Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009096.1 Hibiscus syriacus cultivar Beakdansim tig00112543_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: 48855
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:18 original size:13 final size:13
Alignment explanation
Indices: 1--27 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1 TTTTTATTTTTTA
1 TTTTTATTTTTTA
14 TTTTTATTTTTTA
1 TTTTTATTTTTTA
27 T
1 T
28 ATCCTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:9192 original size:137 final size:137
Alignment explanation
Indices: 8946--9463 Score: 770
Period size: 137 Copynumber: 3.8 Consensus size: 137
8936 GATATTTTAG
8946 GAAACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTT
1 GAAACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTT
*
9011 TAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCA-TCGATCAAAACTCCTCATC
66 TAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACT-GATCAGAACTCCTCATC
*
9075 ATGAAGGA
130 ACGAAGGA
* * *
9083 GAAACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAATCGTGTTATCTCAAATATCTT
1 GAAACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTT
* * *
9148 TAAAGATGGCCAGACGTTCTCATCACCAAGGAACAATGTCATCCACTAATCAGAACTCCTCATCA
66 TAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAACTCCTCATCA
9213 CGAAGGA
131 CGAAGGA
* * * * * *
9220 GCAACATCATCCTTAGATAGCCAGATGTCCTTATCACGAAGAAACCATGTTATCTCAAATATCTT
1 GAAACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTT
* * * *
9285 TAAAGATGGCTAGACATCCTCATCACGAAGGAACAATTTCATCCACTGACCAGAACTCCTCATCA
66 TAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAACTCCTCATCA
*
9350 CGTAGGA
131 CGAAGGA
** * * *
9357 GCTGA-GTCATCCTCAGATAACTAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCT
1 G-AAACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCT
* *
9421 TCAAAGATGGCCAGACGTCCTCATCACGAAGGAATAATGTCAT
65 TTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCAT
9464 ACACCAGTTG
Statistics
Matches: 343, Mismatches: 36, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
137 341 0.99
138 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (137 bp):
GAAACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTT
TAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAACTCCTCATCA
CGAAGGA
Found at i:10193 original size:20 final size:22
Alignment explanation
Indices: 10156--10206 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
10146 ATAGTGATCA
* *
10156 GAATAGTAACCAGTGGTGG-T-
1 GAATAGTGACCAGCGGTGGCTG
*
10176 GAATAGTGACCGGCGGTGGCTG
1 GAATAGTGACCAGCGGTGGCTG
10198 GAATAGTGA
1 GAATAGTGA
10207 TCGTCCGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 16 0.62
21 1 0.04
22 9 0.35
ACGTcount: A:0.27, C:0.12, G:0.39, T:0.22
Consensus pattern (22 bp):
GAATAGTGACCAGCGGTGGCTG
Found at i:11091 original size:2 final size:2
Alignment explanation
Indices: 11084--11125 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
11074 GTCATGTTTA
11084 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
11126 TACTTTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15760 original size:15 final size:14
Alignment explanation
Indices: 15736--15777 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
15726 TGACAGTAAG
*
15736 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
15751 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
15765 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
15778 GTATCTCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:15768 original size:20 final size:20
Alignment explanation
Indices: 15736--15777 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
15726 TGACAGTAAG
*
15736 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
15756 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
15776 TT
1 TT
15778 GTATCTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:16251 original size:3 final size:3
Alignment explanation
Indices: 16235--16317 Score: 150
Period size: 3 Copynumber: 28.0 Consensus size: 3
