Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000389.1 Hibiscus syriacus cultivar Beakdansim tig00000715_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: 2672246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 15
Found at i:2022765 original size:33 final size:33
Alignment explanation
Indices: 2022656--2022788 Score: 133
Period size: 33 Copynumber: 3.8 Consensus size: 33
2022646 GACATTCATT
*
2022656 TGACTATCGCAACGCG-GAAATCGCAACGCGAATA
1 TGACTATCGCAACGAGAG-AATCGCAACGCGAA-A
*
2022690 TGACTATCGCAACACGGAAATGACTATCGCAACGCGGAAA
1 TGACTATCGC-A-AC-GAGA-GA--ATCGCAACGC-GAAA
*
2022730 TGACTATCGCAACGAGAGAATCGCAATGCGAAA
1 TGACTATCGCAACGAGAGAATCGCAACGCGAAA
**
2022763 TGAAAATCGCAACGAGAGAATCGCAA
1 TGACTATCGCAACGAGAGAATCGCAA
2022789 TGCAAAAATG
Statistics
Matches: 85, Mismatches: 6, Indels: 17
0.79 0.06 0.16
Matches are distributed among these distances:
33 28 0.33
34 19 0.22
35 1 0.01
36 4 0.05
37 4 0.05
38 3 0.04
39 2 0.02
40 21 0.25
41 3 0.04
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.14
Consensus pattern (33 bp):
TGACTATCGCAACGAGAGAATCGCAACGCGAAA
Found at i:2022789 original size:33 final size:34
Alignment explanation
Indices: 2022715--2022810 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 34
2022705 GGAAATGACT
* * **
2022715 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCAGAAATGAAAATCGCAACGAGAGA
2022749 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCAGAAATGAAAATCGCAACGAGAGA
* *
2022782 ATCGCAATGCAAAAATGAAAATCGTAACG
1 ATCGCAATGCAGAAATGAAAATCGCAACG
2022811 CGAATTTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 31 0.55
34 25 0.45
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCAGAAATGAAAATCGCAACGAGAGA
Found at i:2022868 original size:34 final size:34
Alignment explanation
Indices: 2022825--2022920 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
2022815 TTTAGTTTCG
2022825 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
2022859 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** * *
2022892 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
2022921 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:2022899 original size:14 final size:14
Alignment explanation
Indices: 2022847--2022900 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
2022837 CATTTTCGCA
2022847 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
2022861 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
2022878 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
2022894 TTGCGAT
1 TTGCGAT
2022901 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2023045 original size:14 final size:14
Alignment explanation
Indices: 2023026--2023062 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2023016 CATCAATTAA
2023026 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2023040 ACAAATCATCTTTT
1 ACAAATCAACATTT
2023054 ACAAATCAA
1 ACAAATCAA
2023063 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2025051 original size:19 final size:19
Alignment explanation
Indices: 2025023--2025071 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2025013 AACTTAAAAT
*
2025023 TGCAACGCGAAAATGACTA
1 TGCAATGCGAAAATGACTA
**
2025042 TGCAATGCGAATTTGACTA
1 TGCAATGCGAAAATGACTA
2025061 TCGCAATGCGA
1 T-GCAATGCGA
2025072 TAGTCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (19 bp):
TGCAATGCGAAAATGACTA
Found at i:2025090 original size:20 final size:20
Alignment explanation
Indices: 2025061--2025242 Score: 194
Period size: 20 Copynumber: 9.8 Consensus size: 20
2025051 AATTTGACTA
*
2025061 TCGCAATGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
2025081 TCGTATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
2025101 TCGCGTTGCGAT--T--TTGT
1 TCGCATTGCGATAGTCATT-T
**
2025118 T-G--TTGCGATTTTCA-TT
1 TCGCATTGCGATAGTCATTT
*
2025134 TCGCATTGCGAT--TC--TC
1 TCGCATTGCGATAGTCATTT
2025150 TCG--TTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
*
2025168 TCGCGTTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
2025188 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
2025208 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
2025228 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
2025243 AAACTATTCT
Statistics
Matches: 141, Mismatches: 7, Indels: 28
0.80 0.04 0.16
Matches are distributed among these distances:
14 14 0.10
16 12 0.09
17 6 0.04
18 5 0.04
19 7 0.05
20 97 0.69
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATTT
Found at i:2025143 original size:33 final size:34
Alignment explanation
Indices: 2025086--2025219 Score: 135
Period size: 33 Copynumber: 3.8 Consensus size: 34
2025076 CATTTTCGTA
* * *
2025086 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
** *
2025120 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
*
2025153 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCG
1 TTGCGATAGTCATTTTCGCGTTGCGAT--TC--TCTCG
*
2025191 CATTGCGATAGTCATTTTCGCATTGCGAT
1 --TTGCGATAGTCATTTTCGCGTTGCGAT
2025220 AGTCATTTTC
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
33 27 0.33
34 23 0.28
36 2 0.02
38 4 0.05
40 26 0.32
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.43
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
Found at i:2027146 original size:20 final size:19
Alignment explanation
Indices: 2027123--2027245 Score: 103
Period size: 20 Copynumber: 6.6 Consensus size: 19
2027113 TCTGAAACTT
2027123 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACG-AAATG
2027143 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACG-AAATG
** *
2027163 ACTATCGC-A-ACGCAA-G
1 AAAATCGCAACACGAAATG
* *
2027179 --AATTGCAACGCGAAATG
1 AAAATCGCAACACGAAATG
2027196 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACG-AAATG
** * *
2027216 ACTATCGTAACGCGAAATG
1 AAAATCGCAACACGAAATG
2027235 AAAATCGCAAC
1 AAAATCGCAAC
2027246 GACAGAATCG
Statistics
Matches: 81, Mismatches: 16, Indels: 13
0.74 0.15 0.12
Matches are distributed among these distances:
14 4 0.05
15 1 0.01
16 5 0.06
17 3 0.04
18 3 0.04
19 24 0.30
20 41 0.51
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACACGAAATG
Found at i:2027255 original size:53 final size:52
Alignment explanation
Indices: 2027142--2027257 Score: 135
Period size: 53 Copynumber: 2.2 Consensus size: 52
2027132 ACACGAAAAT
* * * *
2027142 GAAAATCGCAACACGAAAATGACTATCGCAACGCAAGAATTGCAACGCGAAAT
1 GAAAATCGCAACACGAAAATGACTATCGCAACGC-AGAAATGAAAAGCGAAAC
* * *
2027195 GAAAATCGCAACACGAAAATGACTATCGTAACGC-GAAATGAAAATCGCAAC
1 GAAAATCGCAACACGAAAATGACTATCGCAACGCAGAAATGAAAAGCGAAAC
2027246 GACAGAATCGCA
1 GA-A-AATCGCA
2027258 TTGCGATAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 13 0.24
52 1 0.02
53 40 0.74
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (52 bp):
GAAAATCGCAACACGAAAATGACTATCGCAACGCAGAAATGAAAAGCGAAAC
Found at i:2027619 original size:22 final size:22
Alignment explanation
Indices: 2027582--2027665 Score: 114
Period size: 22 Copynumber: 3.8 Consensus size: 22
2027572 TGACCGTGAA
*
2027582 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
* * *
2027604 TAATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGAGAC
* *
2027626 TGATTTCGTCGGAGATGAAGAT
1 TGATTTCGTCGGAGATGGAGAC
2027648 TGATTTCGTCGGAGATGG
1 TGATTTCGTCGGAGATGG
2027666 GGACGGATGT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.24, C:0.13, G:0.36, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGAGAC
Found at i:2027657 original size:44 final size:44
Alignment explanation
Indices: 2027582--2027679 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
2027572 TGACCGTGAA
*
2027582 TGATTTCGCCGGAGATGGAGACTAATATCGTCGGAGATGGGGAC
1 TGATTTCGCCGGAGATGAAGACTAATATCGTCGGAGATGGGGAC
* * * *
2027626 TGATTTCGTCGGAGATGAAGATTGATTTCGTCGGAGATGGGGAC
1 TGATTTCGCCGGAGATGAAGACTAATATCGTCGGAGATGGGGAC
* *
2027670 GGATGTCGCC
1 TGATTTCGCC
2027680 TTAGAGAATG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.22, C:0.15, G:0.37, T:0.26
Consensus pattern (44 bp):
TGATTTCGCCGGAGATGAAGACTAATATCGTCGGAGATGGGGAC
Found at i:2027891 original size:20 final size:20
Alignment explanation
Indices: 2027868--2027917 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2027858 CGATAGTCAG
*
2027868 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2027888 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2027908 ATTCGCATTG
1 ATTCGCATTG
2027918 AGAATTAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2027981 original size:20 final size:20
Alignment explanation
Indices: 2027927--2027974 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
2027917 GAGAATTAGG
2027927 AAAATCGCAACGCGATAGTC
1 AAAATCGCAACGCGATAGTC
2027947 AAAATCGCAACGCGATAGTC
1 AAAATCGCAACGCGATAGTC
*
2027967 AGAATCGC
1 AAAATCGC
2027975 GTTGCGAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATAGTC
Found at i:2032279 original size:21 final size:21
Alignment explanation
Indices: 2032254--2032328 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2032244 TTTGGAATAA
2032254 ATCGCAACGCGAATTTCGACT
1 ATCGCAACGCGAATTTCGACT
* * **
2032275 TTCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAATTTCGACT
2032294 ATCGCAACGCGAATTTCGACT
1 ATCGCAACGCGAATTTCGACT
*
2032315 ATCGCAATGCGAAT
1 ATCGCAACGCGAAT
2032329 ATGTAAATCG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 15 0.35
21 28 0.65
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGAATTTCGACT
Found at i:2032300 original size:40 final size:42
Alignment explanation
Indices: 2032243--2032321 Score: 135
Period size: 40 Copynumber: 1.9 Consensus size: 42
2032233 ATCCATTGTC
*
2032243 ATTTGGAATAAATCGCAACGCGAATTTCGACTTTCGCAACGA
1 ATTTGGAATAAATCGCAACGCGAATTTCGACTATCGCAACGA
2032285 ATTTGG-A-AAATCGCAACGCGAATTTCGACTATCGCAA
1 ATTTGGAATAAATCGCAACGCGAATTTCGACTATCGCAA
2032322 TGCGAATATG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 29 0.81
41 1 0.03
42 6 0.17
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (42 bp):
ATTTGGAATAAATCGCAACGCGAATTTCGACTATCGCAACGA
Found at i:2032677 original size:178 final size:178
Alignment explanation
Indices: 2032378--2032729 Score: 607
Period size: 178 Copynumber: 2.0 Consensus size: 178
2032368 ATCTAGAAAC
*
