Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 37
Found at i:2845711 original size:20 final size:20
Alignment explanation
Indices: 2845686--2845728 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2845676 AAAAAAAACA
2845686 TTCCAACTCATATTTACCCT
1 TTCCAACTCATATTTACCCT
2845706 TTCCAACTCATATTTACCCT
1 TTCCAACTCATATTTACCCT
2845726 TTC
1 TTC
2845729 TTTTCAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCCAACTCATATTTACCCT
Found at i:2858415 original size:2 final size:2
Alignment explanation
Indices: 2858408--2858433 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2858398 TCATCGATAA
2858408 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
2858434 TGTTAATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2869995 original size:16 final size:16
Alignment explanation
Indices: 2869976--2870006 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2869966 TAAATGTTAA
*
2869976 AATGAATAAAGAATAT
1 AATGAATAAAAAATAT
2869992 AATGAATAAAAAATA
1 AATGAATAAAAAATA
2870007 GGGTAGATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (16 bp):
AATGAATAAAAAATAT
Found at i:2873234 original size:25 final size:25
Alignment explanation
Indices: 2873193--2873240 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2873183 TTTTATAATA
*
2873193 ATAAATTTTTATAATTTTAAAAATT
1 ATAAATTTATATAATTTTAAAAATT
*
2873218 ATAAATTTCATAT-ATTTTGAAAA
1 ATAAATTT-ATATAATTTTAAAAA
2873241 CAATATTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
ATAAATTTATATAATTTTAAAAATT
Found at i:2876262 original size:24 final size:24
Alignment explanation
Indices: 2876246--2876292 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2876236 GAGGGTTTTG
*
2876246 TTGATTGTGCTGCTGAGAGGGTTA
1 TTGATTGTGCTACTGAGAGGGTTA
2876270 TTGATTGTGCTACTGAGAGGGTT
1 TTGATTGTGCTACTGAGAGGGTT
2876293 GCTGAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.09, G:0.36, T:0.38
Consensus pattern (24 bp):
TTGATTGTGCTACTGAGAGGGTTA
Found at i:2891320 original size:2 final size:2
Alignment explanation
Indices: 2891313--2891347 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2891303 AAGATGATAA
2891313 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2891348 CATATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2898484 original size:30 final size:29
Alignment explanation
Indices: 2898425--2898500 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
2898415 TATATTTAAA
* *
2898425 TGATATTATAAAGTAAAAAATATATATTT
1 TGATATTAAAAAGTAAAAAATATAAATTT
*
2898454 TAGATATTAAAAAGTATAAAAT-TAAAATTT
1 T-GATATTAAAAAGTAAAAAATAT-AAATTT
*
2898484 TGAAATTAAAAA-TAAAA
1 TGATATTAAAAAGTAAAA
2898501 TTGTTAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 4 0.10
29 12 0.30
30 24 0.60
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (29 bp):
TGATATTAAAAAGTAAAAAATATAAATTT
Found at i:2899983 original size:30 final size:32
Alignment explanation
Indices: 2899948--2900015 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 32
2899938 ATAGTTATTA
2899948 TATTTTATATT-AAT-ATATTTATATAAATAT
1 TATTTTATATTAAATAATATTTATATAAATAT
* *
2899978 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATATTTATATAAATAT
2900011 TATTT
1 TATTT
2900016 ATTTAGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 10 0.30
32 3 0.09
33 20 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TATTTTATATTAAATAATATTTATATAAATAT
Found at i:2900184 original size:17 final size:16
Alignment explanation
Indices: 2900162--2900215 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
2900152 TAATGTTAAT
2900162 ATTTAAATTTATTTTTA
1 ATTTAAA-TTATTTTTA
* *
2900179 ATTTAAAGTTATTATGA
1 ATTTAAA-TTATTTTTA
* *
2900196 ATTTATATTAATTTTA
1 ATTTAAATTATTTTTA
2900212 ATTT
1 ATTT
2900216 TTTATAATGT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
ATTTAAATTATTTTTA
Found at i:2901779 original size:21 final size:20
Alignment explanation
Indices: 2901751--2901792 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
2901741 GGGTACATGC
2901751 CCAACCCACCACTTCATATG
1 CCAACCCACCACTTCATATG
*
2901771 CCAATCCCACCAGTTCATATG
1 CCAA-CCCACCACTTCATATG
2901792 C
1 C
2901793 TATCTTCGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.29, C:0.43, G:0.07, T:0.21
Consensus pattern (20 bp):
CCAACCCACCACTTCATATG
Found at i:2901828 original size:21 final size:21
Alignment explanation
Indices: 2901802--2901912 Score: 145
Period size: 21 Copynumber: 5.3 Consensus size: 21
2901792 CTATCTTCGT
*
2901802 AGGGTTACATTCCGAGCCCGC
1 AGGGTTACATTCCTAGCCCGC
* *
2901823 AGGGTTATATTCCTAGACCGCC
1 AGGGTTACATTCCTAGCCCG-C
*
2901845 A-GGTTACATTCCGAGCCCGC
1 AGGGTTACATTCCTAGCCCGC
2901865 AGGGTTACATTCCTAGCCCGCC
1 AGGGTTACATTCCTAGCCCG-C
*
2901887 A-GGTTACATGCCTAGCCCGC
1 AGGGTTACATTCCTAGCCCGC
2901907 AGGGTT
1 AGGGTT
2901913 TTATACCATA
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.05
21 70 0.90
22 4 0.05
ACGTcount: A:0.20, C:0.32, G:0.26, T:0.23
Consensus pattern (21 bp):
AGGGTTACATTCCTAGCCCGC
Found at i:2901863 original size:42 final size:42
Alignment explanation
Indices: 2901804--2901912 Score: 182
Period size: 42 Copynumber: 2.6 Consensus size: 42
2901794 ATCTTCGTAG
*
2901804 GGTTACATTCCGAGCCCGCAGGGTTATATTCCTAGACCGCCA
1 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGACCGCCA
*
2901846 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGACCGCCA
* *
2901888 GGTTACATGCCTAGCCCGCAGGGTT
1 GGTTACATTCCGAGCCCGCAGGGTT
2901913 TTATACCATA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (42 bp):
GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGACCGCCA
Found at i:2902523 original size:34 final size:34
Alignment explanation
Indices: 2902433--2902539 Score: 117
Period size: 34 Copynumber: 3.1 Consensus size: 34
2902423 ATAAATGTTT
* *
2902433 TTAAAATACAAAATATATTATTCGAAATTTAAAA
1 TTAAAATAAAAAATATAATATTCGAAATTTAAAA
* * *
2902467 TAAAAACAAAAACA-ATAATATTCAAAATTTAAAA
1 TTAAAATAAAAA-ATATAATATTCGAAATTTAAAA
* * * *
2902501 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAAATATAATATTCGAAATTTAAAA
2902535 TTAAA
1 TTAAA
2902540 TTTCAACTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
34 58 0.98
35 1 0.02
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.33
Consensus pattern (34 bp):
TTAAAATAAAAAATATAATATTCGAAATTTAAAA
Found at i:2903209 original size:128 final size:128
Alignment explanation
Indices: 2902934--2903550 Score: 955
Period size: 128 Copynumber: 4.7 Consensus size: 128
2902924 ACAATCCATC
* *
2902934 TAGTGTCCCCGAGGGACATGATTAACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * * *
2902999 GGAAGACGCCCCCCCCGGGAACGCGGCTTCAAGTCCCCTGAGAAATAATATGTACTGATATGAA
66 GGAAGGCG-CGCCCCCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
2903063 TAGTGTCCCCGAGAGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
2903128 AGAAGGCGCGCCCCCAGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATAAA
66 GGAAGGCGCGCCCCCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
2903191 TAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
2903256 GGAAGGCACGCCCCCAGGAACGCGCCTTCAAGTCCCCTGATAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
2903319 TAGTGTCCCCGAGGAACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
2903384 GGAAGGCGCGCCCCCATGAACGCGCCTTCAAGTCCCCTTAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
2903447 TAGTGTCCCCTAGGGACATGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
1 TAGTGT-CCC------C--GAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
* * **
2903512 CAAAATAATGGAAGACGCCCCCCCAATAACGCGCCTTCA
57 CAAAATAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCA
2903551 TGTGAATAGT
Statistics
Matches: 450, Mismatches: 29, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
128 298 0.66
129 71 0.16
135 1 0.00
137 80 0.18
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:2903644 original size:8 final size:8
Alignment explanation
Indices: 2903631--2903671 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2903621 TCACAAGCTT
2903631 TCAAATTC
1 TCAAATTC
2903639 TCAAATTC
1 TCAAATTC
* *
2903647 CCAAACTC
1 TCAAATTC
2903655 T-AAATTC
1 TCAAATTC
2903662 TCAAATTC
1 TCAAATTC
2903670 TC
1 TC
2903672 TGAAAATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:2911385 original size:2 final size:2
Alignment explanation
Indices: 2911378--2911403 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2911368 CAGACTTTTA
2911378 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
2911404 TAATCTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2917845 original size:16 final size:17
Alignment explanation
Indices: 2917807--2917853 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
2917797 TATTTATAAG
2917807 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
*
2917825 GGAATTAGAATCTGT-A
1 GGAATTGGAATCTGTAA
2917841 GGAATTGGAATCT
1 GGAATTGGAATCT
2917854 AATTCCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:2918446 original size:34 final size:37
Alignment explanation
Indices: 2918403--2918475 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 37
2918393 TTTTCACCCT
2918403 AAACCCGAA-C-C-CGACCCGAATATCACACTTAAAA
1 AAACCCGAACCACTCGACCCGAATATCACACTTAAAA
2918437 AAACCCGAACCGACTCGACCCGAATATCACACTTAAAA
1 AAACCCGAACC-ACTCGACCCGAATATCACACTTAAAA
2918475 A
1 A
2918476 TCCCGACCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
34 9 0.26
35 1 0.03
37 1 0.03
38 24 0.69
ACGTcount: A:0.44, C:0.34, G:0.10, T:0.12
Consensus pattern (37 bp):
AAACCCGAACCACTCGACCCGAATATCACACTTAAAA
Found at i:2918709 original size:38 final size:37
Alignment explanation
Indices: 2918660--2918732 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
2918650 AACCCGAACC
*
