Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008165.1 Hibiscus syriacus cultivar Beakdansim tig00110745_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: 2894944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:2475848 original size:25 final size:24
Alignment explanation
Indices: 2475796--2475849 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2475786 AAAATAAGAT
2475796 AAAATAAATAAGAATAGTAATAAA
1 AAAATAAATAAGAATAGTAATAAA
*
2475820 AAAATAAA-AAGTATATATTAATAACA
1 AAAATAAATAAG-A-ATAGTAATAA-A
2475846 AAAA
1 AAAA
2475850 GATGAAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 3 0.12
24 9 0.35
25 9 0.35
26 5 0.19
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (24 bp):
AAAATAAATAAGAATAGTAATAAA
Found at i:2480751 original size:48 final size:48
Alignment explanation
Indices: 2480697--2480788 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
2480687 TTGTTTTGGA
2480697 AAAACTCCCCCTTAATAAAACATTTAATGAAAAAGAGACATATTAGGC
1 AAAACTCCCCCTTAATAAAACATTTAATGAAAAAGAGACATATTAGGC
* *
2480745 AAAACTCTCCCTTAGTAAAACATTTAATGAAAAAGAGACATATT
1 AAAACTCCCCCTTAATAAAACATTTAATGAAAAAGAGACATATT
2480789 TTGGAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25
Consensus pattern (48 bp):
AAAACTCCCCCTTAATAAAACATTTAATGAAAAAGAGACATATTAGGC
Found at i:2481849 original size:18 final size:18
Alignment explanation
Indices: 2481823--2481887 Score: 121
Period size: 18 Copynumber: 3.6 Consensus size: 18
2481813 GTGTAAAGTA
2481823 GTATCGGTACCCCCTTGG
1 GTATCGGTACCCCCTTGG
*
2481841 GTATTGGTACCCCCTTGG
1 GTATCGGTACCCCCTTGG
2481859 GTATCGGTACCCCCTTGG
1 GTATCGGTACCCCCTTGG
2481877 GTATCGGTACC
1 GTATCGGTACC
2481888 TATTTTGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.12, C:0.31, G:0.28, T:0.29
Consensus pattern (18 bp):
GTATCGGTACCCCCTTGG
Found at i:2483453 original size:65 final size:64
Alignment explanation
Indices: 2483325--2483465 Score: 178
Period size: 65 Copynumber: 2.2 Consensus size: 64
2483315 ACACCCCATT
* * *
2483325 TCGAATGAATTTTATGCACTGATGCACAGTCATGCTTCGATGCACTCTGGATTTTATTGAAACA
1 TCGAATGAATTTTATGCACCGATGCACAGTCATGCATCGATGCACTCTGGATTGTATTGAAACA
* * *
2483389 TCGAATGCATTTTATGCACCGATGCATA-TACCATGCATCGATGCACTCCTGGCTTGT-TTGAAA
1 TCGAATGAATTTTATGCACCGATGCACAGT--CATGCATCGATGCACT-CTGGATTGTATTGAAA
2483452 CA
63 CA
2483454 TCGAATGTAATT
1 TCGAATG-AATT
2483466 AGTGTACTGA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
63 1 0.02
64 25 0.38
65 30 0.45
66 10 0.15
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (64 bp):
TCGAATGAATTTTATGCACCGATGCACAGTCATGCATCGATGCACTCTGGATTGTATTGAAACA
Found at i:2492114 original size:65 final size:64
Alignment explanation
Indices: 2491985--2492120 Score: 186
Period size: 65 Copynumber: 2.1 Consensus size: 64
2491975 ACACCCTATT
* * *
2491985 TCGAATGCATTTTATGCACTGATGCACAGTCATGCATCGATGCACTCTGGATTTTATTGAAACA
1 TCGAATGCATTTTATGCACCGATGCACAGTCATGCATCAATGCACTCTGGATTGTATTGAAACA
* *
2492049 TCGAATGCATTTTATGCACCGATGCATA-TACCATGCATCAATGCACTCCTGGCTTGT-TTGAAA
1 TCGAATGCATTTTATGCACCGATGCACAGT--CATGCATCAATGCACT-CTGGATTGTATTGAAA
2492112 CA
63 CA
2492114 TCGAATG
1 TCGAATG
2492121 TAATTAGTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.02
64 26 0.41
65 30 0.47
66 7 0.11
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGCACCGATGCACAGTCATGCATCAATGCACTCTGGATTGTATTGAAACA
Found at i:2495573 original size:21 final size:20
Alignment explanation
Indices: 2495549--2495587 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2495539 CAAATACAAT
2495549 AAATAATATTATTTATTAACA
1 AAATAATATTATTT-TTAACA
**
2495570 AAATTTTATTATTTTTAA
1 AAATAATATTATTTTTAA
2495588 AATATTAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATAATATTATTTTTAACA
Found at i:2495686 original size:33 final size:34
Alignment explanation
Indices: 2495649--2495712 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
2495639 ATTATTAAAA
**
2495649 TTATTAATAAATA-TAATTTAATA-ATTAATAATT
1 TTATTAA-AAATACTAAAATAATATATTAATAATT
2495682 TTATTAAAAATACTAAAATAATATATTAATA
1 TTATTAAAAATACTAAAATAATATATTAATA
2495713 TTAAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 5 0.19
33 15 0.56
34 7 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (34 bp):
TTATTAAAAATACTAAAATAATATATTAATAATT
Found at i:2505421 original size:21 final size:20
Alignment explanation
Indices: 2505406--2505451 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
2505396 AGAAAAAGGT
*
2505406 AAAAA-TAAGAATGAAAGAG
1 AAAAAGTAAGAATGAAAAAG
*
2505425 AAAAAGTTAAGAATGAAAGAG
1 AAAAAG-TAAGAATGAAAAAG
2505446 AAAAAG
1 AAAAAG
2505452 AAAAAGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 5 0.20
21 20 0.80
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (20 bp):
AAAAAGTAAGAATGAAAAAG
Found at i:2505424 original size:27 final size:27
Alignment explanation
Indices: 2505387--2505464 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
2505377 GAAGATGAAG
* *
2505387 AAATGAGAGAGAAAAAGGTAAAAAT-A
1 AAATGAAAGAGAAAAAGTTAAAAATGA
*
2505413 AGAATGAAAGAGAAAAAGTTAAGAATGA
1 A-AATGAAAGAGAAAAAGTTAAAAATGA
*
2505441 AAGA-GAAAAAGAAAAAGTTAAAAA
1 AA-ATGAAAGAGAAAAAGTTAAAAA
2505465 AATGAGAGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
26 1 0.02
27 40 0.91
28 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.12
Consensus pattern (27 bp):
AAATGAAAGAGAAAAAGTTAAAAATGA
Found at i:2505472 original size:27 final size:27
Alignment explanation
Indices: 2505396--2505472 Score: 63
Period size: 27 Copynumber: 2.9 Consensus size: 27
2505386 GAAATGAGAG
* *
2505396 AGAAAAAGGTAAAAATAA-GA-ATGAAAG
1 AGAAAAAGTTAAAAA-AATGAGA-GAAAA
*
2505423 AGAAAAAGTT--AAGAATGAAAGAGAAAA
1 AGAAAAAGTTAAAAAAATG--AGAGAAAA
2505450 AGAAAAAGTTAAAAAAATGAGAG
1 AGAAAAAGTTAAAAAAATGAGAG
2505473 GGAAATGGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
24 2 0.05
25 3 0.08
27 28 0.70
28 1 0.03
29 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (27 bp):
AGAAAAAGTTAAAAAAATGAGAGAAAA
Found at i:2505769 original size:17 final size:17
Alignment explanation
Indices: 2505745--2505786 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2505735 AATTATTTAC
2505745 AAAA-TAAAAT-AAGAA
1 AAAATTAAAATAAAGAA
*
2505760 TAAAATTAAAATAAAGGA
1 -AAAATTAAAATAAAGAA
2505778 AAAATTAAA
1 AAAATTAAA
2505787 TTTTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (17 bp):
AAAATTAAAATAAAGAA
Found at i:2524641 original size:2 final size:2
Alignment explanation
Indices: 2524636--2524662 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2524626 TAACAGTAAG
2524636 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2524663 CATTAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2526924 original size:20 final size:19
