Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000717.1 Hibiscus syriacus cultivar Beakdansim tig00001389_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: 73196
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6658 original size:20 final size:19
Alignment explanation
Indices: 6630--6684 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
6620 GCATACATGC
*
6630 ATTTACATTTTATTTGTGTT
1 ATTTGCATTTTATTTGT-TT
*
6650 ATTTGCATTATTA-TTATTT
1 ATTTGCATT-TTATTTGTTT
6669 ATTTGGCATTTT-TTTG
1 ATTT-GCATTTTATTTG
6685 CATTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 10 0.34
20 16 0.55
21 3 0.10
ACGTcount: A:0.20, C:0.05, G:0.11, T:0.64
Consensus pattern (19 bp):
ATTTGCATTTTATTTGTTT
Found at i:14893 original size:137 final size:137
Alignment explanation
Indices: 14642--15416 Score: 868
Period size: 137 Copynumber: 5.8 Consensus size: 137
14632 TATTTTAGGA
* * * *
14642 AACATCACCCTTAGATAACCATACGTCCTCATCACGAAGGAACCGTATTATCTCAAATATCTTTA
1 AACATCATCCTTAGATAACCAAACGTCCTCATCATGAAGGAACCGTGTTATCTCAAATATCTTTA
* * *
14707 AAGATGGCTAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCTTCATCACG
66 AAGATGGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACA
*
14772 AAGGAGG
131 AAGGAGC
* *
14779 AACATCATCCTTAGATAACCAGACGTCCTCATCATGAAGGAACCGTGCTATCTCAAATATCTTTA
1 AACATCATCCTTAGATAACCAAACGTCCTCATCATGAAGGAACCGTGTTATCTCAAATATCTTTA
* * * * *
14844 AAGATGGCCAAACATCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCACATCACA
66 AAGATGGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACA
14909 AAGGAGC
131 AAGGAGC
* *
14916 AACATCATCCTTAGATAACCAAAAGTCCTCATCATGAAAGAACCGTGTTATCTCAAATATCTTTA
1 AACATCATCCTTAGATAACCAAACGTCCTCATCATGAAGGAACCGTGTTATCTCAAATATCTTTA
* * *
14981 AAGATGGCCAGACGTCTTTATCACGAAGGAATAATGTCATCCACCGATCAGAACT-C-C-T----
66 AAGATGGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACA
15039 -------
131 AAGGAGC
** * * * *
15039 --CATCATCCTTAGATAGGCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATATTTA
1 AACATCATCCTTAGATAACCAAACGTCCTCATCATGAAGGAACCGTGTTATCTCAAATATCTTTA
* * * * *
15102 AAGATGGCCAGACGTCCTCATCACAAAGGAACAATGCCATCCACCGATCAGAACTCCTCATCACG
66 AAGATGGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACA
15167 AAGGAGC
131 AAGGAGC
* * * * * *
15174 AACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTTAAATATATTTA
1 AACATCATCCTTAGATAACCAAACGTCCTCATCATGAAGGAACCGTGTTATCTCAAATATCTTTA
* * ** * * * *
15239 AAGATGACTAGATATCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTTCTCATCACG
66 AAGATGGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACA
15304 AAGGAGTC
131 AAGGAG-C
* * * * *
15312 -ACTTCATTCTTAGATAACCAGACGTCCTCATCACGAAGGAATCGTGTTA--TCAATATTTATCT
1 AACATCATCCTTAGATAACCAAACGTCCTCATCATGAAGGAACCGTGTTATCTCAA-A--TATCT
* * * * * * *
15374 CTAAAAATGACCAAATGTCCTCAACACGAAGGAACAATGTCAT
63 TTAAAGATGGCCAGACGTCTTCATCACGAAGGAACAATGTCAT
15417 ACACCAGTTT
Statistics
Matches: 559, Mismatches: 59, Indels: 39
0.85 0.09 0.06
Matches are distributed among these distances:
121 106 0.19
122 1 0.00
123 1 0.00
124 1 0.00
134 1 0.00
135 4 0.01
136 2 0.00
137 401 0.72
138 42 0.08
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (137 bp):
AACATCATCCTTAGATAACCAAACGTCCTCATCATGAAGGAACCGTGTTATCTCAAATATCTTTA
AAGATGGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACA
AAGGAGC
Found at i:15125 original size:258 final size:258
Alignment explanation
Indices: 14781--15301 Score: 781
Period size: 258 Copynumber: 2.0 Consensus size: 258
14771 GAAGGAGGAA
* *
14781 CATCATCCTTAGATAACCAGACGTCCTCATCATGAAGGAACCGTGCTATCTCAAATATCTTTAAA
1 CATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGCTATCTCAAATATATTTAAA
* * **
14846 GATGGCCAAACATCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCACATCACAAA
66 GATGGCCAAACATCCTCATCACAAAGGAACAATGCCATCCACCGATCAGAACTCCACATCACAAA
*
14911 GGAGCAACATCATCCTTAGATAACCAAAAGTCCTCATCATGAAAGAACCGTGTTATCTCAAATAT
131 GGAGCAACATCATCCTTAGATAACCAAAAGTCCTCATCACGAAAGAACCGTGTTATCTCAAATAT
* * * * * *
14976 CTTTAAAGATGGCCAGACGTCTTTATCACGAAGGAATAATGTCATCCACCGATCAGAACTCCT
196 ATTTAAAGATGACCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCT
** * *
15039 CATCATCCTTAGATAGGCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATATTTAAA
1 CATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGCTATCTCAAATATATTTAAA
* * * *
15104 GATGGCCAGACGTCCTCATCACAAAGGAACAATGCCATCCACCGATCAGAACTCCTCATCACGAA
66 GATGGCCAAACATCCTCATCACAAAGGAACAATGCCATCCACCGATCAGAACTCCACATCACAAA
* * * * *
15169 GGAGCAACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTTAAATAT
131 GGAGCAACATCATCCTTAGATAACCAAAAGTCCTCATCACGAAAGAACCGTGTTATCTCAAATAT
* * *
15234 ATTTAAAGATGACTAGATATCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTTCT
196 ATTTAAAGATGACCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCT
15297 CATCA
1 CATCA
15302 CGAAGGAGTC
Statistics
Matches: 234, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
258 234 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (258 bp):
CATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGCTATCTCAAATATATTTAAA
GATGGCCAAACATCCTCATCACAAAGGAACAATGCCATCCACCGATCAGAACTCCACATCACAAA
GGAGCAACATCATCCTTAGATAACCAAAAGTCCTCATCACGAAAGAACCGTGTTATCTCAAATAT
ATTTAAAGATGACCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCT
Found at i:15132 original size:121 final size:121
Alignment explanation
Indices: 14918--15301 Score: 462
Period size: 121 Copynumber: 3.0 Consensus size: 121
14908 AAAGGAGCAA
* * * * * *
14918 CATCATCCTTAGATAACCAAAAGTCCTCATCATGAAAGAACCGTGTTATCTCAAATATCTTTAAA
1 CATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATATTTAAA
* * *
14983 GATGGCCAGACGTCTTTATCACGAAGGAATAATGTCATCCACCGATCAGAACTCCT
66 GATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCT
*
15039 CATCATCCTTAGATAGGCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATATTTAAA
1 CATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATATTTAAA
* *
15104 GATGGCCAGACGTCCTCATCACAAAGGAACAATGCCATCCACCGATCAGAACTCCTCAT
66 GATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACT-C-C-T
*
15163 CACGAAGGAGCAACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTT
1 -------------CATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTC
* * **
15228 AAATATATTTAAAGATGACTAGATATCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAAC
53 AAATATATTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAAC
*
15293 TTCT
118 TCCT
15297 CATCA
1 CATCA
15302 CGAAGGAGTC
Statistics
Matches: 226, Mismatches: 21, Indels: 32
0.81 0.08 0.11
Matches are distributed among these distances:
121 111 0.49
122 1 0.00
123 1 0.00
124 1 0.00
134 1 0.00
135 1 0.00
137 110 0.49
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (121 bp):
CATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATATTTAAA
GATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCT
Found at i:15584 original size:3 final size:3
Alignment explanation
Indices: 15576--15603 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15566 TGTCACATAC
15576 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
15604 AATAATTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:16710 original size:19 final size:18
Alignment explanation
Indices: 16680--16715 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16670 TATTTTACGC
16680 ATTTTAATTTTAATTTGA
1 ATTTTAATTTTAATTTGA
*
16698 ATTTTAGATTTTATTTTG
1 ATTTTA-ATTTTAATTTG
16716 TTATGTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (18 bp):
ATTTTAATTTTAATTTGA
Found at i:22665 original size:40 final size:40
Alignment explanation
Indices: 22593--22716 Score: 151
Period size: 42 Copynumber: 3.0 Consensus size: 40
22583 TCTTTGTCAT
*
22593 TGGGTGTTAGTGTGAGTTTTTGTTGTGGTTTGGGGTATGTA
1 TGGGTGTTTGTGTGAG-TTTTGTTGTGGTTTGGGGTATGTA
*
22634 TGGGTGTTTGTGTGAGTTTTGTTGTGGTTTGGGGTATATATA
1 TGGGTGTTTGTGTGAGTTTTGTTGTGGTTTGGGG--TATGTA
* * * *
22676 TGAGTGTTTATGTGTGTGTTTGTTGT-GTTTGAGGTATGTA
1 TGGGTGTTTGTGTGAGT-TTTGTTGTGGTTTGGGGTATGTA
22716 T
1 T
22717 TATTTGTTGC
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
40 24 0.33
41 15 0.21
42 26 0.36
43 8 0.11
ACGTcount: A:0.11, C:0.00, G:0.38, T:0.51
Consensus pattern (40 bp):
TGGGTGTTTGTGTGAGTTTTGTTGTGGTTTGGGGTATGTA
Found at i:24825 original size:31 final size:31
Alignment explanation
Indices: 24787--24893 Score: 205
Period size: 31 Copynumber: 3.5 Consensus size: 31
24777 TCTCTAAAAT
24787 TGTGGCTGCAACCACAGCATCAAGGGTTTAA
1 TGTGGCTGCAACCACAGCATCAAGGGTTTAA
24818 TGTGGCTGCAACCACAGCATCAAGGGTTTAA
1 TGTGGCTGCAACCACAGCATCAAGGGTTTAA
*
24849 TGTGGCTGCAACCACAACATCAAGGGTTTAA
1 TGTGGCTGCAACCACAGCATCAAGGGTTTAA
24880 TGTGGCTGCAACCA
1 TGTGGCTGCAACCA
24894 TGATTAGTTT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.22
Consensus pattern (31 bp):
TGTGGCTGCAACCACAGCATCAAGGGTTTAA
Found at i:26329 original size:40 final size:41
Alignment explanation
Indices: 26257--26333 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 41
26247 TCTTTGTCAT
26257 TGGGTGTTAGTGTGAGTTTTTGTTGTGGTTTGGGGTATGTA
1 TGGGTGTTAGTGTGAGTTTTTGTTGTGGTTTGGGGTATGTA
*
26298 TGGGTGTTTGTGTGAG-TTTTGTTGTGGTTTGGGGTA
1 TGGGTGTTAGTGTGAGTTTTTGTTGTGGTTTGGGGTA
26334 ATGTGTGTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 20 0.57
41 15 0.43
ACGTcount: A:0.08, C:0.00, G:0.43, T:0.49
Consensus pattern (41 bp):
TGGGTGTTAGTGTGAGTTTTTGTTGTGGTTTGGGGTATGTA
Found at i:26354 original size:27 final size:29
Alignment explanation
Indices: 26306--26360 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
26296 TATGGGTGTT
*
26306 TGTGTGAGTTTTGTTGTGGTTTGGGGTAA
1 TGTGTGAGTTTTGTTGTGGTTTGAGGTAA
*
26335 TGTGTGTG-TTTGTTGT-GTTTGAGGTA
1 TGTGTGAGTTTTGTTGTGGTTTGAGGTA
26361 TGTATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.38
28 8 0.33
29 7 0.29
ACGTcount: A:0.09, C:0.00, G:0.40, T:0.51
Consensus pattern (29 bp):
TGTGTGAGTTTTGTTGTGGTTTGAGGTAA