2032378 TGATTTGCGATACTGGAGATCGCGTTGCGAATTATCGATCGCATTACGATTTAGTTGGTCATTTT
1 TGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGATCGCATTACGATTTAGTTGGTCATTTT
* *
2032443 GGCAAATTCAAAAAAAATTGGTTAAAATCGTATATTATAAGGCATTTTTGGTCACTGA-AGTTAT
66 GACAAATACAAAAAAAATTGGTTAAAATCGTATATTATAAGGCATTTTTGGTCACTGAGA-TTAT
2032507 TTTCTCCTCTTTAAGAACTCCGGCGGCGGTCACCGGGGATTGCAAAAAT
130 TTTCTCCTCTTTAAGAACTCCGGCGGCGGTCACCGGGGATTGCAAAAAT
* *
2032556 TGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGATCGCATTGCGATTTAGTTTGTCATTTT
1 TGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGATCGCATTACGATTTAGTTGGTCATTTT
* *
2032621 GACAAATACAAAAAAATTTGGTTAAAATCGTATATTATAAGGTATTTTTGGTCACTGAGATTATT
66 GACAAATACAAAAAAAATTGGTTAAAATCGTATATTATAAGGCATTTTTGGTCACTGAGATTATT
* *
2032686 TTCTCCTCTTTAAGAACTCTGGCGGCGGTCATCGGGGATTGCAA
131 TTCTCCTCTTTAAGAACTCCGGCGGCGGTCACCGGGGATTGCAA
2032730 GAATCGATGT
Statistics
Matches: 164, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
178 163 0.99
179 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (178 bp):
TGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGATCGCATTACGATTTAGTTGGTCATTTT
GACAAATACAAAAAAAATTGGTTAAAATCGTATATTATAAGGCATTTTTGGTCACTGAGATTATT
TTCTCCTCTTTAAGAACTCCGGCGGCGGTCACCGGGGATTGCAAAAAT
Found at i:2034143 original size:2 final size:2
Alignment explanation
Indices: 2034136--2034160 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2034126 AGGGTCAGTT
2034136 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
2034161 TGTTATTTTA
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:2034702 original size:33 final size:33
Alignment explanation
Indices: 2034662--2034773 Score: 91
Period size: 33 Copynumber: 3.2 Consensus size: 33
2034652 ACAATATTAT
2034662 CTTCTGACTGGAGAAAAAAGAAATATATGATTG
1 CTTCTGACTGGAGAAAAAAGAAATATATGATTG
* ** * *
2034695 CTTCTGACTAGTTGTGGTTTAAAAGAAAGAACAAT-ATTG
1 CTTCTGACT-G--G-AG-AAAAAAGAAA-TA-TATGATTG
*
2034734 TCTTCTGACTGGAGACAAAAGAAATATATGATTG
1 -CTTCTGACTGGAGAAAAAAGAAATATATGATTG
2034768 CTTCTG
1 CTTCTG
2034774 GAAATTGCAT
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
33 17 0.28
34 6 0.10
35 8 0.13
36 2 0.03
37 2 0.03
38 8 0.13
39 6 0.10
40 11 0.18
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (33 bp):
CTTCTGACTGGAGAAAAAAGAAATATATGATTG
Found at i:2034725 original size:73 final size:73
Alignment explanation
Indices: 2034628--2034773 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
2034618 ATGAAAGAAT
2034628 ACTAGTTGTGGTTTAAAAGAAAGAACAATATTATCTTCTGACTGGAGAAAAAAGAAATATATGAT
1 ACTAGTTGTGGTTTAAAAGAAAGAACAATATTATCTTCTGACTGGAGAAAAAAGAAATATATGAT
2034693 TGCTTCTG
66 TGCTTCTG
* *
2034701 ACTAGTTGTGGTTTAAAAGAAAGAACAATATTGTCTTCTGACTGGAGACAAAAGAAATATATGAT
1 ACTAGTTGTGGTTTAAAAGAAAGAACAATATTATCTTCTGACTGGAGAAAAAAGAAATATATGAT
2034766 TGCTTCTG
66 TGCTTCTG
2034774 GAAATTGCAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (73 bp):
ACTAGTTGTGGTTTAAAAGAAAGAACAATATTATCTTCTGACTGGAGAAAAAAGAAATATATGAT
TGCTTCTG
Found at i:2035244 original size:27 final size:27
Alignment explanation
Indices: 2035213--2035307 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
2035203 TCTATTTACA
*
2035213 AAATCATATCTCTATAGGAATGACAAC
1 AAATCATATCTCTATAGGAATGATAAC
2035240 AAATCATATCTCTATAGGAATGATAAC
1 AAATCATATCTCTATAGGAATGATAAC
*
2035267 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGATAAC
2035294 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
2035308 ATTCCTACAC
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 9 0.14
27 57 0.86
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGATAAC
Found at i:2039036 original size:27 final size:27
Alignment explanation
Indices: 2039003--2039124 Score: 203
Period size: 27 Copynumber: 4.6 Consensus size: 27
2038993 TCTATTTACA
* **
2039003 AAATCATATCTCTATAAGAATGACAAC
1 AAATCATATCTCTATAGGAATGGTAAC
2039030 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
2039057 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
2039084 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
2039111 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
2039125 ATTCCTACAC
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
25 9 0.10
27 83 0.90
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:2041955 original size:25 final size:25
Alignment explanation
Indices: 2041926--2041983 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
2041916 ATATGATATG
2041926 AACAGTAACCTATTACAGTAACGTA
1 AACAGTAACCTATTACAGTAACGTA
* * *
2041951 AACAGTAACCTGTTATAGTACCGTA
1 AACAGTAACCTATTACAGTAACGTA
2041976 AACAGTAA
1 AACAGTAA
2041984 TCTGCTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (25 bp):
AACAGTAACCTATTACAGTAACGTA
Found at i:2041997 original size:25 final size:25
Alignment explanation
Indices: 2041947--2042020 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 25
2041937 ATTACAGTAA
* * * *
2041947 CGTAAACAGTAACCTGTTATAGTAC
1 CGTAAACAGTAATCTGCTACAATAC
2041972 CGTAAACAGTAATCTGCTACAATAC
1 CGTAAACAGTAATCTGCTACAATAC
* * *
2041997 CGTGAACAGTATTTTGCTACAATA
1 CGTAAACAGTAATCTGCTACAATA
2042021 TCCTGCTACA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (25 bp):
CGTAAACAGTAATCTGCTACAATAC
Found at i:2042662 original size:18 final size:18
Alignment explanation
Indices: 2042639--2042675 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2042629 ACTGAATATT
2042639 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
2042657 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
2042675 T
1 T
2042676 ATATCCCTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTG
Found at i:2045066 original size:30 final size:29
Alignment explanation
Indices: 2045032--2045094 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
2045022 CCTGATATAT
2045032 CACCGGTGAACAGTATATTTCCCGATCTAA
1 CACCGGT-AACAGTATATTTCCCGATCTAA
* * * **
2045062 CACCGGTCAGATTATATTTTTCGATCTAA
1 CACCGGTAACAGTATATTTCCCGATCTAA
2045091 CACC
1 CACC
2045095 CTTAGCAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (29 bp):
CACCGGTAACAGTATATTTCCCGATCTAA
Found at i:2045182 original size:51 final size:51
Alignment explanation
Indices: 2045114--2045233 Score: 143
Period size: 51 Copynumber: 2.4 Consensus size: 51
2045104 AAAGCGCGCC
* * * * *
2045114 CCCCTGCACTGCACTATACGATGATTTGACA-CCACGTGAGGTATAGCGCGT
1 CCCCTGCACCGCGCTATACGATGATCTGACATACACGTG-GGTATAGCGCGG
* * *
2045165 CCCCTGCACCGCGCTATACGGTGATCTGGCATACACGTGGGTATAGTGCGG
1 CCCCTGCACCGCGCTATACGATGATCTGACATACACGTGGGTATAGCGCGG
*
2045216 CCCCTGCAGCGCGCTATA
1 CCCCTGCACCGCGCTATA
2045234 TGCCACGTAG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 53 0.90
52 6 0.10
ACGTcount: A:0.20, C:0.32, G:0.27, T:0.22
Consensus pattern (51 bp):
CCCCTGCACCGCGCTATACGATGATCTGACATACACGTGGGTATAGCGCGG
Found at i:2051219 original size:110 final size:111
Alignment explanation
Indices: 2051025--2051245 Score: 399
Period size: 110 Copynumber: 2.0 Consensus size: 111
2051015 ATTACAAAAA
* *
2051025 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
2051090 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
2051136 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
2051200 AATTAAAACGTTAAAATGTTACCGTATCAGCGAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
2051246 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 71 0.67
111 35 0.33
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:2051610 original size:51 final size:51
Alignment explanation
Indices: 2051555--2051653 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
2051545 GGGGCTGTGT
* * *
2051555 TATA-CCCACGTGTATGCCAGATCACCGTATAGCGCGGTGCAGGGGGCGCAC
1 TATACCCCACGTG-ACGCCAAATCACCGTATAGCACGGTGCAGGGGGCGCAC
* * *
2051606 TATACCCCACGTGGCGCTAAATCATCGTATAGCACGGTGCAGGGGGCG
1 TATACCCCACGTGACGCCAAATCACCGTATAGCACGGTGCAGGGGGCG
2051654 TTTTACTGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 33 0.80
52 8 0.20
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.18
Consensus pattern (51 bp):
TATACCCCACGTGACGCCAAATCACCGTATAGCACGGTGCAGGGGGCGCAC
Found at i:2051729 original size:30 final size:29
Alignment explanation
Indices: 2051667--2051742 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
2051657 TACTGCTAAG
*
2051667 GGTGTTAGATCGGGAAATATAATCTGACC
1 GGTGTTAGATCGGGAAATATAATCTCACC
* *
2051696 GGTGTTAGATCGGGAAATATACTGTTCACC
1 GGTGTTAGATCGGGAAATATAAT-CTCACC
* *
2051726 GGTGATATATCGGGAAA
1 GGTGTTAGATCGGGAAA
2051743 ATCGCCTCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 22 0.54
30 19 0.46
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.28
Consensus pattern (29 bp):
GGTGTTAGATCGGGAAATATAATCTCACC
Found at i:2052381 original size:26 final size:28
Alignment explanation
Indices: 2052338--2052390 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 28
2052328 AATTAATGAA
2052338 TTTTTATATTTCACTTT-ATACGTTAAAC
1 TTTTTATATTTCACTTTAATAC-TTAAAC
*
2052366 TTTTTAT-TTT-ATTTTAATACTTAAA
1 TTTTTATATTTCACTTTAATACTTAAA
2052391 GTATATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 9 0.39
27 7 0.30
28 7 0.30
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTTTATATTTCACTTTAATACTTAAAC
Found at i:2053986 original size:23 final size:23
Alignment explanation
Indices: 2053960--2054005 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2053950 AGATGTAAAT
2053960 TTGTACAACATCAATATTTTAAG
1 TTGTACAACATCAATATTTTAAG
2053983 TTGTACAACATCAATATTTTAAG
1 TTGTACAACATCAATATTTTAAG
2054006 CATAAACCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (23 bp):
TTGTACAACATCAATATTTTAAG
Found at i:2054337 original size:16 final size:17
Alignment explanation
Indices: 2054311--2054343 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2054301 CACATCAATG
*
2054311 TTTATTAAAAATGTATT
1 TTTATTAAAAATATATT
2054328 TTTA-TAAAAATATATT
1 TTTATTAAAAATATATT
2054344 AAAAAGACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTATTAAAAATATATT
Found at i:2057526 original size:23 final size:23
Alignment explanation
Indices: 2057496--2057541 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2057486 AAGGGAGATC
2057496 GACGTTCGATGCCAAAGACTCGT
1 GACGTTCGATGCCAAAGACTCGT
2057519 GACGTTCGATGCCAAAGACTCGT
1 GACGTTCGATGCCAAAGACTCGT
