Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001521.1 Hibiscus syriacus cultivar Beakdansim tig00002969_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: 57962
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:3122 original size:149 final size:148
Alignment explanation
Indices: 2763--3208 Score: 738
Period size: 149 Copynumber: 3.0 Consensus size: 148
2753 GAGTCGAGGG
* * * * * * *
2763 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTT-TGAGGCACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
* * *
2827 ACTTGGTCCTTAGTATATGTATATGATTCTT-AGGAATGATATGTGGTCCTTATGGACACTATT-
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
2890 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
2909 TCTACGCGGTCCTTCGGG-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
*
2973 CTTGATCCCTAGTATATGTATATGATTCTTAAGGTATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
3038 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
3056 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
3121 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
3186 TATGGCACTACGGTGTAAT
130 TATGGCACTACGGTGCAAT
3205 TCTA
1 TCTA
3209 TGTGCACTTC
Statistics
Matches: 282, Mismatches: 13, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
144 29 0.10
145 37 0.13
146 48 0.17
147 37 0.13
149 131 0.46
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:3446 original size:21 final size:21
Alignment explanation
Indices: 3422--3482 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
3412 ATAAATAATT
*
3422 TGATGATAATGATAGA-GATAA
1 TGATAATAAT-ATAGATGATAA
*
3443 TGATAATAATATATATGATAA
1 TGATAATAATATAGATGATAA
* * *
3464 TGCTAAGAAAATAGATGAT
1 TGATAATAATATAGATGAT
3483 GATATATGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (21 bp):
TGATAATAATATAGATGATAA
Found at i:3488 original size:33 final size:33
Alignment explanation
Indices: 3424--3489 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
3414 AAATAATTTG
*
3424 ATGATAATGATAGAGATAATGATAATAATATAT
1 ATGATAATGATAGAGAAAATGATAATAATATAT
* * *
3457 ATGATAATGCTA-AGAAAATAGATGATGATATAT
1 ATGATAATGATAGAGAAAAT-GATAATAATATAT
3490 GTACATGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGATAATGATAGAGAAAATGATAATAATATAT
Found at i:5949 original size:15 final size:15
Alignment explanation
Indices: 5925--5957 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5915 GAGAGAATTA
5925 TCCAGATTCTTCTTC
1 TCCAGATTCTTCTTC
*
5940 TCCAGCTTCTTCTTC
1 TCCAGATTCTTCTTC
5955 TCC
1 TCC
5958 CCGTAAGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.39, G:0.06, T:0.45
Consensus pattern (15 bp):
TCCAGATTCTTCTTC
Found at i:6547 original size:64 final size:64
Alignment explanation
Indices: 6479--6635 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
6469 TTGAAGGTGT
** * *
6479 ATCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAATGCATCGATGCATC-CCTATAATAATA-AAACATCGAATGCATATTA-T
6541 GC
63 GC
* * *
6543 ATCGATGCATAAGTCATGCATCGATGCATCCCTATAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
* * *
6607 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
6636 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
64 71 0.90
65 8 0.10
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
Found at i:8247 original size:149 final size:149
