Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000596.1 Hibiscus syriacus cultivar Beakdansim tig00001152_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: 42868
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:113 original size:26 final size:26
Alignment explanation
Indices: 8--106 Score: 118
Period size: 26 Copynumber: 4.0 Consensus size: 26
1 CATTAAG
*
8 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCCATAAATGAAAT
34 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATAAATGAAAT
* * * *
60 GGATGAAAGGGT-ACATTAATG----
1 GCATGAAAGGATGCCATAAATGAAAT
81 GCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATAAATGAAAT
107 TAATGAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
21 10 0.17
22 7 0.12
25 7 0.12
26 35 0.59
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.20
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAAATGAAAT
Found at i:6248 original size:17 final size:17
Alignment explanation
Indices: 6226--6264 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
6216 TGTGCAAGTA
*
6226 GTATCGATGTAGATAGG
1 GTATCGATGCAGATAGG
6243 GTATCGATGCAGATAGG
1 GTATCGATGCAGATAGG
6260 GTATC
1 GTATC
6265 AATACTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.33, T:0.28
Consensus pattern (17 bp):
GTATCGATGCAGATAGG
Found at i:6422 original size:20 final size:20
Alignment explanation
Indices: 6394--6448 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
6384 TACAATAGTA
*
6394 TAGAAGTATCGATACAGTGG
1 TAGAGGTATCGATACAGTGG
6414 TAGAGGTATCGATACAGTGG
1 TAGAGGTATCGATACAGTGG
6434 TAGAGGTATCGATAC
1 TAGAGGTATCGATAC
6449 TATTGAGCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.25
Consensus pattern (20 bp):
TAGAGGTATCGATACAGTGG
Found at i:6901 original size:46 final size:46
Alignment explanation
Indices: 6843--7018 Score: 275
Period size: 46 Copynumber: 3.8 Consensus size: 46
6833 AACTTCTCTA
* *
6843 AAATGA-ATCCATAAATGAAATACATGAAAGGATGCATTAAGGGATG
1 AAATGATA-CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATG
6889 AAATGATACCATAAATGAAATGCATGAAAGGATGCATTAAGGCATG
1 AAATGATACCATAAATGAAATGCATGAAAGGATGCATTAAGGCATG
*
6935 AAAGGATACCATAAATGAAATGCATGAAAGGATGCATTAAGGCATG
1 AAATGATACCATAAATGAAATGCATGAAAGGATGCATTAAGGCATG
* *
6981 -AATGGATGCCATAAATGAAATGCATGAAAGTATGCATT
1 AAAT-GATACCATAAATGAAATGCATGAAAGGATGCATT
7019 GCATGAAAGT
Statistics
Matches: 122, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
45 2 0.02
46 119 0.98
47 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.22
Consensus pattern (46 bp):
AAATGATACCATAAATGAAATGCATGAAAGGATGCATTAAGGCATG
Found at i:6961 original size:26 final size:25
Alignment explanation
Indices: 6897--7010 Score: 95
Period size: 20 Copynumber: 4.9 Consensus size: 25
6887 TGAAATGATA
6897 CCATAAATGAAATGCATGAAAGGAT
1 CCATAAATGAAATGCATGAAAGGAT
* *
6922 GCAT---T--AAGGCATGAAAGGAT
1 CCATAAATGAAATGCATGAAAGGAT
6942 ACCATAAATGAAATGCATGAAAGGAT
1 -CCATAAATGAAATGCATGAAAGGAT
* * *
6968 GCAT---T--AAGGCATGAATGGAT
1 CCATAAATGAAATGCATGAAAGGAT
6988 GCCATAAATGAAATGCATGAAAG
1 -CCATAAATGAAATGCATGAAAG
7011 TATGCATTGC
Statistics
Matches: 67, Mismatches: 10, Indels: 23
0.67 0.10 0.23
Matches are distributed among these distances:
20 27 0.40
21 6 0.09
22 2 0.03
24 2 0.03
25 6 0.09
26 24 0.36
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.20