Alignment explanation
Indices: 2526899--2526950 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
2526889 CCTCAAGGGG
*
2526899 TATCGATACTA-TGGGTCCAA
1 TATCGATACTAGAGGGT--AA
2526919 TATCGATACTCAGAGGGTAA
1 TATCGATACT-AGAGGGTAA
2526939 TATCGATACTAG
1 TATCGATACTAG
2526951 TGGAAAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 22 0.76
21 1 0.03
22 4 0.14
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (19 bp):
TATCGATACTAGAGGGTAA
Found at i:2528803 original size:22 final size:18
Alignment explanation
Indices: 2528767--2528829 Score: 81
Period size: 18 Copynumber: 3.3 Consensus size: 18
2528757 ATTCGTCCGT
2528767 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
2528785 AGGACCACTGTATATGTCCCGT
1 AGGACCAC----TATGTCCCGA
2528807 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
2528825 AGGAC
1 AGGAC
2528830 TACTCCTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 22 0.56
22 17 0.44
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:2530473 original size:64 final size:63
Alignment explanation
Indices: 2530340--2530500 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 63
2530330 TAATGAAGGT
* * *
2530340 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATAGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATAGGA
* **
2530405 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAA-ATTA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTTAATAGGA
* * *
2530469 ATGCATCGATGCAGTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
2530501 CCTTAAAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 58 0.69
65 25 0.30
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATAGGA
Found at i:2531440 original size:2 final size:2
Alignment explanation
Indices: 2531433--2531472 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
2531423 CTTTTTCCTT
2531433 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
2531473 CATGTCACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2533851 original size:18 final size:18
Alignment explanation
Indices: 2533791--2533860 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
2533781 TTTAGTATTC
2533791 GTCCCGTAGGACCACTAT
1 GTCCCGTAGGACCACTAT
* *
2533809 GTCCTGAAGGACCACTGTATAT
1 GTCCCGTAGGACCAC----TAT
*
2533831 GTCCCGTATGACCACTAT
1 GTCCCGTAGGACCACTAT
*
2533849 GTCCCGAAGGAC
1 GTCCCGTAGGAC
2533861 TACTCCTTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
18 26 0.63
22 15 0.37
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.23
Consensus pattern (18 bp):
GTCCCGTAGGACCACTAT
Found at i:2535507 original size:64 final size:63
Alignment explanation
Indices: 2535374--2535534 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
2535364 TAATGAAGGT
* * *
2535374 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * *
2535439 ATGCATCGATGCACTACTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
2535503 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
2535535 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 58 0.68
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:2536685 original size:25 final size:25
Alignment explanation
Indices: 2536656--2536708 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
2536646 GGTTCCATCT
2536656 AAATAA-AATAATAAATAA-AAATTAA
1 AAATAAGAATAA-AAA-AATAAATTAA
*
2536681 AAATAAGGATAAAAAAATAAATTAA
1 AAATAAGAATAAAAAAATAAATTAA
2536706 AAA
1 AAA
2536709 ATTTACTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 2 0.08
25 19 0.76
26 4 0.16
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (25 bp):
AAATAAGAATAAAAAAATAAATTAA
Found at i:2536707 original size:12 final size:12
Alignment explanation
Indices: 2536674--2536735 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
2536664 TAATAAATAA
2536674 AAATT-AAAAAT
1 AAATTAAAAAAT
*
2536685 AAGGATAAAAAAAT
1 AA--ATTAAAAAAT
2536699 AAATTAAAAAAT
1 AAATTAAAAAAT
** *
2536711 TTACTAAAAAAT
1 AAATTAAAAAAT
2536723 AAAGTTAAAAAAT
1 AAA-TTAAAAAAT
2536736 TACCTTGCAG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
11 2 0.05
12 19 0.49
13 10 0.26
14 8 0.21
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (12 bp):
AAATTAAAAAAT
Found at i:2540185 original size:22 final size:22
Alignment explanation
Indices: 2540159--2540215 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
2540149 CCGGAAGGGG
*
2540159 GTATCAATACCATAGTATGATA
1 GTATCAATACCATACTATGATA
* *
2540181 GTATCAGTACCATACTATGGTA
1 GTATCAATACCATACTATGATA
*
2540203 GTATCGATACCAT
1 GTATCAATACCAT
2540216 GGTAGGGGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (22 bp):
GTATCAATACCATACTATGATA
Found at i:2540302 original size:22 final size:22
Alignment explanation
Indices: 2540276--2540338 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
2540266 ATGGAAGGGG
*
2540276 TATCGATATCATAGTAGGGTAC
1 TATCGATACCATAGTAGGGTAC
2540298 TATCGATACCATAGTAGGGTAC
1 TATCGATACCATAGTAGGGTAC
*
2540320 TATCGATACCATGGTAGGG
1 TATCGATACCATAGTAGGG
2540339 GTGTCGATAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (22 bp):
TATCGATACCATAGTAGGGTAC
Found at i:2540337 original size:116 final size:117
Alignment explanation
Indices: 2540092--2540347 Score: 336
Period size: 116 Copynumber: 2.2 Consensus size: 117
2540082 GGTAGTAACA
* * *
2540092 ATACCATGGTAAGGGTATCGATATCAAGCAACATCGAACCTAAAATTGGTATCGATACCGGAAGG
1 ATACCATGGTAGGGGTATCGATATCAAGCAACATCGAACCTAAAATTGGTATCAATAACGGAAGG
* * * *
2540157 GGGTATCAATACCATAGTATGATAGTATCAGTACCATACTATGGTAGTATCG
66 GGGTATCAATACCATAGTAGGATACTATCAGTACCATACTAGGGTACTATCG
* * * * *
2540209 ATACCATGGTAGGGGTATCGATGTCAGGCCACATCGAATCTAAAATTGGTATCAATAATGGAA-G
1 ATACCATGGTAGGGGTATCGATATCAAGCAACATCGAACCTAAAATTGGTATCAATAACGGAAGG
* * * *
2540273 GGGTATCGATATCATAGTAGGGTACTATC-GATACCATAGTAGGGTACTATCG
66 GGGTATCAATACCATAGTAGGATACTATCAG-TACCATACTAGGGTACTATCG
*
2540325 ATACCATGGTAGGGGTGTCGATA
1 ATACCATGGTAGGGGTATCGATA
2540348 CTAAAGAGCC
Statistics
Matches: 120, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
115 1 0.01
116 64 0.53
117 55 0.46
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (117 bp):
ATACCATGGTAGGGGTATCGATATCAAGCAACATCGAACCTAAAATTGGTATCAATAACGGAAGG
GGGTATCAATACCATAGTAGGATACTATCAGTACCATACTAGGGTACTATCG
Found at i:2540771 original size:55 final size:58
Alignment explanation
Indices: 2540678--2540817 Score: 209
Period size: 55 Copynumber: 2.5 Consensus size: 58
2540668 ATGGCACTAA
* * *
2540678 GTGTGTAAAATGCTAAGAAATTT-ATA-TGAGTGTATGAATTTCTGTATTGGGCACTTC
1 GTGTGCAAAATGTTAAGAAATTTCATACT-AGTGTATGAATTTCCGTATTGGGCACTTC
