Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001268.1 Hibiscus syriacus cultivar Beakdansim tig00002489_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: 64209
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:2671 original size:22 final size:22
Alignment explanation
Indices: 2639--2692 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2629 TTTTCCAAAT
*
2639 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAATCTACAGTTG
* *
2661 TTGTTGTGATAATCTACAGTTG
1 TCGTTGCGATAATCTACAGTTG
2683 TCGTTGCGAT
1 TCGTTGCGAT
2693 TTTGCAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.41
Consensus pattern (22 bp):
TCGTTGCGATAATCTACAGTTG
Found at i:2754 original size:21 final size:21
Alignment explanation
Indices: 2730--2783 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
2720 TATCGCAAAT
2730 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
2751 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
2772 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2784 TTTTCATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:2829 original size:41 final size:42
Alignment explanation
Indices: 2775--2909 Score: 177
Period size: 41 Copynumber: 3.2 Consensus size: 42
2765 TTGAAAATCG
* *
2775 CGTTGCGATTTTTCATTTCGCGTTGCGATAG-CATACAGTTAT
1 CGTTGCGATTTTTCAATTCGCGTTGCGATAGTC-TACAGTTGT
*
2817 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTTC-AATTCGCGTTGCGATAGTCTACAGTTGT
* *
2858 CGTTGCGATTTTGTAAATTCGCATTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTT-TCAATTCGCGTTGCGATAGTCTACAGTTGT
2901 CGTTGCGAT
1 CGTTGCGAT
2910 AGTTGAAAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
41 35 0.43
42 14 0.17
43 33 0.40
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (42 bp):
CGTTGCGATTTTTCAATTCGCGTTGCGATAGTCTACAGTTGT
Found at i:2863 original size:22 final size:22
Alignment explanation
Indices: 2835--2912 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
2825 TTTTCCAAAT
2835 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
** * *
2857 TCGTTGCGATTTTGTA-AATTCG
1 TCGTTGCGATAGTCTACAGTT-G
*
2879 -CATTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
2900 TCGTTGCGATAGT
1 TCGTTGCGATAGT
2913 TGAAAATCGC
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
21 15 0.35
22 28 0.65
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:2909 original size:196 final size:190
Alignment explanation
Indices: 2512--3042 Score: 531
Period size: 196 Copynumber: 2.8 Consensus size: 190
2502 TGCGATCTCT
*
2512 AATTCGCATTGCGATCTCCACTATCGCAAATTCGCGTTGC---ATT-TCGCATTGCGATAGTTGA
1 AATTCGCATTGCGATCTCCACTATCGCAAATTCGCGTTGCGATATTATCGCGTTGCGATAGTTGA
* *
2573 AAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGCCTATAGTTGTTGTTGCGATTTTCCAAA
66 AAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAG-CTACAGTTGTCGTTGCGATTTTCCAAA
* * * * * *
2638 TTCGTTGCGATAGTCTACAGTTGTTGTTGTGATAATCTACAGTTGTCGTTGCGATTTTGCA
130 TTCGTTGCGATAGTCTACAGTTGTCGTTGCGATAATCTACAATTGTCATTGCGATTCTACA
2699 AATTCGCATTGCGATCTCCACTATCGCAAATTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATA
1 AATTCGCATTGCGATCTCCACTATCGCAAATTCGCGTTGCGATA-TT----ATCGCGTTGCGATA
*
2764 GTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGCATACAGTTATCGTTGCGATTTT
61 GTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGC-TACAGTTGTCGTTGCGATTTT
** *
2829 CCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTGTA-AATTCG-CATTGCGATAGTC
125 CCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATAATCTACAATT-GTCATTGCGAT--TC
2892 TAC-
187 TACA
* * * * *
2895 AGTT-GTCGTTGCGA--T--AGT-T-G-AAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATA
1 AATTCG-CATTGCGATCTCCACTATCGCAAATTCGCGTTGCGATATT--A--TCGCGTTGCG--A
*
2952 GTTGAAAATCGTTGAAAATCGCGTTGCGATTTTCCATTT--CGTTGCGATAGTCTACAGTTGTCG
59 --T----A--GTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAG-CTACAGTTGTCG
3015 TTGCG-TTTTCCAAATTCGTTGCGATAGT
115 TTGCGATTTTCCAAATTCGTTGCGATAGT
3043 TAAAAAAAAA
Statistics
Matches: 295, Mismatches: 22, Indels: 46
0.81 0.06 0.13
Matches are distributed among these distances:
186 1 0.00
187 40 0.14
188 12 0.04
189 15 0.05
190 3 0.01
191 3 0.01
192 3 0.01
194 1 0.00
195 36 0.12
196 149 0.51
197 4 0.01
198 28 0.09
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (190 bp):
AATTCGCATTGCGATCTCCACTATCGCAAATTCGCGTTGCGATATTATCGCGTTGCGATAGTTGA
AAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGCTACAGTTGTCGTTGCGATTTTCCAAAT
TCGTTGCGATAGTCTACAGTTGTCGTTGCGATAATCTACAATTGTCATTGCGATTCTACA
