Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 35
Found at i:4775332 original size:6 final size:6
Alignment explanation
Indices: 4775321--4775369 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
4775311 GATAAAGGGT
4775321 TGCGTA TGCGTA TGCGTA TGCGTA TGCGTA TGCGTA TGCGTA TGCGTA
1 TGCGTA TGCGTA TGCGTA TGCGTA TGCGTA TGCGTA TGCGTA TGCGTA
4775369 T
1 T
4775370 CTGTATCTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.16, C:0.16, G:0.33, T:0.35
Consensus pattern (6 bp):
TGCGTA
Found at i:4775375 original size:6 final size:6
Alignment explanation
Indices: 4775324--4775416 Score: 78
Period size: 6 Copynumber: 15.5 Consensus size: 6
4775314 AAAGGGTTGC
* * * * * * * *
4775324 GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATGC GTATCT
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT
* * * *
4775372 GTATCT ATATCT GTATAT GTATGT GTATGT GTATGT GTATGT GTA
1 GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTATGT GTA
4775417 CACATATACA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.42
Consensus pattern (6 bp):
GTATGT
Found at i:4775436 original size:16 final size:16
Alignment explanation
Indices: 4775415--4775446 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4775405 TGTGTATGTG
4775415 TACACATATACATATA
1 TACACATATACATATA
4775431 TACACATATACATATA
1 TACACATATACATATA
4775447 CATATCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACATATACATATA
Found at i:4781899 original size:38 final size:38
Alignment explanation
Indices: 4781857--4781933 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
4781847 AAGTTCATCA
*
4781857 ACTATTATGAAATCAAGACTAATATAAGTAGAACTGAG
1 ACTATTATGAAATCAAGACTAATACAAGTAGAACTGAG
*
4781895 ACTATTATGAAATCAAGATTAATACAAGTAGAACTGAG
1 ACTATTATGAAATCAAGACTAATACAAGTAGAACTGAG
4781933 A
1 A
4781934 TAAGCTGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (38 bp):
ACTATTATGAAATCAAGACTAATACAAGTAGAACTGAG
Found at i:4789185 original size:13 final size:13
Alignment explanation
Indices: 4789167--4789202 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
4789157 CGTGAGTCAT
4789167 TCGAGATCGATTC
1 TCGAGATCGATTC
*
4789180 TCGAGATCAATTC
1 TCGAGATCGATTC
*
4789193 TAGAGATCGA
1 TCGAGATCGA
4789203 CTCGATCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (13 bp):
TCGAGATCGATTC
Found at i:4791797 original size:283 final size:279
Alignment explanation
Indices: 4791283--4791844 Score: 982
Period size: 283 Copynumber: 2.0 Consensus size: 279
4791273 TATGATTATA
4791283 TATGTAGGACATTCGATGCCGGAGTTGCTGATTTAGTTTTAGGGGTAAGAAATTCGAATCTTCGA
1 TATGTAGGACATTCGATGCCGGAGTTGCTGATTTAGTTTTAGGGGTAAGAAATTCGAATCTTCGA
*
4791348 TGTGTAATGCGCTACTCGTGTTTATGCTAACCAAAATGATTCTACTGTTACGATTGTTTTGTCTG
66 TATGTAATGCGCTACTCGTGTTTATGCTAACCAAAATGATTCTACTGTTACGATTGTTTTGTCTG
4791413 GCATTGAAAATTTTGGTATATTCAATTAGCAATCTAATGTCTACAAGAATGAAAGACTTTGTGAT
131 GCATTGAAAATTTTGGTATATTCAATTAGCAATCTAATGTCTACAAGAATGAAAGACTTTGTGAT
* *
4791478 GGCATATTAATTAATTTTTCATATCATAGGATGTGCATATTATTAATTAGTCAATTACCATATTT
196 GGCATATTAATTAATTTTTCATATCATAGCATGTGC--A-TATTAATTAATCAATTA-CATATTT
*
4791543 GAATGAGCAAATAGCTTTAGCTT
257 GAATGAGCAAATAGCTGTAGCTT
* *
4791566 TATGTAGGACATTTGGTGCCGGAGTTGCTGATTTAGTTTTAGGGGTAAGAAATTCGAATCTTCGA
1 TATGTAGGACATTCGATGCCGGAGTTGCTGATTTAGTTTTAGGGGTAAGAAATTCGAATCTTCGA
* *
4791631 TATGTAATGCGCTACTCGTGTTTATGCTAACCAAAATGATTTTACTGTTAGGATTGTTTTGTCTG
66 TATGTAATGCGCTACTCGTGTTTATGCTAACCAAAATGATTCTACTGTTACGATTGTTTTGTCTG
*
4791696 GCATTGAAAA-TTTGGTATATTCAATTAGCAATCTAGTGTCTACAAGAATGAAAGACTTTGTGAT
131 GCATTGAAAATTTTGGTATATTCAATTAGCAATCTAATGTCTACAAGAATGAAAGACTTTGTGAT
*
4791760 GGCGTATTTAATTAATTTTTCATATCATAGCATGTGCATATTAATTAATCAATTACATATTTGAA
196 GGCATA-TTAATTAATTTTTCATATCATAGCATGTGCATATTAATTAATCAATTACATATTTGAA
4791825 TGAGCAAATAGCTGTAGCTT
260 TGAGCAAATAGCTGTAGCTT
4791845 ATGGTTCCCT
Statistics
Matches: 268, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
279 29 0.11
280 16 0.06
281 1 0.00
282 58 0.22
283 164 0.61
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (279 bp):
TATGTAGGACATTCGATGCCGGAGTTGCTGATTTAGTTTTAGGGGTAAGAAATTCGAATCTTCGA
TATGTAATGCGCTACTCGTGTTTATGCTAACCAAAATGATTCTACTGTTACGATTGTTTTGTCTG
GCATTGAAAATTTTGGTATATTCAATTAGCAATCTAATGTCTACAAGAATGAAAGACTTTGTGAT
GGCATATTAATTAATTTTTCATATCATAGCATGTGCATATTAATTAATCAATTACATATTTGAAT
GAGCAAATAGCTGTAGCTT
Found at i:4796425 original size:186 final size:187
Alignment explanation
Indices: 4796070--4796432 Score: 671
Period size: 186 Copynumber: 1.9 Consensus size: 187
4796060 CACCAAACTG
4796070 CATGATGATAGCAATGCCGATGAACAAAAGCCCAATCTTTTGCCCCGTATTGAGCTTGTGATTAC
1 CATGATGATAGCAATGCCGATGAACAAAAGCCCAATCTTTTGCCCCGTATTGAGCTTGTGATTAC
4796135 GTGACAGTTGTGGTGGCTTGTCCCAACTACCATGATTGGTTCGATTCTGGTGTGCTCTGCAGGCG
66 GTGACAGTTGTGGTGGCTTGTCCCAACTACCATGATTGGTTCGATTCTGGTGTGCTCTGCAGGCG
4796200 GCGATGGCCGAGAAGGCGCTGGAGGAGGCGATGGGGGAAGGTGGTGGCGGTGGCGAA
131 GCGATGGCCGAGAAGGCGCTGGAGGAGGCGATGGGGGAAGGTGGTGGCGGTGGCGAA
4796257 CATGATGATAGCAATGCCGATG-ACACAAAGCCCAATC-TTTGCCCCGTATTGAGCTTGTGATTA
1 CATGATGATAGCAATGCCGATGAACA-AAAGCCCAATCTTTTGCCCCGTATTGAGCTTGTGATTA
4796320 CGTGACAGTTGTGGTGGC-TGTCCCCAACTACCATGATTGGTTCGATTCTGGTTGTGCTCTGCAG
65 CGTGACAGTTGTGGTGGCTTGT-CCCAACTACCATGATTGGTTCGATTCTGG-TGTGCTCTGCAG
4796384 GCGGCGATGGCCGAGAAGGCGCTGGAGGAGGCGAT-GGGGAAGGTGGTGG
128 GCGGCGATGGCCGAGAAGGCGCTGGAGGAGGCGATGGGGGAAGGTGGTGG
4796433 TGGCGGTGGC
Statistics
Matches: 173, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
185 3 0.02
186 90 0.52
187 80 0.46
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.24
Consensus pattern (187 bp):
CATGATGATAGCAATGCCGATGAACAAAAGCCCAATCTTTTGCCCCGTATTGAGCTTGTGATTAC
GTGACAGTTGTGGTGGCTTGTCCCAACTACCATGATTGGTTCGATTCTGGTGTGCTCTGCAGGCG
GCGATGGCCGAGAAGGCGCTGGAGGAGGCGATGGGGGAAGGTGGTGGCGGTGGCGAA
Found at i:4796504 original size:15 final size:15
Alignment explanation
Indices: 4796484--4796536 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
4796474 GTGGGGGCGA
*
4796484 TGGCGGGGGAGGAGG
1 TGGCGGGGGTGGAGG
*
4796499 TGGCGGGGGTGGGGG
1 TGGCGGGGGTGGAGG
* *
4796514 AGGCGGAGGTGGAGG
1 TGGCGGGGGTGGAGG
4796529 -GGCGGGGG
1 TGGCGGGGG
4796537 CGGACTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 7 0.22
15 25 0.78
ACGTcount: A:0.09, C:0.08, G:0.75, T:0.08
Consensus pattern (15 bp):
TGGCGGGGGTGGAGG
Found at i:4799573 original size:20 final size:20
Alignment explanation
Indices: 4799537--4799575 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4799527 TCTTGCCTCT
*
4799537 ATATATATTAATTATATATA
1 ATATATATTAATCATATATA
4799557 ATATACTATTAA-CATATAT
1 ATATA-TATTAATCATATAT
4799576 TAGGCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATATATTAATCATATATA
Found at i:4811326 original size:45 final size:45
Alignment explanation
Indices: 4811262--4811487 Score: 341
Period size: 45 Copynumber: 5.0 Consensus size: 45
4811252 ATAAAATTTC
* *
4811262 TTACCAATATATTTTCCATTTATCTCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATT
* *
4811307 TTACGAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATT
*
4811352 TTACCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATT
4811397 TTACCAATATACTTACCATTTAT-TCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCT-CATAAGCTCGTAAGCTTATT
* **
4811442 TTACCAATATATTTGTCA-TTAT-TCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATCT-CATAAGCTCGTAAGCTTATT
4811486 TT
1 TT
4811488 CATGTTTACC
Statistics
Matches: 171, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
44 28 0.16
45 143 0.84
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (45 bp):
TTACCAATATACTTACCATTTATCTCATAAGCTCGTAAGCTTATT
Found at i:4811352 original size:25 final size:25
Alignment explanation
Indices: 4811324--4811397 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
4811314 TATACTTACC
4811324 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
* *
4811349 ATTT-TACCAATATA-CT--T-A-C-C
1 ATTTAT-CCCATA-AGCTCGTAAGCTT
4811369 ATTTATCCCATAAGCTCGTAAGCTT
1 ATTTATCCCATAAGCTCGTAAGCTT
4811394 ATTT
1 ATTT
4811398 TACCAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 2 0.06
22 2 0.06
23 2 0.06
24 2 0.06
25 15 0.42
26 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (25 bp):
ATTTATCCCATAAGCTCGTAAGCTT
Found at i:4814717 original size:35 final size:35
Alignment explanation
Indices: 4814661--4814735 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
4814651 TTCATGTTCA
*
4814661 AAATTCCAAAACACTTCAATTACATTCTAAACCTT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
* * *
4814696 AAATTCTAAAATACTTTAATTACATTCTAAACCCT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
