Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008587.1 Hibiscus syriacus cultivar Beakdansim tig00111524_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: 68498
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1430 original size:30 final size:30
Alignment explanation
Indices: 1394--1451 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
1384 ACATAGAAAA
1394 CATGAAAAAAGAAATTGAATATACCCATTT
1 CATGAAAAAAGAAATTGAATATACCCATTT
1424 CATGAAAAAAGAAATTGAATATACCCAT
1 CATGAAAAAAGAAATTGAATATACCCAT
1452 GTTGGAAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.24
Consensus pattern (30 bp):
CATGAAAAAAGAAATTGAATATACCCATTT
Found at i:1459 original size:29 final size:29
Alignment explanation
Indices: 1397--1459 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 29
1387 TAGAAAACAT
*
1397 GAAAAAAGAAATTGAATATACCCATTTCAT
1 GAAAAAAGAAATTGAATATACCCATTT-AG
1427 GAAAAAAGAAATTGAATATACCCATGTT-G
1 GAAAAAAGAAATTGAATATACCCAT-TTAG
1456 GAAA
1 GAAA
1460 CATACTTGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 4 0.13
30 25 0.81
31 2 0.06
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (29 bp):
GAAAAAAGAAATTGAATATACCCATTTAG
Found at i:7981 original size:21 final size:21
Alignment explanation
Indices: 7940--7992 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
7930 GTGCTGGTGA
* *
7940 TGGAGTTGGGGGCTTATATGG
1 TGGAGTTGGAGCCTTATATGG
7961 TGGAGTTGGAGCCTT-TGATGG
1 TGGAGTTGGAGCCTTAT-ATGG
* *
7982 GGGTGTTGGAG
1 TGGAGTTGGAG
7993 TAGGGGGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.13, C:0.06, G:0.49, T:0.32
Consensus pattern (21 bp):
TGGAGTTGGAGCCTTATATGG
Found at i:11092 original size:20 final size:21
Alignment explanation
Indices: 11062--11101 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
11052 AGCCGTTAGG
11062 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
*
11083 GCCT-ATGGTATCGGTACTA
1 GCCTGATGGTATCGATACTA
11102 CTATGTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:11137 original size:18 final size:18
Alignment explanation
Indices: 11114--11154 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
11104 ATGTAAAGTA
*
11114 GTATCGGTATCTCTTTGG
1 GTATCGATATCTCTTTGG
* *
11132 GTATCGATATTTTTTTGG
1 GTATCGATATCTCTTTGG
11150 GTATC
1 GTATC
11155 AGTACCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.24, T:0.49
Consensus pattern (18 bp):
GTATCGATATCTCTTTGG
Found at i:12775 original size:31 final size:31
Alignment explanation
Indices: 12737--12796 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
12727 GAGTGGAGGG
*
12737 TTACCTATGTCTTTCGAGACATATGGACAAT
1 TTACCTATGTCATTCGAGACATATGGACAAT
*
12768 TTACCTATGTCATTCGCGACATATGGACA
1 TTACCTATGTCATTCGAGACATATGGACA
12797 GTTGCATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (31 bp):
TTACCTATGTCATTCGAGACATATGGACAAT
Found at i:17077 original size:30 final size:30
Alignment explanation
Indices: 17009--17097 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 30
16999 AGAGTCGAGG
*
17009 GTTACCTATGTCTTTC-GATACATATGAACAA
1 GTTACCTATGTC-TTCGGA-ACATATGGACAA
* *
17040 TTTACCTATGTCATTCGGGACATATGGAC-A
1 GTTACCTATGTC-TTCGGAACATATGGACAA
*
17070 GTTACCTAAGTTCTTCGGAACATATGGA
1 GTTACCTATG-TCTTCGGAACATATGGA
17098 TAGGTCCTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
30 23 0.47
31 25 0.51
32 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (30 bp):
GTTACCTATGTCTTCGGAACATATGGACAA
Found at i:27662 original size:20 final size:21
Alignment explanation
Indices: 27637--27688 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
27627 TTTTCCCAAT
*
27637 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
27657 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
27678 TCGCAATGCGA
1 TCGCAATGCGA
27689 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:27701 original size:41 final size:41
Alignment explanation
Indices: 27674--27751 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
27664 GCGAATTGGG
* * *
27674 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
27715 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
27752 CTGTCTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:27702 original size:20 final size:20
Alignment explanation
Indices: 27677--27771 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
27667 AATTGGGAAA
*
27677 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
27697 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
27718 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
27738 TTCGCAACGCGATACTGTCT
1 ATCGCAACGCGATACTGACT
*
27758 TTCGCAACGCGATA
1 ATCGCAACGCGATA
27772 ATACATAATC
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:28291 original size:20 final size:20
Alignment explanation
