Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007474.1 Hibiscus syriacus cultivar Beakdansim tig00020540_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: 55324
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1110 original size:21 final size:22
Alignment explanation
Indices: 1086--1127 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1076 CATTTTACAA
*
1086 TTAAGATAAAAA-AAATTATAG
1 TTAAGATAAAAATAAAATATAG
1107 TTAAGATAAAAATAAAATATA
1 TTAAGATAAAAATAAAATATA
1128 TTATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (22 bp):
TTAAGATAAAAATAAAATATAG
Found at i:1149 original size:29 final size:29
Alignment explanation
Indices: 1107--1334 Score: 97
Period size: 29 Copynumber: 8.0 Consensus size: 29
1097 AAAATTATAG
*
1107 TTAAGATAAAAATAAAATATATTATTAAA
1 TTAAGATAAGAATAAAATATATTATTAAA
*
1136 TTAAGATAAGAATAAATATAAATT-TTAAA
1 TTAAGATAAGAATAAA-ATATATTATTAAA
*
1165 TT-A-A-AATAA-AAAATAT-TT-TTAAA
1 TTAAGATAAGAATAAAATATATTATTAAA
* * * *
1188 CTAATATAAAAAT-AAATAATATTAAT-AA
1 TTAAGATAAGAATAAAAT-ATATTATTAAA
* * * * *
1216 TTTAGGTAA-AATATAAT-TATTAATAATT
1 TTAAGATAAGAATAAAATATATTATTAA-A
* * * *
1244 TATAAGTTAATAAGATTAAAATATATTTTTTAG
1 T-TAAG---ATAAGAATAAAATATATTATTAAA
* * *
1277 TCAATATAAGAATAAAATATATTCAATAAA
1 TTAAGATAAGAATAAAATATATT-ATTAAA
*
1307 TTAACGA-AA-AATAAAATATGTT-TTAAA
1 TTAA-GATAAGAATAAAATATATTATTAAA
1334 T
1 T
1335 GTTAAGATGT
Statistics
Matches: 148, Mismatches: 32, Indels: 40
0.67 0.15 0.18
Matches are distributed among these distances:
23 8 0.05
24 4 0.03
25 4 0.03
26 19 0.13
27 12 0.08
28 14 0.09
29 55 0.37
30 13 0.09
31 1 0.01
32 5 0.03
33 7 0.05
34 6 0.04
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (29 bp):
TTAAGATAAGAATAAAATATATTATTAAA
Found at i:1174 original size:23 final size:22
Alignment explanation
Indices: 1146--1204 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
1136 TTAAGATAAG
*
1146 AATAAATATAAATTTTAAATTAA
1 AATAAA-ATAAATTTTAAACTAA
1169 AATAAAA-AATATTTTTAAACTAA
1 AATAAAATAA-A-TTTTAAACTAA
*
1192 TATAAAAATAAAT
1 AAT-AAAATAAAT
1205 AATATTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 2 0.07
22 2 0.07
23 19 0.63
24 5 0.17
25 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAAATAAATTTTAAACTAA
Found at i:2978 original size:9 final size:9
Alignment explanation
Indices: 2959--2994 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
2949 TTTATTAAAG
2959 AAATAAAAAT
1 AAAT-AAAAT
2969 AAATAAAAT
1 AAATAAAAT
2978 AAATAAAAT
1 AAATAAAAT
2987 AAATAAAA
1 AAATAAAA
2995 AGGAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:7966 original size:15 final size:15
Alignment explanation
Indices: 7946--7975 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
7936 TTTATTAAGA
7946 ATTTAAATCAAATAT
1 ATTTAAATCAAATAT
7961 ATTTAAATCAAATAT
1 ATTTAAATCAAATAT
7976 TAATCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAAATCAAATAT
Found at i:9958 original size:3 final size:3
Alignment explanation
Indices: 9937--10040 Score: 163
Period size: 3 Copynumber: 34.7 Consensus size: 3
9927 TTTTTACCCA
* *
9937 TAT TAT AAT TAT AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
9985 CAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
10033 TAT TAT TA
1 TAT TAT TA
10041 AATATATATT
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:10070 original size:10 final size:11
Alignment explanation
Indices: 10036--10075 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
10026 TTATCATTAT
*
10036 TATTAAATATA
1 TATTAAATACA
10047 TATTAAATACA
1 TATTAAATACA
*
10058 TATAAAATA-A
1 TATTAAATACA
10068 TATTAAAT
1 TATTAAAT
10076 TACAAAGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
TATTAAATACA
Found at i:11501 original size:13 final size:13
