Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008427.1 Hibiscus syriacus cultivar Beakdansim tig00111212_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: 451641
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13537 original size:2 final size:2
Alignment explanation
Indices: 13530--13563 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
13520 AGTAATTATC
*
13530 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13564 GTTATTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15097 original size:17 final size:17
Alignment explanation
Indices: 15075--15111 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
15065 ACAAAATTAG
15075 AATACAAAAAGAAAAAA
1 AATACAAAAAGAAAAAA
*
15092 AATACAAAAAGAAGAAA
1 AATACAAAAAGAAAAAA
15109 AAT
1 AAT
15112 TCAGGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.08, T:0.08
Consensus pattern (17 bp):
AATACAAAAAGAAAAAA
Found at i:15121 original size:21 final size:19
Alignment explanation
Indices: 15080--15144 Score: 71
Period size: 21 Copynumber: 3.4 Consensus size: 19
15070 ATTAGAATAC
* *
15080 AAAAAGAA-AAAAAAT-AC
1 AAAAAGAAGAAAAAGTCAA
*
15097 AAAAAGAAGAAAAATTCAGGA
1 AAAAAGAAGAAAAAGTCA--A
15118 AAAAAGAAGAAAAAGTCAA
1 AAAAAGAAGAAAAAGTCAA
15137 AAAAAGAA
1 AAAAAGAA
15145 AGCAAGCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 8 0.20
18 6 0.15
19 10 0.24
21 17 0.41
ACGTcount: A:0.75, C:0.05, G:0.14, T:0.06
Consensus pattern (19 bp):
AAAAAGAAGAAAAAGTCAA
Found at i:27598 original size:16 final size:18
Alignment explanation
Indices: 27562--27598 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
27552 GTTCAAAGAC
27562 AAAAAGAAGAAAAAATCAG
1 AAAAAGAAGAAAAAA-CAG
27581 AAAAAGAA-AAAAAA-AG
1 AAAAAGAAGAAAAAACAG
27597 AA
1 AA
27599 TTTCAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (18 bp):
AAAAAGAAGAAAAAACAG
Found at i:30660 original size:22 final size:22
Alignment explanation
Indices: 30634--30684 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
30624 GATAAAACTC
30634 CATGCCTATTCGGCCACACCCA
1 CATGCCTATTCGGCCACACCCA
*
30656 TATGCCTATTCGGCCACACCCA
1 CATGCCTATTCGGCCACACCCA
30678 CATGCCT
1 CATGCCT
30685 TGCATAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.43, G:0.14, T:0.22
Consensus pattern (22 bp):
CATGCCTATTCGGCCACACCCA
Found at i:31308 original size:9 final size:9
Alignment explanation
Indices: 31294--31319 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
31284 GCCAACTCTA
31294 TTCATTTCT
1 TTCATTTCT
31303 TTCATTTCT
1 TTCATTTCT
31312 TTCATTTC
1 TTCATTTC
31320 ATTAATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (9 bp):
TTCATTTCT
Found at i:33817 original size:19 final size:19
Alignment explanation
Indices: 33762--33822 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
33752 GAGCACTTAA
33762 AAAG-AAGCTCAAATTATG
1 AAAGTAAGCTCAAATTATG
*
33780 AAA-TAAGCTCAAAAATATGG
1 AAAGTAAGCTC-AAATTAT-G
*
33800 AAAGT-ATCTCAAATTATG
1 AAAGTAAGCTCAAATTATG
33818 AAAGT
1 AAAGT
33823 TTACCCTCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 15 0.42
19 12 0.33
20 8 0.22
21 1 0.03
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.25
Consensus pattern (19 bp):
AAAGTAAGCTCAAATTATG
Found at i:35433 original size:9 final size:10
Alignment explanation
Indices: 35418--35474 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
35408 TTTTTCAAAA
*
35418 AAAAAAAACC
1 AAAAAAAGCC
*
35428 AAAAAAAAGGCA
1 -AAAAAAA-GCC
*
35440 AAAAAAAGGC
1 AAAAAAAGCC
*
35450 AAAAAAA-CA
1 AAAAAAAGCC
35459 AAAAAAAGCC
1 AAAAAAAGCC
35469 AAAAAA
1 AAAAAA
35475 TCCAAAAGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 7 0.19
10 15 0.41
11 14 0.38
12 1 0.03
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCC
Found at i:35433 original size:11 final size:11
Alignment explanation
Indices: 35417--35474 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
35407 TTTTTTCAAA
*
35417 AAAAAAAAACC
1 AAAAAAAAGCC
*
35428 AAAAAAAAGGC
1 AAAAAAAAGCC
*
35439 AAAAAAAAGGC
1 AAAAAAAAGCC
35450 -AAAAAAA--C
1 AAAAAAAAGCC
35458 AAAAAAAAGCC
1 AAAAAAAAGCC
35469 AAAAAA
1 AAAAAA
35475 TCCAAAAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
8 1 0.02
9 7 0.17
10 7 0.17
11 27 0.64
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGCC
Found at i:35444 original size:19 final size:20
Alignment explanation
Indices: 35417--35481 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 20
35407 TTTTTTCAAA
* *
35417 AAAAAAAAACCAAAAAAAAGGC
1 AAAAAAAAGCCAAAAAATA--C
*
35439 AAAAAAAAGGCAAAAAA-AC
1 AAAAAAAAGCCAAAAAATAC
*
35458 AAAAAAAAGCCAAAAAATCC
1 AAAAAAAAGCCAAAAAATAC
35478 AAAA
1 AAAA
35482 GTTCAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 17 0.45
20 5 0.13
21 1 0.03
22 15 0.39
ACGTcount: A:0.77, C:0.14, G:0.08, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGCCAAAAAATAC
Found at i:38987 original size:15 final size:15
Alignment explanation
Indices: 38953--38993 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
38943 TCTCTGATAA
38953 CATTTCTTTCCATTT
1 CATTTCTTTCCATTT
38968 CATTT-TTTCCATTT
1 CATTTCTTTCCATTT
38982 CTATTTCATTTC
1 C-ATTTC-TTTC
38994 TTAATATCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.43
15 9 0.39
17 4 0.17
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (15 bp):
CATTTCTTTCCATTT
Found at i:39472 original size:18 final size:18
Alignment explanation
Indices: 39451--39494 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
39441 ATTTCATTTC
*
39451 CTTATTCTTTCATCTATT
1 CTTATTCCTTCATCTATT
39469 CTTATTCCTTCATCTATT
1 CTTATTCCTTCATCTATT
39487 CTTATTCC
1 CTTATTCC
39495 ACTACCTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (18 bp):
CTTATTCCTTCATCTATT
Found at i:48728 original size:43 final size:46
Alignment explanation
Indices: 48623--48728 Score: 123
Period size: 50 Copynumber: 2.3 Consensus size: 46
48613 AGGATTAGAT
48623 TTATTATTTTATTAGGAATTAAGTTTGAGTTAAAACATTATCTTTAGTTA
1 TTATTATTTTATTAGGAATTAA---TGAGTTAAAACATTA-CTTTAGTTA
48673 TTATTATTTTATTAGGAATT-A-GAGTTAAAACA-TA-TTTAGTT-
1 TTATTATTTTATTAGGAATTAATGAGTTAAAACATTACTTTAGTTA
48714 TGCTATTATTTTATT
1 T--TATTATTTTATT
48729 CATTAGTTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
41 1 0.02
42 7 0.13
43 12 0.22
44 2 0.04
45 11 0.20
49 1 0.02
50 20 0.37
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAATGAGTTAAAACATTACTTTAGTTA
Found at i:56658 original size:19 final size:19
Alignment explanation
Indices: 56621--56676 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
56611 GAAACCCCTT
56621 TGAAAATACATGAATTTTAA
1 TGAAAATACATG-ATTTTAA
56641 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
* *
56660 TGAAAGTACATGCTTTT
1 TGAAAATACATGATTTT
56677 GGCCGAATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 22 0.65
20 12 0.35
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:58831 original size:21 final size:21
Alignment explanation