Consensus pattern (25 bp):
CCATAAATGAAATGCATGAAAGGAT
Found at i:7023 original size:17 final size:17
Alignment explanation
Indices: 7001--7035 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6991 ATAAATGAAA
7001 TGCATGAAAGTATGCAT
1 TGCATGAAAGTATGCAT
7018 TGCATGAAAGTATGCAT
1 TGCATGAAAGTATGCAT
7035 T
1 T
7036 AAGGCATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (17 bp):
TGCATGAAAGTATGCAT
Found at i:7023 original size:109 final size:110
Alignment explanation
Indices: 6909--7111 Score: 338
Period size: 109 Copynumber: 1.9 Consensus size: 110
6899 ATAAATGAAA
6909 TGCATGAAAGGATGCATTAAGGCATGAAAGGATACCATAAATGAAATGCAT-GAAAGGATGCATT
1 TGCATGAAAGGATGCATTAAGGCATGAAAGGATACCATAAATGAAATGC-TCGAAAGGATGCATT
*
6973 -AAGGCATGAATGGATGCCATAAATGAAATGCATGAAAGTATGCAT
65 AAAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGTATGCAT
* * *
7018 TGCATGAAAGTATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGCTCGAAAGGGTGCATTA
1 TGCATGAAAGGATGCATTAAGGCATGAAAGGATACCATAAATGAAATGCTCGAAAGGATGCATTA
*
7083 AAGGCATGAAAGGATGCGATAAATGAAAT
66 AAGGCATGAAAGGATGCCATAAATGAAAT
7112 TAATGAATAT
Statistics
Matches: 87, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
108 1 0.01
109 59 0.68
110 27 0.31
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.22
Consensus pattern (110 bp):
TGCATGAAAGGATGCATTAAGGCATGAAAGGATACCATAAATGAAATGCTCGAAAGGATGCATTA
AAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGTATGCAT
Found at i:7080 original size:63 final size:63
Alignment explanation
Indices: 6955--7099 Score: 202
Period size: 63 Copynumber: 2.2 Consensus size: 63
6945 ATAAATGAAA
* *
6955 TGCATGAAAGGATGCATTAAGGCATGAATGGATGCCATAAATGAAATGCATGAAAGTATGCAT
1 TGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCAT
* *
7018 TGCATGAAAGTATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGC-TCGAAAGGGTGCAT
1 TGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGCAT-GAAAGGATGCAT
7081 TAAAGGCATGAAAGGATGC
1 T----GCATGAAAGGATGC
7100 GATAAATGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
62 1 0.01
63 58 0.81
67 13 0.18
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (63 bp):
TGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCAT
Found at i:7862 original size:19 final size:18
Alignment explanation
Indices: 7838--7878 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
7828 TGGGCCCGAT
*
7838 TTTATAATATTAATAATAA
1 TTTATAATAATAATAAT-A
*
7857 TTTATACTAATAATAATA
1 TTTATAATAATAATAATA
7875 TTTA
1 TTTA
7879 ATGGTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATAATAATAATAATA
Found at i:8207 original size:42 final size:42
Alignment explanation
Indices: 8138--8293 Score: 206
Period size: 42 Copynumber: 3.7 Consensus size: 42
8128 TGACCCAAGG
*
8138 TGATGCTGATCCAACTCCTTATGTGATGGACGAGTGAAATGA
1 TGATGCTGAACCAACTCCTTATGTGATGGACGAGTGAAATGA
* * *
8180 TAATGTTGAACCAACTCCTTATGTGATGGACGAGTGGAATGA
1 TGATGCTGAACCAACTCCTTATGTGATGGACGAGTGAAATGA
* * * **
8222 TGATGCTGATCCAACTCCTTATATGATGGACAAGCAAAATGA
1 TGATGCTGAACCAACTCCTTATGTGATGGACGAGTGAAATGA
*
8264 TGATGCT-AATCCAACTCCTTATGCGATGGA
1 TGATGCTGAA-CCAACTCCTTATGTGATGGA
8294 TGAGGCAAGG
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 1 0.01
42 97 0.99
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (42 bp):
