Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001977.1 Hibiscus syriacus cultivar Beakdansim tig00004012_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: 82504
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4781 original size:18 final size:19
Alignment explanation
Indices: 4760--4813 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
4750 CATTTGGTCA
4760 AAAG-CATGTATTTTCATT
1 AAAGTCATGTATTTTCATT
* *
4778 AAAGTCTTGTTTTTTCATT
1 AAAGTCATGTATTTTCATT
*
4797 AAAAATCATGTCATTTT
1 -AAAGTCATGT-ATTTT
4814 AGGAAGGTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 4 0.14
19 12 0.43
20 8 0.29
21 4 0.14
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (19 bp):
AAAGTCATGTATTTTCATT
Found at i:7546 original size:24 final size:21
Alignment explanation
Indices: 7511--7553 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
7501 GGCTCATTCT
*
7511 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
7534 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
7554 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:10000 original size:24 final size:24
Alignment explanation
Indices: 9973--10028 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
9963 AGAGAACATT
9973 CTTTGGAATACCAAATGTTCCAAC
1 CTTTGGAATACCAAATGTTCCAAC
**
9997 CTTTGGAATACCAAATGTTTGAAC
1 CTTTGGAATACCAAATGTTCCAAC
10021 CTTTGGAA
1 CTTTGGAA
10029 CTTCAATGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (24 bp):
CTTTGGAATACCAAATGTTCCAAC
Found at i:11546 original size:13 final size:11
Alignment explanation
Indices: 11505--11589 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
11495 ACAATCTGTC
11505 CATCACCATTAT
1 CATCACCA-TAT
* *
11517 CA-CGCCTATGT
1 CATCACC-ATAT
11528 CATCACCATAGT
1 CATCACCATA-T
11540 CCATCACCATTAT
1 -CATCACCA-TAT
*
11553 CA-CGCCTATAT
1 CATCACC-ATAT
11564 CATCACCATATT
1 CATCACCATA-T
11576 CCATCACCATAT
1 -CATCACCATAT
11588 CA
1 CA
11590 CGCCTATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
11 22 0.38
12 15 0.26
13 19 0.33
14 2 0.03
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:11549 original size:36 final size:36
Alignment explanation
Indices: 11502--11606 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
11492 GATACAATCT
*
11502 GTCCATCACCATTATCACGCCTATGTCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
11538 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
11574 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
11607 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:12066 original size:14 final size:15
Alignment explanation
Indices: 12043--12087 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
12033 TTTGGAGTGC
12043 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
12058 AAAAG-AAGAAAAGC
1 AAAAGAAAGAAAAGA
12072 AAAAGCAAACGAAAAG
1 AAAAG-AAA-GAAAAG
12088 TGAAGCAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 13 0.50
15 5 0.19
16 2 0.08
17 6 0.23
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:17014 original size:18 final size:16
Alignment explanation
Indices: 16972--17026 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
16962 GTAAGTTATC
16972 TTCATTTTTCTTACTAT
1 TTCATTTTTCTTA-TAT
16989 TTCA-TTTTCTTATACT
1 TTCATTTTTCTTATA-T
17005 TTCATCTTTTCTTAT-T
1 TTCAT-TTTTCTTATAT
17021 TTCATT
1 TTCATT
17027 ACTTTATCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.09
16 19 0.54
17 4 0.11
18 9 0.26
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.65
Consensus pattern (16 bp):
TTCATTTTTCTTATAT
Found at i:17038 original size:25 final size:25
Alignment explanation
Indices: 16992--17044 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
16982 TTACTATTTC
*
16992 ATTTTCTTATACTTTCATCTTTTCTT
1 ATTTTCATATACTTTCATCTTTT-TT
17018 ATTTTCAT-TACTTT-ATCCTTTTTT
1 ATTTTCATATACTTTCAT-CTTTTTT
17042 ATT
1 ATT
17045 AACCTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 7 0.28
25 11 0.44
26 7 0.28
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (25 bp):
ATTTTCATATACTTTCATCTTTTTT
Found at i:20474 original size:19 final size:20
Alignment explanation
Indices: 20450--20500 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
20440 CGGCCAAGAG
* *
20450 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
20469 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
20489 CATGTATTTTCA
1 CATGTATTTTCA
20501 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:24661 original size:19 final size:19
Alignment explanation
Indices: 24637--24686 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
24627 CGGCCAAGAG
*
24637 CATGTATCTTCAT-TAAAAT
1 CATGTAT-TTCATCAAAAAT
24656 CATGTATTTTCATCAAAAAT
1 CATGTA-TTTCATCAAAAAT
