Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007374.1 Hibiscus syriacus cultivar Beakdansim tig00019791_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: 77085
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:1750 original size:3 final size:3
Alignment explanation
Indices: 1744--1788 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
1734 TATTATAATT
*
1744 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1789 TTTAAAATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2926 original size:6 final size:5
Alignment explanation
Indices: 2903--2936 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
2893 AAATCGGTCT
2903 GACCC GACCC GA-CC GACCCC GACCC GACCC GACC
1 GACCC GACCC GACCC GA-CCC GACCC GACCC GACC
2937 GTTGACCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.21, C:0.59, G:0.21, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:9266 original size:72 final size:70
Alignment explanation
Indices: 9159--9297 Score: 233
Period size: 72 Copynumber: 2.0 Consensus size: 70
9149 AATGAAATCG
* * *
9159 TTGTGTGTTTGATGAGTTTTCTCTCTTCAATTTATCTATTCATTCTCTCAGATCGTTGTGTGTTG
1 TTGTGTGTTGGAAGAGTTTTCTCTCTCCAATTTATCTATTCATTCTCTCAGATCGTTGTGTGTTG
9224 GAAAT
66 GAAAT
9229 TTGTGTGTTGGAAGAGTGTTTCTCTCTCCAACTTTATCTATTCATTCTCTCAGATCGTTGTGTGT
1 TTGTGTGTTGGAAGAGT-TTTCTCTCTCCAA-TTTATCTATTCATTCTCTCAGATCGTTGTGTGT
9294 TGGA
64 TGGA
9298 TGAGTGTTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 15 0.23
71 12 0.19
72 37 0.58
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (70 bp):
TTGTGTGTTGGAAGAGTTTTCTCTCTCCAATTTATCTATTCATTCTCTCAGATCGTTGTGTGTTG
GAAAT
Found at i:9317 original size:57 final size:57
Alignment explanation
Indices: 9229--9337 Score: 200
Period size: 57 Copynumber: 1.9 Consensus size: 57
9219 TGTTGGAAAT
*
9229 TTGTGTGTTGGAAGAGTGTTTCTCTCTCCAACTTTATCTATTCATTCTCTCAGATCG
1 TTGTGTGTTGGAAGAGTGTTTCTCTATCCAACTTTATCTATTCATTCTCTCAGATCG
*
9286 TTGTGTGTTGGATGAGTGTTTCTCTATCCAACTTTATCTATTCATTCTCTCA
1 TTGTGTGTTGGAAGAGTGTTTCTCTATCCAACTTTATCTATTCATTCTCTCA
9338 TACTTTTTCG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (57 bp):
TTGTGTGTTGGAAGAGTGTTTCTCTATCCAACTTTATCTATTCATTCTCTCAGATCG
Found at i:9413 original size:70 final size:70
Alignment explanation
Indices: 9300--9434 Score: 234
Period size: 70 Copynumber: 1.9 Consensus size: 70
9290 GTGTTGGATG
*
9300 AGTGTTTCTCTATCCAACTTTATCTATTCATTCTCTCATACTTTTTCGAGATATGCAAATTCAGA
1 AGTGTTTCTCTATCCAACTTTATCTATTCATTCTCTCAGACTTTTTCGAGATATGCAAATTCAGA
9365 AAGAT
66 AAGAT
* * *
9370 AGTGTTTTTCTCTCCAACTTTATCTATTCATTCTCTTAGACTTTTTCGAGATATGCAAATTCAGA
1 AGTGTTTCTCTATCCAACTTTATCTATTCATTCTCTCAGACTTTTTCGAGATATGCAAATTCAGA
9435 CTGAAAATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (70 bp):
AGTGTTTCTCTATCCAACTTTATCTATTCATTCTCTCAGACTTTTTCGAGATATGCAAATTCAGA
AAGAT
Found at i:12904 original size:37 final size:37
Alignment explanation
Indices: 12835--12939 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
12825 CATTTTCGTC
* * * *
12835 CTACTAGAATTTAAATTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