Alignment explanation
Indices: 11483--11520 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
11473 AATATATAAA
11483 TAAATATTTATTT
1 TAAATATTTATTT
*
11496 TAAATAAATTATTT
1 TAAAT-ATTTATTT
11510 T-AATATTTATT
1 TAAATATTTATT
11521 ATCGAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 8 0.36
14 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:12180 original size:29 final size:28
Alignment explanation
Indices: 12138--12247 Score: 73
Period size: 28 Copynumber: 3.9 Consensus size: 28
12128 AAAAGTTCAT
* *
12138 ATATTTAATTTTTAATTATTTCTTTTCAAA
1 ATATTT-ATATTTAATTA-TTATTTTCAAA
* * *
12168 ATTTTTATATTTACTTATTATTTTCATA
1 ATATTTATATTTAATTATTATTTTCAAA
* *
12196 ATATTTATATGTTTTATT-TTATTTGC-AA
1 ATATTTATA--TTTAATTATTATTTTCAAA
* *
12224 GTATTT-TATTTCATTATTTATTTT
1 ATATTTATATTTAATTA-TTATTTT
12248 TCTGTCAAAG
Statistics
Matches: 63, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
25 6 0.10
27 8 0.13
28 23 0.37
29 16 0.25
30 10 0.16
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (28 bp):
ATATTTATATTTAATTATTATTTTCAAA
Found at i:14862 original size:113 final size:113
Alignment explanation
Indices: 14654--15899 Score: 1782
Period size: 114 Copynumber: 10.9 Consensus size: 113
14644 CAAAGATTCA
* * * *
14654 AATTTATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAA
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
14719 AGGAAGAAGAAATTCATAGTGAGAAGAATTTGTTCAACCTTTTGCCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
*
14767 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAA
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
14832 AGGAAGAAGAAATTCATAGTGAGAAGAATTTGTTCAACCTTTTGCCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
*
14880 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAA
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
14945 AGGAAGAAGAAATTCATAGTGAGAAGAATTTGTTCAACCTTTTTGCCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGCCTG
* * *
14994 AATTCATCACTGGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAA
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
15059 AGGAAGAAGAAATTCATAGTGAGAAGAATTTGTTCAACCTTTTTGCCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGCCTG
15108 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
*
15173 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * *
15221 AATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATC-ACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
* *
15286 AAGGAATAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * *
15335 AATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATC-ACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
*
15400 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * * *
15449 AATTCATCAAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATTCATC-ACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
* * *
15514 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * * *
15563 AATTCATCATTTGATGGATCA-ATATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCAGCT-TTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCT
* * *
15626 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
61 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * * * *
15679 AGTTCATCATTTGATGGATCA-ATATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCAGCT-TTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCT
* * *
15742 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
61 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
* * * * *
15795 AATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTTATCTG
1 AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAG-GTTCATAATGAGAAGAACTC---ATCTG
* *
