Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008610.1 Hibiscus syriacus cultivar Beakdansim tig00111566_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: 2108335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 11
Found at i:630140 original size:199 final size:199
Alignment explanation
Indices: 629799--631157 Score: 2459
Period size: 199 Copynumber: 6.8 Consensus size: 199
629789 GGCAAATTTA
* * *
629799 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAA
* * *
629864 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGAGAATATGTCTAA
65 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAA
629929 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
130 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
629994 TGCAC
195 TGCAC
* * *
629999 CCATAAAGTGTTGATCCATATATAAAAAGTGTTGATCCGAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
630064 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAA
630129 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
*
630194 GAAC
196 GCAC
* * *
630198 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAA
* * *
630263 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGAGAATATGTCTAA
65 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAA
*
630328 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGT
130 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
630393 TGCAC
195 TGCAC
*
630398 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
630463 GTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTTTTATGAGATAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAA
630528 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
*
630593 GAAC
196 GCAC
630597 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
630662 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAGTATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAA
630727 TAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
630791 GCAC
196 GCAC
*
630795 TCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
630860 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTATAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAA
630925 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
630990 GCAC
196 GCAC
630994 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* *
631059 GTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAA
66 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAA
631124 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 TAATGTGTCGACACTAATATAGTTTGTGTCGATA
631158 CTAATTTAAA
Statistics
Matches: 1115, Mismatches: 42, Indels: 5
0.96 0.04 0.00
Matches are distributed among these distances:
198 195 0.17
199 686 0.62
200 234 0.21
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (199 bp):
CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGTCTAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGT
GCAC
Found at i:630927 original size:397 final size:399
Alignment explanation
Indices: 629799--631157 Score: 2517
Period size: 399 Copynumber: 3.4 Consensus size: 399
629789 GGCAAATTTA
629799 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
*
629864 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGAGAATATGTCTAA
66 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
629929 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
131 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
* *
629994 TGCACCCATAAAGTGTTGATCCATATATAAAAAGTGTTGATCCGAAAATCATCGAACCCAAAAGT
196 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGAAAATCATCGAACCCAAAAGT
630059 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGT
261 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGT
630124 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAAC
326 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAAC
630189 AGGGTGAAC
391 AGGGTGAAC
630198 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
*
630263 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGAGAATATGTCTAA
66 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
*
630328 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGT
131 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
630393 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGAAAATCATCGAACCCAAAAGT
196 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGAAAATCATCGAACCCAAAAGT
*
630458 ATAATGTAATATGTAATTTTTCAATCTAACCGGTATAATTATACCGGTTTTATGAGATAATATGT
261 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGT
630523 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAAC
326 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAAC
630588 AGGGTGAAC
391 AGGGTGAAC
* * *
630597 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
* * * *
630661 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAGTATGTATAA
66 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
630726 ATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGG
131 ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
* *
630790 TGCACTCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
196 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGAAAATCATCGAACCCAAAAGT
630855 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGT
261 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGT
*
630920 ATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAAC
326 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAAC
*
630985 AGGGTGCAC
391 AGGGTGAAC
* * *
630994 CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AACCCAAAAGTATAA
1 CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
631058 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
66 TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
631123 ATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 ATAATGTGTCGACACTAATATAGTTTGTGTCGATA
631158 CTAATTTAAA
Statistics
Matches: 938, Mismatches: 22, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
397 387 0.41
398 109 0.12
399 442 0.47
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (399 bp):
CCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAACCAAAAGTATAA
TGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAA
ATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGG
TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGAAAATCATCGAACCCAAAAGT
ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGATAATATGT
CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAAC
AGGGTGAAC
Found at i:632640 original size:18 final size:18
Alignment explanation
Indices: 632619--632680 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
632609 AGCGGTCGCA
632619 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
632637 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
632655 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
632673 GAAGATGA
1 GAAGATGA
632681 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:632654 original size:3 final size:3
Alignment explanation
Indices: 632634--632714 Score: 81
Period size: 3 Copynumber: 27.0 Consensus size: 3
632624 TGAAGCTGAC
* * * * * ** *
632634 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
632682 GAC GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
632715 CCAAACAAGT
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:632673 original size:36 final size:36
Alignment explanation
Indices: 632622--632698 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
632612 GGTCGCAGAA
*
632622 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
632658 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
632694 GATGA
1 GATGA
632699 TGATGATGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:634573 original size:183 final size:182
Alignment explanation
Indices: 634180--634851 Score: 1193
Period size: 183 Copynumber: 3.7 Consensus size: 182
634170 TTCAACATAT
* *
634180 TATAAATATACCGGTTTTTTGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
*
634245 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGT-TAAAAGTGTCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTGTCGACATTT
634309 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
*
634362 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
*
634427 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTGTCGACATTT
634492 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
130 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
634545 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
* *
634610 TCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACATTT
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTGTCGACATTT
* * *
634675 ACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACTGG
130 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
* *
634728 TATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTG
1 TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
634793 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGTGTCG
634852 GTAATTTTAA
Statistics
Matches: 474, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
182 111 0.23
183 359 0.76
184 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (182 bp):
TATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTG
TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTGTCGACATTTA
CACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGG
Found at i:637352 original size:25 final size:25
Alignment explanation
Indices: 637318--637382 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
637308 TTATCATTAA
637318 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
637343 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
637368 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
637383 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:637759 original size:23 final size:23
Alignment explanation