Indices: 58792--58833 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
58782 AATAGGCATA
* *
58792 TAGTTATTCAGCGAGCCCTTC
1 TAGTTATTCAGCCAACCCTTC
*
58813 TAGTTATTCGGCCAACCCTTC
1 TAGTTATTCAGCCAACCCTTC
58834 AAAATCCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (21 bp):
TAGTTATTCAGCCAACCCTTC
Found at i:66103 original size:25 final size:24
Alignment explanation
Indices: 66040--66104 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 24
66030 CTTTTCTTTT
*
66040 CTTT-ATTTTTTTCTTTTTGAGTG
1 CTTTAATTTTTTTCTTTTGGAGTG
**
66063 CTGAATATTTTCTTTCTTTTGGAGTG
1 CTTTA-ATTTT-TTTCTTTTGGAGTG
66089 CTTTAATTTCTTTTCT
1 CTTTAATTT-TTTTCT
66105 GATTTTTCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
23 2 0.06
25 14 0.42
26 17 0.52
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.63
Consensus pattern (24 bp):
CTTTAATTTTTTTCTTTTGGAGTG
Found at i:67999 original size:25 final size:25
Alignment explanation
Indices: 67967--68022 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
67957 AAAAATCAGA
*
67967 AAAG-AAATTGAAGCACTCCAAAAG
1 AAAGAAAATTGAAGCACTCAAAAAG
**
67991 AAAGAAAATTTTAGCACTCAAAAAG
1 AAAGAAAATTGAAGCACTCAAAAAG
68016 -AAGAAAA
1 AAAGAAAA
68023 AAATAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.59, C:0.12, G:0.14, T:0.14
Consensus pattern (25 bp):
AAAGAAAATTGAAGCACTCAAAAAG
Found at i:77790 original size:24 final size:24
Alignment explanation
Indices: 77714--77797 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
77704 CTTTGGAACG
* * *
77714 TCAAGAGACATAAATATTGGTTCT
1 TCAAAAGACATGACTATTGGTTCT
* ** * *
77738 TCAAAAGACATGTCTCGTGGATCA
1 TCAAAAGACATGACTATTGGTTCT
* *
77762 CCAAAAGTCATGACTATTGGTTCT
1 TCAAAAGACATGACTATTGGTTCT
77786 TCAAAAGACATG
1 TCAAAAGACATG
77798 TTTCTTGAAT
Statistics
Matches: 43, Mismatches: 17, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (24 bp):
TCAAAAGACATGACTATTGGTTCT
Found at i:80898 original size:13 final size:13
Alignment explanation
Indices: 80880--80918 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
80870 AACACCTCTC
80880 ACATACCTTTTCA
1 ACATACCTTTTCA
80893 ACATACCTTTTCA
1 ACATACCTTTTCA
80906 ACATACCTTTTCA
1 ACATACCTTTTCA
80919 TCTTTGGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:86458 original size:19 final size:20
Alignment explanation
Indices: 86436--86485 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
86426 CTTATGAGTG
*
86436 TTTTGATTTCTTT-GCTGGA
1 TTTTGATTTCTTTCGATGGA
86455 TTTTGATTT-TTTCGATGGA
1 TTTTGATTTCTTTCGATGGA
86474 TTTTGATTTCTT
1 TTTTGATTTCTT
86486 CACTTGTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 3 0.11
19 23 0.82
20 2 0.07
ACGTcount: A:0.12, C:0.08, G:0.18, T:0.62
Consensus pattern (20 bp):
TTTTGATTTCTTTCGATGGA
Found at i:93360 original size:10 final size:9
Alignment explanation
Indices: 93301--93364 Score: 53
Period size: 9 Copynumber: 6.8 Consensus size: 9
93291 TCACTAAATT
93301 ATGAAAGAA
1 ATGAAAGAA
93310 ATGTATTAATGAA
1 ATG-A--AA-GAA
93323 AT-AAA-AA
1 ATGAAAGAA
93330 ATGAAAGAA
1 ATGAAAGAA
93339 A-GAAACGAA
1 ATGAAA-GAA
93348 ATGATAAGAA
1 ATGA-AAGAA
93358 ATGAAAG
1 ATGAAAG
93365 GGATAGAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
7 4 0.09
8 7 0.15
9 15 0.33
10 10 0.22
11 3 0.07
12 2 0.04
13 5 0.11
ACGTcount: A:0.62, C:0.02, G:0.19, T:0.17
Consensus pattern (9 bp):
ATGAAAGAA
Found at i:95305 original size:28 final size:28
Alignment explanation
Indices: 95265--95331 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
95255 GCATTCTATG
*
95265 CCACCTATGTGAGTGCCTCATGACCATC
1 CCACCTATGTGAGTGCCTCATGACCAGC
*
95293 CCACCCATGTGAGTGCCTCATGACCAGC
1 CCACCTATGTGAGTGCCTCATGACCAGC
95321 CCACCTATGTG
1 CCACCTATGTG
95332 CCATTCGTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.22
Consensus pattern (28 bp):
CCACCTATGTGAGTGCCTCATGACCAGC
Found at i:96207 original size:18 final size:18
Alignment explanation
Indices: 96186--96220 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
96176 AACAAAAATA
96186 AAAAGA-AATAAGAAAAAC
1 AAAAGAGAA-AAGAAAAAC
96204 AAAAGAGAAAAGAAAAA
1 AAAAGAGAAAAGAAAAA
96221 GAATCCTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (18 bp):
AAAAGAGAAAAGAAAAAC
Found at i:99837 original size:27 final size:28
Alignment explanation
Indices: 99776--99837 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 28
99766 AAAGAAAATC
99776 AGAAAAGAAATTGAAGCACTACAAAAGA
1 AGAAAAGAAATTGAAGCACTACAAAAGA
* *
99804 A-ATAAAGAAATT-CAGCA-TTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTAC-AAAAGA
99831 AGAAAAG
1 AGAAAAG
99838 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
26 2 0.07
27 16 0.55
28 11 0.38
ACGTcount: A:0.61, C:0.10, G:0.16, T:0.13
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTACAAAAGA
Found at i:104218 original size:27 final size:27
Alignment explanation
Indices: 104169--104225 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
104159 GAAAATCAGA
*
104169 AAAGAAATTGAAGCACTCCAAAAGAAAG
1 AAAGAAATTGAAGCACTCAAAAAG-AAG
*
104197 AAAGAAATT-AAGCATTCAAAAAGAAG
1 AAAGAAATTGAAGCACTCAAAAAGAAG
104223 AAA
1 AAA
104226 AACAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 6 0.22
27 12 0.44
28 9 0.33
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.12
Consensus pattern (27 bp):
AAAGAAATTGAAGCACTCAAAAAGAAG
Found at i:104913 original size:120 final size:121
Alignment explanation
Indices: 104699--104940 Score: 441
Period size: 120 Copynumber: 2.0 Consensus size: 121
104689 GAAGACTCAA
*
104699 AGAAGAACCGATGTTAAAGAACAACGACCCCGACTTTATATTGCTTCAATAAGGGATGGTAAATC
1 AGAAGAACCGATGTTAAAGAACAAAGACCCCGACTTTATATTGCTTCAATAAGGGATGGTAAATC
*
104764 GGACTTTGACCCGCTATCTATAAAGAGATAGGAACCATAAGTATCAAGGTGATAGG
66 AGACTTTGACCCGCTATCTATAAAGAGATAGGAACCATAAGTATCAAGGTGATAGG
* *
104820 AGAAGAACCGATGTTAAAGAA-AAATACCCCGACTTTATATTGCTTCGATAAGGGATGGTAAATC
1 AGAAGAACCGATGTTAAAGAACAAAGACCCCGACTTTATATTGCTTCAATAAGGGATGGTAAATC
104884 AGACTTTGACCCGCTATCTATAAAGAGATAGGAACCATAAGTATCAAGGTGATAGG
66 AGACTTTGACCCGCTATCTATAAAGAGATAGGAACCATAAGTATCAAGGTGATAGG
104940 A
1 A
104941 ATGACGCCAC
Statistics
Matches: 117, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
120 96 0.82
121 21 0.18
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.24
Consensus pattern (121 bp):
AGAAGAACCGATGTTAAAGAACAAAGACCCCGACTTTATATTGCTTCAATAAGGGATGGTAAATC
AGACTTTGACCCGCTATCTATAAAGAGATAGGAACCATAAGTATCAAGGTGATAGG
Found at i:108389 original size:18 final size:19
Alignment explanation
Indices: 108354--108390 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
108344 CACGGAATGT
108354 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
108374 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
108391 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:126269 original size:238 final size:240
Alignment explanation
Indices: 125854--126335 Score: 866
Period size: 238 Copynumber: 2.0 Consensus size: 240
125844 GTTAATTAAA
