Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004856.1 Hibiscus syriacus cultivar Beakdansim tig00010947_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: 77214
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1935 original size:23 final size:22
Alignment explanation
Indices: 1909--1976 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
1899 AAGTGCCATA
*
1909 TTTGTCTCGAATGACCACATAGT
1 TTTGTC-CGAATGACCACATAGG
1932 TTTGTCCCGAATGACCACATAGG
1 TTTGT-CCGAATGACCACATAGG
* *
1955 ATTGTCCAGAAGGACCACATAG
1 TTTGTCC-GAATGACCACATAG
1977 AACCCTCGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 2 0.05
23 37 0.93
24 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (22 bp):
TTTGTCCGAATGACCACATAGG
Found at i:3636 original size:14 final size:14
Alignment explanation
Indices: 3598--3636 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3588 TTTTATCTAT
* *
3598 TTTTAAATATATAA
1 TTTTAAATTTTTAA
*
3612 TTTTAATTTTTTAA
1 TTTTAAATTTTTAA
3626 TTTTAAATTTT
1 TTTTAAATTTT
3637 CAAAATTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAATTTTTAA
Found at i:4068 original size:22 final size:22
Alignment explanation
Indices: 4042--4084 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4032 CTAAACTTCA
* *
4042 TTTAATTTATTAATTATTAATT
1 TTTAATTTAATAATAATTAATT
4064 TTTAATTTAATAATAATTAAT
1 TTTAATTTAATAATAATTAAT
4085 AATTTTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAATTTAATAATAATTAATT
Found at i:4303 original size:21 final size:22
Alignment explanation
Indices: 4274--4316 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4264 CATATTTTAC
*
4274 TTTAGAACTACTAAA-TAATTT
1 TTTAAAACTACTAAATTAATTT
*
4295 TTTAAAACTATTAAATTAATTT
1 TTTAAAACTACTAAATTAATTT
4317 ATAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTAAAACTACTAAATTAATTT
Found at i:4321 original size:21 final size:21
Alignment explanation
Indices: 4279--4321 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4269 TTTACTTTAG
*
4279 AACTACTAAATAATTTTTTAA
1 AACTACTAAATAATTTTATAA
*
4300 AACTATTAAATTAA-TTTATAA
1 AACTACTAAA-TAATTTTATAA
4321 A
1 A
4322 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (21 bp):
AACTACTAAATAATTTTATAA
Found at i:4487 original size:12 final size:12
Alignment explanation
Indices: 4470--4504 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
4460 ATAATAATAT
4470 AATATATTTATA
1 AATATATTTATA
4482 AATATATTTA-A
1 AATATATTTATA
4493 AATAATATTTAT
1 AAT-ATATTTAT
4505 TCAAACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATATATTTATA
Found at i:9026 original size:2 final size:2
Alignment explanation
Indices: 9019--9108 Score: 171
Period size: 2 Copynumber: 45.0 Consensus size: 2
9009 CCTGTATTCA
9019 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
9061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9103 AT AT AT
1 AT AT AT
9109 TGTTTTCAAA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11633 original size:13 final size:13
Alignment explanation
Indices: 11633--11675 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
11623 CCGTTGACCC
11633 GACCCGACCCGTT
1 GACCCGACCCGTT
*
11646 TACCCGACCCGTT
1 GACCCGACCCGTT
* *
11659 GACTCGACCTGTT
1 GACCCGACCCGTT
11672 GACC
1 GACC
11676 GGCGTTGACC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.42, G:0.21, T:0.21
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:11634 original size:18 final size:18
Alignment explanation
Indices: 11611--11656 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
11601 ACCGGTCACA
11611 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
11629 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
11647 ACCCGACCCG
1 ACCCGACCCG
11657 TTGACTCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:13014 original size:18 final size:18
Alignment explanation
Indices: 12988--13023 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12978 TCGAAAGGAC
*
12988 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
13006 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
13024 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:14321 original size:24 final size:24
Alignment explanation
Indices: 14225--14333 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
14215 GAATATTTTA
* *
14225 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
14249 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
14273 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
14297 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
14321 TTTGATTTCTGAT
