Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001541.1 Hibiscus syriacus cultivar Beakdansim tig00003028_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: 65449
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:8319 original size:24 final size:23
Alignment explanation
Indices: 8262--8357 Score: 95
Period size: 23 Copynumber: 4.1 Consensus size: 23
8252 GGTGTCGACA
* *
8262 TCACGAACATGTTCGTTTAATGT
1 TCACGAACGTGTTCATTTAATGT
8285 TCACGAACGTGTTCATTTATATGT
1 TCACGAACGTGTTCATTTA-ATGT
* **
8309 TCA-TAAGCGTGTTCATTTAGCGT
1 TCACGAA-CGTGTTCATTTAATGT
* * *
8332 TCACGAACATGCTCATTTAGTGT
1 TCACGAACGTGTTCATTTAATGT
8355 TCA
1 TCA
8358 TTTATCATTA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
23 40 0.66
24 21 0.34
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (23 bp):
TCACGAACGTGTTCATTTAATGT
Found at i:14317 original size:29 final size:29
Alignment explanation
Indices: 14275--14332 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
14265 TGCAAAAAGG
*
14275 GGGAGCTGAACATTTTCACATATTTTTCC
1 GGGAGCTGAACATTTTAACATATTTTTCC
*
14304 GGGAGCTGAACATTTTAATATATTTTTCC
1 GGGAGCTGAACATTTTAACATATTTTTCC
14333 AACAATTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (29 bp):
GGGAGCTGAACATTTTAACATATTTTTCC
Found at i:18635 original size:6 final size:6
Alignment explanation
Indices: 18624--18652 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
18614 ATCGAATAGA
18624 CTCGAG CTCGAG CTCGAG CTCGA- CTCGAG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG
18653 TTCTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (6 bp):
CTCGAG
Found at i:20227 original size:19 final size:18
Alignment explanation
Indices: 20187--20231 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
20177 ATTTAAATAT
*
20187 TTTTTAAAAATATGATTT
1 TTTTTAAAAATATGATTA
20205 TTTTTAAAAATGATCGA-TA
1 TTTTTAAAAAT-AT-GATTA
20224 TTTTTAAA
1 TTTTTAAA
20232 TGTTTTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 11 0.46
19 11 0.46
20 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
TTTTTAAAAATATGATTA
Found at i:29858 original size:19 final size:17
Alignment explanation
Indices: 29799--29862 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 17
29789 TTCAATGTGC
29799 ATCGATGCACAAGTGGT
1 ATCGATGCACAAGTGGT
29816 ATCGAATGTCATC-AGT-GT
1 ATCG-ATG-CA-CAAGTGGT
29834 ATCGATGCACAAGTGGT
1 ATCGATGCACAAGTGGT
29851 GCATCGATGCAC
1 --ATCGATGCAC
29863 CCCCTAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
15 1 0.03
16 5 0.12
17 9 0.22
18 9 0.22
19 15 0.38
20 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (17 bp):
ATCGATGCACAAGTGGT
Found at i:30479 original size:18 final size:18
Alignment explanation
Indices: 30456--30528 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
30446 AGGGATTATC
30456 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
30474 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
30493 CAGTGGTCCTCCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
30512 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
30529 AATATTTCGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 29 0.63
19 4 0.09
20 13 0.28
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:30788 original size:2 final size:2
Alignment explanation
Indices: 30781--30826 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
30771 TGTATTGTTT
30781 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
30823 -A TA T
1 TA TA T
30827 GCCTCAGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31552 original size:2 final size:2
Alignment explanation
Indices: 31545--31582 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31535 TTATATGGTC
31545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31583 TGCTTTCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33089 original size:8 final size:8
Alignment explanation
Indices: 33064--33134 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 8
33054 ACAAATGAAG
33064 AATAAAAA
1 AATAAAAA
33072 TAAGTAAAAA
1 -AA-TAAAAA
33082 AATAAAAA
