Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003040.1 Hibiscus syriacus cultivar Beakdansim tig00006323_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: 128346
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9116 original size:18 final size:17
Alignment explanation
Indices: 9094--9126 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9084 GCTTCTAATT
9094 TTTTTTTGAGTTCAAGC
1 TTTTTTTGAGTTCAAGC
9111 TTTTTTTGAGTTCAAG
1 TTTTTTTGAGTTCAAG
9127 TTTCAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (17 bp):
TTTTTTTGAGTTCAAGC
Found at i:11790 original size:21 final size:21
Alignment explanation
Indices: 11742--11801 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
11732 TATTTTGTAC
11742 CCGTATCAGATGGCACCACAA
1 CCGTATCAGATGGCACCACAA
* * * *
11763 CCATATCAGATGGCATCGCAG
1 CCGTATCAGATGGCACCACAA
* *
11784 TCGTATCAGATGACACCA
1 CCGTATCAGATGGCACCA
11802 TAGCCATTTC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.18
Consensus pattern (21 bp):
CCGTATCAGATGGCACCACAA
Found at i:12330 original size:19 final size:19
Alignment explanation
Indices: 12308--12346 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12298 GTTTACCAAC
*
12308 AATTATAAAGTTTTTATTT
1 AATTATAAACTTTTTATTT
*
12327 AATTATGAACTTTTTATTT
1 AATTATAAACTTTTTATTT
12346 A
1 A
12347 CTTTTCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (19 bp):
AATTATAAACTTTTTATTT
Found at i:12415 original size:26 final size:25
Alignment explanation
Indices: 12356--12416 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
12346 ACTTTTCTTG
12356 TTAATGTTTTTATTATTTAATTGTT
1 TTAATGTTTTTATTATTTAATTGTT
** *
12381 CGAATTGTTTTTATTATTTAGTTGTTT
1 TTAA-TGTTTTTATTATTTAATTG-TT
12408 TTAATGTTT
1 TTAATGTTT
12417 GAGTTGTATC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.07
26 23 0.79
27 4 0.14
ACGTcount: A:0.21, C:0.02, G:0.11, T:0.66
Consensus pattern (25 bp):
TTAATGTTTTTATTATTTAATTGTT
Found at i:12421 original size:18 final size:18
Alignment explanation
Indices: 12371--12423 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
12361 GTTTTTATTA
* *
12371 TTTAATTGTTCGAATTGTT
1 TTTAA-TGTTTGAGTTGTT
* *
12390 TTTATTATTT-AGTTGTT
1 TTTAATGTTTGAGTTGTT
12407 TTTAATGTTTGAGTTGT
1 TTTAATGTTTGAGTTGT
12424 ATCGTTTTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
17 14 0.52
18 9 0.33
19 4 0.15
ACGTcount: A:0.19, C:0.02, G:0.17, T:0.62
Consensus pattern (18 bp):
TTTAATGTTTGAGTTGTT
Found at i:15439 original size:29 final size:28
Alignment explanation
Indices: 15405--15483 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 28
15395 CGGCGACCGA
*
15405 TATATTTACCGATCTAACACCGGTCAGAC
1 TATATTT-CCGATCTAACACCAGTCAGAC
15434 TATATTTCCCGATCTAACACCAGTCAGAC
1 TATATTT-CCGATCTAACACCAGTCAGAC
*
15463 TATATTTCTTGATCTAACACC
1 TATATTTC-CGATCTAACACC
15484 CTTTGCAGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 1 0.02
29 45 0.98
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (28 bp):
TATATTTCCGATCTAACACCAGTCAGAC
Found at i:17953 original size:3 final size:3
Alignment explanation
Indices: 17947--17986 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
17937 TCAGGATGAT
*
17947 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAT GAC G
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC G
17987 GTGATGATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.30, G:0.35, T:0.03
Consensus pattern (3 bp):
GAC
Found at i:21598 original size:29 final size:30
Alignment explanation
Indices: 21535--21603 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
21525 CATTTTACAG
*
21535 AAATAGCACCCCTTTTCAAATTAATTACCA
1 AAATAGCACCCATTTTCAAATTAATTACCA
* *
21565 AAATAGCACCCATTTT-GAATTAATTCCCA
1 AAATAGCACCCATTTTCAAATTAATTACCA
*
21594 TAATAGCACC
1 AAATAGCACC
21604 AAAATCGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (30 bp):
AAATAGCACCCATTTTCAAATTAATTACCA
Found at i:21613 original size:29 final size:29
Alignment explanation
Indices: 21553--21632 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 29
21543 CCCCTTTTCA
