Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007763.1 Kokia drynarioides strain JFW-HI SEQ_122396, 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: 237200
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1912 original size:21 final size:21
Alignment explanation
Indices: 1869--1927 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
1859 AACCACAAAG
* *
1869 TTTAAAGTTT-GGGTTCAAGA
1 TTTAAAGTTTAGGGTTTAAAA
*
1889 TTTAAAATTTAGGGTTTAAAA
1 TTTAAAGTTTAGGGTTTAAAA
*
1910 TTT-AAGTTTAAGGTTTAA
1 TTTAAAGTTTAGGGTTTAA
1928 GAGTTTAGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 22 0.67
21 11 0.33
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.44
Consensus pattern (21 bp):
TTTAAAGTTTAGGGTTTAAAA
Found at i:2636 original size:3 final size:3
Alignment explanation
Indices: 2630--2655 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2620 CAACAACAAC
2630 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2656 CTTAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3388 original size:37 final size:37
Alignment explanation
Indices: 3346--3416 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
3336 TATAACATTT
* *
3346 TTTTTTTTA-CTTTTTTAAGATTTTCTTTTATTTTTAA
1 TTTTTTTTATCTTTTTTAAG-GTTTCCTTTATTTTTAA
*
3383 TTTTTTTTATTTTTTTTAAGGTTTCCTTTATTTT
1 TTTTTTTTATCTTTTTTAAGGTTTCCTTTATTTT
3417 CACTCTATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 21 0.70
38 9 0.30
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (37 bp):
TTTTTTTTATCTTTTTTAAGGTTTCCTTTATTTTTAA
Found at i:3815 original size:8 final size:8
Alignment explanation
Indices: 3783--3829 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
3773 TAATGATAAA
3783 TAAAATAT
1 TAAAATAT
*
3791 TACAAAAAT
1 TA-AAATAT
*
3800 TTAAATAT
1 TAAAATAT
3808 TAAAATA-
1 TAAAATAT
3815 TAAAATAT
1 TAAAATAT
*
3823 TTAAATA
1 TAAAATA
3830 ATTTGATATG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
7 7 0.22
8 19 0.59
9 6 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAATAT
Found at i:3820 original size:15 final size:15
Alignment explanation
Indices: 3782--3829 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3772 TTAATGATAA
*
3782 ATAAAATATTACAAAA
1 ATAAAATATTA-AAAT
*
3798 ATTTAAATATTAAAAT
1 A-TAAAATATTAAAAT
*
3814 ATAAAATATTTAAAT
1 ATAAAATATTAAAAT
3829 A
1 A
3830 ATTTGATATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 13 0.48
16 5 0.19
17 9 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:3828 original size:23 final size:25
Alignment explanation
Indices: 3783--3829 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
3773 TAATGATAAA
3783 TAAAATATTACAAAAATTTAAATAT
1 TAAAATATTACAAAAATTTAAATAT
*
3808 TAAAATA-TA-AAATATTTAAATA
1 TAAAATATTACAAAAATTTAAATA
3830 ATTTGATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 2 0.10
25 7 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAAATATTACAAAAATTTAAATAT
Found at i:4882 original size:29 final size:29
Alignment explanation
Indices: 4850--4906 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
4840 ATTTGAATAG
* * * *
4850 TTTTAAAAGATTAAATTAAATTTTTATTA
1 TTTTAAAAAAATAAAATAAAATTTTATTA
4879 TTTTAAAAAAATAAAATAAAATTTTATT
1 TTTTAAAAAAATAAAATAAAATTTTATT
4907 TTTAATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTTAAAAAAATAAAATAAAATTTTATTA
Found at i:6052 original size:11 final size:11
Alignment explanation
Indices: 6036--6060 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6026 ACATCTCTAT
6036 ATTAAGGAAGC
1 ATTAAGGAAGC
6047 ATTAAGGAAGC
1 ATTAAGGAAGC
6058 ATT
1 ATT
6061 TTTATTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (11 bp):
ATTAAGGAAGC
Found at i:6281 original size:24 final size:24
Alignment explanation
Indices: 6261--6370 Score: 159
Period size: 24 Copynumber: 4.6 Consensus size: 24
6251 TCCACCGTGA
* *
6261 CCGCCGTGTCCACCACCACCGTGA-
1 CCGCCGTGGCCACCACCACCAT-AC
6285 CCGCCGTGGCCACCACCACCATAC
1 CCGCCGTGGCCACCACCACCATAC
*
6309 CCTCCGTGGCCACCACCACCATAC
1 CCGCCGTGGCCACCACCACCATAC
*
6333 CCTCCGTGGCCACCACCACCATAC
1 CCGCCGTGGCCACCACCACCATAC
*
6357 CCTCCGTGGCCACC
1 CCGCCGTGGCCACC
6371 TCCGTACCCT
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
23 1 0.01
24 81 0.99
ACGTcount: A:0.18, C:0.54, G:0.16, T:0.12
Consensus pattern (24 bp):
CCGCCGTGGCCACCACCACCATAC
Found at i:6321 original size:21 final size:22
Alignment explanation
Indices: 6288--6404 Score: 121
Period size: 24 Copynumber: 5.1 Consensus size: 22
6278 ACCGTGACCG
6288 CCGTGGCCACCACCACCATACCCT
1 CCGTGG-C-CCACCACCATACCCT
6312 CCGTGGCCACCACCACCATACCCT
1 CCGTGG-C-CCACCACCATACCCT
6336 CCGTGGCCACCACCACCATACCCT
1 CCGTGG-C-CCACCACCATACCCT
* *
6360 CCGTGG-CCACCTCCGTACCCT
1 CCGTGGCCCACCACCATACCCT
* * *
6381 CCG-CGTCCACCTCCATACCCT
1 CCGTGGCCCACCACCATACCCT
6402 CCG
1 CCG
6405 CGTCCACCTC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
20 1 0.01
21 33 0.38
24 54 0.61
ACGTcount: A:0.17, C:0.55, G:0.14, T:0.15
Consensus pattern (22 bp):
CCGTGGCCCACCACCATACCCT
Found at i:6405 original size:21 final size:21
Alignment explanation
Indices: 6345--6417 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
6335 TCCGTGGCCA
* * *
6345 CCACCACCATACCCTCCGTGG
1 CCACCTCCATACCCTCCGCGT
*
6366 CCACCTCCGTACCCTCCGCGT
1 CCACCTCCATACCCTCCGCGT
6387 CCACCTCCATACCCTCCGCGT
1 CCACCTCCATACCCTCCGCGT
6408 CCACCTCCAT
1 CCACCTCCAT
6418 TATAACCTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.15, C:0.56, G:0.11, T:0.18
Consensus pattern (21 bp):
CCACCTCCATACCCTCCGCGT
Found at i:6431 original size:24 final size:21
Alignment explanation
Indices: 6345--6439 Score: 91
Period size: 21 Copynumber: 4.4 Consensus size: 21
6335 TCCGTGGCCA
* * * *
6345 CCACCACCATACCCTCCGTGG
1 CCACCTCCATAACCTCCGCGT
* *
6366 CCACCTCCGTACCCTCCGCGT
1 CCACCTCCATAACCTCCGCGT
*
6387 CCACCTCCATACCCTCCGCGT
1 CCACCTCCATAACCTCCGCGT
6408 CCACCTCCATTATAACCTCCGCGT
1 CCACCTCC---ATAACCTCCGCGT
*
6432 CCATCTCC
1 CCACCTCC
6440 TAGCTCAGCC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
21 45 0.70
24 19 0.30
ACGTcount: A:0.16, C:0.54, G:0.11, T:0.20
Consensus pattern (21 bp):
CCACCTCCATAACCTCCGCGT
Found at i:8585 original size:26 final size:24
Alignment explanation
Indices: 8544--8592 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
8534 AAAAATTATT
8544 TAATTGATAAATTAATTTATTTAAAC
1 TAATTGATAAATTAA--TATTTAAAC
8570 TAATTGAGTAAA-TAATATTTAAA
1 TAATTGA-TAAATTAATATTTAAA
8593 TTGGTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 8 0.36
26 10 0.45
27 4 0.18
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (24 bp):
TAATTGATAAATTAATATTTAAAC
Found at i:13848 original size:90 final size:88
Alignment explanation
Indices: 13737--13925 Score: 215
Period size: 90 Copynumber: 2.1 Consensus size: 88
13727 ATATAATATA
* * * *
13737 TGGTACTTGAACTTAACACTTTATTTTTAATTTGGTA--TGTAAATTTTTTTGGTCCAATTTTGT
1 TGGTACCTAAACTTAACACTTT-TTTTTAAGTTGGTACTTG-AAATTTTTTGGGTCCAA-TTTG-
13800 GC-CAAAACTTCACACTTT-TTCCTAATT
62 GCACAAAACTT--CACTTTATTCCTAATT
* *
13827 TGGTACCTAAACTTGACACTTTTTTTTAAGTTGGTACTTGAACTTTTTTGGGTCCAATTTGGCAT
1 TGGTACCTAAACTTAACACTTTTTTTTAAGTTGGTACTTGAAATTTTTTGGGTCCAATTTGGCA-
* *
13892 CTAAACTTGACTTTATTCCTAATT
65 CAAAACTTCACTTTATTCCTAATT
13916 TGGTACCTAA
1 TGGTACCTAA
13926 TCTTTTTTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
88 7 0.08
89 36 0.42
90 41 0.48
91 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (88 bp):
TGGTACCTAAACTTAACACTTTTTTTTAAGTTGGTACTTGAAATTTTTTGGGTCCAATTTGGCAC
AAAACTTCACTTTATTCCTAATT
Found at i:13871 original size:31 final size:31
Alignment explanation
Indices: 13804--13863 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
13794 TTTTGTGCCA
*
13804 AAACTTCACACTTTTTCCTAATTTGGTACCT
1 AAACTTCACACTTTTTCCTAAGTTGGTACCT
* **
13835 AAACTTGACACTTTTTTTTAAGTTGGTAC
1 AAACTTCACACTTTTTCCTAAGTTGGTAC
13864 TTGAACTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (31 bp):
AAACTTCACACTTTTTCCTAAGTTGGTACCT
Found at i:14920 original size:57 final size:57
Alignment explanation
Indices: 14851--14966 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
14841 AATCAAAGCT
14851 TATGCATAATTGCATTTACCAAACAATTAATTATTACTTATAAATCTGTCATATTTC
1 TATGCATAATTGCATTTACCAAACAATTAATTATTACTTATAAATCTGTCATATTTC
14908 TATGCATAATTGCATTTACCAAACAATTAATTATTACTTATAAATCTGTCATATTTC
1 TATGCATAATTGCATTTACCAAACAATTAATTATTACTTATAAATCTGTCATATTTC
14965 TA
1 TA
14967 ATTTTTTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (57 bp):
TATGCATAATTGCATTTACCAAACAATTAATTATTACTTATAAATCTGTCATATTTC
Found at i:15250 original size:30 final size:29
Alignment explanation
Indices: 15204--15271 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
15194 CTTAAAATTT
**
15204 TAAAAAAATATAAAAATTGTTTTTAAAAG
1 TAAAAAAATATAAAAATTGTTTAAAAAAG
*
15233 TAAAAAAATCATTAAAATTGTTTAAAAAAG
1 TAAAAAAAT-ATAAAAATTGTTTAAAAAAG
*
15263 TATAAAAAT
1 TAAAAAAAT
15272 TTTAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.32
Consensus pattern (29 bp):
TAAAAAAATATAAAAATTGTTTAAAAAAG
Found at i:15307 original size:20 final size:18
Alignment explanation
Indices: 15243--15298 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
15233 TAAAAAAATC
15243 ATTAAAATTGTTTAAAAAA
1 ATTAAAATT-TTTAAAAAA
* *
15262 GTATAAAAATTTTAAAAAAA
1 --ATTAAAATTTTTAAAAAA
15282 ATTAAAATTTTTAAAAA
1 ATTAAAATTTTTAAAAA
15299 TTAATTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 15 0.48
20 8 0.26
21 8 0.26
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (18 bp):
ATTAAAATTTTTAAAAAA
Found at i:15308 original size:19 final size:19
Alignment explanation
Indices: 15233--15298 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 19
15223 TTTTTAAAAG
15233 TAAAAAAATCATTAAAATTGTT
1 TAAAAAAA--ATTAAAATT-TT
* *
15255 T-AAAAAAGTATAAAAATTT
1 TAAAAAAAAT-TAAAATTTT
15274 TAAAAAAAATTAAAATTTT
1 TAAAAAAAATTAAAATTTT
15293 TAAAAA
1 TAAAAA
15299 TTAATTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 18 0.47
20 13 0.34
21 6 0.16
22 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAAAAAAATTAAAATTTT
Found at i:17592 original size:21 final size:21
Alignment explanation
Indices: 17540--17592 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
17530 ACTGTTACGT
* *
17540 AGGTATCGGTAATTTTAAAGA
1 AGGTATCGATAATTTCAAAGA
* *
