Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008003.1 Hibiscus syriacus cultivar Beakdansim tig00110462_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: 3297763
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 14
Found at i:2198516 original size:94 final size:93
Alignment explanation
Indices: 2198329--2198702 Score: 585
Period size: 94 Copynumber: 4.0 Consensus size: 93
2198319 GATTGCTTAA
* *
2198329 TAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TG--TTCATTAACACTGTGAAGTTAGTAT
1 TAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
2198390 TTGTCTTTTGTTTTATCTTTTGGTTGAAG
66 TTGTC-TTTGTTTTATCTTTTGGTTGAAG
2198419 TAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
1 TAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
2198484 TTGTCTTTGTTTTATCTTTTGGTTGAAAG
66 TTGTCTTTGTTTTATCTTTTGGTTG-AAG
*
2198513 TAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
1 TAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
* * *
2198578 TTGTCTTTATTTTGTCTTTTGGTCGAAAG
66 TTGTCTTTGTTTTATCTTTTGGTTG-AAG
* * * * *
2198607 TAAATTTGTTCGTTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAATACTTTGAAGTTAGTAT
1 TAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
*
2198672 TTGTCTTTGTTTTGTCTTTTGGTTGAAG
66 TTGTCTTTGTTTTATCTTTTGGTTGAAG
2198700 TAA
1 TAA
2198703 TGCAATCCAT
Statistics
Matches: 267, Mismatches: 12, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
90 33 0.12
92 2 0.01
93 26 0.10
94 206 0.77
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (93 bp):
TAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTAT
TTGTCTTTGTTTTATCTTTTGGTTGAAG
Found at i:2198820 original size:19 final size:19
Alignment explanation
Indices: 2198793--2198869 Score: 92
Period size: 19 Copynumber: 4.3 Consensus size: 19
2198783 TCTTTCGGTT
*
2198793 GAAATGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
2198812 GAAACGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGC
2198829 G--AC-AAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
2198845 GAAACCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
2198865 GAAAC
1 GAAAC
2198870 TATAATCGAG
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 2 0.04
17 2 0.04
18 1 0.02
19 17 0.33
20 17 0.33
ACGTcount: A:0.49, C:0.26, G:0.18, T:0.06
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:2198841 original size:33 final size:34
Alignment explanation
Indices: 2198799--2198863 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
2198789 GGTTGAAATG
*
2198799 AAAATCGCAACGCGAAA-CGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAAATCGCAACGAC
2198832 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAAATCGCAACGCGAAACCAAAAATCGCAACG
2198864 CGAAACTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.49, C:0.28, G:0.17, T:0.06
Consensus pattern (34 bp):
AAAATCGCAACGCGAAACCAAAAATCGCAACGAC
Found at i:2198857 original size:20 final size:18
Alignment explanation
Indices: 2198799--2198869 Score: 87
Period size: 20 Copynumber: 4.0 Consensus size: 18
2198789 GGTTGAAATG
2198799 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
2198817 GAAAATCGCAA--CG--AC
1 -AAAATCGCAACGCGAAAC
2198832 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-C
2198851 AAAAATCGCAACGCGAAAC
1 -AAAATCGCAACGCGAAAC
2198870 TATAATCGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
14 10 0.22
15 2 0.04
16 2 0.04
17 2 0.04
18 1 0.02
19 12 0.26
20 17 0.37
ACGTcount: A:0.49, C:0.28, G:0.17, T:0.06
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAC
Found at i:2198921 original size:33 final size:33
Alignment explanation
Indices: 2198879--2198971 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2198869 CTATAATCGA
* *
2198879 GTTGCGATTTTAATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTTATTTCGCGTTGCGATTCTCTC
2198912 GTTGCGATTTTTATTTCGCGTTGCGATTCTCTC
1 GTTGCGATTTTTATTTCGCGTTGCGATTCTCTC
2198945 GTTGCGATTTTTATTTCGCGTTGCGAT
1 GTTGCGATTTTTATTTCGCGTTGCGAT
2198972 AGTCATTTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
GTTGCGATTTTTATTTCGCGTTGCGATTCTCTC
Found at i:2198935 original size:19 final size:19
Alignment explanation
Indices: 2198911--2198971 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
2198901 GCGATTCTCT
2198911 CGTTGCGATTTTTATTTCG
1 CGTTGCGATTTTTATTTCG
* *
2198930 CGTTGCGA----T-TCTCT
1 CGTTGCGATTTTTATTTCG
2198944 CGTTGCGATTTTTATTTCG
1 CGTTGCGATTTTTATTTCG
2198963 CGTTGCGAT
1 CGTTGCGAT
2198972 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
18 1 0.03
19 20 0.61
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTTATTTCG
Found at i:2199472 original size:21 final size:21
Alignment explanation
Indices: 2199448--2199514 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2199438 TCATTCCTCG
2199448 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2199469 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2199490 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2199511 AGAG
1 AGAG
2199515 CCCGATTCAC
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:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2199472 original size:42 final size:42
Alignment explanation
Indices: 2199407--2199514 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 42
2199397 CATCCCTTAG
* * * * *
2199407 GAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCG-A
1 GAGTCCCCTCCCACCGTTCAAGAGGCCACTATCA-TCCTCGAA
* * *
2199449 GAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCGTTGAA
1 GAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCCTCGAA
*
2199491 GAGGT-CCCTCCCACCATTCAAGAG
1 GA-GTCCCCTCCCACCGTTCAAGAG
2199515 CCCGATTCAC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 4 0.07
42 49 0.89
43 2 0.04
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.22
Consensus pattern (42 bp):
GAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCCTCGAA
Found at i:2201050 original size:19 final size:19
Alignment explanation
Indices: 2200982--2201043 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2200972 AAAAATGACT
*
2200982 ATCGCAATGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
2201001 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
2201020 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
*
2201039 TTCGC
1 ATCGC
2201044 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 39 0.98
20 1 0.03
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:2201061 original size:19 final size:19
Alignment explanation
Indices: 2201039--2201156 Score: 94
Period size: 19 Copynumber: 6.7 Consensus size: 19
2201029 CGAAACTAAA
2201039 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2201058 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2201073 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2201091 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2201106 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
2201124 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
2201143 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2201157 AGACATTAAG
Statistics
Matches: 76, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
14 18 0.24
16 6 0.08
17 6 0.08
19 36 0.47
20 10 0.13
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2201083 original size:14 final size:14
Alignment explanation
Indices: 2201064--2201118 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2201054 TCATTTCGCA
2201064 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
2201078 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
2201095 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
2201111 TTGCGATT
1 TTGCGATT
2201119 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2201085 original size:33 final size:33
Alignment explanation
Indices: 2201043--2201136 Score: 188
Period size: 33 Copynumber: 2.8 Consensus size: 33
2201033 ACTAAATTCG
2201043 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2201076 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2201109 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2201137 AGTCATTTCC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:2201155 original size:20 final size:20
Alignment explanation
Indices: 2201109--2201202 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
2201099 GCGATTCTCT
**
2201109 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
2201128 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
2201148 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
2201167 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
2201189 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
2201203 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:2203705 original size:24 final size:24
Alignment explanation
Indices: 2203671--2203724 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2203661 CTGAAAAATC
2203671 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2203695 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2203719 ATCAAA
1 ATCAAA
2203725 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2203738 original size:24 final size:24
Alignment explanation
Indices: 2203671--2203738 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2203661 CTGAAAAATC
* * *
2203671 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2203695 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2203719 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2203739 TAATACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2204611 original size:21 final size:21
Alignment explanation
Indices: 2204587--2204655 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