* * ** *
21553 AATTAATTACCAAAATAGCACCCATTTTG
1 AATTAATTCCCAAAATAGCACCAAAATCG
*
21582 AATTAATTCCCATAATAGCACCAAAATCG
1 AATTAATTCCCAAAATAGCACCAAAATCG
* * *
21611 AATAAATTCTCAGAATAGCACC
1 AATTAATTCCCAAAATAGCACC
21633 GGTCAACGGT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (29 bp):
AATTAATTCCCAAAATAGCACCAAAATCG
Found at i:21663 original size:18 final size:18
Alignment explanation
Indices: 21633--21685 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
21623 GAATAGCACC
21633 GGTCAAC-GGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
21650 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
21668 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
21686 TGACCGGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 7 0.20
18 28 0.80
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:28849 original size:29 final size:30
Alignment explanation
Indices: 28786--28854 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
28776 CATTTTACAG
*
28786 AAATAGCACCCCTTTTCGAATTAATTACCA
1 AAATAGCACCCATTTTCGAATTAATTACCA
*
28816 AAATAGCACCCATTTT-GAATTAATTCCCA
1 AAATAGCACCCATTTTCGAATTAATTACCA
*
28845 TAATAGCACC
1 AAATAGCACC
28855 AAAATCGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATAGCACCCATTTTCGAATTAATTACCA
Found at i:28864 original size:29 final size:29
Alignment explanation
Indices: 28801--28870 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
28791 GCACCCCTTT
* * **
28801 TCGAATTAATTACCAAAATAGCACCCATT
1 TCGAATTAATTCCCAAAATAGCACCAAAA
* *
28830 TTGAATTAATTCCCATAATAGCACCAAAA
1 TCGAATTAATTCCCAAAATAGCACCAAAA
*
28859 TCGAATAAATTC
1 TCGAATTAATTC
28871 TCAGAATATT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (29 bp):
TCGAATTAATTCCCAAAATAGCACCAAAA
Found at i:28892 original size:7 final size:7
Alignment explanation
Indices: 28880--28916 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
28870 CTCAGAATAT
28880 TCAACGG
1 TCAACGG
28887 TCAACGG
1 TCAACGG
*
28894 TCAACGA
1 TCAACGG
*
28901 TCAACGA
1 TCAACGG
28908 TCAACGG
1 TCAACGG
28915 TC
1 TC
28917 GGGTCAACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.32, C:0.30, G:0.22, T:0.16
Consensus pattern (7 bp):
TCAACGG
Found at i:33501 original size:137 final size:137
Alignment explanation
Indices: 33255--33530 Score: 543
Period size: 137 Copynumber: 2.0 Consensus size: 137
33245 TTTTCATGTG
*
33255 TAGTTTCAAAAAAAGAAAAGGATATGAAGTGAGGAGCTTTGCGAGTATCTTTTGAAAATCAAACC
1 TAGTTTCAAAAAAAGAAAAGGACATGAAGTGAGGAGCTTTGCGAGTATCTTTTGAAAATCAAACC
33320 TACCGATAGTATCAATAAAACATCTTATCTTTGACTTATTAGTGACATGTACATTATATTTGTAG
66 TACCGATAGTATCAATAAAACATCTTATCTTTGACTTATTAGTGACATGTACATTATATTTGTAG
33385 GTTGCTT
131 GTTGCTT
33392 TAGTTTCAAAAAAAGAAAAGGACATGAAGTGAGGAGCTTTGCGAGTATCTTTTGAAAATCAAACC
1 TAGTTTCAAAAAAAGAAAAGGACATGAAGTGAGGAGCTTTGCGAGTATCTTTTGAAAATCAAACC
33457 TACCGATAGTATCAATAAAACATCTTATCTTTGACTTATTAGTGACATGTACATTATATTTGTAG
66 TACCGATAGTATCAATAAAACATCTTATCTTTGACTTATTAGTGACATGTACATTATATTTGTAG
33522 GTTGCTT
131 GTTGCTT
33529 TA
1 TA
33531 TCGAATTTAT
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 138 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (137 bp):
TAGTTTCAAAAAAAGAAAAGGACATGAAGTGAGGAGCTTTGCGAGTATCTTTTGAAAATCAAACC
TACCGATAGTATCAATAAAACATCTTATCTTTGACTTATTAGTGACATGTACATTATATTTGTAG
GTTGCTT
Found at i:37726 original size:20 final size:20
Alignment explanation
Indices: 37696--37795 Score: 103
Period size: 20 Copynumber: 5.0 Consensus size: 20
37686 GTTTCCAAAT
37696 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
** * * *
37716 TCGCATTGCGATTTTCCG-AAT
1 TCGCAACGCGAATAT--GTAAA
*
37737 TCGCAATGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
37757 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
*
37777 TCGCAACGCGAATCTGTAA
1 TCGCAACGCGAATATGTAA
37796 TTCGTAACAC
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.02
20 50 0.76
21 14 0.21
22 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:37819 original size:20 final size:20
Alignment explanation