17561 AGCTATTGATAATTTCACAAG-
1 AGGTATCGATAATTTCA-AAGA
17582 AGGTATCGATA
1 AGGTATCGATA
17593 CTATTTGGAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (21 bp):
AGGTATCGATAATTTCAAAGA
Found at i:19103 original size:53 final size:53
Alignment explanation
Indices: 19041--19147 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
19031 ATTGTCTGTC
19041 ATCTAAGAAATTTGAATTATATAATTAATCATTTTAATAATAATAAGTAAGAA
1 ATCTAAGAAATTTGAATTATATAATTAATCATTTTAATAATAATAAGTAAGAA
19094 ATCTAAGAAATTTGAATTATATAATTAATCATTTTAATAATAATAAGTAAGAA
1 ATCTAAGAAATTTGAATTATATAATTAATCATTTTAATAATAATAAGTAAGAA
19147 A
1 A
19148 ATAAAATATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.37
Consensus pattern (53 bp):
ATCTAAGAAATTTGAATTATATAATTAATCATTTTAATAATAATAAGTAAGAA
Found at i:20003 original size:50 final size:50
Alignment explanation
Indices: 19924--20237 Score: 378
Period size: 50 Copynumber: 6.3 Consensus size: 50
19914 AAATTTTGAA
* * * * * *
19924 TAAACGCATAATTAAGCAGACGAGCGTAAATGTGTGGAAGTTGGCAAGCG
1 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTAGCGAGCG
* *
19974 TAAACGCATAATTAAGTTGACGAGTGTAAACGTGTGCAAGCTAGCGAGCG
1 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTAGCGAGCG
* * ** *
20024 TAAACGCATGATTAAGTTGAC-ATGCGTAAACGTGTGCAAATTGGCGAGCG
1 TAAACGCATAATTAAGCTGACGA-GCGTAAACGTGTGCAAGCTAGCGAGCG
* *
20074 TAAACGCATAATTAAGCTGACGAGCATAAACGTGTGCAAGTTAGCGAGCG
1 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTAGCGAGCG
* * * * * *
20124 TAAATGCATAATTAGGATGACGAGCTTAAACGTGTACAAGCTGGCGAGCG
1 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTAGCGAGCG
* * * *
20174 TAAACACATAATTAAGCTGACGAGCATAAATGTGTACAAGCTAGCGAGCG
1 TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTAGCGAGCG
*
20224 TAAACACATAATTA
1 TAAACGCATAATTA
20238 TGATAAAGAG
Statistics
Matches: 230, Mismatches: 32, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 1 0.00
50 228 0.99
51 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (50 bp):
TAAACGCATAATTAAGCTGACGAGCGTAAACGTGTGCAAGCTAGCGAGCG
Found at i:20097 original size:100 final size:100
Alignment explanation
Indices: 19924--20237 Score: 425
Period size: 100 Copynumber: 3.1 Consensus size: 100
19914 AAATTTTGAA
* * *
19924 TAAACGCATAATTAAGCA-GACGAGCGTAAATGTGTGGAAGTTGGCAAGCGTAAACGCATAATTA
1 TAAACGCATAATTAAG-ATGACGAGCGTAAACGTGTGCAAGTTGGCGAGCGTAAACGCATAATTA
* **
19988 AGTTGACGAGTGTAAACGTGTGCAAGCTAGCGAGCG
65 AGCTGACGAGCATAAACGTGTGCAAGCTAGCGAGCG
* * *
20024 TAAACGCATGATTAAGTTGAC-ATGCGTAAACGTGTGCAAATTGGCGAGCGTAAACGCATAATTA
1 TAAACGCATAATTAAGATGACGA-GCGTAAACGTGTGCAAGTTGGCGAGCGTAAACGCATAATTA
*
20088 AGCTGACGAGCATAAACGTGTGCAAGTTAGCGAGCG
65 AGCTGACGAGCATAAACGTGTGCAAGCTAGCGAGCG
* * * * * *
20124 TAAATGCATAATTAGGATGACGAGCTTAAACGTGTACAAGCTGGCGAGCGTAAACACATAATTAA
1 TAAACGCATAATTAAGATGACGAGCGTAAACGTGTGCAAGTTGGCGAGCGTAAACGCATAATTAA
* *
20189 GCTGACGAGCATAAATGTGTACAAGCTAGCGAGCG
66 GCTGACGAGCATAAACGTGTGCAAGCTAGCGAGCG
*
20224 TAAACACATAATTA
1 TAAACGCATAATTA
20238 TGATAAAGAG
Statistics
Matches: 187, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
99 1 0.01
100 185 0.99
101 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (100 bp):
TAAACGCATAATTAAGATGACGAGCGTAAACGTGTGCAAGTTGGCGAGCGTAAACGCATAATTAA
GCTGACGAGCATAAACGTGTGCAAGCTAGCGAGCG
Found at i:20104 original size:26 final size:26
Alignment explanation
Indices: 19970--20203 Score: 91
Period size: 26 Copynumber: 9.3 Consensus size: 26
19960 GAAGTTGGCA
*
19970 AGCGTAAACGCATAATTAAGTTGACG
1 AGCGTAAACGCATAATTAAGCTGACG
* * *
19996 AGTGTAAACG--T-GTGCAAGCT-AGCG
1 AGCGTAAACGCATAAT-TAAGCTGA-CG
* *
20020 AGCGTAAACGCATGATTAAGTTGAC-
1 AGCGTAAACGCATAATTAAGCTGACG
* * ** *
20045 ATGCGTAAACG--T-GTGCAAATTGGCG
1 A-GCGTAAACGCATAAT-TAAGCTGACG
20070 AGCGTAAACGCATAATTAAGCTGACG
1 AGCGTAAACGCATAATTAAGCTGACG
* * * *
20096 AGCATAAACG--T-GTGCAAG-TTAGCG
1 AGCGTAAACGCATAAT-TAAGCTGA-CG
* * *
20120 AGCGTAAATGCATAATTAGGATGACG
1 AGCGTAAACGCATAATTAAGCTGACG
* ** * *
20146 AGCTTAAACGTGT-A-CAAGCTGGCG
1 AGCGTAAACGCATAATTAAGCTGACG
*
20170 AGCGTAAACACATAATTAAGCTGACG
1 AGCGTAAACGCATAATTAAGCTGACG
*
20196 AGCATAAA
1 AGCGTAAA
20204 TGTGTACAAG
Statistics
Matches: 146, Mismatches: 42, Indels: 40
0.64 0.18 0.18
Matches are distributed among these distances:
23 6 0.04
24 61 0.42
25 4 0.03
26 69 0.47
27 6 0.04
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (26 bp):
AGCGTAAACGCATAATTAAGCTGACG
Found at i:20127 original size:24 final size:23
Alignment explanation
Indices: 19987--20127 Score: 72
Period size: 24 Copynumber: 5.7 Consensus size: 23
19977 ACGCATAATT
*
19987 AAGTTGACGAGTGTAAACGTGTGC
1 AAGTTG-CGAGCGTAAACGTGTGC
* *
20011 AAGCTAGCGAGCGTAAACGCATGAT-T
1 AAG-TTGCGAGCGTAAACG--TG-TGC
20037 AAGTTGAC-ATGCGTAAACGTGTGC
1 AAGTTG-CGA-GCGTAAACGTGTGC
* * *
20061 AAATTGGCGAGCGTAAACGCATAAT-T
1 AAGTT-GCGAGCGTAAACG--T-GTGC
* *
20087 AAGCTGACGAGCATAAACGTGTGC
1 AAGTTG-CGAGCGTAAACGTGTGC
20111 AAGTTAGCGAGCGTAAA
1 AAGTT-GCGAGCGTAAA
20128 TGCATAATTA
Statistics
Matches: 87, Mismatches: 15, Indels: 30
0.66 0.11 0.23
Matches are distributed among these distances:
23 2 0.02
24 44 0.51
25 9 0.10
26 30 0.34
27 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.21
Consensus pattern (23 bp):
AAGTTGCGAGCGTAAACGTGTGC
Found at i:24479 original size:50 final size:50
Alignment explanation
Indices: 24198--24479 Score: 314
Period size: 50 Copynumber: 5.6 Consensus size: 50
24188 TATATAGATA
* ** * * **
24198 TAAACGCATAAATAAACTCTCGAGCATAAACGTGTGCAAGTTGACGAGTG
1 TAAACGCATAAATAAGCTGACGAGCGTAAACATGTGCAAGTTGGTGAGTG
* * *
24248 TAAACACATAAATAAGTTGACAAGCGTAAACATGTGCAAGTTGGTGAGTG
1 TAAACGCATAAATAAGCTGACGAGCGTAAACATGTGCAAGTTGGTGAGTG
* * * * * * *
24298 TAAAAGCATAAATAAGTTGACGAGCGCAAACGTGTGCAAGCTGGCGAGAG
1 TAAACGCATAAATAAGCTGACGAGCGTAAACATGTGCAAGTTGGTGAGTG
* * * *
24348 TAAATGCATAAATAAGCTAACGAGCGTAAACGTGTGCAAGCTGGCT-AGTG
1 TAAACGCATAAATAAGCTGACGAGCGTAAACATGTGCAAGTTGG-TGAGTG
* *
24398 TAAACACATAATTAAGCTGACGAGCGTAAACATGTGCAAGTTGGTGAGTG
1 TAAACGCATAAATAAGCTGACGAGCGTAAACATGTGCAAGTTGGTGAGTG
* * *
24448 TAAACGCATAAATTAGCTAACGAGTGTAAACA
1 TAAACGCATAAATAAGCTGACGAGCGTAAACA
24480 AATAAATATT
Statistics
Matches: 195, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
49 1 0.01
50 194 0.99
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (50 bp):
TAAACGCATAAATAAGCTGACGAGCGTAAACATGTGCAAGTTGGTGAGTG
Found at i:31643 original size:26 final size:26
Alignment explanation
Indices: 31612--31690 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 26
31602 AAATATATGC
* *
31612 AAGCTGGTGAGCGTAAATGCATAAAT
1 AAGCTGGCGAGCGTAAACGCATAAAT
*
31638 AAGCTGGCGAGTGTAAACGCATAAAT
1 AAGCTGGCGAGCGTAAACGCATAAAT
* ** *
31664 TAGCTAACGAGCGTAAACACATAAAT
1 AAGCTGGCGAGCGTAAACGCATAAAT
31690 A
1 A
31691 TTTTGATAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (26 bp):
AAGCTGGCGAGCGTAAACGCATAAAT
Found at i:35962 original size:3 final size:3
Alignment explanation
Indices: 35954--35978 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35944 GTTCAACTGT
35954 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
35979 TTGTTTCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:37832 original size:16 final size:16
Alignment explanation
Indices: 37811--37854 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
37801 TTGGATTAAG
37811 AAAATTATTTAATTGA
1 AAAATTATTTAATTGA
* *
37827 AAAATTAATTAATTTA
1 AAAATTATTTAATTGA
*
37843 ATAAATAATTTA
1 A-AAATTATTTA
37855 TATTTTGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AAAATTATTTAATTGA
Found at i:39864 original size:47 final size:47
Alignment explanation
Indices: 39717--39848 Score: 192
Period size: 47 Copynumber: 2.8 Consensus size: 47
39707 ACAGTAATGT
* * * *
39717 AGATAAACTGTCACTTAATAATATTGTGGAAAAGCCACCACTTTTGC
1 AGATAAATTGACACTTTATAATATTGTGGACAAGCCACCACTTTTGC
* * *
39764 AGATAAATTGACACTTTATAATACTGTGAACAAGCCACCACTTTTGT
1 AGATAAATTGACACTTTATAATATTGTGGACAAGCCACCACTTTTGC
*
39811 AGATAAATTGCCACTTTATAATATTGTGGACAAGCCAC
1 AGATAAATTGACACTTTATAATATTGTGGACAAGCCAC
39849 AAGTTTTAGA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 75 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30
Consensus pattern (47 bp):
AGATAAATTGACACTTTATAATATTGTGGACAAGCCACCACTTTTGC
Found at i:39944 original size:20 final size:20
Alignment explanation
Indices: 39919--39958 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
39909 ATATGACCAC
*
39919 AAAAATCACTTTTTCACTTT
1 AAAAATCAATTTTTCACTTT
39939 AAAAATCAATTTTTCACTTT
1 AAAAATCAATTTTTCACTTT
39959 GGCATGTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAATCAATTTTTCACTTT
Found at i:47994 original size:25 final size:25
Alignment explanation
Indices: 47893--48085 Score: 156
Period size: 25 Copynumber: 7.6 Consensus size: 25
47883 TCCAAAAATT
* *
47893 TAGCTCATACAAGCCTAGACAGAATA
1 TAGCTCTTACGAGCC-AGACAGAATA
* *
47919 TTGCTCTTACTAGCCCAGACAGAATA
1 TAGCTCTTACGAG-CCAGACAGAATA
* * * *
47945 TTGCGCTTACGAG-TATATCAGAATA
1 TAGCTCTTACGAGCCAGA-CAGAATA
*
47970 TAGCTCTTACGAGCCAGACAAAATA
1 TAGCTCTTACGAGCCAGACAGAATA
* * * * **
47995 TCGCACCTACAAGCCAGTTAGAATA
1 TAGCTCTTACGAGCCAGACAGAATA
*
48020 TCGCTCTTACGAGCCAGACAGAATA
1 TAGCTCTTACGAGCCAGACAGAATA
* * *
48045 TCGCTCTTACGAGTCAGACAAAATA
1 TAGCTCTTACGAGCCAGACAGAATA
*
48070 TCA-CTCTTTCGAGCCA
1 T-AGCTCTTACGAGCCA
48086 AATATAATAT
Statistics
Matches: 134, Mismatches: 29, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
24 2 0.01
25 97 0.72
26 33 0.25
27 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (25 bp):
TAGCTCTTACGAGCCAGACAGAATA
Found at i:48070 original size:50 final size:50
Alignment explanation
Indices: 47909--48085 Score: 185
Period size: 50 Copynumber: 3.5 Consensus size: 50
47899 ATACAAGCCT
* * * *
47909 AGACAGAATATTGCTCTTACTAGCCCAGACAGAATATTGCGCTTACGAGT-
1 AGACAGAATATCGCTCTTACGAG-CCAGACAGAATATCGCACTTACGAGTC
* * * * * *
47959 ATATCAGAATATAGCTCTTACGAGCCAGACAAAATATCGCACCTACAAGCC
1 AGA-CAGAATATCGCTCTTACGAGCCAGACAGAATATCGCACTTACGAGTC
** *
48010 AGTTAGAATATCGCTCTTACGAGCCAGACAGAATATCGCTCTTACGAGTC
1 AGACAGAATATCGCTCTTACGAGCCAGACAGAATATCGCACTTACGAGTC
* * *
48060 AGACAAAATATCACTCTTTCGAGCCA
1 AGACAGAATATCGCTCTTACGAGCCA
48086 AATATAATAT
Statistics
Matches: 102, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
