Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001360.1 Hibiscus syriacus cultivar Beakdansim tig00002652_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: 69574
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:657 original size:22 final size:21
Alignment explanation
Indices: 632--672 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
622 ATACTGATTT
* *
632 TGTATATTAATAATTTATTTAG
1 TGTATAATAA-AAATTATTTAG
654 TGTATAATAAAAATTATTT
1 TGTATAATAAAAATTATTT
673 CATTGAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
TGTATAATAAAAATTATTTAG
Found at i:1929 original size:22 final size:22
Alignment explanation
Indices: 1895--1936 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1885 ATAATTGTAA
*
1895 TTTTTTTATTTAA-TTATTTAC
1 TTTTTTTACTTAATTTATTTAC
1916 TTTTTATTACTTAATTTATTT
1 TTTTT-TTACTTAATTTATTT
1937 TGTTTGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTTACTTAATTTATTTAC
Found at i:5267 original size:15 final size:16
Alignment explanation
Indices: 5247--5287 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
5237 TTTTTTTTCC
5247 AAATAATTATAT-ATA
1 AAATAATTATATAATA
5262 AAATAAATATATATAATA
1 AAAT-AAT-TATATAATA
5280 AAATAATT
1 AAATAATT
5288 TTACCTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.17
16 4 0.17
17 8 0.35
18 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATAATTATATAATA
Found at i:5801 original size:22 final size:22
Alignment explanation
Indices: 5776--5845 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
5766 AATCGAACAA
5776 TAAACAAACGATAAACAAATAC
1 TAAACAAACGATAAACAAATAC
5798 TAAACAAACGATAAACAAATAC
1 TAAACAAACGATAAACAAATAC
* *
5820 TAAACAAACAATAAACAAACAC
1 TAAACAAACGATAAACAAATAC
5842 TAAA
1 TAAA
5846 TTAACATAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.66, C:0.19, G:0.03, T:0.13
Consensus pattern (22 bp):
TAAACAAACGATAAACAAATAC
Found at i:5840 original size:11 final size:11
Alignment explanation
Indices: 5771--5845 Score: 87
Period size: 11 Copynumber: 6.8 Consensus size: 11
5761 TATATAATCG
5771 AACAATAAACA
1 AACAATAAACA
*
5782 AACGATAAACA
1 AACAATAAACA
* *
5793 AATACTAAACA
1 AACAATAAACA
*
5804 AACGATAAACA
1 AACAATAAACA
* *
5815 AATACTAAACA
1 AACAATAAACA
5826 AACAATAAACA
1 AACAATAAACA
*
5837 AACACTAAA
1 AACAATAAA
5846 TTAACATAAA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 51 1.00
ACGTcount: A:0.67, C:0.19, G:0.03, T:0.12
Consensus pattern (11 bp):
AACAATAAACA
Found at i:5851 original size:22 final size:21
Alignment explanation
Indices: 5771--5861 Score: 101
Period size: 22 Copynumber: 4.2 Consensus size: 21
5761 TATATAATCG
*
5771 AACAATAAACAAACGATAAACA
1 AACACTAAACAAAC-ATAAACA
*
5793 AATACTAAACAAACGATAAACA
1 AACACTAAACAAAC-ATAAACA
*
5815 AATACTAAACAAACAATAAACA
1 AACACTAAACAAAC-ATAAACA
** *
5837 AACACTAAATTAACATAAACG
1 AACACTAAACAAACATAAACA
5858 AACA
1 AACA
5862 GTAGTGGGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
21 10 0.16
22 52 0.84
ACGTcount: A:0.65, C:0.19, G:0.03, T:0.13
Consensus pattern (21 bp):
AACACTAAACAAACATAAACA
Found at i:11098 original size:3 final size:3
Alignment explanation
Indices: 11086--11171 Score: 74
Period size: 3 Copynumber: 30.0 Consensus size: 3
11076 CATTTGTTTT
*
11086 TTA TTA -TA TTA TTA TTA TTA TTA ATA TTA TT- TTA TT- TTA TT- TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * * *
11131 CTA TTA TTT TTA TTT TTA -TA TTA TTA TAA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11172 AATAATATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
2 9 0.13
3 58 0.87
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:11113 original size:23 final size:23
Alignment explanation
Indices: 11087--11180 Score: 72
Period size: 23 Copynumber: 4.2 Consensus size: 23
11077 ATTTGTTTTT
11087 TATTATATTATTATTATTATTAA
1 TATTATATTATTATTATTATTAA
* *
11110 TATTATTTTATT-TTATT-TATAC
1 TATTATATTATTATTATTAT-TAA
* *
11132 TATTAT-TT-TTATTTTTA-TAT
1 TATTATATTATTATTATTATTAA
* *
11152 TATTATAATAATTATTATTAAATAA
1 TATTAT-ATTATTATTATT-ATTAA
11177 TATT
1 TATT
11181 TTGTACATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
20 10 0.18
21 7 0.12
22 14 0.25
23 18 0.32
24 1 0.02
25 6 0.11
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTATATTATTATTATTATTAA
Found at i:12578 original size:146 final size:143
Alignment explanation
Indices: 12424--12739 Score: 356
Period size: 146 Copynumber: 2.2 Consensus size: 143
12414 TTTACTTTTT
12424 TAAA-ATCCTATTTATAAATT-TA-A-T-TTTATATAAATTACTTTTAGACAAAAATAATCATAT
1 TAAATATCCTATTTATAAATTATATATTATTTATATAAATTACTTTTAG--AAAAAT-AT--T-T
* * *
12484 TTTTAATATTTATTTATTTTTTAATATTAAAGAAAA-AGGTTGTCTTAAAGCAACTAGAAATCAT
60 TATTAATATTTATTTATTTTTAAATATT-AAGAAAAGA-GCTGTCTTAAAGCAACTAGAAATCAT
*
12548 TTTCTGATATTCTTAAATAAA
123 TTTCTGATATTCCTAAATAAA
* * * * *
12569 TAAATATCCTATTTTTATAAATTATATATTAATTTATTTTAATTATTTTTAGAGAAATGTTTTAT
1 TAAATATCCTA--TTTATAAATTATATATT-ATTTATATAAATTACTTTTAGAAAAATATTTTAT
* * * *
