Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003733.1 Hibiscus syriacus cultivar Beakdansim tig00007982_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: 65128
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:10193 original size:29 final size:29
Alignment explanation
Indices: 10160--10246 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
10150 CAGTCCCGGG
*
10160 GGTAGGTCGCCATGCACGCCCGGCGACCT
1 GGTAGGTCGCCATGCACGCCCAGCGACCT
10189 GGTAGGTCGCCATGCACGCCCAGCGACCT
1 GGTAGGTCGCCATGCACGCCCAGCGACCT
* *
10218 GGTAGGTCGCCATGCATGCCCTGCGACCT
1 GGTAGGTCGCCATGCACGCCCAGCGACCT
10247 ACCAGCACCT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.15, C:0.37, G:0.32, T:0.16
Consensus pattern (29 bp):
GGTAGGTCGCCATGCACGCCCAGCGACCT
Found at i:10264 original size:10 final size:10
Alignment explanation
Indices: 10257--10338 Score: 59
Period size: 10 Copynumber: 8.3 Consensus size: 10
10247 ACCAGCACCT
10257 CCATGCACGC
1 CCATGCACGC
10267 CCATGCACGC
1 CCATGCACGC
*
10277 CCAGGCACGC
1 CCATGCACGC
*
10287 CCA-ACGAC-C
1 CCATGC-ACGC
10296 TCCATG-AC-C
1 -CCATGCACGC
10305 TACCA-GCAC-C
1 --CCATGCACGC
10315 TCCATGCACGC
1 -CCATGCACGC
10326 CCATGCACGC
1 CCATGCACGC
10336 CCA
1 CCA
10339 ACGACCTCCA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
9 9 0.15
10 50 0.83
11 1 0.02
ACGTcount: A:0.23, C:0.50, G:0.17, T:0.10
Consensus pattern (10 bp):
CCATGCACGC
Found at i:11027 original size:21 final size:21
Alignment explanation
Indices: 11002--11045 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
10992 AATTTAGTTA
11002 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
11023 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
11044 AT
1 AT
11046 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:14217 original size:60 final size:59
Alignment explanation
Indices: 14145--14564 Score: 571
Period size: 60 Copynumber: 7.2 Consensus size: 59
14135 TTTATAAGAT
* *
14145 TTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTAATAGTAATTTGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAA--TGA
*
14206 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAA-TATTTAATGATTTGATAGTAATGA
* *
14264 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
14324 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
* *
14384 TTTACTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAA-TATTTAATGATTTGATAGTAATGA
*
14444 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
14504 TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTGATATTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
14552 TTTAGTAATGATT
1 -TTAGTAATGATT
14565 TGATAGTAAT
Statistics
Matches: 331, Mismatches: 15, Indels: 32
0.88 0.04 0.08
Matches are distributed among these distances:
48 32 0.10
49 4 0.01
52 8 0.02
53 2 0.01
55 1 0.00
56 1 0.00
58 3 0.01
59 10 0.03
60 263 0.79
61 7 0.02
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
Found at i:14370 original size:35 final size:35
Alignment explanation
Indices: 14323--14491 Score: 92
Period size: 35 Copynumber: 5.4 Consensus size: 35
14313 GATATTAATG
14323 ATTTAGTAATGATTAGTAATAATGAAATTATTATTA
1 ATTT-GTAATGATTAGTAATAATGAAATTATTATTA
* * * *
14359 ATTTTTAATGATT--TGAT-A-GTAATGA-T-TT-
1 ATTTGTAATGATTAGTAATAATGAAATTATTATTA
*
14387 A---CTAATGATTAGTAATAATGAAATTATTATTA
1 ATTTGTAATGATTAGTAATAATGAAATTATTATTA
* * *
14419 ATTATGT-ATGATT--TGAT-A-GTAATGA-T-TT-
1 ATT-TGTAATGATTAGTAATAATGAAATTATTATTA
14447 A---GTAATGATTAGTAATAATGAAATTATTATTA
1 ATTTGTAATGATTAGTAATAATGAAATTATTATTA
*
14479 ATTTTTAATGATT
1 ATTTGTAATGATT
14492 TGATAGTAAT
Statistics
Matches: 95, Mismatches: 16, Indels: 45
0.61 0.10 0.29
Matches are distributed among these distances:
24 2 0.02
25 14 0.15
27 6 0.06
28 4 0.04
29 14 0.15
30 4 0.04
31 14 0.15
32 4 0.04
33 6 0.06
35 22 0.23
36 5 0.05
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (35 bp):