Indices: 637728--637800 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
637718 ATAGGTAAAC
*
637728 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
637751 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
637774 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
637797 ATAT
1 ATAT
637801 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:638249 original size:18 final size:18
Alignment explanation
Indices: 638228--638264 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
638218 GTAATTGGAG
638228 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
638246 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
638264 T
1 T
638265 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:638272 original size:24 final size:24
Alignment explanation
Indices: 638220--638266 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
638210 TTTCATATGT
* *
638220 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
638244 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
638267 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:638577 original size:34 final size:34
Alignment explanation
Indices: 638539--638604 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
638529 AAATCCAAAG
*
638539 CTCATATGGTGCCAAGCAAAAGGAAATCAAAAAT
1 CTCATATGATGCCAAGCAAAAGGAAATCAAAAAT
638573 CTCATATGATGCCAAGCAAAAGGAAATCAAAA
1 CTCATATGATGCCAAGCAAAAGGAAATCAAAA
638605 TCTACAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.48, C:0.18, G:0.17, T:0.17
Consensus pattern (34 bp):
CTCATATGATGCCAAGCAAAAGGAAATCAAAAAT
Found at i:639004 original size:22 final size:21
Alignment explanation
Indices: 638960--639004 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
638950 ATTACATAAC
*
638960 TTTTAAAAAAAGTATCGATCT
1 TTTTAAAAAAAGTATCGAACT
* *
638981 TTTTATAAAAAGTATGGACACT
1 TTTTAAAAAAAGTATCGA-ACT
639003 TT
1 TT
639005 CAATATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (21 bp):
TTTTAAAAAAAGTATCGAACT
Found at i:639053 original size:23 final size:23
Alignment explanation
Indices: 639022--639094 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
639012 ATAGGTAAAC
*
639022 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
639045 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
639068 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
639091 ATAT
1 ATAT
639095 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:639299 original size:30 final size:29
Alignment explanation
Indices: 639240--639306 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
639230 GTTACGATAT
* *
639240 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
639270 ATATTTTATAAAATATCAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
639300 ATTTTTT
1 ATATTTT
639307 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:646380 original size:2 final size:2
Alignment explanation
Indices: 646368--646397 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
646358 ATTATTATTC
646368 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
646398 TATTTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:649398 original size:42 final size:42
Alignment explanation
Indices: 649328--649417 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
649318 TATATAAATC
*
649328 GGTTTTACGAAAAAAGTTTTCTAATGTTTGATAGTTGTAATT
1 GGTTTTACGAAAAAAGTTTTCTAATGTTTGACAGTTGTAATT
* * *
649370 GGTTTTACGGAAAATATTTTTC-AGTGTTTGACAGTTGTAATT
1 GGTTTTAC-GAAAAAAGTTTTCTAATGTTTGACAGTTGTAATT
*
649412 GATTTT
1 GGTTTT
649418 CCCAATGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 31 0.74
43 11 0.26
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.47
Consensus pattern (42 bp):
GGTTTTACGAAAAAAGTTTTCTAATGTTTGACAGTTGTAATT
Found at i:649570 original size:21 final size:21
Alignment explanation
Indices: 649545--649614 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
649535 ATTATTTCAT
649545 TTATTTAATATTAATTTAATA
1 TTATTTAATATTAATTTAATA
649566 TTATTATAATA-TAATTTAATA
1 TTATT-TAATATTAATTTAATA
*
649587 ATA-TT-A-ATT--TTTAATA
1 TTATTTAATATTAATTTAATA
649603 TTATATTAATAT
1 TTAT-TTAATAT
649615 ATACTCAGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
16 9 0.22
17 1 0.02
18 4 0.10
19 2 0.05
20 3 0.07
21 17 0.41
22 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTTAATATTAATTTAATA
Found at i:649599 original size:16 final size:17
Alignment explanation
Indices: 649580--649612 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
649570 TATAATATAA
649580 TTTAATA-ATATTAATT
1 TTTAATATATATTAATT
649596 TTTAATATTATATTAAT
1 TTTAATA-TATATTAAT
649613 ATATACTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATATATATTAATT
Found at i:649613 original size:11 final size:10
Alignment explanation
Indices: 649534--649614 Score: 73
Period size: 11 Copynumber: 8.3 Consensus size: 10
649524 CTCAAAAAAT
*
649534 TATTATTTCA
1 TATTATTTAA
649544 T-TTATTTAA
1 TATTATTTAA
649553 TATTAATTTAA
1 TATT-ATTTAA
649564 TATTATTATAA
1 TATTATT-TAA
*
649575 TATAATTTAA
1 TATTATTTAA
*
649585 TAATA-TT-A
1 TATTATTTAA
649593 -ATT-TTTAA
1 TATTATTTAA
649601 TATTATATTAA
1 TATTAT-TTAA
649612 TAT
1 TAT
649615 ATACTCAGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
7 4 0.07
8 2 0.03
9 13 0.22
10 13 0.22
11 26 0.45
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (10 bp):
TATTATTTAA
Found at i:650122 original size:30 final size:30
Alignment explanation
Indices: 650058--650158 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 30
650048 AATGTAATTC
** * * *
650058 ATTTTACGCAAAATAGTTTT-AGATAATTT
1 ATTTTACATAAAACAGTTTTCAGGTAATAT
*
650087 ATTTTACGTAAAACAGTTTTCAGGTAATAT
1 ATTTTACATAAAACAGTTTTCAGGTAATAT
* *
650117 ATTTTACATAAAACAATTTTCAGGTAATCT
1 ATTTTACATAAAACAGTTTTCAGGTAATAT
650147 ATTTTACATAAA
1 ATTTTACATAAA
650159 TTGTGTATTG
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
29 18 0.28
30 46 0.72
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.42
Consensus pattern (30 bp):
ATTTTACATAAAACAGTTTTCAGGTAATAT
Found at i:651163 original size:2 final size:2
Alignment explanation
Indices: 651156--651180 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
651146 TAAAATACGA
651156 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 A
651181 CTAGAAGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:653665 original size:14 final size:13
Alignment explanation
Indices: 653628--653671 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
653618 AGGTGAGTAC
653628 ATATCTATGTGAT
1 ATATCTATGTGAT
653641 A-ATCTATGTGAT
1 ATATCTATGTGAT
*
653653 ATTATCTACGTGAAT
1 A-TATCTATGTG-AT
653668 ATAT
1 ATAT
653672 TAAAAAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 12 0.44
13 1 0.04
14 11 0.41
15 3 0.11
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (13 bp):
ATATCTATGTGAT
Found at i:654219 original size:65 final size:64
Alignment explanation
Indices: 654094--654249 Score: 206
Period size: 65 Copynumber: 2.4 Consensus size: 64
654084 ACACCCTATT
*
654094 TCAAATGCATTTTGTGTACCGATGCACAGCCATGCATCGATGCACTCTTGAATTTATTGAAACA
1 TCAAATGCATTTTGTGTACCGATGCACAACCATGCATCGATGCACTCTTGAATTTATTGAAACA
* * * **
654158 TCGAATGCATTTTGTGTACCAATGCACAAACCATGCATCGATGTACTCTTGGCTCTT-TTGAAAC
1 TCAAATGCATTTTGTGTACCGATGCAC-AACCATGCATCGATGCACTCTTGAAT-TTATTGAAAC
654222 A
64 A
* * *
654223 TCAAATGTAATTAGTGTACCGATGCAC
1 TCAAATGCATTTTGTGTACCGATGCAC
654250 TCCTAGTGTA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 25 0.32
65 52 0.66
66 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (64 bp):
TCAAATGCATTTTGTGTACCGATGCACAACCATGCATCGATGCACTCTTGAATTTATTGAAACA
Found at i:660097 original size:23 final size:22
Alignment explanation
Indices: 660035--660106 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 22
660025 GAGTGTACTA
*
660035 ATGCATCCCTTGAATGTGCATCG
1 ATGCAT-CCTTGAATGTGCACCG
* * * *
660058 ATTCA-CCATGAAGGTGCACCT
1 ATGCATCCTTGAATGTGCACCG
**
660079 ATGCATTCCTTGAATGTGCTTCG
1 ATGCA-TCCTTGAATGTGCACCG
660102 ATGCA
1 ATGCA
660107 CTAATCTGTG
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
21 16 0.44
23 20 0.56
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (22 bp):
ATGCATCCTTGAATGTGCACCG
Found at i:662773 original size:64 final size:65
Alignment explanation
Indices: 662699--662854 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 65
662689 ACACCCTATT
*
662699 TCGAATGCATTTTGTGTACCGATGCAC-AACCATGCATCGATGCACTCTTGAAT-TTATTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCTGAATCTT-TTGAAAC
662762 A
65 A
* * ** * *
662763 TCGAATGCATTTTGTGTATCGATGCACAAACCATGCATCGATGTACTCCTGGCTCTTTTGCAATA
1 TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCTGAATCTTTTGAAACA
* *
662828 TCGAATGCAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
662855 TCCTAGTGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 26 0.32
65 52 0.65
66 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAACCATGCATCGATGCACTCCTGAATCTTTTGAAACA
Found at i:663692 original size:22 final size:22
Alignment explanation
Indices: 663612--663686 Score: 82
Period size: 21 Copynumber: 3.4 Consensus size: 22
663602 GTTCTTTGCT
* *
663612 GTCCTTCGGGACATTTCTACGCG
1 GTCCTTCGGGACA-TTCTATGTG
**
663635 GTCCTTTAGGACA-TCTATGTG
1 GTCCTTCGGGACATTCTATGTG
663656 GTCCTTCGGGACATTCTATGTG
1 GTCCTTCGGGACATTCTATGTG
663678 G-CACTTCGG
1 GTC-CTTCGG
663687 TGCATTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 18 0.41
22 15 0.34
23 11 0.25
ACGTcount: A:0.15, C:0.25, G:0.27, T:0.33
Consensus pattern (22 bp):
GTCCTTCGGGACATTCTATGTG
Found at i:667746 original size:18 final size:19
Alignment explanation
Indices: 667711--667746 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
667701 AAGTCAAAGT
667711 ATGCAGTAAAACATATTTC
1 ATGCAGTAAAACATATTTC
*
667730 ATGCAGTCAAA-ATATTT
1 ATGCAGTAAAACATATTT