4814731 AAATT
1 AAATT
4814736 AAATTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCCT
Found at i:4814806 original size:35 final size:34
Alignment explanation
Indices: 4814730--4814807 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 34
4814720 TTCTAAACCC
*
4814730 TAAATTAAATTATTTTAGAATTTAGGATTTAAAA
1 TAAATTGAATTATTTTAGAATTTAGGATTTAAAA
* *
4814764 TATAATTGAATTATTTTAGAATTTAGGGTTTAGAA
1 TA-AATTGAATTATTTTAGAATTTAGGATTTAAAA
4814799 TGAAATTGA
1 T-AAATTGA
4814808 GGATTGTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
34 2 0.05
35 36 0.92
36 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (34 bp):
TAAATTGAATTATTTTAGAATTTAGGATTTAAAA
Found at i:4816343 original size:35 final size:35
Alignment explanation
Indices: 4816287--4816361 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
4816277 TTCATGTTCA
4816287 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
* * * *
4816322 AAATTCTAAAATACTTTAATTATATTCTAAACCCT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
4816357 AAATT
1 AAATT
4816362 AAATTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCCT
Found at i:4822271 original size:6 final size:6
Alignment explanation
Indices: 4822238--4822270 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
4822228 ATTAATGACT
*
4822238 AAAATA AAAATA AAAATA AAAATA AAACTA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA
4822271 CAAAATGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:4822978 original size:191 final size:184
Alignment explanation
Indices: 4822623--4822994 Score: 564
Period size: 191 Copynumber: 2.0 Consensus size: 184
4822613 AACCGGAATA
* ** *
4822623 TAGATGTCCAGTAGTTTAATTTTCTCGCATTTTTTAGCATCTTCTATTACTCCTCTCTTGCCCAA
1 TAGATGTCCAGTAGTTTAATTTTCTCGCATTTTGTAGCATCGGCTATTACTCATCTCTTGCCCAA
*
4822688 TTGTGGTGGGTAAAGAGGATCTGAATGATGCTTATATTAAAGTTGGGAGTTTTTTAGTTCTCTCT
66 TTATGGTGGGTAAAGAGGATCTGAATGATGCTTATATTAAAGTTGGGAGTTTTTTAGTTCTCTCT
*
4822753 GAACTTATTCATTCATAGTTCTTGGAGTTCGGGAACTCGTAAATTTCTTCAATG
131 GAACTTATTCATTCATAGTTCTTGGAGTTCGGGAACTCCTAAATTTCTTCAATG
* * * *
4822807 TAGATGTCTAGTAGTTTCATTTTCTCGCATTTTGTAGCATCGGGTATTACTCATCTCTTGCTCAA
1 TAGATGTCCAGTAGTTTAATTTTCTCGCATTTTGTAGCATCGGCTATTACTCATCTCTTGCCCAA
* *
4822872 TTATGGTGGGTAAAGAGTATCTGAATTCTGAATGATGCTTATATTAAATTTTGGAGTTTTTTAGT
66 TTATGGTGGGTAAAGAG-----G-A-TCTGAATGATGCTTATATTAAAGTTGGGAGTTTTTTAGT
*
4822937 TCTCTCTGAACTTATTTATTCATAGTTCTTGGAGTTCGGGAACTCCTAAATTTCTTCA
124 TCTCTCTGAACTTATTCATTCATAGTTCTTGGAGTTCGGGAACTCCTAAATTTCTTCA
4822995 TTTGGTTTTG
Statistics
Matches: 168, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
184 73 0.43
189 1 0.01
190 1 0.01
191 93 0.55
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.43
Consensus pattern (184 bp):
TAGATGTCCAGTAGTTTAATTTTCTCGCATTTTGTAGCATCGGCTATTACTCATCTCTTGCCCAA
TTATGGTGGGTAAAGAGGATCTGAATGATGCTTATATTAAAGTTGGGAGTTTTTTAGTTCTCTCT
GAACTTATTCATTCATAGTTCTTGGAGTTCGGGAACTCCTAAATTTCTTCAATG
Found at i:4824302 original size:26 final size:26
Alignment explanation
Indices: 4824225--4824289 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
4824215 AAGGAAGAAA
*
4824225 TTATAAAATTTTAAGGGACGATAAAC
1 TTATAAAATTTTAAGGGACGATAAAT
4824251 TTATAAAATTTTAAGGGACGATAAAT
1 TTATAAAATTTTAAGGGACGATAAAT
4824277 TTATAAAATTTTA
1 TTATAAAATTTTA
4824290 CATGAACAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (26 bp):
TTATAAAATTTTAAGGGACGATAAAT
Found at i:4824632 original size:8 final size:9
Alignment explanation
Indices: 4824604--4824647 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
4824594 ATTTAGAATA
4824604 AAAATATTT
1 AAAATATTT
4824613 AAAAATATTT
1 -AAAATATTT
4824623 AAAA-ATTT
1 AAAATATTT
4824631 AAAATCAATTT
1 AAAAT--ATTT
4824642 AAAATA
1 AAAATA
4824648 AAAACATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 8 0.26
9 5 0.16
10 9 0.29
11 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATATTT
Found at i:4843499 original size:22 final size:22
Alignment explanation
Indices: 4843451--4843501 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
4843441 ACCCCTCTAT
*
4843451 ATATTTTTTTTCAATTAAATCA
1 ATATTTTTATTCAATTAAATCA
* *
4843473 CTATTTTTATTGAATTAAAAT-A
1 ATATTTTTATTCAATT-AAATCA
4843495 ATATTTT
1 ATATTTT
4843502 ATTATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATTTTTATTCAATTAAATCA
Found at i:4849926 original size:20 final size:20
Alignment explanation
Indices: 4849898--4849943 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
4849888 TTTATCAGAA
*
4849898 ATATTAAAA-AATAATATTTT
1 ATATAAAAACAATAAT-TTTT
4849918 ATATAAAAACAATAATTTTT
1 ATATAAAAACAATAATTTTT
*
4849938 AAATAA
1 ATATAA
4849944 TTTTTTATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATAAAAACAATAATTTTT
Found at i:4850484 original size:9 final size:9
Alignment explanation
Indices: 4850470--4850503 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4850460 TAAAAGGGAA
4850470 AAATAAAAT
1 AAATAAAAT
4850479 AAATAAAAT
1 AAATAAAAT
4850488 AAAT-AAAT
1 AAATAAAAT
4850496 AAGATAAA
1 AA-ATAAA
4850504 GGAAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:4850491 original size:13 final size:13
Alignment explanation
Indices: 4850469--4850503 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
4850459 GTAAAAGGGA
4850469 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
4850483 AAAATAAATAAAT
1 AAAATAAATAAAT
*
4850496 AAGATAAA
1 AAAATAAA
4850504 GGAAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:4850990 original size:11 final size:11
Alignment explanation
Indices: 4850973--4851011 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
4850963 ATATACATAT
4850973 AATAATAATAA
1 AATAATAATAA
*
4850984 CATAATAATAA
1 AATAATAATAA
4850995 AATAAATGAATAA
1 AAT-AAT-AATAA
4851008 AATA
1 AATA
4851012 TCCATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 12 0.50
12 4 0.17
13 8 0.33
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAATAATAA
Found at i:4851408 original size:37 final size:37
Alignment explanation
Indices: 4851367--4851471 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
4851357 GTGCTTGTGG
* *
4851367 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTAT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTAT
* * * * *
4851404 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTAT
*
4851441 ATCCTATTTTTAGGAGTTTGAATCTTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
4851472 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTAT
Found at i:4852181 original size:167 final size:168
Alignment explanation
Indices: 4851936--4852274 Score: 466
Period size: 167 Copynumber: 2.0 Consensus size: 168
4851926 AACTCAACAA
* * * *
4851936 TTTTGATGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATTTGCCTCTGAGTTGA
1 TTTTGATGGCAAATAACCCTTCTTGCCTTGAGCTATGCTGCAAA-TTGATGTGCCTCTGAGCTGA
* * * *
4852001 ATGTAATCGAACTCGAAGGTCTTTGATGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
65 ACGTAATCGAACTCGAAGGTCTTTGATGACAGATAACCCTTCTAGCATTGAGCTATGCTATAAAT
* *
4852066 GATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
130 GATGCGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC
* * * *
4852105 TTTTGTTGGCAAATAGCCCTTTTTGCCTTGAGCTATGTTGCAAA-TGATGTGCCT-TGGAGCTGA
1 TTTTGATGGCAAATAACCCTTCTTGCCTTGAGCTATGCTGCAAATTGATGTGCCTCT-GAGCTGA
* * * * *
4852168 GCGTAGTCGAACTCGAAGGTCTTTGCTGACAGATAGCCCTTCTAGTATTGAGCTATGCTATAAAT
65 ACGTAATCGAACTCGAAGGTCTTTGATGACAGATAACCCTTCTAGCATTGAGCTATGCTATAAAT
*
4852233 GATGCGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTC
130 GATGCGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC
4852272 TTT
1 TTT
4852275 ATTGACAGAT
Statistics
Matches: 149, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
166 1 0.01
167 110 0.74
169 38 0.26
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (168 bp):
TTTTGATGGCAAATAACCCTTCTTGCCTTGAGCTATGCTGCAAATTGATGTGCCTCTGAGCTGAA
CGTAATCGAACTCGAAGGTCTTTGATGACAGATAACCCTTCTAGCATTGAGCTATGCTATAAATG
ATGCGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC
Found at i:4852261 original size:83 final size:83
Alignment explanation
Indices: 4851945--4852285 Score: 423
Period size: 83 Copynumber: 4.1 Consensus size: 83
4851935 ATTTTGATGG
* * * * **
4851945 CAGATAACCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATTTGCCTCT-GAGTTGAATGTAATC
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAA--TGATGTGCCT-TGGAGCTGAGCGTAATC
*
4852009 GAACTCGAAGGTCTTTGATGA
63 GAACTCGAAGGTCTTTGTTGA
* * *
4852030 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAATCGAA
*
4852095 CTCGAAGGTCTTTTGTTGG
66 CTCGAAGGTC-TTTGTTGA
* * * * * *
4852114 CAAATAGCCCTTTTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAATCGAA
*
4852179 CTCGAAGGTCTTTGCTGA
66 CTCGAAGGTCTTTGTTGA
** * * *
4852197 CAGATAGCCCTTCTAGTATTGAGCTATGCTATAAATGATGCGCCTTGGAGCTGAGTGTAATCGAA
1 CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAATCGAA
*
4852262 CTCGAAGGTCTTTATTGA
66 CTCGAAGGTCTTTGTTGA
4852280 CAGATA
1 CAGATA
4852286 CTCCTTTTTT
Statistics
Matches: 223, Mismatches: 31, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
82 1 0.00
83 115 0.52
84 74 0.33
85 33 0.15
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (83 bp):
CAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAATCGAA
CTCGAAGGTCTTTGTTGA
Found at i:4852588 original size:106 final size:106
Alignment explanation
Indices: 4852459--4853416 Score: 1445
Period size: 106 Copynumber: 9.0 Consensus size: 106
4852449 GTACTGTTCC
* * * * * * ** *
4852459 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTACTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * * * * * *
4852524 TCAGTC-GCCCCTTCG-CTATGAAGTTGAGCTTGTGCTGTCTC
66 CCAG-CGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTG
* * * * *
4852565 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTAGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
4852630 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4852671 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
4852736 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
4852777 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
4852842 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
4852883 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
4852948 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
4852989 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
4853054 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
4853095 GAGTCAAATATCCTTCACTGTGAAGTTGAAATTAGCTCCGAAATTGTGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
4853160 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
4853201 GAGTCCAATATCCTTCGTTGTGAAGCTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
4853266 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
4853307 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
4853372 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
4853413 GAGT
1 GAGT
4853417 GGCACGATAT
Statistics
Matches: 787, Mismatches: 62, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
106 785 1.00
107 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:4854426 original size:21 final size:22
Alignment explanation
Indices: 4854375--4854428 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
4854365 TTGTGTTTGG
*
4854375 TCAAATGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
4854397 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
4854419 TC-AAGGTTTG
1 TCAAAGGTTTG
4854429 ATGGGGTAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 8 0.26
22 23 0.74
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.39
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:4855135 original size:16 final size:16
Alignment explanation
Indices: 4855109--4855142 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
4855099 TCTTTGTTTT
4855109 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
4855126 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
4855141 TT
1 TT
4855143 GATTAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:4858170 original size:9 final size:9
Alignment explanation
Indices: 4858156--4858189 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4858146 TAAAAGGGAA
4858156 AAATAAAAT
1 AAATAAAAT
4858165 AAATAAAAT
1 AAATAAAAT
4858174 AAAT-AAAT
1 AAATAAAAT
4858182 AAGATAAA
1 AA-ATAAA
4858190 GGAAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:4858177 original size:13 final size:13
Alignment explanation
Indices: 4858155--4858189 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
4858145 GTAAAAGGGA
4858155 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
4858169 AAAATAAATAAAT
1 AAAATAAATAAAT
*
4858182 AAGATAAA
1 AAAATAAA
4858190 GGAAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:4858497 original size:14 final size:14
Alignment explanation
Indices: 4858480--4858506 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4858470 ATATATACGT
4858480 AAATAAAAATAATC
1 AAATAAAAATAATC
4858494 AAATAAAAATAAT
1 AAATAAAAATAAT
4858507 TAAGAATATA
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:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATAAAAATAATC
Found at i:4858691 original size:14 final size:13
Alignment explanation
Indices: 4858654--4858692 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
4858644 ATATACATAT
4858654 AATAATAATAACATA
1 AATAATAA-AA-ATA
4858669 AATAATAAAAATA
1 AATAATAAAAATA
4858682 AATGAATAAAA
1 AAT-AATAAAA
4858693 TCCATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:4859081 original size:37 final size:37
Alignment explanation
Indices: 4859040--4859147 Score: 153
Period size: 37 Copynumber: 2.9 Consensus size: 37
4859030 GTGCTTGTGG
* * *
4859040 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
4859077 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
4859114 ATCATATTTTTAGGAGTTTGAATCTTAGTAAAAC
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAAC
4859148 GAAAATGTGT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:4862311 original size:18 final size:18
Alignment explanation
Indices: 4862277--4862318 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4862267 TAAATATATT
*
4862277 AAATTTTATTATGTTTAA
1 AAATTTTATTATCTTTAA
4862295 AAATATTTA-TATCTTT-A
1 AAAT-TTTATTATCTTTAA
4862312 AAATTTT
1 AAATTTT
4862319 GTTTGAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 5 0.23
18 10 0.45
19 4 0.18
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
AAATTTTATTATCTTTAA
Found at i:4866089 original size:17 final size:18
Alignment explanation
Indices: 4866044--4866094 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
4866034 CTGAAATAAT
4866044 AATAAAAAATATTATTTATTC
1 AATAAAAAATA--A-TTATTC
*
4866065 AAT-AAAAATAATTATTT
1 AATAAAAAATAATTATTC
*
4866082 AATTAAAAATAAT
1 AATAAAAAATAAT
4866095 ATATATAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 8 0.29
18 10 0.36
20 7 0.25
21 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAAAAATAATTATTC
Found at i:4866095 original size:21 final size:20
Alignment explanation
Indices: 4866047--4866095 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
4866037 AAATAATAAT
4866047 AAAAAAT-ATTATTTATTCA
1 AAAAAATAATTATTTATTCA
4866066 ATAAAAATAATTATTTAATT-A
1 A-AAAAATAATTATTT-ATTCA
4866087 AAAATAATA
1 AAAA-AATA
4866096 TATATAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.04
20 9 0.35
21 13 0.50
22 3 0.12
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATAATTATTTATTCA
Found at i:4867255 original size:20 final size:20
Alignment explanation
Indices: 4867230--4867283 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
4867220 TATTCCCTGA
*
4867230 TAATCTTACATTTCCACTGG
1 TAATCTTACATTCCCACTGG
4867250 TAATCTTACATTCCCACTGG
1 TAATCTTACATTCCCACTGG
*
4867270 CAATCTTACATTCC
1 TAATCTTACATTCC
4867284 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (20 bp):
TAATCTTACATTCCCACTGG
Found at i:4884672 original size:29 final size:29
Alignment explanation
Indices: 4884627--4884684 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
4884617 GTGTTGGCCG
4884627 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCGGGCGACCTAC
* *
4884656 TAGGTCGCCATGTCTTCCGGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCGGGCGACCTAC
4884685 AAGAGATTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.14, C:0.34, G:0.29, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCGGGCGACCTAC
Found at i:4884767 original size:20 final size:20
Alignment explanation
Indices: 4884742--4884794 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
4884732 GCCATCCGAA
4884742 CGAGGCCATCCGAGAGCATC
1 CGAGGCCATCCGAGAGCATC
*
4884762 CGAGGCCATTCGAGAGCATC
1 CGAGGCCATCCGAGAGCATC
4884782 CGAGGCCATCCGA
1 CGAGGCCATCCGA
4884795 CCGAGGCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.34, G:0.30, T:0.11
Consensus pattern (20 bp):
CGAGGCCATCCGAGAGCATC
Found at i:4884808 original size:10 final size:10
Alignment explanation
Indices: 4884742--4884794 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
4884732 GCCATCCGAA
4884742 CGAGGCCATC
1 CGAGGCCATC
4884752 CGAGAG-CATC
1 CGAG-GCCATC
*
4884762 CGAGGCCATT
1 CGAGGCCATC
4884772 CGAGAG-CATC
1 CGAG-GCCATC
4884782 CGAGGCCATC
1 CGAGGCCATC
4884792 CGA
1 CGA
