Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 26
Found at i:4398636 original size:4 final size:4
Alignment explanation
Indices: 4398623--4398713 Score: 55
Period size: 4 Copynumber: 21.8 Consensus size: 4
4398613 CATGAAGTAT
*
4398623 CTCC CT-C CTCC CT-C CTCC C-CC TCCCC CTCC CTCTC CTTCC CTCC CTCTC
1 CTCC CTCC CTCC CTCC CTCC CTCC -CTCC CTCC CTC-C C-TCC CTCC CTC-C
* *
4398672 CTTCC CTCC CTCC CCCC CTCTC TCTCT CTCC C-CC TCTCC CTC
1 C-TCC CTCC CTCC CTCC CTC-C -CTCC CTCC CTCC -CTCC CTC
4398714 TCCCTCTCTG
Statistics
Matches: 70, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
3 10 0.14
4 40 0.57
5 13 0.19
6 7 0.10
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (4 bp):
CTCC
Found at i:4398654 original size:10 final size:10
Alignment explanation
Indices: 4398623--4398687 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
4398613 CATGAAGTAT
4398623 CTCCCTCCTCC
1 CTCCC-CCTCC
*
4398634 CTCCTCC-CC
1 CTCCCCCTCC
4398643 CTCCCCCTCC
1 CTCCCCCTCC
* *
4398653 CTCTCCTTCC
1 CTCCCCCTCC
*
4398663 CTCCCTCT-C
1 CTCCCCCTCC
*
4398672 CT-TCCCTCC
1 CTCCCCCTCC
4398681 CTCCCCC
1 CTCCCCC
4398688 CCTCTCTCTC
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
8 3 0.07
9 14 0.34
10 20 0.49
11 4 0.10
ACGTcount: A:0.00, C:0.72, G:0.00, T:0.28
Consensus pattern (10 bp):
CTCCCCCTCC
Found at i:4398666 original size:14 final size:14
Alignment explanation
Indices: 4398647--4398683 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
4398637 CTCCCCCTCC
4398647 CCCTCCCTCTCCTT
1 CCCTCCCTCTCCTT
4398661 CCCTCCCTCTCCTT
1 CCCTCCCTCTCCTT
4398675 CCCTCCCTC
1 CCCTCCCTC
4398684 CCCCCCTCTC
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:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (14 bp):
CCCTCCCTCTCCTT
Found at i:4398714 original size:14 final size:14
Alignment explanation
Indices: 4398622--4398722 Score: 70
Period size: 14 Copynumber: 7.2 Consensus size: 14
4398612 ACATGAAGTA
4398622 TCTCCCTCCTCCCTCC
1 TCTCCCT-CTCCC-CC
4398638 TC-CCC-CT-CCCC
1 TCTCCCTCTCCCCC
*
4398649 -CTCCCTCTCCTTCC
1 TCTCCCTCTCC-CCC
*
4398663 -CTCCCTCTCCTTCC
1 TCTCCCTCTCC-CCC
*
4398677 -CTCCCTCCCCCCC
1 TCTCCCTCTCCCCC
4398690 TCTCTCTCTCTCCCCC
1 TCTC-C-CTCTCCCCC
*
4398706 TCTCCCTCTCCCTC
1 TCTCCCTCTCCCCC
4398720 TCT
1 TCT
4398723 GAACACCAAG
Statistics
Matches: 73, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
10 1 0.01
11 5 0.07
12 4 0.05
13 5 0.07
14 39 0.53
15 5 0.07
16 14 0.19
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (14 bp):
TCTCCCTCTCCCCC
Found at i:4398720 original size:6 final size:6
Alignment explanation
Indices: 4398622--4398721 Score: 65
Period size: 6 Copynumber: 15.7 Consensus size: 6
4398612 ACATGAAGTA
* * *
4398622 TCTCCC TCCTCCC TCCTCCC CCTCCC CCTCCC TCTCCTTC CCTCCC TCTCCTTC
1 TCTCCC T-CTCCC T-CTCCC TCTCCC TCTCCC TCTCC--C TCTCCC TCTCC--C
* * * * * *
4398676 CCTCCC TCCCCC CCTCTC TCTCTC TCCCCC TCTCCC TCTCCC TCTC
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTC
4398722 TGAACACCAA
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
6 53 0.71
7 12 0.16
8 10 0.13
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
TCTCCC
Found at i:4409271 original size:35 final size:34
Alignment explanation
Indices: 4409212--4409323 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 34
4409202 AAAACATTCC
* * * *
4409212 TCAATTTCATTATAAATCACAAATTTCAAAGTAAT
1 TCAATTTCATTCTAAA-CCCAAATTCCAAAATAAT
4409247 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * * *
4409282 TCAATTACATTCTAAACCCCCAATTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTCCAAAATAAT
4409317 TCAATTT
1 TCAATTT
4409324 AAGGAGAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.03
35 61 0.92
36 3 0.05
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:4410421 original size:34 final size:34
Alignment explanation
Indices: 4410346--4410457 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
4410336 AAAAAAGACA
* *
4410346 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
4410381 GTAATTGAATTATTTTGGAATTTAGGG-TTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
4410415 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
4410450 GAAATTGA
1 GAAATTGA
4410458 GAATTGTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
33 1 0.01
34 30 0.43
35 35 0.51
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:4425526 original size:31 final size:32
Alignment explanation
Indices: 4425488--4425549 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
4425478 TGTTTTGGAA
*
4425488 GTTACAAAAGGGTCATTAAAC-TTCTCAAATG
1 GTTACAAAAGAGTCATTAAACTTTCTCAAATG
*
4425519 GTTACAAAATAGTCATTAAACTTTCTCAAAT
1 GTTACAAAAGAGTCATTAAACTTTCTCAAAT
4425550 TATTATAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32
Consensus pattern (32 bp):
GTTACAAAAGAGTCATTAAACTTTCTCAAATG
Found at i:4425570 original size:32 final size:32
Alignment explanation
Indices: 4425489--4425573 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
4425479 GTTTTGGAAG
* *
4425489 TTACAAAAGGGTCATTAAAC-TTCTCAAATGG
1 TTACAAAATGGTCATTAAACTTTCTCAAATGA
* *
4425520 TTACAAAATAGTCATTAAACTTTCTCAAATTA
1 TTACAAAATGGTCATTAAACTTTCTCAAATGA
* * *
4425552 TTATAGAATGGTCCTTAAACTT
1 TTACAAAATGGTCATTAAACTT
4425574 ATTGAAATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 18 0.40
32 27 0.60
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (32 bp):
TTACAAAATGGTCATTAAACTTTCTCAAATGA
Found at i:4426358 original size:219 final size:220
Alignment explanation
Indices: 4425976--4426416 Score: 803
Period size: 219 Copynumber: 2.0 Consensus size: 220
4425966 GACTTGTCCC
4425976 ACTGATTTACATGCCTCTTTTTTTTTTTTTTTGAAAGGTAAAAATTTTATTCAAATCAAAGGAAA
1 ACTGATTTACATGCCTC--TTTTTTTTTTTTTGAAAGGTAAAAATTTTATTCAAATCAAAGGAAA
4426041 CTAAGCATTGTTAGGGGCCTCATTAAAAAACCTCCCTAAGCCTCGGTGGAGGAAAAAGAGTGCAC
64 CTAAGCATTGTTAGGGGCCTCATTAAAAAACCTCCCTAAGCCTCGGTGGAGGAAAAAGAGTGCAC
*
4426106 CCTAGACAATGCCTCTTCTTTCAAATGCTTTGACACATTAATCCTCCTTTTCTTTTTGGTTCGGG
129 CCTAGACAATGCCTCTTCTTTCAAATACTTTGACACATTAATCCTCCTTTTCTTTTTGGTTCGGG
4426171 AAGCTGGGTGGGAAGATTGGGGGGAGG
194 AAGCTGGGTGGGAAGATTGGGGGGAGG
*
4426198 ACTGATTTGCATGCCTC-TTTTTTTTTTTTGAAAGGTAAAAATTTTATTCAAATCAAAGGAAACT
1 ACTGATTTACATGCCTCTTTTTTTTTTTTTGAAAGGTAAAAATTTTATTCAAATCAAAGGAAACT
* * *
4426262 AAGCATTGTTAGGGGTCTCATTAAAAAACCTTCCTAAGCCTCGGTTGAGGAAAAAGAGTGCACCC
66 AAGCATTGTTAGGGGCCTCATTAAAAAACCTCCCTAAGCCTCGGTGGAGGAAAAAGAGTGCACCC
*
4426327 TAGACAATGCCTCTTCTTTCAAATACTTTGACACATTAATCCTTCTTTTCTTTTTGGTTCGGGAA
131 TAGACAATGCCTCTTCTTTCAAATACTTTGACACATTAATCCTCCTTTTCTTTTTGGTTCGGGAA
4426392 GCTGGGTGGGAAGATTGGGGGGAGG
196 GCTGGGTGGGAAGATTGGGGGGAGG
4426417 GGGGATATTT
Statistics
Matches: 213, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
219 197 0.92
222 16 0.08
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (220 bp):
ACTGATTTACATGCCTCTTTTTTTTTTTTTGAAAGGTAAAAATTTTATTCAAATCAAAGGAAACT
AAGCATTGTTAGGGGCCTCATTAAAAAACCTCCCTAAGCCTCGGTGGAGGAAAAAGAGTGCACCC
TAGACAATGCCTCTTCTTTCAAATACTTTGACACATTAATCCTCCTTTTCTTTTTGGTTCGGGAA
GCTGGGTGGGAAGATTGGGGGGAGG
Found at i:4431825 original size:33 final size:33
Alignment explanation
Indices: 4431780--4431846 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4431770 AACTTAAGGA
* *
4431780 GGGCAAAATATAATTAATCAAAGAAAATTAGGG
1 GGGCAAAATATAATTAACCAAAGAAAATGAGGG
* *
4431813 GGGCAAAGTATAATTAACCATAGAAAATGAGGG
1 GGGCAAAATATAATTAACCAAAGAAAATGAGGG
4431846 G
1 G
4431847 CAAAATCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.07, G:0.25, T:0.19
Consensus pattern (33 bp):
GGGCAAAATATAATTAACCAAAGAAAATGAGGG
Found at i:4434912 original size:2 final size:2
Alignment explanation
Indices: 4434865--4434898 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4434855 AACATTCTTA
4434865 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
4434899 TAACATCCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4435251 original size:97 final size:97
Alignment explanation
Indices: 4435150--4435357 Score: 353
Period size: 97 Copynumber: 2.1 Consensus size: 97
4435140 TTATGTCTTG
* * *
4435150 AAAAATATTTTTGTGTTTGAAGAACTTTTCGCTAAAAATAGTTGTCTAATATTTTTTTCAGTTAT
1 AAAAATATTTTTATGTCTGAAGAACTTTTCGCTAAAAATAATTGTCTAATATTTTTTTCAGTTAT
4435215 ACATTTAGGTGCCTGCCATTTTTTAATAATAA
66 ACATTTAGGTGCCTGCCATTTTTTAATAATAA
*
4435247 AAAAACATTTTTATGTCTGAAGAACTTTTCGCTAAAAATAATTGTCTAATATTTTTTTCAGTTAT
1 AAAAATATTTTTATGTCTGAAGAACTTTTCGCTAAAAATAATTGTCTAATATTTTTTTCAGTTAT
*
4435312 ACATTTAGGTGCCTGTCATTTTTTAATAATAA
66 ACATTTAGGTGCCTGCCATTTTTTAATAATAA
*
4435344 AAATATTATTTTTA
1 AAA-AATATTTTTA
4435358 ATTAAAAATG
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
97 95 0.92
98 8 0.08
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.46
Consensus pattern (97 bp):
AAAAATATTTTTATGTCTGAAGAACTTTTCGCTAAAAATAATTGTCTAATATTTTTTTCAGTTAT
ACATTTAGGTGCCTGCCATTTTTTAATAATAA
Found at i:4438053 original size:38 final size:37
Alignment explanation
Indices: 4437995--4438128 Score: 160