667747 AAAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (19 bp):
ATGCAGTAAAACATATTTC
Found at i:669613 original size:24 final size:23
Alignment explanation
Indices: 669581--669628 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
669571 AAATATGTTG
669581 TATATTATT-TACATTATAATATTA
1 TATATTATTATACATTA-AAT-TTA
669605 TATATTATTATACATTAAATTTA
1 TATATTATTATACATTAAATTTA
669628 T
1 T
669629 GTTGGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.17
24 12 0.52
25 7 0.30
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATTATTATACATTAAATTTA
Found at i:672105 original size:12 final size:12
Alignment explanation
Indices: 672088--672147 Score: 75
Period size: 12 Copynumber: 4.8 Consensus size: 12
672078 TTAGAGCATT
672088 ACCTCCTCCACC
1 ACCTCCTCCACC
**
672100 ACCTCCTCGAACATT
1 ACCTCCTC---CACC
672115 ACCTCCTCCACC
1 ACCTCCTCCACC
672127 ACCTCCTCCACC
1 ACCTCCTCCACC
672139 ACCTCCTCC
1 ACCTCCTCC
672148 TCAATCTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 31 0.76
15 10 0.24
ACGTcount: A:0.18, C:0.60, G:0.02, T:0.20
Consensus pattern (12 bp):
ACCTCCTCCACC
Found at i:672134 original size:15 final size:15
Alignment explanation
Indices: 672116--672149 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
672106 TCGAACATTA
*
672116 CCTCCTCCACCACCT
1 CCTCCACCACCACCT
*
672131 CCTCCACCACCTCCT
1 CCTCCACCACCACCT
672146 CCTC
1 CCTC
672150 AATCTCAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.68, G:0.00, T:0.21
Consensus pattern (15 bp):
CCTCCACCACCACCT
Found at i:672134 original size:27 final size:27
Alignment explanation
Indices: 672007--672133 Score: 166
Period size: 27 Copynumber: 4.7 Consensus size: 27
671997 AGACCCTGCC
* *
672007 ACCTCCCCCGCCACCTCCTAGAA-ATTT
1 ACCTCCTCCACCACCTCCTAGAACA-TT
* *
672034 ACCTCCTCCTCCACCTCCTAGAGCATT
1 ACCTCCTCCACCACCTCCTAGAACATT
* * *
672061 ACCTCCTCCACGACCTCTTAGAGCATT
1 ACCTCCTCCACCACCTCCTAGAACATT
*
672088 ACCTCCTCCACCACCTCCTCGAACATT
1 ACCTCCTCCACCACCTCCTAGAACATT
672115 ACCTCCTCCACCACCTCCT
1 ACCTCCTCCACCACCTCCT
672134 CCACCACCTC
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
27 88 0.99
28 1 0.01
ACGTcount: A:0.20, C:0.50, G:0.06, T:0.24
Consensus pattern (27 bp):
ACCTCCTCCACCACCTCCTAGAACATT
Found at i:672146 original size:27 final size:27
Alignment explanation
Indices: 672033--672149 Score: 92
Period size: 27 Copynumber: 4.3 Consensus size: 27
672023 CCTAGAAATT
* ** * *
672033 TACCTCCTCCTCCACCTCCTAGAGCAT
1 TACCTCCTCCACCACCTCCTCCAACAC
* * ** * *
672060 TACCTCCTCCACGACCTCTTAGAGCAT
1 TACCTCCTCCACCACCTCCTCCAACAC
* *
672087 TACCTCCTCCACCACCTCCTCGAACAT
1 TACCTCCTCCACCACCTCCTCCAACAC
*
672114 TACCTCCTCCACCACCTCCTCCACCACC
1 TACCTCCTCCACCACCTCCTCCAACA-C
672142 T-CCTCCTC
1 TACCTCCTC
672150 AATCTCAAGG
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 78 0.99
28 1 0.01
ACGTcount: A:0.19, C:0.52, G:0.05, T:0.24
Consensus pattern (27 bp):
TACCTCCTCCACCACCTCCTCCAACAC
Found at i:674388 original size:30 final size:30
Alignment explanation
Indices: 674348--674594 Score: 368
Period size: 30 Copynumber: 8.2 Consensus size: 30
674338 TGTTTTAGTT
*
674348 GGTCTTCCAGAAACCGGAGAAGCAGGAGCA
1 GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
*
674378 GGTCTCCCAGAAACCGTAGAAGCAGGAGCA
1 GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
674408 GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
1 GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
* *
674438 GGTCTCCCAGAAACCGAAGAAGCCGGAGCA
1 GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
* *
674468 GGTCTCCCAGAAGCCGGAGAAGCAAGAGCA
1 GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
*
674498 TGTCTCCCAGAAACCGGAGAAGCAGGAGCA
1 GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
* **
674528 TGTCTCCCAGAAATGGGAGAAGCAGGAGCA
1 GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
* * *
674558 GATCTCCCAGAAATCGGAGAAGCAGGAGTA
1 GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
*
674588 GATCTCC
1 GGTCTCC
674595 TAGTTTTCAG
Statistics
Matches: 199, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 199 1.00
ACGTcount: A:0.33, C:0.26, G:0.31, T:0.10
Consensus pattern (30 bp):
GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
Found at i:675464 original size:6 final size:6
Alignment explanation
Indices: 675453--675491 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
675443 TGACTTCCTT
675453 ACCTCC ACCTCC ACCTCC ACCTCC ACCTCC ACCTCC ACC
1 ACCTCC ACCTCC ACCTCC ACCTCC ACCTCC ACCTCC ACC
675492 ACCATCAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.67, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCTCC
Found at i:677863 original size:22 final size:21
Alignment explanation
Indices: 677812--677863 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
677802 TTAACTTTGC
*
677812 ATTTAAAAGGATAAATTATTA
1 ATTTAAAAGGATAAATAATTA
* * * *
677833 ATGTCAAAGCGATTAATAATTT
1 ATTTAAAAG-GATAAATAATTA
677855 ATTTAAAAG
1 ATTTAAAAG
677864 ATGGGTAAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.37
Consensus pattern (21 bp):
ATTTAAAAGGATAAATAATTA
Found at i:678220 original size:4 final size:4
Alignment explanation
Indices: 678211--678255 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
678201 ATTTATATCA
*
678211 AATT AATT AATT TATT AA-T AATT AATT ATATTT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT A-A-TT AATT AATT AATT
678256 TAAATTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
3 3 0.08
4 28 0.78
5 2 0.06
6 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
AATT
Found at i:678224 original size:19 final size:17
Alignment explanation
Indices: 678200--678257 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
678190 AATTGACTAA
678200 AATTTATATCAAATTAATT
1 AATTTATAT--AATTAATT
678219 AATTTAT-TAA-TAATT
1 AATTTATATAATTAATT
*
678234 AATTATATTTAATTAATT
1 AATT-TATATAATTAATT
678252 AATTTA
1 AATTTA
678258 AATTATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
15 9 0.25
16 5 0.14
17 5 0.14
18 10 0.28
19 7 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTTATATAATTAATT
Found at i:678261 original size:14 final size:14
Alignment explanation
Indices: 678215--678262 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
678205 ATATCAAATT
* *
678215 AATTAATTTATTAA
1 AATTAATTAATTTA
678229 TAATTAATTATATTT-
1 -AATTAATTA-ATTTA
678244 AATTAATTAATTTA
1 AATTAATTAATTTA
678258 AATTA
1 AATTA
678263 TAAATTCAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 4 0.14
14 14 0.48
15 8 0.28
16 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTAATTAATTTA
Found at i:682548 original size:64 final size:62
Alignment explanation
Indices: 682431--682590 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 62
682421 AGGTAAGTGT
* * * * *
682431 ACCGATGCATGAATCCATGCATCGATGCACCCTTATTTTAATTGAACAGCGAATGGCTTTTGTGC
1 ACCGATGCA-CAAGCCATGCATCGATGCACCCTTATATTAA-T-AACAGCGAATGGATTTTATGC
* * *
682496 ACCGATGCACATA-TCATGCATCGATGCACTCCATATATATTAA-AACATCGAATTGATTTTATG
1 ACCGATGCACA-AGCCATGCATCGATGCAC-CC-T-TATATTAATAACAGCGAATGGATTTTATG
682559 C
62 C
682560 ACCGATGCACAAGCCATGCATCGATGCACCC
1 ACCGATGCACAAGCCATGCATCGATGCACCC
682591 AGGCTTTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
63 3 0.04
64 59 0.72
65 12 0.15
66 1 0.01
67 7 0.09
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (62 bp):
ACCGATGCACAAGCCATGCATCGATGCACCCTTATATTAATAACAGCGAATGGATTTTATGC
Found at i:682605 original size:64 final size:63
Alignment explanation
Indices: 682488--682633 Score: 163
Period size: 64 Copynumber: 2.3 Consensus size: 63
682478 AGCGAATGGC
* * * *
682488 TTTTGTGCACCGATGCACATATCATGCATCGATGCACTCCATATATATTAAAACATCGAATTGA
1 TTTTATGCACCGATGCACATACCATGCATCGATGCACTCCAGATATATTAAAACATCGAAGT-A
* *
682552 TTTTATGCACCGATGCACA-AGCCATGCATCGATGCAC-CCAGGCT-TTTTCAAAACATCGAAGT
1 TTTTATGCACCGATGCACATA-CCATGCATCGATGCACTCCA-GATATATT-AAAACATCGAAGT
682614 A
63 A
*
682615 TATTTATGCATCGATGCAC
1 T-TTTATGCACCGATGCAC
682634 TATCAGTGTA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
63 9 0.13
64 62 0.87
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (63 bp):
TTTTATGCACCGATGCACATACCATGCATCGATGCACTCCAGATATATTAAAACATCGAAGTA
Found at i:685675 original size:26 final size:26
Alignment explanation
Indices: 685645--685707 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
685635 GGTGAAATTC
*
685645 TTGGTCATTTGCATACTAGAGGTATT
1 TTGGTCATTTCCATACTAGAGGTATT
*
685671 TTGGTCATTTCCATACTAGGGGTATT
1 TTGGTCATTTCCATACTAGAGGTATT
685697 TTGGTCATTTC
1 TTGGTCATTTC
685708 ACAGATCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.44
Consensus pattern (26 bp):
TTGGTCATTTCCATACTAGAGGTATT
Found at i:693276 original size:45 final size:44
Alignment explanation
Indices: 693201--693298 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 44
693191 TTGTGCATAA
* * *
693201 TGCATCGATACACTATTAAGGTGCATCGATGCA-TCCCTTTGAATG
1 TGCATCGATACACTATGAAGATGCACCGATGCACT-CC-TTGAATG
693246 TGCATCGATACA-TCATGAAGATGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACT-ATGAAGATGCACCGATGCACTCCTTGAATG
693290 TGCATCGAT
1 TGCATCGAT
693299 GCACAAGGCC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
44 17 0.35
45 30 0.62
46 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
TGCATCGATACACTATGAAGATGCACCGATGCACTCCTTGAATG
Found at i:693302 original size:23 final size:22
Alignment explanation
Indices: 693221--693301 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
693211 CACTATTAAG
693221 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CC-TTGAAT
* *
693245 GTGCATCGATACAT-CATGAA-
1 GTGCATCGATGCATCCTTGAAT
*
693265 GATGCACCGATGCACTCCTTGAAT
1 G-TGCATCGATGCA-TCCTTGAAT
693289 GTGCATCGATGCA
1 GTGCATCGATGCA
693302 CAAGGCCATG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 2 0.04
23 16 0.34
24 14 0.30
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:695596 original size:20 final size:20
