Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007771.1 Hibiscus syriacus cultivar Beakdansim tig00110052_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 186237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:340 original size:24 final size:24
Alignment explanation
Indices: 306--412 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
296 AAACGGAGAT
* *
306 ATCAGAAATCAAAATATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
330 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
354 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
378 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
402 ATCAGAAATCA
1 ATCAGAAATCA
413 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:412 original size:48 final size:48
Alignment explanation
Indices: 306--414 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
296 AAACGGAGAT
* * * * *
306 ATCAGAAATCAAAATATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
354 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
402 ATCAGAAATCAGA
1 ATCAGAAATCAGA
415 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1547 original size:18 final size:18
Alignment explanation
Indices: 1526--1563 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1516 TCCTTCCATC
*
1526 CAATCTTATTATTTAATT
1 CAATCTTATCATTTAATT
*
1544 CAATCTTATCATTTACTT
1 CAATCTTATCATTTAATT
1562 CA
1 CA
1564 GTCCTTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (18 bp):
CAATCTTATCATTTAATT
Found at i:2888 original size:8 final size:8
Alignment explanation
Indices: 2868--2922 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
2858 GGTCAACTCC
2868 GGTCAAC-
1 GGTCAACG
2875 GGTCAACG
1 GGTCAACG
2883 GGTCAAC-
1 GGTCAACG
2890 GGTCAACG
1 GGTCAACG
2898 GGT---CG
1 GGTCAACG
2903 GGTCAACG
1 GGTCAACG
2911 GGTCAACG
1 GGTCAACG
2919 GGTC
1 GGTC
2923 GGGTAAATGG
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 24 0.56
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:2888 original size:15 final size:15
Alignment explanation
Indices: 2868--2919 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
2858 GGTCAACTCC
2868 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
2883 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
2898 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
2911 GGTCAACGG
1 GGTCAACGG
2920 GTCGGGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.36
15 21 0.64
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:2916 original size:21 final size:21
Alignment explanation
Indices: 2881--2935 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
2871 CAACGGTCAA
2881 CGGGTCAAC-GGTCAACGGGT
1 CGGGTCAACGGGTCAACGGGT
2901 CGGGTCAACGGGTCAACGGGT
1 CGGGTCAACGGGTCAACGGGT
* *
2922 CGGGTAAATGGGTC
1 CGGGTCAACGGGTC
2936 GGTTCGGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 9 0.28
21 23 0.72
ACGTcount: A:0.20, C:0.22, G:0.42, T:0.16
Consensus pattern (21 bp):
CGGGTCAACGGGTCAACGGGT
Found at i:2944 original size:18 final size:18
Alignment explanation
Indices: 2896--2962 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
2886 CAACGGTCAA
*
2896 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
2914 CAACGGGTCGGGTAAATGGGT
1 ---CGGGTCGGGTAAACGGGT
*
2935 CGGTTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
2953 CGGGTCGGGT
1 CGGGTCGGGT
2963 TGTGACCGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 25 0.61
21 16 0.39
ACGTcount: A:0.15, C:0.18, G:0.48, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:11389 original size:90 final size:89
Alignment explanation
Indices: 11237--11409 Score: 310
Period size: 90 Copynumber: 1.9 Consensus size: 89
11227 ACACACCTTT
11237 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
11302 ATTAATTGAAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* *
11326 TTATATCCAAGTTACCCTGATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
11391 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
11410 TTTGGGATTA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 29 0.36
90 51 0.64
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:13925 original size:133 final size:134
Alignment explanation
Indices: 13645--13974 Score: 450
Period size: 134 Copynumber: 2.5 Consensus size: 134
13635 TGGAATATGA
* * *
13645 TGAGGGAATATTAGATCTGGGGACGTTGATTCATTCCACTGTCACTCAGGGAAGATTGAATCGAG
1 TGAGGGAATATCAGATCTAGGGACGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGAG
* * *
13710 GTAGACTTGATCAAATGTTACTCAGGGAATATCAAATCTTGGAAGAAAGGGACATGTTTCACTTC
66 GCAGACTTGATCAAATGTTACTCAGGGAATATCAAATCTTGGAAGAAAGGGACATGTTCCACTTA
13775 TTCT
131 TTCT
* * * * * *
13779 GGAGGGAATATCAGATCTAAGGACATTGATTCATTTCGCTGTCACTCAAGGAAGATTGAATCGGG
1 TGAGGGAATATCAGATCTAGGGACGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGAG
* * * **
13844 GCAGACTTGTTC-ATTGTTACTCAGGGAATATCAAATCTTGGAAGAGAGGGATC-TGTTCCGTTT
66 GCAGACTTGATCAAATGTTACTCAGGGAATATCAAATCTTGGAAGAAAGGGA-CATGTTCCACTT
13907 ATTCT
130 ATTCT
* * *
13912 TGAGGGAAAATCAGAT-TTGGGATGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGA
1 TGAGGGAATATCAGATCTAGGGACGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGA
13975 CTTCGATTTT
Statistics
Matches: 169, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
132 40 0.24
133 62 0.37
134 67 0.40
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (134 bp):
TGAGGGAATATCAGATCTAGGGACGTTGATTCATTTCACTGTCACTCAGGGAAGATTGAATCGAG
GCAGACTTGATCAAATGTTACTCAGGGAATATCAAATCTTGGAAGAAAGGGACATGTTCCACTTA
TTCT
Found at i:14221 original size:16 final size:16
Alignment explanation
Indices: 14196--14228 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14186 ACTATGAATC
14196 ATTTATTTTTCA-AAA
1 ATTTATTTTTCAGAAA
14211 ATTTCATTTTTCAGAAA
1 ATTT-ATTTTTCAGAAA
14228 A
1 A
14229 GATTGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.48
Consensus pattern (16 bp):
ATTTATTTTTCAGAAA
Found at i:14359 original size:41 final size:42
Alignment explanation
Indices: 14309--14405 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
14299 ATAACTTATG
* * * *
14309 GATGGCCCGATGGACTTA-TCATCTTGCTCGAAAGACTTACA
1 GATGACCCGAAGGACTTAGGCATCATGCTCGAAAGACTTACA
* *
14350 GATGACCCGAAGGATTTAGGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTTAGGCATCATGCTCGAAAGACTTACA
14392 GATTG-CCCGAAGGA
1 GA-TGACCCGAAGGA
14406 ATTACCAACT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 15 0.31
42 31 0.65
43 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (42 bp):
GATGACCCGAAGGACTTAGGCATCATGCTCGAAAGACTTACA
Found at i:14636 original size:42 final size:41
Alignment explanation
Indices: 14540--14636 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
14530 AGGTCTTATG
* * *
14540 GATGGCCCGAAGGACTTATCATCTTGCTCAAAATACTTACA
1 GATGGCCCGAAGGACTTAACATCATGCTCAAAAGACTTACA
* * * * *
14581 GATGACTCGAAGGATTTAGACATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTTA-ACATCATGCTCAAAAGACTTACA
*
14623 GATGGCCCAAAGGA
1 GATGGCCCGAAGGA
14637 ATTACCAATT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
41 15 0.34
42 29 0.66
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAACATCATGCTCAAAAGACTTACA
Found at i:15234 original size:232 final size:233
Alignment explanation
Indices: 14257--15284 Score: 1211
Period size: 231 Copynumber: 4.4 Consensus size: 233
14247 TGGAAATTGT
** * * * * ***
14257 TTTCTCATTTTTCGAAAAATCATACGAAAATATCCTACCCTAATAACTTATGGATGGCCCG-ATG
1 TTTCTCATTTTTCGAAAAA-CATGTGAAAACATCTTGCCCAAAGGTCTTATGGATGGCCCGAAT-
*
14321 GACTTATCATCTTGCTCGAAAGACTTACAGATGACC-CGAAGGATTTAGGCATCATGCTCGAAAG
64 GACTTATCATCTTGCTCGAAAGACTTACAGATGACCTCGAAGGATTTAAGCATCATGCTCGAAAG
* * * * *
14385 ACTTACTGATTGCCCGAAGGAATTACCAACTCGGAAATAGTTTACTAGGCAAAAAACCTTCCTTA
129 ACTTACTGATGGCCCGAAGGAATTACCAATTTGGAAATAGTTTACTAGGTAAGAAACCTTCCTTA
* * *
14450 C-TTTTCAAAATTTCAATTTCCATATTTAAATGAG-AACC
194 CTTTTTAAAAATTTCAATTTTCAGATTTAAATGAGAAACC
* *
14488 TTTTCTCATTTTTCGAAAAACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGG
1 -TTTCTCATTTTTCGAAAAACATGTGAAAACATCTTGCCCAAAGGTCTTATGGATGGCCCGAATG
* *
14553 ACTTATCATCTTGCTCAAAATACTTACAGATGA-CTCGAAGGATTT-AGACATCATGCTCGAAAG
65 ACTTATCATCTTGCTCGAAAGACTTACAGATGACCTCGAAGGATTTAAG-CATCATGCTCGAAAG
* *
14616 ACTTACTGATGGCCCAAAGGAATTACCAATTTTGGAAATAGTTTACTAGTTAAGAAACCTTCCTT
129 ACTTACTGATGGCCCGAAGGAATTACCAA-TTTGGAAATAGTTTACTAGGTAAGAAACCTTCCTT
* * * *
14681 ACTTTTCAAAAATTTTAATTTTCAGATTTAGATAAGAAACC
193 ACTTTTTAAAAATTTCAATTTTCAGATTTAAATGAGAAACC
*
14722 TTTCTCATTTTTCAAAAAACATGTGAAAACAT-TCTGCCCAAAGGTCTTATGGATGGCCCGAA-G
1 TTTCTCATTTTTCGAAAAACATGTGAAAACATCT-TGCCCAAAGGTCTTATGGATGGCCCGAATG
* * * * * * *
14785 AACTTACCACCTTGCTTGAAAGACTTACAAAT-AACTCAAAGGATTTAAGCATCATGTTCGAAAG
65 -ACTTATCATCTTGCTCGAAAGACTTACAGATGACCTCGAAGGATTTAAGCATCATGCTCGAAAG
* * * * * * *
14849 A--AACTGATGGCCCGGAGGACTTACCAAATTCGAGAATAGTTTACTAGGTAAGAAACTTTACTT
129 ACTTACTGATGGCCCGAAGGAATTACCAATTTGGA-AATAGTTTACTAGGTAAGAAACCTTCCTT
* *