50 83 0.81
51 19 0.19
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (50 bp):
AGACAGAATATCGCTCTTACGAGCCAGACAGAATATCGCACTTACGAGTC
Found at i:48085 original size:75 final size:77
Alignment explanation
Indices: 47961--48129 Score: 198
Period size: 75 Copynumber: 2.2 Consensus size: 77
47951 TTACGAGTAT
* * ** *
47961 ATCAGAATATAGCTCTTACGAGCCAGACAAAATATCGCACCTACAAGCCAGTTAGAATATCGCTC
1 ATCAGAATATCGCTCTTACGAGCCAGACAAAATATCACACCTACAAGCCAAATAGAATATCACTC
48026 TTACGAGCCAG-
66 TTACGAGCCAGA
* * * * * *
48037 A-CAGAATATCGCTCTTACGAGTCAGACAAAATATCACTCTTTCGAGCCAAATATAATATCACTC
1 ATCAGAATATCGCTCTTACGAGCCAGACAAAATATCACACCTACAAGCCAAATAGAATATCACTC
* *
48101 TTTCGAGCTAGA
66 TTACGAGCCAGA
*
48113 ATCAGAATAACGCTCTT
1 ATCAGAATATCGCTCTT
48130 TCAAGCAAGA
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
75 61 0.79
76 2 0.03
77 14 0.18
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (77 bp):
ATCAGAATATCGCTCTTACGAGCCAGACAAAATATCACACCTACAAGCCAAATAGAATATCACTC
TTACGAGCCAGA
Found at i:48129 original size:27 final size:27
Alignment explanation
Indices: 47961--48191 Score: 167
Period size: 25 Copynumber: 8.9 Consensus size: 27
47951 TTACGAGTAT
* * *
47961 ATCAGAATATAGCTCTTACGAGCCAG-
1 ATCAAAATATCGCTCTTTCGAGCCAGA
* * * *
47987 A-CAAAATATCGCACCTACAAGCCAG-
1 ATCAAAATATCGCTCTTTCGAGCCAGA
* * *
48012 -TTAGAATATCGCTCTTACGAGCCAG-
1 ATCAAAATATCGCTCTTTCGAGCCAGA
* * *
48037 A-CAGAATATCGCTCTTACGAGTCAG-
1 ATCAAAATATCGCTCTTTCGAGCCAGA
*
48062 A-CAAAATATCACTCTTTCGAGCCA-A
1 ATCAAAATATCGCTCTTTCGAGCCAGA
* * *
48087 AT-ATAATATCACTCTTTCGAGCTAGA
1 ATCAAAATATCGCTCTTTCGAGCCAGA
* * * *
48113 ATCAGAATAACGCTCTTTCAAGCAAGA
1 ATCAAAATATCGCTCTTTCGAGCCAGA
* * *
48140 ATCAAAATAACGCTCATTCGAGCCAAA
1 ATCAAAATATCGCTCTTTCGAGCCAGA
*
48167 ATCAAAATAACGCTCTTTCGAGCCA
1 ATCAAAATATCGCTCTTTCGAGCCA
48192 AAGTCAGATT
Statistics
Matches: 170, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
25 101 0.59
26 4 0.02
27 65 0.38
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.23
Consensus pattern (27 bp):
ATCAAAATATCGCTCTTTCGAGCCAGA
Found at i:48192 original size:27 final size:27
Alignment explanation
Indices: 48063--48193 Score: 142
Period size: 27 Copynumber: 4.9 Consensus size: 27
48053 ACGAGTCAGA
* *
48063 CAAAATATCACTCTTTCGAGCC-AAAT
1 CAAAATAACGCTCTTTCGAGCCAAAAT
* * * * *
48089 -ATAATATCACTCTTTCGAGCTAGAAT
1 CAAAATAACGCTCTTTCGAGCCAAAAT
* *
48115 CAGAATAACGCTCTTTCAAG-CAAGAAT
1 CAAAATAACGCTCTTTCGAGCCAA-AAT
*
48142 CAAAATAACGCTCATTCGAGCCAAAAT
1 CAAAATAACGCTCTTTCGAGCCAAAAT
48169 CAAAATAACGCTCTTTCGAGCCAAA
1 CAAAATAACGCTCTTTCGAGCCAAA
48194 GTCAGATTAC
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
25 19 0.22
26 4 0.05
27 62 0.70
28 3 0.03
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.24
Consensus pattern (27 bp):
CAAAATAACGCTCTTTCGAGCCAAAAT
Found at i:57122 original size:20 final size:20
Alignment explanation
Indices: 57093--57130 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57083 ATATATTTCA
* *
57093 TTTATGCTTGTTTTTATTCT
1 TTTATACTTGCTTTTATTCT
57113 TTTATACTTGCTTTTATT
1 TTTATACTTGCTTTTATT
57131 TATTATCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.11, G:0.08, T:0.68
Consensus pattern (20 bp):
TTTATACTTGCTTTTATTCT
Found at i:58013 original size:2 final size:2
Alignment explanation
Indices: 58006--58051 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
57996 TTAACATACA
*
58006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58048 AT AT
1 AT AT
58052 TAAAAATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62524 original size:20 final size:20
Alignment explanation
Indices: 62501--62561 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
62491 AAAACTCCTC
*
62501 TTCTACTGATACAACTATAG
1 TTCTACCGATACAACTATAG
62521 TTCTACCGATACAACTAT-G
1 TTCTACCGATACAACTATAG
62540 TTGCTACCGGA-ACAACTA-AG
1 TT-CTACC-GATACAACTATAG
62560 TT
1 TT
62562 ACAGACTGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 3 0.08
20 32 0.86
21 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (20 bp):
TTCTACCGATACAACTATAG
Found at i:63390 original size:20 final size:20
Alignment explanation
Indices: 63365--63410 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
63355 TGGTTGGGAA
63365 GGTTCTATTGCTGATGGACG
1 GGTTCTATTGCTGATGGACG
* *
63385 GGTTCTGTTGCTGATGGATG
1 GGTTCTATTGCTGATGGACG
63405 GGTTCT
1 GGTTCT
63411 TCGAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.11, C:0.13, G:0.37, T:0.39
Consensus pattern (20 bp):
GGTTCTATTGCTGATGGACG
Found at i:65633 original size:24 final size:24
Alignment explanation
Indices: 65592--65638 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
65582 GTTATATATT
*
65592 ATTTTTCTAATATTATATATTAAA
1 ATTTTTCTAATATCATATATTAAA
*
65616 ATTTTTACTAAT-TCATATTTTAA
1 ATTTTT-CTAATATCATATATTAA
65639 TAATAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTTCTAATATCATATATTAAA
Found at i:65740 original size:58 final size:57
Alignment explanation
Indices: 65625--65770 Score: 161
Period size: 57 Copynumber: 2.5 Consensus size: 57
65615 AATTTTTACT
* *
65625 AATTCATATTTTAATAATAATATATTAAAAATGTTATTAAATTATATATTATTTTATTA
1 AATT-ATA-TTTAATAATAATATATTAAAAATATAATTAAATTATATATTATTTTATTA
* * *
65684 TATTGTATTTAATAATAAT-TATGTTAAAATATAATTAAATTA-ATTATTATTTTTATTA
1 AATTATATTTAATAATAATATAT-TAAAAATATAATTAAATTATA-TATTA-TTTTATTA
* *
65742 AATTATATTTAGTAATAATCTTATTAAAA
1 AATTATATTTAATAATAAT-ATATTAAAA
65771 TTTAATAACA
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
56 4 0.05
57 33 0.45
58 26 0.36
59 7 0.10
60 3 0.04
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (57 bp):
AATTATATTTAATAATAATATATTAAAAATATAATTAAATTATATATTATTTTATTA
Found at i:65771 original size:58 final size:57
Alignment explanation
Indices: 65616--65776 Score: 166
Period size: 58 Copynumber: 2.8 Consensus size: 57
65606 ATATATTAAA
* * * *
65616 ATTTTTACT-AATTCATATTTTAATAATAATATATTAAAAATGTTATTAAATTATATATT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTTATT-AAAATATAATTAAATTATATATT
* * *
65675 A-TTTTATTATATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTA-ATTATT
1 ATTTTTATTAAATTATATTTAATAATAATT-TATTAAAATATAATTAAATTATA-TATT
* *
65732 ATTTTTATTAAATTATATTTAGTAATAATCTTATTAAAATTTAAT
1 ATTTTTATTAAATTATATTTAATAATAAT-TTATTAAAATATAAT
65777 AACAATAATC
Statistics
Matches: 85, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
56 1 0.01
57 32 0.38
58 47 0.55
59 5 0.06
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (57 bp):
ATTTTTATTAAATTATATTTAATAATAATTTATTAAAATATAATTAAATTATATATT
Found at i:65953 original size:16 final size:16
Alignment explanation
Indices: 65932--65971 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
65922 TGAATTACTG
65932 ATTACAGCCCTATTCC
1 ATTACAGCCCTATTCC
* *
65948 ATTACAACTCTATTCC
1 ATTACAGCCCTATTCC
65964 ATTACAGC
1 ATTACAGC
65972 GAACCAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.33
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:66244 original size:57 final size:56
Alignment explanation
Indices: 66118--66306 Score: 186
Period size: 57 Copynumber: 3.3 Consensus size: 56
66108 AATATTTAAT
* *
66118 AAATTTAGGTATCAAATTGAATATAAAAAAGTTTATG-TACCAAATTAGGAAAAAATATC
1 AAATTTAGATATCAAATTG-ATA-AAAAAAATTTA-GATACCAAATTA-GAAAAAATATC
* * * * *
66177 AAGTTCAGATATCAAATTTGATAAAAAAAAATTAGATACCAAATTAGAAAAACTGTC
1 AAATTTAGATATCAAA-TTGATAAAAAAAATTTAGATACCAAATTAGAAAAAATATC
* *
66234 AAATTTAGATACCAAATTGAGTCAAAAAAAATTTA-AGTACCAAATTA-AAAAAAAATC
1 AAATTTAGATATCAAATTGA-T-AAAAAAAATTTAGA-TACCAAATTAGAAAAAATATC
* *
66291 AAATTCAAATATCAAA
1 AAATTTAGATATCAAA
66307 GATTATATTA
Statistics
Matches: 108, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
56 4 0.04
57 45 0.42
58 40 0.37
59 16 0.15
60 3 0.03
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (56 bp):
AAATTTAGATATCAAATTGATAAAAAAAATTTAGATACCAAATTAGAAAAAATATC
Found at i:67423 original size:2 final size:2
Alignment explanation
Indices: 67412--67444 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
67402 CCCTATAATC
67412 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67445 AGTACAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:69031 original size:16 final size:16
Alignment explanation
Indices: 69004--69056 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 16
68994 ATATCTTAAA
*
69004 TTTTCAATACTTAACT
1 TTTTCAACACTTAACT
*
69020 TTTTTAACACTT-ACT
1 TTTTCAACACTTAACT
*
69035 TTTTCAACATTTAA-T
1 TTTTCAACACTTAACT
69050 TTTTCAA
1 TTTTCAA
69057 ATTATCAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 21 0.66
16 11 0.34
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTCAACACTTAACT
Found at i:77100 original size:39 final size:39
Alignment explanation
Indices: 77039--77221 Score: 188
Period size: 39 Copynumber: 4.7 Consensus size: 39
77029 CGATTTGCAC
* * *
77039 TGAACTGGCAGTAACACTGTAAACACTACAATGATATAT
1 TGAACTAGCAGTGACACTGTAAACACTGCAATGATATAT
* * * *
77078 TGGACTAGCAGTGACATTGTAAACACTGCAAAGATATAC
1 TGAACTAGCAGTGACACTGTAAACACTGCAATGATATAT
* * * *
77117 TGAACTGGCAGTTACATTGTAAACACTGCAATGCTATAT
1 TGAACTAGCAGTGACACTGTAAACACTGCAATGATATAT
* * * * * *
77156 TGAACTAGCGGTGATACTGTAAACACCGCGATGCTATAC
1 TGAACTAGCAGTGACACTGTAAACACTGCAATGATATAT
*
77195 TGAAGC-AGTAGTGACACTGTAAACACT
1 TGAA-CTAGCAGTGACACTGTAAACACT
77222 ACTAGACTAT
Statistics
Matches: 118, Mismatches: 25, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
39 117 0.99
40 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (39 bp):
TGAACTAGCAGTGACACTGTAAACACTGCAATGATATAT
Found at i:77122 original size:78 final size:78
Alignment explanation
Indices: 77037--77223 Score: 223
Period size: 78 Copynumber: 2.4 Consensus size: 78
77027 ATCGATTTGC
* *
77037 ACTGAACTGGCAGTAACACTGTAAACACTACAATGATATATTGGACTAGCAGTGACATTGTAAAC
1 ACTGAACTGGCAGTAACACTGTAAACACTACAATGATATATTGAACTAGCAGTGACACTGTAAAC
*
77102 ACTGCAAAGATAT
66 ACCGCAAAGATAT
* * * * * *
77115 ACTGAACTGGCAGTTACATTGTAAACACTGCAATGCTATATTGAACTAGCGGTGATACTGTAAAC
1 ACTGAACTGGCAGTAACACTGTAAACACTACAATGATATATTGAACTAGCAGTGACACTGTAAAC
* * *
77180 ACCGCGATGCTAT
66 ACCGCAAAGATAT
* * *
77193 ACTGAAGC-AGTAGTGACACTGTAAACACTAC
1 ACTGAA-CTGGCAGTAACACTGTAAACACTAC
77224 TAGACTATCA
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 90 0.99