4884795 CCGAGGCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 2 0.05
10 33 0.89
11 2 0.05
ACGTcount: A:0.25, C:0.34, G:0.30, T:0.11
Consensus pattern (10 bp):
CGAGGCCATC
Found at i:4884849 original size:33 final size:34
Alignment explanation
Indices: 4884795--4884879 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 34
4884785 GGCCATCCGA
* * * *
4884795 CCGA-GGCAATCCGAACTAGCTATGCAAGGGCAT
1 CCGAGGGCAAGCCGAGCGAGCTATGCAAGGGAAT
*
4884828 CCGAGGGCAA-CCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAAGCCGAGCGAGCTATGCAAGGGAAT
4884861 CCGAGGG-AAGCCGAGCGAG
1 CCGAGGGCAAGCCGAGCGAG
4884880 GGTAGGTCGC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
32 2 0.04
33 39 0.85
34 5 0.11
ACGTcount: A:0.28, C:0.26, G:0.36, T:0.09
Consensus pattern (34 bp):
CCGAGGGCAAGCCGAGCGAGCTATGCAAGGGAAT
Found at i:4884916 original size:29 final size:29
Alignment explanation
Indices: 4884883--4884938 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
4884873 GAGCGAGGGT
*
4884883 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGAGCATGGCGACCTACA
4884912 AGGTCGCCCGGAGAGCATGGCGACCTA
1 AGGTCGCCCGGAGAGCATGGCGACCTA
4884939 TGTGTTGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.36, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGAGCATGGCGACCTACA
Found at i:4885039 original size:29 final size:29
Alignment explanation
Indices: 4884997--4885053 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
4884987 GAGCAAGGGT
*
4884997 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
*
4885026 AGGTCTCCAGGAGTGCATGGCGACCTAC
1 AGGTCGCCAGGAGTGCATGGCGACCTAC
4885054 GGCTAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (29 bp):
AGGTCGCCAGGAGTGCATGGCGACCTACA
Found at i:4886376 original size:21 final size:21
Alignment explanation
Indices: 4886350--4886392 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4886340 TAAAAAAATA
*
4886350 TAAAATATTATTATTTTTAAT
1 TAAAATATTAATATTTTTAAT
4886371 TAAAATATTAATATTTTTAAT
1 TAAAATATTAATATTTTTAAT
4886392 T
1 T
4886393 TTTTTAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAAATATTAATATTTTTAAT
Found at i:4896374 original size:3 final size:3
Alignment explanation
Indices: 4896366--4896405 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
4896356 TGTTATTTAT
*
4896366 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4896406 AACGGGACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:4898938 original size:22 final size:23
Alignment explanation
Indices: 4898895--4898951 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
4898885 AAATTAATAA
4898895 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
4898918 TATATTATGTAAAA-GTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
4898940 TATA--ATGTAAAA
1 TATATTATGTAAAA
4898952 ATTATAACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.24
22 12 0.35
23 14 0.41
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (23 bp):
TATATTATGTAAAATGTTTCGAT
Found at i:4898987 original size:13 final size:13
Alignment explanation
Indices: 4898969--4898996 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4898959 CTAATAATAT
4898969 TAAATATATTAAA
1 TAAATATATTAAA
4898982 TAAATATATTAAA
1 TAAATATATTAAA
4898995 TA
1 TA
4898997 TATTTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAATATATTAAA
Found at i:4899775 original size:8 final size:8
Alignment explanation
Indices: 4899762--4899802 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
4899752 CTCATTTTCA
4899762 GAGAATTT
1 GAGAATTT
4899770 GAGAATTT
1 GAGAATTT
*
4899778 -AGAGTTT
1 GAGAATTT
*
4899785 GGGAATTT
1 GAGAATTT
4899793 GAGAATTT
1 GAGAATTT
4899801 GA
1 GA
4899803 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:4900095 original size:126 final size:126
Alignment explanation
Indices: 4899870--4900153 Score: 559
Period size: 126 Copynumber: 2.3 Consensus size: 126
4899860 CTATAATCGG
4899870 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
4899935 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
4899996 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
4900061 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
4900122 TTCACTATTCACGTGAAGGCGCGTTCCCGGGG
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGG
4900154 ACACTAGATA
Statistics
Matches: 157, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 157 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
Found at i:4902286 original size:2 final size:2
Alignment explanation
Indices: 4902279--4902331 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
4902269 ATACTCAATA
4902279 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4902320 AT AT AC AT AT AT
1 AT AT AT AT AT AT
4902332 GAACAGTTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4907355 original size:3 final size:3
Alignment explanation
Indices: 4907347--4907398 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
4907337 AGATTAAAAC
4907347 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4907394 AAT AA
1 AAT AA
4907399 AAGATTTGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4909473 original size:13 final size:13
Alignment explanation
Indices: 4909431--4909473 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
4909421 AATAGTAAAA
4909431 TATATGACGAAAT
1 TATATGACGAAAT
* *
4909444 TATAGGATGTAAA-
1 TATATGACG-AAAT
4909457 TATATGACGAAAT
1 TATATGACGAAAT
4909470 TATA
1 TATA
4909474 GGAAACTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 3 0.12
13 18 0.75
14 3 0.12
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (13 bp):
TATATGACGAAAT
Found at i:4909486 original size:26 final size:26
Alignment explanation
Indices: 4909428--4909477 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
4909418 CTAAATAGTA
**
4909428 AAATATATGACGAAATTATAGGATGT
1 AAATATATGACGAAATTATAGGAACT
4909454 AAATATATGACGAAATTATAGGAA
1 AAATATATGACGAAATTATAGGAA
4909478 ACTTCTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.18, T:0.28
Consensus pattern (26 bp):
AAATATATGACGAAATTATAGGAACT
Found at i:4917279 original size:30 final size:30
Alignment explanation
Indices: 4917212--4917269 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
4917202 CAGCGGGTGT
*
4917212 AATAAATTATTTATAGGATATAAAACTTGA
1 AATAAATTATTTACAGGATATAAAACTTGA
4917242 AATAAATTATTTACAGGATATAAAACTT
1 AATAAATTATTTACAGGATATAAAACTT
4917270 TAGGTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (30 bp):
AATAAATTATTTACAGGATATAAAACTTGA
Found at i:4918938 original size:2 final size:2
Alignment explanation
Indices: 4918931--4918966 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4918921 AGACGGAGAA
4918931 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
4918967 TATGACAAAT
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:4919375 original size:23 final size:25
Alignment explanation
Indices: 4919349--4919402 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
4919339 TTTGTTTTTT
* *
4919349 ATTTTATAATTTGATGAT-TTT-AA
1 ATTTTATAATTTAATCATATTTAAA
*
4919372 ATTTTGTAATTTAATCATATTTAAA
1 ATTTTATAATTTAATCATATTTAAA
4919397 ATTTTA
1 ATTTTA
4919403 ATAAATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 15 0.60
24 3 0.12
25 7 0.28
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (25 bp):
ATTTTATAATTTAATCATATTTAAA
Found at i:4921515 original size:6 final size:6
Alignment explanation
Indices: 4921279--4921511 Score: 367
Period size: 6 Copynumber: 38.8 Consensus size: 6
4921269 TCGTGCTCGT
4921279 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
4921327 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
*
4921375 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGT
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* * * *
4921423 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* * * * * *
4921471 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCG
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCG
4921512 TGGTAATACG
Statistics
Matches: 224, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 224 1.00
ACGTcount: A:0.12, C:0.17, G:0.50, T:0.21
Consensus pattern (6 bp):
GGTCGA
Found at i:4921808 original size:22 final size:22
Alignment explanation
Indices: 4921783--4921837 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
4921773 TCAGGAGTTA
* *
4921783 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
4921805 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
4921827 CGGGAGTTATA
1 CAGGAGTTATA
4921838 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:4927384 original size:5 final size:5
Alignment explanation
Indices: 4927370--4927413 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
