Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_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: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 21
Found at i:2161282 original size:33 final size:33
Alignment explanation
Indices: 2161231--2161320 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
2161221 AAATCGCAAC
* * *
2161231 GCGAATTTAATTTCGCGTTGTGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
2161264 TCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
2161297 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
2161321 AGTACTTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:2161287 original size:19 final size:19
Alignment explanation
Indices: 2161260--2161320 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
2161250 GTGATTCTCT
*
2161260 CGTTTCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2161279 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
2161293 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2161312 CATTGCGAT
1 CGTTGCGAT
2161321 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 10 0.30
16 3 0.09
17 3 0.09
19 17 0.52
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2161453 original size:14 final size:14
Alignment explanation
Indices: 2161436--2161462 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2161426 AACAACTCAA
2161436 CTTTTACAAATCAC
1 CTTTTACAAATCAC
2161450 CTTTTACAAATCA
1 CTTTTACAAATCA
2161463 ATTAAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (14 bp):
CTTTTACAAATCAC
Found at i:2162904 original size:42 final size:42
Alignment explanation
Indices: 2162858--2162937 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
2162848 CGATGACAGT
* * *
2162858 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
2162900 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
2162938 CAGGTGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:2163338 original size:91 final size:90
Alignment explanation
Indices: 2163159--2163343 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
2163149 ATTTCAAACT
*
2163159 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
2163224 AGAATTGCCAGCAACCGAATAAATTTAC
63 AGAATTGCCAGCAACCGAATAAATTTAC
*
2163252 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCTCAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
2163316 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGCCAGCAACCGAATAAATTTAC
2163343 T
1 T
2163344 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGCCAGCAACCGAATAAATTTAC
Found at i:2165119 original size:19 final size:18
Alignment explanation
Indices: 2165032--2165177 Score: 101
Period size: 19 Copynumber: 8.1 Consensus size: 18
2165022 TCTTTTGGTT
*
2165032 GAAATGAAAATCGCAACGA
1 GAAATG-AAATCGCAACGC
2165051 GATAATGAGAATCGCAACGC
1 GA-AATGA-AATCGCAACGC
* *
2165071 GGAAATGACTATCACAA--C
1 -GAAATGA-AATCGCAACGC
*
2165089 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
*
2165105 GAAATGACTATCGCAA--C
1 GAAATGA-AATCGCAACGC
*
2165122 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
2165138 GAAATGAAAATCGCAACGC
1 GAAATG-AAATCGCAACGC
*
2165157 GAAATGAAAATCGCAATGC
1 GAAATG-AAATCGCAACGC
2165176 GA
1 GA
2165178 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 13, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
14 13 0.13
16 10 0.10
17 9 0.09
18 1 0.01
19 41 0.41
20 25 0.25
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (18 bp):
GAAATGAAATCGCAACGC
Found at i:2165133 original size:14 final size:14
Alignment explanation
Indices: 2165085--2165136 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
2165075 ATGACTATCA
2165085 CAACGAGAGAATCG
1 CAACGAGAGAATCG
*
2165099 CAACGCGAAATGACTATCG
1 CAA--CGAGA-GA--ATCG
2165118 CAACGAGAGAATCG
1 CAACGAGAGAATCG
2165132 CAACG
1 CAACG
2165137 CGAAATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 12 0.39
16 6 0.19
17 6 0.19
19 7 0.23
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.10
Consensus pattern (14 bp):
CAACGAGAGAATCG
Found at i:2165151 original size:33 final size:33
Alignment explanation
Indices: 2165057--2165155 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
2165047 ACGAGATAAT
*
2165057 GAGAATCGCAACGCGGAAATGACTATCACAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
2165091 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
2165124 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
2165156 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 48 0.77
34 14 0.23
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:2165206 original size:19 final size:19
Alignment explanation
Indices: 2165173--2165239 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
2165163 AAAATCGCAA
**
2165173 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
2165192 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
2165211 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
2165231 TGCGATTTT
1 TGCGATTTT
2165240 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:2165800 original size:20 final size:20
Alignment explanation
Indices: 2165759--2165933 Score: 86
Period size: 20 Copynumber: 8.6 Consensus size: 20
2165749 GCTATGTAAA
* *
2165759 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
2165779 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * *
2165799 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
* * * *
2165820 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGATTTACG-TAT
** * * * *
2165841 TCGCAACGCGAATTAGGAAAA
1 TCGCATTGCGATTTACG-TAT
*
2165862 TCGCATTGCGATAGT-CAGTA-
1 TCGCATTGCGAT-TTAC-GTAT
* **
2165882 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACGTAT
*
2165903 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACGTAT
2165923 TCGCATTGCGA
1 TCGCATTGCGA
2165934 ATTGGGAAAA
Statistics
Matches: 120, Mismatches: 27, Indels: 16
0.74 0.17 0.10
Matches are distributed among these distances:
19 3 0.03
20 59 0.49
21 56 0.47
22 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:2165824 original size:41 final size:41
Alignment explanation
Indices: 2165777--2165933 Score: 138
Period size: 41 Copynumber: 3.8 Consensus size: 41
2165767 CGATAGTAAG
* *
2165777 ATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCAA
* * * * ** * ***
2165818 ATTCGCATTGCGAATTATGAAAATCGCAACGCGAATTAGGAA
1 ATTCGCATTGCGATTTACG-TATTCGCATTGCGATTTTCCAA
* *
2165860 AATCGCATTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGAT-TTAC-GTATTCGCATTGCGATTTTCCAA
*
2165901 ATTCGCATTGCGATTTACTTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
2165934 ATTGGGAAAA
Statistics
Matches: 85, Mismatches: 26, Indels: 10
0.70 0.21 0.08
Matches are distributed among these distances:
40 3 0.04
41 55 0.65
42 25 0.29
43 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (41 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCAA
Found at i:2165844 original size:21 final size:21
Alignment explanation
Indices: 2165820--2165975 Score: 81
Period size: 21 Copynumber: 7.5 Consensus size: 21
2165810 TTTTCCTAAT
2165820 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGAATTATGAAAA
** *
2165841 TCGCAACGCGAATTAGGAAAA
1 TCGCATTGCGAATTATGAAAA
* **
2165862 TCGCATTGCG-A-TAGTCAGTA
1 TCGCATTGCGAATTA-TGAAAA
* * *
2165882 TCGCATTGCG-ATTTTCCAAAT
1 TCGCATTGCGAATTAT-GAAAA
* * *
2165903 TCGCATTGCGATTTACT--TAT
1 TCGCATTGCGAATTA-TGAAAA
**
2165923 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATTATGAAAA
** *
2165944 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCG-AATTATGAAAA
2165965 TCGCATTGCGA
1 TCGCATTGCGA
2165976 TAGTCATAAT
Statistics
Matches: 102, Mismatches: 25, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
19 2 0.02
20 31 0.30
21 62 0.61
22 6 0.06
23 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGAATTATGAAAA
Found at i:2165935 original size:103 final size:103
Alignment explanation
Indices: 2165756--2165995 Score: 326
Period size: 103 Copynumber: 2.3 Consensus size: 103
2165746 GACGCTATGT
* ** * *
2165756 AAATCGCATTGCGATAGTAAG-ATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCCTAAT
1 AAATCGCATTGCGATAGTCAGTA-TCGCATTGCGATTTACAAATTCGCATTGCGATTTTACTAAT
*
2165820 TCGCATTGCGAATTATGAAAATCGCAACGCG-AATTAGGA
65 TCGCATTGCGAATTAGGAAAATCGCAACGCGAAATT-GGA
* *
2165859 AAATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCATTGCGA-TTTACTTAT
1 AAATCGCATTGCGATAGTCAGTATCGCATTGCGA-TTTACAAATTCGCATTGCGATTTTACTAAT
*
2165923 TCGCATTGCGAATTGGGAAAATCGCAACGCGAAATTGGA
65 TCGCATTGCGAATTAGGAAAATCGCAACGCGAAATTGGA
*
2165962 AAATCGCATTGCGATAGTCA-TAATCGCGTTGCGA
1 AAATCGCATTGCGATAGTCAGT-ATCGCATTGCGA
2165996 ATCTGGAAAC
Statistics
Matches: 123, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
102 1 0.01
103 101 0.82
104 21 0.17
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (103 bp):
AAATCGCATTGCGATAGTCAGTATCGCATTGCGATTTACAAATTCGCATTGCGATTTTACTAATT
CGCATTGCGAATTAGGAAAATCGCAACGCGAAATTGGA
Found at i:2165948 original size:41 final size:41
Alignment explanation
Indices: 2165848--2165948 Score: 98
Period size: 41 Copynumber: 2.5 Consensus size: 41
2165838 AAATCGCAAC
*
