Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002174.1 Hibiscus syriacus cultivar Beakdansim tig00004431_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: 50563
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:11734 original size:23 final size:23
Alignment explanation
Indices: 11705--11761 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
11695 CCTAAACACA
11705 AAACCGTTCCGACCCCTCTTTGC
1 AAACCGTTCCGACCCCTCTTTGC
11728 AAACCGTTCCGACCCCTCTTTGC
1 AAACCGTTCCGACCCCTCTTTGC
11751 AAACCGTTCCG
1 AAACCGTTCCG
11762 GTTGTCGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.19, C:0.42, G:0.14, T:0.25
Consensus pattern (23 bp):
AAACCGTTCCGACCCCTCTTTGC
Found at i:12451 original size:20 final size:20
Alignment explanation
Indices: 12417--12465 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
12407 AATGATTTTC
*
12417 TTTTGAAAACAAAAAAT-AGA
1 TTTTGAAAAC-AAAAATGAAA
* *
12437 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
12457 TTTTGAAAA
1 TTTTGAAAA
12466 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:13882 original size:20 final size:20
Alignment explanation
Indices: 13857--13894 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13847 AGAATGTCTA
13857 GGGGTACAGATTCCCCCTAG
1 GGGGTACAGATTCCCCCTAG
*
13877 GGGGTACCGATTCCCCCT
1 GGGGTACAGATTCCCCCT
13895 GTCTAACGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.34, G:0.29, T:0.21
Consensus pattern (20 bp):
GGGGTACAGATTCCCCCTAG
Found at i:14794 original size:21 final size:19
Alignment explanation
Indices: 14766--14820 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
14756 GAAATTAGGG
14766 CCTT-AGTATCGATACTGTCA
1 CCTTGAGTATCGATA-T-TCA
*
14786 CCTTGAGTATCGATATTGA
1 CCTTGAGTATCGATATTCA
14805 -CTTGAGTATCGATATT
1 CCTTGAGTATCGATATT
14821 GCCTTACAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 16 0.48
19 2 0.06
20 5 0.15
21 10 0.30
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (19 bp):
CCTTGAGTATCGATATTCA
Found at i:14810 original size:18 final size:18
Alignment explanation
Indices: 14787--14821 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
14777 ATACTGTCAC
14787 CTTGAGTATCGATATTGA
1 CTTGAGTATCGATATTGA
14805 CTTGAGTATCGATATTG
1 CTTGAGTATCGATATTG
14822 CCTTACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (18 bp):
CTTGAGTATCGATATTGA
Found at i:14835 original size:19 final size:18
Alignment explanation
Indices: 14793--14837 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
14783 TCACCTTGAG
* *
14793 TATCGATATTGACTTGAG
1 TATCGATATTGACTTCAA
*
14811 TATCGATATTGCCTTACAA
1 TATCGATATTGACTT-CAA
14830 TATCGATA
1 TATCGATA
14838 CTCCATATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (18 bp):
TATCGATATTGACTTCAA
Found at i:16742 original size:18 final size:18
Alignment explanation
Indices: 16719--16753 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16709 AGGGATTATC
* *
16719 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTACGGGACAT
16737 AGTGGTCCTACGGGACA
1 AGTGGTCCTACGGGACA
16754 AATTCTACGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:20313 original size:2 final size:2
Alignment explanation
Indices: 20306--20340 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
20296 TAATAACACT
* *
20306 TA TA TA TA TG TA TA TG 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 T
20341 CAAATGCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20947 original size:56 final size:56
Alignment explanation
Indices: 20886--20992 Score: 214
Period size: 56 Copynumber: 1.9 Consensus size: 56
20876 GCCACCGCCC
20886 CAGATAGTGTATCATCCTGCAGTATTTTCCTTTTTCTTTCATATATATATATATAT
1 CAGATAGTGTATCATCCTGCAGTATTTTCCTTTTTCTTTCATATATATATATATAT
20942 CAGATAGTGTATCATCCTGCAGTATTTTCCTTTTTCTTTCATATATATATA
1 CAGATAGTGTATCATCCTGCAGTATTTTCCTTTTTCTTTCATATATATATA
20993 AGAAAAAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (56 bp):
CAGATAGTGTATCATCCTGCAGTATTTTCCTTTTTCTTTCATATATATATATATAT
Found at i:22911 original size:20 final size:20
Alignment explanation
Indices: 22870--22911 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
22860 TTTAAGAATT
*
22870 ATTTTTTAAATTTTGGAACC
1 ATTTTTTAAATTTTAGAACC
* *
22890 ATTTTTTAATTTTTAGATCC
1 ATTTTTTAAATTTTAGAACC
22910 AT
1 AT
22912 AAATGCTTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.55
Consensus pattern (20 bp):
ATTTTTTAAATTTTAGAACC
Found at i:23187 original size:92 final size:94
Alignment explanation
Indices: 23030--23215 Score: 331
Period size: 92 Copynumber: 2.0 Consensus size: 94
23020 CTATATAAAA
*
23030 AAATATCGATCAAATGTGAACGATGACGGCATGTATGCTTGTTATAATTCTTCACGATGATCATG
1 AAATATCGATCAAATGTGAAAGATGACGGCATGTATGCTTGTTATAATTCTTCACGATGATCATG
23095 TCTATGCATG-AT-TGCATACCAAATAAC
66 TCTATGCATGCATATGCATACCAAATAAC
23122 AAATATCGATCAAATGTGAAAGATGACGGCATGTATGCTTGTTATAATTCTTCACGATGATCATG
1 AAATATCGATCAAATGTGAAAGATGACGGCATGTATGCTTGTTATAATTCTTCACGATGATCATG
