Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000491.1 Hibiscus syriacus cultivar Beakdansim tig00000935_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: 94263
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:873 original size:3 final size:3
Alignment explanation
Indices: 865--891 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
855 CAAAGCCAGG
865 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
892 GCACTCGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:26269 original size:21 final size:18
Alignment explanation
Indices: 26258--26295 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
26248 ACCAGTTACT
26258 TCTGCTCCACCACCTTCA
1 TCTGCTCCACCACCTTCA
26276 TCTGCTCCACCACCTTCA
1 TCTGCTCCACCACCTTCA
26294 TC
1 TC
26296 CCCACCGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.50, G:0.05, T:0.29
Consensus pattern (18 bp):
TCTGCTCCACCACCTTCA
Found at i:27842 original size:7 final size:7
Alignment explanation
Indices: 27830--27893 Score: 128
Period size: 7 Copynumber: 9.1 Consensus size: 7
27820 GACTTCCAAG
27830 GAAGTGA
1 GAAGTGA
27837 GAAGTGA
1 GAAGTGA
27844 GAAGTGA
1 GAAGTGA
27851 GAAGTGA
1 GAAGTGA
27858 GAAGTGA
1 GAAGTGA
27865 GAAGTGA
1 GAAGTGA
27872 GAAGTGA
1 GAAGTGA
27879 GAAGTGA
1 GAAGTGA
27886 GAAGTGA
1 GAAGTGA
27893 G
1 G
27894 CGATGGACAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 57 1.00
ACGTcount: A:0.42, C:0.00, G:0.44, T:0.14
Consensus pattern (7 bp):
GAAGTGA
Found at i:28290 original size:22 final size:21
Alignment explanation
Indices: 28256--28322 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
28246 TTATAATTTA
28256 TTAAATGTA-TTATATTAGTATT
1 TTAAAT-TATTTATATTA-TATT
*
28278 TTAAATTATTTATCTTA-ATT
1 TTAAATTATTTATATTATATT
* *
28298 TTAAAATATTT-TAATATTATT
1 TTAAATTATTTATATTA-TATT
28319 TTAA
1 TTAA
28323 CTTAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.08
20 13 0.34
21 9 0.24
22 13 0.34
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (21 bp):
TTAAATTATTTATATTATATT
Found at i:28345 original size:28 final size:30
Alignment explanation
Indices: 28314--28385 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
28304 TATTTTAATA
*
28314 TTATTTTAACTTAAAA-A-ATACTTCATTC
1 TTATCTTAACTTAAAACATATACTTCATTC
* * *
28342 TTATCTAAACTTAAAACATATATTTTATTC
1 TTATCTTAACTTAAAACATATACTTCATTC
*
28372 TTATCTTATCTTAA
1 TTATCTTAACTTAA
28386 CTTAATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 14 0.39
29 1 0.03
30 21 0.58
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.49
Consensus pattern (30 bp):
TTATCTTAACTTAAAACATATACTTCATTC
Found at i:28385 original size:30 final size:28
Alignment explanation
Indices: 28287--28385 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
28277 TTTAAATTAT
** * *
28287 TTATCTTAA-TTTTAAAATATTTTAATA
1 TTATCTTAACTTAAAAAATATTTTATTC
* * *
28314 TTATTTTAACTTAAAAAATACTTCATTC
1 TTATCTTAACTTAAAAAATATTTTATTC
*
28342 TTATCTAAACTTAAAACATATATTTTATTC
1 TTATCTTAACTTAAAA-A-ATATTTTATTC
*
28372 TTATCTTATCTTAA
1 TTATCTTAACTTAA
28386 CTTAATATAT
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
27 8 0.14
28 26 0.46
29 1 0.02
30 21 0.38
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (28 bp):
TTATCTTAACTTAAAAAATATTTTATTC
Found at i:28502 original size:30 final size:30
Alignment explanation
Indices: 28466--28531 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
28456 TATTTTTAAC
*
28466 ATATATTTAATAAGTTAA-AGTAAAAATAAA
1 ATATATTTAATAAATTAATA-TAAAAATAAA
*
28496 ATATATTTAATAAATTAATATAAGAATAAA
1 ATATATTTAATAAATTAATATAAAAATAAA
28526 ATATAT
1 ATATAT
28532 ATTTAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (30 bp):
ATATATTTAATAAATTAATATAAAAATAAA
Found at i:28759 original size:21 final size:21
Alignment explanation
Indices: 28710--28760 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
28700 TATGACTATT
28710 GCAATGCGATTTTCCAATTTC
1 GCAATGCGATTTTCCAATTTC
**
28731 GCGTTGCGATTTTCTCAA-TTC
1 GCAATGCGATTTTC-CAATTTC
28752 GCAATGCGA
1 GCAATGCGA
28761 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (21 bp):
GCAATGCGATTTTCCAATTTC
Found at i:28775 original size:20 final size:21
Alignment explanation
Indices: 28750--28801 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
28740 TTTTCTCAAT
*
28750 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
28770 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
28791 TCGCAATGCGA
1 TCGCAATGCGA
28802 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:28815 original size:20 final size:20
Alignment explanation
Indices: 28790--28924 Score: 155