Found at i:2923 original size:147 final size:146
Alignment explanation
Indices: 2754--3042 Score: 397
Period size: 147 Copynumber: 1.9 Consensus size: 146
2744 TTGAAAATCG
* *
2754 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGCAT-ACA-GTT-A
1 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAG-ATAAAACGTTAA
**
2816 T-CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTGTAAATTCGC
65 TCCGTTGCGATTTTCC-AATTCGTTGCGATAGTCTACAGTTGTCGTTGCG-TTTTCCAAATTCG-
2880 ATTGCGATAGTCTACAGTTGT
127 -TTGCGATAGTCTACAGTTGT
*
2901 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGTTG
1 CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGAT-AAAA-CGTT-
*
2966 AAAATCGCGTTGCGATTTTCCATTTCGTTGCGATAGTCTACAGTTGTCGTTGCGTTTTCCAAATT
63 --AATC-CGTTGCGATTTTCCAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGTTTTCCAAATT
3031 CGTTGCGATAGT
125 CGTTGCGATAGT
3043 TAAAAAAAAA
Statistics
Matches: 126, Mismatches: 6, Indels: 15
0.86 0.04 0.10
Matches are distributed among these distances:
146 1 0.01
147 51 0.40
148 2 0.02
150 3 0.02
152 10 0.08
154 13 0.10
155 32 0.25
156 14 0.11
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (146 bp):
CGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGATAAAACGTTAAT
CCGTTGCGATTTTCCAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGTTTTCCAAATTCGTTGC
GATAGTCTACAGTTGT
Found at i:2927 original size:21 final size:21
Alignment explanation
Indices: 2901--2962 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
2891 CTACAGTTGT
2901 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
* ** **
2922 CGTTGCGAT-TTTCCATTTCG
1 CGTTGCGATAGTTGAAAATCG
2942 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
2963 TTGAAAATCG
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTTGAAAATCG
Found at i:2946 original size:84 final size:84
Alignment explanation
Indices: 2733--2950 Score: 223
Period size: 84 Copynumber: 2.6 Consensus size: 84
2723 CGCAAATTCG
* * * * *
2733 CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGA-AAATCGCGTTGCGATTTTTCATTTCGCG
1 CGTTGCGATAGTTGAAAATCGCGTTGCGATA-TTTACAATTCGCGTTGCGATTTTTAAATTCGCA
2797 TTGCGATAGCATACAGTTAT
65 TTGCGATAGCATACAGTTAT
* ** * * *
2817 CGTTGCGAT-TTTCCAAAT-TCGTTGCGATAGTCTACAGTT-GTCGTTGCGATTTTGTAAATTCG
1 CGTTGCGATAGTTGAAAATCGCGTTGCGATA-TTTACAATTCG-CGTTGCGATTTT-TAAATTCG
*
2879 CATTGCGATAGTC-TACAGTTGT
63 CATTGCGATAG-CATACAGTTAT
* *
2901 CGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGAT
1 CGTTGCGATAGTTGAAAATCGCGTTGCGATATTTACAATTCGCGTTGCGAT
2951 AGTTGAAAAT
Statistics
Matches: 108, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
82 14 0.13
83 20 0.19
84 57 0.53
85 8 0.07
86 9 0.08
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (84 bp):
CGTTGCGATAGTTGAAAATCGCGTTGCGATATTTACAATTCGCGTTGCGATTTTTAAATTCGCAT
TGCGATAGCATACAGTTAT
Found at i:2996 original size:18 final size:18
Alignment explanation
Indices: 2973--3039 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 18
2963 TTGAAAATCG
2973 CGTTGCGATTTTCCATTT
1 CGTTGCGATTTTCCATTT
* *
2991 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGAT--TTTCCA-TT-T
*
3013 CGTTGCG-TTTTCCAAATT
1 CGTTGCGATTTTCC-ATTT
3031 CGTTGCGAT
1 CGTTGCGAT
3040 AGTTAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
18 17 0.45
19 5 0.13
20 5 0.13
21 3 0.08
22 8 0.21
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.42
Consensus pattern (18 bp):
CGTTGCGATTTTCCATTT
Found at i:3131 original size:6 final size:6
Alignment explanation
Indices: 3120--3146 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3110 GACACGTATT
3120 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
3147 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3394 original size:19 final size:19
Alignment explanation
Indices: 3370--3417 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
3360 ACTGTAGACT
3370 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
3389 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
3408 ATCGCAACGA
1 ATCGCAACGA
3418 CAACTGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:3453 original size:42 final size:41
Alignment explanation
Indices: 3402--3486 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 41
3392 GCAACGAATT
3402 TGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * *
3444 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
3485 TG
1 TG
3487 CAATGCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 23 0.59
42 16 0.41