Indices: 28266--28303 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28256 CGATTCTCTC
28266 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
28286 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
28304 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:29644 original size:18 final size:18
Alignment explanation
Indices: 29623--29667 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
29613 TCCACTTCGG
*
29623 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
29641 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
29659 GAGCCATCA
1 GAGCCATCA
29668 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:30165 original size:20 final size:20
Alignment explanation
Indices: 30140--30185 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
30130 TAGTTTACTT
30140 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
30160 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
30180 TCGCAA
1 TCGCAA
30186 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:30213 original size:14 final size:14
Alignment explanation
Indices: 30194--30252 Score: 73
Period size: 14 Copynumber: 3.9 Consensus size: 14
30184 AATGCGAAAT
30194 AAAAATCGCAACGA
1 AAAAATCGCAACGA
30208 AAAAATCGCAATGCGA
1 AAAAATCGCAA--CGA
30224 AATGAAATCGCAACGA
1 AA--AAATCGCAACGA
*
30240 CAAAATCGCAACG
1 AAAAATCGCAACG
30253 CGAAATGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 22 0.55
16 9 0.22
18 9 0.22
ACGTcount: A:0.51, C:0.22, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAAATCGCAACGA
Found at i:30237 original size:32 final size:32
Alignment explanation
Indices: 30179--30269 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 32
30169 GGAAATGGCT
*
30179 ATCGCAATGCGAAATAAAAATCGCAACGAAAAA
1 ATCGCAATGCGAAAT-GAAATCGCAACGAAAAA
*
30212 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGAAAAA
*
30244 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATG-AAATCGCAA
30270 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGAAAAA
Found at i:30305 original size:14 final size:14
Alignment explanation
Indices: 30286--30343 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
30276 TTGTGTTTCG
30286 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
30300 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
30316 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
30332 CGTTGCGATTTT
1 CGTTGCGATTTT
30344 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:30320 original size:32 final size:33
Alignment explanation
Indices: 30281--30359 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
30271 GCGATTTGTG
30281 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
30313 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
30346 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
30360 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:30358 original size:19 final size:19
Alignment explanation
Indices: 30300--30417 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
30290 GCGATTTTGT
30300 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
30318 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
30332 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
30351 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
30371 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
30390 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
30410 TGTTGCGA
1 CGTTGCGA
30418 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:32445 original size:19 final size:19
Alignment explanation
Indices: 32423--32490 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
32413 ATCGCAACGA
32423 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
32442 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
32461 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
32475 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
32491 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:32566 original size:20 final size:20
Alignment explanation
Indices: 32509--32566 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
32499 TCGCATTGCG
* *
32509 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
32529 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
32549 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
32567 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:33649 original size:24 final size:24
Alignment explanation
Indices: 33622--33675 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
33612 GTATTCGAAA
* *
33622 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
33646 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
33670 TTTGAT
1 TTTGAT
33676 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:33867 original size:12 final size:12