1 AATAAAAA
33090 TAA-AAGGAAA
1 -AATAA--AAA
*
33100 AATAAATA
1 AATAAAAA
*
33108 AATAAATA
1 AATAAAAA
*
33116 AATAAATA
1 AATAAAAA
*
33124 AATAAATA
1 AATAAAAA
33132 AAT
1 AAT
33135 GAAATATTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
8 37 0.66
9 8 0.14
10 11 0.20
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (8 bp):
AATAAAAA
Found at i:33108 original size:4 final size:4
Alignment explanation
Indices: 33099--33140 Score: 75
Period size: 4 Copynumber: 10.2 Consensus size: 4
33089 ATAAAAGGAA
33099 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A
33141 TTAAATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:33259 original size:12 final size:13
Alignment explanation
Indices: 33231--33266 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
33221 ATAATATAAT
33231 AAACAAATAAAAA
1 AAACAAATAAAAA
*
33244 AAACAAA-AACAA
1 AAACAAATAAAAA
33256 AAACAAATAAA
1 AAACAAATAAA
33267 TATATAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (13 bp):
AAACAAATAAAAA
Found at i:33440 original size:2 final size:2
Alignment explanation
Indices: 33435--33468 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
33425 TAAAAAAAAG
33435 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
33469 ATAATATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33526 original size:23 final size:24
Alignment explanation
Indices: 33495--33543 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
33485 ACCAAATGAA
33495 TATAAATAAATAA-AAAATAT-ATG
1 TATAAAT-AATAATAAAATATAATG
* *
33518 TATATATAATAATAATATATAATG
1 TATAAATAATAATAAAATATAATG
33542 TA
1 TA
33544 AAAAAAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 12 0.55
24 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
TATAAATAATAATAAAATATAATG
Found at i:34054 original size:37 final size:37
Alignment explanation
Indices: 34013--34116 Score: 163
Period size: 37 Copynumber: 2.8 Consensus size: 37
34003 GTGCTTGTGG
* * *
34013 ATCCTATCTTTAGGAGTTTAAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
* *
34050 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
34087 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
34117 GGACGAAAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:36447 original size:5 final size:5
Alignment explanation
Indices: 36437--36500 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
36427 AACGGTCAAT
* * *
36437 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC- AGTCG GTTCG GGTCG GGTC-
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
* *
36487 AGTCA GGTCG GGTC
1 GGTCG GGTCG GGTC
36501 AGACCGGTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
4 6 0.13
5 36 0.78
7 4 0.09
ACGTcount: A:0.08, C:0.22, G:0.48, T:0.22
Consensus pattern (5 bp):
GGTCG
Found at i:36452 original size:17 final size:17
Alignment explanation
Indices: 36430--36487 Score: 80
Period size: 17 Copynumber: 3.3 Consensus size: 17
36420 CACTGTCAAC
36430 GGTCAATGGTCGGGTCG
1 GGTCAATGGTCGGGTCG
*
36447 GGTCAACGGTCGGGTCG
1 GGTCAATGGTCGGGTCG
*
36464 GGTCAGTCGGTTCGGGTCG
1 GGTCAAT-GG-TCGGGTCG
36483 GGTCA
1 GGTCA
36488 GTCAGGTCGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 21 0.58
18 2 0.06
19 13 0.36
ACGTcount: A:0.10, C:0.21, G:0.47, T:0.22
Consensus pattern (17 bp):
GGTCAATGGTCGGGTCG
Found at i:36480 original size:19 final size:18
Alignment explanation
Indices: 36437--36500 Score: 94
Period size: 19 Copynumber: 3.5 Consensus size: 18
36427 AACGGTCAAT
*
36437 GGTCGGGTCGGGTCA-AC
1 GGTCGGGTCGGGTCAGTC
36454 GGTCGGGTCGGGTCAGTC
1 GGTCGGGTCGGGTCAGTC
36472 GGTTCGGGTCGGGTCAGTC
1 GG-TCGGGTCGGGTCAGTC
36491 AGGTCGGGTC
1 -GGTCGGGTC
36501 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
17 15 0.35
18 3 0.07
19 23 0.53
20 2 0.05
ACGTcount: A:0.08, C:0.22, G:0.48, T:0.22
Consensus pattern (18 bp):
GGTCGGGTCGGGTCAGTC
Found at i:43582 original size:5 final size:5
Alignment explanation
Indices: 43572--43623 Score: 54
Period size: 5 Copynumber: 10.8 Consensus size: 5
43562 AACGGTCAAC
* * * *