1 TCTGATATCTGAT
14334 ATCTCCGTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:16425 original size:13 final size:13
Alignment explanation
Indices: 16406--16473 Score: 88
Period size: 13 Copynumber: 5.5 Consensus size: 13
16396 GTCACAACCC
16406 GACCCGACCCGTT
1 GACCCGACCCGTT
*
16419 TACCCGACCCGTT
1 GACCCGACCCGTT
16432 GACCCGACCC---
1 GACCCGACCCGTT
16442 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
16455 GACTCGACCAGTT
1 GACCCGACCCGTT
16468 GACCCG
1 GACCCG
16474 TTGACCGGCG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
10 10 0.21
13 37 0.79
ACGTcount: A:0.18, C:0.46, G:0.22, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:16449 original size:36 final size:36
Alignment explanation
Indices: 16402--16473 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
16392 ACCGGTCACA
* *
16402 ACCCGACCCGACCCGTTTACCCGACCCGTTGACCCG
1 ACCCGACCCGACCCGTTGACCCGACCAGTTGACCCG
*
16438 ACCCGACCCGACCCGTTGACTCGACCAGTTGACCCG
1 ACCCGACCCGACCCGTTGACCCGACCAGTTGACCCG
16474 TTGACCGGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.14
Consensus pattern (36 bp):
ACCCGACCCGACCCGTTGACCCGACCAGTTGACCCG
Found at i:17821 original size:18 final size:18
Alignment explanation
Indices: 17795--17830 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17785 TCGAAAGGAC
*
17795 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
17813 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
17831 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:19017 original size:24 final size:24
Alignment explanation
Indices: 18925--19024 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
18915 CTTATATGAA
* * *
18925 TGATTTGAATTATGTTTTGACATC
1 TGATCTGAATTATGTTCTGATATC
18949 TGATCTGAAATT-TGTTCTGAT-TCC
1 TGATCTG-AATTATGTTCTGATAT-C
* * * *
18973 TAACCTGGATTCTGTTCTGATATC
1 TGATCTGAATTATGTTCTGATATC
* *
18997 TGATCTGAATTATGTTTTGATTTC
1 TGATCTGAATTATGTTCTGATATC
19021 TGAT
1 TGAT
19025 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
23 4 0.07
24 51 0.85
25 5 0.08
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TGATCTGAATTATGTTCTGATATC
Found at i:21102 original size:13 final size:13
Alignment explanation
Indices: 21084--21108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21074 CAACCCGACC
21084 CGACCCGTTGACT
1 CGACCCGTTGACT
21097 CGACCCGTTGAC
1 CGACCCGTTGAC
21109 CCGTTGACCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (13 bp):
CGACCCGTTGACT
Found at i:21337 original size:16 final size:17
Alignment explanation
Indices: 21306--21338 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21296 TTGATTTTGA
*
21306 CCGAAAATTCCAAATTT
1 CCGAAAAGTCCAAATTT
21323 CCGAAAAGT-CAAATTT
1 CCGAAAAGTCCAAATTT
21339 TATGCTTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (17 bp):
CCGAAAAGTCCAAATTT
Found at i:22455 original size:18 final size:18
Alignment explanation
Indices: 22429--22464 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22419 TCGAAAGGAC
*
22429 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
22447 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
22465 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:23766 original size:24 final size:24
Alignment explanation
Indices: 23665--23766 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 24
23655 GAATATTTTA
* *
23665 TCTGATTTCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
23689 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTATGT
* * * *
23713 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
*
23737 TCTGATATCTGATTTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
*
23761 TTTGAT
1 TCTGAT
23767 TTTTGATATC
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:23940 original size:2 final size:2
Alignment explanation
Indices: 23933--23963 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23923 ACGGATGGGG
23933 TA TA TA TA TA TA 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 T
23964 GTTTTAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25063 original size:27 final size:27
Alignment explanation
Indices: 25013--25065 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
25003 ATCAATTTTA
*
25013 TGAAAAATATAAAATTAAGGAATAAAT
1 TGAAAAATATAAAATTAAGAAATAAAT
*
25040 TGAACAAATATGAAATTAA-AAATAAA
1 TGAA-AAATATAAAATTAAGAAATAAA
25066 AATTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (27 bp):
TGAAAAATATAAAATTAAGAAATAAAT
Found at i:25546 original size:2 final size:2
Alignment explanation
Indices: 25541--26001 Score: 132