23187 TCTATGCATGCATGCATGCATACCAAATA
66 TCTATGCATGCAT--ATGCATACCAAATA
23216 GGTCCTTATG
Statistics
Matches: 89, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
92 74 0.83
93 2 0.02
96 13 0.15
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (94 bp):
AAATATCGATCAAATGTGAAAGATGACGGCATGTATGCTTGTTATAATTCTTCACGATGATCATG
TCTATGCATGCATATGCATACCAAATAAC
Found at i:23447 original size:21 final size:21
Alignment explanation
Indices: 23407--23461 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
23397 GATTCTTGAC
23407 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
23427 AAGTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
*
23449 AATCGCAACGCGA
1 AATCGCAATGCGA
23462 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:23563 original size:20 final size:20
Alignment explanation
Indices: 23449--23697 Score: 245
Period size: 20 Copynumber: 12.4 Consensus size: 20
23439 GATTTTACAG
* ** *
23449 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
23469 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
* *
23489 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
23509 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23529 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
23549 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23569 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23589 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
23609 AATCGCAACG-ATAATCAGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
23629 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
23649 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
23669 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
23689 AATCACAAC
1 AATCGCAAC
23698 ACTGAAATTT
Statistics
Matches: 198, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 194 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:24429 original size:24 final size:24
Alignment explanation
Indices: 24390--24436 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
24380 AAATTTGGTC
24390 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
24414 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
24437 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:24628 original size:12 final size:12
Alignment explanation
Indices: 24611--24635 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24601 ATATAATCCT
24611 GAAGAAGAAAAA
1 GAAGAAGAAAAA
24623 GAAGAAGAAAAA
1 GAAGAAGAAAAA
24635 G
1 G
24636 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:27002 original size:19 final size:19
Alignment explanation
Indices: 26933--27051 Score: 167
Period size: 19 Copynumber: 6.4 Consensus size: 19
26923 GCAATGAGAG
26933 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
26952 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
26966 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
26986 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
27005 AATCGCAACGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
27025 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
27044 AATCGCAA
1 AATCGCAA
27052 CGAGAGAATC
Statistics
Matches: 89, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.11
15 2 0.02
16 1 0.01
17 1 0.01
19 43 0.48
20 32 0.36
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:27018 original size:39 final size:39
Alignment explanation
Indices: 26933--27053 Score: 173
Period size: 39 Copynumber: 3.3 Consensus size: 39
26923 GCAATGAGAG
* *
26933 AATCGCAATGC-GAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGCGGAAATGAAAATCGCAATGCGAAATGAA
*
26966 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGGAAATGAAAATCGCAATGCGAAATGAA
27005 AATCGCAACGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGGAAATGAAAATCGCAATGCGAAATGAA
27044 AATCGCAACG
1 AATCGCAACG
27054 AGAGAATCGC
Statistics
Matches: 80, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
33 11 0.14
34 15 0.19
36 1 0.01
38 2 0.03
39 51 0.64
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (39 bp):
AATCGCAACGCGGAAATGAAAATCGCAATGCGAAATGAA
Found at i:27114 original size:19 final size:19
Alignment explanation
Indices: 27090--27176 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
27080 GATTCTCTCG
27090 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
27109 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
27128 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
27142 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
27161 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
27177 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 41 0.67
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:27150 original size:52 final size:52
Alignment explanation
Indices: 27072--27176 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
27062 GCAATGCGTC
27072 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
27124 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
