Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 135 of 143
Found at i:40083300 original size:17 final size:18
Alignment explanation
Indices: 40083278--40083318 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40083268 GTTATTAATT
*
40083278 TTAATTTGA-ATGTCAAA
1 TTAATTTGAGATATCAAA
*
40083295 TTAATTTGAGATATCAAT
1 TTAATTTGAGATATCAAA
40083313 TTAATT
1 TTAATT
40083319 AAATATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (18 bp):
TTAATTTGAGATATCAAA
Found at i:40084319 original size:30 final size:30
Alignment explanation
Indices: 40084283--40084342 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40084273 CGAGTCACAG
40084283 ATAATTTTTTACCATTGGTATAAATATTCT
1 ATAATTTTTTACCATTGGTATAAATATTCT
40084313 ATAATTTTTTACCATTGGTATAAATATTCT
1 ATAATTTTTTACCATTGGTATAAATATTCT
40084343 GTTTCTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (30 bp):
ATAATTTTTTACCATTGGTATAAATATTCT
Found at i:40097865 original size:7 final size:7
Alignment explanation
Indices: 40097853--40097877 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40097843 GGCAGCTTTG
40097853 TTGTTAT
1 TTGTTAT
40097860 TTGTTAT
1 TTGTTAT
40097867 TTGTTAT
1 TTGTTAT
40097874 TTGT
1 TTGT
40097878 CCTCCGCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (7 bp):
TTGTTAT
Found at i:40104452 original size:5 final size:5
Alignment explanation
Indices: 40104436--40104473 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
40104426 TTTCTCAAAA
40104436 TTTCT ATTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TT
1 TTTCT -TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TT
40104474 CTTCATCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:40110880 original size:20 final size:19
Alignment explanation
Indices: 40110857--40110909 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
40110847 AAAAATTTAA
*
40110857 AAAAAATCAAAATAATTTTC
1 AAAAATTCAAAATAA-TTTC
* *
40110877 AAAATTTTAAAATAATTTC
1 AAAAATTCAAAATAATTTC
*
40110896 TAAAATTCAAAATA
1 AAAAATTCAAAATA
40110910 TTTATAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTC
Found at i:40110919 original size:19 final size:20
Alignment explanation
Indices: 40110850--40110921 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
40110840 TCTCAACAAA
* *
40110850 AATTTAAAAAAAATCAAAAT
1 AATTTATAAAAATTCAAAAT
* *
40110870 AATTT-TCAAAATTTTAAAAT
1 AATTTAT-AAAAATTCAAAAT
*
40110890 AATTTCT-AAAATTCAAAAT
1 AATTTATAAAAATTCAAAAT
40110909 -ATTTATAAAAATT
1 AATTTATAAAAATT
40110922 TTGAATTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 5 0.12
19 16 0.38
20 20 0.48
21 1 0.02
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTATAAAAATTCAAAAT
Found at i:40111236 original size:23 final size:23
Alignment explanation
Indices: 40111203--40111247 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40111193 TCACTATTTA
* *
40111203 AAATAATAATAATATTCAATATT
1 AAATAAAAATAATATTAAATATT
*
40111226 AAATAAAAATATTATTAAATAT
1 AAATAAAAATAATATTAAATAT
40111248 GAATTTAGGT
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:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATAAAAATAATATTAAATATT
Found at i:40111378 original size:15 final size:15
Alignment explanation
Indices: 40111358--40111389 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40111348 TAATACATTT
40111358 ATATTTCCTTTTAAA
1 ATATTTCCTTTTAAA
40111373 ATATTTCCTTTTAAA
1 ATATTTCCTTTTAAA
40111388 AT
1 AT
40111390 TTTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTCCTTTTAAA
Found at i:40111790 original size:30 final size:31
Alignment explanation
Indices: 40111730--40111791 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
40111720 AAGTTTTAAG
*
40111730 AAAATTCTTTCCTTCCTAAAAAATAAATATT
1 AAAATTCTTTCCTTCCTAAAAAAGAAATATT
*
40111761 AAAATTCTTTCCTTCCT-CAAAAGAAATATT
1 AAAATTCTTTCCTTCCTAAAAAAGAAATATT
40111791 A
1 A
40111792 TTATTTCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.37
Consensus pattern (31 bp):
AAAATTCTTTCCTTCCTAAAAAAGAAATATT
Found at i:40117899 original size:21 final size:21
Alignment explanation
Indices: 40117873--40117920 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
40117863 TATTGTTAAT
*
40117873 TTTGTTATTATTTTAGAGCCA
1 TTTGTTATTATTTTAGAGACA
40117894 TTTGTTATTATTTTAGAGACA
1 TTTGTTATTATTTTAGAGACA
40117915 TTTGTT
1 TTTGTT
40117921 TGTTAAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.56
Consensus pattern (21 bp):
TTTGTTATTATTTTAGAGACA
Found at i:40119341 original size:58 final size:58
Alignment explanation
Indices: 40119278--40119525 Score: 356
Period size: 58 Copynumber: 4.2 Consensus size: 58
40119268 CCGCAGGTGC
* *
40119278 AAAATGGTGATTTTCGGTGAAATCGGGGTCAAAAATAGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGT
* * *
40119337 -AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGAGGGT
1 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGT
* * * *
40119395 AAAATGGTAATTTTGGTGCAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGT
*
40119453 AAAATAGTAAATTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGT-AATTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGT
40119512 CAAAAT-GTAATTTT
1 -AAAATGGTAATTTT
40119526 TGAAAGCTTG
Statistics
Matches: 170, Mismatches: 15, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
58 104 0.61
59 61 0.36
60 5 0.03
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGT
Found at i:40119350 original size:29 final size:30
Alignment explanation
Indices: 40119318--40119531 Score: 134
Period size: 29 Copynumber: 7.3 Consensus size: 30
40119308 AAAAATAGAA
40119318 TTTTGGAAAGTTCGGGGGT-AAATGGTAAT
1 TTTTGGAAAGTTCGGGGGTAAAATGGTAAT
*
40119347 TTTTGGTGAAA--TCGGGGTTAAAAATGG-AA-
1 TTTT-G-GAAAGTTCGGGGGT-AAAATGGTAAT
* *
40119376 TTTTAGAAAGTTCGAGGGTAAAATGGTAAT
1 TTTTGGAAAGTTCGGGGGTAAAATGGTAAT
* * * *
40119406 TTTGGTGCAA--TCGAGGTTAAAAATGG-AA-
1 TTTTG-GAAAGTTCGGGGGT-AAAATGGTAAT
* *
40119434 TTTTGGAAAGTTTGGGGGTAAAATAGTAAAT
1 TTTTGGAAAGTTCGGGGGTAAAATGGT-AAT
* * *
40119465 TTTGGTGAAA--TCGGGGTTAAAAATAG-AA-
1 TTTTG-GAAAGTTCGGGGGT-AAAATGGTAAT
40119493 TTTTGGAAAGTTCGGGGGTCAAAAT-GTAAT
1 TTTTGGAAAGTTCGGGGGT-AAAATGGTAAT
40119523 TTTT-GAAAG
1 TTTTGGAAAG
40119532 CTTGAGGATC
Statistics
Matches: 144, Mismatches: 20, Indels: 42
0.70 0.10 0.20
Matches are distributed among these distances:
27 11 0.08
28 22 0.15
29 58 0.40
30 25 0.17
31 24 0.17
32 4 0.03
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (30 bp):
TTTTGGAAAGTTCGGGGGTAAAATGGTAAT
Found at i:40119431 original size:30 final size:29
Alignment explanation
Indices: 40119278--40119498 Score: 111
Period size: 29 Copynumber: 7.5 Consensus size: 29
40119268 CCGCAGGTGC
* * *
40119278 AAAATGGTGATTTTCGGTGAAATCGGGGTCA
1 AAAATGG-AATTTT-GGTGAAATCGAGGTTA
* * *
40119309 AAAATAGAATTTT-G-GAAAGTTCGGGGGT-
1 AAAATGGAATTTTGGTGAAA--TCGAGGTTA
*
40119337 -AAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGG-AA-TTTTGGTGAAATCGAGGTTA
* *
40119367 AAAATGGAATTTT--AGAAAGTTCGAGGGT-
1 AAAATGGAATTTTGGTGAAA--TCGAGGTTA
*
40119395 AAAATGGTAATTTTGGTGCAATCGAGGTTA
1 AAAATGG-AATTTTGGTGAAATCGAGGTTA
* * *
40119425 AAAATGGAATTTT-G-GAAAGTTTGGGGGT-
1 AAAATGGAATTTTGGTGAAA--TCGAGGTTA
* *
40119453 AAAATAGTAAATTTTGGTGAAATCGGGGTTA
1 AAAAT-G-GAATTTTGGTGAAATCGAGGTTA
*
40119484 AAAATAGAATTTTGG
1 AAAATGGAATTTTGG
40119499 AAAGTTCGGG
Statistics
Matches: 148, Mismatches: 21, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
27 16 0.11
28 16 0.11
29 60 0.41
30 27 0.18
31 25 0.17
32 4 0.03
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTGGTGAAATCGAGGTTA
Found at i:40121370 original size:23 final size:22
Alignment explanation
Indices: 40121351--40121392 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
40121341 AACAAATTCA
40121351 AATTCAAA-TAAATTTAAAATT
1 AATTCAAACTAAATTTAAAATT
40121372 AATTCAAACTTAAATTTAAAA
1 AATTCAAAC-TAAATTTAAAA
40121393 ATCCCAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTCAAACTAAATTTAAAATT
Found at i:40122977 original size:89 final size:88
Alignment explanation
Indices: 40122822--40123145 Score: 321
Period size: 89 Copynumber: 3.6 Consensus size: 88
40122812 CTCAAGAGGT
* * ** ** * * *
40122822 CCCCAAACTTTTCTAAAATTATATTTTAACCCTTAAACCTTT-TTAAAATCATATTTTAACCTCT
1 CCCCAAACTTTT-TAAAATCACATTTTAACCCCCAAA-CTTTCCCAAAATTACATTTTAACCCCT
40122886 AAACTTTTCCAAAATTACATTTTGA
64 AAACTTTTCCAAAATTACATTTTGA
40122911 CCCCAAAACATTTTTAAAATCACATTTTAACCCCCAAAC-TTCCCAAAATTACATTTTAACCCCT
1 CCCC-AAAC-TTTTTAAAATCACATTTTAACCCCCAAACTTTCCCAAAATTACATTTTAACCCCT
*
40122975 AAACTTTTCCAAAATTACATTTTAA