Alignment explanation
Indices: 7978--8429 Score: 771
Period size: 149 Copynumber: 3.0 Consensus size: 149
7968 GAGTCGAGGG
* * * * * * * *
7978 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTT-TGAGGCACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
* *
8042 ACTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
8107 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
8126 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
8191 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
8256 TATGGCACTACGGTACAAT
131 TATGGCACTACGGTGCAAT
* *
8275 TCTAAGCGGTCCTTCAGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
8340 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
8405 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
8424 TCTACG
1 TCTACG
8430 TGCACTTCGG
Statistics
Matches: 287, Mismatches: 16, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
148 48 0.17
149 239 0.83
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:8665 original size:21 final size:21
Alignment explanation
Indices: 8641--8701 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
8631 ATAAATAATT
*
8641 TGATGATAATGATAGA-GATAA
1 TGATAATAAT-ATAGATGATAA
*
8662 TGATAATAATATATATGATAA
1 TGATAATAATATAGATGATAA
* * *
8683 TGCTAAGAAAATAGATGAT
1 TGATAATAATATAGATGAT
8702 GATATATGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (21 bp):
TGATAATAATATAGATGATAA
Found at i:8707 original size:33 final size:33
Alignment explanation
Indices: 8643--8708 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
8633 AAATAATTTG
*
8643 ATGATAATGATAGAGATAATGATAATAATATAT
1 ATGATAATGATAGAGAAAATGATAATAATATAT
* * *
8676 ATGATAATGCTA-AGAAAATAGATGATGATATAT
1 ATGATAATGATAGAGAAAAT-GATAATAATATAT
8709 GTACATGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGATAATGATAGAGAAAATGATAATAATATAT
Found at i:11792 original size:10 final size:10
Alignment explanation
Indices: 11779--11829 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
11769 GACCGGTCCA
11779 AACCGGTCTG
1 AACCGGTCTG
*
11789 AACCGATCTG
1 AACCGGTCTG
11799 AACCGGTCTG
1 AACCGGTCTG
*
11809 AACCCGTCTG
1 AACCGGTCTG
*
11819 ACCCGGTCTG
1 AACCGGTCTG
11829 A
1 A
11830 CCCGACCTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.20
Consensus pattern (10 bp):
AACCGGTCTG
Found at i:11804 original size:30 final size:30
Alignment explanation
Indices: 11770--11829 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
11760 GACCGGCTTG
*
11770 ACCGGTCCAAACCGGTCTGAACCGATCTGA
1 ACCGGTCCAAACCCGTCTGAACCGATCTGA
** * *
11800 ACCGGTCTGAACCCGTCTGACCCGGTCTGA
1 ACCGGTCCAAACCCGTCTGAACCGATCTGA
11830 CCCGACCTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (30 bp):
ACCGGTCCAAACCCGTCTGAACCGATCTGA
Found at i:11899 original size:29 final size:30
Alignment explanation
Indices: 11857--11925 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
11847 CCCGACCCGA
* *
11857 TGACATTTTGGG-AATTATTTTGAAAATGG
1 TGACATTCTGGGAAATTATTTTGAAAAAGG
*
11886 TGACATTCTGGGAAATTGTTTTGAAAAAGG
1 TGACATTCTGGGAAATTATTTTGAAAAAGG
11916 TGACATTCTG
1 TGACATTCTG
11926 AAATTTTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 11 0.31
30 25 0.69
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (30 bp):
TGACATTCTGGGAAATTATTTTGAAAAAGG