16225 TGTAATTTTA
*
16235 AAT AAT -AT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16282 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16318 GAGTAAAAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 2 0.03
3 75 0.97
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:16721 original size:114 final size:112
Alignment explanation
Indices: 16574--16916 Score: 571
Period size: 112 Copynumber: 3.0 Consensus size: 112
16564 TTTTGATGAG
* *
16574 TTCTTCTCATTATGAACTTTCTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
** * * * *
16639 AAAAAAATAACCCATCAAGTAATAGATTTGAG-CAAAAAGGTTGAACAAA
65 GCAAAAATAATCCATCAAGTGAT-GAATTCAGAC-AAAAGGTTGAACAAA
16688 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGG
1 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGG
16753 CAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 CAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
*
16800 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGG
1 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGG
16865 CAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 CAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
16912 TTCTT
1 TTCTT
16917 AATTCTTCAG
Statistics
Matches: 219, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
112 137 0.63
113 27 0.12
114 55 0.25
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGG
CAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
Found at i:16969 original size:92 final size:92
Alignment explanation
Indices: 16827--17008 Score: 337
Period size: 92 Copynumber: 2.0 Consensus size: 92
16817 TTCTTCTTCC
* **
16827 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGCAAAAATAATCCATCAAGTGATGAATT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTATGAAAAAAATAATCCATCAAGTGATGAATT
16892 CAGACAAAAGGTTGAACAAATTCTTAA
66 CAGACAAAAGGTTGAACAAATTCTTAA
16919 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTATGAAAAAAATAATCCATCAAGTGATGAATT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTATGAAAAAAATAATCCATCAAGTGATGAATT
16984 CAGACAAAAGGTTGAACAAATTCTT
66 CAGACAAAAGGTTGAACAAATTCTT
17009 CTCATTATGA
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 87 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (92 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTATGAAAAAAATAATCCATCAAGTGATGAATT
CAGACAAAAGGTTGAACAAATTCTTAA
Found at i:17205 original size:116 final size:112
Alignment explanation
Indices: 16919--17289 Score: 566
Period size: 116 Copynumber: 3.3 Consensus size: 112
16909 AAATTCTTAA
* ** * **
16919 TTCTTCAGATGAGTTCTTCTCATTATGAACTTCTA-TGAAAAAAATAATCCATCAAGTGAT-GAA
1 TTCTTCAGATGAGTTCTTCTCATTATGAAC-TCTACTGGAAAAGCTGATCCATCAAGTGATGGGT
* * *
16982 TTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
65 TTGAG-CAAAAGGTTGAACAAATTCTTCTCATTGTGAATTTCTTCTTCC
*
17031 TTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATCAAGTGATGGGT
1 TTCTTCAGATGAGTTCTTCTCATTATGAACTC-TACTGGAAAAGCTGATCCATCAAGTGATGGGT
17096 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTGTGAATTTCTTCTTCC
65 TTGAGCAAAAGGTTGAACAAATTCTTCTCATTGTGAATTTCTTCTTCC
17144 TTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGCTGATCCATCAAGTGATG
1 TTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTA-CTGGAAAAGCTGATCCATCAAGTGATG
*
17209 GGTTTGAGTAAAAGGTTGAACAAATTCTTCTCATTGTGAATTTCTTCTTCC
62 GGTTTGAGCAAAAGGTTGAACAAATTCTTCTCATTGTGAATTTCTTCTTCC
17260 TTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTCTTCAGATGAGTTCTTCTCATTATGAAC
17290 CTTCTCTTCG
Statistics
Matches: 240, Mismatches: 12, Indels: 13
0.91 0.05 0.05
Matches are distributed among these distances:
111 2 0.01
112 31 0.13
113 92 0.38
114 5 0.02
115 1 0.00
116 109 0.45
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (112 bp):
TTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGGAAAAGCTGATCCATCAAGTGATGGGTT
TGAGCAAAAGGTTGAACAAATTCTTCTCATTGTGAATTTCTTCTTCC
Found at i:18593 original size:83 final size:83
Alignment explanation
Indices: 17998--18592 Score: 1048
