Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006961.1 Hibiscus syriacus cultivar Beakdansim tig00017907_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: 73199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:837 original size:14 final size:14
Alignment explanation
Indices: 818--847 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
808 ATTAAAAATC
818 AATTTCAGTGACTA
1 AATTTCAGTGACTA
832 AATTTCAGTGACTA
1 AATTTCAGTGACTA
846 AA
1 AA
848 AATCAACTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (14 bp):
AATTTCAGTGACTA
Found at i:1866 original size:3 final size:3
Alignment explanation
Indices: 1851--1927 Score: 75
Period size: 3 Copynumber: 25.0 Consensus size: 3
1841 TCTGGGCTTG
* * *
1851 TAA TAA TAT TAA TAA TAA TAA -ATA TATA TAA TATA TAA TAA TAT TTA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TA-A TAA TAA TAA TAA
**
1898 TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1928 ATTAAGTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 1 0.02
3 52 0.85
4 8 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:7180 original size:82 final size:82
Alignment explanation
Indices: 7039--7337 Score: 438
Period size: 82 Copynumber: 3.6 Consensus size: 82
7029 ATTTGAATGG
* * * *
7039 AAATTATTTCAATTTCTCTGATTTGATGTGATATGTCAATGAAAAGCAAATGATGTGAATAATAT
1 AAATTATTTCAATTTATCTGAATTGATGTGATATGTCAATGAAAAGCAAATGACGTGAATAGTAT
* *
7104 AGATTATCTAATTCTCT
66 AGATTCTCTGATTCTCT
*
7121 AAATTATTTCAATTTATCTGAATTGATGTGATATGTCAATGAAAAGCAAATGACATGAATAGTAT
1 AAATTATTTCAATTTATCTGAATTGATGTGATATGTCAATGAAAAGCAAATGACGTGAATAGTAT
*
7186 AGATTCTCCGATTCTCT
66 AGATTCTCTGATTCTCT
* *
7203 AAATTATTTCAGTTTATCT-AAGTTGATGTGATATGTCAATGAAAAGCAAATGACGTGAATAGTT
1 AAATTATTTCAATTTATCTGAA-TTGATGTGATATGTCAATGAAAAGCAAATGACGTGAATAGTA
*
7267 TAGATTCTATGATTCTCT
65 TAGATTCTCTGATTCTCT
* *
7285 AAATAATTATTTCAATTTATCTGAGTTGATGTGATATGTCAATGAAAAACAAA
1 --A-AATTATTTCAATTTATCTGAATTGATGTGATATGTCAATGAAAAGCAAA
7338 GGATGTGTAT
Statistics
Matches: 196, Mismatches: 16, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
81 2 0.01
82 148 0.76
84 1 0.01
85 44 0.22
86 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (82 bp):
AAATTATTTCAATTTATCTGAATTGATGTGATATGTCAATGAAAAGCAAATGACGTGAATAGTAT
AGATTCTCTGATTCTCT
Found at i:9462 original size:24 final size:24
Alignment explanation
Indices: 9435--9486 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
9425 GTCGTCTTCT
9435 TCTTCTCATTTTCCTTCATTTTCA
1 TCTTCTCATTTTCCTTCATTTTCA
* * *
9459 TCTTTTCCTTTTCCTTTATTTTCA
1 TCTTCTCATTTTCCTTCATTTTCA
9483 TCTT
1 TCTT
9487 ATTCTTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (24 bp):
TCTTCTCATTTTCCTTCATTTTCA
Found at i:19927 original size:17 final size:17
Alignment explanation
Indices: 19879--19930 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
19869 ATTAGGGCTA
*
19879 TTAATTTA-TATATTTT
1 TTAATTTATTTTATTTT
* *
19895 TGTAAATTAATATTATTTT
1 T-T-AATTTATTTTATTTT
19914 TTAATTTATTTTATTTT
1 TTAATTTATTTTATTTT
19931 GGTCATTGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 1 0.04
17 14 0.50
18 6 0.21
19 7 0.25
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTAATTTATTTTATTTT
Found at i:20062 original size:2 final size:2
Alignment explanation
Indices: 20055--20080 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20045 ACACGTTAAG
20055 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
20081 GAAAAATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25880 original size:12 final size:12
Alignment explanation
Indices: 25863--25887 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25853 TTATTAGGTT
25863 TATTTTACTTGC
1 TATTTTACTTGC
25875 TATTTTACTTGC
1 TATTTTACTTGC
25887 T
1 T
25888 GTCTAAGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TATTTTACTTGC
Found at i:27957 original size:2 final size:2
Alignment explanation
Indices: 27950--27985 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
27940 GTAAGCTTGT
*
27950 TA TA TA TA TA TA CA 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
27986 GCCGATAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:32796 original size:23 final size:23
Alignment explanation
Indices: 32770--32817 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
32760 ATAAAGTACA
* *
32770 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
**
32793 ATAATGTAATAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
32816 AT
1 AT
32818 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:33225 original size:21 final size:22
Alignment explanation