12872 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
12909 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
12940 CTACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:13447 original size:21 final size:21
Alignment explanation
Indices: 13406--13500 Score: 70
Period size: 21 Copynumber: 4.4 Consensus size: 21
13396 TGATTTTTTT
13406 TACACTATATATTATTA-TTATA
1 TACA-TATAT-TTATTATTTATA
* *
13428 TACATATATTTTTTATTTATT
1 TACATATATTTATTATTTATA
* * *
13449 TATAT-TCATTTGGTTATTTTTAA
1 TACATAT-ATTT-ATTATTTAT-A
13472 TAC-TATATTTATTATTTATA
1 TACATATATTTATTATTTATA
*
13492 TATATATAT
1 TACATATAT
13501 ACTTTTTTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
20 9 0.16
21 29 0.51
22 16 0.28
23 3 0.05
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (21 bp):
TACATATATTTATTATTTATA
Found at i:13546 original size:2 final size:2
Alignment explanation
Indices: 13539--13577 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
13529 GTATTATTAC
13539 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
13578 TGTAATTATT
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:13706 original size:29 final size:29
Alignment explanation
Indices: 13674--13743 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
13664 ATTATATGTA
13674 TATTTTTATATTTGGTTTATATATTTAT-T
1 TATTTTTATATTTGGTTT-TATATTTATAT
* *
13703 TATTTTTGGT-TTTGGTTTTTTATTTATAT
1 TATTTTT-ATATTTGGTTTTATATTTATAT
*
13732 TA-TATTATATTT
1 TATTTTTATATTT
13744 TCATATTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
27 1 0.03
28 14 0.41
29 18 0.53
30 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (29 bp):
TATTTTTATATTTGGTTTTATATTTATAT
Found at i:13828 original size:4 final size:4
Alignment explanation
Indices: 13792--13842 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
13782 TATTTTACTC
* * *
13792 ATTT ATAT ATAT ATTT -TTT A-AT ATTT CATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT ATTT
13839 ATTT
1 ATTT
13843 TTTTTACTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 5 0.12
4 31 0.77
5 4 0.10
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:13848 original size:17 final size:17
Alignment explanation
Indices: 13793--13896 Score: 63
Period size: 17 Copynumber: 6.1 Consensus size: 17
13783 ATTTTACTCA
* *
13793 TTTATATATATATTTTT
1 TTTATTTATTTATTTTT
* *
13810 TAATATTTCATTTA-TTTA
1 T-TTATTT-ATTTATTTTT
13828 TTTATTTATTTATTTTT
1 TTTATTTATTTATTTTT
* *
13845 TTTACTTATTT-TTATTC
1 TTTATTTATTTATT-TTT
*
13862 TTCATTT-TTTCATTTTT
1 TTTATTTATTT-ATTTTT
*
13879 TTCATTT-TTTCATTTTT
1 TTTATTTATTT-ATTTTT
13896 T
1 T
13897 CCCTCTAACA
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
16 10 0.14
17 46 0.66
18 10 0.14
19 4 0.06
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTATTTATTTTT
Found at i:13880 original size:9 final size:8
Alignment explanation
Indices: 13862--13897 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
13852 ATTTTTATTC
13862 TTCATTTT
1 TTCATTTT
13870 TTCATTTTT
1 TTCA-TTTT
13879 TTCATTTT
1 TTCATTTT
13887 TTCATTTT
1 TTCATTTT
13895 TTC
1 TTC