79 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (78 bp):
ACTGAACTGGCAGTAACACTGTAAACACTACAATGATATATTGAACTAGCAGTGACACTGTAAAC
ACCGCAAAGATAT
Found at i:79738 original size:55 final size:55
Alignment explanation
Indices: 79654--79764 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
79644 ATACATGCCA
79654 AAGTACGTAAACGTACGATGGAAAGGAAATTCCCGTTTGAACCTAGAGAATACTT
1 AAGTACGTAAACGTACGATGGAAAGGAAATTCCCGTTTGAACCTAGAGAATACTT
79709 AAGTACGTAAACGTACGATGGAAAGGAAATTCCCGTTTGAACCTAGAGAATACTT
1 AAGTACGTAAACGTACGATGGAAAGGAAATTCCCGTTTGAACCTAGAGAATACTT
79764 A
1 A
79765 GGATGCAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (55 bp):
AAGTACGTAAACGTACGATGGAAAGGAAATTCCCGTTTGAACCTAGAGAATACTT
Found at i:88096 original size:11 final size:11
Alignment explanation
Indices: 88080--88135 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
88070 TTAACATAAA
88080 TTTTAATATAT
1 TTTTAATATAT
88091 TTTTAATA-AT
1 TTTTAATATAT
* *
88101 TTAT-ATTTAT
1 TTTTAATATAT
88111 TTTTAATATAT
1 TTTTAATATAT
88122 TTTTAA-AT-T
1 TTTTAATATAT
88131 TTTTA
1 TTTTA
88136 GAATTGTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 8 0.21
10 12 0.31
11 19 0.49
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:88133 original size:20 final size:21
Alignment explanation
Indices: 88080--88135 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
88070 TTAACATAAA
88080 TTTTAATATATTTTTAATA-AT
1 TTTTAA-ATATTTTTAATATAT
* **
88101 TTATATTTATTTTTAATATAT
1 TTTTAAATATTTTTAATATAT
88122 TTTTAAAT-TTTTTA
1 TTTTAAATATTTTTA
88136 GAATTGTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTAAATATTTTTAATATAT
Found at i:88146 original size:31 final size:31
Alignment explanation
Indices: 88080--88147 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
88070 TTAACATAAA
* * *
88080 TTTTAATATATTTTTAATAATTTATATTTAT
1 TTTTAATATATTTTTAATAATTTAGAATTAG
**
88111 TTTTAATATATTTTTAAATTTTTTAGAATT-G
1 TTTTAATATATTTTT-AATAATTTAGAATTAG
88142 TTTTAA
1 TTTTAA
88148 GGAAATTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (31 bp):
TTTTAATATATTTTTAATAATTTAGAATTAG
Found at i:88746 original size:18 final size:18
Alignment explanation
Indices: 88723--88757 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88713 ATATTTTTTA
* *
88723 AAATTAATTTAATTAATC
1 AAATTAACTAAATTAATC
88741 AAATTAACTAAATTAAT
1 AAATTAACTAAATTAAT
88758 TTTTCAATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTAACTAAATTAATC
Found at i:90911 original size:21 final size:20
Alignment explanation
Indices: 90887--90940 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
90877 TCTCTTTCTC
*
90887 TAATTTTTGTAAAATTTATTA
1 TAATTTTTGTAAAATAT-TTA
90908 TAATTCTTT-TAAAATATTTA
1 TAATT-TTTGTAAAATATTTA
90928 TATATTTTATGTA
1 TA-ATTTT-TGTA
90941 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 7 0.25
21 16 0.57
22 5 0.18
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
TAATTTTTGTAAAATATTTA
Found at i:97910 original size:20 final size:20
Alignment explanation
Indices: 97869--97922 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
97859 AATAATTTTT
97869 AAAATTCT-AAATATTAATA
1 AAAATTCTAAAATATTAATA
*
97888 AAAATTCTAAAATTTGTAA-A
1 AAAATTCTAAAATAT-TAATA
* *
97908 AAAAATCTAATATAT
1 AAAATTCTAAAATAT
97923 ATATATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.28
20 18 0.62
21 3 0.10
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAATTCTAAAATATTAATA
Found at i:98970 original size:34 final size:34
Alignment explanation
Indices: 98905--98974 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
98895 TATTGTTTTT
* * *
98905 TTTTTTTAAATAAATTCAAAATATCATAAAAAAA
1 TTTTTTTAAACAAATACAAAAAATCATAAAAAAA
*
98939 TTTTTTTAAACAAATAGAAAAAATC-TCAAAAAAA
1 TTTTTTTAAACAAATACAAAAAATCAT-AAAAAAA
98973 TT
1 TT
98975 AAAAATTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 1 0.03
34 30 0.97
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (34 bp):
TTTTTTTAAACAAATACAAAAAATCATAAAAAAA
Found at i:99127 original size:17 final size:18
Alignment explanation
Indices: 99090--99132 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
99080 TGCGGATTTC
*
99090 TTAAGAAAATTATTTTAT
1 TTAATAAAATTATTTTAT
99108 TT-ATAAAATTATTATT-T
1 TTAATAAAATTATT-TTAT
99125 TTAATAAA
1 TTAATAAA
99133 CAAATTTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTAATAAAATTATTTTAT
Found at i:99254 original size:8 final size:9
Alignment explanation
Indices: 99235--99264 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
99225 TGAATATTTA
99235 TTTTTAATT
1 TTTTTAATT
99244 TTTTTAATTT
1 TTTTTAA-TT
99254 TTTTTAATT
1 TTTTTAATT
99263 TT
1 TT
99265 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTAATT
Found at i:99255 original size:10 final size:10
Alignment explanation
Indices: 99230--99264 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
99220 AAAAATGAAT
99230 ATTTATTTTTA
1 ATTT-TTTTTA
99241 A-TTTTTTTA
1 ATTTTTTTTA
99250 ATTTTTTTTA
1 ATTTTTTTTA
99260 ATTTT
1 ATTTT
99265 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.30
10 15 0.65
11 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:100269 original size:20 final size:20
Alignment explanation
Indices: 100240--100280 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
100230 AAATACAAAC
*
100240 AATGTTTCAAATACATCATA
1 AATGTCTCAAATACATCATA
100260 AATGTCTCAAATACATCATA
1 AATGTCTCAAATACATCATA
100280 A
1 A
100281 TATGCTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (20 bp):
AATGTCTCAAATACATCATA
Found at i:104233 original size:18 final size:19
Alignment explanation
Indices: 104202--104239 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
104192 ATGATTGCTT
104202 TAATCATAACTTACACCGG
1 TAATCATAACTTACACCGG
104221 TAATCAT-ACTTACACCGG
1 TAATCATAACTTACACCGG
104239 T
1 T
104240 GTAAGTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (19 bp):
TAATCATAACTTACACCGG
Found at i:114604 original size:21 final size:21
Alignment explanation
Indices: 114570--114609 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
114560 TACCATTTCT
*
114570 ATTCATTTGGTTGAACATGCA
1 ATTCATTTAGTTGAACATGCA
* *
114591 ATTCATTTATTTGATCATG
1 ATTCATTTAGTTGAACATG
114610 AGGTGGTTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (21 bp):
ATTCATTTAGTTGAACATGCA
Found at i:115783 original size:25 final size:25
Alignment explanation
Indices: 115749--115797 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
115739 TGATCGCTAT
*
115749 TTGTTATTTGTTTAATTTTATTTAA
1 TTGTTATTTGTTTAATTTAATTTAA
115774 TTGTTATTTGTTTAATTTAATTTA
1 TTGTTATTTGTTTAATTTAATTTA
115798 TTTTACAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.67
Consensus pattern (25 bp):
TTGTTATTTGTTTAATTTAATTTAA
Found at i:129699 original size:23 final size:22
Alignment explanation
Indices: 129669--129750 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
129659 GGAACTCAAT
129669 TTTAAATTTTAATTTATTTAAAG
1 TTTAAA-TTTAATTTATTTAAAG
**
129692 TTTAAATTTAATTTTATTTTGAG
1 TTTAAATTTAA-TTTATTTAAAG
*
129715 TTTAAATTTATTTTAAATTTAAA-
1 TTTAAATTTAATTT--ATTTAAAG
129738 TTTAAATTTAATT
1 TTTAAATTTAATT
129751 AAAAATTGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
22 8 0.16
23 37 0.74
24 5 0.10
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (22 bp):
TTTAAATTTAATTTATTTAAAG
Found at i:129701 original size:6 final size:6
Alignment explanation
Indices: 129669--129748 Score: 69
Period size: 6 Copynumber: 13.8 Consensus size: 6
129659 GGAACTCAAT
* * * * *
129669 TTTAAA TTTTAA TTT--A TTTAAA GTTTAAA TTT-AA TTTTAT TTTGAG
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA
*
129715 TTTAAA TTT-AT TTTAAA TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
129749 TTAAAAATTG
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
4 4 0.07
5 9 0.15
6 42 0.69
7 6 0.10
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:129750 original size:17 final size:18
Alignment explanation
Indices: 129669--129748 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 18
129659 GGAACTCAAT
*
129669 TTTAAATTTTAATTT--A
1 TTTAAATTTAAATTTAAA
129685 TTTAAAGTTTAAATTT-AA
1 TTTAAA-TTTAAATTTAAA
* * * *
129703 TTTTATTTTGAGTTTAAA
1 TTTAAATTTAAATTTAAA
*
129721 TTT-ATTTTAAATTTAAA
1 TTTAAATTTAAATTTAAA
129738 TTTAAATTTAA
1 TTTAAATTTAA
129749 TTAAAAATTG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
16 6 0.12
17 30 0.58
18 16 0.31
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
TTTAAATTTAAATTTAAA
Found at i:131536 original size:30 final size:30
Alignment explanation
Indices: 131500--131731 Score: 126
Period size: 30 Copynumber: 8.0 Consensus size: 30
131490 AAAAGGTCCC
* *
131500 TAAACTTTCCAAAAATCACATTTTAATCCT
1 TAAACTTTCCAAAAATTACATTTTAACCCT
** * *
131530 TAAACTTTTTAAAAATTACA-TTTGACCCC
1 TAAACTTTCCAAAAATTACATTTTAACCCT
* *
131559 TAAACTATTTC-AAAATTACATTTTTACCCT
1 TAAACT-TTCCAAAAATTACATTTTAACCCT
* *
131589 TAAAC-TTCTTAAAAATTACATTTTTACCCT
1 TAAACTTTC-CAAAAATTACATTTTAACCCT
** * * *
131619 CGAAC-TCCCAAAAATCACATTTT-ACCCC
1 TAAACTTTCCAAAAATTACATTTTAACCCT
* * * *
131647 CAAGC-TTCCAAAAATTATATTTT--GCCT
1 TAAACTTTCCAAAAATTACATTTTAACCCT
* * *
131674 CTAAAC-TTCTAAAAATCACATTTTTACCC-
1 -TAAACTTTCCAAAAATTACATTTTAACCCT
* * *
131703 CAGATCTTTCC-AAAATTATATTTTAACCC
1 TA-AACTTTCCAAAAATTACATTTTAACCC
131732 CGAACTCTCT
Statistics
Matches: 157, Mismatches: 36, Indels: 19
0.74 0.17 0.09
Matches are distributed among these distances:
27 2 0.01
28 43 0.27
29 51 0.32
30 61 0.39
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
TAAACTTTCCAAAAATTACATTTTAACCCT
Found at i:131563 original size:29 final size:30
Alignment explanation
Indices: 131497--131617 Score: 127
Period size: 30 Copynumber: 4.1 Consensus size: 30
131487 CTCAAAAGGT
** * *
131497 CCCTAAACTTTCCAAAAATCACATTTTAAT
1 CCCTAAACTTTTTAAAAATTACATTTTAAC
* *
131527 CCTTAAACTTTTTAAAAATTACA-TTTGAC
1 CCCTAAACTTTTTAAAAATTACATTTTAAC
* * *
131556 CCCTAAACTATTTCAAAATTACATTTTTAC
1 CCCTAAACTTTTTAAAAATTACATTTTAAC
* * *
131586 CCTTAAACTTCTTAAAAATTACATTTTTAC
1 CCCTAAACTTTTTAAAAATTACATTTTAAC
131616 CC
1 CC
131618 TCGAACTCCC
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
29 24 0.32
30 52 0.68
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (30 bp):
CCCTAAACTTTTTAAAAATTACATTTTAAC
Found at i:131574 original size:59 final size:59