TGATGCTGAACCAACTCCTTATGTGATGGACGAGTGAAATGA
Found at i:8249 original size:84 final size:84
Alignment explanation
Indices: 8138--8293 Score: 233
Period size: 84 Copynumber: 1.9 Consensus size: 84
8128 TGACCCAAGG
* * ** *
8138 TGATGCTGATCCAACTCCTTATGTGATGGACGAGTGAAATGATAATGTTGAA-CCAACTCCTTAT
1 TGATGCTGATCCAACTCCTTATATGATGGACAAGCAAAATGATAATGCT-AATCCAACTCCTTAT
*
8202 GTGATGGACGAGTGGAATGA
65 GCGATGGACGAGTGGAATGA
*
8222 TGATGCTGATCCAACTCCTTATATGATGGACAAGCAAAATGATGATGCTAATCCAACTCCTTATG
1 TGATGCTGATCCAACTCCTTATATGATGGACAAGCAAAATGATAATGCTAATCCAACTCCTTATG
8287 CGATGGA
66 CGATGGA
8294 TGAGGCAAGG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
83 2 0.03
84 62 0.97
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (84 bp):
TGATGCTGATCCAACTCCTTATATGATGGACAAGCAAAATGATAATGCTAATCCAACTCCTTATG
CGATGGACGAGTGGAATGA
Found at i:8609 original size:203 final size:202
Alignment explanation
Indices: 8230--8657 Score: 508
Period size: 203 Copynumber: 2.1 Consensus size: 202
8220 GATGATGCTG
* * *
8230 ATCCAACTCCTTATATGATGG-A-CAAGCAAAATGATGATGCTAATCCAACTCCTTATGCGATGG
1 ATCCACCTCCTTCTATGATGGAATCAAACAAAATGATGATGCTAATCCAACTCCTTATGCGATGG
* * * * * **
8293 ATGAGGCAAGGTCGATGATTTTTCAACTTCTTATGTGATGGAATCGAGCTGAGGCTGAACAAGTT
66 ATGAGCCAAGATCGATGATTTCTCAACTCCTTATATGATGGAATCGAGCCAAGGCTGAACAAGTT
* * * *
8358 CTTCTCATTATGAACTTCTTCTTCCTCATCGGATGAGTTCTTCTCATTATGAACA-CTACACTGG
131 CTTCTCATTATGAAATTATTATTCCCCATCGGATGAGTTCTTCTCATTATGAA-ATCTACACTGG
* *
8422 AAGTGTTG
195 AAATGTTA
* * * * * *
8430 ATCCACCTTCTTCTGTGATTGAATCAAACAAAGTGATGATGTTGATCCAACT-CTATATGCGATG
1 ATCCACCTCCTTCTATGATGGAATCAAACAAAATGATGATGCTAATCCAACTCCT-TATGCGATG
* * * * *
8494 GATGAGCCAAGTATTGGTGCTGTTCT-AACTCCTTATATGATGGAATTGAGCCAAGGTTGAACAA
65 GATGAGCCAAG-ATCGATGAT-TTCTCAACTCCTTATATGATGGAATCGAGCCAAGGCTGAACAA
* *
8558 GTTCTTCTCATTATGAAATTATTATTCCCCAT-GAGATGAGTTCTTCTCATTATGAAATCTCCAT
128 GTTCTTCTCATTATGAAATTATTATTCCCCATCG-GATGAGTTCTTCTCATTATGAAATCTACAC
8622 TGGAAATGTTA
192 TGGAAATGTTA
8633 ATCCACCTCCTTCTATGATGGAATC
1 ATCCACCTCCTTCTATGATGGAATC
8658 GAACCTAGGT
Statistics
Matches: 189, Mismatches: 32, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
200 16 0.08
201 3 0.02
202 45 0.24
203 122 0.65
204 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (202 bp):
ATCCACCTCCTTCTATGATGGAATCAAACAAAATGATGATGCTAATCCAACTCCTTATGCGATGG
ATGAGCCAAGATCGATGATTTCTCAACTCCTTATATGATGGAATCGAGCCAAGGCTGAACAAGTT
CTTCTCATTATGAAATTATTATTCCCCATCGGATGAGTTCTTCTCATTATGAAATCTACACTGGA
AATGTTA
Found at i:8806 original size:118 final size:118
Alignment explanation
Indices: 8522--9010 Score: 472
Period size: 118 Copynumber: 4.1 Consensus size: 118
8512 GCTGTTCTAA
* * * * * *
8522 CTCCTTATATGATGGAATTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAAATTATTATTCCC
1 CTCCTTCTATGATGGAATCGAGCCAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT-CTCCC
* *
8587 -CAT-GAGATGAGTTCTTCTCATTATGAAA-TCT-CCATTGGAAATGTTAATCCAC
65 TCATCG-GATGAGTTCTTCTCATTAT-AAACTCTCCCATTGGAAATATTGATCCAC
* * * * ** *
8639 CTCCTTCTATGATGGAATCGAACCTAGGTTTAATAGTTTATTCTCATTATGAACTTCTTCTCCCT
1 CTCCTTCTATGATGGAATCGAGCCAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCT
* *
8704 CATCGGATGAGTTCTTCTCATTATAAACTTTCCCATTGGAAATATTGATCCAT
66 CATCGGATGAGTTCTTCTCATTATAAACTCTCCCATTGGAAATATTGATCCAC
* * * * *