Period size: 20 Copynumber: 6.7 Consensus size: 20
28780 AATTTGGAAA
*
28790 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
28810 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
28831 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
28851 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
28871 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
28891 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
28911 ATCGCAACGAGATA
1 ATCGCAACGCGATA
28925 ATACAGAATC
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
19 2 0.02
20 83 0.81
21 15 0.15
22 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:28863 original size:41 final size:42
Alignment explanation
Indices: 28787--28899 Score: 151
Period size: 41 Copynumber: 2.8 Consensus size: 42
28777 GCGAATTTGG
* *
28787 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT-AC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
*
28828 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
** *
28870 --TTTCGCAACGCGATTCTGACTTTCGCAACG
1 AAAATCGCAACGCGATACTGACTTTCGCAACG
28900 AGATTCTGAC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
40 27 0.42
41 36 0.55
42 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
Found at i:29693 original size:24 final size:24
Alignment explanation
Indices: 29666--29719 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
29656 GTATTCGAAA
*
29666 TTTGATCTTGGTCAATA-TCCGGAC
1 TTTGATATTGGTCAATACT-CGGAC
*
29690 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACTCGGAC
29714 TTTGAT
1 TTTGAT
29720 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCGGAC
Found at i:33910 original size:21 final size:21
Alignment explanation
Indices: 33881--33941 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
33871 GAATGGTGGG
*
33881 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
33902 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
33923 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
33942 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:33938 original size:42 final size:41
Alignment explanation
Indices: 33854--33945 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 41
33844 CCTCTTCAAC
* * *
33854 GATGACAGTGGCCTCTTGAATGGTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGGTGGAGGGGACTCTTGAGG
* *
33895 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACG-GTGGAGGGGACTCTTGAGG
33937 GATGACAGG
1 GATGACAGG
33946 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 19 0.43
42 25 0.57
ACGTcount: A:0.21, C:0.14, G:0.42, T:0.23
Consensus pattern (41 bp):
GATGACAGGGGCCTCTTGAACGGTGGAGGGGACTCTTGAGG
Found at i:34430 original size:19 final size:19
Alignment explanation
Indices: 34352--34430 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
34342 ATGGCTATCA
*
34352 CAATGCGAAATGAAAATCG
1 CAATGCGAAATCAAAATCG
34371 CAA--CG--A-CAAAATCG
1 CAATGCGAAATCAAAATCG
*
34385 CAATGCGAAATGAAAATCG
1 CAATGCGAAATCAAAATCG
*
34404 CAACGCGAAA-CACAAATCG
1 CAATGCGAAATCA-AAATCG
*
34423 CATTGCGA
1 CAATGCGA
34431 TTTTCATTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
14 10 0.21
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 31 0.65
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.13
Consensus pattern (19 bp):
CAATGCGAAATCAAAATCG
Found at i:34479 original size:20 final size:20
Alignment explanation
Indices: 34456--34503 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
34446 GCGATTTTGT
34456 CGTTGCGATA-TCCATTTCCG
1 CGTTGCGATAGT-CATTTCCG
*
34476 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
*
34496 TGTTGCGA
1 CGTTGCGA
34504 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:35061 original size:18 final size:18
Alignment explanation
Indices: 35038--35085 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
35028 CGGGTCGATC
35038 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
35056 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
35074 AGGTGATGGCTC
1 AGGTGATGGCTC
35086 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:36457 original size:20 final size:20
Alignment explanation
Indices: 36434--36471 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
36424 AACACAAAAA
36434 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATT
36454 TGACTATCGCAACGCGAA
1 TGACTATCGCAACGCGAA
36472 CCTAAAATCG
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:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATT
Found at i:36742 original size:22 final size:22
Alignment explanation
Indices: 36716--36759 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
