Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006147.1 Hibiscus syriacus cultivar Beakdansim tig00014597_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: 64397
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2050 original size:44 final size:44
Alignment explanation
Indices: 1930--2055 Score: 171
Period size: 48 Copynumber: 2.8 Consensus size: 44
1920 AATAAAATCC
*
1930 CTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1974 CTTACCATTTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCA--TT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
2022 CTTGCCATTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTT
2056 GTATGCTTAC
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
44 31 0.42
46 4 0.05
48 38 0.52
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (44 bp):
CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:2255 original size:59 final size:59
Alignment explanation
Indices: 2163--2291 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
2153 CCGTGTGCTA
* * * **
2163 TCCCGAATATGATACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
2222 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
2281 TCCCGAATATG
1 TCCCGAATATG
2292 CAGCCTGCTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:3874 original size:22 final size:19
Alignment explanation
Indices: 3834--3885 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
3824 TTGAGAGCAT
*
3834 TTCATCTTAATTAACATAATA
1 TTCAT-TTAATGAACATAA-A
*
3855 TCTCACTTTAATGAATATAAA
1 T-TCA-TTTAATGAACATAAA
3876 TTCATTTAAT
1 TTCATTTAAT
3886 TGGGATAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 6 0.22
20 3 0.11
21 3 0.11
22 14 0.52
23 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (19 bp):
TTCATTTAATGAACATAAA
Found at i:8848 original size:6 final size:6
Alignment explanation
Indices: 8837--8867 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
8827 TCTTAATTTC
8837 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT T
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT T
8868 TAAAGATTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAAAT
Found at i:9133 original size:16 final size:16
Alignment explanation
Indices: 9103--9133 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9093 GTTAAAATAG
*
9103 AAAATAAAATCAAAAC
1 AAAATAAAATAAAAAC
9119 AAAATAAAATAAAAA
1 AAAATAAAATAAAAA
9134 AGTGGGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAATAAAATAAAAAC
Found at i:9144 original size:37 final size:37
Alignment explanation
Indices: 9102--9172 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
9092 TGTTAAAATA
9102 GAAAATAA-AATCAAAACAAAATAAAATAAAAAAGTGG
1 GAAAATAATAAT-AAAACAAAATAAAATAAAAAAGTGG
* *
9139 GAAAATAATGATAAAATAAAATAAAATAAAAAAG
1 GAAAATAATAATAAAACAAAATAAAATAAAAAAG
9173 GAAATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 29 0.94
38 2 0.06
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (37 bp):
GAAAATAATAATAAAACAAAATAAAATAAAAAAGTGG
Found at i:9265 original size:19 final size:19
Alignment explanation
Indices: 9239--9282 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
9229 GTTGTTTTTA
*
9239 AAAT-AAAAGATAAGAATT
1 AAATAAAAAGAAAAGAATT
*
9257 AAATAAAAAGAAAATAATT
1 AAATAAAAAGAAAAGAATT
9276 AAATAAA
1 AAATAAA
9283 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (19 bp):
AAATAAAAAGAAAAGAATT
Found at i:14400 original size:31 final size:30
Alignment explanation
Indices: 14354--14440 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
14344 TTCGATAATA
*
14354 TAATAATTATTTTATAGTA-TTTAGATAAATT
1 TAATAA-TATTTTATAATATTTTA-ATAAATT
*
14385 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAAT-ATTTTATAATATTTTAATAAATT
*
14416 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATATTTTAA
14441 ACTTTATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.88
32 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTTAATAAATT
Found at i:24921 original size:18 final size:18
Alignment explanation