2918660 CGACCTGAATATCACACTTAAAAAAACCCGAACCGACT
1 CGACCCGAATATCACACTT-AAAAAACCCGAACCGACT
*
2918698 CGACCCGAATATCACACTTAAAAAACCCGACCCGA
1 CGACCCGAATATCACACTTAAAAAACCCGAACCGA
2918733 ACAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.41, C:0.34, G:0.11, T:0.14
Consensus pattern (37 bp):
CGACCCGAATATCACACTTAAAAAACCCGAACCGACT
Found at i:2918823 original size:246 final size:244
Alignment explanation
Indices: 2918363--2918928 Score: 983
Period size: 246 Copynumber: 2.3 Consensus size: 244
2918353 TATAAGGTAA
*
2918363 AATTATATAT-TTTTCGGGTAGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGAATATC
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGAATATC
*
2918427 ACACTTAAAAAAACCCGAACCGACTCGACCCGAATATCACACTTAAAAATCCCGACCCGAACAAA
66 ACACTTAAAAAAACCCGAACCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAA
2918492 ATAAAGTTTCATCCGACCTGACCCGAATATATGAATTAGAAATACGACCCGACCCGAAATAATAA
131 ATAAAGTTTCATCCGACCTGACCCGAATATATGAATTAGAAATACGACCCGACCCGAAATAATAA
* *
2918557 TAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCTG
196 AAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
* * *
2918606 AATTATATATATATTTTCAGGTCGGTCCAGTTTTTTTCACCCTAAACCCGAACCCGACCTGAATA
1 AA-T-TATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGAATA
2918671 TCACACTTAAAAAAACCCGAACCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGAACA
64 TCACACTTAAAAAAACCCGAACCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGAACA
* *
2918736 AAATAAAGTTTCATCCGAACC-GACCTGAATATATGAATTAGAAATATGACCCGACCCGAAATAA
129 AAATAAAGTTTCATCCG-ACCTGACCCGAATATATGAATTAGAAATACGACCCGACCCGAAATAA
2918800 TAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
193 TAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
* **
2918852 AATTATATATATTTTCGGGTCGGTTCGGTTTTTTTCACCCTAAACTTGAACCCGACCCGAATATC
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGAATATC
2918917 ACACTTAAAAAA
66 ACACTTAAAAAA
2918929 TCTGACCCGA
Statistics
Matches: 304, Mismatches: 15, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
243 2 0.01
244 69 0.23
245 8 0.03
246 222 0.73
247 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (244 bp):
AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGAATATC
ACACTTAAAAAAACCCGAACCGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAA
ATAAAGTTTCATCCGACCTGACCCGAATATATGAATTAGAAATACGACCCGACCCGAAATAATAA
AAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
Found at i:2919090 original size:208 final size:209
Alignment explanation
Indices: 2918683--2919188 Score: 736
Period size: 208 Copynumber: 2.4 Consensus size: 209
2918673 ACACTTAAAA
*
2918683 AAACCCGAACCGACTCGACCCGAATATCACACTT-AAAAA--ACCCGACCCGAACAAAATAAAGT
1 AAACCCGAA-C-ACCCGACCCGAATATCACACTTAAAAAACGACCCGACCCGAACAAAATAAAGT
* * *
2918745 TTCATCCGAACCGACCTGAATATATGAATTAGAAATATGACCCGACCCGAAATAATAAAAAAATA
64 TTCATCCGACCCGACCCGAATATATGAATTAGAAATACGACCCGACCCGAAATAAT--AAAAATA
2918810 TTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGG
127 TTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGG
2918875 TTCGGTTTTTTTCACCCT
192 TTCGGTTTTTTTCACCCT
**
2918893 AAACTTG-A-ACCCGACCCGAATATCACACTTAAAAAATCTGACCCGACCCGAACAAAATAAAGT
1 AAACCCGAACACCCGACCCGAATATCACACTTAAAAAA-C-GACCCGACCCGAACAAAATAAAGT
* * *
2918956 TTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCGACCCGAAATAAT-AAATTTTT
64 TTCATCCGACCCGACCCGAATATATGAATTAGAAATACGACCCGACCCGAAATAATAAAAATATT
*
2919020 TTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCTGAATTATATATATTTTCGGGTCGGTT
129 TTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTT
2919085 CGGTTTTTTTCACCCT
194 CGGTTTTTTTCACCCT
*
2919101 AAACCCGAATCCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGACCAAAATA
1 AAACCCGAA--C-ACCCGACCCGAATATCACACTT-AAAAAA--CGACCCGACCCGAACAAAATA
* * *
2919166 AAATTTCACCCAACCCGACCCGA
60 AAGTTTCATCCGACCCGACCCGA
2919189 TCCGAATACA
Statistics
Matches: 267, Mismatches: 17, Indels: 20
0.88 0.06 0.07
Matches are distributed among these distances:
206 21 0.08
207 5 0.02
208 91 0.34
209 2 0.01
210 5 0.02
211 75 0.28
213 22 0.08
214 45 0.17
215 1 0.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (209 bp):
AAACCCGAACACCCGACCCGAATATCACACTTAAAAAACGACCCGACCCGAACAAAATAAAGTTT
CATCCGACCCGACCCGAATATATGAATTAGAAATACGACCCGACCCGAAATAATAAAAATATTTT
TATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTTCG
GTTTTTTTCACCCT
Found at i:2928633 original size:62 final size:62
Alignment explanation
Indices: 2928536--2928659 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
2928526 CTATGTCAAT
2928536 ACTCTGGTTTTGCTTGCGACAATTTCTTGTGTGTTTTTATTACAAGTTCATTACAGAATCTC
1 ACTCTGGTTTTGCTTGCGACAATTTCTTGTGTGTTTTTATTACAAGTTCATTACAGAATCTC
2928598 ACTCTGGTTTTGCTTGCGACAATTTCTTGTGTGTTTTTATTACAAGTTCATTACAGAATCTC
1 ACTCTGGTTTTGCTTGCGACAATTTCTTGTGTGTTTTTATTACAAGTTCATTACAGAATCTC
2928660 TTGCCTTAAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (62 bp):
ACTCTGGTTTTGCTTGCGACAATTTCTTGTGTGTTTTTATTACAAGTTCATTACAGAATCTC
Found at i:2945330 original size:19 final size:21
Alignment explanation
Indices: 2945285--2945342 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
2945275 TTGGTGTTGA
2945285 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TT-AAG
2945308 GGGAACCGATTCCCCC-T-AG
1 GGGAACCGATTCCCCCTTAAG
* *
2945327 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
2945343 CATGGGGTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.48
21 1 0.03
23 16 0.48
ACGTcount: A:0.22, C:0.34, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTTAAG
Found at i:2945349 original size:20 final size:19
Alignment explanation
Indices: 2945306--2945349 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2945296 CCCCCTTTGA
* *
2945306 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCCC
*
2945325 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2945344 ATGGGG
1 A-GGGG
2945350 TTCTGGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.23, C:0.32, G:0.32, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCC
Found at i:2947638 original size:21 final size:21
Alignment explanation
Indices: 2947612--2947653 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2947602 TTTTAAATGG
*
2947612 TTTTAAATGGGAGAAGTGTTA
1 TTTTAAATGAGAGAAGTGTTA
2947633 TTTTAAATGAGAGAAGTGTTA
1 TTTTAAATGAGAGAAGTGTTA
2947654 AAGTAAGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (21 bp):
TTTTAAATGAGAGAAGTGTTA
Found at i:2951167 original size:43 final size:43
Alignment explanation
Indices: 2951113--2951196 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
2951103 GAATAGTGTC
*
2951113 CCCGAGAGACATGAGTGACATAATAGGGTAATAATAACATAGT
1 CCCGAGAGACATGAGTGACATAATAGGGCAATAATAACATAGT
* * *
2951156 CCCGAGGGACATGGGTGACATAATAGGGCAATGATAACATA
1 CCCGAGAGACATGAGTGACATAATAGGGCAATAATAACATA
2951197 TTCTCTGACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.19
Consensus pattern (43 bp):
CCCGAGAGACATGAGTGACATAATAGGGCAATAATAACATAGT
Found at i:2951682 original size:25 final size:25
Alignment explanation
Indices: 2951645--2951703 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 25
2951635 TATGTACACC
*
2951645 TAAATAATTTTTT-TTAATTTTTATT
1 TAAATAATTTTTTATT-ATATTTATT
2951670 TAAA-AATTATTTTATTATATTTATT
1 TAAATAATT-TTTTATTATATTTATT
2951695 TAATATAAT
1 TAA-ATAAT
2951704 AATTAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 4 0.14
25 19 0.66
26 3 0.10
27 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TAAATAATTTTTTATTATATTTATT
Found at i:2954275 original size:34 final size:37
Alignment explanation
Indices: 2954237--2954315 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 37
2954227 ATTATTATAT
2954237 ATATATATAATAT-TAATAAATT-TA-ATTTAAATT-A
1 ATATATATAATATATAAT-AATTATATATTTAAATTAA
* *
2954271 ATATATAT-ATATATAATATTTATATATTTAATTTAA
1 ATATATATAATATATAATAATTATATATTTAAATTAA
2954307 ATATATATA
1 ATATATATA
2954316 CCTGGCCCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
33 7 0.18
34 14 0.37
35 8 0.21
36 9 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
ATATATATAATATATAATAATTATATATTTAAATTAA
Found at i:2954276 original size:40 final size:40
Alignment explanation
Indices: 2954226--2954315 Score: 139
Period size: 40 Copynumber: 2.3 Consensus size: 40
2954216 TATTAAAAAT
*
2954226 AATTATTATATATATATATAATATTAATAAATTTAATTTA
1 AATTAATATATATATATATAATATTAATAAATTTAATTTA
* *
2954266 AATTAATATATATATATATAATATTTATATATTTAATTTA
1 AATTAATATATATATATATAATATTAATAAATTTAATTTA
2954306 AA-T-ATATATA
1 AATTAATATATA
2954316 CCTGGCCCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 7 0.15
39 1 0.02
40 39 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (40 bp):
AATTAATATATATATATATAATATTAATAAATTTAATTTA
Found at i:2974734 original size:7 final size:7
Alignment explanation
Indices: 2974722--2974748 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2974712 TACATTCGGA
2974722 CTTTGGC
1 CTTTGGC
2974729 CTTTGGC
1 CTTTGGC
2974736 CTTTGGC
1 CTTTGGC
2974743 CTTTGG
1 CTTTGG
2974749 TAGACGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.30, T:0.44
Consensus pattern (7 bp):
CTTTGGC
Found at i:2975365 original size:22 final size:20
Alignment explanation
Indices: 2975330--2975376 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2975320 ATAATTATTT
2975330 AAAAATTAAATAAAAATACGA
1 AAAAATTAAATAAAAA-ACGA
* *
2975351 AAAATATTTAATAAAAAACTA
1 AAAA-ATTAAATAAAAAACGA
2975372 AAAAA
1 AAAAA
2975377 CATTTAGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 11 0.48
22 11 0.48
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAAATTAAATAAAAAACGA
Found at i:2979630 original size:59 final size:59
Alignment explanation
Indices: 2979538--2979668 Score: 169