13898 CCTCTAACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (8 bp):
TTCATTTT
Found at i:15519 original size:2 final size:2
Alignment explanation
Indices: 15512--15556 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
15502 TAATCTTGAC
15512 TA 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 TA TA
15553 TA TA
1 TA TA
15557 GAGAATAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20667 original size:19 final size:19
Alignment explanation
Indices: 20624--20667 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
20614 AAATGACCAA
**
20624 CGAATTCGCAACGCGGTCT
1 CGAATTCGCAACGCGAACT
20643 CGAATTCGCAACGCGAACT
1 CGAATTCGCAACGCGAACT
*
20662 CTAATT
1 CGAATT
20668 TTGCAACACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (19 bp):
CGAATTCGCAACGCGAACT
Found at i:20747 original size:20 final size:20
Alignment explanation
Indices: 20724--20799 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
20714 CACATAAGTC
*
20724 AAATTCGCAACGCGATTTCT
1 AAATTCGCAACACGATTTCT
20744 AAATTCGCAACACTGAATTTC-
1 AAATTCGCAACAC-G-ATTTCT
* *
20765 GAATTCGCAACTCGATTT-T
1 AAATTCGCAACACGATTTCT
*
20784 CGAATTCGCAACACGA
1 -AAATTCGCAACACGA
20800 ATTTTAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.08
20 27 0.56
21 12 0.25
22 5 0.10
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (20 bp):
AAATTCGCAACACGATTTCT
Found at i:20781 original size:41 final size:40
Alignment explanation
Indices: 20725--20803 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 40
20715 ACATAAGTCA
20725 AATTCGCAACGCGA-TTTCTAAATTCGCAACACTGAATTTCG
1 AATTCGCAACGCGATTTTC-AAATTCGCAACAC-GAATTTCG
* *
20766 AATTCGCAACTCGATTTTCGAATTCGCAACACGAATTT
1 AATTCGCAACGCGATTTTCAAATTCGCAACACGAATTT
20804 TAATTTCACA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 6 0.17
41 25 0.71
42 4 0.11
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (40 bp):
AATTCGCAACGCGATTTTCAAATTCGCAACACGAATTTCG
Found at i:20901 original size:27 final size:27
Alignment explanation
Indices: 20868--20930 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
20858 CGCAGCAGCA
20868 GCAACTCATAACCTAAATCCCTAAATT
1 GCAACTCATAACCTAAATCCCTAAATT
*
20895 GTAACTCATAACCTAAATCCCTAAATT
1 GCAACTCATAACCTAAATCCCTAAATT
20922 GCAACTCAT
1 GCAACTCAT
20931 TCCATCTCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.40, C:0.29, G:0.05, T:0.27
Consensus pattern (27 bp):
GCAACTCATAACCTAAATCCCTAAATT
Found at i:21020 original size:16 final size:16
Alignment explanation
Indices: 20999--21038 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20989 TCCCTATCTC
*
20999 TAATTTTTTTTTTACA
1 TAATTTTTTTTCTACA
* *
21015 TAATTTTATTTCTATA
1 TAATTTTTTTTCTACA
21031 TAATTTTT
1 TAATTTTT
21039 CAATGATTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TAATTTTTTTTCTACA
Found at i:21814 original size:24 final size:24
Alignment explanation
Indices: 21782--21835 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
21772 GTATTCGAAA
*
21782 TTTGATCTTGGTCTATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
21806 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
21830 TTTGAT
1 TTTGAT