4927360 GTCCGTCCGT
* * * *
4927370 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
4927414 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.07, C:0.41, G:0.36, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:4927422 original size:6 final size:6
Alignment explanation
Indices: 4927411--4927471 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
4927401 TCGGCTCGGC
* * * *
4927411 TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
4927459 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
4927472 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.07, C:0.16, G:0.49, T:0.28
Consensus pattern (6 bp):
TCGTGG
Found at i:4927770 original size:22 final size:22
Alignment explanation
Indices: 4927745--4927799 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
4927735 TCAGGAGTTA
* *
4927745 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
4927767 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
4927789 CGGGAGTTATA
1 CAGGAGTTATA
4927800 ACAGTTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:4934609 original size:2 final size:2
Alignment explanation
Indices: 4934596--4934626 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4934586 ATGAGACATA
*
4934596 AT AT AA 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 A
4934627 ACAATGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4934924 original size:20 final size:18
Alignment explanation
Indices: 4934877--4934949 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
4934867 ACTGAATATT
*
4934877 TGTCCCAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
4934895 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
4934914 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
4934933 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
4934950 GATAATCCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 31 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:4935640 original size:64 final size:64
Alignment explanation
Indices: 4935572--4935693 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
4935562 TCATAAATCT
* * * * *
4935572 CATTCGATGTTTGTATTTTAAGGGGGTGCAACGATGCACTACTTGTGCATCGATACACTAATGA
1 CATTCGATGTTTGTATTTTAAAGGAGTGCAACGATACACCACATGTGCATCGATACACTAATGA
* * *
4935636 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATACACCCCATGTGCATCGATACAC
1 CATTCGATGTTTGTATTTTAAAGGAGTGCAACGATACACCACATGTGCATCGATACAC
4935694 CTTGAACAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAAGGAGTGCAACGATACACCACATGTGCATCGATACACTAATGA
Found at i:4936408 original size:2 final size:2
Alignment explanation
Indices: 4936401--4936431 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4936391 GGATGTTACA
4936401 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 A
4936432 AGAAATGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4937316 original size:21 final size:21
Alignment explanation
Indices: 4937286--4937479 Score: 179
Period size: 21 Copynumber: 9.2 Consensus size: 21
4937276 GATTTACATA
*
4937286 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
4937307 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
4937330 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
4937349 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
4937372 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
4937391 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
4937414 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
4937433 TTCGCGTTGCGATTTATTCCAA-
1 TTCGCGTTGCGA--TAGTCCAAG
*
4937455 ATC-CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
4937475 TTCGC
1 TTCGC
4937480 CACGACACGA
Statistics
Matches: 140, Mismatches: 17, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
19 34 0.24
20 2 0.01
21 68 0.49
22 2 0.01
23 34 0.24
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:4937343 original size:42 final size:42
Alignment explanation
Indices: 4937292--4937479 Score: 331
Period size: 42 Copynumber: 4.5 Consensus size: 42
4937282 CATATTCGCA
*
4937292 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
4937334 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
4937376 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
4937418 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATCCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
4937460 TTGCGATAGTCCAAGTTCGC
1 TTGCGATAGTCCAAGTTCGC
4937480 CACGACACGA
Statistics
Matches: 138, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 138 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:4937412 original size:84 final size:84
Alignment explanation
Indices: 4937292--4937479 Score: 367
Period size: 84 Copynumber: 2.2 Consensus size: 84
4937282 CATATTCGCA
4937292 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
*
4937357 GCGATTTATTCCAAATTCG
66 GCGATTTATTCCAAATCCG
4937376 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
4937441 GCGATTTATTCCAAATCCG
66 GCGATTTATTCCAAATCCG
4937460 TTGCGATAGTCCAAGTTCGC
1 TTGCGATAGTCCAAGTTCGC
4937480 CACGACACGA
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 103 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (84 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATCCG
Found at i:4937994 original size:5 final size:5
Alignment explanation
Indices: 4937984--4938008 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4937974 CCGCCGTCGT
4937984 CCGTC CCGTC CCGTC CCGTC CCGTC
1 CCGTC CCGTC CCGTC CCGTC CCGTC
4938009 TCGAATACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.20, T:0.20
Consensus pattern (5 bp):
CCGTC
Found at i:4939790 original size:95 final size:94
Alignment explanation
Indices: 4939671--4939870 Score: 355
Period size: 95 Copynumber: 2.1 Consensus size: 94
4939661 AAGTAGTGTC
* *
4939671 ACAAAATTGTCAGCATTTGCTTTTCCTTAAAATATATATTACTAATTTAGTATAAATTTGTGATA
1 ACAAAATGGTAAGCATTTGCTTTTCCTTAAAATATATATTACTAATTTAGTATAAATTTGTGATA
4939736 ATAAAAATAAAAATAAAAAAAGATTTACTG
66 ATAAAAATAAAAAT-AAAAAAGATTTACTG
4939766 ACAAAATGGTAAGCATTTGCTTTTCCTTAAAATATATATTACTAATTTAGTATAAATTTGTGATA
1 ACAAAATGGTAAGCATTTGCTTTTCCTTAAAATATATATTACTAATTTAGTATAAATTTGTGATA
* *
4939831 ATAATAATAAAAATAAAAAATATTTACTG
66 ATAAAAATAAAAATAAAAAAGATTTACTG
4939860 ACAAAATGGTA
1 ACAAAATGGTA
4939871 GGATACAAGA
Statistics
Matches: 101, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
94 25 0.25
95 76 0.75
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (94 bp):
ACAAAATGGTAAGCATTTGCTTTTCCTTAAAATATATATTACTAATTTAGTATAAATTTGTGATA
ATAAAAATAAAAATAAAAAAGATTTACTG
Found at i:4940484 original size:2 final size:2
Alignment explanation
Indices: 4940477--4940506 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4940467 TTGGATTTTA
4940477 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
4940507 GGTCTGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4941089 original size:22 final size:23
Alignment explanation
Indices: 4941061--4941107 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
4941051 TTGATTATTT
4941061 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* * *
4941083 TATTATATTGTTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
4941106 TA
1 TA
4941108 AATGTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:4956350 original size:2 final size:2
Alignment explanation
Indices: 4956343--4956371 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4956333 ACACTGTTGA
4956343 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4956372 GTTTTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4968405 original size:2 final size:2
Alignment explanation
Indices: 4968398--4968449 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4968388 CAGAGCTAAC
4968398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4968440 AT AT AT AT AT
1 AT AT AT AT AT
4968450 TTGGATAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4972555 original size:3 final size:3
Alignment explanation
Indices: 4972549--4972576 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4972539 CCCGTTGTAG
4972549 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC C
4972577 ACATACCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:4973827 original size:12 final size:12
Alignment explanation
Indices: 4973810--4973846 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
4973800 TTATAACTAA
4973810 TATATTAAATAT
1 TATATTAAATAT
*
4973822 TATATTAAATAAA
1 TATATTAAAT-AT
4973835 TATATTAAATAT
1 TATATTAAATAT
4973847 ATTTATGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TATATTAAATAT
Found at i:4973840 original size:13 final size:13