Period size: 38 Copynumber: 3.5 Consensus size: 37
4437985 CTCGTATAAA
* * * *
4437995 TGTCACGAAGGACCTATCATCCCGAAGAATATCATCTG
1 TGTCCCGAAGGACCTGTCATCCCGAAG-ATGTAATCTG
* * *
4438033 TGTCCCGAAGGACTTGTCATCTCGAATGATGTAATATG
1 TGTCCCGAAGGACCTGTCATCCCGAA-GATGTAATCTG
4438071 TGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTGTCATCCCGAA-GATGTAATCTG
**
4438109 TGTCCCGAATAACCTGTCAT
1 TGTCCCGAAGGACCTGTCAT
4438129 ATGTCTTATA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
38 81 0.99
39 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (37 bp):
TGTCCCGAAGGACCTGTCATCCCGAAGATGTAATCTG
Found at i:4444211 original size:38 final size:38
Alignment explanation
Indices: 4444158--4444292 Score: 180
Period size: 38 Copynumber: 3.6 Consensus size: 38
4444148 GCTCGTATAA
* * * *
4444158 ATGTCTCGAATGACCTATCATCCCGAAGGATGTCATCT
1 ATGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCT
*
4444196 ATGTCCCGAAGGACCTGTCATCCCGAAAGATGTAATCT
1 ATGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCT
* * *
4444234 GTGTCCCAAAGGACCTGTCATCCCGAAGGATGTAATAT
1 ATGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCT
* *
4444272 GTGTCCCGAAAGACCTGTCAT
1 ATGTCCCGAAGGACCTGTCAT
4444293 AGGACATATG
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 86 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (38 bp):
ATGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCT
Found at i:4444221 original size:17 final size:17
Alignment explanation
Indices: 4444199--4444263 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
4444189 GTCATCTATG
4444199 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTGTCA
* *
4444216 TCCCGAAAGATGTAATCTGT-G
1 TCCCG-AAG--G--ACCTGTCA
*
4444237 TCCCAAAGGACCTGTCA
1 TCCCGAAGGACCTGTCA
4444254 TCCCGAAGGA
1 TCCCGAAGGA
4444264 TGTAATATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
16 5 0.14
17 14 0.39
18 4 0.11
20 4 0.11
21 4 0.11
22 5 0.14
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (17 bp):
TCCCGAAGGACCTGTCA
Found at i:4444240 original size:21 final size:21
Alignment explanation
Indices: 4444216--4444284 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
4444206 GGACCTGTCA
4444216 TCCCGAAAGATGTAATCTGTG
1 TCCCGAAAGATGTAATCTGTG
* *
4444237 TCCC-AAAG--G--ACCTGTCA
1 TCCCGAAAGATGTAATCTGT-G
* *
4444254 TCCCGAAGGATGTAATATGTG
1 TCCCGAAAGATGTAATCTGTG
4444275 TCCCGAAAGA
1 TCCCGAAAGA
4444285 CCTGTCATAG
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
16 5 0.14
17 4 0.11
18 4 0.11
20 5 0.14
21 13 0.37
22 4 0.11
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
TCCCGAAAGATGTAATCTGTG
Found at i:4445033 original size:20 final size:20
Alignment explanation
Indices: 4445010--4445047 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4445000 TTTCCTTTAG
*
4445010 GGGGGAATAGATTCCCCCCA
1 GGGGGAATAGATACCCCCCA
*
4445030 GGGGGAATCGATACCCCC
1 GGGGGAATAGATACCCCC
4445048 TGAACATACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.13
Consensus pattern (20 bp):
GGGGGAATAGATACCCCCCA
Found at i:4453807 original size:2 final size:2
Alignment explanation
Indices: 4453800--4453839 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
4453790 ATAATGATTT
* * *
4453800 TA TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4453840 AAAGTGGGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4455473 original size:3 final size:3
Alignment explanation
Indices: 4455467--4455511 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
4455457 ATACTACTTC
4455467 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4455512 CAACAACAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4459543 original size:35 final size:35
Alignment explanation
Indices: 4459482--4459556 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
4459472 TTCATGTTCA
* *
4459482 AAATTTCAAAACACCTTAATTTCATTCTAAACCCT
1 AAATTTCAAAACACATTAATTACATTCTAAACCCT
* *
4459517 AAATTTCAAAATA-ATTCAATTACATTCTAAACCTT
1 AAATTTCAAAACACATT-AATTACATTCTAAACCCT
4459552 AAATT
1 AAATT
4459557 GAAGTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 2 0.06
35 33 0.94
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (35 bp):
AAATTTCAAAACACATTAATTACATTCTAAACCCT
Found at i:4459632 original size:35 final size:35
Alignment explanation
Indices: 4459552--4459664 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 35
4459542 TCTAAACCTT
* * * *
4459552 AAATTGAAGTATTTTAGAGTTTGGGGTTTAAAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATA
* * *
4459587 TAATTGAATTATTTTGGAATTTAGGGTTTATAATA
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATA
* * * * *
4459622 AAATTAAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATA
4459657 AAATTGAA
1 AAATTGAA
4459665 GACTGTTTTG
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAAAATA
Found at i:4459982 original size:36 final size:35
Alignment explanation
Indices: 4459917--4459991 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 35
4459907 TTAAAAGGAT
*
4459917 ATAATTATCTTTTTAATATTCAAAGTTCAATAAATA
1 ATAAATATCTTTTTAATATTCAAAGTTCAA-AAATA
*
4459953 ATAAATATCTTTTTAAT-TTGACATA-TTCAAAAATA
1 ATAAATATCTTTTTAATATT--CAAAGTTCAAAAATA
4459988 ATAA
1 ATAA
4459992 TAATATCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 11 0.31
36 21 0.60
37 3 0.09
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.43
Consensus pattern (35 bp):
ATAAATATCTTTTTAATATTCAAAGTTCAAAAATA
Found at i:4462602 original size:90 final size:90
Alignment explanation
Indices: 4462444--4462610 Score: 271
Period size: 90 Copynumber: 1.9 Consensus size: 90
4462434 CCTAACACAC
* * * *
4462444 CCTTTTATAGCCAAGTTACCATAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTGT
1 CCTTTTATAGCCAAGTTACCATAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
4462509 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGGAATTTAATAAT
* * *
4462534 CCTTTTTTATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCATAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
4462599 ATTTAATTAATT
66 ATTTAATTAATT
4462611 AAAATTAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 70 1.00
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCATAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGGAATTTAATAAT
Found at i:4469072 original size:14 final size:16
Alignment explanation
Indices: 4469042--4469078 Score: 60
Period size: 14 Copynumber: 2.4 Consensus size: 16
4469032 TTTTATAGTA
4469042 AATATTTATTAATTTT
1 AATATTTATTAATTTT
4469058 AATATTTA-T-ATTTT
1 AATATTTATTAATTTT
4469072 AATATTT
1 AATATTT
4469079 TTTATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATATTTATTAATTTT
Found at i:4479642 original size:33 final size:33
Alignment explanation
Indices: 4479578--4479642 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
4479568 CGACCAATCT
* * * *
4479578 GACCCGACCCGAAAATTTTATATCCTTCACCCC
1 GACCCGACCCGAAAAATATATATCATCCACCCC
* *
4479611 GACCCGATCTGAAAAATATATATCATCCACCC
1 GACCCGACCCGAAAAATATATATCATCCACCC
4479643 GACTTGAACT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.32, C:0.35, G:0.09, T:0.23
Consensus pattern (33 bp):
GACCCGACCCGAAAAATATATATCATCCACCCC
Found at i:4486338 original size:26 final size:25
Alignment explanation
Indices: 4486300--4486358 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
4486290 TGACGTGGCA
* *
4486300 TCTTCTAC-TTCTTCCTCCTCCTCT
1 TCTTCTTCTTTCTTCCTCCTCCTCC
*
4486324 TCTTCCTTCTTTCTTCTTCCTCCTCC
1 TCTT-CTTCTTTCTTCCTCCTCCTCC
4486350 TCTTCTTCT
1 TCTTCTTCT
4486359 CACACACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.13
25 8 0.27
26 18 0.60
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (25 bp):
TCTTCTTCTTTCTTCCTCCTCCTCC
Found at i:4486959 original size:21 final size:21
Alignment explanation
Indices: 4486935--4486974 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4486925 AATTCCTTCT
4486935 TTTTTGCTAATATCCGATCAC
1 TTTTTGCTAATATCCGATCAC
*
4486956 TTTTTGCTGATATCCGATC
1 TTTTTGCTAATATCCGATC
4486975 CGCCAGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (21 bp):
TTTTTGCTAATATCCGATCAC
Found at i:4493743 original size:2 final size:2
Alignment explanation
Indices: 4493738--4493763 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4493728 TTTCTACCAC
4493738 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
4493764 CTCACACACG
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):
TA
Found at i:4512057 original size:21 final size:22
Alignment explanation
Indices: 4512033--4512073 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4512023 TCAGGACAGG
*
4512033 GAGTATTGGTACT-CCTTTAAT
1 GAGTATCGGTACTACCTTTAAT
4512054 GAGTATCGGTACTACCTTTA
1 GAGTATCGGTACTACCTTTA
4512074 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (22 bp):
GAGTATCGGTACTACCTTTAAT
Found at i:4512841 original size:19 final size:19
Alignment explanation
Indices: 4512817--4512853 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4512807 ACATGCATGA
4512817 CATTATTTGTAAGGTCAAG
1 CATTATTTGTAAGGTCAAG