43572 GGTCG GGTCG GGTCG GGTC- AGTCA GGTCG GGTCG GGTC- AGTCG AGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
43620 GGTC
1 GGTC
43624 AGACTGGTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
4 6 0.15
5 34 0.85
ACGTcount: A:0.08, C:0.21, G:0.50, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:43599 original size:19 final size:18
Alignment explanation
Indices: 43577--43623 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 18
43567 TCAACGGTCG
43577 GGTCGGGTCGGGTCAGTC
1 GGTCGGGTCGGGTCAGTC
43595 AGGTCGGGTCGGGTCAGTC
1 -GGTCGGGTCGGGTCAGTC
43614 GAGTCGGGTC
1 G-GTCGGGTC
43624 AGACTGGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 1 0.04
19 26 0.96
ACGTcount: A:0.09, C:0.21, G:0.49, T:0.21
Consensus pattern (18 bp):
GGTCGGGTCGGGTCAGTC
Found at i:43614 original size:14 final size:14
Alignment explanation
Indices: 43572--43625 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
43562 AACGGTCAAC
*
43572 GGTCGGGTCGGGTCG
1 GGTCGGGTC-AGTCG
*
43587 GGTC-AGTCAGGTCG
1 GGTCGGGTCA-GTCG
43601 GGTCGGGTCAGTCG
1 GGTCGGGTCAGTCG
*
43615 AGTCGGGTCAG
1 GGTCGGGTCAG
43626 ACTGGTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 25 0.76
15 8 0.24
ACGTcount: A:0.09, C:0.20, G:0.50, T:0.20
Consensus pattern (14 bp):
GGTCGGGTCAGTCG
Found at i:43676 original size:10 final size:9
Alignment explanation
Indices: 43650--43685 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
43640 TTCAGACTGA
43650 TCAAACCGG
1 TCAAACCGG
43659 TCAAACCGG
1 TCAAACCGG
43668 TCGAAACCGG
1 TC-AAACCGG
43678 TCAAACCG
1 TCAAACCG
43686 ATTTCCAGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (9 bp):
TCAAACCGG
Found at i:44643 original size:106 final size:106
Alignment explanation
Indices: 44415--46230 Score: 2784
Period size: 106 Copynumber: 17.2 Consensus size: 106
44405 GGTTGTTACA
* * *
44415 GAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * * * *
44476 A-AT-TTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * *
44515 -AAGCTTGTGTTGTCTTGG-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGG
1 GAA-CTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
44578 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
64 GAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
44621 AAACTTGCATTGTCTTGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* *
44686 AATTGTTTATTGACAACCAGCGGTCCCTTTGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * * * **
44727 GAACTTGCGTTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTCAAATTAGCTCTAAAATTAAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * *
44792 AGTTCTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
44833 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* **
44898 AGTTGTTTATTGACAACCAACGGTCCCTTTTTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * *
44939 GAACTTGCGTTGTATTGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* *
45004 AATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
45045 GAACTTGCGTTGTCTGTAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
45110 AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * *
45151 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGCTCTGAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
45216 AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
45257 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGCTCTAAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * * *
45322 AGTTATTTGTTGACAACCAGCGGTCCCTTTGTTGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
45363 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
45428 AGTTGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * * *
45469 GAACTTGCGTTGTCTTGAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTGGAA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
45534 AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * *
45575 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
45640 AGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