15859 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
15900 TAATTCTATC
Statistics
Matches: 1090, Mismatches: 32, Indels: 19
0.96 0.03 0.02
Matches are distributed among these distances:
112 3 0.00
113 266 0.24
114 552 0.51
115 1 0.00
116 268 0.25
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
AATTCATCACTTGATGGATCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTG
Found at i:16231 original size:3 final size:3
Alignment explanation
Indices: 16216--16337 Score: 217
Period size: 3 Copynumber: 40.7 Consensus size: 3
16206 TTTTTACCCA
* *
16216 TAT TAT AAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16264 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
16312 TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
16338 AATATATATT
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 113 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:16349 original size:11 final size:10
Alignment explanation
Indices: 16333--16373 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
16323 TTATTATTAT
16333 TATTAAATATA
1 TATTAAATA-A
16344 TATTAAATACA
1 TATTAAATA-A
16355 TATATAAATAA
1 TAT-TAAATAA
16366 TATTAAAT
1 TATTAAAT
16374 TACAAAGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:16488 original size:14 final size:14
Alignment explanation
Indices: 16469--16506 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
16459 ATCCCATGCT
16469 CAGCCGCCTCTAGC
1 CAGCCGCCTCTAGC
16483 CAGCCGCCTCTAGC
1 CAGCCGCCTCTAGC
16497 CAGCCGCCTC
1 CAGCCGCCTC
16507 AGACTGACCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.13, C:0.53, G:0.21, T:0.13
Consensus pattern (14 bp):
CAGCCGCCTCTAGC
Found at i:17221 original size:11 final size:10
Alignment explanation
Indices: 17205--17245 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
17195 TTATTATTAT
17205 TATTAAATATA
1 TATTAAATA-A
17216 TATTAAATACA
1 TATTAAATA-A
17227 TATATAAATAA
1 TAT-TAAATAA
17238 TATTAAAT
1 TATTAAAT
17246 TACAAAGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:17934 original size:13 final size:13
Alignment explanation
Indices: 17918--17955 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
17908 ATATAATAAA
17918 TAAATATTTATTT
1 TAAATATTTATTT
*
17931 TAAATAAATTATTT
1 TAAAT-ATTTATTT
17945 T-AATATTTATT
1 TAAATATTTATT
17956 ATCGAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 8 0.36
14 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:21940 original size:18 final size:18
Alignment explanation
Indices: 21899--21941 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
21889 TACCTTTTTG
21899 TAAATATTATTTATTTAAT
1 TAAATA-TATTTATTTAAT
21918 T-AATATATTT-TTTAAAT
1 TAAATATATTTATTT-AAT
21935 TAAATAT
1 TAAATAT
21942 GAACAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 9 0.41
18 9 0.41
19 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATATATTTATTTAAT
Found at i:23310 original size:17 final size:18
Alignment explanation
Indices: 23288--23321 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23278 TCAGCCGGTC
23288 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
23305 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
23322 CTAGTAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:27303 original size:5 final size:5
Alignment explanation
Indices: 27293--27317 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
27283 TTTGCACGCT
27293 TGTGG TGTGG TGTGG TGTGG TGTGG
1 TGTGG TGTGG TGTGG TGTGG TGTGG
27318 GCCCCATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
TGTGG
Found at i:27371 original size:6 final size:6
Alignment explanation
Indices: 27360--27391 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
27350 TTGGTCTCAT
27360 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CT
