Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006940.1 Hibiscus syriacus cultivar Beakdansim tig00017824_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: 56989
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3799 original size:19 final size:19
Alignment explanation
Indices: 3777--3813 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3767 AAAAAATAAT
3777 GTAATTAAT-AATAATAAAA
1 GTAA-TAATAAATAATAAAA
3796 GTAATAATAAATAATAAA
1 GTAATAATAAATAATAAA
3814 GACCCGGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
GTAATAATAAATAATAAAA
Found at i:4574 original size:18 final size:19
Alignment explanation
Indices: 4533--4575 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
4523 TTTTTAATAT
*
4533 TAAAAAATAATTTTACAAA
1 TAAAAAATAATGTTACAAA
4552 TAAAAAATAA-GTTA-AAA
1 TAAAAAATAATGTTACAAA
4569 TGAAAAA
1 T-AAAAA
4576 CAATTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 8 0.36
19 10 0.45
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (19 bp):
TAAAAAATAATGTTACAAA
Found at i:4861 original size:20 final size:20
Alignment explanation
Indices: 4836--4949 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
4826 ATTTGGGAAA
*
4836 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
4856 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
4876 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
4897 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
4917 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
4937 TTCGCAACGCGAT
1 ATCGCAACGCGAT
4950 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:4881 original size:61 final size:60
Alignment explanation
Indices: 4815--4954 Score: 163
Period size: 61 Copynumber: 2.3 Consensus size: 60
4805 GAATAAGTAA
** * * * *
4815 ATCGCAACGCGATTTGGGAAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACT
1 ATCGCAACGCGATTT-ACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
* * * *
4876 ATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGAT-TTACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
*
4937 TTCGCAACGCGATTTACA
1 ATCGCAACGCGATTTACA
4955 TAGCGCCATT
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
60 4 0.06
61 60 0.92
62 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (60 bp):
ATCGCAACGCGATTTACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
Found at i:5525 original size:19 final size:18
Alignment explanation
Indices: 5463--5528 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 18
5453 TTCGAGAATG
5463 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGC-GAAAT
*
5482 AACTATCGCAACGCGAAAT
1 AA-AATCGCAACGCGAAAT
*
5501 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-T
5520 AAAATCGCA
1 AAAATCGCA
5529 TTGCGATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 14 0.33
19 18 0.43
20 10 0.24
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAT
Found at i:5546 original size:19 final size:19
Alignment explanation
Indices: 5524--5574 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
5514 GAAACCAAAA
*
5524 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5543 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5562 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5575 CTCTCGTCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5635 original size:32 final size:31
Alignment explanation
Indices: 5546--5641 Score: 113
Period size: 32 Copynumber: 3.0 Consensus size: 31
5536 TTTCATTTCG
**
5546 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGA-T-TCT
* * *
5579 CGTCGCGATAGTCA-TTCTCATTGCGATTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCT
5609 CGTTGCGATAGTCATTTCCGCGTTGCGATTCT
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCT
5641 C
1 C
5642 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 16 0.30
31 3 0.06
32 23 0.43
33 11 0.21
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (31 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCT
Found at i:5643 original size:20 final size:20
Alignment explanation
Indices: 5609--5666 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
5599 TTGCGATTCT
**
5609 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
5629 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
5649 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
5667 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:5791 original size:32 final size:28
Alignment explanation
Indices: 5720--5793 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 28
5710 AACTACTATT
5720 TATGTTTATTGTTTTTGGTATATCTTGA
1 TATGTTTATTGTTTTTGGTATATCTTGA
* *
5748 CA-GTGTA--GTTTTTGGTATATCTAACTTGA