Alignment explanation
Indices: 33850--33874 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33840 ATATAATCCT
33850 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33862 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33874 G
1 G
33875 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:36207 original size:33 final size:33
Alignment explanation
Indices: 36160--36286 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
36150 GGAAATTACT
36160 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
36193 ATCGTAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
36225 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
36259 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
36287 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:36243 original size:66 final size:66
Alignment explanation
Indices: 36161--36293 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
36151 GAAATTACTA
* *
36161 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
36226 T
66 T
*
36227 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
36292 T
66 T
36293 T
1 T
36294 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:36308 original size:19 final size:20
Alignment explanation
Indices: 36286--36328 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
36276 AAATCGCAAC
36286 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
36305 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
36325 GCGA
1 GCGA
36329 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:36313 original size:14 final size:14
Alignment explanation
Indices: 36314--36347 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
36304 TGCGATTTTC
36314 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
36328 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
36342 ATTTTC
1 ATTTTC
36348 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:36488 original size:14 final size:14
Alignment explanation
Indices: 36469--36519 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
36459 CATCAATTAA
36469 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
36483 ACAAATCACCTTTT
1 ACAAATCAACTTTT
*
36497 ACAAATCACCTTTT
1 ACAAATCAACTTTT
36511 ACAAATCAA
1 ACAAATCAA
36520 TTAAACAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:37941 original size:21 final size:21
Alignment explanation
Indices: 37875--37941 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
37865 GTGAATCGGG
*
37875 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
37895 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
37917 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
37938 CTCT
1 CTCT
37942 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:37960 original size:42 final size:41
Alignment explanation
Indices: 37875--37997 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
37865 GTGAATCGGG
* * * * *
37875 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
37917 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
37959 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
37998 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:40074 original size:33 final size:33
Alignment explanation
Indices: 40017--40115 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
40007 ACGAGATAAT
40017 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
* *
40051 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
40084 GACAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
40116 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:40134 original size:24 final size:19
Alignment explanation
Indices: 39992--40156 Score: 143
Period size: 19 Copynumber: 9.1 Consensus size: 19
39982 TCTTTTGGTT
*
39992 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
40011 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
40031 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
40049 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
40065 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
40083 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
40098 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
40117 GAAATGAAAATCGCATCGC
1 GAAATGAAAATCGCAACGC
*
40136 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
40155 GA
1 GA
40157 TTTTGGTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 24
0.75 0.09 0.15
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 61 0.51
20 27 0.23
21 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:40185 original size:19 final size:19
Alignment explanation
Indices: 40152--40232 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
40142 AAAATCGCAA
**
40152 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