Period size: 2 Copynumber: 219.5 Consensus size: 2
25531 ATAAACTATT
* * *
25541 TA TA TA GTA TA TA CTA TA TA TA TA TA AA CTA TA GTT TA TA TT TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA
*
25585 TA TA CTA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA T- TA TA
1 TA TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA TA TA TA
* * * *
25628 TA TA TA AA CTA TA TA TA T- TA TA TA GTT TA CA TA TGA AA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA T-A TA TA TA
* * * * *
25670 TA TA TA TA TA TA TA AA CTA TA TA AA T- TA TA GTT TA TA TG TA AA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
25713 CTA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA CA -A TA TA TA TA
1 -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
25756 -A TT TA TA TA TGA -A CTA TA TA T- TG TT TA T- TA AA TA -A CTA
1 TA TA TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
25794 TA TA AA CTA TT TA TA TA GTA TA TA CTA TA TA TA TA AA CTA TA GTT
1 TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA -TA
* *
25839 TA TA TT TA TA TA T- TA TA TA CTA TA GT- TGA TA TT TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA
* * * * *
25881 AA TA T- TA TG TA TA TA AA CTA TA TA GTT TA CA TA TGA -A CTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA T-A TA -TA TA
*
25923 TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA -A T- TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
25963 TA TA GT- TGA TA TT TA TA TA CTA TA TA CTA TA TA CTA TA T
1 TA TA -TA T-A TA TA TA TA TA -TA TA TA -TA TA TA -TA TA T
26002 GTATGAATAC
Statistics
Matches: 338, Mismatches: 61, Indels: 120
0.65 0.12 0.23
Matches are distributed among these distances:
1 19 0.06
2 264 0.78
3 55 0.16
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:25553 original size:7 final size:6
Alignment explanation
Indices: 25541--26001 Score: 132
Period size: 7 Copynumber: 73.2 Consensus size: 6
25531 ATAAACTATT
* * *
25541 TATATA GTATATA CTATATA TATATA AACTATA GTTTATA TTTATA TACTATA
1 TATATA -TATATA -TATATA TATATA TA-TATA -TATATA TATATA TA-TATA
* *
25594 TACTATA GT-TGATA TTTATA TACTATA TAT-TA TATATA TAAACTA TATATA
1 TA-TATA -TAT-ATA TATATA TA-TATA TATATA TATATA TATA-TA TATATA
* * * * *
25645 T-TATA TAGTTTA CATATGA AATATA TATATA TATATA TAAACTA TATAAA
1 TATATA TA-TATA TATAT-A TATATA TATATA TATATA TATA-TA TATATA
* * * * *
25695 T-TATA GTTTATA TGTAAA CTATATA CTATAGT- TGATATT TATATA CTATACA
1 TATATA -TATATA TATATA -TATATA -TATA-TA T-ATATA TATATA -TATATA
* * * *
25747 -ATATA TATA-A TTTATA TATGA-A CTATATA T-TGTT TAT-TA AATA-A
1 TATATA TATATA TATATA TAT-ATA -TATATA TATATA TATATA TATATA
* * * *
25791 CTATATA AACTATT TATATA GTATATA CTATATA TATAAA CTATAGTT
1 -TATATA TA-TATA TATATA -TATATA -TATATA TATATA -TATA-TA
* * *
25839 TATATT TATATA T-TATA TACTATA GT-TGATA TTTATA TACTAAA TAT-TA
1 TATATA TATATA TATATA TA-TATA -TAT-ATA TATATA TA-TATA TATATA
* * * *
25888 TGTATA TAAACTA TATAGTT TACATA TGA-ACTA TATATA TATATA TATATA
1 TATATA TATA-TA TATA-TA TATATA T-ATA-TA TATATA TATATA TATATA
* *
25939 TATAGTT TATATA TA-AT- TATATA T-TATA GT-TGATA TTTATA TACTATA
1 TATA-TA TATATA TATATA TATATA TATATA -TAT-ATA TATATA TA-TATA
25987 TACTATA TACTATA T
1 TA-TATA TA-TATA T
26002 GTATGAATAC
Statistics
Matches: 349, Mismatches: 54, Indels: 102
0.69 0.11 0.20
Matches are distributed among these distances:
4 2 0.01
5 44 0.13
6 133 0.38
7 167 0.48
8 3 0.01
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (6 bp):
TATATA
Found at i:25564 original size:20 final size:19
Alignment explanation
Indices: 25528--26001 Score: 172
Period size: 20 Copynumber: 23.7 Consensus size: 19
25518 ATTAATGAAC
*
25528 TATATAAACTAT-T-TATA
1 TATATATACTATATATATA
25545 TAGTATATACTATATATATA
1 TA-TATATACTATATATATA
* * *
25565 TAAACTATAGTTTATATTTATA
1 TATA-TATA--CTATATATATA
25587 TACTATATACTATAGT-TGATA
1 TA-TATATACTATA-TAT-ATA
*
25608 TTTATATACTATATATTATA
1 TATATATACTATATA-TATA
*
25628 TATATAAACTATATATATTA
1 TATATATACTATATATA-TA
*
25648 TATAGTTTACATATGAAATATATA
1 TATA-TATAC-TAT---ATATATA
*
25672 TATATATA-TATAAACTATA
1 TATATATACTATATA-TATA
* * * *
25691 TAAATTATAGTTTATATGTA
1 TATA-TATACTATATATATA
*
25711 AACTATATACTATAGT-TGATA
1 TA-TATATACTATA-TAT-ATA
* *
25732 TTTATATACTATACA-ATA
1 TATATATACTATATATATA
*
25750 TATATA-A-TTTATATATGAA
1 TATATATACTATATATAT--A
** * *
25769 CTATATATTGTTTATTAAATAA
1 -TATATATACTATA-TATAT-A
*
25791 CTATATAAACTAT-T-TATA
1 -TATATATACTATATATATA
25809 TAGTATATACTATATATATA