Indices: 33200--33251 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
33190 ACACTTTACA
*
33200 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
33223 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
33246 ATATAA
1 ATATAA
33252 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:33236 original size:23 final size:23
Alignment explanation
Indices: 33210--33272 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
33200 ATATAACCAC
33210 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
33233 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
33256 TACCTATTACATCATAT
1 TACCTATTACATTATAT
33273 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:33649 original size:39 final size:39
Alignment explanation
Indices: 33595--33681 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
33585 TCAAGTTGTA
*
33595 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
33634 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
33673 GATTTTGAT
1 GATTTTGAT
33682 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:33962 original size:18 final size:18
Alignment explanation
Indices: 33939--33975 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
33929 CGAAATATAT
33939 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
33957 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
33975 A
1 A
33976 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:34252 original size:25 final size:25
Alignment explanation
Indices: 34224--34274 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
34214 TTAATCCAAA
*
34224 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
34249 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
34274 T
1 T
34275 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:34568 original size:21 final size:22
Alignment explanation
Indices: 34543--34594 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
34533 ACACTTTACA
*
34543 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
34566 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
34589 ATATAA
1 ATATAA
34595 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:34579 original size:23 final size:23
Alignment explanation
Indices: 34553--34615 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
34543 ATATAACCAC
34553 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
34576 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
34599 TACCTATTACATCATAT
1 TACCTATTACATTATAT
34616 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:35010 original size:23 final size:23
Alignment explanation
Indices: 34984--35046 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
34974 ATATAACCAC
34984 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* ** *
35007 TACCTATTTCATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
35030 TACCTATTACATCATAT
1 TACCTATTACATTATAT
35047 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:35112 original size:431 final size:431
Alignment explanation
Indices: 34309--35573 Score: 2401
Period size: 431 Copynumber: 2.9 Consensus size: 431
34299 GAATTATTTA
* *
34309 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
* *
34374 GAATTTTTAATTTAATAATAATATATATCGCAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
34439 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAA
34504 AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
196 AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
34569 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
261 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
34634 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
326 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
*
34699 ATTTTTTTAACATTGTTTCATGTTTTCCACCTACAATATTG
391 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
34740 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
34805 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
*
34870 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACATTGAAAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAA
34935 AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
196 AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
*
35000 TAAACGATACCTATTTCATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
261 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
35065 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
326 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
35130 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
391 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
*