2540735 GTGTGC-AAATGTTAAG-AA-TTCATACTAGTGTATGAATTTCCGTATTGGGCACTTC
1 GTGTGCAAAATGTTAAGAAATTTCATACTAGTGTATGAATTTCCGTATTGGGCACTTC
2540790 GTGTGCAAAATGTTAAGAAATTTCATAC
1 GTGTGCAAAATGTTAAGAAATTTCATAC
2540818 AAAATGTTAA
Statistics
Matches: 75, Mismatches: 3, Indels: 9
0.86 0.03 0.10
Matches are distributed among these distances:
54 2 0.03
55 39 0.52
56 20 0.27
57 7 0.09
58 7 0.09
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.36
Consensus pattern (58 bp):
GTGTGCAAAATGTTAAGAAATTTCATACTAGTGTATGAATTTCCGTATTGGGCACTTC
Found at i:2540870 original size:28 final size:28
Alignment explanation
Indices: 2540828--2540881 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
2540818 AAAATGTTAA
2540828 GTATGTAATTTCATAATGGGCACTTCGT
1 GTATGTAATTTCATAATGGGCACTTCGT
*
2540856 GTATG-AATTTCCATATTGGGCACTTC
1 GTATGTAATTT-CATAATGGGCACTTC
2540882 CTGTGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (28 bp):
GTATGTAATTTCATAATGGGCACTTCGT
Found at i:2540955 original size:58 final size:58
Alignment explanation
Indices: 2540854--2540987 Score: 187
Period size: 58 Copynumber: 2.3 Consensus size: 58
2540844 TGGGCACTTC
*
2540854 GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAATGTTAAGAAATTCATACTAA
1 GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAACGTTAAGAAATTCATACTAA
* * ** * * *
2540912 GTGTATGAATTTTCGTATTGGGCACTTTGTGTGCAAAACGTTAAGAGATTCATATTAA
1 GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAACGTTAAGAAATTCATACTAA
*
2540970 ATGTATGAATTTCCATAT
1 GTGTATGAATTTCCATAT
2540988 GGGAAATGTG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (58 bp):
GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAACGTTAAGAAATTCATACTAA
Found at i:2543394 original size:12 final size:11
Alignment explanation
Indices: 2543376--2543405 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
2543366 GGGCAAGGAC
2543376 TTAATTATTAG
1 TTAATTATTAG
2543387 TATAATTATTAG
1 T-TAATTATTAG
2543399 TTAATTA
1 TTAATTA
2543406 AACTAGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (11 bp):
TTAATTATTAG
Found at i:2552810 original size:21 final size:21
Alignment explanation
Indices: 2552778--2552836 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
2552768 TGATTTATTA
*
2552778 TTATAGATTTCAAGTTTCTTG
1 TTATTGATTTCAAGTTTCTTG
*
2552799 TT-TTGAATTTCAAGTTTGTTG
1 TTATTG-ATTTCAAGTTTCTTG
*
2552820 TTATTGATGTCAAGTTT
1 TTATTGATTTCAAGTTT
2552837 ATTGGATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.06
21 28 0.85
22 3 0.09
ACGTcount: A:0.22, C:0.07, G:0.17, T:0.54
Consensus pattern (21 bp):
TTATTGATTTCAAGTTTCTTG
Found at i:2553122 original size:44 final size:43
Alignment explanation
Indices: 2553050--2553141 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 43
2553040 GTTTACATTC
*
2553050 ACAAACGCCACTATATGATATAACATTTAGCGGCGTTTTTGGG
1 ACAAACACCACTATATGATATAACATTTAGCGGCGTTTTTGGG
*
2553093 AACAAACACCACTATATG-TCATAATATTTAGCGGCGTTTTTGGG
1 -ACAAACACCACTATATGAT-ATAACATTTAGCGGCGTTTTTGGG
2553137 ACAAA
1 ACAAA
2553142 ATGCCACAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 6 0.13
44 39 0.87
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (43 bp):
ACAAACACCACTATATGATATAACATTTAGCGGCGTTTTTGGG
Found at i:2556561 original size:28 final size:28
Alignment explanation
Indices: 2556521--2556703 Score: 262
Period size: 28 Copynumber: 6.5 Consensus size: 28
2556511 ACCCGATGAC
2556521 ACATTTTGGGAATTATTTTGAAAAAGTG
1 ACATTTTGGGAATTATTTTGAAAAAGTG
* *
2556549 ACATTTTGAGAATTATTTTGACAAAGGTG
1 ACATTTTGGGAATTATTTTGA-AAAAGTG
*
2556578 ACATTCTGGGAATTATTTTGAAAAAAAGTG
1 ACATTTTGGGAATTATTTTG--AAAAAGTG
* *
2556608 ATATTTTAGGAATTATTTTG-AAAAGTG
1 ACATTTTGGGAATTATTTTGAAAAAGTG
* *
2556635 ACATTTTGGGAATTATTTTGAAGAGGTG
1 ACATTTTGGGAATTATTTTGAAAAAGTG
2556663 ACATTTTGGGAATTATTTTGAAAAA-TG
1 ACATTTTGGGAATTATTTTGAAAAAGTG
2556690 ACATTTTGGGAATT
1 ACATTTTGGGAATT
2556704 TTCGAATGTG
Statistics
Matches: 137, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
27 41 0.30
28 48 0.35
29 24 0.18
30 23 0.17
31 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.39
Consensus pattern (28 bp):
ACATTTTGGGAATTATTTTGAAAAAGTG
Found at i:2556636 original size:57 final size:54
Alignment explanation
Indices: 2556521--2556703 Score: 258
Period size: 55 Copynumber: 3.3 Consensus size: 54
2556511 ACCCGATGAC
2556521 ACATTTTGGGAATTATTTTGAAAAAGTGACATTTTGAGAATTATTTTGACAAAGGTG
1 ACATTTTGGGAATTATTTTGAAAAAGTGACATTTTG-GAATTATTTTGA-AAA-GTG
* *
2556578 ACATTCTGGGAATTATTTTGAAAAAAAGTGATATTTTAGGAATTATTTTGAAAAGTG
1 ACATTTTGGGAATTATTTTG--AAAAAGTGACATTTT-GGAATTATTTTGAAAAGTG
* * *
2556635 ACATTTTGGGAATTATTTTGAAGAGGTGACATTTTGGGAATTATTTTGAAAAATG
1 ACATTTTGGGAATTATTTTGAAAAAGTGACATTTT-GGAATTATTTTGAAAAGTG
2556690 ACATTTTGGGAATT
1 ACATTTTGGGAATT
2556704 TTCGAATGTG
Statistics
Matches: 115, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
55 44 0.38
57 41 0.36
58 3 0.03
59 26 0.23
60 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.39
Consensus pattern (54 bp):
ACATTTTGGGAATTATTTTGAAAAAGTGACATTTTGGAATTATTTTGAAAAGTG
Found at i:2560784 original size:12 final size:12
Alignment explanation
Indices: 2560725--2560784 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
2560715 GATACATGAC
2560725 CTGAATTCTGTT
1 CTGAATTCTGTT
*
2560737 CT-AATTTCTGAT
1 CTGAA-TTCTGTT
*
2560749 CTGGATTCTGTT
1 CTGAATTCTGTT
* *
2560761 ATG-ATATATGTT
1 CTGAAT-TCTGTT
2560773 CTGAATTCTGTT
1 CTGAATTCTGTT
2560785 TTGATTTATG
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
11 4 0.11
12 30 0.81
13 3 0.08
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:2560794 original size:24 final size:24
Alignment explanation
Indices: 2560704--2560796 Score: 87
Period size: 24 Copynumber: 3.9 Consensus size: 24
2560694 TTCCGACTTA
* ** *
2560704 AATTCTGTTCTGATACATGACCTG
1 AATTCTGTTATGATTTATGATCTG
* * *
2560728 AATTCTGTTCTAATTTCTGATCTG
1 AATTCTGTTATGATTTATGATCTG
* * *
2560752 GATTCTGTTATGATATATGTTCTG
1 AATTCTGTTATGATTTATGATCTG
*
2560776 AATTCTGTTTTGATTTATGAT
1 AATTCTGTTATGATTTATGAT
2560797 ATCTTCGGTT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (24 bp):
AATTCTGTTATGATTTATGATCTG
Found at i:2562875 original size:18 final size:18
Alignment explanation
Indices: 2562840--2562885 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2562830 ACCGGTCATA
*
2562840 ACCCGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTT
* *
2562858 ACCTGACCCGACCTGTTT
1 ACCCGACCCGACCCGTTT
2562876 ACCCGACCCG
1 ACCCGACCCG
2562886 TTGACCCGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.48, G:0.15, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:2562879 original size:13 final size:13