1 TA-TATATACTATATATATA
* * *
25829 AACTATAGT-TTATATTTATA
1 TA-TATA-TACTATATATATA
25849 TATTATATACTATAGT-TGATA
1 TA-TATATACTATA-TAT-ATA
* * *
25870 TTTATATACTAAATATTATG
1 TATATATACTATATA-TATA
* *
25890 TATATAAACTATATAGTTTA
1 TATATATACTATATA-TATA
*
25910 CATATGA-ACTATATATATA
1 TATAT-ATACTATATATATA
*
25929 TATATATA-TATATAGTTTA
1 TATATATACTATATA-TATA
*
25948 TATATA-ATTATATAT-TA
1 TATATATACTATATATATA
*
25965 TAGT-TGATATTTATATACTATA
1 TA-TAT-ATA-CTATATA-TATA
25987 TACTATATACTATAT
1 TA-TATATACTATAT
26002 GTATGAATAC
Statistics
Matches: 348, Mismatches: 58, Indels: 98
0.69 0.12 0.19
Matches are distributed among these distances:
16 4 0.01
17 12 0.03
18 40 0.11
19 42 0.12
20 155 0.45
21 34 0.10
22 41 0.12
23 9 0.03
24 6 0.02
25 5 0.01
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (19 bp):
TATATATACTATATATATA
Found at i:25571 original size:42 final size:39
Alignment explanation
Indices: 25500--25600 Score: 105
Period size: 42 Copynumber: 2.5 Consensus size: 39
25490 AACTATGTAG
* * *
25500 TTTATATATATATAGTTTATTAATGAACTATA-TAAACTA
1 TTTATATATATATACTATATTAATAAACTATAGTAAA-TA
**
25539 TTTATATAGTATATACTATATATATATAAACTATAGTTTATA
1 TTTATATA-TATATACTATAT-TA-ATAAACTATAGTAAATA
25581 TTTATATACTATATACTATA
1 TTTATATA-TATATACTATA
25601 GTTGATATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
39 8 0.15
40 10 0.19
41 2 0.04
42 30 0.58
43 2 0.04
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (39 bp):
TTTATATATATATACTATATTAATAAACTATAGTAAATA
Found at i:25573 original size:27 final size:27
Alignment explanation
Indices: 25526--25651 Score: 91
Period size: 27 Copynumber: 4.6 Consensus size: 27
25516 TTATTAATGA
* *
25526 ACTATATAAACTATTTA-TATAGTATAT
1 ACTATATATA-TATATACTATAGTATAT
* *
25553 ACTATATATATATAAACTATAGTTTAT
1 ACTATATATATATATACTATAGTATAT
*
25580 A-TTTATATACTATATACTATAGT-TGAT
1 ACTATATATA-TATATACTATAGTAT-AT
* *
25607 ATTTATATACTATATATTA-TATA-TATAA
1 A-CTATATA-TATATA-TACTATAGTATAT
25635 ACTATATATATTATATA
1 ACTATATATA-TATATA
25652 GTTTACATAT
Statistics
Matches: 81, Mismatches: 9, Indels: 19
0.74 0.08 0.17
Matches are distributed among these distances:
26 16 0.20
27 44 0.54
28 3 0.04
29 14 0.17
30 4 0.05
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (27 bp):
ACTATATATATATATACTATAGTATAT
Found at i:25941 original size:27 final size:27
Alignment explanation
Indices: 25610--25966 Score: 157
Period size: 27 Copynumber: 12.9 Consensus size: 27
25600 AGTTGATATT
25610 TATATACTATATAT-TATATATATAAAC
1 TATATA-TATATATATATATATATAAAC
* *
25637 TATATATAT-TATATA-GT-T-TACA-
1 TATATATATATATATATATATATAAAC
*
25659 TATGAAATATATATATATATATATAAAC
1 TAT-ATATATATATATATATATATAAAC
* * *
25687 TATATAAAT-TATAGTTTATATGTAAAC
1 TATATATATATATA-TATATATATAAAC
*
25714 TATATACTATAGT-TGATAT-T-TATATAC
1 TATATA-TATA-TAT-ATATATATATAAAC
* * *
25741 TATACAATATATATAATTTATATATGAAC
1 TATA-TATATATAT-ATATATATATAAAC
* * *
25770 TATATATTGTTTATTAAATAACTATATAAAC
1 TATATA-TATATA-TATAT-A-TATATAAAC
25801 TATTTATATAGTATATACTATATATATAAAC
1 TAT--ATATA-TATATA-TATATATATAAAC
* * *
25832 TATAGTTTATATTTATATAT-TATATAC
1 TATA-TATATATATATATATATATAAAC
* * * **
25859 TATAGTTGATATTTATATACTAAATATTATG
1 TATA--T-ATATATATATA-TATATATAAAC
* * * *
25890 TATATAAACTATATAGTTTACATATGAAC
1 TATATATA-TATATA-TATATATATAAAC
***
25919 TATATATATATATATATATATATAGTT
1 TATATATATATATATATATATATAAAC
25946 TATATATA-AT-TATATAT-TATA
1 TATATATATATATATATATATATA
25967 GTTGATATTT
Statistics
Matches: 246, Mismatches: 53, Indels: 65
0.68 0.15 0.18
Matches are distributed among these distances:
22 3 0.01
23 8 0.03
24 11 0.04
25 12 0.05
26 13 0.05
27 72 0.29
28 23 0.09
29 52 0.21
30 10 0.04
31 30 0.12
32 4 0.02
33 8 0.03
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (27 bp):
TATATATATATATATATATATATAAAC
Found at i:25986 original size:27 final size:26
Alignment explanation
Indices: 25576--25993 Score: 138
Period size: 27 Copynumber: 16.0 Consensus size: 26
25566 AAACTATAGT
25576 TTATATTTATATACTATATACTATAG
1 TTATATTTATATACTATATACTATAG
25602 TTGATATTTATATACTATATA-T-TA-
1 TT-ATATTTATATACTATATACTATAG
*
25626 -TATA--TATAAACTATATA-TAT--
1 TTATATTTATATACTATATACTATAG
* *
25646 TATATAGTTTACATA-TGAAATA-TATA-
1 T-TATA-TTTATATACT-ATATACTATAG
* * *
25672 TATATATATATAAACTATATAAATTATAG
1 T-TATATTTATATACTATAT--ACTATAG
*
25701 TTTATATGTA-A-ACTATATACTATAG
1 -TTATATTTATATACTATATACTATAG
* *
25726 TTGATATTTATATACTATACAATATA-
1 TT-ATATTTATATACTATATACTATAG
*
25752 -TATAATTTATATA-TGAACTATA-TATTG
1 TTAT-ATTTATATACT--A-TATACTATAG