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (41 bp):
TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:5588 original size:2 final size:2
Alignment explanation
Indices: 5583--5610 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5573 ACACACACAC
5583 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
5611 CAGATTAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14454 original size:3 final size:3
Alignment explanation
Indices: 14446--14507 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
14436 ATTTTCTCTT
* * *
14446 TTA TTA TTA CTA TTA CTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14494 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
14508 TATGATAGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:20175 original size:29 final size:29
Alignment explanation
Indices: 20132--20214 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
20122 CTCACCTAAC
20132 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
20162 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
20191 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
20215 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:24941 original size:29 final size:29
Alignment explanation
Indices: 24898--24980 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
24888 CTCACCTAAC
24898 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
24928 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
24957 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
24981 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:26301 original size:27 final size:27
Alignment explanation
Indices: 26252--26303 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
26242 TATTTATAAA
* * **
26252 TAAATTAAAATTTTTTATTTTTTATTT
1 TAAAATAAAATTTTTAAAATTTTATTT
26279 TAAAATAAAATTTTTAAAATTTTAT
1 TAAAATAAAATTTTTAAAATTTTAT
26304 AAACTTGACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TAAAATAAAATTTTTAAAATTTTATTT
Found at i:27933 original size:20 final size:20
Alignment explanation
Indices: 27908--28059 Score: 182
Period size: 20 Copynumber: 7.5 Consensus size: 20
27898 TTTTCCTAAT
*
27908 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
27928 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
*
27948 TCGCAACGCGTAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
*
27968 TCGCAACGAGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* * *
27988 TCGCAATGCGTATCCGTAAA
1 TCGCAACGCGAATACGTAAA
28008 TCGCAACGAC-AATACGTAAAA
1 TCGCAACG-CGAATACGT-AAA
* *
28029 TCGCAACGCGTATCCGTAAA
1 TCGCAACGCGAATACGTAAA
28049 TCGCAACGCGA
1 TCGCAACGCGA
28060 TTTTTAAAGC
Statistics
Matches: 111, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.01
20 92 0.83
21 18 0.16
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:27967 original size:40 final size:40
Alignment explanation
Indices: 27908--28059 Score: 216
Period size: 40 Copynumber: 3.8 Consensus size: 40
27898 TTTTCCTAAT
* * * *
27908 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAAA
* *
27948 TCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAA
1 TCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAAA
*
27988 TCGCAATGCGTATCCGTAAATCGCAACGAC-AATACGTAAAA
1 TCGCAACGCGTATCCGTAAATCGCAACG-CGAATACGT-AAA
28029 TCGCAACGCGTATCCGTAAATCGCAACGCGA
1 TCGCAACGCGTATCCGTAAATCGCAACGCGA
28060 TTTTTAAAGC
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
40 68 0.69
41 31 0.31
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (40 bp):
TCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAAA
Found at i:28646 original size:20 final size:20
Alignment explanation
Indices: 28617--28688 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
28607 TTCTAAACTT
* *
28617 AAAATCGCAACATGAAAATG
1 AAAATAGCAACACGAAAATG
28637 AAAATAGCAACACGAAAATG
1 AAAATAGCAACACGAAAATG
** *
28657 ACTATCGCAACGAGCG-AAATG
1 AAAATAGCAAC-A-CGAAAATG
*
28678 AAAATCGCAAC
1 AAAATAGCAAC
28689 GAGATAATCG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 26 0.60
21 15 0.35
22 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAATAGCAACACGAAAATG
Found at i:28677 original size:21 final size:21
Alignment explanation
Indices: 28632--28691 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
28622 CGCAACATGA
*
28632 AAATGAAAATAGCAAC-A-CG
1 AAATGAAAATCGCAACGAGCG
**
28651 AAAATGACTATCGCAACGAGCG
1 -AAATGAAAATCGCAACGAGCG
28673 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGAG
28692 ATAATCGCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 13 0.39