4512836 CATTATTTGTAAGGTCAA
1 CATTATTTGTAAGGTCAA
4512854 ATTCGAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (19 bp):
CATTATTTGTAAGGTCAAG
Found at i:4513164 original size:37 final size:37
Alignment explanation
Indices: 4513123--4513201 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
4513113 TATTAACATT
4513123 ATGATGCCATGGATGTCAAAATTCCAGGAGAAAATGA
1 ATGATGCCATGGATGTCAAAATTCCAGGAGAAAATGA
4513160 ATGATGCCATGGATGTCAAAATTCCAGGAGAAAATGA
1 ATGATGCCATGGATGTCAAAATTCCAGGAGAAAATGA
4513197 A-GATG
1 ATGATG
4513202 TGAATAGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 4 0.10
37 38 0.90
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.22
Consensus pattern (37 bp):
ATGATGCCATGGATGTCAAAATTCCAGGAGAAAATGA
Found at i:4513505 original size:17 final size:18
Alignment explanation
Indices: 4513478--4513511 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4513468 TTATATATTT
4513478 TTTTATATTTACTTTTAG
1 TTTTATATTTACTTTTAG
*
4513496 TTTT-TATTTATTTTTA
1 TTTTATATTTACTTTTA
4513512 TTTGGTTGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTATATTTACTTTTAG
Found at i:4513850 original size:111 final size:111
Alignment explanation
Indices: 4513692--4513905 Score: 338
Period size: 111 Copynumber: 1.9 Consensus size: 111
4513682 ACGTTTGACG
* * * * *
4513692 AGCACCAATGAACACTACTAACTATGAGCATCGTTAATTTAATTTATAAAATTTTAAAATTATAA
1 AGCACCAATGAACACCACTAAATATGAGCACCATTAATTTAATTTATAAAACTTTAAAATTATAA
4513757 AATACTCAACATATAATTATAAATTAGTTAAAAATCTAGCTCGACA
66 AATACTCAACATATAATTATAAATTAGTTAAAAATCTAGCTCGACA
* * * *
4513803 AGCACCGATGAATACCACTAAATATGAGCACCATTTATTTAATTTATAAAACTTTGAAATTATAA
1 AGCACCAATGAACACCACTAAATATGAGCACCATTAATTTAATTTATAAAACTTTAAAATTATAA
*
4513868 AGTACTCAACATATAATTATAAATTAGTTAAAAATCTA
66 AATACTCAACATATAATTATAAATTAGTTAAAAATCTA
4513906 AACGTAAATT
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 93 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (111 bp):
AGCACCAATGAACACCACTAAATATGAGCACCATTAATTTAATTTATAAAACTTTAAAATTATAA
AATACTCAACATATAATTATAAATTAGTTAAAAATCTAGCTCGACA
Found at i:4517312 original size:17 final size:17
Alignment explanation
Indices: 4517275--4517311 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
4517265 CTAATACTTC
4517275 TTTT-TTTTCTTCATTT
1 TTTTATTTTCTTCATTT
4517291 TTTTATTTTCTCTCATTT
1 TTTTATTTTCT-TCATTT
4517309 TTT
1 TTT
4517312 AAATTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 6 0.32
18 9 0.47
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTTCTTCATTT
Found at i:4518421 original size:34 final size:34
Alignment explanation
Indices: 4518378--4518450 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
4518368 TGTTTCGTAC
*
4518378 AATAATTTGATTGGAACTTAAATGCGTCTAACTT
1 AATAATTTGATTGGAACTTAAATGCGCCTAACTT
*
4518412 AATAATTTGATTGGAACTTGAATGCGCCTAACTT
1 AATAATTTGATTGGAACTTAAATGCGCCTAACTT
*
4518446 GATAA
1 AATAA
4518451 ATCTAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (34 bp):
AATAATTTGATTGGAACTTAAATGCGCCTAACTT
Found at i:4523709 original size:28 final size:28
Alignment explanation
Indices: 4523677--4523730 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
4523667 AGGTTTAAAA
*
4523677 TTTAAAATAAATT-TATCATTTTTATATT
1 TTTAAAATAAATTCAAT-ATTTTTATATT
*
4523705 TTTAAATTAAATTCAATATTTTTATA
1 TTTAAAATAAATTCAATATTTTTATA
4523731 CTTACTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTAAAATAAATTCAATATTTTTATATT
Found at i:4524491 original size:18 final size:18
Alignment explanation
Indices: 4524468--4524503 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4524458 CATAACACCG
4524468 TTGAAAAGTTAACGACAA
1 TTGAAAAGTTAACGACAA
4524486 TTGAAAAGTTAACGACAA
1 TTGAAAAGTTAACGACAA
4524504 AGTGAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (18 bp):
TTGAAAAGTTAACGACAA
Found at i:4526521 original size:16 final size:17
Alignment explanation
Indices: 4526494--4526526 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4526484 AATATTAATA
*
4526494 TTAATATTTTATTTATT
1 TTAATATTTTATATATT
4526511 TTAAT-TTTTATATATT
1 TTAATATTTTATATATT
4526527 CAAATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTAATATTTTATATATT
Found at i:4528712 original size:21 final size:21
Alignment explanation
Indices: 4528672--4528722 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
4528662 TTTTTAGCCG
*
4528672 TTTGTAACTCATATAGTTAT-
1 TTTGTAACTCATATAATTATA
* *
4528692 TTCTGTAACTCCTGTAATTATA
1 TT-TGTAACTCATATAATTATA
4528714 TTTGTAACT
1 TTTGTAACT
4528723 AGTTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (21 bp):
TTTGTAACTCATATAATTATA
Found at i:4531803 original size:31 final size:31
Alignment explanation
Indices: 4531765--4531829 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
4531755 TAATATATGG
* * *
4531765 TGATCGAACTGTATTAGATGCATCAGTGTTT
1 TGATCGAACTGCATTAGATACATCAGTGTCT
4531796 TGATCGAACTGCATTAGATACATCAGTGTCT
1 TGATCGAACTGCATTAGATACATCAGTGTCT
4531827 TGA
1 TGA
4531830 AAATTTCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (31 bp):
TGATCGAACTGCATTAGATACATCAGTGTCT
Found at i:4544048 original size:35 final size:35
Alignment explanation
Indices: 4544008--4544089 Score: 155
Period size: 35 Copynumber: 2.3 Consensus size: 35
4543998 TTTATGTACC
4544008 GATGCATAGATAGTGCATCGATGCACCCGTCAAGG
1 GATGCATAGATAGTGCATCGATGCACCCGTCAAGG
4544043 GATGCATAGATAGTGCATCGATGCACCCGTCAAGG
1 GATGCATAGATAGTGCATCGATGCACCCGTCAAGG
*
4544078 GATGCATCGATA
1 GATGCATAGATA
4544090 TACGGTGTAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (35 bp):
GATGCATAGATAGTGCATCGATGCACCCGTCAAGG
Found at i:4545229 original size:12 final size:12
Alignment explanation
Indices: 4545212--4545242 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4545202 TACAATTATA
4545212 TGTGATAAGCTC
1 TGTGATAAGCTC
4545224 TGTGATAAGCTC
1 TGTGATAAGCTC
4545236 TGTGATA
1 TGTGATA
4545243 TGTGAATCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (12 bp):
TGTGATAAGCTC
Found at i:4545594 original size:23 final size:23
Alignment explanation
Indices: 4545563--4545623 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
4545553 ACTTATATAG
4545563 CACTTCGGTGCATTTCTACGTGA
1 CACTTCGGTGCATTTCTACGTGA
* * * *
4545586 CACTACGGTGTAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGTGA
4545609 CACTTCGGTGCATTT
1 CACTTCGGTGCATTT
4545624 GAGTATGGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGTGA
Found at i:4549738 original size:14 final size:15
Alignment explanation
Indices: 4549711--4549739 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4549701 GTATCATATA
4549711 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
4549726 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
4549740 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:4550118 original size:19 final size:20
Alignment explanation
Indices: 4550082--4550119 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4550072 TTTTCATTAG
4550082 GGGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
4550102 GGGGGAATCGATACCCCC
1 GGGGGAATCGATACCCCC
4550120 TGGACATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGGAATCGATACCCCCCA
Found at i:4552304 original size:22 final size:22
Alignment explanation
Indices: 4552279--4552323 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
4552269 CAGATTACAA
*
4552279 ATAGGGAACCGGTTCCCCTGCT
1 ATAGGGAACCGATTCCCCTGCT
4552301 ATAGGGAACCGATTCCCCTGCT
1 ATAGGGAACCGATTCCCCTGCT
4552323 A
1 A
4552324 CAGTACTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.22
Consensus pattern (22 bp):
ATAGGGAACCGATTCCCCTGCT
Found at i:4552946 original size:2 final size:2
Alignment explanation
Indices: 4552941--4552982 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
4552931 ATTATATATA
4552941 TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4552982 T
1 T
4552983 ATTGTATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:4554677 original size:13 final size:13
Alignment explanation
Indices: 4554659--4554684 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4554649 TTCACGGGAG
4554659 GAAGAAGATGAAA
1 GAAGAAGATGAAA
4554672 GAAGAAGATGAAA
1 GAAGAAGATGAAA
4554685 AATGTTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.08
Consensus pattern (13 bp):
GAAGAAGATGAAA
Found at i:4570988 original size:30 final size:30
Alignment explanation
Indices: 4570936--4571010 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
4570926 TAATGATTGT
* * * *
4570936 TAACGTCGAGTGACTATTTTGTAACATACGA
1 TAACGTC-AGTGACCATATTGTAACAAACAA
*
4570967 TAACGTCAGTGACCATATTGTATCAAACAA
1 TAACGTCAGTGACCATATTGTAACAAACAA
*
4570997 TAACGTTAGTGACC
1 TAACGTCAGTGACC
4571011 GATTTATGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
30 31 0.82
31 7 0.18
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (30 bp):
TAACGTCAGTGACCATATTGTAACAAACAA
Found at i:4572835 original size:42 final size:42
Alignment explanation
Indices: 4572751--4572839 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
4572741 TATGATTGGA
* *