14912 ACTTTTTAAAATTTTCAATTTTCAGATTTAAATGAGAAGCC
193 ACTTTTTAAAAATTTCAATTTTCAGATTTAAATGAGAAACC
* * * * *
14953 TTTCTCATTTTTCGAGAGACGTGTGAAAACATCTTTCCCGAAGGTCTTATGGATGGCCCGAATGA
1 TTTCTCATTTTTCGAAAAACATGTGAAAACATCTTGCCCAAAGGTCTTATGGATGGCCCGAATGA
* * * *
15018 CTTATCACCTTGCTCGAAAGACTTACAGGTGACCT-GAAGGATTTAAGTATCATGCTTGAAAGAC
66 CTTATCATCTTGCTCGAAAGACTTACAGATGACCTCGAAGGATTTAAGCATCATGCTCGAAAGAC
* * * * *
15082 TTACTAATGGCCCGAATGACTTA-TAGATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTA
131 TTACTGATGGCCCGAAGGAATTACCA-A-TTTGGAAATAGTTTACTAGGTAAGAAACCTTCCTTA
* ** * *
15146 C-TTTAAAAAAAATCAATTTTTAGATTTAAATGAGAAATC
194 CTTTTTAAAAATTTCAATTTTCAGATTTAAATGAGAAACC
* * * * * * *
15185 TTTCTCATTTTTCGAGAGACATGTGAAAACATCTTGCTCGAATGTCTTATGGATGGTCCGAAAGA
1 TTTCTCATTTTTCGAAAAACATGTGAAAACATCTTGCCCAAAGGTCTTATGGATGGCCCGAATGA
* *
15250 CTTATCATCTTGCTCGAAATACTTACAGATAACCT
66 CTTATCATCTTGCTCGAAAGACTTACAGATGACCT
15285 TTCTTACTTT
Statistics
Matches: 686, Mismatches: 92, Indels: 36
0.84 0.11 0.04
Matches are distributed among these distances:
230 6 0.01
231 305 0.44
232 181 0.26
233 184 0.27
234 10 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (233 bp):
TTTCTCATTTTTCGAAAAACATGTGAAAACATCTTGCCCAAAGGTCTTATGGATGGCCCGAATGA
CTTATCATCTTGCTCGAAAGACTTACAGATGACCTCGAAGGATTTAAGCATCATGCTCGAAAGAC
TTACTGATGGCCCGAAGGAATTACCAATTTGGAAATAGTTTACTAGGTAAGAAACCTTCCTTACT
TTTTAAAAATTTCAATTTTCAGATTTAAATGAGAAACC
Found at i:17906 original size:32 final size:32
Alignment explanation
Indices: 17850--17925 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
17840 TATATTCCTT
* * *
17850 AGAACATATGT-ATATTGTCTATATGTCCCGA
1 AGAACATAGGTAATTTTGTCCATATGTCCCGA
* *
17881 A-AGACATAGGTAATTTTGTCCATATGTTCCGT
1 AGA-ACATAGGTAATTTTGTCCATATGTCCCGA
17913 AGAACATAGGTAA
1 AGAACATAGGTAA
17926 ACTCTCGACT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
30 1 0.03
31 8 0.22
32 27 0.73
33 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (32 bp):
AGAACATAGGTAATTTTGTCCATATGTCCCGA
Found at i:19537 original size:25 final size:27
Alignment explanation
Indices: 19495--19544 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
19485 ATTTAGTTTT
**
19495 AAATTCAACTTATCAACTC-TTTTCCA
1 AAATTCAACTTAAAAACTCATTTTCCA
19521 AAATTC-ACTTAAAAACTCATTTTC
1 AAATTCAACTTAAAAACTCATTTTC
19545 TTTAATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATTCAACTTAAAAACTCATTTTCCA
Found at i:20456 original size:16 final size:16
Alignment explanation
Indices: 20435--20498 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
20425 AAATATTTGA
20435 TTTATTTTCTCTCTTT
1 TTTATTTTCTCTCTTT
20451 TTTATTTT-TCCTCTTT
1 TTTATTTTCT-CTCTTT
* *
20467 TTT-TCTTCT-TTTTT
1 TTTATTTTCTCTCTTT
*
20481 TCTTCTTTTCTCT-TTT
1 T-TTATTTTCTCTCTTT
20497 TT
1 TT
20499 CCTAATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
14 5 0.12
15 7 0.17
16 27 0.68
17 1 0.03
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTTCTCTCTTT
Found at i:20469 original size:11 final size:11
Alignment explanation
Indices: 20455--20489 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
20445 CTCTTTTTTA
*
20455 TTTTTCCTCTT
1 TTTTTCTTCTT
20466 TTTTTCTTCTT
1 TTTTTCTTCTT
20477 TTTTTCTTCTT
1 TTTTTCTTCTT
20488 TT
1 TT
20490 CTCTTTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:20499 original size:28 final size:28
Alignment explanation
Indices: 20439--20518 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
20429 ATTTGATTTA
* *
20439 TTTTC-TCTCTTTTTTATTTTTCCTCTTT
1 TTTTCTTCT-TTTTTTCTTTTTTCTCTTT
20467 TTTTCTTCTTTTTTTCTTCTTTTCTCTTT
1 TTTTCTTCTTTTTTTCTT-TTTTCTCTTT
* **
20496 TTTCCTAATTTTTTTCTATTTTT
1 TTTTCTTCTTTTTTTCT-TTTTT
20519 TCTCAATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 13 0.30
29 30 0.68
30 1 0.02
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTCTTCTTTTTTTCTTTTTTCTCTTT
Found at i:20507 original size:18 final size:19
Alignment explanation
Indices: 20467--20540 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 19
20457 TTTCCTCTTT
* **
20467 TTTTCTTCTTTTTTTCTTC
1 TTTTCTTCTTTTTTCCTAA
20486 TTTTC-TCTTTTTTCCTAA
1 TTTTCTTCTTTTTTCCTAA
* *
20504 TTTTTTTCTATTTTTTCTCAA
1 TTTTCTTCT-TTTTTCCT-AA
*
20525 TTATCTTTCTTTTTTC
1 TTTTC-TTCTTTTTTC
20541 TTTTTCATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
18 14 0.33
19 8 0.19
20 7 0.16
21 10 0.23
22 4 0.09
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTCTTCTTTTTTCCTAA
Found at i:20518 original size:39 final size:39
Alignment explanation
Indices: 20434--20519 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 39
20424 GAAATATTTG
*
20434 ATTTATTTTCTCTCTTTTTTATTTTTCCTCTTTTTTTCTT
1 ATTT-TTTTCTCTCTTTTTTATTTTTCCTATTTTTTTCTT
*
20474 CTTTTTTTCT-TCTTTTCTCT-TTTTTCCTAATTTTTTTC-T
1 ATTTTTTTCTCTCTTTT-T-TATTTTTCCT-ATTTTTTTCTT
20513 ATTTTTT
1 ATTTTTT
20520 CTCAATTATC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
38 6 0.15
39 22 0.55
40 12 0.30
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (39 bp):
ATTTTTTTCTCTCTTTTTTATTTTTCCTATTTTTTTCTT
Found at i:20526 original size:21 final size:21
Alignment explanation
Indices: 20486--20539 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
20476 TTTTTTCTTC
20486 TTTTCTCTTTTTTCCTAATT-T
1 TTTTCT-TTTTTTCCTAATTAT
20507 TTTTCTATTTTTT-CTCAATTAT
1 TTTTCT-TTTTTTCCT-AATTAT
*
20529 CTTTCTTTTTT
1 TTTTCTTTTTT
20540 CTTTTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 21 0.72
22 6 0.21
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCTTTTTTTCCTAATTAT
Found at i:22058 original size:20 final size:20
Alignment explanation
Indices: 22030--22081 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
22020 GAATGTAAAG
*
22030 ATGCAAAAATGC-ACATATGA
1 ATGC-AAAATGCAAAATATGA
*
22050 ATGCGAAAATACATAAATATGA
1 ATGC-AAAATGCA-AAATATGA
22072 ATGCAAAATG
1 ATGCAAAATG
22082 TGAGATGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.38
21 5 0.19
22 11 0.42
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.21
Consensus pattern (20 bp):
ATGCAAAATGCAAAATATGA
Found at i:26439 original size:6 final size:6
Alignment explanation
Indices: 26428--26458 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
26418 ACAACATGCA
26428 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
26459 GGACTAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:27764 original size:3 final size:3
Alignment explanation
Indices: 27758--27784 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27748 TTTTGGGTCT
27758 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
27785 GCGAGACGAA
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:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29029 original size:64 final size:63
Alignment explanation
Indices: 28944--29104 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
28934 TTGTTTAAGG
* * * *
28944 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAAAAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAAAAGGATTTA
* * * *
29008 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAAAAGGATTTA
*
29072 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
29105 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAAAAGGATTTA
Found at i:30696 original size:149 final size:149
Alignment explanation
Indices: 30453--30757 Score: 495
Period size: 149 Copynumber: 2.0 Consensus size: 149
30443 GAGTCGAGGG
* * * * *
30453 TCTACGCGGTCCTTCGGGACATATATATATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACA
1 TCTACGCGGTCCTTCGGGA-ATATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACA
* * *
30518 TACTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATT
65 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGAACATTATT
30583 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
*
30603 TCTACGCGGTCCTTCGGG-ATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
1 TCTACGCGGTCCTTCGGGAATATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACA
30667 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGAACATTATT
65 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGAACATTATT
*
30732 ATATGGCACTACGGTGTAAT
130 ATATGGCACTACGGTGCAAT
30752 TCTACG
1 TCTACG
30758 TGCACTTCGG
Statistics
Matches: 144, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
148 32 0.22
149 94 0.65
150 18 0.12
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGAATATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGAACATTATTA
TATGGCACTACGGTGCAAT
Found at i:30994 original size:18 final size:18
Alignment explanation
Indices: 30971--31035 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
30961 AAATAATTTG
30971 ATGATAATGATATAGATA
1 ATGATAATGATATAGATA
*
30989 ATGATAAT-A-ATATAT-
1 ATGATAATGATATAGATA
* *
31004 ATGATAATGCTA-AGAAA
1 ATGATAATGATATAGATA
*
31021 ATAGATGATGATATA
1 AT-GATAATGATATA
31036 TGTACATGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
15 8 0.22
16 7 0.19
17 4 0.11
18 16 0.44
19 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.32