125854 GTCTACTCTAGATATCAAGAAAAAATAGATGGGATATACAAGTGTGACTAATCCAAGACTTGTGC
1 GTCTACTCTAGATATCAAGAAAAAATAGATGGGATATACAAGTGTGACTAATCCAAGACTTGTGC
125919 CTATTCTAGATAAAGGACATAAGGATGTAATCATAAAAGAGTAATCACCAAGATGATATGTCCAA
66 CTATTCTAGATAAAGGACATAAGGATGTAATCATAAAAGAGTAATCACCAAGATGATATGTCCAA
125984 TCATATTTTCTTGTAATTTAGGTGACAATGATATATTGCTAGATGTCACTCA-TGTATGTAATAT
131 TCATATTTTCTTGTAATTTAGGTGACAATGATATATTGCTAGATGTCACTCATTGTATGTAATAT
126048 TAG-ATTGTTATAAT-A-ATTGCTAACGTTACAAGAA-CTACAAG
196 TAGAATTGTTATAATAATATTGCTAACGTTACAAGAACCTACAAG
* * *
126089 GTCTACTCTAGATATCAAGAAACAATAGATGGGATATACAAGTGTGACTATTCCAAGACTTGTTC
1 GTCTACTCTAGATATCAAGAAAAAATAGATGGGATATACAAGTGTGACTAATCCAAGACTTGTGC
126154 CTATTCTAGATATAAAGGACATAAGGATGTAATACATAAAAGAGTAATCACCAAGATGATATGTC
66 CTATTCTAG--ATAAAGGACATAAGGATGTAAT-CATAAAAGAGTAATCACCAAGATGATATGTC
126219 CAATCATATTTTCTTGTAATTTAGGTGACAATGATATATTGCTAGATGTCACTCATTGTATGTAA
128 CAATCATATTTTCTTGTAATTTAGGTGACAATGATATATTGCTAGATGTCACTCATTGTATGTAA
126284 TATTAGAATTGTTATAATAATTATTGCTAACGTTACAAGAACCTACAAG
193 TATTAGAATTGTTATAATAA-TATTGCTAACGTTACAAGAACCTACAAG
126333 GTC
1 GTC
126336 ACACCCTAGG
Statistics
Matches: 235, Mismatches: 3, Indels: 9
0.95 0.01 0.04
Matches are distributed among these distances:
235 71 0.30
237 22 0.09
238 86 0.37
239 15 0.06
240 11 0.05
241 1 0.00
243 19 0.08
244 10 0.04
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (240 bp):
GTCTACTCTAGATATCAAGAAAAAATAGATGGGATATACAAGTGTGACTAATCCAAGACTTGTGC
CTATTCTAGATAAAGGACATAAGGATGTAATCATAAAAGAGTAATCACCAAGATGATATGTCCAA
TCATATTTTCTTGTAATTTAGGTGACAATGATATATTGCTAGATGTCACTCATTGTATGTAATAT
TAGAATTGTTATAATAATATTGCTAACGTTACAAGAACCTACAAG
Found at i:130183 original size:10 final size:10
Alignment explanation
Indices: 130168--130195 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
130158 CTTTAGGACT
130168 TCTCACAAAG
1 TCTCACAAAG
130178 TCTCACAAAG
1 TCTCACAAAG
130188 TCTCACAA
1 TCTCACAA
130196 GTACACTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.21
Consensus pattern (10 bp):
TCTCACAAAG
Found at i:135140 original size:23 final size:23
Alignment explanation
Indices: 135112--135167 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
135102 GGATGAAGAT
135112 GATGGTGTTGATGATGAAATGGA
1 GATGGTGTTGATGATGAAATGGA
135135 GATGGTGTTGATGATGAAATGGA
1 GATGGTGTTGATGATGAAATGGA
135158 GATGGTGTTG
1 GATGGTGTTG
135168 TTGTTGTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.41, T:0.32
Consensus pattern (23 bp):
GATGGTGTTGATGATGAAATGGA
Found at i:147361 original size:5 final size:5
Alignment explanation
Indices: 147351--147387 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
147341 TCTCTAATCC
147351 TTCAT TTCATT TTCAT TTCAT TTC-T TTCA- TTCAT TTC
1 TTCAT TTCA-T TTCAT TTCAT TTCAT TTCAT TTCAT TTC
147388 TTTTTCCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.28
5 16 0.55
6 5 0.17
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (5 bp):
TTCAT
Found at i:149385 original size:53 final size:50
Alignment explanation
Indices: 149287--149389 Score: 134
Period size: 53 Copynumber: 2.0 Consensus size: 50
149277 TAAATACCAC
* * * *
149287 TTGATGTAAGGTACTCGTACCTTCAATTGATTGTGGATCTAGGAAGGAAG
1 TTGATGTAAGGTAATCGTACCTACAATTGATTCTAGATCTAGGAAGGAAG
*
149337 TTGATGTAAGGTAATTGTACCTCAACAAATTGATTCTAGATCTAGGAAGGAAG
1 TTGATGTAAGGTAATCGTACCT--AC-AATTGATTCTAGATCTAGGAAGGAAG
149390 CAAACAACCT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
50 20 0.44
52 1 0.02
53 24 0.53
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (50 bp):
TTGATGTAAGGTAATCGTACCTACAATTGATTCTAGATCTAGGAAGGAAG
Found at i:161405 original size:29 final size:29
Alignment explanation
Indices: 161346--161406 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
161336 TCCTATTAGG
* *
161346 GTATGCATGAATTTCTTTGAATCCTTTAA
1 GTATGCATGAATTTCTTTGAATCCATCAA
161375 GTATGCATGAATTTCTTTGAATCCATCAA
1 GTATGCATGAATTTCTTTGAATCCATCAA
161404 GTA
1 GTA
161407 GGTAATCACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (29 bp):
GTATGCATGAATTTCTTTGAATCCATCAA
Found at i:165401 original size:17 final size:17
Alignment explanation
Indices: 165369--165418 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
165359 TACAGTCATC
165369 TCTA-TCATTTCTTTATT
1 TCTATTCATTTC-TTATT
165386 TCTATTCATTTCTTATCT
1 TCTATTCATTTCTTAT-T
165404 T-TATT-ATTTCTTATT
1 TCTATTCATTTCTTATT
165419 CTTCCTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.03
16 9 0.29
17 12 0.39
18 9 0.29
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (17 bp):
TCTATTCATTTCTTATT
Found at i:165737 original size:17 final size:19
Alignment explanation
Indices: 165705--165749 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
165695 TACAGTCATC
165705 TCTA-TCATTTCTTTAT-T
1 TCTATTCATTTCTTTATCT
165722 TCTATTCATTTC-TTATCT
1 TCTATTCATTTCTTTATCT
165740 T-TATT-ATTTC
1 TCTATTCATTTC
165750 ACTTATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 12 0.46
18 9 0.35
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (19 bp):
TCTATTCATTTCTTTATCT
Found at i:165921 original size:341 final size:336
Alignment explanation
Indices: 165288--165965 Score: 1302
Period size: 341 Copynumber: 2.0 Consensus size: 336
165278 ATACAACATC
165288 ACCACCATTGCCATTTCATCATCATCCATCATTAACATCCTTTATCAAGACCATCATCAATTCCA
1 ACCACCATTGCCATTTCATCATCATCCATCATTAACATCCTTTATCAAGACCATCATCAATTCCA
165353 TAATTCTACAGTCATCTCTATCATTTCTTTATTTCTATTCATTTCTTATCTTTATTATTTCTTAT
66 TAATTCTACAGTCATCTCTATCATTTCTTTATTTCTATTCATTTCTTATCTTTATTATTTCTTAT
165418 TCTTCCTTTATTAATCATATTCTTTTTCTTATCTTGTTAGCCAAGCTTATAATTCAAGGGCATCA
131 TCTTCCTTTATTAATCATATTCTTTTTCTTATCTTGTTAGCCAAGCTTATAATTCAAGGGCATCA
165483 GTACTTGTTAATCCTAGATCGGTATACAATAAGGCTATCTACTCCCTTCCACCAAAGCGTGTAGA
196 GTACTTGTTAATCCTAGATCGGTATACAATAAGGCTATCTACTCCCTTCCACCAAAGCGTGTAGA
*
165548 TCACCTTACATCAAGCGATAATCAGAGCATAGTTGGATTGACAACAAAAGTTTCATTGGCGTGCA
261 TCACCTTACATCAAGCGATAATCAGAGCATAGTTGGATTGACAACAAAAGTGTCATTGGCGTGCA
165613 AAACAAAAACA
326 AAACAAAAACA
165624 ACCACCATTGCCATTTCATCATCATCCATCATTAACATCCTTTATCAAGACCATCATCAATTCCA
1 ACCACCATTGCCATTTCATCATCATCCATCATTAACATCCTTTATCAAGACCATCATCAATTCCA
165689 TAATTCTACAGTCATCTCTATCATTTCTTTATTTCTATTCATTTCTTATCTTTATTATTTCACTT
66 TAATTCTACAGTCATCTCTATCATTTCTTTATTTCTATTCATTTCTTATCTTTATTATTT--CTT
165754 ATTCTTCCTTTATTAATCATATTCTTTTTCTTATCTTTGTTGTAGCCAAGCTTATAATTCAAGGG
129 ATTCTTCCTTTATTAATCATATTCTTTTTCTTATC-TTG-T-TAGCCAAGCTTATAATTCAAGGG
165819 CATCAGTACTTGTTAATCCTAGATCGGTATACAATAAGGCTATCTACTCCCTTCCACCAAAGCGT
191 CATCAGTACTTGTTAATCCTAGATCGGTATACAATAAGGCTATCTACTCCCTTCCACCAAAGCGT
165884 GTAGATCACCTTACATCAAGCGATAATCAGAGCATAGTTGGATTGACAACAAAAGTGTCATTGGC
256 GTAGATCACCTTACATCAAGCGATAATCAGAGCATAGTTGGATTGACAACAAAAGTGTCATTGGC
165949 GTGCAAAACAAAAACA
321 GTGCAAAACAAAAACA
165965 A
1 A
165966 GTTCAAAAGA
Statistics
Matches: 336, Mismatches: 1, Indels: 5
0.98 0.00 0.01
Matches are distributed among these distances:
336 125 0.37
338 38 0.11
339 3 0.01
340 1 0.00
341 169 0.50
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (336 bp):
ACCACCATTGCCATTTCATCATCATCCATCATTAACATCCTTTATCAAGACCATCATCAATTCCA
TAATTCTACAGTCATCTCTATCATTTCTTTATTTCTATTCATTTCTTATCTTTATTATTTCTTAT
TCTTCCTTTATTAATCATATTCTTTTTCTTATCTTGTTAGCCAAGCTTATAATTCAAGGGCATCA
GTACTTGTTAATCCTAGATCGGTATACAATAAGGCTATCTACTCCCTTCCACCAAAGCGTGTAGA
TCACCTTACATCAAGCGATAATCAGAGCATAGTTGGATTGACAACAAAAGTGTCATTGGCGTGCA
AAACAAAAACA
Found at i:166017 original size:5 final size:5
Alignment explanation
Indices: 166007--166041 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
165997 TTGGAGTTCA
*
166007 AAAAG AAAAG AAAAG AAAAG AAAAA AAGAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AAAA
166042 TTCAGAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:166035 original size:8 final size:8
Alignment explanation
Indices: 166006--166079 Score: 51
Period size: 8 Copynumber: 9.2 Consensus size: 8
165996 ATTGGAGTTC
166006 AAAAAGAA
1 AAAAAGAA
*
166014 AAGAA-AA
1 AAAAAGAA
*
166021 GAAAAGAA
1 AAAAAGAA
166029 AAAAAGAA
1 AAAAAGAA
***
166037 GAAAATTCA
1 -AAAAAGAA
* *
166046 GAAAGGAA
1 AAAAAGAA
* *
166054 GAAAAGAT
1 AAAAAGAA
166062 AAAAAGAA
1 AAAAAGAA
166070 AAAAAGAA
1 AAAAAGAA
166078 AA
1 AA
166080 GAAATTCAAA
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
7 5 0.10
8 39 0.80
9 5 0.10
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (8 bp):
AAAAAGAA
Found at i:168962 original size:22 final size:22
Alignment explanation
Indices: 168931--168981 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
168921 GAGGTACCTT
*
168931 TTCACAAGGAGCTGCCATAATA
1 TTCACCAGGAGCTGCCATAATA
168953 TTCACCAGGAGCTGCCATAATA
1 TTCACCAGGAGCTGCCATAATA
168975 TTCACCA
1 TTCACCA
168982 TGCTACAAGT
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:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (22 bp):
TTCACCAGGAGCTGCCATAATA
Found at i:173193 original size:24 final size:24
Alignment explanation
Indices: 173144--173227 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
173134 TGTAATGAAC
*
173144 TTGGAGCTTCAA-TGATCATAACTT
1 TTGGAACTTCAAGTGA-CATAACTT
*
173168 TTGGCACTTCAAGTGACATATA-TT
1 TTGGAACTTCAAGTGACATA-ACTT
* * *
173192 TTTGAACTTCAAGTGGCATAACTG
1 TTGGAACTTCAAGTGACATAACTT
*
173216 TTGGAACGTCAA
1 TTGGAACTTCAA
173228 AGGACATGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
23 1 0.02
24 44 0.90
25 4 0.08
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (24 bp):
TTGGAACTTCAAGTGACATAACTT
Found at i:174612 original size:18 final size:19
Alignment explanation
Indices: 174586--174623 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
174576 GATGTAGAAG
*
174586 TCTTTTTTC-TTTTGTTTT
1 TCTTCTTTCTTTTTGTTTT
174604 TCTTCTTTCTTTTTGTTTT
1 TCTTCTTTCTTTTTGTTTT
174623 T
1 T
174624 GTTGTAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (19 bp):
TCTTCTTTCTTTTTGTTTT
Found at i:180873 original size:71 final size:71
Alignment explanation
Indices: 180744--180882 Score: 167
Period size: 71 Copynumber: 2.0 Consensus size: 71
180734 TTTGTGAGTG
* * * * **
180744 GTTTGTGAGTTGTTTATGTCTTCCAAGTGCTCCACCAAGTTGTCCCAACATTTTTCATGCTCCAA
1 GTTTGTGAGTTGTATATGTCTTCCAAATGCTCCACCAAGCTATCCCAACATTAGTCATGCTCCAA
180809 TGTGTT
66 TGTGTT
*
180815 GTTTGTGAGTTGTATATGTC-TCCTAAATGCTCCACCAAGCTAT-CCAA-ATGTGAGTCATGGTC
1 GTTTGTGAGTTGTATATGTCTTCC-AAATGCTCCACCAAGCTATCCCAACAT-T-AGTCATGCTC
180877 CAATGT
63 CAATGT
180883 ACCTTCTCAC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
69 2 0.03
70 8 0.14
71 48 0.83
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (71 bp):
GTTTGTGAGTTGTATATGTCTTCCAAATGCTCCACCAAGCTATCCCAACATTAGTCATGCTCCAA
TGTGTT
Found at i:198923 original size:27 final size:26
Alignment explanation
Indices: 198893--198955 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
198883 CAATGTAACT
*
198893 CTTTTTCTCTTTTTTTTCAAAAATATC
1 CTTTTTCTCTTCTTTTTCAAAAA-ATC
* * *
198920 CTTTTTCCCCTCTTTTTCAAAAAATT
1 CTTTTTCTCTTCTTTTTCAAAAAATC
198946 CTTTTTCTCT
1 CTTTTTCTCT
198956 GCTCTCAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (26 bp):
CTTTTTCTCTTCTTTTTCAAAAAATC
Found at i:200030 original size:27 final size:26
Alignment explanation
Indices: 200000--200062 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
199990 CAATGTAACT
*
200000 CTTTTTCTCTTTTTTTTCAAAAATATC
1 CTTTTTCTCTTCTTTTTCAAAAA-ATC
* * *
200027 CTTTTTCCCCTCTTTTTCAAAAAATT
1 CTTTTTCTCTTCTTTTTCAAAAAATC
200053 CTTTTTCTCT
1 CTTTTTCTCT
200063 GCTCTCAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (26 bp):
CTTTTTCTCTTCTTTTTCAAAAAATC
Found at i:201138 original size:27 final size:26
Alignment explanation
Indices: 201108--201170 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
201098 CAATGTAACT
*
201108 CTTTTTCTCTTTTTTTTCAAAAATATC
1 CTTTTTCTCTTCTTTTTCAAAAA-ATC
* * *
201135 CTTTTTCCCCTCTTTTTCAAAAAATT
1 CTTTTTCTCTTCTTTTTCAAAAAATC
201161 CTTTTTCTCT
1 CTTTTTCTCT
201171 GCTCTCAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (26 bp):
CTTTTTCTCTTCTTTTTCAAAAAATC
Found at i:205770 original size:27 final size:24
Alignment explanation
Indices: 205735--205813 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 24
205725 TTTTTTAATT
205735 TCTTTTTCAATATAACTCTTTTTCTC
1 TCTTTTTCAA-A-AACTCTTTTTCTC
* *
205761 TTTTTCTTCAAAAATCTCCTTTTTCCC
1 TCTTT-TTCAAAAA-CT-CTTTTTCTC
*
205788 TCTTTTTCAAAAAATTCTTTTTCTC
1 TCTTTTTC-AAAAACTCTTTTTCTC
205813 T
1 T
205814 GCTCTCAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
25 11 0.25
26 11 0.25
27 22 0.50
ACGTcount: A:0.20, C:0.24, G:0.00, T:0.56
Consensus pattern (24 bp):
TCTTTTTCAAAAACTCTTTTTCTC
Found at i:208054 original size:27 final size:26
Alignment explanation
Indices: 208024--208086 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
208014 CAATGTAACT
*
208024 CTTTTTCTCTTTTTTTTCAAAAATATC
1 CTTTTTCTCTTCTTTTTCAAAAA-ATC
* * *
208051 CTTTTTCCCCTCTTTTTCAAAAAATT
1 CTTTTTCTCTTCTTTTTCAAAAAATC
208077 CTTTTTCTCT
1 CTTTTTCTCT
208087 GCTCTCAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (26 bp):
CTTTTTCTCTTCTTTTTCAAAAAATC
Found at i:218563 original size:3 final size:3
Alignment explanation
Indices: 218555--218584 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
218545 TTTGGTATTT
218555 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
218585 CACGTTGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:219539 original size:71 final size:71
Alignment explanation
Indices: 219450--219588 Score: 197
Period size: 71 Copynumber: 2.0 Consensus size: 71
219440 TTTGTGAGTG
* * ** * * * *
219450 GTTTGTGAGTTGTCTATGTCTTCCAAGTTCTCCACCAAGTTGTCCCAACGTGTGTCATTCTCCAA
1 GTTTGTGAGATGTATATGTCCCCCAAATGCTCCACCAAGTTGTCCCAACGTGAGTCATGCTCCAA
219515 TGTGTT
66 TGTGTT
*
219521 GTTTGTGAGATGTATATGTCCCCCAAATGCTCCACCAAGTTGTCCCAACGTGAGTCATGGTCCAA
1 GTTTGTGAGATGTATATGTCCCCCAAATGCTCCACCAAGTTGTCCCAACGTGAGTCATGCTCCAA