1 TATGTTTATTGTTTTTGGTATA--T--CTTGA
5777 TATGTTTATTGTTTTTG
1 TATGTTTATTGTTTTTG
5794 TAGAAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
25 12 0.34
27 5 0.14
28 1 0.03
29 6 0.17
30 4 0.11
32 7 0.20
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57
Consensus pattern (28 bp):
TATGTTTATTGTTTTTGGTATATCTTGA
Found at i:7817 original size:21 final size:21
Alignment explanation
Indices: 7793--7943 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
7783 TCATTCCTCG
7793 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
7814 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
7835 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
7856 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
7877 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
7898 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
7919 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
7940 AGAG
1 AGAG
7944 CCCGATTCAC
Statistics
Matches: 86, Mismatches: 37, Indels: 15
0.62 0.27 0.11
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 78 0.91
22 3 0.03
23 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:7820 original size:42 final size:42
Alignment explanation
Indices: 7741--7943 Score: 194
Period size: 42 Copynumber: 4.8 Consensus size: 42
7731 GACTCGCCTG
* * * * * * * *
7741 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAAAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
7783 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * * * * * *
7825 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
7867 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
7909 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
7944 CCCGATTCAC
Statistics
Matches: 131, Mismatches: 28, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
41 4 0.03
42 125 0.95
43 2 0.02
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:7922 original size:84 final size:84
Alignment explanation
Indices: 7738--7913 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
7728 CCCGACTCGC
7738 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAAAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAAAGGCCCCTATCATTCCTCGAGAGTCCCCT
7803 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
*
7822 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAAAGGCCCCTATCATTCCTCGAGAGTCCCCT
7887 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
7906 CTGTCATC
1 CTGTCATC
7914 GTTGAAGAGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAAAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:7943 original size:84 final size:84
Alignment explanation
Indices: 7738--7943 Score: 288
Period size: 84 Copynumber: 2.5 Consensus size: 84
7728 CCCGACTCGC
* * * * *
7738 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAAAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
7803 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
7822 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
7887 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
7906 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
7944 CCCGATTCAC
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
84 109 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:9335 original size:14 final size:14
Alignment explanation
Indices: 9300--9326 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9290 ATTGTTTAAT
9300 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
9314 TGATTTGTAAAAG
1 TGATTTGTAAAAG
9327 TTTATTTGTT
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:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:9466 original size:19 final size:19
Alignment explanation
Indices: 9442--9488 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
9432 AAAAAGTACT
*
9442 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
9461 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
9480 ATCGCAACG
1 ATCGCAACG
9489 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:9535 original size:19 final size:19
Alignment explanation
Indices: 9513--9630 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
9503 CGAAATTAAA
9513 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
9532 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
9547 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
9565 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
9580 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
9598 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
9617 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
9631 AGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:9559 original size:33 final size:33