Alignment explanation
Indices: 2562861--2562898 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2562851 CCCGTTTACC
2562861 TGACCCGACCTGT
1 TGACCCGACCTGT
* *
2562874 TTACCCGACCCGT
1 TGACCCGACCTGT
2562887 TGACCCGACCTG
1 TGACCCGACCTG
2562899 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.42, G:0.21, T:0.21
Consensus pattern (13 bp):
TGACCCGACCTGT
Found at i:2562914 original size:10 final size:10
Alignment explanation
Indices: 2562901--2562930 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2562891 CCGACCTGAC
2562901 CCGTTGACCA
1 CCGTTGACCA
2562911 CCGTTGACCA
1 CCGTTGACCA
*
2562921 CTGTTGACCA
1 CCGTTGACCA
2562931 AAACTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (10 bp):
CCGTTGACCA
Found at i:2565404 original size:12 final size:12
Alignment explanation
Indices: 2565389--2565448 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
2565379 GATACATTAC
2565389 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
2565401 CTGATTTCTGAT
1 CTGAATTCTGTT
*
2565413 CTGGATTCTGTT
1 CTGAATTCTGTT
*
2565425 CTG-ATATCTATT
1 CTGAAT-TCTGTT
2565437 CTGAATTCTGTT
1 CTGAATTCTGTT
2565449 TTGATTTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:2565408 original size:48 final size:48
Alignment explanation
Indices: 2565352--2565455 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
2565342 AAATATTTTA
2565352 TCTGATTTCCGA-CTTGAATTATGTTCTGATA-C-ATTACCTGAATTCTGT
1 TCTGATTTCCGATC-TGAATTATGTTCTGATATCTATT--CTGAATTCTGT
* * *
2565400 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTATTCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTATGTTCTGATATCTATTCTGAATTCTGT
*
2565448 TTTGATTT
1 TCTGATTT
2565456 ATGATATCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
48 44 0.90
49 2 0.04
50 3 0.06
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.49
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTATGTTCTGATATCTATTCTGAATTCTGT
Found at i:2565420 original size:24 final size:24
Alignment explanation
Indices: 2565389--2565460 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
2565379 GATACATTAC
2565389 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
2565413 CTGGATTCTGTTCTGATATCT-ATT
1 CTGAATTCTGTTCTGATTTCTGA-T
* *
2565437 CTGAATTCTGTTTTGATTTATGAT
1 CTGAATTCTGTTCTGATTTCTGAT
2565461 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 1 0.03
24 38 0.95
25 1 0.03
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:2566517 original size:26 final size:26
Alignment explanation
Indices: 2566464--2566517 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
2566454 AGGGTAACTC
* *
2566464 TTTTATGGGATTTACTACAGTATAAT
1 TTTTATGAGATTTACTACACTATAAT
* *
2566490 TTTTATGAGATTTACTAGACTATGAT
1 TTTTATGAGATTTACTACACTATAAT
2566516 TT
1 TT
2566518 GTTTAGTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (26 bp):
TTTTATGAGATTTACTACACTATAAT
Found at i:2570623 original size:19 final size:19
Alignment explanation
Indices: 2570599--2570642 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
2570589 GATTCTGAGT
2570599 TGAGGCAGATTATTCTTAA
1 TGAGGCAGATTATTCTTAA
2570618 TGAGGCAGATTATTCTTAA
1 TGAGGCAGATTATTCTTAA
2570637 TGAGGC
1 TGAGGC
2570643 TCACAATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (19 bp):
TGAGGCAGATTATTCTTAA
Found at i:2572679 original size:28 final size:29
Alignment explanation
Indices: 2572615--2572746 Score: 169
Period size: 29 Copynumber: 4.6 Consensus size: 29
2572605 GACCCGACCC
**
2572615 GGTGACATTTTGACAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
*
2572644 GGTAACATTTTGGGAATTATTTT-AAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
* * *
2572672 AGTGACATTCTGGGTATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
* *
2572701 TGTGACATTCTGGGAATTATTTTG-AAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
*
2572729 GGTGACATTTTAGGAATT
1 GGTGACATTTTGGGAATT
2572747 TTCGAATGTG
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 43 0.48
29 47 0.52
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (29 bp):
GGTGACATTTTGGGAATTATTTTGAAAAA
Found at i:2572709 original size:57 final size:57
Alignment explanation
Indices: 2572630--2572737 Score: 171
Period size: 57 Copynumber: 1.9 Consensus size: 57
2572620 CATTTTGACA
*
2572630 ATTATTTTGAAAAAGGTAACATTTTGGGAATTATTTTAAAAAAGTGACATTCTGGGT
1 ATTATTTTGAAAAAGGTAACATTCTGGGAATTATTTTAAAAAAGTGACATTCTGGGT
* * * *
2572687 ATTATTTTGAAAAATGTGACATTCTGGGAATTATTTTGAAAAGGTGACATT
1 ATTATTTTGAAAAAGGTAACATTCTGGGAATTATTTTAAAAAAGTGACATT
2572738 TTAGGAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (57 bp):
ATTATTTTGAAAAAGGTAACATTCTGGGAATTATTTTAAAAAAGTGACATTCTGGGT
Found at i:2573692 original size:31 final size:30
Alignment explanation
Indices: 2573621--2573751 Score: 111
Period size: 31 Copynumber: 4.2 Consensus size: 30
2573611 CTAATGTGAC
* *
2573621 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-AT
** *
2573652 TCTCGGGTAGGCCCTACGGCCCTAAGATGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATAT
* *
2573682 GTCTTAGGTAGGCCCCACGGCCCTAAAATAT
1 -TCTTAGGTAGGCCCTACGGCCCTAAGATAT
* * * *
2573713 ATCTTGGGTAGG-CTTTCAGGCCCTAAGATGT
1 -TCTTAGGTAGGCCCTAC-GGCCCTAAGATAT
2573744 TCCTTAGG
1 T-CTTAGG
2573752 ATAATTCTTT
Statistics
Matches: 79, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
30 4 0.05
31 75 0.95
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.27
Consensus pattern (30 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATAT
Found at i:2573722 original size:62 final size:61
Alignment explanation
Indices: 2573621--2573751 Score: 149
Period size: 62 Copynumber: 2.1 Consensus size: 61
2573611 CTAATGTGAC
* * * *
2573621 TCTTAGGTAGGCTCTACGGCCCTGAGATCATTCTCGGGTAGGCCCTAC-GGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCTAAAATCATTCTCGGGTAGG-CCTACAGGCCCTAAGATGT
* * *
2573682 GTCTTAGGTAGGCCCCACGGCCCTAAAAT-ATATCTTGGGTAGGCTTTCAGGCCCTAAGATGT
1 -TCTTAGGTAGGCCCCACGGCCCTAAAATCAT-TCTCGGGTAGGCCTACAGGCCCTAAGATGT
2573744 TCCTTAGG
1 T-CTTAGG
2573752 ATAATTCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
61 6 0.10
62 53 0.90
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.27
Consensus pattern (61 bp):
TCTTAGGTAGGCCCCACGGCCCTAAAATCATTCTCGGGTAGGCCTACAGGCCCTAAGATGT
Found at i:2575967 original size:19 final size:19
Alignment explanation
Indices: 2575943--2575992 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
2575933 CTCTCTCTGG
*
2575943 TTCTTCCCTTTCATCACAT
1 TTCTTCCCTTTCATCAAAT
**
2575962 TTCTTCATTTTCATCAAAT
1 TTCTTCCCTTTCATCAAAT
2575981 TTCTTCCTCTTT
1 TTCTTCC-CTTT
2575993 ATCCGACCAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.16, C:0.30, G:0.00, T:0.54