219586 TGT
66 TGT
219589 ACCTTCTTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (71 bp):
GTTTGTGAGATGTATATGTCCCCCAAATGCTCCACCAAGTTGTCCCAACGTGAGTCATGCTCCAA
TGTGTT
Found at i:228847 original size:23 final size:24
Alignment explanation
Indices: 228775--228852 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 24
228765 TGGTTGCAAC
228775 AAAGATAAGAAATGAATATGATTAAT
1 AAAGATAAGAAATGAAT-TGA-TAAT
* * *
228801 AAA-AGAA-AAATAAATGGAATAAT
1 AAAGATAAGAAATGAATTG-ATAAT
228824 AAAGATAAGAAATGAATTGA-AAT
1 AAAGATAAGAAATGAATTGATAAT
228847 AAAGAT
1 AAAGAT
228853 GGAATAAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
23 17 0.40
24 12 0.28
25 11 0.26
26 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (24 bp):
AAAGATAAGAAATGAATTGATAAT
Found at i:231306 original size:24 final size:24
Alignment explanation
Indices: 231260--231314 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
231250 TTGTGAATCA
*
231260 CCAAAAGTCATAGCTATTGGTTTT
1 CCAAAAGTCACAGCTATTGGTTTT
* * * *
231284 TCAAAAGTCACATCTTTTTGTTTT
1 CCAAAAGTCACAGCTATTGGTTTT
231308 CCAAAAG
1 CCAAAAG
231315 CCATTATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (24 bp):
CCAAAAGTCACAGCTATTGGTTTT
Found at i:232629 original size:17 final size:17
Alignment explanation
Indices: 232599--232631 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
232589 CTTTTTGAAT
232599 TTCTTCTTTTTCTTTTC
1 TTCTTCTTTTTCTTTTC
232616 TTCTT-TTTTGTCTTTT
1 TTCTTCTTTT-TCTTTT
232632 ATTTGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
TTCTTCTTTTTCTTTTC
Found at i:240071 original size:24 final size:24
Alignment explanation
Indices: 240043--240098 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 24
240033 GCCCATTCCA
**
240043 CTCAATGTTTGCAAAGCATAAATC
1 CTCAATGTCAGCAAAGCATAAATC
240067 CTCAAGAATGTCAGCAAAGCATAAATC
1 CTC---AATGTCAGCAAAGCATAAATC
240094 CTCAA
1 CTCAA
240099 GAAAGTCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
24 5 0.19
27 22 0.81
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (24 bp):
CTCAATGTCAGCAAAGCATAAATC
Found at i:240083 original size:27 final size:27
Alignment explanation
Indices: 240053--240109 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
240043 CTCAATGTTT
*
240053 GCAAAGCATAAATCCTCAAGAATGTCA
1 GCAAAGCATAAATCCTCAAGAAAGTCA
240080 GCAAAGCATAAATCCTCAAGAAAGTCA
1 GCAAAGCATAAATCCTCAAGAAAGTCA
240107 GCA
1 GCA
240110 TAAGTGTGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.16
Consensus pattern (27 bp):
GCAAAGCATAAATCCTCAAGAAAGTCA
Found at i:249475 original size:22 final size:22
Alignment explanation
Indices: 249448--249496 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
249438 TGAATGGATG
249448 AACTTAAAAACCTTTGAATGAA
1 AACTTAAAAACCTTTGAATGAA
*
249470 AACTTAAAAGCCTTTGAATGAA
1 AACTTAAAAACCTTTGAATGAA
249492 AACTT
1 AACTT
249497 GAAACTTCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (22 bp):
AACTTAAAAACCTTTGAATGAA
Found at i:257121 original size:15 final size:14
Alignment explanation
Indices: 257101--257130 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
257091 TGTTCTTGTC
257101 TCCTCAAAACGTTCT
1 TCCTCAAAAC-TTCT
257116 TCCTCAAAACTTCT
1 TCCTCAAAACTTCT
257130 T
1 T
257131 TTTATGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.27, C:0.33, G:0.03, T:0.37
Consensus pattern (14 bp):
TCCTCAAAACTTCT
Found at i:261334 original size:19 final size:20
Alignment explanation
Indices: 261287--261337 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
261277 GAAACCCCTT
**
261287 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
261307 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
261326 TGAAGATACATG
1 TGAAAATACATG
261338 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:265539 original size:28 final size:28
Alignment explanation
Indices: 265507--265566 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
265497 TTTAAATCAT
*
265507 CTAGTTCGCTTAGGCTTCGTTAATTAAA
1 CTAGTTCACTTAGGCTTCGTTAATTAAA
*
265535 CTAGTTCATTTAGGCTTCGTTAATTAAA
1 CTAGTTCACTTAGGCTTCGTTAATTAAA
265563 CTAG
1 CTAG
265567 GCCATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (28 bp):
CTAGTTCACTTAGGCTTCGTTAATTAAA
Found at i:265572 original size:28 final size:28
Alignment explanation
Indices: 265516--265574 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
265506 TCTAGTTCGC
**
265516 TTAGGCTTCGTTAATTAAACTAGTTCAT
1 TTAGGCTTCGTTAATTAAACTAGGCCAT
265544 TTAGGCTTCGTTAATTAAACTAGGCCAT
1 TTAGGCTTCGTTAATTAAACTAGGCCAT
265572 TTA
1 TTA
265575 TTAAATTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (28 bp):
TTAGGCTTCGTTAATTAAACTAGGCCAT
Found at i:269972 original size:21 final size:21
Alignment explanation
Indices: 269926--269974 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
269916 CCGGGTTAGT
* *
269926 AAAAAAATCAAAAAAATAAAT
1 AAAAAAATCAAAAAAAGAAAG
*
269947 TAAAAAAT-AAAAGAAAGAAAG
1 AAAAAAATCAAAA-AAAGAAAG
269968 AAAAAAA
1 AAAAAAA
269975 AGTTTAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.82, C:0.02, G:0.06, T:0.10
Consensus pattern (21 bp):
AAAAAAATCAAAAAAAGAAAG
Found at i:283563 original size:19 final size:20
Alignment explanation
Indices: 283525--283575 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
283515 GAAACCCCTT
283525 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
283545 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
283564 TGAAGATACATG
1 TGAAAATACATG
283576 CTCTTAGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:298287 original size:90 final size:90
Alignment explanation
Indices: 298122--298299 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
298112 TAATCCCGAA
* * * * *
298122 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTAAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
298187 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGGAACTTGGATATAAAAGGAT
298212 TATTAAATTCCAATTAATTAAATATAGATTAAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTAAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
298277 TAGGGGAACTTGGTTATAAAAGG
66 TAGGGGAACTTGGATATAAAAGG
298300 GTGCGTTAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTAAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGGAACTTGGATATAAAAGGAT
Found at i:305041 original size:90 final size:90
Alignment explanation
Indices: 304878--305055 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
304868 TAATCCTGAA
* * * * *
304878 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
304943 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
304968 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
305033 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
305056 GTGCGTTAGG
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:311760 original size:90 final size:90
Alignment explanation
Indices: 311653--311816 Score: 251
Period size: 90 Copynumber: 1.8 Consensus size: 90