Found at i:12998 original size:25 final size:25
Alignment explanation
Indices: 12946--12998 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
12936 AGGGTAACTC
*
12946 TTTTATGAGATTTACTGCAGTATAA
1 TTTTATGAGATTTACTGCACTATAA
* *
12971 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATAA
12996 TTT
1 TTT
12999 GTTTAGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATAA
Found at i:13676 original size:45 final size:45
Alignment explanation
Indices: 13615--13886 Score: 386
Period size: 45 Copynumber: 6.1 Consensus size: 45
13605 ATAAAAGACT
* *
13615 AAATGCATAACAGTGCATTATCGACATGAAAAGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAATG
* ** *
13660 AAATGCATAACGGTGCATTAT-TAGCATGAAAATATGCAATAAATG
1 AAATGCATAACGGTGCATTATCGA-CATGAAAGGATGCCATAAATG
* * *
13705 AAGTGCATAACGATGCATTATCGATATGAAAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAATG
*
13750 AAATGCATAACAGTGCATTATCGACATGAAAGGATGCCATAAATG
1 AAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAATG
* *
13795 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGTCATAAATG
1 AAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAATG
* * *
13840 AAATGCATAACGGTGCATTATTG-CATGAAATGATTCCATAAATG
1 AAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAATG
13884 AAA
1 AAA
13887 ATAAATTATA
Statistics
Matches: 203, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.11
45 180 0.89
46 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.25
Consensus pattern (45 bp):
AAATGCATAACGGTGCATTATCGACATGAAAGGATGCCATAAATG
Found at i:15127 original size:19 final size:19
Alignment explanation
Indices: 15103--15175 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
15093 AATGACCAAC
*
15103 AAAATCGTAACGAATTTAG
1 AAAATCGCAACGAATTTAG
*
15122 AAAATCGCAACGACAACTATAG
1 AAAATCGCAACG--AA-TTTAG
**
15144 ACTATCGCAACGAATTTAG
1 AAAATCGCAACGAATTTAG
*
15163 AAAATCGTAACGA
1 AAAATCGCAACGA
15176 CAACTGTAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 25 0.58
20 2 0.05
21 2 0.05
22 14 0.33
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (19 bp):
AAAATCGCAACGAATTTAG
Found at i:15150 original size:22 final size:22
Alignment explanation
Indices: 15125--15196 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
15115 AATTTAGAAA
15125 ATCGCAACGACAACTATAGACT
1 ATCGCAACGACAACTATAGACT
* **
15147 ATCGCAACG--AA-TTTAGAAA
1 ATCGCAACGACAACTATAGACT
* *
15166 ATCGTAACGACAACTGTAGACT
1 ATCGCAACGACAACTATAGACT
15188 ATCGCAACG
1 ATCGCAACG
15197 CGAATTAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTATAGACT
Found at i:15157 original size:41 final size:41
Alignment explanation
Indices: 15106--15215 Score: 159
Period size: 41 Copynumber: 2.7 Consensus size: 41
15096 GACCAACAAA
*
15106 ATCGTAACGAATTTAGAAAATCGCAACGACAACTATAGACT
1 ATCGCAACGAATTTAGAAAATCGCAACGACAACTATAGACT
* *
15147 ATCGCAACGAATTTAGAAAATCGTAACGACAACTGTAGACT
1 ATCGCAACGAATTTAGAAAATCGCAACGACAACTATAGACT
*
15188 ATCGCAACGCGAA-TTAAAAAATCGCAAC
1 ATCGCAA--CGAATTTAGAAAATCGCAAC
15216 ACGATTTTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 45 0.73
42 13 0.21
43 4 0.06
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAATTTAGAAAATCGCAACGACAACTATAGACT
Found at i:15213 original size:20 final size:20
Alignment explanation