1 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CT
27392 AATTAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (6 bp):
CTTTTC
Found at i:27434 original size:6 final size:6
Alignment explanation
Indices: 27423--27454 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
27413 ATCATCTCAT
27423 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CT
1 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC CT
27455 AATTAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (6 bp):
CTTTTC
Found at i:27441 original size:63 final size:63
Alignment explanation
Indices: 27354--27499 Score: 292
Period size: 63 Copynumber: 2.3 Consensus size: 63
27344 TGGCCATTGG
27354 TCTCATCTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCTAATTAAGAAAATACATATATTATCA
1 TCTCATCTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCTAATTAAGAAAATACATATATTATCA
27417 TCTCATCTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCTAATTAAGAAAATACATATATTATCA
1 TCTCATCTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCTAATTAAGAAAATACATATATTATCA
27480 TCTCATCTTTTCCTTTTCCT
1 TCTCATCTTTTCCTTTTCCT
27500 AGTTAAGAAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 83 1.00
ACGTcount: A:0.21, C:0.25, G:0.01, T:0.52
Consensus pattern (63 bp):
TCTCATCTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCTAATTAAGAAAATACATATATTATCA
Found at i:28619 original size:14 final size:15
Alignment explanation
Indices: 28594--28625 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
28584 TTAGTTAAAA
28594 ATTTGAAGATAAATT
1 ATTTGAAGATAAATT
28609 ATTTGAA-ATAAATT
1 ATTTGAAGATAAATT
28623 ATT
1 ATT
28626 AATGTAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (15 bp):
ATTTGAAGATAAATT
Found at i:30494 original size:117 final size:116
Alignment explanation
Indices: 30290--30503 Score: 340
Period size: 117 Copynumber: 1.8 Consensus size: 116
30280 ATAATTAATT
* * * * *
30290 TTTTTATGAGACAAAAAACTCTAGTTATTAATTTTTATTTTAATATTTAATTATAACTTGATGCA
1 TTTTTATGAGACAAAAAAATATAGTTATTAATTTTTATTGTAAGATTTAATCATAACTTGATGCA
* *
30355 TAGATATAGTGAAATGATAATATTTAAAAATTTAACTATTATTGTTAACTA
66 TAGATACAGTGAAACGATAATATTTAAAAATTTAACTATTATTGTTAACTA
30406 TTTTTATGAGACAAAAAAAAATATAGTTATTAA-TTTTATTGTAAGATTTAATCATAACTTGATG
1 TTTTTATGAGAC--AAAAAAATATAGTTATTAATTTTTATTGTAAGATTTAATCATAACTTGATG
30470 CATAGATACAGTGAAACGATAATATTTAAAAATT
64 CATAGATACAGTGAAACGATAATATTTAAAAATT
30504 CATGATAAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
116 12 0.13
117 60 0.67
118 17 0.19
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.42
Consensus pattern (116 bp):
TTTTTATGAGACAAAAAAATATAGTTATTAATTTTTATTGTAAGATTTAATCATAACTTGATGCA
TAGATACAGTGAAACGATAATATTTAAAAATTTAACTATTATTGTTAACTA
Found at i:37526 original size:2 final size:2
Alignment explanation
Indices: 37519--37591 Score: 75
Period size: 2 Copynumber: 39.0 Consensus size: 2
37509 TTTTACACAA
*
37519 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA AT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
37558 A- AA AC AA AT AT A- 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
37592 TAGATTATAG
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
1 5 0.08
2 56 0.92
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:37931 original size:14 final size:14
Alignment explanation
Indices: 37914--37941 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37904 AATAATATAT
37914 AAATTATATTAAAA
1 AAATTATATTAAAA
37928 AAATTATATTAAAA
1 AAATTATATTAAAA
37942 TTATTTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTATATTAAAA
Found at i:37976 original size:114 final size:117
Alignment explanation
Indices: 37617--37982 Score: 543
Period size: 118 Copynumber: 3.2 Consensus size: 117