311643 TAATTTTAAT
* * *
311653 TAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCAC-GATATGAT-TAGTGTAACTTG
1 TAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACC-CTAATATG-TCTAGGGTAACTTG
311716 GATATAAAAGGATTATTAAATTCCAAA
64 GATATAAAAGGATTATTAAATTCCAAA
* *
311743 TAATTAAATATATATTTAATTAATTTGAAATAATAAAAACCCTAATATGTCTAGGGTAACTTGGC
1 TAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGTCTAGGGTAACTTGGA
311808 TATAAAAGG
66 TATAAAAGG
311817 GAGTGTTAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
89 2 0.03
90 65 0.97
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (90 bp):
TAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGTCTAGGGTAACTTGGA
TATAAAAGGATTATTAAATTCCAAA
Found at i:314634 original size:26 final size:26
Alignment explanation
Indices: 314591--314658 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
314581 CCCTAGAACA
* * **
314591 CCCATGTGCTTTGTATATGATTAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
314617 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
314643 CCCATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
314659 GTGGGTTCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.18, C:0.32, G:0.19, T:0.31
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:314730 original size:23 final size:23
Alignment explanation
Indices: 314697--314741 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
314687 AGCTCTCTCC
*
314697 CTATTCGGCCAAGCATCATTTCA
1 CTATTCAGCCAAGCATCATTTCA
* *
314720 CTATTCAGCCAAGGATTATTTC
1 CTATTCAGCCAAGCATCATTTC
314742 CCTCCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (23 bp):
CTATTCAGCCAAGCATCATTTCA
Found at i:315490 original size:26 final size:27
Alignment explanation
Indices: 315455--315505 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
315445 AACAAAGTGA
315455 AGCACTC-AAAAGAAAGAAAA-AAAACC
1 AGCACTCAAAAAG-AAGAAAAGAAAACC
315481 AGCACTCAAAAAGAAGAAAAGAAAA
1 AGCACTCAAAAAGAAGAAAAGAAAA
315506 GAAAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.67, C:0.16, G:0.14, T:0.04
Consensus pattern (27 bp):
AGCACTCAAAAAGAAGAAAAGAAAACC
Found at i:316770 original size:24 final size:21
Alignment explanation
Indices: 316736--316778 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
316726 TCCACAAGAT
*
316736 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
316758 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
316779 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:318518 original size:26 final size:26
Alignment explanation
Indices: 318479--318546 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
318469 CCCTAGAACA
* * *
318479 CCCATATGCTTTGCATATGATCAACC
1 CCCATGTGCCTTGCATATGACCAACC
*
318505 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAACC
318531 CCCATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
318547 GTGGGTTCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAACC
Found at i:319347 original size:19 final size:20
Alignment explanation
Indices: 319309--319360 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
319299 GAAACTGTTT
*
319309 TGAAAATACATGATTTTTTTTA
1 TGAAAATACATGA--TTTTTAA
319331 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
319350 TGAAGATACAT
1 TGAAAATACAT
319361 ATTCTTGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 15 0.54
22 13 0.46
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:324265 original size:15 final size:15
Alignment explanation
Indices: 324245--324273 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
324235 AAATTCATCC
324245 TTTTCAACTCTCTCA
1 TTTTCAACTCTCTCA
324260 TTTTCAACTCTCTC
1 TTTTCAACTCTCTC
324274 CATGCTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTCAACTCTCTCA
Found at i:325505 original size:2 final size:2
Alignment explanation
Indices: 325498--325526 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
325488 TGGCAGTGAA
325498 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 A
325527 ATGGTGATAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:329390 original size:7 final size:6
Alignment explanation
Indices: 329369--329410 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
329359 TGTAGGAGTC
*
329369 TTTTCT TTTTCT TTTTCT TTTTCT TCTTTCT TGTTGCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT T-TTTCT TTTT
329411 GTTGCAGCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
6 21 0.66
7 11 0.34
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:342337 original size:19 final size:20
Alignment explanation
Indices: 342313--342363 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
342303 CGGCCAAGAG
* *
342313 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
342332 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
342352 CATGTATTTTCA
1 CATGTATTTTCA
342364 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:347573 original size:30 final size:30
Alignment explanation
Indices: 347539--347636 Score: 196
Period size: 30 Copynumber: 3.3 Consensus size: 30
347529 CCATGTTCTT
347539 TAGCTCATTTGCATGTATGCATCTTTTTTC
1 TAGCTCATTTGCATGTATGCATCTTTTTTC
347569 TAGCTCATTTGCATGTATGCATCTTTTTTC
1 TAGCTCATTTGCATGTATGCATCTTTTTTC
347599 TAGCTCATTTGCATGTATGCATCTTTTTTC
1 TAGCTCATTTGCATGTATGCATCTTTTTTC
347629 TAGCTCAT
1 TAGCTCAT
347637 ACATGTTTTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.17, C:0.20, G:0.13, T:0.49
Consensus pattern (30 bp):
TAGCTCATTTGCATGTATGCATCTTTTTTC
Found at i:350004 original size:17 final size:19
Alignment explanation
Indices: 349972--350016 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
349962 CGCAGCCATC
349972 TCTATTC-TTTCTTTAT-T
1 TCTATTCATTTCTTTATCT
349989 TCTATTCATTTC-TTATCT
1 TCTATTCATTTCTTTATCT
350007 T-TATT-ATTTC
1 TCTATTCATTTC
350017 ACTTATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.67
Consensus pattern (19 bp):
TCTATTCATTTCTTTATCT
Found at i:350332 original size:19 final size:18
Alignment explanation
Indices: 350269--350331 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
350259 AATTGGAGTG
*
350269 CAAAAAGAA-AAGAAAAAGA
1 CAAAAAGAAGAA-AAAAA-T
350288 CAAAAAGAAGAAAAAAAT
1 CAAAAAGAAGAAAAAAAT
350306 CAGAAAAGAAGAAAAGAAATT
1 CA-AAAAGAAGAAAA-AAA-T
350327 CAAAA
1 CAAAA
350332 GGTAAAGCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 2 0.05
19 26 0.67
20 8 0.21
21 3 0.08
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.05
Consensus pattern (18 bp):
CAAAAAGAAGAAAAAAAT
Found at i:355467 original size:13 final size:13
Alignment explanation
Indices: 355449--355493 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
355439 CATTGCCATT
*
355449 TCATCATCATCCA
1 TCATCAACATCCA
*
355462 TCATCAACATCCT
1 TCATCAACATCCA
*
355475 TCATCAAGA-CCA
1 TCATCAACATCCA
355487 TCATCAA
1 TCATCAA
355494 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:355547 original size:17 final size:19
Alignment explanation