4572751 AAAAAATTAGGGACCTCAATTATAAAGGTAAAAATGAGATTG
1 AAAAAATCAGGGACCTCAATTATAAAGGCAAAAATGAGATTG
* * *
4572793 AAAAAATCA-GGAGCTCAATTATAAAGGCACAAAGTGATATTG
1 AAAAAATCAGGGACCTCAATTATAAAGGCA-AAAATGAGATTG
4572835 AAAAA
1 AAAAA
4572840 CTTACAATCA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 18 0.44
42 23 0.56
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.21
Consensus pattern (42 bp):
AAAAAATCAGGGACCTCAATTATAAAGGCAAAAATGAGATTG
Found at i:4575181 original size:18 final size:19
Alignment explanation
Indices: 4575163--4575296 Score: 67
Period size: 20 Copynumber: 6.8 Consensus size: 19
4575153 AATGACCAAC
*
4575163 AAAATCGCAATGCGAAACA
1 AAAATCGCAACGCGAAACA
***
4575182 AAAATCGCAACGCGATTTA
1 AAAATCGCAACGCGAAACA
* *
4575201 GAAAATCGCAATGTTGAAA-A
1 -AAAATCGCAACG-CGAAACA
4575221 GAAAATCGCAACG-GTCAAA-A
1 -AAAATCGCAACGCG--AAACA
***
4575241 GAAAATCGCAACGCGATTGA
1 -AAAATCGCAACGCGAAACA
**
4575261 GAAAATCGCAACGCGATTCCA
1 -AAAATCGCAACGCGA-AACA
*
4575282 AGAATCGCAACGCGA
1 AAAATCGCAACGCGA
4575297 TTCCAAGAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 13
0.78 0.12 0.11
Matches are distributed among these distances:
18 1 0.01
19 16 0.17
20 72 0.77
21 5 0.05
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:4575207 original size:20 final size:20
Alignment explanation
Indices: 4575182--4575298 Score: 100
Period size: 20 Copynumber: 5.8 Consensus size: 20
4575172 ATGCGAAACA
*
4575182 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
4575202 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
4575222 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
*
4575242 AAAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTAAG
4575262 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
4575284 --AATCGCAACGCGATT
1 AAAATCGCAACGCGATT
4575299 CCAAGAATCG
Statistics
Matches: 81, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
18 1 0.01
20 74 0.91
21 3 0.04
22 3 0.04
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:4575299 original size:20 final size:20
Alignment explanation
Indices: 4575244--4575311 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
4575234 GTCAAAAGAA
* *
4575244 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
4575264 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
4575284 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
4575304 AATCGCAA
1 AATCGCAA
4575312 AACGGCAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 44 0.98
21 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:4575433 original size:6 final size:6
Alignment explanation
Indices: 4575422--4575463 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
4575412 GACACGTATT
4575422 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
4575464 TCCGTTGCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:4577348 original size:15 final size:15
Alignment explanation
Indices: 4577328--4577358 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4577318 ACTCCTATGA
4577328 GAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAG
*
4577343 GAGAGAGAGGGAGAG
1 GAGAGAGAGAGAGAG
4577358 G
1 G
4577359 GAAACTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (15 bp):
GAGAGAGAGAGAGAG
Found at i:4586933 original size:28 final size:28
Alignment explanation
Indices: 4586889--4586953 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
4586879 GGAGTGGTCT
4586889 TTCGGGACATATATGTTATATGTGATCC
1 TTCGGGACATATATGTTATATGTGATCC
* * *
4586917 TTCGGGATATATGTGTTATATGTGGTCC
1 TTCGGGACATATATGTTATATGTGATCC
4586945 TTCGGGACA
1 TTCGGGACA
4586954 AATCCTATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (28 bp):
TTCGGGACATATATGTTATATGTGATCC
Found at i:4587822 original size:17 final size:16
Alignment explanation
Indices: 4587802--4587844 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
4587792 ATTTAAAAAT
4587802 AAAAATATTTTATTTTAA
1 AAAAATA-TTT-TTTTAA
4587820 AAAACATA-TTTTTTAA
1 AAAA-ATATTTTTTTAA
4587836 AAAAATATT
1 AAAAATATT
4587845 AAAAATAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.13
16 11 0.48
17 2 0.09
18 4 0.17
19 3 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAAATATTTTTTTAA
Found at i:4587832 original size:15 final size:15
Alignment explanation
Indices: 4587814--4587844 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
4587804 AAATATTTTA
4587814 TTTTAAAAAACATATT
1 TTTTAAAAAA-ATATT
4587830 TTTTAAAAAAATATT
1 TTTTAAAAAAATATT
4587845 AAAAATAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTTAAAAAAATATT
Found at i:4597299 original size:45 final size:46
Alignment explanation
Indices: 4597248--4597342 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 46
4597238 TTTTGCTCCC
*
4597248 TAAAGTTTAAAT-GATTATCTCGATTAATCCAAACTGTTAATTCC-T
1 TAAAGTTTAAATCG-TTATCTCGATTAATCCAAAATGTTAATTCCGT
* * * *
4597293 TAAAGTTTAAATCGTTATTTTGTTTACTCCAAAATGTTAATTCCGT
1 TAAAGTTTAAATCGTTATCTCGATTAATCCAAAATGTTAATTCCGT
4597339 TAAA
1 TAAA
4597343 AAATAACATG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
45 37 0.86
46 6 0.14
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (46 bp):
TAAAGTTTAAATCGTTATCTCGATTAATCCAAAATGTTAATTCCGT
Found at i:4599935 original size:20 final size:20
Alignment explanation
Indices: 4599882--4599929 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
4599872 ATATTCTCTA
4599882 GTAATCTTTTATTCTCATTG
1 GTAATCTTTTATTCTCATTG
*
4599902 ATAATCTTTTATTCTCATTG
1 GTAATCTTTTATTCTCATTG
4599922 GTAATCTT
1 GTAATCTT
4599930 ACATTCCGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (20 bp):
GTAATCTTTTATTCTCATTG
Found at i:4602665 original size:5 final size:5
Alignment explanation
Indices: 4602649--4602728 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
4602639 AACGGTCAAC
* * *
4602649 GGTCG GGCCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
4602698 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
4602729 AGACCGGTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 49 0.80
7 12 0.20
ACGTcount: A:0.07, C:0.24, G:0.51, T:0.17
Consensus pattern (5 bp):
GGTCG
Found at i:4602687 original size:27 final size:22
Alignment explanation
Indices: 4602642--4602728 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
4602632 GAAGGTCAAC
*
4602642 GGTCAACGGTCGGGCCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
4602664 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
4602686 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
4602708 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
4602729 AGACCGGTTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.09, C:0.24, G:0.49, T:0.17
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:4609950 original size:22 final size:22
Alignment explanation
Indices: 4609922--4609964 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4609912 AACGGTCAAC
*
4609922 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCAGGTCG
4609944 GGTCAACGGTCGGGTCAGGTC
1 GGTCAACGGTCGGGTCAGGTC
4609965 AGACCGGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCAGGTCG
Found at i:4609954 original size:12 final size:12
Alignment explanation
Indices: 4609922--4609960 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
4609912 AACGGTCAAC
4609922 GGTCAACGGTCG
1 GGTCAACGGTCG
*
4609934 GGTC--GGGTCG
1 GGTCAACGGTCG
4609944 GGTCAACGGTCG
1 GGTCAACGGTCG
4609956 GGTCA
1 GGTCA
4609961 GGTCAGACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:4609999 original size:20 final size:22
Alignment explanation
Indices: 4609974--4610023 Score: 79
Period size: 20 Copynumber: 2.4 Consensus size: 22
4609964 CAGACCGGTC
4609974 AAACCGGTTC-GAACCGGTTG-
1 AAACCGGTTCAGAACCGGTTGA
4609994 AAACCGG-TCAGAACCGGTTGA
1 AAACCGGTTCAGAACCGGTTGA
4610015 AAACCGGTT
1 AAACCGGTT
4610024 AAACTGGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.07
20 17 0.63
21 7 0.26
22 1 0.04
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (22 bp):
AAACCGGTTCAGAACCGGTTGA
Found at i:4610032 original size:9 final size:9
Alignment explanation
Indices: 4609967--4610032 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 9
4609957 GTCAGGTCAG
*
4609967 ACCGGTCAA
1 ACCGGTTAA
*
4609976 ACCGGTTCGA
1 ACCGGTT-AA
4609986 ACCGGTTGAA
1 ACCGGTT-AA
*
4609996 ACCGGTCAGA
1 ACCGGTTA-A
4610006 ACCGGTTGAAA
1 ACCGGTT--AA
4610017 ACCGGTTAA
1 ACCGGTTAA
*
4610026 ACTGGTT
1 ACCGGTT
4610033 TCAGCAGCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
9 15 0.33
10 22 0.48
11 8 0.17
12 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:4610032 original size:20 final size:19
Alignment explanation
Indices: 4609974--4610032 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
4609964 CAGACCGGTC
*
4609974 AAACCGGTTCGAACCGGTTG
1 AAACCGGTT-AAACCGGTTG
*
4609994 AAACCGGTCAGAACCGGTTG
1 AAACCGGTTA-AACCGGTTG
*
4610014 AAAACCGGTTAAACTGGTT
1 -AAACCGGTTAAACCGGTT
4610033 TCAGCAGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 24 0.73
21 9 0.27
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (19 bp):
