Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007352.1 Hibiscus syriacus cultivar Beakdansim tig00019703_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: 70384
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3446 original size:22 final size:23
Alignment explanation
Indices: 3421--3479 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
3411 GGGTCATCTG
* *
3421 TAAGACCTACAGTGCAAGAT-GA
1 TAAGACCTACAGTGCAACATCCA
*
3443 TAAGACCT-CAGGGC--CATCCA
1 TAAGACCTACAGTGCAACATCCA
3463 TAAGACCTACAGTGCAA
1 TAAGACCTACAGTGCAA
3480 AATGTTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.07
20 9 0.31
21 10 0.34
22 8 0.28
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.17
Consensus pattern (23 bp):
TAAGACCTACAGTGCAACATCCA
Found at i:3545 original size:116 final size:116
Alignment explanation
Indices: 3341--3905 Score: 932
Period size: 116 Copynumber: 4.9 Consensus size: 116
3331 CTATTTCCCA
* *
3341 CATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAA
1 CATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
3406 CCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
66 CCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
* * *
3457 CATCCATAAGACCTACAGTGCAAAATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAGG
1 CATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
3522 CCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
66 CCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
* * * * *
3573 CATCCATAGGACCTACAGTGCAGGATATTTTCAAAAATCCTTTGGGAGCTTTTTGATATTTAAAG
1 CATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
*
3638 CCTCCGGGTCATTTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
66 CCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
* *
3689 CATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCCTTTTGATATTTAAAG
1 CATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
* * *
3754 CCTCTGGGTCATCTGTAAGACCTACAGTGCAAGATAATAAGACCTCAAGGC
66 CCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
* * * * *
3805 CATCCATAAGACCTAAAGTGCCAGATATTTTCAAAAAGCCTTCGGGATCTTTTTGATATTAAAAG
1 CATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
*
3870 CCTCCGGGTCATCTGTAAGACCTACAGTGCAGGATG
66 CCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATG
3906 TTTTCAAAAA
Statistics
Matches: 416, Mismatches: 33, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 416 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (116 bp):
CATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
CCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
Found at i:3681 original size:22 final size:21
Alignment explanation
Indices: 3653--3711 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
3643 GGGTCATTTG
3653 TAAGACCTACAGTGCAAGATGA
1 TAAGACCTACAGTGC-AGATGA
* * *
3675 TAAGACCT-CAGGGC-CATCCA
1 TAAGACCTACAGTGCAGAT-GA
3695 TAAGACCTACAGTGCAG
1 TAAGACCTACAGTGCAG
3712 GATGTTTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.07
20 9 0.31
21 10 0.34
22 8 0.28
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (21 bp):
TAAGACCTACAGTGCAGATGA
Found at i:3925 original size:190 final size:190
Alignment explanation
Indices: 3695--4087 Score: 637
Period size: 190 Copynumber: 2.1 Consensus size: 190
3685 GGGCCATCCA
* *
3695 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCCTTTTGATATTTAAAGCCTCTG
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCCTTTTGATATTTAAAACCTCCG
3760 GGTCATCTGTAAGACCTACAGTGCAAGATAATAAGACCTCAAGGCCATCCATAAGACCTAAAGTG
66 GGTCATCTGTAAGACCTACAGTGCAAGATAATAAGACCTCAAGGCCATCCATAAGACCTAAAGTG
* * * *
3825 CCA-GATATTTTCAAAAAGCCTTCGGGATCTTTTTGATA-TTAAAAGCCTCCGGGTCATCTG
131 -AAGGATATTTTCAAAAAGCCTTCAGGAGCTTTCTGATATTTAAAA-CCTCCGGGTCATCTG
*
3885 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCCG
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCCTTTTGATATTTAAAACCTCCG
* * * *
3950 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTTAGGGCCATCCATAAGACCTACAGTG
66 GGTCATCTGTAAGACCTACAGTGCAAGATAATAAGACCTCAAGGCCATCCATAAGACCTAAAGTG
* *
4015 AAGGATGTTTTCAAAAAGCCTTCATGAGCTTTCTGATATTTAAAACCTCCGGGTCATCTG
131 AAGGATATTTTCAAAAAGCCTTCAGGAGCTTTCTGATATTTAAAACCTCCGGGTCATCTG
4075 TAAGACCTACAGT
1 TAAGACCTACAGT
4088 AAAAGATGAT
Statistics
Matches: 188, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
189 1 0.01
190 181 0.96
191 6 0.03
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (190 bp):
TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCCTTTTGATATTTAAAACCTCCG
GGTCATCTGTAAGACCTACAGTGCAAGATAATAAGACCTCAAGGCCATCCATAAGACCTAAAGTG
AAGGATATTTTCAAAAAGCCTTCAGGAGCTTTCTGATATTTAAAACCTCCGGGTCATCTG
Found at i:3932 original size:74 final size:73
Alignment explanation
Indices: 3811--3979 Score: 268
Period size: 74 Copynumber: 2.3 Consensus size: 73
3801 AGGCCATCCA
* * *
3811 TAAGACCTAAAGTGCCAGATATTTTCAAAAAGCCTTCGGGATCTTTTTGATA-TTAAAAGCCTCC
1 TAAGACCTACAGTG-CAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAA-CCTCC