37607 GTAAGACTTA
* * *
37617 AAAATAAAAATGAGTTTAATATTTTT-GTT--ATT-TTTTATAATTATTTTTAAATAATAATATA
1 AAAATAAAAATAAGTTTAATATTTTTATTTAAATTATTTTACAATTA-TTTTAAATAATAATATA
* *
37678 TAAATTATATTAAAAATAAAATTATAATAAGATTATTTAGAGAATCCAAATCAC
65 TAAATTATATT-AAAATAAAATTATATTAAAATTATTTAGAGAATCCAAATCAC
37732 AAAATAAAAATAAGTTTAATATTTTTATTTAAATTATTTTTACAATT-TTTTAAATAATAATATA
1 AAAATAAAAATAAGTTTAATATTTTTATTTAAATTA-TTTTACAATTATTTTAAATAATAATATA
* * *
37796 GAAATTATATTAAAAATAAAATTATATTAAAATTATTTAGAGATTACAAATCAC
65 TAAATTATATT-AAAATAAAATTATATTAAAATTATTTAGAGAATCCAAATCAC
*
37850 AAAATAAAAATAAGTTTAATATTTTTATTTAAATTATTTTA-AGTTATTTTAAATAATAATATAT
1 AAAATAAAAATAAGTTTAATATTTTTATTTAAATTATTTTACAATTATTTTAAATAATAATATAT
*
37914 AAATTATATT-AAA-AAAATTATATTAAAATTATTTAGAGAATCCAAATCAT
66 AAATTATATTAAAATAAAATTATATTAAAATTATTTAGAGAATCCAAATCAC
37964 AAAATAAAAATAA-TTTAAT
1 AAAATAAAAATAAGTTTAAT
37983 TAAAAAAATA
Statistics
Matches: 232, Mismatches: 13, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
113 6 0.03
114 47 0.20
115 28 0.12
116 5 0.02
117 32 0.14
118 105 0.45
120 9 0.04
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (117 bp):
AAAATAAAAATAAGTTTAATATTTTTATTTAAATTATTTTACAATTATTTTAAATAATAATATAT
AAATTATATTAAAATAAAATTATATTAAAATTATTTAGAGAATCCAAATCAC
Found at i:39105 original size:22 final size:22
Alignment explanation
Indices: 39060--39109 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
39050 AACTATACTA
* *
39060 TATAATATATATTTTTTATCAT
1 TATAATATATATTATATATCAT
39082 TATAATATATATATATATAT-AT
1 TATAATATATAT-TATATATCAT
39104 TATAAT
1 TATAAT
39110 TTGAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TATAATATATATTATATATCAT
Found at i:39117 original size:28 final size:29
Alignment explanation
Indices: 39053--39110 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
39043 GAATATTAAC
* * * *
39053 TATACTATATAATATATATTTTTTATCAT
1 TATAATATATAATATATATATATTATAAT
39082 TATAATATAT-ATATATATATATTATAAT
1 TATAATATATAATATATATATATTATAAT
39110 T
1 T
39111 TGAATATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (29 bp):
TATAATATATAATATATATATATTATAAT
Found at i:44324 original size:68 final size:68
Alignment explanation
Indices: 44243--44384 Score: 230
Period size: 68 Copynumber: 2.1 Consensus size: 68
44233 TATATTTTTC
44243 TTTTTAGGCATTTTAGTTTAAATAAATTTTAGTATTTTAATTAGGATTTAAAATATTATTTAAAA
1 TTTTTAGGCATTTTAGTTTAAATAAATTTTAGTATTTTAATTAGGATTTAAAATATTATTTAAAA
44308 TAT
66 TAT
* * ** *
44311 TTTTTAGGTATTTTAGTTTAAATAGATTTTAGTATTTTAATTAGGATTTAGGATATTATTTTAAA
1 TTTTTAGGCATTTTAGTTTAAATAAATTTTAGTATTTTAATTAGGATTTAAAATATTATTTAAAA
44376 TAT
66 TAT
44379 TATTTT
1 T-TTTT
44385 TGTTTTAGAT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
68 64 0.94
69 4 0.06
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.54
Consensus pattern (68 bp):
TTTTTAGGCATTTTAGTTTAAATAAATTTTAGTATTTTAATTAGGATTTAAAATATTATTTAAAA
TAT
Found at i:45149 original size:38 final size:38
Alignment explanation
Indices: 45104--45176 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
45094 ATTTAAAACC
45104 CCCTTTTA-TAATTATTA-CTATTTATTATTTTATTATTT
1 CCCTTTTATTAATTATTATCTA-TT-TTATTTTATTATTT
* *
45142 CCCTTTTATTTATTTTTATCTATTTTATTTTATTA
1 CCCTTTTATTAATTATTATCTATTTTATTTTATTA
45177 AATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 19 0.61
39 9 0.29
40 3 0.10
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (38 bp):
CCCTTTTATTAATTATTATCTATTTTATTTTATTATTT
Found at i:45150 original size:19 final size:20
Alignment explanation
Indices: 45128--45176 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
45118 TTACTATTTA
*
45128 TTATTTTATTATT-TCCCTT
1 TTATTTTATTATTATCCATT
* *
45147 TTA-TTTATTTTTATCTATT