Consensus pattern (18 bp):
ATGATAATGATATAGATA
Found at i:31028 original size:21 final size:21
Alignment explanation
Indices: 30985--31029 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
30975 TAATGATATA
* * *
30985 GATAATGATAATAATATATAT
1 GATAATGATAAGAAAATAGAT
*
31006 GATAATGCTAAGAAAATAGAT
1 GATAATGATAAGAAAATAGAT
31027 GAT
1 GAT
31030 GATATATGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.31
Consensus pattern (21 bp):
GATAATGATAAGAAAATAGAT
Found at i:34175 original size:64 final size:63
Alignment explanation
Indices: 34090--34250 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
34080 TTGTTTAAGG
* * * * *
34090 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGAATTTA
* * *
34154 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGAATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGAATTTA
*
34218 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
34251 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGAATTTA
Found at i:35269 original size:14 final size:15
Alignment explanation
Indices: 35239--35271 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35229 AATAGAATAA
35239 ATAAATAAATATTAT
1 ATAAATAAATATTAT
*
35254 ATAAATATAT-TTAT
1 ATAAATAAATATTAT
35268 ATAA
1 ATAA
35272 CTTAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATAAATATTAT
Found at i:35359 original size:15 final size:16
Alignment explanation
Indices: 35320--35388 Score: 65
Period size: 15 Copynumber: 4.4 Consensus size: 16
35310 TTAAACATAT
35320 ATTAAAAGTAATAATAA
1 ATTAAAAGTAATAAT-A
* *
35337 AATAAAA-TAACAATA
1 ATTAAAAGTAATAATA
*
35352 ATTAAAA-TGAA-AAAA
1 ATTAAAAGT-AATAATA
35367 ATTAAAAGTAATAAT-
1 ATTAAAAGTAATAATA
35382 ATTAAAA
1 ATTAAAA
35389 ACTAATGGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
15 27 0.61
16 11 0.25
17 6 0.14
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (16 bp):
ATTAAAAGTAATAATA
Found at i:35389 original size:25 final size:25
Alignment explanation
Indices: 35303--35389 Score: 60
Period size: 25 Copynumber: 3.6 Consensus size: 25
35293 ATCATGAAGA
* *
35303 TAATAAT-TTAAACATATATTAAAAG
1 TAATAATATTAAA-AAAAATTAAAAG
*
35328 TAATAATA--AAATAAAA-TAACAA-
1 TAATAATATTAAAAAAAATTAA-AAG
* *
35350 TAATTAA-AATGAAAAAAATTAAAAG
1 TAA-TAATATTAAAAAAAATTAAAAG
35375 TAATAATATTAAAAA
1 TAATAATATTAAAAA
35390 CTAATGGATC
Statistics
Matches: 47, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
22 7 0.15
23 7 0.15
24 14 0.30
25 19 0.40
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (25 bp):
TAATAATATTAAAAAAAATTAAAAG
Found at i:36760 original size:15 final size:15
Alignment explanation
Indices: 36707--36761 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
36697 TTTGGGCTTG
36707 TAATAAT-ATATTTAA
1 TAATAATAAT-TTTAA
*
36722 TAATAATTATTATT-A
1 TAATAATAATT-TTAA
36737 TAATAATAATTTTAA
1 TAATAATAATTTTAA
36752 TAATAATAAT
1 TAATAATAAT
36762 AAAAATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 2 0.06
15 30 0.83
16 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATAATAATTTTAA
Found at i:36762 original size:18 final size:18
Alignment explanation
Indices: 36719--36763 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
36709 ATAATATATT
*
36719 TAATAATAATTATTATTA
1 TAATAATAATTATTATAA
36737 TAATAATAATT-TTAATAA
1 TAATAATAATTATT-ATAA
36755 TAATAATAA
1 TAATAATAA
36764 AAATAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATAATAATTATTATAA
Found at i:37019 original size:76 final size:76
Alignment explanation
Indices: 36921--37558 Score: 1195
Period size: 76 Copynumber: 8.4 Consensus size: 76
36911 GAGGTCTTAA
* *
36921 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
36986 AGGCTTTTTGG
66 AGGCTTTTTGG
36997 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
37062 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
37073 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAATCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
37138 AGGCTTTTTGG
66 AGGCTTTTTGG
*
37149 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
37214 AGGCTTTTTGG
66 AGGCTTTTTGG
*
37225 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
37290 AGGCTTTTTGG
66 AGGCTTTTTGG
37301 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
37366 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
37377 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATTAAAAAGCTTCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
37442 AGGCTTTTTGG
66 AGGCTTTTTGG
*
37453 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
37518 AGGCTTTTTGG
66 AGGCTTTTTGG
37529 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
37559 TGGGAAATAG
Statistics
Matches: 549, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 549 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:38423 original size:22 final size:22
Alignment explanation
Indices: 38389--38440 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
38379 CATAAAGCTT
* * *
38389 TCATATTTGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
*
38411 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
38433 TCATCTTT
1 TCATCTTT
38441 GAAGAGTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:41382 original size:115 final size:114
Alignment explanation
Indices: 40948--41379 Score: 702
Period size: 114 Copynumber: 3.8 Consensus size: 114
40938 CATGCAGTTC
* * * *
40948 ATCTTTCAACTCCAATGATTGGTTCTGAGGTTCCTACCAAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
* * * **
41013 CTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATAAGCAAATTC
66 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCACATGG
*
41062 ATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACTAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
* * *
41127 CCTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCACATGG
66 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCACATGG
* *
41176 ATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
* *
41241 CTTTCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATGG
66 CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCACATGG
41290 ATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
1 ATCTTTCAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
41355 ACTTCCAGAAGATGCTATTGGGTCT
65 ACTTCCAGAAGATGCTATTGGGTCT
41380 TCTACTATGA
Statistics
Matches: 293, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
114 228 0.78
115 65 0.22
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (114 bp):
ATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCACATGG
Found at i:43445 original size:11 final size:11
Alignment explanation
Indices: 43409--43445 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
43399 CTTGATTCAA
43409 TTTTTTTTCTT
1 TTTTTTTTCTT
* *
43420 TTTGTTTTGTT
1 TTTTTTTTCTT
43431 TTTTTTTTCTT
1 TTTTTTTTCTT
43442 TTTT
1 TTTT
43446 CCTTTATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.89
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:46787 original size:14 final size:14
Alignment explanation
Indices: 46753--46806 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
46743 CATAAAAATA
* *
46753 CAAATGCAAAGATG
1 CAAATGTAAATATG
46767 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
46782 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
46796 TAAATGTAAAT
1 CAAATGTAAAT
46807 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:49281 original size:14 final size:15
Alignment explanation
Indices: 49251--49283 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
49241 AATAGAATAA
49251 ATAAATAAATGTTAT
1 ATAAATAAATGTTAT
*
49266 ATAAATATAT-TTAT
1 ATAAATAAATGTTAT
49280 ATAA
1 ATAA
49284 CTTAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATAAATAAATGTTAT
Found at i:52109 original size:147 final size:148
Alignment explanation
Indices: 51875--52175 Score: 462
Period size: 147 Copynumber: 2.0 Consensus size: 148
51865 GAGTCGAGGG
* * * * * * *
51875 TCTACGCGGTCTTTCGAGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* * *
51940 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATAATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
52005 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* *
52023 TCTACGCGGTCCTTCG-G-GATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
52086 ACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
52151 TATGGCACTACGGTGTAAT
130 TATGGCACTACGGTGCAAT
52170 TCTACG
1 TCTACG
52176 TGCACTTCGG
Statistics
Matches: 139, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
146 29 0.21
147 95 0.68
148 15 0.11
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATAATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:52435 original size:31 final size:31
Alignment explanation
Indices: 52359--52437 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
52349 CAAGATCATG
* *
52359 TGATAAATAATTTGATGATAATGATAGAGATAA
1 TGAT-AATAATAT-ATGATAATGATAGAGAAAA