Indices: 355515--355559 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
355505 CGCAGCCATC
355515 TCTA-TCATTTCTTTAT-T
1 TCTATTCATTTCTTTATCT
355532 TCTATTCATTTC-TTATCT
1 TCTATTCATTTCTTTATCT
355550 T-TATT-ATTTC
1 TCTATTCATTTC
355560 ACTTATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 12 0.46
18 9 0.35
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (19 bp):
TCTATTCATTTCTTTATCT
Found at i:360298 original size:21 final size:21
Alignment explanation
Indices: 360272--360323 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
360262 AAGTCACCTC
*
360272 TTCCTTTTCTATACCTTCATT
1 TTCCTTATCTATACCTTCATT
360293 TTCCTTATCTATACCTTCATT
1 TTCCTTATCTATACCTTCATT
360314 TTCCTTATCT
1 TTCCTTATCT
360324 TCAACCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.15, C:0.29, G:0.00, T:0.56
Consensus pattern (21 bp):
TTCCTTATCTATACCTTCATT
Found at i:363181 original size:47 final size:47
Alignment explanation
Indices: 363109--363202 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
363099 TTGATGCTTA
*
363109 AGTGGAGAAAAACACCTTGCTTTGCTGGTCACGCACATGGGTTGTTT
1 AGTGGAGAAAAACACCTTGCCTTGCTGGTCACGCACATGGGTTGTTT
* * *
363156 AGTGGAGACAAGCATCTTGCCTTGCTGGTCACGCACATGGGTTGTTT
1 AGTGGAGAAAAACACCTTGCCTTGCTGGTCACGCACATGGGTTGTTT
363203 TTGTAGTGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (47 bp):
AGTGGAGAAAAACACCTTGCCTTGCTGGTCACGCACATGGGTTGTTT
Found at i:365704 original size:35 final size:35
Alignment explanation
Indices: 365630--365746 Score: 171
Period size: 35 Copynumber: 3.3 Consensus size: 35
365620 TACTATCTGT
*
365630 TCATCACCATCGTCCATCACCATTTTCATGCCTATA
1 TCATCACCATCTTCCATCACCA-TTTCATGCCTATA
* * *
365666 TCATCACCATCTTCCATCATCATTGCTTGCCTATA
1 TCATCACCATCTTCCATCACCATTTCATGCCTATA
* *
365701 TCATCACCATCTTCTATCACCATTTCGTGCCTATA
1 TCATCACCATCTTCCATCACCATTTCATGCCTATA
365736 TCATCACCATC
1 TCATCACCATC
365747 CCCTTACCAT
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 53 0.73
36 20 0.27
ACGTcount: A:0.24, C:0.36, G:0.05, T:0.35
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTTCATGCCTATA
Found at i:365775 original size:71 final size:70
Alignment explanation
Indices: 365630--365777 Score: 156
Period size: 71 Copynumber: 2.1 Consensus size: 70
365620 TACTATCTGT
* * *
365630 TCATCACCATCGTCCATCACCATTTTCATGCCTATATCATCACCATCTTCCATCATCATTGCTTG
1 TCATCACCATCGTCCATCACCATTTTCATGCCTATATCATCACCATC-TCCATCACCATTGATTA
*
365695 CCTATA
65 CCTAAA
* * * * * *
365701 TCATCACCATCTTCTATCACCA-TTTCGTGCCTATATCATCACCATC-CCCTTACCATTTATTCA
1 TCATCACCATCGTCCATCACCATTTTCATGCCTATATCATCACCATCTCCATCACCATTGATT-A
365764 CCATTAAA
65 CC--TAAA
365772 TCATCA
1 TCATCA
365778 TTCATTCATC
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
68 10 0.16
69 2 0.03
70 23 0.36
71 29 0.45
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (70 bp):
TCATCACCATCGTCCATCACCATTTTCATGCCTATATCATCACCATCTCCATCACCATTGATTAC
CTAAA
Found at i:367593 original size:16 final size:17
Alignment explanation
Indices: 367572--367610 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
367562 ATTGGATCAC
367572 ATCAATTT-CATTCCTT
1 ATCAATTTCCATTCCTT
*
367588 ATCAATTTCCATTTCTT
1 ATCAATTTCCATTCCTT
367605 -TCAATT
1 ATCAATT
367611 GTTATTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (17 bp):
ATCAATTTCCATTCCTT
Found at i:371005 original size:19 final size:20
Alignment explanation
Indices: 370981--371023 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
370971 AGCATTTATC
*
370981 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
371000 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
371020 TTCA
1 TTCA
371024 AATGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:381545 original size:15 final size:14
Alignment explanation
Indices: 381507--381533 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
381497 TTTGCACTTA
381507 TTTTTGTATTTTTC
1 TTTTTGTATTTTTC
381521 TTTTTGTATTTTT
1 TTTTTGTATTTTT
381534 TTTGTTGTTA
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:0.07, C:0.04, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTTGTATTTTTC
Found at i:385949 original size:17 final size:19
Alignment explanation
Indices: 385917--385961 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
385907 AAGAATAATT
385917 GAAAT-AATA-AAGAT-AA
1 GAAATGAATAGAAGATAAA
385933 GAAATGAATAGAA-ATAAA
1 GAAATGAATAGAAGATAAA
385951 GAAATG-ATAGA
1 GAAATGAATAGA
385962 GATGGCTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 11 0.42
18 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (19 bp):
GAAATGAATAGAAGATAAA
Found at i:393726 original size:18 final size:18
Alignment explanation
Indices: 393688--393749 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
393678 GTGCAAAAAG
*
393688 AAAGA-AAAAGACAA-AA
1 AAAGAGAAAAGAAAAGAA
*
393704 GAAGAGAAAA-AAATCAG-A
1 AAAGAGAAAAGAAA--AGAA
393722 AAAGAAGAAAAGAAAAGAA
1 AAAG-AGAAAAGAAAAGAA
393741 AAAGAGAAA
1 AAAGAGAAA
393750 GCAAGCCAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
16 6 0.17
17 4 0.11
18 12 0.33
19 11 0.31
20 3 0.08
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAGAGAAAAGAAAAGAA
Found at i:408659 original size:13 final size:13
Alignment explanation
Indices: 408636--408674 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
408626 AAGTGAAGAA
408636 AAACTAAAGAAAGG
1 AAAC-AAAGAAAGG
408650 AAACAAAGAAAGG
1 AAACAAAGAAAGG
408663 AAACAAAGAAAG
1 AAACAAAGAAAG
408675 CAAAATACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.69, C:0.08, G:0.21, T:0.03
Consensus pattern (13 bp):
AAACAAAGAAAGG
Found at i:418046 original size:30 final size:31
Alignment explanation
Indices: 418007--418066 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
417997 ACATGCTGCC
418007 ATGATATCT-AAATGATATGCAAACATAATAA
1 ATGATATCTAAAAT-ATATGCAAACATAATAA
*
418038 ATGA-ATCTAAAATATATGTAAACATAATA
1 ATGATATCTAAAATATATGCAAACATAATA
418067 TAAAGCTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.30
Consensus pattern (31 bp):
ATGATATCTAAAATATATGCAAACATAATAA
Found at i:419124 original size:24 final size:24
Alignment explanation
Indices: 419091--419174 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
419081 TGTAATGAAC
*
419091 TTGGAGCTTCAA-TGATCATAACTT
1 TTGGAACTTCAAGTGA-CATAACTT
* *
419115 TTGGCACTTCAAGTGACATATCTT
1 TTGGAACTTCAAGTGACATAACTT
* * *
419139 TTTGAACTTCAAGTGGCATAACTG
1 TTGGAACTTCAAGTGACATAACTT
*
419163 TTGGAACGTCAA
1 TTGGAACTTCAA
419175 AGAACATGTC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
24 46 0.94
25 3 0.06
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (24 bp):
TTGGAACTTCAAGTGACATAACTT
Found at i:421533 original size:19 final size:21
Alignment explanation
Indices: 421509--421562 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
421499 TTCGGCCAAG
*
421509 ATCATGTATCTTCA-TT-AAA
1 ATCATGTATTTTCATTTAAAA
421528 ATCATGTATTTTCATTTAAAA
1 ATCATGTATTTTCATTTAAAA
421549 ATCATGTATTTTCA