Alignment explanation
Indices: 9517--9610 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
9507 ATTAAATTCG
9517 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
9550 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
9583 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
9611 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:11919 original size:12 final size:12
Alignment explanation
Indices: 11902--11926 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11892 CTTCGGGGGA
11902 CTTTTTCTTCTT
1 CTTTTTCTTCTT
11914 CTTTTTCTTCTT
1 CTTTTTCTTCTT
11926 C
1 C
11927 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:12888 original size:21 final size:21
Alignment explanation
Indices: 12847--12916 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
12837 TTTTCCTAAT
**
12847 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGTAAA
12867 TCGCAATGCGAATTTGGTAAA
1 TCGCAATGCGAATTTGGTAAA
*
12888 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGTAAA
12909 TCGCAATG
1 TCGCAATG
12917 TGATACTGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 12 0.26
21 34 0.74
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGTAAA
Found at i:12993 original size:20 final size:20
Alignment explanation
Indices: 12904--12995 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
12894 TGCGAATTTG
* *
12904 GAAAATCGCAATGTGATACT
1 GAAAATCGCAACGAGATACT
** *
12924 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
12944 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
12965 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
12985 GAAAATCGCAA
1 GAAAATCGCAA
12996 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:13234 original size:20 final size:20
Alignment explanation
Indices: 13209--13276 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
13199 CAACGGGGAA
13209 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*** ***
13229 ATCGCAATTAG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
13249 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
13269 ATCGCAAC
1 ATCGCAAC
13277 TAGAAAATCG
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
19 5 0.15
20 24 0.71
21 5 0.15
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:13262 original size:40 final size:40
Alignment explanation
Indices: 13207--13282 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
13197 CGCAACGGGG
*
13207 AAATCGCAACGCGAAAATGGCTATCGCAATTAGAAATGAA
1 AAATCGCAACGCGAAAATGGCTATCGCAACTAGAAATGAA
13247 AAATCGCAACGCGAAAATGGCTATCGCAACTAGAAA
1 AAATCGCAACGCGAAAATGGCTATCGCAACTAGAAA
13283 ATCGCAATGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.16
Consensus pattern (40 bp):
AAATCGCAACGCGAAAATGGCTATCGCAACTAGAAATGAA
Found at i:13282 original size:20 final size:20
Alignment explanation
Indices: 13209--13284 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
13199 CAACGGGGAA
*
13209 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGAGAAAATGGCT
** ***
13229 ATCGCAATTAG-AAATGAAAA
1 ATCGCAACGAGAAAATG-GCT
*
13249 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGAGAAAATGGCT
*
13269 ATCGCAACTAGAAAAT
1 ATCGCAACGAGAAAAT
13285 CGCAATGCGA
Statistics
Matches: 40, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
19 5 0.12
20 30 0.75
21 5 0.12
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGAGAAAATGGCT
Found at i:13288 original size:34 final size:34
Alignment explanation
Indices: 13193--13296 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
13183 ATTCATTTGA
** *
13193 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACTAGAAAATCGCAACGCGAAAATGG
*
13227 CTATCGCAATTAGAAATGAAAAATCGCAACGCGAAAATGG
1 CTATCGCAACT----A-G-AAAATCGCAACGCGAAAATGG
*
13267 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACTAGAAAATCGCAACGCGAAA
13297 TGAAAATCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 25 0.43
35 1 0.02
36 1 0.02
39 1 0.02
40 30 0.52
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.15
Consensus pattern (34 bp):
CTATCGCAACTAGAAAATCGCAACGCGAAAATGG
Found at i:13327 original size:14 final size:16
Alignment explanation
Indices: 13307--13380 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
13297 TGAAAATCGC
13307 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
13322 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
13339 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
13358 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
13374 -TTGCGAT
1 ATTGCGAT
13381 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:13344 original size:19 final size:19
Alignment explanation