Found at i:28937 original size:26 final size:27
Alignment explanation
Indices: 28878--28943 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
28868 ATTTAGTATT
*
28878 TAATTTTTAAAAATATAAATGAATAAA
1 TAATTATTAAAAATATAAATGAATAAA
*
28905 TAGTTATTAAAAAT-TAAAT-AA-AACTA
1 TAATTATTAAAAATATAAATGAATAA--A
28931 TAATTATTAAAAA
1 TAATTATTAAAAA
28944 CAATCATTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 2 0.06
25 2 0.06
26 18 0.53
27 12 0.35
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (27 bp):
TAATTATTAAAAATATAAATGAATAAA
Found at i:30825 original size:17 final size:17
Alignment explanation
Indices: 30786--30844 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
30776 AAGTATGTTG
* *
30786 TTCATTAAAGAATGCAT
1 TTCATTTAAGAATGTAT
* *
30803 TGCATTTAAGCATGTAT
1 TTCATTTAAGAATGTAT
* * *
30820 TTCATTTAGGGATGTAG
1 TTCATTTAAGAATGTAT
30837 TTCATTTA
1 TTCATTTA
30845 TGGATCTATT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (17 bp):
TTCATTTAAGAATGTAT
Found at i:30849 original size:17 final size:17
Alignment explanation
Indices: 30814--30849 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30804 GCATTTAAGC
*
30814 ATGTATTTCATTTAGGG
1 ATGTAGTTCATTTAGGG
*
30831 ATGTAGTTCATTTATGG
1 ATGTAGTTCATTTAGGG
30848 AT
1 AT
30850 CTATTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (17 bp):
ATGTAGTTCATTTAGGG
Found at i:30926 original size:17 final size:17
Alignment explanation
Indices: 30902--30951 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
30892 TGAAGAAAGT
*
30902 TAGTTCATTAATTAAAT
1 TAGTTCATTAATTAAAC
* * *
30919 TGGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
30936 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
30952 ATAACTCTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:31946 original size:2 final size:2
Alignment explanation
Indices: 31939--31991 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
31929 CCAAACATAA
31939 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
31981 AT AT AT AT AT A
1 AT AT AT AT AT A
31992 CCATTTCCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32447 original size:23 final size:23
Alignment explanation
Indices: 32421--32489 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
32411 CACCACAGCT
* *
32421 CGTATAAATGCATCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
32444 CGTAGAATTGCACCTAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
32467 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
32490 TATAAGATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:32772 original size:30 final size:29
Alignment explanation
Indices: 32719--32777 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
32709 TGTAAACATA
* *
32719 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
32749 TCACATATACATTTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
32778 GTAAATTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:38276 original size:17 final size:17
Alignment explanation
Indices: 38234--38276 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
38224 AAGTATGTTG
*
38234 TTCATTAAAGCATGCAT
1 TTCATTTAAGCATGCAT
*
38251 TTGCATTTAAGCATGTAT
1 TT-CATTTAAGCATGCAT
38269 TTCATTTA
1 TTCATTTA
38277 GGGAAGTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (17 bp):
TTCATTTAAGCATGCAT