Alignment explanation
Indices: 695571--695608 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
695561 AAGGGGGAGT
695571 AATTTCAAAACTTTATTTCA
1 AATTTCAAAACTTTATTTCA
695591 AATTTCAAAACTTTATTT
1 AATTTCAAAACTTTATTT
695609 TAAAAATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTTCAAAACTTTATTTCA
Found at i:696022 original size:19 final size:19
Alignment explanation
Indices: 695977--696042 Score: 125
Period size: 19 Copynumber: 3.5 Consensus size: 19
695967 GAATTTGTGT
695977 ATCGATGCACATACCATGC
1 ATCGATGCACATACCATGC
695996 AT-GATGCACATACCATGC
1 ATCGATGCACATACCATGC
696014 ATCGATGCACATACCATGC
1 ATCGATGCACATACCATGC
696033 ATCGATGCAC
1 ATCGATGCAC
696043 TCCATTTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.39
19 28 0.61
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (19 bp):
ATCGATGCACATACCATGC
Found at i:699221 original size:80 final size:80
Alignment explanation
Indices: 699088--699243 Score: 278
Period size: 80 Copynumber: 1.9 Consensus size: 80
699078 TTCGTTACAT
**
699088 GAGAGTAAGTATCAAAGAAGTCTAAACTGAATTTTTGAGTGAACCCTTTGACAACTAGCCTTT-C
1 GAGAGTAAGTATCAAAGAAGTCTAAACCAAATTTTTGAGTGAACCCTTTGACAACTAG-CTTTGC
699152 CTTGTATCTCTGGCTA
65 CTTGTATCTCTGGCTA
699168 GAGAGTAAGTATCAAAGAAGTCTAAACCAAATTTTTGAGTGAACCCTTTGACAACTAGCTTTGCC
1 GAGAGTAAGTATCAAAGAAGTCTAAACCAAATTTTTGAGTGAACCCTTTGACAACTAGCTTTGCC
699233 TTGTATCTCTG
66 TTGTATCTCTG
699244 AATATAACCA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
79 4 0.05
80 69 0.95
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (80 bp):
GAGAGTAAGTATCAAAGAAGTCTAAACCAAATTTTTGAGTGAACCCTTTGACAACTAGCTTTGCC
TTGTATCTCTGGCTA
Found at i:702630 original size:3 final size:3
Alignment explanation
Indices: 702624--702661 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
702614 ATAATAATAA
702624 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
702662 ACAAAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:703248 original size:24 final size:24
Alignment explanation
Indices: 703200--703247 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
703190 GAACCAAACT
*
703200 AGAAGAAAAGCGAGAGAAAGCAAA
1 AGAAGAAAAGCGAGAGAAAACAAA
703224 AGAA-AAAAG-GAGAGAAAAACAAA
1 AGAAGAAAAGCGAGAG-AAAACAAA
703247 A
1 A
703248 ACAACCAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.69, C:0.06, G:0.25, T:0.00
Consensus pattern (24 bp):
AGAAGAAAAGCGAGAGAAAACAAA
Found at i:703423 original size:20 final size:20
Alignment explanation
Indices: 703400--703438 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
703390 AGGAGTTTAT
703400 GGGTT-GTTTTAGGCTAAATA
1 GGGTTGGTTTTAGG-TAAATA
703420 GGGTTGGGTTTTAGGTAAA
1 GGGTT-GGTTTTAGGTAAA
703439 ACAAGGTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 4 0.24
22 8 0.47
ACGTcount: A:0.23, C:0.03, G:0.36, T:0.38
Consensus pattern (20 bp):
GGGTTGGTTTTAGGTAAATA
Found at i:704150 original size:30 final size:30
Alignment explanation
Indices: 704116--704183 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
704106 CCCTTAGTTT
*
704116 CTATTTTTTCTATTTTCGACCTTTAAATTC
1 CTATTTTTACTATTTTCGACCTTTAAATTC
* * * * *
704146 CTATTTGTACTATTTTTGTCCTTTAAGTTT
1 CTATTTTTACTATTTTCGACCTTTAAATTC
704176 CTATTTTT
1 CTATTTTT
704184 CCCATTCTGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.18, C:0.16, G:0.06, T:0.60
Consensus pattern (30 bp):
CTATTTTTACTATTTTCGACCTTTAAATTC
Found at i:709109 original size:32 final size:31
Alignment explanation
Indices: 709063--709125 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
709053 AAGAAATGAT
709063 GAATGATGGGCATCTTTGGAGATTCAACATC
1 GAATGATGGGCATCTTTGGAGATTCAACATC
* *
709094 GAATGTTGGGACATCTTTGGGGATTCAACATC
1 GAATGATGGG-CATCTTTGGAGATTCAACATC
709126 CTAATATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (31 bp):
GAATGATGGGCATCTTTGGAGATTCAACATC
Found at i:709489 original size:64 final size:67
Alignment explanation
Indices: 709416--709590 Score: 257
Period size: 68 Copynumber: 2.6 Consensus size: 67
709406 GTTTCTCTTA
* * *
709416 AAACAAAATTTTGTCTCTCTTGAGACATTTTCTTTTGAAA-AA-ACATCTTTGAGTC-GTTTCCC
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAACACATCTTTAAGTCTGTTTCCC
709478 TCG
65 TCG
*
709481 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAACCCATCTTTAAGTCTGTTTCCCT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAACACATCTTTAAGTCTGTTTCCCT
*
709546 TG
66 CG
*
709548 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
709591 AATTTTGTGT
Statistics
Matches: 100, Mismatches: 6, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
64 33 0.33
65 6 0.06
66 11 0.11
67 16 0.16
68 34 0.34
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (67 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAACACATCTTTAAGTCTGTTTCCCT
CG
Found at i:709571 original size:68 final size:66
Alignment explanation
Indices: 709353--709591 Score: 267
Period size: 64 Copynumber: 3.7 Consensus size: 66
709343 ATTTTTCTCA
* * * * * *
709353 AAACAAACTTTGTCTCACTTAAGACAGTCTTCT-TT-AAGACAAAC-T-TTGAAAT-TGTTTCTC
1 AAACAAATTTTGTCTCTCTTGAGACAGT-TTCTCTTGAA-ACAAACATCTTTAAGTCTGTTTCCC
*
709413 TTA
64 TTG
* * *
709416 AAACAAAATTTTGTCTCTCTTGAGACATTTTCTTTTGAAA-AAACATCTTTGAGTC-GTTTCCCT
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAACATCTTTAAGTCTGTTTCCCT
*
709479 CG
65 TG
*
709481 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAACCCATCTTTAAGTCTGTTTCCCT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA-ACATCTTTAAGTCTGTTTCCCT
709546 TG
65 TG
*
709548 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
709592 ATTTTGTGTC
Statistics
Matches: 149, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
63 12 0.08
64 57 0.38
65 19 0.13
66 11 0.07
67 16 0.11
68 34 0.23
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (66 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAACATCTTTAAGTCTGTTTCCCTT
G
Found at i:709588 original size:37 final size:36
Alignment explanation
Indices: 709471--709598 Score: 124
Period size: 37 Copynumber: 3.6 Consensus size: 36
709461 TCTTTGAGTC
*
709471 GTTTCCCTCGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* ** * * *
709507 GTTTCTCTTGAAAC-AA----CCCATCT-TTAAGTCT
1 GTTTCCCTTGAAACAAATTTTGTC-TCTCTTGAGACA
709538 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
709575 GTTTCCCTTGAAACAAAATTTTGT
1 GTTTCCCTTGAAAC-AAATTTTGT
709599 GTCACTCGAC
Statistics
Matches: 70, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
31 19 0.27
32 5 0.07
35 2 0.03
36 15 0.21
37 26 0.37
38 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:709645 original size:103 final size:104
Alignment explanation
Indices: 709471--709657 Score: 243
Period size: 103 Copynumber: 1.8 Consensus size: 104
709461 TCTTTGAGTC
* * * *
709471 GTTTCCCTCGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAACCCATCTTTAAGT
1 GTTTCCCTCGAAACAAATTTTGTCTCACTCGACACAGTTTCTCTTGAAACAAACCATCTTTAAGT
*
709536 CTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
66 CGGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
* * * * * *
709575 GTTTCCCTTGAAACAAAATTTTGTGTCACTCGACACATTTTCT-TTTAAA-AAATCATCTTTGAG
1 GTTTCCCTCGAAAC-AAATTTTGTCTCACTCGACACAGTTTCTCTTGAAACAAACCATCTTTAAG
*
709638 TCGGTTTCTCTTGAAACAAA
65 TCGGTTTCCCTTGAAACAAA
709658 AATCCCTAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
103 29 0.41
104 18 0.26
105 23 0.33
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (104 bp):
GTTTCCCTCGAAACAAATTTTGTCTCACTCGACACAGTTTCTCTTGAAACAAACCATCTTTAAGT
CGGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
Found at i:710212 original size:3 final size:3
Alignment explanation
Indices: 710204--710280 Score: 68
Period size: 3 Copynumber: 25.7 Consensus size: 3
710194 TCAACAAAAA
* *
710204 TAT TAT TA- TAT ATAT ATAT TAT AAT AAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
710250 TAT TAC TAC CAC TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
710281 ACAAAAATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.06
3 54 0.83
4 7 0.11
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:710641 original size:11 final size:11
Alignment explanation
Indices: 710615--710652 Score: 58
Period size: 11 Copynumber: 3.3 Consensus size: 11
710605 ATGCCAAGGG
710615 GATTTAACATAGA
1 GATTTAAC--AGA
710628 GATTTAACAGA
1 GATTTAACAGA
710639 GATTTAACAGA
1 GATTTAACAGA
710650 GAT
1 GAT
710653 CAGAGACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 17 0.68
13 8 0.32
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (11 bp):
GATTTAACAGA
Found at i:720638 original size:24 final size:24
Alignment explanation
Indices: 720602--720648 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
720592 TTAAATAAAT
*
720602 AATATATTATTTA-AAATATAACGC
1 AATAAATTATTTACAAATA-AACGC
*
720626 AATAAATTTTTTACAAATAAACG
1 AATAAATTATTTACAAATAAACG
720649 TAAATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (24 bp):
AATAAATTATTTACAAATAAACGC
Found at i:721522 original size:39 final size:35
Alignment explanation
Indices: 721443--721510 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
721433 TTGTAAAAGG
*
721443 AAAGGTTTTAGCTGAGCCCTTGAAAAACTAGGGAT
1 AAAGGTTCTAGCTGAGCCCTTGAAAAACTAGGGAT
* *
721478 -AAGGTTCTAGTTTAGCCCTTGAAAAACTAGGGA
1 AAAGGTTCTAGCTGAGCCCTTGAAAAACTAGGGA
721511 GTTGTAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (35 bp):
AAAGGTTCTAGCTGAGCCCTTGAAAAACTAGGGAT
Found at i:722402 original size:19 final size:19
Alignment explanation
Indices: 722358--722407 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
722348 CTCAAAATTG
* *
722358 AAAATAAATCGATTTTGAA
1 AAAAAAAATTGATTTTGAA
** *
722377 AGCAAAAGTTGATTTTGAA
1 AAAAAAAATTGATTTTGAA
722396 AAAAAAAATTGA
1 AAAAAAAATTGA
722408 AAAATGATTT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.14, T:0.28
Consensus pattern (19 bp):