Period size: 59 Copynumber: 2.2 Consensus size: 59
2979528 CTCGAACTAG
* *
2979538 ATTAGATATCTAGTAACACAATTCTGGTATAATTTACTCAGA-TGACAAAATATGATTGA
1 ATTAGATATCTAGTAACACAATTCTGGTATAATTCACTCAGACT-ACAAAATATGACTGA
* * *
2979597 ATTAGTTATCTAGTAACACAATTCAT-GTATAATTCACTCGGACTACAAAATATTACTGA
1 ATTAGATATCTAGTAACACAATTC-TGGTATAATTCACTCAGACTACAAAATATGACTGA
2979656 ATT-GAATATCTAG
1 ATTAG-ATATCTAG
2979669 AATAATTCAC
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 1 0.02
59 60 0.95
60 2 0.03
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (59 bp):
ATTAGATATCTAGTAACACAATTCTGGTATAATTCACTCAGACTACAAAATATGACTGA
Found at i:2979700 original size:45 final size:45
Alignment explanation
Indices: 2979625--2979713 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
2979615 CAATTCATGT
* * * *
2979625 ATAATTCACTCGGACTACAAAATATTACTGAATTGAATATCTAGA
1 ATAATTCACTCAGACTACAAAACATAACTGAATTGAACATCTAGA
* *
2979670 ATAATTCACTCAGATTATAAAACATAACTGAATTGAACATCTAG
1 ATAATTCACTCAGACTACAAAACATAACTGAATTGAACATCTAG
2979714 TAACCCAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (45 bp):
ATAATTCACTCAGACTACAAAACATAACTGAATTGAACATCTAGA
Found at i:2984677 original size:20 final size:20
Alignment explanation
Indices: 2984652--2984689 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2984642 TTTGGTTCAC
*
2984652 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
2984672 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
2984690 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:2984692 original size:18 final size:19
Alignment explanation
Indices: 2984652--2984695 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2984642 TTTGGTTCAC
*
2984652 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
2984672 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
2984690 GGAATA
1 GGAATA
2984696 GGATTACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:2984928 original size:22 final size:22
Alignment explanation
Indices: 2984903--2984947 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2984893 TATTATTTTT
*
2984903 AATATATATACTTTTTTAATAA
1 AATATATATAATTTTTTAATAA
*
2984925 AATATATATAATTTTTTTATAA
1 AATATATATAATTTTTTAATAA
2984947 A
1 A
2984948 TTTAAAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATATATAATTTTTTAATAA
Found at i:2986104 original size:19 final size:20
Alignment explanation
Indices: 2986082--2986124 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2986072 ATTCATGGTT
* *
2986082 AATAAACATAG-AGCAGTTC
1 AATAAACAGAGTAGAAGTTC
2986101 AAT-AACAGAGTAGAAGTTC
1 AATAAACAGAGTAGAAGTTC
2986120 AATAA
1 AATAA
2986125 CATGATGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 6 0.30
19 13 0.65
20 1 0.05
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (20 bp):
AATAAACAGAGTAGAAGTTC
Found at i:2988730 original size:2 final size:2
Alignment explanation
Indices: 2988723--2988761 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2988713 ATTTTGAGTT
2988723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2988762 GATGAATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2994709 original size:86 final size:87
Alignment explanation
Indices: 2994553--2994712 Score: 250
Period size: 86 Copynumber: 1.9 Consensus size: 87
2994543 CTTGAAATGA
* * *
2994553 TGGAAGCGGTTGATCTCTCTAATAACCCATCCTTGCAATGATGCAAGACCTTTTACCAGTAATCA
1 TGGAAGCGGTTGATCTCTCAAATAACCAATCCCTGCAATGATGCAAGACCTTTTACCAGTAATCA
*
2994618 TCACAAGAATAAATGCTATCGT
66 CCACAAGAATAAATGCTATCGT
* * *
2994640 TGGAAGC-TTTGATCTCTCAAATAAGCAATCCCTGCAATGATGCAAGGCCTTTTACCAGTAATCA
1 TGGAAGCGGTTGATCTCTCAAATAACCAATCCCTGCAATGATGCAAGACCTTTTACCAGTAATCA
2994704 CCACAAGAA
66 CCACAAGAA
2994713 CATAAGCCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
86 59 0.89
87 7 0.11
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (87 bp):
TGGAAGCGGTTGATCTCTCAAATAACCAATCCCTGCAATGATGCAAGACCTTTTACCAGTAATCA
CCACAAGAATAAATGCTATCGT
Found at i:2997375 original size:18 final size:18
Alignment explanation
Indices: 2997352--2997386 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2997342 TTCCATCCGG
*
2997352 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
2997370 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
2997387 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:2998688 original size:7 final size:7
Alignment explanation
Indices: 2998675--2998708 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
2998665 TGGTCAACTC
2998675 CGGTCAA
1 CGGTCAA
*
2998682 TGGTCAA
1 CGGTCAA
2998689 CGGGTCAA
1 C-GGTCAA
2998697 CGGTCAA
1 CGGTCAA
2998704 CGGTC
1 CGGTC
2998709 GGGTCAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.24, C:0.26, G:0.32, T:0.18
Consensus pattern (7 bp):
CGGTCAA
Found at i:2998696 original size:15 final size:15
Alignment explanation
Indices: 2998676--2998706 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2998666 GGTCAACTCC
*
2998676 GGTCAATGGTCAACG
1 GGTCAACGGTCAACG
2998691 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
2998706 G
1 G
2998707 TCGGGTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.35, T:0.16
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:2998728 original size:18 final size:18
Alignment explanation
Indices: 2998705--2998779 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
2998695 AACGGTCAAC
2998705 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
2998723 GGTCGGGTCAA----T-G
1 GGTCGGGTCAACGGGTCG
* *
2998736 GGTCAGGTAAACGGGTCG
1 GGTCGGGTCAACGGGTCG
2998754 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
2998772 GGTCGGGT
1 GGTCGGGT
2998780 TGTGACCGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
17 1 0.02
18 36 0.75
ACGTcount: A:0.13, C:0.19, G:0.49, T:0.19
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:2998739 original size:13 final size:13
Alignment explanation
Indices: 2998683--2998726 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
2998673 TCCGGTCAAT
*
2998683 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
2998698 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
2998710 GGTCAACGGGTCG
1 GGTCAACGGGTCG
2998723 GGTC
1 GGTC
2998727 GGGTCAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 4 0.15
15 7 0.26
ACGTcount: A:0.18, C:0.25, G:0.41, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:2998750 original size:31 final size:31
Alignment explanation
Indices: 2998698--2998770 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
2998688 ACGGGTCAAC
* *
2998698 GGTCAAC-GGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
*
2998728 GGTCAATGGGTCAGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
2998759 GGTCAACGGGTC
1 GGTCAACGGGTC
2998771 GGGTCGGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
Found at i:3002584 original size:18 final size:18
Alignment explanation
Indices: 3002561--3002595 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3002551 TTCCATCCGG
*
3002561 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
3002579 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
3002596 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:3003896 original size:7 final size:7
Alignment explanation
Indices: 3003883--3003916 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3003873 TGGTCAACTC
3003883 CGGTCAA
1 CGGTCAA
*
3003890 TGGTCAA
1 CGGTCAA
3003897 CGGGTCAA
1 C-GGTCAA
3003905 CGGTCAA
1 CGGTCAA
3003912 CGGTC
1 CGGTC
3003917 GGGTCAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.24, C:0.26, G:0.32, T:0.18
Consensus pattern (7 bp):
CGGTCAA
Found at i:3003904 original size:15 final size:15
Alignment explanation
Indices: 3003884--3003914 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3003874 GGTCAACTCC
*
3003884 GGTCAATGGTCAACG
1 GGTCAACGGTCAACG
3003899 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
3003914 G
1 G
3003915 TCGGGTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.35, T:0.16
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:3003936 original size:18 final size:18
Alignment explanation
Indices: 3003913--3003987 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
3003903 AACGGTCAAC
3003913 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
3003931 GGTCGGGTCAA----T-G
1 GGTCGGGTCAACGGGTCG
* *
3003944 GGTCAGGTAAACGGGTCG
1 GGTCGGGTCAACGGGTCG
3003962 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
3003980 GGTCGGGT
1 GGTCGGGT
3003988 TGTGACCGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
17 1 0.02
18 36 0.75
ACGTcount: A:0.13, C:0.19, G:0.49, T:0.19
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:3003947 original size:13 final size:13
Alignment explanation
Indices: 3003891--3003934 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
3003881 TCCGGTCAAT
*
3003891 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
3003906 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
3003918 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3003931 GGTC
1 GGTC
3003935 GGGTCAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 4 0.15
15 7 0.26
ACGTcount: A:0.18, C:0.25, G:0.41, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3003958 original size:31 final size:31
Alignment explanation
Indices: 3003906--3003978 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
3003896 ACGGGTCAAC
* *
3003906 GGTCAAC-GGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
*
3003936 GGTCAATGGGTCAGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
3003967 GGTCAACGGGTC
1 GGTCAACGGGTC
3003979 GGGTCGGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCAGGTAAACGGGTCGGGTCG
Found at i:3010325 original size:104 final size:104