35171 ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
35236 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
* **
35301 ACTAAATTAATATCTTAAAACTCACTCAAAA-TTAATATTAAATTAATG-TTTCCACAGTGAAAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAA
*
35364 AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
196 AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
35429 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
261 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
35494 AAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAACTTATGTAATTTATGTTTCA
326 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
35558 ATTTTTTTAACAGTGT
391 ATTTTTTTAACAGTGT
35574 ACTGCGAATT
Statistics
Matches: 820, Mismatches: 14, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
428 46 0.06
429 176 0.21
430 14 0.02
431 584 0.71
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (431 bp):
ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAA
AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
Found at i:35428 original size:21 final size:22
Alignment explanation
Indices: 35403--35454 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
35393 AAACTTTACA
*
35403 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
35426 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
35449 ATATAA
1 ATATAA
35455 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:35439 original size:23 final size:23
Alignment explanation
Indices: 35413--35475 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
35403 ATATAACCAC
35413 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
35436 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
35459 TACCTATTACATCATAT
1 TACCTATTACATTATAT
35476 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:38547 original size:183 final size:183
Alignment explanation
Indices: 38049--38574 Score: 926
Period size: 184 Copynumber: 2.9 Consensus size: 183
38039 TTCAAATTAC
*
38049 CGACACTTTTTAAATGGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAATA
1 CGACACTTTTTAAATCGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAATA
38114 TTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
66 TTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
38179 TATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTAAAATGT
131 TATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTAAAATGT
38232 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACAC-TTTTTAAATCGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAT
38297 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
65 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
*
38362 ATATTATAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTAAAATGT
130 ATATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTAAAATGT
* * *
38416 CGACACTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACACTA
1 CGACACTTTTTAAATCGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAATA
* * *
38481 TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTTA
66 TTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
* * * **
38546 TATTGCAAATTTACCTATTTTATTATAAT
131 TATTACAAAATTATCTATTACATTATAAT
38575 ATGTTGAAAG
Statistics
Matches: 328, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
183 147 0.45
184 181 0.55
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (183 bp):
CGACACTTTTTAAATCGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAATA
TTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTA
TATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTAAAATGT
Found at i:40047 original size:3 final size:3
Alignment explanation
Indices: 40039--40122 Score: 87
Period size: 3 Copynumber: 28.0 Consensus size: 3
40029 ACTTGTTTGG
* * ** *
40039 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC ATC ATC TTC ATC GCC AGC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * *
40087 TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
40123 GTCAGCTTCA
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:40056 original size:12 final size:12
Alignment explanation
Indices: 40039--40137 Score: 81
Period size: 12 Copynumber: 8.0 Consensus size: 12
40029 ACTTGTTTGG
40039 ATCATCATCTTC
1 ATCATCATCTTC
40051 ATCATCATCATCATC
1 ATCATCATC-T--TC
40066 ATCATCATCTTC
1 ATCATCATCTTC
** *
40078 ATCGCCAGCTTC
1 ATCATCATCTTC
* *
40090 ATCGTCATCATC
1 ATCATCATCTTC
*
40102 ATCATCATCGTC
1 ATCATCATCTTC
* *
40114 ATCTTCATCGTC
1 ATCATCATCTTC
* *
40126 AGCTTCATCTTC
1 ATCATCATCTTC
40138 TGCGACCGCT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
12 60 0.82