AAAAAAAATTGATTTTGAA
Found at i:723772 original size:19 final size:20
Alignment explanation
Indices: 723748--723807 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
723738 AAAATGTTTT
*
723748 TATGAATAATA-CTGTACTG
1 TATGAATAATACCTATACTG
* *
723767 TATGAACAATACCTATATTG
1 TATGAATAATACCTATACTG
* *
723787 TATGAATAGTACCGATACTG
1 TATGAATAATACCTATACTG
723807 T
1 T
723808 GTGCACAATA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
19 10 0.30
20 23 0.70
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
TATGAATAATACCTATACTG
Found at i:725837 original size:14 final size:14
Alignment explanation
Indices: 725818--725852 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
725808 AATTTAAATA
725818 AAATATAATTAAGT
1 AAATATAATTAAGT
**
725832 AAATATAATTATTT
1 AAATATAATTAAGT
725846 AAATATA
1 AAATATA
725853 TTTACATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (14 bp):
AAATATAATTAAGT
Found at i:726075 original size:15 final size:15
Alignment explanation
Indices: 726055--726084 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
726045 TGACTTGAGT
726055 AAGACGTTTAAACTA
1 AAGACGTTTAAACTA
726070 AAGACGTTTAAACTA
1 AAGACGTTTAAACTA
726085 GGGATGGGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
AAGACGTTTAAACTA
Found at i:727108 original size:13 final size:13
Alignment explanation
Indices: 727090--727131 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
727080 TGCATCATGA
727090 ATTTATGACGCGC
1 ATTTATGACGCGC
*
727103 ATTTATGACACGC
1 ATTTATGACGCGC
*
727116 ATTTATGACGCTC
1 ATTTATGACGCGC
727129 ATT
1 ATT
727132 GCGCGTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:727250 original size:85 final size:84
Alignment explanation
Indices: 727103--727269 Score: 205
Period size: 85 Copynumber: 2.0 Consensus size: 84
727093 TATGACGCGC
* * * * *
727103 ATTTATGACACGCATTTATGACGCTCATTGCGCGTCATTGAAGCCCCCGTCATAAATTAAGATGA
1 ATTTATGACACGCATATATGACGCTCATTACGCGTCATTGAAGCACACGTCATAAATAAAGATGA
727168 CACAC-ATTTGTGTGTCATAA
66 CACACGA--TGTGTGTCATAA
* * *
727188 ATTTATGACACGCATATATGAC-TTACATTATGTGTCATTGAAGCACACGTCATTAAA-AAAGAT
1 ATTTATGACACGCATATATGACGCT-CATTACGCGTCATTGAAGCACACGTCA-TAAATAAAGAT
727251 GACACACGATGTGTGTCAT
64 GACACACGATGTGTGTCAT
727270 GATTGTATTT
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
84 11 0.15
85 55 0.77
86 5 0.07
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (84 bp):
ATTTATGACACGCATATATGACGCTCATTACGCGTCATTGAAGCACACGTCATAAATAAAGATGA
CACACGATGTGTGTCATAA
Found at i:730284 original size:203 final size:204
Alignment explanation
Indices: 729922--730422 Score: 665
Period size: 203 Copynumber: 2.4 Consensus size: 204
729912 TAGTCAAGTT
*
729922 AAGACTTTTCCTCAAT-CCAAACAGAAAAATGCAGATTCCCCAGAATTTTGCATGCATTCAAAAG
1 AAGACTTTTCCTCAATCCCAAACAGAAAAATGCAGATTCCCCAGAATTTTGCTTGCATTCAAAAG
*
729986 AAGAAAACAACAAACAAATTGAAAATCAGAAACACACACAAGCATGGGACTAAAACTTATAAGCT
66 AAGAAAAC-ACAAACAAATTGAAAACCAGAAACACACACAAGCATGGGACTAAAACTTATAAGCT
* * * * *
730051 AATAACTTTGCTCACGTAAAAGAGAACAACACAACTAAATCAACAATATATTGTGGTTCAAG-AA
130 AATAACTTTGCTCACGCAAAAGAAAACAACACAACTAAATCAACAACATATTATGATTCAAGCAA
730115 ATTGATAGTC
195 ATTGATAGTC
* *
730125 AAGACTTTCCCTCAATCCCAAACAGAAAAAAATGTAGATTCCCCAGAATTTTGCTTGCATTCAAA
1 AAGACTTTTCCTCAATCCCAAACAG--AAAAATGCAGATTCCCCAGAATTTTGCTTGCATTCAAA
*
730190 AGAAGAAAAC-C-AACAAATTGAAAACCA-ACAACACACACAAGCATGGGACTTAAACTTATAA-
64 AGAAGAAAACACAAACAAATTGAAAACCAGA-AACACACACAAGCATGGGACTAAAACTTATAAG
* * ** *
730251 ATCAATAATTTTGCTCGTGCAACAGAAAACAACACAACTAAATCAACAACATATTATGATTCAAG
128 CT-AATAACTTTGCTCACGCAAAAGAAAACAACACAACTAAATCAACAACATATTATGATTCAAG
* *
730316 CTAATTGATATTC
192 CAAATTGATAGTC
* *
730329 AAGTTAAAACTTTTCCTCAATCCCAAACAGAAAAATGCAGATTTCCCAGAATTTT-TTGTGCATT
1 AAG-----ACTTTTCCTCAATCCCAAACAGAAAAATGCAGATTCCCCAGAATTTTGCT-TGCATT
*
730393 CAAAAGAAGAAAACAACTAACAAATTGAAA
60 CAAAAGAAGAAAAC-ACAAACAAATTGAAA
730423 GTGTGTCAAA
Statistics
Matches: 262, Mismatches: 21, Indels: 23
0.86 0.07 0.08
Matches are distributed among these distances:
202 2 0.01
203 114 0.44
204 22 0.08
206 47 0.18
207 43 0.16
209 22 0.08
210 12 0.05
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (204 bp):
AAGACTTTTCCTCAATCCCAAACAGAAAAATGCAGATTCCCCAGAATTTTGCTTGCATTCAAAAG
AAGAAAACACAAACAAATTGAAAACCAGAAACACACACAAGCATGGGACTAAAACTTATAAGCTA
ATAACTTTGCTCACGCAAAAGAAAACAACACAACTAAATCAACAACATATTATGATTCAAGCAAA
TTGATAGTC
Found at i:732954 original size:139 final size:136
Alignment explanation
Indices: 732781--733187 Score: 426
Period size: 139 Copynumber: 2.9 Consensus size: 136
732771 GAACTCAAGG
** * * *
732781 ATTAAACCTAAAATGTGAGCTCTAATATTAAAACCTAACCAATTTTAACAATTTATTAGATCGAA
1 ATTAAACCTAAAATGAAAGCTCTAATA-TAAAACCTAATCAATTTTATCAATTTATTAGA-CAAA
* ** *
732846 TGACTAAAATGGAACCTCAAGCATAAATGTAAGGACCAAATTAAAAAATCTCCTAATTTAAGGAC
64 TAACTAAAATGGAACCTC-AGCATAAATGCGAGGACCAAATTAAAAATTCTCCTAATTTAAGGAC
* *
732911 TAAGGTGAA
128 AAAAGTGAA
* *
732920 ATTAAACCTAAAATGAAAGCTCTAATATGAAAACCTAGTCAATTTTATC-ATATTATTAGGACTA
1 ATTAAACCTAAAATGAAAGCTCTAATAT-AAAACCTAATCAATTTTATCAAT-TTATTA-GACAA
* * * ** *
732984 ATAACTAAAATGGAACATCTGATATAAATGCGAGGACCAAA-TAAGAAATTCTGTTAATTTAAAG
63 ATAACTAAAATGGAACCTCAG-CATAAATGCGAGGACCAAATTAA-AAATTCTCCTAATTTAAGG
733048 ACAAAAGTGAA
126 ACAAAAGTGAA
* * * *
733059 ATTAAACCAAAAAT-AAAGGCTCTAATACTAAAACC-AAGTCAATTTTATCAAATTATTGGGCCA
1 ATTAAACCTAAAATGAAA-GCTCTAATA-TAAAACCTAA-TCAATTTTATCAATTTATT-AGACA
* * * *
733122 AATAACTGAAATGGACCCTCGAGCATAAATGCGAGGACCGAATCAAAAATTCTCCTAATTTAAGG
62 AATAACTAAAATGGAACCTC-AGCATAAATGCGAGGACCAAATTAAAAATTCTCCTAATTTAAGG
733187 A
126 A
733188 ACATCTTTGC
Statistics
Matches: 222, Mismatches: 34, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
138 11 0.05
139 204 0.92
140 7 0.03
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (136 bp):
ATTAAACCTAAAATGAAAGCTCTAATATAAAACCTAATCAATTTTATCAATTTATTAGACAAATA
ACTAAAATGGAACCTCAGCATAAATGCGAGGACCAAATTAAAAATTCTCCTAATTTAAGGACAAA
AGTGAA
Found at i:736006 original size:12 final size:12
Alignment explanation
Indices: 735989--736013 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
735979 TTAAATAGGG
735989 AAAAATTATAAA
1 AAAAATTATAAA
736001 AAAAATTATAAA
1 AAAAATTATAAA
736013 A
1 A
736014 GGGTTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:741348 original size:12 final size:12
Alignment explanation
Indices: 741331--741358 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
741321 GAAACTCAAC
741331 GGTCAACGGTCG
1 GGTCAACGGTCG
741343 GGTCAACGGTCG
1 GGTCAACGGTCG
741355 GGTC
1 GGTC
741359 GGGTCGGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:744607 original size:15 final size:15
Alignment explanation
Indices: 744580--744647 Score: 50
Period size: 16 Copynumber: 4.3 Consensus size: 15
744570 ACTATAACTT
744580 AAATAACTG-AAATTA
1 AAAT-ACTGAAAATTA
744595 AAATACTGAAAATTTA
1 AAATACTGAAAA-TTA
**
744611 AAA-AAGGCAAGAATTA
1 AAATACTG-AA-AATTA
744627 AAAGGTACTGAAAATTA
1 AAA--TACTGAAAATTA
744644 AAAT
1 AAAT
744648 GTTGAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
14 4 0.10
15 10 0.24
16 14 0.33
17 10 0.24
18 2 0.05
19 2 0.05
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (15 bp):
AAATACTGAAAATTA
Found at i:746410 original size:21 final size:22
Alignment explanation
Indices: 746386--746441 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
746376 TTTGTGAAGG
746386 AAAAGGATCAATCTCTTC-ACC
1 AAAAGGATCAATCTCTTCGACC
* **
746407 AAAAGGATCGAT-TCTTCGATG
1 AAAAGGATCAATCTCTTCGACC
*
746428 AAAATGATCAATCT
1 AAAAGGATCAATCT
746442 ATTACCCTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 5 0.18
21 22 0.79
22 1 0.04
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (22 bp):
AAAAGGATCAATCTCTTCGACC
Found at i:746587 original size:21 final size:20
Alignment explanation
Indices: 746558--746612 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
746548 ACAAGAAAGA
*
746558 GATCGATCCTTTTCATTGAGG
1 GATCGATCCTTTTC-TCGAGG
*
746579 GATCAATCCTTTTTCTCGAGG
1 GATCGATCC-TTTTCTCGAGG
746600 GATCGATCCTTTT
1 GATCGATCCTTTT
746613 GTGAAGGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 21 0.70
22 5 0.17
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (20 bp):
GATCGATCCTTTTCTCGAGG
Found at i:746620 original size:20 final size:19
Alignment explanation
Indices: 746558--746622 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
746548 ACAAGAAAGA
746558 GATCGATCCTTTTCATTGAGG
1 GATCGATCCTTTTC--TGAGG
*
746579 GATCAATCCTTTTTCTCGAGG
1 GATCGATCC-TTTTCT-GAGG
*
746600 GATCGATCCTTTTGTGAAGG
1 GATCGATCCTTTTCTG-AGG
746620 GAT
1 GAT
746623 TAATCCAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.03
20 12 0.32
21 20 0.53
22 5 0.13
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (19 bp):
GATCGATCCTTTTCTGAGG
Found at i:746974 original size:20 final size:20
Alignment explanation
Indices: 746930--746977 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
746920 TGAGTTAATC
*
746930 AAAACATGTTTAAAGTGTTT
1 AAAATATGTTTAAAGTGTTT
*
746950 GAAATATGTTTAAAG-GTTTT
1 AAAATATGTTTAAAGTG-TTT
746970 AAAATATG
1 AAAATATG
746978 AAAAACACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.40
Consensus pattern (20 bp):
AAAATATGTTTAAAGTGTTT
Found at i:748425 original size:20 final size:20
Alignment explanation
Indices: 748391--748439 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
748381 AATGATTTTC
* * *
748391 TTTTG-AAAGCAAAATTAGA
1 TTTTGAAAAACAAAATGAAA
748410 TTTTGAAAAACAAAATGAAA
1 TTTTGAAAAACAAAATGAAA
*
748430 CTTTGAAAAA
1 TTTTGAAAAA
748440 TGAATTTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAAA
Found at i:750540 original size:20 final size:19
Alignment explanation
Indices: 750514--750583 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
750504 GTGTCTTTCG
750514 AAGTTTCGAAACTTTCACA
1 AAGTTTCGAAACTTTCACA
* * *