Alignment explanation
Indices: 3010145--3010357 Score: 417
Period size: 104 Copynumber: 2.0 Consensus size: 104
3010135 TAGTAATTAA
3010145 TTTAAATAATGTGTCTTTAGAACGTATAATATTTTATAATCACCCTAAGTTAATCGATTAAATCC
1 TTTAAATAATGTGTCTTTAGAACGTATAATATTTTATAATCACCCTAAGTTAATCGATTAAATCC
3010210 AAAACTTACTTTTCACTTTATCAAACAATACCTTAACCT
66 AAAACTTACTTTTCACTTTATCAAACAATACCTTAACCT
3010249 TTTAAATAATGTGTCTTTAGAACGTATAATATTTTATAATCACCCTAAGTTAATCGATTAAATCC
1 TTTAAATAATGTGTCTTTAGAACGTATAATATTTTATAATCACCCTAAGTTAATCGATTAAATCC
3010314 AAAACTTACTTTTCACTTTATCAAACAATACCTTAACCT
66 AAAACTTACTTTTCACTTTATCAAACAATACCTTAACCT
*
3010353 CTTAA
1 TTTAA
3010358 CTATTATATT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 108 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (104 bp):
TTTAAATAATGTGTCTTTAGAACGTATAATATTTTATAATCACCCTAAGTTAATCGATTAAATCC
AAAACTTACTTTTCACTTTATCAAACAATACCTTAACCT
Found at i:3028083 original size:109 final size:109
Alignment explanation
Indices: 3027943--3028163 Score: 338
Period size: 109 Copynumber: 2.0 Consensus size: 109
3027933 ATTTTTTCGC
* * *
3027943 TAAGGTTTTAAAAGTAATAAATTTATTATTAACTTTATCGATATGTAATAAATCGAACATTCAAT
1 TAAGGTTTTAAAAGTAATAAATTGATCATTAACTTTATCAATATGT-ATAAATCGAACATTCAAT
* *
3028008 GTTAATAGA-T-TTAATGTGAGTGACAAAAAACTTACATAGTTCAT
65 GTTAACA-ACTGTTAACGTGAGTGACAAAAAACTTACATAGTTCAT
* * *
3028052 TAAGGTTTTAAAAGTAATAAATTGATCATTAACTTTATCAATCTGTATAAATCGATCATTCGATG
1 TAAGGTTTTAAAAGTAATAAATTGATCATTAACTTTATCAATATGTATAAATCGAACATTCAATG
3028117 TTAACAACTGTTAACGTGAGTGACAAAAAACTTACATAGTTCAT
66 TTAACAACTGTTAACGTGAGTGACAAAAAACTTACATAGTTCAT
3028161 TAA
1 TAA
3028164 TCACTTATCT
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 23 0.23
109 78 0.76
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (109 bp):
TAAGGTTTTAAAAGTAATAAATTGATCATTAACTTTATCAATATGTATAAATCGAACATTCAATG
TTAACAACTGTTAACGTGAGTGACAAAAAACTTACATAGTTCAT
Found at i:3029278 original size:19 final size:18
Alignment explanation
Indices: 3029250--3029286 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3029240 ATAATTAAAA
3029250 TTTTATAAATTAAATTAT
1 TTTTATAAATTAAATTAT
*
3029268 TTTTCATAAATTTAATTAT
1 TTTT-ATAAATTAAATTAT
3029287 AAACTAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTATAAATTAAATTAT
Found at i:3033801 original size:37 final size:37
Alignment explanation
Indices: 3033725--3033801 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
3033715 TTTTTATATT
*
3033725 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
3033762 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
3033799 TTT
1 TTT
3033802 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:3037711 original size:17 final size:18
Alignment explanation
Indices: 3037681--3037714 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3037671 TTTTTTATTA
*
3037681 ATAATAATAGTTAAAAAG
1 ATAATAATAATTAAAAAG
3037699 ATAA-AATAATTAAAAA
1 ATAATAATAATTAAAAA
3037715 CGTAAAGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
ATAATAATAATTAAAAAG
Found at i:3056098 original size:2 final size:2
Alignment explanation
Indices: 3056091--3056124 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3056081 ACCTTGATCA
3056091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3056125 GAGAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3056315 original size:21 final size:20
Alignment explanation
Indices: 3056289--3056529 Score: 231
Period size: 21 Copynumber: 11.7 Consensus size: 20
3056279 ATTCTGACTA
3056289 TCGCATTGCGATTTTCTAAAT
1 TCGCATTGCGATTTTCT-AAT
*
3056310 TCGCATTGCGATTTTTTAAAT
1 TCGCATTGCGATTTTCT-AAT
*
3056331 TCGCATTGCGATTTCTCAAAT
1 TCGCATTGCGATTT-TCTAAT
* *
3056352 TCGCGTTGCGATTTACGTAA-
1 TCGCATTGCGATTTTC-TAAT
3056372 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTT-CTAAT
*
3056393 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTTC-TAAT
*
3056413 CCGCATTGCGATTTTACTAAT
1 TCGCATTGCGATTTT-CTAAT
* *
3056434 TCACATTGCAATTTTACTAAT
1 TCGCATTGCGATTTT-CTAAT
* *
3056455 TCGCAATGCGATTTACGTAA-
1 TCGCATTGCGATTTTC-TAAT
*
3056475 TCGCATTGAGATTTTCCTAAT
1 TCGCATTGCGATTTT-CTAAT
*
3056496 TCGCACTT-CGATTTACGTAA-
1 TCGCA-TTGCGATTTTC-TAAT
3056516 TCGCATTGCGATTT
1 TCGCATTGCGATTT
3056530 AATAAATCGC
Statistics
Matches: 184, Mismatches: 23, Indels: 27
0.79 0.10 0.12
Matches are distributed among these distances:
19 2 0.01
20 62 0.34
21 117 0.64
22 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTTCTAAT
Found at i:3056321 original size:41 final size:40
Alignment explanation
Indices: 3056260--3056540 Score: 211
Period size: 41 Copynumber: 6.8 Consensus size: 40
3056250 CGCAAATCAG
* **
3056260 TTTCCAAATTCGCAACGCGATTCTGACT-ATCGCATTGCGAT
1 TTTCTAAATTCGCATTGCGATT-T-ACTAATCGCATTGCGAT
**
3056301 TTTCTAAATTCGCATTGCGATTTTTTAAATTCGCATTGCGA-
1 TTTCTAAATTCGCATTGCGATTTACT-AA-TCGCATTGCGAT
*
3056342 TTTCTCAAATTCGCGTTGCGATTTACGTAATCGCATTGCGAT
1 TTTCT-AAATTCGCATTGCGATTTAC-TAATCGCATTGCGAT
*
3056384 TTTCCT-AATTCGCATTGCGATTTACGTAACCGCATTGCGAT
1 TTT-CTAAATTCGCATTGCGATTTAC-TAATCGCATTGCGAT
* * *
3056425 TTTACT-AATTCACATTGCAATTTTACTAATTCGCAATGCGAT
1 TTT-CTAAATTCGCATTGCGA-TTTACTAA-TCGCATTGCGAT
* * *
3056467 TTACGT-AA-TCGCATTGAGATTTTCCTAATTCGCACTT-CGAT
1 TTTC-TAAATTCGCATTGCGA-TTTACTAA-TCGCA-TTGCGAT
* *
3056508 TTACGT-AA-TCGCATTGCGATTTAATAAATCGCA
1 TTTC-TAAATTCGCATTGCGATTTACT-AATCGCA
3056541 ACGAGATTCT
Statistics
Matches: 204, Mismatches: 24, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
39 1 0.00
40 10 0.05
41 136 0.67
42 54 0.26
43 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (40 bp):
TTTCTAAATTCGCATTGCGATTTACTAATCGCATTGCGAT
Found at i:3056342 original size:62 final size:62
Alignment explanation
Indices: 3056266--3056530 Score: 255
Period size: 62 Copynumber: 4.3 Consensus size: 62
3056256 TCAGTTTCCA
* *
3056266 AATTCGCAACGCGATTCTGAC-T-ATCGCATTGCGATTTT-CTAAATTCGCATTGCGATTTT-TT
1 AATTCGCAATGCGATT-T-ACGTAATCGCATTGCGATTTTACT-AATTCGCATTGCGATTTTACT
* * *
3056327 AAATTCGCATTGCGATTT-C-TCAAATTCGCGTTGCGA-TTTACGTAA-TCGCATTGCGATTTTC
1 -AATTCGCAATGCGATTTACGT--AA-TCGCATTGCGATTTTAC-TAATTCGCATTGCGATTTTA
3056388 CT
61 CT
* * * *
3056390 AATTCGCATTGCGATTTACGTAACCGCATTGCGATTTTACTAATTCACATTGCAATTTTACT
1 AATTCGCAATGCGATTTACGTAATCGCATTGCGATTTTACTAATTCGCATTGCGATTTTACT
* *
3056452 AATTCGCAATGCGATTTACGTAATCGCATTGAGATTTTCCTAATTCGCACTT-CGA-TTTACGT
1 AATTCGCAATGCGATTTACGTAATCGCATTGCGATTTTACTAATTCGCA-TTGCGATTTTAC-T
*
3056514 AA-TCGCATTGCGATTTA
1 AATTCGCAATGCGATTTA
3056531 ATAAATCGCA
Statistics
Matches: 174, Mismatches: 16, Indels: 27
0.80 0.07 0.12
Matches are distributed among these distances:
59 2 0.01
61 32 0.18
62 121 0.70
63 17 0.10
64 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (62 bp):
AATTCGCAATGCGATTTACGTAATCGCATTGCGATTTTACTAATTCGCATTGCGATTTTACT
Found at i:3056418 original size:103 final size:103
Alignment explanation
Indices: 3056289--3056529 Score: 328
Period size: 103 Copynumber: 2.3 Consensus size: 103
3056279 ATTCTGACTA
* * * *
3056289 TCGCATTGCGATTTTC-TAAATTCGCATTGCGATTTT-TTAAATTCGCATTGCGATTTCT-CAAA
1 TCGCATTGCGATTTACGT-AA-TCGCATTGCGATTTTACT-AATTCACATTGCAATTT-TACAAA
** *
3056351 TTCGCGTTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
62 TTCGCAATGCGATTTACGTAATCGCATTGAGATTTTCCTAAT
* *
3056393 TCGCATTGCGATTTACGTAACCGCATTGCGATTTTACTAATTCACATTGCAATTTTACTAATTCG
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTACTAATTCACATTGCAATTTTACAAATTCG
3056458 CAATGCGATTTACGTAATCGCATTGAGATTTTCCTAAT
66 CAATGCGATTTACGTAATCGCATTGAGATTTTCCTAAT
3056496 TCGCACTT-CGATTTACGTAATCGCATTGCGATTT
1 TCGCA-TTGCGATTTACGTAATCGCATTGCGATTT
3056530 AATAAATCGC
Statistics
Matches: 123, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
102 1 0.01
103 101 0.82
104 20 0.16
105 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (103 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTTACTAATTCACATTGCAATTTTACAAATTCG
CAATGCGATTTACGTAATCGCATTGAGATTTTCCTAAT
Found at i:3057455 original size:24 final size:24
Alignment explanation
Indices: 3057402--3057448 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
3057392 GTATTTGAAA
*
3057402 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATCTTGGTCAATACCAGAAC
3057426 TTTGATCTTGGTCAATACTCAGA
1 TTTGATCTTGGTCAATAC-CAGA
3057449 TTTTGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGAAC
Found at i:3059990 original size:20 final size:19
Alignment explanation
Indices: 3059962--3060016 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
3059952 CAATCATCTT
*
3059962 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
3059982 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
3060001 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
3060017 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:3060026 original size:14 final size:14
Alignment explanation
Indices: 3060007--3060063 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3059997 GCGAAATGAA
3060007 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3060021 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
3060040 AATCGCAACGAGGG
1 AATCGCAACGAGAG
3060054 AATCGCAACG
1 AATCGCAACG
3060064 CGAATTTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3060031 original size:33 final size:33
Alignment explanation
Indices: 3059989--3060067 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
3059979 GGAAATGACT
3059989 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3060022 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3060055 ATCGCAACGCGAA
1 ATCGCAATGCGAA
3060068 TTTAGTTTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3060045 original size:19 final size:19
Alignment explanation