Found at i:38401 original size:17 final size:17
Alignment explanation
Indices: 38351--38403 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
38341 TGAAGAAAGT
*
38351 TAGTTCGTTAATTAAAC
1 TAGTTCATTAATTAAAC
* * *
38368 TGGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
38385 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
38402 TA
1 TA
38404 ACTCTTAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:42174 original size:15 final size:15
Alignment explanation
Indices: 42093--42181 Score: 60
Period size: 15 Copynumber: 5.7 Consensus size: 15
42083 TCCTAAAAAC
42093 TAATATTTTATAAATAT
1 TAATATTTTAT-AAT-T
42110 T-ATATTTTAATTAATT
1 TAATATTTT-A-TAATT
42126 TAGAT-TTTTAACTAATT
1 TA-ATATTTT-A-TAATT
* *
42143 T-ATA-ATTATGTATT
1 TAATATTTTAT-AATT
42157 TAATATTTTATAATT
1 TAATATTTTATAATT
42172 TAATATTTTA
1 TAATATTTTA
42182 CAAATTAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
13 1 0.02
14 5 0.08
15 20 0.34
16 13 0.22
17 17 0.29
18 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (15 bp):
TAATATTTTATAATT
Found at i:42178 original size:22 final size:23
Alignment explanation
Indices: 42111--42179 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 23
42101 TATAAATATT
*
42111 ATATTTTAATTAATTTAGATTTTTA
1 ATATTTT-A-TAATTTAGATATTTA
*
42136 ACTAATTTATAA-TTATG-TATTTA
1 A-TATTTTATAATTTA-GATATTTA
42159 ATATTTTATAATTTA-ATATTT
1 ATATTTTATAATTTAGATATTT
42180 TACAAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
22 14 0.38
23 12 0.32
24 4 0.11
25 2 0.05
26 5 0.14
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (23 bp):
ATATTTTATAATTTAGATATTTA
Found at i:42189 original size:15 final size:15
Alignment explanation
Indices: 42156--42190 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42146 AATTATGTAT
* *
42156 TTAATATTTTATAAT
1 TTAATATTTTACAAA
42171 TTAATATTTTACAAA
1 TTAATATTTTACAAA
42186 TTAAT
1 TTAAT
42191 TTAATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAATATTTTACAAA
Found at i:43975 original size:24 final size:24
Alignment explanation
Indices: 43946--43993 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
43936 TGTATACTAC
*
43946 ATTATTATCCTGCACGCAATACAT
1 ATTATTATCCTGCACACAATACAT
43970 ATTATTATCCTGCACACAATACAT
1 ATTATTATCCTGCACACAATACAT
43994 GCTTTTGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.33
Consensus pattern (24 bp):
ATTATTATCCTGCACACAATACAT
Found at i:46278 original size:2 final size:2
Alignment explanation
Indices: 46271--46302 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46261 ATGTACCAAA
46271 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
46303 TATGTGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46472 original size:15 final size:15
Alignment explanation
Indices: 46448--46481 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
46438 GCAAAAATTA
46448 AAATTATAAAGACTT
1 AAATTATAAAGACTT
*
46463 AAATTCTAAAGACTT
1 AAATTATAAAGACTT
46478 AAAT
1 AAAT
46482 GTAAACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (15 bp):
AAATTATAAAGACTT
Found at i:49221 original size:9 final size:9
Alignment explanation
Indices: 49207--49239 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
49197 GTAGATCATA
49207 TTATTTTAT
1 TTATTTTAT
49216 TTATTTTAT
1 TTATTTTAT
49225 TT-TATTTAT