24676 CATGTATTTCA
1 CATGTATTTCA
24687 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (19 bp):
CATGTATTTCATCAAAAAT
Found at i:24676 original size:20 final size:19
Alignment explanation
Indices: 24637--24684 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
24627 CGGCCAAGAG
* *
24637 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATAAAAAT
24656 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCAT-AAAAAT
24676 CATGTATTT
1 CATGTATTT
24685 CAAAGGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Found at i:28828 original size:19 final size:20
Alignment explanation
Indices: 28804--28854 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
28794 CGGCCAAGAG
* *
28804 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
28823 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
28843 CATGTATTTTCA
1 CATGTATTTTCA
28855 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:32060 original size:16 final size:16
Alignment explanation
Indices: 32028--32073 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
32018 ATAGTAATGA
32028 AATAAGAAAAGATGAAAG
1 AATAAG-AAA-ATGAAAG
*
32046 AATAAGAAAATGAAAT
1 AATAAGAAAATGAAAG
*
32062 AGTAAGAAAATG
1 AATAAGAAAATG
32074 GAGATAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 17 0.65
17 3 0.12
18 6 0.23
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:32816 original size:16 final size:16
Alignment explanation
Indices: 32795--32826 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
32785 TAGTTAGCTC
32795 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
32811 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
32827 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:34282 original size:5 final size:5
Alignment explanation
Indices: 34240--34329 Score: 84
Period size: 5 Copynumber: 18.8 Consensus size: 5
34230 TTGGAGTGCA
* * **
34240 AAAAG -AAAG AAAAG -ACA- AAAAG AAGAG AAAA- ATCAG AAAAG --AAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
34284 AAAAG AAGAAG AAAAG AAAAG AAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
34330 AAGAGAAGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
3 3 0.04
4 10 0.14
5 46 0.67
6 10 0.14
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.01
Consensus pattern (5 bp):
AAAAG
Found at i:34285 original size:8 final size:8
Alignment explanation
Indices: 34240--34322 Score: 73
Period size: 8 Copynumber: 9.9 Consensus size: 8
34230 TTGGAGTGCA
34240 AAAAGAAAG
1 AAAAG-AAG
34249 AAAAGACA-
1 AAAAGA-AG
34257 AAAAGAAG
1 AAAAGAAG
*
34265 AGAAAAATCAG
1 A-AAAGA--AG
34276 AAAAGAAG
1 AAAAGAAG
34284 AAAAGAAG
1 AAAAGAAG
34292 AAGAA-AAG
1 AA-AAGAAG
34300 AAAAGAAG
1 AAAAGAAG
34308 AAGAA-AAG
1 AA-AAGAAG
34316 AAAAGAA
1 AAAAGAA
34323 AAGAAAAAAG
Statistics
Matches: 63, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
7 5 0.08
8 37 0.59
9 14 0.22
10 4 0.06
11 3 0.05
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.01
Consensus pattern (8 bp):
AAAAGAAG
Found at i:34330 original size:16 final size:16
Alignment explanation
Indices: 34281--34329 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
34271 ATCAGAAAAG
34281 AAGAAAAGAAGAAGAA
1 AAGAAAAGAAGAAGAA
34297 AAGAAAAGAAGAAGAA
1 AAGAAAAGAAGAAGAA
34313 AAGAAAAGAA-AAGAA
1 AAGAAAAGAAGAAGAA
34328 AA
1 AA
34330 AAGAGAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 7 0.21
16 26 0.79
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAGAAGAA
Found at i:34336 original size:27 final size:27
Alignment explanation
Indices: 34240--34337 Score: 103
Period size: 27 Copynumber: 3.6 Consensus size: 27
34230 TTGGAGTGCA
34240 AAAAGAAAGAAAAGACA-AAAAGAAGA-G
1 AAAAGAAA-AAAAGA-AGAAAAGAAGAAG
** *
34267 AAAAATCAGAAAAGAAGAAAAGAAGAAG
1 -AAAAGAAAAAAAGAAGAAAAGAAGAAG
*
34295 AAAAGAAAAGAAGAAGAAAAGAA-AAG
1 AAAAGAAAAAAAGAAGAAAAGAAGAAG
34321 AAAAGAAAAAAGAGAAG
1 AAAAGAAAAAA-AGAAG
34338 TTCAAAAAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
26 14 0.24
27 39 0.66
28 6 0.10
ACGTcount: A:0.74, C:0.02, G:0.22, T:0.01
Consensus pattern (27 bp):
AAAAGAAAAAAAGAAGAAAAGAAGAAG
Found at i:36452 original size:16 final size:16
Alignment explanation
Indices: 36431--36462 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
36421 TAGTTAGCTC
36431 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
36447 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
36463 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:38140 original size:19 final size:21
Alignment explanation
Indices: 38097--38147 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
38087 GAAACCCCTT
38097 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