Indices: 3059969--3060047 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
3059959 CTTAATGTCT
* **
3059969 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
3059989 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3060008 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3060022 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3060041 ATCGCAA
1 ATCGCAA
3060048 CGAGGGAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 24 0.49
20 9 0.18
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3060115 original size:33 final size:33
Alignment explanation
Indices: 3060073--3060152 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
3060063 GCGAATTTAG
* * * *
3060073 TTTCGCGTTGTGATTTTGTCGTTTCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
3060106 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
3060139 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
3060153 AGTCATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.10, C:0.20, G:0.21, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:3060119 original size:19 final size:19
Alignment explanation
Indices: 3060092--3060152 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
3060082 GTGATTTTGT
*
3060092 CGTTTCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3060111 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
3060125 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3060144 CATTGCGAT
1 CGTTGCGAT
3060153 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 10 0.30
16 3 0.09
17 3 0.09
19 17 0.52
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3060277 original size:14 final size:14
Alignment explanation
Indices: 3060258--3060294 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3060248 CATCAATTAA
3060258 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3060272 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3060286 ACAAATCAA
1 ACAAATCAA
3060295 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3062292 original size:20 final size:20
Alignment explanation
Indices: 3062267--3062304 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3062257 CGCGATTATA
3062267 GTTTCGCGTTGCAATTTTTG
1 GTTTCGCGTTGCAATTTTTG
*
3062287 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCAATTTT
3062305 GTCGTTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.16, G:0.26, T:0.50
Consensus pattern (20 bp):
GTTTCGCGTTGCAATTTTTG
Found at i:3062331 original size:33 final size:33
Alignment explanation
Indices: 3062288--3062371 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
3062278 CAATTTTTGG
*
3062288 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
* * *
3062321 TTTCGTGTTGCGATTCTCTCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
3062354 TTTCGCGTTGCGATTTTC
1 TTTCGCGTTGCGATTTTC
3062372 ATTCTCTCGT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.07, C:0.20, G:0.24, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
Found at i:3062332 original size:19 final size:18
Alignment explanation
Indices: 3062308--3062396 Score: 87
Period size: 19 Copynumber: 4.9 Consensus size: 18
3062298 CGATTTTGTC
3062308 GTTGCGATTTTCATTTCGT
1 GTTGCGATTTTCATTTC-T
*
3062327 GTTGCGA--TTC-TCTC-
1 GTTGCGATTTTCATTTCT
* *
3062341 GTTGCGATTTTCGTTTCGC
1 GTTGCGATTTTCATTTC-T
3062360 GTTGCGATTTTCATTCTCT
1 GTTGCGATTTTCATT-TCT
3062379 CGTTGCGATTTTCATTTC
1 -GTTGCGATTTTCATTTC
3062397 AACCAAAAGA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
14 7 0.12
16 6 0.10
17 6 0.10
19 23 0.39
20 17 0.29
ACGTcount: A:0.09, C:0.21, G:0.20, T:0.49
Consensus pattern (18 bp):
GTTGCGATTTTCATTTCT
Found at i:3062597 original size:94 final size:94
Alignment explanation
Indices: 3062485--3062857 Score: 543
Period size: 94 Copynumber: 4.1 Consensus size: 94
3062475 ATGGATTGCA
* *
3062485 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3062549 TTAGCAGAATTGGCAGCAAACAAACAAAT
66 TTAGCAGAATTGGCAGCAAACGAACAAAT
*
3062578 TTACTTTCAACCAAAAGACAAAACAAAGATAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
3062643 TTATCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAAACGAACAAAT
*
3062672 TTACTTTCAACCAAAAGACAAAAC---GACAATTACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3062734 TTAGCAGAATTGGCAGC-AACTGAATAAAT
66 TTAGCAGAATTGGCAGCAAAC-GAACAAAT
3062763 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT----A
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAA-AGAATACACA
* * *
3062822 GTTTAGCAGTATTGGCAGCAACCGAATAAAT
64 GTTTAGCAGAATTGGCAGCAAACGAACAAAT
3062853 TTACT
1 TTACT
3062858 AAGCAATCTA
Statistics
Matches: 257, Mismatches: 14, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
90 52 0.20
91 65 0.25
93 4 0.02
94 135 0.53
95 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAAACGAACAAAT
Found at i:3062727 original size:185 final size:182
Alignment explanation
Indices: 3062485--3062857 Score: 549
Period size: 185 Copynumber: 2.0 Consensus size: 182
3062475 ATGGATTGCA
*
3062485 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAAC--AGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
*
3062549 TTAGCAGAATTGGCAGCAAAC-AAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAGATAAAT
64 TTAGCAGAATTGGCAGC-AACTAAACAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAAT
*
3062612 ACTAACTTCACAGTGTTAA-AGAATACACAGTTTATCAGAATTGGCAGCAACCGAACAAAT
127 ACTAACTTCACAGTGTTAATA-AAT----AGTTTAGCAGAATTGGCAGCAACCGAACAAAT
* *
3062672 TTACTTTCAACCAAAAGACAAAAC-GACAATTACTAACTTCACAGTGTTAAAGAATACACAGTTT
1 TTACTTTCAACCAAAAGACAAAACAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTT
* *
3062736 AGCAGAATTGGCAGCAACTGAATAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAATACTA
66 AGCAGAATTGGCAGCAACTAAACAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAATACTA
* *
3062801 ACTTCACAGTGTTAATAAATAGTTTAGCAGTATTGGCAGCAACCGAATAAAT
131 ACTTCACAGTGTTAATAAATAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
3062853 TTACT
1 TTACT
3062858 AAGCAATCTA
Statistics
Matches: 173, Mismatches: 9, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
181 34 0.20
184 22 0.13
185 93 0.54
186 1 0.01
187 4 0.02
188 19 0.11
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (182 bp):
TTACTTTCAACCAAAAGACAAAACAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTT
AGCAGAATTGGCAGCAACTAAACAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAATACTA
ACTTCACAGTGTTAATAAATAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3064608 original size:19 final size:19
Alignment explanation
Indices: 3064544--3064642 Score: 144
Period size: 19 Copynumber: 5.1 Consensus size: 19
3064534 TCTTTTGGTT
*
3064544 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
3064563 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3064583 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
3064603 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3064622 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3064641 GA
1 GA
3064643 TTTTGGTTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 39 0.54
20 31 0.43
21 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3064660 original size:19 final size:20
Alignment explanation
Indices: 3064638--3064689 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3064628 AAAATCGCAA
**
3064638 TGCGATTTTGGTTTC-GCGT
1 TGCGATTTTCATTTCTGCGT
**
3064657 TGCGATAGTCATTTCTGCGT
1 TGCGATTTTCATTTCTGCGT
3064677 TGCGATTTTCATT
1 TGCGATTTTCATT
3064690 CTCGAAACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.12, C:0.17, G:0.25, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTCTGCGT
Found at i:3065285 original size:21 final size:20
Alignment explanation
Indices: 3065255--3065305 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3065245 ATTTACGTAT
* *
3065255 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGAAAA
*
3065276 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGAAAA
*
3065296 TCGTAATGCG
1 TCGCAATGCG
3065306 GTAGTCAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGAAAA
Found at i:3075764 original size:11 final size:11
Alignment explanation
Indices: 3075731--3075765 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3075721 ATAATTTCTT
*
3075731 AAATATTATAA
1 AAATATTATTA
3075742 AAATATTATTA
1 AAATATTATTA
*
3075753 AAATATTGTTA
1 AAATATTATTA
3075764 AA
1 AA
3075766 CTTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
AAATATTATTA
Found at i:3077390 original size:3 final size:3
Alignment explanation
Indices: 3077382--3077459 Score: 75
Period size: 3 Copynumber: 25.3 Consensus size: 3
3077372 TGTATTTATT
* * * *
3077382 TAA TAA TAAA TAA TAA TAA TAA TAA TGTA TAT TAA TAA TAA CAG TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
** *
3077429 TAA TAA TAA TAA TAA TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3077460 TTAAGTAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
3 54 0.92
4 5 0.08
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3077648 original size:45 final size:45
Alignment explanation
Indices: 3077584--3078068 Score: 835
Period size: 45 Copynumber: 10.8 Consensus size: 45
3077574 GATGGAAATG
* * *
3077584 TTTGAAAACATCATGCACTGAAGGTCTTATAGATGACCCGAAGGC
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3077629 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
3077674 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3077719 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
3077764 TTTGAAAACATCAAGCACTGAAGGGCTTATAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3077809 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
3077854 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCTGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3077899 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