21836 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:24104 original size:18 final size:18
Alignment explanation
Indices: 24071--24106 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24061 AAGCAAAAGG
**
24071 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
24089 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
24107 CAACTGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:25925 original size:21 final size:21
Alignment explanation
Indices: 25901--25966 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
25891 AAACGGTGGG
*
25901 AGGGACCTCTTGAATGATGAC
1 AGGGGCCTCTTGAATGATGAC
* * **
25922 AGGGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAATGATGAC
25943 AGGGGCCTCTTGAATGATGAC
1 AGGGGCCTCTTGAATGATGAC
25964 AGG
1 AGG
25967 TGAATCGGGC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTGAATGATGAC
Found at i:25945 original size:42 final size:42
Alignment explanation
Indices: 25886--25966 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
25876 GTGAATCGGG
25886 CTCTTAAACGGTGGGAGGGACCTCTTGAATGATGACAGGGGC
1 CTCTTAAACGGTGGGAGGGACCTCTTGAATGATGACAGGGGC
* *
25928 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGACAGG
1 CTCTTAAACGGTGGGAGGGACCTCTTGAATGATGACAGG
25967 TGAATCGGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (42 bp):
CTCTTAAACGGTGGGAGGGACCTCTTGAATGATGACAGGGGC
Found at i:26323 original size:63 final size:64
Alignment explanation
Indices: 26213--26350 Score: 163
Period size: 63 Copynumber: 2.2 Consensus size: 64
26203 GTAAAGTAGA
* * * * * *
26213 TACCTCACCACGTAAAGCACCATTGTCATCGCGTAAAACATCTACCTCACCACATAAAG-ACTG
1 TACCTCATCACGCAAAGCACCATTGTCATCACGTAAAACACCGACCTCACCACAGAAAGCACTG
* ** * *
26276 TACCTCATCACGCCAAGCACCATTGTCATCACGTAAAGTACCGACCTCATCACGGAAAGCACTG
1 TACCTCATCACGCAAAGCACCATTGTCATCACGTAAAACACCGACCTCACCACAGAAAGCACTG
26340 -ACCTCATCACG
1 TACCTCATCACG
26351 TAACTCTCCT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 59 0.94
64 4 0.06
ACGTcount: A:0.33, C:0.35, G:0.13, T:0.20
Consensus pattern (64 bp):
TACCTCATCACGCAAAGCACCATTGTCATCACGTAAAACACCGACCTCACCACAGAAAGCACTG
Found at i:26325 original size:21 final size:21
Alignment explanation
Indices: 26193--26353 Score: 85
Period size: 21 Copynumber: 7.7 Consensus size: 21
26183 TAGAGTGGCT
* ***
26193 ACCTCATCACGTAAAGTAGAT
1 ACCTCATCACGTAAAGCACCG
*
26214 ACCTCACCACGTAAAGCACC-
1 ACCTCATCACGTAAAGCACCG
** * * * *
26234 ATTGTCATCGCGTAAAACATCT
1 A-CCTCATCACGTAAAGCACCG
* * *
26256 ACCTCACCACATAAAG-ACTG
1 ACCTCATCACGTAAAGCACCG
**
26276 TACCTCATCACGCCAAGCACC-
1 -ACCTCATCACGTAAAGCACCG
** *
26297 ATTGTCATCACGTAAAGTACCG
1 A-CCTCATCACGTAAAGCACCG
* *
26319 ACCTCATCACGGAAAGCACTG
1 ACCTCATCACGTAAAGCACCG
26340 ACCTCATCACGTAA
1 ACCTCATCACGTAA
26354 CTCTCCTAAC
Statistics
Matches: 99, Mismatches: 35, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
20 3 0.03
21 92 0.93
22 4 0.04
ACGTcount: A:0.34, C:0.33, G:0.13, T:0.20
Consensus pattern (21 bp):
ACCTCATCACGTAAAGCACCG
Found at i:27947 original size:20 final size:20
Alignment explanation
