Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007965.1 Hibiscus syriacus cultivar Beakdansim tig00110395_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: 37538
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:5190 original size:64 final size:63
Alignment explanation
Indices: 5104--5290 Score: 241
Period size: 64 Copynumber: 2.9 Consensus size: 63
5094 ATGCACTCTT
5104 TTAA-AATAAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCA
1 TTAATAAT-AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCA
** *
5167 TTAATAATGAAACATCGAATGCAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCA
1 TTAATAAT-AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCA
** * ** * * *
5231 GCAATAATAATACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 TTAATAATAA-ACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCAT
5291 ACCTTCATTA
Statistics
Matches: 108, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
63 6 0.06
64 102 0.94
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (63 bp):
TTAATAATAAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCA
Found at i:5616 original size:12 final size:12
Alignment explanation
Indices: 5598--5633 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5588 TATATATGTT
5598 CATGTGATATGA
1 CATGTGATATGA
*
5610 TATGTGATATGA
1 CATGTGATATGA
5622 CATGTGATATGA
1 CATGTGATATGA
5634 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:5644 original size:13 final size:13
Alignment explanation
Indices: 5626--5683 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
5616 ATATGACATG
5626 TGATATGAGAACA
1 TGATATGAGAACA
5639 TGATATGAGATACA
1 TGATATGAGA-ACA
*
5653 TGATCACAAGAGAA-A
1 TGAT---ATGAGAACA
*
5668 TGATATGAGTACA
1 TGATATGAGAACA
5681 TGA
1 TGA
5684 ACATATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 5 0.14
13 14 0.38
14 7 0.19
15 5 0.14
16 1 0.03
17 5 0.14
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24
Consensus pattern (13 bp):
TGATATGAGAACA
Found at i:5786 original size:15 final size:15
Alignment explanation
Indices: 5768--5800 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5758 GAGGGTATAA
5768 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
5783 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
5798 TAG
1 TAG
5801 GGGTCCTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:8174 original size:2 final size:2
Alignment explanation
Indices: 8167--8215 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
8157 GCTTGGTACG
8167 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
8209 TC TC TC T
1 TC TC TC T
8216 ATTTATCTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:9702 original size:29 final size:29
Alignment explanation
Indices: 9669--9737 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
9659 ATTCATTTCT
*
9669 AAACTTTTGGACGTTCCAAATTTATTCCC
1 AAACTTTTGAACGTTCCAAATTTATTCCC
* **
9698 AAACTTTTGAACGTTTCAAATTTATTCTG
1 AAACTTTTGAACGTTCCAAATTTATTCCC
9727 AAACTTTTGAA
1 AAACTTTTGAA
9738 TGATTTTGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (29 bp):
AAACTTTTGAACGTTCCAAATTTATTCCC
Found at i:11496 original size:2 final size:2
Alignment explanation
Indices: 11489--11525 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
11479 GTTTCCCCTT
*
11489 GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
11526 CTATGTTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17146 original size:20 final size:21
Alignment explanation
Indices: 17113--17162 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
17103 AACAATTATT
*
17113 TAATAATGAT-ATAATATATA
1 TAATAATAATGATAATATATA
*
17133 TAAT-ATAATGATAATATTTA
1 TAATAATAATGATAATATATA