3875 GGGTCATCTG
64 GGGTCATCTG
3885 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCCG
1 TAAGACCTACAGTGCA-GATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCCG
3950 GGTCATCTG
65 GGTCATCTG
3959 TAAGACCTACAGTGCAAGATG
1 TAAGACCTACAGTGC-AGATG
3980 ATAAGACCTT
Statistics
Matches: 89, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
73 2 0.02
74 80 0.90
75 7 0.08
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (73 bp):
TAAGACCTACAGTGCAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCCGG
GTCATCTG
Found at i:3954 original size:306 final size:306
Alignment explanation
Indices: 3582--4211 Score: 987
Period size: 306 Copynumber: 2.1 Consensus size: 306
3572 CCATCCATAG
* * * *
3582 GACCTACAGTGCAGGATATTTTCAAAAATCCTTTGGGAGCTTTTTGATATTTAAAGCCTCCGGGT
1 GACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCCGGGT
* *
3647 CATTTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAG
66 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGAAG
* * *
3712 GATGTTTTCAAAAAGCCTTCGGGAGCCTTT-TGATATTTAAAGCCTCTGGGTCATCTGTAAGACC
131 GATGTTTTCAAAAAGCCTTCAGGAG-CTTTCTGATATTTAAAACCTCCGGGTCATCTGTAAGACC
**
3776 TACAGTGCAAGATAATAAGACCTCAAGGCCATCCATAAGACCTAAAGTGCCAG-ATATTTTCAAA
195 TACAGTAAAAGATAATAAGACCTCAAGGCCATCCATAAGACCTAAAGTG-CAGAATATTTTCAAA
*
3840 AAGCCTTCGGGATCTTTTTGATA-TTAAAAGCCTCCGGGTCATCTGTAA
259 AAGCCTTCGGGAACTTTTTGATATTTAAAA-CCTCCGGGTCATCTGTAA
3888 GACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCCGGGT
1 GACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCCGGGT
*
3953 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTTAGGGCCATCCATAAGACCTACAGTGAAG
66 CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGAAG
*
4018 GATGTTTTCAAAAAGCCTTCATGAGCTTTCTGATATTTAAAACCTCCGGGTCATCTGTAAGACCT
131 GATGTTTTCAAAAAGCCTTCAGGAGCTTTCTGATATTTAAAACCTCCGGGTCATCTGTAAGACCT
* * * * *
4083 ACAGTAAAAGATGATAAGACCTTAGGGCCATCCATAAGACCTACAGTGCAGAATGTTTTCAAAAA
196 ACAGTAAAAGATAATAAGACCTCAAGGCCATCCATAAGACCTAAAGTGCAGAATATTTTCAAAAA
* *
4148 GCCTTCGTGAACTTTTTGATATTTAAAACCTCTGGGTCATCTGTAA
261 GCCTTCGGGAACTTTTTGATATTTAAAACCTCCGGGTCATCTGTAA
* * * *
4194 AACATAAAGTGCAAGATG
1 GACCTACAGTGCAGGATG
4212 ATAAGACCTC
Statistics
Matches: 296, Mismatches: 25, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
305 7 0.02
306 283 0.96
307 6 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (306 bp):
GACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCCGGGT
CATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGAAG
GATGTTTTCAAAAAGCCTTCAGGAGCTTTCTGATATTTAAAACCTCCGGGTCATCTGTAAGACCT
ACAGTAAAAGATAATAAGACCTCAAGGCCATCCATAAGACCTAAAGTGCAGAATATTTTCAAAAA
GCCTTCGGGAACTTTTTGATATTTAAAACCTCCGGGTCATCTGTAA
Found at i:4094 original size:116 final size:116
Alignment explanation
Indices: 3885--4259 Score: 581
Period size: 116 Copynumber: 3.2 Consensus size: 116
3875 GGGTCATCTG
*
3885 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCCG
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGTGAGCTTTTTGATATTTAAAACCTCCG
3950 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTTAGGGCCATCCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTTAGGGCCATCCA
* * *
4001 TAAGACCTACAGTGAAGGATGTTTTCAAAAAGCCTTCATGAGCTTTCTGATATTTAAAACCTCCG
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGTGAGCTTTTTGATATTTAAAACCTCCG
**
4066 GGTCATCTGTAAGACCTACAGTAAAAGATGATAAGACCTTAGGGCCATCCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTTAGGGCCATCCA
* * *
4117 TAAGACCTACAGTGCAGAATGTTTTCAAAAAGCCTTCGTGAACTTTTTGATATTTAAAACCTCTG
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGTGAGCTTTTTGATATTTAAAACCTCCG
* * * * *
4182 GGTCATCTGTAAAACATAAAGTGCAAGATGATAAGACCTCAGGGCCATTCA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTTAGGGCCATCCA
* * * *
4233 TAAAACCT-CTGGGCAGAATGTTTTCAA
1 TAAGACCTACAGTGCAGGATGTTTTCAA
4260 CATTTCCATC
Statistics
Matches: 237, Mismatches: 22, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
115 17 0.07
116 220 0.93
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (116 bp):
TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGTGAGCTTTTTGATATTTAAAACCTCCG
GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTTAGGGCCATCCA
Found at i:4131 original size:422 final size:422
Alignment explanation
Indices: 3463--4240 Score: 1277
Period size: 422 Copynumber: 1.8 Consensus size: 422
3453 GGGCCATCCA
**
3463 TAAGACCTACAGTGCAAAATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAGGCCTCCG
1 TAAGACCTACAGTGCAAAATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAAACCTCCG
*
3528 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAGGACCTACAGTG
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTG
* * ** * * *
3593 CAGGATATTTTCAAAAATCCTTTGGGAGCTTTTTGATATTTAAAGCCTCCGGGTCATTTGTAAGA
131 AAGGATATTTTCAAAAAGCCTTCAGGAGCTTTCTGATATTTAAAACCTCCGGGTCATCTGTAAGA
** *
3658 CCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAA
196 CCTACAGTAAAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAGAATGTTTTCAA
* * * * *
3723 AAAGCCTTCGGGAGCCTTTTGATATTTAAAGCCTCTGGGTCATCTGTAAGACCTACAGTGCAAGA
261 AAAGCCTTCGGGAACCTTTTGATATTTAAAACCTCTGGGTCATCTGTAAAACATAAAGTGCAAGA
*
3788 TAATAAGACCTCAAGGCCATCCATAAGACCTAAAGTGCCAGATATTTTCAAAAAGCCTTCGGGAT
326 TAATAAGACCTCAAGGCCATCCATAAAACCTAAAGTGCCAGATATTTTCAAAAAGCCTTCGGGAT
3853 CTTTTTGATATTAAAAGCCTCCGGGTCATCTG
391 CTTTTTGATATTAAAAGCCTCCGGGTCATCTG
** *
3885 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAACCTCCG
1 TAAGACCTACAGTGCAAAATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAAACCTCCG
*
3950 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTTAGGGCCATCCATAAGACCTACAGTG
66 GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTG
* *
4015 AAGGATGTTTTCAAAAAGCCTTCATGAGCTTTCTGATATTTAAAACCTCCGGGTCATCTGTAAGA
131 AAGGATATTTTCAAAAAGCCTTCAGGAGCTTTCTGATATTTAAAACCTCCGGGTCATCTGTAAGA
*
4080 CCTACAGTAAAAGATGATAAGACCTTAGGGCCATCCATAAGACCTACAGTGCAGAATGTTTTCAA
196 CCTACAGTAAAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAGAATGTTTTCAA
* *
4145 AAAGCCTTCGTGAACTTTTTGATATTTAAAACCTCTGGGTCATCTGTAAAACATAAAGTGCAAGA
261 AAAGCCTTCGGGAACCTTTTGATATTTAAAACCTCTGGGTCATCTGTAAAACATAAAGTGCAAGA
* * *
4210 TGATAAGACCTCAGGGCCATTCATAAAACCT
326 TAATAAGACCTCAAGGCCATCCATAAAACCT
4241 CTGGGCAGAA
Statistics
Matches: 325, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
422 325 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (422 bp):
TAAGACCTACAGTGCAAAATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAAACCTCCG
GGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTG
AAGGATATTTTCAAAAAGCCTTCAGGAGCTTTCTGATATTTAAAACCTCCGGGTCATCTGTAAGA
CCTACAGTAAAAGATGATAAGACCTCAGGGCCATCCATAAGACCTACAGTGCAGAATGTTTTCAA
AAAGCCTTCGGGAACCTTTTGATATTTAAAACCTCTGGGTCATCTGTAAAACATAAAGTGCAAGA
TAATAAGACCTCAAGGCCATCCATAAAACCTAAAGTGCCAGATATTTTCAAAAAGCCTTCGGGAT
CTTTTTGATATTAAAAGCCTCCGGGTCATCTG
Found at i:4363 original size:15 final size:16
Alignment explanation
Indices: 4343--4373 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4333 TCATGTTTAC
4343 ACAAGAAT-GAGCAAA
1 ACAAGAATAGAGCAAA
4358 ACAAGAATAGAGCAAA
1 ACAAGAATAGAGCAAA
4374 GAGGGGCAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.61, C:0.13, G:0.19, T:0.06
Consensus pattern (16 bp):
ACAAGAATAGAGCAAA
Found at i:4419 original size:3 final size:3
Alignment explanation
Indices: 4411--4440 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4401 CATTTTACTT
4411 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4441 AATAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:7814 original size:32 final size:32
Alignment explanation
Indices: 7718--7814 Score: 99
Period size: 32 Copynumber: 3.1 Consensus size: 32
7708 ATTTATATAC
* * **
7718 CATGCTAAATAAAAGTC-GTCCAATGTGGACG
1 CATGCTAAATAAAAGCCACTCCAATGTGGGTG
* * *
7749 CATGATAAATAAAAGCCACT-CAATTTTGAGTG
1 CATGCTAAATAAAAGCCACTCCAA-TGTGGGTG
*
7781 CATGCTAAATAAAAACCACTCCAATGTGGGTG
1 CATGCTAAATAAAAGCCACTCCAATGTGGGTG
7813 CA
1 CA
7815 ATGTTGAGAT
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
31 18 0.35
32 31 0.60
33 3 0.06
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.24
Consensus pattern (32 bp):
CATGCTAAATAAAAGCCACTCCAATGTGGGTG
Found at i:8552 original size:79 final size:79
Alignment explanation
Indices: 8466--8706 Score: 369
Period size: 79 Copynumber: 3.1 Consensus size: 79
8456 ATAAAATATA
* * * * * *
8466 CTTTTATGCTAATAATGAACCCATATGCATTTCAACGATGACATCCTTAT-ATGCCAATAATGCA
1 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATCCTT-TCATGCCAATAATGCA
8530 CCCATATGCATTATT
65 CCCATATGCATTATT
*
8545 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGAAATCCTTTCATGCCAATAATGCAC
1 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATCCTTTCATGCCAATAATGCAC
8610 CCATATGCATTATT
66 CCATATGCATTATT
* * *
8624 CTTTTATACTGACAATTTACCCGTATACATTTCAGCTATGACATCCTTTCATGCCAATAATGCAC
1 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATCCTTTCATGCCAATAATGCAC
8689 CCATATGCATTA-T
66 CCATATGCATTATT
8702 CTTTT
1 CTTTT
8707 TCATTTGTTT
Statistics
Matches: 150, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
78 7 0.05
79 143 0.95
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (79 bp):
CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGACATCCTTTCATGCCAATAATGCAC
CCATATGCATTATT
Found at i:8553 original size:34 final size:34
Alignment explanation
Indices: 8515--8630 Score: 79
Period size: 34 Copynumber: 3.1 Consensus size: 34
8505 GACATCCTTA
8515 TATGCCAATAATGCACCCATATGCATTATTCTTT
1 TATGCCAATAATGCACCCATATGCATTATTCTTT
** * * *
8549 TATGCTGACAATGTACCCATATACATTTCAGCTATGAAATCCTTT
1 TATGCCAATAATGCACCCATATGCA--T----TAT----T-CTTT
*
8594 CATGCCAATAATGCACCCATATGCATTATTCTTT
1 TATGCCAATAATGCACCCATATGCATTATTCTTT
8628 TAT
1 TAT
8631 ACTGACAATT
Statistics
Matches: 59, Mismatches: 12, Indels: 22
0.63 0.13 0.24
Matches are distributed among these distances:
34 26 0.44
35 1 0.02