38118 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
38137 TGAAGATACAT
1 TGAAAATACAT
38148 ACTCTTGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:41446 original size:13 final size:13
Alignment explanation
Indices: 41416--41466 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
41406 CTTGGCTTGC
**
41416 TTTCTCTTTTTGAA
1 TTTCTCTTTTT-CT
41430 TTTCTCTTTTTCT
1 TTTCTCTTTTTCT
41443 TTTCT-TTTCTTCT
1 TTTCTCTTT-TTCT
41456 TTTCTTCTTTT
1 TTTC-TCTTTT
41467 CAGATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 3 0.09
13 13 0.41
14 13 0.41
15 3 0.09
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTCTCTTTTTCT
Found at i:41503 original size:17 final size:18
Alignment explanation
Indices: 41474--41507 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
41464 TTTCAGATTT
41474 TTTTCTCTTCTTTTTGCC
1 TTTTCTCTTCTTTTTGCC
41492 TTTTCT-TTCTTTTTGC
1 TTTTCTCTTCTTTTTGC
41508 ACTCCAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.24, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTCTCTTCTTTTTGCC
Found at i:41833 original size:14 final size:14
Alignment explanation
Indices: 41814--41840 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41804 ATGAAATAAA
41814 TAGAGGAAGAACAT
1 TAGAGGAAGAACAT
41828 TAGAGGAAGAACA
1 TAGAGGAAGAACA
41841 ACAAAGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.30, T:0.11
Consensus pattern (14 bp):
TAGAGGAAGAACAT
Found at i:57431 original size:24 final size:24
Alignment explanation
Indices: 57404--57455 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
57394 GACATGTCCT
* * *
57404 TTGACGTTCCAACAGTTATGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
* *
57428 TTGATGTTCAAAAAGATGTGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
57452 TTGA
1 TTGA
57456 AGTGCCAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (24 bp):
TTGACGTTCAAAAAGATATGCCAC
Found at i:61196 original size:11 final size:11
Alignment explanation
Indices: 61176--61208 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
61166 TAACATTGGT
61176 TCTTCTTTGAG
1 TCTTCTTTGAG
*
61187 TCTTCGTTGAG
1 TCTTCTTTGAG
61198 TCTTCTTTGAG
1 TCTTCTTTGAG
61209 ATACTACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.18, G:0.21, T:0.52
Consensus pattern (11 bp):
TCTTCTTTGAG
Found at i:61691 original size:27 final size:27
Alignment explanation
Indices: 61629--61683 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
61619 CTAAATAATG
*
61629 GAAACAAAGAAATTAAAATGCAAAGAA
1 GAAACAAAGAAATCAAAATGCAAAGAA
61656 GAAACAAAGAAATCAAAATGCAAAGAA
1 GAAACAAAGAAATCAAAATGCAAAGAA
61683 G
1 G
61684 TGCCAAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.65, C:0.09, G:0.16, T:0.09
Consensus pattern (27 bp):
GAAACAAAGAAATCAAAATGCAAAGAA
Found at i:64788 original size:11 final size:11
Alignment explanation
Indices: 64768--64800 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
64758 TAACATTGGT
64768 TCTTCTTTGAG
1 TCTTCTTTGAG
*
64779 TCTTCGTTGAG
1 TCTTCTTTGAG
64790 TCTTCTTTGAG
1 TCTTCTTTGAG
64801 ATACTACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.18, G:0.21, T:0.52
Consensus pattern (11 bp):
TCTTCTTTGAG
Found at i:74187 original size:19 final size:20
Alignment explanation
Indices: 74163--74213 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
74153 CGGCCAAGAG
* *
74163 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
74182 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
74202 CATGTATTTTCA
1 CATGTATTTTCA
74214 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:78353 original size:18 final size:19
Alignment explanation
Indices: 78318--78364 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
78308 CGGCCAAGAG
*
78318 CATGTATCTTCAT-TAAAAT
1 CATGTAT-TTCATCAAAAAT
78337 CATGTATTTCATCAAAAAT
1 CATGTATTTCATCAAAAAT
78356 CATGTATTT
1 CATGTATTT
78365 TCAAAGGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.43
Consensus pattern (19 bp):
CATGTATTTCATCAAAAAT
Found at i:82480 original size:19 final size:19
Alignment explanation
Indices: 82456--82492 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
82446 CGGCCAAGAG
*
82456 CATGTATCTTCATTAAAAC
1 CATGTATCTTCATCAAAAC
*
82475 CATGTATTTTCATCAAAA
1 CATGTATCTTCATCAAAA
82493 ATCATGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (19 bp):
CATGTATCTTCATCAAAAC
Found at i:82498 original size:20 final size:19
Alignment explanation
Indices: 82456--82504 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
82446 CGGCCAAGAG
* *
82456 CATGTATCTTCATTAAAAC
1 CATGTATTTTCATAAAAAC
*
82475 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCAT-AAAAAC
82495 CATGTATTTT
1 CATGTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAC
Done.