40171 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
40190 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
40204 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
40224 TGCGATTTT
1 TGCGATTTT
40233 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:40775 original size:20 final size:20
Alignment explanation
Indices: 40750--40801 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
40740 CGCTATGTAA
* *
40750 ATCGCGTTGCGAAATTCAGT
1 ATCGCGTTGCGAAAGTAAGT
40770 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
40790 ATCTCGTTGCGA
1 ATCGCGTTGCGA
40802 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:40821 original size:41 final size:41
Alignment explanation
Indices: 40769--40846 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
40759 CGAAATTCAG
* * *
40769 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* * *
40810 TATCGCATTGCGATAGTCAGTCTCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
40847 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:40861 original size:21 final size:21
Alignment explanation
Indices: 40832--40887 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
40822 ATAGTCAGTC
*
40832 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
40853 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
*
40874 TTGCGTTGCGATTT
1 TCGCGTTGCGATTT
40888 ACTTATTCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:42273 original size:55 final size:55
Alignment explanation
Indices: 42207--42313 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 55
42197 GCAACATACA
* * * *
42207 CCATACAAATATTAAATTGGGAAATATTCTTAGTCATAAATTATTACCACCTACT
1 CCATACAAATATTAAATCGAGAAATATTCATAGCCATAAATTATTACCACCTACT
* *
42262 CCATACAAATATTAAATCGAGAAATATTCATAGCCATACATTATTATCACCT
1 CCATACAAATATTAAATCGAGAAATATTCATAGCCATAAATTATTACCACCT
42314 GTCGAAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.33
Consensus pattern (55 bp):
CCATACAAATATTAAATCGAGAAATATTCATAGCCATAAATTATTACCACCTACT
Found at i:44484 original size:3 final size:3
Alignment explanation
Indices: 44476--44546 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
44466 GTCCATATAC
44476 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
44523 A-T ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
44547 GGGCGTGGTT
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 62 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:45515 original size:17 final size:18
Alignment explanation
Indices: 45495--45536 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
45485 ATTAATAGTG
45495 TTTTATAT-AAAATATTT
1 TTTTATATCAAAATATTT
**
45512 TTTTATTATCATTATATTT
1 TTTTA-TATCAAAATATTT
45531 TTTTAT
1 TTTTAT
45537 TTTTATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 4 0.19
19 12 0.57
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATATCAAAATATTT
Found at i:51287 original size:20 final size:20
Alignment explanation
Indices: 51264--51338 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
51254 ATAGGTTCCA
51264 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
**
51284 AAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATATGT
*
51304 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATATGT
51324 AAATCGCAACGCGAA
1 AAATCGCAACGCGAA
51339 CTCTAATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:51924 original size:20 final size:20
Alignment explanation
Indices: 51899--51951 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
51889 GGCTTTCCAA
51899 GTGCATCGGTGCACTAGGGT
1 GTGCATCGGTGCACTAGGGT
51919 GTGCATCGGTGCACTAGGGT
1 GTGCATCGGTGCACTAGGGT
*
51939 GTCCATCGGTGCA
1 GTGCATCGGTGCA
51952 TAAATCAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (20 bp):
GTGCATCGGTGCACTAGGGT
Found at i:52018 original size:64 final size:63
Alignment explanation
Indices: 51942--52084 Score: 216
Period size: 64 Copynumber: 2.2 Consensus size: 63
51932 CTAGGGTGTC
*
51942 CATCGGTGCATAAATCAACTTCGATGTTTCAAAATAACCAGGGTGCATCGATGCAT-GTCTTGTG
1 CATCGGTGCATAAATCAA-TTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGT-TTGTG
* *
52006 CATCGGTGCATAAAATCAATTCGGTGTTTTAAAATAACCAGAGTGCATCGATGCATGGTTTGTG
1 CATCGGTGCAT-AAATCAATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGTTTGTG
*
52070 CATCGATGCATAAAT
1 CATCGGTGCATAAAT
52085 TGTATTCGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
63 4 0.05
64 60 0.82
65 9 0.12
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (63 bp):
CATCGGTGCATAAATCAATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGTTTGTG
Found at i:52087 original size:19 final size:19
Alignment explanation
Indices: 52048--52087 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
52038 AATAACCAGA
***
52048 GTGCATCGATGCATGGTTT
1 GTGCATCGATGCATAAATT
52067 GTGCATCGATGCATAAATT