1 ATCATGTATTTTCA
421563 AAGGGGTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.41
20 2 0.06
21 17 0.53
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
ATCATGTATTTTCATTTAAAA
Found at i:425483 original size:19 final size:21
Alignment explanation
Indices: 425459--425510 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
425449 CGGCCAAGAG
*
425459 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
425478 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
425499 CATGTATTTTCA
1 CATGTATTTTCA
425511 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:429427 original size:19 final size:21
Alignment explanation
Indices: 429403--429454 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
429393 CGGCCAAGAG
*
429403 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
429422 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
429443 CATGTATTTTCA
1 CATGTATTTTCA
429455 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:430459 original size:19 final size:19
Alignment explanation
Indices: 430428--430469 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
430418 ATGGGATAAT
430428 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
430447 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
430466 AATA
1 AATA
430470 AAGAAAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:430926 original size:19 final size:21
Alignment explanation
Indices: 430883--430934 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
430873 GAAACCCCTT
430883 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
430904 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
430923 TGAAGATACATG
1 TGAAAATACATG
430935 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:431870 original size:30 final size:31
Alignment explanation
Indices: 431831--431890 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
431821 ACATGCTGCC
**
431831 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
431862 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
431891 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:432951 original size:24 final size:24
Alignment explanation
Indices: 432918--433001 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
432908 TGTAATGAAC
*
432918 TTGGAGCTTCAA-TGATCATAACTT
1 TTGGAACTTCAAGTGA-CATAACTT
* *
432942 TTGGCACTTCAAGTGACATATCTT
1 TTGGAACTTCAAGTGACATAACTT
* *
432966 TTTGAACTTCAAGTGGA-ATAACTG
1 TTGGAACTTCAAGT-GACATAACTT
*
432990 TTGGAACGTCAA
1 TTGGAACTTCAA
433002 AGGACATGTC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
24 44 0.90
25 5 0.10
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (24 bp):
TTGGAACTTCAAGTGACATAACTT
Found at i:437601 original size:17 final size:17
Alignment explanation
Indices: 437546--437607 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
437536 TTTTCCTTGG
*
437546 CTTTC-TTTTCTCTTTT
1 CTTTCTTTTTGTCTTTT
**
437562 -TCTTCTTTTCTGAATTTT
1 CT-TTCTTTT-TGTCTTTT
437580 C-TTCTTTTTGTCTTTT
1 CTTTCTTTTTGTCTTTT
437596 CTTTCTTTTTGT
1 CTTTCTTTTTGT
437608 ACTCCAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
15 1 0.03
16 10 0.28
17 20 0.56
18 5 0.14
ACGTcount: A:0.03, C:0.19, G:0.05, T:0.73
Consensus pattern (17 bp):
CTTTCTTTTTGTCTTTT
Found at i:437604 original size:25 final size:25
Alignment explanation
Indices: 437546--437604 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
437536 TTTTCCTTGG
*
437546 CTTTCTTTTCTCTTTTTCTTCTTTT
1 CTTTCTTTTCTCTTTTTCGTCTTTT
***
437571 CTGAATTTTCTTCTTTTT-GTCTTTT
1 CTTTCTTTTC-TCTTTTTCGTCTTTT
437596 CTTTCTTTT
1 CTTTCTTTT
437605 TGTACTCCAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.73
Consensus pattern (25 bp):
CTTTCTTTTCTCTTTTTCGTCTTTT
Found at i:440451 original size:10 final size:11
Alignment explanation
Indices: 440436--440465 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
440426 TCTATTCTGA
440436 TTTTTTTTTCT
1 TTTTTTTTTCT
440447 TTTTTTTTTCT
1 TTTTTTTTTCT
440458 TTCTTTTT
1 TT-TTTTT
440466 GCACTCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:440460 original size:15 final size:14
Alignment explanation
Indices: 440436--440465 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
440426 TCTATTCTGA
440436 TTTTTTTTTCTTTT
1 TTTTTTTTTCTTTT
440450 TTTTTTCTTTCTTTT
1 TTTTTT-TTTCTTTT
440465 T
1 T
440466 GCACTCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTCTTTT
Found at i:440752 original size:18 final size:18
Alignment explanation
Indices: 440718--440759 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
440708 AGGGGATAAT
440718 AATATAAGTAATAAAATG
1 AATATAAGTAATAAAATG
*
440736 AATATTAAG-AATGAAATG
1 AATA-TAAGTAATAAAATG
440754 AA-ATAA
1 AATATAA
440760 AGAAACGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 1 0.05
18 14 0.64
19 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (18 bp):
AATATAAGTAATAAAATG
Found at i:441209 original size:19 final size:21
Alignment explanation
Indices: 441166--441217 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
441156 GAAACCCCTT
441166 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
441187 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
441206 TGAAGATACATG
1 TGAAAATACATG
441218 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:444408 original size:149 final size:148
Alignment explanation
Indices: 444211--444504 Score: 498
Period size: 149 Copynumber: 2.0 Consensus size: 148
444201 GTTGTGTTCT
444211 TACTAAGCATTTATTAACTACATAACAAGAATTCTTATCATAAAATGTATTATAAAAGCATATAG
1 TACTAAGCATTTATTAACTACATAACAAGAATTCTTATCATAAAATGTATTATAAAAGCATATAG
*
444276 TATATAACTAATATAAAGTAAATTCAATATAAAGATGTTCAAGAGTACTCCCTTTGTAGGTGAAA
66 TATAGAACTAATATAAAGTAAATTCAATATAAAGATGTTCAAGAGTACTCCCTTTGTAGGTGAAA
444341 ACGTGCTTGCATCATTCA
131 ACGTGCTTGCATCATTCA
* * * * *
444359 TACTAAGTTATTTATTAACTACATAACTAGTATTCTTATCATGAAATGTATTATAATAGCATATA
1 TACTAAG-CATTTATTAACTACATAACAAGAATTCTTATCATAAAATGTATTATAAAAGCATATA
* *
444424 GTATAGAACTAGTATAAAGTAAATTCAGTATAAAGATGTTCAAGAGTACTCCCTTTGTAGGTGAA
65 GTATAGAACTAATATAAAGTAAATTCAATATAAAGATGTTCAAGAGTACTCCCTTTGTAGGTGAA
*
444489 AATGTGCTTGCATCAT
130 AACGTGCTTGCATCAT
444505 CCCCCTTCTT
Statistics
Matches: 136, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
148 7 0.05
149 129 0.95
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (148 bp):
TACTAAGCATTTATTAACTACATAACAAGAATTCTTATCATAAAATGTATTATAAAAGCATATAG
TATAGAACTAATATAAAGTAAATTCAATATAAAGATGTTCAAGAGTACTCCCTTTGTAGGTGAAA
ACGTGCTTGCATCATTCA
Found at i:446145 original size:11 final size:11
Alignment explanation
Indices: 446125--446151 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
446115 AACAAAAAAA
446125 CAAAAAAAAGC
1 CAAAAAAAAGC
446136 CAAAAAAAAGC
1 CAAAAAAAAGC
446147 CAAAA
1 CAAAA
446152 TTTCAAAAAA
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:0.74, C:0.19, G:0.07, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGC
Done.