Alignment explanation
Indices: 4973808--4973845 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
4973798 AATTATAACT
4973808 AATATATTAAAT-
1 AATATATTAAATA
*
4973820 ATTATATTAAATA
1 AATATATTAAATA
4973833 AATATATTAAATA
1 AATATATTAAATA
4973846 TATTTATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATATATTAAATA
Found at i:4974217 original size:4 final size:4
Alignment explanation
Indices: 4974208--4975700 Score: 2591
Period size: 4 Copynumber: 382.8 Consensus size: 4
4974198 ATCAGTTTGA
4974208 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974256 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974304 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974352 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974400 TATG TATG T-TG TATG TATG TA-G TA-G TATG TATG TA-G TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974444 --TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974490 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974537 TATG TATG TATG TATG TATG TATG TATG -ATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974584 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974632 TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974678 TATG TATG TATG TATG TATG TATG TATG T-TG TATG --TG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974723 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-TG TATG
4974771 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974819 TATG --TG TATG TATG TATG -ATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974864 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974912 TA-G TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4974958 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4975005 TATG TATG TATG TA-G TATG TATG TATG TATG TATG TATG T-TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4975051 TATG TATG TATG TATG --TG TATG TATG TATG TATG TATG TATG -ATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4975096 TATG TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4975142 TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
4975188 TATG TATG TATG TATG TATG TCTG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4975236 TA-G TATG TATG T-TG TATG TAT- TATG TATG TATG -ATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4975280 TATG TATG TATG TATG TATG TATG TATG TATTGG TATG TATG TA-G TATG
1 TATG TATG TATG TATG TATG TATG TATG TA-T-G TATG TATG TATG TATG
4975329 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4975375 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T-TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4975422 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4975468 TATG TATG TATG TATG TATG TATG TATG TATG TA-G TAT- TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4975514 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * *
4975562 TATG TATG TATG TATG TATG TATG TATG CATG CATG CATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
4975610 CATG CATG CATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
4975658 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
4975701 ATTGGCGTTG
Statistics
Matches: 1442, Mismatches: 4, Indels: 86
0.94 0.00 0.06
Matches are distributed among these distances:
2 18 0.01
3 69 0.05
4 1347 0.93
5 5 0.00
6 3 0.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:4976156 original size:8 final size:8
Alignment explanation
Indices: 4976143--4976183 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
4976133 CTCATTTTCA
4976143 GAGAATTT
1 GAGAATTT
4976151 GAGAATTT
1 GAGAATTT
*
4976159 -AGAGTTT
1 GAGAATTT
*
4976166 GGGAATTT
1 GAGAATTT
4976174 GAGAATTT
1 GAGAATTT
4976182 GA
1 GA
4976184 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:4976944 original size:28 final size:30
Alignment explanation
Indices: 4976885--4976948 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
4976875 ATATTTTAAA
* *
4976885 TTTAAATTTGAATATATTATTTATTTTTAT
1 TTTAAATTTGAATATATTATTAATTTGTAT
4976915 TTTAAATTTCGAATA-A-TA-TAATTTGTAT
1 TTTAAATTT-GAATATATTATTAATTTGTAT
4976943 TTTAAA
1 TTTAAA
4976949 AAACATTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 14 0.45
29 2 0.06
30 10 0.32
31 5 0.16
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (30 bp):
TTTAAATTTGAATATATTATTAATTTGTAT
Found at i:4977495 original size:21 final size:20
Alignment explanation
Indices: 4977468--4977537 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
4977458 GGTATAAAAC
*
4977468 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
4977488 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
4977509 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
4977530 CCCTGCGG
1 -CCTGCGG
4977538 AGATGGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:4977567 original size:21 final size:21
Alignment explanation
Indices: 4977541--4977588 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4977531 CCTGCGGAGA
*
4977541 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
4977562 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
4977583 GGGCAT
1 TGGCAT
4977589 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:4979311 original size:31 final size:32
Alignment explanation
Indices: 4979276--4979346 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
4979266 TAATTCTAAT
* *
4979276 AAATAATAATTATAAATATTAT-TTAATA-AAA
1 AAATAATAATT-TAAATAATATAGTAATATAAA
*
4979307 AAATAAT-ATTTACATAATATAGTAATATAAA
1 AAATAATAATTTAAATAATATAGTAATATAAA
4979338 AAATAATAA
1 AAATAATAA
4979347 CTATTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 8 0.24
30 8 0.24
31 17 0.50
32 1 0.03
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (32 bp):
AAATAATAATTTAAATAATATAGTAATATAAA
Found at i:4979371 original size:34 final size:33
Alignment explanation
Indices: 4979303--4979371 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 33
4979293 ATTATTTAAT
* * * *
4979303 AAAAAAATAATATTTACATAATATAGTAATATA
1 AAAAAAATAATATTTAAAAAATACAGTAAAATA
4979336 AAAAATAATAACTATTTAAAAAATACA-TAAAATA
1 AAAAA-AATAA-TATTTAAAAAATACAGTAAAATA
4979370 AA
1 AA
4979372 TTTTTTACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
33 5 0.17
34 13 0.43
35 12 0.40
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (33 bp):
AAAAAAATAATATTTAAAAAATACAGTAAAATA
Found at i:4981418 original size:22 final size:22
Alignment explanation
Indices: 4981393--4981435 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
4981383 TAATAAATTA
4981393 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
4981415 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
4981436 GTAATAAATT
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:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:4981444 original size:22 final size:22
Alignment explanation
Indices: 4981395--4981443 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
4981385 ATAAATTATT
**
4981395 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
4981417 TAAAATAAATCAATCCATAGTAA
1 TAAAATAAATCAATCCATA-TAA
4981440 TAAA
1 TAAA
4981444 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:4981453 original size:32 final size:32
Alignment explanation
Indices: 4981415--4981544 Score: 154
Period size: 32 Copynumber: 4.4 Consensus size: 32
4981405 CAATCCATAT
*
4981415 TTTAAAATAAATCAATCCATAGTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
4981447 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
4981479 TTTAAAATAAATC-A---AT-C-GAT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
4981501 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
4981533 TTTAAAATAAAT
1 TTTAAAATAAAT
4981545 TATTTTAAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 20
0.78 0.04 0.19
Matches are distributed among these distances:
22 13 0.15
23 2 0.02
24 1 0.01
26 4 0.05
27 2 0.02
28 4 0.05
30 1 0.01
31 2 0.02
32 55 0.65
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:4981457 original size:14 final size:14
Alignment explanation
Indices: 4981438--4981490 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
4981428 AATCCATAGT
4981438 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
4981452 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
4981470 AATAAATTATTTAA
1 AATAAATTATTTAA
4981484 AATAAAT
1 AATAAAT
4981491 CAATCGATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 5 0.16
17 5 0.16
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:4981481 original size:86 final size:86
Alignment explanation
Indices: 4981383--4981544 Score: 297
Period size: 86 Copynumber: 1.9 Consensus size: 86