*
52392 TGATAATAATATATGATAATGCTA-AGAAAA
1 TGATAATAATATATGATAATGATAGAGAAAA
* *
52422 TAGATGATGATATATG
1 T-GATAATAATATATG
52438 TACATGAGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 6 0.15
31 23 0.57
32 7 0.17
33 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.18, T:0.33
Consensus pattern (31 bp):
TGATAATAATATATGATAATGATAGAGAAAA
Found at i:53014 original size:2 final size:2
Alignment explanation
Indices: 53009--53051 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
52999 TGGGTGGAAG
53009 TA TA TA TA TA TA TA 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 TA TA TA TA
53051 T
1 T
53052 TAATAACATT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56951 original size:64 final size:63
Alignment explanation
Indices: 56879--56999 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 63
56869 ATTGTTCAAG
* * * * *
56879 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCAATGCACCCCCTT-AAATAAAAACATCGAATGCCATCA
* *
56943 GTGTATCGATGCACAAGTAGTGCATCAATGCACCCCCTTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCAATGCACCCCCTTAAATAAAAACATCGAATG
57000 GAATTTATGC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 17 0.34
64 33 0.66
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCAATGCACCCCCTTAAATAAAAACATCGAATGCCATCA
Found at i:58782 original size:17 final size:17
Alignment explanation
Indices: 58756--58788 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
58746 CCTTGATTGA
58756 TGAATCTAAATTAAGAG
1 TGAATCTAAATTAAGAG
*
58773 TGAATTTAAATTAAGA
1 TGAATCTAAATTAAGA
58789 TATTCTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.33
Consensus pattern (17 bp):
TGAATCTAAATTAAGAG
Found at i:60271 original size:65 final size:65
Alignment explanation
Indices: 60138--60298 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
60128 GTGCACTAAG
* *
60138 TGTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCATGTCT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGTCA
* *
60202 TGTGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATC-AGTGCATGG
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATACCCTGAGTGCATCGA-TGCAT-G
60265 T-A
63 TCA
* *
60267 TGTGCATCGCTGCATAAAATGCATTCAATGTT
1 TGTGCATCGATGCATAAAATGCATTCGATGTT
60299 CAATTTATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 29 0.34
65 51 0.60
66 5 0.06
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (65 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATACCCTGAGTGCATCGATGCATGTCA
Found at i:75370 original size:2 final size:2
Alignment explanation
Indices: 75363--75392 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
75353 TAAAATATTA
75363 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
75393 GGTTGCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81378 original size:16 final size:16
Alignment explanation
Indices: 81357--81389 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
81347 ACCGAATTAA
81357 ATTTAAGAA-TTTTTCT
1 ATTTAA-AACTTTTTCT
81373 ATTTAAAACTTTTTCT
1 ATTTAAAACTTTTTCT
81389 A
1 A
81390 GCTTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTTAAAACTTTTTCT
Found at i:82030 original size:23 final size:23
Alignment explanation
Indices: 82000--82045 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
81990 TTAATAGAGG
82000 ATTGATTCAATTGCAACAAATTT
1 ATTGATTCAATTGCAACAAATTT
82023 ATTGATTCAATTGCAACAAATTT
1 ATTGATTCAATTGCAACAAATTT
82046 TAAATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (23 bp):
ATTGATTCAATTGCAACAAATTT
Found at i:87989 original size:26 final size:26
Alignment explanation
Indices: 87953--88025 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
87943 TGGCCGATGC
*
87953 TTGTAAATGAAAACTAAAACAAATTA
1 TTGTAAATGAAAACAAAAACAAATTA
87979 TTGTAAATGAAAACAAAAACAAATTA
1 TTGTAAATGAAAACAAAAACAAATTA
* *
88005 TTGCAAATGAAAACAGAAACA
1 TTGTAAATGAAAACAAAAACA
88026 TGCAATTGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (26 bp):
TTGTAAATGAAAACAAAAACAAATTA
Found at i:92313 original size:39 final size:39
Alignment explanation
Indices: 92270--92345 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
92260 TAAGAGGTTA
92270 AGAAAGAAGTAA-AAAAGGTATAAAACTATTGAAATTTAG
1 AGAAAGAAGTAACAAAA-GTATAAAACTATTGAAATTTAG
* *
92309 AGAAAGAAGTAACAACAGTATTAAACTATTGAAATTT
1 AGAAAGAAGTAACAAAAGTATAAAACTATTGAAATTT
92346 GGGAATAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 31 0.91
40 3 0.09
ACGTcount: A:0.54, C:0.05, G:0.16, T:0.25
Consensus pattern (39 bp):
AGAAAGAAGTAACAAAAGTATAAAACTATTGAAATTTAG
Found at i:94219 original size:60 final size:59
Alignment explanation
Indices: 94112--94223 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 59
94102 AGTACATATG
* * * * * *
94112 TATAGTTTAGGATGAAATTGGATTTTTAAAAAGTTTGAAGATCAATTTAGAATGAAGGT
1 TATAGTTTAGGATAAAATTGAAATGTTAAAAACTTTAAAGATCAATTTAGAATGAAGGT
*
94171 TATAGTTTAGGGATAAAATTGAAATGTTCAAAACTTTAAAGAAT-AATTTAGAA
1 TATAGTTTA-GGATAAAATTGAAATGTTAAAAACTTTAAAG-ATCAATTTAGAA
94224 CCATAGTCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
59 9 0.20
60 33 0.75
61 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.36
Consensus pattern (59 bp):
TATAGTTTAGGATAAAATTGAAATGTTAAAAACTTTAAAGATCAATTTAGAATGAAGGT
Found at i:94401 original size:18 final size:18
Alignment explanation
Indices: 94378--94431 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
94368 AATATTTTTA
94378 TATTTTCTATTAATAATT
1 TATTTTCTATTAATAATT
94396 TA-TTT-TATCTAAT-ATT
1 TATTTTCTAT-TAATAATT
94412 TATATTTCTATTAATAATT
1 TAT-TTTCTATTAATAATT
94431 T
1 T
94432 GTTGTCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
16 8 0.26
17 7 0.23
18 9 0.29
19 7 0.23
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTTCTATTAATAATT
Found at i:105914 original size:30 final size:29
Alignment explanation
Indices: 105846--105971 Score: 137
Period size: 30 Copynumber: 4.3 Consensus size: 29
105836 CTGGAAGTGC
* *
105846 CTAAATAGCAAAAACAAAAATTTAAAGGA
1 CTAAATAGAAAAAACAAAAAGTTAAAGGA
105875 CTAAATAGAAAAAACAAAAAGTTAAAGGA
1 CTAAATAGAAAAAACAAAAAGTTAAAGGA
* * * *
105904 CTAGAATAGAAAAAATAGAAACTTAAAAGA
1 CTA-AATAGAAAAAACAAAAAGTTAAAGGA
* *
105934 CTAAAATA-ACTAAAACAAAAAGTTAATGGA
1 CT-AAATAGA-AAAAACAAAAAGTTAAAGGA
*
105964 CTACATAG
1 CTAAATAG
105972 TAATTATGAA
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
29 35 0.44
30 44 0.55
31 1 0.01
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.17
Consensus pattern (29 bp):
CTAAATAGAAAAAACAAAAAGTTAAAGGA
Found at i:106918 original size:15 final size:15
Alignment explanation
Indices: 106900--106937 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
106890 GTTTCCCCTC
106900 TCCCTCTTCTTCTAA
1 TCCCTCTTCTTCTAA
106915 TCCCTCTTCTTCTAA
1 TCCCTCTTCTTCTAA
106930 TCCCTCTT
1 TCCCTCTT
106938 TGTTCTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.11, C:0.42, G:0.00, T:0.47
Consensus pattern (15 bp):
TCCCTCTTCTTCTAA
Found at i:108068 original size:137 final size:137
Alignment explanation
Indices: 107738--108129 Score: 364
Period size: 137 Copynumber: 2.9 Consensus size: 137
107728 TAGGAGGGGT
* * * *
107738 GATAACACGATTCCTACGCGATGAGGAC-ATCTAGTTATCA-AGGGTGACAC-AGCTCCTACGTG
1 GATAACACGATTCCTACGTGATGAGAACGA-CTGGTTATCAGAGGGTAACACGA-CTCCTACGTG
** * * * * * *
107800 ATGAGGAATTCTGGTCAGTGG-ATGACACAGTTCCTATGTGATAAGGATGGCATA-CCATC----
64 ATGAGGAGGTCTGGTCAG-GGAATGACACGGTTCCTACGCGATGAGGACGACA-AGCCATCTTTA
107859 TTTA-GCA--T-
127 TTTATG-AGGTA
* * * * * * *
107867 GATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCAGGGGGTGACACGGCTTCTATGTGAT
1 GATAACACGATTCCTACGTGATGAGAACGACTGGTTATCAGAGGGTAACACGACTCCTACGTGAT
* * * * *
107932 GAGGAGGTTTGGTCGGGGGATGACACGGTTCCTACGCGATGTGGACGGCAAGCCATCTTTATTTA
66 GAGGAGGTCTGGTCAGGGAATGACACGGTTCCTACGCGATGAGGACGACAAGCCATCTTTATTTA
107997 TGAGGTA
131 TGAGGTA
*
108004 GATAACACGATTCCTACGTGATGAGAACGGC-GTGTTATCTA-AGGGTAACACGACTCCTACGTG
1 GATAACACGATTCCTACGTGATGAGAACGACTG-GTTATC-AGAGGGTAACACGACTCCTACGTG
* * *
108067 ATGAGGAGGTCTGGTCAGGGAATGACACGGTTCCTATGCGATGAGGATGACATGCCATCTTTA
64 ATGAGGAGGTCTGGTCAGGGAATGACACGGTTCCTACGCGATGAGGACGACAAGCCATCTTTA
108130 GGGATAATGG
Statistics
Matches: 215, Mismatches: 33, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
129 38 0.18
130 62 0.29
134 5 0.02
135 1 0.00
136 2 0.01
137 106 0.49
138 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (137 bp):
GATAACACGATTCCTACGTGATGAGAACGACTGGTTATCAGAGGGTAACACGACTCCTACGTGAT
GAGGAGGTCTGGTCAGGGAATGACACGGTTCCTACGCGATGAGGACGACAAGCCATCTTTATTTA
TGAGGTA
Found at i:108176 original size:29 final size:30
Alignment explanation
Indices: 108132--108188 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
108122 CATCTTTAGG
*
108132 GATAATGGTTTCAAGAGAAACTGACTCATA
1 GATAATGGCTTCAAGAGAAACTGACTCATA
* *
108162 GATAAT-GCTTCAAGAGAAGCTGTCTCA
1 GATAATGGCTTCAAGAGAAACTGACTCA
108189 AAAGACACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (30 bp):
GATAATGGCTTCAAGAGAAACTGACTCATA