2057542 TACTGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (23 bp):
GACGTTCGATGCCAAAGACTCGT
Found at i:2058061 original size:2 final size:2
Alignment explanation
Indices: 2058054--2058078 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2058044 GAAAAGATAA
2058054 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2058079 AAATAATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2058164 original size:15 final size:16
Alignment explanation
Indices: 2058144--2058185 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
2058134 TATACCAAAG
*
2058144 AAATAAAAT-TAAATT
1 AAATAAAATAAAAATT
2058159 AAATAAAATAAAAATT
1 AAATAAAATAAAAATT
2058175 AAAT-AAATAAA
1 AAATAAAATAAA
2058186 TAATAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAAAATAAAAATT
Found at i:2058167 original size:20 final size:20
Alignment explanation
Indices: 2058144--2058185 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2058134 TATACCAAAG
2058144 AAAT-AAAATTAAATTAAATA
1 AAATAAAAATTAAA-TAAATA
2058164 AAATAAAAATTAAATAAATA
1 AAATAAAAATTAAATAAATA
2058184 AA
1 AA
2058186 TAATAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATAAAAATTAAATAAATA
Found at i:2059337 original size:12 final size:12
Alignment explanation
Indices: 2059313--2059355 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
2059303 ATTTGGACCC
2059313 TAAAAAATGAAAA
1 TAAAAAAT-AAAA
2059326 TAAAAAATAAAA
1 TAAAAAATAAAA
* *
2059338 TTAATAATAATAA
1 TAAAAAATAA-AA
2059351 TAAAA
1 TAAAA
2059356 TAAAAAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:2059378 original size:2 final size:2
Alignment explanation
Indices: 2059373--2059401 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2059363 AGAGTAAATA
2059373 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2059402 TTTTCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2059454 original size:36 final size:37
Alignment explanation
Indices: 2059374--2059491 Score: 123
Period size: 37 Copynumber: 3.2 Consensus size: 37
2059364 GAGTAAATAA
* * * *
2059374 TATATATATATATATATATATATAA-TATTTTTCAAAAA
1 TATATATA-ATATATATTTTTAAAAGTA-TTTTCAAAAT
*
2059412 TCTATATAATATATATTTTTAAAAGTATTTT-AAAAT
1 TATATATAATATATATTTTTAAAAGTATTTTCAAAAT
* * *
2059448 TATATATATTATAATTTTTTTAAAAGTGTTTTCAAAAT
1 TATATATAATAT-ATATTTTTAAAAGTATTTTCAAAAT
2059486 TATATA
1 TATATA
2059492 GTTTAAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
36 14 0.21
37 34 0.50
38 20 0.29
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (37 bp):
TATATATAATATATATTTTTAAAAGTATTTTCAAAAT
Found at i:2059593 original size:104 final size:103
Alignment explanation
Indices: 2059408--2059595 Score: 231
Period size: 104 Copynumber: 1.8 Consensus size: 103
2059398 ATATTTTTCA
* * * * *
2059408 AAAATCTATATAATATATATTTTTAAAAGTATTTTAAAATTATATATATTATAATTTTTTTAAAA
1 AAAATCTATATAATATATATTTTCAAAAGTATTTCAAAACTATATATATTATAATGTTTTCAAAA
*
2059473 GTGTTTTCAAAATTATATAGTTTAAAAAAAATGTTTTT
66 GTGTTTTAAAAATTATATAGTTTAAAAAAAATGTTTTT
*
2059511 AAAA-CTATATATTATATAAGTTTTCAAAA-TGATTTCAAAACTATATA-A-TATATATGTTTTC
1 AAAATCTATATAATATAT-A-TTTTCAAAAGT-ATTTCAAAACTATATATATTATA-ATGTTTTC
*
2059572 AAAATGTTTTTTAAAAATTATATA
62 AAAA-GTGTTTTAAAAATTATATA
2059596 TTTTTTCAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
102 16 0.22
103 17 0.24
104 39 0.54
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (103 bp):
AAAATCTATATAATATATATTTTCAAAAGTATTTCAAAACTATATATATTATAATGTTTTCAAAA
GTGTTTTAAAAATTATATAGTTTAAAAAAAATGTTTTT
Found at i:2059594 original size:38 final size:36
Alignment explanation
Indices: 2059500--2059631 Score: 134
Period size: 36 Copynumber: 3.8 Consensus size: 36
2059490 TAGTTTAAAA
*
2059500 AAAATGTTTTTAAAACTATATATTATATAAGTTTTC
1 AAAATGTTTTTAAAACTATATAATATATAAGTTTTC
* * *
2059536 AAAATGATTTCAAAACTATATAATATATATGTTTTC
1 AAAATGTTTTTAAAACTATATAATATATAAGTTTTC
*
2059572 AAAATGTTTTTTAAAA--AT-T-ATATAT--TTTTTC
1 AAAATG-TTTTTAAAACTATATAATATATAAGTTTTC
**
2059603 AAAATG-TTTTAAAAAAAGTATAATATATA
1 AAAATGTTTTTAAAACTA-TATAATATATA
2059632 TATATATATA
Statistics
Matches: 82, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
29 8 0.10
31 12 0.15
32 1 0.01
33 7 0.09
34 7 0.09
35 2 0.02
36 38 0.46
37 7 0.09
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (36 bp):
AAAATGTTTTTAAAACTATATAATATATAAGTTTTC
Found at i:2059619 original size:31 final size:31
Alignment explanation
Indices: 2059523--2059624 Score: 96
Period size: 31 Copynumber: 3.1 Consensus size: 31
2059513 AACTATATAT
* * *
2059523 TATATAAGTTTTCAAAATGATTTCAAAACTATATAA
1 TATATATGTTTTCAAAATG-TTTTAAAA--A-A-AG
** *
2059559 TATATATGTTTTCAAAATGTTTTTTAAAAAT
1 TATATATGTTTTCAAAATGTTTTAAAAAAAG
*
2059590 TATATATTTTTTCAAAATGTTTTAAAAAAAG
1 TATATATGTTTTCAAAATGTTTTAAAAAAAG
2059621 TATA
1 TATA
2059625 ATATATATAT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
31 32 0.56
32 1 0.02
33 1 0.02
35 5 0.09
36 18 0.32
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (31 bp):
TATATATGTTTTCAAAATGTTTTAAAAAAAG
Found at i:2059630 original size:2 final size:2
Alignment explanation
Indices: 2059621--2059656 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2059611 TTAAAAAAAG
2059621 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2059657 TCAAAAATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2059684 original size:41 final size:41
Alignment explanation
Indices: 2059639--2059787 Score: 149
Period size: 39 Copynumber: 3.6 Consensus size: 41
2059629 ATATATATAT
2059639 ATATATATATATATATATTCAAAAATGTTTTAAAAAAAACA
1 ATATATATATATATATATTCAAAAATGTTTTAAAAAAAACA
* * * *
2059680 ATATAT-TATATTTATTTTC-AAAATGTTTTTAAAAAAACT
1 ATATATATATATATATATTCAAAAATGTTTTAAAAAAAACA
* * * * * * *
2059719 ATATAATATATAAATGTTTTCAAACATGTTTTCAAAACTATATA
1 ATAT-ATATATATATATATTCAAAAATGTTTT-AAAA-AAAACA
*
2059763 TTATATATATATATATATTCAAAAA
1 ATATATATATATATATATTCAAAAA
2059788 CCATTTGAAA
Statistics
Matches: 85, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
39 22 0.26
40 13 0.15
41 16 0.19
42 9 0.11
43 20 0.24
44 5 0.06
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (41 bp):
ATATATATATATATATATTCAAAAATGTTTTAAAAAAAACA
Found at i:2059821 original size:41 final size:41
Alignment explanation
Indices: 2059713--2059821 Score: 105
Period size: 41 Copynumber: 2.7 Consensus size: 41
2059703 TGTTTTTAAA
* ***
2059713 AAAACTATATAATATATAAATGT-T-TTCAAACATGTTTTC
1 AAAACTATATAATATATAAATGTATATTCAAAAACCATTTC
* * *
2059752 AAAACTATATATTATATATATATATATATTCAAAAACCATTTG
1 AAAACTATATA--ATATATAAATGTATATTCAAAAACCATTTC
* *
2059795 AAAACTATATAATATATAGACGTATAT
1 AAAACTATATAATATATAAATGTATAT
2059822 GTAATAAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
39 11 0.20
41 23 0.41
42 1 0.02
43 21 0.38
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (41 bp):
AAAACTATATAATATATAAATGTATATTCAAAAACCATTTC
Found at i:2062773 original size:44 final size:44
Alignment explanation
Indices: 2062665--2062888 Score: 394
Period size: 44 Copynumber: 5.1 Consensus size: 44
2062655 AATTTACGAT
* * * *
2062665 TTATCCCATAAGCTCGTAAGTTTATTTTACCAACATACTTACCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
2062709 TTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
1 -TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
*
2062754 TTATTCCATAAGCTTGTAAGCTTATTTTACCAATATACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
2062798 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
2062842 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
2062886 TTA
1 TTA
2062889 ACCTCATTTA
Statistics
Matches: 173, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
44 133 0.77
45 40 0.23
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.39
Consensus pattern (44 bp):
TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
Found at i:2063084 original size:59 final size:59
Alignment explanation
Indices: 2063021--2063133 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 59
2063011 CTTCCCCTTT
* *
2063021 CATTTTAGCACACGAAGTGCCCTAT-TCAAAAATTCATATAATTAATATGATTTTGTTAC
1 CATTTTAGCACACGAAATGCCCTATGT-AAAAATCCATATAATTAATATGATTTTGTTAC
* * * *
2063080 CATTTTAGCACATGAAATGCCCTATGTGAAAATCCATATCATTAGTATGATTTT
1 CATTTTAGCACACGAAATGCCCTATGTAAAAATCCATATAATTAATATGATTTT
2063134 CTTATCTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 46 0.98
60 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (59 bp):
CATTTTAGCACACGAAATGCCCTATGTAAAAATCCATATAATTAATATGATTTTGTTAC
Found at i:2063347 original size:59 final size:59
Alignment explanation
Indices: 2063165--2063570 Score: 310
Period size: 58 Copynumber: 6.9 Consensus size: 59
2063155 GTGCTTTAGC
* * *
2063165 TGGAAATCCATACACTCATTATGATTCCCTTAGCATTTTAGCACATAAAATGCCCCTATC
1 TGGAAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACATAAAATG-CCCTATA
*** * * ***
2063225 TGGAAATCCATATTTTCAATATGATTTCCTTATCA-TTTAGCACACT-CCGTGCTCC-ATA
1 TGGAAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACA-TAAAATGC-CCTATA
** * * *
2063283 TGGAAATATATACCCTCAGTATGATCCCCTTACCATTTTAGCACATAAAATGCCCTATA
1 TGGAAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACATAAAATGCCCTATA
*** * * *
2063342 TGGAAATCCATATTTTCAATATGACTT-CCTTATCA-TTTAGCACACT-CAGTGCTCC-ATA
1 TGGAAATCCATACACTCAATATGA-TTCCCTTACCATTTTAGCACA-TAAAATGC-CCTATA
* *
2063400 TGGAAATCTATACACTCAGTATGATTCCCTTACCATTTTAGCACATAAAATGCCCTATA
1 TGGAAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACATAAAATGCCCTATA
*** * * * * *
2063459 TGGAAATCCATATTTTCAATATGATTTCATTATCA-TTTAGCACACT-CAATGCTCC-ATT
1 TGGAAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACA-TAAAATGC-CCTATA
* * ** * * * *
2063517 TGGAAATCTATACACTCATTATGATTTACATATCATTTTAGCACACAAAGTGCC
1 TGGAAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACATAAAATGCC
2063571 ATTCGGTAAT
Statistics
Matches: 269, Mismatches: 61, Indels: 34
0.74 0.17 0.09
Matches are distributed among these distances:
57 2 0.01
58 121 0.45
59 115 0.43
60 31 0.12
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (59 bp):
TGGAAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACATAAAATGCCCTATA
Found at i:2063385 original size:117 final size:117
Alignment explanation
Indices: 2063076--2063570 Score: 668