12634 TAATATTTATTTATTTTTAAATATTAAGAAATGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTCT
63 TAATATTTATTTATTTTTAAATATTAAGAAAAGAGCTGTCTTAAAGCAACTAGAAATCATTTTCT
12699 GATATTCCTAAATAAA
128 GATATTCCTAAATAAA
*
12715 TAAATATCTTATTTATAAAATTATA
1 TAAATATCCTATTTAT-AAATTATA
12740 AAAAATATAA
Statistics
Matches: 147, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
144 5 0.03
145 12 0.08
146 64 0.44
147 28 0.19
148 11 0.07
149 2 0.01
150 2 0.01
151 6 0.04
153 17 0.12
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (143 bp):
TAAATATCCTATTTATAAATTATATATTATTTATATAAATTACTTTTAGAAAAATATTTTATTAA
TATTTATTTATTTTTAAATATTAAGAAAAGAGCTGTCTTAAAGCAACTAGAAATCATTTTCTGAT
ATTCCTAAATAAA
Found at i:14696 original size:43 final size:44
Alignment explanation
Indices: 14635--14721 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
14625 TGGCTTTAGA
* *
14635 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
* *
14678 GAAGTTAGGACTGAAAGTTGTCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
14722 TGATGCACGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.34
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
Found at i:17422 original size:72 final size:72
Alignment explanation
Indices: 17335--17470 Score: 220
Period size: 72 Copynumber: 1.9 Consensus size: 72
17325 ATACAATAAA
*
17335 GCTTGATTTATCCCCCTAAAACAATTGGTTAATAGCCCC-AGCTTTATGGATAATATTCAGCTAA
1 GCTTGAGTTATCCCCCTAAAACAATTGGTTAATAGCCCCGA-CTTTATGGATAATATTCAGCTAA
17399 TCTGTTAT
65 TCTGTTAT
** *
17407 GCTTGAGTTATCCCCCTAAAGTAATTGGTTAATCGCCCCGACTTTATGGATAATATTCAGCTAA
1 GCTTGAGTTATCCCCCTAAAACAATTGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAA
17471 CCTATTATAC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 58 0.98
73 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (72 bp):
GCTTGAGTTATCCCCCTAAAACAATTGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAAT
CTGTTAT
Found at i:22747 original size:112 final size:112
Alignment explanation
Indices: 22586--22916 Score: 529
Period size: 112 Copynumber: 2.9 Consensus size: 112
22576 GATTCGGATC
* *
22586 CATCATTCGATGGATCAACATTCCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTGCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
22651 AGAATAATTTCATAATGAAAAGAACTTGTTCAACCTTTTTCTCAAATT
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATT
*
22699 CATCACTCGATGGATCAACATTGCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 CATCACTCGATGGATCAACATTGCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
22764 GAAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTTTGCTCGAATT
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATT
22811 CATCACTCGATGGATCAACATTGCCAAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGA
1 CATCACTCGATGGATCAACATTGCC-AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
22875 AGAAGAAGTTCATAATGAGAAGAACTCGTTTAATCTTTTGCT
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
22917 TGACTCCATT
Statistics
Matches: 203, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
112 145 0.71
113 58 0.29
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (112 bp):
CATCACTCGATGGATCAACATTGCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATT
Found at i:23015 original size:38 final size:39
Alignment explanation
Indices: 22964--23063 Score: 166
Period size: 38 Copynumber: 2.6 Consensus size: 39
22954 ATTTCCAGGT
22964 AGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGA
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
*
23002 AGAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGA
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
*
23041 ATAAGTTCATAATGAGAAGAACT
1 A-GAGTTCATAATGAGAAGAACT
23064 TGTTCAACCT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
38 31 0.53
39 7 0.12
40 20 0.34
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (39 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
Found at i:23518 original size:3 final size:3
Alignment explanation
Indices: 23506--23582 Score: 65
Period size: 3 Copynumber: 27.0 Consensus size: 3
23496 CATTTGTTTT
* *
23506 TTA TTA -TA TTA TTA TTA ATA TTA TT- TTA TT- TTA TT- TATA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* * *
23548 TTA TTT TTA TTT TTA -TA TTA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23583 AATAATATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
2 9 0.16
3 49 0.84
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:23529 original size:17 final size:17
Alignment explanation
Indices: 23507--23580 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
23497 ATTTGTTTTT
23507 TATTATATTATTATTAA
1 TATTATATTATTATTAA
*
23524 TATTATTTTATT-TT-A
1 TATTATATTATTATTAA
* * *
23539 TTTATACTATTATTTTTAT
1 TAT-TA-TATTATTATTAA
*
23558 TTTTATATTATTA-TAA
1 TATTATATTATTATTAA
23574 TTATTAT
1 -TATTAT
23581 TAAATAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
15 3 0.07
16 6 0.13
17 29 0.64
18 4 0.09
19 3 0.07