Alignment explanation
Indices: 131497--131702 Score: 183
Period size: 59 Copynumber: 3.5 Consensus size: 59
131487 CTCAAAAGGT
* *
131497 CCCTAAACTTTCCAAAAATCACATTTTAATCCTTAAACTTTTTAAAAATTACATTTGAC
1 CCCTAAACTTTCCAAAAATCACATTTTAACCCTTAAACTTCTTAAAAATTACATTTGAC
* * * *
131556 CCCTAAACTATTTC-AAAATTACATTTTTACCCTTAAACTTCTTAAAAATTACATTTTTA-
1 CCCTAAACT-TTCCAAAAATCACATTTTAACCCTTAAACTTCTTAAAAATTACA-TTTGAC
* * ** * * *
131615 CCCTCGAAC-TCCCAAAAATCACATTTT-ACCCCCAAGCTTC-CAAAAATTATATTTTG-C
1 CCCT-AAACTTTCCAAAAATCACATTTTAACCCTTAAACTTCTTAAAAATTACA-TTTGAC
* * *
131672 CTCTAAAC-TTCTAAAAATCACATTTTTACCC
1 CCCTAAACTTTCCAAAAATCACATTTTAACCC
131703 CAGATCTTTC
Statistics
Matches: 121, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
56 19 0.16
57 20 0.17
58 12 0.10
59 60 0.50
60 10 0.08
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (59 bp):
CCCTAAACTTTCCAAAAATCACATTTTAACCCTTAAACTTCTTAAAAATTACATTTGAC
Found at i:131632 original size:29 final size:29
Alignment explanation
Indices: 131570--131702 Score: 110
Period size: 28 Copynumber: 4.6 Consensus size: 29
131560 AAACTATTTC
* **
131570 AAAATTACATTTTTACCCTTAAACTTCTTA
1 AAAATTACATTTTTACCCTCAAAC-TCCCA
*
131600 AAAATTACATTTTTACCCTCGAACTCCCA
1 AAAATTACATTTTTACCCTCAAACTCCCA
* * * *
131629 AAAATCACA-TTTTACCCCCAAGCTTCCA
1 AAAATTACATTTTTACCCTCAAACTCCCA
* * * *
131657 AAAATTATA-TTTT-GCCTCTAAACTTCTA
1 AAAATTACATTTTTACCCTC-AAACTCCCA
*
131685 AAAATCACATTTTTACCC
1 AAAATTACATTTTTACCC
131703 CAGATCTTTC
Statistics
Matches: 82, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
27 3 0.04
28 40 0.49
29 15 0.18
30 24 0.29
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTCAAACTCCCA
Found at i:131910 original size:16 final size:16
Alignment explanation
Indices: 131880--131923 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
131870 TATTTTTATC
131880 ATATTTATT--TTCGT
1 ATATTTATTCATTCGT
131894 ATATTTATTCATTCGT
1 ATATTTATTCATTCGT
*
131910 ATATTTGTTCATTC
1 ATATTTATTCATTC
131924 TTTGTGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 9 0.33
16 18 0.67
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.59
Consensus pattern (16 bp):
ATATTTATTCATTCGT
Found at i:132162 original size:37 final size:37
Alignment explanation
Indices: 132103--132176 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
132093 ACTTACTAGG
* *
132103 CGCAAATTTTCTTTAAATCGAGATAATCGAATATCCT
1 CGCAAATTTTCTTCAAACCGAGATAATCGAATATCCT
*
132140 CGCAATTTTTCTTCAAACCGAGATAATCGAATATCCT
1 CGCAAATTTTCTTCAAACCGAGATAATCGAATATCCT
132177 TCTTCAAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.34
Consensus pattern (37 bp):
CGCAAATTTTCTTCAAACCGAGATAATCGAATATCCT
Found at i:142867 original size:3 final size:3
Alignment explanation
Indices: 142859--142885 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
142849 TTATGATATT
142859 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
142886 AGGGATGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:146568 original size:21 final size:21
Alignment explanation
Indices: 146525--146585 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
146515 TAGTTGCATG
*
146525 ACTTGTAACGGTAGAAATCAT
1 ACTTGTAACAGTAGAAATCAT
* * *
146546 ACTTGTATCAGTAGAACTTAT
1 ACTTGTAACAGTAGAAATCAT
** *
146567 ACAGGTACCAGTAGAAATC
1 ACTTGTAACAGTAGAAATC
146586 TGCACCATTC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (21 bp):
ACTTGTAACAGTAGAAATCAT
Found at i:153565 original size:78 final size:78
Alignment explanation
Indices: 153385--153694 Score: 408
Period size: 78 Copynumber: 4.0 Consensus size: 78
153375 TCAAGAAGGA
* * * *
153385 CAGCCATTCGATCTTTTACCCCGAGCTTAGGGCAAATCACCATTAGCCAATCTCTTACCCCGAGC
1 CAGCCATTCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGC
153450 CT-GGGCAGATTG
66 CTGGGGCAGATTG
* * * * * *
153462 CAGCTATTAGATCTCTTACCCCGAGCCTGGGGCAGATCACTATCAGCAAATCTCTTACCCCAAGC
1 CAGCCATTCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGC
153527 CTGGGGCAGATTG
66 CTGGGGCAGATTG
* * * *
153540 CAGCCATTTGATCTCTTACCCCGAGCCT-GGTGTAGATCACCATCATCCAATCTCTTACCCTGAG
1 CAGCCATTCGATCTCTTACCCCGAGCCTAGG-GCAGATCACCATCAGCCAATCTCTTACCCCGAG
**
153604 TTTGGGGCAGATTG
65 CCTGGGGCAGATTG
* * * *
153618 CAACCATTCGATCTTTTACCCCGAGCCTAGGGCAGATCACCATCATCTAATCTCTTACCCCGAGC
1 CAGCCATTCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGC
*
153683 CTGAGGCAGATT
66 CTGGGGCAGATT
153695 ACCATTAGCC
Statistics
Matches: 201, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
77 59 0.29
78 140 0.70
79 2 0.01
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (78 bp):
CAGCCATTCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGC
CTGGGGCAGATTG
Found at i:153638 original size:117 final size:117
Alignment explanation
Indices: 153388--153808 Score: 332
Period size: 117 Copynumber: 3.6 Consensus size: 117
153378 AGAAGGACAG
* * * * * *
153388 CCATTCGATCTTTTACCCCGAGCTTAGGGCA-AATCACCATTAGCCAATCTCTTACCCCGAGCCT
1 CCATTCAATCTTTTACCCCAAGCCTAGGGCAGATTCACCA-TATCTAATCTCTTACCCCGAGCCT
* * * * * *
153452 G-GGCAGATTGCAGCTATTAG---AT-CTCTTACCCCGAGCCTGGGGCAGATCACTA
65 GAGGCAGA-T-CA-CCATCAGCCAATCCT-TTACCCCGAGCTTGAGGCAGATTACAA
* * * * *
153504 TCA-GCAAATCTCTTACCCCAAGCCTGGGGCAGATTGCAGCCAT-T-TGATCTCTTACCCCGAGC
1 CCATTC-AATCTTTTACCCCAAGCCTAGGGCAGATT-CA-CCATATCTAATCTCTTACCCCGAGC
* * * * * *
153566 CTG-GTGTAGATCACCATCATCCAAT-CTCTTACCCTGAGTTTGGGGCAGATTGCAA
63 CTGAG-GCAGATCACCATCAGCCAATCCT-TTACCCCGAGCTTGAGGCAGATTACAA
* *
153621 CCATTCGATCTTTTACCCCGAGCCTAGGGCAGA-TCACCATCATCTAATCTCTTACCCCGAGCCT
1 CCATTCAATCTTTTACCCCAAGCCTAGGGCAGATTCACCAT-ATCTAATCTCTTACCCCGAGCCT
* * *
153685 GAGGCAGATTACCATTAGCCAATCCTTTACCCCGAGCTTGAGGCAGATTACAG
65 GAGGCAGATCACCATCAGCCAATCCTTTACCCCGAGCTTGAGGCAGATTACAA
*
153738 CCATTCAATCTTTTACCTCGAA-CCTAGGGCAGA-TCACCATCAGTC-AATCTCTTACCCCGAGC
1 CCATTCAATCTTTTACC-CCAAGCCTAGGGCAGATTCACCAT-A-TCTAATCTCTTACCCCGAGC
*
153800 TTGGAGGCA
63 CT-GAGGCA
153809 AATTGCAGTC
Statistics
Matches: 247, Mismatches: 41, Indels: 32
0.77 0.13 0.10
Matches are distributed among these distances:
114 8 0.03
115 5 0.02
116 45 0.18
117 169 0.68
118 17 0.07
119 3 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (117 bp):
CCATTCAATCTTTTACCCCAAGCCTAGGGCAGATTCACCATATCTAATCTCTTACCCCGAGCCTG
AGGCAGATCACCATCAGCCAATCCTTTACCCCGAGCTTGAGGCAGATTACAA
Found at i:153730 original size:78 final size:78
Alignment explanation
Indices: 153395--153889 Score: 360
Period size: 78 Copynumber: 6.3 Consensus size: 78
153385 CAGCCATTCG
* * * *
153395 ATCTTTTACCCCGAGCTT-AGGGCAAATCACCATTAGCCAATCTCTTACCCCGAGCCTG-GGCAG
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCATCATCCAATCTCTTACCCCGAGCCTGAGGCAG
*
153458 ATTGCAGCTATTAG--
65 ATT-CA-CCATTAGCA
* * * * * * *
153472 ATCTCTTACCCCGAGCCTGGGGCAGATCACTATCAGCAAATCTCTTACCCCAAGCCTGGGGCAGA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCATCCAATCTCTTACCCCGAGCCTGAGGCAGA
*
153537 TTGCAGCCATTTG--
66 TT-CA-CCATTAGCA
* * * ** *
153550 ATCTCTTACCCCGAGCCTG-GTGTAGATCACCATCATCCAATCTCTTACCCTGAGTTTGGGGCAG
1 ATCTCTTACCCCGAGCTTGAG-GCAGATCACCATCATCCAATCTCTTACCCCGAGCCTGAGGCAG
*
153614 ATTGCAACCATT--CG
65 ATT-C-ACCATTAGCA
* * *
153628 ATCTTTTACCCCGAGCCT-AGGGCAGATCACCATCATCTAATCTCTTACCCCGAGCCTGAGGCAG
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCATCATCCAATCTCTTACCCCGAGCCTGAGGCAG
153692 ATT-ACCATTAGCCA
65 ATTCACCATTAG-CA
* * * * * *
153706 ATC-CTTTACCCCGAGCTTGAGGCAGATTA-CAGCCATTCAATCTTTTACCTCGAACCT-AGGGC
1 ATCTC-TTACCCCGAGCTTGAGGCAGATCACCA-TCATCCAATCTCTTACCCCGAGCCTGA-GGC
*
153768 AGA-TCACCATCAGTCA
63 AGATTCACCATTAG-CA
* ** * * *
153784 ATCTCTTACCCCGAGCTTGGAGGCAAAT-TGCAGTCATTCGATCTTTTACCCCGAGCCT-AGGAC
1 ATCTCTTACCCCGAGCTT-GAGGCAGATCACCA-TCATCCAATCTCTTACCCCGAGCCTGAGG-C
*
153847 AGA-TCACCATCAGCTA
63 AGATTCACCATTAGC-A
*
153863 ATCTCTTACCTCGAGCTTGAGGCAGAT
1 ATCTCTTACCCCGAGCTTGAGGCAGAT
153890 TGCAACCATC
Statistics
Matches: 352, Mismatches: 45, Indels: 41
0.80 0.10 0.09
Matches are distributed among these distances:
75 6 0.02
77 54 0.15
78 223 0.63
79 69 0.20
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCATCCAATCTCTTACCCCGAGCCTGAGGCAGA
TTCACCATTAGCA
Found at i:153905 original size:39 final size:39
Alignment explanation
Indices: 153431--153905 Score: 264
Period size: 39 Copynumber: 12.2 Consensus size: 39
153421 TCACCATTAG
* * *
153431 CCAATCTCTTACCCCGAGCCTG-GGCAGATTGCAGCTAT
1 CCAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCAT
* * * * * *
153469 -TAGATCTCTTACCCCGAGCCTGGGGCAGATCACTATCAG
1 CCA-ATCTCTTACCCCGAGCCTGAGGCAGATTACAACCAT
* * * * *
153508 CAAATCTCTTACCCCAAGCCTGGGGCAGATTGCAGCCAT
1 CCAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCAT
*** * * * *
153547 TTGATCTCTTACCCCGAGCCTG-GTGTAGATCACCATCAT
1 CCAATCTCTTACCCCGAGCCTGAG-GCAGATTACAACCAT
* ** * *
153586 CCAATCTCTTACCCTGAGTTTGGGGCAGATTGCAACCAT
1 CCAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCAT
* * * * * *
153625 TCGATCTTTTACCCCGAGCCT-AGGGCAGATCACCATCAT
1 CCAATCTCTTACCCCGAGCCTGA-GGCAGATTACAACCAT
* * ** *
153664 CTAATCTCTTACCCCGAGCCTGAGGCAGATTACCATTAG
1 CCAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCAT
* *
153703 CCAATC-CTTTACCCCGAGCTTGAGGCAGATTACAGCCAT
1 CCAATCTC-TTACCCCGAGCCTGAGGCAGATTACAACCAT
* * * * * * *
153742 TCAATCTTTTACCTCGAACCT-AGGGCAGATCACCATCAGT
1 CCAATCTCTTACCCCGAGCCTGA-GGCAGATTACAACCA-T
* * * **
153782 -CAATCTCTTACCCCGAGCTTGGAGGCAAATTGCAGTCAT
1 CCAATCTCTTACCCCGAGCCT-GAGGCAGATTACAACCAT
* * * * * * *
153821 TCGATCTTTTACCCCGAGCCT-AGGACAGATCACCATCAG
1 CCAATCTCTTACCCCGAGCCTGAGG-CAGATTACAACCAT
* * * *
153860 CTAATCTCTTACCTCGAGCTTGAGGCAGATTGCAACCAT
1 CCAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCAT
153899 CCAATCT
1 CCAATCT
153906 AAAACGAAAA
Statistics
Matches: 320, Mismatches: 101, Indels: 31
0.71 0.22 0.07
Matches are distributed among these distances:
37 1 0.00
38 25 0.08
39 259 0.81
40 34 0.11
41 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (39 bp):
CCAATCTCTTACCCCGAGCCTGAGGCAGATTACAACCAT
Found at i:154381 original size:16 final size:17
Alignment explanation
Indices: 154360--154392 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
154350 GGAACCCAAT
*
154360 TTTAAA-TTTTAATTTA
1 TTTAAAGTTTAAATTTA
154376 TTTAAAGTTTAAATTTA
1 TTTAAAGTTTAAATTTA