21 18 0.55
22 2 0.06
ACGTcount: A:0.50, C:0.18, G:0.20, T:0.12
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGCG
Found at i:28737 original size:19 final size:19
Alignment explanation
Indices: 28715--28846 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
28705 GAAACCAAAA
*
28715 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
28734 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
28753 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
28772 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
28786 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
28805 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
* *
28825 CTCTCGTTGCGATTTTTATT
1 -TCGCGTTGCGATTTTCATT
28845 TC
1 TC
28847 AACCAAAAGA
Statistics
Matches: 96, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.10
16 2 0.02
17 3 0.03
19 49 0.51
20 31 0.32
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:32504 original size:19 final size:19
Alignment explanation
Indices: 32482--32540 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
32472 AAAAATGACT
32482 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
32501 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
32515 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
32534 ATCGCAA
1 ATCGCAA
32541 CGACAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.52
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:32528 original size:33 final size:33
Alignment explanation
Indices: 32486--32561 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
32476 ATGACTATCG
* *
32486 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
32519 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
32552 CAACGCGAAA
1 CAATGCGAAA
32562 CTAAATTCGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.49, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCA
Found at i:32676 original size:20 final size:19
Alignment explanation
Indices: 32567--32681 Score: 114
Period size: 19 Copynumber: 6.3 Consensus size: 19
32557 CGAAACTAAA
*
32567 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
32586 TTCGCTTTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
32602 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
32619 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
32638 TTCGCATTGCGATAGTCAT
1 TTCGCATTGCGATTTTCAT
* *
32657 TTCCGCTTTACGATTTTCAT
1 TT-CGCATTGCGATTTTCAT
32677 TTCGC
1 TTCGC
32682 GTTGTGATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
14 6 0.08
16 6 0.08
17 6 0.08
19 46 0.58
20 15 0.19
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:32680 original size:39 final size:38
Alignment explanation
Indices: 32606--32681 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
32596 GATTCCCTCG
** *
32606 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATAGTCATTTCGCATTACGATTTTCATTTCGCA
*
32644 TTGCGATAGTCATTTCCGCTTTACGATTTTCATTTCGC
1 TTGCGATAGTCATTT-CGCATTACGATTTTCATTTCGC
32682 GTTGTGATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 13 0.39
39 20 0.61
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.46
Consensus pattern (38 bp):
TTGCGATAGTCATTTCGCATTACGATTTTCATTTCGCA
Found at i:32769 original size:20 final size:20
Alignment explanation
Indices: 32696--32769 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
32686 TGATTCTCTC
* * *
32696 GTTGCGATAGTAATTTTCGC
1 GTTGCGATAGTCATTTACGT
* *
32716 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTACG-T
*
32736 GATTGCGA-ATGTCATTTCCGT
1 G-TTGCGATA-GTCATTTACGT
32757 GTTGCGATAGTCA
1 GTTGCGATAGTCA
32770 AATGAATGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCATTTACGT
Found at i:35306 original size:24 final size:24
Alignment explanation
Indices: 35239--35298 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
35229 CTGAAAAATC
35239 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
35263 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
35287 ATCAAATTTCGA
1 ATCAAAATTCGA
35299 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:36180 original size:20 final size:20
Alignment explanation
Indices: 36157--36196 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
36147 AATCTCGTTA
36157 CGATTAAGTAAATCGCAATG
1 CGATTAAGTAAATCGCAATG
* *
36177 CGATTACGTAAATTGCAATG
1 CGATTAAGTAAATCGCAATG
36197 TGAATCCGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (20 bp):
CGATTAAGTAAATCGCAATG
Found at i:36206 original size:20 final size:20
Alignment explanation