AAACCGGTTAAACCGGTTG
Found at i:4612316 original size:29 final size:29
Alignment explanation
Indices: 4612283--4612360 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
4612273 GTCCCTGGGG
4612283 GTAGGTCGCCATGCACGCCCAACGACCTA
1 GTAGGTCGCCATGCACGCCCAACGACCTA
**
4612312 GTAGGTCGCCATGCACGCCCAGGGACCTA
1 GTAGGTCGCCATGCACGCCCAACGACCTA
** *
4612341 CCAGGTCGCTATGCACGCCC
1 GTAGGTCGCCATGCACGCCC
4612361 CAACACGCTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.21, C:0.38, G:0.27, T:0.14
Consensus pattern (29 bp):
GTAGGTCGCCATGCACGCCCAACGACCTA
Found at i:4612442 original size:33 final size:33
Alignment explanation
Indices: 4612390--4612474 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
4612380 GACCATCCGA
* * * * *
4612390 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAAGGAAT
4612423 CCGAGGGCAACCGAGCGAGCTATGCGAAGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAAGGAAT
4612456 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
4612475 AATAGGTCGC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.27, C:0.28, G:0.36, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAAGGAAT
Found at i:4612535 original size:23 final size:23
Alignment explanation
Indices: 4612505--4612576 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
4612495 GGGCGACCTA
*
4612505 CCCTCGCATAGCTCGCTCGGTTG
1 CCCTCGCATAGCTCGCTCGGATG
*
4612528 CCCTCGCATAGCTCGTTCGGATG
1 CCCTCGCATAGCTCGCTCGGATG
* *
4612551 GCCTCGGAT-GCT--CTCGGATG
1 CCCTCGCATAGCTCGCTCGGATG
*
4612571 GCCTCG
1 CCCTCG
4612577 GATGCTTTCG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
20 13 0.30
22 3 0.07
23 28 0.64
ACGTcount: A:0.10, C:0.36, G:0.29, T:0.25
Consensus pattern (23 bp):
CCCTCGCATAGCTCGCTCGGATG
Found at i:4612559 original size:10 final size:10
Alignment explanation
Indices: 4612544--4612600 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
4612534 CATAGCTCGT
4612544 TCGGATGGCC
1 TCGGATGGCC
4612554 TCGGAT-GCTC
1 TCGGATGGC-C
4612564 TCGGATGGCC
1 TCGGATGGCC
*
4612574 TCGGAT-GCTT
1 TCGGATGGC-C
4612584 TCGGATGGCC
1 TCGGATGGCC
4612594 TCGGATG
1 TCGGATG
4612601 CATTGCATGG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.10
10 33 0.80
11 4 0.10
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:4612569 original size:20 final size:20
Alignment explanation
Indices: 4612544--4612601 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
4612534 CATAGCTCGT
4612544 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
4612564 TCGGATGGCCTCGGATGCTT
1 TCGGATGGCCTCGGATGCTC
4612584 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGGATGC
4612602 ATTGCATGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.10, C:0.28, G:0.36, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:4622191 original size:35 final size:37
Alignment explanation
Indices: 4622131--4622201 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 37
4622121 GTCCTACTAT
*
4622131 GATTCAAACTCTCAAAAATATGATAGAATTCTGCTAG
1 GATTCAAACTCTCAAAAATAGGATAGAATTCTGCTAG
* *
4622168 GATTC-AACTC-CTAAAATAGGATAGAATTTTGCTA
1 GATTCAAACTCTCAAAAATAGGATAGAATTCTGCTA
4622202 TATTTTAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 21 0.68
36 5 0.16
37 5 0.16
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (37 bp):
GATTCAAACTCTCAAAAATAGGATAGAATTCTGCTAG
Found at i:4622758 original size:10 final size:10
Alignment explanation
Indices: 4622729--4622762 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4622719 TATATGTATA
*
4622729 TTTTTTATTG
1 TTTTTTATTT
*
4622739 TATTTTATTT
1 TTTTTTATTT
4622749 TTTTTTATTT
1 TTTTTTATTT
4622759 TTTT
1 TTTT
4622763 AAACATATGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:4622856 original size:16 final size:16
Alignment explanation
Indices: 4622835--4622869 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4622825 TTTCATGTAT
4622835 TTATTATATTACATTA
1 TTATTATATTACATTA
* *
4622851 TTATTATTTTACTTTA
1 TTATTATATTACATTA
4622867 TTA
1 TTA
4622870 AATTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTATATTACATTA
Found at i:4623173 original size:19 final size:21
Alignment explanation
Indices: 4623144--4623193 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
4623134 TTTATTCCTC
*
4623144 TTTTAGTTTTT-CATC-ATTT
1 TTTTATTTTTTCCATCTATTT
4623163 TTTTATTTTTTTCCATCTATTT
1 TTTTA-TTTTTTCCATCTATTT
4623185 TCTTTATTT
1 T-TTTATTT
4623194 CATTTACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 5 0.19
21 4 0.15
22 8 0.31
23 4 0.15
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTATTTTTTCCATCTATTT
Found at i:4623175 original size:20 final size:23
Alignment explanation
Indices: 4623150--4623193 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4623140 CCTCTTTTAG
4623150 TTTTT-CATC-ATTTT-TTTATT
1 TTTTTCCATCTATTTTCTTTATT
4623170 TTTTTCCATCTATTTTCTTTATT
1 TTTTTCCATCTATTTTCTTTATT
4623193 T
1 T
4623194 CATTTACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 5 0.24
23 7 0.33
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTCCATCTATTTTCTTTATT
Found at i:4626268 original size:20 final size:20
Alignment explanation
Indices: 4626216--4626285 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
4626206 CAAAAAGGGC
*
4626216 AAAAAGAAAAAAGAAAAGGAGCA
1 AAAAAGAAAAAACAAAA--A-CA
*
4626239 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAAAACA
* *
4626260 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAAAACA
4626280 AAAAAG
1 AAAAAG
4626286 GGGACAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 18 0.44
21 7 0.17
22 1 0.02
23 5 0.12
24 10 0.24
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAAAACA
Found at i:4626919 original size:22 final size:22
Alignment explanation
Indices: 4626891--4626941 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
4626881 CCCCATCAAT
4626891 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
4626913 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
4626935 CCTTTGA
1 CCTTTGA
4626942 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:4627839 original size:36 final size:37
Alignment explanation
Indices: 4627792--4627893 Score: 143
Period size: 36 Copynumber: 2.8 Consensus size: 37
4627782 CTCACCATTA
4627792 TCTCTCTTGAGACAGTTTCCCTTGAAACAAA-CTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATCTTTG
* * *
4627828 TCTCTGTTGAGACAGTTTCCCTTGAAACAAATTTTTT
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATCTTTG
* * *
4627865 TCTCCCTTGAGACAGTTTCTCTTAAAACA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACA
4627894 TAAACATTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 30 0.52
37 28 0.48
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (37 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAATCTTTG
Found at i:4628058 original size:36 final size:36
Alignment explanation
Indices: 4628011--4628096 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
4628001 ATTGAAAACA
** * * *
4628011 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAG
4628047 TTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAG
*
4628083 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
4628097 TAAACATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAG
Found at i:4628127 original size:101 final size:101
Alignment explanation
Indices: 4627807--4628161 Score: 548
Period size: 102 Copynumber: 3.5 Consensus size: 101
4627797 CTTGAGACAG
** * * * * *
4627807 TTTCCCTTGAAACAAACTTTGTCTCTGTTGAGACAGTTTCCCTTGAAACAAATTTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA-ATTTGTCTCCCT
*
4627872 TGAGACAGTTTCTCTTAAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
4627909 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATT-TGTCTCCCT
* *
4627974 TGAGGCAATTTCTCTTGAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
4628011 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTGTCTCCCTT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTGTCTCCCTT
4628076 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
** *
4628112 TTTCCCTTGAAATGAATTCCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
4628162 TAAACATTGA
Statistics
Matches: 231, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
101 91 0.39
102 140 0.61
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (101 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTGTCTCCCTT
GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:4628151 original size:65 final size:65
Alignment explanation
Indices: 4628067--4628226 Score: 293
Period size: 65 Copynumber: 2.5 Consensus size: 65
4628057 AACAAAATTT
*
4628067 GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTCC
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTCC
* *
4628132 GTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTC
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTCC
4628197 GTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACA
4628227 AAATTTTGTC