750533 ATAGTTTCAAAACTTTGATTA
1 A-AGTTTCGAAACTTTCA-CA
* *
750554 AAGTTTTGAAACTTTCCCCA
1 AAGTTTCGAAACTTT-CACA
750574 AAGTTTCGAA
1 AAGTTTCGAA
750584 GTTGCATGTG
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.03
20 36 0.92
21 2 0.05
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (19 bp):
AAGTTTCGAAACTTTCACA
Found at i:753266 original size:23 final size:23
Alignment explanation
Indices: 753225--753270 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
753215 TAAAAATCAA
753225 AAAAAATAATTCCTAATAAATTGT
1 AAAAAATAATTCCTAAT-AATTGT
* *
753249 AAAAGATAATT-CTCATAATTGT
1 AAAAAATAATTCCTAATAATTGT
753271 TTGAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 4 0.20
24 10 0.50
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.35
Consensus pattern (23 bp):
AAAAAATAATTCCTAATAATTGT
Found at i:756276 original size:38 final size:38
Alignment explanation
Indices: 756234--756369 Score: 112
Period size: 38 Copynumber: 3.6 Consensus size: 38
756224 GGTTACATAT
* * *
756234 TGGAAAACATATTTCAAGTT-GAAAATTAGATTTTAGGC
1 TGGAAAACAGATTTCAAGTTGGAAAA-TAGATTTCAGGA
* * *
756272 TGGAAACCAGATTTTAGGTTGGAAAATAGATTTCAGGA
1 TGGAAAACAGATTTCAAGTTGGAAAATAGATTTCAGGA
* * * ** * * *
756310 TGGAAAATAGATTTTAGGTTGGAAACCATATTTCAAGT
1 TGGAAAACAGATTTCAAGTTGGAAAATAGATTTCAGGA
* *
756348 TGGAAACCAGATTTTAAGTTGG
1 TGGAAAACAGATTTCAAGTTGG
756370 GAACCAGATC
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
38 76 0.94
39 5 0.06
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (38 bp):
TGGAAAACAGATTTCAAGTTGGAAAATAGATTTCAGGA
Found at i:756283 original size:19 final size:19
Alignment explanation
Indices: 756261--756378 Score: 128
Period size: 19 Copynumber: 6.2 Consensus size: 19
756251 GTTGAAAATT
*
756261 AGATTTTAGGCTGGAAACC
1 AGATTTTAGGTTGGAAACC
**
756280 AGATTTTAGGTTGGAAAAT
1 AGATTTTAGGTTGGAAACC
* * **
756299 AGATTTCAGGATGGAAAAT
1 AGATTTTAGGTTGGAAACC
756318 AGATTTTAGGTTGGAAACC
1 AGATTTTAGGTTGGAAACC
* * *
756337 ATATTTCAAGTTGGAAACC
1 AGATTTTAGGTTGGAAACC
* *
756356 AGATTTTAAGTTGGGAACC
1 AGATTTTAGGTTGGAAACC
756375 AGAT
1 AGAT
756379 CCCTAAGGGT
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 84 1.00
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.31
Consensus pattern (19 bp):
AGATTTTAGGTTGGAAACC
Found at i:756295 original size:57 final size:56
Alignment explanation
Indices: 756233--756368 Score: 164
Period size: 57 Copynumber: 2.4 Consensus size: 56
756223 AGGTTACATA
* * *
756233 TTGGAAAACATATTTCAAGTTGAAAATTAGATTTTAGGCTGGAAACCAGATTTTAGG
1 TTGGAAAACAGATTTCAAGTTGAAAA-TAGATTTTAGGCTGGAAACCAGATTTCAAG
* * * * *
756290 TTGGAAAATAGATTTCAGGATGGAAAATAGATTTTAGGTTGGAAACCATATTTCAAG
1 TTGGAAAACAGATTTCAAG-TTGAAAATAGATTTTAGGCTGGAAACCAGATTTCAAG
* *
756347 TTGGAAACCAGATTTTAAGTTG
1 TTGGAAAACAGATTTCAAGTTG
756369 GGAACCAGAT
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
56 2 0.03
57 57 0.88
58 6 0.09
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (56 bp):
TTGGAAAACAGATTTCAAGTTGAAAATAGATTTTAGGCTGGAAACCAGATTTCAAG
Found at i:762055 original size:26 final size:26
Alignment explanation
Indices: 762014--762078 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
762004 AAGGGTAAAC
* *
762014 AAAAATAACAAA-TAAATTCATACTA-
1 AAAAATAA-AAATTAAAATAATACTAT
762039 AAAAATAAAGAATTAAAATAATACTAT
1 AAAAATAAA-AATTAAAATAATACTAT
*
762066 AAAAACAAAAATT
1 AAAAATAAAAATT
762079 GACAATCCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 1 0.03
25 10 0.29
26 15 0.44
27 8 0.24
ACGTcount: A:0.68, C:0.08, G:0.02, T:0.23
Consensus pattern (26 bp):
AAAAATAAAAATTAAAATAATACTAT
Found at i:763010 original size:53 final size:53
Alignment explanation
Indices: 762930--763087 Score: 235
Period size: 53 Copynumber: 3.0 Consensus size: 53
762920 CAAGGTAACA
* * *
762930 AAATGGAAATTCACAAACTCATAATGAATACCATGGGTGCACACATAGTGCCG
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCG
* * ** *
762983 AAATGGTAATTCAAAAACTCATTATGAATACAATGGATGTGCACATAGTGTCG
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCG
*
763036 AAATGGTAATTCACAAACTCATTATGAATACCACGGATGCACACATAGTGCC
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCC
763088 AAAAGTACAC
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 91 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (53 bp):
AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCG
Found at i:763512 original size:53 final size:53
Alignment explanation
Indices: 763448--763609 Score: 216
Period size: 53 Copynumber: 3.1 Consensus size: 53
763438 TAAGGTAACA
* * * *
763448 AAATGGAAATTCACAAACTCATAATGAATACTATGGGTGCACACATAGTGCCG
1 AAATGGTAATTCACAAACTCATTATGAATACAATGGATGCACACATAGTGCCG
* * ** *
763501 AAATGGTAATTCAAAAACTCCTTATGAATACAATGGATGTGCACATAGTGTCG
1 AAATGGTAATTCACAAACTCATTATGAATACAATGGATGCACACATAGTGCCG
* * *
763554 AAATTGTAATTCACAAACTCATTATGAATACCACGGATGCACACATAGTGCCG
1 AAATGGTAATTCACAAACTCATTATGAATACAATGGATGCACACATAGTGCCG
763607 AAA
1 AAA
763610 GTACACATAG
Statistics
Matches: 92, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 92 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (53 bp):
AAATGGTAATTCACAAACTCATTATGAATACAATGGATGCACACATAGTGCCG
Found at i:763748 original size:518 final size:518
Alignment explanation
Indices: 762771--763811 Score: 1992
Period size: 518 Copynumber: 2.0 Consensus size: 518
762761 TGAAACAATA
762771 TTTAGTATGCCCAACATACCTATAAATCAATATTTTTCCAAAGTATACATTTATTTTCCCAATAT
1 TTTAGTATGCCCAACATACCTATAAATCAATATTTTTCCAAAGTATACATTTATTTTCCCAATAT
762836 ATGTCGAATGAGAATACAAGGTACATGAGTTGCACCTAAGTGCTAAACGAAAGCATAGGTTTTGT
66 ATGTCGAATGAGAATACAAGGTACATGAGTTGCACCTAAGTGCTAAACGAAAGCATAGGTTTTGT
*
762901 GATGACAACAACACTATACCAAGGTAACAAAATGGAAATTCACAAACTCATAATGAATACCATGG
131 GATGAAAACAACACTATACCAAGGTAACAAAATGGAAATTCACAAACTCATAATGAATACCATGG
762966 GTGCACACATAGTGCCGAAATGGTAATTCAAAAACTCATTATGAATACAATGGATGTGCACATAG
196 GTGCACACATAGTGCCGAAATGGTAATTCAAAAACTCATTATGAATACAATGGATGTGCACATAG
763031 TGTCGAAATGGTAATTCACAAACTCATTATGAATACCACGGATGCACACATAGTGCCAAAAGTAC
261 TGTCGAAATGGTAATTCACAAACTCATTATGAATACCACGGATGCACACATAGTGCCAAAAGTAC
*
763096 ACATAGTACTGATACGAAAATGCAACATATGCATTAAAAAAATCGATCGATAACCATTATACACA
326 ACATAGTACTGATACGAAAATGCAACATATGCATTAAAAAAATCGATCGATAAACATTATACACA
763161 AAGTATGTCAAAATGCACCTATTACTCTCAATGCACATACAATAGGCTTTTAAATCAATTTCGCA
391 AAGTATGTCAAAATGCACCTATTACTCTCAATGCACATACAATAGGCTTTTAAATCAATTTCGCA
763226 TATTAAACATTTATTCAGAAACATCAATAGTTGTTAAAACAATATAAAAGTTCATCCATCTAT
456 TATTAAACATTTATTCAGAAACATCAATAGTTGTTAAAACAATATAAAAGTTCATCCATCTAT
* *
763289 TTTAGTATGCCCAACATACCTATAAATCAATATTTTTCCAAATTATACATTTATTTTCCCAATGT
1 TTTAGTATGCCCAACATACCTATAAATCAATATTTTTCCAAAGTATACATTTATTTTCCCAATAT
763354 ATGTCGAATGAGAATACAAGGTACATGAGTTGCACCTAAGTGCTAAACGAAAGCATAGGTTTTGT
66 ATGTCGAATGAGAATACAAGGTACATGAGTTGCACCTAAGTGCTAAACGAAAGCATAGGTTTTGT
* *
763419 GATGAAAACAACACTATACTAAGGTAACAAAATGGAAATTCACAAACTCATAATGAATACTATGG
131 GATGAAAACAACACTATACCAAGGTAACAAAATGGAAATTCACAAACTCATAATGAATACCATGG
*
763484 GTGCACACATAGTGCCGAAATGGTAATTCAAAAACTCCTTATGAATACAATGGATGTGCACATAG
196 GTGCACACATAGTGCCGAAATGGTAATTCAAAAACTCATTATGAATACAATGGATGTGCACATAG
* *
763549 TGTCGAAATTGTAATTCACAAACTCATTATGAATACCACGGATGCACACATAGTGCCGAAAGTAC
261 TGTCGAAATGGTAATTCACAAACTCATTATGAATACCACGGATGCACACATAGTGCCAAAAGTAC
763614 ACATAGTACTGATACGAAAATGCAACATATGCATTAAAAAAATCGATCGATAAACATTATACACA
326 ACATAGTACTGATACGAAAATGCAACATATGCATTAAAAAAATCGATCGATAAACATTATACACA
763679 AAGTATGTCAAAATGCACCTATTACTCTCAATGCACATACAATAGGCTTTTAAATCAATTTCGCA
391 AAGTATGTCAAAATGCACCTATTACTCTCAATGCACATACAATAGGCTTTTAAATCAATTTCGCA
*
763744 TATTAAACATTTATTCAGAAACATCAATAGTTGTTAAAACAATATAAAAGTTTATCCATCTAT
456 TATTAAACATTTATTCAGAAACATCAATAGTTGTTAAAACAATATAAAAGTTCATCCATCTAT
763807 TTTAG
1 TTTAG
763812 AGCATTTCAC
Statistics
Matches: 513, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
518 513 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (518 bp):
TTTAGTATGCCCAACATACCTATAAATCAATATTTTTCCAAAGTATACATTTATTTTCCCAATAT
ATGTCGAATGAGAATACAAGGTACATGAGTTGCACCTAAGTGCTAAACGAAAGCATAGGTTTTGT
GATGAAAACAACACTATACCAAGGTAACAAAATGGAAATTCACAAACTCATAATGAATACCATGG
GTGCACACATAGTGCCGAAATGGTAATTCAAAAACTCATTATGAATACAATGGATGTGCACATAG
TGTCGAAATGGTAATTCACAAACTCATTATGAATACCACGGATGCACACATAGTGCCAAAAGTAC
ACATAGTACTGATACGAAAATGCAACATATGCATTAAAAAAATCGATCGATAAACATTATACACA
AAGTATGTCAAAATGCACCTATTACTCTCAATGCACATACAATAGGCTTTTAAATCAATTTCGCA
TATTAAACATTTATTCAGAAACATCAATAGTTGTTAAAACAATATAAAAGTTCATCCATCTAT
Found at i:764301 original size:21 final size:20
Alignment explanation
Indices: 764258--764306 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
764248 TTACCCTTGG
*
764258 TATTGATACCTTCACATCAA
1 TATTGATACCTTCACACCAA
764278 TATTGATACTTCTTCA-ACCAA
1 TATTGATAC--CTTCACACCAA
*
764299 TATCGATA
1 TATTGATA
764307 ATGTCCATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.36
21 11 0.44
22 5 0.20
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (20 bp):
TATTGATACCTTCACACCAA
Found at i:769841 original size:53 final size:53
Alignment explanation
Indices: 769761--769922 Score: 252
Period size: 53 Copynumber: 3.1 Consensus size: 53
769751 TAAGGTAACA
** * *
769761 AAATGGTAATTCACAAACTCATTATGAATGTCATGGGTGCACACATAGTTCTG
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCTG
**
769814 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCA
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCTG
* *
769867 AAATGGTAATTCATAAACTCATTATGAATACCATGGACGCACACATAGTGCTG
1 AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCTG
769920 AAA
1 AAA
769923 ATACATATAA
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 99 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (53 bp):
AAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCTG
Found at i:770524 original size:22 final size:23
Alignment explanation