Found at i:108316 original size:66 final size:62
Alignment explanation
Indices: 108234--108371 Score: 188
Period size: 66 Copynumber: 2.2 Consensus size: 62
108224 AGATGTTTGT
* *
108234 TTTGTTTCAAGGGAAACATAA-TCAAAGATTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAA
1 TTTGTTTCAAGAGAAACA-AACTCAAAGATTTTTT-TCAAAAGAAACTGTCTC--GAGAGACAAA
108298 A
62 A
* *
108299 CTTTGTTTCCAGAGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTCGAGCGACAAAA
1 -TTTGTTTCAAGAGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTCGAGAGACAAAA
108362 TTTGTTTCAA
1 TTTGTTTCAA
108372 AATAAATAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
62 9 0.14
63 10 0.15
65 18 0.27
66 29 0.44
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (62 bp):
TTTGTTTCAAGAGAAACAAACTCAAAGATTTTTTTCAAAAGAAACTGTCTCGAGAGACAAAA
Found at i:113428 original size:18 final size:18
Alignment explanation
Indices: 113399--113441 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
113389 TTGTATGTGC
*
113399 TTCTTATCTTTTTTTCTTT
1 TTCTT-TCTTTTGTTCTTT
113418 TTCTTTCTTTTGTTCTTT
1 TTCTTTCTTTTGTTCTTT
113436 TTCTTT
1 TTCTTT
113442 GATTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTCTTTTGTTCTTT
Found at i:113454 original size:18 final size:18
Alignment explanation
Indices: 113415--113477 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
113405 TCTTTTTTTC
*
113415 TTTTTCTTT-CTTTTGTT
1 TTTTTCTTTGATTTTGTT
*
113432 CTTTTTCTTTGATTTT-CT
1 -TTTTTCTTTGATTTTGTT
113450 TTTTTCTTTGATATTTGTT
1 TTTTTCTTTGAT-TTTGTT
113469 TTTTT-TTTG
1 TTTTTCTTTG
113478 CTTCTTTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
17 12 0.31
18 17 0.44
19 10 0.26
ACGTcount: A:0.05, C:0.10, G:0.08, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTGATTTTGTT
Found at i:113496 original size:24 final size:24
Alignment explanation
Indices: 113408--113496 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 24
113398 CTTCTTATCT
*
113408 TTTTTTCTTT-TTCTTTCTTTTGTTC
1 TTTTCTCTTTGTT-TTT-TTTTGTTC
*
113433 TTTT-TCTTTGATTTTCTTTT-TTC
1 TTTTCTCTTTG-TTTTTTTTTGTTC
** *
113456 TTTGATATTTGTTTTTTTTTTGCTTC
1 TTTTCTCTTTG-TTTTTTTTTG-TTC
113482 TTTTCTCTTTGTTTT
1 TTTTCTCTTTGTTTT
113497 GATTTGATCT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
23 6 0.12
24 22 0.43
25 10 0.20
26 13 0.25
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTTCTCTTTGTTTTTTTTTGTTC
Found at i:116691 original size:13 final size:15
Alignment explanation
Indices: 116658--116701 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
116648 CTAATGGGCA
116658 AAGTTTTGAAAAATT
1 AAGTTTTGAAAAATT
*
116673 ATG-TTTGAAAAA-T
1 AAGTTTTGAAAAATT
116686 AAGTTTTG-AAAATT
1 AAGTTTTGAAAAATT
116700 AA
1 AA
116702 TATGCGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 7 0.28
14 16 0.64
15 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.39
Consensus pattern (15 bp):
AAGTTTTGAAAAATT
Found at i:120988 original size:23 final size:23
Alignment explanation
Indices: 120938--121020 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
120928 AATCTTATAT
*
120938 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACAC
*
120961 AGCACTACGGTGCAATTCTACAC
1 GGCACTACGGTGCAATTCTACAC
*** * *
120984 GGCACTTTAGTGTAATTCTACAT
1 GGCACTACGGTGCAATTCTACAC
*
121007 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
121021 TTTATACGAG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACAC
Found at i:127157 original size:65 final size:64
Alignment explanation
Indices: 127081--127237 Score: 181
Period size: 65 Copynumber: 2.4 Consensus size: 64
127071 CCATTCAATA
* * * * * *
127081 GGTACCGATACCCTCTCAAACG-AGAAATTCCATAATGTTATGGGGGTACCGATTCCCCCCAGAG
1 GGTACCGATACCCCCT-AAACGAAAAAATTACAGAATGTCATAGGGGTACCGATT-CCCCCAGAG
127145 G
64 G
** *
127146 GGTACCGATACCCCCTTGACGAAAAAATTACAGAATGTCATAGGGGTACCGATTCCCCCATAGG
1 GGTACCGATACCCCCTAAACGAAAAAATTACAGAATGTCATAGGGGTACCGATTCCCCCAGAGG
* *
127210 GGTATCGATACCCCTCTAAAAGAAAAAA
1 GGTACCGATACCCC-CTAAACGAAAAAA
127238 AATGAAACAT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 25 0.32
65 52 0.68
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (64 bp):
GGTACCGATACCCCCTAAACGAAAAAATTACAGAATGTCATAGGGGTACCGATTCCCCCAGAGG
Found at i:127209 original size:20 final size:20
Alignment explanation
Indices: 127184--127223 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
127174 TACAGAATGT
*
127184 CATAGGGGTACCGATTCCCC
1 CATAGGGGTACCGATACCCC
*
127204 CATAGGGGTATCGATACCCC
1 CATAGGGGTACCGATACCCC
127224 TCTAAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (20 bp):
CATAGGGGTACCGATACCCC
Found at i:127864 original size:23 final size:23
Alignment explanation
Indices: 127838--127885 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
127828 TATGGAATTA
127838 CGGTGCAATTCTACGCGGCACTT
1 CGGTGCAATTCTACGCGGCACTT
*
127861 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTT
127884 CG
1 CG
127886 ATGTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.27
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTT
Found at i:127898 original size:23 final size:23
Alignment explanation
Indices: 127841--127898 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
127831 GGAATTACGG
* *
127841 TGCAATTCTACGCGGCACTTCGG
1 TGCAATTATACGCGGCACTTCGA
* *
127864 TGCAATTCTACGTGGCACTTCGA
1 TGCAATTATACGCGGCACTTCGA
* *
127887 TGTATTTATACG
1 TGCAATTATACG
127899 AGTTGTGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (23 bp):
TGCAATTATACGCGGCACTTCGA
Found at i:130110 original size:21 final size:21
Alignment explanation
Indices: 130059--130098 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
130049 GTGATTATTT
130059 TCATTTTTCA-ATTTTAAAATA
1 TCATTTTT-ATATTTTAAAATA
130080 TCATTTTTATATTTTAAAA
1 TCATTTTTATATTTTAAAA
130099 ACAATTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
TCATTTTTATATTTTAAAATA
Found at i:132064 original size:21 final size:22
Alignment explanation
Indices: 132021--132064 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
132011 CCGTTGAACA
*
132021 GGGGGAATCGGTACCCCTTTGG
1 GGGGGAATCGGTACCCCTCTGG
132043 GGGGGAATCGGTACCCC-CTGG
1 GGGGGAATCGGTACCCCTCTGG
132064 G
1 G
132065 AAATCTGCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCTCTGG
Found at i:135767 original size:29 final size:29
Alignment explanation
Indices: 135734--135836 Score: 91
Period size: 29 Copynumber: 3.4 Consensus size: 29
135724 CTACAAGGGC
*
135734 CTAAATAGCAAAATCAAAAATTTAAAGGA
1 CTAAATAGCAAAATCAAAAACTTAAAGGA
* * *
135763 CTAAATGGCAAAAACAAAAAGTTAAAGGA
1 CTAAATAGCAAAATCAAAAACTTAAAGGA
* * * *
135792 CCAAAATAGAAAAAAT-AGAAACTTAAATGA
1 -CTAAATAG-CAAAATCAAAAACTTAAAGGA
135822 CTAAAATAGCTAAAA
1 CT-AAATAGC-AAAA
135837 CATAATGTTA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
29 27 0.47
30 27 0.47
31 4 0.07
ACGTcount: A:0.60, C:0.11, G:0.12, T:0.17
Consensus pattern (29 bp):
CTAAATAGCAAAATCAAAAACTTAAAGGA
Found at i:149397 original size:23 final size:23
Alignment explanation
Indices: 149371--149432 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
149361 ACATGTAAAA
* * *
149371 ATATGATGTAATAGGTATCGCTT
1 ATATAATGTAATAGGTAGCGATT
149394 ATATAATGTAATAGGTAGCGATT
1 ATATAATGTAATAGGTAGCGATT
**
149417 ATATAATAAAATAGGT
1 ATATAATGTAATAGGT
149433 TAATTACTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.35
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGATT
Found at i:149495 original size:23 final size:23
Alignment explanation
Indices: 149469--149533 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
149459 AATAACATAT
149469 TAGGTACTTCTTATATAATGTAA
1 TAGGTACTTCTTATATAATGTAA
*
149492 TAGGTAGC-GCTTATATAATGTAA
1 TAGGTA-CTTCTTATATAATGTAA
* *
149515 TATGTAGTTCTTATATAAT
1 TAGGTACTTCTTATATAAT
149534 AAAAGGTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (23 bp):
TAGGTACTTCTTATATAATGTAA
Found at i:149582 original size:108 final size:108
Alignment explanation
Indices: 149371--149615 Score: 345
Period size: 110 Copynumber: 2.3 Consensus size: 108
149361 ACATGTAAAA
*
149371 ATATGATGTAATAGGTATCGCTTATATAATGTAATAGGTAGCGATTATATAATAAAATAGGTTAA
1 ATAT-ATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGATTATATAATAAAATAGGTTAA
**
149436 TTACTGTAAACATTACCAAGCACAATAACATATTAGGTACTTCTT
65 TTACTGTAAACATTACCAAGCACAATAACATATTAGGTACAGC-T
* ***
149481 ATATAATGTAATAGGTAGCGCTTATATAATGTAATATGTAGTTCTTATATAAT-AAA-AGGTTAA
1 ATAT-ATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGATTATATAATAAAATAGGTTAA
* *
149544 TTACTAG-AAACATTATCAAGCACAATAACATATTAGGTAGAGCT
65 TTACT-GTAAACATTACCAAGCACAATAACATATTAGGTACAGCT
149588 -TATATGTAATAGGTAGCGCTTATATAAT
1 ATATATGTAATAGGTAGCGCTTATATAAT
149616 AAAATAAGTT
Statistics
Matches: 124, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
105 25 0.20
106 3 0.02
107 1 0.01
108 44 0.35
109 4 0.03
110 47 0.38
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (108 bp):
ATATATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGATTATATAATAAAATAGGTTAAT
TACTGTAAACATTACCAAGCACAATAACATATTAGGTACAGCT
Found at i:149645 original size:84 final size:84
Alignment explanation
Indices: 149509--149717 Score: 287
Period size: 84 Copynumber: 2.5 Consensus size: 84
149499 CGCTTATATA
* **
149509 ATGTAATATGTAGTTCTTATATAAT-AAA-AGGTTAATTACTAGAAACATTATCAAGCACAATAA
1 ATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCACAATAA
149572 CATATTAGGTAGAGCTTAT
66 CATATTAGGTAGAGCTTAT
* * *
149591 ATGTAATAGGTAGCGCTTATATAATAAAATAAGTTAATTACTGGAAACATTATCAAGCACAATAA
1 ATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCACAATAA
*
149656 CATATTAGGTAGCGCTTAT
66 CATATTAGGTAGAGCTTAT
* * *
149675 ATAACATAATAGATAACACTTATATAATAAAATAGGTTAATTA
1 AT---GTAATAGGTAGCACTTATATAATAAAATAGGTTAATTA
149718 TTTAATTTGT
Statistics
Matches: 111, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
82 22 0.20
83 3 0.03
84 53 0.48
87 33 0.30
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (84 bp):
ATGTAATAGGTAGCACTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCACAATAA
CATATTAGGTAGAGCTTAT
Found at i:149678 original size:23 final size:23
Alignment explanation
Indices: 149652--149701 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
149642 ATCAAGCACA
* * * *
149652 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGATAACACTTAT
149675 ATAACATAATAGATAACACTTAT
1 ATAACATAATAGATAACACTTAT
149698 ATAA
1 ATAA
149702 TAAAATAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGATAACACTTAT
Found at i:150043 original size:14 final size:14
Alignment explanation
Indices: 150032--150105 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 14
150022 TAATTTATGT
150032 AAATATTATTATTA
1 AAATATTATTATTA
150046 AAATATTA-TATCTA
1 AAATATTATTAT-TA
* * * *
150060 TAATTTTATAAATA
1 AAATATTATTATTA
* *
150074 AAAAATTATGATTA
1 AAATATTATTATTA
**
150088 TTATATT-TTATTA
1 AAATATTATTATTA
150101 AAATA
1 AAATA
150106 AAATTATTAT
Statistics
Matches: 43, Mismatches: 15, Indels: 5
0.68 0.24 0.08
Matches are distributed among these distances:
13 11 0.26
14 31 0.72
15 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (14 bp):
AAATATTATTATTA
Found at i:150068 original size:28 final size:28
Alignment explanation
Indices: 149982--150105 Score: 88
Period size: 28 Copynumber: 4.7 Consensus size: 28
149972 TAACAAAATA
*
149982 ATAATATTATTTTTAAAATATTA-GA--
1 ATAATATTATTATTAAAATATTATGATT
* *
150007 ATAAT-TTATTTAATATAAT-TTATG--T
1 ATAATATTA-TTATTAAAATATTATGATT
150032 A-AATATTATTATTAAAATATTAT-ATCT
1 ATAATATTATTATTAAAATATTATGAT-T
* * * *
150059 ATAATTTTATAAATAAAAAATTATGATT
1 ATAATATTATTATTAAAATATTATGATT
*
150087 ATTATATT-TTATTAAAATA
1 ATAATATTATTATTAAAATA
150106 AAATTATTAT
Statistics
Matches: 75, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
24 17 0.23
25 21 0.28
27 10 0.13
28 25 0.33
29 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (28 bp):
ATAATATTATTATTAAAATATTATGATT
Found at i:150836 original size:28 final size:28
Alignment explanation
Indices: 150801--150890 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 28
150791 TATTTATGTC
150801 AATATTATTATTAAAATATTAT-ATCTAT
1 AATATTATTATTAAAATATTATGAT-TAT
* * * *
150829 AATTTTATAAATAAAAAATTATGATTAT
1 AATATTATTATTAAAATATTATGATTAT
* ** *
150857 TATATT-TTATTAAAATAAAATTATTAT
1 AATATTATTATTAAAATATTATGATTAT
150884 AA-ATTAT
1 AATATTAT
150891 ATTTATTATT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
26 3 0.06
27 17 0.36
28 25 0.53
29 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTATTATTAAAATATTATGATTAT
Found at i:150893 original size:31 final size:31
Alignment explanation
Indices: 150830--150898 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
150820 TATATCTATA
*
150830 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
150860 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
150891 A-TTTATTA
1 ATTTTATTA
150899 TTTATTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Found at i:151444 original size:199 final size:198
Alignment explanation
Indices: 150999--151668 Score: 940
Period size: 199 Copynumber: 3.4 Consensus size: 198
150989 CACATATGTT
* * *
150999 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAACCAATATAAATATACCGG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGT-ACCGATAGAAATATACCGG
* * ***
151064 TTTTATGAGAGAATATG-TCTACATAATGTATCGACACAAATTTAA-AAAGTGTCGATACATTTT
65 TTTTATGAGAAAATA-GATCTACATAATGTATCGACAC-ATTTTAAGTTTGTGTCGATAC-TTTT
* * *
151127 GTCTAGAATGAATG-CCAAACTAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGA
127 TTCTAGAATGAATGTCC-AACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATTGA
151191 TCCCAAAA
191 TCCCAAAA
* *
151199 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACTCGGTAGAAATATATCGG
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTAC-CGATAGAAATATACCGG
* *
151264 TTTTATGAGAAAATAGATATGCATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
65 TTTTATGAGAAAATAGATCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
* * *
151329 CAGAAAGAATGTCCAACGAGGTGCACACATAAAGTGTCGATACATTTATTAAAAGTATTGATCCC
130 TAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATTGATCCC
151394 AAAA
195 AAAA
* * *
151398 A-TTCGAAACCGATAATTACAATGTTAATAGGTAAATTTACAATGTACCCGGTAGAAATATATCG
1 ACATCGAAACCGATAATTACAATG-TAATAGGTAAATTTACAATGTA-CCGATAGAAATATACCG
* *
151462 GTTTTATGAGAAAATA-AGTCTACATAATGTATCGACACGTTTTAAGTTTGTGTAGATACTTTTT
64 GTTTTATGAGAAAATAGA-TCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTT
*
151526 TCTAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA--AAATTGTATTGAT
128 TCTAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTATTGAT
151589 CCCAAAA
192 CCCAAAA
* * * *
151596 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTATAATGTTACCGATATAAATATACCGA
1 ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATG-TACCGATAGAAATATACCGG
151661 TTTTATGA
65 TTTTATGA
151669 TAGAATAAGT
Statistics
Matches: 426, Mismatches: 34, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
197 3 0.01
198 79 0.19
199 242 0.57
200 102 0.24
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (198 bp):
ACATCGAAACCGATAATTACAATGTAATAGGTAAATTTACAATGTACCGATAGAAATATACCGGT
TTTATGAGAAAATAGATCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTCT
AGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATTGATCCCA
AAA
Found at i:151841 original size:87 final size:87
Alignment explanation
Indices: 151695--151920 Score: 337
Period size: 87 Copynumber: 2.6 Consensus size: 87
151685 AAACGTTGCA
*
151695 TATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTTCTAGTAATTAACCT
1 TATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTTCTAGTAATTAACCT
*
151760 ATTTTATTATATCAGCGCTACC
66 ATTTTATTATATAAGCGCTACC
* * * *
151782 TATTACATTATATAAACACAACCTAATATGTTATTGTGTTTGATAATGTTT-TCAGTAATTAACC
1 TATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTTCT-AGTAATTAACC
151846 TATTTTATTATATAAGCGCTACC
65 TATTTTATTATATAAGCGCTACC
* * * * *
151869 TATTACATTATATAAACGCTACCTAATTTATTATTTTACTTAATAATATTTC
1 TATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTTC
151921 CGATTAAATG
Statistics
Matches: 122, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
86 1 0.01
87 121 0.99
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.44
Consensus pattern (87 bp):
TATTACATTATATAAACGCTACCTAATATGTTATTGTGCTTGATAATATTTCTAGTAATTAACCT
ATTTTATTATATAAGCGCTACC
Found at i:151901 original size:23 final size:23
Alignment explanation
Indices: 151843--151902 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
151833 TCAGTAATTA
* *
151843 ACCTATTTTATTATATAAGCGCT
1 ACCTAATTTATTATATAAACGCT
*
151866 ACCT-ATTACATTATATAAACGCT
1 ACCTAATT-TATTATATAAACGCT
151889 ACCTAATTTATTAT
1 ACCTAATTTATTAT
151903 TTTACTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 2 0.06
23 26 0.84
24 3 0.10
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (23 bp):
ACCTAATTTATTATATAAACGCT
Found at i:152081 original size:15 final size:15
Alignment explanation
Indices: 152061--152089 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
152051 ACGCATAAAA
152061 ATTTTAAAAATATAT
1 ATTTTAAAAATATAT
152076 ATTTTAAAAATATA
1 ATTTTAAAAATATA
152090 CACTTTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTAAAAATATAT
Found at i:153012 original size:20 final size:21
Alignment explanation
Indices: 152987--153079 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
152977 TTTTCCCAAT
*
152987 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
153007 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
153028 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
153048 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
153069 TCGCAATGCGA
1 TCGCAATGCGA
153080 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:153032 original size:41 final size:41
Alignment explanation
Indices: 152987--153079 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
152977 TTTTCCCAAT
