Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007586.1 Hibiscus syriacus cultivar Beakdansim tig00021741_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: 110541
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:6686 original size:19 final size:19
Alignment explanation
Indices: 6662--6700 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6652 TATCTTTTAT
6662 TTATTTCATTTCATT-CTTA
1 TTATTT-ATTTCATTACTTA
*
6681 TTATTTTTTTCATTACTTA
1 TTATTTATTTCATTACTTA
6700 T
1 T
6701 ATTATTACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTATTTCATTACTTA
Found at i:6962 original size:5 final size:5
Alignment explanation
Indices: 6952--7020 Score: 54
Period size: 5 Copynumber: 13.8 Consensus size: 5
6942 GGAGTGCAAA
* * **
6952 AAAAG AAAAG -ACA- AAAAG AAGAG AAAA- ATCAG AAAGAAG AAAAG AAGAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA-A-G AAAAG AA-AAG
7002 AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAA
7021 AGAGAAGTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
4 6 0.12
5 33 0.66
6 7 0.14
7 4 0.08
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:6978 original size:11 final size:11
Alignment explanation
Indices: 6951--7023 Score: 62
Period size: 11 Copynumber: 6.6 Consensus size: 11
6941 TGGAGTGCAA
6951 AAAAAGAAAAG
1 AAAAAGAAAAG
*
6962 ACAAAA-AGAAG
1 A-AAAAGAAAAG
**
6973 AGAAAA-ATCAG
1 A-AAAAGAAAAG
6984 AAAGAAGAAAAG
1 AAA-AAGAAAAG
*
6996 AAGAAGAAAAG
1 AAAAAGAAAAG
7007 -AAAAGAAAAG
1 AAAAAGAAAAG
7017 AAAAAGA
1 AAAAAGA
7024 GAAGTTCAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
10 11 0.22
11 30 0.60
12 9 0.18
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:6978 original size:18 final size:17
Alignment explanation
Indices: 6955--7027 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 17
6945 GTGCAAAAAA
6955 AGAAAAGACAAAAAGAAG
1 AGAAAAGA-AAAAAGAAG
*
6973 AGAAAA-ATCAGAAAGAAG
1 AGAAAAGA--AAAAAGAAG
* *
6991 AAAAGAAGAAGAAAAGAAA
1 AGAA-AAGAA-AAAAGAAG
7010 AGAAAAGAAAAAGAGAAG
1 AGAAAAGAAAAA-AGAAG
7028 TTCAAAAGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
17 4 0.09
18 28 0.64
19 11 0.25
20 1 0.02
ACGTcount: A:0.73, C:0.03, G:0.23, T:0.01
Consensus pattern (17 bp):
AGAAAAGAAAAAAGAAG
Found at i:6979 original size:26 final size:27
Alignment explanation
Indices: 6949--7027 Score: 90
Period size: 26 Copynumber: 2.9 Consensus size: 27
6939 ATTGGAGTGC
6949 AAAAAAAGAAAAGACAAAAAGAAG-AGA
1 AAAAAAAGAAAAGA-AAAAAGAAGAAGA
**
6976 AAAATCAG-AAAGAAGAAAAGAAGAAGA
1 AAAAAAAGAAAAGAA-AAAAGAAGAAGA
7003 AAAGAAAAGAAAAGAAAAAGAGAAG
1 AAA-AAAAGAAAAGAAAAA-AGAAG
7028 TTCAAAAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
25 1 0.02
26 13 0.30
27 12 0.28
28 6 0.14
29 11 0.26
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.01
Consensus pattern (27 bp):
AAAAAAAGAAAAGAAAAAAGAAGAAGA
Found at i:15228 original size:19 final size:20
Alignment explanation
Indices: 15206--15269 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
15196 TTTGAACTTC
15206 TCTTTTTCTT-TTCTTT-TCT
1 TCTTTTTCTTATT-TTTCTCT
15225 TC-TTTTCTTATTTTTCTCT
1 TCTTTTTCTTATTTTTCTCT
* *
15244 TC-TTTTCTGATTTTTGTCT
1 TCTTTTTCTTATTTTTCTCT
15263 TCTTTTT
1 TCTTTTT
15270 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.25
19 26 0.65
20 4 0.10
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (20 bp):
TCTTTTTCTTATTTTTCTCT
Found at i:34500 original size:13 final size:11
Alignment explanation
Indices: 34479--34543 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 11
34469 ATCACGCCTT
34479 TATCATCACCA
1 TATCATCACCA
34490 TAGTCCATCACCA
1 TA-T-CATCACCA
*
34503 TTATCA-CGCCTA
1 -TATCATCACC-A
34515 TATCATCACCA
1 TATCATCACCA
34526 TATTCCATCACCA
1 TA-T-CATCACCA
34539 TATCA
1 TATCA
34544 CGCCTATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 15 0.33
12 9 0.20
13 19 0.42
14 2 0.04
ACGTcount: A:0.32, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
TATCATCACCA