64 AAACTTTTCCAAAATTACATTTTGA
* ** * * * * *
40123000 CCCCTAACTTTTTCTAATCATATTTTGACCCCTAAACTTTTTCCAAAATTGCATTTTAACCCC-A
1 CCCCAAACTTTTTAAAATCACATTTTAACCCCCAAAC-TTTCCCAAAATTACATTTTAACCCCTA
* * *
40123064 AACTTTTCCAAAATCATATTTTGGC
65 AACTTTTCCAAAATTACATTTT-GA
* ** * * *
40123089 CCCCAAACTTCTCTAAAATCACATTTTAACCCATAAACTTTTCCAAAGTCACATTTT
1 CCCCAAACTT-TTTAAAATCACATTTTAACCCCCAAACTTTCCCAAAATTACATTTT
40123146 GACCTCGAAG
Statistics
Matches: 196, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
87 24 0.12
88 26 0.13
89 97 0.49
90 45 0.23
91 4 0.02
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (88 bp):
CCCCAAACTTTTTAAAATCACATTTTAACCCCCAAACTTTCCCAAAATTACATTTTAACCCCTAA
ACTTTTCCAAAATTACATTTTGA
Found at i:40123141 original size:30 final size:30
Alignment explanation
Indices: 40122822--40123145 Score: 311
Period size: 30 Copynumber: 10.9 Consensus size: 30
40122812 CTCAAGAGGT
* * *
40122822 CCCC-AAACTTTTCTAAAATTATATTTTAA
1 CCCCTAAACTTTTCCAAAATCACATTTTAA
* * *
40122851 CCCTTAAACCTTTT-TAAAATCATATTTTAA
1 CCCCTAAA-CTTTTCCAAAATCACATTTTAA
* * *
40122881 CCTCTAAACTTTTCCAAAATTACATTTTGA
1 CCCCTAAACTTTTCCAAAATCACATTTTAA
* *
40122911 CCCCAAAACATTTT-TAAAATCACATTTTAA
1 CCCCTAAAC-TTTTCCAAAATCACATTTTAA
* * *
40122941 CCCCCAAAC-TTCCCAAAATTACATTTTAA
1 CCCCTAAACTTTTCCAAAATCACATTTTAA
*
40122970 CCCCTAAACTTTTCCAAAATTACATTTTAA
1 CCCCTAAACTTTTCCAAAATCACATTTTAA
* * * *
40123000 CCCCT-AACTTTTTC-TAATCATATTTTGA
1 CCCCTAAACTTTTCCAAAATCACATTTTAA
**
40123028 CCCCTAAACTTTTTCCAAAATTGCATTTTAA
1 CCCCTAAAC-TTTTCCAAAATCACATTTTAA
* **
40123059 CCCC-AAACTTTTCCAAAATCATATTTTGG
1 CCCCTAAACTTTTCCAAAATCACATTTTAA
* * *
40123088 CCCCCAAACTTCTCTAAAATCACATTTTAA
1 CCCCTAAACTTTTCCAAAATCACATTTTAA
* *
40123118 CCCATAAACTTTTCCAAAGTCACATTTT
1 CCCCTAAACTTTTCCAAAATCACATTTT
40123146 GACCTCGAAG
Statistics
Matches: 240, Mismatches: 45, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
28 17 0.07
29 61 0.25
30 140 0.58
31 22 0.09
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (30 bp):
CCCCTAAACTTTTCCAAAATCACATTTTAA
Found at i:40124034 original size:25 final size:24
Alignment explanation
Indices: 40124002--40124052 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
40123992 ATATATTTTT
40124002 TAAAATTTATTTTCAAT-TTATTAG
1 TAAAATTTATTTT-AATGTTATTAG
*
40124026 TAAATATTTATTTTAATGTTTTTAG
1 TAAA-ATTTATTTTAATGTTATTAG
40124051 TA
1 TA
40124053 TTTTTAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (24 bp):
TAAAATTTATTTTAATGTTATTAG
Found at i:40124261 original size:2 final size:2
Alignment explanation
Indices: 40124256--40124298 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
40124246 CAAAAAAATA
40124256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40124298 A
1 A
40124299 AGAGAATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40133635 original size:35 final size:37
Alignment explanation
Indices: 40133581--40133651 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 37
40133571 TAAATCATTT
40133581 AAATTTTATAAATAAATAT-AATTA-AATTAAAATTA
1 AAATTTTATAAATAAATATAAATTATAATTAAAATTA
** * *
40133616 AAATTTTATGTATATATATAAATTATAATTTAAATT
1 AAATTTTATAAATAAATATAAATTATAATTAAAATT
40133652 TCATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 16 0.53
36 5 0.17
37 9 0.30
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (37 bp):
AAATTTTATAAATAAATATAAATTATAATTAAAATTA
Found at i:40133638 original size:25 final size:27
Alignment explanation
Indices: 40133610--40133673 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 27
40133600 AATTAAATTA
*
40133610 AAATTAAAATTT-TATGT-ATATATAT
1 AAATTAAAATTTAAATGTCATATATAT
* *
40133635 AAATTATAATTTAAATTTCATATATAT
1 AAATTAAAATTTAAATGTCATATATAT
40133662 -AATTAAAATTTA
1 AAATTAAAATTTA
40133674 TATATCAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 11 0.33
26 14 0.42
27 8 0.24
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
AAATTAAAATTTAAATGTCATATATAT
Found at i:40133638 original size:31 final size:31
Alignment explanation
Indices: 40133596--40133662 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
40133586 TTATAAATAA
*
40133596 ATATA-AT-TAAATTAAAATTAAAATTTTAT
1 ATATATATATAAATTAAAATTAAAATTTCAT
* * *
40133625 GTATATATATAAATTATAATTTAAATTTCAT
1 ATATATATATAAATTAAAATTAAAATTTCAT
40133656 ATATATA
1 ATATATA
40133663 ATTAAAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 4 0.13
30 2 0.06
31 25 0.81
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
ATATATATATAAATTAAAATTAAAATTTCAT
Found at i:40133676 original size:19 final size:20
Alignment explanation
Indices: 40133639--40133678 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40133629 ATATATAAAT
*
40133639 TATAATTTAAATTTCATATA
1 TATAATTAAAATTTCATATA
40133659 TATAATTAAAATTT-ATATA
1 TATAATTAAAATTTCATATA
40133678 T
1 T
40133679 CAAACTATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAATTAAAATTTCATATA
Found at i:40138946 original size:15 final size:15
Alignment explanation
Indices: 40138926--40138956 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40138916 TTGTCACCCA
*
40138926 TCGTAATCAAATTTG
1 TCGTAATCAAAATTG
40138941 TCGTAATCAAAATTG
1 TCGTAATCAAAATTG
40138956 T
1 T
40138957 TATTAACTTT
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:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (15 bp):
TCGTAATCAAAATTG
Found at i:40140867 original size:32 final size:32
Alignment explanation
Indices: 40140825--40140898 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
40140815 CCTCCTGAAC
*
40140825 TTGTCC-AAAAGTAAC-TAGTTGATACCAAAAT
1 TTGTCCAAAAAGT-ACGTAATTGATACCAAAAT
* *
40140856 TTGTCCAAAAAGTACGTAATTGGTACCTAAAT
1 TTGTCCAAAAAGTACGTAATTGATACCAAAAT
*
40140888 TTATCCAAAAA
1 TTGTCCAAAAA
40140899 ATTTATGCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 8 0.22
32 29 0.78
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (32 bp):
TTGTCCAAAAAGTACGTAATTGATACCAAAAT
Found at i:40140930 original size:19 final size:20
Alignment explanation
Indices: 40140894--40140938 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
40140884 AAATTTATCC
*
40140894 AAAA-AATTTATGCTTTTTTT
1 AAAATAATTTATGC-TTTTTA
40140914 AAAATAATTTATG-TTTTTA
1 AAAATAATTTATGCTTTTTA
40140933 AAAATA
1 AAAATA
40140939 TTTTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 11 0.48
20 4 0.17
21 8 0.35
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (20 bp):
AAAATAATTTATGCTTTTTA
Found at i:40140930 original size:20 final size:20
Alignment explanation
Indices: 40140894--40140931 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40140884 AAATTTATCC
40140894 AAAAAATTTATGCTTTTTTT
1 AAAAAATTTATGCTTTTTTT
40140914 AAAATAATTTATG-TTTTT
1 AAAA-AATTTATGCTTTTT
40140932 AAAAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (20 bp):
AAAAAATTTATGCTTTTTTT
Found at i:40146484 original size:21 final size:20
Alignment explanation
Indices: 40146439--40146486 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
40146429 AAACATTTTA
40146439 TATTTATAATAAATTAAAAT
1 TATTTATAATAAATTAAAAT
*
40146459 T-TTTATACATATAATT-TAAT
1 TATTTATA-ATA-AATTAAAAT
40146479 TATTTATA
1 TATTTATA
40146487 TTATACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 6 0.25
20 8 0.33
21 10 0.42
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTTATAATAAATTAAAAT
Found at i:40149726 original size:25 final size:26
Alignment explanation
Indices: 40149675--40149728 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
40149665 AGTCGAATTA
40149675 AAAAAATATTTTTATGAAATAATTATT
1 AAAAAATATTTTTA-GAAATAATTATT
*
40149702 AAAATATATTTTTA-AATATAA-TATT
1 AAAAAATATTTTTAGAA-ATAATTATT
40149727 AA
1 AA
40149729 TTTAGAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 8 0.32
26 4 0.16
27 13 0.52
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
AAAAAATATTTTTAGAAATAATTATT
Found at i:40151968 original size:2 final size:2
Alignment explanation
Indices: 40151961--40151991 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
40151951 GACTTCATGA
40151961 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40151992 TAAATAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:40154984 original size:16 final size:16
Alignment explanation
Indices: 40154963--40155003 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
40154953 TCCTTCCTTA
40154963 TTTCTTTCTCT-TTTCT
1 TTTCTTT-TCTATTTCT
40154979 TTTCTTTTCTATTTCT
1 TTTCTTTTCTATTTCT
40154995 TTCTCTTTT
1 TT-TCTTTT
40155004 AATCACTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.13
16 14 0.61
17 6 0.26