4981373 ACAAATACAA
*
4981383 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAGTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
4981448 TTAAAATAAATCAATTCATAC
66 TTAAAATAAATCAATTCATAC
* *
4981469 TAATAAATTATTTAAAATAAATCAATCGATATTTTAAAATAAATCAATCTATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
4981534 TTAAAATAAAT
66 TTAAAATAAAT
4981545 TATTTTAAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.37
Consensus pattern (86 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATTCATAC
Found at i:4981530 original size:22 final size:22
Alignment explanation
Indices: 4981481--4981529 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4981471 ATAAATTATT
**
4981481 TAAAATAAATCAATCGATATTT
1 TAAAATAAATCAATCGATATAA
*
4981503 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCGATA-TAA
4981526 TAAA
1 TAAA
4981530 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCGATATAA
Found at i:4981553 original size:15 final size:15
Alignment explanation
Indices: 4981524--4981626 Score: 100
Period size: 15 Copynumber: 6.5 Consensus size: 15
4981514 AATCTATACT
4981524 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
4981538 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
4981553 AATAAATCAATCTATATTTTAT
1 AAT--A--AA--T-TATTTTAA
*
4981575 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
4981590 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
4981605 AATAATTTATTTTAA
1 AATAAATTATTTTAA
4981620 AATAAAT
1 AATAAAT
4981627 AACCTTATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.12
15 47 0.64
16 1 0.01
17 1 0.01
18 1 0.01
19 2 0.03
20 1 0.01
21 1 0.01
22 10 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:4981570 original size:69 final size:67
Alignment explanation
Indices: 4981470--4981626 Score: 201
Period size: 67 Copynumber: 2.3 Consensus size: 67
4981460 AATTCATACT
*
4981470 AATAAATTA-TTTAAAATAAATCAATCGATATTTTAAAATAAATCAATCTATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCGATATTTTAAAAT-AATCAAT-TATA-AAATAAATTAT
4981533 TTTAA
63 TTTAA
* * ** *
4981538 AATAAATTATTTTAAAATAAATCAATCTATATTTTATAATAATTTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCGATATTTTAAAATAATCAATTATAAAATAAATTATTTT
*
4981603 AT
66 AA
*
4981605 AATAATTTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
4981627 AACCTTATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
66 9 0.11
67 28 0.35
68 14 0.18
69 28 0.35
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCGATATTTTAAAATAATCAATTATAAAATAAATTATTTT
AA
Found at i:4981603 original size:30 final size:30
Alignment explanation
Indices: 4981567--4981626 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4981557 AATCAATCTA
4981567 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTATAATAATTTATTTTAAAATAAAT
4981597 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTATAATAATTTATTTTAAAATAAAT
4981627 AACCTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TATTTTATAATAATTTATTTTAAAATAAAT
Found at i:4985432 original size:43 final size:43
Alignment explanation
Indices: 4985371--4985457 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
4985361 TAAGGGAATT
4985371 TGTTGTTACGATAAGGAAACTGCATATATAAGGACAAGAACTG
1 TGTTGTTACGATAAGGAAACTGCATATATAAGGACAAGAACTG
4985414 TGTTGTTACGATAAGGAAACTGCATATATAAGGACAAGAACTG
1 TGTTGTTACGATAAGGAAACTGCATATATAAGGACAAGAACTG
4985457 T
1 T
4985458 TATTATATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.26
Consensus pattern (43 bp):
TGTTGTTACGATAAGGAAACTGCATATATAAGGACAAGAACTG
Found at i:4985456 original size:21 final size:21
Alignment explanation
Indices: 4985388--4985456 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
4985378 ACGATAAGGA
4985388 AACTGCATATATAAGGACAAG
1 AACTGCATATATAAGGACAAG
** * * * *
4985409 AACTGTGT-TGTTACGATAAGG
1 AACTGCATATATAAGGACAA-G
4985430 AAACTGCATATATAAGGACAAG
1 -AACTGCATATATAAGGACAAG
4985452 AACTG
1 AACTG
4985457 TTATTATATT
Statistics
Matches: 33, Mismatches: 12, Indels: 6
0.65 0.24 0.12
Matches are distributed among these distances:
20 7 0.21
21 12 0.36
22 7 0.21
23 7 0.21
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (21 bp):
AACTGCATATATAAGGACAAG
Found at i:4987909 original size:24 final size:24
Alignment explanation
Indices: 4987881--4987928 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4987871 TGAGAATAAT
*
4987881 TTATAATTTTA-ATAATATAAAATA
1 TTATAAATTTACATAATA-AAAATA
4987905 TTATAAATTTAGCATAATAAAAAT
1 TTATAAATTTA-CATAATAAAAAT
4987929 GTATTATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 5 0.24
26 6 0.29
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
TTATAAATTTACATAATAAAAATA
Found at i:4988414 original size:22 final size:23
Alignment explanation
Indices: 4988376--4988418 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
4988366 TAGAGATTTT
4988376 TATTTTATAATATTAAAAATAGA
1 TATTTTATAATATTAAAAATAGA
4988399 TATTTT-TAAT-TATAAAAATA
1 TATTTTATAATAT-TAAAAATA
4988419 ATAAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.05
22 12 0.63
23 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TATTTTATAATATTAAAAATAGA
Found at i:4988424 original size:29 final size:29
Alignment explanation
Indices: 4988366--4988424 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
4988356 TTTAAGGTTT
* * *
4988366 TAGAGATTTTTATTTTATAATATTAAAAA
1 TAGAGATTTTTATATTATAAAAATAAAAA
*
4988395 TAGATATTTTTA-ATTATAAAAATAATAAA
1 TAGAGATTTTTATATTATAAAAATAA-AAA
4988424 T
1 T
4988425 TATTATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (29 bp):
TAGAGATTTTTATATTATAAAAATAAAAA
Found at i:4989094 original size:20 final size:20
Alignment explanation
Indices: 4989069--4989106 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4989059 TAATTAATAA
4989069 TTTTTAT-TTATAAATAAAGT
1 TTTTTATCTTA-AAATAAAGT
4989089 TTTTTATCTTAAAATAAA
1 TTTTTATCTTAAAATAAA
4989107 ATATTGGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTTATCTTAAAATAAAGT
Found at i:4989604 original size:21 final size:21
Alignment explanation
Indices: 4989579--4989622 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4989569 AGAAATATTA
4989579 AAAAAT-ATTAATATTTTAAAT
1 AAAAATGA-TAATATTTTAAAT
*
4989600 AAAAATGATAATATTTTTAAT
1 AAAAATGATAATATTTTAAAT
4989621 AA
1 AA
4989623 TCTTTTACCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAATGATAATATTTTAAAT
Found at i:4989843 original size:95 final size:95
Alignment explanation
Indices: 4989680--4989867 Score: 376
Period size: 95 Copynumber: 2.0 Consensus size: 95
4989670 ACCAAAATCG
4989680 TATATTAAAGGTTGAGCACGGAAGGGGATTTCAAACGTACTAGAAACAAAAGAAGAAAATTTAAG
1 TATATTAAAGGTTGAGCACGGAAGGGGATTTCAAACGTACTAGAAACAAAAGAAGAAAATTTAAG
4989745 GCAACAAATTCAAACGCAAAGTGGGCCCAC
66 GCAACAAATTCAAACGCAAAGTGGGCCCAC
4989775 TATATTAAAGGTTGAGCACGGAAGGGGATTTCAAACGTACTAGAAACAAAAGAAGAAAATTTAAG
1 TATATTAAAGGTTGAGCACGGAAGGGGATTTCAAACGTACTAGAAACAAAAGAAGAAAATTTAAG
4989840 GCAACAAATTCAAACGCAAAGTGGGCCC
66 GCAACAAATTCAAACGCAAAGTGGGCCC
4989868 CACACGAGTG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.18
Consensus pattern (95 bp):
TATATTAAAGGTTGAGCACGGAAGGGGATTTCAAACGTACTAGAAACAAAAGAAGAAAATTTAAG
GCAACAAATTCAAACGCAAAGTGGGCCCAC
Found at i:5009199 original size:2 final size:2
Alignment explanation
Indices: 5009192--5009219 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5009182 TGAGTATTAA
5009192 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
5009220 TTGTCAACAA
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):
AT
Found at i:5018408 original size:34 final size:36
Alignment explanation
Indices: 5018365--5018434 Score: 117
Period size: 34 Copynumber: 2.0 Consensus size: 36
5018355 ATGTGTCAGT
5018365 TTTGATCCAGAAAAC-CCCTAC-AAGTGACCTCCCA
1 TTTGATCCAGAAAACACCCTACAAAGTGACCTCCCA
*
5018399 TTTGATCCAGAAAACACCCTACAAAGTGTCCTCCCA
1 TTTGATCCAGAAAACACCCTACAAAGTGACCTCCCA
5018435 AAATGGACAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 15 0.45
35 6 0.18
36 12 0.36
ACGTcount: A:0.33, C:0.34, G:0.11, T:0.21
Consensus pattern (36 bp):
TTTGATCCAGAAAACACCCTACAAAGTGACCTCCCA
Found at i:5022021 original size:186 final size:183
Alignment explanation
Indices: 5021689--5022057 Score: 663
Period size: 186 Copynumber: 2.0 Consensus size: 183
5021679 TGACTAATAT
5021689 GTCTGATTCAAGTCTCCAGGCAATTAGTTATGGTTCTAAGCCATCTCATGTTGAAGTTCGTCGCA
1 GTCTGATTCAAGTCTCCAGGCAATTAGTTATGGTTCTAAGCCATCTCATGTTGAAGTTCGTCGCA
5021754 TACAATTTCTGCTGCACTACCACAACGTGCAGGTAATTTTTCACTGTATGTTACATCATTTTAAA
66 TACAATTTCTGCTGCACTACCACAACGTGCAGGTAATTTTTCACTGTATGTTACATCATTTTAAA
5021819 ACCAATTCATCTGCTGGTT-AATGGTTTAAATGATATATATA-CGTACAGAAA