27176 C
1 C
27177 AACATAATGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (52 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
Found at i:27286 original size:14 final size:14
Alignment explanation
Indices: 27267--27303 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
27257 CATCAATTAC
27267 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
27281 ACAAATCATCTTTT
1 ACAAATCAACTTTT
27295 ACAAATCAA
1 ACAAATCAA
27304 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:29227 original size:19 final size:19
Alignment explanation
Indices: 29185--29338 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
29175 TAGTTTACTT
* *
29185 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
29205 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
29224 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
29243 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
29262 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
29276 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
29295 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
29309 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
29328 TCGCAATGCGA
1 TCGCAACGCGA
29339 TTTTGGTTTC
Statistics
Matches: 109, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
14 18 0.17
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 63 0.58
20 12 0.11
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:29279 original size:14 final size:14
Alignment explanation
Indices: 29260--29316 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
29250 GCGAAATGAA
*
29260 AATCGCAACGACAG
1 AATCGCAACGAAAG
29274 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
29291 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
29307 AATCGCAACG
1 AATCGCAACG
29317 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:29287 original size:33 final size:33
Alignment explanation
Indices: 29203--29333 Score: 181
Period size: 33 Copynumber: 3.8 Consensus size: 33
29193 CGAAACTTAA
* *
29203 AATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
29241 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
29274 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
29307 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
29334 TGCGATTTTG
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
33 59 0.67
34 1 0.01
36 1 0.01
38 27 0.31
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:29330 original size:52 final size:51
Alignment explanation
Indices: 29202--29338 Score: 141
Period size: 52 Copynumber: 2.6 Consensus size: 51
29192 ACGAAACTTA
* * * *
29202 AAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAATCGCAACGCG
1 AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
* ** * * **
29253 AAAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AAATCGCAACGCGAAATGA-A-AATCGCAATGCGAAACCAAAATCGCAACGAG
29305 AGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 A-AATCGCAACGCGAAATGAAAATCGCAATGCGA
29339 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
50 9 0.14
51 4 0.06
52 40 0.61
53 4 0.06
54 9 0.14
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (51 bp):
AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
Found at i:29369 original size:14 final size:14
Alignment explanation
Indices: 29350--29408 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
29340 TTTGGTTTCG
29350 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
29364 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
29381 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
29397 CGTTGCGATTTT
1 CGTTGCGATTTT
29409 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:29376 original size:33 final size:33
Alignment explanation
Indices: 29334--29457 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
29324 AAAATCGCAA
*
29334 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
29367 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
29400 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
29433 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
29458 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:29388 original size:19 final size:18
Alignment explanation
Indices: 29334--29425 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
29324 AAAATCGCAA
29334 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
29353 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
29367 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
29386 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
29400 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
29419 TGCGATT
1 TGCGATT
29426 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:29435 original size:14 final size:14
Alignment explanation
Indices: 29383--29439 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
29373 TTTGGTTTCG
*
29383 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
