914397 ATTATTATAAT-ATAAATGAA
1 ATTATTATAATAATTAAT-AA
* * *
914417 TTTATAATAATAATAATATAA
1 ATTATTATAATAATTA-ATAA
* *
914438 ATTATTAAAATTATTAATAA
1 ATTATTATAATAATTAATAA
*
914458 ATATATTTTAATAATTAATA
1 AT-TATTATAATAATTAATA
914478 TTATATTGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
20 15 0.31
21 31 0.65
22 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (20 bp):
ATTATTATAATAATTAATAA
Found at i:914737 original size:41 final size:41
Alignment explanation
Indices: 914680--914757 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
914670 ATATACTATA
* *
914680 AATTTGATTGAGTATTATTATATATAACTATAGATAATAAT
1 AATTTAATTGAGTATTATAATATATAACTATAGATAATAAT
914721 AATTTAATTGAGTATTATAATATATAACTATAGATAA
1 AATTTAATTGAGTATTATAATATATAACTATAGATAA
914758 GATCAAACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (41 bp):
AATTTAATTGAGTATTATAATATATAACTATAGATAATAAT
Found at i:914786 original size:2 final size:2
Alignment explanation
Indices: 914779--914805 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
914769 TTATGATAAC
914779 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 A
914806 AGGTTGATTT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:919061 original size:59 final size:60
Alignment explanation
Indices: 918945--919060 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
918935 TTGGATGATC
* * * ** *
918945 ATTTTGTAATTTTTTAATAATTAAAAGACTTAATAAAAAACATTTTATAATTAAAAATTT
1 ATTTTATAATTTTTTAATAAGTAAAAAACTTAATAAAAAACATCATAAAATTAAAAATTT
*
919005 ATTTTATAA-TTTTTAAT-AGTAAAATAACTTAATAAAACAACGTCATAAAATTAAAA
1 ATTTTATAATTTTTTAATAAGTAAAA-AACTTAATAAAA-AACATCATAAAATTAAAA
919061 TACCATTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
58 6 0.13
59 19 0.40
60 22 0.47
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (60 bp):
ATTTTATAATTTTTTAATAAGTAAAAAACTTAATAAAAAACATCATAAAATTAAAAATTT
Found at i:919222 original size:2 final size:2
Alignment explanation
Indices: 919215--919265 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
919205 TTCATCGAAT
919215 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
*
919257 TA TG TA TA T
1 TA TA TA TA T
919266 CCTATAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:920043 original size:3 final size:3
Alignment explanation
Indices: 920037--920071 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
920027 AAAAAACATC
*
920037 ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
920072 TTCAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:928375 original size:16 final size:16
Alignment explanation
Indices: 928335--928375 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
928325 TTAGGGTTGC
*
928335 TTTCGATTCAAGTTTT
1 TTTCGGTTCAAGTTTT
* *
928351 GTTCAGTTCAAGTTTT
1 TTTCGGTTCAAGTTTT
928367 TTTCGGTTC
1 TTTCGGTTC
928376 GGGTTGATTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.54
Consensus pattern (16 bp):
TTTCGGTTCAAGTTTT
Found at i:929193 original size:17 final size:17
Alignment explanation
Indices: 929171--929214 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
929161 ATGTAAAAAT
929171 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
929188 AAATATACAAATTTATT
1 AAATATTTAAATTTAAA
929205 AAATATTTAA
1 AAATATTTAA
929215 TTAAGTAGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:935260 original size:19 final size:19
Alignment explanation
Indices: 935236--935285 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
935226 AAAAACGTTT
* *
935236 TATGAATAGTATTATATTG
1 TATGAATAGTACTATAATG
935255 TATGAATAGTACTATAATG
1 TATGAATAGTACTATAATG
935274 TATGAATAGTAC
1 TATGAATAGTAC
935286 CGTGAACAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (19 bp):
TATGAATAGTACTATAATG
Found at i:942427 original size:101 final size:101
Alignment explanation
Indices: 942249--942452 Score: 381
Period size: 101 Copynumber: 2.0 Consensus size: 101
942239 AATATTTTTA
* *
942249 CATGGAAAACCCCTCTAAATTAAGGATAAAAATCATAAAACTTTAGGGTACGATCAAAAGCTCCA
1 CATGGAAAACCCCTCTAAATTAAGAATAAAAACCATAAAACTTTAGGGTACGATCAAAAGCTCCA
*
942314 CTATCATTAAATGTTCAACTACAATATCACAATATC
66 CTATCATCAAATGTTCAACTACAATATCACAATATC
942350 CATGGAAAACCCCTCTAAATTAAGAATAAAAACCATAAAACTTTAGGGTACGATCAAAAGCTCCA
1 CATGGAAAACCCCTCTAAATTAAGAATAAAAACCATAAAACTTTAGGGTACGATCAAAAGCTCCA
942415 CTATCATCAAATGTTCAACTACAATATCACAATATC
66 CTATCATCAAATGTTCAACTACAATATCACAATATC
942451 CA
1 CA
942453 GCCTCCAACA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (101 bp):
CATGGAAAACCCCTCTAAATTAAGAATAAAAACCATAAAACTTTAGGGTACGATCAAAAGCTCCA
CTATCATCAAATGTTCAACTACAATATCACAATATC
Found at i:949700 original size:18 final size:18
Alignment explanation
Indices: 949673--949711 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
949663 TACTCATACA
**
949673 AAAGAAACAATTAAAAAT
1 AAAGAAACAAAGAAAAAT
*
949691 AAAGATACAAAGAAAAAT
1 AAAGAAACAAAGAAAAAT
949709 AAA
1 AAA
949712 ACCTTCCGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAGAAACAAAGAAAAAT
Found at i:950068 original size:24 final size:24
Alignment explanation
Indices: 950009--950069 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
949999 AAACCATGAG
*
950009 AATCATGCCATAAAAGTAGAGAAA
1 AATCATGCCACAAAAGTAGAGAAA
** *
950033 ACGCGTGCCACAAAAGTAGAGAAA
1 AATCATGCCACAAAAGTAGAGAAA
*
950057 AATCATGTCACAA
1 AATCATGCCACAA
950070 TGACAAAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (24 bp):
AATCATGCCACAAAAGTAGAGAAA
Found at i:953901 original size:31 final size:31
Alignment explanation
Indices: 953829--953894 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
953819 CAGTTACGTC
953829 GGGACCATATTACAAACGGACTAAATGTTGA
1 GGGACCATATTACAAACGGACTAAATGTTGA
953860 GGGACCATATTACAAACGGACTAAATGTTGA
1 GGGACCATATTACAAACGGACTAAATGTTGA
953891 GGGA
1 GGGA
953895 TTATATTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (31 bp):
GGGACCATATTACAAACGGACTAAATGTTGA
Found at i:955579 original size:18 final size:18
Alignment explanation
Indices: 955552--955593 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
955542 AATATTTTTA
*
955552 TATTTCTTATTAATAATT
1 TATTTTTTATTAATAATT
955570 TATTTTTTATTAATAATT
1 TATTTTTTATTAATAATT
955588 TATTTT
1 TATTTT
955594 CATCTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTTTTATTAATAATT
Found at i:956209 original size:22 final size:22
Alignment explanation
Indices: 956166--956211 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
956156 ATAATTTTCG
* *
956166 TAAATATGATATTTATATATAT
1 TAAATATAATATATATATATAT
956188 TAAATATAATATA-ATATAATAT
1 TAAATATAATATATATAT-ATAT
956210 TA
1 TA
956212 TAGTATCGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAAATATAATATATATATATAT
Found at i:958232 original size:8 final size:7
Alignment explanation
Indices: 958202--958251 Score: 55
Period size: 7 Copynumber: 6.6 Consensus size: 7
958192 AAGATAAAGA
958202 AAAAAAT
1 AAAAAAT
958209 AAATGAAAT
1 AAA--AAAT
958218 AAAAAAT
1 AAAAAAT
958225 ACAAAAAT
1 A-AAAAAT
*
958233 AAAAAAA
1 AAAAAAT
958240 ACAAAAAT
1 A-AAAAAT
958248 AAAA
1 AAAA
958252 TAAAGGTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 17 0.46
8 13 0.35
9 7 0.19
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:958232 original size:15 final size:15
Alignment explanation
Indices: 958214--958251 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
958204 AAAATAAATG
*
958214 AAATAAAAAATACAA
1 AAATAAAAAAAACAA
958229 AAATAAAAAAAACAA
1 AAATAAAAAAAACAA
958244 AAATAAAA
1 AAATAAAA
958252 TAAAGGTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (15 bp):
AAATAAAAAAAACAA
Found at i:958332 original size:2 final size:2
Alignment explanation
Indices: 958325--958370 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
958315 AAATAACAAA
958325 AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
958366 AT AT A
1 AT AT A
958371 ATAATAGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:959488 original size:14 final size:15
Alignment explanation
Indices: 959446--959494 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 15
959436 AATTAAATGA
*
959446 ATAAAATAATAATAAT
1 ATAAACTAAT-ATAAT
*
959462 AATATACTAATATAAT
1 -ATAAACTAATATAAT
959478 ATAAACT-ATATAAT
1 ATAAACTAATATAAT
959492 ATA
1 ATA
959495 TATATTTCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 10 0.34
15 6 0.21
16 5 0.17
17 8 0.28
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAACTAATATAAT
Found at i:959558 original size:34 final size:34
Alignment explanation
Indices: 959480--959665 Score: 166
Period size: 36 Copynumber: 5.4 Consensus size: 34
959470 AATATAATAT
* *
959480 AAACTATATAATATATA-TATTTCCAAAATATTTTT-
1 AAACTATAT-AT-TATAGT-TTTCAAAAATGTTTTTA
* * *
959515 AAACTATATATTATATTTTTTAAAGAA-GTTTTCA
1 AAACTATATATTATAGTTTTCAAA-AATGTTTTTA
* *
959549 AAACTATATACTATATAGTTTTCAAAAATGATTTAA
1 AAACTATATA-T-TATAGTTTTCAAAAATGTTTTTA
*
959585 AAAATATCATA-TA-AGTTTTCAAAAATGTTTTTA
1 AAACTAT-ATATTATAGTTTTCAAAAATGTTTTTA
* *
959618 AAACTATATATTATATAATTTTCAACAATGTTTTTA
1 AAACTATATA-T-TATAGTTTTCAAAAATGTTTTTA
959654 AAACTATATATT
1 AAACTATATATT
959666 TAAAATGTTT
Statistics
Matches: 126, Mismatches: 14, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
32 3 0.02
33 37 0.29
34 18 0.14
35 15 0.12
36 50 0.40
37 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (34 bp):
AAACTATATATTATAGTTTTCAAAAATGTTTTTA
Found at i:959615 original size:69 final size:61
Alignment explanation
Indices: 959533--959707 Score: 170
Period size: 69 Copynumber: 2.7 Consensus size: 61
959523 TATTATATTT
* * *
959533 TTTAAAGAAGTTTTCAAAACTATATACTATATAGTTTTCAAAAATGATTTAAAAAATATCATATA
1 TTTAAA-ATGTTTTAAAAACTATATATTATATAGTTTTCAAAAATG-TTTAAAAAA-AT-ATAT-
959598 A
61 A
* * * ** *
959599 GTTTTCAAAAATGTTTTTAAAACTATATATTATATAATTTTCAACAATGTTTTTAAAACTATATA
1 --TTT--AAAATGTTTTAAAAACTATATATTATATAGTTTTCAAAAATGTTTAAAAAAATATATA
*
959664 TTTAAAATGTTTTAAAAACTATATATTATACAAGTTTTCAAAAA
1 TTTAAAATGTTTTAAAAACTATATATTATA-TAGTTTTCAAAAA
959708 AATGTTTCGA
Statistics
Matches: 92, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
61 26 0.28
62 10 0.11
63 3 0.03
65 1 0.01
66 4 0.04
67 1 0.01
68 10 0.11
69 34 0.37
70 3 0.03
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (61 bp):