36706 GATGGAGATA
36716 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
36738 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
36760 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:36969 original size:20 final size:20
Alignment explanation
Indices: 36946--37052 Score: 108
Period size: 20 Copynumber: 5.3 Consensus size: 20
36936 TATTATCTAG
* *
36946 TTGCAAAAGTCAGTATCGCT
1 TTGCGAAAGTCAGTATCGCA
*
36966 TTGCGAAAGTAAGTATCGCA
1 TTGCGAAAGTCAGTATCGCA
*
36986 TTGCGAAAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCA
** * *
37006 TTGCGATTTTGT-ATTATCGCG
1 TTGCGA--AAGTCAGTATCGCA
*
37027 TTGCGATAGTCAGTATCGCA
1 TTGCGAAAGTCAGTATCGCA
37047 TTGCGA
1 TTGCGA
37053 TTTTCCCAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 3 0.04
20 54 0.74
21 14 0.19
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TTGCGAAAGTCAGTATCGCA
Found at i:37056 original size:41 final size:41
Alignment explanation
Indices: 36919--37054 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
36909 CGCTTTGAAA
** *
36919 ATCGCATTGCGATTATGTATTATCTAGTTGCAAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
36960 ATCGCTTTGCGA--AAGTAAGTATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * *
37000 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
37041 ATCGCATTGCGATT
1 ATCGCATTGCGATT
37055 TTCCCAATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 29 0.37
41 44 0.56
42 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:37067 original size:41 final size:41
Alignment explanation
Indices: 36979--37074 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
36969 CGAAAGTAAG
* * * ** *
36979 TATCGCATTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA
37020 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAA
37062 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
37075 TTACTTATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA
Found at i:37135 original size:21 final size:22
Alignment explanation
Indices: 37083--37135 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
37073 ATTTACTTAT
37083 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
37104 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
37125 TCGCATTGCGA
1 TCGCATTGCGA
37136 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:37366 original size:28 final size:28
Alignment explanation
Indices: 37333--37432 Score: 89
Period size: 30 Copynumber: 3.5 Consensus size: 28
37323 ATGTATATTT
37333 TTAAATA-AAAAAGTAAAATATTTTTAAA
1 TTAAATATAAAAA-TAAAATATTTTTAAA
* * *
37361 TTAAAT-TAATAATAAAATAAATTTAATAAG
1 TTAAATATAAAAATAAAAT--ATTT-TTAAA
*
37391 TT-AATATTAAAATAAAATATTTTTCAAA
1 TTAAATATAAAAATAAAATATTTTT-AAA
37419 TTAATATATAAAAA
1 TTAA-ATATAAAAA
37433 ATATTATGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
27 7 0.12
28 18 0.32
29 8 0.14
30 23 0.41
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (28 bp):
TTAAATATAAAAATAAAATATTTTTAAA
Found at i:37673 original size:10 final size:10
Alignment explanation
Indices: 37660--37731 Score: 54
Period size: 10 Copynumber: 6.5 Consensus size: 10
37650 TGAACGGAAG
37660 TAAACAAACA
1 TAAACAAACA
*
37670 TAAATAAACA
1 TAAACAAACA
37680 TAAACAAACGAA
1 TAAACAAAC--A
37692 CGTAAACAAACACAA
1 --TAAAC-AA-AC-A
**
37707 TAAATGAACA
1 TAAACAAACA
37717 TAAACAAACA
1 TAAACAAACA
37727 TAAAC
1 TAAAC
37732 GAACCTTCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 31 0.62
11 2 0.04
12 2 0.04
13 4 0.08
14 5 0.10
15 4 0.08
16 2 0.04
ACGTcount: A:0.65, C:0.18, G:0.04, T:0.12
Consensus pattern (10 bp):
TAAACAAACA
Found at i:37790 original size:23 final size:22
Alignment explanation
Indices: 37689--37787 Score: 78
Period size: 23 Copynumber: 4.5 Consensus size: 22
37679 ATAAACAAAC
*
37689 GAACGTAAACAAACACAATAAAT
1 GAACATAAAC-AACACAATAAAT
*
37712 GAACATAAACAA-AC-ATAAAC
1 GAACATAAACAACACAATAAAT
* * *
37732 GAACCTTCAAA-AACATAACAAAT
1 GAA-CAT-AAACAACACAATAAAT
*
37755 GAACATAATCGAACACAATAAAT
1 GAACATAAAC-AACACAATAAAT
*
37778 GAACGTAAAC
1 GAACATAAAC
37788 GAATGTAAAC
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
20 8 0.14
21 8 0.14
22 8 0.14
23 34 0.59
ACGTcount: A:0.59, C:0.19, G:0.08, T:0.14
Consensus pattern (22 bp):
GAACATAAACAACACAATAAAT
Found at i:37929 original size:16 final size:18
Alignment explanation
Indices: 37899--37935 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
37889 CATTTTCTTT
*
37899 AATTGATTTGTG-TTTAA
1 AATTGATTTGGGTTTTAA
37916 AATT-ATTTGGGTTTTAA
1 AATTGATTTGGGTTTTAA
37933 AAT
1 AAT
37936 ATTAATGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (18 bp):