ATTTGTAATGATTAGTAATAATGAAATTATTATTA
Found at i:14444 original size:180 final size:171
Alignment explanation
Indices: 14142--14564 Score: 658
Period size: 180 Copynumber: 2.4 Consensus size: 171
14132 GTATTTATAA
* *
14142 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTAATAGTAAT--TTG
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT-
14205 ATAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGT
65 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGT
14270 AATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
129 AATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TG--ATT--T
*
14322 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
*
14387 ACTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAA
66 AGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAA
14452 TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTT
131 TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTT
* *
14493 GA--TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
14555 AGTAATGATT
66 AGTAATGATT
14565 TGATAGTAAT
Statistics
Matches: 233, Mismatches: 8, Indels: 16
0.91 0.03 0.06
Matches are distributed among these distances:
168 46 0.20
169 20 0.09
171 3 0.01
173 3 0.01
175 2 0.01
177 1 0.00
179 1 0.00
180 155 0.67
182 2 0.01
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (171 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
AGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAA
TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTT
Found at i:14535 original size:21 final size:22
Alignment explanation
Indices: 14511--14580 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 22
14501 TGATTAGTAA
14511 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
14532 TAATGATTTGATATTAATGATTT
1 TAATAATTTGATATTAATGA-TT
* *
14555 AGTAATGATTTGATAGTAATGATT
1 --TAATAATTTGATATTAATGATT
14579 TA
1 TA
14581 CGACTTGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 15 0.36
22 4 0.10
23 2 0.05
24 2 0.05
25 19 0.45
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:14538 original size:48 final size:49
Alignment explanation
Indices: 14446--14560 Score: 187
Period size: 48 Copynumber: 2.3 Consensus size: 49
14436 AGTAATGATT
*
14446 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
14495 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
14543 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
14561 GATTTGATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 34 0.55
49 28 0.45
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:14548 original size:14 final size:14
Alignment explanation
Indices: 14532--14579 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
14522 TATTAATATT
*
14532 TAATGATTTGATAT
1 TAATGATTTGATAG
14546 TAATGA-TT--TAG
1 TAATGATTTGATAG
14557 TAATGATTTGATAG
1 TAATGATTTGATAG
14571 TAATGATTT
1 TAATGATTT
14580 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:16915 original size:30 final size:31
Alignment explanation
Indices: 16878--16953 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
16868 TTTCCCTTAA
16878 ACAACTAATAAACTATTCTTTAA-TATAAATT
1 ACAACTAATAAACTATT-TTTAATTATAAATT
*
16909 A-AACTAATAAA-TGATTTTTAATTATAATTT
1 ACAACTAATAAACT-ATTTTTAATTATAAATT
* *
16939 ACTACTAAAAAACTA
1 ACAACTAATAAACTA
16954 ATTAACTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 6 0.16
30 21 0.55
31 10 0.26
32 1 0.03
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.38
Consensus pattern (31 bp):
ACAACTAATAAACTATTTTTAATTATAAATT
Found at i:17154 original size:21 final size:21
Alignment explanation
Indices: 17130--17169 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
17120 TTTCTATATG
17130 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
17151 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