154393 AACTTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTAAAGTTTAAATTTA
Found at i:154390 original size:23 final size:23
Alignment explanation
Indices: 154360--154415 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
154350 GGAACCCAAT
* *
154360 TTTAAATTTTAATTTATTTAAAG
1 TTTAAATTTAAACTTATTTAAAG
**
154383 TTTAAATTTAAACTTATTTTGAG
1 TTTAAATTTAAACTTATTTAAAG
154406 TTTAAATTTA
1 TTTAAATTTA
154416 TTCTAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTAAATTTAAACTTATTTAAAG
Found at i:154392 original size:6 final size:6
Alignment explanation
Indices: 154360--154479 Score: 83
Period size: 6 Copynumber: 20.8 Consensus size: 6
154350 GGAACCCAAT
* * * * *
154360 TTTAAA TTTTAA TTT--A TTTAAA GTTTAAA TTTAAA CTT-AT TTTGAG
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA
* * *
154406 TTTAAA TTT--A TTCTAAA TTTAAA TTT-AT TTTAAA TTAAAA TTAAAA
1 TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
154452 TTT-AT TTTAAA TTAAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
154480 TTAAACATTG
Statistics
Matches: 90, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
4 7 0.08
5 12 0.13
6 62 0.69
7 9 0.10
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:154432 original size:23 final size:23
Alignment explanation
Indices: 154420--154478 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
154410 AATTTATTCT
154420 AAATTTAAATTTATTTTAAATTA
1 AAATTTAAATTTATTTTAAATTA
*
154443 AAATTAAAATTTATTTTAAATTA
1 AAATTTAAATTTATTTTAAATTA
154466 AAATTTAAATTTA
1 AAATTTAAATTTA
154479 ATTAAACATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATTTAAATTTATTTTAAATTA
Found at i:154472 original size:17 final size:17
Alignment explanation
Indices: 154383--154447 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
154373 TTATTTAAAG
*
154383 TTTAAATTTAAACTTAT
1 TTTAAATTTAAATTTAT
* *
154400 TTTGAGTTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
154417 TCTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
154434 TTTAAATTAAAATT
1 TTTAAATTTAAATT
154448 AAAATTTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:154481 original size:17 final size:17
Alignment explanation
Indices: 154434--154484 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
154424 TTAAATTTAT
*
154434 TTTAAATTAAAATTAAAA
1 TTTAAATT-TAATTAAAA
*
154452 TTT-ATTTTAAATTAAAA
1 TTTAAATTT-AATTAAAA
154469 TTTAAATTTAATTAAA
1 TTTAAATTTAATTAAA
154485 CATTGTCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 21 0.75
18 7 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAATTAAAA
Found at i:154482 original size:40 final size:40
Alignment explanation
Indices: 154409--154484 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
154399 TTTTGAGTTT
* *
154409 AAATTTATTCTAAATTTAAATTTATTTTAAATTAAAATTA
1 AAATTTATTCTAAATTAAAATTTAATTTAAATTAAAATTA
*
154449 AAATTTATTTTAAATTAAAATTTAAATTT-AATTAAA
1 AAATTTATTCTAAATTAAAATTT-AATTTAAATTAAA
154485 CATTGTCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 28 0.88
41 4 0.12
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (40 bp):
AAATTTATTCTAAATTAAAATTTAATTTAAATTAAAATTA
Found at i:155170 original size:4 final size:4
Alignment explanation
Indices: 155161--155228 Score: 54
Period size: 4 Copynumber: 17.5 Consensus size: 4
155151 TTAAATGCAT
* * *
155161 AATA AATA AATA TAAT- ATTA AATA GAT- AATA AATA AATA TAAT- ATTA
1 AATA AATA AATA -AATA AATA AATA AATA AATA AATA AATA -AATA AATA
*
155208 AATA GAT- AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AA
155229 AAGGAATTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
3 8 0.16
4 36 0.72
5 6 0.12
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (4 bp):
AATA
Found at i:155227 original size:11 final size:11
Alignment explanation
Indices: 155159--155227 Score: 56
Period size: 11 Copynumber: 6.4 Consensus size: 11
155149 TATTAAATGC
155159 ATAATAAATAA
1 ATAATAAATAA
155170 AT-ATAATATTAA
1 ATAATAA-A-TAA
155182 ATAGAT-AATAA
1 ATA-ATAAATAA
*
155193 ATAA-ATAT-A
1 ATAATAAATAA
* *
155202 ATATTAAATAG
1 ATAATAAATAA
155213 ATAATAAATAA
1 ATAATAAATAA
155224 ATAA
1 ATAA
155228 AAAGGAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
9 4 0.09
10 10 0.22
11 22 0.49
12 6 0.13
13 1 0.02
14 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
ATAATAAATAA
Found at i:155228 original size:31 final size:27
Alignment explanation
Indices: 155149--155226 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
155139 TACTAAATGC
155149 TATTAAAT-GCATAATAAATAAATATAA
1 TATTAAATAG-ATAATAAATAAATATAA
155176 TATTAAATAGATAATAAATAAATATAA
1 TATTAAATAGATAATAAATAAATATAA
155203 TATTAAATAGATAATAAATAAATA
1 TATTAAATAGATAATAAATAAATA
155227 AAAAGGAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (27 bp):
TATTAAATAGATAATAAATAAATATAA
Found at i:156311 original size:29 final size:29
Alignment explanation
Indices: 156251--156464 Score: 247
Period size: 29 Copynumber: 7.3 Consensus size: 29
156241 CCCATAAGGT
*
156251 CCTTAAACTTTTCAAAAATCACATTTTGAC
1 CCTTAAACTTTTC-AAAATTACATTTTGAC
*
156281 CCTTAAACTTTTCAAAATTACATTTTAAC
1 CCTTAAACTTTTCAAAATTACATTTTGAC
* *
156310 CCCTAAACTTTTTAAAATTACATTTTGAC
1 CCTTAAACTTTTCAAAATTACATTTTGAC
* * *
156339 CCCTAAATTTTTCAAAATTACATTTT-AA
1 CCTTAAACTTTTCAAAATTACATTTTGAC
*
156367 CCTCCAAACTTTTCCAAAATTACATTTTGAC
1 CCT-TAAACTTTT-CAAAATTACATTTTGAC
*
156398 CC-TAAACTTTTTCAAAATTACATTTTTAC
1 CCTTAAAC-TTTTCAAAATTACATTTTGAC
* *
156427 CC-TAAACTTCTCAAAATTTATATTTTG-C
1 CCTTAAACTTTTCAAAA-TTACATTTTGAC
*
156455 CCCTAAACTT
1 CCTTAAACTT
156465 CCAAAAATCA
Statistics
Matches: 161, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
28 14 0.09
29 113 0.70
30 31 0.19
31 3 0.02
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (29 bp):
CCTTAAACTTTTCAAAATTACATTTTGAC
Found at i:156333 original size:58 final size:58
Alignment explanation
Indices: 156254--156544 Score: 272
Period size: 58 Copynumber: 5.0 Consensus size: 58
156244 ATAAGGTCCT
* *
156254 TAAACTTTTCAAAAATCACATTTTGACCCTTAAACTTTTCAAAATTACATTTTAACCCC
1 TAAACTTTT-AAAAATTACATTTTGACCCCTAAACTTTTCAAAATTACATTTTAACCCC
* *
156313 TAAACTTTTTAAAATTACATTTTGACCCCTAAATTTTTCAAAATTACATTTTAACCTCC
1 TAAACTTTTAAAAATTACATTTTGACCCCTAAACTTTTCAAAATTACATTTTAACC-CC
* *
156372 -AAACTTTTCCAAAATTACATTTTGA-CCCTAAACTTTTTCAAAATTACATTTTTA-CCC
1 TAAACTTTT-AAAAATTACATTTTGACCCCTAAAC-TTTTCAAAATTACATTTTAACCCC
* * * * * * *
156429 TAAACTTCTCAAAATTTATATTTTG-CCCCTAAAC-TTCCAAAAATCACATTTTTATCTCC
1 TAAACTT-TTAAAAATTACATTTTGACCCCTAAACTTTTC-AAAATTACA-TTTTAACCCC
* * * * * * **
156488 -GAACTTTCAAAAATCACATTTTTA-CCCTCAATCTTTCCAAAATTATGTTTTAACCCC
1 TAAACTTTTAAAAATTACATTTTGACCCCT-AAACTTTTCAAAATTACATTTTAACCCC
156545 GAACTCTTCG
Statistics
Matches: 193, Mismatches: 27, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
56 3 0.02
57 35 0.18
58 103 0.53
59 52 0.27
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (58 bp):
TAAACTTTTAAAAATTACATTTTGACCCCTAAACTTTTCAAAATTACATTTTAACCCC
Found at i:156523 original size:29 final size:29
Alignment explanation
Indices: 156255--156532 Score: 198
Period size: 29 Copynumber: 9.6 Consensus size: 29
156245 TAAGGTCCTT
* *
156255 AAACTTTTCAAAAATCACATTTTGACCCTT
1 AAAC-TTTCAAAAATTACATTTTGACCCTC
*
156285 AAACTTTTC-AAAATTACATTTTAACCC-C
1 AAAC-TTTCAAAAATTACATTTTGACCCTC
**
156313 TAAACTTTTTAAAATTACATTTTGACCC-C
1 -AAACTTTCAAAAATTACATTTTGACCCTC
* *
156342 TAAATTTTTC-AAAATTACATTTT-AACCTCC
1 -AAA-CTTTCAAAAATTACATTTTGACCCT-C
*
156372 AAACTTTTCCAAAATTACATTTTGACCCT-
1 AAAC-TTTCAAAAATTACATTTTGACCCTC
*
156401 AAACTTTTTC-AAAATTACATTTTTACCCT-
1 AAAC--TTTCAAAAATTACATTTTGACCCTC
* * *
156430 AAACTTCTCAAAATTTATATTTTGCCCCT-
1 AAACTT-TCAAAAATTACATTTTGACCCTC
* * * *
156459 AAACTTCCAAAAATCACATTTTTA-TCTCC
1 AAACTTTCAAAAATTACATTTTGACCCT-C
* * *
156488 GAACTTTCAAAAATCACATTTTTACCCTC
1 AAACTTTCAAAAATTACATTTTGACCCTC
* *
156517 AATCTTTCCAAAATTA
1 AAACTTTCAAAAATTA
156533 TGTTTTAACC
Statistics
Matches: 205, Mismatches: 29, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
27 4 0.02
28 20 0.10
29 144 0.70
30 33 0.16
31 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (29 bp):
AAACTTTCAAAAATTACATTTTGACCCTC
Found at i:162548 original size:15 final size:15
Alignment explanation
Indices: 162528--162571 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
162518 TAAATAAATA
*
162528 AATAAATATAAAATT
1 AATAAATATAAAACT
* *
162543 ATTAAATATTAAACT
1 AATAAATATAAAACT
162558 AATATAATATAAAA
1 AATA-AATATAAAA
162572 AAAAATTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAAATATAAAACT
Found at i:164124 original size:15 final size:14
Alignment explanation
Indices: 164094--164128 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
164084 TGTTTGATTG
164094 AAAATGATTTTCGA
1 AAAATGATTTTCGA
* *
164108 AAAATGATTTTTGG
1 AAAATGATTTTCGA
164122 AAAATGA
1 AAAATGA
164129 ATTACTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (14 bp):
AAAATGATTTTCGA
Found at i:166648 original size:14 final size:14
Alignment explanation
Indices: 166629--166664 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
166619 GGGTGGCAAT
166629 GAAGGGGGAAAGGG
1 GAAGGGGGAAAGGG
166643 GAAGGGGG-AAGGG
1 GAAGGGGGAAAGGG
*
166656 GAAGAGGGA
1 GAAGGGGGA
166665 TTTTCCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (14 bp):
GAAGGGGGAAAGGG
Found at i:175749 original size:24 final size:24
Alignment explanation
Indices: 175722--175804 Score: 85
Period size: 24 Copynumber: 3.3 Consensus size: 24
175712 TTACACTAGC
175722 CAGCTTACACACGTTTATGCTCAT
1 CAGCTTACACACGTTTATGCTCAT
* * *
175746 CAGCTTATATATATGCGTTTATGCTCAC
1 CAGC-T-TACACA--CGTTTATGCTCAT
* *
175774 CAGCTTGCACACGTTTATGCTCGT
1 CAGCTTACACACGTTTATGCTCAT
175798 CAGCTTA
1 CAGCTTA
175805 TATATATGCG
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
24 21 0.46
25 1 0.02
26 7 0.15
27 1 0.02
28 16 0.35
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.35
Consensus pattern (24 bp):
CAGCTTACACACGTTTATGCTCAT
Found at i:175777 original size:28 final size:28
Alignment explanation
Indices: 175733--175831 Score: 107
Period size: 28 Copynumber: 3.7 Consensus size: 28
175723 AGCTTACACA
*
175733 CGTTTATGCTCATCAGCTTATATATATG
1 CGTTTATGCTCACCAGCTTATATATATG
** *
175761 CGTTTATGCTCACCAGC-T-TGCACA--
1 CGTTTATGCTCACCAGCTTATATATATG