Period size: 117 Copynumber: 4.2 Consensus size: 117
2063066 TATGATTTTG
* * * * * *
2063076 TTACCATTTTAGCACATGAAATGCCCTATGTGAAAATCCATATCATT-AGTATGATTTTCTTATC
1 TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATAT-TTTCAATATGATTTCCTTATC
* * * ** ** * *
2063140 TTTGTAGCACCCTTAGTGCTTTAGCTGGAAATCCATACACTCATTATGATTCCC
65 ATT-TAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
* *
2063194 TTAGCATTTTAGCACATAAAATGCCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATC
1 TTACCATTTTAGCACATAAAATG-CCCTATATGGAAATCCATATTTTCAATATGATTTCCTTATC
* * * *
2063259 ATTTAGCACACTCCGTGCTCCATATGGAAATATATACCCTCAGTATGATCCCC
65 ATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
*
2063312 TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATATTTTCAATATGACTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATATTTTCAATATGATTTCCTTATCA
2063377 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
*
2063429 TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATATTTTCAATATGATTTCATTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATATTTTCAATATGATTTCCTTATCA
* * * **
2063494 TTTAGCACACTCAATGCTCCATTTGGAAATCTATACACTCATTATGATTTAC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
* * * *
2063546 ATATCATTTTAGCACACAAAGTGCC
1 TTACCATTTTAGCACATAAAATGCC
2063571 ATTCGGTAAT
Statistics
Matches: 337, Mismatches: 38, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
117 219 0.65
118 83 0.25
119 35 0.10
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (117 bp):
TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATATTTTCAATATGATTTCCTTATCA
TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
Found at i:2063542 original size:58 final size:61
Alignment explanation
Indices: 2063064--2063562 Score: 363
Period size: 59 Copynumber: 8.5 Consensus size: 61
2063054 TCATATAATT
** * * * * *
2063064 AATATGATTTTGTTACCATTTTAGCACA-TGAAATGC-CCTATGTGAAAATCCATATCA-TT
1 AATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATGGAAATCCATA-CACTC
* * * * * * **
2063123 AGTATGATTTTCTTATC-TTTGTAGCACCCT-TAGTGCT-TTAGCTGGAAATCCATACACTC
1 AATATGATTTCCTTATCATTT-TAGCACACTAAAATGCTCCTATATGGAAATCCATACACTC
* * * * * ***
2063182 ATTATGATTCCCTTAGCATTTTAGCACA-TAAAATGCCCCTATCTGGAAATCCATATTTTC
1 AATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATGGAAATCCATACACTC
*** ** *
2063242 AATATGATTTCCTTATCA-TTTAGCACACT-CCGTGCTCC-ATATGGAAATATATACCCTC
1 AATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATGGAAATCCATACACTC
* ** * ***
2063300 AGTATGATCCCCTTACCATTTTAGCACA-TAAAATGC-CCTATATGGAAATCCATATTTTC
1 AATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATGGAAATCCATACACTC
* * * *
2063359 AATATGACTTCCTTATCA-TTTAGCACACT-CAGTGCTCC-ATATGGAAATCTATACACTC
1 AATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATGGAAATCCATACACTC
* * * ***
2063417 AGTATGATTCCCTTACCATTTTAGCACA-TAAAATGC-CCTATATGGAAATCCATATTTTC
1 AATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATGGAAATCCATACACTC
* * * *
2063476 AATATGATTTCATTATCA-TTTAGCACACT-CAATGCTCC-ATTTGGAAATCTATACACTC
1 AATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATGGAAATCCATACACTC
* * *
2063534 ATTATGATTTACATATCATTTTAGCACAC
1 AATATGATTTCCTTATCATTTTAGCACAC
2063563 AAAGTGCCAT
Statistics
Matches: 337, Mismatches: 84, Indels: 38
0.73 0.18 0.08
Matches are distributed among these distances:
58 126 0.37
59 174 0.52
60 37 0.11
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (61 bp):
AATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATGGAAATCCATACACTC
Found at i:2069198 original size:21 final size:21
Alignment explanation
Indices: 2069172--2069211 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2069162 TAAAATGTGT
* *
2069172 ATCGATGCACTGTTACAGTGC
1 ATCGATACACTGCTACAGTGC
2069193 ATCGATACACTGCTACAGT
1 ATCGATACACTGCTACAGT
2069212 ACTGTTACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (21 bp):
ATCGATACACTGCTACAGTGC
Found at i:2069751 original size:44 final size:44
Alignment explanation
Indices: 2069643--2069910 Score: 473
Period size: 44 Copynumber: 6.1 Consensus size: 44
2069633 AATTTACCAT
* * **
2069643 TTATCCCATAAGCTCGTAAGCTTATTTTACCAACATACTTATCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
*
2069687 TTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAATTGCCA
1 -TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
2069732 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
2069776 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
*
2069820 TTATTCCATAAGCTCTTAAGCTTATTTTACCAATATACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
2069864 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
2069908 TTA
1 TTA
2069911 ACCTCATTTA
Statistics
Matches: 215, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
44 176 0.82
45 39 0.18
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.39
Consensus pattern (44 bp):
TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
Found at i:2070107 original size:59 final size:59
Alignment explanation
Indices: 2070027--2070139 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 59
2070017 CTTCCCCTTT
* * *
2070027 CATTTTAGCACACGAAGTGCCCTAT-TCAAAAATTCATACCATTAGTATGATTTTGTTAC
1 CATTTTAGCACACGAAATGCCCTATGT-AAAAATCCACACCATTAGTATGATTTTGTTAC
* *
2070086 CATTTTAGCACATGAAATGCCCTATGTGAAAATCCACACCATTAGTATGATTTT
1 CATTTTAGCACACGAAATGCCCTATGTAAAAATCCACACCATTAGTATGATTTT
2070140 CTTATCTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 47 0.98
60 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (59 bp):
CATTTTAGCACACGAAATGCCCTATGTAAAAATCCACACCATTAGTATGATTTTGTTAC
Found at i:2070320 original size:58 final size:61
Alignment explanation
Indices: 2070173--2070568 Score: 399
Period size: 58 Copynumber: 6.7 Consensus size: 61
2070163 GCTTTATCTA
* * * * *
2070173 GAAATCCATACACTCAGTATGATTCCCTTAGCATTTTAGCACA-TAAAATGCCCCTATCTG
1 GAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATG
*** ***
2070233 GAAATCCATATTTTCAATATGATTTCCTTATCA-TTTAGCACACT-CCGTGCTCC-ATATG
1 GAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATG
* * * *
2070291 GAAATCTATACACTCAGTATGATTCCCTTACCATTTTAGCACA-TAAAATGC-CCTATATG
1 GAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATG
*** * * *
2070350 GAAATCCATATTTTCAATATGTTTTCCTTATCA-TTTAGCACACT-CAGTGCTCC-ATATG
1 GAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATG
* *
2070408 GAAATCTATACACTCAATATGA-TTCCTTTACCATTTTAGCACA-TAAAATGC-CCTATATG
1 GAAATCCATACACTCAATATGATTTCC-TTATCATTTTAGCACACTAAAATGCTCCTATATG
**** * *
2070467 GAAATCCATTTTTTCAATATGATTTCCTTATCA-TTTAGCACACT-CAGTGCTCC-ATATG
1 GAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATG
* *
2070525 GAAATCTATACACTCAGTATGATTTCCTTATCATTTTAGCACAC
1 GAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACAC
2070569 AAAGTGCCAT
Statistics
Matches: 269, Mismatches: 53, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
57 4 0.01
58 121 0.45
59 112 0.42
60 32 0.12
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (61 bp):
GAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACACTAAAATGCTCCTATATG
Found at i:2070400 original size:117 final size:117
Alignment explanation
Indices: 2070082--2070576 Score: 713
Period size: 117 Copynumber: 4.2 Consensus size: 117
2070072 TATGATTTTG
* * * * ** * *
2070082 TTACCATTTTAGCACATGAAATGCCCTATGTGAAAATCCACACCATT-AGTATGATTTTCTTATC
1 TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATA-TTTTCAATATGATTTCCTTATC
* * * ** * * *
2070146 TTTGTAGCACCCTTAGTGCTTTATCTAGAAATCCATACACTCAGTATGATTCCC
65 ATT-TAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
* *
2070200 TTAGCATTTTAGCACATAAAATGCCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATC
1 TTACCATTTTAGCACATAAAATG-CCCTATATGGAAATCCATATTTTCAATATGATTTCCTTATC
*
2070265 ATTTAGCACACTCCGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
65 ATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
*
2070318 TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATATTTTCAATATGTTTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATATTTTCAATATGATTTCCTTATCA
* *
2070383 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAATATGATTCCT
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
*
2070435 TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATTTTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATATTTTCAATATGATTTCCTTATCA
*
2070500 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
* * *
2070552 TTATCATTTTAGCACACAAAGTGCC
1 TTACCATTTTAGCACATAAAATGCC
2070577 ATTCGGTAAT
Statistics
Matches: 343, Mismatches: 32, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
117 223 0.65
118 87 0.25
119 33 0.10
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (117 bp):
TTACCATTTTAGCACATAAAATGCCCTATATGGAAATCCATATTTTCAATATGATTTCCTTATCA
TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTCCC
Found at i:2077202 original size:17 final size:17
Alignment explanation
Indices: 2077182--2077226 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
2077172 TAAATAAAAG
2077182 AATT-AAAAGAAAATTCA
1 AATTGAAAAGAAAATT-A
*
2077199 AATTGAAAA-AGAATTA
1 AATTGAAAAGAAAATTA
2077215 AATTGAAAAGAA
1 AATTGAAAAGAA
2077227 TTAAAAGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 10 0.42
17 10 0.42
18 4 0.17
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.22
Consensus pattern (17 bp):
AATTGAAAAGAAAATTA
Found at i:2077225 original size:15 final size:16
Alignment explanation
Indices: 2077193--2077231 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
2077183 ATTAAAAGAA
2077193 AATTCAAATTGAAAAAG
1 AATT-AAATTGAAAAAG
2077210 AATTAAATTG-AAAAG
1 AATTAAATTGAAAAAG
2077225 AATTAAA
1 AATTAAA
2077232 AGTCAATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 12 0.55
16 6 0.27
17 4 0.18
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (16 bp):
AATTAAATTGAAAAAG
Found at i:2078288 original size:2 final size:2
Alignment explanation
Indices: 2078281--2078412 Score: 104
Period size: 2 Copynumber: 68.0 Consensus size: 2
2078271 TAATAAATTA
*
2078281 AT AT AT AT A- AT AA AT AT A- AT AT AGT AT AT A- AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT -AT AT
* * *