2204577 AGAATCTCGT
2204587 TGCGATTTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
2204608 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
2204629 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
*
2204649 TGAGATT
1 TGCGATT
2204656 AAATCACAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:2204643 original size:20 final size:20
Alignment explanation
Indices: 2204587--2204656 Score: 95
Period size: 20 Copynumber: 3.4 Consensus size: 20
2204577 AGAATCTCGT
2204587 TGCGATTTACGTAAATCGCAA
1 TGCGA-TTACGTAAATCGCAA
* *
2204608 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
2204629 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
*
2204649 TGAGATTA
1 TGCGATTA
2204657 AATCACAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 21 0.49
21 21 0.49
22 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:2205132 original size:30 final size:30
Alignment explanation
Indices: 2205066--2205161 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
2205056 TACTTAGCAC
* * * *
2205066 AAAAAATAATTA-ATTAATA-AAGTTAAAT
1 AAAAAATAATTATATAAATATTATTTTAAT
*
2205094 AAATAATAATTATATAAATATTATTTTAAT
1 AAAAAATAATTATATAAATATTATTTTAAT
* * *
2205124 AAAAAATAA-TATTTATATAATTATATTAAT
1 AAAAAATAATTATATAAAT-ATTATTTTAAT
*
2205154 ATAAAATA
1 AAAAAATA
2205162 TAATAACTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
28 11 0.20
29 13 0.24
30 31 0.56
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (30 bp):
AAAAAATAATTATATAAATATTATTTTAAT
Found at i:2210080 original size:17 final size:15
Alignment explanation
Indices: 2210044--2210074 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2210034 AAATTCTAAA
2210044 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
2210059 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
2210074 T
1 T
2210075 TTATTTGTTG
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:2213618 original size:18 final size:18
Alignment explanation
Indices: 2213595--2213655 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
2213585 TAAAGCTCCA
*
2213595 AAGCAAGCTAACGGGGAG
1 AAGCAAGATAACGGGGAG
*
2213613 AAGCAAGATAACGAGGAG
1 AAGCAAGATAACGGGGAG
*
2213631 AAGCAAGATAACGGGAAG
1 AAGCAAGATAACGGGGAG
2213649 AATGCAA
1 AA-GCAA
2213656 CAACTCTAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 34 0.89
19 4 0.11
ACGTcount: A:0.48, C:0.13, G:0.33, T:0.07
Consensus pattern (18 bp):
AAGCAAGATAACGGGGAG
Found at i:2214147 original size:2 final size:2
Alignment explanation
Indices: 2214140--2214164 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2214130 ATAAAAGGTT
2214140 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 T
2214165 GTGTTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2215449 original size:27 final size:29
Alignment explanation
Indices: 2215390--2215449 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
2215380 TATATTAAAA
2215390 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
2215419 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
2215445 AAATA
1 AAATA
2215450 GTAAAGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 1 0.04
27 12 0.43
28 15 0.54
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.47
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:2215607 original size:18 final size:18
Alignment explanation
Indices: 2215584--2215638 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
2215574 AATAATTATT
2215584 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
2215602 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
2215614 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
2215631 TAAATTAG
1 TAAATTAG
2215639 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:2215692 original size:21 final size:21
Alignment explanation
Indices: 2215666--2215705 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2215656 GATAATGAGT
2215666 TTGTTAGTTTAAATTATATTA
1 TTGTTAGTTTAAATTATATTA
*
2215687 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAATTATAT
2215706 CATATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAATTATATTA
Found at i:2215970 original size:15 final size:15
Alignment explanation
Indices: 2215921--2215971 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2215911 AAAAATCGTT
*
2215921 TATTAGTTTAAGTTAA
1 TATTAGTTAAAGTT-A
**
2215937 TATTAAATAATAGTT-
1 TATTAGTTAA-AGTTA
2215952 TATTAGTTAAAGTTA
1 TATTAGTTAAAGTTA
2215967 TATTA
1 TATTA
2215972 AAGAATAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 4 0.14
15 13 0.46
16 7 0.25
17 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (15 bp):
TATTAGTTAAAGTTA
Found at i:2215970 original size:30 final size:29
Alignment explanation
Indices: 2215885--2216011 Score: 108
Period size: 31 Copynumber: 4.4 Consensus size: 29
2215875 TTTAGTTAAT
*
2215885 TAGTTTTTTAGTAGTAAA-TTATAATTAAAAA
1 TAGTTTATTAGT--TAAAGTTAT-ATTAAAAA
* *
2215916 TCGTTTATTAGTTTAAGTTAATATTAAATAA
1 TAGTTTATTAGTTAAAGTT-ATATTAAA-AA
2215947 TAGTTTATTAGTTAAAGTTATATT---AA
1 TAGTTTATTAGTTAAAGTTATATTAAAAA
*
2215973 -AG---AATAGTTAAAGTTATATTAAAGAA
1 TAGTTTATTAGTTAAAGTTATATTAAA-AA
2215999 TAGTTTATTAGTT
1 TAGTTTATTAGTT
2216012 GTTTAAGGGA
Statistics
Matches: 78, Mismatches: 7, Indels: 23
0.72 0.06 0.21
Matches are distributed among these distances:
22 17 0.22
25 2 0.03
26 4 0.05
27 2 0.03
29 3 0.04
30 19 0.24
31 31 0.40
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.46
Consensus pattern (29 bp):
TAGTTTATTAGTTAAAGTTATATTAAAAA
Found at i:2215974 original size:11 final size:11
Alignment explanation
Indices: 2215958--2215996 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2215948 AGTTTATTAG
2215958 TTAAAGTTATA
1 TTAAAGTTATA
*
2215969 TTAAAG-AATA
1 TTAAAGTTATA
2215979 GTTAAAGTTATA
1 -TTAAAGTTATA
2215991 TTAAAG
1 TTAAAG
2215997 AATAGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (11 bp):
TTAAAGTTATA
Found at i:2215982 original size:22 final size:22
Alignment explanation
Indices: 2215955--2216003 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
2215945 AATAGTTTAT
2215955 TAGTTAAAGTTATATTAAAGAA
1 TAGTTAAAGTTATATTAAAGAA
2215977 TAGTTAAAGTTATATTAAAGAA
1 TAGTTAAAGTTATATTAAAGAA
2215999 TAGTT
1 TAGTT
2216004 TATTAGTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (22 bp):
TAGTTAAAGTTATATTAAAGAA
Found at i:2216066 original size:8 final size:8
Alignment explanation
Indices: 2216053--2216083 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2216043 TTTAAAAAGT
2216053 TTAGTTTG
1 TTAGTTTG
2216061 TTAGTTTG
1 TTAGTTTG
*
2216069 TTAGTTTA
1 TTAGTTTG
2216077 TTAGTTT
1 TTAGTTT
2216084 AATATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (8 bp):
TTAGTTTG
Found at i:2217002 original size:64 final size:64
Alignment explanation
Indices: 2216929--2217152 Score: 213
Period size: 64 Copynumber: 3.5 Consensus size: 64
2216919 TGTTTGAATG
* * **
2216929 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
2216992 A
64 A
* * **
2216993 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* ** ** * * ** *
2217057 TGCATCGATGCATAAGG-AGTGCATCGATACATCCCAGCAATAATACTATATCGAATACCTTTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
*
2217121 TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCAT
2217153 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
63 1 0.01
64 123 0.93
65 8 0.06
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:2217480 original size:12 final size:12
Alignment explanation
Indices: 2217463--2217497 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
2217453 ATATATGTTC
2217463 ATGTGATATGAT
1 ATGTGATATGAT
2217475 ATGTGATATGAT
1 ATGTGATATGAT
2217487 ATGTGATATGA
1 ATGTGATATGA
2217498 GAACATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:2217660 original size:15 final size:15
Alignment explanation
Indices: 2217642--2217674 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2217632 GAGGGTATAA
2217642 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
2217657 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
2217672 TAG
1 TAG
2217675 GAGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:2223815 original size:64 final size:64
Alignment explanation
Indices: 2223732--2223952 Score: 218
Period size: 64 Copynumber: 3.5 Consensus size: 64
2223722 TGTTTGAATG
* ** ** *
2223732 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 TGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATACAATTC
2223795 A
64 A
* **
2223796 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATACAATTGG
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATACAATTCA
* * * ** ** *
2223860 TGCATCGATGAATATGGAGTGCATCGATGCATCCCAGCAATAAT---ACATCGAATACCTTTTA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATACAATTCA
* *
2223921 TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAGTAGTGCATCGATGCAT
2223953 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
61 40 0.30
64 86 0.65
65 6 0.05
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATACAATTCA
Found at i:2224330 original size:28 final size:29
Alignment explanation
Indices: 2224287--2224359 Score: 123
Period size: 28 Copynumber: 2.6 Consensus size: 29
2224277 TGATATGAAG
2224287 TGACATGAGCTACATGATCAC-AGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
2224315 TGACATGAGCTCCATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
2224344 TGACATGAG-TACATGA
1 TGACATGAGCTACATGA
2224360 ACATGAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 26 0.62
29 16 0.38
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:2226195 original size:21 final size:21
Alignment explanation