Consensus pattern (19 bp):
TTCTTCCCTTTCATCAAAT
Found at i:2578082 original size:43 final size:43
Alignment explanation
Indices: 2578019--2578254 Score: 203
Period size: 43 Copynumber: 5.5 Consensus size: 43
2578009 GTGACGATAT
* * *
2578019 AAACGCCGCTCAATAGGTGTTGATATTTAGCGGCGTTTGTCTTAC
1 AAACGCCG--CAATAAGTGTTGATATTTAGCGGCGTTTTTCTCAC
* * * *
2578064 AAACGTCGCAATAGGTGTT-ATTGTTTAGCGGTGTTTTTAC-CAC
1 AAACGCCGCAATAAGTGTTGA-TATTTAGCGGCGTTTTT-CTCAC
* * * * * *
2578107 AAACGCCGCAGTAGGTGTTGATATTTAGCGGTGATTTTATCAT
1 AAACGCCGCAATAAGTGTTGATATTTAGCGGCGTTTTTCTCAC
**
2578150 AAACGCCGCAATAAGTAATG-TGATTTAGCGGCGTTTTTCTCAC
1 AAACGCCGCAATAAGTGTTGAT-ATTTAGCGGCGTTTTTCTCAC
* * * * *
2578193 AAACGCCACAATAAGTGTTGAGAATTAG-GGCGTTTCTCT-AA
1 AAACGCCGCAATAAGTGTTGATATTTAGCGGCGTTTTTCTCAC
*
2578234 AAACGCCGCAAAAAGTGTTGA
1 AAACGCCGCAATAAGTGTTGA
2578255 GATGTATCGT
Statistics
Matches: 157, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
41 20 0.13
42 12 0.08
43 116 0.74
44 2 0.01
45 7 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (43 bp):
AAACGCCGCAATAAGTGTTGATATTTAGCGGCGTTTTTCTCAC
Found at i:2578828 original size:21 final size:21
Alignment explanation
Indices: 2578771--2578828 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
2578761 ATTTCTCTCT
* *
2578771 CTGCTTCCGCTGCTGCTTTGA
1 CTGCTTCCGATGATGCTTTGA
2578792 CTGCTT-CGATGATGCTTTCGA
1 CTGCTTCCGATGATGCTTT-GA
*
2578813 -TGCTTCCGATGTTGCT
1 CTGCTTCCGATGATGCT
2578829 CTCTCTGCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.09, C:0.28, G:0.24, T:0.40
Consensus pattern (21 bp):
CTGCTTCCGATGATGCTTTGA
Found at i:2578837 original size:21 final size:21
Alignment explanation
Indices: 2578765--2578840 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 21
2578755 GCCACTATTT
* *
2578765 CTCTCTCTGCTTCCGCTGCTG
1 CTCTCTCTGCTTCCGATGATG
* **
2578786 CTTTGACTGCTT-CGATGATG
1 CTCTCTCTGCTTCCGATGATG
* ** *
2578806 CTTTCGATGCTTCCGATGTTG
1 CTCTCTCTGCTTCCGATGATG
2578827 CTCTCTCTGCTTCC
1 CTCTCTCTGCTTCC
2578841 CTTGCTTCAT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.07, C:0.33, G:0.20, T:0.41
Consensus pattern (21 bp):
CTCTCTCTGCTTCCGATGATG
Found at i:2582201 original size:42 final size:42
Alignment explanation
Indices: 2582154--2582345 Score: 233
Period size: 42 Copynumber: 4.6 Consensus size: 42
2582144 ACTACTATGA
* * * *
2582154 CGTTTATTACGAAAATGCCACTAACGGAGAAAACAATTGCGA
1 CGTTTATTACAAAAATGCCACTAAAGGAGAAAACAATTACGG
* * * * *
2582196 CGTTTATTACGAATACGCCAATAAAGGAGAAAATAATTACGG
1 CGTTTATTACAAAAATGCCACTAAAGGAGAAAACAATTACGG
* * * *
2582238 CGTTTATTTCAAAAATGCCACTAACGGAGAAAAGAATTATGG
1 CGTTTATTACAAAAATGCCACTAAAGGAGAAAACAATTACGG
*
2582280 CGTTTATTACAAAAATGCCACTAAAGGAG-AAACAATTGCGG
1 CGTTTATTACAAAAATGCCACTAAAGGAGAAAACAATTACGG
* *
2582321 TGTTTATTTCAAAAATGCCACTAAA
1 CGTTTATTACAAAAATGCCACTAAA
2582346 TTACAACTCT
Statistics
Matches: 128, Mismatches: 22, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
41 32 0.25
42 96 0.75
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (42 bp):
CGTTTATTACAAAAATGCCACTAAAGGAGAAAACAATTACGG
Found at i:2583940 original size:41 final size:41
Alignment explanation
Indices: 2583902--2584004 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
2583892 TACAAAAAAA
* *
2583902 CCACTATTGATTAACACTATTGTGGCATTTGTCTAAAAATG
1 CCACTATTGATTAACACTATTGCGACATTTGTCTAAAAATG
**
2583943 CCACTATTGATTAACACTATTGCGATGTTTGTCTAAAAATG
1 CCACTATTGATTAACACTATTGCGACATTTGTCTAAAAATG
*
2583984 CCACTATTGATAAACACTATT
1 CCACTATTGATTAACACTATT
2584005 ACACGTTTGA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (41 bp):
CCACTATTGATTAACACTATTGCGACATTTGTCTAAAAATG
Found at i:2594501 original size:13 final size:14
Alignment explanation
Indices: 2594464--2594501 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
2594454 ATAAGTTTTC
*
2594464 TTTATCTAATTTAT
1 TTTATTTAATTTAT
2594478 TTTATTT-ATTTA-
1 TTTATTTAATTTAT
2594490 TTTATTTAATTT
1 TTTATTTAATTT
2594502 TTATCTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 9 0.41
14 6 0.27
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTTAATTTAT
Found at i:2594608 original size:17 final size:17
Alignment explanation
Indices: 2594543--2594612 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 17
2594533 AAACTCTCCC
*
2594543 ATTTTATCTTTATCCTT
1 ATTTTATCTTTATCTTT
* ** *
2594560 ATCTTATAATTATTATTT
1 ATTTTATCTTTA-TCTTT
2594578 A-TTTAT-TTTA---TT
1 ATTTTATCTTTATCTTT
2594590 ATTTTATCTTTATCTTT
1 ATTTTATCTTTATCTTT
2594607 ATTTTA
1 ATTTTA
2594613 AACGATTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
12 3 0.08
13 5 0.12
14 4 0.10
16 3 0.08
17 21 0.52
18 4 0.10
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTATCTTTATCTTT
Found at i:2600136 original size:17 final size:16
Alignment explanation
Indices: 2600110--2600147 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2600100 AGGCAACTCA
2600110 TTTTTTT-TTTT-ATT
1 TTTTTTTGTTTTAATT
2600124 TTGTTTTTGTTTTAATT
1 TT-TTTTTGTTTTAATT
2600141 TTTTTTT
1 TTTTTTT
2600148 ATTCTTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.10
15 5 0.24
16 9 0.43
17 5 0.24
ACGTcount: A:0.08, C:0.00, G:0.05, T:0.87
Consensus pattern (16 bp):
TTTTTTTGTTTTAATT
Found at i:2601067 original size:9 final size:9
Alignment explanation
Indices: 2601035--2601059 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2601025 AAAAGGGAAA
2601035 AAATAAAAT
1 AAATAAAAT
2601044 AAATAAAAT
1 AAATAAAAT
2601053 AAATAAA
1 AAATAAA
2601060 TAAGATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2601190 original size:38 final size:40
Alignment explanation
Indices: 2601122--2601200 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
2601112 AAAATGAAAA
*
2601122 ATATATATATACATCAAAGTATTAATAAAATA-AATAAGCT
1 ATATATATATACAACAAAGTATTAATAAAATAGAA-AAGCT
*
2601162 ATATATATATACAACAAA-TATTTA-AAAATAGAAAAGCT
1 ATATATATATACAACAAAGTATTAATAAAATAGAAAAGCT
2601200 A
1 A
2601201 CCCTCTCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 12 0.33
39 7 0.19
40 17 0.47
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (40 bp):
ATATATATATACAACAAAGTATTAATAAAATAGAAAAGCT
Found at i:2601608 original size:2 final size:2
Alignment explanation
Indices: 2601601--2601635 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2601591 TTAAAGAAAC
2601601 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2601636 AAATAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2601718 original size:18 final size:17
Alignment explanation
Indices: 2601695--2601737 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2601685 ATATATATGT