36 1 0.02
39 3 0.05
40 3 0.05
43 1 0.02
44 1 0.02
45 23 0.39
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.37
Consensus pattern (34 bp):
TATGCCAATAATGCACCCATATGCATTATTCTTT
Found at i:9248 original size:22 final size:23
Alignment explanation
Indices: 9204--9248 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
9194 TTGGTATCGA
*
9204 TACCCTTACCATGGTATCAATAC
1 TACCCTTACCATGGTACCAATAC
* *
9227 TACCC-TACTATGGTACCGATAC
1 TACCCTTACCATGGTACCAATAC
9249 CCCTTTATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.29
Consensus pattern (23 bp):
TACCCTTACCATGGTACCAATAC
Found at i:9363 original size:96 final size:95
Alignment explanation
Indices: 9163--9341 Score: 227
Period size: 96 Copynumber: 1.9 Consensus size: 95
9153 CTTCCTCCGG
*
9163 GTATCGATACCAAAATTAGGTTCGATGTTTCTTGGTATCGATACCCTTACCATGGTATCAATACT
1 GTATCGATACCAAAATTAGGTTCGATGTTTCTTGGTATCGATACCCTTACAATGGTATCAATACT
* * * * * *
9228 ACCCTACTATGGTACCGATACCCCTTTATG
66 ACCATACAACGGTACCGATACCCATTAATA
* **
9258 GTATCGATACCAAAATTAGTTTCGATGTTTGCTTGGTATCGATACCCTTACAATGGTATTGATAC
1 GTATCGATACCAAAATTAGGTTCGATGTTT-CTTGGTATCGATACCCTTACAATGGTATCAATAC
* *
9323 T-TCAT-CAACGGTATCGATA
65 TACCATACAACGGTACCGATA
9342 TTGATTGAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
94 11 0.15
95 31 0.42
96 32 0.43
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (95 bp):
GTATCGATACCAAAATTAGGTTCGATGTTTCTTGGTATCGATACCCTTACAATGGTATCAATACT
ACCATACAACGGTACCGATACCCATTAATA
Found at i:15709 original size:78 final size:79
Alignment explanation
Indices: 15504--15823 Score: 489
Period size: 79 Copynumber: 4.1 Consensus size: 79
15494 ATAAAATATA
* * * * * *
15504 CTTTTATGCTAATAATGCACCCATATGCATTTCAGCGATGGAATCCTTTCATGCCAATAATGCAC
1 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCAC
* *
15569 CCATACGCGTTATT
66 CCATATGCATTATT
* * *
15583 CTTTTATGCTGACAATGTACCCGTACACATTTCAGCTATGGCAACCTTTCATGCCAATAATGCAC
1 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCAC
15648 CCATATGCATTATT
66 CCATATGCATTATT
15662 CTTTTA-GCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCAC
1 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCAC
15726 CCATATGCATTATT
66 CCATATGCATTATT
* * * *
15740 CTTTTATACTGACAATGTACCCATATACATTTCAGCTATGACATCCTTTCATGCTACTAATGCAC
1 CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCAC
15805 CCATATGCATTATT
66 CCATATGCATTATT
*
15819 TTTTT
1 CTTTT
15824 TCATTCGTTT
Statistics
Matches: 221, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
78 75 0.34
79 146 0.66
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (79 bp):
CTTTTATGCTGACAATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCAC
CCATATGCATTATT
Found at i:15808 original size:157 final size:157
Alignment explanation
Indices: 15517--15823 Score: 488
Period size: 157 Copynumber: 2.0 Consensus size: 157
15507 TTATGCTAAT
* *
15517 AATGCACCCATATGCATTTCAGCGATGGAATCCTTTCATGCCAATAATGCACCCATACGCGTTAT
1 AATGCACCCATATACATTTCAGCGATGGAATCCTTTCATGCCAATAATGCACCCATACGCATTAT
* * *
15582 TCTTTTATGCTGACAATGTACCCGTACACATTTCAGCTATGGCAACCTTTCATGCCAATAATGCA
66 TCTTTTATACTGACAATGTACCCATACACATTTCAGCTATGACAACCTTTCATGCCAATAATGCA
15647 CCCATATGCATTATTCTTTTAGCTGAC
131 CCCATATGCATTATTCTTTTAGCTGAC
* * * *
15674 AATGTACCCATATACATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTAT
1 AATGCACCCATATACATTTCAGCGATGGAATCCTTTCATGCCAATAATGCACCCATACGCATTAT
* * * *
15739 TCTTTTATACTGACAATGTACCCATATACATTTCAGCTATGACATCCTTTCATGCTACTAATGCA
66 TCTTTTATACTGACAATGTACCCATACACATTTCAGCTATGACAACCTTTCATGCCAATAATGCA
*
15804 CCCATATGCATTATTTTTTT
131 CCCATATGCATTATTCTTTT
15824 TCATTCGTTT
Statistics
Matches: 136, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
157 136 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (157 bp):
AATGCACCCATATACATTTCAGCGATGGAATCCTTTCATGCCAATAATGCACCCATACGCATTAT
TCTTTTATACTGACAATGTACCCATACACATTTCAGCTATGACAACCTTTCATGCCAATAATGCA
CCCATATGCATTATTCTTTTAGCTGAC
Found at i:16308 original size:19 final size:19
Alignment explanation
Indices: 16260--16301 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
16250 TCAATACTAT
*
16260 GGTACCGATACTTTCTCCG
1 GGTACCGATACTTCCTCCG
16279 GGTACCGATACTTCCTCCG
1 GGTACCGATACTTCCTCCG
16298 GGTA
1 GGTA
16302 TCTATACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.31, G:0.24, T:0.29
Consensus pattern (19 bp):
GGTACCGATACTTCCTCCG
Found at i:16471 original size:20 final size:20
Alignment explanation
Indices: 16448--16500 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
16438 CCCTTACAAT
16448 GGTATCGATACTGCCTCAAC
1 GGTATCGATACTGCCTCAAC
16468 GGTATCGATACTGCCTCAAC
1 GGTATCGATACTGCCTCAAC
16488 GGTATCGATACTG
1 GGTATCGATACTG
16501 ATTGAATCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (20 bp):
GGTATCGATACTGCCTCAAC
Found at i:21006 original size:12 final size:11
Alignment explanation
Indices: 20989--21022 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
20979 TGCTATTTTT
20989 AAAAAACAAAA