131 ACCAATTCATCTGCTGGTTAAATGGTTTAAATGATATATATACCGTACAGAAA
5021870 GTCTGATTCAAGTCTCCAGGCAATTAGTTATGGTTCTAATGCCATCTCATGTTGAAGTTCGTCGC
1 GTCTGATTCAAGTCTCCAGGCAATTAGTTATGGTTCTAA-GCCATCTCATGTTGAAGTTCGTCGC
5021935 ATACAATTTTCTGCTGCACTACCACAACGTGATGCAGGTAATTTTTCACTGTATGTTACATCA-T
65 ATACAA-TTTCTGCTGCACTACCACAAC--G-TGCAGGTAATTTTTCACTGTATGTTACATCATT
5021999 TTAAAACCAATTCATCCTGCTGGTTAAATGGTTTAAATGATATATATACCGTACAGAAA
126 TTAAAACCAATTCAT-CTGCTGGTTAAATGGTTTAAATGATATATATACCGTACAGAAA
5022058 TCAGAAGCAG
Statistics
Matches: 180, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
181 39 0.22
182 31 0.17
183 21 0.12
185 17 0.09
186 40 0.22
187 22 0.12
188 10 0.06
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (183 bp):
GTCTGATTCAAGTCTCCAGGCAATTAGTTATGGTTCTAAGCCATCTCATGTTGAAGTTCGTCGCA
TACAATTTCTGCTGCACTACCACAACGTGCAGGTAATTTTTCACTGTATGTTACATCATTTTAAA
ACCAATTCATCTGCTGGTTAAATGGTTTAAATGATATATATACCGTACAGAAA
Found at i:5037313 original size:21 final size:20
Alignment explanation
Indices: 5037275--5037312 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5037265 AAAAAATTAT
*
5037275 TTAAAAATTATTAATTTTAC
1 TTAAAAATTAATAATTTTAC
5037295 TTAAAATATTAAT-ATTTT
1 TTAAAA-ATTAATAATTTT
5037313 TTTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAAAATTAATAATTTTAC
Found at i:5038868 original size:18 final size:17
Alignment explanation
Indices: 5038828--5038870 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
5038818 ATTAAAAAAA
*
5038828 AGTTTTAATATTTTTAT
1 AGTTTTAAGATTTTTAT
**
5038845 TCTTTTAAGAGTTTTTAT
1 AGTTTTAAGA-TTTTTAT
5038863 AGTTTTAA
1 AGTTTTAA
5038871 ATTGTTTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.60
Consensus pattern (17 bp):
AGTTTTAAGATTTTTAT
Found at i:5039762 original size:21 final size:21
Alignment explanation
Indices: 5039737--5039779 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5039727 TTTTTATTGT
*
5039737 AATTTATACAAAATAAAATAA
1 AATTTAAACAAAATAAAATAA
* *
5039758 AATTTAAACATAATATAATAA
1 AATTTAAACAAAATAAAATAA
5039779 A
1 A
5039780 TTCAAGTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTTAAACAAAATAAAATAA
Found at i:5039796 original size:15 final size:17
Alignment explanation
Indices: 5039776--5039807 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5039766 CATAATATAA
5039776 TAAATT-CAAG-TAGAT
1 TAAATTGCAAGATAGAT
5039791 TAAATTGCAAGATAGAT
1 TAAATTGCAAGATAGAT
5039808 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (17 bp):
TAAATTGCAAGATAGAT
Found at i:5039845 original size:21 final size:21
Alignment explanation
Indices: 5039803--5039845 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5039793 AATTGCAAGA
**
5039803 TAGATAAAAATACATTGAAAT
1 TAGATAAAAATACATACAAAT
* *
5039824 TAGATAAATATACATACTAAT
1 TAGATAAAAATACATACAAAT
5039845 T
1 T
5039846 TTTTGAAACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (21 bp):
TAGATAAAAATACATACAAAT
Found at i:5040353 original size:3 final size:3
Alignment explanation
Indices: 5040345--5040379 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5040335 TGGCCACGCT
5040345 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5040380 TCTTTCTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5046102 original size:250 final size:253
Alignment explanation
Indices: 5045644--5046143 Score: 907
Period size: 250 Copynumber: 2.0 Consensus size: 253
5045634 GCTCAACACA
*
5045644 GTACTGCATATGTTCTTTTAGTTTTCGCCTGCAGTTAATAGCACGTTATATATGCCACAATAATA
1 GTACTGCATATGTTCTTTTAGTTTTCGCCCGCAGTTAATAGCACGTTATATATGCCACAATAATA
* *
5045709 GGAAACAGATACCCCCTCCGATTCATTATTTTTATAAACAGTCATAGAAAGATACCCAAATTCCT
66 GGAAAAAGATACCCCCTCCGATTCATTATTTTTATAAACAGTCATAGAAAAATACCCAAATTCCT
*
5045774 TGTTCATGCTGTTGGCAGGAGCTGTAGCAGCCTTTCCACTACCATATTTTGACACAAAATCATCC
131 TGTTCAGGCTGTTGGCAGGAGCTGTAGCAGCCTTTCCACTACCATATTTTGACACAAAATCATCC
* *
5045839 TTGACACGCTCCAGAGATGCAATAGGTACTTGCCTTCCAGCCGACTCATCTGCAATAG
196 TTGACACGCTCCAGAAATGCAACAGGTACTTGCCTTCCAGCCGACTCATCTGCAATAG
*
5045897 GTACTGCATATGTT-TTTTAGTTTTGGCCCGCAGTTAATAGCACG-T-TATATGCCACAATAATA
1 GTACTGCATATGTTCTTTTAGTTTTCGCCCGCAGTTAATAGCACGTTATATATGCCACAATAATA
5045959 GGAAAAAGATACCCCCTCCGATTCATTATTTTTATAAACAGTCATAGAAAAATACCCAAATTCCT
66 GGAAAAAGATACCCCCTCCGATTCATTATTTTTATAAACAGTCATAGAAAAATACCCAAATTCCT
5046024 TGTTCAGGCTGTTGGCAGGAGCTGTAGCAGCCTTTCCACTACCATATTTTGACACAAAATCATCC
131 TGTTCAGGCTGTTGGCAGGAGCTGTAGCAGCCTTTCCACTACCATATTTTGACACAAAATCATCC
*
5046089 TTGGCACGCTCCAGAAATGCAACAGGTACTTGCCTTCCAGCCGACTCATCTGCAA
196 TTGACACGCTCCAGAAATGCAACAGGTACTTGCCTTCCAGCCGACTCATCTGCAA
5046144 CAACACAAAA
Statistics
Matches: 239, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
250 196 0.82
251 1 0.00
252 28 0.12
253 14 0.06
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (253 bp):
GTACTGCATATGTTCTTTTAGTTTTCGCCCGCAGTTAATAGCACGTTATATATGCCACAATAATA
GGAAAAAGATACCCCCTCCGATTCATTATTTTTATAAACAGTCATAGAAAAATACCCAAATTCCT
TGTTCAGGCTGTTGGCAGGAGCTGTAGCAGCCTTTCCACTACCATATTTTGACACAAAATCATCC
TTGACACGCTCCAGAAATGCAACAGGTACTTGCCTTCCAGCCGACTCATCTGCAATAG
Found at i:5047139 original size:11 final size:11
Alignment explanation
Indices: 5047106--5047140 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
5047096 TACTGTTGGC
5047106 TTTTTGTTTTT
1 TTTTTGTTTTT
*
5047117 CTTTTGTTTTT
1 TTTTTGTTTTT
5047128 TTTTTGTTTTT
1 TTTTTGTTTTT
5047139 TT
1 TT
5047141 ATATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.89
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:5054394 original size:2 final size:2
Alignment explanation
Indices: 5054387--5054444 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
5054377 ATATAATTAC
5054387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5054429 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
5054445 TATTTAGGGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5065154 original size:18 final size:18
Alignment explanation
Indices: 5065121--5065155 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5065111 AGATAACATA
5065121 ATAATTAATAAAATTAAT
1 ATAATTAATAAAATTAAT
5065139 ATAA-TAATAAATATTAA
1 ATAATTAATAAA-ATTAA
5065156 AAAGAGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATTAATAAAATTAAT
Found at i:5065610 original size:4 final size:4
Alignment explanation
Indices: 5065603--5065666 Score: 101
Period size: 4 Copynumber: 16.0 Consensus size: 4
5065593 TTTCTTTCAT
* *
5065603 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA CTTA CTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
5065651 TTTA CTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA
5065667 CATTGAATGG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 56 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:5082903 original size:2 final size:2
Alignment explanation
Indices: 5082896--5082958 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
5082886 TTAACATTCC
5082896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5082938 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
5082959 CCCTTCCACT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5091152 original size:21 final size:20
Alignment explanation
Indices: 5091128--5091178 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
5091118 TTTTTTATAA
* *
5091128 TTATATTTAATGTAAATTTTT
1 TTATA-TTAATATAAACTTTT
5091149 TTATA-TAATATAAACTTTT
1 TTATATTAATATAAACTTTT
5091168 TTATA-TAATAT
1 TTATATTAATAT
5091179 TTTTATTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 23 0.82
21 5 0.18
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATATTAATATAAACTTTT
Found at i:5091162 original size:19 final size:19
Alignment explanation
Indices: 5091135--5091178 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
5091125 TAATTATATT
* *
5091135 TAATGTAAATTTTTTTATA
1 TAATATAAACTTTTTTATA
5091154 TAATATAAACTTTTTTATA
1 TAATATAAACTTTTTTATA
5091173 TAATAT
1 TAATAT
5091179 TTTTATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TAATATAAACTTTTTTATA
Found at i:5094558 original size:7 final size:7
Alignment explanation
Indices: 5094546--5094638 Score: 186
Period size: 7 Copynumber: 13.3 Consensus size: 7
5094536 TACAACTTAT
5094546 CAGTTAC
1 CAGTTAC
5094553 CAGTTAC
1 CAGTTAC
5094560 CAGTTAC
1 CAGTTAC
5094567 CAGTTAC
1 CAGTTAC
5094574 CAGTTAC
1 CAGTTAC
5094581 CAGTTAC
1 CAGTTAC
5094588 CAGTTAC
1 CAGTTAC
5094595 CAGTTAC
1 CAGTTAC
5094602 CAGTTAC
1 CAGTTAC
5094609 CAGTTAC
1 CAGTTAC
5094616 CAGTTAC
1 CAGTTAC
5094623 CAGTTAC
1 CAGTTAC
5094630 CAGTTAC
1 CAGTTAC
5094637 CA
1 CA
5094639 TACCAGTAGA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 86 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (7 bp):
CAGTTAC
Done.