152987 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
153028 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
153069 TCGCAATGCGA
1 TCGCAATGCGA
153080 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:153092 original size:41 final size:41
Alignment explanation
Indices: 153006--153140 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
152996 GAATAAGTAA
* *
153006 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
153047 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
153088 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
153129 TTCGCAACGCGA
1 ATCGCAACGCGA
153141 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:153093 original size:20 final size:20
Alignment explanation
Indices: 153068--153162 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
153058 AATTGGGAAA
*
153068 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
153088 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
153109 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
153129 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
153149 TTCGCAACGCGATA
1 ATCGCAACGCGATA
153163 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:153378 original size:22 final size:22
Alignment explanation
Indices: 153350--153393 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
153340 CACTCTCTCA
153350 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
153372 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
153394 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:155016 original size:18 final size:18
Alignment explanation
Indices: 154995--155039 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
154985 TCCACTTCGG
*
154995 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
155013 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
155031 GAGCCATCA
1 GAGCCATCA
155040 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:155562 original size:20 final size:20
Alignment explanation
Indices: 155512--155578 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
155502 TAGTTTACTT
*
155512 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
155532 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
155552 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
155571 TCGCAACG
1 TCGCAACG
155579 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:155586 original size:14 final size:14
Alignment explanation
Indices: 155567--155624 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
155557 ATGCGAAATG
155567 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
155581 AAAATCGCAATACGAA
1 AAAATCGC-A-ACGAC
155597 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
155613 AAAATCGCAACG
1 AAAATCGCAACG
155625 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 19 0.50
15 1 0.03
16 10 0.26
17 1 0.03
18 7 0.18
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:155609 original size:32 final size:33
Alignment explanation
Indices: 155551--155641 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
155541 GAAAATGGCT
155551 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
155584 ATCGCAATACGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
155616 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
155642 TGTGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:155676 original size:13 final size:14
Alignment explanation
Indices: 155658--155714 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
155648 TTGTGTTTCG
155658 CGTTGCGA-TTTGT
1 CGTTGCGATTTTGT
*
155671 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
155687 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
155703 CGTTGCGATTTT
1 CGTTGCGATTTT
155715 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.22
14 14 0.38
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:155702 original size:32 final size:33
Alignment explanation
Indices: 155653--155730 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
155643 GTGATTTGTG
155653 TTTCGCGTTGCGA-TTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
155684 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
155717 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
155731 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 13 0.30
32 13 0.30
33 18 0.41
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:155729 original size:19 final size:19
Alignment explanation
Indices: 155671--155788 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
155661 TGCGATTTGT
155671 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
155689 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
155703 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
155722 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
155742 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
155761 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
155781 TGTTGCGA
1 CGTTGCGA
155789 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:157805 original size:33 final size:33
Alignment explanation
Indices: 157760--157875 Score: 133
Period size: 33 Copynumber: 3.4 Consensus size: 33
157750 AAAACAGACT
* ***
157760 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
* *
157793 ATCGCAATGCGAAATGAAAATCGCAATGCGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
157826 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
157864 ATCGCAATGCGA
1 ATCGCAATGCGA
157876 TAACCATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
33 53 0.76
35 1 0.01
38 16 0.23
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:157811 original size:19 final size:19
Alignment explanation
Indices: 157789--157875 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
157779 ATCGCAACGA
157789 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
157808 GAAAATCGCAATGC-----
1 GAAAATCGCAATGCGAAAT
157822 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
157841 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
157860 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
157876 TAACCATTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
14 14 0.22
19 49 0.78
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:157858 original size:14 final size:14
Alignment explanation
Indices: 157808--157839 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
157798 AATGCGAAAT
157808 GAAAATCGCAATGC
1 GAAAATCGCAATGC
157822 GAAAATCGCAATGC
1 GAAAATCGCAATGC
157836 GAAA
1 GAAA
157840 TGAAAATCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAATGC
Found at i:158984 original size:24 final size:24
Alignment explanation
Indices: 158957--159010 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
158947 GTATTCGAAA
*
158957 TTTGATCTTGGTCAATACACGGAC
1 TTTGATATTGGTCAATACACGGAC
*
158981 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
159005 TTTGAT
1 TTTGAT
159011 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:161523 original size:19 final size:19
Alignment explanation
Indices: 161501--161565 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
161491 GTAAATTACT
161501 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
161520 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
161534 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
161553 ATCGCAACGCGAA
1 ATCGCAATGCGAA
161566 TTTAATTTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:161524 original size:39 final size:35
Alignment explanation
Indices: 161501--161565 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 35
161491 GTAAATTACT
*
161501 ATCGCAATGCGAAATGAAAATCGCAA--CGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAAGGA
161534 ATCGCAATGCGAAATGAAAATCGCAACGCGAA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAA
161566 TTTAATTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 26 0.90
35 3 0.10
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (35 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAAGGA
Found at i:161583 original size:19 final size:20
Alignment explanation
Indices: 161561--161603 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
161551 AAATCGCAAC
161561 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
161580 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
161600 GCGA
1 GCGA
161604 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:161588 original size:14 final size:14
Alignment explanation
Indices: 161589--161622 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
161579 TGCGATTTTC
161589 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
161603 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
161617 ATTTTC
1 ATTTTC
161623 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:161769 original size:14 final size:14
Alignment explanation
Indices: 161746--161779 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
161736 TCAATTAAAC
161746 AATCAACTTTTACA
1 AATCAACTTTTACA
*
161760 AATCACCTTTTACA