*
25779 TT-TA-TTAAATAACTATATAAACTATTTA-
1 TTATATTTATAT-ACTATAT--ACTA--TAG
*
25807 TATAGTATATACTATATA-TATAAACTATAG
1 T-TA-TAT-T--TATATACTATATACTATAG
*
25837 TTTATATTTATATATTATATACTATAG
1 -TTATATTTATATACTATATACTATAG
* *
25864 TTGATATTTATATACTAAATATTAT-G
1 TT-ATATTTATATACTATATACTATAG
** * *
25890 -TATATAAACTATA-TAGTTTACATATGAAC
1 TTATATTTA-TATACTA-TATAC-TAT--AG
*
25919 TATATATATATATA-TATATA-TATAG
1 T-TATATTTATATACTATATACTATAG
* * *
25944 TT-TATATATA-ATTATATATTATAG
1 TTATATTTATATACTATATACTATAG
25968 TTGATATTTATATACTATATACTATA
1 TT-ATATTTATATACTATATACTATA
25994 TACTATATGT
Statistics
Matches: 302, Mismatches: 35, Indels: 109
0.68 0.08 0.24
Matches are distributed among these distances:
20 13 0.04
21 1 0.00
22 8 0.03
23 15 0.05
24 24 0.08
25 58 0.19
26 37 0.12
27 88 0.29
28 8 0.03
29 17 0.06
30 9 0.03
31 14 0.05
33 5 0.02
34 1 0.00
35 4 0.01
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (26 bp):
TTATATTTATATACTATATACTATAG
Found at i:26001 original size:27 final size:25
Alignment explanation
Indices: 25919--26001 Score: 53
Period size: 25 Copynumber: 3.2 Consensus size: 25
25909 ACATATGAAC
*
25919 TATATATATATATATATA-TATATA
1 TATATATATATTTATATACTATATA
* * *
25943 GTTTATATATAATTATATATTATAGT-
1 -TATATATATATTTATATACTATA-TA
* *
25969 TGATATTTATATACTATATACTATATA
1 T-ATATATATAT-TTATATACTATATA
25996 CTATAT
1 -TATAT
26002 GTATGAATAC
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
25 16 0.36
26 12 0.27
27 15 0.34
28 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (25 bp):
TATATATATATTTATATACTATATA
Found at i:26579 original size:12 final size:12
Alignment explanation
Indices: 26562--26591 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
26552 AGGATTTTTG
26562 TTTTATATATTT
1 TTTTATATATTT
26574 TTTTATATATTT
1 TTTTATATATTT
*
26586 ATTTAT
1 TTTTAT
26592 GCATATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATATATTT
Found at i:26770 original size:16 final size:16
Alignment explanation
Indices: 26751--26800 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
26741 AATATATAGT
*
26751 ATATACTAACTATATA
1 ATATACTAATTATATA
*
26767 ATATA--AATTATGTA
1 ATATACTAATTATATA
*
26781 ATATACTAATTATTTA
1 ATATACTAATTATATA
26797 ATAT
1 ATAT
26801 CAAATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 12 0.41
16 17 0.59
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (16 bp):
ATATACTAATTATATA
Found at i:26820 original size:27 final size:29
Alignment explanation
Indices: 26751--26836 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 29
26741 AATATATAGT
* * *
26751 ATATACTAACTATATAATAT-AAATTATGTA
1 ATATACTAATTATTTAATATCAAACTA--TA
26781 ATATACTAATTATTTAATATCAAA-TATA
1 ATATACTAATTATTTAATATCAAACTATA
* * *
26809 ATATGC-AATTATTTGATATGAAACTATA
1 ATATACTAATTATTTAATATCAAACTATA
26837 TGATATACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
27 15 0.31
28 11 0.22
30 20 0.41
31 3 0.06
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (29 bp):
ATATACTAATTATTTAATATCAAACTATA
Found at i:27504 original size:14 final size:14
Alignment explanation
Indices: 27487--27519 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
27477 TTGAAGATTT
*
27487 ATAATATAAGAATC
1 ATAATATAAAAATC
27501 ATAATATAAAAATC
1 ATAATATAAAAATC
27515 ATAAT
1 ATAAT
27520 TAATATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (14 bp):
ATAATATAAAAATC
Found at i:27525 original size:18 final size:18
Alignment explanation
Indices: 27502--27564 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
27492 ATAAGAATCA
27502 TAATATAAAAATCATAAT
1 TAATATAAAAATCATAAT
* *
27520 TAATATAATAAAACTATTTAT
1 TAATATAA-AAATC-A-TAAT
* **
27541 TAATTTAATTATCATAAT
1 TAATATAAAAATCATAAT
27559 TAATAT
1 TAATAT
27565 TTTATTATAC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 16 0.47
19 5 0.15
20 3 0.09
21 10 0.29
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATATAAAAATCATAAT
Found at i:27731 original size:16 final size:16
Alignment explanation
Indices: 27710--27760 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
27700 TCATTTACAG
27710 GTCAGGTTGAAAACAA
1 GTCAGGTTGAAAACAA
* * *
27726 GTCAGGTTCATAACAT
1 GTCAGGTTGAAAACAA
27742 GTCAGGTTGAAAACAA
1 GTCAGGTTGAAAACAA
27758 GTC
1 GTC
27761 GGGTAATAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (16 bp):
GTCAGGTTGAAAACAA
Found at i:28773 original size:20 final size:22
Alignment explanation
Indices: 28748--28787 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
28738 AGTCGTATAT