Indices: 37794--37841 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
37784 GCGAATCTGT
* *
37794 AATTCGTAACACATAAGTCA
1 AATTCGCAACACAGAAGTCA
37814 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
37834 AATTCGCA
1 AATTCGCA
37842 GTGCGATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.21
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:37878 original size:21 final size:20
Alignment explanation
Indices: 37811--37899 Score: 74
Period size: 20 Copynumber: 4.4 Consensus size: 20
37801 AACACATAAG
*
37811 TCAAATTCGCAACACAGAA-G
1 TCAAATTCGCAACAC-GAATT
***
37831 TCAAATTCGCAGTGCG-ATT
1 TCAAATTCGCAACACGAATT
37850 TCCAAATTCGCAACACTGAATT
1 T-CAAATTCGCAACAC-GAATT
* *
37872 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACACGAATT
*
37892 TCGAATTC
1 TCAAATTC
37900 CTAAATCCCT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.02
19 2 0.04
20 34 0.62
21 14 0.25
22 4 0.07
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (20 bp):
TCAAATTCGCAACACGAATT
Found at i:37899 original size:41 final size:40
Alignment explanation
Indices: 37812--37891 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
37802 ACACATAAGT
*
37812 CAAATTCGCAACACAGAAGTCAAATTCGCAGTGCGATTTC
1 CAAATTCGCAACACAGAAGTCAAATTCGCACTGCGATTTC
* *
37852 CAAATTCGCAACACTGAATTTCAAATTCGCAACT-CGATTT
1 CAAATTCGCAACACAGAA-GTCAAATTCGC-ACTGCGATTT
37892 TCGAATTCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 17 0.49
41 16 0.46
42 2 0.06
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (40 bp):
CAAATTCGCAACACAGAAGTCAAATTCGCACTGCGATTTC
Found at i:39333 original size:19 final size:19
Alignment explanation
Indices: 39305--39351 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
39295 CGTGGCGCAT
39305 GATTGCAAAGAGGATAAAA
1 GATTGCAAAGAGGATAAAA
*
39324 GATTGTAAAGAGGATAAAA
1 GATTGCAAAGAGGATAAAA
39343 GATTGCAAA
1 GATTGCAAA
39352 ATATTTCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.51, C:0.04, G:0.26, T:0.19
Consensus pattern (19 bp):
GATTGCAAAGAGGATAAAA
Found at i:40291 original size:46 final size:46
Alignment explanation
Indices: 40224--40320 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 46
40214 CAAACACTAG
40224 AAGATGTCAGGTTTGAAAGATGGTCAAGAGTACATCAACTTGGAGC
1 AAGATGTCAGGTTTGAAAGATGGTCAAGAGTACATCAACTTGGAGC
**
40270 AAGATGTTGGGTTTGAAAGATGGTCAAGAGTACATCAACTTGGAGC
1 AAGATGTCAGGTTTGAAAGATGGTCAAGAGTACATCAACTTGGAGC
40316 AAGAT
1 AAGAT
40321 ATGGTTTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.25
Consensus pattern (46 bp):
AAGATGTCAGGTTTGAAAGATGGTCAAGAGTACATCAACTTGGAGC
Found at i:42942 original size:21 final size:21
Alignment explanation
Indices: 42918--43009 Score: 80
Period size: 21 Copynumber: 4.5 Consensus size: 21
42908 GTGAATCGGG
*
42918 CTCTTGAACGGCGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* * *
42939 CTCTTGAATGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* *
42960 CTATTGAACGGTGGGAAGGGC
1 CTCTTGAACGGTGGGAGGGGC
* * * *
42981 CTTTTGAAAGAT-AGA-GGGC
1 CTCTTGAACGGTGGGAGGGGC
43000 CTCTTGAACG
1 CTCTTGAACG
43010 ATGACAGGTG
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
19 12 0.21
20 2 0.04
21 42 0.75
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:42981 original size:42 final size:40
Alignment explanation
Indices: 42921--43009 Score: 115
Period size: 42 Copynumber: 2.2 Consensus size: 40
42911 AATCGGGCTC
* *
42921 TTGAACGGCGGGAGGGGCCTCTTGAATGATGAGAGGGGCCTA
1 TTGAACGGCGGGAAGGGCCTCTTGAAAGAT-AGA-GGGCCTA
* * *
42963 TTGAACGGTGGGAAGGGCCTTTTGAAAGATAGAGGGCCTC
1 TTGAACGGCGGGAAGGGCCTCTTGAAAGATAGAGGGCCTA
43003 TTGAACG
1 TTGAACG
43010 ATGACAGGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 13 0.31
41 3 0.07
42 26 0.62
ACGTcount: A:0.24, C:0.16, G:0.39, T:0.21
Consensus pattern (40 bp):
TTGAACGGCGGGAAGGGCCTCTTGAAAGATAGAGGGCCTA
Found at i:43320 original size:21 final size:21
Alignment explanation
Indices: 43294--43347 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
43284 TGCGATAATC
* *
43294 TCACGTAGAGCAGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
*