2078322 AA AT AT AT AT AT -T AT ACT AC A- AT AT AT AT A- AT AT CT ACT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT
2078363 -T AT A- AT AT A- AT AT AT AT AT AT AT AT A- AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
2078402 AT ACT AT AT AT
1 AT A-T AT AT AT
2078413 TATCCCAGAC
Statistics
Matches: 107, Mismatches: 7, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
1 10 0.09
2 85 0.79
3 12 0.11
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2078292 original size:17 final size:19
Alignment explanation
Indices: 2078270--2078393 Score: 79
Period size: 17 Copynumber: 6.9 Consensus size: 19
2078260 ACATATAAAA
2078270 ATAATAAAT-TAATATA-T
1 ATAATAAATATAATATAGT
2078287 ATAATAAATATAATATAGT
1 ATAATAAATATAATATAGT
2078306 AT-AT-AATAT-ATCATA-T
1 ATAATAAATATAAT-ATAGT
* * *
2078322 A-AATATATATATTATACT
1 ATAATAAATATAATATAGT
* * *
2078340 ACAATATATATAATAT-CT
1 ATAATAAATATAATATAGT
*
2078358 ACTATTATAATATAATATA-T
1 A-TAATA-AATATAATATAGT
*
2078378 AT-ATATATATAATATA
1 ATAATAAATATAATATA
2078394 TACTATATAT
Statistics
Matches: 88, Mismatches: 8, Indels: 22
0.75 0.07 0.19
Matches are distributed among these distances:
16 6 0.07
17 34 0.39
18 17 0.19
19 20 0.23
20 11 0.12
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (19 bp):
ATAATAAATATAATATAGT
Found at i:2078379 original size:46 final size:44
Alignment explanation
Indices: 2078280--2078408 Score: 117
Period size: 46 Copynumber: 2.9 Consensus size: 44
2078270 ATAATAAATT
* *
2078280 AATATATATA-ATAAATATAATATAGTA-TATA-ATA-TATCATATA
1 AATATATATATATATATACAATATA-TACTATATATACTAT--TATA
*
2078323 AATATATATAT-TATACTACAATATATA-TAATATCTACTATTATA
1 AATATATATATATATA-TACAATATATACT-ATATATACTATTATA
*
2078367 ATATAATATATATATATATATAATATATACTATATATACTAT
1 A-AT-ATATATATATATATACAATATATACTATATATACTAT
2078409 ATATTATCCC
Statistics
Matches: 72, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
43 16 0.22
44 16 0.22
45 4 0.06
46 31 0.43
47 5 0.07
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (44 bp):
AATATATATATATATATACAATATATACTATATATACTATTATA
Found at i:2078409 original size:7 final size:6
Alignment explanation
Indices: 2078281--2078412 Score: 104
Period size: 5 Copynumber: 22.7 Consensus size: 6
2078271 TAATAAATTA
* *
2078281 ATATAT ATA-AT AAATAT A-ATAT AGTATAT A-ATAT ATCATAT AAATAT
1 ATATAT ATATAT ATATAT ATATAT A-TATAT ATATAT AT-ATAT ATATAT
* *
2078328 ATATAT -TATACT ACA-AT ATATAT A-ATAT CTACTAT -TATA- ATATA-
1 ATATAT ATATA-T ATATAT ATATAT ATATAT ATA-TAT ATATAT ATATAT
2078372 ATATAT ATATAT ATATA- ATATAT ACTATAT ATACTAT ATAT
1 ATATAT ATATAT ATATAT ATATAT A-TATAT ATA-TAT ATAT
2078413 TATCCCAGAC
Statistics
Matches: 105, Mismatches: 6, Indels: 30
0.74 0.04 0.21
Matches are distributed among these distances:
5 41 0.39
6 38 0.36
7 26 0.25
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (6 bp):
ATATAT
Found at i:2078412 original size:9 final size:9
Alignment explanation
Indices: 2078270--2078404 Score: 113
Period size: 9 Copynumber: 15.1 Consensus size: 9
2078260 ACATATAAAA
*
2078270 ATAATAAAT
1 ATAATATAT
2078279 -TAATATAT
1 ATAATATAT
*
2078287 ATAATAAAT
1 ATAATATAT
2078296 ATAATATAGT
1 ATAATATA-T
2078306 AT-ATA-AT
1 ATAATATAT
2078313 AT-ATCATAT
1 ATAAT-ATAT
2078322 A-AATATAT
1 ATAATATAT
*
2078330 ATATTATACT
1 ATAATATA-T
*
2078340 ACAATATAT
1 ATAATATAT
*
2078349 ATAATATCT
1 ATAATATAT
*
2078358 ACTATTATAAT
1 A-TAATAT-AT
2078369 ATAATATAT
1 ATAATATAT
2078378 AT-ATATAT
1 ATAATATAT
2078386 ATAATATAT
1 ATAATATAT
2078395 ACT-ATATAT
1 A-TAATATAT
2078404 A
1 A
2078405 CTATATATTA
Statistics
Matches: 104, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
7 5 0.05
8 22 0.21
9 54 0.52
10 21 0.20
11 2 0.02
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (9 bp):
ATAATATAT
Found at i:2080073 original size:14 final size:14
Alignment explanation
Indices: 2080054--2080086 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2080044 GGGGTAAGGC
2080054 GCGCCCCCTGAAAA
1 GCGCCCCCTGAAAA
2080068 GCGCCCCCTGAAAA
1 GCGCCCCCTGAAAA
2080082 GCGCC
1 GCGCC
2080087 TTATGCTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.45, G:0.24, T:0.06
Consensus pattern (14 bp):
GCGCCCCCTGAAAA
Found at i:2088090 original size:69 final size:69
Alignment explanation
Indices: 2088009--2088150 Score: 284
Period size: 69 Copynumber: 2.1 Consensus size: 69
2087999 GTTAATCAAG
2088009 AGGAGAGGATATTAAGGTTAAAGACAAGATAAATGAATAAAAATGAATCTAAGCATGTATATGTA
1 AGGAGAGGATATTAAGGTTAAAGACAAGATAAATGAATAAAAATGAATCTAAGCATGTATATGTA
2088074 AGTT
66 AGTT
2088078 AGGAGAGGATATTAAGGTTAAAGACAAGATAAATGAATAAAAATGAATCTAAGCATGTATATGTA
1 AGGAGAGGATATTAAGGTTAAAGACAAGATAAATGAATAAAAATGAATCTAAGCATGTATATGTA
2088143 AGTT
66 AGTT
2088147 AGGA
1 AGGA
2088151 TTATAAAAGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.48, C:0.04, G:0.23, T:0.25
Consensus pattern (69 bp):
AGGAGAGGATATTAAGGTTAAAGACAAGATAAATGAATAAAAATGAATCTAAGCATGTATATGTA
AGTT
Found at i:2089617 original size:30 final size:29
Alignment explanation
Indices: 2089578--2089636 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
2089568 GAGAATTTAC
* *
2089578 ATGAACTACGTGATTAAATGTATATGTGA
1 ATGAACTACGAGATTAAATGAATATGTGA
* *
2089607 ATGAAGCTACGAGTTTATATGAATATGTGA
1 ATGAA-CTACGAGATTAAATGAATATGTGA
2089637 TATGTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTAAATGAATATGTGA
Found at i:2089903 original size:23 final size:23
Alignment explanation
Indices: 2089877--2089932 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2089867 GACACTTCGA
* *
2089877 TGCATTTCTACGCGGTACTTAGG
1 TGCATTTATACGCGGCACTTAGG
* * *
2089900 TGCAATTATACGTGGCACTTCGG
1 TGCATTTATACGCGGCACTTAGG
2089923 TGCATTTATA
1 TGCATTTATA
2089933 AAAGCTGTGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (23 bp):
TGCATTTATACGCGGCACTTAGG
Found at i:2098491 original size:6 final size:6
Alignment explanation
Indices: 2098482--2098506 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2098472 GCCGTCCGTC
2098482 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
2098507 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:2102183 original size:15 final size:15
Alignment explanation
Indices: 2102158--2102201 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2102148 AGACCATGGA
*
2102158 AGAAGAGGTGG-AGT
1 AGAAGAAGTGGAAGT
2102172 ACGAAGAAGTGGAAGT
1 A-GAAGAAGTGGAAGT
*
2102188 AGAAGAAGAGGAAG
1 AGAAGAAGTGGAAG
2102202 AAATAGAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 1 0.04
15 21 0.81
16 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.43, T:0.09
Consensus pattern (15 bp):
AGAAGAAGTGGAAGT
Found at i:2112477 original size:56 final size:56
Alignment explanation
Indices: 2112391--2112497 Score: 178
Period size: 56 Copynumber: 1.9 Consensus size: 56
2112381 GATCAAAATG
* *
2112391 ATTGTGCATGAAACAGATATACTTCATTTGACGATGCGGTCATGTTCATATTGATC
1 ATTGTCCATGAAACAAATATACTTCATTTGACGATGCGGTCATGTTCATATTGATC
* *
2112447 ATTGTCCATGAAACAAATATACTTCATTTGATGATGCTGTCATGTTCATAT
1 ATTGTCCATGAAACAAATATACTTCATTTGACGATGCGGTCATGTTCATAT
2112498 CCATATTTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (56 bp):
ATTGTCCATGAAACAAATATACTTCATTTGACGATGCGGTCATGTTCATATTGATC
Found at i:2118084 original size:2 final size:2
Alignment explanation
Indices: 2118077--2118102 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2118067 TTTAAAATGA
2118077 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
2118103 GATAGCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2122964 original size:28 final size:28
Alignment explanation
Indices: 2122924--2123004 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
2122914 GAATGACCAC
2122924 TATGTCCCGAAGGACCACATAGAACACA
1 TATGTCCCGAAGGACCACATAGAACACA
* *
2122952 TATGTCCTGAAGGACCACGTAGAACACA
1 TATGTCCCGAAGGACCACATAGAACACA
* *
2122980 TATGTCCCAAAAGACCACATAGAAC
1 TATGTCCCGAAGGACCACATAGAAC
2123005 CCTCGACTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.40, C:0.27, G:0.17, T:0.16
Consensus pattern (28 bp):
TATGTCCCGAAGGACCACATAGAACACA
Found at i:2123906 original size:26 final size:23
Alignment explanation
Indices: 2123877--2123935 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 23
2123867 GAAATTCCCC
2123877 AGGTATCGATACCTTACCTTCCACAT
1 AGGTATCGATACC-T--CTTCCACAT
* *
2123903 AGGTATCGAAACCTCTTCCATAT
1 AGGTATCGATACCTCTTCCACAT
2123926 -GGTATCGATA
1 AGGTATCGATA
2123936 TTGTTCATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 9 0.30
23 8 0.27
25 1 0.03
26 12 0.40
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (23 bp):
AGGTATCGATACCTCTTCCACAT
Found at i:2123916 original size:21 final size:22
Alignment explanation
Indices: 2123892--2123933 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2123882 TCGATACCTT
2123892 ACCT-TCCACATA-GGTATCGAA
1 ACCTCTCC-CATATGGTATCGAA
*
2123913 ACCTCTTCCATATGGTATCGA
1 ACCTCTCCCATATGGTATCGA
2123934 TATTGTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (22 bp):
ACCTCTCCCATATGGTATCGAA
Found at i:2125531 original size:20 final size:20
Alignment explanation
Indices: 2125486--2125539 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
2125476 AGAACCAGTT
**
2125486 TGAGTCAACTCGAACTGTTC
1 TGAGTCAACTCGAACTGAAC
* *
2125506 TTAGTCAACTCGGACTGAAC
1 TGAGTCAACTCGAACTGAAC
*
2125526 TGAGTCAACCCGAA
1 TGAGTCAACTCGAA
2125540 TCGTTCTGAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
TGAGTCAACTCGAACTGAAC
Found at i:2126211 original size:23 final size:23
Alignment explanation
Indices: 2126149--2126212 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
2126139 AGTAAACATG
2126149 CAGTTACATACTTTCATA--ACA
1 CAGTTACATACTTTCATATCACA
* *
2126170 CACTTACATACTTTCATATCATA
1 CAGTTACATACTTTCATATCACA
*
2126193 CAGTCACATACTTTCATATC
1 CAGTTACATACTTTCATATC
2126213 TTACCTGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 17 0.46
23 20 0.54
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (23 bp):
CAGTTACATACTTTCATATCACA
Found at i:2126444 original size:23 final size:23
Alignment explanation
Indices: 2126418--2126510 Score: 111
Period size: 23 Copynumber: 4.1 Consensus size: 23
2126408 TGAGTGCCAT
2126418 ATAGAATTGTCCCGAATGACCAC
1 ATAGAATTGTCCCGAATGACCAC
*
2126441 ATAGAAATGTCCCGAATGACCAC