45681 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
*
45746 AGTTGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
45787 GAACTTGCGTTGTCTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* *
45852 AATTGTTTATTGACAACCAGCGGTCCCTTCGTCTTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
45893 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * *
45958 AGTCGTTTATTGACAACCAGCGGTCCCTTCATTGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
45999 GAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * *
46064 AATTGTTTATTGATAACCAGAGGTCCCTTCGTCGTGAAGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
46105 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
1 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
* * * * *
46170 AGTTGTTTGTTGACAACCAGAGGTCCCTTCGTTGAGATGTT
66 AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* *
46211 GAACTTGTGTTGTCTTGAGT
1 GAACTTGCGTTGTCTGGAGT
46231 GGCACGATAT
Statistics
Matches: 1577, Mismatches: 129, Indels: 14
0.92 0.08 0.01
Matches are distributed among these distances:
99 2 0.00
100 46 0.03
101 4 0.00
102 1 0.00
104 3 0.00
105 3 0.00
106 1516 0.96
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGA
AGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
Found at i:47759 original size:172 final size:173
Alignment explanation
Indices: 47463--47809 Score: 547
Period size: 172 Copynumber: 2.0 Consensus size: 173
47453 TAAATAGGCC
* *
47463 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGCGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTG
* *
47528 CTCAAACTGTCTCTGTCTTGATGCTCTATGATCTTCGAATGAAGTGATTCAGTGATTCGGGAATG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAATGAAGTGATTCAGTGATTCGGGAATG
*
47593 ACTATGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ACTATGCTTGATCAATCTCATAGTTTGAAGCTTGATGAGCCATTT
* *
47638 CAAACAAGTGTTTTAGGGCGTTGAACCAAGGATCAATTCATTATGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTGTTTCAGGGCGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
*
47700 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
66 CAAAATG--TCTCTCTCTTGATGCTCTATGATCTTCGAATGAAGTGATTCAGTGATTCGGGAATG
* *
47765 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGAGCCATTT
129 ACTATGCTTGATCAATCTCATAGTTTGAAGCTTGATGAGCCATTT
47810 GTCTTTAGGG
Statistics
Matches: 160, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
170 13 0.08
172 97 0.61
174 1 0.01
175 49 0.31
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (173 bp):
CAAACAAGTGTTTCAGGGCGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAATGAAGTGATTCAGTGATTCGGGAATGAC
TATGCTTGATCAATCTCATAGTTTGAAGCTTGATGAGCCATTT
Found at i:47856 original size:7 final size:7
Alignment explanation
Indices: 47844--47918 Score: 55
Period size: 7 Copynumber: 10.0 Consensus size: 7
47834 TTTTTTGTCC
47844 CTTTTTT
1 CTTTTTT
47851 CTTTTTT
1 CTTTTTT
47858 CTTTTTGTT
1 C-TTTT-TT
*
47867 ATTGTTTCT
1 CTT-TTT-T
47876 CTTTTTT
1 CTTTTTT
47883 CTTTGTTT
1 CTTT-TTT
47891 -TTTTGTT
1 CTTTT-TT
*
47898 -TTTTTG
1 CTTTTTT
47904 CTTCTTTT
1 CTT-TTTT
47912 CTTTTTT
1 CTTTTTT
47919 GTTCTTGATT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
6 2 0.04
7 28 0.50
8 19 0.34
9 7 0.12
ACGTcount: A:0.01, C:0.12, G:0.07, T:0.80
Consensus pattern (7 bp):
CTTTTTT
Found at i:47899 original size:17 final size:16
Alignment explanation
Indices: 47845--47921 Score: 61
Period size: 16 Copynumber: 4.8 Consensus size: 16
47835 TTTTTGTCCC
*
47845 TTTTTTCTT-TTTTCT
1 TTTTTTTTTGTTTTCT
*
47860 TTTTGTTATTGTTTCTCT
1 TTTT-TTTTTGTTT-TCT
*
47878 TTTTTCTTTGTTTT-T
1 TTTTTTTTTGTTTTCT
*
47893 TTGTTTTTTTG-CTTCT
1 TT-TTTTTTTGTTTTCT
47909 TTTCTTTTTTGTT
1 TTT-TTTTTTGTT
47922 CTTGATTGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
15 10 0.20
16 22 0.45
17 10 0.20
18 7 0.14
ACGTcount: A:0.01, C:0.10, G:0.08, T:0.81
Consensus pattern (16 bp):
TTTTTTTTTGTTTTCT
Found at i:52371 original size:2 final size:2
Alignment explanation
Indices: 52364--52394 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52354 AAAATATTAA