Indices: 24878--24921 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
24868 TTTTAGCTCG
* *
24878 CTAGCTCCTCTCGGACGC
1 CTAGCTCGTCTCAGACGC
24896 CTAGCTCGTCTCAGACGC
1 CTAGCTCGTCTCAGACGC
24914 CTAGCTCG
1 CTAGCTCG
24922 CTACTCCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.41, G:0.23, T:0.23
Consensus pattern (18 bp):
CTAGCTCGTCTCAGACGC
Found at i:28608 original size:2 final size:2
Alignment explanation
Indices: 28601--28639 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28591 ATAGGAAAAT
28601 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28640 GAAACAAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28690 original size:13 final size:14
Alignment explanation
Indices: 28672--28704 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28662 AACTATTCTA
28672 ATATATTTT-GGAT
1 ATATATTTTAGGAT
*
28685 ATATATTTTAGTAT
1 ATATATTTTAGGAT
28699 ATATAT
1 ATATAT
28705 ATATATATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (14 bp):
ATATATTTTAGGAT
Found at i:28729 original size:73 final size:73
Alignment explanation
Indices: 28610--28769 Score: 295
Period size: 73 Copynumber: 2.2 Consensus size: 73
28600 TTATATATAT
*
28610 ATATATATATATA-TATATATATATATATATGAAACAAATCATGTGAACATGCAACTATTCTAAT
1 ATATATAT-TTTAGTATATATATATATATATGAAACAAATCATGTGAACATGCAACTATTCTAAT
28674 ATATTTTGG
65 ATATTTTGG
28683 ATATATATTTTAGTATATATATATATATATGAAACAAATCATGTGAACATGCAACTATTCTAATA
1 ATATATATTTTAGTATATATATATATATATGAAACAAATCATGTGAACATGCAACTATTCTAATA
28748 TATTTTGG
66 TATTTTGG
28756 ATATATATTTTAGT
1 ATATATATTTTAGT
28770 TTATTTTTTA
Statistics
Matches: 85, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
72 3 0.04
73 82 0.96
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (73 bp):
ATATATATTTTAGTATATATATATATATATGAAACAAATCATGTGAACATGCAACTATTCTAATA
TATTTTGG
Found at i:31969 original size:50 final size:50
Alignment explanation
Indices: 31854--31975 Score: 156
Period size: 50 Copynumber: 2.4 Consensus size: 50
31844 TCGTAAAGCA
* *
31854 CGCCCCCTGAACCACGCTATACGCTGATTTGGCGCCACGTGGGTATAACG
1 CGCCCCCTGAACCGCGCTATACGCTGATCTGGCGCCACGTGGGTATAACG
*** * *
31904 CGCCCCCTTCCCCGCGATATACAG-TGATCTGGCGCCACGTGGGTATAGCG
1 CGCCCCCTGAACCGCGCTATAC-GCTGATCTGGCGCCACGTGGGTATAACG
*
31954 CGCCCCCTGATCCGCGCTATAC
1 CGCCCCCTGAACCGCGCTATAC
31976 CTGGGTATCT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 59 0.98
51 1 0.02
ACGTcount: A:0.17, C:0.38, G:0.25, T:0.20
Consensus pattern (50 bp):
CGCCCCCTGAACCGCGCTATACGCTGATCTGGCGCCACGTGGGTATAACG
Found at i:32130 original size:19 final size:19
Alignment explanation
Indices: 32106--32142 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
32096 ACCAAATTCT
*
32106 CTCAAATTCTCTAACTTTC
1 CTCAAATACTCTAACTTTC
*
32125 CTCAAATACTCTATCTTT
1 CTCAAATACTCTAACTTT
32143 GTAAGGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (19 bp):
CTCAAATACTCTAACTTTC
Found at i:32457 original size:111 final size:111
Alignment explanation
Indices: 32263--32484 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 111
32253 TGGAAATCAT
*
32263 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
*
32328 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
32374 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
32439 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
32485 TTTTTGTAAT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:38314 original size:51 final size:51
Alignment explanation
Indices: 38209--38332 Score: 124
Period size: 51 Copynumber: 2.4 Consensus size: 51
38199 CTACGTGGCG
* * * * *
38209 TATAGCGCGG-AGCAGGGGGTGCGCTATACCCCACGTGTAACCCAGTCAGCA
1 TATAGCGCGGTA-CAGGGGGCGCACTATACCCCACGTGGAACCAAATCAGCA
* ** *
38260 TATAGCGCGGTACAGGGGGCGCACTATACTCCACGTGGCGCCAAATCAGTA
1 TATAGCGCGGTACAGGGGGCGCACTATACCCCACGTGGAACCAAATCAGCA
* * *
38311 TATAACGCGGTTCAGAGGGCGC
1 TATAGCGCGGTACAGGGGGCGC
38333 GCTTTACTGC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
51 59 0.98