TTTAAAATGTTTTAAAAACTATATATTATATAGTTTTCAAAAATGTTTAAAAAAATATATA
Found at i:959700 original size:25 final size:25
Alignment explanation
Indices: 959642--959707 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
959632 ATAATTTTCA
*
959642 ACAATGTTTTTAAAACTATATATTT
1 ACAATGTTTTAAAAACTATATATTT
*
959667 AAAATGTTTTAAAAACTATATATTAT
1 ACAATGTTTTAAAAACTATATATT-T
959693 ACAA-GTTTTCAAAAA
1 ACAATGTTTT-AAAAA
959708 AATGTTTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 27 0.75
26 9 0.25
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (25 bp):
ACAATGTTTTAAAAACTATATATTT
Found at i:960569 original size:80 final size:80
Alignment explanation
Indices: 960365--961432 Score: 1217
Period size: 84 Copynumber: 12.9 Consensus size: 80
960355 TGACATATAG
** * * * * * * *
960365 CCCTTCTTGCCTTGAGCTATGCTATAAATTTGATATGTCTTTAAGCTTAATGTAATCAAACTTGA
1 CCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
*
960430 AGGTCTTTTGTTAGCATATAA
64 AGGTC-TTTG---GCAGATAA
* * * *
960451 CACTTCTTGCCTTGAGCTATGCTGAAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
960516 GTCTTTGGCAGATAA
66 GTCTTTGGCAGATAA
* * * *
960531 CCCTTATTGCCTTGAGCTATGATGCAAATGATGCGCCTTTGAGCTGAGTATAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
960596 GTCTTTGGCAGATAG
66 GTCTTTGGCAGATAA
* * ** *
960611 CCCTTCTTGCATTGAGTTATGCTGCAAATGATGTATCTTTGAGATGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* *
960676 GTCTTTGGAAGATAG
66 GTCTTTGGCAGATAA
* *
960691 CCCTTCTTGCCTTGAGTTATGCTGCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
960756 TTCTTTGGCAGATAA
66 GTCTTTGGCAGATAA
*
960771 CCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
960836 GTCTTTGGCAGATAG
66 GTCTTTGGCAGATAA
* * *
960851 CCCTTCTTGCCTTGAGCTATACTGTAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
960916 GTCTTTCGAAGGTCTTTGGAAGATAA
66 GTCTTT----GG-C------AGATAA
* *
960942 CCCTTCTTTCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTTAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
961007 GTTTTTTGTTGGCAGATAA
66 G---TCT-TTGGCAGATAA
* * * *
961026 CCCTTCTTGGCTTGATCTATGCTGCAAATAATGTGCCTTTGAACTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
961091 GTCTTTTGTTGGCAGATAA
66 GTC---T-TTGGCAGATAA
* * * * * *
961110 CCCTTATTGCCTTGAGTTATGTTGTACTAAAT-A--TGCCTTTAAGCTGAATGTAATTGAACTCG
1 CCCTTCTTGCCTTGAGCTATGCTG--C-AAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCG
* * * *
961172 AAGGTTTTTTTTTGACATATAG
63 AAGG----TCTTTGGCAGATAA
* * *
961194 CTCTTCTTGCCTTGAGTTATGCTGCAAAT-ATTGTGCCTTTGAGTTGAGTGTAATCGAACTCGAA
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGA-TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
961258 GGTCTTTTGTTGGCAGATAA
65 GGTC---T-TTGGCAGATAA
*
961278 CCCTTCTTGCCTTGAGCTATGCTGCAAAAGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
961343 GTCTTTCGTTGGCAGATAA
66 GTC--T--TTGGCAGATAA
* * *
961362 CCCTTCTTTCCTTGAGCTATGCTACAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
961427 GTCTTT
66 GTCTTT
961433 TGTTGAAGGT
Statistics
Matches: 855, Mismatches: 93, Indels: 74
0.84 0.09 0.07
Matches are distributed among these distances:
80 365 0.43
81 6 0.01
82 2 0.00
83 8 0.01
84 366 0.43
85 3 0.00
86 27 0.03
87 4 0.00
88 1 0.00
90 1 0.00
91 68 0.08
94 2 0.00
95 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (80 bp):
CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
GTCTTTGGCAGATAA
Found at i:960653 original size:160 final size:160
Alignment explanation
Indices: 960365--961432 Score: 1217
Period size: 160 Copynumber: 6.4 Consensus size: 160
960355 TGACATATAG
** * * * * * * *
960365 CCCTTCTTGCCTTGAGCTATGCTATAAATTTGATATGTCTTTAAGCTTAATGTAATCAAACTTGA
1 CCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
* * * *
960430 AGGTCTTTTGTTAGCATATAACACTTCTTGCCTTGAGCTATGCTGAAAATAATGTGCCTTTGAGC
64 AGGTC-TTTG---GCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGC
*
960495 TGAGTGTAATCGAACTTGAAGGTCTTTGGCAGATAA
125 TGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAA
* * * *
960531 CCCTTATTGCCTTGAGCTATGATGCAAATGATGCGCCTTTGAGCTGAGTATAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* * * ** *
960596 GTCTTTGGCAGATAGCCCTTCTTGCATTGAGTTATGCTGCAAATGATGTATCTTTGAGATGAGTG
66 GTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
* *
960661 TAATCGAACTCGAAGGTCTTTGGAAGATAG
131 TAATCGAACTCGAAGGTCTTTGGCAGATAA
* *
960691 CCCTTCTTGCCTTGAGTTATGCTGCAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* *
960756 TTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTG
66 GTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
*
960821 TAATCGAACTCGAAGGTCTTTGGCAGATAG
131 TAATCGAACTCGAAGGTCTTTGGCAGATAA
* * *
960851 CCCTTCTTGCCTTGAGCTATACTGTAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
960916 GTCTTTCGAAGGTCTTTGGAAGATAACCCTTCTTTCCTTGAGCTATGCTGCAAATGATGTGCCTT
66 GTCTTT----GG-C------AGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTT
* *
960981 TGAGCTTAGTGTAATCGAACTCGAAGGTTTTTTGTTGGCAGATAA
120 TGAGCTGAGTGTAATCGAACTCGAAGG---TCT-TTGGCAGATAA
* * * *
961026 CCCTTCTTGGCTTGATCTATGCTGCAAATAATGTGCCTTTGAACTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
* * * *
961091 GTCTTTTGTTGGCAGATAACCCTTATTGCCTTGAGTTATGTTGTACTAAAT-A--TGCCTTTAAG
66 GTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG--C-AAATGATGTGCCTTTGAG
* * * * * *
961153 CTGAATGTAATTGAACTCGAAGGTTTTTTTTTGACATATAG
124 CTGAGTGTAATCGAACTCGAAGG----TCTTTGGCAGATAA
* * *
961194 CTCTTCTTGCCTTGAGTTATGCTGCAAAT-ATTGTGCCTTTGAGTTGAGTGTAATCGAACTCGAA
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGA-TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
*
961258 GGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAAAGATGTGCCTTTGAGCT
65 GGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCT
961323 GAGTGTAATCGAACTCGAAGGTCTTTCGTTGGCAGATAA
126 GAGTGTAATCGAACTCGAAGGTC--T--TTGGCAGATAA
* * *
961362 CCCTTCTTTCCTTGAGCTATGCTACAAATGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
961427 GTCTTT
66 GTCTTT
961433 TGTTGAAGGT
Statistics
Matches: 777, Mismatches: 93, Indels: 66
0.83 0.10 0.07
Matches are distributed among these distances:
160 285 0.37
163 4 0.01
164 36 0.05
165 5 0.01
166 27 0.03
167 1 0.00
168 258 0.33
169 7 0.01
170 2 0.00
171 73 0.09
174 3 0.00
175 73 0.09
178 1 0.00
179 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (160 bp):
CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
GTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
TAATCGAACTCGAAGGTCTTTGGCAGATAA
Found at i:964135 original size:54 final size:54
Alignment explanation
Indices: 964053--964160 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
964043 ACATGCTTAT
964053 TATTCCTACCCGGACATGATCTATATCTTGGAAGTTGATTTTGAACCAGTCCTA
1 TATTCCTACCCGGACATGATCTATATCTTGGAAGTTGATTTTGAACCAGTCCTA
964107 TATTCCTACCCGGACATGATCTATATCTTGGAAGTTGATTTTGAACCAGTCCTA
1 TATTCCTACCCGGACATGATCTATATCTTGGAAGTTGATTTTGAACCAGTCCTA
964161 ACCGCATAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (54 bp):
TATTCCTACCCGGACATGATCTATATCTTGGAAGTTGATTTTGAACCAGTCCTA
Found at i:965170 original size:19 final size:18
Alignment explanation
Indices: 965146--965203 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
965136 AAAAAAAAGG
*
965146 AAAAAAAAACAAATGAAAT
1 AAAAAAAAACAAAT-AAAA
* *
965165 AAAAAAATATAAATAAAA
1 AAAAAAAAACAAATAAAA
965183 AATAAAAAAACGAAAATAAAA
1 AA-AAAAAAAC--AAATAAAA
965204 TTAATGTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 5 0.16
19 18 0.58
21 8 0.26
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.12
Consensus pattern (18 bp):
AAAAAAAAACAAATAAAA
Found at i:965199 original size:21 final size:21
Alignment explanation
Indices: 965161--965203 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
965151 AAAACAAATG
*
965161 AAATAAAAAAATATAAATAAA
1 AAATAAAAAAAGATAAATAAA
965182 AAATAAAAAAACGA-AAATAAA
1 AAATAAAAAAA-GATAAATAAA
965203 A
1 A
965204 TTAATGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (21 bp):
AAATAAAAAAAGATAAATAAA
Found at i:966431 original size:23 final size:23
Alignment explanation
Indices: 966405--966470 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
966395 CACCAGAGCT
*
966405 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
966428 CGTAGAATTGCACC-AGAGTACCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
966451 CGTAGAATTGCACCGTAGTG
1 CGTAGAATTGCACCGAAGTG
966471 ACATATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:972824 original size:30 final size:28
Alignment explanation
Indices: 972761--972843 Score: 114
Period size: 28 Copynumber: 2.9 Consensus size: 28
972751 TAAACACCAA
* *
972761 TTTTCAACACCAACACCTACCACCCCAT
1 TTTTCAACACCAACACCCATCACCCCAT
*
972789 TTTTCAACACCAACACCCATCATCCCATTT
1 TTTTCAACACCAACACCCATCACCCCA--T
972819 TTTTCAACACCAAC-CCCATCACCCC
1 TTTTCAACACCAACACCCATCACCCC
972844 TTGTTCCCTG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
28 24 0.49
29 10 0.20
30 15 0.31
ACGTcount: A:0.30, C:0.46, G:0.00, T:0.24
Consensus pattern (28 bp):
TTTTCAACACCAACACCCATCACCCCAT
Found at i:986215 original size:116 final size:111
Alignment explanation
Indices: 986012--986230 Score: 294
Period size: 116 Copynumber: 1.9 Consensus size: 111
986002 GCTCGATTCT
* * *
986012 ATCACAGAAGGAGGTAGATCAGCATCGACTTTTGCTCAATTCTATCACAGATGAGGATCAGCATC
1 ATCACAGAAGGAGGTAGATCAGCATCAACTTTTGCTCAATTCTATCACAGAGGAGGAACAGCATC
*
986077 GACATCTCGTTCTATTCCATCACAAAAGGAGGTGGATCTCAAATCC
66 GACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCTCAAATCC
* * * ** *
986123 ATCACAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAAGGAGGTAGACCG
1 ATCACAGAAGGAGGTAGATCAGCATCAAC-TTTTGCTCAATTCTATCACAG-AGGAGG-A-ACAG
*
986188 ACATCGACATCTCGTTCGATTCCATCACAAAATGAGGTGGATC
62 -CATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATC
986231 GACATTTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
111 25 0.27
112 19 0.21
113 5 0.05
114 1 0.01
115 2 0.02
116 40 0.43
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (111 bp):
ATCACAGAAGGAGGTAGATCAGCATCAACTTTTGCTCAATTCTATCACAGAGGAGGAACAGCATC
GACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCTCAAATCC
Found at i:987106 original size:44 final size:44
Alignment explanation
Indices: 986931--987918 Score: 152
Period size: 44 Copynumber: 22.3 Consensus size: 44
986921 TTTTTGCTTG
*
986931 ATCACAGAATGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
* * * * **** * * *
986975 ATCACAAAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATC-TCGTTCGATTCC
* * * * * * * * * * *
987020 ATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTT-GATTCT
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCG-TTCGATTCC
987064 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
* * * * ***** * * *
987108 ATCACAAAAGGAGGTGGATCGACATTTTTTTCTTCGCTCAAATCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATC-TCGTTCGATTCC
* * * * * * * * * * * *
987153 ATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCT
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
* * * **
987197 ATCACAGAATGAGGTAAATCAACATCGACATCTCGTTCGATTCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
* * * * * **** * * *
987241 ATCACAAAATGAGGTGGATCGACATTTTTATCTTCGCTCAAATCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATC-TCGTTCGATTCC
* * * * * * * * * * * * *
987286 ATCGCAGAATGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCT
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
* * *
987330 ATCACAGAATGAGGTAGATCAGCATCGACATCTCGTTCGATTCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
* * * * **** * * *
987374 ATCACAAAATGAGGTGGATCGGCATTTTTATCTTCGCTCAAATCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATC-TCGTTCGATTCC
* * * * * * * * * * * * *
987419 ATCGCAGAATGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCT
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
* * * *
987463 ATCACAGAATGAGGTATATCAGCATCGACATCTCGTTCGATTCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
* * * * * **** * * * *
987507 ATCACAAAATGAGGTGGATCGACATTTTTATCTTCGCTCAAATCT
1 ATCACAGAAGGAGGTAGACCGGCATCGACATC-TCGTTCGATTCC
* * * * * * * * * * * *
987552 TTCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTT-GATTCT
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCG-TTCGATTCC
* * * *
987596 ATCACAGAATGAGGTATATCAGCATCGACATCTCGTTCGATTCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
* * * * **** * * *
987640 ATCACAAAAGGAGGTGGATCGACATTTTTATCTTCGCTCAAATCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATC-TCGTTCGATTCC
* * * * * * * * * * * *
987685 ATCGCAGAATGAGTTGGATCAGCGTCAACTTTTTGCTT-GATTCT
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCG-TTCGATTCC
* * *
987729 ATCACAGAATGAGGTAGATCAGCATCGACATCTCGTTCGATTCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
* * * * *** * * *
987773 ATCA-AAAAGGAGGTGGATCGACAT-TTTATCTTCGCTCAAATCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATC-TCGTTCGATTCC
* * * * * * * * * * *
987816 ATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTT-GATTCT
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCG-TTCGATTCC
* *
987860 ATCACAGAATGAGGTAGATCGGCATCGACATCTCGTTCGATTCC
1 ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
*
987904 ATCACAAAAGGAGGT
1 ATCACAGAAGGAGGT
987919 GGATCGACAT
Statistics
Matches: 651, Mismatches: 276, Indels: 34
0.68 0.29 0.04
Matches are distributed among these distances:
42 3 0.00
43 35 0.05
44 436 0.67
45 177 0.27
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
ATCACAGAAGGAGGTAGACCGGCATCGACATCTCGTTCGATTCC
Found at i:987120 original size:133 final size:133
Alignment explanation
Indices: 986114--988000 Score: 3103
Period size: 133 Copynumber: 14.5 Consensus size: 133
986104 GGAGGTGGAT
* *
986114 CTCAAATCCATCACAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAAGGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
* *
986179 GGTAGA-CCGACATCGACATCTCGTTCGATTCCATCACAAAATGAGGTGGATCGACA-TTTTATC
66 GGTAGATCAG-CATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATC
986242 TTCG
130 TTCG
*
986246 CTCAAATCCATCGCA-AAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCAC---A-GA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
*
986306 GGT--ATCA-TATCGACATCTCGTTCGATTCCATCAC-AAAGGAGGTGGATCGACA-TTTT-TCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
986365 TCG
131 TCG
*
986368 CTC-AATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAAGGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
* * * *
986432 GGTAGACCGGCATCGACATCTCGTTCGATTCCATCACAAAAGGATGTGGATTGACATTTTTATCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
986497 TCG
131 TCG
* *
986500 CTTAAATCCATCGCAGAAGGAGTTGGATCA--G-CAACTTTTTGCTCGATTCTATCACAGAA-GA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
986561 GGTAGATCAGCATCGACATCTCGTTCGATTCCAT--CAAAAGGAGGTGGATCGACATTTTTATCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
986624 TCG
131 TCG
* * *
986627 CTCAAATCCATCGCATAAGGAGTTGGATCAACGTCAACTTTTTGCTTGATTCTATCACAGAAGGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
* *
986692 GGTAGACCGGCATCGACATCTCGTTCGATTCCAT--CAAAAGGA-G-GGATCGACA-TTTTATCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
986752 TCG
131 TCG
*
986755 CTCAAATCCATCGCAGAA-G-GTTGGATCAGCGTCAACTTTTTGC-TCATTCTATCACAGAATGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
*
986817 GGTATATCA-CATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
986881 TCG
131 TCG
986884 CTC-AATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTG-----ATCACAGAATGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
* *
986943 GGTAGACCGGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
987008 TCG
131 TCG
*
987011 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAAGGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
* * *
987076 GGTAGACCGGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTTTCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
987141 TCG
131 TCG
*
987144 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAATGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
* * *
987209 GGTAAATCAACATCGACATCTCGTTCGATTCCATCACAAAATGAGGTGGATCGACATTTTTATCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
987274 TCG
131 TCG
* *
987277 CTCAAATCCATCGCAGAATGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAATGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
* *
987342 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAATGAGGTGGATCGGCATTTTTATCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
987407 TCG
131 TCG
* *
987410 CTCAAATCCATCGCAGAATGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAATGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
* *
987475 GGTATATCAGCATCGACATCTCGTTCGATTCCATCACAAAATGAGGTGGATCGACATTTTTATCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
987540 TCG
131 TCG
**
987543 CTCAAATCTTTCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
*
987608 GGTATATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
987673 TCG
131 TCG
*
987676 CTCAAATCCATCGCAGAATGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
987741 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCA-AAAAGGAGGTGGATCGACA-TTTTATCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
987804 TCG
131 TCG
987807 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
*
987872 GGTAGATCGGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
66 GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
987937 TCG
131 TCG
*
987940 CTCAAATCCATCGCA-AAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAA
1 CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAA
988001 GGAGAATGAG
Statistics
Matches: 1660, Mismatches: 61, Indels: 68
0.93 0.03 0.04
Matches are distributed among these distances:
121 11 0.01
122 50 0.03
123 21 0.01
124 50 0.03
125 25 0.02
126 55 0.03
127 126 0.08
128 98 0.06
129 85 0.05
130 95 0.06
131 199 0.12
132 105 0.06
133 740 0.45
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (133 bp):
CTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTTGATTCTATCACAGAATGA
GGTAGATCAGCATCGACATCTCGTTCGATTCCATCACAAAAGGAGGTGGATCGACATTTTTATCT
TCG
Found at i:988097 original size:49 final size:50
Alignment explanation
Indices: 987955--988102 Score: 255
Period size: 50 Copynumber: 3.0 Consensus size: 50
987945 ATCCATCGCA
987955 AAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAG
1 AAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAG
* * *
988005 AATGAGTTGGATCAGAGGCAACTTTTTGCTCGATTCTATCACAGAAGGAG
1 AAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAG
988055 AAGGAGTTGGATCAGCGTC-ACTTTTTGCTCGATTCTATCACAG-AGGAG
1 AAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAG
988103 TTGAATCGAC
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
48 5 0.05
49 24 0.26
50 63 0.68
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (50 bp):
AAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGGAG
Found at i:988196 original size:224 final size:225
Alignment explanation
Indices: 987937--988385 Score: 875
Period size: 224 Copynumber: 2.0 Consensus size: 225
987927 ATTTTTATCT
987937 TCGCTCAAATCCATCGCAAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAG
1 TCGCTCAAATCCATCGCAAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAG
988002 GAGAATGAGTTGGATCAGAGGCAACTTTTTGCTCGATTCTATCACAGAAGGAGAAGGAGTTGGAT
66 GAGAATGAGTTGGATCAGAGGCAACTTTTTGCTCGATTCTATCACAGAAGGAGAAGGAGTTGGAT
988067 CAGCGTC-ACTTTTTGCTCGATTCTATCACA-GAGGAGTTGAATCGACAATTTAATTCATTACAA
131 CAGCGTCAACTTTTTGCTCGATTCTATCACAGGAGGAGTTGAATCGACAATTTAATTCATTACAA
988130 AAGGCAGTGGATTGACATCCCCAACAAAAA
196 AAGGCAGTGGATTGACATCCCCAACAAAAA
988160 TCGCTCAAATCCATCGCAGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAA
1 TCGCTCAAATCCATCGCA-AAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAA
988225 GGAGAATGAGTTGGATCAGAGGCAACTTTTTGCTCGATTCTATCACAGAAGGAGAAGGAGTTGGA
65 GGAGAATGAGTTGGATCAGAGGCAACTTTTTGCTCGATTCTATCACAGAAGGAGAAGGAGTTGGA
988290 TCAGCGTCAACTTTTTGCTCGATTCTATCACAGGAGGAGTTGAATCGACAATTTAATTCATTACA
130 TCAGCGTCAACTTTTTGCTCGATTCTATCACAGGAGGAGTTGAATCGACAATTTAATTCATTACA
988355 AAAGGCAGTGGATTGACATCCCCAACAAAAA
195 AAAGGCAGTGGATTGACATCCCCAACAAAAA
988386 GTTCCTAATG
Statistics
Matches: 223, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