Indices: 27924--27961 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27914 CGCGTTGCGC
27924 TTTTCGTGTTACGAATTTCA
1 TTTTCGTGTTACGAATTTCA
*
27944 TTTTCGTGTTGCGAATTT
1 TTTTCGTGTTACGAATTT
27962 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53
Consensus pattern (20 bp):
TTTTCGTGTTACGAATTTCA
Found at i:27968 original size:20 final size:20
Alignment explanation
Indices: 27925--27968 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
27915 GCGTTGCGCT
* *
27925 TTTCGTGTTACGAATTTCAT
1 TTTCGTGTTACGAATTTAAG
*
27945 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTACGAATTTAAG
27965 TTTC
1 TTTC
27969 AAAATTCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTACGAATTTAAG
Found at i:28325 original size:22 final size:20
Alignment explanation
Indices: 28287--28328 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
28277 CTCTGAGAGA
*
28287 TGGAGATAGACGGATTTCGC
1 TGGAGATAGACGAATTTCGC
28307 TGGAGATAGGGACGAATTTCGC
1 TGGAGATA--GACGAATTTCGC
28329 CAAAGATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.26, C:0.14, G:0.36, T:0.24
Consensus pattern (20 bp):
TGGAGATAGACGAATTTCGC
Found at i:28478 original size:19 final size:20
Alignment explanation
Indices: 28456--28493 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28446 ACTATTGTGT
28456 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
28475 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
28494 TACGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:28494 original size:19 final size:20
Alignment explanation
Indices: 28464--28506 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
28454 GTTTCGAATT
*
28464 CGAAAATAAAATTCGCGTTG
1 CGAAAATAAAATACGCGTTG
*
28484 CGAAAAT-AAATACGCTTTG
1 CGAAAATAAAATACGCGTTG
28503 CGAA
1 CGAA
28507 TTTGACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (20 bp):
CGAAAATAAAATACGCGTTG
Found at i:28542 original size:20 final size:20
Alignment explanation
Indices: 28519--28609 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
28509 TGACTTCTGT
28519 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
* *
28539 GTTGCGATTTACATATTCGC
1 GTTGCGAATTACAAATTCGC
*
28559 GTTGCGAATTTGA-AAAATCGC
1 GTTGCGAA-TT-ACAAATTCGC
* * *
28580 GTTGTGATTTACATATTCGC
1 GTTGCGAATTACAAATTCGC
*
28600 ATTGCGAATT
1 GTTGCGAATT
28610 TGAAAACTAT
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.71
21 14 0.25
22 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:28579 original size:21 final size:21
Alignment explanation
Indices: 28555--28615 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
28545 ATTTACATAT
28555 TCGCGTTGCGAATTTGAAAAA
1 TCGCGTTGCGAATTTGAAAAA
* * *
28576 TCGCGTTGTG-ATTT-ACATAT
1 TCGCGTTGCGAATTTGA-AAAA
*
28596 TCGCATTGCGAATTTGAAAA
1 TCGCGTTGCGAATTTGAAAA
28616 CTATGTTCCG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.45
21 15 0.48
22 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGAAAAA
Found at i:28589 original size:41 final size:41
Alignment explanation
Indices: 28519--28615 Score: 144
Period size: 41 Copynumber: 2.4 Consensus size: 41
28509 TGACTTCTGT
*
28519 GTTGCGAA-TT-ACAAATTCGCGTTGCGATTTACATATTCGC