52 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.31, T:0.17
Consensus pattern (51 bp):
TATAGCGCGGTACAGGGGGCGCACTATACCCCACGTGGAACCAAATCAGCA
Found at i:39041 original size:19 final size:19
Alignment explanation
Indices: 39017--39053 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39007 ATGACCAACA
*
39017 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
39036 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
39054 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:39141 original size:20 final size:20
Alignment explanation
Indices: 39082--39232 Score: 137
Period size: 20 Copynumber: 7.5 Consensus size: 20
39072 TCCAGATTCA
* *
39082 CAACGAGATTTTGACTATCG
1 CAACGCGATTATGACTATCG
* * *
39102 CAATGCGAATATGTA-AATCG
1 CAACGCGATTATG-ACTATCG
*
39122 CAACGCGATTCTGACTATCG
1 CAACGCGATTATGACTATCG
*
39142 CAACGCGATAAT-ACATAATCG
1 CAACGCGATTATGAC-T-ATCG
*
39163 CAACGCGATTCTGACTATCG
1 CAACGCGATTATGACTATCG
* *
39183 CAACGAGATAAT-ACATAATCG
1 CAACGCGATTATGAC-T-ATCG
*
39204 CAACGCGATTCTGACTATCG
1 CAACGCGATTATGACTATCG
39224 CAACGCGAT
1 CAACGCGAT
39233 AATACAAAAT
Statistics
Matches: 104, Mismatches: 19, Indels: 16
0.75 0.14 0.12
Matches are distributed among these distances:
19 5 0.05
20 65 0.62
21 30 0.29
22 4 0.04
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (20 bp):
CAACGCGATTATGACTATCG
Found at i:39169 original size:41 final size:41
Alignment explanation
Indices: 39082--39252 Score: 247
Period size: 41 Copynumber: 4.2 Consensus size: 41
39072 TCCAGATTCA
* * * **
39082 CAACGAGATTTTGACTATCGCAATGCG--AATATGTAAATCG
1 CAACGCGATTCTGACTATCGCAACGCGATAATACAT-AATCG
39122 CAACGCGATTCTGACTATCGCAACGCGATAATACATAATCG
1 CAACGCGATTCTGACTATCGCAACGCGATAATACATAATCG
*
39163 CAACGCGATTCTGACTATCGCAACGAGATAATACATAATCG
1 CAACGCGATTCTGACTATCGCAACGCGATAATACATAATCG
*
39204 CAACGCGATTCTGACTATCGCAACGCGATAATACAAAATCG
1 CAACGCGATTCTGACTATCGCAACGCGATAATACATAATCG
*
39245 CAATGCGA
1 CAACGCGA
39253 ATTTCAAAGC
Statistics
Matches: 120, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
40 24 0.20
41 91 0.76
42 5 0.04
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (41 bp):
CAACGCGATTCTGACTATCGCAACGCGATAATACATAATCG
Found at i:41854 original size:20 final size:20
Alignment explanation
Indices: 41829--41897 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
41819 CGAAACTTAA
41829 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
41849 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
41869 ATCGCAACGCGAAGTTGACT
1 ATCGCAACGCGAAAATGACT
41889 ATCGCAACG
1 ATCGCAACG
41898 GGATAATCTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:42048 original size:32 final size:33
Alignment explanation
Indices: 41979--42052 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 33
41969 TTTAGTTTTG
* * *
41979 CGTTGCGATTTTTGTGTCGCGTTGCGATTTTCT
1 CGTTGCGATTTTTGTGTCGCATTGCGATTATCC
42012 CGTTGCGATTTTAT-T-TCGCATTGCGATTATCC
1 CGTTGCGATTTT-TGTGTCGCATTGCGATTATCC
42044 CGTTGCGAT
1 CGTTGCGAT
42053 AGTTAAATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 23 0.62
33 13 0.35
34 1 0.03
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTTGTGTCGCATTGCGATTATCC
Found at i:42096 original size:20 final size:19
Alignment explanation
Indices: 42044--42112 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
42034 GCGATTATCC
* *
42044 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAG-TCATTTCG
42064 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
42084 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
42104 TGTTGCGAT
1 CGTTGCGAT
42113 TTAAGTTTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.09
20 37 0.84
21 3 0.07
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:42712 original size:21 final size:21
Alignment explanation
Indices: 42617--42719 Score: 91
Period size: 21 Copynumber: 4.9 Consensus size: 21
42607 ACTCGACTCA
42617 CCTGTCATCATTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGCC
* *
42638 TCT-CCTATCATTCAAGAGGCC
1 CCTGTC-ATCATTCAAGAGGCC