17153 TAATAATAAT
1 TAATAATAAT
17163 TTTAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 17 0.65
21 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
TAATAATAATGATAATATATA
Found at i:17156 original size:15 final size:14
Alignment explanation
Indices: 17136--17179 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
17126 ATATATATAA
*
17136 TATAATGATAATATT
1 TATAATAATAAT-TT
17151 TATAATAATAATTT
1 TATAATAATAATTT
17165 TAATAATAATAATTT
1 T-ATAATAATAATTT
17180 AAGTAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 3 0.11
15 24 0.89
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
TATAATAATAATTT
Found at i:17597 original size:46 final size:46
Alignment explanation
Indices: 17390--18052 Score: 962
Period size: 46 Copynumber: 14.5 Consensus size: 46
17380 TCAAAAAGCT
* * * * * *
17390 CCCGAAGGCTTTTTGAAAATATCCTGTACTGCAGGGCTTACGGATGA
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
17437 CCCG-AGGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * * * *
17482 CCTGAAGG-TTTTGAAAACATCATGCAATGAAGGGCTTATAGATTA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
17527 CTCGAAGG-TTTTGAAAACATCATGCACTGAAGAACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
17572 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
17618 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
17664 CCTGAAGATTTTTGAAAACATCATGCACTGAATGG-CTTATAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAA-GGACTTACAGATGA
*
17710 CTCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
17755 CCTGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
17801 CCCGAAGGTTTTTGAAAACATCATGCACTGTAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * * *
17847 CCCGAAGGTTTTTGAAAGCATCATGCATTGAAGGGCTTATAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
17893 CCTGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
17938 CCCAAAGGTTTTTGAAAATATCATGCACTGAAGGACTTACAAATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
17984 CCCGAAGGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAA-GGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
18031 CCCGAAGG-CTTTGAAAATATCA
1 CCCGAAGGTTTTTGAAAACATCA
18053 AAAAGCTCCA
Statistics
Matches: 559, Mismatches: 50, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
44 2 0.00
45 204 0.36
46 304 0.54
47 49 0.09
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (46 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:17730 original size:183 final size:182
Alignment explanation
Indices: 17390--18052 Score: 1033
Period size: 183 Copynumber: 3.6 Consensus size: 182
17380 TCAAAAAGCT
* * * * * * *
17390 CCCGAAGGCTTTTTGAAAATATCCTGTACTGCAGGGCTTACGGATGACCCG-AGGGTTTTGAAAA
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAA
* * *
17454 CATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACATCATGCAATGAAGGGCTT
65 CATCATGCACTGAAGGACTTACAGATGACCCGAAGTTTTTGAAAACATCATGCAATGAAGGGCTT
* *
17519 ATAGATTACTCGAAGGTTTTGAAAACATCATGCACTGAAGAACTTACAGATGA
130 ATAGATGACTCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
17572 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAAC
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAAC
* * *
17637 ATCATGCACTGAAGGACTTACAGATGACCTGAAGATTTTTGAAAACATCATGCACTGAATGGCTT
66 ATCATGCACTGAAGGACTTACAGATGACCCGAAG-TTTTTGAAAACATCATGCAATGAAGGGCTT
17702 ATAGATGACTCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
130 ATAGATGACTCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
17755 CCTGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAAC
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAAC
* * *
17820 ATCATGCACTGTAGGACTTACAGATGACCCGAAGGTTTTTGAAAGCATCATGCATTGAAGGGCTT