1 AAAAAACAAAA
21000 CAAAAAACAAAA
1 -AAAAAACAAAA
*
21012 AAAAACCAAAA
1 AAAAAACAAAA
21023 TTTCAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:25722 original size:19 final size:20
Alignment explanation
Indices: 25688--25732 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
25678 AAAAACAAAA
* *
25688 AAAAAAGAACAAAAAAAGGC
1 AAAAAACAACAAAAAAAGCC
25708 AAAAAACAA-AAAAAAAGCC
1 AAAAAACAACAAAAAAAGCC
25727 AAAAAA
1 AAAAAA
25733 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (20 bp):
AAAAAACAACAAAAAAAGCC
Found at i:26834 original size:16 final size:16
Alignment explanation
Indices: 26813--26846 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
26803 TAAAGGTCCT
26813 AAATAACTAATAAA-TA
1 AAATAA-TAATAAACTA
26829 AAATAATAATAAACTA
1 AAATAATAATAAACTA
26845 AA
1 AA
26847 CATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAATAATAAACTA
Found at i:30642 original size:1 final size:1
Alignment explanation
Indices: 30638--30692 Score: 65
Period size: 1 Copynumber: 55.0 Consensus size: 1
30628 CTTTTTTGGC
* * * * *
30638 TTTTTTTGTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTGTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
30693 GAAAAAAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:30642 original size:10 final size:10
Alignment explanation
Indices: 30629--30692 Score: 76
Period size: 10 Copynumber: 6.5 Consensus size: 10
30619 AAATTTTGGC
*
30629 TTTTTTGGCT
1 TTTTTTGGTT
*
30639 TTTTTTGTTT
1 TTTTTTGGTT
*
30649 TTTTTTGTTT
1 TTTTTTGGTT
*
30659 TTTTTTGTTT
1 TTTTTTGGTT
*
30669 TTTTTTTGTT
1 TTTTTTGGTT
30679 TTTTTT-GTT
1 TTTTTTGGTT
30688 TTTTT
1 TTTTT
30693 GAAAAAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
9 8 0.16
10 42 0.84
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (10 bp):
TTTTTTGGTT
Found at i:30650 original size:9 final size:10
Alignment explanation
Indices: 30638--30692 Score: 94
Period size: 10 Copynumber: 5.5 Consensus size: 10
30628 CTTTTTTGGC
30638 TTTTTTTGTT
1 TTTTTTTGTT
30648 TTTTTTTGTT
1 TTTTTTTGTT
30658 TTTTTTTGTT
1 TTTTTTTGTT
30668 TTTTTTT-TGT
1 TTTTTTTGT-T
30678 TTTTTTTGTT
1 TTTTTTTGTT
30688 TTTTT
1 TTTTT
30693 GAAAAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
9 1 0.02
10 41 0.95
11 1 0.02
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:30654 original size:20 final size:20
Alignment explanation
Indices: 30629--30692 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
30619 AAATTTTGGC
*
30629 TTTTTTGGCTTTTTTTGTTT
1 TTTTTTGGTTTTTTTTGTTT
*
30649 TTTTTTGTTTTTTTTTGTTT
1 TTTTTTGGTTTTTTTTGTTT
*
30669 TTTTTTTGTTTTTTTTGTTT
1 TTTTTTGGTTTTTTTTGTTT
30689 TTTT
1 TTTT
30693 GAAAAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (20 bp):
TTTTTTGGTTTTTTTTGTTT
Found at i:31067 original size:15 final size:16
Alignment explanation
Indices: 31047--31083 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
31037 GATTAGAATA
31047 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
*
31062 AAATAAACAGAAGATG
1 AAATAAACAAAAGATG
31078 AAATAA
1 AAATAA
31084 GATAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:31569 original size:25 final size:22
Alignment explanation
Indices: 31540--31585 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31530 TTTTTAACCC
31540 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
31565 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
31586 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:37979 original size:24 final size:24
Alignment explanation
Indices: 37949--38021 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
37939 AAACATAATT
* * *
37949 CAGGTCAAGTAGCAAATCAGAATC
1 CAGGTCAAGTATCATATCAAAATC
* * *
37973 CATGTCATGTATCATATAAAAATC
1 CAGGTCAAGTATCATATCAAAATC
37997 CAGGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCATATCAAAATC
38021 C
1 C
38022 CGTCAAAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAAAATC
Found at i:38786 original size:17 final size:18
Alignment explanation
Indices: 38761--38815 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
38751 TTCAAAATAA
38761 TTTCTAAAATATCACCAT
1 TTTCTAAAATATCACCAT
38779 TTTC--AAA-AT-A--A-
1 TTTCTAAAATATCACCAT
38790 TTTCTAAAATATCACCAT
1 TTTCTAAAATATCACCAT
38808 TTTC-AAAA
1 TTTCTAAAA
38816 CAATTACCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 15
0.67 0.00 0.33
Matches are distributed among these distances:
11 4 0.13
12 1 0.03
13 3 0.10
14 3 0.10
15 3 0.10
16 3 0.10
17 5 0.17
18 8 0.27
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTCTAAAATATCACCAT
Found at i:38894 original size:28 final size:29
Alignment explanation
Indices: 38741--38946 Score: 206
Period size: 29 Copynumber: 7.2 Consensus size: 29
38731 TTTACATAAT
* *
38741 TATCATCATTTTCAAAATAATTTCTAAAA
1 TATCACCATTTTCAAAATAATTACTAAAA
*
38770 TATCACCATTTTCAAAATAATTTCTAAAA
1 TATCACCATTTTCAAAATAATTACTAAAA
* *
38799 TATCACCATTTTCAAAACAATTACCAAAA
1 TATCACCATTTTCAAAATAATTACTAAAA
* ** *