Indices: 2226169--2226221 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2226159 GTTACACCAT
2226169 TGATCAATTTTTCTTTTGTTG
1 TGATCAATTTTTCTTTTGTTG
2226190 TGATCAATTTTTCTTTTGTTG
1 TGATCAATTTTTCTTTTGTTG
*
2226211 AGATCCAATTT
1 TGAT-CAATTT
2226222 GGGGATAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.19, C:0.11, G:0.13, T:0.57
Consensus pattern (21 bp):
TGATCAATTTTTCTTTTGTTG
Found at i:2227112 original size:59 final size:58
Alignment explanation
Indices: 2227006--2227154 Score: 200
Period size: 59 Copynumber: 2.6 Consensus size: 58
2226996 ACAATGATTT
* * * * *
2227006 TTAGTATCAAATCATT-ATTATTATAAT--TTCATTACTAGTAATCATTAGTAAATCA
1 TTAGTATCAAATAATTAAATATTATAATAAATCATTACTAATAATAATTAGTAAATCA
*
2227061 TTAGTATCAAATAATTAAATATTAATAATAAATCATTATTAATAATAATTAGTAAATCA
1 TTAGTATCAAATAATTAAATATT-ATAATAAATCATTACTAATAATAATTAGTAAATCA
2227120 TTAGTATCAAATAATTAAATATT-TAA-AAATCATTA
1 TTAGTATCAAATAATTAAATATTATAATAAATCATTA
2227155 ATAAATTCGA
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
55 15 0.18
56 14 0.17
57 8 0.10
59 47 0.56
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (58 bp):
TTAGTATCAAATAATTAAATATTATAATAAATCATTACTAATAATAATTAGTAAATCA
Found at i:2227300 original size:26 final size:26
Alignment explanation
Indices: 2227239--2227512 Score: 213
Period size: 26 Copynumber: 11.0 Consensus size: 26
2227229 ATTAGTAATA
* *
2227239 ATTATTAAATCATTATTATAA-AATC
1 ATTATTAAATCATTATTATAATCATT
* *
2227264 ATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATCATT
2227290 ATTATTAAATCATTA-T-T-ATCATT
1 ATTATTAAATCATTATTATAATCATT
*
2227313 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATCATT
* *
2227339 ATTACTAAATCATTATTATAATAATT
1 ATTATTAAATCATTATTATAATCATT
* * * *
2227365 ATTATAAAATCACTACTA-AATCATCAA
1 ATTATTAAATCATTATTATAATCAT--T
* *
2227392 ATCATTAAAT-ATTA--A-AGTC---
1 ATTATTAAATCATTATTATAATCATT
*
2227411 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATCATT
2227437 ATT-TCTAAATCATTATTA-AATCA-T
1 ATTAT-TAAATCATTATTATAATCATT
* *
2227461 AATATTAAAATCATTACTA-AATCATT
1 ATTATT-AAATCATTATTATAATCATT
* *
2227487 AAATATTAAAATCATTACTA-AATCAT
1 -ATTATT-AAATCATTATTATAATCAT
2227513 CAAATCATTA
Statistics
Matches: 207, Mismatches: 24, Indels: 34
0.78 0.09 0.13
Matches are distributed among these distances:
19 9 0.04
20 4 0.02
22 1 0.00
23 22 0.11
24 10 0.05
25 49 0.24
26 79 0.38
27 33 0.16
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.43
Consensus pattern (26 bp):
ATTATTAAATCATTATTATAATCATT
Found at i:2227304 original size:23 final size:23
Alignment explanation
Indices: 2227278--2227368 Score: 101
Period size: 23 Copynumber: 3.8 Consensus size: 23
2227268 CTAAATCATT
2227278 ATTATAATGATTATTATTAAATC
1 ATTATAATGATTATTATTAAATC
* *
2227301 ATTATTATCATTATTATTAAATC
1 ATTATAATGATTATTATTAAATC
*
2227324 ATTATTATAATGATTATTACTAAATC
1 ---ATTATAATGATTATTATTAAATC
* * *
2227350 ATTATTATAATAATTATTA
1 ATTATAATGATTATTATTA
2227369 TAAAATCACT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
23 36 0.64
26 20 0.36
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTATAATGATTATTATTAAATC
Found at i:2227324 original size:49 final size:49
Alignment explanation
Indices: 2227239--2227503 Score: 213
Period size: 49 Copynumber: 5.3 Consensus size: 49
2227229 ATTAGTAATA
* *
2227239 ATTATTAAATCATTATTATAAAATCATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTAT--AATTATTATTAAATCATTATTATAATGATT
*
2227290 ATTATTAAATCATTATTATCATTATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATTATTATTAAATCATTATTATAATGATT
* * * * * *
2227339 ATTACTAAATCATTATTATAATAATTATTATAAAATCACTACTA-AATCATCAA
1 ATTATTAAATCATTA-T-T-ATAATTATTATTAAATCATTATTATAATGAT--T
* * *
2227392 ATCATTAAAT-ATTA--A-AGTCATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATTATTATTAAATCATTATTATAATGATT
* * *
2227437 ATT-TCTAAATCATTATTA-AATCATAATATTAAAATCATTACTA-AATCATT
1 ATTAT-TAAATCATTATTATAAT--TATTATT-AAATCATTATTATAATGATT
*
2227487 AAATATTAAAATCATTA
1 -ATTATT-AAATCATTA
2227504 CTAAATCATC
Statistics
Matches: 172, Mismatches: 26, Indels: 31
0.75 0.11 0.14
Matches are distributed among these distances:
44 1 0.01
45 7 0.04
46 21 0.12
47 6 0.03
48 3 0.02
49 41 0.24
50 12 0.07
51 39 0.23
52 34 0.20
53 8 0.05
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (49 bp):
ATTATTAAATCATTATTATAATTATTATTAAATCATTATTATAATGATT
Found at i:2227405 original size:98 final size:96
Alignment explanation
Indices: 2227313--2227496 Score: 289
Period size: 98 Copynumber: 1.9 Consensus size: 96
2227303 TATTATCATT
*
2227313 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATAATTAT-TATAAAATCA
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTA-AATAATAATAT-TAAAATCA
2227377 CTACTAAATCATCAAATCATTAAATATTAAAGTC
64 CTACTAAATCATCAAAT-ATTAAATATTAAAGTC
* * *
2227411 ATTATTAAATCATTATTATAATGATTATTTCTAAATCATTATTAAATCATAATATTAAAATCATT
1 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTAAATAATAATATTAAAATCACT
*
2227476 ACTAAATCATTAAATATTAAA
66 ACTAAATCATCAAATATTAAA
2227497 ATCATTACTA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
96 6 0.08
97 30 0.38
98 44 0.55
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (96 bp):
ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTAAATAATAATATTAAAATCACT
ACTAAATCATCAAATATTAAATATTAAAGTC
Found at i:2227498 original size:8 final size:9
Alignment explanation
Indices: 2227464--2227534 Score: 62
Period size: 8 Copynumber: 8.0 Consensus size: 9
2227454 AAATCATAAT
2227464 ATTAAAATC
1 ATTAAAATC
2227473 ATTACTAAATC
1 ATTA--AAATC
2227484 ATT-AAAT-
1 ATTAAAATC
2227491 ATTAAAATC
1 ATTAAAATC
2227500 ATTACTAAATC
1 ATTA--AAATC
*
2227511 A-TCAAATC
1 ATTAAAATC
2227519 ATT-AAAT-
1 ATTAAAATC
2227526 ATTAAAATC
1 ATTAAAATC
2227535 CTTATTAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
7 6 0.12
8 22 0.42
9 9 0.17
10 1 0.02
11 14 0.27
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAAATC
Found at i:2227508 original size:19 final size:18
Alignment explanation
Indices: 2227486--2227544 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
2227476 ACTAAATCAT
2227486 TAAATATTAAAATCATTA
1 TAAATATTAAAATCATTA
*
2227504 CTAAATCA-TCAAATCA-T-
1 -TAAAT-ATTAAAATCATTA
*
2227521 TAAATATTAAAATCCTTA
1 TAAATATTAAAATCATTA
2227539 TTAAAT
1 -TAAAT
2227545 TTTTTATGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
15 1 0.03
16 11 0.34
17 1 0.03
18 1 0.03
19 17 0.53
20 1 0.03
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAATATTAAAATCATTA
Found at i:2227512 original size:11 final size:11
Alignment explanation
Indices: 2227239--2227487 Score: 129
Period size: 11 Copynumber: 20.4 Consensus size: 11
2227229 ATTAGTAATA
2227239 ATTATTAAATC
1 ATTATTAAATC
2227250 ATTATTATAAAATC
1 ATTA-T-T-AAATC
*
2227264 ATTACTAAATC
1 ATTATTAAATC
*
2227275 ATTATTATAATGATT
1 ATTA-T-TAA--ATC
2227290 ATTATTAAATC
1 ATTATTAAATC
* *
2227301 ATTATTATCATT
1 ATTATTA-AATC
2227313 ATTATTAAATC
1 ATTATTAAATC
*
2227324 ATTATTATAATG
1 ATTATTA-AATC
2227336 ATTATTACTAAATC
1 ATTA-T--TAAATC
*
2227350 ATTATTATAATA
1 ATTATTA-AATC
2227362 ATTATTATAAAATC
1 ATTA-T-T-AAATC
* *
2227376 ACTACTAAATC
1 ATTATTAAATC
* * * * *
2227387 ATCAAATCATTA
1 AT-TATTAAATC
*
2227399 AATATTAAAGTC
1 ATTATTAAA-TC
2227411 ATTATTAAATC
1 ATTATTAAATC
*
2227422 ATTATTATAATG
1 ATTATTA-AATC
2227434 ATTATTTCTAAATC
1 ATTA--T-TAAATC
2227448 ATTATTAAATC
1 ATTATTAAATC
2227459 ATAATATTAAAATC
1 AT--TATT-AAATC
*
2227473 ATTACTAAATC
1 ATTATTAAATC
2227484 ATTA
1 ATTA
2227488 AATATTAAAA
Statistics
Matches: 183, Mismatches: 30, Indels: 50
0.70 0.11 0.19
Matches are distributed among these distances:
11 68 0.37
12 51 0.28
13 14 0.08
14 39 0.21
15 11 0.06
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:2227525 original size:27 final size:26
Alignment explanation
Indices: 2227443--2227524 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 26
2227433 GATTATTTCT
*
2227443 AAATCATTATTAAATCAT-AATATTA
1 AAATCATTACTAAATCATAAATATTA
2227468 AAATCATTACTAAATCATTAAATATTA
1 AAATCATTACTAAATCA-TAAATATTA
2227495 AAATCATTACTAAATCATCAAATCATTA
1 AAATCATTACTAAATCAT-AAAT-ATTA
2227523 AA
1 AA
2227525 TATTAAAATC
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
25 16 0.31
26 2 0.04
27 28 0.54
28 6 0.12
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (26 bp):
AAATCATTACTAAATCATAAATATTA
Found at i:2227542 original size:124 final size:120
Alignment explanation
Indices: 2227290--2227544 Score: 336
Period size: 124 Copynumber: 2.1 Consensus size: 120
2227280 TATAATGATT
* * * *
2227290 ATTATTAAATCATTATTATCATTATTATTAAATCATTATTATAATGATTATTACTAAATCATTAT
1 ATTATTAAATCATTATTATAATGATTATTAAATCATTATTATAATCATTATTAC-AAATCATTAC
* *
2227355 TATAATAATTATTATAAAATCACTACTAAATCATCAAATCATTAAATATTAAAGTC
65 TATAATAATTAATATAAAATCACTACTAAATCATCAAATCATTAAATATTAAAATC
2227411 ATTATTAAATCATTATTATAATGATTATTTCTAAATCATTATTA-AATCATAATATTA-AAATCA
1 ATTATTAAATCATTATTATAATGATTA--T-TAAATCATTATTATAATCAT--TATTACAAATCA
* *
2227474 TTACTA-AATCATTAAATATTAAAATCATTACTAAATCATCAAATCATTAAATATTAAAATC
61 TTACTATAATAATT-AATA-TAAAATCACTACTAAATCATCAAATCATTAAATATTAAAATC
*
2227535 CTTATTAAAT
1 ATTATTAAAT
2227545 TTTTTATGGT
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
121 25 0.21
122 6 0.05
123 20 0.17
124 62 0.53
125 5 0.04
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (120 bp):
ATTATTAAATCATTATTATAATGATTATTAAATCATTATTATAATCATTATTACAAATCATTACT
ATAATAATTAATATAAAATCACTACTAAATCATCAAATCATTAAATATTAAAATC
Found at i:2228387 original size:23 final size:23
Alignment explanation
Indices: 2228361--2228420 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2228351 CACCACAGCT
*