17170 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:17251 original size:18 final size:18
Alignment explanation
Indices: 17198--17252 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
17188 TTGTTTTACC
*
17198 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
17216 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
17228 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
17245 CTAATTTA
1 CTAATTTA
17253 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:17311 original size:35 final size:37
Alignment explanation
Indices: 17267--17345 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 37
17257 ATTATTCTTT
* *
17267 TATATAACTT-AA-ACTAATAAACT-ATTTTTTATTA
1 TATAAAACTTAAACACTAATAAACTAATTTTTTATAA
17301 TAATAAAACTTAAACTACTAATAAACTAATTTTTTATAA
1 T-ATAAAACTTAAAC-ACTAATAAACTAATTTTTTATAA
17340 TATAAA
1 TATAAA
17346 TTCAACAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
34 1 0.03
35 8 0.21
36 2 0.05
38 16 0.42
39 11 0.29
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (37 bp):
TATAAAACTTAAACACTAATAAACTAATTTTTTATAA
Found at i:17401 original size:27 final size:29
Alignment explanation
Indices: 17366--17430 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
17356 AAAATATAAC
*
17366 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
17393 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
17421 TTAATTATTT
1 TTAAATATTT
17431 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:17544 original size:9 final size:9
Alignment explanation
Indices: 17512--17549 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
17502 CTAACAAACT
17512 AATAATTTAA
1 AATAA-TTAA
17522 AATAA-TAA
1 AATAATTAA
*
17530 ACTAATTAA
1 AATAATTAA
17539 AATAATTAA
1 AATAATTAA
17548 AA
1 AA
17550 AAAAACTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:17750 original size:12 final size:11
Alignment explanation
Indices: 17719--17754 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
17709 ACGTTCACGG
17719 GCTGCAATAAT
1 GCTGCAATAAT
*
17730 GCAGCAATAAGT
1 GCTGCAATAA-T
17742 GCTGCAATAAT
1 GCTGCAATAAT
17753 GC
1 GC
17755 AGTTGATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (11 bp):
GCTGCAATAAT
Found at i:18040 original size:30 final size:30
Alignment explanation
Indices: 17999--18078 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
17989 CTTTGGCGAG
*
17999 ATGGGCATGCATGGAGGTCGTTGGGCGTGC
1 ATGGGCGTGCATGGAGGTCGTTGGGCGTGC
18029 ATGGGCGTGCATGGAGGTCGTTGGGCGTGC
1 ATGGGCGTGCATGGAGGTCGTTGGGCGTGC
18059 AT--G-G-GCATGGAGGTCGTTGG
1 ATGGGCGTGCATGGAGGTCGTTGG
18079 CTGGTAGGTC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
26 16 0.33
27 1 0.02
28 1 0.02
30 31 0.63
ACGTcount: A:0.12, C:0.15, G:0.49, T:0.24
Consensus pattern (30 bp):
ATGGGCGTGCATGGAGGTCGTTGGGCGTGC
Found at i:18119 original size:29 final size:29
Alignment explanation
Indices: 18084--18170 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 29
18074 GTTGGCTGGT
*
18084 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
18113 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* *
18142 AGGTCGCCGAGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
18171 CCCGGGACTG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.16, C:0.30, G:0.38, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:22136 original size:8 final size:7
Alignment explanation
Indices: 22077--22138 Score: 74
Period size: 7 Copynumber: 9.0 Consensus size: 7
22067 AATTCCTTTG
22077 TTGCA-T
1 TTGCATT
*
22083 TTACATT
1 TTGCATT
*
22090 TTGTATT
1 TTGCATT
*
22097 TTGTATT
1 TTGCATT
22104 TTGCATT
1 TTGCATT
22111 TTGCATT
1 TTGCATT
22118 TTGCA-T
1 TTGCATT
22124 TTGCATCT
1 TTGCAT-T
22132 TTGCATT
1 TTGCATT
22139 AGCATCAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
6 10 0.20
7 32 0.65
8 7 0.14
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (7 bp):
TTGCATT
Found at i:23216 original size:2 final size:2