1 GTTGCGAATTTGA-AAAATCGCGTTGCGATTTACATATTCGC
*
28559 GTTGCGAATTTGAAAAATCGCGTTGTGATTTACATATTCGC
1 GTTGCGAATTTGAAAAATCGCGTTGCGATTTACATATTCGC
*
28600 ATTGCGAATTTGAAAA
1 GTTGCGAATTTGAAAA
28616 CTATGTTCCG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 8 0.15
41 43 0.83
42 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (41 bp):
GTTGCGAATTTGAAAAATCGCGTTGCGATTTACATATTCGC
Found at i:30826 original size:7 final size:7
Alignment explanation
Indices: 30809--30839 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
30799 ACGAAAGAAA
30809 AAAAAAT
1 AAAAAAT
30816 -AAAAAT
1 AAAAAAT
30822 AAAAAAT
1 AAAAAAT
30829 AAAAAAT
1 AAAAAAT
30836 AAAA
1 AAAA
30840 TATTAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:30827 original size:14 final size:15
Alignment explanation
Indices: 30808--30839 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
30798 AACGAAAGAA
30808 AAAAAAAT-AAAAAT
1 AAAAAAATAAAAAAT
30822 -AAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
30836 AAAA
1 AAAA
30840 TATTAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.44
14 6 0.38
15 3 0.19
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:32757 original size:54 final size:53
Alignment explanation
Indices: 32600--32973 Score: 321
Period size: 54 Copynumber: 6.9 Consensus size: 53
32590 ATACTTGAAA
* * * * *
32600 AATCTTCAAATAACGGGTCGGCTCCCTTTCTTTCAAGGAGTATA-AGACTCGAAC
1 AATCTTCACA-AACGGGTCCGCTCCCTATCCTTCAGGGAGTATAGA-ACTCGAAC
** * * * *
32654 AATCCTTGGC-AACGTGTCTGCTCCCTATTCGTTCA-GGAGTATA-AGACTCGAAT
1 AAT-CTTCACAAACGGGTCCGCTCCCTA-TCCTTCAGGGAGTATAGA-ACTCGAAC
*
32707 AATCTTCGACAAACGGGTCCGCTCCCTATCCGTCAGGGAGTATAGAACTCGAAC
1 AATCTTC-ACAAACGGGTCCGCTCCCTATCCTTCAGGGAGTATAGAACTCGAAC
*
32761 AATCTTCATAAAACGGGTCCGCTCCCTATCCGTTCAGGGAGTAT-GAACTCGAAC
1 AATCTTCA-CAAACGGGTCCGCTCCCTATCC-TTCAGGGAGTATAGAACTCGAAC
* * * *
32815 AATCTTCATAAAACGTGTTCGCTCTCTATTCCTTCA-GGAGTATAGAACTCGAAC
1 AATCTTCA-CAAACGGGTCCGCTCCCTA-TCCTTCAGGGAGTATAGAACTCGAAC
** * * *
32869 AATCTTCATGAACGGGGTCCGCTCTCTATTTCTTCAGAGAGTATAG-ACTCGAAC
1 AATCTTCACAAAC-GGGTCCGCTCCCTA-TCCTTCAGGGAGTATAGAACTCGAAC
* *** * *
32923 AATCTTCAACGAATTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 AATCTTC-ACAAACGGGTCCGCTCCCTA-TCCTTCAGGGAGTATAGAACTC
32974 AATCTTCAAC
Statistics
Matches: 274, Mismatches: 32, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
52 3 0.01
53 51 0.19
54 186 0.68
55 34 0.12
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (53 bp):
AATCTTCACAAACGGGTCCGCTCCCTATCCTTCAGGGAGTATAGAACTCGAAC
Found at i:32829 original size:108 final size:105
Alignment explanation
Indices: 32600--32973 Score: 362
Period size: 108 Copynumber: 3.5 Consensus size: 105
32590 ATACTTGAAA
* * * **
32600 AATCTTCAAATAACGGGTCGGCTCCCTTTCTTTCAAGGAGTATA-AGACTCGAACAATCCTT-GG
1 AATCTTCAAA-AACGGGTCCGCTCCCTATCCTTC-AGGAGTATAGA-ACTCGAACAAT-CTTCAT
* * * *
32663 CAACGTGTCTGCTCCCTATTCGTTCA-GGAGTATAAGACTCGAAT
62 AAACGGGTCCGCTCCCTATTCGTTCAGGGAGTAT-AGACTCGAAC
* *
32707 AATCTTCGACAAACGGGTCCGCTCCCTATCCGTCAGGGAGTATAGAACTCGAACAATCTTCATAA