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTTTTCTATTTCT
Found at i:40154986 original size:10 final size:10
Alignment explanation
Indices: 40154963--40155003 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
40154953 TCCTTCCTTA
40154963 TTTCTTTCTCT
1 TTTCTTT-TCT
40154974 TTTCTTTTCT
1 TTTCTTTTCT
40154984 TTTCTATTTCT
1 TTTCT-TTTCT
40154995 TTCTCTTTT
1 TT-TCTTTT
40155004 AATCACTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.29
11 17 0.61
12 3 0.11
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTCTTTTCT
Found at i:40155001 original size:6 final size:5
Alignment explanation
Indices: 40154963--40155003 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
40154953 TCCTTCCTTA
40154963 TTTCT TTCTCT TTTCT TTTCT TTTCT ATTTCT TTCTCT TTT
1 TTTCT TT-TCT TTTCT TTTCT TTTCT -TTTCT TT-TCT TTT
40155004 AATCACTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 18 0.55
6 15 0.45
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTCT
Found at i:40155542 original size:22 final size:22
Alignment explanation
Indices: 40155511--40155598 Score: 106
Period size: 22 Copynumber: 4.0 Consensus size: 22
40155501 ACCAAGTCAA
*
40155511 ATCGTTGACCGATCGTTGACCG
1 ATCGTTGACCGACCGTTGACCG
* *
40155533 ATTGTTGACCGACCGTTGATCG
1 ATCGTTGACCGACCGTTGACCG
*
40155555 ATCGTTGACCTACCGTTGACCG
1 ATCGTTGACCGACCGTTGACCG
* *
40155577 ACCATTGACCTG-CCGTTGACCG
1 ATCGTTGACC-GACCGTTGACCG
40155599 TTGACAGTTG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.27
Consensus pattern (22 bp):
ATCGTTGACCGACCGTTGACCG
Found at i:40155550 original size:33 final size:33
Alignment explanation
Indices: 40155513--40155586 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
40155503 CAAGTCAAAT
**
40155513 CGTTGACCGATCGTTGACCGATTGTTGACCGAC
1 CGTTGACCGATCGTTGACCGACCGTTGACCGAC
* *
40155546 CGTTGATCGATCGTTGACCTACCGTTGACCGAC
1 CGTTGACCGATCGTTGACCGACCGTTGACCGAC
*
40155579 CATTGACC
1 CGTTGACC
40155587 TGCCGTTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (33 bp):
CGTTGACCGATCGTTGACCGACCGTTGACCGAC
Found at i:40155584 original size:11 final size:11
Alignment explanation
Indices: 40155513--40155598 Score: 93
Period size: 11 Copynumber: 7.8 Consensus size: 11
40155503 CAAGTCAAAT
*
40155513 CGTTGACCGAT
1 CGTTGACCGAC
*
40155524 CGTTGACCGAT
1 CGTTGACCGAC
*
40155535 TGTTGACCGAC
1 CGTTGACCGAC
* *
40155546 CGTTGATCGAT
1 CGTTGACCGAC
*
40155557 CGTTGACCTAC
1 CGTTGACCGAC
40155568 CGTTGACCGAC
1 CGTTGACCGAC
*
40155579 CATTGACCTG-C
1 CGTTGACC-GAC
40155590 CGTTGACCG
1 CGTTGACCG
40155599 TTGACAGTTG
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
10 1 0.02
11 61 0.97
12 1 0.02
ACGTcount: A:0.17, C:0.30, G:0.26, T:0.27
Consensus pattern (11 bp):
CGTTGACCGAC
Found at i:40155622 original size:21 final size:20
Alignment explanation
Indices: 40155595--40155644 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
40155585 CCTGCCGTTG
40155595 ACCGTTGACAGTTGACTGTTA
1 ACCGTTGACAGTTGACT-TTA
* *
40155616 ATCGTTGACTGTTGACTTTA
1 ACCGTTGACAGTTGACTTTA
40155636 ACCGTTGAC
1 ACCGTTGAC
40155645 TTTTTCGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
ACCGTTGACAGTTGACTTTA
Found at i:40158020 original size:41 final size:41
Alignment explanation
Indices: 40157975--40158067 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
40157965 TTTTATTTTA
*
40157975 ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACATTT
1 ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACATTG
* * * *
40158016 ACAAGAATTCTAGTTACCTAATTCTAATAATCTCCACCTTG
1 ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACATTG
40158057 ACAAGAATTCT
1 ACAAGAATTCT
40158068 CTACGAACAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (41 bp):
ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACATTG
Found at i:40158079 original size:17 final size:17
Alignment explanation
Indices: 40158057--40158095 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
40158047 CTCCACCTTG
* *
40158057 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
40158074 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
40158091 ACAAG
1 ACAAG
40158096 TCCTCCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:40172185 original size:37 final size:37
Alignment explanation
Indices: 40172113--40172185 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
40172103 TTTAACAGTG
*
40172113 TTTTTAAAAAATGCTTTTAAAAAATATGGTAAAAAAA
1 TTTTTAAAAAATGCTTTTAAAAAATATGATAAAAAAA
* * * *
40172150 TTTTTAAAAAGTGTTTTTAAAAAATTTGATTAAAAA
1 TTTTTAAAAAATGCTTTTAAAAAATATGATAAAAAA
40172186 TTTAATTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (37 bp):
TTTTTAAAAAATGCTTTTAAAAAATATGATAAAAAAA
Found at i:40172484 original size:14 final size:14
Alignment explanation
Indices: 40172358--40172488 Score: 53
Period size: 14 Copynumber: 9.2 Consensus size: 14
40172348 TGTTAATATT
*
40172358 TTAATATATGAAATA
1 TTAATAT-TTAAATA
40172373 TTAAT-TTTAAATA
1 TTAATATTTAAATA
*
40172386 TTTTCAAGTAATT-AATA
1 --TT-AA-TATTTAAATA
*
40172403 TTAATTATTTAAAAA
1 TTAA-TATTTAAATA
*
40172418 TT--TAATTAAATTA
1 TTAATATTTAAA-TA
* *
40172431 TATAA-A-TTATATT
1 T-TAATATTTAAATA
40172444 TTAAATATTTAAATA
1 TT-AATATTTAAATA
40172459 -TAATCA-TTAAATA
1 TTAAT-ATTTAAATA
*
40172472 TTTATATTTAAATA
1 TTAATATTTAAATA
40172486 TTA
1 TTA
40172489 GCATAATTGT
Statistics
Matches: 87, Mismatches: 13, Indels: 33
0.65 0.10 0.25
Matches are distributed among these distances:
12 8 0.09
13 23 0.26
14 27 0.31
15 20 0.23
16 2 0.02
17 5 0.06
18 2 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (14 bp):
TTAATATTTAAATA
Found at i:40174406 original size:19 final size:20
Alignment explanation
Indices: 40174366--40174406 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40174356 ATCATCAATG
* *
40174366 AAAATTTTAAAATATTATAT
1 AAAATTTAAAAATATTACAT
40174386 AAAATTTAAAAATA-TACAT
1 AAAATTTAAAAATATTACAT
40174405 AA
1 AA
40174407 TTGGCTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATTTAAAAATATTACAT
Found at i:40176598 original size:19 final size:20
Alignment explanation
Indices: 40176558--40176598 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40176548 ATCATCAATG
* *
40176558 AAAATTTTAAAATATTATAT
1 AAAATTTAAAAATATTACAT
40176578 AAAATTTAAAAATA-TACAT
1 AAAATTTAAAAATATTACAT
40176597 AA
1 AA
40176599 TTGGCTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATTTAAAAATATTACAT
Found at i:40177981 original size:19 final size:21
Alignment explanation
Indices: 40177954--40177992 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
40177944 CTACTTATTT
40177954 TTATATCTG-ATA-AATATAA
1 TTATATCTGTATATAATATAA
*
40177973 TTATTTCTGTATATAATATA
1 TTATATCTGTATATAATATA
40177993 TAAACATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (21 bp):
TTATATCTGTATATAATATAA
Found at i:40180672 original size:13 final size:13
Alignment explanation
Indices: 40180642--40180684 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
40180632 TGGAGTTAAA
**
40180642 AAAAAAGAATCAG
1 AAAAAAGAAAAAG
*
40180655 CAAAAAGAAAAAG
1 AAAAAAGAAAAAG
40180668 AAAAAAGAACAAAG
1 AAAAAAGAA-AAAG
40180682 AAA
1 AAA
40180685 GGAAAAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:40180673 original size:14 final size:14
Alignment explanation
Indices: 40180656--40180684 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
40180646 AAGAATCAGC
40180656 AAAAAGAA-AAAGA
1 AAAAAGAACAAAGA
40180669 AAAAAGAACAAAGA
1 AAAAAGAACAAAGA
40180683 AA
1 AA
40180685 GGAAAAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAACAAAGA
Found at i:40190673 original size:28 final size:29
Alignment explanation
Indices: 40190642--40190700 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
40190632 GTTAAATAAA
40190642 ATTATTCAAATA-TTTTTTTAACAATTTT
1 ATTATTCAAATATTTTTTTTAACAATTTT
*
40190670 ATTATTCGAATATTTTTTTTAACAATTTT
1 ATTATTCAAATATTTTTTTTAACAATTTT
40190699 AT
1 AT
40190701 GATAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.58
Consensus pattern (29 bp):
ATTATTCAAATATTTTTTTTAACAATTTT
Found at i:40190710 original size:29 final size:28
Alignment explanation
Indices: 40190649--40190710 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
40190639 AAAATTATTC
* **
40190649 AAATATTTTTTTAACAATTTTATTATTC
1 AAATATTTTTTTAACAATTTTATGATAA
*
40190677 GAATATTTTTTTTAACAATTTTATGATAA
1 AAATA-TTTTTTTAACAATTTTATGATAA
40190706 AAATA
1 AAATA
40190711 AATAGATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (28 bp):
AAATATTTTTTTAACAATTTTATGATAA
Found at i:40191066 original size:16 final size:15