AATTGATTTGGGTTTTAA
Found at i:41924 original size:13 final size:13
Alignment explanation
Indices: 41906--41930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41896 GATTATTCAT
41906 ATTTTTTAAATTC
1 ATTTTTTAAATTC
41919 ATTTTTTAAATT
1 ATTTTTTAAATT
41931 ATCAACTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTTTAAATTC
Found at i:45971 original size:21 final size:21
Alignment explanation
Indices: 45947--46079 Score: 64
Period size: 20 Copynumber: 6.5 Consensus size: 21
45937 CAGTTCCCAG
45947 AATCGCAACGCGATTATGAAT
1 AATCGCAACGCGATTATGAAT
*
45968 AATCGCAATGCGA-TA-GTACA-
1 AATCGCAACGCGATTATG-A-AT
** * **
45988 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGATTATGAAT
* *
46010 AATCGCAACTCGAATATGAA-
1 AATCGCAACGCGATTATGAAT
* **
46030 AATCACAACGCGAACAT--AT
1 AATCGCAACGCGATTATGAAT
* *
46049 AAATCGCAACGCGATTCTGACT
1 -AATCGCAACGCGATTATGAAT
46071 -ATCGCAACG
1 AATCGCAACG
46080 AGTATCCGTA
Statistics
Matches: 82, Mismatches: 20, Indels: 21
0.67 0.16 0.17
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 41 0.50
21 35 0.43
22 4 0.05
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (21 bp):
AATCGCAACGCGATTATGAAT
Found at i:46115 original size:20 final size:20
Alignment explanation
Indices: 46010--46244 Score: 208
Period size: 20 Copynumber: 11.7 Consensus size: 20
46000 GATTTTCCAT
* * *
46010 AATCGCAACTCGAATATGAA
1 AATCGCAACGCGAATACGTA
* * **
46030 AATCACAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
46050 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
46069 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
46091 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
46111 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATACGT-A
46132 AATCGCAACGTC-AATACGTA
1 AATCGCAACG-CGAATACGTA
*
46152 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
46172 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
46192 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
46212 AATCGCAACGCGAATACGTA
1 AATCGCAACGCGAATACGTA
46232 AATCGCAACGCGA
1 AATCGCAACGCGA
46245 TTTTTAAAGC
Statistics
Matches: 177, Mismatches: 29, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.01
19 4 0.02
20 131 0.74
21 39 0.22
22 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:46188 original size:40 final size:41
Alignment explanation
Indices: 46071--46243 Score: 235
Period size: 40 Copynumber: 4.3 Consensus size: 41
46061 GATTCTGACT
* * *
46071 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACGTAA
* * *
46112 ATCGCAACGAGAATACGTAAAATCGCAACGTC-AATACGTAA
1 ATCGCAACGCGTATCCGTAAAATCGCAACG-CGAATACGTAA
* *
46153 ATCGCAACGCGTATCTGT-AAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACGTAA
*
46193 ATCGCAATGCGTATCCGT-AAATCGCAACGCGAATACGTAA
1 ATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACGTAA
46233 ATCGCAACGCG
1 ATCGCAACGCG
46244 ATTTTTAAAG
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
40 67 0.57
41 49 0.42
42 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (41 bp):
ATCGCAACGCGTATCCGTAAAATCGCAACGCGAATACGTAA
Found at i:46772 original size:21 final size:21
Alignment explanation
Indices: 46712--46790 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
46702 TTCTAAACTT
46712 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
46732 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
** *
46752 ACTATCGTAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
46773 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
46791 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 29 0.58
21 21 0.42
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:46813 original size:19 final size:19
Alignment explanation
Indices: 46712--46833 Score: 83
Period size: 20 Copynumber: 6.5 Consensus size: 19
46702 TTCTAAACTT
**
46712 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
*
46732 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** * *
46752 ACTATCGTAACGAGAGAAATG
1 AAAATCGCAAC--GCGAAATG
46773 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
46787 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
46806 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
46825 AAAATCGCA
1 AAAATCGCA
46834 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 26 0.32
20 27 0.33
21 12 0.15
22 1 0.01
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:46851 original size:19 final size:19
Alignment explanation
Indices: 46829--46974 Score: 116
Period size: 19 Copynumber: 8.1 Consensus size: 19
46819 GAAACCAAAA
*
46829 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