* ** *
42659 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCATTCAAGAGGCC
* * *
42680 CCTCTCACCGTTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGCC
* *
42701 CCTGTCATCGTTGAAGAGG
1 CCTGTCATCATTCAAGAGG
42720 TCACTCCCAC
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.24
Consensus pattern (21 bp):
CCTGTCATCATTCAAGAGGCC
Found at i:42736 original size:42 final size:42
Alignment explanation
Indices: 42617--42739 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
42607 ACTCGACTCA
* * * *
42617 CCTGTCATCATTCAAGAGGCCTCTCCTATCATTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGTCACTCCCACCATTCAAGAGGCC
* ** * * *
42659 CCTATCATCCCTCAAGA-GTCCCCTCTCACCGTTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGT-CACTCCCACCATTCAAGAGGCC
* *
42701 CCTGTCATCGTTGAAGAGGTCACTCCCACCATTCAAGAG
1 CCTGTCATCATTCAAGAGGTCACTCCCACCATTCAAGAG
42740 CCCGATTCAT
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
41 1 0.02
42 60 0.95
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTGTCATCATTCAAGAGGTCACTCCCACCATTCAAGAGGCC
Found at i:43079 original size:12 final size:12
Alignment explanation
Indices: 43062--43096 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
43052 GGGGGGTAAG
43062 TCTTATATTTCT
1 TCTTATATTTCT
43074 TCTTATATTTCT
1 TCTTATATTTCT
43086 TCTTATATTTC
1 TCTTATATTTC
43097 ATTTTGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (12 bp):
TCTTATATTTCT
Found at i:44156 original size:14 final size:14
Alignment explanation
Indices: 44137--44198 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
44127 TTGCTTGTTT
44137 AATTGATTTGTAAA
1 AATTGATTTGTAAA
44151 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
44165 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
44180 TATTGATGTGTAAA
1 AATTGATTTGTAAA
44194 TAATT
1 -AATT
44199 CTTATTTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 13 0.33
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:44171 original size:28 final size:29
Alignment explanation
Indices: 44139--44193 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
44129 GCTTGTTTAA
*
44139 TTGATTTG-TAAAAATTGATTTGTAAAAG
1 TTGATTTGTTAAAAATTGATGTGTAAAAG
* *
44167 TTGATTTGTTTAATATTGATGTGTAAA
1 TTGATTTGTTAAAAATTGATGTGTAAA
44194 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (29 bp):
TTGATTTGTTAAAAATTGATGTGTAAAAG
Found at i:44419 original size:20 final size:19
Alignment explanation
Indices: 44394--44509 Score: 108
Period size: 20 Copynumber: 5.8 Consensus size: 19
44384 CGATTTTCTC
44394 GTTGCGATAGTCAAATACCA
1 GTTGCGATAGTCAAAT-CCA
* *
44414 GTTGCGATAATCAAATTCA
1 GTTGCGATAGTCAAATCCA
*
44433 CGTTGCGATAGTCAAATTTGC-
1 -GTTGCGATAGTCAAA--TCCA
*
44454 GTTGCGATAGTCAAATTCA
1 GTTGCGATAGTCAAATCCA
**
44473 CGTTGCGATAGTCAAATTCGT
1 -GTTGCGATAGTCAAA-TCCA
*
44494 GTTGCGATATTCAAAT
1 GTTGCGATAGTCAAAT
44510 GAATGTGTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 13
0.79 0.09 0.13
Matches are distributed among these distances:
18 2 0.02
19 3 0.04
20 73 0.90
21 1 0.01
22 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (19 bp):
GTTGCGATAGTCAAATCCA
Found at i:44448 original size:40 final size:39
Alignment explanation
Indices: 44393--44509 Score: 162
Period size: 40 Copynumber: 2.9 Consensus size: 39
44383 GCGATTTTCT
*
44393 CGTTGCGATAGTCAAATACCAGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCC-GTTGCGATAATCAAATTCA
* *
44433 CGTTGCGATAGTCAAATTTGCGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAA-TTCCGTTGCGATAATCAAATTCA
* *
44473 CGTTGCGATAGTCAAATTCGTGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAATTC-CGTTGCGATAATCAAAT
44510 GAATGTGTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
39 2 0.03
40 65 0.94
41 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (39 bp):
CGTTGCGATAGTCAAATTCCGTTGCGATAATCAAATTCA
Found at i:44488 original size:60 final size:60
Alignment explanation
Indices: 44393--44509 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