1 GTGCATCGATGCATAAATT
52086 GT
1 GT
52088 ATTCGAAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.35
Consensus pattern (19 bp):
GTGCATCGATGCATAAATT
Found at i:53138 original size:14 final size:14
Alignment explanation
Indices: 53121--53148 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53111 ACCATAACAA
53121 AATTATATAACTAT
1 AATTATATAACTAT
53135 AATTATATAACTAT
1 AATTATATAACTAT
53149 TCTTTCACTT
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:55028 original size:14 final size:14
Alignment explanation
Indices: 55009--55036 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54999 AAGTGAAAGA
55009 ATAGTTATATAATT
1 ATAGTTATATAATT
55023 ATAGTTATATAATT
1 ATAGTTATATAATT
55037 TTGTATGGTT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:56116 original size:64 final size:63
Alignment explanation
Indices: 56048--56202 Score: 195
Period size: 64 Copynumber: 2.4 Consensus size: 63
56038 ATACCCATTT
* *
56048 CGAATACAATTTATGCATCGATGCACAA-ACCATGCATCGATGCACTCTGGTTATTTTAAAACAC
1 CGAAT-CAATTTATGCACCGATGCACAAGA-CATGCATCGATGCACCCTGGTTATTTTAAAACAC
* * * *
56112 CGAATTGATTTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGTTATTTTGAAACAT
1 CGAA-TCAATTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGTTATTTTAAAACAC
**
56176 CGAAGTTGATTTATGCACCGATGCACA
1 CGAA-TCAATTTATGCACCGATGCACA
56203 CCCTAGTGCA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 77 0.97
65 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (63 bp):
CGAATCAATTTATGCACCGATGCACAAGACATGCATCGATGCACCCTGGTTATTTTAAAACAC
Found at i:56214 original size:20 final size:20
Alignment explanation
Indices: 56189--56241 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
56179 AGTTGATTTA
56189 TGCACCGATGCACACCCTAG
1 TGCACCGATGCACACCCTAG
56209 TGCACCGATGCACACCCTAG
1 TGCACCGATGCACACCCTAG
56229 TGCACCGATGCAC
1 TGCACCGATGCAC
56242 TTGGAAAGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.40, G:0.21, T:0.15
Consensus pattern (20 bp):
TGCACCGATGCACACCCTAG
Found at i:57671 original size:19 final size:19
Alignment explanation
Indices: 57649--57685 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57639 ATTATTTTCT
57649 GAAAATAAAAACAAAAAAC
1 GAAAATAAAAACAAAAAAC
* *
57668 GAAAATAGAAATAAAAAA
1 GAAAATAAAAACAAAAAA
57686 TATTTTTTAG
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:0.78, C:0.05, G:0.08, T:0.08
Consensus pattern (19 bp):
GAAAATAAAAACAAAAAAC
Found at i:60787 original size:15 final size:16
Alignment explanation
Indices: 60767--60804 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
60757 AATTAAATAT
*
60767 TATTTTA-AATAATTA
1 TATTTTACAATAATGA
60782 TATTTTTACAATAATGA
1 TA-TTTTACAATAATGA
60799 TATTTT
1 TATTTT
60805 CACCTCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 9 0.45
17 9 0.45
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
TATTTTACAATAATGA
Found at i:60794 original size:17 final size:16
Alignment explanation
Indices: 60769--60804 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
60759 TTAAATATTA
*
60769 TTTTAAATAATTATAT
1 TTTTAAATAATGATAT
60785 TTTTACAATAATGATAT
1 TTTTA-AATAATGATAT
60802 TTT
1 TTT
60805 CACCTCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTTAAATAATGATAT
Found at i:61684 original size:19 final size:19
Alignment explanation
Indices: 61660--61698 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
61650 ATACATCATA
*
61660 TTACCTAACCGCTTATTTC
1 TTACCTAACCACTTATTTC
61679 TTACCTAACCACTTATTTC
1 TTACCTAACCACTTATTTC
61698 T
1 T
61699 AACTAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.31, G:0.03, T:0.44
Consensus pattern (19 bp):
TTACCTAACCACTTATTTC
Found at i:64050 original size:102 final size:100
Alignment explanation
Indices: 63857--64086 Score: 234
Period size: 102 Copynumber: 2.3 Consensus size: 100
63847 GGTTGTCTCA
* *
63857 CTTTCTTCCATGCAAAATCCACCTCCCATTTCCAGGTAATCGTTAGTCGGTTCGGTTTCAAAAGA
1 CTTTCTTCCATGCAAAATCCACCTCCCATTTCCAGGTAATCATTAGTCGGTTCAGTTTC--AAGA
* * *
63922 GGGATCATGTTGGCTTGCCTCGGGTTGATCATCGTCT
64 GGGATCATCTTGGCTTGCATCAGGTTGATCATCGTCT
* *
63959 CTTTC-TCCAGTGCAAAATCCGCCTCCCATTTTCAGGTAATCATTAG-CTGGTTCAGTTTC-AGA
1 CTTTCTTCCA-TGCAAAATCCACCTCCCATTTCCAGGTAATCATTAGTC-GGTTCAGTTTCAAGA
* * * *
64021 GGGATCAACTTCTTGGTTTTCATCAGGTTGATCAGTTG-CC
64 GGGATC-A--TCTTGGCTTGCATCAGGTTGATCA-TCGTCT
* * *
64061 CTCTCATCCATGCAGAATCCACCTCC
1 CTTTCTTCCATGCAAAATCCACCTCC
64087 TGTTTCAAGA
Statistics
Matches: 107, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
99 9 0.08
100 1 0.01
101 5 0.05
102 86 0.80
103 6 0.06
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.33
Consensus pattern (100 bp):
CTTTCTTCCATGCAAAATCCACCTCCCATTTCCAGGTAATCATTAGTCGGTTCAGTTTCAAGAGG
GATCATCTTGGCTTGCATCAGGTTGATCATCGTCT
Done.