29397 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
29416 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
29430 CGTTGCGATT
1 CGTTGCGATT
29440 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:29718 original size:93 final size:93
Alignment explanation
Indices: 29555--29870 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
29545 TCAGGGTATT
29555 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
29620 TACTATTTCACAGTGTTAAAGAATACAC
66 GACTATTTCACAGTGTTAAAGAATACAC
29648 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
29713 GACTATTTCACAGTGTTAAAGAATACAC
66 GACTATTTCACAGTGTTAAAGAATACAC
29741 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
29806 GACTATTTCACAGTGTTAAAGAATACAC
66 GACTATTTCACAGTGTTAAAGAATACAC
*
29834 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
29871 AAGCAATCTA
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 221 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
GACTATTTCACAGTGTTAAAGAATACAC
Found at i:31580 original size:14 final size:14
Alignment explanation
Indices: 31561--31617 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
31551 TTGAAATGAA
31561 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
31575 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
31594 AATCGCAACGAGAG
1 AATCGCAACGAGAG
31608 AATCGCAACG
1 AATCGCAACG
31618 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:31593 original size:33 final size:33
Alignment explanation
Indices: 31553--31634 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
31543 TCTTTTGGTT
31553 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
31586 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
31619 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
31635 TGCGATTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:31599 original size:19 final size:19
Alignment explanation
Indices: 31575--31639 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
31565 GCAACGAGAG
31575 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
31594 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
31608 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
31627 AATCGCAATGCGA
1 AATCGCAACGCGA
31640 TTTTGGCTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:31687 original size:21 final size:21
Alignment explanation
Indices: 31662--31735 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
31652 GTTGCGATTC
31662 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
31683 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
*
31704 TCAT-GTTGCGATTTTCATTTA
1 TC-TCGTTGCGATTTTCATTTT
*
31725 TCTTGTTGCGA
1 TCTCGTTGCGA
31736 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 7 0.16
21 30 0.68
22 7 0.16
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.50
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:31857 original size:33 final size:33
Alignment explanation
Indices: 31815--31885 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
31805 AATACTAACT
31815 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
31848 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
31881 TGAAA
1 TGAAA
31886 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:32290 original size:20 final size:20
Alignment explanation
Indices: 32265--32436 Score: 213
Period size: 20 Copynumber: 8.6 Consensus size: 20
32255 CTTTAAAAAT
32265 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
32285 CGCGTTGCGATTTACTGATTA
1 CGCGTTGCGATTTACGGA-TA
*
32306 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
32325 CACGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
32345 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
32365 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
32385 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
32405 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
32425 CGCGTTGCGATT
1 CGCGTTGCGATT
32437 CTTGAAAATC
Statistics
Matches: 133, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 128 0.96
21 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:40737 original size:25 final size:25
Alignment explanation
Indices: 40698--40747 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
40688 TTATTAAATC
* *
40698 GGGTAAAGTATTTAAACGACCATTT
1 GGGTAAACTACTTAAACGACCATTT
*
40723 GGGTAAACTACTTAAACGATCATTT
1 GGGTAAACTACTTAAACGACCATTT
40748 AATTATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (25 bp):
GGGTAAACTACTTAAACGACCATTT
Found at i:48535 original size:32 final size:32
Alignment explanation
Indices: 48494--48558 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
48484 GCCTATTGCT
48494 AACTTTTCAACAATCTCCCACTTGAAGATTTG
1 AACTTTTCAACAATCTCCCACTTGAAGATTTG
48526 AACTTTTCAACAATCTCCCACTTGAAGATTTG
1 AACTTTTCAACAATCTCCCACTTGAAGATTTG
48558 A
1 A
48559 TTGGAACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (32 bp):
AACTTTTCAACAATCTCCCACTTGAAGATTTG
Done.