1 ATAGAATTGTCCCGAATGACCAC
* *
2126464 ATA-TA-TGTCCCGAAGGACCAC
1 ATAGAATTGTCCCGAATGACCAC
* *
2126485 ATAAAATTGTCCCTAA-GAACCAC
1 ATAGAATTGTCCCGAATG-ACCAC
2126508 ATA
1 ATA
2126511 TATGTTCCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
21 18 0.29
22 3 0.05
23 41 0.66
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (23 bp):
ATAGAATTGTCCCGAATGACCAC
Found at i:2126473 original size:21 final size:21
Alignment explanation
Indices: 2126425--2126585 Score: 135
Period size: 21 Copynumber: 7.5 Consensus size: 21
2126415 CATATAGAAT
*
2126425 TGTCCCGAATGACCACATAGAAA
1 TGTCCCGAATGACCACAT--ATA
2126448 TGTCCCGAATGACCACATATA
1 TGTCCCGAATGACCACATATA
* *
2126469 TGTCCCGAAGGACCACATAAAA
1 TGTCCCGAATGACCACAT-ATA
*
2126491 TTGTCCCTAA-GAACCACATATA
1 -TGTCCCGAATG-ACCACATATA
* * * *
2126513 TGTTCCAAAGGACCAAATATA
1 TGTCCCGAATGACCACATATA
* * * * *
2126534 TATTCCAAAGGACCGCATATA
1 TGTCCCGAATGACCACATATA
* *
2126555 TGTTCCAAATGACCACATATA
1 TGTCCCGAATGACCACATATA
2126576 TGTCCCGAAT
1 TGTCCCGAAT
2126586 AATCGCGTAG
Statistics
Matches: 118, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
21 79 0.67
22 6 0.05
23 33 0.28
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.23
Consensus pattern (21 bp):
TGTCCCGAATGACCACATATA
Found at i:2126483 original size:44 final size:44
Alignment explanation
Indices: 2126425--2126527 Score: 138
Period size: 44 Copynumber: 2.3 Consensus size: 44
2126415 CATATAGAAT
*
2126425 TGTCCCGAATGACCACATAGAAA-TGTCCCGAATG-ACCACATATA
1 TGTCCCGAAGGACCACATA-AAATTGTCCCGAA-GAACCACATATA
*
2126469 TGTCCCGAAGGACCACATAAAATTGTCCCTAAGAACCACATATA
1 TGTCCCGAAGGACCACATAAAATTGTCCCGAAGAACCACATATA
* *
2126513 TGTTCCAAAGGACCA
1 TGTCCCGAAGGACCA
2126528 AATATATATT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
43 4 0.08
44 49 0.92
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.20
Consensus pattern (44 bp):
TGTCCCGAAGGACCACATAAAATTGTCCCGAAGAACCACATATA
Found at i:2132485 original size:2 final size:2
Alignment explanation
Indices: 2132478--2132522 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
2132468 CATACGTTAA
* *
2132478 AT AT AT AT AT AT AT AT GT AT A- AT AT AT A- AT AT -T AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2132517 AT AT AT
1 AT AT AT
2132523 TATGTTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2132530 original size:18 final size:17
Alignment explanation
Indices: 2132480--2132536 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
2132470 TACGTTAAAT
*
2132480 ATATATATATATATGTATA
1 ATATATA-ATAT-TATATA
2132499 ATATATAATATTATATA
1 ATATATAATATTATATA
* * *
2132516 CATATATTATGTTATTTA
1 -ATATATAATATTATATA
2132534 ATA
1 ATA
2132537 ATGACATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.24
18 18 0.55
19 7 0.21
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (17 bp):
ATATATAATATTATATA
Found at i:2133163 original size:12 final size:12
Alignment explanation
Indices: 2133148--2133220 Score: 53
Period size: 13 Copynumber: 6.0 Consensus size: 12
2133138 TTTCTCTTTG
*
2133148 ATTTTTTCCTTT
1 ATTTTTTCATTT
*
2133160 ATTTTTTTCTTTT
1 A-TTTTTTCATTT
2133173 ATTTATTT-ATTT
1 ATTT-TTTCATTT
* *
2133185 ATCTTTTGATTT
1 ATTTTTTCATTT
2133197 ATTATTTT-ATTTT
1 ATT-TTTTCA-TTT
2133210 ATTTTTT-ATTT
1 ATTTTTTCATTT
2133221 TTACATTTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
11 6 0.12
12 22 0.42
13 24 0.46
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.77
Consensus pattern (12 bp):
ATTTTTTCATTT
Found at i:2133193 original size:45 final size:44
Alignment explanation
Indices: 2133111--2133220 Score: 116
Period size: 45 Copynumber: 2.4 Consensus size: 44
2133101 CTTTGATTCA
* * *
2133111 TTTATTATTTTTATTTAATTTAATTTTTTTCTCTTTGATTTTTTCC
1 TTTATT-TTTTT-TTTTATTTAATTTTTTTCTCTTTGATTTATTAC
*
2133157 TTTATTTTTTTCTTTTATTT-ATTTATTTATCT-TTTGATTTATTAT
1 TTTATTTTTTT-TTTTATTTAATTT-TTT-TCTCTTTGATTTATTAC
*
2133202 TTTATTTTATTTTTTATTT
1 TTTATTTTTTTTTTTATTT
2133221 TTACATTTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
44 12 0.21
45 35 0.62
46 9 0.16
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.75
Consensus pattern (44 bp):
TTTATTTTTTTTTTTATTTAATTTTTTTCTCTTTGATTTATTAC
Found at i:2133221 original size:12 final size:12
Alignment explanation
Indices: 2133157--2133221 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 12
2133147 GATTTTTTCC
*
2133157 TTTATTTTTTTCT
1 TTTA-TTTTTTAT
2133170 TTTATTTATTTA-
1 TTTATTT-TTTAT
*
2133182 TTTATCTTTTGA-
1 TTTAT-TTTTTAT
2133194 TTTATTATTTTAT
1 TTTATT-TTTTAT
2133207 TTTATTTTTTAT
1 TTTATTTTTTAT
2133219 TTT
1 TTT
2133222 TACATTTTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
11 1 0.02
12 29 0.64
13 15 0.33
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTATTTTTTAT
Found at i:2133228 original size:20 final size:19
Alignment explanation
Indices: 2133163--2133229 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
2133153 TTCCTTTATT
2133163 TTTTTC-TTTTATTTATTTA
1 TTTTTCATTTTATTT-TTTA
* *
2133182 TTTATC-TTTTGATTTATTA
1 TTTTTCATTTT-ATTTTTTA
2133201 -TTTT-ATTTTATTTTTTA
1 TTTTTCATTTTATTTTTTA
2133218 TTTTTACATTTT
1 TTTTT-CATTTT
2133230 CCCCATTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 7 0.18
18 11 0.28
19 12 0.31
20 9 0.23
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (19 bp):
TTTTTCATTTTATTTTTTA
Found at i:2137307 original size:17 final size:17
Alignment explanation
Indices: 2137285--2137328 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
2137275 GAAAGCATTA
2137285 TGTGACCTTGGCTCAAG
1 TGTGACCTTGGCTCAAG
2137302 TGTGACCTTGGCTCAAG
1 TGTGACCTTGGCTCAAG
*
2137319 TGTGAACTTG
1 TGTGACCTTG
2137329 ATGCCTAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (17 bp):
TGTGACCTTGGCTCAAG
Found at i:2149441 original size:97 final size:97
Alignment explanation
Indices: 2149275--2149539 Score: 394
Period size: 97 Copynumber: 2.7 Consensus size: 97
2149265 CCAGATTATA
* * *
2149275 ATAATATATATACAATAAATCTTGAGTTGTCCCTCTAAAGCAATTGCTTAAACGCCCC-ATCTTT
1 ATAATATCTATACAATAAA-CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGA-CTTT
2149339 ATGGAT-A-ATTATGCTAGCCTGATAAAGGTGATT
64 ATGGATAATATTA-GCTAGCCTGATAAAGGTGATT
*
2149372 ATAATATCTATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
1 ATAATATCTATACAATAAA-CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTA
2149437 TGGATAATATTCAGCTAGCCTGATAAAGGTGATT
65 TGGATAATATT-AGCTAGCCTGATAAAGGTGATT
* *
2149471 ATAATATCTATACAATGATA-TTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCCGACTTTA
1 ATAATATCTATACAAT-AAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTA
2149535 TGGAT
65 TGGAT
2149540 CCAGCTAGCT
Statistics
Matches: 155, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
97 64 0.41
98 48 0.31
99 40 0.26
100 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (97 bp):
ATAATATCTATACAATAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTAT
GGATAATATTAGCTAGCCTGATAAAGGTGATT
Found at i:2150893 original size:124 final size:123
Alignment explanation
Indices: 2150672--2151035 Score: 559
Period size: 124 Copynumber: 2.9 Consensus size: 123
2150662 GGACTCGAAG
*
2150672 CAACATTCATCTTTAGATTGGATTTCAACTTCACGAC-AAAGGATATCCAATTCAATGCTCAACT
1 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAA-GATATCCAATTCAAGGCTCAACT
* ** *
2150736 TCACAACGAATGGGCCATCCACAGTTTCAACTTCACGACGAAGTGAATCGTGGTCACCAG
65 TCACAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAA-TGAATCGTGCCCACCAA
* *
2150796 TAACATTCATATTTAGATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTT
1 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTT
2150861 CACAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAATGGAATCGTGCCCACCAA
66 CACAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAAT-GAATCGTGCCCACCAA
* * *
2150920 CAACATTCATCTTTATATTTGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTT
1 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTT
* * * *
2150985 CACAATGAAGGGGTCATCCACGATTTCAACTTCACGACGAATGATATCGTG
66 CACAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAATGA-ATCGTG
2151036 TTTACTTGAA
Statistics
Matches: 221, Mismatches: 16, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
123 3 0.01
124 215 0.97
125 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (123 bp):
CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAGGCTCAACTT
CACAACGAATGGGCCATCCACGGTTTCAACTTCACGACGAATGAATCGTGCCCACCAA
Found at i:2151186 original size:84 final size:84
Alignment explanation
Indices: 2151073--2151934 Score: 1064
Period size: 84 Copynumber: 10.3 Consensus size: 84
2151063 AAAGGCTATT
* * * *
2151073 TGCCAATAAAAAACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACT
1 TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
*
2151138 CAAGGCTATAAGGGTTATC
66 CAAGGCTAGAAGGGTTATC
* * * *
2151157 TGCCAACAAAAGACCTTCGAGTTAGACTACGGTCAGCTCCAAGGCACATCATTTGCAGCAGAGCT
1 TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* * * *
2151222 CAAGGCAATAAGGGATATT
66 CAAGGCTAGAAGGGTTATC
* * * * * * *
2151241 TGCCAACAAAAAATCTTCGAGTTCGACTACACTCAGCTCAAAGACATATCATTTGCAGCATAACT
1 TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
2151306 CAAGGCTAGAAGGGTTATC
66 CAAGGCTAGAAGGGTTATC
* * *
2151325 TGTCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACT
1 TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
2151390 CAAGGCTAGAAGGGTTATC
66 CAAGGCTAGAAGGGTTATC
* * *
2151409 TGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCT
1 TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* * *
2151474 CAAGGCAAGAAAGGTTATT
66 CAAGGCTAGAAGGGTTATC
*
2151493 TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCT-CATAGGCATATCATTTGCAGCATAAC
1 TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCA-AGGCACATCATTTGCAGCATAAC
*
2151557 TCAAGGCTAGAAAGGTTATC
65 TCAAGGCTAGAAGGGTTATC
* * * * * *
2151577 TGACAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTTGCAACATATCT
1 TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* * * *
2151642 TAAGGCAATAAGGGTTATT
66 CAAGGCTAGAAGGGTTATC
* * * *
2151661 TACCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACGTCTTTTGCATCATAACT
1 TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