**
175785 CGTTTATGCTCGTCAGCTTATATATATG
1 CGTTTATGCTCACCAGCTTATATATATG
*
175813 CGTTTACGCTCACCAGCTT
1 CGTTTATGCTCACCAGCTT
175832 GCAGACGTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
24 15 0.27
25 1 0.02
26 6 0.11
27 1 0.02
28 32 0.58
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.37
Consensus pattern (28 bp):
CGTTTATGCTCACCAGCTTATATATATG
Found at i:175777 original size:52 final size:52
Alignment explanation
Indices: 175672--175858 Score: 241
Period size: 52 Copynumber: 3.6 Consensus size: 52
175662 TGCTCGTCAA
* ** *
175672 CTTACATACGTTTACACTCGTCAGCTATATATATATGCGTTTACACT-AGCCAG
1 CTTACACACGTTTATGCTCGTCAGCT-TATATATATGCGTTTACGCTCA-CCAG
* *
175725 CTTACACACGTTTATGCTCATCAGCTTATATATATGCGTTTATGCTCACCAG
1 CTTACACACGTTTATGCTCGTCAGCTTATATATATGCGTTTACGCTCACCAG
*
175777 CTTGCACACGTTTATGCTCGTCAGCTTATATATATGCGTTTACGCTCACCAG
1 CTTACACACGTTTATGCTCGTCAGCTTATATATATGCGTTTACGCTCACCAG
* * ** *
175829 CTTGCAGACGTTTACACTCGTAAGCTTATA
1 CTTACACACGTTTATGCTCGTCAGCTTATA
175859 CATGCGTTTA
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
52 97 0.81
53 23 0.19
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (52 bp):
CTTACACACGTTTATGCTCGTCAGCTTATATATATGCGTTTACGCTCACCAG
Found at i:177457 original size:21 final size:21
Alignment explanation
Indices: 177433--177490 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
177423 CAGCACAGAT
*
177433 TTCTACCGATACAAGTG-ACAG
1 TTCTACCGATACAAGTGTA-AC
*
177454 TTCTAACGATACAAGTGTAAC
1 TTCTACCGATACAAGTGTAAC
*
177475 TTCTACCGAAACAAGT
1 TTCTACCGATACAAGT
177491 CATGCTTCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (21 bp):
TTCTACCGATACAAGTGTAAC
Found at i:177925 original size:21 final size:21
Alignment explanation
Indices: 177899--177940 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
177889 TTTATTGCTC
177899 ATAGATTCTCAAGAACTTTAT
1 ATAGATTCTCAAGAACTTTAT
177920 ATAGATTCTCAAGAACTTTAT
1 ATAGATTCTCAAGAACTTTAT
177941 CATAACTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATAGATTCTCAAGAACTTTAT
Found at i:178080 original size:20 final size:22
Alignment explanation
Indices: 178034--178084 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
178024 TACTTCATTT
178034 TAGGGGCATCATAGATGCAAGA
1 TAGGGGCATCATAGATGCAAGA
178056 TAGGGGCATCGA-AG-TGCAA-A
1 TAGGGGCATC-ATAGATGCAAGA
178076 TAGGGGCAT
1 TAGGGGCAT
178085 AAATGTGCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.36
21 5 0.18
22 12 0.43
23 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.35, T:0.18
Consensus pattern (22 bp):
TAGGGGCATCATAGATGCAAGA
Found at i:178092 original size:20 final size:21
Alignment explanation
Indices: 178034--178092 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
178024 TACTTCATTT
*
178034 TAGGGGCATCATAGATGCAAGA
1 TAGGGGCATCAAAG-TGCAAGA
*
178056 TAGGGGCATCGAAGTGCAA-A
1 TAGGGGCATCAAAGTGCAAGA
178076 TAGGGGCAT-AAATGTGC
1 TAGGGGCATCAAA-GTGC
178093 GAACAGTGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 2 0.06
20 14 0.42
21 5 0.15
22 12 0.36
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.19
Consensus pattern (21 bp):
TAGGGGCATCAAAGTGCAAGA
Found at i:180292 original size:41 final size:41
Alignment explanation
Indices: 180236--180327 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
180226 AACTCGATAT
* * *
180236 TTAAATGGAAGACTCATGTCTAGGGATGAGAATGAGATTATA
1 TTAAA-GGAAAACTCATGTCTAGAGATGAAAATGAGATTATA
**
180278 TTAAAGGAAAACTCATGTCTCTAGATGAAAATGAGATTATA
1 TTAAAGGAAAACTCATGTCTAGAGATGAAAATGAGATTATA
180319 TTAAAGGAA
1 TTAAAGGAA
180328 GACATGTCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 40 0.89
42 5 0.11
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (41 bp):
TTAAAGGAAAACTCATGTCTAGAGATGAAAATGAGATTATA
Found at i:180422 original size:40 final size:40
Alignment explanation
Indices: 180367--180503 Score: 220
Period size: 40 Copynumber: 3.4 Consensus size: 40
180357 TTTTTAAAAA
* * *
180367 AAAAGGATGACTTATGACTCGGTAGAGCATAAGAGAGATT
1 AAAAGGAAGACTTATGACTCAGTAGAGCATAAGAGTGATT
*
180407 AAAAGGAAGACTTATGACTCAGTAGAGCATAAAAGTGATT
1 AAAAGGAAGACTTATGACTCAGTAGAGCATAAGAGTGATT
* *
180447 AAAAGGAAGACTTATGACTAAGTAGAGAATAAGAGTGATT
1 AAAAGGAAGACTTATGACTCAGTAGAGCATAAGAGTGATT
180487 AAAAGGAAGACTTATGA
1 AAAAGGAAGACTTATGA
180504 ACCCATGAAG
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 90 1.00
ACGTcount: A:0.45, C:0.08, G:0.25, T:0.22
Consensus pattern (40 bp):
AAAAGGAAGACTTATGACTCAGTAGAGCATAAGAGTGATT
Found at i:181752 original size:3 final size:3
Alignment explanation
Indices: 181744--181787 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
181734 TGGGTTGAAG
*
181744 GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G-AA GAA G
181788 GAAAAAAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:181796 original size:12 final size:12
Alignment explanation
Indices: 181745--181810 Score: 71
Period size: 12 Copynumber: 5.2 Consensus size: 12
181735 GGGTTGAAGG
*
181745 AAGAAGAAGAAG
1 AAGAAGAAGAAA
181757 AAGAAGAAGAAA
1 AAGAAGAAGAAA
181769 AAGAAGAAGAAGA
1 AAGAAGAAGAA-A
181782 AAGAAGGAA-AAA
1 AAGAA-GAAGAAA
181794 AAGGAACGATAGAAA
1 AA-GAA-GA-AGAAA
181809 AA
1 AA
181811 TTGGGCGGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
12 25 0.53
13 13 0.28
14 4 0.09
15 5 0.11
ACGTcount: A:0.70, C:0.02, G:0.27, T:0.02
Consensus pattern (12 bp):
AAGAAGAAGAAA
Found at i:181808 original size:25 final size:22
Alignment explanation
Indices: 181748--181793 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
181738 TTGAAGGAAG
181748 AAGAAGAAGAAG-AAGAAGAAA
1 AAGAAGAAGAAGAAAGAAGAAA
181769 AAGAAGAAGAAGAAAGAAGGAAA
1 AAGAAGAAGAAGAAAGAA-GAAA
181792 AA
1 AA
181794 AAGGAACGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.52
22 5 0.22
23 6 0.26
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAGAAGAAGAAGAAAGAAGAAA
Found at i:183833 original size:42 final size:42
Alignment explanation
Indices: 183787--183897 Score: 143
Period size: 42 Copynumber: 2.6 Consensus size: 42
183777 TTCGAAAAGG
*
183787 GACACACGGTCATGTCTCAACCCGTGTAACTCACTGACTTAA
1 GACACACGGTCATGTCTTAACCCGTGTAACTCACTGACTTAA
* ** * *
183829 GACACACGATTGTGTCTTAGA-CCTTGTAACTCACTGACTTGA
1 GACACACGGTCATGTCTTA-ACCCGTGTAACTCACTGACTTAA
*
183871 GACACACGGTCATGTCTTAGCCCGTGT
1 GACACACGGTCATGTCTTAACCCGTGT
183898 CTCATACCGT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 55 0.98
43 1 0.02
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (42 bp):
GACACACGGTCATGTCTTAACCCGTGTAACTCACTGACTTAA
Found at i:184936 original size:20 final size:20
Alignment explanation
Indices: 184857--184945 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
184847 AGATGCAAGA
*
184857 CAAGGGCACCAAAGTGCAAAT
1 CAAGGGCACCGAAGTGC-AAT
* * *
184878 -AGGGGCATCGAAGTGCAAA
1 CAAGGGCACCGAAGTGCAAT
* **
184897 CAGGGGCATAGAAGTGCAAT
1 CAAGGGCACCGAAGTGCAAT
184917 CAAGGGCACCGAAGTGCAAT
1 CAAGGGCACCGAAGTGCAAT
184937 CAAGGGCAC
1 CAAGGGCAC
184946 TTCTTCATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
19 2 0.03
20 56 0.97
ACGTcount: A:0.37, C:0.21, G:0.31, T:0.10
Consensus pattern (20 bp):
CAAGGGCACCGAAGTGCAAT
Found at i:186996 original size:19 final size:19
Alignment explanation
Indices: 186974--187018 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
186964 AACTAGGGTT
*
186974 AAAGGAAGAA-GAAGAAGAA
1 AAAGGAAGAAGGAA-AAAAA
*
186993 AAAGAAAGAAGGAAAAAAA
1 AAAGGAAGAAGGAAAAAAA
187012 AAAGGAA
1 AAAGGAA
187019 CGATAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (19 bp):
AAAGGAAGAAGGAAAAAAA
Found at i:187016 original size:12 final size:14
Alignment explanation
Indices: 186975--187018 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 14
186965 ACTAGGGTTA
*
186975 AAGGAAGAAG-AAG
1 AAGGAAAAAGAAAG
186988 AA-GAAAAAGAAAG
1 AAGGAAAAAGAAAG
187001 AAGGAAAAA-AAA-
1 AAGGAAAAAGAAAG
187013 AAGGAA
1 AAGGAA
187019 CGATAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 12 0.43
13 10 0.36
14 6 0.21
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AAGGAAAAAGAAAG
Found at i:192326 original size:2 final size:2
Alignment explanation
Indices: 192319--192346 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
192309 TGTATGTTAG
192319 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
192347 TTGTGTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:201097 original size:34 final size:34
Alignment explanation
Indices: 201059--201125 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
201049 TTAGTAATGG
201059 TTCAAGGGTTTAATTGGCAAATGACCACTTTTTT
1 TTCAAGGGTTTAATTGGCAAATGACCACTTTTTT
201093 TTCAAGGGTTTAATTGGCAAATGACCACTTTTT
1 TTCAAGGGTTTAATTGGCAAATGACCACTTTTT
201126 AAAGGTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (34 bp):
TTCAAGGGTTTAATTGGCAAATGACCACTTTTTT
Found at i:203003 original size:16 final size:15
Alignment explanation
Indices: 202984--203068 Score: 62
Period size: 16 Copynumber: 5.3 Consensus size: 15
202974 AAAACTGAGT
202984 CCAAAAAATCCCAAAC
1 CCAAAAAAT-CCAAAC
* * *
203000 CCAAGAAATTTCAAGC
1 CCAA-AAAATCCAAAC
**
203016 CCATAATAAATAAAAAC
1 CCA-AA-AAATCCAAAC
* *
203033 TCAAAAAATTCAAAC
1 CCAAAAAATCCAAAC
203048 CCAAACAAATCCAAAC
1 CCAAA-AAATCCAAAC
203064 CCAAA
1 CCAAA
203069 TTAATCCGAG
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
15 12 0.23
16 28 0.53
17 13 0.25
ACGTcount: A:0.56, C:0.28, G:0.02, T:0.13
Consensus pattern (15 bp):
CCAAAAAATCCAAAC
Found at i:206226 original size:29 final size:29
Alignment explanation
Indices: 206101--206673 Score: 277
Period size: 29 Copynumber: 19.6 Consensus size: 29
206091 CCCCTAAACT
* *
206101 TTCCAAAAATTACATTTTGACCC-CTAAAC
1 TTCCAAAAATTACATTTTTACCCTC-GAAC
* * * *
206130 TTTCCACAAATTATATTTTGACCC-CTAAAC
1 -TTCCAAAAATTACATTTTTACCCTC-GAAC
* * *
206160 TTTCCAAAAATTACATTTTGA-CTTCAAAC
1 -TTCCAAAAATTACATTTTTACCCTCGAAC
* *
206189 TTCTTAAAAAATACATTTTTACCCTCGAAC
1 TTC-CAAAAATTACATTTTTACCCTCGAAC
** *
206219 TTCCAAAATATCCCA-TTTTACCC-CTAAAC
1 TTCCAAAA-ATTACATTTTTACCCTC-GAAC
*
206248 TTCCAAAAATTACCA-TTTTACCCTCGGA-
1 TTCCAAAAATTA-CATTTTTACCCTCGAAC
* *
206276 TGTCTAAAAATTTCATTTTTGA-CCTCGAAC
1 T-TCCAAAAATTACATTTTT-ACCCTCGAAC
206306 TTTCCAAAAATTACCA-TTTTA-CCTCGAAC
1 -TTCCAAAAATTA-CATTTTTACCCTCGAAC
*
206335 ATT-CAAAAATTAC-TATTTTACCCCCGAA-
1 -TTCCAAAAATTACAT-TTTTACCCTCGAAC