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 91 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (65 bp):
GTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTCC
Found at i:4628155 original size:166 final size:169
Alignment explanation
Indices: 4627945--4628261 Score: 525
Period size: 166 Copynumber: 1.9 Consensus size: 169
4627935 CTTGAGATAG
*
4627945 TTTCCCTTGAAACAAAATTCCGTCTCCATTGAGGCAATTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAATTTCTCTTGAAACATAAACATTGAAAAC
* *
4628010 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA-TTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCC
4628074 TTGAGACAG-TTTCTCTTGAAACATAAACATTGAAAACA
131 TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
** * *
4628112 TTTCCCTTGAAA-TGAATTCCGTCTCTC-TTGAGATAGTTTCTCTTGAAACATAAACATTGAAAA
1 TTTCCCTTGAAACAAAATTCCGTCTC-CATTGAGACAATTTCTCTTGAAACATAAACATTGAAAA
*
4628175 CATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCC
65 CATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCC
4628240 CTTGAGACAGTTTTCTCTTGAA
130 CTTGAGACAGTTTTCTCTTGAA
4628262 GCATCATCTT
Statistics
Matches: 139, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
166 96 0.69
167 32 0.23
168 11 0.08
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (169 bp):
TTTCCCTTGAAACAAAATTCCGTCTCCATTGAGACAATTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCC
TTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:4628234 original size:203 final size:194
Alignment explanation
Indices: 4627792--4628261 Score: 523
Period size: 203 Copynumber: 2.3 Consensus size: 194
4627782 CTCACCATTA
* *
4627792 TCTCTCTTGAGACAGTTTCCCTTGAAACAAACTTTGTCTCTGTTGAGACAGTTTCCCTTGAAACA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
* *
4627857 AATTTTTTTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAACATTTCCCTTGAAAT
66 AATATTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAACATTTCCCTTGAAAT
* ** * *
4627922 GAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCATTGAGGCAATTTC
131 GAATTCCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTACATCTCCATTGAGGCAATTTC
* ** *
4627986 TCTTGAAACATAAACATTGAAAACA-TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTT
1 TC-T----C-T---C-TTG-AGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTT
*
4628050 CCCTTGAAACAAA-ATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATT
55 CCCTTGAAACAAATATTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAACATT
* *
4628114 TCCCTTGAAATGAATTCCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATT
120 TCCCTTGAAATGAATTCCGTCTCTCTTGAGATAGTTTCCCTTGAAAC--AAA-ATT----ACATC
* *
4628179 TCCCTTGAAATG-AATTTC
178 TCCATTG--AGGCAATTTC
* * *
4628197 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTTCTCTTGAA
1 -TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAA
4628262 GCATCATCTT
Statistics
Matches: 227, Mismatches: 25, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
194 2 0.01
195 1 0.00
199 1 0.00
200 1 0.00
201 4 0.02
202 14 0.06
203 113 0.50
204 60 0.26
205 7 0.03
206 4 0.02
207 1 0.00
210 8 0.04
211 7 0.03
212 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (194 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
AATATTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAACATTTCCCTTGAAAT
GAATTCCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTACATCTCCATTGAGGCAATTTC
Found at i:4628288 original size:103 final size:102
Alignment explanation
Indices: 4628132--4628357 Score: 242
Period size: 103 Copynumber: 2.2 Consensus size: 102
4628122 AATGAATTCC
*
4628132 GTCTCTCTTGAGATAG-TTTCTCTTGAAACATAAACATTGAAAACATTTCCCTT-GAAATGAATT
1 GTCTCTCTTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGGAAAT-AATT
* * * * *
4628195 TCGTCT-CTCTTGAGACAGTTTCTCTTGAAACAAAATTTT
65 TCATCTCCCCGTGAGACAATTTCT-TTGAAAC-AAAGTTT
* * * * * * ** * *
4628234 GTCTCCCTTGAGACAGTTTTCTCTTGAAGCATCATCTTTGAATATGTTTTCCTTGGAACTAATTT
1 GTCTCTCTTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGGAAATAATTT
* *
4628299 CATCTCCCCGTGAGACAATTTCTTTGGAACTAAGTTT
66 CATCTCCCCGTGAGACAATTTCTTTGAAACAAAGTTT
4628336 GTCTCTCTTGAGACAGTTTTCT
1 GTCTCTCTTGAGACAGTTTTCT
4628358 TAAAACAAAA
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
102 40 0.39
103 44 0.43
104 18 0.18
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (102 bp):
GTCTCTCTTGAGACAGTTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGGAAATAATTT
CATCTCCCCGTGAGACAATTTCTTTGAAACAAAGTTT
Found at i:4628909 original size:98 final size:98
Alignment explanation
Indices: 4628662--4629581 Score: 773
Period size: 109 Copynumber: 8.9 Consensus size: 98
4628652 TATCTAGAGT
* * *
4628662 CAATTTCGACTTCACAGCGAAGGCTATTGGACTCGAGACAACACAAGTTCAGCTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
*
4628727 GGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGG-GC
66 GGACGGCTGGTTGTCAAC-A-AA-----CAATTTC-GGAGC
* * * * *
4628767 CAATTT-AACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* ** *
4628831 GGGCGGCTGACTGTCGACAAACAATTTCGGAGC
66 GGACGGCTGGTTGTCAACAAACAATTTCGGAGC
* *
4628864 CAATCTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
*
4628929 GGACGGCTGGTTGTCAACAATAATTTCCTAGTTTCAGG-GC
66 GGACGGCTGGTTGTCAAC-A-AA----C-AATTTC-GGAGC
* * * * *
4628969 CAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* ** * *
4629034 GGGCGGCTGACTGTCGATAAGA-AATTTCGGAGC
66 GGACGGCTGGTTGTCAACAA-ACAATTTCGGAGC
* * * *
4629067 CAATCTCAACTTCACAGTGAAGGATTTTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
*
4629132 GGACGGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGC
66 GGACGGCTGGTTGTCAACAAACAA--T-----TT-CGGAGC
* * * * *
4629173 CGATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAAC
1 CAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAAC
* *
4629237 GAAGGGACGGCTGGTTGTCAACGAAA-AACTTTTCAGTTTCATCC
62 GAAGGGACGGCTGGTTGTCAAC-AAACAA--TTTC-G---GA-GC
* * * * *
4629281 GCGATTTTAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAA
1 -CAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAA
*
4629345 CGAAGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGC
61 CGAAGGGACGGCTGGTTGTCAAC-AA-A-----C-AATTTCGGAGC
*
4629391 CAATTTCAACTTCGCAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * *
4629456 GGACGGCTGATTGTCAAC-AA-GATTTCGTTCAGAGT
66 GGACGGCTGGTTGTCAACAAACAATTTCG----GAGC
* * * * *
4629491 CAATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCAC-AGCTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* **
4629555 GGGCGG-TGACTGTCAACAAACAATTTC
66 GGACGGCTGGTTGTCAACAAACAATTTC
4629582 CCAGTTCCAG
Statistics
Matches: 678, Mismatches: 90, Indels: 99
0.78 0.10 0.11
Matches are distributed among these distances:
96 7 0.01
97 16 0.02
98 158 0.23
99 26 0.04
100 51 0.08
102 2 0.00
103 4 0.01
104 70 0.10
105 87 0.13
106 78 0.12
107 3 0.00
108 3 0.00
109 160 0.24
110 6 0.01
111 1 0.00
115 4 0.01
117 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (98 bp):
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
GGACGGCTGGTTGTCAACAAACAATTTCGGAGC
Found at i:4629074 original size:203 final size:202
Alignment explanation
Indices: 4628670--4629625 Score: 1064
Period size: 203 Copynumber: 4.6 Consensus size: 202
4628660 GTCAATTTCG
* * *
4628670 ACTTCACAGCGAAGGCTATTGGACTCGAGACAACACAAGTTCAGCTTCACAACGAAGGGACGGCT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* *
4628735 GGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTT-AACTTCACAGCGAAGGATATTGGACC
66 GGTTGTCAACAACAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
* * * *
4628799 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAACAATTTCGGAGC
131 CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAA-AATTTCGGAGC
4628864 CAATCTCA
195 CAATCTCA
4628872 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* * *
4628937 GGTTGTCAACAATAATTTCCTAGTTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
66 GGTTGTCAACAACAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
* * * * *
4629002 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGATAAGAAATTTCGGAGC
131 CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAA-AAATTTCGGAGC
4629067 CAATCTCA
195 CAATCTCA
* * * *
4629075 ACTTCACAGTGAAGGATTTTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGGACGGCT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* * * * *
4629140 GGTTGTCAACAAACAATTTCCCAATTCCAGAGCCGATTTCAACTCCAC-GACGGAGGATATCGTG
66 GGTTGTCAAC-AACAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATAT--TG
* * * **
4629204 CTACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAAAAACTTT
127 -GACCCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAAC-AAAAA--TT
* * * * *
4629269 TCAGTTTCATCCGCGATTTTA
188 TC-G---GA-GC-CAATCTCA
* * *
4629290 ACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGAC
1 ACTTCACAG-CGAAGGATAT--TG-AACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGAC
* * * * *
4629354 GGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTTCAACTTCGCAGCGAAGGATATT