Alignment explanation
Indices: 23209--23234 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23199 ATCCTTTCAA
23209 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
23235 TGTTGTCCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23513 original size:9 final size:9
Alignment explanation
Indices: 23501--23605 Score: 61
Period size: 9 Copynumber: 10.9 Consensus size: 9
23491 AAACACACAA
23501 AAAAGAAAG
1 AAAAGAAAG
23510 AAAA-AAGAG
1 AAAAGAA-AG
23519 AAACACGAAAAAG
1 AAA-A-G--AAAG
23532 AAATAGAAA-
1 AAA-AGAAAG
* *
23541 AAGAGAAAA
1 AAAAGAAAG
*
23550 AAAAGAAAC
1 AAAAGAAAG
*
23559 AAAAGAAAC
1 AAAAGAAAG
*
23568 AAAAGAAAA
1 AAAAGAAAG
23577 AGAAAGAAAAG
1 A-AAAG-AAAG
*
23588 AAAAGAAAA
1 AAAAGAAAG
23597 AAGAAGAAA
1 AA-AAGAAA
23606 ATGGACAGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.09
9 41 0.52
10 18 0.23
11 4 0.05
12 1 0.01
13 6 0.08
14 2 0.03
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.01
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:23539 original size:6 final size:6
Alignment explanation
Indices: 23500--23597 Score: 60
Period size: 6 Copynumber: 15.8 Consensus size: 6
23490 AAAACACACA
* * *
23500 AAAAAG AAAGAA- AAAAGAG AAACACG AAAAAG AAATAG AAAAAG AGAAA-
1 AAAAAG AAA-AAG AAAA-AG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG
* *
23549 AAAAAG AAACAA- AAGAAA- CAAAAG AAAAAG AAAGAAA AGAAAAG AAAAA
1 AAAAAG AAA-AAG AA-AAAG AAAAAG AAAAAG AAA-AAG A-AAAAG AAAAA
23598 AGAAGAAAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
5 8 0.11
6 43 0.60
7 18 0.25
8 3 0.04
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:23541 original size:27 final size:26
Alignment explanation
Indices: 23495--23548 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
23485 TATAAAAAAC
23495 ACACAAAAAAGAAAGAAAAAAGAGAA
1 ACACAAAAAAGAAAGAAAAAAGAGAA
* *
23521 ACACGAAAAAGAAATAGAAAAAGAGAA
1 ACACAAAAAAGAAAGA-AAAAAGAGAA
23548 A
1 A
23549 AAAAAGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.74, C:0.07, G:0.17, T:0.02
Consensus pattern (26 bp):
ACACAAAAAAGAAAGAAAAAAGAGAA
Found at i:23542 original size:38 final size:37
Alignment explanation
Indices: 23501--23605 Score: 117
Period size: 36 Copynumber: 2.8 Consensus size: 37
23491 AAACACACAA
* * *
23501 AAAAGAAAGAAAAAAGAGAAACACGAA-AAAGAAATAGA
1 AAAAGAAAGAAAAAAAAGAAACA-AAAGAAACAAA-AGA
23539 AAAAG--AGAAAAAAAAGAAACAAAAGAAACAAAAGA
1 AAAAGAAAGAAAAAAAAGAAACAAAAGAAACAAAAGA
*
23574 AAAAGAAAGAAAAGAAAAGAAAAAAGAAGAAA
1 AAAAGAAAGAAAA-AAAAGAAACAA-AAGAAA
23606 ATGGACAGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
35 10 0.17
36 21 0.36
37 6 0.10
38 15 0.26
39 6 0.10
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.01
Consensus pattern (37 bp):
AAAAGAAAGAAAAAAAAGAAACAAAAGAAACAAAAGA
Found at i:23572 original size:29 final size:29
Alignment explanation
Indices: 23539--23606 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
23529 AAGAAATAGA
23539 AAAAGAGAAAAAAAAG-AAACAAAAGAAAC
1 AAAAGA-AAAAAAAAGAAAACAAAAGAAAC
* * *
23568 AAAAGAAAAAGAAAGAAAAGAAAAGAAAA
1 AAAAGAAAAAAAAAGAAAACAAAAGAAAC
23597 AAGAAGAAAA
1 AA-AAGAAAA
23607 TGGACAGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 8 0.24
29 19 0.56
30 7 0.21
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (29 bp):
AAAAGAAAAAAAAAGAAAACAAAAGAAAC
Found at i:23579 original size:15 final size:15
Alignment explanation
Indices: 23500--23606 Score: 74
Period size: 15 Copynumber: 6.9 Consensus size: 15
23490 AAAACACACA
23500 AAAAAGAAAGAAAAAAG
1 AAAAA-AAAG-AAAAAG
* * *
23517 AGAAACACGAAAAAG
1 AAAAAAAAGAAAAAG
* * *
23532 AAATAGAA-AAAGAG
1 AAAAAAAAGAAAAAG
23546 AAAAAAAAGAAACAAAAG
1 AAAAAAAAG--A-AAAAG
*
23564 AAACAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
*
23579 AAAGAAAAG-AAAAG
1 AAAAAAAAGAAAAAG
23593 AAAAAAGAAGAAAA
1 AAAAAA-AAGAAAA
23607 TGGACAGATC
Statistics