2601695 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
2601713 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
2601730 ATAA-AATA
1 ATAATAATA
2601738 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:2603294 original size:106 final size:106
Alignment explanation
Indices: 2603095--2603641 Score: 756
Period size: 106 Copynumber: 5.2 Consensus size: 106
2603085 TCGGTCGCCC
* * * * *
2603095 CTTGTGTTGTCTCGAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTAGGAAAT
1 CTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
* * * * * * *
2603160 TATTTGTTGGCAGCAAGCCGTCCGTTCGTTGTGAATTTGAA
66 TGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAA
*
2603201 CTTGTGTCGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
1 CTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
** *
2603266 TGTTTCCTGACAACCAGTCATCCCTTCGTTGTGAAGTTGAA
66 TGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAA
* *
2603307 CTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACT-GAAAAG
1 CTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-
*
2603371 TGGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAA
65 TTGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAA
* * * * *
2603413 ATTATGTTGTCTTGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAACTGGGAAAT
1 CTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
*
2603478 TGTTTTGTTGACAACCAGTCGTCCCTTCTTTGTGAAGTTGAA
66 TG-TTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAA
* * * *
2603520 CTTGTGTTGTTTTGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTCTAAAATTGGGAAAT
1 CTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
* * *
2603585 TATTTGTTGACAACCAGTCGT-CTTTCGTTGTGAAGTTAAA
66 TGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAA
* *
2603625 CTTGTGTTATCTCGAGT
1 CTTGTGTTGTCTTGAGT
2603642 GGCGTGATAT
Statistics
Matches: 392, Mismatches: 46, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
105 34 0.09
106 259 0.66
107 99 0.25
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.37
Consensus pattern (106 bp):
CTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAT
TGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAA
Found at i:2604551 original size:36 final size:38
Alignment explanation
Indices: 2604497--2604573 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 38
2604487 GAAACAATTT
* *
2604497 CAAAGGTTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGGAAACTATCTCAAGAGAGA
2604535 CAAA-GTTTGTTT-CAAGGGAAACTATCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGGAAACTATCTCAAGAGAGA
2604571 CAA
1 CAA
2604574 TGGTGAGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 26 0.70
37 7 0.19
38 4 0.11
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (38 bp):
CAAAGGTTTGTTTCCAAGGGAAACTATCTCAAGAGAGA
Found at i:2606155 original size:15 final size:17
Alignment explanation
Indices: 2606130--2606163 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2606120 TTCCTTTTGA
2606130 TTTTTGCTTCTT-TTTT
1 TTTTTGCTTCTTGTTTT
2606146 TTTTTG-TTCTTGTTTT
1 TTTTTGCTTCTTGTTTT
2606162 TT
1 TT
2606164 CTTTTTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (17 bp):
TTTTTGCTTCTTGTTTT
Found at i:2606161 original size:16 final size:16
Alignment explanation
Indices: 2606130--2606178 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 16
2606120 TTCCTTTTGA
2606130 TTTTTGCTTCTTTTTT
1 TTTTTGCTTCTTTTTT
*
2606146 TTTTTGTTCTTGTTTTTTCT
1 TTTTTG--CTT-CTTTTT-T
2606166 TTTTTGCTTCTTT
1 TTTTTGCTTCTTT
2606179 ATTGAATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 6 0.22
17 3 0.11
18 6 0.22
19 5 0.19
20 7 0.26
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (16 bp):
TTTTTGCTTCTTTTTT
Found at i:2610595 original size:14 final size:14
Alignment explanation
Indices: 2610544--2610597 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
2610534 CAATGTAAAG
* *
2610544 AAAACAAATAAGAT
1 AAAAGAAATAAAAT
2610558 -AAAGAGAATAAAAT
1 AAAAGA-AATAAAAT
*
2610572 AAAAGGAATAAAAT
1 AAAAGAAATAAAAT
*
2610586 AAAATAAATAAA
1 AAAAGAAATAAA
2610598 TAAGATAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 4 0.12
14 25 0.76
15 4 0.12
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (14 bp):
AAAAGAAATAAAAT
Found at i:2619559 original size:14 final size:14
Alignment explanation
Indices: 2619540--2619576 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2619530 CCGATCCGAC
2619540 CCGTTGACCGTTCA
1 CCGTTGACCGTTCA
*
2619554 CCGTTGACCGTTTA
1 CCGTTGACCGTTCA
*
2619568 CCGCTGACC
1 CCGTTGACC
2619577 AACTGTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.38, G:0.22, T:0.27
Consensus pattern (14 bp):
CCGTTGACCGTTCA
Found at i:2630945 original size:16 final size:17
Alignment explanation
Indices: 2630924--2630956 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2630914 AGATGATCCT
2630924 AATAAATCAT-ATTCTG
1 AATAAATCATGATTCTG
*
2630940 AATAAATGATGATTCTG
1 AATAAATCATGATTCTG
2630957 TCAGCTAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (17 bp):
AATAAATCATGATTCTG
Found at i:2636318 original size:18 final size:18
Alignment explanation
Indices: 2636295--2636335 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2636285 CGTTGAGTCA
2636295 ACATCTGAAACAAGTACC
1 ACATCTGAAACAAGTACC
2636313 ACATCTGAAACAAGTACC
1 ACATCTGAAACAAGTACC
2636331 -CATCT
1 ACATCT
2636336 TCTTTCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (18 bp):
ACATCTGAAACAAGTACC
Found at i:2638183 original size:17 final size:18
Alignment explanation
Indices: 2638144--2638184 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
2638134 TTAATATACC
*
2638144 TAAAATAAAAACGAAAAG
1 TAAAATAAAAAAGAAAAG
*
2638162 T-AAATAAAAAATAAAA-
1 TAAAATAAAAAAGAAAAG
2638178 TAAAATA
1 TAAAATA
2638185 CTAATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.90
18 1 0.05
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (18 bp):
TAAAATAAAAAAGAAAAG
Found at i:2638194 original size:3 final size:3
Alignment explanation
Indices: 2638171--2638217 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
2638161 GTAAATAAAA
* * *
2638171 AAT AA- AAT AA- AAT ACT AAT AAT AAT AAT AAT AAC AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2638217 A
1 A
2638218 TATTATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:2638251 original size:17 final size:15
Alignment explanation
Indices: 2638233--2638266 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2638223 TATATATATA
*
2638233 TATATATTCAAAAAC
1 TATATATTTAAAAAC
2638248 TATATATTTAAAAAC
1 TATATATTTAAAAAC
2638263 TATA
1 TATA
2638267 AAAATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (15 bp):