2165848 GCGAATTAGGAAAATCGCATTGCGATAGTCAGTATCGCATT
1 GCGAATTAGGAAAATCGCATTGCGATACTCAGTATCGCATT
* *** * *
2165889 GCGATTTTCCAAATTCGCATTGCGATTTACTTA-T-TCGCATT
1 GCGAATTAGGAAAATCGCATTGCGA--TACTCAGTATCGCATT
*
2165930 GCGAATTGGGAAAATCGCA
1 GCGAATTAGGAAAATCGCA
2165949 ACGCGAAATT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
41 41 0.89
42 1 0.02
43 4 0.09
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (41 bp):
GCGAATTAGGAAAATCGCATTGCGATACTCAGTATCGCATT
Found at i:2168784 original size:64 final size:65
Alignment explanation
Indices: 2168712--2168867 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 65
2168702 ACACCCTAAT
* *
2168712 TCGAATGCATTTTGTGTACTGATGCACAG-CCATGCATCGATGCACTCCT-GATTTTATTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTT-TTGAAAC
2168775 A
65 A
* * * *
2168776 TCGAATGCATTTTATTTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTCTTTTGTAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTTTTGAAACA
* * *
2168841 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
2168868 CCCAAAGTAT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 26 0.33
65 49 0.62
66 4 0.05
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTTTTGAAACA
Found at i:2171511 original size:45 final size:45
Alignment explanation
Indices: 2171433--2171535 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
2171423 CATATTCAAT
* * *
2171433 GTGCATCGATGCA-CTCTTTAAAGAAGAAACATCGAATGCAATTC
1 GTGCATCGATGCATCCCCTTAAAGAAGAAACATCGAAGGCAATTC
* * *
2171477 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCGAAGGTAATTT
1 GTGCATCGATGCATCCCCTTAAAGAAG-AAACATCGAAGGCAATTC
*
2171522 GTGTATCGATGCAT
1 GTGCATCGATGCAT
2171536 GGGTAGTGCA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 15 0.30
45 35 0.70
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (45 bp):
GTGCATCGATGCATCCCCTTAAAGAAGAAACATCGAAGGCAATTC
Found at i:2171569 original size:24 final size:20
Alignment explanation
Indices: 2171542--2171599 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
2171532 GCATGGGTAG
2171542 TGCATCGATACACATGTTAAAGAA
1 TGCATCGATACAC-TG-T--AGAA
*
2171566 TGCATCGATGCACTGTAGAA
1 TGCATCGATACACTGTAGAA
*
2171586 TGCATCGATGCACT
1 TGCATCGATACACT
2171600 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 18 0.55
22 1 0.03
23 2 0.06
24 12 0.36
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCATCGATACACTGTAGAA
Found at i:2171587 original size:20 final size:20
Alignment explanation
Indices: 2171562--2171599 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2171552 CACATGTTAA
2171562 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
2171582 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
2171600 TCAAGGGGAA
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:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:2174586 original size:2 final size:2
Alignment explanation
Indices: 2174579--2174611 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2174569 AAGTGACATG
2174579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2174612 AAGGAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2175619 original size:64 final size:63
Alignment explanation
Indices: 2175503--2175643 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
2175493 CATATTCAAT
* * * *
2175503 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGAATCGATGTATAAGG-A
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGAATCGATGCAT-AGGTA
* * * * * *
2175566 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATTGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTGGTGAATCGATGCATAGGTA
2175630 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2175644 ATGTTAAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 18 0.28
64 47 0.72
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTGGTGAATCGATGCATAGGTA
Found at i:2175676 original size:20 final size:22
Alignment explanation
Indices: 2175631--2175688 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
2175621 GCATGGGTAG
2175631 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
2175655 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
2175675 TGCATCGATGCACT
1 TGCATCGATGCACT
2175689 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:2177654 original size:18 final size:18
Alignment explanation
Indices: 2177633--2177672 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2177623 AATTAGAAGT
2177633 GGTTAAGGAAAATTTTAA
1 GGTTAAGGAAAATTTTAA
2177651 GGTTAAGGAAAATTTTAA
1 GGTTAAGGAAAATTTTAA
2177669 GGTT
1 GGTT
2177673 CAGAGATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (18 bp):
GGTTAAGGAAAATTTTAA
Found at i:2196690 original size:28 final size:28
Alignment explanation
Indices: 2196658--2196733 Score: 134
Period size: 28 Copynumber: 2.7 Consensus size: 28
2196648 TCATTTTTAC
2196658 GATAGATAGAATATTGAATGGTTTGTAT
1 GATAGATAGAATATTGAATGGTTTGTAT
2196686 GATAGATAGAATATTGAATGGTTTGTAT
1 GATAGATAGAATATTGAATGGTTTGTAT
* *
2196714 GATAGGTAGAACATTGAATG
1 GATAGATAGAATATTGAATG
2196734 AATGGACCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.36
Consensus pattern (28 bp):
GATAGATAGAATATTGAATGGTTTGTAT
Found at i:2200914 original size:31 final size:31
Alignment explanation
Indices: 2200876--2200941 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2200866 ATATATTTCT
* * *
2200876 ATAAGTGTAAAAATCATTTTATAATAGTTTA
1 ATAAGTGTAAAAATCATTTGACAATAATTTA
* *
2200907 ATAAGTGTAAAGATTATTTGACAATAATTTA
1 ATAAGTGTAAAAATCATTTGACAATAATTTA
2200938 ATAA
1 ATAA
2200942 ATTTAATGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (31 bp):
ATAAGTGTAAAAATCATTTGACAATAATTTA
Found at i:2200990 original size:31 final size:31
Alignment explanation
Indices: 2200890--2201021 Score: 115
Period size: 31 Copynumber: 4.3 Consensus size: 31
2200880 GTGTAAAAAT
* * * * *
2200890 CATTTTATAATAGTTTAATAAGTGTAAAGAT
1 CATTTTATAATAATTTAATAAATTTAATGAC
* * *
2200921 TATTTGACAATAATTTAATAAATTTAATGAC
1 CATTTTATAATAATTTAATAAATTTAATGAC
* *
2200952 TATTTTATAATAATTTGATAAATTTTAATGAC
1 CATTTTATAATAATTTAATAAA-TTTAATGAC
* * * *
2200984 CA-TTTATAATTA-TTAAAAAAATTAATGAT
1 CATTTTATAATAATTTAATAAATTTAATGAC
2201013 CATTTTATA
1 CATTTTATA
2201022 TTATCTAAAA
Statistics
Matches: 82, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
29 9 0.11
30 12 0.15
31 51 0.62
32 10 0.12
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (31 bp):
CATTTTATAATAATTTAATAAATTTAATGAC
Found at i:2201024 original size:29 final size:30
Alignment explanation
Indices: 2200976--2201041 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
2200966 TTGATAAATT
2200976 TTAATGACCATTTATAATTAT-TAAAAAAA
1 TTAATGACCATTTATAATTATCTAAAAAAA
*
2201005 TTAATGATCATTT-TATATTATCT-AAAAAA
1 TTAATGACCATTTATA-ATTATCTAAAAAAA
*
2201034 TTAGTGAC
1 TTAATGAC
2201042 TAAAAGATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.06
29 29 0.91
30 1 0.03
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (30 bp):
TTAATGACCATTTATAATTATCTAAAAAAA
Found at i:2203881 original size:3 final size:3
Alignment explanation
Indices: 2203873--2203916 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
2203863 GGCATAGGAC
2203873 AAG AAG AAG AAG AAG AAG AAG AAG AAG CAA- AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AA
2203917 AATTATTATC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2204038 original size:4 final size:4
Alignment explanation
Indices: 2204029--2204055 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2204019 TGGGGGTGTT
2204029 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
2204056 TTTTTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:2204905 original size:23 final size:26
Alignment explanation
Indices: 2204878--2204952 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 26
2204868 ATTTTGATTT
2204878 TAATATTAATTTTTAA-A-TAAATTA
1 TAATATTAATTTTTAATATTAAATTA
*
2204902 -AATATTAATATTTTAATATTATATTA
1 TAATATTAAT-TTTTAATATTAAATTA
2204928 TAGATATTAA-TTTTAATATTAAATT
1 TA-ATATTAATTTTTAATATTAAATT
2204953 TTTAAATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
23 9 0.20
24 6 0.14
25 1 0.02
26 20 0.45
27 1 0.02
28 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
TAATATTAATTTTTAATATTAAATTA
Found at i:2204956 original size:40 final size:38
Alignment explanation
Indices: 2204902--2204986 Score: 95
Period size: 38 Copynumber: 2.2 Consensus size: 38
2204892 AAATAAATTA
*
2204902 AATATT-AATATTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAAATATTTTAA-A-TAAATTA-A-ATATTAATTTTT
2204942 AATATTAAAT-TTTTAAATAAATTAAATATTAATTTTTT
1 AATATTAAATATTTTAAATAAATTAAATATTAA-TTTTT
2204980 AATATTA
1 AATATTA
2204987 TATTATAGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
36 7 0.17
37 1 0.02
38 17 0.41
39 1 0.02
40 12 0.29
41 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (38 bp):
AATATTAAATATTTTAAATAAATTAAATATTAATTTTT
Found at i:2204964 original size:64 final size:63
Alignment explanation
Indices: 2204851--2205007 Score: 248
Period size: 64 Copynumber: 2.5 Consensus size: 63
2204841 GTTTTATTTA
* *
2204851 ATTTT-ATATTATATT-T-GATTTTGATTTTAATATTAATTTTTAAATAAATTAAATATTAAT