Indices: 15188--15260 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
15178 ACTGTAGACT
15188 ATCGCAACGCGAATTAAAAA
1 ATCGCAACGCGAATTAAAAA
* * * **
15208 ATCGCAACACGATTTTCAACT
1 ATCGCAACGCGA-ATTAAAAA
* * *
15229 ATCGTAACGCGAAATGAAAA
1 ATCGCAACGCGAATTAAAAA
15249 ATCGCAACGCGA
1 ATCGCAACGCGA
15261 TTTTCAACTA
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAATTAAAAA
Found at i:15230 original size:41 final size:41
Alignment explanation
Indices: 15185--15281 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
15175 ACAACTGTAG
*
15185 ACTATCGCAACGCGAATTAAAAAATCGCAACACGATTTTCA
1 ACTATCGCAACGCGAAATAAAAAATCGCAACACGATTTTCA
* * *
15226 ACTATCGTAACGCGAAATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATAAAAAATCGCAACACGATTTTCA
15267 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
15282 TTTTCAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.39, C:0.25, G:0.15, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATAAAAAATCGCAACACGATTTTCA
Found at i:15275 original size:21 final size:21
Alignment explanation
Indices: 15185--15298 Score: 106
Period size: 21 Copynumber: 5.5 Consensus size: 21
15175 ACAACTGTAG
* *
15185 ACTATCGCAACGCGA-ATTAA
1 ACTATCGCAACGCGATTTTCA
** *
15205 AAAATCGCAACACGATTTTCA
1 ACTATCGCAACGCGATTTTCA
* ** *
15226 ACTATCGTAACGCGA-AATGA
1 ACTATCGCAACGCGATTTTCA
**
15246 AAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
15267 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGATTTTCA
*
15288 ATTATCGCAAC
1 ACTATCGCAAC
15299 ACGAAATGCA
Statistics
Matches: 71, Mismatches: 21, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
20 26 0.37
21 45 0.63
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.24
Consensus pattern (21 bp):
ACTATCGCAACGCGATTTTCA
Found at i:15352 original size:19 final size:19
Alignment explanation
Indices: 15328--15380 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
15318 TATGATAGTG
15328 GAGATCGCAATGCGAATTA
1 GAGATCGCAATGCGAATTA
15347 GAGATCGCAATGCGAATTA
1 GAGATCGCAATGCGAATTA
*
15366 GAGATCGCATTGCGA
1 GAGATCGCAATGCGA
15381 TTTTGTTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (19 bp):
GAGATCGCAATGCGAATTA
Found at i:21047 original size:22 final size:22
Alignment explanation
Indices: 21020--21072 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
21010 CATCAAAGTG
21020 TCAAATCATT-TATAAAA-AAT
1 TCAAATCATTCTATAAAACAAT
*
21040 TAACAAATTCTTTCTATAAAACAAT
1 T--CAAA-TCATTCTATAAAACAAT
21065 TCAAATCA
1 TCAAATCA
21073 GAAATTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
20 1 0.04
22 6 0.23
23 8 0.31
24 7 0.27
25 4 0.15
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (22 bp):
TCAAATCATTCTATAAAACAAT
Found at i:22112 original size:6 final size:6
Alignment explanation
Indices: 22098--22129 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
22088 AGCCTTTATT
*
22098 TTACTA TTACAA TTACTA TTACTA TTACTA TT
1 TTACTA TTACTA TTACTA TTACTA TTACTA TT
22130 TAGTAGTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
TTACTA
Found at i:22767 original size:74 final size:74
Alignment explanation
Indices: 22646--22800 Score: 238
Period size: 74 Copynumber: 2.1 Consensus size: 74
22636 AATCTAAAAA
* * * *
22646 TTGGGAGGGCCAAAGACCTTATTTGATTACTATTTAAACTAAAAAGGACCTAAGATACTATTATA