2228361 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
2228384 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
2228407 CATAGAATTGCACC
1 CGTAGAATTGCACC
2228421 ATTGTGCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:2231015 original size:48 final size:49
Alignment explanation
Indices: 2230936--2231145 Score: 356
Period size: 48 Copynumber: 4.3 Consensus size: 49
2230926 ATTACTAATA
* * *
2230936 ATTACTAAATCATTACTATCAAATCATTAAATATTAACAATAATTTAATT
1 ATTACT-AATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
2230986 ATTACTAATCATTACTACC-AATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
2231034 ATTACTAATCATTACTACCAAATCATTAAATA-TAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
2231082 ATTACTAATCATTACTACCAAATC-TTAAATATTAATAAT-ATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
2231129 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
2231146 ACATTATTAT
Statistics
Matches: 155, Mismatches: 3, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
47 32 0.21
48 93 0.60
49 24 0.15
50 6 0.04
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
Found at i:2234397 original size:26 final size:25
Alignment explanation
Indices: 2234375--2234425 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
2234365 ATTTGATATT
2234375 TAATGATTTAATAATAATATGATTTA
1 TAATGA-TTAATAATAATATGATTTA
*
2234401 GTAATGATTACTAATAAT-T-ATTTA
1 -TAATGATTAATAATAATATGATTTA
2234425 T
1 T
2234426 TATAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 1 0.04
24 5 0.22
25 1 0.04
26 10 0.43
27 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TAATGATTAATAATAATATGATTTA
Found at i:2234694 original size:17 final size:17
Alignment explanation
Indices: 2234672--2234709 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2234662 TTTTAAAAAA
2234672 AAACACTAA-ATATTTTT
1 AAACAC-AATATATTTTT
*
2234689 AAACACAATATTTTTTT
1 AAACACAATATATTTTT
2234706 AAAC
1 AAAC
2234710 GGAAATTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (17 bp):
AAACACAATATATTTTT
Found at i:2235256 original size:28 final size:28
Alignment explanation
Indices: 2235191--2235252 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
2235181 TTTATATAAT
2235191 ATAATATATAACTTAAACTAACAAACTAC
1 ATAAT-TATAACTTAAACTAACAAACTAC
2235220 TATAA-TATAACTTAAACTAACAAACTA-
1 -ATAATTATAACTTAAACTAACAAACTAC
2235247 ATAATT
1 ATAATT
2235253 TATACTAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
28 22 0.71
30 4 0.13
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.31
Consensus pattern (28 bp):
ATAATTATAACTTAAACTAACAAACTAC
Found at i:2235259 original size:21 final size:21
Alignment explanation
Indices: 2235226--2235274 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2235216 CTACTATAAT
2235226 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
2235247 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2235268 ATTAACT
1 A-TAACT
2235275 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2235741 original size:23 final size:23
Alignment explanation
Indices: 2235709--2235752 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2235699 GCTTGGCTGC
* *
2235709 AATCTCCCAGCTTTGGATGCAGG
1 AATCTCCCAGATATGGATGCAGG
*
2235732 AATCTTCCAGATATGGATGCA
1 AATCTCCCAGATATGGATGCA
2235753 ACGCATGCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (23 bp):
AATCTCCCAGATATGGATGCAGG
Found at i:2244703 original size:29 final size:29
Alignment explanation
Indices: 2244644--2244705 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
2244634 TTATAAGTCC
* * * *
2244644 TAAACACATAAATTCGTACATTCTTTAAA
1 TAAACACACAAATTCATAAATTATTTAAA
* *
2244673 TAAACACACAAATTTATAAATTATTTGAA
1 TAAACACACAAATTCATAAATTATTTAAA
2244702 TAAA
1 TAAA
2244706 GATAAAGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (29 bp):
TAAACACACAAATTCATAAATTATTTAAA
Found at i:2257278 original size:19 final size:19
Alignment explanation
Indices: 2257254--2257293 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2257244 TATGCACACA
2257254 TATAGGATTAAAATTCACT
1 TATAGGATTAAAATTCACT
2257273 TATAGGATTAAAATTCACT
1 TATAGGATTAAAATTCACT
2257292 TA
1 TA
2257294 CAATTAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (19 bp):
TATAGGATTAAAATTCACT
Found at i:2265137 original size:100 final size:100
Alignment explanation
Indices: 2264953--2265150 Score: 297
Period size: 100 Copynumber: 2.0 Consensus size: 100
2264943 CTCGTAACCG
*
2264953 GTTAAAATAAAATAGGCGCTACTTATTACATTAAATTACTTACCGATTTGTTTAAAGGTATAATA
1 GTTAAAATAAAATAGGCGCTACCTATTACATTAAATTACTTACCGATTTGTTTAAAGGTATAATA
* * * *
2265018 TTAATGCAAAGAGTTAAATATTTACAACTTAACAT
66 ATAATACAAAGAATAAAATATTTACAACTTAACAT
* * * *
2265053 GTTAAAATAAAATAGGTGTTACCTATTACATTAAATTATTTACCGGTTTGTTTAAAGGTATAATA
1 GTTAAAATAAAATAGGCGCTACCTATTACATTAAATTACTTACCGATTTGTTTAAAGGTATAATA
* *
2265118 ATAATATAAATAATAAAATATTTACAACTTAAC
66 ATAATACAAAGAATAAAATATTTACAACTTAAC
2265151 CGTTTGCTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 87 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (100 bp):
GTTAAAATAAAATAGGCGCTACCTATTACATTAAATTACTTACCGATTTGTTTAAAGGTATAATA
ATAATACAAAGAATAAAATATTTACAACTTAACAT
Found at i:2265631 original size:21 final size:20
Alignment explanation
Indices: 2265605--2265670 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
2265595 TCCTAAATAT
2265605 GTATCGATACATATACACTAA
1 GTATCGATACAT-TACACTAA
*
2265626 GTATCGGT--ATTA-A-TAA
1 GTATCGATACATTACACTAA
* *
2265642 TTTTC-ATACATCTACACTAA
1 GTATCGATACAT-TACACTAA
2265662 GTATCGATA
1 GTATCGATA
2265671 TTTTTACAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
15 1 0.03
16 6 0.18
17 3 0.09
18 4 0.12
19 3 0.09
20 6 0.18
21 10 0.30
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (20 bp):
GTATCGATACATTACACTAA
Found at i:2266375 original size:108 final size:107
Alignment explanation
Indices: 2266045--2266357 Score: 400
Period size: 108 Copynumber: 2.9 Consensus size: 107
2266035 GCCTCATCAT
* * * * * *
2266045 CTTAAACTTTGGTAACATATTAGACGC-AGTCTAATATGTTGATAATATTTATAACAAAGTAAGT
1 CTTAAACTTTGATAACATTTTAGGCGCTA-CCTAATATGTTGATAATATTAATAACAAAATAAGT
* *
2266109 AATTAACTTATTTTGTTATCGT-GAGATTTCTAAAGCCCTGTTAG
65 AATTAACTTATTTTGTTATCATCG-GATTTCTAAAG-CCTATTAG
* * * *
2266153 CTTAAACTTTGGA-AACATTTTAGGTGTTACATAATATGTTGATAATATTAATAACAAAATAAAT
1 CTTAAACTTT-GATAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAGT
** *
2266217 AATTAACTTATTTTAATATCATCGGATTTCTAAAGTCTCATTAG
65 AATTAACTTATTTTGTTATCATCGGATTTCTAAAGCCT-ATTAG
*
2266261 CTTAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGGTAATATTAATAACAAAATAAGTA
1 CTTAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTA
2266326 ATTAA-TCTATTTTGTTATCATCGGATTTCTAA
66 ATTAACT-TATTTTGTTATCATCGGATTTCTAA
2266358 GGCTAATCAG
Statistics
Matches: 177, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
107 5 0.03
108 169 0.95
109 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (107 bp):
CTTAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTA
ATTAACTTATTTTGTTATCATCGGATTTCTAAAGCCTATTAG
Found at i:2267627 original size:41 final size:41
Alignment explanation
Indices: 2267582--2267663 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
2267572 GATAGTGTTA
2267582 AGAAAATTTTAATGATAAATTTAATAATACCTAGAAGATAT
1 AGAAAATTTTAATGATAAATTTAATAATACCTAGAAGATAT
*
2267623 AGAAAATTTTAATGATAAATTTAGTAATACCTAGAAGATAT
1 AGAAAATTTTAATGATAAATTTAATAATACCTAGAAGATAT
2267664 GCTTTCTGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (41 bp):
AGAAAATTTTAATGATAAATTTAATAATACCTAGAAGATAT
Found at i:2272979 original size:8 final size:8
Alignment explanation
Indices: 2272966--2273006 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2272956 CTCATTTTCA
2272966 GAGAATTT
1 GAGAATTT
2272974 GAGAATTT
1 GAGAATTT
*
2272982 -AGAGTTT
1 GAGAATTT
*
2272989 GGGAATTT
1 GAGAATTT
2272997 GAGAATTT
1 GAGAATTT
2273005 GA
1 GA
2273007 AAGATTGTGA
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:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:2273307 original size:128 final size:128
Alignment explanation
Indices: 2273079--2274084 Score: 1587
Period size: 128 Copynumber: 7.9 Consensus size: 128
2273069 ATCGGAGTAT
*
2273079 TATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
2273144 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
2273207 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCATTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
2273272 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * *
2273335 -AGGGGACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
* **
2273399 ATTGCCCTATTATGTCACTCATGTCCATCGGGGACACCCGATATATCAGTACCTATTATTTCAC
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
2273463 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGA-AATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
2273527 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * * * * *
2273590 -AGGGGACATGAAGGCGCGTTCCCGGGGGAGTGCCTTCCATTATTTTGCCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
**
2273654 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCAC
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* * *
2273718 TATTCACATGAATGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
* *
2273783 TTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * * *
2273846 -AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGCCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
** *
2273910 ATTG-CCTATTATGTC-CTCATGTCCCTCGGGGACACCCGATATATCGGTACCT-TTATTTCAC
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
2273971 TATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