1 ATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTAAT
2204911 ATTTTAATATTATATTATAGATATTAATTTTAATATTAAATTTTTAAATAAATTAAATATTAAT
1 ATTTTAATATTATATTATAGATATTAATTTTAATATT-AATTTTTAAATAAATTAAATATTAAT
*
2204975 TTTTTAATATTATATTATAGATATTTAATTTTA
1 ATTTTAATATTATATTATAGATA-TTAATTTTA
2205008 TATCATATAA
Statistics
Matches: 89, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
60 5 0.06
61 10 0.11
62 1 0.01
63 16 0.18
64 48 0.54
65 9 0.10
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (63 bp):
ATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAATAAATTAAATATTAAT
Found at i:2205062 original size:20 final size:19
Alignment explanation
Indices: 2205002--2205063 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
2204992 TAGATATTTA
*
2205002 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
2205021 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
2205039 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
2205059 ATTTT
1 ATTTT
2205064 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:2205583 original size:31 final size:31
Alignment explanation
Indices: 2205524--2205584 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
2205514 GTAGTTGTAT
* * **
2205524 AAATTATTTAAATTTTAGTATTGTAAAACTA
1 AAATTATTTAAATATCAGTATTACAAAACTA
2205555 AAATTATTTAAATATCAGTATTACAAAACT
1 AAATTATTTAAATATCAGTATTACAAAACT
2205585 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (31 bp):
AAATTATTTAAATATCAGTATTACAAAACTA
Found at i:2206034 original size:15 final size:15
Alignment explanation
Indices: 2206016--2206102 Score: 131
Period size: 15 Copynumber: 5.9 Consensus size: 15
2206006 ATAAGGTTAT
* *
2206016 TTATTTTAAAATAAT
1 TTATTATAAAATAAA
*
2206031 TTATT-TAAAATAAT
1 TTATTATAAAATAAA
2206045 TTATTATAAAATAAA
1 TTATTATAAAATAAA
2206060 TTATTATAAAATAAA
1 TTATTATAAAATAAA
*
2206075 TTATTTTAAAATAAA
1 TTATTATAAAATAAA
2206090 TTATTATAAAATA
1 TTATTATAAAATA
2206103 TGGAATGATT
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
14 14 0.21
15 54 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTATTATAAAATAAA
Found at i:2206037 original size:32 final size:30
Alignment explanation
Indices: 2205995--2206102 Score: 114
Period size: 30 Copynumber: 3.6 Consensus size: 30
2205985 AAAATAATTT
* *
2205995 TAAATAATTTAATAAGGTTATTTATTTTAAAA
1 TAAATTATTTAATAA--TAATTTATTTTAAAA
* *
2206027 TAATTTATTTAA-AATAATTTATTATAAAA
1 TAAATTATTTAATAATAATTTATTTTAAAA
*
2206056 TAAATTATTATAA-AATAAATTATTTTAAAA
1 TAAATTATT-TAATAATAATTTATTTTAAAA
2206086 TAAATTATTATAA-AATA
1 TAAATTATT-TAATAATA
2206103 TGGAATGATT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
29 21 0.31
30 35 0.51
31 2 0.03
32 10 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (30 bp):
TAAATTATTTAATAATAATTTATTTTAAAA
Found at i:2206144 original size:32 final size:31
Alignment explanation
Indices: 2206108--2206207 Score: 119
Period size: 32 Copynumber: 3.5 Consensus size: 31
2206098 AAATATGGAA
2206108 TGATTTATTTTAAATAATTTATTAGTATAAAT
1 TGATTTATTTTAAATAATTTATTAGTAT-AAT
2206140 TGATTTATTTT-AA-AA--TA-T-G---AAT
1 TGATTTATTTTAAATAATTTATTAGTATAAT
2206162 TGATTTATTTTAAATAATTTATTAGTATGAAT
1 TGATTTATTTTAAATAATTTATTAGTAT-AAT
2206194 TGATTTATTTTAAA
1 TGATTTATTTTAAA
2206208 ATATGGATTG
Statistics
Matches: 58, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 14 0.24
23 2 0.03
24 2 0.03
26 3 0.05
27 2 0.03
28 3 0.05
30 2 0.03
31 2 0.03
32 28 0.48
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (31 bp):
TGATTTATTTTAAATAATTTATTAGTATAAT
Found at i:2206155 original size:54 final size:54
Alignment explanation
Indices: 2206090--2206390 Score: 294
Period size: 54 Copynumber: 5.5 Consensus size: 54
2206080 TTAAAATAAA
* **
2206090 TTATTATAAAATATGGAATGATTTATTTTAAATAATTTATTAGTATAAATTGAT
1 TTATTTTAAAATATGGAATGATTTATTTTAAATAATTTATTAGTATGGATTGAT
*
2206144 TTATTTTAAAATAT-GAATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
1 TTATTTTAAAATATGGAA-TGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* *
2206198 TTATTTTAAAATATGGATTGATTTATTTTAAATGATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATGGAATGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* * *
2206252 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-TAG-ATTGATTTA-
1 TTA-TTT---TAA---A--A-TATGGAATGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* *** *
2206309 TTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGGAATGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* *
2206364 TTATTTTAAAATATGGATTGATATATT
1 TTATTTTAAAATATGGAATGATTTATT
2206391 ATTGTAGTTG
Statistics
Matches: 208, Mismatches: 19, Indels: 40
0.78 0.07 0.15
Matches are distributed among these distances:
48 18 0.09
49 2 0.01
50 2 0.01
52 2 0.01
53 8 0.04
54 121 0.58
55 12 0.06
56 2 0.01
57 3 0.01
58 10 0.05
59 3 0.01
60 2 0.01
61 1 0.00
62 1 0.00
63 3 0.01
64 18 0.09
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.51
Consensus pattern (54 bp):
TTATTTTAAAATATGGAATGATTTATTTTAAATAATTTATTAGTATGGATTGAT
Found at i:2206212 original size:22 final size:22
Alignment explanation
Indices: 2206187--2206229 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2206177 AATTTATTAG
2206187 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
2206209 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
2206230 TGATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:2206249 original size:32 final size:32
Alignment explanation
Indices: 2206209--2206293 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
2206199 TATTTTAAAA
*
2206209 TATGGATTGATTTATTTTAAATGATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
2206241 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
2206273 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2206294 ATATAGATTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:2206328 original size:26 final size:25
Alignment explanation
Indices: 2206299--2206416 Score: 89
Period size: 26 Copynumber: 4.5 Consensus size: 25
2206289 TTAAAATATA
2206299 GATTGATTTATTATTGTAGTTGTATG
1 GATTGATTTATTATTGTA-TTGTATG
*
2206325 GATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTA--TT--AT--TGTATT-GTATG
***
2206357 GATTGATTTA-T-TT-TAAAATATG
1 GATTGATTTATTATTGTATTGTATG
*
2206379 GATTGATATATTATTGTAGTTGTATG
1 GATTGATTTATTATTGTA-TTGTATG
2206405 GATTGATTTATT
1 GATTGATTTATT
2206417 TTAAATAATT
Statistics
Matches: 72, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
22 13 0.18
23 3 0.04
24 3 0.04
25 2 0.03
26 26 0.36
28 2 0.03
29 1 0.01
30 2 0.03
31 2 0.03
32 18 0.25
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.53
Consensus pattern (25 bp):
GATTGATTTATTATTGTATTGTATG
Found at i:2206362 original size:80 final size:80
Alignment explanation
Indices: 2206155--2206470 Score: 508
Period size: 80 Copynumber: 3.9 Consensus size: 80
2206145 TATTTTAAAA
* *
2206155 TATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
2206220 TTATTTTAAATGATTTA-TTAG
66 TTA--TT--AT--TGTAGTT-G
*
2206241 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
2206306 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
2206321 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
2206386 ATATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
2206401 TATGGATTGATTTATTTTAAATAATTCATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
2206466 TTATT
66 TTATT
2206471 TTAAATAATC
Statistics
Matches: 221, Mismatches: 8, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
80 150 0.68
81 2 0.01
82 2 0.01
84 2 0.01
86 65 0.29
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:2206441 original size:32 final size:30
Alignment explanation
Indices: 2206400--2206561 Score: 158
Period size: 32 Copynumber: 5.7 Consensus size: 30
2206390 TATTGTAGTT
2206400 GTATGGATTGATTTATTTTAAATAATTCATTA
1 GTATGGATTGATTTATTTTAAATAA-T-ATTA
2206432 GTATGGATTGATTTA-TTT---TAA-A--A
1 GTATGGATTGATTTATTTTAAATAATATTA
2206455 -TATGGATTGATTTATTTTAAATAATCTATTA
1 GTATGGATTGATTTATTTTAAATAA--TATTA
2206486 GTATGGATTGATTTATTTT-AA-AATA-TA
1 GTATGGATTGATTTATTTTAAATAATATTA
2206513 G-AT---TT-ATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAA--TATTA
2206540 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
2206562 ATATAGATTG
Statistics
Matches: 110, Mismatches: 0, Indels: 40
0.73 0.00 0.27
Matches are distributed among these distances:
22 23 0.21
23 8 0.07
24 2 0.02
25 1 0.01
26 7 0.06
27 6 0.05
28 7 0.06
29 1 0.01
30 2 0.02
31 8 0.07
32 45 0.41
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.51
Consensus pattern (30 bp):
GTATGGATTGATTTATTTTAAATAATATTA
Found at i:2206461 original size:22 final size:22
Alignment explanation
Indices: 2206433--2206475 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2206423 AATTCATTAG
2206433 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
2206455 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
2206476 TAATCTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:2206465 original size:54 final size:54
Alignment explanation
Indices: 2206241--2206593 Score: 375
Period size: 54 Copynumber: 6.6 Consensus size: 54