3077944 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3077989 TTTGAAGACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3078034 TTTGAAGACATCATGCACTGAAGGGCTTACAGATG
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
3078069 TGAGAAGTAG
Statistics
Matches: 425, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 425 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.22
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
Found at i:3077896 original size:20 final size:20
Alignment explanation
Indices: 3077871--3077942 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 20
3077861 ACATCAAGCA
3077871 CTGAAGGGCTTACAGATGAC
1 CTGAAGGGCTTACAGATGAC
** *
3077891 CTGAAGGTTTTGAAAACATCATG-C
1 CTGAAGGGCTT----ACA-GATGAC
3077915 ACTGAAGGGCTTACAGATGAC
1 -CTGAAGGGCTTACAGATGAC
3077936 CTGAAGG
1 CTGAAGG
3077943 TTTTGAAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 19 0.49
21 4 0.10
24 4 0.10
25 12 0.31
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (20 bp):
CTGAAGGGCTTACAGATGAC
Found at i:3078356 original size:22 final size:22
Alignment explanation
Indices: 3078331--3078379 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
3078321 AATCTTCTTG
*
3078331 TTCATATGAAGATCTGTAAAAC
1 TTCATACGAAGATCTGTAAAAC
3078353 TTCATACGAAGATCTGTAAAAC
1 TTCATACGAAGATCTGTAAAAC
3078375 TTCAT
1 TTCAT
3078380 GTTTGAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (22 bp):
TTCATACGAAGATCTGTAAAAC
Found at i:3078698 original size:3 final size:3
Alignment explanation
Indices: 3078690--3078770 Score: 81
Period size: 3 Copynumber: 26.3 Consensus size: 3
3078680 TGTATTTATT
* * * *
3078690 TAA TAA TAA TAAA TAA TAA TAA TAA TGTA TAT TAA TAA TAA CAG TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
** *
3078737 TAA TAA TAA TAA TAA TAA TTT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3078771 TTAAATAATT
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
3 57 0.92
4 5 0.08
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3079350 original size:20 final size:20
Alignment explanation
Indices: 3079325--3079362 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3079315 GAACCGTTCG
*
3079325 AACCGGAAAAAATCGGGAAA
1 AACCGGAAAAAACCGGGAAA
3079345 AACCGGAAAAAACCGGGA
1 AACCGGAAAAAACCGGGA
3079363 TTTTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.26, T:0.03
Consensus pattern (20 bp):
AACCGGAAAAAACCGGGAAA
Found at i:3079355 original size:10 final size:10
Alignment explanation
Indices: 3079325--3079360 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
3079315 GAACCGTTCG
3079325 AACCGGAAAA
1 AACCGGAAAA
* *
3079335 AATCGGGAAA
1 AACCGGAAAA
3079345 AACCGGAAAA
1 AACCGGAAAA
3079355 AACCGG
1 AACCGG
3079361 GATTTTTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.25, T:0.03
Consensus pattern (10 bp):
AACCGGAAAA
Found at i:3089896 original size:20 final size:20
Alignment explanation
Indices: 3089847--3089896 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
3089837 AAAATTACCG
*
3089847 ATTAAATATTAATTGAATAA
1 ATTAAATTTTAATTGAATAA
* * *
3089867 ATTAAAATTTTAATTTACTCA
1 ATT-AAATTTTAATTGAATAA
3089888 ATTAAATTT
1 ATTAAATTT
3089897 GTAACTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (20 bp):
ATTAAATTTTAATTGAATAA
Found at i:3094744 original size:211 final size:210
Alignment explanation
Indices: 3094403--3094820 Score: 640
Period size: 211 Copynumber: 2.0 Consensus size: 210
3094393 AATGTCCCCG
* *
3094403 ATTTCAACATCAGGAACAACCCCTATTGAACCAAAATTTTCTCTTTGCACAAAATCTAGTGATAC
1 ATTTCAACACCAGGAACAACCCCTATTGAACCAAAATTTTCTCTTTACACAAAATCTAGTGATAC
* *
3094468 CCACTTCAGTACTTTACTCCTTTAACTTGTTTACACACAAACTAAAGCTCTAGTGAACCAAATTA
66 CCACTTCAGTACTTTACTCCTTTAACTTGTTTACACACAAACTAAAGCTCCAGTAAACCAAATTA
*
3094533 CACAAAATTCGGACTTTTTTTTCTTCAAAACAAGGAAATACCCACTTCATTTTTCTCCAACGTTA
131 CACAAAATTCAGA-TTTTTTTTCTTCAAAACAAGGAAATACCCACTTCATTTTTCTCCAACGTT-
*
3094598 ACTGTTTATGCACACTT
194 ACTGTTAATGCACACTT
*
3094615 ATTTCAACACCAGGAACAACCCCTATTGAACC-AAATTTTCTCTTTACGCAAAATCTAGTGATAC
1 ATTTCAACACCAGGAACAACCCCTATTGAACCAAAATTTTCTCTTTACACAAAATCTAGTGATAC
* * * * *
3094679 CCACTTTAGTTCTTTACTCCTTTAACTTGTTTACGCACAAACTGAAGCTCCAGTAAACTAAATTA
66 CCACTTCAGTACTTTACTCCTTTAACTTGTTTACACACAAACTAAAGCTCCAGTAAACCAAATTA
* * * * * * *
3094744 CACAAAATTCATATTTTTTTTCTTCAAAACCAGGAAATATCGAGTTTATTTTTCTCCGACGTTAC
131 CACAAAATTCAGATTTTTTTTCTTCAAAACAAGGAAATACCCACTTCATTTTTCTCCAACGTTAC
3094809 TGTTAATGCACA
196 TGTTAATGCACA
3094821 AAACAATGGC
Statistics
Matches: 187, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
209 13 0.07
210 44 0.24
211 99 0.53
212 31 0.17
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (210 bp):
ATTTCAACACCAGGAACAACCCCTATTGAACCAAAATTTTCTCTTTACACAAAATCTAGTGATAC
CCACTTCAGTACTTTACTCCTTTAACTTGTTTACACACAAACTAAAGCTCCAGTAAACCAAATTA
CACAAAATTCAGATTTTTTTTCTTCAAAACAAGGAAATACCCACTTCATTTTTCTCCAACGTTAC
TGTTAATGCACACTT
Found at i:3096540 original size:14 final size:14
Alignment explanation
Indices: 3096518--3096574 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
3096508 GGTTCGTGAA
*
3096518 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
3096532 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
3096546 CG--T--TTATGTT
1 CGTTTGGTTATGTT
* *
3096556 CGTTCGATTATGTT
1 CGTTTGGTTATGTT
3096570 CGTTT
1 CGTTT
3096575 ATGTTCATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.25
12 1 0.03
14 26 0.72
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:3096546 original size:24 final size:24
Alignment explanation
Indices: 3096519--3096593 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
3096509 GTTCGTGAAC
* * *
3096519 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
3096543 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
3096567 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
3096591 GTT
1 GTT
3096594 TAACCCAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.12, C:0.11, G:0.21, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:3097338 original size:16 final size:16
Alignment explanation
Indices: 3097317--3097383 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
3097307 GTCTCCAACG
3097317 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
3097333 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
3097349 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
3097365 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
3097379 TTTAT
1 TTTAT
3097384 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:3097356 original size:32 final size:32
Alignment explanation
Indices: 3097315--3097375 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
3097305 GGGTCTCCAA
3097315 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
3097347 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
3097376 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:3097469 original size:16 final size:16
Alignment explanation
Indices: 3097445--3097477 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3097435 AAAAAAATTT
*
3097445 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3097461 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
3097477 T
1 T
3097478 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.24, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:3109696 original size:7 final size:7
Alignment explanation
Indices: 3109684--3109735 Score: 79
Period size: 7 Copynumber: 7.3 Consensus size: 7
3109674 ATAGTTATTA
3109684 AAAAAAT
1 AAAAAAT
3109691 AAAAAA-
1 AAAAAAT
3109697 AAATAAAT
1 AAA-AAAT
3109705 AAAAAAAT
1 -AAAAAAT
3109713 AAAAAAT
1 AAAAAAT
3109720 AAAAAAT
1 AAAAAAT
3109727 AAAAAAT
1 AAAAAAT
3109734 AA
1 AA
3109736 TAATGAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
6 3 0.07
7 32 0.76
8 4 0.10
9 3 0.07
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:3109708 original size:22 final size:22
Alignment explanation
Indices: 3109682--3109732 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
3109672 ACATAGTTAT
3109682 TAAAAAAATAAAAAA-AAATAAA
1 TAAAAAAATAAAAAATAAA-AAA
3109704 TAAAAAAATAAAAAATAAAAAA
1 TAAAAAAATAAAAAATAAAAAA
3109726 TAAAAAA
1 TAAAAAA
3109733 TAATAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (22 bp):
TAAAAAAATAAAAAATAAAAAA
Found at i:3110024 original size:21 final size:21
Alignment explanation
Indices: 3110000--3110044 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3109990 TGATTTCATA
*
3110000 TAACATAATAATTTATGATAT
1 TAACATAATAATTTATAATAT
* *
3110021 TAACGTGATAATTTATAATAT
1 TAACATAATAATTTATAATAT
3110042 TAA
1 TAA
3110045 TGTGATCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (21 bp):
TAACATAATAATTTATAATAT
Found at i:3110049 original size:21 final size:21
Alignment explanation
Indices: 3110007--3110069 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
3109997 ATATAACATA
*
3110007 ATAATTTATGATATTAACGTG
1 ATAATTTATGATATTAATGTG
*
3110028 ATAATTTATAATATTAATGTG
1 ATAATTTATGATATTAATGTG
* *
3110049 ATCATTTATGATGTTAATGTG
1 ATAATTTATGATATTAATGTG
3110070 TTCGATCCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (21 bp):
ATAATTTATGATATTAATGTG
Found at i:3111769 original size:211 final size:211
Alignment explanation
Indices: 3111500--3112122 Score: 1022
Period size: 211 Copynumber: 2.9 Consensus size: 211
3111490 AACTGACCCG
3111500 ACCCGACCCG-AAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
1 ACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
*
3111564 TATATATAATTTTTTTCAATTAAGTCG-TCATTTTTATTGAATAAAAATAATTTTTTTATTATTT
66 TATATATAATTTTTTTCAATTAAGTCGCT-GTTTTTATTGAATAAAAATAATTTTTTTATTATTT