66 ATCATGCACTGAAGGACTTACAGATGACCCGAA-GTTTTTGAAAACATCATGCAATGAAGGGCTT
17885 ATAGATGAC-CTGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
130 ATAGATGACTC-GAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
17938 CCCAAAGGTTTTTGAAAATATCATGCACTGAAGGACTTACAAATGACCCGAAGGGTTTTTGAAAA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAA-GGTTTTTGAAAA
* ** *
18003 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCA
65 CATCATGCACTGAAGGACTTACAGATGACCCGAAGTTTTTGAAAACATCA
18053 AAAAGCTCCA
Statistics
Matches: 447, Mismatches: 29, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
181 36 0.08
182 55 0.12
183 311 0.70
184 45 0.10
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (182 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAAC
ATCATGCACTGAAGGACTTACAGATGACCCGAAGTTTTTGAAAACATCATGCAATGAAGGGCTTA
TAGATGACTCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:17740 original size:137 final size:136
Alignment explanation
Indices: 17390--18052 Score: 963
Period size: 137 Copynumber: 4.8 Consensus size: 136
17380 TCAAAAAGCT
* * * * * *
17390 CCCGAAGGCTTTTTGAAAATATCCTGTACTGCAGGGCTTACGGATGACCCG-AGGGTTTTGAAAA
1 CCCGAAGG-TTTTTGAAAACATCATGCACTG-AAGGCTTACAGATGACCCGAAGGTTTTTGAAAA
* *
17454 CATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACATCATGCAATGAAGGGCTT
64 CATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGACTT
* *
17519 ATAGATTA
129 ACAGATGA
* *
17527 CTCGAAGG-TTTTGAAAACATCATGCACTGAAGAACTTACAGATGACCCGAAGGTTTTTGAAAAC
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAG-GCTTACAGATGACCCGAAGGTTTTTGAAAAC
* *
17591 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTT
65 ATCATGCACTGAAGGGCTTACAGATGACCTGAAGG-TTTTGAAAACATCATGCACTGAAGGACTT
17656 ACAGATGA
129 ACAGATGA
* * * *
17664 CCTGAAGATTTTTGAAAACATCATGCACTGAATGGCTTATAGATGACTCGAAGG-TTTTGAAAAC
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAA-GGCTTACAGATGACCCGAAGGTTTTTGAAAAC
*
17728 ATCATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTTGAAAACATCATGCACTGAAGGACTT
65 ATCATGCACTGAAGGGCTTACAGATGACCTGAAGG-TTTTGAAAACATCATGCACTGAAGGACTT
17793 ACAGATGA
129 ACAGATGA
* *
17801 CCCGAAGGTTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGTTTTTGAAAGC
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGG-CTTACAGATGACCCGAAGGTTTTTGAAAAC
* *
17866 ATCATGCATTGAAGGGCTTATAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGACTTA
65 ATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGACTTA
17931 CAGATGA
130 CAGATGA
* * *
17938 CCCAAAGGTTTTTGAAAATATCATGCACTGAAGGACTTACAAATGACCCGAAGGGTTTTTGAAAA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGG-CTTACAGATGACCCGAA-GGTTTTTGAAAA
* * *
18003 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCA
64 CATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACATCA
18053 AAAAGCTCCA
Statistics
Matches: 478, Mismatches: 40, Indels: 15
0.90 0.08 0.03
Matches are distributed among these distances:
134 2 0.00
135 32 0.07
136 48 0.10
137 258 0.54
138 137 0.29
139 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (136 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGCTTACAGATGACCCGAAGGTTTTTGAAAACA
TCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGACTTAC
AGATGA
Found at i:18784 original size:22 final size:22
Alignment explanation
Indices: 18759--18868 Score: 175
Period size: 22 Copynumber: 5.0 Consensus size: 22
18749 AAATCCAATA
* *
18759 AATCTTTCATCTTTGAAAAGTG
1 AATCTATCATCTTTGAAGAGTG
* *
18781 AATCTATCATCTTTGAATAGAG
1 AATCTATCATCTTTGAAGAGTG
18803 AATCTATCATCTTTGAAGAGTG
1 AATCTATCATCTTTGAAGAGTG
*
18825 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGTG
18847 AATCTATCATCTTTGAAGAGTG