Alignment explanation
Indices: 40191042--40191071 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40191032 AATTTTATCA
40191042 TTTTAAAATTTTAAT
1 TTTTAAAATTTTAAT
40191057 TTTTATAAATTTTAA
1 TTTTA-AAATTTTAA
40191072 AAAATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTAAAATTTTAAT
Found at i:40191120 original size:84 final size:84
Alignment explanation
Indices: 40191010--40191170 Score: 209
Period size: 84 Copynumber: 1.9 Consensus size: 84
40191000 TTAAATTGTA
* * * * *
40191010 ATTTTTATGATAGTAAAAATATAATTTTATCATTTTA-AAATTTTAATTTTTATAAATTTTAAAA
1 ATTTTTAAGAAAGTAAAAATATAATTTTA-C-TTTTATAAATTTAAAATTTTAAAAATTTTAAAA
*
40191074 AAT-TAAATTAAAATTTTATT
64 AATCTAAATGAAAATTTTATT
* * *
40191094 ATTTTTAAGAAAGTCAAAATATAATTTTACTTTTATTAATTTAAAATTTTAAAAATTTTAAAATA
1 ATTTTTAAGAAAGTAAAAATATAATTTTACTTTTATAAATTTAAAATTTTAAAAATTTTAAAAAA
40191159 TCTAAATGAAAA
66 TCTAAATGAAAA
40191171 AAAAAATCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
82 5 0.08
83 26 0.39
84 35 0.53
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (84 bp):
ATTTTTAAGAAAGTAAAAATATAATTTTACTTTTATAAATTTAAAATTTTAAAAATTTTAAAAAA
TCTAAATGAAAATTTTATT
Found at i:40203175 original size:23 final size:23
Alignment explanation
Indices: 40203149--40203192 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
40203139 CAATTACATA
40203149 TAATAAGATTTCAAATTAGATTT
1 TAATAAGATTTCAAATTAGATTT
*
40203172 TAATAAGATTTTAAATTAGAT
1 TAATAAGATTTCAAATTAGAT
40203193 ACTCAGAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
TAATAAGATTTCAAATTAGATTT
Found at i:40203646 original size:3 final size:3
Alignment explanation
Indices: 40203638--40203667 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
40203628 GTGGGGGACT
*
40203638 CTG CTG CTG CTG CTG CTG CTG GTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
40203668 ATGATGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.37, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:40204561 original size:3 final size:3
Alignment explanation
Indices: 40204553--40204589 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
40204543 AATCTTTTCA
40204553 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40204590 TATTATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40211160 original size:17 final size:18
Alignment explanation
Indices: 40211138--40211171 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40211128 TTTTCAGTTG
*
40211138 TAATTAGTT-TAAATTTT
1 TAATTAATTATAAATTTT
40211155 TAATTAATTATAAATTT
1 TAATTAATTATAAATTT
40211172 ATTCTCATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TAATTAATTATAAATTTT
Found at i:40211554 original size:14 final size:15
Alignment explanation
Indices: 40211535--40211569 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
40211525 AAATAATTTT
40211535 TTATCTTAAAA-TAA
1 TTATCTTAAAATTAA
40211549 TTATCTTAAAATTAA
1 TTATCTTAAAATTAA
40211564 TTATCT
1 TTATCT
40211570 AATTACATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATCTTAAAATTAA
Found at i:40225760 original size:21 final size:21
Alignment explanation
Indices: 40225736--40225776 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40225726 AGATTAATTA
*
40225736 TATAAATATATCCAACTTTTC
1 TATAAATATATACAACTTTTC
* *
40225757 TATAGATATATAGAACTTTT
1 TATAAATATATACAACTTTT
40225777 ATCCGTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (21 bp):
TATAAATATATACAACTTTTC
Found at i:40231865 original size:15 final size:15
Alignment explanation
Indices: 40231845--40231874 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40231835 TGAAGAATCG
40231845 AGCTTGGGGTTGAAT
1 AGCTTGGGGTTGAAT
40231860 AGCTTGGGGTTGAAT
1 AGCTTGGGGTTGAAT
40231875 TCGGAAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.40, T:0.33
Consensus pattern (15 bp):
AGCTTGGGGTTGAAT
Found at i:40232942 original size:31 final size:31
Alignment explanation
Indices: 40232907--40232968 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
40232897 TTTCTGATCC
40232907 AATTTAGTA-CTCAAACTTGACACTTTTTTCT
1 AATTTAGTACCT-AAACTTGACACTTTTTTCT
* *
40232938 AATTTGGTACCTAAACTTGACATTTTTTTCT
1 AATTTAGTACCTAAACTTGACACTTTTTTCT
40232969 TAAGTTGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (31 bp):
AATTTAGTACCTAAACTTGACACTTTTTTCT
Found at i:40232985 original size:32 final size:31
Alignment explanation
Indices: 40232914--40232987 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
40232904 TCCAATTTAG
* * *
40232914 TACTCAAACTTGACACTTTTTTCTAATTTGG
1 TACTTAAACTTGACACTTTTTTCTAAGTTGA
* *
40232945 TACCTAAACTTGACATTTTTTTCTTAAGTTGA
1 TACTTAAACTTGACACTTTTTTC-TAAGTTGA
40232977 TACTTAAACTT
1 TACTTAAACTT
40232988 TTTGGGGTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 20 0.56
32 16 0.44
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (31 bp):
TACTTAAACTTGACACTTTTTTCTAAGTTGA
Found at i:40233015 original size:91 final size:92
Alignment explanation
Indices: 40232870--40233042 Score: 233
Period size: 91 Copynumber: 1.9 Consensus size: 92
40232860 AATTTGACAC
* * * *
40232870 TTTTTCTTAATTTGGTACTTAAATTTTTTTCTGATCCAATTTAGTACTCAAACTTGACACTTTTT
1 TTTTTCTTAAGTTGATACTTAAATCTTTTTCGGATCCAATTTAGTACTCAAACTTGACACTTTTT
*
40232935 TCTAATTTGGTACCTAAACTTGACATT
66 CCTAATTTGGTACCTAAACTTGACATT
* * * * *
40232962 TTTTTCTTAAGTTGATACTTAAA-CTTTTTGGGGTCCAATTTGGTAC-CTGAACTTGACTCTTTT
1 TTTTTCTTAAGTTGATACTTAAATCTTTTTCGGATCCAATTTAGTACTC-AAACTTGACACTTTT
40233025 TCCTAATTTGGTACCTAA
65 TCCTAATTTGGTACCTAA
40233043 TTTTTTTAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
90 1 0.01
91 48 0.69
92 21 0.30
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (92 bp):
TTTTTCTTAAGTTGATACTTAAATCTTTTTCGGATCCAATTTAGTACTCAAACTTGACACTTTTT
CCTAATTTGGTACCTAAACTTGACATT
Found at i:40233272 original size:61 final size:59
Alignment explanation
Indices: 40233207--40233353 Score: 160
Period size: 56 Copynumber: 2.5 Consensus size: 59
40233197 AATTGAATCT
* *
40233207 AAAAAAAGCTTAAG-TGCCAAATTAGGAAAAAAA-TGCCAAGTTCAGGTACCAAATTGGGTCC
1 AAAAAAAG-TTAAGATACCAAATTA--AAAAAAAGTGCCAAATTCA-GTACCAAATTGGGTCC
* * * *
40233268 AAAAAAAGTTTAGATACCAAATTAAAAAAAAGTGTCAAATTCAGTACCAAATTAGAT--
1 AAAAAAAGTTAAGATACCAAATTAAAAAAAAGTGCCAAATTCAGTACCAAATTGGGTCC
*
40233325 AAAAAAAATT-AGATACCAAATTAAAAAAA
1 AAAAAAAGTTAAGATACCAAATTAAAAAAA
40233354 TATCAAATTT
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
56 19 0.25
57 9 0.12
59 19 0.25
60 13 0.17
61 17 0.22
ACGTcount: A:0.54, C:0.12, G:0.13, T:0.21
Consensus pattern (59 bp):
AAAAAAAGTTAAGATACCAAATTAAAAAAAAGTGCCAAATTCAGTACCAAATTGGGTCC
Found at i:40233369 original size:55 final size:57
Alignment explanation
Indices: 40233268--40233374 Score: 148
Period size: 55 Copynumber: 1.9 Consensus size: 57
40233258 AATTGGGTCC
* * * *
40233268 AAAAAAAGTTTAGATACCAAATTAAAAAAAAGTGTCAAATTCAGTACCAAATTAGAT
1 AAAAAAAGATTAGATACCAAATTAAAAAAAAGTATCAAATTAAGTACAAAATTAGAT
40233325 AAAAAAA-ATTAGATACCAAATT-AAAAAAA-TATCAAATTTAAGTACAAAAT
1 AAAAAAAGATTAGATACCAAATTAAAAAAAAGTATCAAA-TTAAGTACAAAAT
40233375 ATTATATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
54 6 0.13
55 18 0.40
56 14 0.31
57 7 0.16
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.24
Consensus pattern (57 bp):
AAAAAAAGATTAGATACCAAATTAAAAAAAAGTATCAAATTAAGTACAAAATTAGAT
Found at i:40237229 original size:24 final size:25
Alignment explanation
Indices: 40237187--40237240 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
40237177 ATGAATTTTT
*
40237187 CTTTTAAAAATAATTTAAAAA-ATA
1 CTTTTAAAAATAATATAAAAATATA
40237211 CTTTTAAAAACT-ATATAAAAATATA
1 CTTTTAAAAA-TAATATAAAAATATA
*
40237236 TTTTT
1 CTTTT
40237241 TTAAAACATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.43
Consensus pattern (25 bp):
CTTTTAAAAATAATATAAAAATATA
Found at i:40237663 original size:3 final size:3
Alignment explanation
Indices: 40237655--40237683 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40237645 AAATTGTTAT
40237655 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
40237684 TCGATTCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40239408 original size:19 final size:18
Alignment explanation
Indices: 40239384--40239419 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40239374 CTAATCAATA
40239384 AAAAATATATATATTTGAG
1 AAAAATATATAT-TTTGAG
*
40239403 AAAAATATTTATTTTGA
1 AAAAATATATATTTTGA
40239420 TTAATTACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
AAAAATATATATTTTGAG
Found at i:40240491 original size:58 final size:58
Alignment explanation
Indices: 40240422--40240541 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 58