13 1 0.01
14 1 0.01
15 11 0.15
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.36
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:40116 original size:42 final size:42
Alignment explanation
Indices: 40052--40134 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
40042 ATCATCTTCA
40052 TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATCG
* *
40094 TCATCATCATCATCATCGTCATCTTCATCGTCAGCTTCATC
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATC
40135 TTCTGCGACC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.35
Consensus pattern (42 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCTTCATCG
Found at i:40133 original size:18 final size:18
Alignment explanation
Indices: 40070--40137 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
40060 ATCATCATCA
*
40070 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
* *
40088 TCATCGTCATCATCATCATCAT
1 TCATC-T--TCATCGTCAGC-T
40110 CGTCATCTTCATCGTCAGCT
1 --TCATCTTCATCGTCAGCT
40130 TCATCTTC
1 TCATCTTC
40138 TGCGACCGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:42319 original size:199 final size:199
Alignment explanation
Indices: 41590--43083 Score: 2861
Period size: 199 Copynumber: 7.5 Consensus size: 199
41580 TTTAAATTAG
*
41590 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
41655 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
41720 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
41784 AAAA
196 AAAA
41788 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
41853 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
41918 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTAATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
41982 AAAA
196 AAAA
41986 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
42051 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
42116 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
42181 AAAA
196 AAAA
*
42185 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
42250 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
42315 CGACACTTTTTATATATGAATCGACACTTTATGGGTGTACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
42380 AAAA
196 AAAA
*
42384 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
42449 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
42514 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
42579 AAAA
196 AAAA
42583 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
42648 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
42713 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
42778 AAAA
196 AAAA
*
42782 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
42847 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
42912 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTAATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
42975 AAAA
196 AAAA
42979 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
43044 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATA
43084 TGGATCGACA
Statistics
Matches: 1278, Mismatches: 17, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
197 111 0.09
198 399 0.31
199 768 0.60
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:43257 original size:18 final size:18
Alignment explanation
Indices: 43231--43278 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
43221 TTATATTCAC
*
43231 ATACAAAAATATAAATCGT
1 ATACAAAATTAT-AATCGT
*
43250 ATACAAAATTATAATCTT
1 ATACAAAATTATAATCGT
43268 ATACAAAATTA
1 ATACAAAATTA
43279 ACTCGACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (18 bp):
ATACAAAATTATAATCGT
Found at i:45101 original size:33 final size:33
Alignment explanation
Indices: 45064--45129 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
45054 CATCTTAATA
*
45064 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
45097 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
45130 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:47452 original size:17 final size:18
Alignment explanation
Indices: 47430--47472 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
47420 ATATATCCGG
47430 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
47447 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
47467 TATCAT
1 TATCAT
47473 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:47490 original size:20 final size:19
Alignment explanation
Indices: 47435--47481 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
47425 TCCGGTATCA
47435 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
47454 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