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATATTATTATTAA
Found at i:23539 original size:22 final size:23
Alignment explanation
Indices: 23503--23578 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 23
23493 ATCCATTTGT
*
23503 TTTTTATTATATTATTATTAATATTA
1 TTTTTATTTTA-T-TTA-TAATATTA
*
23529 -TTTTATTTTATTTATACTATTA
1 TTTTTATTTTATTTATAATATTA
*
23551 TTTTTATTTTTATATTATTATAATTA
1 TTTTTA-TTTTAT-TTATAAT-ATTA
23577 TT
1 TT
23579 ATTAAATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
22 7 0.17
23 8 0.19
24 7 0.17
25 14 0.33
26 6 0.14
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTATTTTATTTATAATATTA
Found at i:24464 original size:11 final size:11
Alignment explanation
Indices: 24448--24480 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
24438 TCTCTCTCCT
24448 AGAGAAAAAAA
1 AGAGAAAAAAA
24459 AGAGAAAAAAA
1 AGAGAAAAAAA
24470 A-AGAAAAAAA
1 AGAGAAAAAAA
24480 A
1 A
24481 ATTTGGCCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AGAGAAAAAAA
Found at i:24480 original size:10 final size:10
Alignment explanation
Indices: 24450--24481 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
24440 TCTCTCCTAG
24450 AGAAAAAAAA
1 AGAAAAAAAA
24460 GAGAAAAAAAA
1 -AGAAAAAAAA
24471 AGAAAAAAAA
1 AGAAAAAAAA
24481 A
1 A
24482 TTTGGCCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:25374 original size:10 final size:9
Alignment explanation
Indices: 25346--25372 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
25336 AATATCTTAT
25346 TTATAAAAA
1 TTATAAAAA
25355 TTATAAAAA
1 TTATAAAAA
25364 TTATAAAAA
1 TTATAAAAA
25373 ATAATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TTATAAAAA
Found at i:36530 original size:287 final size:287
Alignment explanation
Indices: 36014--36562 Score: 1098
Period size: 287 Copynumber: 1.9 Consensus size: 287
36004 ATGAATCATT
36014 GAGATGCCTCTTAAAGTCCGACTAATGTCAGGACGCCTCTCACTCTTACTAATACAACTTAGAGT
1 GAGATGCCTCTTAAAGTCCGACTAATGTCAGGACGCCTCTCACTCTTACTAATACAACTTAGAGT
36079 CATATCCAAATAATGTTGAGATACCTTTTCTACGGTGTCGAGATGCATTTGCATTGGCAAAGGGA
66 CATATCCAAATAATGTTGAGATACCTTTTCTACGGTGTCGAGATGCATTTGCATTGGCAAAGGGA
36144 AAGTTGACATTTTCCCATTTGTTTTCACTTTTCACCATGACAATAACCAAATCTCTTTGAGAGTG
131 AAGTTGACATTTTCCCATTTGTTTTCACTTTTCACCATGACAATAACCAAATCTCTTTGAGAGTG
36209 AAGAGATACATTCTATGTAGATAAGGGCTTAGAGAAACCTTTGCCCTATATCTTACTACAATAAC
196 AAGAGATACATTCTATGTAGATAAGGGCTTAGAGAAACCTTTGCCCTATATCTTACTACAATAAC
36274 TTAGATAAGGTCATTGATAGGAGTGAA
261 TTAGATAAGGTCATTGATAGGAGTGAA
36301 GAGATGCCTCTTAAAGTCCGACTAATGTCAGGACGCCTCTCACTCTTACTAATACAACTTAGAGT
1 GAGATGCCTCTTAAAGTCCGACTAATGTCAGGACGCCTCTCACTCTTACTAATACAACTTAGAGT
36366 CATATCCAAATAATGTTGAGATACCTTTTCTACGGTGTCGAGATGCATTTGCATTGGCAAAGGGA
66 CATATCCAAATAATGTTGAGATACCTTTTCTACGGTGTCGAGATGCATTTGCATTGGCAAAGGGA
36431 AAGTTGACATTTTCCCATTTGTTTTCACTTTTCACCATGACAATAACCAAATCTCTTTGAGAGTG
131 AAGTTGACATTTTCCCATTTGTTTTCACTTTTCACCATGACAATAACCAAATCTCTTTGAGAGTG
36496 AAGAGATACATTCTATGTAGATAAGGGCTTAGAGAAACCTTTGCCCTATATCTTACTACAATAAC
196 AAGAGATACATTCTATGTAGATAAGGGCTTAGAGAAACCTTTGCCCTATATCTTACTACAATAAC
36561 TT
261 TT
36563 TGCCACCCCT
Statistics
Matches: 262, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
287 262 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (287 bp):
GAGATGCCTCTTAAAGTCCGACTAATGTCAGGACGCCTCTCACTCTTACTAATACAACTTAGAGT
CATATCCAAATAATGTTGAGATACCTTTTCTACGGTGTCGAGATGCATTTGCATTGGCAAAGGGA
AAGTTGACATTTTCCCATTTGTTTTCACTTTTCACCATGACAATAACCAAATCTCTTTGAGAGTG
AAGAGATACATTCTATGTAGATAAGGGCTTAGAGAAACCTTTGCCCTATATCTTACTACAATAAC
TTAGATAAGGTCATTGATAGGAGTGAA
Found at i:36725 original size:19 final size:19
Alignment explanation
Indices: 36673--36726 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
36663 CTATCCTCCC
36673 CGAGAGAAGTCATCCTTTA
1 CGAGAGAAGTCATCCTTTA
* * *
36692 TGTGA-AATGTTATCCTTTA
1 CGAGAGAA-GTCATCCTTTA
36711 CGAGAGAAGTCATCCT
1 CGAGAGAAGTCATCCT
36727 CCGCGTGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
18 2 0.07
19 23 0.85
20 2 0.07
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (19 bp):
CGAGAGAAGTCATCCTTTA
Found at i:36746 original size:38 final size:38
Alignment explanation
Indices: 36646--36747 Score: 114
Period size: 38 Copynumber: 2.7 Consensus size: 38
36636 CATTTCTCTT
* * * ***
36646 ATCCTCCACATGAGATGCTATCCTCCCCGAGAGAAGTC
1 ATCCTCCACGTGAAATGTTATCCTTTACGAGAGAAGTC
** *
36684 ATCCTTTATGTGAAATGTTATCCTTTACGAGAGAAGTC
1 ATCCTCCACGTGAAATGTTATCCTTTACGAGAGAAGTC
*
36722 ATCCTCCGCGTGAAATGTTATCCTTT
1 ATCCTCCACGTGAAATGTTATCCTTT
36748 GTGAGATAAG
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (38 bp):
ATCCTCCACGTGAAATGTTATCCTTTACGAGAGAAGTC
Found at i:37164 original size:26 final size:26
Alignment explanation
Indices: 37134--37194 Score: 92
Period size: 23 Copynumber: 2.5 Consensus size: 26
37124 CTCAGAGGGA
37134 ACCGATTCCCCCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCCCCCAAGGGGGT
*
37160 ACCGATT---CCCCCCCTAAGGGGGT
1 ACCGATTCCCCCCCCCCCAAGGGGGT