38828 TGTCACTTTTTTTAAAA-AATTA-TGAAAA
1 TATCACCATTTTCAAAATAATTACT-AAAA
* * *
38856 TATCA--ATTTTTAAAAAAATTACAAAAA
1 TATCACCATTTTCAAAATAATTACTAAAA
* * *
38883 TAGCACCATTTTCAAAATAATGACCAAAA
1 TATCACCATTTTCAAAATAATTACTAAAA
* *
38912 TACCACCATTTT-GAAATAATTACTAAAA
1 TATCACCATTTTCAAAATAATTACTAAAA
*
38940 TACCACC
1 TATCACC
38947 CGGTCAACGG
Statistics
Matches: 151, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
26 9 0.06
27 13 0.09
28 33 0.22
29 96 0.64
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.33
Consensus pattern (29 bp):
TATCACCATTTTCAAAATAATTACTAAAA
Found at i:38933 original size:84 final size:85
Alignment explanation
Indices: 38747--38941 Score: 214
Period size: 84 Copynumber: 2.3 Consensus size: 85
38737 TAATTATCAT
* * * * * *
38747 CATTTTCAAAATAATTTCTAAAATATCACCATTTTCAAAATAATTTCTAAAATATCACCATTTTC
1 CATTTTGAAAA-AATTACTAAAATATCA-CATTTTCAAAAAAATTACAAAAATAGCACCATTTTC
* **
38812 AAAACAATTACCAAAATGTCAC
64 AAAACAATGACCAAAATACCAC
** * *
38834 TTTTTTTAAAAAATTA-TGAAAATATCA-ATTTTTAAAAAAATTACAAAAATAGCACCATTTTCA
1 CATTTTGAAAAAATTACT-AAAATATCACATTTTCAAAAAAATTACAAAAATAGCACCATTTTCA
*
38897 AAATAATGACCAAAATACCAC
65 AAACAATGACCAAAATACCAC
*
38918 CATTTTGAAATAATTACTAAAATA
1 CATTTTGAAAAAATTACTAAAATA
38942 CCACCCGGTC
Statistics
Matches: 89, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
84 66 0.74
85 2 0.02
86 13 0.15
87 8 0.09
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (85 bp):
CATTTTGAAAAAATTACTAAAATATCACATTTTCAAAAAAATTACAAAAATAGCACCATTTTCAA
AACAATGACCAAAATACCAC
Found at i:38978 original size:5 final size:5
Alignment explanation
Indices: 38968--38992 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38958 CAACGTTCAA
38968 CGGGT CGGGT CGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT CGGGT
38993 TGGAATTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
CGGGT
Found at i:45237 original size:24 final size:24
Alignment explanation
Indices: 45199--45269 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
45189 AACATAATTC
* *
45199 AGGTCAAGTAGCATATCAGAATCT
1 AGGTCAAGTATCATATCAAAATCT
* * *
45223 ATGTCATGTATCATATAAAAATCT
1 AGGTCAAGTATCATATCAAAATCT
45247 AGGTCAAGTATCATATCAAAATC
1 AGGTCAAGTATCATATCAAAATC
45270 CCGTCAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (24 bp):
AGGTCAAGTATCATATCAAAATCT
Found at i:46018 original size:29 final size:29
Alignment explanation
Indices: 45980--46158 Score: 184
Period size: 29 Copynumber: 6.2 Consensus size: 29
45970 TTTACACAAT
* * *
45980 TATCACCATTTTCAAAATAATTTCTACAA
1 TATCACCATTTTCAAAATAATTACCAAAA
**
46009 TATCACCATTTTCAAACCAATTACCAAAA
1 TATCACCATTTTCAAAATAATTACCAAAA
* * *
46038 TATCA-CTTTTTTAAAATAAATTACAAAAA
1 TATCACCATTTTCAAAAT-AATTACCAAAA
* * *
46067 TATCAAC-TTTT-AAAAAAATTACGAAAA
1 TATCACCATTTTCAAAATAATTACCAAAA
* *
46094 TAGCACCATTTTCGAAATAATTACCAAAA
1 TATCACCATTTTCAAAATAATTACCAAAA
* *
46123 TACCACCATTTTCGAAATAATTACCAAAA
1 TATCACCATTTTCAAAATAATTACCAAAA
*
46152 TACCACC
1 TATCACC
46159 CGGTCAACGT
Statistics
Matches: 128, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 15 0.12
28 16 0.12
29 96 0.75
30 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (29 bp):
TATCACCATTTTCAAAATAATTACCAAAA
Found at i:47063 original size:34 final size:34
Alignment explanation
Indices: 47020--47099 Score: 124
Period size: 34 Copynumber: 2.3 Consensus size: 34
47010 TGAAAATGTG
47020 TGATGAAAACATCATAACTTTTGGAGGCACCTTTT
1 TGAT-AAAACATCATAACTTTTGGAGGCACCTTTT
* *
47055 TGATAAAACATCATGACTTTTGGAGGTACCTTTT
1 TGATAAAACATCATAACTTTTGGAGGCACCTTTT
*
47089 AGATAAAACAT
1 TGATAAAACAT
47100 GTCTTTTGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 38 0.90
35 4 0.10
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (34 bp):
TGATAAAACATCATAACTTTTGGAGGCACCTTTT
Found at i:47333 original size:43 final size:42
Alignment explanation
Indices: 47285--47575 Score: 296
Period size: 43 Copynumber: 6.8 Consensus size: 42
47275 ATAGGTCCAG
* * * * *
47285 ATCTATAGTAGCGTTTATGAAATAAACGCCGTAAAAGATCGAT
1 ATCTATAGTGGCGTTTTTGAAACAAACGCCGCAAAAGGTC-AT
* *
47328 ATCTATAGCGGCATTTTTTG-AACAAACGCCGCAAAAGGTCTAT
1 ATCTATAGTGGC-GTTTTTGAAACAAACGCCGCAAAAGGTC-AT
* * * *
47371 ATTTATAGTGGCGTTTTTTGGAACAAACGCCGCAAAATGTCAAG
1 ATCTATAGTGGCG-TTTTTGAAACAAACGCCGCAAAAGGTC-AT
* * *
47415 ATCTATAGTGACGTTTCTGGAACAAACGCCGCAAAAGGTCAT
1 ATCTATAGTGGCGTTTTTGAAACAAACGCCGCAAAAGGTCAT
* * *
47457 ATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATCAT
1 ATCTATAGTGGCGTTTTT-GAAACAAACGCCGCAAAAGGTCAT
* * *
47500 ATATATAGAGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAT
1 ATCTATAGTGGCGTTTTT-GAAACAAACGCCGCAAAAGGTCAT
* * *
47543 ATCTATAGCGGCATTTTTGGATACAAACGCCGC
1 ATCTATAGTGGCGTTTTT-GAAACAAACGCCGC
47576 TAATTACCTT
Statistics
Matches: 213, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
42 16 0.08
43 161 0.76
44 36 0.17
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (42 bp):
ATCTATAGTGGCGTTTTTGAAACAAACGCCGCAAAAGGTCAT