43315 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGCAGATACCTCA
*
43336 CCACGTAAAGCA
1 TCACGTAAAGCA
43348 CCATTGTCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.19
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:43384 original size:21 final size:21
Alignment explanation
Indices: 43307--43403 Score: 56
Period size: 21 Copynumber: 4.6 Consensus size: 21
43297 CGTAGAGCAG
* *
43307 CTACCTCATCACGTAAAGTA-G
1 CTACCTCACCACGTAAAG-ACC
*
43328 ATACCTCACCACGTAAAGCACC
1 CTACCTCACCACGTAAAG-ACC
* ** * *
43350 AT-TGTCATCGCGTAAA-ACC
1 CTACCTCACCACGTAAAGACC
43369 TCTACCTCACCACGTAAAGACC
1 -CTACCTCACCACGTAAAGACC
* *
43391 GTACCTCATCACG
1 CTACCTCACCACG
43404 CCATGCACCA
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
19 3 0.05
20 1 0.02
21 48 0.84
22 5 0.09
ACGTcount: A:0.32, C:0.35, G:0.12, T:0.21
Consensus pattern (21 bp):
CTACCTCACCACGTAAAGACC
Found at i:43659 original size:42 final size:42
Alignment explanation
Indices: 43584--43682 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 42
43574 GTGATAGAAT
* ** * * *
43584 AGGTGATGGCTCTCGTTGTGGAGGTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCAAGCTGTAGAATCGACTCGATC
* *
43626 AGGTGATGGCTCTGGGTGTCAAGCTGTAGAATCGACTTGATC
1 AGGTGATGGCTCTCGGTGTCAAGCTGTAGAATCGACTCGATC
*
43668 AGGTGATGACTCTCG
1 AGGTGATGGCTCTCG
43683 AAGTGGGGGG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.29
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCAAGCTGTAGAATCGACTCGATC
Found at i:45177 original size:20 final size:20
Alignment explanation
Indices: 45167--45210 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
45157 ATCGCAATGT
45167 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
45187 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
45207 GAAA
1 GAAA
45211 CTAAATTCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.18, G:0.18, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:45258 original size:20 final size:20
Alignment explanation
Indices: 45216--45258 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
45206 CGAAACTAAA
* * *
45216 TTCGCGTTGCGATTTTTATT
1 TTCGCGTTGCGAATTTAAGT
45236 TTCGCGTTGCGAATTTAAGT
1 TTCGCGTTGCGAATTTAAGT
45256 TTC
1 TTC
45259 AAAAACTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.49
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTAAGT
Found at i:45620 original size:22 final size:22
Alignment explanation
Indices: 45593--45651 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
45583 GAGATAGACG
45593 GATTTCGCCGGAGATGGGGACA
1 GATTTCGCCGGAGATGGGGACA
*
45615 GATTTCGCCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACA
* *
45637 GATGTCGCCGTAGAT
1 GATTTCGCCGGAGAT
45652 AATGAAAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.20, C:0.19, G:0.41, T:0.20
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACA
Found at i:45819 original size:20 final size:20
Alignment explanation
Indices: 45794--45842 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
45784 TAAACGCGCT
*
45794 TTGCGAATTTAACTTCTGTG
1 TTGCGAATTTAACTTATGTG
*
45814 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTAACTTATGTG
45834 TTGCGAATT
1 TTGCGAATT
45843 ACAAATTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTAACTTATGTG
Found at i:45890 original size:20 final size:20
Alignment explanation
Indices: 45833--45899 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
45823 TGACTTATGT
*
45833 GTTGCGAATTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
45853 GTTACGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
* *
45873 GTTGCGATTTATATATTCGC
1 GTTGCGATTTACAAATTCGC
*
45893 TTTGCGA
1 GTTGCGA
45900 ATTTGGAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:46955 original size:71 final size:75
Alignment explanation
Indices: 46744--46957 Score: 242
Period size: 76 Copynumber: 2.9 Consensus size: 75
46734 TAGGATAATA
* ** * * *
46744 TTTTAAACATTATATTT-TTTCTTTGTATTTTAGTTTAAATTGGTTTTAGTATTTTAATTAAGTT
1 TTTTAAATATTATATTTGTTTC-AGGTATTTTAGTTTAAA-TAGTTTTAGTATTTTAATTAGGAT
*