37183 ACCGATTCCCCC
1 ACCGATTCCCCC
37195 TGAATGGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 22 0.71
26 9 0.29
ACGTcount: A:0.16, C:0.48, G:0.21, T:0.15
Consensus pattern (26 bp):
ACCGATTCCCCCCCCCCCAAGGGGGT
Found at i:37178 original size:23 final size:23
Alignment explanation
Indices: 37144--37194 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
37134 ACCGATTCCC
37144 CCCCCCCCAAGGGGGTACCGATT
1 CCCCCCCCAAGGGGGTACCGATT
*
37167 CCCCCCCTAAGGGGGTACCGATT
1 CCCCCCCCAAGGGGGTACCGATT
37190 CCCCC
1 CCCCC
37195 TGAATGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.16, C:0.47, G:0.24, T:0.14
Consensus pattern (23 bp):
CCCCCCCCAAGGGGGTACCGATT
Found at i:46365 original size:54 final size:54
Alignment explanation
Indices: 46283--46391 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
46273 CTTTTCAGGT
46283 TGCAATAAAAAAGGTTACAAATTTATATAATCTTTGAAGTTGAAAAGGATAACA
1 TGCAATAAAAAAGGTTACAAATTTATATAATCTTTGAAGTTGAAAAGGATAACA
46337 TGCAATAAAAAAGGTTACAAATTTATATAATCTTTGAAGTTGAAAAGGATAACA
1 TGCAATAAAAAAGGTTACAAATTTATATAATCTTTGAAGTTGAAAAGGATAACA
46391 T
1 T
46392 TTTAGGTTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (54 bp):
TGCAATAAAAAAGGTTACAAATTTATATAATCTTTGAAGTTGAAAAGGATAACA
Found at i:47041 original size:13 final size:13
Alignment explanation
Indices: 47020--47049 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
47010 ACTTTGTGAA
*
47020 TTGTGTCTCAAAG
1 TTGTATCTCAAAG
47033 TTGTATCTCAAAG
1 TTGTATCTCAAAG
47046 TTGT
1 TTGT
47050 TTCTAAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.43
Consensus pattern (13 bp):
TTGTATCTCAAAG
Found at i:49639 original size:12 final size:12
Alignment explanation
Indices: 49622--49649 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
49612 AACAAACGAT
49622 CACAACTGTAAG
1 CACAACTGTAAG
49634 CACAACTGTAAG
1 CACAACTGTAAG
49646 CACA
1 CACA
49650 GCCGTAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (12 bp):
CACAACTGTAAG
Found at i:52180 original size:707 final size:709
Alignment explanation
Indices: 49996--53051 Score: 3607
Period size: 707 Copynumber: 4.3 Consensus size: 709
49986 CCATCAAAGA
* * *
49996 TTTCATCTTTCATGATGAAAATTACACTAGTCATGGATTTAAATAGCGGTTACCGAAT-GTAATA
1 TTTCATCTTTCATGATGAACATTACACTAGTCATGGATTTAAATAGCGGTCACCG-ATCGCAATA
* * * * * *
50060 GCGTCCGTTAGATAGCGATAGCGGTGTCTTCCATAATCGTTATTGTATAACCGCTATACCTGAAA
65 GCGTCCGTTATATAGCGATAACGGTGTCTTCCACAACCGTTATTGTATAACCGCAATACCTGCAA
* * * * * * **
50125 TCATTGTAATAGCGTCTATTATGTACGCAATCGT-GATAAATGTATGTAACCGAAAATGTGACCA
130 TCATTGAAATAGCGTCTATTATGT-CGCAAT-TTCGATAAACGTACGTAACCGAAAACGCGACTG
* ** *
50189 CAAACATAATTTAGATCCGTGGTACTAGTGCTGCTTATCAA-ATGTTGAGACCCTTTGATCATTT
193 CAATCATAATTTAGATATGTGGTAC---T--TGCTTATCAACCT-TTGAGACCCTTTGATCATTT
* *
50253 TCATTTTATCGTCTCCTAGTGGAATATTGAGCCAATAATAACTCTTGGATAGTTTTTTCCATGGA
252 TCATTTTGTCGTCTCCTAGTGGAATATTGAGCCAATAAAAACTCTTGGATAGTTTTTTCCATGGA
* * *
50318 TTTCAATGAAGGATCATATGTTTATGCTTATGGGTTTTTCGGTGAGACTAG-AAAAATATAGTTG
317 TTTCAATGAAAGATCATATGTTTATGCTTATGGGTTTTTCGCTGAGACTAGAAAAAATAGAGTTG
* *
50382 AATTTAACTACAACACTTTGAGCAAAGTGTTGGTAGAAGTGGTGTATGCAAGACATTTTTTAAGG
382 AATTTAACTACAACACTTGGAGCAAAGTGTTGGTAGAAGTGGTGTATGCAAGACATATTTTAAGG
* * * * *
50447 CTAAGAGCTACGTTGAACAGGATAATATTTTAGGTTGAAAATCGTCTTAAATTAACTTTAAATTA
447 TTGAGAGCTATGTTGAACAGGATAATATTTTAGGTTGAAAACCTTCTTAAATTAACTTTAAATTA
* * *
50512 AGTTACCATGAAG-AGGAACTACCTGTATTAGCTACCAACATAGCTCTCAACTCTCCAATCTGTT
512 AGCTACCGTGAAGCA-GAACTACCTGTATTAGCTACCAACA-A---CTCAACTCTTCAATCTGTT
* * *
50576 TGGTCAGTTTTTCCACCTCTTCCCTTCCTTCTATCTT-ATTTGGATTTACAGGTTGGGGGATACA
572 TGGTCAGCTTTTCCACCTCTTCCCTTACTTCTATCTTCA-TTGGATTTACAGGTTGGGGGATATA
*
50640 CTTTTGATATTTACACTATGGTGGTTCGTGATAAGCTGTCTAGGAATTCAGAGCATTATTTCTAA
636 CTTTTGATATTTACACTATGGTGGTTCGTGATAAGCTGTCTAGAAATTCAGAGCATTATTTCTAA
50705 CATGTAGGG
701 CATGTAGGG
* * ** *
50714 TTTCATCTTTTATGATAAACATTACACTAGTCATGGATTTAAATAAAGGTCA-CGATCGTAATAG
1 TTTCATCTTTCATGATGAACATTACACTAGTCATGGATTTAAATAGCGGTCACCGATCGCAATAG
* * * * * * *
50778 CGTCTGTTATATAGCAATAGCGGTGTCTTTCGCAACCGTTATTGCATAACCACAATA-CTCGCAA
66 CGTCCGTTATATAGCGATAACGGTGTCTTCCACAACCGTTATTGTATAACCGCAATACCT-GCAA
** * * * * * * *
50842 TCATTGAAATAAAGTCTATTATGTCCGTAATTGCGATAAACGTACGTAAGCGAAAATGTGACCGT
130 TCATTGAAATAGCGTCTATTATGT-CGCAATTTCGATAAACGTACGTAACCGAAAACGCGACTGC
* * * *
50907 AACCATAATTTTGAT-TGTGGTACTGGTGTTGCTCATCAACCGTTGAGACCCTTTGATCATTTTC
194 AATCATAATTTAGATATGTGGTAC-----TTGCTTATCAACCTTTGAGACCCTTTGATCATTTTC
* * *
50971 ATTTTGTCGTCTCCTCGTGGAATATTGAGCCAATAAGAACTCTTGGATAGTTTTTTTTCATGGAT
254 ATTTTGTCGTCTCCTAGTGGAATATTGAGCCAATAAAAACTCTTGGATAG-TTTTTTCCATGGAT
* * *
51036 TTCGATGAAAGATCATATGTTTATGTTTATGGGTTCTTCGCTGAGACTAGAAAAAATAGAGTTGA
318 TTCAATGAAAGATCATATGTTTATGCTTATGGGTTTTTCGCTGAGACTAGAAAAAATAGAGTTGA
* * * *
51101 ATTTAACTACAACACTTTGAGCGAAGTGTTGGCAGAAGTGGTGTATG-GA-ACATATTTTTAAGG
383 ATTTAACTACAACACTTGGAGCAAAGTGTTGGTAGAAGTGGTGTATGCAAGACATA-TTTTAAGG