Found at i:47493 original size:86 final size:85
Alignment explanation
Indices: 47347--47575 Score: 327
Period size: 86 Copynumber: 2.7 Consensus size: 85
47337 GGCATTTTTT
* *
47347 GAACAAACGCCGCAAAAGGTCTATATTTATAGTGGCGTTTTTTGGA-ACAAACGCCGCAAAATG-
1 GAACAAACGCCGCAAAAGGTC-ATATCTATAGCGGCG-TTTTTGGATACAAACGCCGCAAAA-GA
* *
47410 TCAAGATCTATAGTGACGTTTCTG
63 TC-AGATATATAGAGACGTTTCTG
47434 GAACAAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATCA
1 GAACAAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATCA
* * *
47499 TATATATAGAGGCGTTTTTG
66 GATATATAGAGACGTTTCTG
*
47519 GATACAAACGCCGCAAAAGGTCATATCTATAGCGGCATTTTTGGATACAAACGCCGC
1 GA-ACAAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGATACAAACGCCGC
47576 TAATTACCTT
Statistics
Matches: 131, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
85 27 0.21
86 83 0.63
87 21 0.16
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (85 bp):
GAACAAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGATCA
GATATATAGAGACGTTTCTG
Found at i:47533 original size:129 final size:129
Alignment explanation
Indices: 47277--47575 Score: 372
Period size: 129 Copynumber: 2.3 Consensus size: 129
47267 ATGCCACCAT
* * *
47277 AGGTCCAGATCTATAGT-AGCGTTTATGAAATAAACGCCGTAAAAGATCGATATCTATAGCGGCA
1 AGGT-CAGATCTATAGTGA-CGTTTATGGAACAAACGCCGCAAAAGATCGATATCTATAGCGGCA
* * * *
47341 TTTTTTGAACAAACGCCGCAAAAGGTCTATATTTATAGTGGCGTTTTTTGGAACAAACGCCGCAA
64 TTTTTGGAACAAACGCCGCAAAAGATCTATATATATAGAGGCGTTTTTTGGAACAAACGCCGCAA
47406 A
129 A
* * * *
47407 ATGTCAAGATCTATAGTGACGTTTCTGGAACAAACGCCGCAAAAGGTC-ATATCTATAGCGGCGT
1 AGGTC-AGATCTATAGTGACGTTTATGGAACAAACGCCGCAAAAGATCGATATCTATAGCGGCAT
47471 TTTTGGATACAAACGCCGCAAAAGATC-ATATATATAGAGGCG-TTTTTGGATACAAACGCCGCA
65 TTTTGGA-ACAAACGCCGCAAAAGATCTATATATATAGAGGCGTTTTTTGGA-ACAAACGCCGCA
47534 AA
128 AA
* * * * *
47536 AGGTCATATCTATAGCGGCATTTTTGGATACAAACGCCGC
1 AGGTCAGATCTATAGTGACGTTTATGGA-ACAAACGCCGC
47576 TAATTACCTT
Statistics
Matches: 147, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
128 26 0.18
129 64 0.44
130 56 0.38
131 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (129 bp):
AGGTCAGATCTATAGTGACGTTTATGGAACAAACGCCGCAAAAGATCGATATCTATAGCGGCATT
TTTGGAACAAACGCCGCAAAAGATCTATATATATAGAGGCGTTTTTTGGAACAAACGCCGCAAA
Found at i:52502 original size:64 final size:64
Alignment explanation
Indices: 52399--52527 Score: 143
Period size: 64 Copynumber: 2.0 Consensus size: 64
52389 TTATAAAAAT
* * * *
52399 GCCGCTGAAGTACTAATCTTTGTGGCATTTGTCGAAAAAACGCCACTATAGATGGACCTATTGC
1 GCCGCTAAAGTACTAATCTTTGTAGCATTTGTCGAAAAAAAGCCACTACAGATGGACCTATTGC
* * * * * * *
52463 GCCGCTAAAGTACTACTCTTTTGTAGCGTTTTTTG-AAAAAATCCACTACATATGTACCTATTGC
1 GCCGCTAAAGTACTAATC-TTTGTAGCATTTGTCGAAAAAAAGCCACTACAGATGGACCTATTGC
52527 G
1 G
52528 GCGTTTATAT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
64 41 0.77
65 12 0.23
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (64 bp):
GCCGCTAAAGTACTAATCTTTGTAGCATTTGTCGAAAAAAAGCCACTACAGATGGACCTATTGC
Found at i:57469 original size:23 final size:23
Alignment explanation
Indices: 57443--57488 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
57433 AAAGCATGCG
57443 AACTAGATACCAAGCGGTCAGGA
1 AACTAGATACCAAGCGGTCAGGA
* *
57466 AACTAGATACCATGGGGTCAGGA
1 AACTAGATACCAAGCGGTCAGGA
57489 TCAATTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.28, T:0.15
Consensus pattern (23 bp):
AACTAGATACCAAGCGGTCAGGA
Found at i:57526 original size:16 final size:17
Alignment explanation
Indices: 57505--57536 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
57495 TCTTGAAAAT
57505 AAAACATGTC-GGGTAG
1 AAAACATGTCTGGGTAG
57521 AAAACATGTCTGGGTA
1 AAAACATGTCTGGGTA
57537 TGATTGCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (17 bp):
AAAACATGTCTGGGTAG
Found at i:58995 original size:11 final size:10
Alignment explanation
Indices: 58975--59023 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
58965 AAATCAAGGT
58975 GAAAAAAAAA
1 GAAAAAAAAA
58985 GAAAAAGAAAA
1 GAAAAA-AAAA
*
58996 GAAGAAAAAGA
1 GAA-AAAAAAA
*
59007 GAAAAAAAAG
1 GAAAAAAAAA
59017 GAAAAAA
1 GAAAAAA
59024 GGAAAAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 18 0.53
11 13 0.38
12 3 0.09
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:59005 original size:20 final size:19
Alignment explanation
Indices: 58978--59038 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
58968 TCAAGGTGAA
58978 AAAAAAAGAAAAAGAAAAG
1 AAAAAAAGAAAAAGAAAAG
58997 AAGAAAAAGAGAAAA-AAAAG
1 AA-AAAAAGA-AAAAGAAAAG
* *
59017 GAAAAAAGGAAAAG-AAAG
1 AAAAAAAGAAAAAGAAAAG
59035 AAAA
1 AAAA
59039 CAAATCAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 11 0.31
19 8 0.22
20 13 0.36
21 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAGAAAAG
Found at i:59029 original size:34 final size:33
Alignment explanation
Indices: 58975--59038 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
58965 AAATCAAGGT
58975 GAAAAAAAAAGAAAAAGAAAAG-AAGAAAAAGA