Indices: 13303--13370 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
13293 GAAATGAAAA
13303 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
13319 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
13336 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
13355 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
13371 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:13526 original size:14 final size:14
Alignment explanation
Indices: 13507--13543 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
13497 CATCAATTAA
13507 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
13521 ACAAATCATCTTTT
1 ACAAATCAACATTT
13535 ACAAATCAA
1 ACAAATCAA
13544 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:15431 original size:20 final size:19
Alignment explanation
Indices: 15408--15474 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
15398 GAAACTTAAA
15408 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
15428 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
15448 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
15467 ATCGCAAC
1 ATCGCAAC
15475 AACAAAATCG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.32
20 26 0.65
21 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:15516 original size:14 final size:14
Alignment explanation
Indices: 15497--15554 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
15487 ATGCGAAATG
*
15497 AAAATCACAACGAC
1 AAAATCGCAACGAC
*
15511 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
15527 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
15543 AAAATCGCAACG
1 AAAATCGCAACG
15555 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:15540 original size:32 final size:33
Alignment explanation
Indices: 15448--15559 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
15438 GGAAATGGCT
*
15448 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
15481 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
15514 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
15546 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
15560 CACAAATTAC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 28 0.37
33 47 0.63
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:15609 original size:14 final size:14
Alignment explanation
Indices: 15590--15645 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
15580 TCATTTCGCA
15590 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
15604 TTGCGATTTCATTTCG
1 TTGCGATTT--TGTCG
15620 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
15636 TTGCGATTTT
1 TTGCGATTTT
15646 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:15652 original size:33 final size:33
Alignment explanation
Indices: 15571--15657 Score: 167
Period size: 32 Copynumber: 2.7 Consensus size: 33
15561 ACAAATTACA
15571 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
15604 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
15636 TTGCGATTTTCATTTCGCATTG
1 TTGCGATTTTCATTTCGCATTG
15658 TGATAGCCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 32 0.60
33 21 0.40
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:15688 original size:20 final size:20
Alignment explanation
Indices: 15659--15700 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
15649 TTCGCATTGT
15659 GATAGCCATTTCCGTGTTGC
1 GATAGCCATTTCCGTGTTGC
* *
15679 GATAGTCATTTTCGTGTTGC
1 GATAGCCATTTCCGTGTTGC
15699 GA
1 GA
15701 AAGTAAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
GATAGCCATTTCCGTGTTGC
Found at i:16208 original size:18 final size:18
Alignment explanation
Indices: 16182--16226 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
16172 GTCGATCAGA
*
16182 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
16200 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
16218 TGATGGCTC
1 TGATGGCTC
16227 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:17595 original size:20 final size:20
Alignment explanation
Indices: 17547--17605 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
17537 AATAGTTTCT
** *
17547 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
17567 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
17587 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
17606 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:18185 original size:20 final size:20
Alignment explanation
Indices: 18079--18213 Score: 130
Period size: 20 Copynumber: 6.7 Consensus size: 20
18069 CACTTTGAAA
*
18079 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
18100 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
18120 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