47475 TTTTACC
1 TTTTACC
47482 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:47628 original size:20 final size:20
Alignment explanation
Indices: 47602--47647 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
47592 CACTTTTAAA
47602 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
47621 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
47642 TTTACC
1 TTTACC
47648 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:48272 original size:226 final size:229
Alignment explanation
Indices: 47713--48387 Score: 1250
Period size: 229 Copynumber: 3.0 Consensus size: 229
47703 TTAAAACTGC
47713 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
47778 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
47843 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
47908 GTATGGACACTTTTATAAAAATGATATATACTTT
196 GTATGGACACTTTTATAAAAATGATATATACTTT
47942 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
48007 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
48072 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
48137 GTATGGACACTTTTATAAAAATGATATATAC-TT
196 GTATGGACACTTTTATAAAAATGATATATACTTT
48170 TTTGAAAGTTATGTAATTTATGTTTCAA-TT-TTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
* **
48233 TTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
* * * *
48298 TTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
*
48362 GTATGGACACTTTTATAAAAAGGATA
196 GTATGGACACTTTTATAAAAATGATA
48388 GATAATTTAC
Statistics
Matches: 438, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
225 37 0.08
226 143 0.33
227 2 0.00
228 30 0.07
229 226 0.52
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (229 bp):
TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
GTATGGACACTTTTATAAAAATGATATATACTTT
Found at i:58572 original size:95 final size:95
Alignment explanation
Indices: 58407--58579 Score: 301
Period size: 95 Copynumber: 1.8 Consensus size: 95
58397 GTACTCATTC
* *
58407 TCTTAACCTGCGACTCAGAAAGTGAAAACCACACAAAAGCATTAAACTAACAGCTCTTAGGCTAG
1 TCTTAACCGGCGACTCAGAAAGTGAAAACCACACAAAAGCATTAAACAAACAGCTCTTAGGCTAG
*
58472 GAAGAAAAGAAAAACTATTAGAAAATCTAA
66 AAAGAAAAGAAAAACTATTAGAAAATCTAA
* *
58502 TCTTAACCGGTGACTCAGAAAGTGAAAACCACACAAAAGCATTAAACAAACGGCTCTTAGGCTAG
1 TCTTAACCGGCGACTCAGAAAGTGAAAACCACACAAAAGCATTAAACAAACAGCTCTTAGGCTAG
58567 AAAGAAAAGAAAA
66 AAAGAAAAGAAAA
58580 GAAAAAAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 73 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.17
Consensus pattern (95 bp):
TCTTAACCGGCGACTCAGAAAGTGAAAACCACACAAAAGCATTAAACAAACAGCTCTTAGGCTAG
AAAGAAAAGAAAAACTATTAGAAAATCTAA
Found at i:61980 original size:20 final size:19
Alignment explanation
Indices: 61948--61985 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
61938 AGAAATGGCC
61948 CATATTTTATTAAATAAAAA
1 CATATTTTATTAAA-AAAAA
61968 CATA-TTTATTTAAAAAAA
1 CATATTTTA-TTAAAAAAA
61986 TATTTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
CATATTTTATTAAAAAAAA
Found at i:61983 original size:16 final size:16
Alignment explanation
Indices: 61962--61994 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
61952 TTTTATTAAA
*
61962 TAAAAACATATTTATT
1 TAAAAAAATATTTATT
61978 TAAAAAAATATTTATT
1 TAAAAAAATATTTATT
61994 T
1 T
61995 GAATAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAAAAATATTTATT
Found at i:64610 original size:36 final size:35
Alignment explanation
Indices: 64549--64645 Score: 99
Period size: 36 Copynumber: 2.7 Consensus size: 35
64539 TTTGAGAAAA
* * *
64549 ATCTTTGAGTCTGTTT-ATTTGGAAACAAAATTTATC
1 ATCTTTGAGTCTGTTTCACTT-GAAACAAAA-TAAAC
*
64585 ATCTTTGAGTCTGTTTCCCTTGAAACAAAATAAAC
1 ATCTTTGAGTCTGTTTCACTTGAAACAAAATAAAC
* *
64620 ATCTTTGAAATC-GTTTCTCTTGAAAC
1 ATCTTTG-AGTCTGTTTCACTTGAAAC
64646 GAATTTTCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
35 23 0.43
36 28 0.53
37 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (35 bp):
ATCTTTGAGTCTGTTTCACTTGAAACAAAATAAAC
Found at i:64636 original size:35 final size:36
Alignment explanation
Indices: 64570--64645 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 36
64560 TGTTTATTTG
* * *
64570 GAAACAAAATTTATCATCTTTGAGTCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
*
64606 GAAACAAAA-TAAACATCTTTGAAATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTG-AATCTGTTTCCCTT
64641 GAAAC
1 GAAAC
64646 GAATTTTCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
Found at i:64833 original size:28 final size:28
Alignment explanation
Indices: 64802--64867 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