40240412 AAAAAGAGTT
*
40240422 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTG-GATTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGTG-TTTAAAAATATTTGGGTTTA
* * *
40240480 GTTTATGAGTGTTTTTTAATAATGAAATTATATTTGTGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGTGTTTAAAAATATTTGGGTTTA
40240538 GTTT
1 GTTT
40240542 GTTGATGAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
58 56 0.98
59 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGTGTTTAAAAATATTTGGGTTTA
Found at i:40240555 original size:58 final size:58
Alignment explanation
Indices: 40240446--40240556 Score: 163
Period size: 58 Copynumber: 1.9 Consensus size: 58
40240436 TTTAGGAATA
**
40240446 AAATTATATTTGGATTTAAAAATATTTGGGTTTAGTTTATGAGTGTTTTTTAATAATG
1 AAATTATATTTGGATTTAAAAATATTTGGGTTTAGTTTATGAGTGAGTTTTAATAATG
*
40240504 AAATTATATTTGTG-TTTAAAAATATTTGGGTTTAGTTTGTTGA-TGAGTTTTAA
1 AAATTATATTTG-GATTTAAAAATATTTGGGTTTAGTTT-ATGAGTGAGTTTTAA
40240557 ATATTAGGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
58 44 0.92
59 4 0.08
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (58 bp):
AAATTATATTTGGATTTAAAAATATTTGGGTTTAGTTTATGAGTGAGTTTTAATAATG
Found at i:40240763 original size:35 final size:36
Alignment explanation
Indices: 40240717--40240789 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 36
40240707 TCAAAAATTA
*
40240717 AACTTGATTCG-AACTCGAAATTCGAAATTTTTTTT
1 AACTCGATTCGAAACTCGAAATTCGAAATTTTTTTT
* *
40240752 AACTCGATTCGAATAATTTGAAATTCGAAATTTTTTTT
1 AACTCGATTCG-A-AACTCGAAATTCGAAATTTTTTTT
40240790 GAATTTTTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 10 0.31
38 22 0.69
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (36 bp):
AACTCGATTCGAAACTCGAAATTCGAAATTTTTTTT
Found at i:40249861 original size:2 final size:2
Alignment explanation
Indices: 40249854--40249888 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
40249844 AGGAACAATA
40249854 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
40249889 TACATACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40249893 original size:4 final size:4
Alignment explanation
Indices: 40249886--40249917 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
40249876 ACACACACAC
40249886 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
40249918 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:40258396 original size:13 final size:13
Alignment explanation
Indices: 40258378--40258408 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40258368 AGAAAAAATA
*
40258378 AAAATGAGAGAGT
1 AAAATGAGAAAGT
40258391 AAAATGAGAAAGT
1 AAAATGAGAAAGT
40258404 AAAAT
1 AAAAT
40258409 AAAAAAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (13 bp):
AAAATGAGAAAGT
Found at i:40259185 original size:56 final size:54
Alignment explanation
Indices: 40259064--40259222 Score: 153
Period size: 56 Copynumber: 2.9 Consensus size: 54
40259054 TTGGAGGTTC
* * * * * *
40259064 CAAAATAGATTTGCAAACTAAAAAAATAAAGCATA-TGGGGTGAATAAGGAGCTCG
1 CAAAATAGATTTACAAACTAAAAAAAAAAAG-ATATTAGAGTGAATGA-GAGCTCA
* *
40259119 CAAAGTAGATTTACAAATTAAAAAGAAAAAAGATAATTAGAGTGAATGAGAGCTCA
1 CAAAATAGATTTACAAACTAAAAA-AAAAAAGAT-ATTAGAGTGAATGAGAGCTCA
* * *
40259175 CAAAATAGATTTATAAACT-GAAAAAAAAAGATCATGA-AGTGAATGAGA
1 CAAAATAGATTTACAAACTAAAAAAAAAAAGAT-ATTAGAGTGAATGAGA
40259223 AAAAAAAAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
53 11 0.13
54 12 0.14
55 26 0.30
56 29 0.33
57 9 0.10
ACGTcount: A:0.52, C:0.08, G:0.19, T:0.21
Consensus pattern (54 bp):
CAAAATAGATTTACAAACTAAAAAAAAAAAGATATTAGAGTGAATGAGAGCTCA
Found at i:40259240 original size:26 final size:27
Alignment explanation
Indices: 40259194--40259255 Score: 99
Period size: 26 Copynumber: 2.3 Consensus size: 27
40259184 TTTATAAACT
* *
40259194 GAAAAAAAAAGATCATGAAGTGAATGA
1 GAAAAAAAAAGATAATAAAGTGAATGA
40259221 GAAAAAAAAA-ATAATAAAGTGAATGA
1 GAAAAAAAAAGATAATAAAGTGAATGA
40259247 GAAAAAAAA
1 GAAAAAAAA
40259256 GAGAAAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
26 23 0.70
27 10 0.30
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.13
Consensus pattern (27 bp):
GAAAAAAAAAGATAATAAAGTGAATGA
Found at i:40286084 original size:31 final size:31
Alignment explanation
Indices: 40286024--40286084 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
40286014 GCCTAGTGAC
** *
40286024 TTGAATAAAATCTTTCAAATTGTTTAGTAAT
1 TTGAATAAAATCTTTCAAATAATTCAGTAAT
40286055 TTGAATGAAAA-CTTTCAAATAATTCAGTAA
1 TTGAAT-AAAATCTTTCAAATAATTCAGTAA
40286085 CCATTTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (31 bp):
TTGAATAAAATCTTTCAAATAATTCAGTAAT
Found at i:40287867 original size:23 final size:21
Alignment explanation
Indices: 40287837--40287972 Score: 112
Period size: 23 Copynumber: 6.0 Consensus size: 21
40287827 ACACTAGCGC
*
40287837 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAGCAC-T-TTGT
40287860 GCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCAC-TT-TGT
* *
40287883 GCTCTCTGATTAGTACTTTGT
1 GCTCTCTGTTTAGCACTTTGT
40287904 GTACTCTCTGTTTAGCACTGTGTGT
1 G--CTCTCTGTTTAGCACT-T-TGT
*
40287929 GCTCTCTATTGCCTAGCACTTATGT
1 GCTCTCTGTT---TAGCACTT-TGT
*
40287954 GCTCTCTG-TTAGTACTTTG
1 GCTCTCTGTTTAGCACTTTG
40287973 ATACTTTCTG
Statistics
Matches: 95, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
20 2 0.02
21 11 0.12
22 3 0.03
23 55 0.58
24 2 0.02
25 15 0.16
26 7 0.07
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (21 bp):
GCTCTCTGTTTAGCACTTTGT
Found at i:40287983 original size:69 final size:69
Alignment explanation
Indices: 40287838--40287985 Score: 187
Period size: 69 Copynumber: 2.1 Consensus size: 69
40287828 CACTAGCGCG
* *
40287838 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTTAGCACTTTGTGTGCTCTCTGATTAGTACTTTG
1 CTCTCTGTTTAGCACGTCTCGTGCTCTCTATTTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
*
40287903 TGTA
66 TATA
*
40287907 CTCTCTGTTTAGCACTGTGT-GTGCTCTCTATTGCCTAGCAC-TTATGTGCTCTCTG-TTAGTAC
1 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTATT---TAGCACTTTATGTGCTCTCTGATTAGTAC
40287969 TTTG-ATA
62 TTTGTATA
*
40287976 CTTTCTGTTT
1 CTCTCTGTTT
40287986 GTTCCGTATA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
69 37 0.53
70 14 0.20
71 13 0.19
72 6 0.09
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (69 bp):
CTCTCTGTTTAGCACGTCTCGTGCTCTCTATTTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
TATA
Found at i:40297006 original size:21 final size:19
Alignment explanation
Indices: 40296982--40297024 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
40296972 AAACTAACAA
40296982 AAAAATTAAAAAAATCAAAAT
1 AAAAATTAAAAAAAT--AAAT
* *
40297003 AAAATTTAGAAAAATAAAT
1 AAAAATTAAAAAAATAAAT
40297022 AAA
1 AAA
40297025 CATAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAATTAAAAAAATAAAT
Found at i:40298134 original size:4 final size:4
Alignment explanation
Indices: 40298125--40298151 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
40298115 TACATTTACA
40298125 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
40298152 ATTTGGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:40302341 original size:18 final size:18
Alignment explanation
Indices: 40302318--40302390 Score: 53
Period size: 18 Copynumber: 4.0 Consensus size: 18
40302308 ATCTTTTATT
40302318 ATAATTTATATTATAATA
1 ATAATTTATATTATAATA
40302336 ATAA-TTATTATTAT-AT-
1 ATAATTTA-TATTATAATA
* * * *
40302352 ATGTATTAATATTTTTAGTA
1 AT-AATTTATA-TTATAATA
40302372 ATAATTATATATTATAATA
1 ATAATT-TATATTATAATA
40302391 TTATATCATG
Statistics
Matches: 40, Mismatches: 8, Indels: 13
0.66 0.13 0.21
Matches are distributed among these distances:
16 2 0.05
17 8 0.20
18 15 0.38
19 10 0.25
20 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
ATAATTTATATTATAATA
Found at i:40302393 original size:15 final size:15
Alignment explanation
Indices: 40302314--40302396 Score: 53
Period size: 15 Copynumber: 5.1 Consensus size: 15
40302304 CTATATCTTT
40302314 TATTATAAT-TTATA
1 TATTATAATATTATA
*
40302328 TTATAATAATAATTAT-
1 -TATTATAAT-ATTATA
40302344 TATTATATATGTATTAATA
1 TATTATA-A--TATT-ATA
*
40302363 TTTTTAGTAATAATTATA
1 -TATTA-TAAT-ATTATA
40302381 TATTATAATATTATA
1 TATTATAATATTATA
40302396 T
1 T
40302397 CATGTATTAG
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
15 21 0.39
16 5 0.09
17 11 0.20
18 7 0.13
19 3 0.06
20 5 0.09
21 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTATAATATTATA
Found at i:40302407 original size:37 final size:36
Alignment explanation