Found at i:34506 original size:36 final size:36
Alignment explanation
Indices: 34466--34560 Score: 156
Period size: 36 Copynumber: 2.7 Consensus size: 36
34456 CCTTACATCA
*
34466 ATTATCACGCCTTTATCATCACCATAGTCCATCACC
1 ATTATCACGCCTATATCATCACCATAGTCCATCACC
*
34502 ATTATCACGCCTATATCATCACCATATTCCATCACC
1 ATTATCACGCCTATATCATCACCATAGTCCATCACC
*
34538 A-TATCACGCCTATATTATCACCA
1 ATTATCACGCCTATATCATCACCA
34561 ACTTATAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 21 0.38
36 35 0.62
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.31
Consensus pattern (36 bp):
ATTATCACGCCTATATCATCACCATAGTCCATCACC
Found at i:42900 original size:16 final size:16
Alignment explanation
Indices: 42879--42910 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42869 TAGTTAGCTC
42879 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
42895 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
42911 TGGTGGAAGA
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:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:44343 original size:16 final size:15
Alignment explanation
Indices: 44324--44408 Score: 66
Period size: 16 Copynumber: 5.2 Consensus size: 15
44314 TCCAAAAATA
44324 AAGAAAAGACAAAAAG
1 AAGAAAAGA-AAAAAG
*
44340 AAGAGAAAAATCAGAAAAG
1 AAGA-AAAGA--A-AAAAG
44359 AAGAAAAGAAGAAGAA-
1 AAGAAAAGAA-AA-AAG
44375 AAGAAAAGAAAAGAA-
1 AAGAAAAGAAAA-AAG
44390 AAGAAAAGAAAAAGAG
1 AAGAAAAGAAAAA-AG
44406 AAG
1 AAG
44409 TTCAAAAAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.02
15 18 0.30
16 21 0.34
17 6 0.10
18 6 0.10
19 9 0.15
ACGTcount: A:0.74, C:0.02, G:0.22, T:0.01
Consensus pattern (15 bp):
AAGAAAAGAAAAAAG
Found at i:44348 original size:11 final size:11
Alignment explanation
Indices: 44323--44404 Score: 71
Period size: 11 Copynumber: 7.5 Consensus size: 11
44313 GTCCAAAAAT
44323 AAAGAAAAGACAA
1 AAAGAAAAG--AA
*
44336 AAAGAAGAGAA
1 AAAGAAAAGAA
* *
44347 AAATCAGAA-AA
1 AAA-GAAAAGAA
*
44358 GAAGAAAAGAA
1 AAAGAAAAGAA
*
44369 GAAGAAAAG-A
1 AAAGAAAAGAA
44379 AAAGAAAAG-A
1 AAAGAAAAGAA
44389 AAAGAAAAGAA
1 AAAGAAAAGAA
44400 AAAGA
1 AAAGA
44405 GAAGTTCAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
10 22 0.38
11 26 0.45
12 2 0.03
13 8 0.14
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.01
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:44357 original size:19 final size:19
Alignment explanation
Indices: 44335--44399 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
44325 AGAAAAGACA
**
44335 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGAGAAAAAGAAG
44354 AAAAGAAGA-AAAGAAGAAG
1 AAAAGAAGAGAAA-AAGAAG
* *
44373 AAAAGAAAAGAAAAGAAAAG
1 AAAAGAAGAGAAAA-AGAAG
44393 AAAAGAA
1 AAAAGAA
44400 AAAGAGAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
18 3 0.08
19 22 0.56
20 14 0.36
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAAGAAGAGAAAAAGAAG
Found at i:44360 original size:5 final size:5
Alignment explanation
Indices: 44323--44401 Score: 78
Period size: 5 Copynumber: 16.6 Consensus size: 5
44313 GTCCAAAAAT
* * **
44323 AAAGA AAAG- ACA-A AAAGA AGAGA AAA-A TCAGA AAAG- -AAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
44368 AGAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1 A-AAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
44402 AGAGAAGTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
3 3 0.05
4 6 0.10
5 46 0.77
6 5 0.08
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAGA
Found at i:46521 original size:16 final size:16
Alignment explanation
Indices: 46500--46531 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46490 TAGTTAGCTC
46500 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
46516 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
46532 TGGTGGAAGA
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:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:47981 original size:5 final size:5