* * *
51164 TTGAGAGCTATGTTGAACATGATAATATTTTAGGTT-TAAA--TTGTCT-AATTAACTTTAAATT
447 TTGAGAGCTATGTTGAACAGGATAATATTTTAGGTTGAAAACCTTCT-TAAATTAACTTTAAATT
* *
51225 AAGCTCCCGTGAAGCAGAACTA-C----TT-G-T-------ACTCAACTCTTCAATTTGTTTGGT
511 AAGCTACCGTGAAGCAGAACTACCTGTATTAGCTACCAACAACTCAACTCTTCAATCTGTTTGGT
* * * * *
51276 CATCTTTTCCACCACTTTCCTTACTTCTATCTTCTTTGGATTTACAGGTTGGAGGATATACTTTT
576 CAGCTTTTCCACCTCTTCCCTTACTTCTATCTTCATTGGATTTACAGGTTGGGGGATATACTTTT
* * *
51341 GATATTTACACTATGGTGGTTCTTGATAAGATGTCTAGAAATTCAGAGCATTATTCCTAACATGT
641 GATATTTACACTATGGTGGTTCGTGATAAGCTGTCTAGAAATTCAGAGCATTATTTCTAACATGT
51406 AGGG
706 AGGG
* * * * *
51410 TTTCATCTTTCCTGATGAACAGTACACTAGTCATGGATTTAAATAGCGGTCACTGACCGCAATAA
1 TTTCATCTTTCATGATGAACATTACACTAGTCATGGATTTAAATAGCGGTCACCGATCGCAATAG
** * * ** * * *
51475 TATCCATTATATAGCGATAACGGTATCTTCCACAATTGTTATTGTATAACCACTATATCCAG-AA
66 CGTCCGTTATATAGCGATAACGGTGTCTTCCACAACCGTTATTGTATAACCGCAATA-CCTGCAA
* * ** *
51539 TCATTGCAATAGCGTTTATTATGTCTGCAATTTCGATAAACACACATAACCGAAAACGCGACTGC
130 TCATTGAAATAGCGTCTATTATGTC-GCAATTTCGATAAACGTACGTAACCGAAAACGCGACTGC
* * *
51604 AATCATAATTTAGATATGTGGTAC-TGCTTATCAACCTTTTAGACCCTTTGATTATTTTCAATTT
194 AATCATAATTTAGATATGTGGTACTTGCTTATCAACCTTTGAGACCCTTTGATCATTTTCATTTT
* * *
51668 GTCGTCTCCTAGTGGAATATTGAGCCAATAACAACTCTTGGATAGTTTTTTTTCCATGGATTACG
259 GTCGTCTCCTAGTGGAATATTGAGCCAATAAAAACTCTTGGATAG--TTTTTTCCATGGATTTCA
* * * *
51733 ATGAAAGATCATTTGTTTA-GATTATGGGTTTTTGGTTGAGACTAGAAAAAATAGAGTTGAATTT
322 ATGAAAGATCATATGTTTATGCTTATGGGTTTTTCGCTGAGACTAGAAAAAATAGAGTTGAATTT
*
51797 CACTACAACACTTGGAGCAAAGTGTTGGTAGAAGTGGTGTATGCAAGACATATTTTAAGGTTGAG
387 AACTACAACACTTGGAGCAAAGTGTTGGTAGAAGTGGTGTATGCAAGACATATTTTAAGGTTGAG
* * **
51862 AGCAATGTTGAACAGGATAATATTTTAGGTTGAAAACCTTCTTAAATTAAATTTAAAAGAAGCTA
452 AGCTATGTTGAACAGGATAATATTTTAGGTTGAAAACCTTCTTAAATTAACTTTAAATTAAGCTA
* * *
51927 CCGTAAAGCAGAATTACCTGTATTAGCTACCAAC-A-T-AACTCTTCAATCTGTTTTGTCAGCTT
517 CCGTGAAGCAGAACTACCTGTATTAGCTACCAACAACTCAACTCTTCAATCTGTTTGGTCAGCTT
* *
51989 TTCCTCCTCTTCCCTTACTTCTATCTTCATTGGATTTACAAGTTGGGGGATATACTTTTGATATT
582 TTCCACCTCTTCCCTTACTTCTATCTTCATTGGATTTACAGGTTGGGGGATATACTTTTGATATT
* * *
52054 TACACTATGGTAGTTCGTGCTAATCTGTCTAGAAATTCAGAGCATTATTTCTAACATGTAGGG
647 TACACTATGGTGGTTCGTGATAAGCTGTCTAGAAATTCAGAGCATTATTTCTAACATGTAGGG
* * * * *
52117 TTTCATATTTTATAATGAACATTATACTAGTCATGGATTTAAATAGCGGTCACCAATCGCAATAG
1 TTTCATCTTTCATGATGAACATTACACTAGTCATGGATTTAAATAGCGGTCACCGATCGCAATAG
* * ** ** *
52182 CGTCCGTTATATAGCGATATCGGTATCTTCTGCAACCGTTATTGTATAGTCGCAATACCCGCAAT
66 CGTCCGTTATATAGCGATAACGGTGTCTTCCACAACCGTTATTGTATAACCGCAATACCTGCAAT
* * * * *
52247 CATTAAAATAGTGTCTATTATGTACGCAATTGT-GATTAACGTACGTAACC-AAAACAC-AATCG
131 CATTGAAATAGCGTCTATTATGT-CGCAATT-TCGATAAACGTACGTAACCGAAAACGCGACT-G
* * * * *
52309 CAATCATAATTTAGATTAT-TGATACTAATGTTGTTCATCAACCATTGAGACCTTTTGATAATTT
193 CAATCATAATTTAGA-TATGTGGTACT--TG--CTT-ATCAACCTTTGAGACCCTTTGATCATTT
* * *
52373 TGATTTTGTCGTCTCCTAGTAGAATATTGAGCCAATAAAAACTCTTGGATAGTTTTTTCCAAGGA
252 TCATTTTGTCGTCTCCTAGTGGAATATTGAGCCAATAAAAACTCTTGGATAGTTTTTTCCATGGA
52438 TTTCAATGAAAGATCATATGTTTATGCTTATGGGTTTTTCGCTGAGACTAGAAAAAATAGAGTTG
317 TTTCAATGAAAGATCATATGTTTATGCTTATGGGTTTTTCGCTGAGACTAGAAAAAATAGAGTTG
*
52503 AGTTTAACTACAACACTTGGAGCAAAATGTTTGGAGCAAAATGTTGGTAGAAGTGGTGTATGCAA
382 AATTTAACTACAACACTTGGAGC--AA-------AG-----TGTTGGTAGAAGTGGTGTATGCAA
* *
52568 GGCATCTTTTAAGGTTGAGAGCTATGTTGAACAGGATAATATTTTAGGTTGAAAACCTTCTTAAA
433 GACATATTTTAAGGTTGAGAGCTATGTTGAACAGGATAATATTTTAGGTTGAAAACCTTCTTAAA
* *
52633 TTAACTTGAAATTAAGCTACCGTGAAGCAGAACTACCCGTATTAGCTACCAACATAGCTCTCAAC
498 TTAACTTTAAATTAAGCTACCGTGAAGCAGAACTACCTGTATTAGCTACCAACA-A---CTCAAC
* * *
52698 TCTTCAATCTGTTTGGTCAACTTTTCCACCTCTT-CC---CTTCTATCTTCTTTGGATTTTCAGG
559 TCTTCAATCTGTTTGGTCAGCTTTTCCACCTCTTCCCTTACTTCTATCTTCATTGGATTTACAGG
* ** * *
52759 TTGGGGGATATACTTTTGATATCTACACTATGGTGGTTTATGATAAGCTTTCTAGGAATTCAGAG
624 TTGGGGGATATACTTTTGATATTTACACTATGGTGGTTCGTGATAAGCTGTCTAGAAATTCAGAG
* *
52824 CATTATGTCTAACATGTAGAG
689 CATTATTTCTAACATGTAGGG
* *
52845 TTTCATCTTTCATGATGAACATTACACTAGTCATGGATTTAAATAGCGGTCACCGATCGTAATAT
1 TTTCATCTTTCATGATGAACATTACACTAGTCATGGATTTAAATAGCGGTCACCGATCGCAATAG
* * * *
52910 CGT-CGTTATATAGCAATAACAGTGTCTTCC-GAACCGTT-TCTGTATAACTGCAATACCTGCAA
66 CGTCCGTTATATAGCGATAACGGTGTCTTCCACAACCGTTAT-TGTATAACCGCAATACCTGCAA
* * *
52972 TCATT-ACAATAGCATCTATTATGTCCGCAATTACGATAAACGTACGTAACCGAAAACACGA-TC
130 TCATTGA-AATAGCGTCTATTATGT-CGCAATTTCGATAAACGTACGTAACCGAAAACGCGACT-
* *
53035 GCAATTATAGTTTAGAT
192 GCAATCATAATTTAGAT
53052 CCGTGGTATT
Statistics
Matches: 2002, Mismatches: 261, Indels: 142
0.83 0.11 0.06
Matches are distributed among these distances:
692 158 0.08
693 78 0.04
694 8 0.00
695 1 0.00
696 223 0.11
697 117 0.06
698 9 0.00
699 2 0.00
701 2 0.00
702 1 0.00
703 1 0.00
705 2 0.00
706 30 0.01
707 284 0.14
708 4 0.00
709 5 0.00
710 33 0.02
711 60 0.03
712 72 0.04