46808 TTAGGATATTAT
64 TTAGAATATTAT
* * * *
46820 TTTTATATTTTATCTTTGTTTCAGTTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATT
1 TTTTAAATATTATATTTGTTTCAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAGGATT
46885 TAGAATATTA-
65 TAGAATATTAT
*
46895 TTTTAAATATTA-ATTT-TTT-AGGTA-TTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATT
1 TTTTAAATATTATATTTGTTTCAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAGGATT
46956 TA
65 TA
46958 AGATGTTTTA
Statistics
Matches: 119, Mismatches: 16, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
70 5 0.04
71 32 0.27
72 4 0.03
73 3 0.03
74 3 0.03
75 11 0.09
76 57 0.48
77 4 0.03
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (75 bp):
TTTTAAATATTATATTTGTTTCAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTT
AGAATATTAT
Found at i:47573 original size:17 final size:18
Alignment explanation
Indices: 47551--47592 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
47541 CTTTAGATTA
47551 TTTATTTAATTATT-TCT
1 TTTATTTAATTATTATCT
* *
47568 TTTATTTAATTCTTATTT
1 TTTATTTAATTATTATCT
47586 TTTATTT
1 TTTATTT
47593 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:47667 original size:20 final size:20
Alignment explanation
Indices: 47642--47691 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
47632 CTATTATTTA
*
47642 TTATTTTATTATT-TCCCCTT
1 TTATTTTATTATTAT-CCATT
*
47662 TTA-TTTATTATTATCTATT
1 TTATTTTATTATTATCCATT
47681 TTATTTTATTA
1 TTATTTTATTA
47692 AATATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTATTATTATCCATT
Found at i:49800 original size:12 final size:12
Alignment explanation
Indices: 49785--49815 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
49775 GAAAATCATT
49785 TTGAAATCAAAA
1 TTGAAATCAAAA
49797 TTGAAATCAAAA
1 TTGAAATCAAAA
49809 TTGAAAT
1 TTGAAAT
49816 TACTCCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (12 bp):
TTGAAATCAAAA
Found at i:52494 original size:15 final size:15
Alignment explanation
Indices: 52474--52507 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
52464 ATATCTTCTT
*
52474 TAATGACATGATCTC
1 TAATGAAATGATCTC
*
52489 TAATGAAATGATGTC
1 TAATGAAATGATCTC
52504 TAAT
1 TAAT
52508 TTCAATGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (15 bp):
TAATGAAATGATCTC
Found at i:56177 original size:117 final size:118
Alignment explanation
Indices: 55957--56178 Score: 299
Period size: 117 Copynumber: 1.9 Consensus size: 118
55947 CTTTCAAGTC
*
55957 AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
56022 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTG
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * * *
56075 AAAA-TTTCTTTTTCAA-AGTTTTCAGATTTCGTTTTTGAAAGCTCTAACTCCTTTCTT-AACAT
1 AAAATTTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCC-TTCTTCAACAT
** *
56137 TTCATTTTGATTTTTTAAATCTATTTTAGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
56179 ATCATTTTTA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
116 1 0.01
117 77 0.85
118 13 0.14
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (118 bp):
AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:61571 original size:21 final size:21
Alignment explanation
Indices: 61518--61580 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
61508 ATTCCCCTGT
61518 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* * *
61541 AGGAGGAATCGGTTCCCTCAG
1 GGGGGGAATCGGTTCCCTCAA
*
61562 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
61581 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 19 0.56
22 3 0.09
23 12 0.35
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:71931 original size:5 final size:5
Alignment explanation
Indices: 71921--72022 Score: 82
Period size: 5 Copynumber: 19.8 Consensus size: 5
71911 TCGTTCCATT
* * *
71921 TTTTA TTTTA TTTCA TTTTA TTTCA TTTTA TTTTTA TTTTA TTTT- TTAGTAAA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TT--T-TA
* * * *
71974 CTTTA TTTTCA TTCTA -TTTA TTTTA TTTTA ATTGA TTTTA TTTTA TTTT
1 TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