Indices: 40302325--40302411 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 36
40302315 ATTATAATTT
*
40302325 ATATTA-TAATAATAATTATTATTATATATGTATTA
1 ATATTATTAGTAATAATTATTATTATATATGTATTA
*
40302360 ATATTTTTAGTAATAATTATATATTATA-A--TATTA
1 ATATTATTAGTAATAATTAT-TATTATATATGTATTA
40302394 TATCATGTATTAGTAATA
1 -AT-AT-TATTAGTAATA
40302412 TACTAATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
34 5 0.11
35 7 0.16
36 15 0.34
37 17 0.39
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.51
Consensus pattern (36 bp):
ATATTATTAGTAATAATTATTATTATATATGTATTA
Found at i:40310583 original size:20 final size:18
Alignment explanation
Indices: 40310540--40310582 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 18
40310530 ATCTAATTGC
40310540 AAAATTTTATAAAAAATTAT
1 AAAATTTTAT--AAAATTAT
40310560 AAAATTTTATAAAATTCAT
1 AAAATTTTATAAAATT-AT
40310579 AAAA
1 AAAA
40310583 AGATTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.27
19 6 0.27
20 10 0.45
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTTTATAAAATTAT
Found at i:40310685 original size:20 final size:20
Alignment explanation
Indices: 40310634--40310692 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
40310624 TTATACAGTA
* *
40310634 GTAAAAAAATTATAAAAAAT
1 GTAAAAAAAATATAAAAATT
*
40310654 GT-AAAGAAATAT-AAAATT
1 GTAAAAAAAATATAAAAATT
*
40310672 CGTAAAAAAAATATGAAAATT
1 -GTAAAAAAAATATAAAAATT
40310693 ATCGTATGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 5 0.16
19 10 0.31
20 11 0.34
21 6 0.19
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.25
Consensus pattern (20 bp):
GTAAAAAAAATATAAAAATT
Found at i:40310926 original size:19 final size:19
Alignment explanation
Indices: 40310904--40310983 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 19
40310894 ACTTTACAAT
40310904 TTTTTATAATTTTTAATGA
1 TTTTTATAATTTTTAATGA
40310923 TTTTTAT-A-TTTT-AT-A
1 TTTTTATAATTTTTAATGA
** *
40310938 TTTTTATTAAAATTTAATAA
1 TTTTTA-TAATTTTTAATGA
* * *
40310958 TATTTATAATGTTTATTGA
1 TTTTTATAATTTTTAATGA
40310977 TTTTTAT
1 TTTTTAT
40310984 TTTTTATAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
15 7 0.14
16 3 0.06
17 5 0.10
18 4 0.08
19 24 0.49
20 6 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTTATAATTTTTAATGA
Found at i:40310933 original size:8 final size:9
Alignment explanation
Indices: 40310869--40310997 Score: 56
Period size: 9 Copynumber: 14.4 Consensus size: 9
40310859 TTTTGATACA
40310869 TTTTATAAT
1 TTTTATAAT
*
40310878 TTTT-TTA-
1 TTTTATAAT
*
40310885 TTTTATAAAA
1 TTTTAT-AAT
* *
40310895 CTTTACAATT
1 TTTTATAA-T
40310905 TTTTATAAT
1 TTTTATAAT
*
40310914 TTTTAATGAT
1 TTTT-ATAAT
40310924 TTTTAT-A-
1 TTTTATAAT
40310931 TTTTAT-AT
1 TTTTATAAT
*
40310939 TTTTATTAAAA
1 TTTTA-T-AAT
*
40310950 TTTAATAAT
1 TTTTATAAT
*
40310959 ATTTATAAT
1 TTTTATAAT
* *
40310968 GTTTATTGAT
1 TTTTA-TAAT
40310978 TTTTAT--T
1 TTTTATAAT
*
40310985 TTTTATAGT
1 TTTTATAAT
40310994 TTTT
1 TTTT
40310998 TGTCACATGT
Statistics
Matches: 92, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
7 18 0.20
8 9 0.10
9 34 0.37
10 26 0.28
11 5 0.05
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:40312006 original size:29 final size:29
Alignment explanation
Indices: 40311959--40312026 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
40311949 ATGATCTAAA
* *
40311959 AAATAATTATTTATGTAAATGATTCTGATTT
1 AAATAA-TAATTATGTAAATGATT-TGATAT
*
40311990 AAA-AATAATTATTTAAATGATTTGATAT
1 AAATAATAATTATGTAAATGATTTGATAT
40312018 AAATAATAA
1 AAATAATAA
40312027 AATAAGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 8 0.24
29 20 0.61
30 2 0.06
31 3 0.09
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (29 bp):
AAATAATAATTATGTAAATGATTTGATAT
Found at i:40313544 original size:12 final size:12
Alignment explanation
Indices: 40313513--40313549 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40313503 TAACGGACTT
40313513 TTTAAATT-AAA
1 TTTAAATTAAAA
40313524 -TTAAATTAAAA
1 TTTAAATTAAAA
*
40313535 TTTAATTTAAAA
1 TTTAAATTAAAA
40313547 TTT
1 TTT
40313550 TGTTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
10 7 0.30
11 3 0.13
12 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TTTAAATTAAAA
Found at i:40315138 original size:22 final size:22
Alignment explanation
Indices: 40315110--40315161 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
40315100 TGGTCAAAGT
*
40315110 TATCATTAAGCCTTAATTTTGC
1 TATCATTAAGACTTAATTTTGC
*
40315132 TATCATTTTAGACTTAATTTTGC
1 TATCA-TTAAGACTTAATTTTGC
40315155 TATCATT
1 TATCATT
40315162 TTAAACTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (22 bp):
TATCATTAAGACTTAATTTTGC
Found at i:40315150 original size:23 final size:23
Alignment explanation
Indices: 40315121--40315169 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
40315111 ATCATTAAGC
*
40315121 CTTAATTTTGCTATCATTTTAGA
1 CTTAATTTTGCTATCATTTTAAA
40315144 CTTAATTTTGCTATCATTTTAAA
1 CTTAATTTTGCTATCATTTTAAA
40315167 CTT
1 CTT
40315170 TAGAGGCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.06, T:0.53
Consensus pattern (23 bp):
CTTAATTTTGCTATCATTTTAAA
Found at i:40316316 original size:11 final size:11
Alignment explanation
Indices: 40316282--40316356 Score: 57
Period size: 11 Copynumber: 6.7 Consensus size: 11
40316272 AACCATTTGA
*
40316282 AAATTAAATTT
1 AAATTTAATTT
*
40316293 -ATTTTAATCTT
1 AAATTTAAT-TT
*
40316304 AAATTTATTTT
1 AAATTTAATTT
*
40316315 AAATTCAATTT
1 AAATTTAATTT
40316326 AAATTTAAATTT
1 AAATTT-AATTT
40316338 -AATATT-ATTAT
1 AAAT-TTAATT-T
40316349 AAATTTAA
1 AAATTTAA
40316357 AAAGAAAAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
10 9 0.18
11 24 0.48
12 17 0.34
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:40318272 original size:30 final size:30
Alignment explanation
Indices: 40318236--40318377 Score: 187
Period size: 30 Copynumber: 4.7 Consensus size: 30
40318226 AAATTGTCCA
* *
40318236 AAAATTATATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* * *
40318266 AAAATTACATTCTAACCCCAAAAATGTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
*
40318296 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* *
40318326 AAAATTACATTTTGACCCCAAAAC-TTTCA
1 AAAATTACATTTTAACCCCAAAACTTTTCC
*
40318355 AAAATTACCATTTTACCCCCAAA
1 AAAATTA-CATTTTAACCCCAAA
40318378 CTTCCCTAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
29 11 0.11
30 88 0.89
ACGTcount: A:0.41, C:0.25, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCAAAACTTTTCC
Found at i:40318318 original size:19 final size:19
Alignment explanation
Indices: 40318294--40318348 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 19
40318284 CAAAAATGTT
40318294 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
40318313 CC-AAA--AC-TTTT----
1 CCAAAATTACATTTTGACC
40318324 CCAAAATTACATTTTGACC
1 CCAAAATTACATTTTGACC
40318343 CCAAAA
1 CCAAAA
40318349 CTTTCAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 2 0.07
12 3 0.11
14 2 0.07
15 8 0.29
16 2 0.07
18 3 0.11
19 8 0.29
ACGTcount: A:0.40, C:0.27, G:0.04, T:0.29
Consensus pattern (19 bp):
CCAAAATTACATTTTGACC
Found at i:40318403 original size:59 final size:60
Alignment explanation
Indices: 40318234--40318403 Score: 175
Period size: 60 Copynumber: 2.9 Consensus size: 60
40318224 CTAAATTGTC
* * * * * *
40318234 CAAAAATTATATTTTAACCCTAAAACTTTTCCAAAATTACATTCTAACCCCAAAAATGTT
1 CAAAAATTACATTTTGACCCCAAAACTTTCCCAAAATCACATTTTAACCCCAAAAATGTT
* * * * *
40318294 CCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACT-TT
1 CAAAAATTACATTTTGACCCCAAAACTTTCCCAAAATCACATTTTAACCCCAAAAATGTT
* * *
40318353 CAAAAATTACCATTTT-ACCCCCAAAC-TTCCCTAAATCCCATTTTTAACCCC
1 CAAAAATTA-CATTTTGACCCCAAAACTTTCCCAAAATCACA-TTTTAACCCC
40318404 GATTTTACCA
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
58 10 0.11
59 28 0.30
60 56 0.60
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (60 bp):
CAAAAATTACATTTTGACCCCAAAACTTTCCCAAAATCACATTTTAACCCCAAAAATGTT
Found at i:40318416 original size:59 final size:58
Alignment explanation
Indices: 40318353--40318548 Score: 180
Period size: 59 Copynumber: 3.4 Consensus size: 58
40318343 CCAAAACTTT
* *
40318353 CAAAAATTACCATTTTACCCCCAAACTTCCCTAAATCCCATTTTTAACCCCGATTTTAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTTAC
* * * * * * * * ** * *
40318412 CAAAACTTATCGTTTTGCCTCCGAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGC
1 CAAAAATTACCATTTTACCCCCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTTAC
* * * *
40318471 CAAAATTTACCATTTTATTCCCCAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA-