2274035 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2274085 AATCAGGTAA
Statistics
Matches: 795, Mismatches: 74, Indels: 20
0.89 0.08 0.02
Matches are distributed among these distances:
124 41 0.05
125 37 0.05
126 66 0.08
127 125 0.16
128 524 0.66
129 2 0.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
Found at i:2273839 original size:383 final size:383
Alignment explanation
Indices: 2273079--2274084 Score: 1589
Period size: 383 Copynumber: 2.6 Consensus size: 383
2273069 ATCGGAGTAT
* *
2273079 TATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGA-AATATGTTATCA
2273144 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
65 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
* *
2273209 TTCACATGAAGGCGCGTTCCCGGGGGCGCGCATTCCATTATTTCATCAGAGAATATGTTATCATT
130 TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATT
*
2273274 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGG
195 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACAGGG
* * *
2273339 GACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCATAGAATATGTTATCATTGC
260 CACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGC
* *
2273404 CCTATTATGTCACTCATGTCCATCGGGGACACCCGATATATCAGTACCTATTATTTCAC
325 CCTATTATGTCACTCATGTCCATCAGGGACACCAGATATATCAGTACCTATTATTTCAC
2273463 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAAATATGTTATCAT
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAAATATGTTATCAT
*
2273528 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC-AG
66 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA-
*** * * * * *
2273592 GGGACATGAAGGCGCGTTCCCGGGGGAGTGCCTTCCATTATTTTGCCATAGAATATGTTATCATT
130 TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATT
** *
2273657 GCCCTATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTA-T
195 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC-AGG
* *
2273721 TCACATGAATGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTG
259 GCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTG
* * *
2273786 CCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTACCTATTATTTCTC
324 CCCTATTATGTCACTCATGTCCATCAGGGACACCAGATATATCAGTACCTATTATTTCAC
***
2273846 -AGGGGACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGCCAT-AG-AATATGTTA
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTA-TTT--CATCAGAAATATGTTA
** *
2273908 TCATTG-CCTATTATGTC-CTCATGTCCCTCGGGGACACCCGATATATCGGTACCT-TTATTTCA
62 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
2273970 CTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
127 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
2274034 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
192 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2274085 AATCAGGTAA
Statistics
Matches: 571, Mismatches: 44, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
380 84 0.15
381 26 0.05
382 37 0.06
383 350 0.61
384 69 0.12
385 2 0.00
386 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (383 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAAATATGTTATCAT
TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTAT
TCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTG
CCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACAGGGC
ACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCC
CTATTATGTCACTCATGTCCATCAGGGACACCAGATATATCAGTACCTATTATTTCAC
Found at i:2273903 original size:256 final size:256
Alignment explanation
Indices: 2273086--2274084 Score: 1810
Period size: 256 Copynumber: 3.9 Consensus size: 256
2273076 TATTATTCAT
* *
2273086 ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCT
1 ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGCCATAGAATATGTTATCATTGCCCT
**
2273151 ATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACAT
66 ATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCACAT
*
2273216 GAAGGCGCGTTCCCGGGGGCGCGCATTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTAT
131 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTAT
2273281 TATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGAC
196 TATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGAC
* *
2273342 ATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCATAGAATATGTTATCATTGCCCT
1 ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGCCATAGAATATGTTATCATTGCCCT
*
2273407 ATTATGTCACTCATGTCCATCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCACAT
66 ATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCACAT
2273472 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGA-AATATGTTATCATTGCCCTAT
131 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTAT
2273536 TATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGAC
196 TATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGAC
* * *
2273597 ATGAAGGCGCGTTCCCGGGGGAGTGCCTTCCATTATTTTGCCATAGAATATGTTATCATTGCCCT
1 ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGCCATAGAATATGTTATCATTGCCCT
2273662 ATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCACAT
66 ATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCACAT
* *
2273727 GAATGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTAT
131 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTAT
*
2273792 TATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGAC
196 TATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGAC
*
2273853 ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGCCATAGAATATGTTATCATTG-CCT
1 ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGCCATAGAATATGTTATCATTGCCCT
*
2273917 ATTATGTC-CTCATGTCCCTCGGGGACACCCGATATATCGGTACCT-TTATTTCACTATTCACAT
66 ATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCACAT
*
2273980 GAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTAT
131 GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTAT
2274044 TATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
196 TATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
2274085 AATCAGGTAA
Statistics
Matches: 721, Mismatches: 21, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
252 88 0.12
253 31 0.04
254 36 0.05
255 259 0.36
256 307 0.43
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (256 bp):
ATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGCCATAGAATATGTTATCATTGCCCT
ATTATGTCACTCATGTCCCTCGGGGACACCCGATATATCAGTACCTATTATTTCACTATTCACAT
GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTAT
TATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGAC
Found at i:2274559 original size:33 final size:34
Alignment explanation
Indices: 2274482--2274578 Score: 121
Period size: 32 Copynumber: 3.0 Consensus size: 34
2274472 AAATTTAATG
*
2274482 TTAAATTTC--ATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * *
2274514 TTAAATTT-GAATAATATTATTT-TATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
2274546 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
2274579 AACATTTATC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
32 24 0.44
33 23 0.43
34 7 0.13
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:2275124 original size:21 final size:21
Alignment explanation
Indices: 2275094--2275187 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
2275084 TATGGTATAA
*
2275094 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
2275115 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
2275136 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
2275157 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
2275178 AACCCTGCGG
1 AACCCTGCGG
2275188 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.28, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:2275217 original size:21 final size:21
Alignment explanation
Indices: 2275191--2275238 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2275181 CCTGCGGAGA
*
2275191 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
2275212 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
2275233 GGGCAT
1 TGGCAT
2275239 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:2276999 original size:17 final size:19
Alignment explanation
Indices: 2276977--2277020 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2276967 ATAATTATAT
2276977 AAATATTAT-TTTA-ATAA
1 AAATATTATATTTACATAA
*
2276994 AAATATAATATTTACATAA
1 AAATATTATATTTACATAA
*
2277013 ATATATTA
1 AAATATTA
2277021 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTATATTTACATAA
Found at i:2277012 original size:19 final size:18
Alignment explanation
Indices: 2276964--2277051 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 18
2276954 TTCTAAATAA
* *
2276964 ATAATAATT-ATATAAAT
1 ATAATATTTAATAAAAAT
*
2276981 ATTAT-TTTAATAAAAAT
1 ATAATATTTAATAAAAAT
*
2276998 ATAATATTTACATAAATAT
1 ATAATATTTA-ATAAAAAT
2277017 ATTAATA--T-A-AAAAAT
1 A-TAATATTTAATAAAAAT
2277032 AATAACTATTTAA-AAAAAT
1 -ATAA-TATTTAATAAAAAT
2277051 A
1 A
2277052 CTAACATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
15 8 0.14
16 6 0.11
17 15 0.27
18 7 0.12
19 15 0.27
20 5 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATATTTAATAAAAAT
Found at i:2277061 original size:34 final size:34
Alignment explanation
Indices: 2276992--2277063 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
2276982 TTATTTTAAT
* * *
2276992 AAAAATATAATATTTACATAAATATATTAATATA
1 AAAAATATAATATTTACATAAAAATACTAACATA
2277026 AAAAATAATAACTATTTA-A-AAAAATACTAACATA
1 AAAAAT-ATAA-TATTTACATAAAAATACTAACATA
2277060 AAAA
1 AAAA
2277064 TAAATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 22 0.67
35 5 0.15
36 6 0.18
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (34 bp):
AAAAATATAATATTTACATAAAAATACTAACATA