44383 GCGATTTTCT
44393 CGTTGCGATAGTCAAATACCAGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATACCAGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTTG
* * ** *
44453 CGTTGCGATAGTCAAAT-TCACGTTGCGATAGTCAAATTCGTGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAATACCA-GTTGCGATAATCAAATTCACGTTGCGATAGTCAAAT
44510 GAATGTGTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 2 0.04
60 49 0.96
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (60 bp):
CGTTGCGATAGTCAAATACCAGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTTG
Found at i:44732 original size:140 final size:140
Alignment explanation
Indices: 44480--44762 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 140
44470 TCACGTTGCG
* * *
44480 ATAGTCAAATTCGTGTTGCGATATTCAAATGAATGTGTATTAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
44545 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTCAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
44610 AATACACATA
131 AATACACATA
44620 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
44685 TAGCAATGTTCATACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
44750 AATACACATA
131 AATACACATA
44760 ATA
1 ATA
44763 CAACGTTTGC
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:44841 original size:18 final size:18
Alignment explanation
Indices: 44815--44855 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
44805 AGGTGAAGCC
*
44815 GATTGTGATTGGGATTTT
1 GATTGTGATTGCGATTTT
*
44833 GATTTTGATTGCGATTTT
1 GATTGTGATTGCGATTTT
44851 GATTG
1 GATTG
44856 CCTTTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.02, G:0.29, T:0.51
Consensus pattern (18 bp):
GATTGTGATTGCGATTTT
Found at i:47141 original size:24 final size:24
Alignment explanation
Indices: 47114--47160 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
47104 CAAAATCCGA
47114 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
47138 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
47161 AATACCGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:48016 original size:21 final size:20
Alignment explanation
Indices: 47975--48145 Score: 177
Period size: 20 Copynumber: 8.4 Consensus size: 20
47965 GAAATTCAGT
*
47975 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
**
47995 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
**
48016 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
*
48037 GTTGCGATAGTCAGAATCAC
1 GTTGCGATAGTCAGAATCGC
48057 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
48077 GTTGCGATAGTCAGAATTGC
1 GTTGCGATAGTCAGAATCGC
**
48097 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
*
48118 GTTGCAATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
48138 GTTGCGAT
1 GTTGCGAT
48146 TTACATATTC
Statistics
Matches: 130, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
19 4 0.03
20 74 0.57
21 48 0.37
22 4 0.03
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:48121 original size:81 final size:82
Alignment explanation
Indices: 47975--48145 Score: 265
Period size: 81 Copynumber: 2.1 Consensus size: 82
47965 GAAATTCAGT
* **
47975 GTTGCGACAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATTATGTATTATCGCGTT
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGTAGAATCGCGTTGCGATTATGTATTATCGCGTT
*
48040 GCGATAGTCAGAATCAC
66 GCAATAGTCAGAATCAC
*
48057 GTTGCGATAGTCAGAATCGCGTTGCGA-TA-GTCAGAATTGCGTTGCGATTATGTATTATCGCGT
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATGT-AGAATCGCGTTGCGATTATGTATTATCGCGT
*
48120 TGCAATAGTCAGAATCGC
65 TGCAATAGTCAGAATCAC
48138 GTTGCGAT
1 GTTGCGAT
48146 TTACATATTC
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
80 2 0.02
81 54 0.66
82 26 0.32
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (82 bp):
GTTGCGATAGTCAGAATCGCGTTGCGATTATGTAGAATCGCGTTGCGATTATGTATTATCGCGTT
GCAATAGTCAGAATCAC
Found at i:48195 original size:21 final size:20
Alignment explanation
Indices: 48171--48248 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 20
48161 GCGATTTTAC