46848 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
46867 TCGC-TACGCGA--TTC---
1 TCGCGT-TGCGATTTTCATT
*
46881 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
46900 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
46914 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
46933 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
46953 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
46973 TC
1 TC
46975 AACCAAATGA
Statistics
Matches: 100, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
14 17 0.17
15 1 0.01
16 5 0.05
17 5 0.05
18 1 0.01
19 38 0.38
20 32 0.32
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:46893 original size:14 final size:14
Alignment explanation
Indices: 46874--46925 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
46864 ATTTCGCTAC
46874 GCGATTCTCTCGTT
1 GCGATTCTCTCGTT
*
46888 GCGATTTTCATTTCGCGTT
1 GCGA--TTC---TCTCGTT
46907 GCGATTCTCTCGTT
1 GCGATTCTCTCGTT
46921 GCGAT
1 GCGAT
46926 AGTCATTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 15 0.48
16 3 0.10
17 3 0.10
19 10 0.32
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (14 bp):
GCGATTCTCTCGTT
Found at i:46893 original size:33 final size:33
Alignment explanation
Indices: 46851--46925 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
46841 TTTCATTTCG
46851 CGTTGCGATTTTAATTTCGC-TACGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCGT-CGCGATTCTCT
* *
46884 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCGTCGCGATTCTCT
46917 CGTTGCGAT
1 CGTTGCGAT
46926 AGTCATTTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 38 0.97
34 1 0.03
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCGTCGCGATTCTCT
Found at i:46932 original size:33 final size:34
Alignment explanation
Indices: 46874--46946 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 34
46864 ATTTCGCTAC
**
46874 GCGATTCTCTCGTTGCGATTTTCATTT-CGCGTT
1 GCGATTCTCTCGTTGCGATAGTCATTTCCGCGTT
46907 GCGATTCTCTCGTTGCGATAGTCATTTCCGCGTT
1 GCGATTCTCTCGTTGCGATAGTCATTTCCGCGTT
46941 GCGATT
1 GCGATT
46947 TTCATTCTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
33 25 0.68
34 12 0.32
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.41
Consensus pattern (34 bp):
GCGATTCTCTCGTTGCGATAGTCATTTCCGCGTT
Found at i:49009 original size:21 final size:21
Alignment explanation
Indices: 48985--49051 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
48975 TCATTCCTCG
48985 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
49006 AGAGACCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
49027 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
49048 AGAG
1 AGAG
49052 CCCAATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:50422 original size:14 final size:14
Alignment explanation
Indices: 50403--50438 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
50393 ATTGTTTAAT
50403 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
50417 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
50431 TGATTTGT
1 TGATTTGT
50439 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:50587 original size:33 final size:32
Alignment explanation
Indices: 50545--50638 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 32
50535 AAAAATGACT
* * *
50545 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
50578 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGACAAA
*
50611 ATCGCAACGCGAAACTAAAATCGCAACG
1 ATCGCAATGCGAAA-TAAAATCGCAACG
50639 CGAAACTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACAAA
Found at i:50660 original size:19 final size:19
Alignment explanation
Indices: 50577--50653 Score: 92
Period size: 19 Copynumber: 4.3 Consensus size: 19
50567 GCAACGAGAG
* *
50577 AATCGCAATGCGAAATTAA
1 AATCGCAACGCGAAACTAA
50596 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
50610 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
50629 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
50648 ATTCGC
1 AATCGC
50654 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 34 0.67
ACGTcount: A:0.45, C:0.25, G:0.16, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:50799 original size:33 final size:33
Alignment explanation
Indices: 50717--50799 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 33
50707 TCATTTCGCA
* *
50717 TTGCAATAGTCATTTCCGCGTTGCGATTTTCACG
1 TTGCAATAGTCATTT-CGCATTGCGATTCTCACG
* ** *
50751 TTGCTATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCAATAGTCATTTCGCATTGCGATTCTCACG
* *
50784 TTGCGATAGTAATTTC
1 TTGCAATAGTCATTTC
50800 CACGTTACGA