Indices: 36164--36206 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
36154 TTACGATTAA
*
36164 GTAAATCGCAATGCGATTAC
1 GTAAATCGCAATGCGAATAC
* * *
36184 GTAAATTGCAATGTGAATCC
1 GTAAATCGCAATGCGAATAC
36204 GTA
1 GTA
36207 TTCGTGTTGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (20 bp):
GTAAATCGCAATGCGAATAC
Found at i:36235 original size:20 final size:20
Alignment explanation
Indices: 36212--36256 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
36202 CCGTATTCGT
36212 GTTGCGATTTACGTAATCGC
1 GTTGCGATTTACGTAATCGC
*
36232 GTTGCGATTTACGTATTCGC
1 GTTGCGATTTACGTAATCGC
36252 GTTGC
1 GTTGC
36257 AAATTAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGTAATCGC
Found at i:44727 original size:29 final size:28
Alignment explanation
Indices: 44662--44727 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
44652 CTTTATCCTA
* *
44662 ATTTTTTTTAAAATTTATTTTAATTTTC
1 ATTTTTTTTAAAATTCATTTGAATTTTC
* *
44690 ATTTGTTTTTTAAATTCATTATGATTTTTC
1 ATTT-TTTTTAAAATTCATT-TGAATTTTC
*
44720 CTTTTTTT
1 ATTTTTTT
44728 AATATGATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.13
29 17 0.55
30 10 0.32
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (28 bp):
ATTTTTTTTAAAATTCATTTGAATTTTC
Found at i:51559 original size:10 final size:10
Alignment explanation
Indices: 51544--51576 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
51534 GTCAATGATC
*
51544 TCCTTCCACT
1 TCCTTCCAAT
51554 TCCTTCCAAT
1 TCCTTCCAAT
51564 TCCTTCCAAT
1 TCCTTCCAAT
51574 TCC
1 TCC
51577 CATCTATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.15, C:0.45, G:0.00, T:0.39
Consensus pattern (10 bp):
TCCTTCCAAT
Found at i:53671 original size:20 final size:21
Alignment explanation
Indices: 53646--53688 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
53636 GAGTCCGTGA
*
53646 TTAGAATCCTCGTATAAT-TT
1 TTAGAATCCTCATATAATATT
53666 TTAGAATCCTCATATAATATT
1 TTAGAATCCTCATATAATATT
53687 TT
1 TT
53689 TTAGCATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.47
Consensus pattern (21 bp):
TTAGAATCCTCATATAATATT
Found at i:55154 original size:2 final size:2
Alignment explanation
Indices: 55147--55183 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
55137 ATATAATACT
55147 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 T
55184 TAGTGGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61339 original size:20 final size:20
Alignment explanation
Indices: 61317--61355 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
61307 AATAAACTTA
*
61317 AAAAATTATA-CTCAAATCC
1 AAAAATTATATCACAAATCC
61336 AAAAATTATATCACAAATCC
1 AAAAATTATATCACAAATCC
61356 TAAATCACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATTATATCACAAATCC
Found at i:63026 original size:11 final size:11
Alignment explanation
Indices: 63010--63063 Score: 65
Period size: 11 Copynumber: 4.7 Consensus size: 11
63000 GTCCGGATCT
*
63010 TTTTATTTTTA
1 TTTTATTATTA
63021 TTTTATTATATTA
1 TTTTA-T-TATTA
63034 TTATTATTATTA
1 TT-TTATTATTA
63046 TTTTATTATTA
1 TTTTATTATTA
63057 -TTTATTA
1 TTTTATTA
63064 CATTTACATT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
10 7 0.18
11 14 0.36
12 8 0.21
13 7 0.18
14 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:63029 original size:14 final size:14
Alignment explanation
Indices: 63012--63058 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
63002 CCGGATCTTT
*
63012 TTATTTTTATTTTA
1 TTATTATTATTTTA
63026 TTA-TATTA--TTA
1 TTATTATTATTTTA
63037 TTATTATTATTTTA
1 TTATTATTATTTTA
63051 TTATTATT
1 TTATTATT
63059 TATTACATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 6 0.21
12 5 0.17
13 4 0.14
14 14 0.48
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTATTATTTTA
Found at i:63035 original size:3 final size:3
Alignment explanation
Indices: 63012--63063 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
63002 CCGGATCTTT
*
63012 TTA TTT TTA TT- TTA TTA -TA TTA TTA TTA TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
63057 TTTA TTA
1 -TTA TTA
63064 CATTTACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 6 0.14
3 34 0.79
4 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:63055 original size:8 final size:8
Alignment explanation
Indices: 63018--63055 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
63008 CTTTTTATTT
63018 TTATTTTA
1 TTATTTTA
*
63026 TTATATTA
1 TTATTTTA
63034 TTATTATTA
1 TTATT-TTA
63043 TTATTTTA
1 TTATTTTA
63051 TTATT
1 TTATT
63056 ATTTATTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTATTTTA
Done.