62 GGCTGGTTGTCAAC-AACAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
* * * * *
4629419 GGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AAGATTTCG
126 GGACCCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAAAATTTCG
* *
4629483 TTCAGAGTCAATTTCA
191 ----GAGCCAATCTCA
* * * * *
4629499 TCTTCACAGCGAAGGATATT-AGACTCGAGACAGCAC-AGCTCAACTTCACAGCGAAGGGGCGG-
1 ACTTCACAGCGAAGGATATTGA-ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGC
** * * *
4629561 TGACTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACAGCGGAGGATA-TGGA
65 TGGTTGTCAAC-AACAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
4629625 C
129 C
4629626 TCGGAACAAT
Statistics
Matches: 655, Mismatches: 75, Indels: 47
0.84 0.10 0.06
Matches are distributed among these distances:
202 99 0.15
203 173 0.26
204 90 0.14
205 23 0.04
206 15 0.02
207 48 0.07
208 2 0.00
209 24 0.04
210 3 0.00
211 6 0.01
213 4 0.01
214 2 0.00
215 69 0.11
216 2 0.00
217 2 0.00
218 92 0.14
219 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (202 bp):
ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
GGTTGTCAACAACAATTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
CAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAAAATTTCGGAGCC
AATCTCA
Found at i:4630152 original size:35 final size:35
Alignment explanation
Indices: 4630089--4630188 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
4630079 TTTCGTCCTA
*
4630089 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
4630126 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
4630161 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
4630189 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:4630863 original size:15 final size:16
Alignment explanation
Indices: 4630834--4630870 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
4630824 GTTTTCATGT
4630834 ATTA-TATTATATTAC
1 ATTATTATTATATTAC
4630849 ATTATTATTAT-TTAC
1 ATTATTATTATATTAC
*
4630864 TTTATTA
1 ATTATTA
4630871 AATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTATTATATTAC
Found at i:4637445 original size:18 final size:18
Alignment explanation
Indices: 4637422--4637459 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4637412 GAAATTATTA
4637422 ACTATTACATGATAATTG
1 ACTATTACATGATAATTG
*
4637440 ACTATTACATGATAGTTG
1 ACTATTACATGATAATTG
4637458 AC
1 AC
4637460 GTGGCAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (18 bp):
ACTATTACATGATAATTG
Found at i:4637555 original size:45 final size:44
Alignment explanation
Indices: 4637480--4637567 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 44
4637470 AGAATTTTGT
*
4637480 ATAAAAATATATTTACTCCTCATTATTTATACATTAATTAATTTAG
1 ATAAAAATATATTTACTCCTCATTAATTATACATT-ATT-ATTTAG
* **
4637526 ATAATAATATATTTA-TTTTCATTAATTATACATTATTATTTA
1 ATAAAAATATATTTACTCCTCATTAATTATACATTATTATTTA
4637568 ATCTTAATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 5 0.13
44 3 0.08
45 16 0.42
46 14 0.37
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.50
Consensus pattern (44 bp):
ATAAAAATATATTTACTCCTCATTAATTATACATTATTATTTAG
Found at i:4638404 original size:20 final size:20
Alignment explanation
Indices: 4638379--4638427 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
4638369 TGAGCAAAGT
4638379 GGTGCTCACAAAAGGTAATC
1 GGTGCTCACAAAAGGTAATC
4638399 GGTGCTCACAAAAGGTAATC
1 GGTGCTCACAAAAGGTAATC
*
4638419 AGTGCTCAC
1 GGTGCTCAC
4638428 CAGTGGGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.20
Consensus pattern (20 bp):
GGTGCTCACAAAAGGTAATC
Found at i:4641627 original size:60 final size:60
Alignment explanation
Indices: 4641550--4641664 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
4641540 CTATATGATA
* * * * *
4641550 TTATTTTATTAAGTTTTTATATTATTAAAATTTATAAAATTAATT-TTAAATTATAGTGTG
1 TTATATTATTAAATTTTTAGACTATTAAAAATTATAAAA-TAATTATTAAATTATAGTGTG
*
4641610 TTATATTATTAAATTTTTCGACTATTAAAAATTATAAAATAATTACTTAAATTAT
1 TTATATTATTAAATTTTTAGACTATTAAAAATTATAAAATAATTA-TTAAATTAT
4641665 TAAATATTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 5 0.11
60 33 0.70
61 9 0.19
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (60 bp):
TTATATTATTAAATTTTTAGACTATTAAAAATTATAAAATAATTATTAAATTATAGTGTG
Found at i:4641706 original size:18 final size:18
Alignment explanation
Indices: 4641683--4641718 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4641673 AATATGATGA
4641683 TTAAAATATAATAATTAT
1 TTAAAATATAATAATTAT
* *
4641701 TTAAAATTTTATAATTAT
1 TTAAAATATAATAATTAT
4641719 ATTTTATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAAATATAATAATTAT
Found at i:4642294 original size:2 final size:2
Alignment explanation
Indices: 4642287--4642316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4642277 AATATTTTTA
4642287 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
4642317 TAACCTTAAA
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:4642928 original size:24 final size:24
Alignment explanation
Indices: 4642901--4642950 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
4642891 TATCCAAAAT
4642901 AGCAAAGTTATGCTACAACCAATC
1 AGCAAAGTTATGCTACAACCAATC
4642925 AGCAAAGTTATGCTACAACCAATC
1 AGCAAAGTTATGCTACAACCAATC
4642949 AG
1 AG
4642951 TAAAATGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (24 bp):
AGCAAAGTTATGCTACAACCAATC
Found at i:4644030 original size:32 final size:32
Alignment explanation
Indices: 4643991--4644055 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
4643981 TAGCAAAAAG
*
4643991 AAGTATTAATTTTTTAGATGTTTTAAATTTAA
1 AAGTATTAATTTTTTAGATGTTTCAAATTTAA
*
4644023 AAGTATTATTTTTTTAGATGTTTCAAATTTAA
1 AAGTATTAATTTTTTAGATGTTTCAAATTTAA
4644055 A
1 A
4644056 CAATTACAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (32 bp):
AAGTATTAATTTTTTAGATGTTTCAAATTTAA
Found at i:4653026 original size:22 final size:23
Alignment explanation
Indices: 4652989--4653037 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
4652979 CAATCTCTAT
* *
4652989 TTATTATCAATTATCTTATATTA
1 TTATTATCAATTATCTAATAATA
*
4653012 TTATTAT-TATTATCTAATAATA
1 TTATTATCAATTATCTAATAATA
4653034 TTAT
1 TTAT
4653038 AAAATAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATTATCAATTATCTAATAATA
Found at i:4653242 original size:13 final size:14
Alignment explanation
Indices: 4653214--4653246 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4653204 TAATATTTAT
4653214 AAATAAAGAATAAA
1 AAATAAAGAATAAA
*
4653228 AAATAAA-ACTAAA
1 AAATAAAGAATAAA
4653241 AAATAA
1 AAATAA
4653247 TTATTTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (14 bp):
AAATAAAGAATAAA
Found at i:4653340 original size:2 final size:2
Alignment explanation
Indices: 4653333--4653359 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4653323 AATATGAAAG
4653333 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 T
4653360 CATAATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4660624 original size:30 final size:31
Alignment explanation
Indices: 4660560--4660631 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
4660550 ATAAAGTTTC
4660560 ACCCGACCCAAATATATGAATTAGAAACCCA
1 ACCCGACCCAAATATATGAATTAGAAACCCA
*
4660591 ACCCTACCCAAATATATGAATTAGAAA-CCA
1 ACCCGACCCAAATATATGAATTAGAAACCCA
4660621 ACCCGACCCAA
1 ACCCGACCCAA
4660632 CCCGAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 13 0.33
31 26 0.67
ACGTcount: A:0.44, C:0.32, G:0.08, T:0.15
Consensus pattern (31 bp):
ACCCGACCCAAATATATGAATTAGAAACCCA
Found at i:4660807 original size:290 final size:285
Alignment explanation
Indices: 4660314--4660893 Score: 801
Period size: 290 Copynumber: 2.0 Consensus size: 285
4660304 ACCCGACCTG
* * *
4660314 ACCCAAATATATGAATTAGAAACCTGACACGACTCGAAATAATAAAAAATTATTTTTATTCAATA
1 ACCCAAATATATGAATTAGAAACCCGACACAACCCGAAATAATAAAAAATTATTTTTATTCAATA
* *
4660379 AAAACAATGACTTAATTGAAAAAAATTTATATGTAGGGGTATTATTGTAATTATTTCTAAATATA
66 AAAACAATGACTTAATTGAAAAAAAATTATATGGAGGGGTATTATTGTAATTATTTCTAAATATA
* * *
4660444 TAAGGTAAAATTATATATTTTTTGGGTCGGATCGAGTATTTTTCACCTTAAACCCGACCCCGACC
131 TAAGGTAAAATTATATATTTTTCGGGTCGGATCGAGTATTTTTCACCGTAAACCCGAACCCGACC
* * *
4660509 CAACCCGAATATCACACTTAAAAAAAACCGACCCGA-C-A-AAAATAAAGTTTCACC-CGACCCA
196 CAACCCGAATATAACACTT-AAAAAAACCGACCCGACCGACAAAATAAAATTTCACCACAACCCA
4660570 AATATATGAATTAGAAACCCAACCCT
260 AATATATGAATTAGAAACCCAACCCT
*
4660596 ACCCAAATATATGAATTAGAAACCAACCCGACCCAACCCGAAATAATAAAAAAATTATTTTTATT
1 ACCCAAATATATGAATTAG--A--AACCCGACACAACCCGAAATAAT-AAAAAATTATTTTTATT
* *
4660661 CAATAAAAATAGTGACTTAATTGAAAAAAAAATTATATAGAGAGGGGTATTATTGTAATTATTTC
61 CAATAAAAACAATGACTTAATTG-AAAAAAAATTATAT-G-GAGGGGTATTATTGTAATTATTTC
* *
4660726 -AAATATATAAGGTAAAATTATATATATTTTCGGGTCGGGTCGGGTATTTTTCACCGTAAACCCG
123 TAAATATATAAGGTAAAATTATATAT-TTTTCGGGTCGGATCGAGTATTTTTCACCGTAAACCCG
* * *
4660790 AACTCGACCCGACCCGAATATAACACTTAAAAAAGCCGACCCGACCTGACCAAAATAAAATTTCA
187 AACCCGACCCAACCCGAATATAACACTTAAAAAAACCGACCCGACC-GA-CAAAATAAAATTTCA
*
4660855 CCTGAATCAACCCAAATATATGAATTAGAAACCCGACCC
250 CC---A-CAACCCAAATATATGAATTAGAAACCCAACCC