1 AATCTTC-AAAAACGGGTCCGCTCCCTATCCTTCA-GGAGTATAGAACTCGAACAATCTTCAT-A
*
32772 AACGGGTCCGCTCCCTATCCGTTCAGGGAGTAT-GAACTCGAAC
63 AACGGGTCCGCTCCCTATTCGTTCAGGGAGTATAG-ACTCGAAC
* * * *
32815 AATCTTCATAAAACGTGTTCGCTCTCTATTCCTTCAGGAGTATAGAACTCGAACAATCTTCATGA
1 AATCTTCA-AAAACGGGTCCGCTCCCTA-TCCTTCAGGAGTATAGAACTCGAACAATCTTCATAA
* *
32880 ACGGGGTCCGCTCTCTATTTC-TTCAGAGAGTATAGACTCGAAC
64 AC-GGGTCCGCTCCCTA-TTCGTTCAGGGAGTATAGACTCGAAC
* *** *
32923 AATCTTCAACGAATTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 AATCTTCAA-AAACGGGTCCGCTCCCTA-TCCTTCAG-GAGTATAGAACTC
32974 AATCTTCAAC
Statistics
Matches: 226, Mismatches: 27, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
106 4 0.02
107 51 0.23
108 143 0.63
109 28 0.12
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (105 bp):
AATCTTCAAAAACGGGTCCGCTCCCTATCCTTCAGGAGTATAGAACTCGAACAATCTTCATAAAC
GGGTCCGCTCCCTATTCGTTCAGGGAGTATAGACTCGAAC
Found at i:32875 original size:162 final size:161
Alignment explanation
Indices: 32600--32931 Score: 390
Period size: 162 Copynumber: 2.1 Consensus size: 161
32590 ATACTTGAAA
* * * **
32600 AATCTTCAAATAACGGGTCGGCTCCCTTTCTTTCAAGGAGTATAAGACTCGAACAATCCTTGGCA
1 AATCTTCAAATAACGGGTCCGCTCCCTTCCGTTCAAGGAGTATAAGACTCGAACAATCCTTGAAA
* *
32665 ACGTGTCTGCTCCCTATTCGTTCAGGAGTATAAGACTCGAATAATCTTCGACAAAC-GGGTCCGC
66 ACGTGTCTGCTCCCTATTCCTTCAGGAGTATAAGACTCGAACAATCTTC-ACAAACGGGGTCCGC
*
32729 TCCCTA-TCCGTCAGGGAGTATAGAACTCGAAC
130 TCCCTATTCCGTCAGAGAGTATAG-ACTCGAAC
* *
32761 AATCTTCATAA-AACGGGTCCGCTCCCTATCCGTTCAGGGAGTATGA-ACTCGAACAAT-CTTCA
1 AATCTTCA-AATAACGGGTCCGCTCCCT-TCCGTTCAAGGAGTATAAGACTCGAACAATCCTT--
* * **
32823 TAAAACGTGT-TCGCTCTCTATTCCTTCAGGAGTAT-AGAACTCGAACAATCTTCATGAACGGGG
62 GAAAACGTGTCT-GCTCCCTATTCCTTCAGGAGTATAAG-ACTCGAACAATCTTCACAAACGGGG
* * *
32886 TCCGCTCTCTATTTCTTCAGAGAGTATAGACTCGAAC
125 TCCGCTCCCTATTCCGTCAGAGAGTATAGACTCGAAC
32923 AATCTTCAA
1 AATCTTCAA
32932 CGAATTTGTC
Statistics
Matches: 146, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
160 3 0.02
161 42 0.29
162 87 0.60
163 14 0.10
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (161 bp):
AATCTTCAAATAACGGGTCCGCTCCCTTCCGTTCAAGGAGTATAAGACTCGAACAATCCTTGAAA
ACGTGTCTGCTCCCTATTCCTTCAGGAGTATAAGACTCGAACAATCTTCACAAACGGGGTCCGCT
CCCTATTCCGTCAGAGAGTATAGACTCGAAC
Found at i:34342 original size:12 final size:12
Alignment explanation
Indices: 34309--34334 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34299 TCTTGAACTC
34309 CTTTTATTTTTT
1 CTTTTATTTTTT
34321 CTTTTATTTTTT
1 CTTTTATTTTTT
34333 CT
1 CT
34335 CTTTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (12 bp):
CTTTTATTTTTT
Found at i:34454 original size:7 final size:7
Alignment explanation
Indices: 34438--34481 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
34428 TTTATTATTA
*
34438 TTTTTCC
1 TTTTTTC
34445 TTTTTTC
1 TTTTTTC
34452 TTTTTTC
1 TTTTTTC
34459 TTTTTTC
1 TTTTTTC
* *
34466 TCTTTTA
1 TTTTTTC
34473 TTTTTTC
1 TTTTTTC
34480 TT
1 TT
34482 CAAGCGAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:34462 original size:21 final size:21
Alignment explanation