2151726 CAAGGCTAGAAGGGTTATC
66 CAAGGCTAGAAGGGTTATC
* * * * * *
2151745 TTCCAACAAAATACCTTCGAGTTTGATTACACTCAGCTCAAAGGCACAACATTTGCAGCATAACT
1 TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* * *
2151810 TAAGGCGAGAAAGGTTATC
66 CAAGGCTAGAAGGGTTATC
* * * * * * * ** * *
2151829 TACCAACCAAAGACATTCGAGTTCGATTACACTTAGC-CCAAAGGCACATCATTCACAGCTTAGC
1 TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCC-AAGGCACATCATTTGCAGCATAAC
*
2151893 TCAAGGCAAGAAGGGTTATC
65 TCAAGGCTAGAAGGGTTATC
* * *
2151913 TGTCAATAAAA-ACCGTCGAGTT
1 TGCCAACAAAAGACCTTCGAGTT
2151935 CAATTCCATT
Statistics
Matches: 670, Mismatches: 105, Indels: 7
0.86 0.13 0.01
Matches are distributed among these distances:
83 12 0.02
84 656 0.98
85 2 0.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (84 bp):
TGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
CAAGGCTAGAAGGGTTATC
Found at i:2151530 original size:252 final size:252
Alignment explanation
Indices: 2151085--2151934 Score: 1204
Period size: 252 Copynumber: 3.4 Consensus size: 252
2151075 CCAATAAAAA
* *
2151085 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTATAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAG
* * *
2151150 GGTTATCTGCCAACAAAAGACCTTCGAGTTAGACTACGGTCAGCTCCAAGGCACATCATTTGCAG
66 GGTTATCTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAA
* * * * *
2151215 CAGAGCTCAAGGCAATAAGGGATATTTGCCAACAAAAAATCTTCGAGTTCGACTACACTCAGCTC
131 CATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAAACCTTCGAGTTTGACTACACTCAGCTC
* * *
2151280 AAAGACATATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAG
196 AAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAAGGTTATCTGACAACCAAAG
* *
2151337 ACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAG
*
2151402 GGTTATCTGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAA
66 GGTTATCTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAA
* * *
2151467 CATAGCTCAAGGCAAGAAAGGTTATTTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTC
131 CATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAAACCTTCGAGTTTGACTACACTCAGCTC
*
2151532 ATAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAAGGTTATCTGACAACCAAAG
196 AAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAAGGTTATCTGACAACCAAAG
* * * *
2151589 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTTGCAACATATCTTAAGGCAATAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAG
* * * * *
2151654 GGTTATTTACCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACGTCTTTTGCAT
66 GGTTATCTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAA
* * * *
2151719 CATAACTCAAGGCTAGAAGGGTTATCTT-CCAACAAAATACCTTCGAGTTTGATTACACTCAGCT
131 CATAGCTCAAGGCAAGAAGGGTTAT-TTGCCAACAAAAAACCTTCGAGTTTGACTACACTCAGCT
* * * *
2151783 CAAAGGCACAACATTTGCAGCATAACTTAAGGCGAGAAAGGTTATCT-ACCAACCAAAG
195 CAAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAAGGTTATCTGA-CAACCAAAG
* * * * ** * * *
2151841 ACATTCGAGTTCGATTACACTTAGC-CCAAAGGCACATCATTCACAGCTTAGCTCAAGGCAAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCC-AAGGCACATCATTTGCAACATAACTCAAGGCAAGAA
* * *
2151905 GGGTTATCTGTCAATAAAA-ACCGTCGAGTT
65 GGGTTATCTGCCAACAAAAGACCTTCGAGTT
2151935 CAATTCCATT
Statistics
Matches: 537, Mismatches: 58, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
251 13 0.02
252 522 0.97
253 2 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (252 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAG
GGTTATCTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAA
CATAGCTCAAGGCAAGAAGGGTTATTTGCCAACAAAAAACCTTCGAGTTTGACTACACTCAGCTC
AAAGGCATATCATTTGCAGCATAACTCAAGGCTAGAAAGGTTATCTGACAACCAAAG
Found at i:2153492 original size:13 final size:12
Alignment explanation
Indices: 2153474--2153511 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
2153464 TTTGTGTTTA
2153474 TTTCATATTATT
1 TTTCATATTATT
2153486 GTTTCATATT-TT
1 -TTTCATATTATT
*
2153498 TTTCATTTTATT
1 TTTCATATTATT
2153510 TT
1 TT
2153512 GGTCCCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 8 0.35
12 6 0.26
13 9 0.39
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTCATATTATT
Found at i:2153585 original size:20 final size:20
Alignment explanation
Indices: 2153555--2153645 Score: 80
Period size: 20 Copynumber: 4.5 Consensus size: 20
2153545 CCTTTGATTC
2153555 ATTTATTATTTTATTATTTTT
1 ATTTATTATTTTATT-TTTTT
2153576 ATTT-TTATTTTATTTTTTT
1 ATTTATTATTTTATTTTTTT
* *
2153595 CTCTT-TGA-TTTATTTTCCTTT
1 AT-TTATTATTTTATTTT--TTT
* * *
2153616 ATTTATTTTTTTATCTTTTG
1 ATTTATTATTTTATTTTTTT
2153636 ATTTATTATT
1 ATTTATTATT
2153646 AATATTATTA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
19 14 0.25
20 27 0.47
21 9 0.16
22 7 0.12
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (20 bp):
ATTTATTATTTTATTTTTTT
Found at i:2153621 original size:14 final size:15
Alignment explanation
Indices: 2153584--2153624 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
2153574 TTATTTTTAT
2153584 TTTATTT-TTTTCTC
1 TTTATTTATTTTCTC
2153598 TTTGATTTATTTTC-C
1 TTT-ATTTATTTTCTC
2153613 TTTATTTATTTT
1 TTTATTTATTTT
2153625 TTTATCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 12 0.48
15 8 0.32
16 5 0.20
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTATTTATTTTCTC
Found at i:2153761 original size:3 final size:3
Alignment explanation
Indices: 2153753--2153809 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
2153743 CCTTTTGATC
*
2153753 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2153801 TTT TAT TAT
1 TAT TAT TAT
2153810 GTTTTTCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:2153774 original size:117 final size:116
Alignment explanation
Indices: 2153559--2153771 Score: 276
Period size: 114 Copynumber: 1.8 Consensus size: 116
2153549 TGATTCATTT
* * *
2153559 ATTATTTTATTATTTTTATTTTTATTTTATTTTTTTCTCTTTGATTTATTTTCCTTTATTTATTT
1 ATTATTTGATTATTTTTATCTTTATTTTATTTTTTTCTCTTTGATATATTTT-CTTTATTTATTT
* *
2153624 TTTTATCTTTTGATTTATTATTAATATTATTATTTACATTTTTTCCCATTGA
65 TTCTACCTTTTGATTTATTATTAATATTATTATTTACATTTTTTCCCATTGA
2153676 ATTATTTGATATATTTTTA-CTTTATTTTATTTTATTT-TCCTTTGATATATTTT-TTT-TTCT-
1 ATTATTTGAT-TATTTTTATCTTTATTTTATTTT-TTTCT-CTTTGATATATTTTCTTTATT-TA
* *
2153736 TTTTTCT-CCTTTTGATCTATTATTATTATTATTATT
62 TTTTTCTACCTTTTGATTTATTATTAATATTATTATT
2153772 ATTATTATTA
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
114 26 0.31
115 8 0.09
116 4 0.05
117 23 0.27
118 24 0.28
ACGTcount: A:0.20, C:0.08, G:0.03, T:0.69
Consensus pattern (116 bp):
ATTATTTGATTATTTTTATCTTTATTTTATTTTTTTCTCTTTGATATATTTTCTTTATTTATTTT
TCTACCTTTTGATTTATTATTAATATTATTATTTACATTTTTTCCCATTGA
Found at i:2154485 original size:24 final size:24
Alignment explanation
Indices: 2154453--2154501 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2154443 TTGAATGTGA
2154453 TTTGTATACCTTTTTTAGTATGGG
1 TTTGTATACCTTTTTTAGTATGGG
2154477 TTTGTATACCTTTTTTAGTATGGG
1 TTTGTATACCTTTTTTAGTATGGG
2154501 T
1 T
2154502 GGACCATGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.08, G:0.20, T:0.55
Consensus pattern (24 bp):
TTTGTATACCTTTTTTAGTATGGG
Found at i:2155023 original size:19 final size:19
Alignment explanation
Indices: 2154999--2155036 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2154989 ACCTTTATAT
*
2154999 ATTTAATACTTTCTTTAAA
1 ATTTAATACTTTCATTAAA
*
2155018 ATTTAATATTTTCATTAAA
1 ATTTAATACTTTCATTAAA
2155037 GTAATGAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTAATACTTTCATTAAA
Found at i:2155292 original size:2 final size:2
Alignment explanation
Indices: 2155285--2155320 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2155275 GGCATATTTA
2155285 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
2155321 TTGATTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2159822 original size:23 final size:23
Alignment explanation
Indices: 2159777--2159828 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
2159767 CATGCGAAGA
*
2159777 AATTGCAGAATTATCAATTTATT
1 AATTGCAGAATTATCAATATATT
*
2159800 AATTGCA-AATTATATAATATATT
1 AATTGCAGAATTAT-CAATATATT
2159823 ACATTG
1 A-ATTG
2159829 TTAATTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 15 0.60
24 4 0.16
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (23 bp):
AATTGCAGAATTATCAATATATT
Found at i:2164313 original size:20 final size:20
Alignment explanation
Indices: 2164259--2164313 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
2164249 TGATCTCTAA
* *
2164259 ATCGCAACACGATCTCCAGT
1 ATCGCAACACGATTTCCAAT
*
2164279 ATCGCAA-ATCAATTTCCAA-
1 ATCGCAACA-CGATTTCCAAT
2164298 ATTCGCAACACGATTT
1 A-TCGCAACACGATTT
2164314 TGACTATCGT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 2 0.07
20 25 0.89
21 1 0.04
ACGTcount: A:0.35, C:0.29, G:0.11, T:0.25
Consensus pattern (20 bp):
ATCGCAACACGATTTCCAAT
Found at i:2164365 original size:21 final size:21
Alignment explanation
Indices: 2164319--2164372 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
2164309 GATTTTGACT
* **
2164319 ATCGTATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTAAAAA
*
2164340 TTCGCATTGCGATTTTAAAAA
1 ATCGCATTGCGATTTTAAAAA
*
2164361 ATCGCAATGCGA
1 ATCGCATTGCGA
2164373 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (21 bp):
ATCGCATTGCGATTTTAAAAA
Found at i:2165304 original size:24 final size:24
Alignment explanation
Indices: 2165253--2165306 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2165243 GTATTCGAAA
* *
2165253 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTAAATACCCAGAC
* *
2165277 TTTGATCTTGGTAAATACTCAGAT
1 TTTGATCTTGGTAAATACCCAGAC
2165301 TTTGAT
1 TTTGAT
2165307 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTAAATACCCAGAC
Found at i:2167577 original size:18 final size:18
Alignment explanation
Indices: 2167554--2167588 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2167544 AGAAAAAGGC
*
2167554 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
2167572 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
2167589 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:2167784 original size:20 final size:20
Alignment explanation
Indices: 2167759--2167943 Score: 187
Period size: 20 Copynumber: 9.8 Consensus size: 20