223 18 0.08
224 119 0.53
225 23 0.10
226 63 0.28
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (225 bp):
TCGCTCAAATCCATCGCAAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAG
GAGAATGAGTTGGATCAGAGGCAACTTTTTGCTCGATTCTATCACAGAAGGAGAAGGAGTTGGAT
CAGCGTCAACTTTTTGCTCGATTCTATCACAGGAGGAGTTGAATCGACAATTTAATTCATTACAA
AAGGCAGTGGATTGACATCCCCAACAAAAA
Found at i:988257 original size:50 final size:50
Alignment explanation
Indices: 988177--988328 Score: 268
Period size: 50 Copynumber: 3.0 Consensus size: 50
988167 AATCCATCGC
988177 AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGG
1 AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGG
* * *
988227 AGAATGAGTTGGATCAGAGGCAACTTTTTGCTCGATTCTATCACAGAAGG
1 AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGG
*
988277 AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGGAGG
1 AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGG
988327 AG
1 AG
988329 TTGAATCGAC
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 95 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (50 bp):
AGAAGGAGTTGGATCAGCGTCAACTTTTTGCTCGATTCTATCACAGAAGG
Found at i:988574 original size:30 final size:29
Alignment explanation
Indices: 988507--988591 Score: 127
Period size: 29 Copynumber: 2.9 Consensus size: 29
988497 GTAAACACCA
* *
988507 TTTTTCAACACCAACACCTACCACCCCAT
1 TTTTTCAACACCAACACCCATCACCCCAT
*
988536 TTTTTCAACACCAACACCCATCATCCCAT
1 TTTTTCAACACCAACACCCATCACCCCAT
988565 TTCTTTCAACACCAAC-CCCATCACCCC
1 TT-TTTCAACACCAACACCCATCACCCC
988592 TTGTTCCCGC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 38 0.75
30 13 0.25
ACGTcount: A:0.29, C:0.46, G:0.00, T:0.25
Consensus pattern (29 bp):
TTTTTCAACACCAACACCCATCACCCCAT
Found at i:990754 original size:27 final size:27
Alignment explanation
Indices: 990704--990763 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
990694 GGTGTTCCAA
990704 TCTCACCTTAAATGATTGGTGGCGACT
1 TCTCACCTTAAATGATTGGTGGCGACT
990731 TCTCACCTTAAATGATTGGTGGCGACT
1 TCTCACCTTAAATGATTGGTGGCGACT
*
990758 CCTCAC
1 TCTCAC
990764 ATTTTGAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (27 bp):
TCTCACCTTAAATGATTGGTGGCGACT
Found at i:991391 original size:23 final size:23
Alignment explanation
Indices: 991325--991393 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
991315 CACCAGAGCT
* *
991325 CGTATAATTGCACCGAAGTGACA
1 CGTAGAATTGCACCGAAGTGCCA
*
991348 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
991371 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
991394 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:992110 original size:63 final size:67
Alignment explanation
Indices: 991973--992110 Score: 146
Period size: 63 Copynumber: 2.1 Consensus size: 67
991963 GCCATTTTCA
*
991973 TCTTTTAATGGAGGTATGCATCGATGCACTACACTATGCATCGATGCATAAATCCTATTCGATGT
1 TCTTTTAATGGAGG-ATGCATCGATGCACTACACTATGCATCGATGCATAAATCCTACTCGATGT
992038 TTG
65 TTG
* * ** *
992041 T-ATTTAATGG-GG-TGCATCGATGCACT-C-CTTATGCATTGATGCATCGATGGC-ACTCGATG
1 TCTTTTAATGGAGGATGCATCGATGCACTACAC-TATGCATCGATGCATAAAT-CCTACTCGATG
992100 TTT-
64 TTTG
992103 TCTTTTAA
1 TCTTTTAA
992111 ATTAATGCAT
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
62 2 0.03
63 32 0.53
64 15 0.25
66 2 0.03
67 8 0.13
68 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (67 bp):
TCTTTTAATGGAGGATGCATCGATGCACTACACTATGCATCGATGCATAAATCCTACTCGATGTT
TG
Found at i:993429 original size:5 final size:5
Alignment explanation
Indices: 993413--993457 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
993403 AAAAACAAAA
* * *
993413 TAAAA TAAAT TAGAT TAGAT TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
993458 GAATATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (5 bp):
TAAAT
Found at i:993505 original size:14 final size:15
Alignment explanation
Indices: 993459--993511 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 15
993449 AAATTAAATG
*
993459 AATATAATAATAATAAT
1 AATATAA-ACTAAT-AT
*
993476 AATAATATACTAATAT
1 AAT-ATAAACTAATAT
993492 AATATAAACT-ATAT
1 AATATAAACTAATAT
993506 AATATA
1 AATATA
993512 TATATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.31
15 6 0.19
16 5 0.16
17 8 0.25
18 3 0.09
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATAAACTAATAT
Found at i:993547 original size:31 final size:31
Alignment explanation
Indices: 993507--993580 Score: 80
Period size: 33 Copynumber: 2.4 Consensus size: 31
993497 AAACTATATA
**
993507 ATATA-TATATTTCAAAAA-TATTTTTAAACT
1 ATATATTATATTTCAAAAAGT-TTTCAAAACT
*
993537 ATATATTATATTTTTTAAAAAGTTTTCAAAACT
1 ATATATTATA--TTTCAAAAAGTTTTCAAAACT
993570 ATATATTATAT
1 ATATATTATAT
993581 AGTTTTCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 5 0.14
31 5 0.14
33 26 0.70
34 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (31 bp):
ATATATTATATTTCAAAAAGTTTTCAAAACT
Found at i:993642 original size:67 final size:62
Alignment explanation
Indices: 993550--993722 Score: 206
Period size: 62 Copynumber: 2.7 Consensus size: 62
993540 TATTATATTT
* *
993550 TTTAAAAAGTTTTCAAAACTATATATTATAT-AGTTTTCAAAAATGATTTAAAAAATCATATAA
1 TTTAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAAATG-TTTAAAAAATCATAT-A
* * ** *
993613 GTTTTCAAAAATGCTTTT-AAAACTATATATTATATAATTTTTCAACAATGTTTTTAAAATTATA
1 --TTT--AAAATG-TTTTAAAAACTATATATTATATAAGTTTTCAAAAATGTTTAAAAAATCATA
993677 TA
61 TA
993679 TTTAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAAA
1 TTTAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAAA
993723 AATGTTTCAA
Statistics
Matches: 95, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
61 4 0.04
62 34 0.36
64 3 0.03
65 3 0.03
66 1 0.01
67 34 0.36
68 16 0.17
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (62 bp):
TTTAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAAATGTTTAAAAAATCATATA
Found at i:993657 original size:37 final size:36
Alignment explanation
Indices: 993497--993787 Score: 198
Period size: 39 Copynumber: 8.5 Consensus size: 36
993487 AATATAATAT
* * * *
993497 AAACTATATAATATAT-ATATTTCAAAAATATTTTT
1 AAACTATATATTATATAATTTTTCAAAAATGTTTTA
993532 AAACTATATATTATAT--TTTTT-AAAAA-GTTTTCA
1 AAACTATATATTATATAATTTTTCAAAAATGTTTT-A
* *
993565 AAACTATATATTATAT-AGTTTTCAAAAATGATTT-
1 AAACTATATATTATATAATTTTTCAAAAATGTTTTA
* *
993599 AAA--A-A-ATCATATAAGTTTTCAAAAATGCTTTTA
1 AAACTATATATTATATAATTTTTCAAAAATG-TTTTA
*
993632 AAACTATATATTATATAATTTTTCAACAATGTTTT-
1 AAACTATATATTATATAATTTTTCAAAAATGTTTTA
*
993667 ----TA-AAATTATAT-A--TTT--AAAATGTTTTAA
1 AAACTATATATTATATAATTTTTCAAAAATGTTTT-A
* *
993694 AAACTATATATTATATAAGTTTTCAAAAAAATGTTTCAA
1 AAACTATATATTATATAATTTTTC--AAAAATGTTT-TA
* *
993733 AAACTATATA-TATATATTTTTTTC-AAAATGATTTCA
1 AAACTATATATTATATA-ATTTTTCAAAAATG-TTTTA
993769 AAACTATAATATATATATA
1 AAACTAT-ATAT-TATATA
993788 TATATATATA
Statistics
Matches: 207, Mismatches: 18, Indels: 58
0.73 0.06 0.20
Matches are distributed among these distances:
25 9 0.04
27 3 0.01
29 1 0.00
30 14 0.07
31 19 0.09
32 16 0.08
33 25 0.12
34 11 0.05
35 24 0.12
36 23 0.11
37 25 0.12
38 6 0.03
39 31 0.15
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (36 bp):
AAACTATATATTATATAATTTTTCAAAAATGTTTTA
Found at i:993715 original size:25 final size:25
Alignment explanation
Indices: 993659--993722 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
993649 ATTTTTCAAC
* *
993659 AATGTTTTTAAAATTATATATTTAA
1 AATGTTTTAAAAACTATATATTTAA
*
993684 AATGTTTTAAAAACTATATATTATAT
1 AATGTTTTAAAAACTATATATT-TAA
993710 AA-GTTTTCAAAAA
1 AATGTTTT-AAAAA
993723 AATGTTTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 25 0.74
26 9 0.26
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (25 bp):
AATGTTTTAAAAACTATATATTTAA
Found at i:993784 original size:2 final size:2
Alignment explanation
Indices: 993773--993840 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
993763 ATTTCAAAAC
993773 TA TA -A 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
993814 T- 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
993841 CGGACGAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 62 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:994759 original size:3 final size:3
Alignment explanation
Indices: 994751--994777 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
994741 AATTCTCTTA
994751 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
994778 TATTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:994782 original size:3 final size:3
Alignment explanation
Indices: 994776--994809 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
994766 AATAATAATA
994776 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
994810 CAACCATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:997119 original size:65 final size:65
Alignment explanation
Indices: 996988--997402 Score: 627
Period size: 65 Copynumber: 6.4 Consensus size: 65
996978 CATCATATAG
* * ** * *
996988 TCACTCCACCTTATGCACCACAAAGTTACACAAGTCCCATTGAGTGAT-TAGTACATTATTCAAT
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCACA-TGAGTGATCT-GTACAGTATTCAAT
997052 TA
64 TA
* *
997054 TCACTCCACCTCATGCACCATAAAGGTACATGAATCACATGAGTGATCTGTA-AGGTATTCAATT
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCACATGAGTGATCTGTACA-GTATTCAATT
997118 A
65 A
* *
997119 TCACTCCATCTCATGTACCACAAAGGTACATGAGTCACATGAGTGATCTGTACAGTATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCACATGAGTGATCTGTACAGTATTCAATTA
* * *
997184 TCATTCCACCTCATGCACCACAAAGGTAAATGAGTCACATGAGTGATCTGTACAATATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCACATGAGTGATCTGTACAGTATTCAATTA
* *
997249 TCACTCTACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACAGTATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCACATGAGTGATCTGTACAGTATTCAATTA
* * *
997314 TCATTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTACAGTATTCAATTA
1 TCACTCCACCTCATGCACCACAAAGGTACATGAGTCACATGAGTGATCTGTACAGTATTCAATTA
997379 TCACTCCACCTCATGCACCACAAA
1 TCACTCCACCTCATGCACCACAAA
997403 TATACGTTAA
Statistics
Matches: 320, Mismatches: 26, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
64 1 0.00
65 285 0.89
66 34 0.11