1 TTAT-TTTAT
49234 TTATTT
1 TTATTT
49240 GAATAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTTTAT
Found at i:49226 original size:14 final size:13
Alignment explanation
Indices: 49207--49239 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
49197 GTAGATCATA
49207 TTATTTTATTTATT
1 TTATTTTATTTA-T
49221 TTATTTTATTTAT
1 TTATTTTATTTAT
49234 TTATTT
1 TTATTT
49240 GAATAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:50400 original size:35 final size:35
Alignment explanation
Indices: 50337--50416 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
50327 AACACAGTCA
*
50337 TCAATTACATTCTAAATCCCAAAATCCAAAATATT
1 TCAATTACATTCTAAATCCCAAAATCCAAAATACT
* *
50372 TCAATTACATTGTAAA-CCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAATCC-CAAAATCCAAAATACT
50407 TCAATTACAT
1 TCAATTACAT
50417 GCCCAACCCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 2 0.05
35 39 0.95
ACGTcount: A:0.44, C:0.23, G:0.01, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAATCCCAAAATCCAAAATACT
Found at i:50430 original size:35 final size:35
Alignment explanation
Indices: 50337--50432 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 35
50327 AACACAGTCA
* * *
50337 TCAATTACATT-CTAAATCCCAAAATCCAAAATATT
1 TCAATTACATTGC-AAACCCCAAATTCCAAAATACT
* *
50372 TCAATTACATTGTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTGCAAACCCCAAATTCCAAAATACT
*
50407 TCAATTACA-TGCCCAACCCCAAATTC
1 TCAATTACATTG-CAAACCCCAAATTC
50433 ATATTCCATT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
34 2 0.04
35 49 0.96
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (35 bp):
TCAATTACATTGCAAACCCCAAATTCCAAAATACT
Found at i:50868 original size:148 final size:143
Alignment explanation
Indices: 50586--50873 Score: 441
Period size: 148 Copynumber: 2.0 Consensus size: 143
50576 AAATACTCAA
** ** *
50586 TTCAGTTTATAAAATAGTTGACTCGGAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGTTTATAAAATAGTTGACTCAAAAAATTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
* * *
50651 GAATTGAATTTTCGAGTTTTTGTTTAAAGTTAATTATAAATATTTATCATATTATAATATTATTT
66 GAATTGAATTTTCGAGTTTCTGTTTAAAGTTAATTATAAATATTTATAATACTATAATATTATTT
50716 GATTCTAATTCAG
131 GATTCTAATTCAG
*
50729 TTCAGTTTATAAAATAGTTTACTCAAAAAATTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGTTTATAAAATAGTTGACTCAAAAAATTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
*
50794 GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
66 -----GAATTGAATTTTCGAGTTTCTGTTTAAAGTTAATTATAAATATTTATAATACTATAATAT
50859 TATTTGATTCTAATT
126 TATTTGATTCTAATT
50874 AAAATAGTTT
Statistics
Matches: 130, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
143 59 0.45
148 71 0.55
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (143 bp):
TTCAGTTTATAAAATAGTTGACTCAAAAAATTTTCAATTTGAGTTTATAAAATTTAAATCAAGTC
GAATTGAATTTTCGAGTTTCTGTTTAAAGTTAATTATAAATATTTATAATACTATAATATTATTT
GATTCTAATTCAG
Found at i:51430 original size:35 final size:36
Alignment explanation
Indices: 51372--51449 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 36
51362 GTTGGGCATG
* *
51372 TAATTGAAGTATTTTTGAAATTTGAGGTTTAGAATA
1 TAATTGAAGCATTTTTGAAATTTGAGGTTTAAAATA
* * *
51408 TAATTGAAGCA-TTTTGGAATTTGGGGTTTAAAATG
1 TAATTGAAGCATTTTTGAAATTTGAGGTTTAAAATA
51443 TAATTGA
1 TAATTGA