8757 CTCCTTCTGTGATGGAATCGAGCCAAGCTTGAACAAATTCTTCTTATTATGAACTTCTTTTGCCT
1 CTCCTTCTATGATGGAATCGAGCCAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCT
* * * * * *
8822 CGTCGGATGGGTTATTCTCATTATGAACTCTCCCATTGGAAACGA-CGATCCAC
66 CATCGGATGAGTTCTTCTCATTATAAACTCTCCCATTGGAAA-TATTGATCCAC
* * ** * *
8875 CTCCTTC-AGTGATGGATTAGAGTAAAAGTTCGAACAAATTCTTCTCATTATGAACTTCTTCTTT
1 CTCCTTCTA-TGATGGAATCGAGCCAAGGTT-GAACAAATTCTTCTCATTATGAACTTCTTC-TC
* * * * * *
8939 TCTCATCAGATGAGTTCTTATCATTATGAGCTC-CTCCATTGGAAATGA-TGATTCAC
63 CCTCATCGGATGAGTTCTTCTCATTATAAACTCTC-CCATTGGAAAT-ATTGATCCAC
*
8995 CTCATTCTATGATGGA
1 CTCCTTCTATGATGGA
9011 TTTGAATCTG
Statistics
Matches: 304, Mismatches: 57, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
116 7 0.02
117 72 0.24
118 137 0.45
119 30 0.10
120 57 0.19
121 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (118 bp):
CTCCTTCTATGATGGAATCGAGCCAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTCCCT
CATCGGATGAGTTCTTCTCATTATAAACTCTCCCATTGGAAATATTGATCCAC
Found at i:11527 original size:20 final size:19
Alignment explanation
Indices: 11502--11542 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
11492 TCTTTTCATA
11502 TTTTCATATTTTC-TTCTTTT
1 TTTTCAT-TTTTCATT-TTTT
11522 TTTTCATTTTTCATTTTTT
1 TTTTCATTTTTCATTTTTT
11541 TT
1 TT
11543 CTTTTCTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCATTTTTCATTTTTT
Found at i:11555 original size:28 final size:29
Alignment explanation
Indices: 11489--11555 Score: 95
Period size: 26 Copynumber: 2.4 Consensus size: 29
11479 TTCCTTCATT
11489 TTTTCTTTTCATATTTTCATATTTTCTTC
1 TTTTCTTTTCATATTTTCATATTTTCTTC
*
11518 TTTT-TTTTCAT-TTTTCAT-TTTTTTTC
1 TTTTCTTTTCATATTTTCATATTTTCTTC
11544 TTTTCTTCTTCA
1 TTTTCTT-TTCA
11556 GATATAATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 11 0.31
27 9 0.26
28 11 0.31
29 4 0.11
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTTCTTTTCATATTTTCATATTTTCTTC
Found at i:17754 original size:17 final size:17
Alignment explanation
Indices: 17732--17772 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
17722 TTTAAATCAT
*
17732 CTAGTTCATT-ATTTAAA
1 CTAGTTCATTCA-TCAAA
17749 CTAGTTCATTCATCAAA
1 CTAGTTCATTCATCAAA
17766 CTAGTTC
1 CTAGTTC
17773 TTTTATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (17 bp):
CTAGTTCATTCATCAAA
Found at i:27868 original size:2 final size:2
Alignment explanation
Indices: 27863--28306 Score: 171
Period size: 2 Copynumber: 226.5 Consensus size: 2
27853 CTTATGTATG
* *
27863 TA TA TA TA TA TA TA TA TA TA -A GTA TA TG TG 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
* * * *
27905 TA TA -A GTA TA TG TG TA TA TA TA TA TA TA TA CT- TA TG TA TA CA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
27947 TA -A TA T- TA -A TA TA TA TA TA TA TA TA T- TA T- TT TA CTT TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * *
27985 TA TT TT TT TA -A AA TA TA AA GTA TGA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA
* * * * * * * * * * *
28028 TA TA TA CA TG CA CCA TA CGA CA TCA TA CA TA TG TA CA TA AA TG
1 TA TA TA TA TA TA -TA TA -TA TA T-A TA TA TA TA TA TA TA TA TA
*
28071 CA 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
* *
28113 TA TA TA TA TA TA TA TG TA TA TA T- TA TA TA TA TG TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