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (65 bp):
TCACTCCACCTCATGCACCACAAAGGTACATGAGTCACATGAGTGATCTGTACAGTATTCAATTA
Found at i:997730 original size:65 final size:65
Alignment explanation
Indices: 997626--997778 Score: 227
Period size: 65 Copynumber: 2.4 Consensus size: 65
997616 CTACTCGAGT
* * * *
997626 ATAGATCACTCATATAACTCGTGTACCTTTGTGGTGCATGAGGTGAAATGA-TAATTGAATATTG
1 ATAGATCACTCATATGACTCATGTACCTTTGTAGTGCATGAGGTGAAAT-ATTAATTGAATAATG
997690 C
65 C
* *
997691 ATAGATCACTCATATGACTCATGTACTTTTGTAGTGCATGAGGTGAAGTATTAATTGAATAATGC
1 ATAGATCACTCATATGACTCATGTACCTTTGTAGTGCATGAGGTGAAATATTAATTGAATAATGC
*
997756 ACAGATCACTCATATGACTCATG
1 ATAGATCACTCATATGACTCATG
997779 CACAGGTGGA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
64 1 0.01
65 79 0.99
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (65 bp):
ATAGATCACTCATATGACTCATGTACCTTTGTAGTGCATGAGGTGAAATATTAATTGAATAATGC
Found at i:997863 original size:65 final size:64
Alignment explanation
Indices: 997782--997987 Score: 254
Period size: 65 Copynumber: 3.2 Consensus size: 64
997772 ACTCATGCAC
* * *
997782 AGGTGGAGTTATAATTGAGTATTGCACAAATCACTCACATGACTCTTGTACCTTTGTGGTGCATG
1 AGGTGGAGTGATAATTGAATACTGCACAAATCACTCA-ATGACTCTTGTACCTTTGTGGTGCATG
* * * *
997847 AGGTGGAGTGATAATTGAATACTACACATATCACTCATATGACTCATGTACCTTCGTGGTGCATG
1 AGGTGGAGTGATAATTGAATACTGCACAAATCACTCA-ATGACTCTTGTACCTTTGTGGTGCATG
* *
997912 AGGTGGAGTGAT-ATTGAATACTGCA-AAGATCACTCAATGAGATTTGTGTACCTTTGTGGTGCA
1 AGGTGGAGTGATAATTGAATACTGCACAA-ATCACTCAATGA-CTCT-TGTACCTTTGTGGTGCA
*
997975 TA
63 TG
*
997977 ATGTGGAGTGA
1 AGGTGGAGTGA
997988 CTATATGATA
Statistics
Matches: 122, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
63 5 0.04
64 21 0.17
65 96 0.79
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (64 bp):
AGGTGGAGTGATAATTGAATACTGCACAAATCACTCAATGACTCTTGTACCTTTGTGGTGCATG
Found at i:997880 original size:116 final size:116
Alignment explanation
Indices: 997676--997894 Score: 323
Period size: 116 Copynumber: 1.9 Consensus size: 116
997666 AGGTGAAATG
* * * *
997676 ATAATTGAATATTGCATAGATCACTCATATGACTCATGTACTTTTGTAGTGCATGAGGTGAAGTA
1 ATAATTGAATATTGCACAAATCACTCACATGACTCATGTACCTTTGTAGTGCATGAGGTGAAGTA
*
997741 TTAATTGAATAATGCACAGATCACTCATATGACTCATGCACAGGTGGAGTT
66 TTAATTGAATAATACACAGATCACTCATATGACTCATGCACAGGTGGAGTT
* * * *
997792 ATAATTGAGTATTGCACAAATCACTCACATGACTCTTGTACCTTTGTGGTGCATGAGGTGGAGTG
1 ATAATTGAATATTGCACAAATCACTCACATGACTCATGTACCTTTGTAGTGCATGAGGTGAAGT-
* *
997857 A-TAATTGAATACTACACATATCACTCATATGACTCATG
65 ATTAATTGAATAATACACAGATCACTCATATGACTCATG
997895 TACCTTCGTG
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
116 90 0.99
117 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (116 bp):
ATAATTGAATATTGCACAAATCACTCACATGACTCATGTACCTTTGTAGTGCATGAGGTGAAGTA
TTAATTGAATAATACACAGATCACTCATATGACTCATGCACAGGTGGAGTT
Found at i:1005248 original size:20 final size:21
Alignment explanation
Indices: 1005205--1005262 Score: 100
Period size: 20 Copynumber: 2.8 Consensus size: 21
1005195 AGTGGTCAAT
*
1005205 AATAACAAAACTGATAGAAAA
1 AATAACAAAACTGGTAGAAAA
1005226 AATAACAAAACTGGTAG-AAA
1 AATAACAAAACTGGTAGAAAA
1005246 AATAACAAAACTGGTAG
1 AATAACAAAACTGGTAG
1005263 CACTTTACCG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.60, C:0.10, G:0.14, T:0.16
Consensus pattern (21 bp):
AATAACAAAACTGGTAGAAAA
Found at i:1005843 original size:32 final size:32
Alignment explanation
Indices: 1005805--1006136 Score: 305
Period size: 32 Copynumber: 10.4 Consensus size: 32
1005795 CAATCCATAT
*
1005805 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1005837 TTTAAAATAAATCAATACATAC-AACTACAA-TA
1 TTTAAAATAAATCAATCCATACTAA-TA-AATTA
* * * * * *
1005869 ATAAATCAATACATACAACTACAATAATAAATCAATCTATA
1 TTTAA--AATAAAT-CAA-T-CCATACT-AAT-AA-AT-TA
*
1005910 TTTTAAAATAAATCAATTCATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
*
1005943 TTTAAAATAAATCAAT-C---C--AT---GT-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1005965 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1005997 TTTAAAATAAATCAA-CACATACTAATAAATTA
1 TTTAAAATAAATCAATC-CATACTAATAAATTA
**
1006029 TTTAAAATAAATCAATATATACTAATAAA-TA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1006060 TTTTAAAATAAATCAATCCATACTAATAAAATA
1 -TTTAAAATAAATCAATCCATACTAATAAATTA
*
1006093 TTTAAAATAAATCAATCCATACTAATTAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1006125 ATTAAAATAAAT
1 TTTAAAATAAAT
1006137 TATTTTAAAA
Statistics
Matches: 247, Mismatches: 25, Indels: 56
0.75 0.08 0.17
Matches are distributed among these distances:
22 16 0.06
23 2 0.01
26 3 0.01
28 3 0.01
31 7 0.03
32 167 0.68
33 6 0.02
34 7 0.03
35 5 0.02
36 4 0.02
37 7 0.03
38 3 0.01
39 6 0.02
40 6 0.02
41 2 0.01
42 3 0.01
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:1005875 original size:26 final size:26
Alignment explanation
Indices: 1005842--1005904 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
1005832 AATTATTTAA
1005842 AATAAATCAATACATACAACTACAAT
1 AATAAATCAATACATACAACTACAAT
1005868 AATAAATCAATACATACAACTACAAT
1 AATAAATCAATACATACAACTACAAT
1005894 AATAAATCAAT
1 AATAAATCAAT
1005905 CTATATTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.59, C:0.17, G:0.00, T:0.24
Consensus pattern (26 bp):
AATAAATCAATACATACAACTACAAT
Found at i:1005971 original size:22 final size:22
Alignment explanation
Indices: 1005943--1005984 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1005933 TAATAAATTA
1005943 TTTAAAATAAATCAATCCATGT
1 TTTAAAATAAATCAATCCATGT
1005965 TTTAAAATAAATCAATCCAT
1 TTTAAAATAAATCAATCCAT
1005985 ACTAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATGT
Found at i:1005994 original size:22 final size:22
Alignment explanation
Indices: 1005945--1005993 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1005935 ATAAATTATT
* **
1005945 TAAAATAAATCAATCCATGTTT
1 TAAAATAAATCAATCCATCTAA
1005967 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCAT-CTAA
1005990 TAAA
1 TAAA
1005994 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATCTAA
Found at i:1007329 original size:3 final size:3
Alignment explanation
Indices: 1007321--1007368 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1007311 GGTGAAGTTT
1007321 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1007369 GAAATCTGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1009278 original size:2 final size:2
Alignment explanation
Indices: 1009266--1009303 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1009256 TTTTGATGCA
*
1009266 AT AT TT 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
1009304 GTGCCTTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1011282 original size:167 final size:166
Alignment explanation
Indices: 1010934--1011438 Score: 976
Period size: 167 Copynumber: 3.0 Consensus size: 166
1010924 AATTTTTTAG
1010934 TTTAATATTAAAATGATTAAAAATATAAATTATTATTTCCATTATTATAATTACTATTACCATGT
1 TTTAATATTAAAATGATTAAAAATATAAATTATTATTTCCATTATTATAATTACTATTACCATGT
1010999 ACTTTTGTTTTGTGAAAATAGTTTTTTTTTCTTTAAAACATTTTAAGGTGTATATTAATTAAATT
66 ACTTTTGTTTTGTGAAAATAGTTTTTTTTTCTTTAAAACATTTTAAGGTGTATATTAATTAAATT
1011064 AGTTGAATTTATAACTTAAATGATGTTAAAAATCTA
131 AGTTGAATTTATAACTTAAATGATGTTAAAAATCTA
1011100 TTTAATATTAAAATGATTAAAAATATAAATTATTATTTCCATTATTATAATTACTATTACCATGT
1 TTTAATATTAAAATGATTAAAAATATAAATTATTATTTCCATTATTATAATTACTATTACCATGT
*
1011165 ACTTTTGTTTTGTGAAAATAGTTTTTTTTTTCTTTAAAACATTTCAAGGTGTATATTAATTAAAT
66 ACTTTTGTTTTGTGAAAATAG-TTTTTTTTTCTTTAAAACATTTTAAGGTGTATATTAATTAAAT
1011230 TAGTTGAATTTATAACTTAAATGATGTTAAAAATCTA
130 TAGTTGAATTTATAACTTAAATGATGTTAAAAATCTA
1011267 TTTAATATTAAAATGATTAAAAATATAAATTATTATTTCCATTATTATAATTACTATTACCATGT
1 TTTAATATTAAAATGATTAAAAATATAAATTATTATTTCCATTATTATAATTACTATTACCATGT
*
1011332 ACTTTTGTTTTGTGAAAATAG-TTTTTTTTCTTTAAAAAATTTTAAGGTGTATATTAATTAAATT
66 ACTTTTGTTTTGTGAAAATAGTTTTTTTTTCTTTAAAACATTTTAAGGTGTATATTAATTAAATT
1011396 AGTTGAATTTATAACTTAAATGATGTTAAAAATCTA
131 AGTTGAATTTATAACTTAAATGATGTTAAAAATCTA
1011432 TTTAATA
1 TTTAATA
1011439 CTGTTTCACG
Statistics
Matches: 335, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
165 84 0.25
166 86 0.26
167 165 0.49
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.48
Consensus pattern (166 bp):
TTTAATATTAAAATGATTAAAAATATAAATTATTATTTCCATTATTATAATTACTATTACCATGT
ACTTTTGTTTTGTGAAAATAGTTTTTTTTTCTTTAAAACATTTTAAGGTGTATATTAATTAAATT
AGTTGAATTTATAACTTAAATGATGTTAAAAATCTA
Found at i:1012882 original size:17 final size:19
Alignment explanation
Indices: 1012847--1012883 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
1012837 TAGTTTTTTC
*
1012847 TTTATCTTTTATATCATTT
1 TTTATCTTTTATATAATTT
1012866 TTTAT-TTTTA-ATAATTT
1 TTTATCTTTTATATAATTT
1012883 T
1 T
1012884 ATTTCTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 5 0.29
19 5 0.29
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATCTTTTATATAATTT
Found at i:1012915 original size:23 final size:26
Alignment explanation
Indices: 1012880--1012936 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 26
1012870 TTTTTAATAA
1012880 TTTTAT-TTCTATGACAC-TTTTT-T
1 TTTTATCTTCTATGACACATTTTTCT
1012903 TTTTATCTT-TATGACACATTTTTCT
1 TTTTATCTTCTATGACACATTTTTCT
*
1012928 TTTTCTCTT
1 TTTTATCTT
1012937 GCATGTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 14 0.47
24 7 0.23
25 9 0.30
ACGTcount: A:0.16, C:0.16, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTATCTTCTATGACACATTTTTCT
Found at i:1013785 original size:14 final size:15
Alignment explanation
Indices: 1013753--1013792 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1013743 TTATAATGAA
*
1013753 TTAATAAAATATTAC
1 TTAATTAAATATTAC
*
1013768 TTAATTAAA-ATTAT
1 TTAATTAAATATTAC
1013782 TTAATTAAATA
1 TTAATTAAATA
1013793 ATAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAATTAAATATTAC
Found at i:1013956 original size:2 final size:2
Alignment explanation
Indices: 1013949--1013980 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1013939 ATTTTAAAAC
1013949 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
1013981 ATTTAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1015168 original size:12 final size:12