2206231 GATTTATTAG
2206241 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
2206295 TATAGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * * * ***
2206342 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATATATTATTGTAGTTG
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG--AT-TTATTTTA-AAA
*
2206401 TATGGATTGATTTATTTTAAATAATTCATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
2206455 TATGGATTGATTTATTTTAAATAATCTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
2206509 TATAGATTTATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
2206563 TATAGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
2206594 TTGTAGTTAT
Statistics
Matches: 246, Mismatches: 36, Indels: 34
0.78 0.11 0.11
Matches are distributed among these distances:
47 4 0.02
48 27 0.11
49 3 0.01
50 5 0.02
51 1 0.00
52 2 0.01
53 1 0.00
54 155 0.63
55 10 0.04
56 7 0.03
57 15 0.06
58 15 0.06
59 1 0.00
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:2206643 original size:31 final size:31
Alignment explanation
Indices: 2206608--2206666 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2206598 AGTTATATTG
* *
2206608 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
2206639 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
2206667 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:2210821 original size:19 final size:20
Alignment explanation
Indices: 2210797--2210847 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2210787 AATGACCAAT
2210797 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
2210816 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
2210836 AAAATCGCAACG
1 AAAATCGCAACG
2210848 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:2210841 original size:20 final size:20
Alignment explanation
Indices: 2210797--2211074 Score: 130
Period size: 20 Copynumber: 13.6 Consensus size: 20
2210787 AATGACCAAT
* *
2210797 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
2210816 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
2210836 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
2210856 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
2210876 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
2210897 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2210920 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
2210940 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
2210960 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
2210980 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2211003 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * * *
2211023 AGAACCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
2211043 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
*
2211063 AGAATCGCAACG
1 AAAATCGCAACG
2211075 TTAAAAAGAA
Statistics
Matches: 203, Mismatches: 44, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
19 17 0.08
20 143 0.70
21 14 0.07
23 29 0.14
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:2211009 original size:63 final size:63
Alignment explanation
Indices: 2210942--2211063 Score: 190
Period size: 63 Copynumber: 1.9 Consensus size: 63
2210932 CGATTGATTG
* * * * * *
2210942 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGACTGAGAGAACCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAGAA
2211005 AATCGCAATGCGACTGAGAGAACCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGA
1 AATCGCAATGCGACTGAGAGAACCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGA
2211064 GAATCGCAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (63 bp):
AATCGCAATGCGACTGAGAGAACCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAGAA
Found at i:2211011 original size:83 final size:83
Alignment explanation
Indices: 2210901--2211074 Score: 258
Period size: 83 Copynumber: 2.1 Consensus size: 83
2210891 GCTTCCAAGT
* ** * * * *
2210901 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAACCGCAATGCGACTGAGAGAATC
* *
2210966 GCAATGCGATTGAGAGAG
66 GCAACGCGATTGAGAGAA
2210984 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAACCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAACCGCAATGCGACTGAGAGAATC
*
2211049 GCAACGCGATTTAGAGAA
66 GCAACGCGATTGAGAGAA
2211067 TCGCAACG
1 TCGCAACG
2211075 TTAAAAAGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.20
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAACCGCAATGCGACTGAGAGAATC
GCAACGCGATTGAGAGAA
Found at i:2211065 original size:40 final size:40
Alignment explanation
Indices: 2210922--2211072 Score: 167
Period size: 40 Copynumber: 3.7 Consensus size: 40
2210912 TTTAGAAGAA
** * *
2210922 AATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* * *
2210962 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGA-TT-G-AGAG
* * *
2211005 AATCGCAATGCGACTGAGAGAACCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
* *
2211045 AATCGCAACGCGATTTAGAGAATCGCAA
1 AATCGCAATGCGATTGAGAGAATCGCAA
2211073 CGTTAAAAAG
Statistics
Matches: 91, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
40 56 0.62
41 3 0.03
42 1 0.01
43 31 0.34
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.20
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
Found at i:2211088 original size:20 final size:20
Alignment explanation
Indices: 2211065--2211104 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2211055 CGATTTAGAG
*
2211065 AATCGCAACGTTAAAAAGAA
1 AATCGCAACGGTAAAAAGAA
*
2211085 AATCGCAACGGTCAAAAGAA
1 AATCGCAACGGTAAAAAGAA
2211105 TAGTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGGTAAAAAGAA
Found at i:2211193 original size:6 final size:6
Alignment explanation
Indices: 2211182--2211220 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
2211172 GACACGTATT
2211182 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
2211221 CGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2211926 original size:6 final size:6
Alignment explanation
Indices: 2211915--2212120 Score: 412
Period size: 6 Copynumber: 34.3 Consensus size: 6
2211905 GTCTCGGGTC
2211915 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
2211963 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
2212011 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
2212059 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
2212107 GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GT
2212121 AATACGTGTC
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 200 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GTCGTG
Found at i:2212223 original size:20 final size:20
Alignment explanation
Indices: 2212198--2212241 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2212188 TTTTTAACTA
*
2212198 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
2212218 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
2212238 TTCT
1 TTCT
2212242 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:2212274 original size:40 final size:40
Alignment explanation
Indices: 2212230--2212400 Score: 207
Period size: 40 Copynumber: 4.2 Consensus size: 40
2212220 CTTTTTAACG
* * *
2212230 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* * * *
2212270 TTGCGATTCTCTCAGTCACATTGCGATTCTCTCAGTCTCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
* *
2212310 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTTCTAAATCGCG
1 TTGCGATTCTCTCAATCGCATTGCGATTCTC-TC--AATCGCA
* **
2212353 TTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCA
1 TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
2212393 TTGCGATT
1 TTGCGATT
2212401 TTCTTCTAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
40 76 0.68
41 2 0.02
42 2 0.02
43 31 0.28
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCA
Found at i:2212392 original size:63 final size:63
Alignment explanation
Indices: 2212228--2212421 Score: 250
Period size: 63 Copynumber: 3.1 Consensus size: 63
2212218 TTCTTTTTAA
* * * * *
2212228 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTC-TC--AGTCA
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
* * * *
2212288 CATTGCGATTCTCTCAGTCTCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTTCTAAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
* ** *
2212351 CGTTGCGACTCTCTCAATCGCATTGCGATTCAATCAATCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
2212414 CGTTGCGA
1 CGTTGCGA
2212422 ACTTGGAAGC
Statistics
Matches: 114, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
60 46 0.40
61 2 0.02
63 66 0.58
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.36
Consensus pattern (63 bp):
CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTCTTCTAAATCG
Found at i:2212515 original size:19 final size:20
Alignment explanation
Indices: 2212228--2212525 Score: 143
Period size: 20 Copynumber: 14.6 Consensus size: 20
2212218 TTCTTTTTAA
2212228 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
2212248 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * * *
2212268 CATTGCGATTCTCTCAGTCA
1 CGTTGCGATTTTCTAAATCG
* * * * *
2212288 CATTGCGATTCTCTCAGTCT
1 CGTTGCGATTTTCTAAATCG
* * * *