Indices: 34403--34481 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
34393 AATTTTCTCA
* *
34403 TTTTTTCCTTTTTCTTCTTCTC
1 TTTTTTCTTTTTTCTTTTTC-C
* * * *
34425 ATTTTT-ATTATTATTTTTCC
1 TTTTTTCTTTTTTCTTTTTCC
*
34445 TTTTTTCTTTTTTCTTTTTTC
1 TTTTTTCTTTTTTCTTTTTCC
* *
34466 TCTTTTATTTTTTCTT
1 TTTTTTCTTTTTTCTT
34482 CAAGCGAAAT
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 6 0.14
21 33 0.75
22 5 0.11
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTTCTTTTTTCTTTTTCC
Found at i:38365 original size:148 final size:146
Alignment explanation
Indices: 38146--38440 Score: 572
Period size: 148 Copynumber: 2.0 Consensus size: 146
38136 TTCAACACGA
38146 AGCCCGGCGGTTCAGGATAAATGCCAAGCTCTCATTTCCTCAAATTCATCTCAGTTATAACATTA
1 AGCCCGGCGGTTCAGGATAAATGCCAAGCTCTCATTTCCTCAAATTCATCTCAGTTATAACATTA
38211 ATGCCTAAATCTCCCAAGGCATTCTCAACCATCACTTCAGTGTTCCTTGAATTCCCTTAAAACAT
66 ATGCCTAAATCTCCCAAGGCATTCTCAACCATCACTTCAGTGTTCCTTGAATTCCCTTAAAACAT
38276 ATGTCCCCTAGATATG
131 ATGTCCCCTAGATATG
38292 AGCCCGGCGGTTCAGGATAAATGCCAATGCTCTCATTTCCTCAAATTCATCATCAGTTATAACAT
1 AGCCCGGCGGTTCAGGATAAATGCCAA-GCTCTCATTTCCTCAAATTCATC-TCAGTTATAACAT
38357 TAATGCCTAAATCTCCCAAGGCATTCTCAACCATCACTTCAGTGTTCCTTGAATTCCCTTAAAAC
64 TAATGCCTAAATCTCCCAAGGCATTCTCAACCATCACTTCAGTGTTCCTTGAATTCCCTTAAAAC
38422 ATATGTCCCCTAGATATG
129 ATATGTCCCCTAGATATG
38440 A
1 A
38441 AAAAATTGCT
Statistics
Matches: 147, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
146 27 0.18
147 23 0.16
148 97 0.66
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (146 bp):
AGCCCGGCGGTTCAGGATAAATGCCAAGCTCTCATTTCCTCAAATTCATCTCAGTTATAACATTA
ATGCCTAAATCTCCCAAGGCATTCTCAACCATCACTTCAGTGTTCCTTGAATTCCCTTAAAACAT
ATGTCCCCTAGATATG
Found at i:45841 original size:6 final size:6
Alignment explanation
Indices: 45830--45861 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
45820 ACGAAAGAAA
45830 AAAAAT AAAAAT AAAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT -AAAAAT AAAAAT AAAAAT A
45862 TTAACATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:45870 original size:14 final size:13
Alignment explanation
Indices: 45829--45859 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
45819 AACGAAAGAA
45829 AAAAAATAAAAAT
1 AAAAAATAAAAAT
45842 AAAAAATAAAAAT
1 AAAAAATAAAAAT
45855 AAAAA
1 AAAAA
45860 TATTAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:55651 original size:16 final size:16
Alignment explanation
Indices: 55630--55661 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
55620 TTACTTGTAA
55630 AGGTGATCTAATTGAC
1 AGGTGATCTAATTGAC
55646 AGGTGATCTAATTGAC
1 AGGTGATCTAATTGAC
55662 CTTCTTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
AGGTGATCTAATTGAC
Found at i:73392 original size:16 final size:17
Alignment explanation
Indices: 73361--73393 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
73351 GCTGATTCGA
*
73361 GAATTGATGCGTTGGTG
1 GAATTGAAGCGTTGGTG
73378 GAATTGAAG-GTTGGTG
1 GAATTGAAGCGTTGGTG
73394 ACAACTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.03, G:0.42, T:0.33
Consensus pattern (17 bp):
GAATTGAAGCGTTGGTG
Done.