TATATATTTAAAAAC
Found at i:2638294 original size:15 final size:16
Alignment explanation
Indices: 2638276--2638310 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2638266 AAAAATATAT
2638276 ATTATAT-TTTCAAAA
1 ATTATATATTTCAAAA
2638291 ATTATATGATTTCAAAA
1 ATTATAT-ATTTCAAAA
2638308 ATT
1 ATT
2638311 TTTGTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
17 11 0.61
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (16 bp):
ATTATATATTTCAAAA
Found at i:2638358 original size:37 final size:38
Alignment explanation
Indices: 2638316--2638398 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 38
2638306 AAATTTTTGT
2638316 ATATATTA-A-ATATGTATTCAAAAATATCTA-ATA-TATA
1 ATATATTATATATATGT-TTCAAAAA-A-CTATATATTATA
*
2638353 ATATATTATATATATGTTTCTAAAAACTATATATTATA
1 ATATATTATATATATGTTTCAAAAAACTATATATTATA
2638391 ATAT-TTAT
1 ATATATTAT
2638399 GCCATATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
36 3 0.07
37 16 0.39
38 16 0.39
39 6 0.15
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (38 bp):
ATATATTATATATATGTTTCAAAAAACTATATATTATA
Found at i:2640414 original size:21 final size:21
Alignment explanation
Indices: 2640384--2640424 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2640374 AACATATTAC
2640384 TAAAACTATCACTTTAAATAT
1 TAAAACTATCACTTTAAATAT
*
2640405 TAAAATTATCACTTTAAATA
1 TAAAACTATCACTTTAAATA
2640425 CCTTACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAACTATCACTTTAAATAT
Found at i:2640901 original size:81 final size:82
Alignment explanation
Indices: 2640782--2641190 Score: 569
Period size: 81 Copynumber: 5.0 Consensus size: 82
2640772 ATTTAGTATA
* * * *
2640782 TCATCTAAAGGCAATTAACCTTTCATATAACTTGCATTATTAGCACTA-TTCTGCCAAATGCACT
1 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCAC-
*
2640846 A-TTAGGCATCTAATCTT
65 AGTTAGGCATTTAATCTT
** * * *
2640863 TCATCCAAAATCATTTAACATTTCATCTAATTTTCATTATTGGCA-TATTTCTGCCAAATGCACA
1 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCACA
2640927 GTTAGGCATTTAATCTT
66 GTTAGGCATTTAATCTT
* * * * *
2640944 TTATCCAAAGGCATTTAACCTTTCATCTAACTTGCAATATTGGCAC-CTTTATGCCAAATGAACA
1 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCACA
2641008 GTTAGGCATTTAATCTT
66 GTTAGGCATTTAATCTT
* *
2641025 TTATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCAC-ATTTCTACCAAATGCACA
1 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCACA
* *
2641089 GTAAGGCATTTAATGTT
66 GTTAGGCATTTAATCTT
* * *
2641106 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCAC-ATTTCTACCAAACGCATA
1 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCACA
2641170 GTTAGGCATTTAATCTT
66 GTTAGGCATTTAATCTT
2641187 TCAT
1 TCAT
2641191 TTTAAAACAA
Statistics
Matches: 293, Mismatches: 32, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
80 3 0.01
81 290 0.99
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.37
Consensus pattern (82 bp):
TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCACA
GTTAGGCATTTAATCTT
Found at i:2641117 original size:22 final size:22
Alignment explanation
Indices: 2641091--2641132 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2641081 AATGCACAGT
**
2641091 AAGGCATTTAATGTTTCATCCA
1 AAGGCATTTAACCTTTCATCCA
2641113 AAGGCATTTAACCTTTCATC
1 AAGGCATTTAACCTTTCATC
2641133 TAACTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (22 bp):
AAGGCATTTAACCTTTCATCCA
Found at i:2641585 original size:20 final size:21
Alignment explanation
Indices: 2641560--2641613 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
2641550 TGGCTGAATA
*
2641560 GTATCGGTAC-CTATACCATG
1 GTATCGATACTCTATACCATG
*
2641580 GTATCGATACTTCTATACTATG
1 GTATCGATAC-TCTATACCATG
*
2641602 GTATCAATACTC
1 GTATCGATACTC
2641614 CTTTTCAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.31
21 2 0.07
22 18 0.62
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (21 bp):
GTATCGATACTCTATACCATG
Found at i:2641597 original size:22 final size:22
Alignment explanation
Indices: 2641570--2641612 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2641560 GTATCGGTAC
*
2641570 CTATACCATGGTATCGATACTT
1 CTATACCATGGTATCAATACTT
*
2641592 CTATACTATGGTATCAATACT
1 CTATACCATGGTATCAATACT
2641613 CCTTTTCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (22 bp):
CTATACCATGGTATCAATACTT
Found at i:2641625 original size:41 final size:41
Alignment explanation
Indices: 2641580--2641724 Score: 114
Period size: 41 Copynumber: 3.2 Consensus size: 41
2641570 CTATACCATG
2641580 GTATCGATACTTCTATACTATGGTATCAATACTCCTTTTCA
1 GTATCGATACTTCTATACTATGGTATCAATACTCCTTTTCA
* * *
2641621 GTATCGATGCCATTTCCATATTCTCGATTCATGGTATCGATA--CCTTTCTCTTA
1 GTATCGAT---ACTT-C-TA---T--ACT-ATGGTATCAATACTCCTTT-TC--A
*
2641674 GTATCGATACTTCTATACTATGGTACCAATACTCCTTTTCA
1 GTATCGATACTTCTATACTATGGTATCAATACTCCTTTTCA
2641715 GTATCGATAC
1 GTATCGATAC
2641725 CATTTCTTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 32
0.68 0.06 0.27
Matches are distributed among these distances:
41 19 0.23
42 10 0.12
43 4 0.05
44 8 0.10
45 2 0.02
46 2 0.02
48 2 0.02
49 2 0.02
50 8 0.10
51 4 0.05
52 11 0.14
53 9 0.11
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (41 bp):
GTATCGATACTTCTATACTATGGTATCAATACTCCTTTTCA
Found at i:2641665 original size:94 final size:94
Alignment explanation
Indices: 2641560--2641779 Score: 273
Period size: 94 Copynumber: 2.3 Consensus size: 94
2641550 TGGCTGAATA
* * *
2641560 GTATCGGTACCTATAC-CATGGTATCGATACTTCTATACTATGGTATCAATACTCCTTTTCAGTA
1 GTATCGATACCT-TACTCATAGTATCGATACTTCTATACTATGGTACCAATACTCCTTTTCAGTA
*
2641624 TCGATGCCATTTCCATATTCTCGATTCATG
65 TCGATACCATTTCCATATTCTCGATTCATG
* *
2641654 GTATCGATACCTTTCTCTTAGTATCGATACTTCTATACTATGGTACCAATACTCCTTTTCAGTAT
1 GTATCGATACCTTACTCATAGTATCGATACTTCTATACTATGGTACCAATACTCCTTTTCAGTAT
** * * * *
2641719 CGATACCATTTCTTTTTTCTGGAATCCCTG
66 CGATACCATTTCCATATTCTCG-ATTCATG
* *
2641749 GTATCGATACATTTA-TCTTAGTATCGATACT
1 GTATCGATAC-CTTACTCATAGTATCGATACT
2641780 AATAGCATCA
Statistics
Matches: 109, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
93 2 0.02
94 74 0.68
95 31 0.28
96 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (94 bp):
GTATCGATACCTTACTCATAGTATCGATACTTCTATACTATGGTACCAATACTCCTTTTCAGTAT
CGATACCATTTCCATATTCTCGATTCATG
Found at i:2642663 original size:53 final size:54
Alignment explanation
Indices: 2642599--2642716 Score: 139
Period size: 54 Copynumber: 2.2 Consensus size: 54
2642589 ACTCGTTTTC
* **
2642599 AGTATCAATACCATTTCCACATTCT-GGATCCATGGTATCGATACCTTTCCCTT
1 AGTATCGATACCATTTCCACATTCTAAAATCCATGGTATCGATACCTTTCCCTT
** * * * *
2642652 AGTATCGATACCATTTCTTCCTTCTAAAATCCCTGGTATTGATACCTTTCTCTT