* * *
3111628 CGGGTCAGGTTTCTAATTCATATATTCGGTTCGGGTCGAGTGAAATTTTATTTTGGTCGGGTTCG
130 CGGGTCGGGTTTCTAATTCATATATTCGGTTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTTCG
*
3111693 GGTTTATGGTGAAAAAT
195 GGTTTAGGGTGAAAAAT
*
3111710 ACCTGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
1 ACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
* *
3111775 TCTATATATTTTTTTTCAATTAAGTCGCTGTTTTTATTGAATAAAAAT-ATTTTTTTATTATTTC
66 TATATATAATTTTTTTCAATTAAGTCGCTGTTTTTATTGAATAAAAATAATTTTTTTATTA-TT-
*
3111839 AGGTCGGGTCGGGTTTCTAATTCATATATTCGGTTCGGGTTGGGTGAAACTTTATTTTGGTCGGG
129 ---TCGGGTCGGGTTTCTAATTCATATATTCGGTTCGGGTCGGGTGAAACTTTATTTTGGTCGGG
3111904 -TCGGGTTTAGGGTGAAAAAT
191 TTCGGGTTTAGGGTGAAAAAT
* **
3111924 ACCCGAACAAAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
1 ACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
*
3111989 TATATATAATTTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTT
66 TATATATAA-TTTTTTTCAATTAAGTCGCTGTTTTTATTGAATAAAAATAATTTTTTTATTATTT
*
3112054 CGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTT-G
130 CGGGTCGGGTTTCTAATTCATATATTCGGTTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTTCG
3112118 GGTTT
195 GGTTT
3112123 TTTAAGTGAT
Statistics
Matches: 385, Mismatches: 18, Indels: 19
0.91 0.04 0.05
Matches are distributed among these distances:
210 21 0.05
211 165 0.43
212 2 0.01
214 87 0.23
215 98 0.25
216 12 0.03
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (211 bp):
ACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
TATATATAATTTTTTTCAATTAAGTCGCTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTC
GGGTCGGGTTTCTAATTCATATATTCGGTTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTTCGG
GTTTAGGGTGAAAAAT
Found at i:3112768 original size:18 final size:18
Alignment explanation
Indices: 3112731--3112830 Score: 157
Period size: 18 Copynumber: 5.6 Consensus size: 18
3112721 TATGGAATTG
*
3112731 GATTCCAATT-CTTGACA
1 GATTCCAATTCCTTCACA
*
3112748 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
3112766 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
3112784 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
3112802 GATTCCAATTCTTTCACA
1 GATTCCAATTCCTTCACA
3112820 GATTCCAATTC
1 GATTCCAATTC
3112831 ACTCATAAAC
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
17 9 0.12
18 69 0.88
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:3116835 original size:29 final size:29
Alignment explanation
Indices: 3116801--3116859 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3116791 CCTAAATTAA
3116801 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
3116830 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
3116859 T
1 T
3116860 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:3121511 original size:29 final size:29
Alignment explanation
Indices: 3121478--3121547 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
3121468 AAATAAGTTC
*
3121478 ACACCTAAATTA-ATTTGATGTCATTGTTT
1 ACACC-AAATTAGATTTGATGTCATTGCTT
* *
3121507 ACACCAATTTAGTTTTGATGTCATTGCTT
1 ACACCAAATTAGATTTGATGTCATTGCTT
* *
3121536 ACATCAATTTAG
1 ACACCAAATTAG
3121548 TTAGGTGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (29 bp):
ACACCAAATTAGATTTGATGTCATTGCTT
Found at i:3121548 original size:29 final size:29
Alignment explanation
Indices: 3121491--3121549 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
3121481 CCTAAATTAA
*
3121491 TTTGATGTCATTGTTTACACCAATTTAGT
1 TTTGATGTCATTGCTTACACCAATTTAGT
*
3121520 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACACCAATTTAGT
3121549 T
1 T
3121550 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACACCAATTTAGT
Found at i:3121949 original size:66 final size:66
Alignment explanation
Indices: 3121874--3122022 Score: 176
Period size: 66 Copynumber: 2.3 Consensus size: 66
3121864 ACCTCCGGTG
* *
3121874 CCAGTTCAATCTCCACTTCAACCAGTCCACTCCTCACCGCCA-TCAGTCTTCTC-CCAACCTATA
1 CCAGTTCAATCTCCACCTCAACCAGTCCACTCCTCACCACCACT-AGTCTTCTCTCC-ACCTATA
3121937 ATA
64 ATA
* * * * * * **
3121940 CCAGTTCAATATCCACCTCCACCAGTTCATTCTTCACCACCACTAGTCTTCTCTCCACCTCTGGT
1 CCAGTTCAATCTCCACCTCAACCAGTCCACTCCTCACCACCACTAGTCTTCTCTCCACCTATAAT
3122005 A
66 A
3122006 CCAGTTCAATCTCCACC
1 CCAGTTCAATCTCCACC
3122023 ATCACTTGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
66 67 0.96
67 3 0.04
ACGTcount: A:0.23, C:0.42, G:0.07, T:0.28
Consensus pattern (66 bp):
CCAGTTCAATCTCCACCTCAACCAGTCCACTCCTCACCACCACTAGTCTTCTCTCCACCTATAAT
A
Found at i:3121977 original size:21 final size:21
Alignment explanation
Indices: 3121939--3121982 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3121929 AACCTATAAT
*
3121939 ACCAGTTCAATATCCACCTCC
1 ACCAGTTCAATATCCACCACC
* * *
3121960 ACCAGTTCATTCTTCACCACC
1 ACCAGTTCAATATCCACCACC
3121981 AC
1 AC
3121983 TAGTCTTCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.43, G:0.05, T:0.25
Consensus pattern (21 bp):
ACCAGTTCAATATCCACCACC
Found at i:3125585 original size:29 final size:31
Alignment explanation
Indices: 3125517--3125582 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
3125507 TGTTCAAAGT
* *
3125517 TTGGCCACCAACCAAGATGAAATTTCTAATAAG
1 TTGGCCACCAACCAAGATGAAATTTC--ACAAC
3125550 TTGGCCACCAACCAAGATGAAATTTC-CAAC
1 TTGGCCACCAACCAAGATGAAATTTCACAAC
3125580 TTG
1 TTG
3125583 CCAACTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.16
33 26 0.84
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCACAAC
Found at i:3127529 original size:21 final size:22
Alignment explanation
Indices: 3127491--3127536 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3127481 ATCTGCTGAA
* **
3127491 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
3127512 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
3127534 ACT
1 ACT
3127537 TGTATGGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:3130334 original size:29 final size:31
Alignment explanation
Indices: 3130266--3130331 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 31
3130256 TGTTCAAAGT
* *
3130266 TTGGCCACCAACCAAGATAAAATTTCTAATAAG
1 TTGGCCACCAACCAAGATAAAATTTC--ACAAC
*
3130299 TTGGCCACCAACCAAGATGAAATTTC-CAAC
1 TTGGCCACCAACCAAGATAAAATTTCACAAC
3130329 TTG
1 TTG
3130332 CCAACTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 5 0.17
33 25 0.83
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATAAAATTTCACAAC
Found at i:3131379 original size:21 final size:21
Alignment explanation
Indices: 3131330--3131407 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
3131320 GTAGAGAGTA
* *
3131330 GACAGGCGGTGGTGGAGAATG
1 GACAGGTGGTGGTGGTGAATG
** *
3131351 GATTGGTGGTGGTGGTGAGTG
1 GACAGGTGGTGGTGGTGAATG
* * *
3131372 TACAGGTGGAGGTGATGAATG
1 GACAGGTGGTGGTGGTGAATG
*
3131393 GACAAGTGGTGGTGG
1 GACAGGTGGTGGTGG
3131408 AGATTGAACT
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.21, C:0.05, G:0.51, T:0.23
Consensus pattern (21 bp):
GACAGGTGGTGGTGGTGAATG
Found at i:3131452 original size:21 final size:20
Alignment explanation
Indices: 3131427--3131498 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
3131417 TGGTACCGGG
3131427 GGTGGGGAATGGACTA-TAGGT
1 GGTGGGGAA-GGACTAGT-GGT
3131448 GGTGGAGAGAA-GACTAGTGGT
1 GGTGG-G-GAAGGACTAGTGGT
*
3131469 GGTGGGGAGAAGACTAGTGGT
1 GGTGGGGA-AGGACTAGTGGT
3131490 GGTGGGGAA
1 GGTGGGGAA
3131499 TGGGCATGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.04
20 3 0.07
21 36 0.78
22 2 0.04
23 3 0.07
ACGTcount: A:0.25, C:0.04, G:0.51, T:0.19
Consensus pattern (20 bp):
GGTGGGGAAGGACTAGTGGT
Found at i:3131546 original size:21 final size:21
Alignment explanation
Indices: 3131506--3131546 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3131496 GAATGGGCAT
* *
3131506 GTGGAGGTGGGGAGTAAATTA
1 GTGGAGGTGGAGAATAAATTA
*
3131527 GTGGAGGTGGAGAATGAATT
1 GTGGAGGTGGAGAATAAATT
3131547 GGTATCGGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.46, T:0.24
Consensus pattern (21 bp):
GTGGAGGTGGAGAATAAATTA
Found at i:3131678 original size:21 final size:21
Alignment explanation
Indices: 3131571--3131727 Score: 95
Period size: 21 Copynumber: 7.1 Consensus size: 21
3131561 TGGTGAATGG
3131571 ACTGGTTGAGGTGGAGATTGA
1 ACTGGTTGAGGTGGAGATTGA
* ** *
3131592 ACTAGTATCAGAGGTGG-GGGTGG
1 ACTGGT-T--GAGGTGGAGATTGA
* * * *
3131615 ACTGGTGGTGGTGGGGAGTGA
1 ACTGGTTGAGGTGGAGATTGA
*
3131636 ACTGGTTGAGGTGTG-GAGTGA
1 ACTGGTTGAGGTG-GAGATTGA
3131657 ACTGGTTGAGGTGGAGATTGA
1 ACTGGTTGAGGTGGAGATTGA
*
3131678 ATTGGTACTCG-GGATGGAGATTGA
1 ACTGGT--T-GAGG-TGGAGATTGA
*
3131702 ACTGATACTGGAGGTGGAGATTGA
1 ACTGGT--T-GAGGTGGAGATTGA
3131726 AC
1 AC
3131728 AGGTACCAGA
Statistics
Matches: 109, Mismatches: 16, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
20 7 0.06
21 49 0.45
22 2 0.02
23 11 0.10
24 38 0.35
25 2 0.02
ACGTcount: A:0.23, C:0.07, G:0.44, T:0.26
Consensus pattern (21 bp):
ACTGGTTGAGGTGGAGATTGA
Found at i:3131739 original size:24 final size:23
Alignment explanation
Indices: 3131664--3132029 Score: 114
Period size: 24 Copynumber: 16.0 Consensus size: 23
3131654 TGAACTGGTT
*
3131664 GAGGTGGAGATTGAATTGGTACTC
1 GAGGTGGAGATTGAACTGGTAC-C
* *
3131688 G-GGATGGAGATTGAACTGATACTG
1 GAGG-TGGAGATTGAACTGGTAC-C
*
3131712 GAGGTGGAGATTGAACAGGTACC
1 GAGGTGGAGATTGAACTGGTACC
* * * * *
3131735 AGAGGTGGGGAGTGGA-TTG-ATC
1 -GAGGTGGAGATTGAACTGGTACC
*
3131757 GAGGTGGAGATTGAACCGGTACC
1 GAGGTGGAGATTGAACTGGTACC
* * * *
3131780 AGAGGTGGGGAGTGGACAGGT--C
1 -GAGGTGGAGATTGAACTGGTACC
* * *
3131802 GAGGTAGAGATTGAACTTGTACAG
1 GAGGTGGAGATTGAACTGGTAC-C
* ** *
3131826 GAGGTGGGGAGAGGACTGGT--C
1 GAGGTGGAGATTGAACTGGTACC
* ** *
3131847 GAGGTGGAGATTGTACCAGTATCG
1 GAGGTGGAGATTGAACTGGTA-CC
* *
3131871 GAGGT-GAGGAGTGGACTGGTTA--