4660894 GAAATAATAA
Statistics
Matches: 259, Mismatches: 20, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
282 19 0.07
284 1 0.00
286 19 0.07
287 38 0.15
288 13 0.05
289 41 0.16
290 82 0.32
292 1 0.00
294 15 0.06
299 30 0.12
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (285 bp):
ACCCAAATATATGAATTAGAAACCCGACACAACCCGAAATAATAAAAAATTATTTTTATTCAATA
AAAACAATGACTTAATTGAAAAAAAATTATATGGAGGGGTATTATTGTAATTATTTCTAAATATA
TAAGGTAAAATTATATATTTTTCGGGTCGGATCGAGTATTTTTCACCGTAAACCCGAACCCGACC
CAACCCGAATATAACACTTAAAAAAACCGACCCGACCGACAAAATAAAATTTCACCACAACCCAA
ATATATGAATTAGAAACCCAACCCT
Found at i:4679716 original size:16 final size:16
Alignment explanation
Indices: 4679692--4679725 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4679682 TATCGCCGAC
*
4679692 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
4679708 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
4679724 CG
1 CG
4679726 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:4682933 original size:27 final size:27
Alignment explanation
Indices: 4682895--4682951 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
4682885 ACCTCTACCT
4682895 CTGCCAAGGATTTGGGATCACTGCCAG
1 CTGCCAAGGATTTGGGATCACTGCCAG
* *
4682922 CTGCCAATGATTTGGGATCACTGCTAG
1 CTGCCAAGGATTTGGGATCACTGCCAG
4682949 CTG
1 CTG
4682952 TCATATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (27 bp):
CTGCCAAGGATTTGGGATCACTGCCAG
Found at i:4693265 original size:15 final size:15
Alignment explanation
Indices: 4693247--4693277 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4693237 TCAATACAAA
4693247 TATAATCATAATAAT
1 TATAATCATAATAAT
4693262 TATAATCATAATAAT
1 TATAATCATAATAAT
4693277 T
1 T
4693278 TTTTTGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
TATAATCATAATAAT
Found at i:4695601 original size:35 final size:35
Alignment explanation
Indices: 4695555--4695634 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
4695545 AACACAATCA
* **
4695555 TCAATTATATTCTAAACC-CTAAATTCTAAAATGTT
1 TCAATTATATTCTAAACCTC-AAATTCAAAAATACT
4695590 TCAATTATATTCTAAACCTCAAATTCAAAAATACT
1 TCAATTATATTCTAAACCTCAAATTCAAAAATACT
4695625 TCAATTATAT
1 TCAATTATAT
4695635 GCCCAACCCG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 40 0.98
36 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.01, T:0.39
Consensus pattern (35 bp):
TCAATTATATTCTAAACCTCAAATTCAAAAATACT
Found at i:4697450 original size:29 final size:29
Alignment explanation
Indices: 4697408--4697518 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
4697398 AAACTAAATT
4697408 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
4697437 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
4697466 GATGTCATTGCTTACATCATTTAAATAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
4697495 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
4697519 GTTAGGTGAG
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
29 74 0.94
30 5 0.06
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:4702236 original size:29 final size:29
Alignment explanation
Indices: 4702194--4702304 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
4702184 AAACTAAATT
4702194 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
4702223 GATGTCATTGCTTATATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
4702252 GATGTCATTGCTTACATCATTTAAATAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
4702281 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
4702305 GTTAGGTGAG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 72 0.94
30 5 0.06
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:4702757 original size:2 final size:2
Alignment explanation
Indices: 4702750--4702777 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4702740 ACCAGCAGTC
4702750 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4702778 AGTTTCGGGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4706097 original size:11 final size:11
Alignment explanation
Indices: 4706081--4706107 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4706071 ATGGGTTATC
4706081 AGCTGAGTATA
1 AGCTGAGTATA
4706092 AGCTGAGTATA
1 AGCTGAGTATA
4706103 AGCTG
1 AGCTG
4706108 GTTGTCACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (11 bp):
AGCTGAGTATA
Found at i:4708190 original size:43 final size:43
Alignment explanation
Indices: 4708128--4708260 Score: 140
Period size: 51 Copynumber: 2.9 Consensus size: 43
4708118 GTCCCTATTA
* * * *
4708128 AGGTGGCTGACCAGGCCGAGGCTGCTCCAATGAGTTCCTGTTG
1 AGGTGACTGGCCAGACCGAGGCTGCTCCAGTGAGTTCCTGTTG
4708171 AGGTGACTGGCCAGACCGAGGCTGCTCCAGTGAGTTCCTTCGTTCCTGTTG
1 AGGTGACTGGCCAGACCGAGGCTGCTCCAGTGA--------GTTCCTGTTG
* *
4708222 AGGTGACTGGTCAGACCGAGGCTGCTCCAGCGAGTTCCT
1 AGGTGACTGGCCAGACCGAGGCTGCTCCAGTGAGTTCCT
4708261 TTGTTTACAA
Statistics
Matches: 76, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
43 35 0.46
51 41 0.54
ACGTcount: A:0.16, C:0.27, G:0.33, T:0.24
Consensus pattern (43 bp):
AGGTGACTGGCCAGACCGAGGCTGCTCCAGTGAGTTCCTGTTG
Found at i:4708237 original size:51 final size:51
Alignment explanation
Indices: 4708161--4708261 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
4708151 GCTCCAATGA
*
4708161 GTTCCTGTTGAGGTGACTGGCCAGACCGAGGCTGCTCCAGTGAGTTCCTTC
1 GTTCCTGTTGAGGTGACTGGCCAGACCGAGGCTGCTCCAGCGAGTTCCTTC
*
4708212 GTTCCTGTTGAGGTGACTGGTCAGACCGAGGCTGCTCCAGCGAGTTCCTT
1 GTTCCTGTTGAGGTGACTGGCCAGACCGAGGCTGCTCCAGCGAGTTCCTT
4708262 TGTTTACAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.14, C:0.27, G:0.32, T:0.28
Consensus pattern (51 bp):
GTTCCTGTTGAGGTGACTGGCCAGACCGAGGCTGCTCCAGCGAGTTCCTTC
Found at i:4712413 original size:80 final size:80
Alignment explanation
Indices: 4712326--4712473 Score: 217
Period size: 80 Copynumber: 1.9 Consensus size: 80
4712316 TGTTATCGTC
* * *
4712326 TCATCTTATTTTGACATCTTTTAATTATTAATAATTATAAATAAA-TGATTTTAAAATTATACTT
1 TCATCTTATTTTGACATATCTTAATTATTAATAATTATAAACAAACT-ATTTTAAAATTATACTT
4712390 TAAGCCACACGTTGAT
65 TAAGCCACACGTTGAT
* * * *
4712406 TCATCTTATTTTGAGATATCTTAATTATTAATCATTATGAACAAACTATTTTAAAATTATATTTT
1 TCATCTTATTTTGACATATCTTAATTATTAATAATTATAAACAAACTATTTTAAAATTATACTTT
4712471 AAG
66 AAG
4712474 TCATATATTG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 59 0.98
81 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (80 bp):
TCATCTTATTTTGACATATCTTAATTATTAATAATTATAAACAAACTATTTTAAAATTATACTTT
AAGCCACACGTTGAT
Found at i:4712485 original size:80 final size:79
Alignment explanation
Indices: 4712326--4712494 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
4712316 TGTTATCGTC
* * *
4712326 TCATCTTATTTTGACATCTTTTAATTATTAATAATTATAAATAAATGATTTTAAAATTATACTTT
1 TCATCTTATTTTGACATATCTTAATTATTAATAATTATAAACAAATGATTTTAAAATTATACTTT
*
4712391 AAGCCACACGTTGA
66 AAGCCACACATTGA
* * * *
4712405 TTCATCTTATTTTGAGATATCTTAATTATTAATCATTATGAACAAACT-ATTTTAAAATTATATT
1 -TCATCTTATTTTGACATATCTTAATTATTAATAATTATAAACAAA-TGATTTTAAAATTATACT
* * *
4712469 TTAAGTCATATATTGA
64 TTAAGCCACACATTGA
4712485 TCATGCTTAT
1 TCAT-CTTAT
4712495 CCTAAAGATA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
79 4 0.05
80 71 0.93
81 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (79 bp):
TCATCTTATTTTGACATATCTTAATTATTAATAATTATAAACAAATGATTTTAAAATTATACTTT
AAGCCACACATTGA
Found at i:4718948 original size:25 final size:22
Alignment explanation
Indices: 4718902--4718947 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
4718892 TAATACTATT
4718902 ATTCCTATCAAAAAAAACAATA
1 ATTCCTATCAAAAAAAACAATA
4718924 ATTCCTATCAAAAAAAACAATA
1 ATTCCTATCAAAAAAAACAATA
4718946 AT
1 AT
4718948 ACTATTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.59, C:0.17, G:0.00, T:0.24
Consensus pattern (22 bp):
ATTCCTATCAAAAAAAACAATA
Found at i:4718952 original size:21 final size:22
Alignment explanation
Indices: 4718906--4718952 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
4718896 ACTATTATTC
*
4718906 CTATCAAAAAAAACAATAATTC
1 CTATCAAAAAAAACAATAATTA
4718928 CTATCAAAAAAAACAATAA-TA
1 CTATCAAAAAAAACAATAATTA
4718949 CTAT
1 CTAT
4718953 TATAGTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (22 bp):
CTATCAAAAAAAACAATAATTA
Found at i:4728203 original size:19 final size:21
Alignment explanation
Indices: 4728181--4728222 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
4728171 TGATAATTAC
*
4728181 TTTTCA-TTACTCAT-AATAT
1 TTTTCATTTAATCATCAATAT
*
4728200 TTTTTATTTAATCATCAATAT
1 TTTTCATTTAATCATCAATAT
4728221 TT
1 TT
4728223 AATATAGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 7 0.37
21 7 0.37
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTCATTTAATCATCAATAT
Found at i:4730629 original size:17 final size:17
Alignment explanation
Indices: 4730607--4730640 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4730597 TTTTTTTGAC
4730607 GAGTTTGAAGAAGATGA
1 GAGTTTGAAGAAGATGA
4730624 GAGTTTGAAGAAGATGA
1 GAGTTTGAAGAAGATGA
4730641 AAGAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (17 bp):
GAGTTTGAAGAAGATGA
Done.