Found at i:2278419 original size:338 final size:338
Alignment explanation
Indices: 2277803--2278481 Score: 1358
Period size: 338 Copynumber: 2.0 Consensus size: 338
2277793 GTAAAGGGCT
2277803 TTCCGATGATAATAATAAAGAAGGGATTGGACAATCTCGATTTTGCTTCTTGTGTTGTGGGGTGT
1 TTCCGATGATAATAATAAAGAAGGGATTGGACAATCTCGATTTTGCTTCTTGTGTTGTGGGGTGT
2277868 TCTCATGTACTATGTTTTCAAATGCACACCTGACCAGATCCCGGTATTTTCCAGACCCAACTTCT
66 TCTCATGTACTATGTTTTCAAATGCACACCTGACCAGATCCCGGTATTTTCCAGACCCAACTTCT
2277933 TCTTCTTCTTGTTTTCTTCAAATTGTAAATGAATTCTTGTGTCTCAGATTTGGAATTGAGATGGA
131 TCTTCTTCTTGTTTTCTTCAAATTGTAAATGAATTCTTGTGTCTCAGATTTGGAATTGAGATGGA
2277998 ATTTAGTAAAGCGGCTATATCACTGCTCAAAATAGCTTGTTTTTTCTTGGATGCTTTAGGATTCT
196 ATTTAGTAAAGCGGCTATATCACTGCTCAAAATAGCTTGTTTTTTCTTGGATGCTTTAGGATTCT
2278063 GATTTACTTGCTGTAGTTGTTGTTAATCATCTTCTGAACTGAAATATTATCGCTAAAGCTTGAGT
261 GATTTACTTGCTGTAGTTGTTGTTAATCATCTTCTGAACTGAAATATTATCGCTAAAGCTTGAGT
2278128 TTCAGATGCTATG
326 TTCAGATGCTATG
2278141 TTCCGATGATAATAATAAAGAAGGGATTGGACAATCTCGATTTTGCTTCTTGTGTTGTGGGGTGT
1 TTCCGATGATAATAATAAAGAAGGGATTGGACAATCTCGATTTTGCTTCTTGTGTTGTGGGGTGT
2278206 TCTCATGTACTATGTTTTCAAATGCACACCTGACCAGATCCCGGTATTTTCCAGACCCAACTTCT
66 TCTCATGTACTATGTTTTCAAATGCACACCTGACCAGATCCCGGTATTTTCCAGACCCAACTTCT
2278271 TCTTCTTCTTGTTTTCTTCAAATTGTAAATGAATTCTTGTGTCTCAGATTTGGAATTGAGATGGA
131 TCTTCTTCTTGTTTTCTTCAAATTGTAAATGAATTCTTGTGTCTCAGATTTGGAATTGAGATGGA
2278336 ATTTAGTAAAGCGGCTATATCACTGCTCAAAATAGCTTGTTTTTTCTTGGATGCTTTAGGATTCT
196 ATTTAGTAAAGCGGCTATATCACTGCTCAAAATAGCTTGTTTTTTCTTGGATGCTTTAGGATTCT
2278401 GATTTACTTGCTGTAGTTGTTGTTAATCATCTTCTGAACTGAAATATTATCGCTAAAGCTTGAGT
261 GATTTACTTGCTGTAGTTGTTGTTAATCATCTTCTGAACTGAAATATTATCGCTAAAGCTTGAGT
2278466 TTCAGATGCTATG
326 TTCAGATGCTATG
2278479 TTC
1 TTC
2278482 ATTGGTTACT
Statistics
Matches: 341, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
338 341 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (338 bp):
TTCCGATGATAATAATAAAGAAGGGATTGGACAATCTCGATTTTGCTTCTTGTGTTGTGGGGTGT
TCTCATGTACTATGTTTTCAAATGCACACCTGACCAGATCCCGGTATTTTCCAGACCCAACTTCT
TCTTCTTCTTGTTTTCTTCAAATTGTAAATGAATTCTTGTGTCTCAGATTTGGAATTGAGATGGA
ATTTAGTAAAGCGGCTATATCACTGCTCAAAATAGCTTGTTTTTTCTTGGATGCTTTAGGATTCT
GATTTACTTGCTGTAGTTGTTGTTAATCATCTTCTGAACTGAAATATTATCGCTAAAGCTTGAGT
TTCAGATGCTATG
Found at i:2294201 original size:24 final size:24
Alignment explanation
Indices: 2294174--2294237 Score: 65
Period size: 29 Copynumber: 2.5 Consensus size: 24
2294164 TTAAGATCAG
* *
2294174 TATATTCTATTGAAATAAAAATAC
1 TATATTATATTAAAATAAAAATAC
2294198 TATAAATTATATGATTAAAATAAAAATAC
1 TAT--A-T-TAT-ATTAAAATAAAAATAC
2294227 TATATTATATT
1 TATATTATATT
2294238 TTAAAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
24 6 0.18
25 3 0.09
26 2 0.06
27 2 0.06
28 2 0.06
29 18 0.55
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (24 bp):
TATATTATATTAAAATAAAAATAC
Found at i:2294350 original size:23 final size:24
Alignment explanation
Indices: 2294324--2294374 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
2294314 ATAATATTGT
* *
2294324 TTATTATTAATAATTTAATAA-TA
1 TTATTATTAAGAAATTAATAACTA
* *
2294347 TTATTTTTAGGAAATTAATAACTA
1 TTATTATTAAGAAATTAATAACTA
2294371 TTAT
1 TTAT
2294375 AAATTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (24 bp):
TTATTATTAAGAAATTAATAACTA
Found at i:2294442 original size:23 final size:24
Alignment explanation
Indices: 2294412--2294469 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
2294402 TATTAAAATA
2294412 ATAATATAATATCA-TATATTATT
1 ATAATATAATATCAGTATATTATT
*
2294435 ATAATATAAT-TGAGTATATTATT
1 ATAATATAATATCAGTATATTATT
*
2294458 ATAATATTATAT
1 ATAATATAATAT
2294470 TAATAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 2 0.06
23 28 0.90
24 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (24 bp):
ATAATATAATATCAGTATATTATT
Found at i:2294470 original size:16 final size:16
Alignment explanation
Indices: 2294449--2294482 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2294439 TATAATTGAG
* *
2294449 TATATTATTATAATAT
1 TATATTAATAAAATAT
2294465 TATATTAATAAAATAT
1 TATATTAATAAAATAT
2294481 TA
1 TA
2294483 ATAAATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATTAATAAAATAT
Found at i:2294486 original size:11 final size:12
Alignment explanation
Indices: 2294465--2294550 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 12
2294455 ATTATAATAT
2294465 TATATTAATAAA
1 TATATTAATAAA
2294477 -ATATTAATAAA
1 TATATTAATAAA
*
2294488 TATATT-TTAAA
1 TATATTAATAAA
*
2294499 TATTTTAATTATTAA
1 TATATTAA-TA--AA
*
2294514 TATTTTAATAAAA
1 TATATTAAT-AAA
2294527 TGATATTAA-AACA
1 T-ATATTAATAA-A
2294540 TTATATTAATA
1 -TATATTAATA
2294551 CTCAATATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
11 20 0.33
12 7 0.12
13 13 0.22
14 9 0.15
15 11 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (12 bp):
TATATTAATAAA
Found at i:2294525 original size:38 final size:39
Alignment explanation
Indices: 2294449--2294550 Score: 104
Period size: 38 Copynumber: 2.7 Consensus size: 39
2294439 TATAATTGAG
2294449 TATATTATTATAATATTATATTAATAAAATATTAATAAA
1 TATATTATTATAATATTATATTAATAAAATATTAATAAA
* * * *
2294488 TATATT-TTA-AATATTTTAATTATTAATATTTTAATAAA
1 TATATTATTATAATATTAT-ATTAATAAAATATTAATAAA
* *
2294526 -ATGA-TATTAAAACATTATATTAATA
1 TAT-ATTATTATAATATTATATTAATA
2294551 CTCAATATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
37 10 0.19
38 30 0.58
39 12 0.23
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (39 bp):
TATATTATTATAATATTATATTAATAAAATATTAATAAA
Found at i:2303255 original size:55 final size:56
Alignment explanation
Indices: 2303142--2303259 Score: 141
Period size: 55 Copynumber: 2.1 Consensus size: 56
2303132 AGGACCTTTA
* * * * * *
2303142 AAAAATAGGGATCTCGAAATTGAATATATCTATCAGTTATTGCCATTAATATATAT
1 AAAAATAGGGACCCCGAAATCGAATATATCTATCAATTATTGCCATTAAGATACAT
* *
2303198 AAAAATAGGG-CCCCGAAATCGAGTATATTTATCAATTATTGCCATTAAGA-AGCAT
1 AAAAATAGGGACCCCGAAATCGAATATATCTATCAATTATTGCCATTAAGATA-CAT
2303253 AAAAATA
1 AAAAATA
2303260 AGGGTTCTGG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
54 1 0.02
55 42 0.79
56 10 0.19
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.31
Consensus pattern (56 bp):
AAAAATAGGGACCCCGAAATCGAATATATCTATCAATTATTGCCATTAAGATACAT
Found at i:2304507 original size:2 final size:2
Alignment explanation
Indices: 2304500--2304539 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2304490 GTGGATCTGC
2304500 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
2304540 TTGGATAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2311098 original size:20 final size:20
Alignment explanation
Indices: 2311075--2311140 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
2311065 TGTAGAATTT
2311075 TCTAGAACATTTCGAAGAAC
1 TCTAGAACATTTCGAAGAAC
* * *
2311095 TCTAGAGA-A-GT-GTAGAATTT
1 TCTAGA-ACATTTCGAAGAA--C
2311115 TCTAGAACATTTCGAAGAAC
1 TCTAGAACATTTCGAAGAAC
2311135 TCTAGA
1 TCTAGA
2311141 GAAGTGTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 5 0.15
19 2 0.06
20 20 0.59
21 2 0.06
22 5 0.15
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (20 bp):
TCTAGAACATTTCGAAGAAC
Found at i:2311161 original size:40 final size:40
Alignment explanation
Indices: 2311055--2311148 Score: 188
Period size: 40 Copynumber: 2.4 Consensus size: 40
2311045 TCTAGAGCTT
2311055 TCTAGAGAAGTGTAGAATTTTCTAGAACATTTCGAAGAAC
1 TCTAGAGAAGTGTAGAATTTTCTAGAACATTTCGAAGAAC
2311095 TCTAGAGAAGTGTAGAATTTTCTAGAACATTTCGAAGAAC
1 TCTAGAGAAGTGTAGAATTTTCTAGAACATTTCGAAGAAC
2311135 TCTAGAGAAGTGTA
1 TCTAGAGAAGTGTA
2311149 TAACACTCTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (40 bp):
TCTAGAGAAGTGTAGAATTTTCTAGAACATTTCGAAGAAC
Found at i:2313213 original size:17 final size:18
Alignment explanation
Indices: 2313180--2313218 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2313170 ATATTGAACC
2313180 AAAAAAATATGTAATATA
1 AAAAAAATATGTAATATA
2313198 TAAAAAAAT-TGT-ATATA
1 -AAAAAAATATGTAATATA
2313215 AAAA
1 AAAA
2313219 TACTATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 5 0.25
18 3 0.15
19 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAAAATATGTAATATA
Found at i:2315316 original size:2 final size:2
Alignment explanation
Indices: 2315311--2315345 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2315301 TTTATTTTTC
2315311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2315346 ACCGAAGCCA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2328983 original size:2 final size:2
Alignment explanation
Indices: 2328976--2329025 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2328966 GTTTTATACT
2328976 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2329017 TA TA TA TA T
1 TA TA TA TA T
2329026 GGTTCTATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2332456 original size:24 final size:25
Alignment explanation
Indices: 2332420--2332467 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
2332410 TAGAGGTGCA
2332420 AGGCTCTATATAAGAAATTAATTTT
1 AGGCTCTATATAAGAAATTAATTTT
2332445 AGGCTC-ATATAAGAAATTAATTT
1 AGGCTCTATATAAGAAATTAATTT
2332468 GCCACTCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (25 bp):
AGGCTCTATATAAGAAATTAATTTT
Found at i:2345169 original size:12 final size:12
Alignment explanation
Indices: 2345134--2345161 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2345124 TTATAGGGCT
2345134 TGGGACTGGAGG
1 TGGGACTGGAGG
2345146 TGGGACTGGAGG
1 TGGGACTGGAGG
2345158 TGGG
1 TGGG
2345162 GTTGGAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.61, T:0.18
Consensus pattern (12 bp):
TGGGACTGGAGG
Found at i:2350956 original size:22 final size:23