1 TTGGGAGGGACAAAGACCTTATTCGATTAATATTTAAACTAAAAAGGACCTAAAATACTATTATA
*
22711 CCAAACATT
66 CCAAAAATT
* *
22720 TTGGGAGGGACAAAGGCCTTATTCGATTAATATTTAAATTAAAAAGGACCTAAAATACTATTATA
1 TTGGGAGGGACAAAGACCTTATTCGATTAATATTTAAACTAAAAAGGACCTAAAATACTATTATA
22785 CCAAAAATT
66 CCAAAAATT
*
22794 TCGGGAG
1 TTGGGAG
22801 TGGCAACAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (74 bp):
TTGGGAGGGACAAAGACCTTATTCGATTAATATTTAAACTAAAAAGGACCTAAAATACTATTATA
CCAAAAATT
Found at i:33064 original size:77 final size:79
Alignment explanation
Indices: 32911--33065 Score: 199
Period size: 77 Copynumber: 2.0 Consensus size: 79
32901 ATATAATTAG
* *
32911 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTTAATAGATTTTTAATTCGGAATAATTA
1 TAAACATTAAAAGAATGTAATTTGGATTACAACTCTTTTAATAGATATTTAATTCGGAATAATTA
32976 AATAAGATTTTAAA
66 AATAAGATTTTAAA
* * * * * *
32990 TAAACATT-AAAGATTGTAATTTGGATTATAAGTC-TTTAATGGATATTTAGTT-TGAATTAATT
1 TAAACATTAAAAGAATGTAATTTGGATTACAACTCTTTTAATAGATATTTAATTCGGAA-TAATT
*
33052 AAATAATATTTTAA
65 AAATAAGATTTTAA
33066 TTAATTCGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
76 3 0.05
77 33 0.50
78 22 0.33
79 8 0.12
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTTGGATTACAACTCTTTTAATAGATATTTAATTCGGAATAATTA
AATAAGATTTTAAA
Found at i:34694 original size:21 final size:21
Alignment explanation
Indices: 34669--34824 Score: 195
Period size: 21 Copynumber: 7.4 Consensus size: 21
34659 TGTTACTAAG
*
34669 TATATTAGAACATATTATTAA
1 TATATTAGTACATATTATTAA
* *** *
34690 TATATTATTGTTTATTATTCA
1 TATATTAGTACATATTATTAA
*
34711 TATATTAGTACATATTATGAA
1 TATATTAGTACATATTATTAA
*
34732 TATATTAGTTCATATTATTAA
1 TATATTAGTACATATTATTAA
*
34753 TATATTAGTACATATTATTAG
1 TATATTAGTACATATTATTAA
* * *
34774 TATATTAATAAATATTACTAA
1 TATATTAGTACATATTATTAA
*
34795 TATATTAGTATATATTATTAA
1 TATATTAGTACATATTATTAA
34816 TATATTAGT
1 TATATTAGT
34825 GTATATTAGT
Statistics
Matches: 112, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 112 1.00
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (21 bp):
TATATTAGTACATATTATTAA
Found at i:34831 original size:63 final size:63
Alignment explanation
Indices: 34661--34832 Score: 215
Period size: 63 Copynumber: 2.7 Consensus size: 63
34651 ACTACGTATG
* * * * * *
34661 TTACTAAGTATATTAGAACATATTATTAATATATTATTGTTTATTATTCATATATTAGTACATA
1 TTACTAA-TATATTAGTATATATTATTAATATATTAGTGTATATTATTCATATATTAATAAATA
**
34725 TTA-TGAATATATTAGT-TCATATTATTAATATATTAGTACATATTATT-AGTATATTAATAAAT
1 TTACT-AATATATTAGTAT-ATATTATTAATATATTAGTGTATATTATTCA-TATATTAATAAAT
34787 A
63 A
34788 TTACTAATATATTAGTATATATTATTAATATATTAGTGTATATTA
1 TTACTAATATATTAGTATATATTATTAATATATTAGTGTATATTA
34833 GTGTAGACAC
Statistics
Matches: 93, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 85 0.91
64 7 0.08
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (63 bp):
TTACTAATATATTAGTATATATTATTAATATATTAGTGTATATTATTCATATATTAATAAATA
Found at i:34837 original size:10 final size:10
Alignment explanation
Indices: 34669--34834 Score: 100
Period size: 10 Copynumber: 15.9 Consensus size: 10
34659 TGTTACTAAG
*
34669 TATATTAGAA
1 TATATTAGTA
* *
34679 CATATTATTAA
1 TATATTAGT-A
* *
34690 TATATTATTG
1 TATATTAGTA
* *
34700 TTTATTATTCA
1 TATATTAGT-A
34711 TATATTAGTA
1 TATATTAGTA
* *
34721 CATATTATGAA