Matches: 70, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
14 21 0.30
15 26 0.37
16 6 0.09
17 5 0.07
18 12 0.17
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.01
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:23585 original size:45 final size:44
Alignment explanation
Indices: 23499--23606 Score: 114
Period size: 45 Copynumber: 2.4 Consensus size: 44
23489 AAAAACACAC
* *
23499 AAAAAAGAAAGAAAAAAGAGAAACACGAAAAAGAAATAGAAAAAG
1 AAAAAAAAAAGAAAAAAGAGAAACAAGAAAAAGAAATAG-AAAAG
*
23544 AGAAAAAAAAGAAACAAA-AGAAACAAAAGAAAAAG-AA-AGAAAAG
1 AAAAAAAAAAGAAA-AAAGAGAAAC--AAGAAAAAGAAATAGAAAAG
23588 AAAAGAAAAAAGAAGAAAA
1 AAAA-AAAAAAGAA-AAAA
23607 TGGACAGATC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
44 8 0.15
45 32 0.59
46 6 0.11
47 8 0.15
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.01
Consensus pattern (44 bp):
AAAAAAAAAAGAAAAAAGAGAAACAAGAAAAAGAAATAGAAAAG
Found at i:23593 original size:20 final size:19
Alignment explanation
Indices: 23499--23606 Score: 87
Period size: 20 Copynumber: 5.6 Consensus size: 19
23489 AAAAACACAC
* *
23499 AAAAAAGAAAGAAAAAAGAG
1 AAAAAAGAAA-AGAAAAGAA
* *
23519 AAACACGAAAAAGAAATAG-A
1 AAAAAAG-AAAAGAAA-AGAA
*
23539 AAAAGAGAAAA-AAAAGAA
1 AAAAAAGAAAAGAAAAGAA
* *
23557 ACAAAAG-AAACAAAAGAA
1 AAAAAAGAAAAGAAAAGAA
23575 AAAGAAAGAAAAGAAAAGAA
1 AAA-AAAGAAAAGAAAAGAA
23595 AAAAGAAGAAAA
1 AAAA-AAGAAAA
23607 TGGACAGATC
Statistics
Matches: 70, Mismatches: 11, Indels: 14
0.74 0.12 0.15
Matches are distributed among these distances:
17 5 0.07
18 18 0.26
19 9 0.13
20 33 0.47
21 5 0.07
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.01
Consensus pattern (19 bp):
AAAAAAGAAAAGAAAAGAA
Found at i:25750 original size:55 final size:55
Alignment explanation
Indices: 25559--25816 Score: 264
Period size: 54 Copynumber: 4.8 Consensus size: 55
25549 ATTTTTTATT
* * * * *
25559 AGTTTTTAAATAAACTAAGTCTGATTTTCAGAAGTTTCTTAACGGTTTTCAAATG
1 AGTTTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGACGATTTTCAAATA
* * * *
25614 AGTTTTT-TAGAAACTAA-TTCCGATTTTCGGAAGTTTCTTGATC-ATTTT-AAATG
1 AGTTTTTAAAGAAACTAAGTT-TGATTTTCAGAAGTTTCTTGA-CGATTTTCAAATA
* * *
25667 AGTTTTTAAAGAAGCTAAGTCTT-ATTTTCATAAGTTTCTTGACGATTTTCAAGTA
1 AGTTTTTAAAGAAACTAAGT-TTGATTTTCAGAAGTTTCTTGACGATTTTCAAATA
* *
25722 AGTTTTTAAAGAAGCTAAGTTTGGTTTTCAGAAGTTTCTTGACG-TTTTCAAAT-
1 AGTTTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGACGATTTTCAAATA
**
25775 -GTGTTTTAAAGAAACTAAGTTCAATTTT-AGGAAGTTTCTTGA
1 AGT-TTTTAAAGAAACTAAGTTTGATTTTCA-GAAGTTTCTTGA
25817 TTTTTCTTAA
Statistics
Matches: 172, Mismatches: 21, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
52 3 0.02
53 47 0.27
54 70 0.41
55 51 0.30
56 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (55 bp):
AGTTTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGACGATTTTCAAATA
Found at i:25802 original size:108 final size:108
Alignment explanation
Indices: 25559--25816 Score: 292
Period size: 108 Copynumber: 2.4 Consensus size: 108
25549 ATTTTTTATT
* * * * * *
25559 AGTTTTTAAATAAACTAAGTCTGATTTTCAGAAGTTTCTTAACGGTTTTCAAATGAGTTTTTTAG
1 AGTTTTTAAAGAAACTAAGTCTAATTTTCAGAAGTTTCTTGACGATTTTCAAATAAGTTTTTAAG
*
25624 AAACTAATTCCGATTTTCGGAAGTTTCTTGATCATTTTAAATG
66 AAACTAATTCCGATTTTCAGAAGTTTCTTGATCATTTTAAATG
* * * *
25667 AGTTTTTAAAGAAGCTAAGTCTTATTTTCATAAGTTTCTTGACGATTTTCAAGTAAGTTTTTAAA
1 AGTTTTTAAAGAAACTAAGTCTAATTTTCAGAAGTTTCTTGACGATTTTCAAATAAGTTTTT-AA
* * * *
25732 GAAGCTAAGTT-TGGTTTTCAGAAGTTTCTTGA-CGTTTTCAAATG
65 GAAACTAA-TTCCGATTTTCAGAAGTTTCTTGATCATTTT-AAATG
*
25776 TG-TTTTAAAGAAACTAAGT-TCAATTTT-AGGAAGTTTCTTGA
1 AGTTTTTAAAGAAACTAAGTCT-AATTTTCA-GAAGTTTCTTGA
25817 TTTTTCTTAA
Statistics
Matches: 127, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
107 2 0.02
108 91 0.72
109 32 0.25
110 2 0.02
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (108 bp):