2212308 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
2212328 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
2212351 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
2212371 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
2212391 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
2212414 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
2212435 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
2212453 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
2212475 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
*
2212495 CGTTGCGATTTT-TATATCG
1 CGTTGCGATTTTCTAAATCG
2212514 CGTTGCGATTTT
1 CGTTGCGATTTT
2212526 ATTGGTCATT
Statistics
Matches: 225, Mismatches: 42, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
18 2 0.01
19 18 0.08
20 158 0.70
21 15 0.07
22 5 0.02
23 27 0.12
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:2212673 original size:2 final size:2
Alignment explanation
Indices: 2212612--2212654 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2212602 TTTTCTCTTT
2212612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2212654 T
1 T
2212655 GGGATAATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2213714 original size:12 final size:12
Alignment explanation
Indices: 2213696--2213729 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2213686 ACCATACGGT
2213696 ATGAACAGTACC
1 ATGAACAGTACC
* *
2213708 GTGAACAATACC
1 ATGAACAGTACC
2213720 ATGAACAGTA
1 ATGAACAGTA
2213730 AAAATTCGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:2234756 original size:15 final size:15
Alignment explanation
Indices: 2234733--2234834 Score: 96
Period size: 15 Copynumber: 6.7 Consensus size: 15
2234723 AATTATGTCA
*
2234733 TATTGTATTTAATGT
1 TATTGTATTTTATGT
* *
2234748 TATTATATTTTATGG
1 TATTGTATTTTATGT
** *
2234763 TATTAAATTTTATAT
1 TATTGTATTTTATGT
* * *
2234778 TTTTGTATTTTCTGG
1 TATTGTATTTTATGT
*
2234793 TATTTTATTTTATGT
1 TATTGTATTTTATGT
*
2234808 TATTGTATCTTATGT
1 TATTGTATTTTATGT
2234823 TATTGTAATTTT
1 TATTGT-ATTTT
2234835 TAATATTGTA
Statistics
Matches: 67, Mismatches: 19, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
15 63 0.94
16 4 0.06
ACGTcount: A:0.24, C:0.02, G:0.11, T:0.64
Consensus pattern (15 bp):
TATTGTATTTTATGT
Found at i:2234787 original size:30 final size:30
Alignment explanation
Indices: 2234747--2234846 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
2234737 GTATTTAATG
*
2234747 TTATTATATTTTATGGTATTAAATTTTATA
1 TTATTGTATTTTATGGTATTAAATTTTATA
* * ** *
2234777 TTTTTGTATTTTCTGGTATTTTATTTTATG
1 TTATTGTATTTTATGGTATTAAATTTTATA
* * *
2234807 TTATTGTATCTTATGTTATTGTAATTTT-TA
1 TTATTGTATTTTATGGTATT-AAATTTTATA
*
2234837 ATATTGTATT
1 TTATTGTATT
2234847 GTGTCCTATT
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
30 49 0.89
31 6 0.11
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.64
Consensus pattern (30 bp):
TTATTGTATTTTATGGTATTAAATTTTATA
Found at i:2234881 original size:25 final size:25
Alignment explanation
Indices: 2234838--2234888 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2234828 TAATTTTTAA
* *
2234838 TATTGTATTGTGTCCTATTTTATTT
1 TATTGTATTGTCTCCTATTATATTT
* *
2234863 TATTGTATTTTCTCTTATTATATTT
1 TATTGTATTGTCTCCTATTATATTT
2234888 T
1 T
2234889 GTATTTTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.67
Consensus pattern (25 bp):
TATTGTATTGTCTCCTATTATATTT
Found at i:2234907 original size:23 final size:22
Alignment explanation
Indices: 2234865--2234909 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2234855 TTTTATTTTA
*
2234865 TTGTATTTTCTCTTATTATATT
1 TTGTATTTTCTCTTAATATATT
2234887 TTGTATTTT-TCATATAATATATT
1 TTGTATTTTCTC-T-TAATATATT
2234910 ATAAGTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 10 0.50
23 8 0.40
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.64
Consensus pattern (22 bp):
TTGTATTTTCTCTTAATATATT
Found at i:2237685 original size:24 final size:25
Alignment explanation
Indices: 2237639--2237690 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
2237629 GTTTGTATTT
*
2237639 TCTCTGTTTTTTTTTTCTATGTCTC
1 TCTCTATTTTTTTTTTCTATGTCTC
2237664 TCTCTATTCTTTTTTTT-T-TGTCTC
1 TCTCTATT-TTTTTTTTCTATGTCTC
2237688 TCT
1 TCT
2237691 GTCTCGTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 8 0.32
26 8 0.32
ACGTcount: A:0.04, C:0.21, G:0.06, T:0.69
Consensus pattern (25 bp):
TCTCTATTTTTTTTTTCTATGTCTC
Found at i:2238191 original size:3 final size:3
Alignment explanation
Indices: 2238183--2238304 Score: 174
Period size: 3 Copynumber: 40.7 Consensus size: 3
2238173 TTAATATATT
* * *
2238183 TAA TAA TAA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2238231 TAA TAA TAT TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2238279 TAA TAA TAA T-A TGGA TAA TAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TA
2238305 TGGATAAAAA
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
2 2 0.02
3 102 0.96
4 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2238875 original size:113 final size:113
Alignment explanation
Indices: 2238625--2239630 Score: 1771
Period size: 113 Copynumber: 8.9 Consensus size: 113
2238615 AGAGTCATTC
* * * *
2238625 AAAAGGTCGAATAAATTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
2238690 TATGAAC-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
2238737 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** * *** *
2238802 TATGAACTATACCTGGCAATGTTGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
2238850 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
2238915 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
2238963 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
2239028 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
2239076 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
2239141 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
2239189 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
2239254 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
2239302 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
2239367 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAAGT
66 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
*
2239415 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
2239480 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
2239528 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** * *
2239593 TATGAACTTTCTCTTCAAAAAATAATCCATCAATTGAT
66 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGAT
2239631 AGATTTGAAT
Statistics
Matches: 863, Mismatches: 30, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
112 68 0.08
113 795 0.92
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
Found at i:2240367 original size:14 final size:14
Alignment explanation
Indices: 2240348--2240375 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2240338 GGTTCTGTAG
2240348 TTCCTACTAAACCA
1 TTCCTACTAAACCA
2240362 TTCCTACTAAACCA
1 TTCCTACTAAACCA
2240376 AATCAGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
TTCCTACTAAACCA
Found at i:2240504 original size:52 final size:52
Alignment explanation
Indices: 2240442--2240598 Score: 305
Period size: 52 Copynumber: 3.0 Consensus size: 52
2240432 AATTCGGTGA
2240442 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
*
2240494 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGT
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
2240546 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
2240598 T
1 T
2240599 ATTGGCAAAT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 103 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (52 bp):
TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
Found at i:2240685 original size:83 final size:83
Alignment explanation
Indices: 2240546--2241297 Score: 1339
Period size: 83 Copynumber: 9.0 Consensus size: 83
2240536 CAGAAGATGT
2240546 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
2240611 ATCTTCTAAATTCAATGA
66 ATCTTCTAAATTCAATGA
*
2240629 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
2240694 ATCTTCTAAATTCAATGA
66 ATCTTCTAAATTCAATGA
* *
2240712 TTGGTTCTGTCTAACCAGATCTGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATT
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATT
2240776 CATCTTCTAAATTCAATGA
65 CATCTTCTAAATTCAATGA
2240795 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
2240860 ATCTTCTAAATTCAATGA
66 ATCTTCTAAATTCAATGA
*
2240878 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
2240943 ATCTTCTAAATTCAATGA
66 ATCTTCTAAATTCAATGA
* *
2240961 TTGGTTCTGTCTAACCAGATCTGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATT
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATT
2241025 CATCTTCTAAATTCAATGA
65 CATCTTCTAAATTCAATGA
2241044 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
2241109 ATCTTCTAAATTCAATGA
66 ATCTTCTAAATTCAATGA
* * *
2241127 TTGGTTCTGTCTAACCATATCTGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATT
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATT
2241191 CATCTTCTAAATTCAATGA
65 CATCTTCTAAATTCAATGA
* * *