1 TATATTA-GTA
34732 TATATTAGT-
1 TATATTAGTA
*
34741 TCATATTATTAA
1 T-ATATTAGT-A
34753 TATATTAGTA
1 TATATTAGTA
* *
34763 CATATTATTA
1 TATATTAGTA
*
34773 GTATATTAATA
1 -TATATTAGTA
* *
34784 AATATTACTAA
1 TATATTAGT-A
34795 TATATTAGTA
1 TATATTAGTA
*
34805 TATATTATTAA
1 TATATTAGT-A
*
34816 TATATTAGTG
1 TATATTAGTA
34826 TATATTAGT
1 TATATTAGT
34835 GTAGACACTC
Statistics
Matches: 121, Mismatches: 26, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
9 1 0.01
10 63 0.52
11 56 0.46
12 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (10 bp):
TATATTAGTA
Found at i:34952 original size:24 final size:24
Alignment explanation
Indices: 34925--34976 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
34915 ATGTTAGTAA
34925 TTTAATTAGGATTAAGGATATTAT
1 TTTAATTAGGATTAAGGATATTAT
34949 TTTAATTAGGATTAAGGATATTAT
1 TTTAATTAGGATTAAGGATATTAT
34973 TTTA
1 TTTA
34977 TGTTATCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (24 bp):
TTTAATTAGGATTAAGGATATTAT
Found at i:35586 original size:18 final size:18
Alignment explanation
Indices: 35563--35605 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
35553 CTTTAGATTA
*
35563 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
35581 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
35599 TTTATTT
1 TTTATTT
35606 TATAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:35761 original size:41 final size:41
Alignment explanation
Indices: 35650--35759 Score: 159
Period size: 41 Copynumber: 2.7 Consensus size: 41
35640 ACTACTATTA
* *
35650 TTTATTATTTAATTTAACAATTCTTTTTTATTTTATTTTGT
1 TTTATTATTAAATTTAACACTTCTTTTTTATTTTATTTTGT
35691 TTTATTATTAAATTTAACACTTCTTTTTTATTTTATTTTGT
1 TTTATTATTAAATTTAACACTTCTTTTTTATTTTATTTTGT
* * **
35732 TTTATT-TTTATTTTTCCACTTCTTTTTT
1 TTTATTATTAAATTTAACACTTCTTTTTT
35760 TAATTTTAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 18 0.29
41 45 0.71
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (41 bp):
TTTATTATTAAATTTAACACTTCTTTTTTATTTTATTTTGT
Found at i:37298 original size:85 final size:85
Alignment explanation
Indices: 37194--37364 Score: 245
Period size: 85 Copynumber: 2.0 Consensus size: 85
37184 AAGAACATCT
* * *
37194 CACATGACTTTCCTATGAAGGGGAGTCATCCAAAGATAATCTCA-CTGGTTCAAACCTGCTAAGG
1 CACATGACTTTCCCATGAA-GGGAGTCATCCAAAGATAATCTCACCTGGTTCAAACCCGCGAAGG
37258 GGAACCACCTGAAGAATATAC
65 GGAACCACCTGAAGAATATAC
* ** * * *
37279 CACATGACTTTCCCGTGAAGGGAGTCATCCAAAGATCTTCTGACCTGGTTTAGACCCGCGAAGGG
1 CACATGACTTTCCCATGAAGGGAGTCATCCAAAGATAATCTCACCTGGTTCAAACCCGCGAAGGG
37344 GAACCACCTGAAGAATATAC
66 GAACCACCTGAAGAATATAC
37364 C
1 C
37365 TTGAATTGTG
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
84 21 0.28
85 55 0.72
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (85 bp):
CACATGACTTTCCCATGAAGGGAGTCATCCAAAGATAATCTCACCTGGTTCAAACCCGCGAAGGG
GAACCACCTGAAGAATATAC
Found at i:40166 original size:48 final size:48
Alignment explanation
Indices: 40110--40221 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
40100 AAATGGAGAT
* *
40110 ATCAGAAATCAAAATAGAATTCAGATCAAATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAATAGAATTCAGATCAAATATCAGAACAGAATCCAA
* * * * ** *
40158 ATCAGAAATTAGAACATAATTCAGGTCATGTATCAGAACAGAATTCAA
1 ATCAGAAATCAGAATAGAATTCAGATCAAATATCAGAACAGAATCCAA
*