1 AATCAACTTTTACA
161774 AATCAA
1 AATCAA
161780 TTAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (14 bp):
AATCAACTTTTACA
Found at i:163203 original size:21 final size:21
Alignment explanation
Indices: 163137--163248 Score: 57
Period size: 21 Copynumber: 5.3 Consensus size: 21
163127 GTGAATCGGG
* *
163137 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGATGGGAGGGGA
* ** * *
163157 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGATGGGAGGGGA
163179 CTCTTGAACGATGGGAGGGGA
1 CTCTTGAACGATGGGAGGGGA
* * ** *
163200 CTCTCG-AGGAATGATAGGGGC
1 CTCTTGAACG-ATGGGAGGGGA
* * *
163221 CTCTTCAACGATAGGAGTGGA
1 CTCTTGAACGATGGGAGGGGA
163242 CTCTTGA
1 CTCTTGA
163249 GGGATGATAG
Statistics
Matches: 62, Mismatches: 26, Indels: 6
0.66 0.28 0.06
Matches are distributed among these distances:
20 2 0.03
21 56 0.90
22 4 0.06
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGA
Found at i:163222 original size:42 final size:42
Alignment explanation
Indices: 163176--163259 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
163166 CGATGACAGT
* *
163176 GGCCTCTTGAACGATGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
163218 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
163260 CAAGTCGGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:165342 original size:33 final size:33
Alignment explanation
Indices: 165285--165383 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
165275 ACGAGATAAT
*
165285 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
165319 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
165352 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
165384 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:165377 original size:19 final size:19
Alignment explanation
Indices: 165261--165425 Score: 134
Period size: 20 Copynumber: 9.1 Consensus size: 19
165251 CTTTTGGTTA
*
165261 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*
165280 ATAATGAGAATCGCAACGCGG
1 A-AATGAAAATCGCAACGC-G
**
165301 AAATGACTATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
165318 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
** *
165334 AAATGACTATCGCGAC-C-
1 AAATGAAAATCGCAACGCG
*
165351 --A-GACAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
165367 AAATGAAAATCGCAACCGCG
1 AAATGAAAATCGCAA-CGCG
*
165387 AAATAAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
*
165406 AAATGAAAATCGCAATGCG
1 AAATGAAAATCGCAACGCG
165425 A
1 A
165426 TTTTGGTTTC
Statistics
Matches: 118, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 42 0.36
20 45 0.38
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:165454 original size:19 final size:19
Alignment explanation
Indices: 165421--165501 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
165411 AAAATCGCAA
**
165421 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
165440 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
165459 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
165473 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
165493 TGCGATTTT
1 TGCGATTTT
165502 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:166088 original size:41 final size:41
Alignment explanation
Indices: 166036--166113 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
166026 CGAAAGTCAG
* * *
166036 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
166077 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
166114 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:166110 original size:20 final size:20
Alignment explanation
Indices: 166017--166110 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
166007 CGCTATGTAA
*
166017 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
166037 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
166057 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
166078 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
166098 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
166111 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:166128 original size:21 final size:21
Alignment explanation
Indices: 166099--166195 Score: 142
Period size: 21 Copynumber: 4.7 Consensus size: 21
166089 ATAGTCAGTA
*
166099 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
166120 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
166141 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
166161 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
166182 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
166196 ACTTATTCGC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
20 16 0.24
21 50 0.76
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:166129 original size:41 final size:41
Alignment explanation
Indices: 166036--166131 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
166026 CGAAAGTCAG
* * * ** *
166036 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
166077 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
166119 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
166132 TTTCCCAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:166151 original size:62 final size:62
Alignment explanation
Indices: 166079--166212 Score: 175
Period size: 62 Copynumber: 2.2 Consensus size: 62
166069 TTTTTTATTA
166079 TCGCATTGCGATAGTCA-GTA-TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAAT
1 TCGCATTGCGAT--TCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAAT
* * * * **
166141 TCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAAT
166202 TCGCATTGCGA
1 TCGCATTGCGA
166213 ATTGGGAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 2 0.03
61 18 0.29
62 43 0.68
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (62 bp):
TCGCATTGCGATTCACGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAAT
Found at i:166163 original size:41 final size:41
Alignment explanation
Indices: 166118--166212 Score: 181
Period size: 41 Copynumber: 2.3 Consensus size: 41
166108 GATTTTCCCA
*
166118 ATTCGCGTTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
166159 ATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
166200 ATTCGCATTGCGA
1 ATTCGCATTGCGA
166213 ATTGGGAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (41 bp):
ATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
Found at i:166164 original size:20 final size:21
Alignment explanation
Indices: 166099--166212 Score: 124
Period size: 21 Copynumber: 5.5 Consensus size: 21
166089 ATAGTCAGTA
* *
166099 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTACCAAT
*
166120 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTACCAAT
**
166141 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTACCAAT
* *
166161 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTACCAAT
**
166182 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTACCAAT
*
166202 TCGCATTGCGA
1 TCGCGTTGCGA
166213 ATTGGGAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
20 32 0.41
21 47 0.59
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTACCAAT
Found at i:166227 original size:62 final size:62
Alignment explanation
Indices: 166079--166227 Score: 156
Period size: 62 Copynumber: 2.4 Consensus size: 62
166069 TTTTTTATTA
* * ** *
166079 TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAAT
1 TCGCATTGCGATTGACAAAATCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTACCAAT
* * ** * **
166141 TCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTGACAAAATCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTACCAAT
**
166202 TCGCATTGCGAATTGGGAAAATCGCA
1 TCGCATTGCG-ATTGACAAAATCGCA
166228 ACGATACTGT
Statistics
Matches: 68, Mismatches: 18, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
61 15 0.22
62 53 0.78
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (62 bp):
TCGCATTGCGATTGACAAAATCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTACCAAT
Found at i:170949 original size:2 final size:2
Alignment explanation
Indices: 170942--170967 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
170932 TTCTGCTCCA
170942 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
170968 TAATCATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:172982 original size:17 final size:18
Alignment explanation
Indices: 172949--172982 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
172939 CCGCTATTAG
172949 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
172967 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
172983 GACCAGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:179151 original size:16 final size:16
Alignment explanation
Indices: 179132--179169 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
179122 ATTTCGCCCT
179132 TATTAT-ATAATGCATA
1 TATTATAAT-ATGCATA
*
179148 TATTATAATATGTATA
1 TATTATAATATGCATA
179164 TATTAT
1 TATTAT
179170 TTACATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (16 bp):
TATTATAATATGCATA
Done.