Alignment explanation
Indices: 2350905--2350957 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
2350895 TCAAATATAT
*
2350905 AATATTTAATAAATAAAAATACC
1 AATATTTTATAAATAAAAATACC
2350928 AA-A-TTTATAAATAAAAA-A-C
1 AATATTTTATAAATAAAAATACC
2350947 AGATATTTTAT
1 A-ATATTTTAT
2350958 TTGTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 2 0.08
20 2 0.08
21 14 0.54
22 6 0.23
23 2 0.08
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (23 bp):
AATATTTTATAAATAAAAATACC
Found at i:2353882 original size:11 final size:11
Alignment explanation
Indices: 2353850--2353892 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
2353840 TTATGAATTT
2353850 AATATTAATAA
1 AATATTAATAA
* *
2353861 AACATTTAATAT
1 AATA-TTAATAA
*
2353873 CATATTAATAA
1 AATATTAATAA
2353884 AATATTAAT
1 AATATTAAT
2353893 TATTAAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATTAATAA
Found at i:2353942 original size:22 final size:22
Alignment explanation
Indices: 2353917--2353962 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2353907 AAAATATATT
2353917 TATTA-ATATTTTAATAATATAA
1 TATTATAT-TTTTAATAATATAA
*
2353939 TATTATATTTTTAATATTATAA
1 TATTATATTTTTAATAATATAA
2353961 TA
1 TA
2353963 AAATAATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTATATTTTTAATAATATAA
Found at i:2353955 original size:30 final size:32
Alignment explanation
Indices: 2353911--2353989 Score: 99
Period size: 30 Copynumber: 2.5 Consensus size: 32
2353901 TATCTAAAAA
* *
2353911 TATATTTATTAATATTTTAATAATATAAT-AT
1 TATATTTATTAATATTATAATAAAATAATAAT
2353942 TATATTT-TTAATATTATAATAAAATAATCAAT
1 TATATTTATTAATATTATAATAAAATAAT-AAT
*
2353974 TATATTATAATAATAT
1 TATATT-TATTAATAT
2353990 AAGATATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 19 0.46
31 7 0.17
32 8 0.20
33 1 0.02
34 6 0.15
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTATAATAAAATAATAAT
Found at i:2354251 original size:31 final size:29
Alignment explanation
Indices: 2354226--2354296 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 29
2354216 ATATAATTTA
2354226 TAATATTTTTATTTCAATAAAATATACCAATAT
1 TAATATTTTTA-TT-AATAAAATATA--AATAT
*
2354259 TAATATTTTTATTAATAAAATTATAAA-AA
1 TAATATTTTTATTAATAAAA-TATAAATAT
2354288 TAATATTTT
1 TAATATTTT
2354297 AATATTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 10 0.28
30 2 0.06
31 7 0.19
32 6 0.17
33 11 0.31
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (29 bp):
TAATATTTTTATTAATAAAATATAAATAT
Found at i:2354303 original size:31 final size:32
Alignment explanation
Indices: 2354225--2354313 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 32
2354215 AATATAATTT
2354225 ATAATATTTT-TATTTCAATAAAA-TATACCAATA
1 ATAATATTTTATA-TT-AATAAAATTATA-CAATA
*
2354258 TTAATATTTT-TATTAATAAAATTATA-AA-A
1 ATAATATTTTATATTAATAAAATTATACAATA
2354287 ATAATATTTTAATATT-ATATAAATTAT
1 ATAATATTTT-ATATTAATA-AAATTAT
2354314 TTTAATATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
29 10 0.20
30 5 0.10
31 18 0.36
32 6 0.12
33 11 0.22
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (32 bp):
ATAATATTTTATATTAATAAAATTATACAATA
Found at i:2354316 original size:20 final size:20
Alignment explanation
Indices: 2354291--2354330 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2354281 ATAAAAATAA
2354291 TATTTTAATATTATATAAAT
1 TATTTTAATATTATATAAAT
*
2354311 TATTTTAATATTTTATAAAT
1 TATTTTAATATTATATAAAT
2354331 AATAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTAATATTATATAAAT
Found at i:2354362 original size:22 final size:21
Alignment explanation
Indices: 2354279--2354362 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 21
2354269 ATTAATAAAA
* * *
2354279 TTATAAAAATAATATTTTAATA
1 TTATATAAATAATA-TTAAATT
* *
2354301 TTATATAAATTATTTTAATATT
1 TTATATAAATAATATTAA-ATT
*
2354323 TTATAAATAATAATATTAAATT
1 TTATATA-AATAATATTAAATT
2354345 TTATGATAAATAATATTA
1 TTAT-ATAAATAATATTA
2354363 TTTATTGTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 3 0.06
22 36 0.72
23 11 0.22
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TTATATAAATAATATTAAATT
Found at i:2354466 original size:14 final size:14
Alignment explanation
Indices: 2354447--2354482 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2354437 CAAATATAGT
* *
2354447 AAAATATTTTTCAG
1 AAAATATATTTCAA
2354461 AAAATATATTTCAA
1 AAAATATATTTCAA
2354475 AAAATATA
1 AAAATATA
2354483 ATTTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (14 bp):
AAAATATATTTCAA
Found at i:2358433 original size:20 final size:19
Alignment explanation
Indices: 2358409--2358461 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
2358399 TATGGTAAAT
*
2358409 AATTTTTTTTTTGAAAACTT
1 AATTTTTTTTTT-AAAACTG
*
2358429 TATTTTTTTTATTAAAACTG
1 AATTTTTTTT-TTAAAACTG
2358449 AATTTTTTTTTTA
1 AATTTTTTTTTTA
2358462 TTTATAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.10
20 24 0.83
21 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (19 bp):
AATTTTTTTTTTAAAACTG
Found at i:2358634 original size:19 final size:19
Alignment explanation
Indices: 2358596--2358635 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2358586 TATTTTTAAA
*
2358596 ATAATGATATTATGTTTTT
1 ATAATGATATTATGTATTT
2358615 ATAATGAATATTAT-TATTT
1 ATAATG-ATATTATGTATTT
2358634 AT
1 AT
2358636 TATATTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (19 bp):
ATAATGATATTATGTATTT
Found at i:2363242 original size:21 final size:21
Alignment explanation
Indices: 2363194--2363234 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2363184 TTACACCTTC
2363194 AACATCATCACATCCATTCAT
1 AACATCATCACATCCATTCAT
*
2363215 AACATCATCACATTCATTCA
1 AACATCATCACATCCATTCA
2363235 CTTCATCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (21 bp):
AACATCATCACATCCATTCAT
Found at i:2363335 original size:6 final size:6
Alignment explanation
Indices: 2363318--2363373 Score: 67
Period size: 6 Copynumber: 8.8 Consensus size: 6
2363308 ATCACTACCA
* *
2363318 CCATCT TCATCT CTATCT CCATCT CCATCT CCATCTT CATCATCT CCATCT
1 CCATCT CCATCT CCATCT CCATCT CCATCT CCATC-T C--CATCT CCATCT
2363369 CCATC
1 CCATC
2363374 ACCTCTATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
6 35 0.81
7 2 0.05
8 2 0.05
9 4 0.09
ACGTcount: A:0.18, C:0.45, G:0.00, T:0.38
Consensus pattern (6 bp):
CCATCT
Found at i:2363339 original size:18 final size:18
Alignment explanation
Indices: 2363318--2363373 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 18
2363308 ATCACTACCA
* *
2363318 CCATCTTCATCTCTATCT
1 CCATCTCCATCTCCATCT
2363336 CCATCTCCATCTCCATCTT
1 CCATCTCCATCTCCATC-T
2363355 CATCATCTCCATCTCCATC
1 C--CATCTCCATCTCCATC
2363374 ACCTCTATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 15 0.45
19 2 0.06
21 16 0.48
ACGTcount: A:0.18, C:0.45, G:0.00, T:0.38
Consensus pattern (18 bp):
CCATCTCCATCTCCATCT
Found at i:2363383 original size:15 final size:15
Alignment explanation
Indices: 2363328--2363391 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
2363318 CCATCTTCAT
*
2363328 CTCTATCTCCATCTC
1 CTCTATCTCCATCAC
* *
2363343 CATCTCCATCTTCATCAT
1 C-TCT--ATCTCCATCAC
*
2363361 CTCCATCTCCATCAC
1 CTCTATCTCCATCAC
*
2363376 CTCTATCTCCACCAC
1 CTCTATCTCCATCAC
2363391 C
1 C
2363392 ACCACCACCA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 24 0.63
16 3 0.08
17 2 0.05
18 9 0.24
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (15 bp):
CTCTATCTCCATCAC
Found at i:2363383 original size:21 final size:21
Alignment explanation
Indices: 2363337--2363386 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2363327 TCTCTATCTC
*
2363337 CATCTCCATCTCCATCTTCAT
1 CATCTCCATCTCCATCTACAT
*
2363358 CATCTCCATCTCCATC-ACCT
1 CATCTCCATCTCCATCTACAT
2363378 CTATCTCCA
1 C-ATCTCCA
2363387 CCACCACCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.20, C:0.46, G:0.00, T:0.34
Consensus pattern (21 bp):
CATCTCCATCTCCATCTACAT
Found at i:2368688 original size:2 final size:2
Alignment explanation
Indices: 2368675--2368716 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2368665 ACTGTTTTCG
*
2368675 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2368717 CCTCTATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2368806 original size:16 final size:15
Alignment explanation
Indices: 2368770--2368808 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2368760 TTAAAGAGAT
2368770 ATTAATTAATTTATAA
1 ATTAA-TAATTTATAA
2368786 ATTAATAATTTATTAA
1 ATTAATAATTTA-TAA
*
2368802 TTTAATA
1 ATTAATA
2368809 TATATTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTAATAATTTATAA
Found at i:2369497 original size:40 final size:41
Alignment explanation
Indices: 2369419--2369509 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 41
2369409 AAATTTGTAT
* * * *
2369419 ACAAACTAAGCACAAACTAAATTTTAGGATGGACACAATCA
1 ACAAAATAAACACAAACTAAATTTTAAGACGGACACAATCA
*
2369460 ACAAAATAAACACAAA-TAAATTTTAAGACGGATACAATCA
1 ACAAAATAAACACAAACTAAATTTTAAGACGGACACAATCA
*
2369500 ATAAAATAAA
1 ACAAAATAAA
2369510 AGAAAGATCG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 30 0.68
41 14 0.32
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.20
Consensus pattern (41 bp):
ACAAAATAAACACAAACTAAATTTTAAGACGGACACAATCA
Found at i:2369580 original size:2 final size:2
Alignment explanation
Indices: 2369573--2369623 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2369563 CACCACAGTA
2369573 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
*
2369615 AT AT CT AT A
1 AT AT AT AT A
2369624 ATACAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2373006 original size:22 final size:22
Alignment explanation
Indices: 2372955--2373015 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