48171 AAAATCGCAACGCGTATTTGG
1 AAAATCGCAACGCG-ATTTGG
* * *
48192 AAAATCGCAATGCGA-TAGTC
1 AAAATCGCAACGCGATTTG-G
48212 AAAATCGCAACGCGAATTTGG
1 AAAATCGCAACGCG-ATTTGG
*
48233 AAAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
48249 AGTCAAAATC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
19 2 0.04
20 16 0.34
21 27 0.57
22 2 0.04
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTGG
Found at i:48217 original size:20 final size:20
Alignment explanation
Indices: 48192--48260 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 20
48182 GCGTATTTGG
48192 AAAATCGCAATGCGATAGTC
1 AAAATCGCAATGCGATAGTC
* * *
48212 AAAATCGCAACGCGA-ATTTGG
1 AAAATCGCAATGCGATA-GT-C
48233 AAAATCGCAATGCGATAGTC
1 AAAATCGCAATGCGATAGTC
48253 AAAATCGC
1 AAAATCGC
48261 GTTGCGAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 23 0.57
21 15 0.38
22 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (20 bp):
AAAATCGCAATGCGATAGTC
Found at i:48269 original size:41 final size:41
Alignment explanation
Indices: 48170--48260 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
48160 TGCGATTTTA
*
48170 CAAAATCGCAACGCGTATTTGGAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATAGT
48211 CAAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATAGT
48252 CAAAATCGC
1 CAAAATCGC
48261 GTTGCGAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATAGT
Found at i:48275 original size:41 final size:41
Alignment explanation
Indices: 48170--48276 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
48160 TGCGATTTTA
* *
48170 CAAAATCGCAACGCGTATTTGGAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGAATATGGAAAATCGCAATGCGATAGT
*
48211 CAAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGAATATGGAAAATCGCAATGCGATAGT
***
48252 CAAAATCGCGTTGCGAATATGGAAA
1 CAAAATCGCAACGCGAATATGGAAA
48277 CTGATTTGTG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATGGAAAATCGCAATGCGATAGT
Found at i:48319 original size:19 final size:19
Alignment explanation
Indices: 48291--48329 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
48281 TTTGTGATAC
*
48291 TAGAGATCGCGTTGCGATT
1 TAGAGATCGCATTGCGATT
* *
48310 TAGAGCTCGCATTGCTATT
1 TAGAGATCGCATTGCGATT
48329 T
1 T
48330 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (19 bp):
TAGAGATCGCATTGCGATT
Found at i:49639 original size:18 final size:18
Alignment explanation
Indices: 49616--49650 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49606 TTTTCTTTTA
*
49616 AAAATTATAATTTAAAAT
1 AAAATTAAAATTTAAAAT
49634 AAAATTAAAATTTAAAA
1 AAAATTAAAATTTAAAA
49651 AAAGTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATTAAAATTTAAAAT
Found at i:50412 original size:21 final size:21
Alignment explanation
Indices: 50386--50446 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
50376 TGCAGAGATT
*
50386 TCATCCCCAAACGGCTAGAAA
1 TCATCCCCAAACAGCTAGAAA
*
50407 TCAT-CCCAAACAGCTCGAAA
1 TCATCCCCAAACAGCTAGAAA
*
50427 TCATCCCC-AATAGCTAGAAA
1 TCATCCCCAAACAGCTAGAAA
50447 CGACCACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 28 0.80
21 7 0.20
ACGTcount: A:0.39, C:0.33, G:0.11, T:0.16
Consensus pattern (21 bp):
TCATCCCCAAACAGCTAGAAA
Found at i:53911 original size:21 final size:20
Alignment explanation
Indices: 53885--53926 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
53875 TACAGAGATT
53885 TCATCCCCAAACGGCTAGAAA
1 TCAT-CCCAAACGGCTAGAAA
*
53906 TCATCCCTAACGGCTAGAAA
1 TCATCCCAAACGGCTAGAAA
53926 T
1 T
53927 GGCCACAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.36, C:0.31, G:0.14, T:0.19
Consensus pattern (20 bp):
TCATCCCAAACGGCTAGAAA
Found at i:54666 original size:22 final size:22
Alignment explanation
Indices: 54641--54682 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
54631 CTTAAGTCAC
54641 TAAA-AATAATGTTTTATTTATA
1 TAAATAATAAT-TTTTATTTATA
*
54663 TAAATAATTATTTTTATTTA
1 TAAATAATAATTTTTATTTA
54683 CATTATATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TAAATAATAATTTTTATTTATA
Done.