18140 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
18161 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
18181 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
18201 ATCGCATTGCGAT
1 ATCGCATTGCGAT
18214 TTTCCCAATT
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
19 5 0.05
20 67 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:18185 original size:61 final size:61
Alignment explanation
Indices: 18079--18216 Score: 204
Period size: 61 Copynumber: 2.3 Consensus size: 61
18069 CACTTTGAAA
* * *
18079 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
* * * * *
18140 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
18201 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
18217 CCCAATTCGC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
Found at i:18232 original size:61 final size:61
Alignment explanation
Indices: 18079--18234 Score: 170
Period size: 61 Copynumber: 2.6 Consensus size: 61
18069 CACTTTGAAA
* ** * * *
18079 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
18140 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGT
18201 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
18235 TTACTTATTC
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
61 78 0.98
62 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGAATCGCATTGCGAAAGTCAGT
Found at i:18324 original size:21 final size:21
Alignment explanation
Indices: 18284--18324 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
18274 ACTGTAGACC
** *
18284 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
18305 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
18325 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:18671 original size:47 final size:48
Alignment explanation
Indices: 18587--18682 Score: 149
Period size: 47 Copynumber: 2.0 Consensus size: 48
18577 GTCTCAGCAA
*
18587 CGACTGGCGACCCAACCCTAGAACTCCAATCGCCTGATTTATCGCCAT
1 CGACTGGCGACCCAACCCTAGAACTCCAATCGCCTGATTTATCACCAT
* * *
18635 CGACTGGCGACCCAACTC-GGCACTCCAATCGCCTGATTTATCACCAT
1 CGACTGGCGACCCAACCCTAGAACTCCAATCGCCTGATTTATCACCAT
18682 C
1 C
18683 ATCTCCCAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 27 0.61
48 17 0.39
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.21
Consensus pattern (48 bp):
CGACTGGCGACCCAACCCTAGAACTCCAATCGCCTGATTTATCACCAT
Found at i:20437 original size:14 final size:14
Alignment explanation
Indices: 20420--20447 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20410 ATCATAACAA
20420 AATTATATAACTAT
1 AATTATATAACTAT
20434 AATTATATAACTAT
1 AATTATATAACTAT
20448 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:20522 original size:16 final size:16
Alignment explanation
Indices: 20501--20531 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20491 TTCTAATTTT
20501 TTTTTGAGTTCAAGTC
1 TTTTTGAGTTCAAGTC
20517 TTTTTGAGTTCAAGT
1 TTTTTGAGTTCAAGT
20532 TTCAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTTTGAGTTCAAGTC
Found at i:22083 original size:25 final size:25
Alignment explanation
Indices: 22055--22105 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
22045 TCATACAGAA
22055 TCTATTA-ATTATATATTCAATATAT
1 TCTATTATA-TATATATTCAATATAT
22080 TCTATTATATATATATTCAATATAT
1 TCTATTATATATATATTCAATATAT
22105 T
1 T
22106 TAAGTGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (25 bp):
TCTATTATATATATATTCAATATAT
Found at i:23737 original size:41 final size:40
Alignment explanation
Indices: 23683--23761 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
23673 AATCTTTTAG
* * * *
23683 ATTTATGATTTTTAGTTTGATTATTTTATTATTACTTTTTT
1 ATTTAGGACTTTTAATTTGATTATTTGATTATTA-TTTTTT
23724 ATTTAGGACTTTTAATTTGATTATTTGATTATTATTTT
1 ATTTAGGACTTTTAATTTGATTATTTGATTATTATTTT
23762 ATTAGGAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.65
Consensus pattern (40 bp):
ATTTAGGACTTTTAATTTGATTATTTGATTATTATTTTTT
Found at i:29401 original size:11 final size:11
Alignment explanation
Indices: 29385--29418 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
29375 TCATATCTAA
29385 TGTTTTGTTTT
1 TGTTTTGTTTT
29396 TGTTTTGTTTT
1 TGTTTTGTTTT
*
29407 TGTTTCGTTTT
1 TGTTTTGTTTT
29418 T
1 T
29419 ACCCCGTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.18, T:0.79
Consensus pattern (11 bp):
TGTTTTGTTTT
Found at i:35098 original size:43 final size:43
Alignment explanation
Indices: 35035--35117 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
35025 GTGATAAACA
*
35035 TTTTATATTTAGGATTTTTAGTTTGATTATTTTATTATTAACT
1 TTTTATATTCAGGATTTTTAGTTTGATTATTTTATTATTAACT
*
35078 TTTTTTATTCAGGATTTTTAGTTTGATTATTTTATTATTA
1 TTTTATATTCAGGATTTTTAGTTTGATTATTTTATTATTA