713 3 0.00
714 34 0.02
715 2 0.00
716 96 0.05
717 223 0.11
718 106 0.05
720 2 0.00
725 134 0.07
726 69 0.03
727 46 0.02
728 160 0.08
731 3 0.00
732 34 0.02
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (709 bp):
TTTCATCTTTCATGATGAACATTACACTAGTCATGGATTTAAATAGCGGTCACCGATCGCAATAG
CGTCCGTTATATAGCGATAACGGTGTCTTCCACAACCGTTATTGTATAACCGCAATACCTGCAAT
CATTGAAATAGCGTCTATTATGTCGCAATTTCGATAAACGTACGTAACCGAAAACGCGACTGCAA
TCATAATTTAGATATGTGGTACTTGCTTATCAACCTTTGAGACCCTTTGATCATTTTCATTTTGT
CGTCTCCTAGTGGAATATTGAGCCAATAAAAACTCTTGGATAGTTTTTTCCATGGATTTCAATGA
AAGATCATATGTTTATGCTTATGGGTTTTTCGCTGAGACTAGAAAAAATAGAGTTGAATTTAACT
ACAACACTTGGAGCAAAGTGTTGGTAGAAGTGGTGTATGCAAGACATATTTTAAGGTTGAGAGCT
ATGTTGAACAGGATAATATTTTAGGTTGAAAACCTTCTTAAATTAACTTTAAATTAAGCTACCGT
GAAGCAGAACTACCTGTATTAGCTACCAACAACTCAACTCTTCAATCTGTTTGGTCAGCTTTTCC
ACCTCTTCCCTTACTTCTATCTTCATTGGATTTACAGGTTGGGGGATATACTTTTGATATTTACA
CTATGGTGGTTCGTGATAAGCTGTCTAGAAATTCAGAGCATTATTTCTAACATGTAGGG
Found at i:52538 original size:14 final size:14
Alignment explanation
Indices: 52519--52547 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52509 ACTACAACAC
52519 TTGGAGCAAAATGT
1 TTGGAGCAAAATGT
52533 TTGGAGCAAAATGT
1 TTGGAGCAAAATGT
52547 T
1 T
52548 GGTAGAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (14 bp):
TTGGAGCAAAATGT
Found at i:55538 original size:2 final size:2
Alignment explanation
Indices: 55531--55566 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
55521 TTTTCCAAGA
55531 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
55567 GAATAAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56043 original size:19 final size:19
Alignment explanation
Indices: 56019--56055 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
56009 ATGACCAACA
*
56019 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
56038 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
56056 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:56173 original size:41 final size:41
Alignment explanation
Indices: 56128--56218 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
56118 AAATTCACGT
* *
56128 TGCGATTTTAGAAAATCGCAATGCGA-ATATA-TAAATCGCAA
1 TGCGATTTT-GAAAATCGCAACGCGATA-ATACAAAATCGCAA
* **
56169 TGCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAA
1 TGCGATTTTGAAAATCGCAACGCGATAATACAAAATCGCAA
56210 TGCGATTTT
1 TGCGATTTT
56219 CAAAGCGCCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
40 16 0.38
41 26 0.62
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (41 bp):
TGCGATTTTGAAAATCGCAACGCGATAATACAAAATCGCAA
Found at i:56855 original size:33 final size:34
Alignment explanation
Indices: 56803--56877 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
56793 TTAGTTTCAT
* ** *
56803 GTTGCGATTTTCTCATTGCGATTTTC-ATTTCGC
1 GTTGCGATTATCTCATTGCGATAGTCAAATTCGC
*
56836 GTTGCGATTATCTCGTTGCGATAGTCAAATTCGC
1 GTTGCGATTATCTCATTGCGATAGTCAAATTCGC
56870 GTTGCGAT
1 GTTGCGAT
56878 AGTCATTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 22 0.61
34 14 0.39
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (34 bp):
GTTGCGATTATCTCATTGCGATAGTCAAATTCGC
Found at i:56905 original size:20 final size:20
Alignment explanation
Indices: 56882--56920 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56872 TGCGATAGTC
*
56882 ATTTTCGTGTTTCGATTTTT
1 ATTTTCGTGTTGCGATTTTT
*
56902 ATTTTTGTGTTGCGATTTT
1 ATTTTCGTGTTGCGATTTT
56921 AAGTTTCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.08, G:0.18, T:0.64
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTT
Found at i:58538 original size:21 final size:21
Alignment explanation
Indices: 58514--58569 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
58504 TGGTGCATGG
* * *
58514 CGTGATGAGGTATCTACTTTA
1 CGTGATGAGGTAGCGACTCTA
*
58535 CGTGGTGAGGTAGCGACTCTA
1 CGTGATGAGGTAGCGACTCTA
58556 CGTGA-GATGGTAGC
1 CGTGATGA-GGTAGC
58570 ATCGTTGCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (21 bp):
CGTGATGAGGTAGCGACTCTA
Found at i:58862 original size:20 final size:20
Alignment explanation
Indices: 58839--58905 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
58829 GAAACTTAAA
58839 ATCGCAAAGCGAAAATGACT
1 ATCGCAAAGCGAAAATGACT
* *
58859 ATCGCAACGCGGAAATGACT
1 ATCGCAAAGCGAAAATGACT
** **
58879 ATCGCAATTCGAATTTGACT
1 ATCGCAAAGCGAAAATGACT
58899 ATCGCAA
1 ATCGCAA
58906 CGGGATAATC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAAAGCGAAAATGACT
Found at i:59057 original size:20 final size:20
Alignment explanation
Indices: 59034--59077 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
59024 ATTCGCATTT
59034 CGATAGTCATTTCCGAGTTG
1 CGATAGTCATTTCCGAGTTG
* *
59054 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTCCGAGTTG
59074 CGAT
1 CGAT
59078 TTTAAGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGATAGTCATTTCCGAGTTG
Found at i:59087 original size:20 final size:20
Alignment explanation
Indices: 59064--59108 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