28153 TG TA CA TA TA TA CA TA TA -A AA CA TA TA TCA T- TGA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A T-A TA TA
** * * * *
28194 TA -A T- TA CG TA TA TA CT- TA T- TG TA T- TA CA TA TA TA CA CA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
28232 TA CA T- TA TA CA TA TG TA TA TA CA TA CA TA TA TA TA CT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
*
28273 TA TA TA TA -A TA T- TA -A TA TC TA TCA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA T
28307 GGTTGTTTTA
Statistics
Matches: 332, Mismatches: 72, Indels: 76
0.69 0.15 0.16
Matches are distributed among these distances:
1 24 0.07
2 289 0.87
3 19 0.06
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:29554 original size:16 final size:16
Alignment explanation
Indices: 29533--29571 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29523 GTGCGGTCGT
*
29533 AATTTTAGAATCTTTA
1 AATTTTAAAATCTTTA
*
29549 AATTTTAAAATTTTTA
1 AATTTTAAAATCTTTA
29565 ATATTTT
1 A-ATTTT
29572 TCATTGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (16 bp):
AATTTTAAAATCTTTA
Found at i:31050 original size:42 final size:41
Alignment explanation
Indices: 31004--31082 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
30994 AATTATTAGA
* * *
31004 TTATATAA-AATTAAATTAAATATTTTAAGTTTAATTTATTTT
1 TTATATAATAATT-AATT-AATAATTTAAATATAATTTATTTT
31046 TTATATAATAATTAATTAATAATTTAAATATAATTTA
1 TTATATAATAATTAATTAATAATTTAAATATAATTTA
31083 ACATAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 17 0.52
42 12 0.36
43 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (41 bp):
TTATATAATAATTAATTAATAATTTAAATATAATTTATTTT
Found at i:31566 original size:2 final size:2
Alignment explanation
Indices: 31561--31731 Score: 265
Period size: 2 Copynumber: 85.5 Consensus size: 2
31551 ATACACACAC
31561 AT AT 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 AT AT
31603 AT AT 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 AT AT
31645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * * *
31687 GT AT TT AT AT AT AT AT ACT -T AT GT AT AC AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
31729 AT A
1 AT A
31732 CTTGTGTACA
Statistics
Matches: 155, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
1 2 0.01
2 151 0.97
3 2 0.01
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35850 original size:29 final size:29
Alignment explanation
Indices: 35814--35901 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
35804 CATTTTACAG
* * *
35814 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
*
35843 AAATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
* *
35872 AAATAACACCCATTTTGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTCCCA
35901 A
1 A
35902 CGGTCAACGG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.31
Consensus pattern (29 bp):
AAATAGCACCCTTTTTGAATTAATTCCCA
Found at i:35931 original size:13 final size:13
Alignment explanation
Indices: 35913--35951 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
35903 GGTCAACGGT
35913 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
35926 CGGGTCGAGTCAA
1 CGGGTCGGGTCAA
* *
35939 CTGGTAGGGTCAA
1 CGGGTCGGGTCAA
35952 AACTAGTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.41, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Done.