72023 TCTCTAAACA
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
4 5 0.07
5 59 0.78
6 11 0.14
8 1 0.01
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:71961 original size:21 final size:20
Alignment explanation
Indices: 71925--71964 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
71915 TCCATTTTTT
71925 ATTTTATTTCATTTTATTTC
1 ATTTTATTTCATTTTATTTC
*
71945 ATTTTATTTTTATTTTATTT
1 ATTTTA-TTTCATTTTATTT
71965 TTTAGTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (20 bp):
ATTTTATTTCATTTTATTTC
Found at i:73755 original size:74 final size:70
Alignment explanation
Indices: 73673--73857 Score: 223
Period size: 72 Copynumber: 2.6 Consensus size: 70
73663 TTTTATCTTT
* * * * *
73673 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATTTTTATC
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATTATTTTAAATATTA--
73738 TTTGTTTAG
64 -TT-TTTAG
*
73747 GTATTTTAGTTTAAATAGGTTTTA-TA-TTTAATTAGGATTTAGAATATTATTTTAAATATTATT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATTATTTTAAATATTATT
73810 TTTAG
66 TTTAG
* * *
73815 TTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTTA
73858 AGATGTTTTA
Statistics
Matches: 100, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
67 5 0.05
68 22 0.22
69 3 0.03
70 15 0.15
72 29 0.29
73 2 0.02
74 24 0.24
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.57
Consensus pattern (70 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATATTATTTTAAATATTATT
TTTAG
Found at i:75247 original size:19 final size:19
Alignment explanation
Indices: 75202--75253 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
75192 TACTATTATT
75202 TATTAT-TTTATTATTTTC
1 TATTATATTTATTATTTTC
** *
75220 CCTTTTATTTATTATTTTC
1 TATTATATTTATTATTTTC
75239 TATTATATTTTATTA
1 TATTATA-TTTATTA
75254 AATCTTTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 3 0.12
19 16 0.62
20 7 0.27
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTATATTTATTATTTTC
Found at i:78068 original size:19 final size:20
Alignment explanation
Indices: 78046--78085 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
78036 GTGGAGATTT
*
78046 ATAGAAG-AAGAGAAATAAA
1 ATAGAAGAAAGAAAAATAAA
78065 ATAGAAGAAAGAAAAATAAA
1 ATAGAAGAAAGAAAAATAAA
78085 A
1 A
78086 ATATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.10
Consensus pattern (20 bp):
ATAGAAGAAAGAAAAATAAA
Found at i:82344 original size:87 final size:87
Alignment explanation
Indices: 82243--82418 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 87
82233 CAAGGGGATA
*
82243 TTTATAACCTTCTAAAACCCTAAAATAGGATAAAAAAAATTAAAGATAATTGTTTAAACTTAAAA
1 TTTATAACCTTCTAAAACCCTAAAATAGGATAAAAAAAATAAAAGATAATTGTTTAAACTTAAAA
82308 TCCTAAAAGATAATTCCTAAAC
66 TCCTAAAAGATAATTCCTAAAC
82330 TTTATAACCTTCTAAAACCCTAAAATAGGATAAAAAAAATAAAAGATAATTGTTTAAACTTAAAA
1 TTTATAACCTTCTAAAACCCTAAAATAGGATAAAAAAAATAAAAGATAATTGTTTAAACTTAAAA
82395 TCCTAAAAGATAATTCCTAAAC
66 TCCTAAAAGATAATTCCTAAAC
82417 TT
1 TT
82419 GAATTTAAAA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.30
Consensus pattern (87 bp):
TTTATAACCTTCTAAAACCCTAAAATAGGATAAAAAAAATAAAAGATAATTGTTTAAACTTAAAA
TCCTAAAAGATAATTCCTAAAC
Found at i:84131 original size:139 final size:135
Alignment explanation
Indices: 83966--84456 Score: 515
Period size: 139 Copynumber: 3.6 Consensus size: 135
83956 CCTAAGACCT
**
83966 ATTTTAGCAATTTATTGGATCAAATAATTAAAATGGAACCTCATGCATAAAAGGGAGGACCAAAT
1 ATTTTAGCAATTTATTGGATCAAATAATTAAAATGGAACCTCA-GCATAAAAACGAGGACCAAAT
* * *
84031 TAAAAAATCTCCTAAAGTAAAGGACTAAAGTGAAATTAAACCTAAGACAAAGGCTCTAATATTAA
65 TAAAAATTCTCCTAAA-TAAAGAACTAAAGTGAAATT-AACCTAA-ATAAAGGCTCTAATATTAA
84096 TCCTAACCA
127 TCCTAACCA
* * * * *
84105 ATTTTAGCAATCTATTGAATCAAATAATTAAAATAGAACCTCGAGTATAAAAACGAGGATCAAAT
1 ATTTTAGCAATTTATTGGATCAAATAATTAAAATGGAACCTC-AGCATAAAAACGAGGACCAAAT
84170 TAAAAATTCTCCTAAATTAAAGAACTAAAGTGAAATTCAACCTAAAATAAAGGCTCTAATATTAA
65 TAAAAATTCTCCTAAA-TAAAGAACTAAAGTGAAATT-AACCT-AAATAAAGGCTCTAATATTAA
* *
84235 TCTTGACCA
127 TCCTAACCA
* * * ** * * * *