35118 TTTTATTAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.64
Consensus pattern (43 bp):
TTTTATATTCAGGATTTTTAGTTTGATTATTTTATTATTAACT
Found at i:41478 original size:622 final size:620
Alignment explanation
Indices: 40280--41486 Score: 1830
Period size: 622 Copynumber: 1.9 Consensus size: 620
40270 GTACTAAACT
*
40280 TTTAATTTGTTTTCAAATCGTACCTAATGTTTTGTTTTGGTTTCATTTTAGTACCCCGTTAAAAA
1 TTTAATTTGTTTTCAAATCATACCTAATGTTTTGTTTTGGTTTCATTTTA-TACCCCGTTAAAAA
* *
40345 CTTAACGTTAAGTTTTGAATTTTTTTTAAAAGTTTAGGTATTAAAACGGGCAAAAACTTATAGTT
65 CTTAACGTTAAGTTTTGAATTTTTTTTAAAAGTTTACGTATTAAAACGGGCAAAAACTGATAGTT
* *
40410 TAGGTACTAAACACATTACGTTTTTAACTGTGGGTACTAAAATGAAACAAAAATTAAATGTTAGG
130 TAGGTACTAAACACATTACGTTTTTAACTGTGGGTACTAAAATGAAACAAAAAATAAACGTTAGG
* *
40475 TATGATTTTCAAAAAATTGAAAGTTTAAGCATTAAAATGGACCAAAACTGATAGGTTAGGTACTA
195 TATGATTTTCAAAAAATTAAAAGTTTAAGCATTAAAATAGACCAAAACTGATAGGTTAGGTACTA
* * * **
40540 AATTTATAGTTTACCCTAGTTTTTAATGCATTATTGTTGCTTAATTCCACACTAATAATTGACTA
260 AAATTATAGTTTACCCAAGTTTTTAATGCATTATTGTTGCTCAAGCCCACACTAATAATTGACTA
40605 AAGACCTTTTAAGAATAATCATATTATTCTTATGATTTTATTAAAATGTAAGTAATTTATATATT
325 AAGACCTTTTAAGAATAATCATATTATTCTTATGATTTTATTAAAATGTAAGTAATTTATATATT
40670 CAAAAAAGTAATTGAAATAAAAATGACAGTATCTTATATTAATAAATAAGATAAAATATATCAAT
390 CAAAAAAGTAATTGAAATAAAAATGACAGTATCTTATATTAATAAATAAGATAAAATATATCAAT
* * * * * *
40735 GAGTGTTAGTACAAGTGGTTGTGATTCATGAATTTGAGTTTGTAAAACTAAGTTTGAATCCTACC
455 GAGTATTAGTACAAGTGGTTGAGATTCAAGAATTTGAGCTTGTAAAACTAAGTTCGAATACTACC
** * * * *
40800 ACCGTCACTCTTGGTGGGCAATCTGTAAATTCTTATATAAATCGCAATTGGGTCTTAGGTATGCC
520 ACCGTCACTCTTGAAGGGCAATCTATAAATTCTTACATAAATCACAATTAGGTCTTAGGTATGCC
40865 TTGGCCCTTAATTAGGGGAGCCATTATTGACCTAAA
585 TTGGCCCTTAATTAGGGGAGCCATTATTGACCTAAA
* *
40901 TTTAATTT-TTTTCCAAATCATACCTAATGTTTTGTTTTTGTTTCGTTTT-TACCCCGTTAAAAA
1 TTTAATTTGTTTT-CAAATCATACCTAATGTTTTGTTTTGGTTTCATTTTATACCCCGTTAAAAA
** *
40964 CTTAACGTTAAGTTTTGTTTTTTTTTTAAAAAGTTTACGTATTAAAACGGGCCAAAACTGATAGT
65 CTTAACGTTAAGTTTTGAATTTTTTTT-AAAAGTTTACGTATTAAAACGGGCAAAAACTGATAGT
* **
41029 TTAGGTACTAAATATGTT-CAGTTTTTAACTGTGGGTTACTAAAATGAAACAAAAAATAAACGTT
129 TTAGGTACTAAACACATTAC-GTTTTTAACTGTGGG-TACTAAAATGAAACAAAAAATAAACGTT
* * * ** *
41093 AGGTATGATTTTGAAAAAATTAAAAG-TTAAGGTATTAAAATATACCAAAGTTGATAGTTTAGGT
192 AGGTATGATTTTCAAAAAATTAAAAGTTTAA-GCATTAAAATAGACCAAAACTGATAGGTTAGGT
* * *
41157 ACTAAAATTGTAGTTTACCCAAATTTTTTAATGCATTATTGTTGGTCAAGCCCACACTAATAATT
256 ACTAAAATTATAGTTTACCC-AAGTTTTTAATGCATTATTGTTGCTCAAGCCCACACTAATAATT
* * *
41222 GACTAAAGATCTTTTAAGAATAATCGTATTATTCTTATGATTTTATTAAAATGTATGTAATTTAT
320 GACTAAAGACCTTTTAAGAATAATCATATTATTCTTATGATTTTATTAAAATGTAAGTAATTTAT
* * *
41287 ATATTCAAAAAAAGTAATTGGAA-AAAAGTGACAGTATCTTATATTAGTAAATAAGATAAAATAT
385 ATATTC-AAAAAAGTAATTGAAATAAAAATGACAGTATCTTATATTAATAAATAAGATAAAATAT
* **
41351 ATCAATGAGTATTAGTACAAGTGGTTGAGTTTCAAGAATTTGAGCTTGTAAGGCTAAGTTCGAAT
449 ATCAATGAGTATTAGTACAAGTGGTTGAGATTCAAGAATTTGAGCTTGTAAAACTAAGTTCGAAT
* * *
41416 ACTACCACTGTCACTCTTGAAGGGCAATCTATAAATTCTTCCATAAATTACAATTAGGTCTTAGG
514 ACTACCACCGTCACTCTTGAAGGGCAATCTATAAATTCTTACATAAATCACAATTAGGTCTTAGG
41481 TATGCC
579 TATGCC
41487 CTGATCCTGA
Statistics
Matches: 526, Mismatches: 53, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
619 40 0.08
620 72 0.14
621 136 0.26
622 263 0.50
623 15 0.03
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (620 bp):
TTTAATTTGTTTTCAAATCATACCTAATGTTTTGTTTTGGTTTCATTTTATACCCCGTTAAAAAC
TTAACGTTAAGTTTTGAATTTTTTTTAAAAGTTTACGTATTAAAACGGGCAAAAACTGATAGTTT
AGGTACTAAACACATTACGTTTTTAACTGTGGGTACTAAAATGAAACAAAAAATAAACGTTAGGT
ATGATTTTCAAAAAATTAAAAGTTTAAGCATTAAAATAGACCAAAACTGATAGGTTAGGTACTAA
AATTATAGTTTACCCAAGTTTTTAATGCATTATTGTTGCTCAAGCCCACACTAATAATTGACTAA
AGACCTTTTAAGAATAATCATATTATTCTTATGATTTTATTAAAATGTAAGTAATTTATATATTC
AAAAAAGTAATTGAAATAAAAATGACAGTATCTTATATTAATAAATAAGATAAAATATATCAATG
AGTATTAGTACAAGTGGTTGAGATTCAAGAATTTGAGCTTGTAAAACTAAGTTCGAATACTACCA
CCGTCACTCTTGAAGGGCAATCTATAAATTCTTACATAAATCACAATTAGGTCTTAGGTATGCCT
TGGCCCTTAATTAGGGGAGCCATTATTGACCTAAA
Found at i:47000 original size:42 final size:42
Alignment explanation
Indices: 46937--47017 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 42
46927 GTGATAAACA
*
46937 TTTTATATTTAGGATTTTAGTTTGATTA-TTTATTATTAACT
1 TTTTATATTCAGGATTTTAGTTTGATTATTTTATTATTAACT
*
46978 TTTTTTATTCAGGATTTTTAGTTTGATTATTTTATTATTA
1 TTTTATATTCAGGA-TTTTAGTTTGATTATTTTATTATTA
47018 TTTTATTAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 12 0.33
42 14 0.39
43 10 0.28
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (42 bp):
TTTTATATTCAGGATTTTAGTTTGATTATTTTATTATTAACT
Done.