Alignment explanation
Indices: 47939--48009 Score: 53
Period size: 5 Copynumber: 14.8 Consensus size: 5
47929 TTGGAGTCCA
* * **
47939 AAAAG -AAAG AAAAG -ACA- AAAAG AAGAG AAAA- ATCAG AAAAG AAGAA-
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG
47985 AAGAAG AAAAG AAAAG AAAAG AAAA
1 AA-AAG AAAAG AAAAG AAAAG AAAA
48010 AGAGAAGTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
4 10 0.19
5 38 0.73
6 4 0.08
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:47984 original size:8 final size:8
Alignment explanation
Indices: 47939--48016 Score: 61
Period size: 8 Copynumber: 9.0 Consensus size: 8
47929 TTGGAGTCCA
47939 AAAAGAAAG
1 AAAAG-AAG
47948 AAAAGACA-
1 AAAAGA-AG
47956 AAAAGAAG
1 AAAAGAAG
*
47964 AGAAAAATCAG
1 A-AAAGA--AG
47975 AAAAGAAG
1 AAAAGAAG
47983 AAAAGAAG
1 AAAAGAAG
47991 AAAAGAAAAG
1 AAAAG--AAG
48001 AAAAGAA-
1 AAAAGAAG
48008 AAAGAGAAG
1 AAA-AGAAG
48017 TTCAAAAAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
7 4 0.07
8 29 0.50
9 10 0.17
10 12 0.21
11 3 0.05
ACGTcount: A:0.74, C:0.03, G:0.22, T:0.01
Consensus pattern (8 bp):
AAAAGAAG
Found at i:51727 original size:16 final size:16
Alignment explanation
Indices: 51706--51737 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
51696 TAGTTAGCTC
51706 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
51722 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
51738 TGGTGGAAGA
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:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:53180 original size:8 final size:8
Alignment explanation
Indices: 53169--53226 Score: 82
Period size: 8 Copynumber: 7.0 Consensus size: 8
53159 AAAGAAGAGA
53169 AAAAGAAG
1 AAAAGAAG
53177 AAAAGAAG
1 AAAAGAAG
53185 AAAAGAAG
1 AAAAGAAG
53193 AAAAGAAG
1 AAAAGAAG
53201 AAAAGAAAAG
1 AAAAG--AAG
53211 AAAAGAA-
1 AAAAGAAG
53218 AAAGAGAAG
1 AAA-AGAAG
53227 TTCAAAAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
7 3 0.07
8 35 0.76
10 8 0.17
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:53182 original size:5 final size:5
Alignment explanation
Indices: 53158--53219 Score: 60
Period size: 5 Copynumber: 12.8 Consensus size: 5
53148 TTGGAGTGCA
* *
53158 AAAAG AAGAG AAAA- AGAAG AAAAG --AAG AAAAG AAGAA- AAGAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AA-AAG AAAAG
53206 AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAA
53220 AGAGAAGTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
3 3 0.06
4 3 0.06
5 38 0.79
6 4 0.08
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:55328 original size:16 final size:16
Alignment explanation
Indices: 55307--55338 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
55297 TAGTTAGCTC
55307 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
55323 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
55339 TGGTGGAAGA
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:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:59840 original size:19 final size:20
Alignment explanation
Indices: 59799--59849 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
59789 GAAACCCCTT
*
59799 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
59819 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
59838 TGAAGATACATG
1 TGAAAATACATG
59850 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:67938 original size:13 final size:13
Alignment explanation
Indices: 67922--67960 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
67912 CTTTTTGAAC
67922 TTCTCTTTTTCTT
1 TTCTCTTTTTCTT
67935 TTCT-TTTCTTCTT
1 TTCTCTTT-TTCTT
67948 TTCTTCTTTTTCT
1 TTC-TCTTTTTCT
67961 CTTGTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.13
13 12 0.52
14 5 0.22
15 3 0.13
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTCTTTTTCTT
Found at i:67955 original size:27 final size:29
Alignment explanation
Indices: 67925--67988 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