84244 ATTTTATCAATTTATTGGATCGAACAATTATTATGGAACATTGAGCATAAAAACGACGATCAAAT
1 ATTTTAGCAATTTATTGGATCAAATAATTAAAATGGAAC-CTCAGCATAAAAACGAGGACCAAAT
* * * * *
84309 TAAAAATTCAT-CTAAATTAAGTAACTAAAGTAAAATTAATCTGAAATGAAGGCTCTAATGTTAA
65 TAAAAATTC-TCCTAAATAAAG-AACTAAAGTGAAATTAACCT-AAATAAAGGCTCTAATATTAA
84373 TCCTAACC-
127 TCCTAACCA
** * * * * * *
84381 ---TTAGTTATTTATTGGATCGAATAGTTAAAATGAAACCTCGGGCATAAAAGCGATGACCAAAT
1 ATTTTAGCAATTTATTGGATCAAATAATTAAAATGGAACCTC-AGCATAAAAACGAGGACCAAAT
*
84443 TAAAAATTCACCTA
65 TAAAAATTCTCCTA
84457 TTTTAAAAAA
Statistics
Matches: 296, Mismatches: 49, Indels: 19
0.81 0.13 0.05
Matches are distributed among these distances:
133 1 0.00
134 58 0.20
138 33 0.11
139 199 0.67
140 5 0.02
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.28
Consensus pattern (135 bp):
ATTTTAGCAATTTATTGGATCAAATAATTAAAATGGAACCTCAGCATAAAAACGAGGACCAAATT
AAAAATTCTCCTAAATAAAGAACTAAAGTGAAATTAACCTAAATAAAGGCTCTAATATTAATCCT
AACCA
Found at i:85111 original size:21 final size:22
Alignment explanation
Indices: 85085--85143 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 22
85075 ATTATCCAAT
**
85085 AAGCTTGGCATCCATAACAA-C
1 AAGCTTGAAATCCATAACAACC
85106 AAGCTTGAAATCCATAACAACC
1 AAGCTTGAAATCCATAACAACC
85128 AA-CTTGAAATCCATAA
1 AAGCTTGAAATCCATAA
85144 TAATAAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 32 0.91
22 3 0.09
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.20
Consensus pattern (22 bp):
AAGCTTGAAATCCATAACAACC
Found at i:86904 original size:110 final size:110
Alignment explanation
Indices: 86715--86923 Score: 382
Period size: 110 Copynumber: 1.9 Consensus size: 110
86705 GAAACTTCCG
86715 TAGATCCAACACCACTCGATTCCTCATTATTTGTTTCTTCATCCTCTTGAGAAGCTCGAACAATC
1 TAGATCCAACACCACTCGATTCCTCATTATTTGTTTCTTCATCCTCTTGAGAAGCTCGAACAATC
* * *
86780 CGCAAATCACTTAATTTTCTCGTGGGCATAATATAGGAACTTTCA
66 CGCAAATCAATTAATTTTCTCCTAGGCATAATATAGGAACTTTCA
86825 TAGATCCAACACCACTCGATTCCTCATTATTTGTTTCTTCATCCTCTTGAGAAGCTCGAACAATC
1 TAGATCCAACACCACTCGATTCCTCATTATTTGTTTCTTCATCCTCTTGAGAAGCTCGAACAATC
*
86890 CGTAAATCAATTAATTTTCTCCTAGGCATAATAT
66 CGCAAATCAATTAATTTTCTCCTAGGCATAATAT
86924 TTGTAATAAA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 95 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.34
Consensus pattern (110 bp):
TAGATCCAACACCACTCGATTCCTCATTATTTGTTTCTTCATCCTCTTGAGAAGCTCGAACAATC
CGCAAATCAATTAATTTTCTCCTAGGCATAATATAGGAACTTTCA
Found at i:95657 original size:64 final size:64
Alignment explanation
Indices: 95459--95658 Score: 219
Period size: 65 Copynumber: 3.1 Consensus size: 64
95449 TTTTCAGAGT
** * * *
95459 GATGCACCAAGCCATGCATCGATGCAC-CATGAATAAATTG-AACATCGAATGAATTTCATGCAC
1 GATGCACC-AGCCATGCATCGATGCACTC-TGAATATTTTGAAACATCGAATGCATTTGATGCAT
95522 C
64 C
* * *
95523 GATGCA-CATACTATGCATCGATGCACTCAGAAT-TTTATGAAAACATCGAATGCATTTGATGCA
1 GATGCACCA-GCCATGCATCGATGCACTCTGAATATTT-TG-AAACATCGAATGCATTTGATGCA
95586 TC
63 TC
** **
95588 GATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACCTGATGCATC
1 GATGCACCAGCCATGCATCGATGCACTCTGAATATTTTGAAACATCGAATGCATTTGATGCATC
95652 GATGCAC
1 GATGCAC
95659 TCTTAGTGCA
Statistics
Matches: 114, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
62 2 0.02
63 22 0.19
64 37 0.32
65 48 0.42
66 5 0.04
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (64 bp):
GATGCACCAGCCATGCATCGATGCACTCTGAATATTTTGAAACATCGAATGCATTTGATGCATC
Found at i:98951 original size:41 final size:41
Alignment explanation
Indices: 98883--99001 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 41
98873 TTATGAACTA
*
98883 TTGCATCATTTGTTTCAAAAACGCCACTAAAGAACTATTCTT
1 TTGCAGCATTTGTTT-AAAAACGCCACTAAAGAACTATTCTT
* **
98925 TTGCGGTGTTTGTTTAAAAACGCCACTAAAGAA-TGATTCTT
1 TTGCAGCATTTGTTTAAAAACGCCACTAAAGAACT-ATTCTT
* *
98966 TTGCAGCATTTGTTTAGAAACGCCACTAAAGTACTA
1 TTGCAGCATTTGTTTAAAAACGCCACTAAAGAACTA
99002 GGTTTTAGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
40 1 0.02
41 53 0.80
42 12 0.18
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (41 bp):
TTGCAGCATTTGTTTAAAAACGCCACTAAAGAACTATTCTT