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
33 27 0.69
34 12 0.31
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (33 bp):
TTGCAATAGTCATTTCGCATTGCGATTCTCACG
Found at i:50856 original size:20 final size:20
Alignment explanation
Indices: 50783--50856 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
50773 CGATTCTCTC
* *
50783 GTTGCGATAGTAATTTCCAC
1 GTTGCGATAGTCATTTCCAT
* ***
50803 GTTACGATA-TACATTAAGAT
1 GTTGCGATAGT-CATTTCCAT
50823 GATTGCGA-ACGTCATTTCCAT
1 G-TTGCGATA-GTCATTTCCAT
50844 GTTGCGATAGTCA
1 GTTGCGATAGTCA
50857 AATGAATGCC
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
19 1 0.03
20 24 0.62
21 13 0.33
22 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCAT
Found at i:54365 original size:74 final size:75
Alignment explanation
Indices: 54267--54410 Score: 227
Period size: 74 Copynumber: 1.9 Consensus size: 75
54257 CAGATTCACA
*
54267 TTGCGATTTACGTATTCGCATTGCGATTTACGGATACGTATTACGA-TTTACGTATTCTCGTTGC
1 TTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCATTACGATTTTACGTATTCTCGTTGC
54331 GATTTCCGCG
66 GATTTCCGCG
* * * * *
54341 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGC
1 TTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCATTACGATTTTACGTATTCTCGTTGC
54406 GATTT
66 GATTT
54411 ACGAATACGC
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 41 0.65
75 22 0.35
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (75 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCATTACGATTTTACGTATTCTCGTTGC
GATTTCCGCG
Found at i:54392 original size:41 final size:40
Alignment explanation
Indices: 54242--54449 Score: 239
Period size: 41 Copynumber: 5.3 Consensus size: 40
54232 ATAGTCAGAA
* * * *
54242 TCTCGTTGCGATTTACAGATTCACATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTACGTAT
* * ** *
54282 TCGCATTGCGATTTACGGATACGTATTACGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTACGTAT
54322 TCTCGTTGCGATTT-C-----CGCGTTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTACGTAT
54356 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTAT
* * *
54397 TGTCGTTGCGATTTACGAATACGCGTTGCGATTTTACGGAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTAT
*
54438 ACTCGTTGCGAT
1 TCTCGTTGCGAT
54450 AATCAGAATC
Statistics
Matches: 144, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
34 30 0.21
35 1 0.01
39 1 0.01
40 55 0.38
41 57 0.40
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (40 bp):
TCTCGTTGCGATTTACGGATACGCGTTGCGATTTACGTAT
Found at i:54393 original size:21 final size:20
Alignment explanation
Indices: 54245--54449 Score: 154
Period size: 20 Copynumber: 10.4 Consensus size: 20
54235 GTCAGAATCT
* * *
54245 CGTTGCGATTTACAGATTCA
1 CGTTGCGATTTACGGATACG
* * *
54265 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATACG
*
54285 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
** * * * *
54305 TATTACGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
54325 CGTTGCGATTT-C-----CG
1 CGTTGCGATTTACGGATACG
* * *
54339 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
54359 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
54379 CGTTGCGATTTTACGTAT-TG
1 CGTTGCGA-TTTACGGATACG
*
54399 TCGTTGCGATTTACGAATACG
1 -CGTTGCGATTTACGGATACG
*
54420 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGGATACG
54441 CGTTGCGAT
1 CGTTGCGAT
54450 AATCAGAATC
Statistics
Matches: 150, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
14 12 0.08
15 1 0.01
19 1 0.01
20 101 0.67
21 35 0.23
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:54466 original size:41 final size:41
Alignment explanation
Indices: 54340--54471 Score: 135
Period size: 41 Copynumber: 3.2 Consensus size: 41
54330 CGATTTCCGC
* * * * *
54340 GTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGC
1 GTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGA
* ** * *
54380 GTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACGC
1 GTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGA
54421 GTTGCGATTTTACGGATACTCGTTGCGATAATCA-GAAT-CGA
1 GTTGCGATTTTACGGATACTCGTTGCGAT--TCACGAATACGA
54462 GTTGCGATTT
1 GTTGCGATTT
54472 ATATGTTCGC
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
40 7 0.09
41 69 0.84
42 4 0.05
43 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (41 bp):
GTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGA
Found at i:54466 original size:61 final size:61
Alignment explanation
Indices: 54340--54472 Score: 153
Period size: 61 Copynumber: 2.2 Consensus size: 61
54330 CGATTTCCGC
* * * * * * * *
54340 GTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTC
1 GTTGCGATTTACGAATACGCGTTGCGATTTACGGATACGCGTTGCGATATCACGAATCGTA
*
54401 GTTGCGATTTACGAATACGCGTTGCGATTTTACGGATACTCGTTGCGATAATCA-GAATCG-A
1 GTTGCGATTTACGAATACGCGTTGCGA-TTTACGGATACGCGTTGCGAT-ATCACGAATCGTA
54462 GTTGCGATTTA
1 GTTGCGATTTA
54473 TATGTTCGCG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
61 35 0.57
62 24 0.39
63 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (61 bp):
GTTGCGATTTACGAATACGCGTTGCGATTTACGGATACGCGTTGCGATATCACGAATCGTA
Found at i:54485 original size:20 final size:20
Alignment explanation
Indices: 54462--54510 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
54452 TCAGAATCGA
*
54462 GTTGCGATTTAT-ATGTTCGC
1 GTTGCGATTT-TCATATTCGC
54482 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTTCATATTCGC
54502 GTTGCGATT
1 GTTGCGATT
54511 ATGGAAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.45
Consensus pattern (20 bp):
GTTGCGATTTTCATATTCGC
Found at i:66631 original size:19 final size:20
Alignment explanation
Indices: 66609--66650 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
66599 AATGCGATTT
66609 TCCAAATT-CGTTGCGATAG
1 TCCAAATTCCGTTGCGATAG
*
66628 TCCAAGTTCGCGTTGCGATAG
1 TCCAAATTC-CGTTGCGATAG
66649 TC
1 TC
66651 TAAAATCGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
TCCAAATTCCGTTGCGATAG
Found at i:66659 original size:21 final size:21
Alignment explanation
Indices: 66617--66659 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
66607 TTTCCAAATT
**
66617 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAAATCG
*
66638 CGTTGCGATAGTCTAAAATCG
1 CGTTGCGATAGTCCAAAATCG
66659 C
1 C
66660 AACGACTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAAATCG
Found at i:67501 original size:21 final size:19
Alignment explanation
Indices: 67486--67565 Score: 88
Period size: 19 Copynumber: 4.0 Consensus size: 19
67476 AATCGCAACG
*
67486 CGAACTTCGACTATCGCAA
1 CGAACTTGGACTATCGCAA
67505 CGAACTTGGACTATCGCAA
1 CGAACTTGGACTATCGCAA
* * *
67524 CGAATTTGTAATAAATCGCAA
1 CGAACTTGGACT--ATCGCAA
67545 CGCGAACTTGGACTATCGCAA
1 --CGAACTTGGACTATCGCAA
67566 TAAATTTGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 27 0.54
21 14 0.28
23 9 0.18
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (19 bp):
CGAACTTGGACTATCGCAA
Found at i:67564 original size:42 final size:42
Alignment explanation
Indices: 67498--67649 Score: 141
Period size: 42 Copynumber: 3.7 Consensus size: 42
67488 AACTTCGACT
*
67498 ATCGCAA--CGAACTTGGACTATCGCAACGAATTTGTAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAATAA
**
67538 ATCGCAACGCGAACTTGGACTATCGCAATAAATTTGAAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAATAA
* * * ** ** * * *
67580 ATCGCAGCGCGAATTTGAAAAATCATAACGCGAACTTGGACT--
1 ATCGCAACGCGAACTTGGACTATCGCAA--CGAATTTGAAATAA
67622 ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTGGACTATCGCAA
67650 TGCGAATATG
Statistics
Matches: 86, Mismatches: 22, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
40 7 0.08
42 72 0.84
44 7 0.08
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAATAA
Found at i:67630 original size:21 final size:21
Alignment explanation
Indices: 67606--67655 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
67596 GAAAAATCAT
67606 AACGCGAACTTGGACTATCGC
1 AACGCGAACTTGGACTATCGC
67627 AACGCGAACTTGGACTATCGC
1 AACGCGAACTTGGACTATCGC
*
67648 AATGCGAA
1 AACGCGAA
67656 TATGTAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (21 bp):
AACGCGAACTTGGACTATCGC
Found at i:67647 original size:63 final size:61
Alignment explanation
Indices: 67449--67649 Score: 226
Period size: 61 Copynumber: 3.2 Consensus size: 61
67439 TGTTGTGATT
** * *
67449 TTGGACTATCGCAACGAATTTAAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAATTTGTAATAAATCACAACGCGAACTTGGACTATCGCAACGAAC
* ** *
67510 TTGGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTGGACTATCGCAATAAAT
1 TTGGACTATCGCAACGAATTTGTAATAAATCACAACGCGAACTTGGACTATCGCAACGAAC
* * * *
67571 TTGAAATAAATCGCAGCGCGAATTTG-AA-AAATCATAACGCGAACTTGGACTATCGCAACGCGA
1 TTGGACT--ATCGCA--ACGAATTTGTAATAAATCACAACGCGAACTTGGACTATCGCAA--CGA
67634 AC
60 AC
67636 TTGGACTATCGCAA
1 TTGGACTATCGCAA
67650 TGCGAATATG
Statistics
Matches: 117, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
61 60 0.51
63 40 0.34
64 2 0.02
65 15 0.13
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (61 bp):
TTGGACTATCGCAACGAATTTGTAATAAATCACAACGCGAACTTGGACTATCGCAACGAAC
Found at i:67655 original size:42 final size:43
Alignment explanation
Indices: 67477--67655 Score: 131
Period size: 42 Copynumber: 4.3 Consensus size: 43