1 AATCTATCATCTTTGAAGAGTG
18869 TAGATGTAGA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 81 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGTG
Found at i:18825 original size:44 final size:44
Alignment explanation
Indices: 18759--18868 Score: 193
Period size: 44 Copynumber: 2.5 Consensus size: 44
18749 AAATCCAATA
* * *
18759 AATCTTTCATCTTTGAAAAGTGAATCTATCATCTTTGAATAGAG
1 AATCTATCATCTTTGAAGAGTGAATCTATCATCTTTGAAGAGAG
18803 AATCTATCATCTTTGAAGAGTGAATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGTGAATCTATCATCTTTGAAGAGAG
18847 AATCTATCATCTTTGAAGAGTG
1 AATCTATCATCTTTGAAGAGTG
18869 TAGATGTAGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (44 bp):
AATCTATCATCTTTGAAGAGTGAATCTATCATCTTTGAAGAGAG
Found at i:19332 original size:54 final size:54
Alignment explanation
Indices: 19237--19340 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
19227 TACTGGTTCT
* * * *
19237 TAAAACACTTGGCAACACATTCATCATTTCTTGTGGCTTCTGCTCAGATGCTCA
1 TAAAACACTTGACAACACATTCATCATCTCATGTGGCTTCTGCCCAGATGCTCA
*
19291 TAAAACATTTGACAACACATTCATCATCTCATGT-GCTTTCTGCCCAGATG
1 TAAAACACTTGACAACACATTCATCATCTCATGTGGC-TTCTGCCCAGATG
19341 TTTGGTCAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 2 0.05
54 42 0.95
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (54 bp):
TAAAACACTTGACAACACATTCATCATCTCATGTGGCTTCTGCCCAGATGCTCA
Found at i:24997 original size:9 final size:9
Alignment explanation
Indices: 24983--25086 Score: 84
Period size: 9 Copynumber: 11.1 Consensus size: 9
24973 CTTGATTCAA
24983 TTTTTTCTT
1 TTTTTTCTT
24992 TTTTTT-TT
1 TTTTTTCTT
*
25000 TTTTTCTTTT
1 TTTTT-TCTT
*
25010 TTTTTTTTT
1 TTTTTTCTT
25019 TTTTTTCTT
1 TTTTTTCTT
*
25028 TTTTTCCCTT
1 TTTTT-TCTT
**
25038 TTTTTCCTCAC
1 TTTTT--TCTT
*
25049 TTTTTCCTT
1 TTTTTTCTT
*
25058 TTTTATCTT
1 TTTTTTCTT
25067 TTTTTTCTT
1 TTTTTTCTT
*
25076 CTTTCTTCTT
1 -TTTTTTCTT
25086 T
1 T
25087 CTTTGCTGGA
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
8 7 0.09
9 41 0.53
10 23 0.29
11 7 0.09
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:24998 original size:10 final size:10
Alignment explanation
Indices: 24990--25086 Score: 74
Period size: 10 Copynumber: 10.0 Consensus size: 10
24980 CAATTTTTTC
24990 TTTTTT-TTT
1 TTTTTTCTTT
24999 TTTTTTCTTT
1 TTTTTTCTTT
*
25009 TTTTTTTTTT
1 TTTTTTCTTT
25019 TTTTTTC-TT
1 TTTTTTCTTT
* *
25028 TTTTTCCCTT
1 TTTTTTCTTT
* **
25038 TTTTTCCTCA
1 TTTTTTCTTT
* *
25048 CTTTTTCCTT
1 TTTTTTCTTT
*
25058 TTTTATC-TT
1 TTTTTTCTTT
*
25067 TTTTTTCTTC
1 TTTTTTCTTT
*
25077 TTTCTTCTTT
1 TTTTTTCTTT
25087 CTTTGCTGGA
Statistics
Matches: 68, Mismatches: 17, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
9 22 0.32
10 46 0.68
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:25002 original size:16 final size:16
Alignment explanation
Indices: 24983--25032 Score: 84
Period size: 16 Copynumber: 3.1 Consensus size: 16
24973 CTTGATTCAA
24983 TTTTTTCTTTTTTTTT
1 TTTTTTCTTTTTTTTT
24999 TTTTTTCTTTTTTTTT
1 TTTTTTCTTTTTTTTT
25015 TTTTTT-TTTTCTTTTT
1 TTTTTTCTTTT-TTTTT
25031 TT
1 TT
25033 CCCTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.12
16 29 0.88
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (16 bp):
TTTTTTCTTTTTTTTT
Found at i:25015 original size:20 final size:20
Alignment explanation
Indices: 24985--25032 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
24975 TGATTCAATT
24985 TTTTCTTTTTTTTTTTTTTTC
1 TTTT-TTTTTTTTTTTTTTTC
25006 TTTTTTTTTTTTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTC
25026 TTTTTTT
1 TTTTTTT
25033 CCCTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (20 bp):
TTTTTTTTTTTTTTTTTTTC