AGTTTTTAAAGAAACTAAGTCTAATTTTCAGAAGTTTCTTGACGATTTTCAAATAAGTTTTTAAG
AAACTAATTCCGATTTTCAGAAGTTTCTTGATCATTTTAAATG
Found at i:25898 original size:54 final size:53
Alignment explanation
Indices: 25755--25977 Score: 224
Period size: 54 Copynumber: 4.2 Consensus size: 53
25745 GTTTTCAGAA
* ** * * *
25755 GTTTCTTGACGTTTTCAAATGTGTTTT-AAAGAAACTAAG-TTCAATTTTAGGAA
1 GTTTCTTGATGTTTTCAAATGAATTTTCAAAGAAATTAAGCCT-AATTTTAGG-G
**
25808 GTTTCTTGAT-TTTTCTTAAATGAACGTTCAAAGAAATTAAGCCTAATTTTTAGGG
1 GTTTCTTGATGTTTTC--AAATGAATTTTCAAAGAAATTAAGCCTAA-TTTTAGGG
**
25863 GTTTCTTGATGTTTTCAAATGAATTTTCAAAGAAATTAAGCCTGGTTTTATGGG
1 GTTTCTTGATGTTTTCAAATGAATTTTCAAAGAAATTAAGCCTAATTTTA-GGG
* * *
25917 GTTTCTTGATGTTTT---TTGAATTTTTGAAAGAAGTTAAGCCTAATTTTAGGG
1 GTTTCTTGATGTTTTCAAATGAA-TTTTCAAAGAAATTAAGCCTAATTTTAGGG
25968 GTTTCTTGAT
1 GTTTCTTGAT
25978 AACTGTAAAT
Statistics
Matches: 145, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
51 17 0.12
52 28 0.19
53 14 0.10
54 50 0.34
55 23 0.16
56 13 0.09
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (53 bp):
GTTTCTTGATGTTTTCAAATGAATTTTCAAAGAAATTAAGCCTAATTTTAGGG
Found at i:26652 original size:139 final size:139
Alignment explanation
Indices: 26399--26892 Score: 816
Period size: 139 Copynumber: 3.6 Consensus size: 139
26389 AGATGAACCA
* *
26399 ATCAACATTTCAAATTGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
* *
26464 AATGAGAAGAACTTGTTCGACCTTAGCTCGATTCATCGCATAAGAAGTTGAATCAGCAACACCTC
66 AATGAGAAGAACTTGTTCGACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
26529 ACTCGAGGG
131 ACTCGAGGG
*
26538 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACCCATCCGATGAAGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
*
26603 AATGAGAAGAGCTTGTTCGACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
66 AATGAGAAGAACTTGTTCGACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
26668 ACTCGAGGG
131 ACTCGAGGG
*
26677 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
* * * *
26742 AATGAGAAGAACTTGTTCAATCTTAGCTCGATTCGTCACATATGGAGTTGAATCAGCAACACCTC
66 AATGAGAAGAACTTGTTCGACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
26807 ACTCGAGGG
131 ACTCGAGGG
* * * *
26816 ATCAACCTTTCC-A-GTAGAGTTCATAATGAGAATAACTCATCCGAT-AAGG-GAAAAAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAG-AAGAAGTTCA
26877 TAATGAGAAGAACTTG
65 TAATGAGAAGAACTTG
26893 AGCTTACTTC
Statistics
Matches: 336, Mismatches: 18, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
135 1 0.00
136 28 0.08
137 30 0.09
138 1 0.00
139 276 0.82
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (139 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCGACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
ACTCGAGGG
Found at i:31827 original size:19 final size:20
Alignment explanation
Indices: 31789--31835 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
31779 GCCCTAGCAG
*
31789 AAAAGGCACAAGAGGGAAAA
1 AAAAAGCACAAGAGGGAAAA
*
31809 AACAAGCACAAGA-GGAAAA
1 AAAAAGCACAAGAGGGAAAA
31828 AAAAAGCA
1 AAAAAGCA
31836 TCAAAGTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.64, C:0.13, G:0.23, T:0.00
Consensus pattern (20 bp):
AAAAAGCACAAGAGGGAAAA
Found at i:38752 original size:51 final size:50
Alignment explanation
Indices: 38627--38752 Score: 166
Period size: 51 Copynumber: 2.5 Consensus size: 50
38617 ATAGCAGTAA
* * *
38627 AGCGC-CCCCTGACCCGCGCTATACGTTGATTTGGCGCCACGTGGGGTAT
1 AGCGCGCCCCTGAACCGCGCTATATGCTGATTTGGCGCCACGTGGGGTAT
*
38676 AGCGCGCCCCATGTAA-CGCGCTATATGCTGATTTGGCTCCACGTGGGGTAT
1 AGCGCGCCCC-TG-AACCGCGCTATATGCTGATTTGGCGCCACGTGGGGTAT
*
38727 AGCGTGCTCCCTGAACCGCGCTATAT
1 AGCGCGC-CCCTGAACCGCGCTATAT
38753 CTGTGTATCT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
49 5 0.07
50 6 0.09
51 52 0.78
52 4 0.06
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.24
Consensus pattern (50 bp):
AGCGCGCCCCTGAACCGCGCTATATGCTGATTTGGCGCCACGTGGGGTAT