Alignment explanation
Indices: 1015151--1015188 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1015141 AAAAAAAATC
1015151 TTTTGAATTGGT
1 TTTTGAATTGGT
*
1015163 TTTTGAGTT-GT
1 TTTTGAATTGGT
1015174 TTTTGAATTGTGT
1 TTTTGAATTG-GT
1015187 TT
1 TT
1015189 AACCTATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 8 0.36
13 4 0.18
ACGTcount: A:0.13, C:0.00, G:0.24, T:0.63
Consensus pattern (12 bp):
TTTTGAATTGGT
Found at i:1018793 original size:24 final size:24
Alignment explanation
Indices: 1018732--1018794 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
1018722 TTATAAAATA
*
1018732 TTAATAT-AATAAT-TTATTGATT
1 TTAATATAAATAATATTAATGATT
* *
1018754 TTAAAATATAGTAATATTAAT-ATTT
1 TTAATATA-AATAATATTAATGA-TT
1018779 TTAATATAAATAATAT
1 TTAATATAAATAATAT
1018795 ATTTATAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 6 0.19
24 13 0.41
25 13 0.41
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (24 bp):
TTAATATAAATAATATTAATGATT
Found at i:1018811 original size:19 final size:20
Alignment explanation
Indices: 1018773--1018833 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
1018763 AGTAATATTA
*
1018773 ATATTTTTAATATAAATAAT
1 ATATTTATAATATAAATAAT
1018793 ATATTTATAATAT-AATAAT
1 ATATTTATAATATAAATAAT
* *
1018812 ATATTTATAAAATCAATAAT
1 ATATTTATAATATAAATAAT
1018832 AT
1 AT
1018834 CAATATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.47
20 20 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTTATAATATAAATAAT
Found at i:1022983 original size:64 final size:64
Alignment explanation
Indices: 1022865--1023028 Score: 163
Period size: 64 Copynumber: 2.6 Consensus size: 64
1022855 ATTGTTCAAG
* * * * ** *
1022865 GTGTATCGATGAACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCA-TCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCAC-CCGCTAAAATAAAAACATCGAATGGCATTCA
* * * *
1022929 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCGCTAAAAGTACAAATATCGAATGGGATTTA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCGCTAAAA-TAAAAACATCGAATGGCATTCA
* *
1022994 -TGTACCGATGCA-TAGATAGTGCATCGATGCACCCG
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCCG
1023029 TCAAGGGATG
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
63 9 0.11
64 73 0.87
65 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCGCTAAAATAAAAACATCGAATGGCATTCA
Found at i:1026215 original size:21 final size:21
Alignment explanation
Indices: 1026100--1026215 Score: 55
Period size: 21 Copynumber: 5.6 Consensus size: 21
1026090 GCGAAATAAA
*
1026100 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
1026120 AATCGCAA----ATTAGTTCCTAG
1 AATCGCAACGCGATT--TTCC-AG
* **
1026140 AATCGCAACGCGATTATGAAG
1 AATCGCAACGCGATTTTCCAG
** ** *
1026161 AATCGCAATACGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
1026181 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
1026203 AATCGCAACGCGA
1 AATCGCAACGCGA
1026216 ATATGAAAAT
Statistics
Matches: 69, Mismatches: 17, Indels: 19
0.66 0.16 0.18
Matches are distributed among these distances:
16 1 0.01
17 1 0.01
19 3 0.04
20 20 0.29
21 38 0.55
22 3 0.04
24 3 0.04
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:1026245 original size:20 final size:20
Alignment explanation
Indices: 1026203--1026255 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1026193 GATTTTCCAG
*
1026203 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAACATGAA
*
1026223 AATCACAACGCGAACAT-ATA
1 AATCGCAACGCGAACATGA-A
*
1026243 AATTGCAACGCGA
1 AATCGCAACGCGA
1026256 TTCTGACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATGAA
Found at i:1026308 original size:20 final size:20
Alignment explanation
Indices: 1026264--1026477 Score: 189
Period size: 20 Copynumber: 10.6 Consensus size: 20
1026254 GATTCTGACT
*
1026264 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
1026285 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1026305 ATCGTAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
1026326 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * **
1026346 ATCTCAACGAGAATATGTAA
1 ATCGCAACGCGTATCCGTAA
*
1026366 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1026386 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1026406 ATTGCAATGCGTATTCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
1026426 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
1026447 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
1026467 ATCGCAACGCG
1 ATCGCAACGCG
1026478 ATTTTTAAAG
Statistics
Matches: 154, Mismatches: 33, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
20 106 0.69
21 48 0.31
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:1026314 original size:41 final size:41
Alignment explanation
Indices: 1026264--1026475 Score: 293
Period size: 41 Copynumber: 5.2 Consensus size: 41
1026254 GATTCTGACT
* * *
1026264 ATCGCAACGAGTATCCGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
1026305 ATCGTAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
1026346 ATCTCAACGAGAATATGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
1026386 ATCGCAACGAGAATACGT-AAATTGCAATGCGTATTCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
1026426 ATCGCAACGACAATACGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
1026467 ATCGCAACG
1 ATCGCAACG
1026476 CGATTTTTAA
Statistics
Matches: 149, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 72 0.48
41 77 0.52
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:1027064 original size:21 final size:21
Alignment explanation
Indices: 1027003--1027081 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
1026993 TTCTAAACTT
1027003 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
1027023 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
1027043 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
1027064 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
1027082 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:1027099 original size:33 final size:33
Alignment explanation
Indices: 1027058--1027138 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
1027048 CGCAACGAGA
1027058 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1027091 GAAATGAAAATTGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1027124 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1027139 TTGCAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1027156 original size:19 final size:19
Alignment explanation
Indices: 1027134--1027217 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
1027124 GAAACCAAAA
* *
1027134 TCGCATTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
1027153 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1027167 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
1027186 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1027205 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1027218 CTCTCATTGC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.19
16 2 0.04
17 3 0.06
19 39 0.72
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1027228 original size:33 final size:34
Alignment explanation
Indices: 1027191--1027276 Score: 93
Period size: 37 Copynumber: 2.5 Consensus size: 34
1027181 TAATTTCGCG
* *
1027191 TTGCGATTTTCATTTCGCGTTGC-GATTCTCTCA
1 TTGCGATTTTCATTTCGCATTGCACATTCTCTCA
** *
1027224 TTGCGATAGTCATTTCCGCATTGCAATCATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGC-A-CATTCTCTCA
1027261 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1027277 AACCAAAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
33 13 0.31
34 7 0.17
36 1 0.02
37 21 0.50
ACGTcount: A:0.15, C:0.24, G:0.16, T:0.44
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCATTGCACATTCTCTCA
Found at i:1027239 original size:52 final size:52
Alignment explanation
Indices: 1027134--1027250 Score: 171
Period size: 52 Copynumber: 2.2 Consensus size: 52
1027124 GAAACCAAAA
* **
1027134 TCGCATTGCAATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTAATT
1 TCGCATTGCAATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTAATT
* * *
1027186 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTCATT
1 TCGCATTGCAATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTAATT
1027238 TCCGCATTGCAAT
1 T-CGCATTGCAAT
1027251 CATTCTCTCG
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 47 0.84
53 9 0.16
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (52 bp):
TCGCATTGCAATTTTCATTTCGCGTTGCGATTCTCTCATTGCGATAGTAATT
Found at i:1029133 original size:94 final size:94
Alignment explanation
Indices: 1028972--1029351 Score: 593
Period size: 94 Copynumber: 4.1 Consensus size: 94
1028962 TAGATTGCTT
* *
1028972 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1029037 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* * *
1029066 AGTAAATTTATTTGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1029131 ATTTGTCTTTGTTTTGTCTTTTAGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
1029160 AGTAAATTTGTTCGGTTGTTGCCAATTCTACTAAACTGTGTATTATTTAACAGTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1029225 ATTTATCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
1029254 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTTTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1029319 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1029347 AGTAA
1 AGTAA
1029352 TGCAATCAAT
Statistics
Matches: 263, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
93 25 0.10
94 238 0.90
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1029545 original size:19 final size:19
Alignment explanation
Indices: 1029452--1029537 Score: 92
Period size: 19 Copynumber: 4.8 Consensus size: 19
1029442 GCAACGAGAG
* *
1029452 AATCGCAACGAGAAATGAA
1 AATCGCAACGCGAAATCAA
*
1029471 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATCAA
* *
1029490 AATCACAA--TG--A-CAA
1 AATCGCAACGCGAAATCAA
1029504 AATCGCAACGCGAAATCAA
1 AATCGCAACGCGAAATCAA
1029523 AATCGCAACGCGAAA
1 AATCGCAACGCGAAA
1029538 CTATAATCAC
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 41 0.75
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAATCAA
Found at i:1029631 original size:22 final size:20
Alignment explanation
Indices: 1029582--1029670 Score: 124
Period size: 20 Copynumber: 4.3 Consensus size: 20
1029572 GATTCTCTCG
**
1029582 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1029602 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1029622 TAATGCGATAGTCATTTTTGCA
1 T--TGCGATAGTCATTTTCGCA
*
1029644 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1029664 TTGCGAT
1 TTGCGAT
1029671 TTTAAGTTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
20 43 0.69
22 19 0.31
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1029645 original size:42 final size:42
Alignment explanation
Indices: 1029583--1029662 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
1029573 ATTCTCTCGT
1029583 TGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATAA
1 TGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATAA
** *
1029625 TGCGATAGTCATTTTTGCATTGCGATAGTCATTTTCGC
1 TGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGC
1029663 GTTGCGATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (42 bp):
TGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATAA
Found at i:1030245 original size:21 final size:21
Alignment explanation
Indices: 1030154--1030258 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
1030144 GACTCACCTG
*
1030154 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
1030176 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1030196 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1030217 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1030238 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1030259 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1030251 original size:42 final size:42
Alignment explanation
Indices: 1030151--1030261 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
1030141 CCCGACTCAC
* * * *
1030151 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
1030193 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
1030235 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
1030262 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:1031634 original size:14 final size:14
Alignment explanation
Indices: 1031615--1031650 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1031605 ATTGTTTAAT
1031615 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1031629 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1031643 TGATTTGT
1 TGATTTGT
1031651 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1031801 original size:20 final size:20
Alignment explanation
Indices: 1031776--1032050 Score: 462
Period size: 20 Copynumber: 13.8 Consensus size: 20
1031766 CCGATTCTCT
1031776 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
1031796 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
1031816 CGTTACGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
1031836 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
1031856 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
1031876 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
*
1031896 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
*
1031916 CGCTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
1031936 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
1031956 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
*
1031976 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
*
1031996 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
*
1032016 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCA-ATTCCG
1032036 CGTTGCGATAGTCAA
1 CGTTGCGATAGTCAA
1032051 ATGAATGTCT
Statistics
Matches: 244, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
19 1 0.00
20 241 0.99
21 2 0.01
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:1035366 original size:20 final size:20
Alignment explanation
Indices: 1035351--1035402 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1035341 GTCAGAATCT
1035351 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTACAGATTCG
*
1035371 CATTGCGATTTAC-GTATTCG
1 CGTTGCGATTTACAG-ATTCG
1035391 CGTTGCGATTTA
1 CGTTGCGATTTA
1035403 GGAAAATCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACAGATTCG
Found at i:1035535 original size:20 final size:20
Alignment explanation
Indices: 1035491--1035684 Score: 180
Period size: 21 Copynumber: 9.6 Consensus size: 20
1035481 TACCGGAGAT
*
1035491 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
* *
1035510 CGCGTTGCGGTTAACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1035530 CGCGTTGCGATTTTACGTATT
1 CGCGTTGCGA-TTTACGGATA
*
1035551 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1035571 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1035591 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
1035612 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1035632 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* *
1035653 CGCGTTACGATTTTATGGATA
1 CGCGTTGCGA-TTTACGGATA
*
1035674 CTCGTTGCGAT
1 CGCGTTGCGAT
1035685 AGTCAGAATC
Statistics
Matches: 142, Mismatches: 23, Indels: 19
0.77 0.12 0.10
Matches are distributed among these distances:
18 1 0.01
19 14 0.10
20 60 0.42
21 67 0.47
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1035568 original size:41 final size:41
Alignment explanation
Indices: 1035512--1035684 Score: 274
Period size: 41 Copynumber: 4.2 Consensus size: 41
1035502 TTATCGATCG
* *
1035512 CGTTGCGGTTAACGGATACGCGTTGCGATTTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1035553 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1035594 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * *
1035635 CGTTGCGATTTACGGATACGCGTTACGATTTTATGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
1035676 CGTTGCGAT
1 CGTTGCGAT
1035685 AGTCAGAATC
Statistics
Matches: 124, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 124 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:1035698 original size:82 final size:82
Alignment explanation
Indices: 1035512--1035706 Score: 259
Period size: 82 Copynumber: 2.4 Consensus size: 82
1035502 TTATCGATCG
* * *
1035512 CGTTGCGGTTAACGGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTCACGAATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
* * **
1035577 GCGATTTTACGTATTGT
66 ACGATTTTACGGATACT
* * *
1035594 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTCACGAATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
*
1035659 ACGATTTTATGGATACT
66 ACGATTTTACGGATACT
1035676 CGTTGCGATAGTCA-GAAT-CGCGTTGCGATTT
1 CGTTGCGAT--TCACGAATACGCGTTGCGATTT
1035707 ATATGTTCGC
Statistics
Matches: 101, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
82 96 0.95
83 3 0.03
84 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (82 bp):
CGTTGCGATTCACGAATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
ACGATTTTACGGATACT
Found at i:1035716 original size:20 final size:20
Alignment explanation
Indices: 1035693--1035747 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1035683 ATAGTCAGAA
*
1035693 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1035713 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
1035733 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1035748 GGAAAATCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1037151 original size:20 final size:20
Alignment explanation
Indices: 1037126--1037494 Score: 460
Period size: 20 Copynumber: 18.4 Consensus size: 20
1037116 GATTTTCCAT
* ** *
1037126 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1037146 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1037166 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1037186 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1037206 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1037226 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1037246 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1037266 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1037286 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
1037306 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1037326 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1037346 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1037366 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1037386 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1037406 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1037426 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1037446 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1037466 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1037486 AATCACAAC
1 AATCGCAAC
1037495 ACTTAAATTT
Statistics
Matches: 307, Mismatches: 32, Indels: 20
0.86 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 299 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1039057 original size:14 final size:14
Alignment explanation
Indices: 1039038--1039127 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
1039028 TTGAAATGAA
1039038 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1039052 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
* *
1039069 ACAATCGCAAAGAGAA
1 --AATCGCAACGAGAG
*
1039085 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1039104 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1039118 AATCGCAACG
1 AATCGCAACG
1039128 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 1 0.02
16 6 0.10
17 7 0.11
18 1 0.02
19 19 0.31
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1039075 original size:33 final size:33
Alignment explanation
Indices: 1039030--1039144 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
1039020 TCTTTTGGTT
1039030 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * * *
1039063 GAGATGACAATCGCAAAGAGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1039096 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1039129 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1039145 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1039076 original size:19 final size:19
Alignment explanation
Indices: 1039033--1039149 Score: 93