1 CAAAAATTACCATTTTA-CCCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTTAC
*
40318529 TAAAAATTACCA-TTTACCCC
1 CAAAAATTACCATTTTACCCC
40318549 TAAAAACCCA
Statistics
Matches: 103, Mismatches: 33, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
56 3 0.03
57 4 0.04
58 10 0.10
59 75 0.73
60 11 0.11
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAATTCCATTTTTAACCCCGATTTTAC
Found at i:40320282 original size:21 final size:21
Alignment explanation
Indices: 40320249--40320290 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40320239 AAAAAATTAT
40320249 AAAAAATAATTAAAATACAAAA
1 AAAAAATAATTAAAATA-AAAA
*
40320271 AAAAAAT-CTTAAAATAAAAA
1 AAAAAATAATTAAAATAAAAA
40320291 TGGTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (21 bp):
AAAAAATAATTAAAATAAAAA
Found at i:40321331 original size:14 final size:14
Alignment explanation
Indices: 40321291--40321331 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
40321281 TATTTATATT
40321291 ATTTTTTAATTT-A
1 ATTTTTTAATTTAA
40321304 ATTTTTTAATTTTAA
1 ATTTTTTAA-TTTAA
40321319 ATATTTTT-ATTTA
1 AT-TTTTTAATTTA
40321332 TTATAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 9 0.36
14 7 0.28
15 4 0.16
16 5 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTTTAATTTAA
Found at i:40321393 original size:34 final size:33
Alignment explanation
Indices: 40321326--40321395 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
40321316 TAAATATTTT
* *
40321326 TATTTATTATAATTTTATATATAATTATCTTAA
1 TATTTATTATAATTTTATATATAATAATATTAA
*
40321359 TATTT-TTTTAATGTTTATATTATAATAATATTAA
1 TATTTATTATAAT-TTTATA-TATAATAATATTAA
40321393 TAT
1 TAT
40321396 AAATTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 6 0.19
33 11 0.34
34 15 0.47
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (33 bp):
TATTTATTATAATTTTATATATAATAATATTAA
Found at i:40321403 original size:34 final size:33
Alignment explanation
Indices: 40321335--40321411 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 33
40321325 TTATTTATTA
* * ***
40321335 TAATTTTATA-TATAATTATCTTAATATTTTTT
1 TAATTTTATATTATAATAATATTAATATAAATT
40321367 TAATGTTTATATTATAATAATATTAATATAAATT
1 TAAT-TTTATATTATAATAATATTAATATAAATT
40321401 TAATTTT-TATT
1 TAATTTTATATT
40321412 TATTATAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
32 8 0.21
33 9 0.24
34 21 0.55
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (33 bp):
TAATTTTATATTATAATAATATTAATATAAATT
Found at i:40328731 original size:4 final size:4
Alignment explanation
Indices: 40328722--40328747 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
40328712 TGTTTAATTC
40328722 TTGT TTGT TTGT TTGT TTGT TTGT TT
1 TTGT TTGT TTGT TTGT TTGT TTGT TT
40328748 TAAATCAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTGT
Found at i:40335150 original size:20 final size:19
Alignment explanation
Indices: 40335104--40335150 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
40335094 TTTATATTTT
*
40335104 TTAAAAAAATTATAAAAAT
1 TTAAAAAAATTATAAAAAG
40335123 TCTAAAAAATATATATAAAAAG
1 T-TAAAAAA-AT-TATAAAAAG
40335145 TTAAAA
1 TTAAAA
40335151 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 7 0.29
21 7 0.29
22 9 0.38
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
TTAAAAAAATTATAAAAAG
Found at i:40335348 original size:14 final size:14
Alignment explanation
Indices: 40335329--40335355 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40335319 TTAGTTTTTT
40335329 TAATTTCATTCGAA
1 TAATTTCATTCGAA
40335343 TAATTTCATTCGA
1 TAATTTCATTCGA
40335356 TTCAACTCTA
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:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (14 bp):
TAATTTCATTCGAA
Found at i:40335396 original size:26 final size:26
Alignment explanation
Indices: 40335344--40335397 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
40335334 TCATTCGAAT
*
40335344 AATTTCATTCGATTCAACTCTACTTG
1 AATTTCATTCGATTCAACTCGACTTG
* *
40335370 AATTTCATTTC-ATTCGACTCGATTTG
1 AATTTCA-TTCGATTCAACTCGACTTG
40335396 AA
1 AA
40335398 AAATTTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (26 bp):
AATTTCATTCGATTCAACTCGACTTG
Found at i:40339937 original size:33 final size:33
Alignment explanation
Indices: 40339900--40339965 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
40339890 AGTGTTCTGA
40339900 TTTTATATGGGCCTTCAAGTCCAGAAGATCTTT
1 TTTTATATGGGCCTTCAAGTCCAGAAGATCTTT
40339933 TTTTATATGGGCCTTCAAGTCCAGAAGATCTTT
1 TTTTATATGGGCCTTCAAGTCCAGAAGATCTTT
40339966 CGGTTTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (33 bp):
TTTTATATGGGCCTTCAAGTCCAGAAGATCTTT
Found at i:40344164 original size:54 final size:54
Alignment explanation
Indices: 40344096--40344213 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 54
40344086 ATGATGATGC
*** *
40344096 TTTTAAAATAGCAAGCTAACATGACATTATGCGTGTAATGATATGTTTGACATA
1 TTTTAAAATAGCAAGCTAACATGACATTATAAATGTAATAATATGTTTGACATA
* * * **
40344150 TTTTGAAATAGCAAGCTGACATGATATTATAAATGTAATAATATGTTTGACGCA
1 TTTTAAAATAGCAAGCTAACATGACATTATAAATGTAATAATATGTTTGACATA
40344204 TTTTAAAATA
1 TTTTAAAATA
40344214 ACAGAATTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (54 bp):
TTTTAAAATAGCAAGCTAACATGACATTATAAATGTAATAATATGTTTGACATA
Found at i:40347617 original size:19 final size:19
Alignment explanation
Indices: 40347562--40347617 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
40347552 TTTATATATT
*
40347562 TTTTTATAAAAATTA-TGA
1 TTTTTAAAAAAATTATTGA
**
40347580 TTTTTAAATATTATT-TTGA
1 TTTTTAAA-AAAATTATTGA
40347599 TTTTTAAAAAAATTATTGA
1 TTTTTAAAAAAATTATTGA
40347618 AAGAGATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTTAAAAAAATTATTGA
Found at i:40352486 original size:18 final size:16
Alignment explanation
Indices: 40352465--40352505 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
40352455 AAAGATCATA
40352465 AATATAATAAAATATATG
1 AATATAAT-AAATAT-TG
40352483 AATATCAATAAATATTG
1 AATAT-AATAAATATTG
40352500 AATATA
1 AATATA
40352506 GTGCTAAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.05
17 7 0.32
18 11 0.50
19 3 0.14
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (16 bp):
AATATAATAAATATTG
Found at i:40360157 original size:20 final size:20
Alignment explanation
Indices: 40360116--40360157 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
40360106 ACGATAATTT
*
40360116 AAATAATCATAAAAATTCAA
1 AAATAATCATAAAAATTAAA
*
40360136 AAATAATTA-AAAAATCTAAA
1 AAATAATCATAAAAAT-TAAA
40360156 AA
1 AA
40360158 TCATAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (20 bp):
AAATAATCATAAAAATTAAA
Found at i:40362572 original size:16 final size:17
Alignment explanation
Indices: 40362551--40362594 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
40362541 CTTGCTTTTG
40362551 TAATTTATAA-TTTATT
1 TAATTTATAATTTTATT
*
40362567 TAATTTATGAATTTTTTT
1 TAATTTAT-AATTTTATT
*
40362585 TAAATTATAA
1 TAATTTATAA
40362595 GAGGAGGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 8 0.33
17 4 0.17
18 12 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TAATTTATAATTTTATT
Found at i:40364964 original size:443 final size:442
Alignment explanation
Indices: 40364138--40365235 Score: 1560
Period size: 443 Copynumber: 2.5 Consensus size: 442
40364128 TTTGTTTTGG
* * * ** * * **
40364138 TTTTGCAGTGTTCAACTTTACTAATGGACAGCATAACGTTGTC-GAAGTGACCGAATCTGCTTAC
1 TTTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTG-CAGAGGTGACCGAAGATGCTTAC
* ** * * *
40364202 GATG-CTTGCAACGCTGCAAAT-CCGGTATCTACGGTGAGCACCGGACCGGCGAGGATTACGCTT
65 GATGAC-TGCAACGCTGCAAATGCC-ATATCTACTTTGACCACCGGACCGGCAAGGATTACCCTT
* * ** * * ** * * * *
40364265 AACAGGACAGGGGAGTACTACTTTATTTGTGGTATCCCTGGTCACTGTTCCGCCGGCCAGAAGAT
128 AACAGGACCGGTGACCATTACTTCATTTGCAGTGTCCCTGGTCATTGTTCCGCCGGCCAAAAGCT
* * * * *
40364330 AAACGTGGAAGTACGAAATGGTAACACCACCGGCGGTGTTACTCCATCGACGCCTGTAACTCCAA
193 CAAGGTCGAAGTACGAAATGGTAACACCACCGGCGGCGTTACTCCATCGACGCCTATAACTCCAA
*
40364395 CCACCACCACTTATACGGTGGGCGACTCCACTGGTTGGCGAGTCCCTACTAATAATGATGATTTT
258 CCACCACCACTTATACGGTGGGCGACTCCACTGGTTGGCGAGTCCCTACCAATAATGATGATTTT
40364460 TATGAGGATTGGGCTGATAATAAACACTTCGTTGTCGGAGATGTTTTAGGTCAGTTTCTTAATTC
323 TATGAGGATTGGGCTGATAATAAACACTTCGTTGTCGGAGATGTTTTAGGTCAGTTTCTTAATTC
*
40364525 AACATTTGAATCGAAATTTGATGAGTTTTTTA-TCGAACTGTTTGA-TTTTTTTTTCT
388 -ACATTTGAATCGAAACTTGATGAGTTTTTTATTC-AACTG-TTGATTTTTTTTTTCT
*
40364581 TTTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAGGTGACGGAAGATGCTTACG
1 TTTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAGGTGACCGAAGATGCTTACG
* * *
40364646 ATGACTGCAACACTGCAAATGCCATATCTACTTTGACCACCGGTCCAGCAAGGATTACCCTTAAC
66 ATGACTGCAACGCTGCAAATGCCATATCTACTTTGACCACCGGACCGGCAAGGATTACCCTTAAC
* *
40364711 AAGACCGGTGACCATTACTTCATTTGCAGTGTCCCCGGTCATTGTTCCGCCGGCCAAAAGCTCAA
131 AGGACCGGTGACCATTACTTCATTTGCAGTGTCCCTGGTCATTGTTCCGCCGGCCAAAAGCTCAA
* * * * * * *
40364776 GGTTGAAGTTCGAACTGGTAACACCACTGGCGGCGTTGCTCCGTC-ACCGCCTATAACTCCAAGC
196 GGTCGAAGTACGAAATGGTAACACCACCGGCGGCGTTACTCCATCGA-CGCCTATAACTCCAACC
* * * * *
40364840 ACCACGACTTTTACGGTGGGTGACTCTACTGGTTGGCGTGTCCCTACCAATAATGATGATTTTTA
260 ACCACCACTTATACGGTGGGCGACTCCACTGGTTGGCGAGTCCCTACCAATAATGATGATTTTTA
40364905 TGAGGATTGGGCTGATAATAAACACTTCGTTGTCGGAGATGTTTTAGGTCAGTTTCTTAATTCAC
325 TGAGGATTGGGCTGATAATAAACACTTCGTTGTCGGAGATGTTTTAGGTCAGTTTCTTAATTCAC
**
40364970 ATTTGAATCGAAACTTGATGCTTTTTTTATTCAACTGTTGATTTTTTTTTTCT
390 ATTTGAATCGAAACTTGATGAGTTTTTTATTCAACTGTTGATTTTTTTTTTCT
* * *
40365023 TCTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAGGTGACTGAAGATGGTTACG
1 TTTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAGGTGACCGAAGATGCTTACG
*
40365088 ACGACTGCAACGCTGCAAATGCCATATCTACTTTGACCACCGGACCGGCAAGGATTACCCTTAAC
66 ATGACTGCAACGCTGCAAATGCCATATCTACTTTGACCACCGGACCGGCAAGGATTACCCTTAAC
40365153 AGGACCGGTGACCATTACTTCATTTGCAGTGTCCCTGGTCATTGTTCCGCCGGCCAAAAGCTCAA
131 AGGACCGGTGACCATTACTTCATTTGCAGTGTCCCTGGTCATTGTTCCGCCGGCCAAAAGCTCAA
*
40365218 GGTCGAAGTCCGAAATGG
196 GGTCGAAGTACGAAATGG
40365236 CAACCGCACC
Statistics
Matches: 584, Mismatches: 65, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
441 4 0.01
442 247 0.42
443 330 0.57
444 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (442 bp):
TTTTGCAGTGTTTAATTTTACGACCGGACAGCATAATGTTGCAGAGGTGACCGAAGATGCTTACG
ATGACTGCAACGCTGCAAATGCCATATCTACTTTGACCACCGGACCGGCAAGGATTACCCTTAAC
AGGACCGGTGACCATTACTTCATTTGCAGTGTCCCTGGTCATTGTTCCGCCGGCCAAAAGCTCAA
GGTCGAAGTACGAAATGGTAACACCACCGGCGGCGTTACTCCATCGACGCCTATAACTCCAACCA
CCACCACTTATACGGTGGGCGACTCCACTGGTTGGCGAGTCCCTACCAATAATGATGATTTTTAT
GAGGATTGGGCTGATAATAAACACTTCGTTGTCGGAGATGTTTTAGGTCAGTTTCTTAATTCACA
TTTGAATCGAAACTTGATGAGTTTTTTATTCAACTGTTGATTTTTTTTTTCT
Found at i:40366755 original size:22 final size:21
Alignment explanation
Indices: 40366722--40366762 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
40366712 CAATTATAAC
40366722 TTTTCTTTTAAAAATTGATTT
1 TTTTCTTTTAAAAATTGATTT
*
40366743 TTTTTTTTATAAAAATTGAT
1 TTTTCTTT-TAAAAATTGAT
40366763 CTTTCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTCTTTTAAAAATTGATTT
Found at i:40366933 original size:29 final size:28
Alignment explanation
Indices: 40366901--40366957 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
40366891 GGTTTTAATA
40366901 TCTATAATATTAATTAATATTTAATATAT
1 TCTATAATA-TAATTAATATTTAATATAT
* * * *
40366930 TCTATTATATACTTTATATTTTATATAT
1 TCTATAATATAATTAATATTTAATATAT
40366958 AAGCTTAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TCTATAATATAATTAATATTTAATATAT
Found at i:40369752 original size:63 final size:63
Alignment explanation
Indices: 40369660--40369850 Score: 242
Period size: 63 Copynumber: 3.0 Consensus size: 63
40369650 CAAGAGTAAG
* * * *
40369660 CCTCCGAGCGCC-CCCACGCCTGGAACTCCGCGCGCCACCCCGCGAGGAACTTCAAGTTCTCCT
1 CCTCCGACCGCCGCCC-CGCCTGGAACTCCGAGCGCCACCCCGCGTGGAACTTCAAGTCCTCCT
* * * *
40369723 CCTCCGACCGCCGCCCCGCGTGGATCTCCGAACGCCACCCCGCGTGGAGCTTCAAGTCCTCCT
1 CCTCCGACCGCCGCCCCGCCTGGAACTCCGAGCGCCACCCCGCGTGGAACTTCAAGTCCTCCT
* * * *
40369786 CCTCCGAGCC-CGGTCACGCCTGGAACTCCGAGCGCCACCGCGCGTGGAACTTCAAGTCCTCCT
1 CCTCCGA-CCGCCGCCCCGCCTGGAACTCCGAGCGCCACCCCGCGTGGAACTTCAAGTCCTCCT
40369849 CC
1 CC
40369851 CGAGGCCAAC
Statistics
Matches: 110, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
63 105 0.95
64 5 0.05
ACGTcount: A:0.15, C:0.47, G:0.24, T:0.15
Consensus pattern (63 bp):
CCTCCGACCGCCGCCCCGCCTGGAACTCCGAGCGCCACCCCGCGTGGAACTTCAAGTCCTCCT
Found at i:40369758 original size:24 final size:24
Alignment explanation
Indices: 40369724--40369770 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
40369714 AGTTCTCCTC
* *
40369724 CTCCGACCGCCGCCCCGCGTGGAT
1 CTCCGAACGCCACCCCGCGTGGAT
40369748 CTCCGAACGCCACCCCGCGTGGA
1 CTCCGAACGCCACCCCGCGTGGA
40369771 GCTTCAAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.49, G:0.28, T:0.11
Consensus pattern (24 bp):
CTCCGAACGCCACCCCGCGTGGAT
Found at i:40379338 original size:17 final size:18
Alignment explanation
Indices: 40379304--40379345 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
40379294 TTTAAGTTAA
40379304 TTATATAAAATGGATAAAT
1 TTATATAAAAT-GATAAAT
*
40379323 TTATATAAAAT-TTAAAT
1 TTATATAAAATGATAAAT
40379340 TTATAT
1 TTATAT
40379346 TTCGAATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
19 11 0.50
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
TTATATAAAATGATAAAT
Found at i:40382535 original size:39 final size:39
Alignment explanation
Indices: 40382423--40382511 Score: 178
Period size: 39 Copynumber: 2.3 Consensus size: 39
40382413 ACCTTCACCA
40382423 TCACCATCACCATCGACGACAACACCACCATCCTCTTCC
1 TCACCATCACCATCGACGACAACACCACCATCCTCTTCC
40382462 TCACCATCACCATCGACGACAACACCACCATCCTCTTCC
1 TCACCATCACCATCGACGACAACACCACCATCCTCTTCC
40382501 TCACCATCACC
1 TCACCATCACC
40382512 TTCAACGGCG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.28, C:0.49, G:0.04, T:0.18
Consensus pattern (39 bp):
TCACCATCACCATCGACGACAACACCACCATCCTCTTCC
Found at i:40384541 original size:24 final size:24
Alignment explanation
Indices: 40384497--40384542 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
40384487 AAACAACAAA
* *
40384497 AACAATCAAAACAGCAGCAAAAAT
1 AACAATCAAAACAACACCAAAAAT
40384521 AACAA-CAAAAGCAACACCAAAA
1 AACAATCAAAA-CAACACCAAAA
40384543 CAGTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.65, C:0.24, G:0.07, T:0.04
Consensus pattern (24 bp):
AACAATCAAAACAACACCAAAAAT
Found at i:40385660 original size:12 final size:12
Alignment explanation
Indices: 40385639--40385675 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
40385629 ATGGGAAGAA
*
40385639 TTGGATTCAGAC
1 TTGGAATCAGAC
40385651 TTGGAATCAGAC
1 TTGGAATCAGAC
40385663 TTGGAATCAGAC
1 TTGGAATCAGAC
40385675 T
1 T
40385676 CGGACTCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (12 bp):
TTGGAATCAGAC
Found at i:40389315 original size:31 final size:28
Alignment explanation
Indices: 40389256--40389338 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 28
40389246 AACATATCAT
*
40389256 TTTTA-ATATAATTTAATCAAATTAAAA
1 TTTTATATATAATTTAATCAAATCAAAA
40389283 TTTTATATATACATTTAAATCATAATCAAAA
1 TTTTATATATA-ATTT-AATCA-AATCAAAA
40389314 TTTCATATATATAATTGT-ATCAAAT
1 TTT--TATATATAATT-TAATCAAAT
40389339 TTAAATTTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
27 5 0.10
28 5 0.10
29 4 0.08
30 8 0.17
31 14 0.29
32 3 0.06
33 9 0.19
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (28 bp):
TTTTATATATAATTTAATCAAATCAAAA
Found at i:40396355 original size:24 final size:24
Alignment explanation
Indices: 40396319--40396368 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
40396309 CAAAGTGCAA
*
40396319 TTTTACTTTTACTAATTTAAATTT
1 TTTTACTTTTACTAATTTAAAATT
40396343 TTTTA-TTTATACTAATTTAAAATT
1 TTTTACTTT-TACTAATTTAAAATT
40396367 TT
1 TT
40396369 AAAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTACTTTTACTAATTTAAAATT
Found at i:40398297 original size:23 final size:24
Alignment explanation
Indices: 40398254--40398332 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
40398244 AACATCCAAA
* **
40398254 CAACTAAAATAACAACCAAAACAG
1 CAACAAAAATAACAAGAAAAACAG
** * *
40398278 CAGTAAAAATAA-TAGAAAAATAG
1 CAACAAAAATAACAAGAAAAACAG
*
40398301 CAACAAAAATAACAATAAAAACAG
1 CAACAAAAATAACAAGAAAAACAG
*
40398325 CACCAAAA
1 CAACAAAA
40398333 TAGTAAAAAA
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
23 17 0.41
24 24 0.59
ACGTcount: A:0.66, C:0.18, G:0.06, T:0.10
Consensus pattern (24 bp):
CAACAAAAATAACAAGAAAAACAG
Found at i:40398308 original size:12 final size:12
Alignment explanation
Indices: 40398293--40398354 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
40398283 AAAATAATAG
40398293 AAAAATAGCAAC
1 AAAAATAGCAAC
* *
40398305 AAAAATAACAAT
1 AAAAATAGCAAC
*
40398317 AAAAACAGC-AC
1 AAAAATAGCAAC
* *
40398328 CAAAATAGTAA-
1 AAAAATAGCAAC
*
40398339 AAAAATAGCACC
1 AAAAATAGCAAC
40398351 AAAA
1 AAAA
40398355 CAGAAACCAA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
11 15 0.41
12 22 0.59
ACGTcount: A:0.68, C:0.16, G:0.06, T:0.10
Consensus pattern (12 bp):
AAAAATAGCAAC
Done.