2241210 TTGATTATGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATT
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATT
2241275 CATCTTCTAAATTCAATGA
65 CATCTTCTAAATTCAATGA
2241294 TTGG
1 TTGG
2241298 ACTAAGATAT
Statistics
Matches: 641, Mismatches: 22, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
82 6 0.01
83 600 0.94
84 35 0.05
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (83 bp):
TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
ATCTTCTAAATTCAATGA
Found at i:2242452 original size:16 final size:14
Alignment explanation
Indices: 2242417--2242498 Score: 71
Period size: 12 Copynumber: 5.6 Consensus size: 14
2242407 CCTTGACCCC
*
2242417 CTTTCTTTTTCTTCT
1 CTTT-TTTTTCTTTT
2242432 C-TTTTTTTCATTTT
1 CTTTTTTTTC-TTTT
2242446 CTATTTTTTTTCTTTT
1 C--TTTTTTTTCTTTT
2242462 C--TTTTTTCTTTT
1 CTTTTTTTTCTTTT
*
2242474 CTTTCTTTTCTTTTT
1 CTTTTTTTTC-TTTT
2242489 CTTTTCTTTT
1 CTTTT-TTTT
2242499 TTCTTCAAGC
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
12 12 0.21
13 6 0.11
14 12 0.21
15 9 0.16
16 9 0.16
17 8 0.14
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTTTTTCTTTT
Found at i:2242463 original size:5 final size:5
Alignment explanation
Indices: 2242418--2242498 Score: 69
Period size: 5 Copynumber: 15.6 Consensus size: 5
2242408 CTTGACCCCC
* *
2242418 TTTCT TTT-T CTTCT CTTT-T TTTCAT TTTCT ATTTTT TTTCT TTTCTTT
1 TTTCT TTTCT TTTCT -TTTCT TTTC-T TTTCT -TTTCT TTTCT TTTC--T
2242466 TTTCT TTTC- TTTCT TTTCTT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTC-T TTTCT TTTCT TTT
2242499 TTCTTCAAGC
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
4 10 0.16
5 32 0.51
6 16 0.25
7 5 0.08
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:2242488 original size:32 final size:32
Alignment explanation
Indices: 2242418--2242503 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
2242408 CTTGACCCCC
* *
2242418 TTTCTTTTTCTTCTCTTTTTT-TCATTTTCTA
1 TTTCTTTTTCTTTTCTTTTTTCTTATTTTCTA
*
2242449 TTT-TTTTTCTTTTCTTTTTTCTTTTCTTTCT-
1 TTTCTTTTTCTTTTCTTTTTTCTTAT-TTTCTA
2242480 TTTCTTTTTCTTTTCTTTTTTCTT
1 TTTCTTTTTCTTTTCTTTTTTCTT
2242504 CAAGCATAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
30 16 0.33
31 8 0.16
32 25 0.51
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (32 bp):
TTTCTTTTTCTTTTCTTTTTTCTTATTTTCTA
Found at i:2253151 original size:18 final size:18
Alignment explanation
Indices: 2253128--2253177 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
2253118 AAAATGCTTG
2253128 TAAATAAAATAAAACAT-A
1 TAAATAAAATAAAA-ATAA
**
2253146 TAAATATTATAAAAATAA
1 TAAATAAAATAAAAATAA
2253164 TAAAT-AAATAAAAA
1 TAAATAAAATAAAAA
2253178 GAATGAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAATAAAATAAAAATAA
Found at i:2254836 original size:24 final size:24
Alignment explanation
Indices: 2254800--2254850 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2254790 GTTTGTATTT
* *
2254800 TCTCTGTTTTTTTTTCTATGTCTC
1 TCTCTATTCTTTTTTCTATGTCTC
* *
2254824 TCTCTATTCTTTTTTTTTTGTCTC
1 TCTCTATTCTTTTTTCTATGTCTC
2254848 TCT
1 TCT
2254851 GTCTCGTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.04, C:0.22, G:0.06, T:0.69
Consensus pattern (24 bp):
TCTCTATTCTTTTTTCTATGTCTC
Found at i:2255354 original size:3 final size:3
Alignment explanation
Indices: 2255346--2255470 Score: 196
Period size: 3 Copynumber: 41.7 Consensus size: 3
2255336 TTAATATATT
* *
2255346 TAA TAA TAA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
2255394 TAG TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2255442 TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2255471 TGGATAAAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 110 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2257752 original size:41 final size:41
Alignment explanation
Indices: 2257707--2257784 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
2257697 GCGAATTTGG
* *
2257707 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATAATGACTATCGCAACGCGATAATAC
*
2257748 AAAATCGCAACGCGATAATGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATAATGACTATCGCAACGCGATA
2257785 CTGACTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATAATGACTATCGCAACGCGATAATAC
Found at i:2257818 original size:21 final size:20
Alignment explanation
Indices: 2257710--2257824 Score: 108
Period size: 20 Copynumber: 5.7 Consensus size: 20
2257700 AATTTGGAAA
* *
2257710 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATGACT
*
2257730 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATAATGAC--T
2257751 ATCGCAACGCGATAATGACT
1 ATCGCAACGCGATAATGACT
* *
2257771 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* *
2257791 TTCGCAACGAGATAAT-ACAT
1 ATCGCAACGCGATAATGAC-T
*
2257811 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
2257825 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.05
20 47 0.59
21 26 0.33
22 2 0.03
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:2258022 original size:22 final size:22
Alignment explanation
Indices: 2257997--2258047 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
2257987 CTACGGCGAC
2257997 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
2258019 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
2258041 ATCCGTC
1 ATCCGTC
2258048 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:2258351 original size:20 final size:20
Alignment explanation
Indices: 2258326--2258374 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2258316 GCGATTCTCT
2258326 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
2258346 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
2258366 TGTTGCGAT
1 CGTTGCGAT
2258375 TTTTATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2258382 original size:20 final size:20
Alignment explanation
Indices: 2258359--2258396 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2258349 TGCGATAGTC
2258359 ATTTTCGTGTTGCGATTTTT
1 ATTTTCGTGTTGCGATTTTT
2258379 ATTTTCGTGTTGCGATTT
1 ATTTTCGTGTTGCGATTT
2258397 CAGAAACTAT
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:0.11, C:0.11, G:0.21, T:0.58
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTT
Found at i:2259738 original size:18 final size:18
Alignment explanation
Indices: 2259717--2259764 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
2259707 TCCACTTTGG
2259717 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2259735 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2259753 AAGCCATCACCT
1 GAGCCATCACCT
2259765 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.46, G:0.10, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2260415 original size:14 final size:15
Alignment explanation
Indices: 2260383--2260416 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
2260373 AATGCGAAAT
2260383 GAAAATCGCAACGAC
1 GAAAATCGCAACGAC
2260398 -AAAATCGCAACG-C
1 GAAAATCGCAACGAC
2260411 GAAAAT
1 GAAAAT
2260417 GAAAATCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 17 0.94
ACGTcount: A:0.50, C:0.24, G:0.18, T:0.09
Consensus pattern (15 bp):
GAAAATCGCAACGAC
Found at i:2260421 original size:20 final size:20
Alignment explanation
Indices: 2260309--2260427 Score: 90
Period size: 20 Copynumber: 6.3 Consensus size: 20
2260299 TAGTTTACTT
* * *
2260309 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAATGAAAA
**
2260329 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGAAAA
* ***
2260349 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGAAAA
*
2260369 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
2260388 TCGCAA--CG---A-CAAAA
1 TCGCAACGCGAAAATGAAAA
2260402 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
2260422 TCGCAA
1 TCGCAA
2260428 TGCAATTTGT
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.03
17 2 0.03
19 13 0.16
20 52 0.65
ACGTcount: A:0.44, C:0.24, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:2260503 original size:19 final size:19
Alignment explanation
Indices: 2260439--2260527 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
2260429 GCAATTTGTG
* *
2260439 TTTCGCGTTGCAATTTTCA
1 TTTCGCATTGCGATTTTCA
2260458 TTTCGCATTGCGATTTT--
1 TTTCGCATTGCGATTTTCA
*
2260475 GTT-G--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
**
2260491 TTTCGCATTGCGATAGTCA
1 TTTCGCATTGCGATTTTCA
*
2260510 TTTTCGCGTTGCGATTTT
1 -TTTCGCATTGCGATTTT
2260528 AAGTTTCGTG
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 3 0.05
19 25 0.45
20 14 0.25
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.48
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:2260534 original size:20 final size:20
Alignment explanation
Indices: 2260438--2260543 Score: 84
Period size: 20 Copynumber: 5.7 Consensus size: 20
2260428 TGCAATTTGT
*
2260438 GTTTCGCGTTGCAATTTTCA
1 GTTTCGCGTTGCGATTTTCA
*
2260458 -TTTCGCATTGCGATTTT--
1 GTTTCGCGTTGCGATTTTCA
2260475 G-TT---GTTGCGATTTTCA
1 GTTTCGCGTTGCGATTTTCA
* **
2260491 -TTTCGCATTGCGATAGTCA
1 GTTTCGCGTTGCGATTTTCA
* *
2260510 TTTTCGCGTTGCGATTTTAA
1 GTTTCGCGTTGCGATTTTCA
*
2260530 GTTTCGTGTTGCGA
1 GTTTCGCGTTGCGA
2260544 AAGTAAACTA
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 25 0.38