59054 CGATAGTCAT
*
59064 TTTCGCGTTGCGATTTTAAG
1 TTTCACGTTGCGATTTTAAG
*
59084 TTTCATGTTGCGATTTTAAG
1 TTTCACGTTGCGATTTTAAG
59104 TTTCA
1 TTTCA
59109 GAAACTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.13, G:0.20, T:0.49
Consensus pattern (20 bp):
TTTCACGTTGCGATTTTAAG
Found at i:59680 original size:42 final size:42
Alignment explanation
Indices: 59586--59766 Score: 130
Period size: 42 Copynumber: 4.3 Consensus size: 42
59576 ACTCATATGT
* ** **
59586 CATCATTCAAGAGGCCTCT-CCTATCGTTCAAGAGGCCCCTAT
1 CATCATTCAAGAGGCCCCTACC-ATCACTCAAGAGGCCCCTCC
** * * * *
59628 CATCCCTCAAGAGTCCCCTCCCATCATTCAAGAGGCCTCTCC
1 CATCATTCAAGAGGCCCCTACCATCACTCAAGAGGCCCCTCC
* * * * *
59670 TATCGTTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCTCC
1 CATCATTCAAGAGGCCCCTACCATCACTCAAGAGGCCCCTCC
** ** * **
59712 CATCATTCAAGAGGCCCCTGTCATCGTTGAAGAGGTTCCTCC
1 CATCATTCAAGAGGCCCCTACCATCACTCAAGAGGCCCCTCC
*
59754 CACCATTCAAGAG
1 CATCATTCAAGAG
59767 CCCGATTCAC
Statistics
Matches: 110, Mismatches: 28, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
42 108 0.98
43 2 0.02
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.24
Consensus pattern (42 bp):
CATCATTCAAGAGGCCCCTACCATCACTCAAGAGGCCCCTCC
Found at i:59744 original size:21 final size:21
Alignment explanation
Indices: 59586--59746 Score: 128
Period size: 21 Copynumber: 7.7 Consensus size: 21
59576 ACTCATATGT
* *
59586 CATCATTCAAGAGGCCTCT-C
1 CATCGTTCAAGAGGCCCCTAC
*
59606 CTATCGTTCAAGAGGCCCCTAT
1 C-ATCGTTCAAGAGGCCCCTAC
** * *
59628 CATCCCTCAAGAGTCCCCTCC
1 CATCGTTCAAGAGGCCCCTAC
* *
59649 CATCATTCAAGAGGCCTCT-C
1 CATCGTTCAAGAGGCCCCTAC
*
59669 CTATCGTTCAAGAGGCCCCTAT
1 C-ATCGTTCAAGAGGCCCCTAC
** * *
59691 CATCCCTCAAGAGTCCCCTCC
1 CATCGTTCAAGAGGCCCCTAC
* **
59712 CATCATTCAAGAGGCCCCTGT
1 CATCGTTCAAGAGGCCCCTAC
*
59733 CATCGTTGAAGAGG
1 CATCGTTCAAGAGG
59747 TTCCTCCCAC
Statistics
Matches: 110, Mismatches: 27, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
20 3 0.03
21 105 0.95
22 2 0.02
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTAC
Found at i:59746 original size:63 final size:63
Alignment explanation
Indices: 59586--59727 Score: 284
Period size: 63 Copynumber: 2.3 Consensus size: 63
59576 ACTCATATGT
59586 CATCATTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCTCC
1 CATCATTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCTCC
59649 CATCATTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCTCC
1 CATCATTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCTCC
59712 CATCATTCAAGAGGCC
1 CATCATTCAAGAGGCC
59728 CCTGTCATCG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 79 1.00
ACGTcount: A:0.23, C:0.39, G:0.15, T:0.23
Consensus pattern (63 bp):
CATCATTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTATCATCCCTCAAGAGTCCCCTCC
Found at i:61334 original size:20 final size:20
Alignment explanation
Indices: 61295--61352 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
61285 AGGTACACTT
* *
61295 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGTCAAAA
* *
61315 TCGTAATGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
61335 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAAGTCAA
61353 TTCGTGTTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:61419 original size:20 final size:20
Alignment explanation
Indices: 61391--61541 Score: 188
Period size: 20 Copynumber: 7.8 Consensus size: 20
61381 GCAATTTTCT
* *
61391 CGTTTCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
61411 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
61431 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
61451 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
61471 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
61485 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
61505 CGTTGCGATGGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
61525 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
61542 GAATATGTAA
Statistics
Matches: 115, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
14 13 0.11
16 1 0.01
18 1 0.01
20 100 0.87
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:61482 original size:94 final size:94
Alignment explanation
Indices: 61342--61541 Score: 260
Period size: 94 Copynumber: 2.1 Consensus size: 94
61332 AAATCGCAAC
* * * * *
61342 GCGAAAGTC-AATTCGTGTTGCGATAGTCTAATACGCTTTGCAATTTTCT-CGTTTCGATAGTCA
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATACGCGTTGCAATTTT-TGCGTTGCGATAGTCA
61405 AATTCCCGTTGCGATAATCAAATTCACGTT
65 AATTCCCGTTGCGATAATCAAATTCACGTT
** *
61435 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTTGCGTTGCGATAGTCAA
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATACGCGTTGCAATTTTTGCGTTGCGATAGTCAA
* ** *
61500 ATTCGCGTTGCGATGGTCAAATTCGCGTT
66 ATTCCCGTTGCGATAATCAAATTCACGTT
*
61529 GCGATATTCAAAT
1 GCGATAGTCAAAT
61542 GAATATGTAA
Statistics
Matches: 92, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