Period size: 83 Copynumber: 7.2 Consensus size: 83
17988 TTCATCTTTT
* * * * *
17998 AATTCCAATGATTGGTTCTG-CCAAACTAGATCAAATAACTCAAAGAACACTTCCAAAAGATACT
1 AATT-CAATGATTGATTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
18062 ATTGGCAAATTCATCTTCCA
64 ATTGGCAAATTCATCTTCCA
18082 AATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
18147 CGGCAAATTCATCTTCCA
66 TGGCAAATTCATCTTCCA
18165 AATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
18230 CGGCAAATTCATCTTCCA
66 TGGCAAATTCATCTTCCA
18248 AATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* *
18313 TGGTAAATTCCTCTTCCA
66 TGGCAAATTCATCTTCCA
*
18331 AATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
18396 TGGCAAATTCATCTTCCA
66 TGGCAAATTCATCTTCCA
18414 AATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* *
18479 TGGTAAATTCCTCTTCCA
66 TGGCAAATTCATCTTCCA
*
18497 AATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
18562 TGGCAAATTCATCTTCCA
66 TGGCAAATTCATCTTCCA
18580 AATTCAATGATTG
1 AATTCAATGATTG
18593 GACTAAGATA
Statistics
Matches: 492, Mismatches: 18, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
83 486 0.99
84 6 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (83 bp):
AATTCAATGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
TGGCAAATTCATCTTCCA
Found at i:19374 original size:16 final size:16
Alignment explanation
Indices: 19353--19389 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
19343 GCATATTCAA
19353 AAATAAATTGAATCTC-
1 AAATAAATTGAA-CTCG
19369 AAATAAATTGAACTCG
1 AAATAAATTGAACTCG
19385 AAATA
1 AAATA
19390 GATAGAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.27
Consensus pattern (16 bp):
AAATAAATTGAACTCG
Found at i:19728 original size:5 final size:5
Alignment explanation
Indices: 19710--19777 Score: 55
Period size: 5 Copynumber: 12.6 Consensus size: 5
19700 CTTGACCCTC
* * *
19710 TTTCTT TTTTT TTTCT TTTCT TTTCT TTCTAT TTTCTAT TTTTT TTTCT
1 TTTC-T TTTCT TTTCT TTTCT TTTCT TT-TCT TTTC--T TTTCT TTTCT
*
19759 TTTCT TTCTTT TTTCT TTT
1 TTTCT TT-TCT TTTCT TTT
19778 TTCTTCAAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
5 35 0.70
6 11 0.22
7 4 0.08
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:19729 original size:16 final size:16
Alignment explanation
Indices: 19710--19777 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
19700 CTTGACCCTC
19710 TTTCTTTTTTTTTTCT
1 TTTCTTTTTTTTTTCT
* * *
19726 TTTCTTTTCTTTCTAT
1 TTTCTTTTTTTTTTCT
19742 TTTCTATTTTTTTTTCT
1 TTTCT-TTTTTTTTTCT
*
19759 TTTCTTTCTTTTTTCT
1 TTTCTTTTTTTTTTCT
19775 TTT
1 TTT
19778 TTCTTCAAGC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 31 0.70
17 13 0.30
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTTTTTTTTCT
Found at i:19745 original size:7 final size:7
Alignment explanation
Indices: 19708--19782 Score: 57
Period size: 7 Copynumber: 10.6 Consensus size: 7
19698 ACCTTGACCC
19708 TCTTTCTT
1 TCTTT-TT
*
19716 TTTTTTT
1 TCTTTTT
19723 TCTTTTCT
1 TCTTTT-T
*
19731 T-TTCTT
1 TCTTTTT
*
19737 TCTATTT
1 TCTTTTT
19744 TCTATTTT
1 TCT-TTTT
19752 T-TTTTCT
1 TCTTTT-T
*
19759 T-TTCTT
1 TCTTTTT
19765 TCTTTTT
1 TCTTTTT
19772 TCTTTTT
1 TCTTTTT
19779 TCTT
1 TCTT
19783 CAAGCATAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
6 7 0.13
7 37 0.69
8 10 0.19
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (7 bp):
TCTTTTT
Found at i:19760 original size:28 final size:26
Alignment explanation
Indices: 19708--19779 Score: 101
Period size: 28 Copynumber: 2.7 Consensus size: 26
19698 ACCTTGACCC
*
19708 TCTTTCTTTTT-TTTTTCTTTTCTTT
1 TCTTTCTTTTTCTTTTTTTTTTCTTT
19733 TCTTTCTATTTTCTATTTTTTTTTCTTT
1 TCTTTCT-TTTTCT-TTTTTTTTTCTTT
19761 TCTTTCTTTTTTCTTTTTT
1 TCTTTC-TTTTTCTTTTTT
19780 CTTCAAGCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
25 7 0.17
26 4 0.10
27 6 0.14
28 24 0.57
29 1 0.02
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (26 bp):
TCTTTCTTTTTCTTTTTTTTTTCTTT
Found at i:30442 original size:52 final size:52
Alignment explanation
Indices: 30376--30482 Score: 139