Found at i:102062 original size:18 final size:18
Alignment explanation
Indices: 102035--102080 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
102025 TGCAAAAATG
102035 GTACCGATACCCAAAGGA
1 GTACCGATACCCAAAGGA
* *
102053 GTATCGATACCCAAAGGG
1 GTACCGATACCCAAAGGA
102071 GTACCGATAC
1 GTACCGATAC
102081 TACTTTGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (18 bp):
GTACCGATACCCAAAGGA
Found at i:115521 original size:30 final size:29
Alignment explanation
Indices: 115485--115543 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
115475 ATGTATGAAG
*
115485 TATTCTACAAGCTTTAGAAAATTTGGGGAC
1 TATTCTACAA-CTTTAGAAAAGTTGGGGAC
* * *
115515 TATTCTATAATTTTTGAAAAGTTGGGGAC
1 TATTCTACAACTTTAGAAAAGTTGGGGAC
115544 CAATTCTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.37
Consensus pattern (29 bp):
TATTCTACAACTTTAGAAAAGTTGGGGAC
Found at i:115539 original size:29 final size:30
Alignment explanation
Indices: 115501--115568 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
115491 ACAAGCTTTA
* *
115501 GAAAATTTGGGGA-CTATTCTATAATTTTT-
1 GAAAAGTTGGGGACCAATTCT-TAATTTTTG
115530 GAAAAGTTGGGGACCAATTCTTAATTTTTG
1 GAAAAGTTGGGGACCAATTCTTAATTTTTG
115560 GAAAAGTTG
1 GAAAAGTTG
115569 TAAATGGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.38
Consensus pattern (30 bp):
GAAAAGTTGGGGACCAATTCTTAATTTTTG
Found at i:116102 original size:20 final size:21
Alignment explanation
Indices: 116077--116116 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
116067 TTATTTGGTG
*
116077 TGATAAGAA-TATGAATTATA
1 TGATAACAAGTATGAATTATA
116097 TGATAACAATGTATGAATTA
1 TGATAACAA-GTATGAATTA
116117 AATATAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (21 bp):
TGATAACAAGTATGAATTATA
Found at i:117364 original size:23 final size:23
Alignment explanation
Indices: 117338--117403 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
117328 TCTTATATGA
* *
117338 CACTACGGTGCATTTCTATGCGG
1 CACTTCGGTGCATTTCTACGCGG
* *
117361 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGCGG
*
117384 CACTTCGGTGCATTTATACG
1 CACTTCGGTGCATTTCTACG
117404 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGG
Found at i:118177 original size:22 final size:22
Alignment explanation
Indices: 118151--118233 Score: 121
Period size: 22 Copynumber: 3.8 Consensus size: 22
118141 TTCGGTATTG
118151 TTTACGGTACTGTTCATTACTA
1 TTTACGGTACTGTTCATTACTA
118173 TTTACGGTACTGTTCATTACTA
1 TTTACGGTACTGTTCATTACTA
* *
118195 TTAACGGTACTGTTCATTACTG
1 TTTACGGTACTGTTCATTACTA
* * *
118217 TTCATGGTATTGTTCAT
1 TTTACGGTACTGTTCAT
118234 ATCGTATAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.46
Consensus pattern (22 bp):
TTTACGGTACTGTTCATTACTA
Found at i:121777 original size:15 final size:16
Alignment explanation
Indices: 121738--121779 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
121728 AAATTACTAT
*
121738 TTTATTTTATTTATTA
1 TTTATATTATTTATTA
121754 TTT-TATTATTTA-TA
1 TTTATATTATTTATTA
*
121768 TTTATCTTATTT
1 TTTATATTATTT
121780 TCAAACAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 15 0.65
16 3 0.13
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATATTATTTATTA
Found at i:123592 original size:2 final size:2
Alignment explanation
Indices: 123585--123614 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
123575 ATTGGACCAC
123585 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
123615 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:123619 original size:2 final size:2
Alignment explanation
Indices: 123614--123640 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
123604 TCTCTCTCTC
123614 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
123641 TCGCACTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:124415 original size:2 final size:2
Alignment explanation
Indices: 124408--124437 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
124398 ATTCTAAATA
124408 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
124438 GCTTATGTGA
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
Done.