Found at i:42627 original size:12 final size:12
Alignment explanation
Indices: 42610--42638 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
42600 ACTCCTCACT
42610 GTCGTCATCGTC
1 GTCGTCATCGTC
42622 GTCGTCATCGTC
1 GTCGTCATCGTC
42634 GTCGT
1 GTCGT
42639 GAGCAGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.31, G:0.28, T:0.34
Consensus pattern (12 bp):
GTCGTCATCGTC
Found at i:43662 original size:17 final size:18
Alignment explanation
Indices: 43621--43659 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
43611 ATTATATTAG
43621 TAAAATA-TTAAATAAAA
1 TAAAATACTTAAATAAAA
*
43638 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAA
43656 TAAA
1 TAAA
43660 TACATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATACTTAAATAAAA
Found at i:43948 original size:51 final size:51
Alignment explanation
Indices: 43812--43967 Score: 139
Period size: 50 Copynumber: 3.1 Consensus size: 51
43802 CCCCTTACAC
* ** * *
43812 CGCGCTATACCCCACGTGTCAGATAAAT-AG-GTATAGCACGGAGCAGGGGG
1 CGCGCTATACCCCACGTGAC-GCCAAATCAGCGTATAGCGCGGTGCAGGGGG
* *
43862 -GACGCTATA-GCCACGTGTAAC-CC-AGTCAGCGTATAGCGCGGTGCAGGGGG
1 CG-CGCTATACCCCACGTG--ACGCCAAATCAGCGTATAGCGCGGTGCAGGGGG
*
43912 CGCGCTATACCCCACGTGACGCCAAATCAGCATATAGCGCAGGT-CA-GGGG
1 CGCGCTATACCCCACGTGACGCCAAATCAGCGTATAGCGC-GGTGCAGGGGG
43962 CGCGCT
1 CGCGCT
43968 TTACTGCTAC
Statistics
Matches: 86, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
48 2 0.02
49 12 0.14
50 44 0.51
51 25 0.29
52 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.15
Consensus pattern (51 bp):
CGCGCTATACCCCACGTGACGCCAAATCAGCGTATAGCGCGGTGCAGGGGG
Found at i:46622 original size:18 final size:17
Alignment explanation
Indices: 46592--46683 Score: 78
Period size: 18 Copynumber: 5.2 Consensus size: 17
46582 TATACATTGC
*
46592 ATTATATTAATATTAAT
1 ATTATATTTATATTAAT
*
46609 ATTATTATTTATATTTAT
1 ATTA-TATTTATATTAAT
*
46627 ATTATATCATATATTATAAT
1 ATTATAT-TTATA-T-TAAT
* *
46647 ATTATATTTTTATTATGT
1 ATTATATTTATATTA-AT
*
46665 ATTAT-TTTATGTTAAT
1 ATTATATTTATATTAAT
46681 ATT
1 ATT
46684 TTTTATTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
16 4 0.07
17 16 0.27
18 26 0.43
19 4 0.07
20 10 0.17
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTATATTTATATTAAT
Found at i:46971 original size:9 final size:9
Alignment explanation
Indices: 46957--46990 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
46947 GAAATCGGTT
46957 AATTAACCG
1 AATTAACCG
*
46966 AATTAATCG
1 AATTAACCG
46975 AATTAACCG
1 AATTAACCG
46984 AAATTAA
1 -AATTAA
46991 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:48357 original size:25 final size:25
Alignment explanation
Indices: 48309--48360 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
48299 CTTTTAGAAA
*
48309 TTAACATTTTTTTTCATTTTTTTATT
1 TTAACATTTTTTTT-ATTTATTTATT
48335 TTAACATTTTTTATT-TTTATTTATT
1 TTAACATTTTTT-TTATTTATTTATT
48360 T
1 T
48361 CTCTTGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 10 0.42
26 12 0.50
27 2 0.08
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (25 bp):
TTAACATTTTTTTTATTTATTTATT
Found at i:49912 original size:7 final size:7
Alignment explanation
Indices: 49902--49927 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
49892 TTTAATGTAT
49902 AATAATA
1 AATAATA
49909 AATAATA
1 AATAATA
49916 AATAATA
1 AATAATA
49923 AATAA
1 AATAA
49928 CATATTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AATAATA
Found at i:51256 original size:27 final size:29
Alignment explanation
Indices: 51198--51258 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 29
51188 AATATGATTG
* *
51198 ATTTAGTCACCTGTTTTTTAATTAAATGC
1 ATTTAGTCACCTGATTTTTAATTAAATAC
*
51227 ATTTAGTC-CC-GATTTTTAATTAAGTAC
1 ATTTAGTCACCTGATTTTTAATTAAATAC
51254 ATTTA
1 ATTTA
51259 ATCTTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 19 0.66
28 2 0.07
29 8 0.28