Period size: 52 Copynumber: 2.1 Consensus size: 52
30366 CTTGACAGAA
* *
30376 AAAAATAATGAAATAAAATACTTGCAAAGAAA-AA-TAAAACATATAAATATTAT
1 AAAAATAATGAAATAAAAAACTTGAAAAGAAAGAATTAAAA-AT-TAAATA-TAT
*
30429 AAAAATAAT-AAATAAAAAATTTGAAAAGAAAGAATTAAAAATTAAATATAT
1 AAAAATAATGAAATAAAAAACTTGAAAAGAAAGAATTAAAAATTAAATATAT
30480 AAA
1 AAA
30483 TTTTTAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
51 6 0.12
52 25 0.51
53 13 0.27
54 5 0.10
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (52 bp):
AAAAATAATGAAATAAAAAACTTGAAAAGAAAGAATTAAAAATTAAATATAT
Found at i:31975 original size:15 final size:14
Alignment explanation
Indices: 31951--31992 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
31941 TGACAGTAAG
*
31951 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
31966 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
31980 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
31993 GTATCTCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:31983 original size:20 final size:20
Alignment explanation
Indices: 31951--31992 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31941 TGACAGTAAG
*
31951 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
31971 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
31991 TT
1 TT
31993 GTATCTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:32466 original size:3 final size:3
Alignment explanation
Indices: 32450--32550 Score: 179
Period size: 3 Copynumber: 34.3 Consensus size: 3
32440 TGTAATTTTA
*
32450 AAT AAT -AT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
32497 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
32544 AAT AAT A
1 AAT AAT A
32551 TGAGTAAAAA
Statistics
Matches: 94, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 4 0.04
3 90 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:40130 original size:54 final size:53
Alignment explanation
Indices: 40017--40190 Score: 226
Period size: 54 Copynumber: 3.2 Consensus size: 53
40007 CTCATAGGGT
** *
40017 GTACCGATACCCTTATGCCAATTTTGG-TGTGAGAAAAACATAATGCCAAATGG
1 GTACCGATACCC-TATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
*
40070 GTACCGATACCTCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCAAATGG
1 GTACCGATACC-CTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
* * *
40124 GCACCGATACCCCTATGCTAATTTTTGGCTCCGAGAAAAACAGAATGCTC-GATGG
1 GTACCGATA-CCCTATGCCAA-TTTTGGCTCCGAGAAAAACAGAATGC-CAAATGG
40179 GTACCGATACCC
1 GTACCGATACCC
40191 CCTTAGAGGT
Statistics
Matches: 107, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
53 25 0.23
54 42 0.39
55 39 0.36
56 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (53 bp):
GTACCGATACCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
Found at i:40179 original size:55 final size:54
Alignment explanation
Indices: 40017--40191 Score: 237
Period size: 55 Copynumber: 3.2 Consensus size: 54
40007 CTCATAGGGT
* ** *
40017 GTACCGATACCCTTATGCCAATTTTGG-TGTGAGAAAAACATAATGCCAAATGG
1 GTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
* *
40070 GTACCGATACCTCTATGCCAATTTTGGCTCCGAGAAAAATAGAATGCCAAATGG
1 GTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
* * *
40124 GCACCGATACCCCTATGCTAATTTTTGGCTCCGAGAAAAACAGAATGCTC-GATGG
1 GTACCGATACCCCTATGCCAA-TTTTGGCTCCGAGAAAAACAGAATGC-CAAATGG
40179 GTACCGATACCCC
1 GTACCGATACCCC
40192 CTTAGAGGTA
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
53 25 0.23
54 40 0.37
55 41 0.38
56 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (54 bp):
GTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGG
Found at i:47862 original size:18 final size:19
Alignment explanation
Indices: 47822--47863 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
47812 TGTTTTGGAA
47822 TTTGGATGTTTGAATTGTTG
1 TTTGGATGTTT-AATTGTTG
*
47842 TTTGGATGTTT-ATTTTTG
1 TTTGGATGTTTAATTGTTG
47860 TTTG
1 TTTG
47864 AATGATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.12, C:0.00, G:0.26, T:0.62
Consensus pattern (19 bp):
TTTGGATGTTTAATTGTTG
Done.