67467 TTTAAAATAA
* *
67477 ATCGCAACGCGAACTTCGACT-ATCGCAA--CGAACTTGGACT
1 ATCGCAACGCGAACTTGGAATAATCGCAACGCGAACTTGGACT
* *
67517 ATCGCAA--CGAATTTGTAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGAAT-AATCGCAACGCGAACTTGGACT
** * * * * * **
67559 ATCGCAA--TAAATTTGAAATAAATCGCAGCGCGAATTTGAAAA
1 ATCGCAACGCGAACTTGGAAT-AATCGCAACGCGAACTTGGACT
** *
67601 ATCATAACGCGAACTTGGACT-ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGAATAATCGCAACGCGAACTTGGACT
*
67643 ATCGCAATGCGAA
1 ATCGCAACGCGAA
67656 TATGTAAATC
Statistics
Matches: 106, Mismatches: 27, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
38 8 0.08
40 14 0.13
42 77 0.73
44 7 0.07
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (43 bp):
ATCGCAACGCGAACTTGGAATAATCGCAACGCGAACTTGGACT
Found at i:69485 original size:37 final size:38
Alignment explanation
Indices: 69400--69485 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 38
69390 TTAAACTTTT
*
69400 TTTTATATTTTTAATTTTGTAAAAAAAATTATATAAATA
1 TTTTATA-ATTTAATTTTGTAAAAAAAATTATATAAATA
* *
69439 --TTATGAATTTAATTTTTTAAAGAAAA-TATATAAATA
1 TTTTAT-AATTTAATTTTGTAAAAAAAATTATATAAATA
69475 TTTTATAATTT
1 TTTTATAATTT
69486 GTAATATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
36 10 0.24
37 26 0.63
38 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (38 bp):
TTTTATAATTTAATTTTGTAAAAAAAATTATATAAATA
Found at i:73319 original size:7 final size:7
Alignment explanation
Indices: 73307--73340 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
73297 CTAGCTGGAT
73307 AAAAAAG
1 AAAAAAG
73314 AAAAAAG
1 AAAAAAG
73321 AAAAAAG
1 AAAAAAG
*
73328 AAACAAG
1 AAAAAAG
73335 ATAAAA
1 A-AAAA
73341 TGGATAGAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 21 0.88
8 3 0.12
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:77715 original size:30 final size:30
Alignment explanation
Indices: 77681--77742 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
77671 TCCTGATTGC
* *
77681 GCTCCTACCTAGTTTCTTTG-ATTCACGGTT
1 GCTCCTACCTACTTTC-TTGAATTCACCGTT
*
77711 GCTCCTACTTACTTTCTTGAATTCACCGTT
1 GCTCCTACCTACTTTCTTGAATTCACCGTT
77741 GC
1 GC
77743 AGAGGAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.42
Consensus pattern (30 bp):
GCTCCTACCTACTTTCTTGAATTCACCGTT
Found at i:80119 original size:44 final size:44
Alignment explanation
Indices: 80056--80146 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
80046 CTGTTGATCG
80056 CAACCAGCATTTTAAAGTTAAAGATAACTTCCTAAGGGCACCAC
1 CAACCAGCATTTTAAAGTTAAAGATAACTTCCTAAGGGCACCAC
80100 CAACCAGCATTTTAAAGTTAAAGATAACTTCCTAAGGGCACCAC
1 CAACCAGCATTTTAAAGTTAAAGATAACTTCCTAAGGGCACCAC
80144 CAA
1 CAA
80147 ACAATCTGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.22
Consensus pattern (44 bp):
CAACCAGCATTTTAAAGTTAAAGATAACTTCCTAAGGGCACCAC
Found at i:91008 original size:16 final size:16
Alignment explanation
Indices: 90987--91017 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
90977 ATGGAGTTTT
*
90987 AAAAAAATATATAAAG
1 AAAAAAATAAATAAAG
91003 AAAAAAATAAATAAA
1 AAAAAAATAAATAAA
91018 ATTCGTCATG
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:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAAAAATAAATAAAG
Found at i:91810 original size:21 final size:21
Alignment explanation
Indices: 91784--91829 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
91774 AATCCTTGTC
* *
91784 TGATATAACATTGGAATGAAG
1 TGATATAACACTGAAATGAAG
*
91805 TGATATAATACTGAAATGAAG
1 TGATATAACACTGAAATGAAG
91826 TGAT
1 TGAT
91830 TAGGCACTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.30
Consensus pattern (21 bp):
TGATATAACACTGAAATGAAG
Found at i:92173 original size:32 final size:32
Alignment explanation
Indices: 92137--92206 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
92127 AAATGTCATT
* *
92137 TTTCTGAAATGAAGTAATATATCACTTAAAAG
1 TTTCTAAAATGAAGTAATATATCACTAAAAAG
* *
92169 TTTCTAAAATGAAGTGATATCTCACTAAAAAG
1 TTTCTAAAATGAAGTAATATATCACTAAAAAG
92201 TTTCTA
1 TTTCTA
92207 TCACTGAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (32 bp):
TTTCTAAAATGAAGTAATATATCACTAAAAAG
Found at i:92916 original size:20 final size:20
Alignment explanation
Indices: 92893--92959 Score: 134
Period size: 20 Copynumber: 3.4 Consensus size: 20
92883 GCTTGGATAG
92893 GTGTTCTAACCCTTCTTCAA
1 GTGTTCTAACCCTTCTTCAA
92913 GTGTTCTAACCCTTCTTCAA
1 GTGTTCTAACCCTTCTTCAA
92933 GTGTTCTAACCCTTCTTCAA
1 GTGTTCTAACCCTTCTTCAA
92953 GTGTTCT
1 GTGTTCT
92960 CAACTTGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.18, C:0.28, G:0.12, T:0.42
Consensus pattern (20 bp):
GTGTTCTAACCCTTCTTCAA
Done.