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (29 bp):
ATTTAGTCACCTGATTTTTAATTAAATAC
Found at i:52303 original size:39 final size:39
Alignment explanation
Indices: 52249--52342 Score: 188
Period size: 39 Copynumber: 2.4 Consensus size: 39
52239 GGTGTTTTGT
52249 TTTAAAAGTTAATGAAGGTGCTTTTGCTTTAGCTTTAGC
1 TTTAAAAGTTAATGAAGGTGCTTTTGCTTTAGCTTTAGC
52288 TTTAAAAGTTAATGAAGGTGCTTTTGCTTTAGCTTTAGC
1 TTTAAAAGTTAATGAAGGTGCTTTTGCTTTAGCTTTAGC
52327 TTTAAAAGTTAATGAA
1 TTTAAAAGTTAATGAA
52343 AGTTAAAAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.43
Consensus pattern (39 bp):
TTTAAAAGTTAATGAAGGTGCTTTTGCTTTAGCTTTAGC
Found at i:55942 original size:27 final size:27
Alignment explanation
Indices: 55904--55965 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
55894 TCGTGTTTCT
55904 GCTTGTGCGTTTGTCTCCGTTGCTCCC
1 GCTTGTGCGTTTGTCTCCGTTGCTCCC
* *
55931 GCTTGTGCGTTTGTCTCCGTTGCTTCT
1 GCTTGTGCGTTTGTCTCCGTTGCTCCC
55958 GCTTGTGC
1 GCTTGTGC
55966 TCTTTGAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.00, C:0.29, G:0.27, T:0.44
Consensus pattern (27 bp):
GCTTGTGCGTTTGTCTCCGTTGCTCCC
Found at i:58695 original size:21 final size:20
Alignment explanation
Indices: 58653--58692 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
58643 TTTTATTTTT
58653 TATTTTTTTATAAATAAAAA
1 TATTTTTTTATAAATAAAAA
58673 TATTATTTTTA-AAATAAAAA
1 TATT-TTTTTATAAATAAAAA
58693 ATAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTTTTTTATAAATAAAAA
Found at i:59549 original size:18 final size:18
Alignment explanation
Indices: 59528--59578 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
59518 AAATAAATAC
*
59528 TATTTATTTAATTACTTA
1 TATTTATTTAATTAATTA
59546 TATTTACTTT-ATTAATTA
1 TATTTA-TTTAATTAATTA
*
59564 -ATCTATTTAAATTAA
1 TATTTATTT-AATTAA
59579 ATAATGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 3 0.11
17 4 0.14
18 18 0.64
19 3 0.11
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTATTTAATTAATTA
Found at i:60584 original size:21 final size:21
Alignment explanation
Indices: 60559--60658 Score: 191
Period size: 21 Copynumber: 4.8 Consensus size: 21
60549 CATATAGCTT
60559 CTTTTCATATAATTCATATCA
1 CTTTTCATATAATTCATATCA
60580 CTTTTCATATAATTCATATCA
1 CTTTTCATATAATTCATATCA
60601 CTTTTCATATAATTCATATCA
1 CTTTTCATATAATTCATATCA
*
60622 CTTTTCACATAATTCATATCA
1 CTTTTCATATAATTCATATCA
60643 CTTTTCATATAATTCA
1 CTTTTCATATAATTCA
60659 CATGTTCACA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (21 bp):
CTTTTCATATAATTCATATCA
Found at i:61064 original size:24 final size:22
Alignment explanation
Indices: 61012--61073 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 22
61002 TCCCCTTGAA
*
61012 GTGCATCGATGCATCCTACCGT
1 GTGCATCGATGCATCCTAACGT
61034 GT--ATCGATGCATCCCTTAACGT
1 GTGCATCGATGCAT-CC-TAACGT
61056 GTGCATCGATGCACTCCT
1 GTGCATCGATGCA-TCCT
61074 TATGCATCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
20 10 0.29
21 2 0.06
22 9 0.26
23 1 0.03
24 11 0.32
25 1 0.03
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (22 bp):
GTGCATCGATGCATCCTAACGT
Found at i:61081 original size:19 final size:19
Alignment explanation
Indices: 61057--61122 Score: 132
Period size: 19 Copynumber: 3.5 Consensus size: 19
61047 CCTTAACGTG
61057 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
61076 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
61095 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
61114 TGCATCGAT
1 TGCATCGAT
61123 TCATTAATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:64618 original size:18 final size:19
Alignment explanation
Indices: 64595--64630 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
64585 TCTAGCTCTC
64595 TTTCAC-ATAACATTTCAT
1 TTTCACTATAACATTTCAT
*
64613 TTTCACTATATCATTTCA
1 TTTCACTATAACATTTCA
64631 CATATACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTCACTATAACATTTCAT
Done.