51450 TGATTGTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 27 0.73
36 10 0.27
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (36 bp):
TAATTGAAGCATTTTTGAAATTTGAGGTTTAAAATA
Found at i:55447 original size:26 final size:26
Alignment explanation
Indices: 55416--55512 Score: 81
Period size: 26 Copynumber: 3.6 Consensus size: 26
55406 CATAGTTTTT
*
55416 CTAAGCTATTTCTCGTCCTTGCTTTG
1 CTAAGCTATTTCTCATCCTTGCTTTG
55442 CTAAGCT-TTT-TCATTCTCTAATAGCTTTG
1 CTAAGCTATTTCTCA-TC-CT--T-GCTTTG
* * * *
55471 TTAAGCTATTTCTCATTCTGGCTTTT
1 CTAAGCTATTTCTCATCCTTGCTTTG
*
55497 CTAAGCTTTTTCTCAT
1 CTAAGCTATTTCTCAT
55513 ATTCCTTCTC
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
24 2 0.04
25 5 0.09
26 28 0.49
28 1 0.02
29 14 0.25
30 4 0.07
31 3 0.05
ACGTcount: A:0.16, C:0.23, G:0.11, T:0.49
Consensus pattern (26 bp):
CTAAGCTATTTCTCATCCTTGCTTTG
Found at i:55477 original size:55 final size:55
Alignment explanation
Indices: 55400--55508 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 55
55390 GCTTCATCTT
* * * *
55400 TTCTCTCATAGTTTTTCTAAGCTATTTCTCGTCCTTGCTTTGCTAAGCTTTTTCA
1 TTCTCTAATAGTTTGTCTAAGCTATTTCTCATCCTGGCTTTGCTAAGCTTTTTCA
* *
55455 TTCTCTAATAGCTTTGT-TAAGCTATTTCTCATTCTGGCTTTTCTAAGCTTTTTC
1 TTCTCTAATAG-TTTGTCTAAGCTATTTCTCATCCTGGCTTTGCTAAGCTTTTTC
55509 TCATATTCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
55 43 0.91
56 4 0.09
ACGTcount: A:0.16, C:0.22, G:0.11, T:0.51
Consensus pattern (55 bp):
TTCTCTAATAGTTTGTCTAAGCTATTTCTCATCCTGGCTTTGCTAAGCTTTTTCA
Found at i:56673 original size:26 final size:26
Alignment explanation
Indices: 56644--56704 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
56634 TGCTAAGCTA
56644 TTTCTCATTCTGGCTTTTCTAAACCT
1 TTTCTCATTCTGGCTTTTCTAAACCT
56670 TTTCTCATTCTGGCTTTTCTAAACCT
1 TTTCTCATTCTGGCTTTTCTAAACCT
56696 TTTCTCATT
1 TTTCTCATT
56705 TTCCTTCTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.15, C:0.26, G:0.07, T:0.52
Consensus pattern (26 bp):
TTTCTCATTCTGGCTTTTCTAAACCT
Found at i:56673 original size:55 final size:55
Alignment explanation
Indices: 56565--56673 Score: 121
Period size: 55 Copynumber: 2.0 Consensus size: 55
56555 GCTTCACCTT
* * * * * * * *
56565 TTCTCTCATAGCTTTTCTAAGTTATTTTTCGTCCTTGCTTTGTTAAGCTTTTTCA
1 TTCTCTAATAGCTTTGCTAAGCTATTTCTCATCCTGGCTTTGTTAAACCTTTTCA
*
56620 TTCTCTAATAGCTTTGCTAAGCTATTTCTCATTCTGGCTTT-TCTAAACCTTTTC
1 TTCTCTAATAGCTTTGCTAAGCTATTTCTCATCCTGGCTTTGT-TAAACCTTTTC
56674 TCATTCTGGC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
54 1 0.02
55 43 0.98
ACGTcount: A:0.17, C:0.22, G:0.10, T:0.51
Consensus pattern (55 bp):
TTCTCTAATAGCTTTGCTAAGCTATTTCTCATCCTGGCTTTGTTAAACCTTTTCA
Found at i:57691 original size:2 final size:2
Alignment explanation
Indices: 57684--57713 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
57674 TGATAATTCT
57684 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57714 TCTATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:57993 original size:16 final size:16
Alignment explanation
Indices: 57972--58002 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
57962 ATGATACCTC
57972 ACAAAAAATGACTTCT
1 ACAAAAAATGACTTCT
57988 ACAAAAAATGACTTC
1 ACAAAAAATGACTTC
58003 GCGATTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (16 bp):
ACAAAAAATGACTTCT
Done.