67915 TTTGAACTTC
*
67925 TCTTTTTCTTTTCTTTTCT-TCTTT-TCT
1 TCTTTTTCTCTTCTTTTCTATCTTTGTCT
* *
67952 TCTTTTTCTCTTGTTTTCTGATTTTTGTCT
1 TCTTTTTCTCTTCTTTTCT-ATCTTTGTCT
67982 TCTTTTT
1 TCTTTTT
67989 GCACTCCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 17 0.55
29 4 0.13
30 10 0.32
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.75
Consensus pattern (29 bp):
TCTTTTTCTCTTCTTTTCTATCTTTGTCT
Found at i:67963 original size:16 final size:17
Alignment explanation
Indices: 67922--67963 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
67912 CTTTTTGAAC
*
67922 TTCTCTTTTTCTTTTCTT
1 TTCTC-TTTTCTTCTCTT
67940 TTCTTCTTTTCTTCT-TT
1 TTC-TCTTTTCTTCTCTT
67957 TTCTCTT
1 TTCTCTT
67964 GTTTTCTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.18
17 5 0.23
18 11 0.50
19 2 0.09
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTCTTTTCTTCTCTT
Found at i:67963 original size:19 final size:17
Alignment explanation
Indices: 67928--67987 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 17
67918 GAACTTCTCT
67928 TTTTCTTTTCTTTTCTTC
1 TTTTCTTTT-TTTTCTTC
*
67946 TTTTCTTCTTTTTCTCTTG
1 TTTTCTT-TTTTT-TCTTC
*
67965 TTTTCTGATTTTTGTCTTC
1 TTTTCT--TTTTTTTCTTC
67984 TTTT
1 TTTT
67988 TGCACTCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 10 0.29
19 20 0.57
20 4 0.11
21 1 0.03
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (17 bp):
TTTTCTTTTTTTTCTTC
Found at i:68278 original size:20 final size:20
Alignment explanation
Indices: 68241--68284 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
68231 ATGGACTTAA
*
68241 GAAATGAATATATAATAAAG
1 GAAATGAATATAGAATAAAG
*
68261 GAAATGAA-ATAGACATAAAT
1 GAAATGAATATAGA-ATAAAG
68281 GAAA
1 GAAA
68285 GAGATGGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.61, C:0.02, G:0.16, T:0.20
Consensus pattern (20 bp):
GAAATGAATATAGAATAAAG
Found at i:70950 original size:19 final size:20
Alignment explanation
Indices: 70926--70976 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
70916 CGGCCAAGAG
* *
70926 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
70945 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
70965 CATGTATTTTCA
1 CATGTATTTTCA
70977 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:75150 original size:19 final size:20
Alignment explanation
Indices: 75126--75176 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
75116 CGGCCAAGAG
* *
75126 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
75145 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
75165 CATGTATTTTCA
1 CATGTATTTTCA
75177 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:90985 original size:19 final size:21
Alignment explanation
Indices: 90942--90993 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
90932 GAAACCCCTT
90942 TGAAGATACATGACTTTTAAA
1 TGAAGATACATGACTTTTAAA
*
90963 TGAAAATACATGA-TTTT-AA
1 TGAAGATACATGACTTTTAAA
90982 TGAAGATACATG
1 TGAAGATACATG
90994 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (21 bp):
TGAAGATACATGACTTTTAAA
Found at i:91918 original size:23 final size:24
Alignment explanation
Indices: 91888--91941 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
91878 ATATTATAAC
91888 TGATGTATGGC-TCTGATACCACT
1 TGATGTATGGCTTCTGATACCACT
*
91911 TGATGTATGGCTTCTGATGCCACT
1 TGATGTATGGCTTCTGATACCACT
91935 TGATGTA
1 TGATGTA
91942 AGGTAATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (24 bp):
TGATGTATGGCTTCTGATACCACT
Found at i:101856 original size:5 final size:5
Alignment explanation
Indices: 101846--101918 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
101836 GAACTTCTCT
*
101846 TTTTC TTTTC TTTTC TTTTC TTCTTA TTTTC TTATT- TTCTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TT-TTC TT-TTC TTTTC
* *
101893 TCTTC -TTT- TTGTC TTTTC -TTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
101919 TGCACTCCAA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
4 8 0.15
5 39 0.71
6 8 0.15