93 9 0.10
94 83 0.90
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (94 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCAAATACGCGTTGCAATTTTTGCGTTGCGATAGTCAA
ATTCCCGTTGCGATAATCAAATTCACGTT
Found at i:61486 original size:14 final size:14
Alignment explanation
Indices: 61467--61493 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
61457 GATAGTCAAA
61467 TTTGCGTTGCGATT
1 TTTGCGTTGCGATT
61481 TTTGCGTTGCGAT
1 TTTGCGTTGCGAT
61494 AGTCAAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
TTTGCGTTGCGATT
Found at i:61496 original size:54 final size:54
Alignment explanation
Indices: 61431--61533 Score: 188
Period size: 54 Copynumber: 1.9 Consensus size: 54
61421 ATCAAATTCA
*
61431 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
*
61485 CGTTGCGATAGTCAAATTCGCGTTGCGATGGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
61534 ATTCAAATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.34
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:61767 original size:140 final size:140
Alignment explanation
Indices: 61515--61794 Score: 533
Period size: 140 Copynumber: 2.0 Consensus size: 140
61505 CGTTGCGATG
*
61515 GTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAAGAACTGAACAGATCATAG
1 GTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCATAG
61580 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAAT
66 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAAT
61645 ACACATAATA
131 ACACATAATA
* *
61655 GTCAAATTCGCGTTGCGATATTCAAATGAATGTGTTATAAGTGATAACAACTGAACAGATCATAG
1 GTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCATAG
61720 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAAT
66 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAAT
61785 ACACATAATA
131 ACACATAATA
61795 CAACGTTTGC
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (140 bp):
GTCAAATTCGCGTTGCGATATTCAAATGAATATGTAATAAGTGATAACAACTGAACAGATCATAG
CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAAT
ACACATAATA
Found at i:63871 original size:12 final size:14
Alignment explanation
Indices: 63838--63875 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
63828 CTCCCGTGGC
63838 ATTTTCTTCGGGGA
1 ATTTTCTTCGGGGA
63852 ATTTTCTTCGGGGA
1 ATTTTCTTCGGGGA
*
63866 TTTCTTCTTC
1 ATT-TTCTTC
63876 TTCTTCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.11, C:0.18, G:0.21, T:0.50
Consensus pattern (14 bp):
ATTTTCTTCGGGGA
Found at i:63875 original size:3 final size:3
Alignment explanation
Indices: 63867--63902 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
63857 CTTCGGGGAT
63867 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
63903 AGGGTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:65018 original size:21 final size:20
Alignment explanation
Indices: 64966--65020 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
64956 CGACAGTCAG
*
64966 AATCGCATTGCGATTTACAT
1 AATCGCATTGCGATTTACAA
* *
64986 ATTCGCATTGCGATTTTCTAA
1 AATCGCATTGCGATTTAC-AA
*
65007 AATCGCAATGCGAT
1 AATCGCATTGCGAT
65021 AGTCAAAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (20 bp):
AATCGCATTGCGATTTACAA
Found at i:66282 original size:18 final size:18
Alignment explanation
Indices: 66259--66299 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
66249 ATCATTGTAT
66259 ATTATAAAATAATTTAA-A
1 ATTATAAAA-AATTTAAGA
*
66277 ATTATAATAAATTTAAGA
1 ATTATAAAAAATTTAAGA
66295 ATTAT
1 ATTAT
66300 TTTATAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTATAAAAAATTTAAGA
Found at i:66648 original size:41 final size:41
Alignment explanation
Indices: 66603--66686 Score: 134
Period size: 41 Copynumber: 2.0 Consensus size: 41
66593 TATTGTTTAA
66603 CAATATTTTGACTTTAAGGATCACAAAATTAAAATAAAA-AG
1 CAATATTTTGACTTTAAGGATCA-AAAATTAAAATAAAATAG
* *
66644 CAATATTTTGACTTTAAGGGTCATAAATTAAAATAAAATAG
1 CAATATTTTGACTTTAAGGATCAAAAATTAAAATAAAATAG
66685 CA
1 CA
66687 TTATCAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 14 0.35
41 26 0.65
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.31
Consensus pattern (41 bp):
CAATATTTTGACTTTAAGGATCAAAAATTAAAATAAAATAG
Found at i:66697 original size:13 final size:13
Alignment explanation
Indices: 66679--66706 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
66669 AATTAAAATA
66679 AAATAGCATTATC
1 AAATAGCATTATC
66692 AAATAGCATTATC
1 AAATAGCATTATC
66705 AA
1 AA
66707 CTTTATCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (13 bp):
AAATAGCATTATC
Found at i:68798 original size:20 final size:20
Alignment explanation
Indices: 68773--68832 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
68763 TCGAGTTGCG
*
68773 ATTTTCGTATTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
68793 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
*
68813 ATTTTCGTGTTGCGATTTTC
1 ATTTTCGTGTTGCGAATTTC
68833 GTGTTACGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.52
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Done.