20 27 0.41
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.46
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTCA
Found at i:2260621 original size:27 final size:26
Alignment explanation
Indices: 2260559--2260623 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 26
2260549 AACTATTCTT
*
2260559 CTTCTGGAATGTTTATATATGTTGTC
1 CTTCTGGAATGTTTATATATGTTGTA
**
2260585 CTT-TTAAATGTTTATATAAGTGTT-TA
1 CTTCTGGAATGTTTATAT-A-TGTTGTA
2260611 CTTCTGGAATGTT
1 CTTCTGGAATGTT
2260624 ATCTGATGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 12 0.39
26 8 0.26
27 11 0.35
ACGTcount: A:0.23, C:0.09, G:0.17, T:0.51
Consensus pattern (26 bp):
CTTCTGGAATGTTTATATATGTTGTA
Found at i:2260924 original size:21 final size:20
Alignment explanation
Indices: 2260898--2260966 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
2260888 CTGTCATCCC
2260898 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
2260919 TCAAGAGACCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
2260940 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
2260960 TCAAGAG
1 TCAAGAG
2260967 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.26, C:0.41, G:0.14, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:2260978 original size:41 final size:42
Alignment explanation
Indices: 2260888--2260978 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
2260878 CCCGACTCAC
* *
2260888 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGACCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGACCA
* * *
2260930 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGACCA
2260971 CTGTCATC
1 CTGTCATC
2260979 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.51
42 21 0.49
ACGTcount: A:0.23, C:0.42, G:0.14, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGACCA
Found at i:2262420 original size:14 final size:14
Alignment explanation
Indices: 2262386--2262424 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2262376 TTGATTGTTT
2262386 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
2262400 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
2262414 TGTTGATTTGT
1 AATTGATTTGT
2262425 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2262641 original size:19 final size:20
Alignment explanation
Indices: 2262608--2262649 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
2262598 ATCGCAATGT
2262608 GATTTTCATTTTCGCATTGC
1 GATTTTCATTTTCGCATTGC
2262628 GATTTTCA-TTTCGCATTGC
1 GATTTTCATTTTCGCATTGC
2262647 GAT
1 GAT
2262650 AGCCATTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.48
Consensus pattern (20 bp):
GATTTTCATTTTCGCATTGC
Found at i:2262656 original size:19 final size:19
Alignment explanation
Indices: 2262617--2262691 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
2262607 TGATTTTCAT
***
2262617 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATAGCCA
2262636 TTTCGCATTGCGATAGCCA
1 TTTCGCATTGCGATAGCCA
*
2262655 TTTCCGCGTTGCGATAGCCA
1 TTT-CGCATTGCGATAGCCA
*
2262675 TTTTCGCGTTGCGATAG
1 -TTTCGCATTGCGATAG
2262692 TCAAATGAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
19 19 0.38
20 28 0.56
21 3 0.06
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (19 bp):
TTTCGCATTGCGATAGCCA
Found at i:2262668 original size:20 final size:19
Alignment explanation
Indices: 2262634--2262691 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 19
2262624 TTGCGATTTT
*
2262634 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
2262653 CATTTCCGCGTTGCGATAGC
1 CATTT-CGCGTTGCGATAGC
2262673 CATTTTCGCGTTGCGATAG
1 CA-TTTCGCGTTGCGATAG
2262692 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 5 0.14
20 28 0.78
21 3 0.08
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2264972 original size:12 final size:12
Alignment explanation
Indices: 2264955--2264979 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2264945 TCTTCGGGGA
2264955 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2264967 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2264979 C
1 C
2264980 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2265948 original size:20 final size:20
Alignment explanation
Indices: 2265927--2265994 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
2265917 TGTATTATCT
* *
2265927 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
*
2265947 CGTTGTGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
* *
2265967 CATTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
2265987 CGTTGCGA
1 CGTTGCGA
2265995 TTTTGTATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:2266028 original size:20 final size:20
Alignment explanation
Indices: 2265922--2266036 Score: 83
Period size: 20 Copynumber: 5.7 Consensus size: 20
2265912 GATTCTGTAT
*
2265922 TATCTCGTTGCGATAGTCAGA
1 TATCGCGTTGCGATAGTCA-A
* * *
2265943 -ATCTCGTTGTGAAAGTCAGA
1 TATCGCGTTGCGATAGTCA-A
* * *
2265963 -ATCGCATTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAA
* *
2265982 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAA
2266003 TATCGCGTTGCGATAGTCAA
1 TATCGCGTTGCGATAGTCAA
*
2266023 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
2266037 TTTCCAAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.04
20 58 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAA
Found at i:2266050 original size:41 final size:41
Alignment explanation
Indices: 2265963--2266057 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
2265953 GAAAGTCAGA
* * * * ** *
2265963 ATCGCATTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAATATCGCATTGCGATTTTCAAAT
2266004 ATCGCGTTGCGATAGTCAATATCGCATTGCGATTTTCCAAAT
1 ATCGCGTTGCGATAGTCAATATCGCATTGCGATTTT-CAAAT
2266046 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
2266058 TTACTTATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAATATCGCATTGCGATTTTCAAAT
Found at i:2266118 original size:21 final size:22
Alignment explanation
Indices: 2266066--2266118 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2266056 ATTTACTTAT
2266066 TCGCATTGCG-AATTGAGAAAA
1 TCGCATTGCGAAATTGAGAAAA
**
2266087 TCGCAACGCGAAATT-AGAAAA
1 TCGCATTGCGAAATTGAGAAAA
2266108 TCGCATTGCGA
1 TCGCATTGCGA
2266119 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:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGAGAAAA
Found at i:2285389 original size:3 final size:3
Alignment explanation
Indices: 2285381--2285455 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
2285371 AAATCAAAGA
2285381 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2285429 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
2285456 AGGATTTTAC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2285527 original size:17 final size:18
Alignment explanation
Indices: 2285507--2285542 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2285497 TAAATACAAG
2285507 GAAAA-GGAAAGATCAGA
1 GAAAAGGGAAAGATCAGA
*
2285524 GAAAAGGGAATGATCAGA
1 GAAAAGGGAAAGATCAGA
2285542 G
1 G
2285543 CTGTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.53, C:0.06, G:0.33, T:0.08
Consensus pattern (18 bp):
GAAAAGGGAAAGATCAGA
Found at i:2288596 original size:39 final size:39
Alignment explanation
Indices: 2288519--2288598 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 39
2288509 TGTGCGTTTA
* * *
2288519 TTTAATAAATGAACGAACATGAACAAGATTTTGTGTTCG
1 TTTAATAAATGAACGAACATGAACAAGAGTCTGCGTTCG
2288558 TTTAATTAAATGAACGAACATGAACATA-AGTCT-CGTTCG
1 TTTAA-TAAATGAACGAACATGAACA-AGAGTCTGCGTTCG
2288597 TT
1 TT
2288599 CATTTACGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 12 0.33
40 23 0.64
41 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (39 bp):
TTTAATAAATGAACGAACATGAACAAGAGTCTGCGTTCG
Found at i:2288643 original size:24 final size:24
Alignment explanation
Indices: 2288616--2288667 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
2288606 GTTCGTGAAC
*
2288616 GTTCGGTTATGTTTGTTCGGTTAT
1 GTTCGGTTATGTTCGTTCGGTTAT
*
2288640 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCGTTCGGTTAT
2288664 GTTC
1 GTTC
2288668 ATTCATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.08, C:0.12, G:0.27, T:0.54
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCGGTTAT
Found at i:2288667 original size:14 final size:14
Alignment explanation
Indices: 2288615--2288667 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
2288605 CGTTCGTGAA
2288615 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
2288629 TGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2288643 CG-T---TTATGTT
1 CGTTCGGTTATGTT
2288653 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
2288667 C
1 C
2288668 ATTCATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 9 0.27
11 1 0.03
13 1 0.03
14 22 0.67
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.53
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:2289547 original size:12 final size:12
Alignment explanation
Indices: 2289530--2289594 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
2289520 TGGGGCAATG
*
2289530 TCGAGCTCGGAA
1 TCGAGCTCAGAA
*
2289542 TCGAGCT-TGAA
1 TCGAGCTCAGAA
2289553 TCGAGCTCAGAA