* *
206363 TGTTCAAAAATTACA-TTTTGCCCTCGAAC
1 T-TCCAAAAATTACATTTTTACCCTCGAAC
* *
206392 TTTTC-AAAATTACCA-TTTTACCCTCAAAC
1 -TTCCAAAAATTA-CATTTTTACCCTCGAAC
* * *
206421 ATCCAAAATTTACCA-TTTTACCATC-AGA-
1 TTCCAAAAATTA-CATTTTTACCCTCGA-AC
* *
206449 TGTCCAAAAATTACATTTTGACCC-CAAAC
1 T-TCCAAAAATTACATTTTTACCCTCGAAC
* *
206478 TTTCCAAAAATTACCATTTTAACCC-CAAAC
1 -TTCCAAAAATTA-CATTTTTACCCTCGAAC
* ** *
206508 ATAAAAAAATTACCA-TTTTACCC-CCAGA-
1 TTCCAAAAATTA-CATTTTTACCCTCGA-AC
*
206536 TGTCCAAAAATTACATTTTTACTCCT-AAAC
1 T-TCCAAAAATTACATTTTTAC-CCTCGAAC
* * *
206566 TTTCCAAAAATTA-TTATTTTACCCCCGGA-
1 -TTCCAAAAATTACAT-TTTTACCCTCGAAC
*
206595 TGTCCAAAAATTACATTTTTGACCC-CGAGC
1 T-TCCAAAAATTACATTTTT-ACCCTCGAAC
*
206625 TTTTCAAAAATTACCA-TTTTACCCTCGAAC
1 -TTCCAAAAATTA-CATTTTTACCCTCGAAC
* *
206655 ATCCAAAGATTATCATTTT
1 TTCCAAAAATTA-CATTTT
206674 GCCTTCGGGT
Statistics
Matches: 435, Mismatches: 61, Indels: 94
0.74 0.10 0.16
Matches are distributed among these distances:
27 2 0.00
28 61 0.14
29 227 0.52
30 138 0.32
31 7 0.02
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.34
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCCTCGAAC
Found at i:206612 original size:87 final size:88
Alignment explanation
Indices: 206102--206724 Score: 465
Period size: 87 Copynumber: 7.1 Consensus size: 88
206092 CCCTAAACTT
* * * * * *
206102 TCCAAAAATTACATTTTGACCC-CTAAACTTTCCACAAATTA-TATTTTGACCCCTAAACTTTCC
1 TCCAAAAATTACATTTTTACCCTC-GAACTTTCCAAAAATTACCATTTT-ACCCCCAAA-TATCC
** *
206165 AAAAATTA-CATTTTGA-CTTCAAACT-
63 AAAAATTACCATTTT-ACCCCCAGA-TG
* * * *
206190 TCTTAAAAAATACATTTTTACCCTCGAAC-TTCC-AAAATATCCCATTTTACCCCTAAACT-TCC
1 TC-CAAAAATTACATTTTTACCCTCGAACTTTCCAAAAAT-TACCATTTTACCCCCAAA-TATCC
* *
206252 AAAAATTACCATTTTACCCTCGGATG
63 AAAAATTACCATTTTACCCCCAGATG
* * * *
206278 TCTAAAAATTTCATTTTTGA-CCTCGAACTTTCCAAAAATTACCATTTTACCTCGAACAT-T-CA
1 TCCAAAAATTACATTTTT-ACCCTCGAACTTTCCAAAAATTACCATTTTACCCCCAA-ATATCCA
*
206340 AAAATTACTATTTTACCCCC-GAATG
64 AAAATTACCATTTTACCCCCAG-ATG
* * * * *
206365 TTCAAAAATTACA-TTTTGCCCTCGAACTTTTC-AAAATTACCATTTTACCCTCAAACATCCAAA
1 TCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCCCAAATATCCAAA
* **
206428 ATTTACCATTTTACCATCAGATG
66 AATTACCATTTTACCCCCAGATG
* * * * **
206451 TCCAAAAATTACATTTTGACCC-CAAACTTTCCAAAAATTACCATTTTAACCCCAAACATAAAAA
1 TCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCCCAAATATCCAAA
206515 AATTACCATTTTACCCCCAGATG
66 AATTACCATTTTACCCCCAGATG
* ** ** *
206538 TCCAAAAATTACATTTTTACTCCT-AAACTTTCCAAAAATTATTATTTTACCCCCGGATGTCCAA
1 TCCAAAAATTACATTTTTAC-CCTCGAACTTTCCAAAAATTACCATTTTACCCCCAAATATCCAA
* * *
206602 AAATTA-CATTTTTGACCCCGAGCTT
65 AAATTACCA-TTTT-ACCCCCAGATG
* * * * * ** *** *
206627 TTCAAAAATTACCA-TTTTACCCTCGAAC-ATCCAAAGATTATCATTTTGCCTTCGGGTGTCCAA
1 TCCAAAAATTA-CATTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCCCAAATATCCAA
* * *
206690 AAATTACCATTTTATCCACGGATG
65 AAATTACCATTTTACCCCCAGATG
206714 TCCAAAAATTA
1 TCCAAAAATTA
206725 TTGTTTTACC
Statistics
Matches: 439, Mismatches: 71, Indels: 51
0.78 0.13 0.09
Matches are distributed among these distances:
84 1 0.00
85 20 0.05
86 58 0.13
87 162 0.37
88 135 0.31
89 60 0.14
90 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.34
Consensus pattern (88 bp):
TCCAAAAATTACATTTTTACCCTCGAACTTTCCAAAAATTACCATTTTACCCCCAAATATCCAAA
AATTACCATTTTACCCCCAGATG
Found at i:206660 original size:59 final size:58
Alignment explanation
Indices: 206205--206673 Score: 272
Period size: 59 Copynumber: 8.1 Consensus size: 58
206195 AAAAATACAT
* * * *
206205 TTTTACCCTCGAAC--TTCCAAAATATCCCATTTTACCC-CTAAACTTCCAAAAATTACCA
1 TTTTACCC-CGAACTTTTCAAAAAT-TACCATTTTACCCTC-GAACGTCCAAAAATTACCA
* * * *
206263 TTTTACCCTCGGA--TGTCTAAAAATT-TCATTTTTGA-CCTCGAACTTTCCAAAAATTACCA
1 TTTTACCC-CGAACTTTTC-AAAAATTACCA-TTTT-ACCCTCGAAC-GTCCAAAAATTACCA
* * * * * *
206322 TTTTACCTCGAAC-ATTCAAAAATTACTATTTTACCCCCGAATGTTCAAAAATTA-CA
1 TTTTACCCCGAACTTTTCAAAAATTACCATTTTACCCTCGAACGTCCAAAAATTACCA
* * * *
206378 TTTTGCCCTCGAACTTTTC-AAAATTACCATTTTACCCTCAAACATCCAAAATTTACCA
1 TTTTACCC-CGAACTTTTCAAAAATTACCATTTTACCCTCGAACGTCCAAAAATTACCA
* * * * *
206436 TTTTACCATC-AGA-TGTCCAAAAATTA-CATTTTGACCC-CAAACTTTCCAAAAATTACCA
1 TTTTACC-CCGA-ACTTTTCAAAAATTACCATTTT-ACCCTCGAAC-GTCCAAAAATTACCA
* * ** * *
206494 TTTTAACCCCAAAC-ATAAAAAAATTACCATTTTACCC-CCAGATGTCCAAAAATTA-CA
1 TTTT-ACCCCGAACTTTTCAAAAATTACCATTTTACCCTCGA-ACGTCCAAAAATTACCA
** * ** * * *
206551 TTTTTACTCCTAAACTTTCCAAAAATTATTATTTTACCCCCGGATGTCCAAAAATTA-CA
1 -TTTTAC-CCCGAACTTTTCAAAAATTACCATTTTACCCTCGAACGTCCAAAAATTACCA
* * * *
206610 TTTTTGACCCCGAGCTTTTCAAAAATTACCATTTTACCCTCGAACATCCAAAGATTATCA
1 -TTTT-ACCCCGAACTTTTCAAAAATTACCATTTTACCCTCGAACGTCCAAAAATTACCA
206670 TTTT
1 TTTT
206674 GCCTTCGGGT
Statistics
Matches: 326, Mismatches: 57, Indels: 55
0.74 0.13 0.13
Matches are distributed among these distances:
56 8 0.02
57 66 0.20
58 123 0.38
59 124 0.38
60 5 0.02
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (58 bp):
TTTTACCCCGAACTTTTCAAAAATTACCATTTTACCCTCGAACGTCCAAAAATTACCA
Found at i:206674 original size:59 final size:57
Alignment explanation
Indices: 206074--206674 Score: 271
Period size: 59 Copynumber: 10.3 Consensus size: 57
206064 TTAAACTGTT
* * * * * *
206074 CAAAAATCATATTTTAACCCCTAAACTTTCCAAAAATTA-CATTTTGACCCCTAAACTTTC
1 CAAAAATTACATTTTGACCCC-AAACTTTTCAAAAATTACCATTTT-ACCCC-GAAC-GTC
* * * ** * *
206134 CACAAATTATATTTTGACCCCTAAACTTTCCAAAAATTA-CATTTTGACTTCAAACTTC
1 CAAAAATTACATTTTGACCCC-AAACTTTTCAAAAATTACCATTTT-ACCCCGAACGTC
* * * * * * * *
206192 TTAAAAAATACATTTTTACCCTCGAAC--TTCCAAAATATCCCATTTTACCCCTAAACTTC
1 -CAAAAATTACATTTTGACCC-CAAACTTTTCAAAAAT-TACCATTTTACCCC-GAACGTC
** * * * *
206251 CAAAAATTACCATTTT-ACCCTCGGA--TGTCTAAAAATT-TCATTTTTGACCTCGAACTTTC
1 CAAAAATTA-CATTTTGACCC-CAAACTTTTC-AAAAATTACCA-TTTT-ACCCCGAAC-GTC
* * * * * *
206310 CAAAAATTACCATTTT-ACCTCGAAC-ATTCAAAAATTACTATTTTACCCCCGAATGTT
1 CAAAAATTA-CATTTTGACCCCAAACTTTTCAAAAATTACCATTTTA-CCCCGAACGTC
* * *
206367 CAAAAATTACATTTTG-CCCTCGAACTTTTC-AAAATTACCATTTTACCCTCAAACATC
1 CAAAAATTACATTTTGACCC-CAAACTTTTCAAAAATTACCATTTTACCC-CGAACGTC
* * * * * * *
206424 CAAAATTTACCATTTT-ACCATCAGA-TGTCCAAAAATTA-CATTTTGACCCCAAACTTTC
1 CAAAAATTA-CATTTTGACC-CCAAACTTTTCAAAAATTACCATTTT-ACCCCGAAC-GTC
* * ** * *
206482 CAAAAATTACCATTTTAACCCCAAAC-ATAAAAAAATTACCATTTTACCCCCAGATGTC
1 CAAAAATTA-CATTTTGACCCCAAACTTTTCAAAAATTACCATTTTACCCCGA-ACGTC
* * * ** * *
206540 CAAAAATTACATTTTTACTCCTAAACTTTCCAAAAATTATTATTTTACCCCCGGATGTC
1 CAAAAATTACATTTTGAC-CCCAAACTTTTCAAAAATTACCATTTTA-CCCCGAACGTC
* * *
206599 CAAAAATTACATTTTTGACCCCGAGCTTTTCAAAAATTACCATTTTACCCTCGAACATC
1 CAAAAATTACA-TTTTGACCCCAAACTTTTCAAAAATTACCATTTTACCC-CGAACGTC
*
206658 CAAAGATTATCATTTTG
1 CAAAAATTA-CATTTTG
206675 CCTTCGGGTG
Statistics
Matches: 430, Mismatches: 77, Indels: 69
0.75 0.13 0.12
Matches are distributed among these distances:
56 11 0.03
57 73 0.17
58 131 0.30
59 156 0.36
60 59 0.14
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.34
Consensus pattern (57 bp):
CAAAAATTACATTTTGACCCCAAACTTTTCAAAAATTACCATTTTACCCCGAACGTC
Found at i:206715 original size:29 final size:29
Alignment explanation
Indices: 206205--206782 Score: 316
Period size: 29 Copynumber: 19.9 Consensus size: 29
206195 AAAAATACAT
*
206205 TTTTACCCTCGAACT-TCC-AAAATATCCCA
1 TTTTACCCTCGAA-TGTCCAAAAAT-TACCA
*
206234 TTTTACCC-CTAAACT-TCCAAAAATTACCA
1 TTTTACCCTC-GAA-TGTCCAAAAATTACCA
* * *
206263 TTTTACCCTCGGATGTCTAAAAATT-TCA
1 TTTTACCCTCGAATGTCCAAAAATTACCA
*
206291 TTTTTGA-CCTCGAACTTTCCAAAAATTACCA
1 -TTTT-ACCCTCGAA-TGTCCAAAAATTACCA
** * *
206322 TTTTA-CCTCGAACATTCAAAAATTACTA
1 TTTTACCCTCGAATGTCCAAAAATTACCA
* *
206350 TTTTACCCCCGAATGTTCAAAAATTA-CA
1 TTTTACCCTCGAATGTCCAAAAATTACCA
* * *
206378 TTTTGCCCTCGAACTTTTC-AAAATTACCA
1 TTTTACCCTCGAA-TGTCCAAAAATTACCA
* ** *
206407 TTTTACCCTCAAACATCCAAAATTTACCA
1 TTTTACCCTCGAATGTCCAAAAATTACCA
*
206436 TTTTACCATC-AGATGTCCAAAAATTA-CA
1 TTTTACCCTCGA-ATGTCCAAAAATTACCA
* *
206464 TTTTGACCC-CAAACTTTCCAAAAATTACCA
1 TTTT-ACCCTCGAA-TGTCCAAAAATTACCA
* ** **
206494 TTTTAACCC-CAAACATAAAAAAATTACCA
1 TTTT-ACCCTCGAATGTCCAAAAATTACCA
*
206523 TTTTACCC-CCAGATGTCCAAAAATTA-CA
1 TTTTACCCTCGA-ATGTCCAAAAATTACCA
* * **
206551 TTTTTACTCCT-AAACTTTCCAAAAATTATTA
1 -TTTTAC-CCTCGAA-TGTCCAAAAATTACCA
* *
206582 TTTTACCCCCGGATGTCCAAAAATTA-CA
1 TTTTACCCTCGAATGTCCAAAAATTACCA
* * *
206610 TTTTTGACCC-CGAGCTTTTCAAAAATTACCA
1 -TTTT-ACCCTCGA-ATGTCCAAAAATTACCA
** * *
206641 TTTTACCCTCGAACATCCAAAGATTATCA
1 TTTTACCCTCGAATGTCCAAAAATTACCA
* * **
206670 TTTTGCCTTCGGGTGTCCAAAAATTACCA
1 TTTTACCCTCGAATGTCCAAAAATTACCA
* * * ***
206699 TTTTATCCACGGATGTCCAAAAATTATTG
1 TTTTACCCTCGAATGTCCAAAAATTACCA
* * * *
206728 TTTTACCCT-TAGACGTCCAAAAATTATCG
1 TTTTACCCTCGA-ATGTCCAAAAATTACCA
*
206757 TTTTGCCCTCGACA--TCCAAAAATTAC
1 TTTTACCCTCGA-ATGTCCAAAAATTAC
206783 ACTTTGACTC
Statistics
Matches: 431, Mismatches: 87, Indels: 63
0.74 0.15 0.11
Matches are distributed among these distances:
28 71 0.16
29 274 0.64
30 81 0.19
31 5 0.01
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.33
Consensus pattern (29 bp):
TTTTACCCTCGAATGTCCAAAAATTACCA
Found at i:206746 original size:58 final size:58
Alignment explanation
Indices: 206512--206753 Score: 195
Period size: 59 Copynumber: 4.1 Consensus size: 58
206502 CCAAACATAA
* * * *
206512 AAAAATTACCATTTTACCCCCAGATGTCCAAAAATTACATTTTTACTCC-TAAACTTTCC
1 AAAAATTACCATTTTACCCCCGGATGTCCAAAAATTA-TTTTTTAC-CCTTAGACTGTCC
** * ** * *
206571 AAAAATTATTATTTTACCCCCGGATGTCCAAAAATTACATTTTTGACCCCGAG-CTTTTC
1 AAAAATTACCATTTTACCCCCGGATGTCCAAAAATT--ATTTTTTACCCTTAGACTGTCC
* * ** * * * * **
206630 AAAAATTACCATTTTACCCTCGAACATCCAAAGATTATCATTTT-GCCTTCGGGTGTCC
1 AAAAATTACCATTTTACCCCCGGATGTCCAAAAATTAT-TTTTTACCCTTAGACTGTCC
* *
206688 AAAAATTACCATTTTATCCACGGATGTCCAAAAATTATTGTTTTACCCTTAGAC-GTCC
1 AAAAATTACCATTTTACCCCCGGATGTCCAAAAATTATT-TTTTACCCTTAGACTGTCC
206746 AAAAATTA
1 AAAAATTA
206754 TCGTTTTGCC
Statistics
Matches: 141, Mismatches: 35, Indels: 15
0.74 0.18 0.08
Matches are distributed among these distances:
57 5 0.04
58 54 0.38
59 74 0.52
60 7 0.05
61 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCCGGATGTCCAAAAATTATTTTTTACCCTTAGACTGTCC
Done.