28748 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
28768 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
28788 TCTGCAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:28851 original size:3 final size:3
Alignment explanation
Indices: 28843--28898 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
28833 AAATTTAAAT
* * * *
28843 TTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TAA ATA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
28889 TTA TTTA TTA
1 TTA -TTA TTA
28899 ATAATACAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:30229 original size:18 final size:18
Alignment explanation
Indices: 30208--30243 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30198 TATAAATATA
*
30208 TATATTATTTATTTATTT
1 TATAATATTTATTTATTT
*
30226 TATAATGTTTATTTATTT
1 TATAATATTTATTTATTT
30244 ATTTTCAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TATAATATTTATTTATTT
Found at i:30544 original size:137 final size:125
Alignment explanation
Indices: 30359--30714 Score: 393
Period size: 137 Copynumber: 2.7 Consensus size: 125
30349 TTTTAATATT
* * *
30359 TATTT-TTTATTTATTAATATCAAAGGAAAGAGATGTCTTAGGGTACCTAGAAGCCCTTTTCTGA
1 TATTTATTTATTT-TTAATATCAAAGAAAAGAGCTGTCTTA-AGTACCTAGAAGCCCTTTTCTGA
30423 TATTTTTAAATAAATAAATATCTTACTGTATTAAAATAAATTTTTTGTTATTATCTTAAGAAAAA
64 TATTTTTAAATAAATAAATATCTTACT-TATT----T-AA---TTT-TTATT-TCTTAAG-AAAA
30488 TGTTTTTA-
117 TGTTTTTAG
*
30496 TATTTATTTATTTTTAATATCAAAGAAAAGAGCTGTCTTAAGTCACCTAGAAGCCATTTTCTGAT
1 TATTTATTTATTTTTAATATCAAAGAAAAGAGCTGTCTTAAGT-ACCTAGAAGCCCTTTTCTGAT
* *
30561 ATTTTTAAATAAATAAGTA---T-CTTATTTAATTTTTATTTTTTAAGAAAATGTTTTTAG
65 ATTTTTAAATAAATAAATATCTTACTTATTTAATTTTTATTTCTTAAGAAAATGTTTTTAG
*
30618 TTATTTATTTTATTTTTTAATATCGAAGAAAATG-GCTGTCTTAAGGTACCTAGAAGCCCTTTTC
1 -TATTTA-TTTA-TTTTTAATATCAAAGAAAA-GAGCTGTCTTAA-GTACCTAGAAGCCCTTTTC
* * *
30682 TGATATTTCTAAATAAGTAAATATCTTATTTAT
61 TGATATTTTTAAATAAATAAATATCTTACTTAT
30715 GTATATTAAT
Statistics
Matches: 195, Mismatches: 12, Indels: 32
0.82 0.05 0.13
Matches are distributed among these distances:
121 12 0.06
122 6 0.03
123 11 0.06
124 7 0.04
125 64 0.33
126 3 0.02
127 2 0.01
128 2 0.01
129 4 0.02
132 4 0.02
133 2 0.01
134 1 0.01
136 2 0.01
137 68 0.35
138 7 0.04
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (125 bp):
TATTTATTTATTTTTAATATCAAAGAAAAGAGCTGTCTTAAGTACCTAGAAGCCCTTTTCTGATA
TTTTTAAATAAATAAATATCTTACTTATTTAATTTTTATTTCTTAAGAAAATGTTTTTAG
Found at i:30648 original size:125 final size:122
Alignment explanation
Indices: 30478--30713 Score: 352
Period size: 125 Copynumber: 1.9 Consensus size: 122
30468 TGTTATTATC
30478 TTAAGAAAAATGTTTTTATATTTATTTATTTTTAATATCAAAGAAAA-GAGCTGTCTTAA-GTCA
1 TTAAGAAAAATGTTTTTATATTTATTTATTTTTAATATCAAAGAAAATG-GCTGTCTTAAGGT-A
* *
30541 CCTAGAAGCCATTTTCTGATATTTTTAAATAAATAAGTATCTTATTTAATTTTTATTTT
64 CCTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTATTTAATTTTTATTTT
*
30600 TTAAG-AAAATGTTTTTAGTTATTTATTTTATTTTTTAATATCGAAGAAAATGGCTGTCTTAAGG
1 TTAAGAAAAATGTTTTTA--TATTTA-TTTA-TTTTTAATATCAAAGAAAATGGCTGTCTTAAGG
* *
30664 TACCTAGAAGCCCTTTTCTGATATTTCTAAATAAGTAAATATCTTATTTA
62 TACCTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTATTTA
30714 TGTATATTAA
Statistics
Matches: 103, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
121 12 0.12
122 5 0.05
123 6 0.06
124 4 0.04
125 73 0.71
126 3 0.03
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (122 bp):
TTAAGAAAAATGTTTTTATATTTATTTATTTTTAATATCAAAGAAAATGGCTGTCTTAAGGTACC
TAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTATTTAATTTTTATTTT
Found at i:31422 original size:17 final size:17
Alignment explanation
Indices: 31402--31456 Score: 110
Period size: 17 Copynumber: 3.2 Consensus size: 17
31392 GCGACGTCTT
31402 CGTGAGAATTTATTCTC
1 CGTGAGAATTTATTCTC
31419 CGTGAGAATTTATTCTC
1 CGTGAGAATTTATTCTC
31436 CGTGAGAATTTATTCTC
1 CGTGAGAATTTATTCTC
31453 CGTG
1 CGTG
31457 TCAGACCTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (17 bp):
CGTGAGAATTTATTCTC
Found at i:38493 original size:114 final size:114
Alignment explanation
Indices: 38290--38515 Score: 353
Period size: 114 Copynumber: 2.0 Consensus size: 114
38280 AAGTGCCATA
* ** *
38290 TGCTCATAGTAGAAATAAGAAGACTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATC
* * *
38355 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
66 TGGTTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
* *
38404 TGCTCATAGTAAAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATT
1 TGCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATC
* *
38469 TGGTTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 TGGTTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
38516 CTACATGATC
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATC
TGGTTCGGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
Found at i:40829 original size:22 final size:22
Alignment explanation
Indices: 40800--40854 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
40790 ATCTACACTC
40800 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
40822 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
40844 TTCAAAAATGA
1 TTCAAAGATGA
40855 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:41617 original size:76 final size:76
Alignment explanation
Indices: 41491--42282 Score: 1500
Period size: 76 Copynumber: 10.5 Consensus size: 76
41481 CTATTTCCCA
*
41491 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41556 AGCCTTAGGGT
66 AGCCTTAGGGT
*
41567 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41632 AGCCTTA-GGT
66 AGCCTTAGGGT
41642 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41706 AGCCTTAGGGT
66 AGCCTTAGGGT
41717 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41782 AGCCTTAGGGT
66 AGCCTTAGGGT
*
41793 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41858 AGCCTTAGGGT
66 AGCCTTAGGGT
41869 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41934 AGCCTTAGGGT
66 AGCCTTAGGGT
*
41945 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42010 AGCCTTAGGGT
66 AGCCTTAGGGT
42021 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42086 AGCCTTAGGGT
66 AGCCTTAGGGT
*
42097 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT-GGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42161 AGCCTTAGGGT
66 AGCCTTAGGGT
*
42172 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGGTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
42237 AGCCTTAGGGT
66 AGCCTTAGGGT
*
42248 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
42283 CATTTTCATC
Statistics
Matches: 703, Mismatches: 10, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
74 22 0.03
75 177 0.25
76 504 0.72
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:42423 original size:3 final size:3
Alignment explanation
Indices: 42415--42476 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
42405 AAATTTAAAT
* * *
42415 TTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA ATA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
42461 TTA TTTA TTA ATA TTA
1 TTA -TTA TTA TTA TTA
42477 CAAAACCCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:44328 original size:121 final size:119
Alignment explanation
Indices: 43947--44329 Score: 296
Period size: 121 Copynumber: 3.0 Consensus size: 119
43937 ACATTTTTAA
* * * *
43947 TATTTATTTTTATTTATTAATATCAAAGGAAAGAGATGTCTTAGGGTACCTAGAAGCCCTTTTCT
1 TATTTA-TTTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCT
* ** * *
44012 GATATTTTTAAATAAATAAATATCTTACTGTATTAAAATAAATTTTTTGTTATTATCTTAAGAAA
65 GATA-TTTTAAATAAATAAATATCTTA-TTTATT---AT--A-TTAAT-ATATTTTCTT----AA
44077 AAT
117 AAT
* *
44080 GT-TTTATATTATTTATTTTTAATATCAAAGAAAAGAGCTGTCTTAA-GTCACCTAGAAGCCATT
1 -TATTTAT-TT-TAT-TTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGT-ACCTAGAAGCCCTT
* * *
44143 TTCTGATATTTT---TAAATAAATATCTTATTTAAATTTTATTTTTTAAGAAAATGTTT-TT--A
61 TTCTGATATTTTAAATAAATAAATATCTTATTT--A--TTA--TATTAA-TATAT-TTTCTTAAA
*
44202 TT
118 AT
*
44204 TATTTATTTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTG
1 TATTTATTTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTG
*
44269 ATATTTCTAAATAAGTAAATATCTTATTTATGTATATTAATATATTTTCTTAAAAT
66 ATATTT-TAAATAAATAAATATCTTATTTAT-TATATTAATATATTTTCTTAAAAT
44325 TATTT
1 TATTT
44330 GAAATAGTAG
Statistics
Matches: 204, Mismatches: 23, Indels: 57
0.72 0.08 0.20
Matches are distributed among these distances:
118 3 0.01
119 5 0.02
120 5 0.02
121 62 0.30
122 7 0.03
123 4 0.02
124 7 0.03
125 17 0.08
130 8 0.04
131 18 0.09
132 2 0.01
133 7 0.03
134 11 0.05
135 48 0.24
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (119 bp):
TATTTATTTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTG
ATATTTTAAATAAATAAATATCTTATTTATTATATTAATATATTTTCTTAAAAT
Found at i:45162 original size:21 final size:19
Alignment explanation
Indices: 45131--45193 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
45121 ATGTTTAATG
*
45131 AAAAAGGTACCAATTGTTT
1 AAAAAGATACCAATTGTTT
*
45150 ACAAAATTATACCAATTG-TT