Found at i:25042 original size:1 final size:1
Alignment explanation
Indices: 24983--25032 Score: 73
Period size: 1 Copynumber: 50.0 Consensus size: 1
24973 CTTGATTCAA
* * *
24983 TTTTTTCTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
25033 CCCTTTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:25072 original size:20 final size:19
Alignment explanation
Indices: 24983--25072 Score: 73
Period size: 17 Copynumber: 4.8 Consensus size: 19
24973 CTTGATTCAA
24983 TTTTTTC-TTTTTTTT--T
1 TTTTTTCTTTTTTTTTCCT
24999 TTTTTTCTTTTTTTTT--T
1 TTTTTTCTTTTTTTTTCCT
*
25016 TTTTTTTTTCTTTTTTTCCCT
1 TTTTTTCTT-TTTTTTT-CCT
***
25037 TTTTTTCCTCACTTTTTCCT
1 TTTTTT-CTTTTTTTTTCCT
25057 TTTTTATCTTTTTTTT
1 TTTTT-TCTTTTTTTT
25073 CTTCTTTCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.12
17 17 0.29
18 7 0.12
20 14 0.24
21 13 0.22
22 1 0.02
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTCTTTTTTTTTCCT
Found at i:27904 original size:14 final size:14
Alignment explanation
Indices: 27885--27915 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27875 AAATGTAATT
*
27885 ATGCAAAGATGAAA
1 ATGCAAAAATGAAA
27899 ATGCAAAAATGAAA
1 ATGCAAAAATGAAA
27913 ATG
1 ATG
27916 TAAATACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.19, T:0.16
Consensus pattern (14 bp):
ATGCAAAAATGAAA
Found at i:27973 original size:14 final size:13
Alignment explanation
Indices: 27904--27960 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 13
27894 TGAAAATGCA
*
27904 AAAATGAAAATGT
1 AAAATGCAAATGT
* *
27917 -AAATACAAACGT
1 AAAATGCAAATGT
27929 AAAAATGCAAAAATGT
1 -AAAATGC--AAATGT
27945 AAAATGCAAATGT
1 AAAATGCAAATGT
27958 AAA
1 AAA
27961 TATGTGAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
12 9 0.26
13 9 0.26
14 5 0.14
15 7 0.20
16 5 0.14
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.19
Consensus pattern (13 bp):
AAAATGCAAATGT
Found at i:29531 original size:22 final size:23
Alignment explanation
Indices: 29504--29560 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
29494 AATACTTGAA
29504 AATAAAATAAAACAT-TAACAAAT
1 AATAAAATAAAACATATAA-AAAT
*
29527 -ATAAAATAATACATATAAAAAT
1 AATAAAATAAAACATATAAAAAT
*
29549 AATAATATAAAA
1 AATAAAATAAAA
29561 ATTTGAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (23 bp):
AATAAAATAAAACATATAAAAAT
Found at i:29544 original size:14 final size:13
Alignment explanation
Indices: 29524--29560 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 13
29514 AACATTAACA
29524 AATATAAAATAAT
1 AATATAAAATAAT
29537 ACATATAAAAATAAT
1 A-ATAT-AAAATAAT
29552 AATATAAAA
1 AATATAAAA
29561 ATTTGAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.23
14 8 0.36
15 9 0.41
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (13 bp):
AATATAAAATAAT
Found at i:29561 original size:14 final size:14
Alignment explanation
Indices: 29524--29562 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
29514 AACATTAACA
29524 AATAT-AAAATAAT
1 AATATAAAAATAAT
29537 ACATATAAAAATAAT
1 A-ATATAAAAATAAT
29552 AATATAAAAAT
1 AATATAAAAAT
29563 TTGAATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 1 0.04
14 14 0.58
15 9 0.38
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (14 bp):
AATATAAAAATAAT
Found at i:36577 original size:24 final size:23
Alignment explanation
Indices: 36548--36603 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
36538 TAAAAGAATC
36548 CAAGAAGACACGCCACCAAAGAAA
1 CAAGAAGACACGCCACCAAAG-AA
**
36572 CAAGAAGATGCGCCACCAAAGAA
1 CAAGAAGACACGCCACCAAAGAA
*
36595 CAAAAAGAC
1 CAAGAAGAC
36604 GAATCTTCGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.54, C:0.27, G:0.18, T:0.02
Consensus pattern (23 bp):
CAAGAAGACACGCCACCAAAGAA
Done.