2372945 ATATAGTTTC
* *
2372955 TATAAAAGT-TATATTAAATTAT
1 TATAAAAATATAT-TTAAAATAT
* *
2372977 TTTTAAAATATATTTAAAATAT
1 TATAAAAATATATTTAAAATAT
2372999 TATAAAAA-ATTATTTAA
1 TATAAAAATA-TATTTAA
2373016 TTTTGAAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 1 0.03
22 27 0.87
23 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TATAAAAATATATTTAAAATAT
Found at i:2377840 original size:29 final size:27
Alignment explanation
Indices: 2377796--2377854 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
2377786 GTTTTTTATT
* *
2377796 TAAGTGTTTAAAATTTATTTTGATCAAAA
1 TAAGTGTGTAAAA-TT-TTTTAATCAAAA
*
2377825 TAAGTGTGTAACATTTTTTAATCAAAA
1 TAAGTGTGTAAAATTTTTTAATCAAAA
2377852 TAA
1 TAA
2377855 AATCCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 14 0.52
28 2 0.07
29 11 0.41
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (27 bp):
TAAGTGTGTAAAATTTTTTAATCAAAA
Found at i:2399413 original size:23 final size:23
Alignment explanation
Indices: 2399369--2399413 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2399359 AATATTGAAC
* **
2399369 GAATATATTCATAAACTTTAAAA
1 GAATATATTCACAAACGCTAAAA
*
2399392 GAATATATTCGCAAACGCTAAA
1 GAATATATTCACAAACGCTAAA
2399414 CATGAACATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (23 bp):
GAATATATTCACAAACGCTAAAA
Found at i:2404062 original size:11 final size:11
Alignment explanation
Indices: 2404046--2404073 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2404036 TTGCTATTTT
2404046 AAAAAAAAACA
1 AAAAAAAAACA
2404057 AAAAAAAAACA
1 AAAAAAAAACA
2404068 AAAAAA
1 AAAAAA
2404074 GCCAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:2407348 original size:37 final size:38
Alignment explanation
Indices: 2407286--2407360 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 38
2407276 AATTTTTCAT
* *
2407286 TATATTATTTTAATTATTATTATTATTATTAAATAAAA
1 TATATTATTATAATTATTATTATTATCATTAAATAAAA
2407324 TATATTATTAT-A-TATATATTATTATCATTAAATAAAA
1 TATATTATTATAATTAT-TATTATTATCATTAAATAAAA
2407361 AAAACATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 3 0.09
37 21 0.62
38 10 0.29
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (38 bp):
TATATTATTATAATTATTATTATTATCATTAAATAAAA
Found at i:2407813 original size:11 final size:11
Alignment explanation
Indices: 2407797--2407839 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
2407787 ACAAAGTAAG
2407797 AAAAAAAAGAA
1 AAAAAAAAGAA
2407808 AAAAAAAAGAA
1 AAAAAAAAGAA
*
2407819 ACGAAAAACAGAA
1 A--AAAAAAAGAA
2407832 AAAAAAAA
1 AAAAAAAA
2407840 AAATGAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 18 0.64
13 10 0.36
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:2407847 original size:23 final size:24
Alignment explanation
Indices: 2407798--2407847 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2407788 CAAAGTAAGA
2407798 AAAAAAAGAAAAAAAAAAGAAACG
1 AAAAAAAGAAAAAAAAAAGAAACG
* *
2407822 AAAAACAGAAAAAAAAAA-AAATG
1 AAAAAAAGAAAAAAAAAAGAAACG
2407845 AAA
1 AAA
2407848 GGAAGGGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.84, C:0.04, G:0.10, T:0.02
Consensus pattern (24 bp):
AAAAAAAGAAAAAAAAAAGAAACG
Found at i:2408770 original size:15 final size:15
Alignment explanation
Indices: 2408750--2408799 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2408740 ATCCATTAGT
2408750 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
2408765 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
2408779 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
2408795 TTTTA
1 TTTTA
2408800 TTTTATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 5 0.18
15 18 0.64
16 1 0.04
17 4 0.14
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:2409763 original size:18 final size:18
Alignment explanation
Indices: 2409742--2409809 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 18
2409732 TTTTATATAC
2409742 TTATTATTTTCATAGTAT
1 TTATTATTTTCATAGTAT
*
2409760 TTATATATTTTCTTATTAATAT
1 TTAT-TATTTTC--A-TAGTAT
*
2409782 TTCATTATTTGCA-AGTATT
1 TT-ATTATTTTCATAGTA-T
2409801 TTATTATTT
1 TTATTATTT
2409810 ATTTTTCTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 14 0.34
19 10 0.24
20 1 0.02
21 1 0.02
22 13 0.32
23 2 0.05
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (18 bp):
TTATTATTTTCATAGTAT
Found at i:2416740 original size:93 final size:93
Alignment explanation
Indices: 2416576--2416848 Score: 476
Period size: 93 Copynumber: 2.9 Consensus size: 93
2416566 AGAAGACCCA
*
2416576 ATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
2416641 TCATTGAATTTGGAAGATGAATGTGCTC
66 TCATTGAATTTGGAAGATGAATGTGCTC
2416669 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
2416734 TCATTGAATTTGGAAGATGAATGTGCTC
66 TCATTGAATTTGGAAGATGAATGTGCTC
* * * *
2416762 ATAGCATCTTCTAGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGTATGAAACCATAGAATCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
*
2416827 TCATT-AGATTTGAAAGATGAAT
66 TCATTGA-ATTTGGAAGATGAAT
2416849 TTTTCTCATA
Statistics
Matches: 173, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
92 1 0.01
93 172 0.99
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (93 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
TCATTGAATTTGGAAGATGAATGTGCTC
Found at i:2420561 original size:76 final size:76
Alignment explanation
Indices: 2420247--2421162 Score: 1613
Period size: 76 Copynumber: 12.0 Consensus size: 76
2420237 CTATTTCCCA
*
2420247 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2420312 AGCC-TCAGGGT
66 AGCCTTC-GGGT
* * *
2420323 CATCTGTAAGTCCTTCAATGCATGATGTTTCCAAAAAAGCCTTCAGGAGCTTTTTAATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
2420388 AAGCC-TCAGGGT
65 AAGCCTTC-GGGT
*
2420400 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAAAGCCTTCGGGAGCTTTTTAATGTTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC---AAAAAGCCTTCGGGAGCTTTTTGATGTTTT
2420465 CAAAGCC-TCAGGGT
63 CAAAGCCTTC-GGGT
*
2420479 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2420544 AGCCTTCGGGT
66 AGCCTTCGGGT
2420555 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
2420620 AAACCTTCGGGT
65 AAGCCTTCGGGT
2420632 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2420697 AACCTTCGGGT
66 AGCCTTCGGGT
2420708 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2420773 AGCTTTCGGGT
66 AGCCTTCGGGT
* *
2420784 CATCTGTAAGCCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2420849 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2420860 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2420925 AGCCTTCGGGT
66 AGCCTTCGGGT
2420936 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2421001 AACCTTCGGGT
66 AGCCTTCGGGT
2421012 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2421077 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2421088 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2421153 AGCCTTCGGG
66 AGCCTTCGGG
2421163 AGCTTTTTGA
Statistics
Matches: 815, Mismatches: 20, Indels: 10
0.96 0.02 0.01
Matches are distributed among these distances:
76 591 0.73
77 148 0.18
79 76 0.09
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:2421190 original size:29 final size:29
Alignment explanation
Indices: 2421122--2421191 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
2421112 ATGTTTCCAA
*
2421122 AAAGCCTTCGAGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
2421151 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 AAAGCCTTCGGGAGCTTTTTGATGTTTTC
2421180 AAAGCCTTCGGG
1 AAAGCCTTCGGG
2421192 TCATCTGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (29 bp):
AAAGCCTTCGGGAGCTTTTTGATGTTTTC
Found at i:2421353 original size:14 final size:15
Alignment explanation
Indices: 2421336--2421396 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 15
2421326 CCACTTTTTC
2421336 ATTATATTATT-TTA
1 ATTATATTATTATTA
2421350 ATTATTATTATTATTA
1 ATTA-TATTATTATTA
* *
2421366 AATAAATATATTATTA
1 ATTATAT-TATTATTA
2421382 TATATATATTATTAT
1 -AT-TATATTATTAT
2421397 CATTAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 4 0.11
15 9 0.24
16 14 0.37
17 7 0.18
18 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATATTATTATTA
Found at i:2421377 original size:16 final size:15
Alignment explanation
Indices: 2421358--2421395 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2421348 TAATTATTAT
2421358 TATTATTAAATAAATA
1 TATTATT-AATAAATA
*
2421374 TATTATT-ATATATA
1 TATTATTAATAAATA
2421388 TATTATTA
1 TATTATTA
2421396 TCATTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 13 0.65
16 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTATTAATAAATA
Found at i:2421835 original size:1 final size:1
Alignment explanation
Indices: 2421829--2421889 Score: 77
Period size: 1 Copynumber: 61.0 Consensus size: 1
2421819 GACACGAAAG
* * * * *
2421829 AAAAAAAAAAGAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAACAAACAGAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2421890 CGAAAGGAAG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.92, C:0.03, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:2421850 original size:20 final size:19
Alignment explanation
Indices: 2421829--2421889 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
2421819 GACACGAAAG
2421829 AAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAGAAAAAAAA
2421848 GAAAAAAAAAA-AAAAAAAA
1 -AAAAAAAAAAGAAAAAAAA
* *
2421867 AAAACAAACAGAAAAAAAA
1 AAAAAAAAAAGAAAAAAAA
2421886 AAAA
1 AAAA
2421890 CGAAAGGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 8 0.21
19 20 0.53
20 10 0.26
ACGTcount: A:0.92, C:0.03, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAAAAA
Done.