1 TCGAGCTCAGAA
* *
2289565 TTGAGCTTA-AA
1 TCGAGCTCAGAA
2289576 TCGAGCTCAGAA
1 TCGAGCTCAGAA
2289588 TCGAGCT
1 TCGAGCT
2289595 TGAATCAAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
11 19 0.42
12 26 0.58
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (12 bp):
TCGAGCTCAGAA
Found at i:2289555 original size:11 final size:11
Alignment explanation
Indices: 2289539--2289600 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
2289529 GTCGAGCTCG
2289539 GAATCGAGCTT
1 GAATCGAGCTT
*
2289550 GAATCGAGCTCA
1 GAATCGAGCT-T
*
2289562 GAATTGAGCTT
1 GAATCGAGCTT
* *
2289573 AAATCGAGCTCA
1 GAATCGAGCT-T
2289585 GAATCGAGCTT
1 GAATCGAGCTT
2289596 GAATC
1 GAATC
2289601 AAGATCTTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 23 0.56
12 18 0.44
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (11 bp):
GAATCGAGCTT
Found at i:2289560 original size:23 final size:23
Alignment explanation
Indices: 2289530--2289600 Score: 115
Period size: 23 Copynumber: 3.1 Consensus size: 23
2289520 TGGGGCAATG
*
2289530 TCGAGCTCGGAATCGAGCTTGAA
1 TCGAGCTCAGAATCGAGCTTGAA
* *
2289553 TCGAGCTCAGAATTGAGCTTAAA
1 TCGAGCTCAGAATCGAGCTTGAA
2289576 TCGAGCTCAGAATCGAGCTTGAA
1 TCGAGCTCAGAATCGAGCTTGAA
2289599 TC
1 TC
2289601 AAGATCTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (23 bp):
TCGAGCTCAGAATCGAGCTTGAA
Found at i:2289810 original size:10 final size:10
Alignment explanation
Indices: 2289795--2289869 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
2289785 GGGTCTCCAA
2289795 CGTTTATGTT
1 CGTTTATGTT
2289805 CGTTTATGTT
1 CGTTTATGTT
2289815 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
2289826 ATGTTTGTGTT
1 -CGTTTATGTT
*
2289837 TGTTTATGTT
1 CGTTTATGTT
2289847 CG----TGTT
1 CGTTTATGTT
2289853 CGTTTATGTT
1 CGTTTATGTT
2289863 CGTTTAT
1 CGTTTAT
2289870 TTATTAAATG
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
6 6 0.11
10 35 0.66
11 8 0.15
12 4 0.08
ACGTcount: A:0.09, C:0.09, G:0.21, T:0.60
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:2289826 original size:16 final size:16
Alignment explanation
Indices: 2289801--2289865 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
2289791 CCAACGTTTA
2289801 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
2289817 TGTTCATTTATGTTTG
1 TGTTCGTTTATGTTCG
*
2289833 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2289849 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2289865 T
1 T
2289866 TTATTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.08, C:0.09, G:0.23, T:0.60
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2289956 original size:16 final size:16
Alignment explanation
Indices: 2289935--2289965 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2289925 AAAAATATTT
2289935 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2289951 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
2289966 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2295284 original size:21 final size:21
Alignment explanation
Indices: 2295254--2295300 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2295244 TAACTCCATT
2295254 TATTA-CGGTTTACAATAATA
1 TATTATCGGTTTACAATAATA
* * *
2295274 TATTATCGGTTTCCAATATTT
1 TATTATCGGTTTACAATAATA
2295295 TATTAT
1 TATTAT
2295301 AATTATTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (21 bp):
TATTATCGGTTTACAATAATA
Found at i:2298959 original size:21 final size:19
Alignment explanation
Indices: 2298923--2298963 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2298913 ATTTCTGAAC
*
2298923 TTATATTTTTATTTTGTTT
1 TTATATTTTTAATTTGTTT
2298942 TTATGATTTTTGAATTTGTTT
1 TTAT-ATTTTT-AATTTGTTT
2298963 T
1 T
2298964 ACAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 9 0.47
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (19 bp):
TTATATTTTTAATTTGTTT
Found at i:2304268 original size:27 final size:29
Alignment explanation
Indices: 2304232--2304292 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
2304222 CCGAACCGAA
*
2304232 TTTTCATTAACCG-AA-TTAATCGAATTT
1 TTTTCATTAACCGTAATTTAACCGAATTT
*
2304259 TTTTCTTTAACCGTTAATTTAACCGAATTT
1 TTTTCATTAACCG-TAATTTAACCGAATTT
2304289 TTTT
1 TTTT
2304293 TTTGAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.41
29 2 0.07
30 15 0.52
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.51
Consensus pattern (29 bp):
TTTTCATTAACCGTAATTTAACCGAATTT
Found at i:2305683 original size:1 final size:1
Alignment explanation
Indices: 2305677--2305701 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2305667 AAAGGTCAGG
2305677 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
2305702 GAAATGGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2308532 original size:17 final size:17
Alignment explanation
Indices: 2308510--2308545 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2308500 TTTTACTTCA
2308510 TTTTCAGTAAGGTTACG
1 TTTTCAGTAAGGTTACG
*
2308527 TTTTCAGTAAGGTTCCG
1 TTTTCAGTAAGGTTACG
2308544 TT
1 TT
2308546 AGCTTATCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.44
Consensus pattern (17 bp):
TTTTCAGTAAGGTTACG
Found at i:2311197 original size:17 final size:18
Alignment explanation
Indices: 2311160--2311203 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2311150 TTTCTGAGAT
2311160 AATTGGAATCTGTGAAGG
1 AATTGGAATCTGTGAAGG
*
2311178 AATTGGAATCTGT-TAGG
1 AATTGGAATCTGTGAAGG
2311195 AATTGGAAT
1 AATTGGAAT
2311204 ACAATTCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.32
Consensus pattern (18 bp):
AATTGGAATCTGTGAAGG
Found at i:2311817 original size:33 final size:33
Alignment explanation
Indices: 2311746--2311859 Score: 103
Period size: 31 Copynumber: 3.4 Consensus size: 33
2311736 ACCCAAACCC
*
2311746 GACCCGAC-CAGAATATCACACTTAAAAAACCCA
1 GACCCGACTC-GAATATCACACTTAAAAAACACA
2311779 -A-CCGACTCGAATATCACACTTAAAAAA-ACA
1 GACCCGACTCGAATATCACACTTAAAAAACACA
*
2311809 TGACCCGACTCGACCCGAATATCACACTTAAAAAAC-CC
1 -GACCCGACT-----CGAATATCACACTTAAAAAACACA
*
2311847 GACCCGACCCGAA
1 GACCCGACTCGAA
2311860 CAAAAATAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 21
0.74 0.03 0.23
Matches are distributed among these distances:
30 2 0.03
31 24 0.35
32 7 0.10
33 6 0.09
37 8 0.12
38 21 0.31
ACGTcount: A:0.42, C:0.34, G:0.11, T:0.13
Consensus pattern (33 bp):
GACCCGACTCGAATATCACACTTAAAAAACACA
Found at i:2311855 original size:32 final size:32
Alignment explanation
Indices: 2311740--2311859 Score: 143
Period size: 32 Copynumber: 3.6 Consensus size: 32
2311730 CCCTAAACCC
*
2311740 AAACCCGACCCGACCAGAATATCACACTTAAA
1 AAACCCGACCCGACCCGAATATCACACTTAAA
* *
2311772 AAACCC-AACCGACTCGAATATCACACTTAAAAAA
1 AAACCCGACCCGACCCGAATATCACACTT---AAA
*
2311806 ACATGACCCGACTCGACCCGAATATCACACTTAAA
1 A-A--ACCCGACCCGACCCGAATATCACACTTAAA
2311841 AAACCCGACCCGACCCGAA
1 AAACCCGACCCGACCCGAA
2311860 CAAAAATAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
31 19 0.26
32 22 0.30
34 5 0.07
35 5 0.07
37 4 0.05
38 19 0.26
ACGTcount: A:0.42, C:0.35, G:0.10, T:0.12
Consensus pattern (32 bp):
AAACCCGACCCGACCCGAATATCACACTTAAA
Found at i:2312466 original size:25 final size:23
Alignment explanation
Indices: 2312433--2312484 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 23
2312423 CATTAAAGGG
2312433 TTTTTAAATTAATAGAAAAATAGAT
1 TTTTTAAATTAAT-GAAAAA-AGAT
*
2312458 TTTTTAAATTAATGAAAAAAGGT
1 TTTTTAAATTAATGAAAAAAGAT
2312481 TTTT
1 TTTT
2312485 AATTAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 7 0.27
24 6 0.23
25 13 0.50
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (23 bp):
TTTTTAAATTAATGAAAAAAGAT
Found at i:2313236 original size:15 final size:15
Alignment explanation
Indices: 2313213--2313243 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2313203 ACTCAGCATT
*
2313213 TCATTTCATTTCATC
1 TCATCTCATTTCATC
2313228 TCATCTCATTTCATC
1 TCATCTCATTTCATC
2313243 T
1 T
2313244 TCTGCACCGT
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:0.19, C:0.29, G:0.00, T:0.52
Consensus pattern (15 bp):
TCATCTCATTTCATC
Found at i:2334313 original size:13 final size:13
Alignment explanation
Indices: 2334295--2334344 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
2334285 CAGAACATGA
2334295 AAATATATTGAAT
1 AAATATATTGAAT
2334308 AAATATATT-AAT
1 AAATATATTGAAT
* * *
2334320 TATTATATTAAAT
1 AAATATATTGAAT
2334333 AAATATATTGAA
1 AAATATATTGAA
2334345 AATATTTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (13 bp):
AAATATATTGAAT
Found at i:2335776 original size:60 final size:60
Alignment explanation
Indices: 2335648--2335777 Score: 152
Period size: 60 Copynumber: 2.2 Consensus size: 60
2335638 AGGTTGATAG
* * * * * * * *
2335648 TTTATGGATGAAATTACAATGTTTAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAA
1 TTTAAGGATAAAATTAAAATATTCAAAAGTTTAAAGACTAATTTAAAATAAAAGTCATAA
* * * *
2335708 ATTGAGGATAAAATTAAAATATTCAAAAGTTTAAAGACTAATTTAAAATAAAATTTATAA
1 TTTAAGGATAAAATTAAAATATTCAAAAGTTTAAAGACTAATTTAAAATAAAAGTCATAA
2335768 TTTAAGGATA
1 TTTAAGGATA
2335778 TATAATGCAA
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (60 bp):
TTTAAGGATAAAATTAAAATATTCAAAAGTTTAAAGACTAATTTAAAATAAAAGTCATAA
Done.