Period size: 19 Copynumber: 6.9 Consensus size: 19
1039023 TTTGGTTGAA
1039033 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
1039050 A-G--AATCGCAACGCGAG
1 ATGAAAATCGCAACGCGAG
*
1039066 ATGACAATCGCAA----AG
1 ATGAAAATCGCAACGCGAG
*
1039081 A-GAAAATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
1039099 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
*
1039116 A-G--AATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
*
1039132 ATGAAAATCGCAATGCGA
1 ATGAAAATCGCAACGCGA
1039150 TTTTGGTTTC
Statistics
Matches: 80, Mismatches: 5, Indels: 28
0.71 0.04 0.25
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 11 0.14
17 7 0.09
18 2 0.03
19 31 0.39
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (19 bp):
ATGAAAATCGCAACGCGAG
Found at i:1039180 original size:14 final size:14
Alignment explanation
Indices: 1039161--1039215 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1039151 TTTGGTTTCG
1039161 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1039175 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1039194 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1039208 CGTTGCGA
1 CGTTGCGA
1039216 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1039193 original size:33 final size:33
Alignment explanation
Indices: 1039145--1039215 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1039135 AAAATCGCAA
**
1039145 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1039178 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1039211 TGCGA
1 TGCGA
1039216 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1039223 original size:33 final size:33
Alignment explanation
Indices: 1039156--1039237 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1039146 GCGATTTTGG
***
1039156 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1039189 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1039222 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1039238 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1039242 original size:20 final size:20
Alignment explanation
Indices: 1039168--1039256 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1039158 TCGCGTTGCG
1039168 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1039188 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1039201 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1039221 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1039241 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1039257 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1039378 original size:33 final size:33
Alignment explanation
Indices: 1039336--1039406 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1039326 AATACTAACT
*
1039336 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1039369 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1039402 TGAAA
1 TGAAA
1039407 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1039637 original size:22 final size:22
Alignment explanation
Indices: 1039585--1039639 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1039575 TGGTTGTGAG
**
1039585 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1039607 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1039629 GGATTTCTTCG
1 GGATTTCTTCG
1039640 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1039810 original size:20 final size:20
Alignment explanation
Indices: 1039785--1039977 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
1039775 CTTTAAATAT
1039785 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1039805 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1039827 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1039846 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1039866 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1039886 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1039906 CACGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1039926 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1039946 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1039966 CGCGTTGCGATT
1 CGCGTTGCGATT
1039978 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1039977 original size:60 final size:60
Alignment explanation
Indices: 1039785--1039977 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
1039775 CTTTAAATAT
**
1039785 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1039846 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * * ** *
1039906 CACGTTACGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1039966 CGCGTTGCGATT
1 CGCGTTGCGATT
1039978 ATGGAAAATC
Statistics
Matches: 109, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 81 0.74
61 28 0.26
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1040058 original size:20 final size:20
Alignment explanation
Indices: 1040033--1040084 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1040023 AAGAATCGCG
*
1040033 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1040053 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1040073 TTGCGATTCTGG
1 TTGCGATTCTGG
1040085 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1042071 original size:29 final size:29
Alignment explanation
Indices: 1042038--1042097 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1042028 AGTTTTCAAG
*
1042038 GGTTTTACTTGACAATGTAGTCTAAGGTT
1 GGTTTTACTAGACAATGTAGTCTAAGGTT
1042067 GGTTTTACTAGACAATGTAGTCTAAGGTT
1 GGTTTTACTAGACAATGTAGTCTAAGGTT
1042096 GG
1 GG
1042098 ACTGTTCCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (29 bp):
GGTTTTACTAGACAATGTAGTCTAAGGTT
Found at i:1044027 original size:14 final size:15
Alignment explanation
Indices: 1043987--1044029 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1043977 TTAGTTTTTC
1043987 GAAAAATGAATTACT
1 GAAAAATGAATTACT
* **
1044002 GGAATTTGAATT-CT
1 GAAAAATGAATTACT
1044016 GAAAAATGAATTAC
1 GAAAAATGAATTAC
1044030 ATTTTTTAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (15 bp):
GAAAAATGAATTACT
Found at i:1044061 original size:19 final size:20
Alignment explanation
Indices: 1044017--1044055 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1044007 TTGAATTCTG
1044017 AAAAATGAATTACATTTTTT
1 AAAAATGAATTACATTTTTT
1044037 AAAAATGAATTACATTTTT
1 AAAAATGAATTACATTTTT
1044056 GGAAATCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAAATGAATTACATTTTTT
Found at i:1044413 original size:23 final size:22
Alignment explanation
Indices: 1044373--1044443 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 22
1044363 TATCTTTACT
*
1044373 AAAATATTAT-TTAAATATATA
1 AAAATATTTTATTAAATATATA
1044394 AATAATATTTTATTAAATATATA
1 AA-AATATTTTATTAAATATATA
* *
1044417 AAAA-A-TTTATTATATATTATT
1 AAAATATTTTATTAAATA-TATA
1044438 AAAATA
1 AAAATA
1044444 AAAAATATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 10 0.23
21 10 0.23
22 10 0.23
23 13 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAATATTTTATTAAATATATA
Found at i:1044437 original size:30 final size:32
Alignment explanation
Indices: 1044398--1044476 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 32
1044388 TATATAAATA
* *
1044398 ATATTTTATTAAATATATAAAAA-AT-TTAT-T
1 ATATATTATTAAATATA-AAAAATATAATATCT
1044428 ATATATTATTAAA-ATAAAAAATATAATATCT
1 ATATATTATTAAATATAAAAAATATAATATCT
1044459 -TATATTATTATAATATAA
1 ATATATTATTA-AATATAA
1044477 TTTGATTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 5 0.12
29 5 0.12
30 25 0.60
31 3 0.07
32 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (32 bp):
ATATATTATTAAATATAAAAAATATAATATCT
Found at i:1044444 original size:27 final size:26
Alignment explanation
Indices: 1044414--1044525 Score: 79
Period size: 27 Copynumber: 4.1 Consensus size: 26
1044404 TATTAAATAT
1044414 ATAAAAAATTTATTATATATTATTAAA
1 ATAAAAAATTTATT-TATATTATTAAA
*
1044441 ATAAAAAATATAATATCTTATATTATTATA
1 ATAAAAAAT-T--TAT-TTATATTATTAAA
*
1044471 AT--ATAATTTGA-TTATATTATTAAA
1 ATAAAAAATTT-ATTTATATTATTAAA
* *
1044495 CT-AAAAATATAATATTATATTATTATAA
1 ATAAAAAAT-TTAT-TTATATTATTA-AA
1044523 ATA
1 ATA
1044526 TTAATAAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
24 13 0.19
25 6 0.09
26 2 0.03
27 21 0.31
28 8 0.12
30 16 0.24
31 1 0.01
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (26 bp):
ATAAAAAATTTATTTATATTATTAAA
Found at i:1044524 original size:22 final size:20
Alignment explanation
Indices: 1044499--1044547 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
1044489 ATTAAACTAA
*
1044499 AAATATAATATTATATTATTAT
1 AAATATAATA-AATA-TATTAT
*
1044521 AAATATTAATAAATATATTTT
1 AAATA-TAATAAATATATTAT
1044542 AAATAT
1 AAATAT
1044548 TTTAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 10 0.42
22 8 0.33
23 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATATAATAAATATATTAT
Found at i:1044535 original size:27 final size:26
Alignment explanation
Indices: 1044446--1044536 Score: 68
Period size: 27 Copynumber: 3.6 Consensus size: 26
1044436 TTAAAATAAA
*
1044446 AAATATAAT--ATCTTATATTATTAT
1 AAATATAATAAATATTATATTATTAT
*
1044470 -AATATAAT--TTGATTATATTATTA-
1 AAATATAATAAAT-ATTATATTATTAT
* *
1044493 AACTAAAAATATAATATTATATTATTAT
1 AAAT-ATAATA-AATATTATATTATTAT
1044521 AAATATTAATAAATAT
1 AAATA-TAATAAATAT
1044537 ATTTTAAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
23 9 0.17
24 13 0.25
25 4 0.08
27 18 0.35
28 8 0.15
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (26 bp):
AAATATAATAAATATTATATTATTAT
Found at i:1044538 original size:51 final size:52
Alignment explanation
Indices: 1044428--1044544 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 52
1044418 AAAATTTATT
*
1044428 ATATATTATTAAAATAAAAAATATAATATCTTATATTATTATAATATAATTTGA
1 ATATATTATTAAAATAAAAAATATAATA-CTTATATTATTATAATATAA-TTAA
* *
1044482 TTATATTATTAAACT-AAAAATATAATA-TTATATTATTATAAATATTAA-TAA
1 ATATATTATTAAAATAAAAAATATAATACTTATATTATTAT-AATA-TAATTAA
1044533 ATATATT-TTAAA
1 ATATATTATTAAA
1044545 TATTTTAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
50 5 0.09
51 20 0.35
52 4 0.07
53 15 0.26
54 13 0.23
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (52 bp):
ATATATTATTAAAATAAAAAATATAATACTTATATTATTATAATATAATTAA
Done.