52364 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52395 AATGAGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52475 original size:27 final size:29
Alignment explanation
Indices: 52445--52521 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 29
52435 TAGTAATATG
52445 AAAATATAATATAATATAAA-CAAA-AAA
1 AAAATATAATATAATATAAATCAAATAAA
* * *
52472 AAAACA-AATAAATATATAAATCAAATATA
1 AAAATATAATATA-ATATAAATCAAATAAA
*
52501 AAAGTATACATATAATGATAA
1 AAAATATA-ATATAAT-ATAA
52522 TTGACTTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
26 5 0.13
27 12 0.32
28 4 0.11
29 6 0.16
30 3 0.08
31 8 0.21
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (29 bp):
AAAATATAATATAATATAAATCAAATAAA
Found at i:53234 original size:37 final size:37
Alignment explanation
Indices: 53168--53268 Score: 121
Period size: 37 Copynumber: 2.7 Consensus size: 37
53158 GTGATTGTGG
* * ** *
53168 ATCCTATATTTAGGAGTTTAAATTATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
*
53205 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
* * *
53242 ATCATAATTTTAAGAGTTTGAATCCTA
1 ATCCTATTTTTAGGAGTTTGAATCCTA
53269 ATAGGATAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:55447 original size:2 final size:2
Alignment explanation
Indices: 55442--55469 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55432 AAGTGTGTCG
55442 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
55470 TTTTCTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58927 original size:21 final size:20
Alignment explanation
Indices: 58878--58933 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
58868 GTTTTTGTAA
58878 TTTT-AAATAAA-TTTAGAT
1 TTTTAAAATAAATTTTAGAT
** *
58896 TTTTATTATAAATTTTAAGTT
1 TTTTAAAATAAATTTT-AGAT
58917 TTTTAAAATAAAATTTT
1 TTTTAAAAT-AAATTTT
58934 CAAGAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 3 0.10
21 10 0.34
22 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTAAAATAAATTTTAGAT
Found at i:59812 original size:29 final size:31
Alignment explanation
Indices: 59744--59820 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 31
59734 AATAATTTAA
* * * *
59744 AGTGAGTAAAATCGGAACAATTCGAAAGTTT
1 AGTGAGTGAAATAGGAAAAATTCGAAAGTAT
*
59775 AGTGA-TGAAATTGGAAAAATT-GAAA-TAT
1 AGTGAGTGAAATAGGAAAAATTCGAAAGTAT
59803 AGTGAGTGAAATAGGAAA
1 AGTGAGTGAAATAGGAAA
59821 TAGAGTAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 7 0.17
29 15 0.38
30 13 0.32
31 5 0.12
ACGTcount: A:0.47, C:0.04, G:0.25, T:0.25
Consensus pattern (31 bp):
AGTGAGTGAAATAGGAAAAATTCGAAAGTAT
Found at i:63412 original size:78 final size:81
Alignment explanation
Indices: 63324--63475 Score: 220
Period size: 82 Copynumber: 1.9 Consensus size: 81
63314 TGATCCTTTG
*
63324 ATATTCAAATTTAAAGAGATAAT-A-T-CTTTTAATTAGAAATATTCAAAAGGATATAATTATCT
1 ATATTCAAATTTAAAGAGATAATAAGTACTTTTAATTAGAAATATTCAAAAGGATATAATTATCA
*
63386 TTTTAATAACTTTTTA
66 TATTAATAACTTTTTA
** * *
63402 ATATTCAAATTTAAAGAGATAATAAGTACCTTTTAATTTTAAATATTTAAAAGGATATGATTATC
1 ATATTCAAATTTAAAGAGATAATAAGTA-CTTTTAATTAGAAATATTCAAAAGGATATAATTATC
63467 ATATTAATA
65 ATATTAATA
63476 TTTAAATTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
78 23 0.36
79 1 0.02
80 1 0.02
82 39 0.61
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (81 bp):
ATATTCAAATTTAAAGAGATAATAAGTACTTTTAATTAGAAATATTCAAAAGGATATAATTATCA
TATTAATAACTTTTTA
Found at i:63437 original size:35 final size:34
Alignment explanation
Indices: 63397--63509 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 34
63387 TTTAATAACT
* *
63397 TTTTAATATTCAAATTTAAAGAGATAATAAGTACC
1 TTTTAATATTAAAATTTAAA-AGATAATAAATACC
* * * *
63432 TTTTAATTTTAAATATTTAAAAGGAT-ATGATTATCA
1 TTTTAATATTAAA-ATTTAAAA-GATAATAAATA-CC
* * *
63468 TATTAATATTTAAATTTAAATAGATAATAAATATC
1 TTTTAATATTAAAATTTAAA-AGATAATAAATACC
63503 TTTTAAT
1 TTTTAAT
63510 TTCTTTTAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
35 33 0.55
36 27 0.45
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (34 bp):
TTTTAATATTAAAATTTAAAAGATAATAAATACC
Done.