1 A-AAAA-GATACCAATTGTTT
*
45170 AAAAAGATACCAATTGTTG
1 AAAAAGATACCAATTGTTT
45189 AAAAA
1 AAAAA
45194 ATATGAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 10 0.27
19 11 0.30
20 7 0.19
21 9 0.24
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTT
Found at i:45179 original size:18 final size:18
Alignment explanation
Indices: 45131--45193 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
45121 ATGTTTAATG
*
45131 AAAAAGGTACCAATTGTTT
1 AAAAAGATACCAATTG-TT
*
45150 ACAAAATTATACCAATTGTT
1 A-AAAA-GATACCAATTGTT
45170 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
45188 GAAAAA
1 -AAAAA
45194 ATATGAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
18 12 0.32
19 10 0.26
20 7 0.18
21 9 0.24
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:48122 original size:20 final size:22
Alignment explanation
Indices: 48097--48136 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
48087 AGTCGTATAT
48097 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGCTTTTGG
48117 AGCCGTTTGGGGATGCTTTT
1 AGCCGTTTGGGGATGCTTTT
48137 TCTACAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.10, C:0.12, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGCTTTTGG
Found at i:51509 original size:28 final size:28
Alignment explanation
Indices: 51460--51529 Score: 113
Period size: 28 Copynumber: 2.4 Consensus size: 28
51450 ATTAAAATTT
51460 CAAACAAACAATTCGGATAAATGATTGATA
1 CAAACAAAC-A-TCGGATAAATGATTGATA
51490 CAAACAAACATCGGATAAATGATTGATA
1 CAAACAAACATCGGATAAATGATTGATA
*
51518 CAAACGAACATC
1 CAAACAAACATC
51530 ATTGTCGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 29 0.74
29 1 0.03
30 9 0.23
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (28 bp):
CAAACAAACATCGGATAAATGATTGATA
Found at i:56852 original size:18 final size:19
Alignment explanation
Indices: 56817--56853 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
56807 CACGGAATGT
56817 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
56837 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
56854 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:56999 original size:17 final size:18
Alignment explanation
Indices: 56969--57007 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
56959 AAATTGTCCT
* *
56969 TATTATAAATTTGTATAA
1 TATTACAAATTTGTAAAA
56987 TATTACAAA-TTGTAAAA
1 TATTACAAATTTGTAAAA
57004 TATT
1 TATT
57008 TATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (18 bp):
TATTACAAATTTGTAAAA
Found at i:57033 original size:36 final size:36
Alignment explanation
Indices: 57000--57067 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
56990 TACAAATTGT
57000 AAAATATTTATAT-ATTTTCTTTA-AAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTACAAAATTAAATTC
*
57035 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTACAAAATTAAA
57068 AATATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 16 0.53
36 14 0.47
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTACAAAATTAAATTC
Found at i:60491 original size:2 final size:2
Alignment explanation
Indices: 60484--60530 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
60474 TTGAATGCCG
60484 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
60526 TC TC T
1 TC TC T
60531 TATAAAATAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:66529 original size:138 final size:137
Alignment explanation
Indices: 66262--66542 Score: 393
Period size: 138 Copynumber: 2.0 Consensus size: 137
66252 GTCATATGTG
* ** * *
66262 CATTTCGACATAAATTGTATATAATGGTTATCGATTGATTTTGTGTAATGCGTAACGGTGCATTT
1 CATTTCGACATAAATTATATATAAAAGTTATCGATCGATTTTGTGTAATGCATAACGGTGCATTT
* * * * *
66327 TCGTATCAGTACTATGTGTACTTTCGGCACTAGATGTGCAACCATGGTATTTATAATGAGTTTGT
66 TCGTATCAATACTATATGTACTTTCGACACTAGATGTGCAACCATGGAATTCATAATGAGTTTGT
66392 GAATTAC
131 GAATTAC
* * *
66399 CATTTCGACATACAATTATTTATAAAAGTTATCGATCGATTTTGTTTAATGCATAATGGTGCATT
1 CATTTCGACATA-AATTATATATAAAAGTTATCGATCGATTTTGTGTAATGCATAACGGTGCATT
* *
66464 TTCGTATCAATATTATATGTACTTTCGACACTATG-TGTGCATCCATGGAATTCATAATGAGTTT
65 TTCGTATCAATACTATATGTACTTTCGACACTA-GATGTGCAACCATGGAATTCATAATGAGTTT
*
66528 GTGAATTTC
129 GTGAATTAC
66537 CATTTC
1 CATTTC
66543 AACACTTAGG
Statistics
Matches: 126, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
137 12 0.10
138 113 0.90
139 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (137 bp):
CATTTCGACATAAATTATATATAAAAGTTATCGATCGATTTTGTGTAATGCATAACGGTGCATTT
TCGTATCAATACTATATGTACTTTCGACACTAGATGTGCAACCATGGAATTCATAATGAGTTTGT
GAATTAC
Done.