Indices: 770488--770530 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
770478 AGTATCGGTA
770488 CTCTTCCTATAGTACCGATACTT
1 CTCTTCCTATAGTACCGATACTT
*
770511 CTCTT-CTATGGTACCGATAC
1 CTCTTCCTATAGTACCGATAC
770531 CTAATTCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (23 bp):
CTCTTCCTATAGTACCGATACTT
Found at i:770648 original size:21 final size:20
Alignment explanation
Indices: 770605--770653 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
770595 TTACCCTTGG
*
770605 TATCGATACCTTCACATCAA
1 TATCGATACCTTCACACCAA
770625 TATCGATACTTCTTCA-ACCAA
1 TATCGATAC--CTTCACACCAA
770646 TATCGATA
1 TATCGATA
770654 ATGTCCATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.35
21 12 0.46
22 5 0.19
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.33
Consensus pattern (20 bp):
TATCGATACCTTCACACCAA
Found at i:773576 original size:36 final size:36
Alignment explanation
Indices: 773531--773770 Score: 182
Period size: 36 Copynumber: 6.7 Consensus size: 36
773521 GCATGCACAA
* * *
773531 GCTAGTAATGGTTATATGCATGATATACATTCTCCT
1 GCTAATAATGATTATATGCATGATATACATTCGCCT
* * * *
773567 ACTAATAATGATTATATGCATGATATACATGCACAT
1 GCTAATAATGATTATATGCATGATATACATTCGCCT
* *
773603 GCTAATAATGATTTTATGTATGATATACATGT-GCCT
1 GCTAATAATGATTATATGCATGATATACAT-TCGCCT
* * *
773639 GCTAACAATGATCATATGCATGATATAC-TTGCGCTT
1 GCTAATAATGATTATATGCATGATATACATT-CGCCT
* * * * *
773675 GCTACTAATGGTTACATGCATGATATACATGT-TCTT
1 GCTAATAATGATTATATGCATGATATACAT-TCGCCT
* ** * * * *
773711 GTTGCTAATAATTATATGCATGACATTCATGT-GCTT
1 GCTAATAATGATTATATGCATGATATACAT-TCGCCT
* *
773747 GCAAATAATGATTATAAGCATGAT
1 GCTAATAATGATTATATGCATGAT
773771 CTTTTACCTG
Statistics
Matches: 161, Mismatches: 38, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
34 1 0.01
35 1 0.01
36 157 0.98
37 1 0.01
38 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (36 bp):
GCTAATAATGATTATATGCATGATATACATTCGCCT
Found at i:773612 original size:72 final size:72
Alignment explanation
Indices: 773517--773706 Score: 229
Period size: 72 Copynumber: 2.6 Consensus size: 72
773507 AATAATGATC
* * * * * *
773517 ATATGCATGCACAAGCTAGTAATGGTTATATGCATGATATACAT-TCTCCTACTAATAATGATTA
1 ATATACATGCACATGCTAATAATGGTTATATGCATGATATACATGT-GCCTACTAACAATGATCA
773581 TATGCATG
65 TATGCATG
* * * *
773589 ATATACATGCACATGCTAATAATGATTTTATGTATGATATACATGTGCCTGCTAACAATGATCAT
1 ATATACATGCACATGCTAATAATGGTTATATGCATGATATACATGTGCCTACTAACAATGATCAT
773654 ATGCATG
66 ATGCATG
* * * * *
773661 ATATACTTGCGCTTGCTACTAATGGTTACATGCATGATATACATGT
1 ATATACATGCACATGCTAATAATGGTTATATGCATGATATACATGT
773707 TCTTGTTGCT
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 98 0.99
73 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (72 bp):
ATATACATGCACATGCTAATAATGGTTATATGCATGATATACATGTGCCTACTAACAATGATCAT
ATGCATG
Found at i:773728 original size:72 final size:72
Alignment explanation
Indices: 773517--773770 Score: 224
Period size: 72 Copynumber: 3.5 Consensus size: 72
773507 AATAATGATC
* * * ** *
773517 ATATGCATGCACAAGCTAGTAATGGTTATATGCATGATATACAT-TCTCCTACTAATAATGATTA
1 ATATACATGCACATGCTAATAATGGTTATATGCATGATATACATGT-TCCTGTTACTAATGATTA
773581 TATGCATG
65 TATGCATG
* * * * * *
773589 ATATACATGCACATGCTAATAATGATTTTATGTATGATATACATGTGCCTGCTAAC-AATGATCA
1 ATATACATGCACATGCTAATAATGGTTATATGCATGATATACATGTTCCTG-TTACTAATGATTA
773653 TATGCATG
65 TATGCATG
* * * * * * * *
773661 ATATACTTGCGCTTGCTACTAATGGTTACATGCATGATATACATGTTCTTGTTGCTAATAATTAT
1 ATATACATGCACATGCTAATAATGGTTATATGCATGATATACATGTTCCTGTTACTAATGATTAT
773726 ATGCATG
66 ATGCATG
* * ** * * * *
773733 ACATTCATGTGCTTGCAAATAATGATTATAAGCATGAT
1 ATATACATGCACATGCTAATAATGGTTATATGCATGAT
773771 CTTTTACCTG
Statistics
Matches: 144, Mismatches: 35, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
71 2 0.01
72 140 0.97
73 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (72 bp):
ATATACATGCACATGCTAATAATGGTTATATGCATGATATACATGTTCCTGTTACTAATGATTAT
ATGCATG
Found at i:773742 original size:108 final size:108
Alignment explanation
Indices: 773544--773770 Score: 240
Period size: 108 Copynumber: 2.1 Consensus size: 108
773534 AGTAATGGTT
* *
773544 ATATGCATGATATACATTCTCCTACTAATAATGATTATATGCATGATATACATGCACATGCTAAT
1 ATATGCATGATATACATTCGCCTACTAATAATGATTACATGCATGATATACATGCACATGCTAAT
* * * * *
773609 AATGATTTTATGTATGATATACATGTGCCTGCTAACAATGATC
66 AATAATTATATGCATGACATACATGTGCCTGCAAACAATGATC
* * * * ** * * **
773652 ATATGCATGATATAC-TTGCGCTTGCTACTAATGGTTACATGCATGATATACATGTTCTTGTTGC
1 ATATGCATGATATACATT-CGCCTACTAATAATGATTACATGCATGATATACATGCACATGCTAA
* * * *
773716 TAATAATTATATGCATGACATTCATGTGCTTGCAAATAATGATT
65 TAATAATTATATGCATGACATACATGTGCCTGCAAACAATGATC
*
773760 ATAAGCATGAT
1 ATATGCATGAT
773771 CTTTTACCTG
Statistics
Matches: 96, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
107 2 0.02
108 94 0.98
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (108 bp):
ATATGCATGATATACATTCGCCTACTAATAATGATTACATGCATGATATACATGCACATGCTAAT
AATAATTATATGCATGACATACATGTGCCTGCAAACAATGATC
Found at i:774031 original size:13 final size:13
Alignment explanation
Indices: 774013--774061 Score: 71
Period size: 13 Copynumber: 3.6 Consensus size: 13
774003 CTTAGGTAAG
*
774013 TATAATGAGCCGA
1 TATAATGAACCGA
774026 TATAATGAACCGA
1 TATAATGAACCGA
774039 TATAATGAACCGA
1 TATAATGAACCGA
774052 CTGATAATGA
1 -T-ATAATGA
774062 TAAGACTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
13 25 0.76
14 1 0.03
15 7 0.21
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.24
Consensus pattern (13 bp):
TATAATGAACCGA
Found at i:780912 original size:24 final size:24
Alignment explanation
Indices: 780867--780916 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
780857 ATAAAGAACC
*
780867 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
780891 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
780915 AA
1 AA
780917 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:783270 original size:15 final size:15
Alignment explanation
Indices: 783237--783279 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
783227 AAAATAATAT
* *
783237 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
783252 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
783266 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
783280 CAAACACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:785749 original size:18 final size:18
Alignment explanation
Indices: 785726--785760 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
785716 TTCCATCTGG
*
785726 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
785744 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
785761 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:787086 original size:18 final size:18
Alignment explanation
Indices: 787063--787103 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
787053 AACGGGTCAA
787063 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
787081 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
787099 CGGGT
1 CGGGT
787104 TGTGACCGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.15, C:0.17, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:787103 original size:13 final size:13
Alignment explanation
Indices: 787055--787085 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
787045 CGACGGTCAA
*
787055 CGGGTCAACGGGT
1 CGGGTAAACGGGT
787068 CGGGTAAACGGGT
1 CGGGTAAACGGGT
787081 CGGGT
1 CGGGT
787086 CGGGTAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTAAACGGGT
Found at i:790993 original size:24 final size:24
Alignment explanation
Indices: 790948--790997 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
790938 ATAAAGAACC
*
790948 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
790972 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
790996 AA
1 AA
790998 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:800235 original size:4 final size:4
Alignment explanation
Indices: 800226--800274 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
800216 ATTCTCAAAG
* * *
800226 CATA CATA CATA CATA CATA CATA TATA CATG CAT- -ATA CTTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
800272 CAT
1 CAT
800275 GAATGAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
2 2 0.05
4 36 0.95
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (4 bp):
CATA
Found at i:801161 original size:2 final size:2
Alignment explanation
Indices: 801150--801182 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
801140 TTTACCTATT
*
801150 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
801183 CACTTCTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:807512 original size:39 final size:39
Alignment explanation
Indices: 807398--807512 Score: 135
Period size: 39 Copynumber: 2.9 Consensus size: 39
807388 CTGTACACCT
*
807398 AGTAAGGACTTACCCTGTGCACAAAGTGGAGGAGCCTGC
1 AGTAAGGACTTACCCTGTGCACAAAGTCGAGGAGCCTGC
* ***
807437 AGTAA-CATCTTATTATGTGCACAAAG-CAGAGGAGCCTGC
1 AGTAAGGA-CTTACCCTGTGCACAAAGTC-GAGGAGCCTGC
* *
807476 AGTAAGGACTTACCCTGAGCACAAAGTCGAGAAGCCT
1 AGTAAGGACTTACCCTGTGCACAAAGTCGAGGAGCCT
807513 ACAGAAAGCG
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
38 1 0.02
39 58 0.95
40 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (39 bp):
AGTAAGGACTTACCCTGTGCACAAAGTCGAGGAGCCTGC
Found at i:809231 original size:20 final size:20
Alignment explanation
Indices: 809180--809233 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
809170 AACTCTACCT
* *
809180 CCTCAACATGAATAATATGA
1 CCTCAACATGGATAATATCA
* *
809200 CCTGGATC-TGGATAATATCA
1 CCT-CAACATGGATAATATCA
809220 CCTCAACATGGATA
1 CCTCAACATGGATA
809234 CATGAAAACC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (20 bp):
CCTCAACATGGATAATATCA
Found at i:810573 original size:18 final size:18
Alignment explanation
Indices: 810550--810588 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