1 GAAAAAAAAAGAAAAAGAAAAGAAAGAAAAAGA
*
59007 GAAAAAAAAGGAAAAAAGGAAAAGAAAGAAAA
1 GAAAAAAAAAG-AAAAA-GAAAAGAAAGAAAA
59039 CAAATCAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 10 0.36
33 5 0.18
34 6 0.21
35 7 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (33 bp):
GAAAAAAAAAGAAAAAGAAAAGAAAGAAAAAGA
Found at i:59929 original size:23 final size:23
Alignment explanation
Indices: 59880--59934 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
59870 AAAGGCAATA
*
59880 TTTTTT-AAAAAATTTATTAAAC
1 TTTTTTAAAAAAATTAATTAAAC
* * *
59902 ATTTTTAAAAAAATTAATTGATC
1 TTTTTTAAAAAAATTAATTAAAC
*
59925 TTTTTCAAAA
1 TTTTTTAAAA
59935 TTTGAAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTTTTAAAAAAATTAATTAAAC
Found at i:61951 original size:66 final size:67
Alignment explanation
Indices: 61802--61963 Score: 218
Period size: 66 Copynumber: 2.4 Consensus size: 67
61792 CCTAAAAAAA
* *
61802 TTGTCTCGCTTGAGACGGTTTCTCTTGAAACATAAACCTTTGAGATTCTTTCTCTCCAAACAAAG
1 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTAGAGATTCTTTCTCTCCAAACAAAG
61867 TT
66 TT
** * ** * * *
61869 TCATCTCGCTTGAGACATTTTCTCTTGAAACATAAGTCTTAGAGATT-TTTCTCTCGAAATATAG
1 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTAGAGATTCTTTCTCTCCAAACAAAG
61933 TT
66 TT
*
61935 TTGTCTCGCTTGAGACAGTTTCACTTGAA
1 TTGTCTCGCTTGAGACAGTTTCTCTTGAA
61964 GCCTAAATTT
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
66 41 0.51
67 40 0.49
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (67 bp):
TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTAGAGATTCTTTCTCTCCAAACAAAG
TT
Found at i:62759 original size:135 final size:135
Alignment explanation
Indices: 62516--62760 Score: 310
Period size: 135 Copynumber: 1.8 Consensus size: 135
62506 CATCTTCAAC
* * * *
62516 ACGAAGGAACAATGTCATCCACCGACCAAATGTCCTAAACGCAAAGGAGAAATGTCATCCTCAAA
1 ACGAAGAAACAATGTCATACACCGACCAAATCTCCTAAACACAAAGGAGAAATGTCATCCTCAAA
* * * * *
62581 CAGTCAGACTTCCTCAACGCAAAATAACCGTGTTGTCTCCAAATTATCCAAATATGTCTAGACGT
66 CAATCAGACTTCCTCAACACAAAAGAACCATGTTATCTCCAAATTATCCAAATATGTCTAGACGT
62646 CCTCT
131 CCTCT
* * * * * * *
62651 ACGAAGAAACAATGTTATACATCGACCAGATCTCCTCAATACAAAGGAGCAATGTCATCCTCAGA
1 ACGAAGAAACAATGTCATACACCGACCAAATCTCCTAAACACAAAGGAGAAATGTCATCCTCAAA
* ** *
62716 TAATCAGACTTCCTCAACATGAAAGAACCATGTTATCTTCAAATT
66 CAATCAGACTTCCTCAACACAAAAGAACCATGTTATCTCCAAATT
62761 TTCTAGATTG
Statistics
Matches: 90, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
135 90 1.00
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (135 bp):
ACGAAGAAACAATGTCATACACCGACCAAATCTCCTAAACACAAAGGAGAAATGTCATCCTCAAA
CAATCAGACTTCCTCAACACAAAAGAACCATGTTATCTCCAAATTATCCAAATATGTCTAGACGT
CCTCT
Found at i:62951 original size:104 final size:104
Alignment explanation
Indices: 62771--62960 Score: 233
Period size: 104 Copynumber: 1.8 Consensus size: 104
62761 TTCTAGATTG
* * *
62771 ACTCGACTTCCTCAACGAAAAGGAACAATGTCATATGAAAGCTGTCGAAAATCTTCAACATGGAT
1 ACTCGACTTCCTCAACGAAAAGGAACAATGTCATATGAAAGCTGGCCAAAATCTTCAACATGAAT
62836 GAGGAGTGTCGTATTT-AACATAAAATTATCTACAAATTT
66 GAGGAGTGTCGT-TTTCAACATAAAATTATCTACAAATTT
* * ** **
62875 ACTCGACTTCCTCGAC-AAGAAGGAACAATGTCATCTGAAAG-TGGCCAGATCTCTTCAATGTGA
1 ACTCGACTTCCTCAACGAA-AAGGAACAATGTCATATGAAAGCTGGCCA-AAATCTTCAACATGA
* *
62938 ATGTGTAGTGTCGTTTTCAACAT
64 ATGAGGAGTGTCGTTTTCAACAT
62961 CAGAATTACC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
103 9 0.12
104 63 0.88
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (104 bp):
ACTCGACTTCCTCAACGAAAAGGAACAATGTCATATGAAAGCTGGCCAAAATCTTCAACATGAAT
GAGGAGTGTCGTTTTCAACATAAAATTATCTACAAATTT
Found at i:64120 original size:51 final size:50
Alignment explanation
Indices: 64047--64143 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 50
64037 ACGTGATACT
* *
64047 TTCAATTTATATATTTTAGTCACCGTTTATTT-TTTATTTGGCTACTGTTC
1 TTCAATTTATATATTTTAGTCACCATTTATTTCTGT-TTTGGCTACTGTTC
* *
64097 TTCAATTT-TATGCATTTTGGTCACTATTTATTTCTGTTTTGGCTACT
1 TTCAATTTATAT--ATTTTAGTCACCATTTATTTCTGTTTTGGCTACT
64144 ATTTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 3 0.08
50 8 0.20
51 27 0.68
52 2 0.05
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (50 bp):
TTCAATTTATATATTTTAGTCACCATTTATTTCTGTTTTGGCTACTGTTC
Found at i:68964 original size:59 final size:59
Alignment explanation
Indices: 68872--68991 Score: 161
Period size: 59 Copynumber: 2.0 Consensus size: 59
68862 ATAGATGGAC
* * * * * * *
68872 AAGTGTCCTATCGAGCCCTCCTAGTTGCTATGAAAAATGCAAAC-CGATAATATGGCTCT
1 AAGTGTCCTATCAAACCCTCCTAGTCGCAATG-AAAAGGAAAACTCGATAATATGACTCT
68931 AAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGACTCT
1 AAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGACTCT
68990 AA
1 AA
68992 CCAACCCTCC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
58 9 0.17
59 44 0.83
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (59 bp):
AAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGACTCT
Done.