64792 GAGACAGTTG
* *
64802 CTTTTGAAAGAAATCTTTGAGTCTGTTT
1 CTTTTGAAACAAATCTTTGAGTCGGTTT
*
64830 CTTTTGAAACAAATCTTTGGGTCGGTTT
1 CTTTTGAAACAAATCTTTGAGTCGGTTT
*
64858 CTCTTGAAAC
1 CTTTTGAAAC
64868 CATAATCCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCGGTTT
Found at i:65331 original size:132 final size:132
Alignment explanation
Indices: 64924--65363 Score: 580
Period size: 135 Copynumber: 3.3 Consensus size: 132
64914 TTCGTCTCTT
* * * * * * *
64924 GACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAACCGTCCTTATCACGTA
1 GACCAGACCTCCTCATCACATAGGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCGCGTA
* *
64989 GGAACCGTGTTATCATTCCTAAAGATGGCC-AGAACTCTTCATCATGTATGAGTCGTGTCATCCA
66 GGAACCGTGTTATCATTCCTAAAGATGGCCAAGAACTCTTCATCAAGTATGAGTCGTGTCATCCC
65053 CC
131 CC
* *
65055 GACCAGACCTCCTTATCACATAGGAGTCGTGTCACCCCTAGATAACCAGCCATCCTCATCGCGTA
1 GACCAGACCTCCTCATCACATAGGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCGCGTA
* *
65120 GGAACCATATTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACA-TATGAGTCGTGTCA
66 GGAACCGTGTTATCA---TTCCTAAAGATGGCCAAGAACTCTTCATCA-AGTATGAGTCGTGTCA
65184 TCCCCC
127 TCCCCC
* ** * * * * *
65190 GACCAGATCTCCTCATCATGTAAGAGTCGTGTCACCCCTAAATAACCAGTCATCCTCATCGCATA
1 GACCAGACCTCCTCATCACATAGGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCGCGTA
* *
65255 GGAACTGTGTTATCGTTCCTAAAGATGGCCAAGAACTCTTCATCAAGTATGAG-CAGTGTCATCC
66 GGAACCGTGTTATCATTCCTAAAGATGGCCAAGAACTCTTCATCAAGTATGAGTC-GTGTCATCC
65319 CCC
130 CCC
* * *
65322 GGCCAGATCTCCTCATCACATAGGAGCCGTGTCACCCTTAGA
1 GACCAGACCTCCTCATCACATAGGAGCCGTGTCACCCCTAGA
65364 CGAAGACCTC
Statistics
Matches: 270, Mismatches: 32, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
131 71 0.26
132 83 0.31
134 15 0.06
135 101 0.37
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (132 bp):
GACCAGACCTCCTCATCACATAGGAGCCGTGTCACCCCTAGATAACCAGCCATCCTCATCGCGTA
GGAACCGTGTTATCATTCCTAAAGATGGCCAAGAACTCTTCATCAAGTATGAGTCGTGTCATCCC
CC
Found at i:65589 original size:3 final size:3
Alignment explanation
Indices: 65565--65617 Score: 79
Period size: 3 Copynumber: 17.0 Consensus size: 3
65555 TAATTTTTTA
*
65565 ATT ATT ATAT ATC ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT AT-T ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
65612 ATT ATT
1 ATT ATT
65618 TATTGTTACA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:68610 original size:14 final size:14
Alignment explanation
Indices: 68556--68603 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
68546 TTTTAAGATT
68556 TTAAAATTATTAAA
1 TTAAAATTATTAAA
*
68570 TTAAAA--GTTAAA
1 TTAAAATTATTAAA
68582 --AAAATTATTAAA
1 TTAAAATTATTAAA
68594 TTAAAATTAT
1 TTAAAATTAT
68604 GTAATTAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 4 0.14
12 10 0.36
14 14 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
TTAAAATTATTAAA
Found at i:68679 original size:22 final size:24
Alignment explanation
Indices: 68621--68679 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
68611 GCTAATCATT
*
68621 AAAATTTAA-GATATTAATATAGTA
1 AAAATTTAATTATA-TAATATAGTA
68645 AAAATTTTAATTATATAATA-AGTA
1 AAAA-TTTAATTATATAATATAGTA
68669 AAAA-TTAATTA
1 AAAATTTAATTA
68680 GTTAAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 7 0.22
24 12 0.38
25 10 0.31
26 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (24 bp):
AAAATTTAATTATATAATATAGTA
Found at i:68844 original size:2 final size:2
Alignment explanation
Indices: 68828--68875 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
68818 ACATACGTAG
68828 TA TA TCA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
68870 TA TA TA
1 TA TA TA
68876 ACATCAAGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:69528 original size:19 final size:18
Alignment explanation
Indices: 69486--69529 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
69476 TCAAAATTAG
* *
69486 ATATTATTTTAAATAATT
1 ATATTTTTTTAAATAATA
*
69504 ACATTTTTTTACAATAATA
1 ATATTTTTTTA-AATAATA
69523 ATATTTT
1 ATATTTT
69530 CACCATATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTTTTTTAAATAATA
Found at i:69529 original size:18 final size:19
Alignment explanation
Indices: 69480--69529 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
69470 AATAACTCAA
*
69480 AATTAGATATTATTTTAAAT
1 AATTACATATT-TTTTAAAT
69500 AATTACAT-TTTTTTACAAT
1 AATTACATATTTTTTA-AAT
69519 AA-TA-ATATTTT
1 AATTACATATTTT
69530 CACCATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.07
18 11 0.41
19 7 0.26
20 7 0.26
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
AATTACATATTTTTTAAAT
Done.