2167749 TTACACATTC
*
2167759 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2167779 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
2167798 A----A-AATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
2167813 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
2167833 ATATGACTATCGCAACGCCA
1 ATTTGACTATCGCAACGCGA
2167853 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2167867 AATTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2167887 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
2167907 ATTTGATTATCGTAACGGGA
1 ATTTGACTATCGCAACGCGA
2167927 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
2167944 AGAAAATCGC
Statistics
Matches: 136, Mismatches: 17, Indels: 24
0.77 0.10 0.14
Matches are distributed among these distances:
14 20 0.15
15 3 0.02
16 1 0.01
18 1 0.01
19 3 0.02
20 108 0.79
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:2167841 original size:54 final size:54
Alignment explanation
Indices: 2167759--2167903 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
2167749 TTACACATTC
* * *
2167759 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACTCAAAAATCGCAATGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGA
* *
2167813 ATTTGACTATCGCAACGCGAATATGACTATCGCAACGCCAAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGA
*
2167867 AATTGACTATCGCAACGCGAATTTGACTATCGCAACG
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
2167904 TGAATTTGAT
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (54 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGA
Found at i:2167936 original size:94 final size:93
Alignment explanation
Indices: 2167801--2167992 Score: 251
Period size: 94 Copynumber: 2.1 Consensus size: 93
2167791 CAACTCAAAA
* * *
2167801 ATCGCAATGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGCCAAAATCGCAACGCG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGACAAAATCGCAAAGCG
2167866 AAATT-GACTATCGCAACGCGAATTTGACT
66 -AATTAGACTATCGCAACGCGAA-TTGACT
* * * * * *
2167895 ATCGCAACGTGAATTTGATTATCGTAACGGGAATTTGACTATCGCAACGAGAAAATCGCAAAGCG
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGACAAAATCGCAAAGCG
* *
2167960 TATTAGACTATTGCAACGCGAATTGACT
66 AATTAGACTATCGCAACGCGAATTGACT
*
2167988 TTCGC
1 ATCGC
2167993 GTTGCGATTT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
93 13 0.15
94 72 0.85
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (93 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGACAAAATCGCAAAGCG
AATTAGACTATCGCAACGCGAATTGACT
Found at i:2167953 original size:74 final size:74
Alignment explanation
Indices: 2167759--2167983 Score: 213
Period size: 74 Copynumber: 3.0 Consensus size: 74
2167749 TTACACATTC
*
2167759 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACTCA-AAAATCGCAATGCGAATTTGACTAT
1 ATTTGAATATCGCAACGCGAATTTGACTATCGCAAC-CAGAAAATCGCAAAGCGAATTTGACTAT
2167823 CGCAACGCGA
65 CGCAACGCGA
* * * * * * *** ** *
2167833 ATATGACTATCGCAACGCCAAAATCG-C-AACGCGAAATTGACTATCGCAACGCGAATTTGACTA
1 ATTTGAATATCGCAACG-CGAATTTGACTATCGC-AACCAGAAAATCGCAAAGCGAATTTGACTA
*
2167896 TCGCAACGTGA
64 TCGCAACGCGA
* * * * * * *
2167907 ATTTGATTATCGTAACGGGAATTTGACTATCGCAACGAGAAAATCGCAAAGCGTATTAGACTATT
1 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACCAGAAAATCGCAAAGCGAATTTGACTATC
2167972 GCAACGCGA
66 GCAACGCGA
2167981 ATT
1 ATT
2167984 GACTTTCGCG
Statistics
Matches: 115, Mismatches: 31, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
73 8 0.07
74 98 0.85
75 9 0.08
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (74 bp):
ATTTGAATATCGCAACGCGAATTTGACTATCGCAACCAGAAAATCGCAAAGCGAATTTGACTATC
GCAACGCGA
Found at i:2168011 original size:20 final size:20
Alignment explanation
Indices: 2167982--2168042 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
2167972 GCAACGCGAA
*
2167982 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
2168002 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
*
2168022 TTGACTTTCGTATTGCGATT
1 TTGACTTTCGCATTGCGATT
2168042 T
1 T
2168043 GAGTTTAGCG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:2168174 original size:36 final size:35
Alignment explanation
Indices: 2168133--2168241 Score: 108
Period size: 36 Copynumber: 3.3 Consensus size: 35
2168123 TTACATTTCA
2168133 ATCAATTAAATAATCACAAATAAGAATTATTTACAC
1 ATCAATTAAATAA-CACAAATAAGAATTATTTACAC
* * *
2168169 ATCAA-T---TAA-ACAAAT--CAACT-TTTACAA
1 ATCAATTAAATAACACAAATAAGAATTATTTACAC
*
2168196 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAATAA-CACAAATAAGAATTATTTACAC
2168232 ATCAATTAAA
1 ATCAATTAAA
2168242 CAAATCAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
27 11 0.19
28 4 0.07
30 6 0.11
31 2 0.04
32 3 0.05
33 6 0.11
35 4 0.07
36 21 0.37
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.28
Consensus pattern (35 bp):
ATCAATTAAATAACACAAATAAGAATTATTTACAC
Found at i:2168220 original size:63 final size:63
Alignment explanation
Indices: 2168132--2168263 Score: 246
Period size: 63 Copynumber: 2.1 Consensus size: 63
2168122 TTTACATTTC
* *
2168132 AATCAATTAAATAATCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACA
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACA
2168195 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACA
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACA
2168258 AATCAA
1 AATCAA
2168264 CTTTTACAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (63 bp):
AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTTACA
Found at i:2168260 original size:14 final size:14
Alignment explanation
Indices: 2168241--2168277 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2168231 CATCAATTAA
2168241 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2168255 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2168269 ACAAATCAA
1 ACAAATCAA
2168278 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2169699 original size:42 final size:42
Alignment explanation
Indices: 2169640--2169762 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 42
2169630 ATGAATCGGG
* *
2169640 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
** *
2169682 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTGAACGATGACAGGGGC
* *
2169724 CTCTTGAACGATAGGAGAGG-CCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATGACAGG
2169763 TGAGTCAGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 63 0.93
43 4 0.06
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:2169700 original size:21 final size:21
Alignment explanation
Indices: 2169640--2169754 Score: 97
Period size: 21 Copynumber: 5.5 Consensus size: 21
2169630 ATGAATCGGG
* *
2169640 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
2169661 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
2169682 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
* **
2169703 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
2169724 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
2169745 CTCTTGAACG
1 CTCTTGAACG
2169755 ATGACAGGTG
Statistics
Matches: 71, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.04
21 66 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:2170068 original size:2 final size:2
Alignment explanation
Indices: 2170061--2170088 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2170051 AGTAAGCACT
2170061 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
2170089 CATTTAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2170295 original size:20 final size:20
Alignment explanation
Indices: 2170272--2170339 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
2170262 GAAACTTAAA
*
2170272 ATCGCAACGCGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * *
2170292 ATCGTAATACGGAAATGACT
1 ATCGCAACACGAAAATGACT
*
2170312 ATCGCAACAC-AAATTTGACT
1 ATCGCAACACGAAA-ATGACT
2170332 ATCGCAAC
1 ATCGCAAC
2170340 GAGATAATCG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 2 0.05
20 37 0.95
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:2170528 original size:20 final size:20
Alignment explanation
Indices: 2170474--2170533 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
2170464 GCGATTATCC
**
2170474 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
* *
2170494 CGTTGCAATCGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2170514 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
2170534 AATTGTGATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2170847 original size:21 final size:21
Alignment explanation
Indices: 2170810--2170849 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2170800 ATTCTGCAAC
*
2170810 GATGCTACCATCTCACGTAGA
1 GATGCTACCATCCCACGTAGA
2170831 GATGCTACC-TCACCACGTA
1 GATGCTACCATC-CCACGTA
2170850 AAATAGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.23
Consensus pattern (21 bp):
GATGCTACCATCCCACGTAGA
Found at i:2172506 original size:20 final size:20
Alignment explanation
Indices: 2172460--2172498 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2172450 TTTGAAACTT
2172460 AAAATCGCAACAAGAAAATG
1 AAAATCGCAACAAGAAAATG
*
2172480 AAAATCGCAACACGAAAAT
1 AAAATCGCAACAAGAAAAT
2172499 AATTATCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.18, G:0.13, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACAAGAAAATG
Found at i:2172582 original size:20 final size:20
Alignment explanation
Indices: 2172537--2172599 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
2172527 CAACGAGATA
**
2172537 ATCGCAACGC-AAAATGAAA
1 ATCGCAACGCAAAAATGACT
* *
2172556 ATTGCAACACAAAAATGACT
1 ATCGCAACGCAAAAATGACT
**
2172576 ATCGCAACGCAAATTTGACT
1 ATCGCAACGCAAAAATGACT
2172596 ATCG
1 ATCG
2172600 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 8 0.23
20 27 0.77
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCAAAAATGACT
Found at i:2172990 original size:22 final size:22
Alignment explanation
Indices: 2172963--2173020 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2172953 GATGGAGATA
2172963 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2172985 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
2173007 GATGGATGTCGCCG
1 GACGGATTTCGCCG
2173021 TAGAGAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Done.