810540 TCCCTGAATG
810550 ATACTCTATCTCACAATC
1 ATACTCTATCTCACAATC
810568 ATACTCTATCTCACAATC
1 ATACTCTATCTCACAATC
810586 ATA
1 ATA
810589 GTCCTTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (18 bp):
ATACTCTATCTCACAATC
Found at i:813232 original size:39 final size:38
Alignment explanation
Indices: 813174--813292 Score: 130
Period size: 39 Copynumber: 3.1 Consensus size: 38
813164 CTGTACACCA
**
813174 AGTAAGGACTTACCATGTGCACAAAGCAGAGGAATTTGC
1 AGTAAGGACTTACC-TGTGCACAAAGCAGAGGAACCTGC
* * *
813213 AGTAAGGTCTTATCCTGTGCACAAAACAGAGGAGCCTGC
1 AGTAAGGACTTA-CCTGTGCACAAAGCAGAGGAACCTGC
* ** *
813252 AGTAAGGACTTACCCTGAGCACAAAGCCTAGGAGCCTGC
1 AGTAAGGACTTA-CCTGTGCACAAAGCAGAGGAACCTGC
813291 AG
1 AG
813293 AAAGCAGTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 66 0.97
40 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (38 bp):
AGTAAGGACTTACCTGTGCACAAAGCAGAGGAACCTGC
Found at i:816617 original size:18 final size:18
Alignment explanation
Indices: 816594--816629 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
816584 TTAATCAAAC
816594 TGAATCGAATATATCAAT
1 TGAATCGAATATATCAAT
816612 TGAATCGAATATATCAAT
1 TGAATCGAATATATCAAT
816630 ATCAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (18 bp):
TGAATCGAATATATCAAT
Found at i:824755 original size:94 final size:94
Alignment explanation
Indices: 824385--825431 Score: 1541
Period size: 94 Copynumber: 11.0 Consensus size: 94
824375 TTCAGAGTCT
* * * * *
824385 ATTTCAACTTCGCAGCGAAGAAAATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
824450 ACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTC----AACAA----ACAATTTC----CCA
*
824491 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
824556 ACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTC----AACAA----ACAATTTC----CCA
* *
824597 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
824662 ACCGCTGGTTGTCAATAAACAATTTCCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCA
* * * *
824691 ATTTCAACTTCACAGCGAAGGATATTGGACGCCAGACAACGCAAGTTCAACTTCATGATGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
824756 ACCGCTGGTTGTCAACAAAGAATTTCCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCA
* *
824785 ATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
824850 ACCACTGGTTGTCAACAAACAATTTCCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCA
* *
824879 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTTAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
824944 ACCGCTGGTTGTCAACAAACAATTTCCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCA
824973 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
825038 ACCGCTGGTTGTCAACAAACAATTTCCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCA
* * *
825067 ATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAGCGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
825132 ACCGCTGGTTGTCAACAAACAATTTCCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCA
*
825161 ATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
825226 ATCGCTGGTTGTCAACAAACAATTTCCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCA
* *
825255 ATTTTAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
825320 ACCGCTGGTTGT-------CAATTTCCCA
66 ACCGCTGGTTGTCAACAAACAATTTCCCA
* * *
825342 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
825407 ACCGCTGGTTGTCAATAAACAATTT
66 ACCGCTGGTTGTCAACAAACAATTT
825432 TCCAGTTCCA
Statistics
Matches: 887, Mismatches: 47, Indels: 26
0.92 0.05 0.03
Matches are distributed among these distances:
87 82 0.09
94 617 0.70
98 7 0.01
102 4 0.00
106 177 0.20
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (94 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAAACAATTTCCCA
Found at i:825391 original size:87 final size:87
Alignment explanation
Indices: 825245--825422 Score: 311
Period size: 87 Copynumber: 2.0 Consensus size: 87
825235 TGTCAACAAA
* *
825245 CAATTTCCCAATTTTAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 CAATTTCCCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACACAAGTTCAACTTCA
*
825310 CGACGAAGGGACCGCTGGTTGT
66 CAACGAAGGGACCGCTGGTTGT
* *
825332 CAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACACAAGTTCAACTTCA
1 CAATTTCCCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACACAAGTTCAACTTCA
825397 CAACGAAGGGACCGCTGGTTGT
66 CAACGAAGGGACCGCTGGTTGT
825419 CAAT
1 CAAT
825423 AAACAATTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (87 bp):
CAATTTCCCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACACAAGTTCAACTTCA
CAACGAAGGGACCGCTGGTTGT
Found at i:833242 original size:18 final size:18
Alignment explanation
Indices: 833219--833263 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
833209 TATGTGATAT
833219 GTGGTCCTTCTG-GACATA
1 GTGGTCCTTC-GAGACATA
*
833237 GTGGTCCTTCGAGACATT
1 GTGGTCCTTCGAGACATA
833255 GTGGTCCTT
1 GTGGTCCTT
833264 TGGGACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.13, C:0.22, G:0.29, T:0.36
Consensus pattern (18 bp):
GTGGTCCTTCGAGACATA
Found at i:833270 original size:18 final size:18
Alignment explanation
Indices: 833218--833270 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
833208 ATATGTGATA
833218 TGTGGTCCTTCT-GGACAT
1 TGTGGTCCTT-TGGGACAT
* * *
833236 AGTGGTCCTTCGAGACAT
1 TGTGGTCCTTTGGGACAT
833254 TGTGGTCCTTTGGGACA
1 TGTGGTCCTTTGGGACA
833271 AATTCTACGC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.34
Consensus pattern (18 bp):
TGTGGTCCTTTGGGACAT
Found at i:837347 original size:21 final size:21
Alignment explanation
Indices: 837305--837347 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
837295 TTTCTGGGCT
*
837305 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
837326 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
837347 A
1 A
837348 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:837399 original size:19 final size:20
Alignment explanation
Indices: 837370--837409 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
837360 TTCCAGAACG
*
837370 CTAGAGGGGAATCGATACCC
1 CTAGAGGGGAACCGATACCC
*
837390 CTAG-GGGGAACCGATTCCC
1 CTAGAGGGGAACCGATACCC
837409 C
1 C
837410 CATAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (20 bp):
CTAGAGGGGAACCGATACCC
Found at i:838116 original size:103 final size:103
Alignment explanation
Indices: 837891--838108 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
837881 GTAGAGGGTT
*
837891 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
837956 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
837994 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
838059 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
838097 TATGTGGTCCTT
1 TATGTGGTCCTT
838109 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:839399 original size:27 final size:27
Alignment explanation
Indices: 839369--839432 Score: 112
Period size: 26 Copynumber: 2.4 Consensus size: 27
839359 CTTTATTCTT
*
839369 AGATGAATTTAAAAACAAGTACATTGG
1 AGATCAATTTAAAAACAAGTACATTGG
839396 AGATCAATTT-AAAACAAGTACATTGG
1 AGATCAATTTAAAAACAAGTACATTGG
839422 AGATCAATTTA
1 AGATCAATTTA
839433 TTCGACAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 26 0.74
27 9 0.26
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (27 bp):
AGATCAATTTAAAAACAAGTACATTGG
Found at i:844292 original size:21 final size:21
Alignment explanation
Indices: 844250--844292 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
844240 ATTTCGGGCT
*
844250 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
844271 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
844292 A
1 A
844293 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:844344 original size:19 final size:19
Alignment explanation
Indices: 844320--844356 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
844310 GAACGCTAGA
*
844320 GGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCAG
*
844339 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
844357 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (19 bp):
GGGGAACCGATACCCCCAG
Found at i:845021 original size:103 final size:103
Alignment explanation
Indices: 844837--845051 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 103
844827 GTAGAGGGTC
* *
844837 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
* *
844902 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
*
844940 TATGTGGTCTTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
*
845005 TTGATCATTGGCATATGTATATGATTCTTAAGGAATTA
66 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
845043 TATGTGGTC
1 TATGTGGTC
845052 GTTACGGACA
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:845122 original size:23 final size:23
Alignment explanation
Indices: 845073--845133 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
845063 TATTATATGG
* *
845073 CACTACGGTGCAATTCTATGCGG
1 CACTACGGTGCAATTCTAAGCGA
* *
845096 CACTCCGGTGCAATTCTAAGTGA
1 CACTACGGTGCAATTCTAAGCGA
845119 CACTTA-GGTGCAATT
1 CAC-TACGGTGCAATT
845134 ATACGAGTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (23 bp):
CACTACGGTGCAATTCTAAGCGA
Found at i:846653 original size:2 final size:2
Alignment explanation
Indices: 846646--846678 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
846636 TCAATCTACA
846646 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
846679 ATTTACGAAA
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:846856 original size:13 final size:13
Alignment explanation
Indices: 846833--846884 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
846823 AATGACGCGC
*
846833 AATGAGCGTCATA
1 AATGCGCGTCATA
*
846846 AATACGCGTCATA
1 AATGCGCGTCATA
*
846859 AATGCGTGTCATA
1 AATGCGCGTCATA
*
846872 AATGCACGTCATA
1 AATGCGCGTCATA
846885 GATTTATGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (13 bp):
AATGCGCGTCATA
Done.