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:101864 original size:16 final size:16
Alignment explanation
Indices: 101846--101919 Score: 64
Period size: 16 Copynumber: 4.6 Consensus size: 16
101836 GAACTTCTCT
101846 TTTTC-TTTTCTTTTC
1 TTTTCTTTTTCTTTTC
* *
101861 TTTTCTTCTTATTTTC
1 TTTTCTTTTTCTTTTC
*
101877 TTATT-TTCTTCTTTTC
1 TT-TTCTTTTTCTTTTC
*
101893 TCTTCTTTTTGTCTTTTC
1 TTTTC-TTTT-TCTTTTC
101911 -TTTCTTTTT
1 TTTTCTTTTT
101920 GCACTCCAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
15 8 0.17
16 25 0.52
17 8 0.17
18 7 0.15
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTC
Found at i:101869 original size:8 final size:8
Alignment explanation
Indices: 101853--101918 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
101843 TCTTTTTCTT
101853 TTCTTTTC
1 TTCTTTTC
101861 TT-TTCTTC
1 TTCTT-TTC
*
101869 TTATTTTC
1 TTCTTTTC
*
101877 TTATTTTC
1 TTCTTTTC
101885 TTCTTTTCTC
1 TTC-TTT-TC
101895 TTCTTTT-
1 TTCTTTTC
101902 TGTCTTTTC
1 T-TCTTTTC
101911 TTTCTTTT
1 -TTCTTTT
101919 TGCACTCCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
7 3 0.06
8 27 0.54
9 14 0.28
10 6 0.12
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:101912 original size:13 final size:12
Alignment explanation
Indices: 101851--101913 Score: 56
Period size: 13 Copynumber: 5.1 Consensus size: 12
101841 TCTCTTTTTC
101851 TTTTCTTTTCTT
1 TTTTCTTTTCTT
*
101863 TTCTTCTTAT-TT
1 TT-TTCTTTTCTT
* *
101875 TCTTATTTTCTT
1 TTTTCTTTTCTT
*
101887 CTTTTCTCTTCTT
1 -TTTTCTTTTCTT
101900 TTTGTCTTTTCTT
1 TTT-TCTTTTCTT
101913 T
1 T
101914 CTTTTTGCAC
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:101917 original size:17 final size:18
Alignment explanation
Indices: 101839--101920 Score: 73
Period size: 18 Copynumber: 4.6 Consensus size: 18
101829 TCTTTTTGAA
101839 CTTCTCTTTT-TCTTTTCT
1 CTTCT-TTTTGTCTTTTCT
* *
101857 TTTCTTTTCT-TCTTATTTT
1 CTTCTTTT-TGTCTT-TTCT
*
101876 CTTATTTTCT-TCTTTTCT
1 CTTCTTTT-TGTCTTTTCT
101894 CTTCTTTTTGTCTTTTCT
1 CTTCTTTTTGTCTTTTCT
101912 -TTCTTTTTG
1 CTTCTTTTTG
101921 CACTCCAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
17 13 0.24
18 27 0.49
19 15 0.27
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (18 bp):
CTTCTTTTTGTCTTTTCT
Found at i:102210 original size:19 final size:20
Alignment explanation
Indices: 102171--102206 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
102161 GGGTAATAAT
102171 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
102191 ATAAG-AATG-AAATAAA
1 ATAAGTAATGAAAATAAA
102207 ATAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 4 0.25
20 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:104954 original size:13 final size:13
Alignment explanation
Indices: 104932--104961 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
104922 ACTAAACACC
104932 TTTC-ACATACCT
1 TTTCAACATACCT
104944 TTTCAACATACCT
1 TTTCAACATACCT
104957 TTTCA
1 TTTCA
104962 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:107728 original size:22 final size:21
Alignment explanation
Indices: 107702--107758 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
107692 ACTTTTCTTT
*
107702 CTTTCTTTTTCTTTTTCAAGTG
1 CTTTCATTTTCTTTTT-AAGTG
* *
107724 CTTTCAATTTCTTCTTTGAGTG
1 CTTTCATTTTCTT-TTTAAGTG
*
107746 CTTT-GTTTTCTTT
1 CTTTCATTTTCTTT
107759 GCTGAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.03
21 6 0.21
22 19 0.66
23 3 0.10
ACGTcount: A:0.09, C:0.18, G:0.11, T:0.63
Consensus pattern (21 bp):
CTTTCATTTTCTTTTTAAGTG
Found at i:108453 original size:23 final size:24
Alignment explanation
Indices: 108423--108476 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
108413 ATATTATAAC
108423 TGATGTATGGC-TCTGATACCACT
1 TGATGTATGGCTTCTGATACCACT
*
108446 TGATGTATGGCTTCTGATGCCACT
1 TGATGTATGGCTTCTGATACCACT
108470 TGATGTA
1 TGATGTA
108477 AGGTAATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (24 bp):
TGATGTATGGCTTCTGATACCACT
Done.