40206 ATCGGAAATCAGAATA
1 ATCAGAAATCAGAATA
40222 AATATTTATG
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAATAGAATTCAGATCAAATATCAGAACAGAATCCAA
Found at i:40171 original size:24 final size:24
Alignment explanation
Indices: 40110--40219 Score: 89
Period size: 24 Copynumber: 4.6 Consensus size: 24
40100 AAATGGAGAT
* * *
40110 ATCAGAAATCAAAATAGAATTCAG
1 ATCAGAAATCAGAACAGAATCCAG
40134 ATCA-AATATCAGAACAGAATCCAG
1 ATCAGAA-ATCAGAACAGAATCCAG
* * *
40158 ATCAGAAATTAGAACATAATTCAG
1 ATCAGAAATCAGAACAGAATCCAG
* * * *
40182 GTCATG-TATCAGAACAGAATTCAA
1 ATCA-GAAATCAGAACAGAATCCAG
*
40206 ATCGGAAATCAGAA
1 ATCAGAAATCAGAA
40220 TAAATATTTA
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
23 3 0.04
24 62 0.91
25 3 0.04
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATCCAG
Found at i:42458 original size:17 final size:17
Alignment explanation
Indices: 42436--42469 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42426 TCAAAGTCAA
42436 CGGTCAAAGATCAACGG
1 CGGTCAAAGATCAACGG
*
42453 CGGTCAAAGGTCAACGG
1 CGGTCAAAGATCAACGG
42470 TCAACGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.32, T:0.12
Consensus pattern (17 bp):
CGGTCAAAGATCAACGG
Found at i:44649 original size:24 final size:24
Alignment explanation
Indices: 44619--44709 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
44609 GATATCAGAA
*
44619 ATCAAAACAGAATTCAAATAAGAT
1 ATCAAAACAGAATTCAAATATGAT
* * * * *
44643 ATCAAAATAGAATCCATATCTGAA
1 ATCAAAACAGAATTCAAATATGAT
* *
44667 ATCAGAACAGAATTCAGAACATG-T
1 ATCAAAACAGAATTCA-AATATGAT
*
44691 ATCAGAACAGAATTCAAAT
1 ATCAAAACAGAATTCAAAT
44710 CAGAAATCTG
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
23 2 0.04
24 47 0.90
25 3 0.06
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAAATATGAT
Found at i:44694 original size:48 final size:48
Alignment explanation
Indices: 44610--44717 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
44600 GTAAACAGAG
* *
44610 ATATCAGAAATCAAAACAGAATTCAAATAAGATATCAAAATAGAATCC
1 ATATCAGAAATCAAAACAGAATTCAAACAAGATATCAAAACAGAATCC
* * * * *
44658 ATATCTGAAATCAGAACAGAATTCAGAACATG-TATCAGAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTCA-AACAAGATATCAAAACAGAATCC
*
44706 AAATCAGAAATC
1 ATATCAGAAATC
44718 TGATAAAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 46 0.92
49 4 0.08
ACGTcount: A:0.52, C:0.16, G:0.11, T:0.21
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCAAACAAGATATCAAAACAGAATCC
Found at i:47013 original size:24 final size:23
Alignment explanation
Indices: 46971--47016 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
46961 TTGACTTTTT
46971 CGGTCAAAGTCAACGGTCAACGG
1 CGGTCAAAGTCAACGGTCAACGG
*
46994 CGGTCAAAGGTCAACTGTCAACG
1 CGGTCAAA-GTCAACGGTCAACG
47017 ATTTTACACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.15
Consensus pattern (23 bp):
CGGTCAAAGTCAACGGTCAACGG
Found at i:50801 original size:30 final size:30
Alignment explanation
Indices: 50767--50826 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
50757 TCCGACTAGA
50767 TCAGTTCAATTTTTTAAGAAAAATGAGTTC
1 TCAGTTCAATTTTTTAAGAAAAATGAGTTC
50797 TCAGTTCAATTTTTTAAGAAAAATGAGTTC
1 TCAGTTCAATTTTTTAAGAAAAATGAGTTC
50827 GGTTTGGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (30 bp):
TCAGTTCAATTTTTTAAGAAAAATGAGTTC
Done.