1 TTATTTTATTATTATCCATT
45166 TTATTTTATTA
1 TTATTTTATTA
45177 AATATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 8 0.33
19 10 0.42
20 6 0.25
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTTATTATTATCCATT
Found at i:49289 original size:23 final size:23
Alignment explanation
Indices: 49254--49302 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
49244 CAGTAGAAAA
*
49254 AAAGTTCAATGTTTCGAACAAAG
1 AAAGTCCAATGTTTCGAACAAAG
* *
49277 AAAGTCCATTGTTTCGAACAGAG
1 AAAGTCCAATGTTTCGAACAAAG
49300 AAA
1 AAA
49303 AAGAAGAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.24
Consensus pattern (23 bp):
AAAGTCCAATGTTTCGAACAAAG
Found at i:50287 original size:69 final size:74
Alignment explanation
Indices: 50197--50379 Score: 261
Period size: 69 Copynumber: 2.5 Consensus size: 74
50187 AAACATTATA
* *
50197 ATTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTAGTTTTTTAATTAGGATTTAAAATAT
1 ATTAT-TTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAAAATAT
50262 TA-TTTAAA-
65 TATTTTAAAT
**
50270 A-TA-TTT-TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGGATATT
1 ATTATTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAAAATATT
50332 ATTTTAAAT
66 ATTTTAAAT
*
50341 ATTATTTTTGTTTTAGGTATTTTAGTTTAATTA-GTTTTA
1 ATTA-TTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
50380 ATTAGGATTT
Statistics
Matches: 99, Mismatches: 5, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
69 53 0.54
70 9 0.09
71 1 0.01
72 4 0.04
73 1 0.01
74 9 0.09
75 22 0.22
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.57
Consensus pattern (74 bp):
ATTATTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAAAATATT
ATTTTAAAT
Found at i:50309 original size:24 final size:23
Alignment explanation
Indices: 50206--50313 Score: 71
Period size: 25 Copynumber: 4.6 Consensus size: 23
50196 AATTATCTTT
50206 GTTTTAGATATTTTAGTTTAAATAG
1 GTTTTAG-TATTTTA-TTTAAATAG
*
50231 GTTTTAG---TTT-TTTAATTAG
1 GTTTTAGTATTTTATTTAAATAG
* ** * *
50250 GATTTAAAATATTATTTAAAATATT
1 GTTTTAGTATTTTATTT-AAATA-G
*
50275 TTTTTAGGTATTTTAGTTTAAATAG
1 GTTTTA-GTATTTTA-TTTAAATAG
50300 GTTTTAGTATTTTA
1 GTTTTAGTATTTTA
50314 ATTAGGATTT
Statistics
Matches: 62, Mismatches: 13, Indels: 17
0.67 0.14 0.18
Matches are distributed among these distances:
19 13 0.21
21 3 0.05
22 2 0.03
23 3 0.05
24 12 0.19
25 16 0.26
26 10 0.16
27 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (23 bp):
GTTTTAGTATTTTATTTAAATAG
Found at i:51103 original size:15 final size:16
Alignment explanation
Indices: 51085--51127 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
51075 TTACTAATTA
51085 TTTTATTATTTTT-TC
1 TTTTATTATTTTTATC
51100 TTTTATTTATTTTTATC
1 TTTTA-TTATTTTTATC
*
51117 TATT-TTATTTT
1 TTTTATTATTTT
51128 ATTAAATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 12 0.48
16 8 0.32
17 5 0.20
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATTATTTTTATC
Found at i:51122 original size:19 final size:18
Alignment explanation
Indices: 51083--51126 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
51073 TATTACTAAT
51083 TATTTTA-TTATTTTTTC
1 TATTTTATTTATTTTTTC
51100 --TTTTATTTATTTTTATC
1 TATTTTATTTATTTTT-TC
51117 TATTTTATTT
1 TATTTTATTT
51127 TATTAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.22
16 8 0.35
17 2 0.09
19 8 0.35
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTTTATTTATTTTTTC
Found at i:54469 original size:17 final size:17
Alignment explanation
Indices: 54447--54479 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
54437 AGATATCATA
54447 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
54464 ATATTATATTTTATAT
1 ATATTATATTTTATAT
54480 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Done.