1 GAGGTGGA-GATTGAACTGG-TACC
**
3131893 -AGGTGGAGATTGAACCAGTACC
1 GAGGTGGAGATTGAACTGGTACC
* * * *
3131915 GAATGTGGGGAGTGGACTGGTACC
1 G-AGGTGGAGATTGAACTGGTACC
* * * *
3131939 GGAGGTGGCGAGTGGACTGGT--T
1 -GAGGTGGAGATTGAACTGGTACC
* * *
3131961 GAGGTGGATATTGAACTGCTATCT
1 GAGGTGGAGATTGAACTGGTA-CC
* *
3131985 GAGGTGGAGATTGAATTGGT--G
1 GAGGTGGAGATTGAACTGGTACC
* * *
3132006 GTGGTGGGGAATGAACTGGTACC
1 GAGGTGGAGATTGAACTGGTACC
3132029 G
1 G
3132030 GTGAACTTGT
Statistics
Matches: 243, Mismatches: 74, Indels: 51
0.66 0.20 0.14
Matches are distributed among these distances:
20 2 0.01
21 82 0.34
22 6 0.02
23 8 0.03
24 140 0.58
25 5 0.02
ACGTcount: A:0.25, C:0.10, G:0.43, T:0.22
Consensus pattern (23 bp):
GAGGTGGAGATTGAACTGGTACC
Found at i:3131778 original size:45 final size:45
Alignment explanation
Indices: 3131559--3131935 Score: 286
Period size: 45 Copynumber: 8.4 Consensus size: 45
3131549 TATCGGAGGT
* * * * *
3131559 GGTGGTGAATGGACTGGTTGAGGTGGAGATTGAACTAGTATCAGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCAGTACCAGA
* * * * ** *
3131604 GGTGGGG-GTGGACTGGTGGTGGTGGGGAGTGAACTGGT---TGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCAGTACCAGA
* * * ***
3131645 GGTGTGGAGTGAACTGGTTGAGGTGGAGATTGAATTGGTACTC-G-
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCAGTAC-CAGA
* * * *
3131689 GGATGGAGATTGAACTGATACTGGAGGTGGAGATTGAA-CAGGTACCAGA
1 GG-TGGGGAGTGGACTGGT-C--GAGGTGGAGATTGAACCA-GTACCAGA
* * *
3131738 GGTGGGGAGTGGATTGATCGAGGTGGAGATTGAACCGGTACCAGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCAGTACCAGA
* * **
3131783 GGTGGGGAGTGGACAGGTCGAGGTAGAGATTGAACTTGTA-CAGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCAGTACCA-GA
* * * *
3131828 GGTGGGGAGAGGACTGGTCGAGGTGGAGATTGTACCAGTATCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCAGTACCAGA
* **
3131873 GGTGAGGAGTGGACTGGTTAAGGTGGAGATTGAACCAGTACC-GAA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCAGTACCAG-A
*
3131918 TGTGGGGAGTGGACTGGT
1 GGTGGGGAGTGGACTGGT
3131936 ACCGGAGGTG
Statistics
Matches: 268, Mismatches: 48, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
41 8 0.03
42 25 0.09
44 30 0.11
45 167 0.62
46 2 0.01
47 2 0.01
48 32 0.12
49 2 0.01
ACGTcount: A:0.24, C:0.09, G:0.45, T:0.23
Consensus pattern (45 bp):
GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCAGTACCAGA
Found at i:3139986 original size:21 final size:21
Alignment explanation
Indices: 3139946--3139989 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3139936 GAATGGACAT
* *
3139946 GTGGAGGTGGGGAGTAAATTG
1 GTGGAGGTGGAGAATAAATTG
*
3139967 GTGGAGGTGGAGAATGAATTG
1 GTGGAGGTGGAGAATAAATTG
3139988 GT
1 GT
3139990 ATCGGAGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (21 bp):
GTGGAGGTGGAGAATAAATTG
Found at i:3140440 original size:45 final size:45
Alignment explanation
Indices: 3140065--3140432 Score: 511
Period size: 45 Copynumber: 8.1 Consensus size: 45
3140055 GACTGGTGGT
* * * *
3140065 GGTGGGGAGTGAACTGGTTGAGGTGGAGATTGAATTGGTACCGGG
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
* * * *
3140110 GGTGGAGATTGAACTGGTACTGGAGGTGGAGATTGAACAGGTACCGGA
1 GGTGGGGAGTGGACTGGT-C--GAGGTGGAGATTGAACTGGTACCGGA
*
3140158 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTTGTACCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
* *
3140203 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCGGCACCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
*
3140248 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTTGTACCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
*
3140293 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCGGTACCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
* *
3140338 GGTGGGGAGTGGACTGGTTGAGGTGGAGATTGAACTGGTATCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
* * * * * * *
3140383 GGTGGAGATTGAACTGGTGGTGGTGGGGAATGAACTGGTACCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
3140428 GGTGG
1 GGTGG
3140433 AGATTGAATT
Statistics
Matches: 290, Mismatches: 30, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
45 251 0.87
47 1 0.00
48 38 0.13
ACGTcount: A:0.21, C:0.10, G:0.48, T:0.21
Consensus pattern (45 bp):
GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
Found at i:3145819 original size:2 final size:2
Alignment explanation
Indices: 3145808--3145892 Score: 163
Period size: 2 Copynumber: 43.0 Consensus size: 2
3145798 CTCTAATAAA
3145808 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3145849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3145891 AT
1 AT
3145893 TAAATAGAAA
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3151610 original size:45 final size:45
Alignment explanation
Indices: 3151561--3151976 Score: 580
Period size: 45 Copynumber: 9.1 Consensus size: 45
3151551 GACTGGTGGT
* * * *
3151561 GGTGGGGAGTGAACTGGTTGAGGTGGAGATTGAATTGGTACCGGG
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
* * * *
3151606 GGTGGAGATTGAACTGGTACTGGAGGTGGAGATTGAACAGGTACCGGA
1 GGTGGGGAGTGGACTGGT-C--GAGGTGGAGATTGAACTGGTACCGGA
* *
3151654 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCGGTACCAGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
*
3151699 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTTGTACCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
* *
3151744 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCGGCACCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
*
3151789 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTTGTACCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
*
3151834 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACCGGTACCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
* *
3151879 GGTGGGGAGTGGACTGGTTGAGGTGGAGATTGAACTGGTATCGGA
1 GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
* * * * *
3151924 GGTGGAGATTGAACTGGTACCGGAGGTGGAGATTGAATTGGTACTGGA
1 GGTGGGGAGTGGACTGGT--C-GAGGTGGAGATTGAACTGGTACCGGA
3151972 GGTGG
1 GGTGG
3151977 AGAAGGAACT
Statistics
Matches: 333, Mismatches: 32, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
45 266 0.80
47 1 0.00
48 66 0.20
ACGTcount: A:0.21, C:0.11, G:0.47, T:0.21
Consensus pattern (45 bp):
GGTGGGGAGTGGACTGGTCGAGGTGGAGATTGAACTGGTACCGGA
Found at i:3155265 original size:170 final size:170
Alignment explanation
Indices: 3154920--3155272 Score: 376
Period size: 170 Copynumber: 2.1 Consensus size: 170
3154910 GACTGACTGA
* * * * * * *
3154920 GTTTTGGTCAGAATGGTGTGATAACTCTAATGGTGGTGGCGGTATGGTGAATAGACGACCTAATC
1 GTTTTGGTCGGAACGGTATGAGAACTCCAATGGTGGTGGCGGTATGGCGAAGAGACGACCTAATC
* * * * * *
3154985 GACCAAAAAATTATGAAAATAGAAAAGGGGTGTTGGGGTTTTCCGATGAGATTCAGGACCCTCTC
66 GACCAAAAAATGATGAAAACAAAAAAAGGGCGTTGGGGTTTTCCGACGAGATTCAGGACCCTCTC
* * *
3155050 TACAGTGAATGGAGGTGAGTCTCAGTAAGTGACCAGAGGG
131 CACAGCGAATGGAGGTGAGTATCAGTAAGTGACCAGAGGG
* *
3155090 GTTTTGGTTGGAACGGTATGAGAACTCCAATGGTGGTGGCGGTATGGCGAACGA-ATGACCTAAT
1 GTTTTGGTCGGAACGGTATGAGAACTCCAATGGTGGTGGCGGTATGGCGAA-GAGACGACCTAAT
* * **
3155154 CGGA-C-AAAAATCGATGAAAACAAAAAAAGGGCGTTGGGGTTTTTCGACGAGATTTGAGG-CTT
65 C-GACCAAAAAAT-GATGAAAACAAAAAAAGGGCGTTGGGGTTTTCCGACGAGA-TTCAGGACCC
* * * *
3155216 TCTCCACGGCGAATGGAGGTGAGTATCCA-TGAGTGGCTA-AGGAG
127 TCTCCACAGCGAATGGAGGTGAGTAT-CAGTAAGTGACCAGAGG-G
3155260 GTTTTGGTCGGAA
1 GTTTTGGTCGGAA
3155273 TGGGGCTATA
Statistics
Matches: 150, Mismatches: 27, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
169 9 0.06
170 131 0.87
171 10 0.07
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (170 bp):
GTTTTGGTCGGAACGGTATGAGAACTCCAATGGTGGTGGCGGTATGGCGAAGAGACGACCTAATC
GACCAAAAAATGATGAAAACAAAAAAAGGGCGTTGGGGTTTTCCGACGAGATTCAGGACCCTCTC
CACAGCGAATGGAGGTGAGTATCAGTAAGTGACCAGAGGG
Found at i:3157396 original size:26 final size:26
Alignment explanation
Indices: 3157360--3157422 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
3157350 TGTCATGGGT
* **
3157360 CTCATCTAAGTTTTTTTTTTAAGTAC
1 CTCACCTAAGTTTTTTTTAAAAGTAC
3157386 CTCACCTAAGTTTTTTTTAAAAGTAC
1 CTCACCTAAGTTTTTTTTAAAAGTAC
3157412 CTCACCTAAGT
1 CTCACCTAAGT
3157423 CTTATTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (26 bp):
CTCACCTAAGTTTTTTTTAAAAGTAC
Found at i:3170848 original size:19 final size:19
Alignment explanation
Indices: 3170824--3170860 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3170814 ATGACCAACA
*
3170824 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
3170843 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
3170861 CAGTATTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:3170991 original size:41 final size:41
Alignment explanation
Indices: 3170946--3171265 Score: 536
Period size: 41 Copynumber: 7.8 Consensus size: 41
3170936 CGAATATGTA
* *
3170946 AATCGCAACACGATTCTAACTATCGCAACGCGATAATACAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
3170987 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
3171028 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
3171069 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
3171110 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
*
3171151 AATCGCAACGCGATTCTGACTATCGCAATGCGATAATACAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
* **
3171192 AATCGCAACTCGATTCTGACTATCGCAACGCGATTCTGAC-T
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAAT-ACAT
* * *
3171233 -ATCGCAACGCAATTTTGACTATCACAACGCGAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGAT
3171266 TCTGACTCTC
Statistics
Matches: 267, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
40 29 0.11
41 236 0.88
42 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (41 bp):
AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
Done.