1 AGTATCGATACCATTTCCACATTCTAAAATCCATGGTATCGATACCTTTCCCTT
*
2642706 AGTATTGATAC
1 AGTATCGATAC
2642717 TCCCATTAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
53 21 0.39
54 33 0.61
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (54 bp):
AGTATCGATACCATTTCCACATTCTAAAATCCATGGTATCGATACCTTTCCCTT
Found at i:2649019 original size:17 final size:17
Alignment explanation
Indices: 2648970--2649039 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
2648960 TTAAGAGTTT
*
2648970 GTTTAATAAATGAACTA
1 GTTTAATTAATGAACTA
* * *
2648987 GTTTGATGAATAAACTA
1 GTTTAATTAATGAACTA
2649004 GTTTAATTAATGAACTAA
1 GTTTAATTAATGAACT-A
*
2649022 CTTT-ATTCAATGAACTA
1 GTTTAATT-AATGAACTA
2649039 G
1 G
2649040 ATACATGAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
17 31 0.72
18 12 0.28
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (17 bp):
GTTTAATTAATGAACTA
Found at i:2650965 original size:162 final size:162
Alignment explanation
Indices: 2650720--2651200 Score: 757
Period size: 162 Copynumber: 3.0 Consensus size: 162
2650710 TCAATCATCT
* * * * *
2650720 AAAGGCAATTAACCTTTCATCTATCTTGGATTATTAGCACCATTCTGCCAAATGCACAGTTAGGC
1 AAAGGCATTTAACCTTTCATCGAACTTGTATTATTAGCACCTTTCTGCCAAATGCACAGTTAGGC
* * * *
2650785 ATTTAATCTTTCATCCAAAGGCATTTAATCTTTCATCTAATTTGCATTATTGGCACATTTCTGCC
66 ATTTAATATTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTACC
*
2650850 AAATGCACAGTTAGGCATTTAATCTTTTATCC
131 AAATGCACAATTAGGCATTTAATCTTTTATCC
** *
2650882 AAAGGCATTTAACCTTTCATCGAACTTGTATTATCGGCACCTTTCTTCCAAATGCACAGTTAGGC
1 AAAGGCATTTAACCTTTCATCGAACTTGTATTATTAGCACCTTTCTGCCAAATGCACAGTTAGGC
* * *
2650947 ATTTAATATTTTATCCAAAGGCATTTAGCCTTTCATCTAACTTGCATTATTGGTA-ACTTTCTAC
66 ATTTAATATTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACA-TTTCTAC
*
2651011 AAAATGCACAATTAGGCATTTAATCTTTTATCC
130 CAAATGCACAATTAGGCATTTAATCTTTTATCC
* *
2651044 AAAGGCATTTAACCTTTCATCGAACTTCTATTATTAGCACCTTTCTGCCAAATGCACAGTTAGAC
1 AAAGGCATTTAACCTTTCATCGAACTTGTATTATTAGCACCTTTCTGCCAAATGCACAGTTAGGC
* *
2651109 ATTTAATATTTCATTCAAAGGCATTTAACCTTTCATCTAACTTACATTATTGGCACATTTCTACC
66 ATTTAATATTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTACC
2651174 AAATGCACAATTAGGCATTTAATCTTT
131 AAATGCACAATTAGGCATTTAATCTTT
2651201 CATTTTAGAA
Statistics
Matches: 289, Mismatches: 28, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
161 1 0.00
162 287 0.99
163 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (162 bp):
AAAGGCATTTAACCTTTCATCGAACTTGTATTATTAGCACCTTTCTGCCAAATGCACAGTTAGGC
ATTTAATATTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTACC
AAATGCACAATTAGGCATTTAATCTTTTATCC
Found at i:2651204 original size:81 final size:81
Alignment explanation
Indices: 2650683--2651203 Score: 670
Period size: 81 Copynumber: 6.4 Consensus size: 81
2650673 GCACTGTTTA
* * * ** * * *
2650683 TGCCAAAATGCACTGTTAAGCATTTAGTCAATCATCTAAAGGCAATTAACCTTTCATCTATCTTG
1 TGCC-AAATGCACAGTTAGGCATTTAATCTTTCATCCAAAGGCATTTAACCTTTCATCTAACTTG
* *
2650748 GATTATTAGCACCA-TTC
65 CATTATTGGCA-CATTTC
* *
2650765 TGCCAAATGCACAGTTAGGCATTTAATCTTTCATCCAAAGGCATTTAATCTTTCATCTAATTTGC
1 TGCCAAATGCACAGTTAGGCATTTAATCTTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGC
2650830 ATTATTGGCACATTTC
66 ATTATTGGCACATTTC
* * *
2650846 TGCCAAATGCACAGTTAGGCATTTAATCTTTTATCCAAAGGCATTTAACCTTTCATCGAACTTGT
1 TGCCAAATGCACAGTTAGGCATTTAATCTTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGC
* *
2650911 ATTATCGGCACCTTTC
66 ATTATTGGCACATTTC
* * * *
2650927 TTCCAAATGCACAGTTAGGCATTTAATATTTTATCCAAAGGCATTTAGCCTTTCATCTAACTTGC
1 TGCCAAATGCACAGTTAGGCATTTAATCTTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGC
*
2650992 ATTATTGGTA-ACTTTC
66 ATTATTGGCACA-TTTC
* * * * *
2651008 TACAAAATGCACAATTAGGCATTTAATCTTTTATCCAAAGGCATTTAACCTTTCATCGAACTT-C
1 TGCCAAATGCACAGTTAGGCATTTAATCTTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGC
* *
2651072 TATTATTAGCACCTTTC
66 -ATTATTGGCACATTTC
* * * *
2651089 TGCCAAATGCACAGTTAGACATTTAATATTTCATTCAAAGGCATTTAACCTTTCATCTAACTTAC
1 TGCCAAATGCACAGTTAGGCATTTAATCTTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGC
2651154 ATTATTGGCACATTTC
66 ATTATTGGCACATTTC
* *
2651170 TACCAAATGCACAATTAGGCATTTAATCTTTCAT
1 TGCCAAATGCACAGTTAGGCATTTAATCTTTCAT
2651204 TTTAGAACAA
Statistics
Matches: 384, Mismatches: 50, Indels: 11
0.86 0.11 0.02
Matches are distributed among these distances:
80 3 0.01
81 376 0.98
82 5 0.01
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (81 bp):
TGCCAAATGCACAGTTAGGCATTTAATCTTTCATCCAAAGGCATTTAACCTTTCATCTAACTTGC
ATTATTGGCACATTTC
Found at i:2651602 original size:20 final size:21
Alignment explanation
Indices: 2651577--2651630 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
2651567 TAGCTCAATA
*
2651577 GTATCGGTAC-CTATACCATG
1 GTATCGATACTCTATACCATG
*
2651597 GTATCGATACTTCTATACTATG
1 GTATCGATAC-TCTATACCATG
*
2651619 GTATCAATACTC
1 GTATCGATACTC
2651631 CTTTTCAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.31
21 2 0.07
22 18 0.62
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (21 bp):
GTATCGATACTCTATACCATG
Found at i:2651614 original size:22 final size:22
Alignment explanation
Indices: 2651587--2651629 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2651577 GTATCGGTAC
*
2651587 CTATACCATGGTATCGATACTT
1 CTATACCATGGTATCAATACTT
*
2651609 CTATACTATGGTATCAATACT
1 CTATACCATGGTATCAATACT
2651630 CCTTTTCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (22 bp):
CTATACCATGGTATCAATACTT
Found at i:2651642 original size:41 final size:41
Alignment explanation
Indices: 2651597--2651741 Score: 114
Period size: 41 Copynumber: 3.2 Consensus size: 41
2651587 CTATACCATG
2651597 GTATCGATACTTCTATACTATGGTATCAATACTCCTTTTCA
1 GTATCGATACTTCTATACTATGGTATCAATACTCCTTTTCA
* * *
2651638 GTATCGATGCCATTTCCATATTCTCGATTCATGGTATCGATA--CCTTTCTCTTA
1 GTATCGAT---ACTT-C-TA---T--ACT-ATGGTATCAATACTCCTTT-TC--A
*
2651691 GTATCGATACTTCTATACTATGGTACCAATACTCCTTTTCA
1 GTATCGATACTTCTATACTATGGTATCAATACTCCTTTTCA
2651732 GTATCGATAC
1 GTATCGATAC
2651742 CATTTCTTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 32
0.68 0.06 0.27
Matches are distributed among these distances:
41 19 0.23
42 10 0.12
43 4 0.05
44 8 0.10
45 2 0.02
46 2 0.02
48 2 0.02
49 2 0.02
50 8 0.10
51 4 0.05
52 11 0.14
53 9 0.11
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (41 bp):
GTATCGATACTTCTATACTATGGTATCAATACTCCTTTTCA
Found at i:2651682 original size:94 final size:94
Alignment explanation
Indices: 2651577--2651796 Score: 282
Period size: 94 Copynumber: 2.3 Consensus size: 94
2651567 TAGCTCAATA
* * *
2651577 GTATCGGTACCTATAC-CATGGTATCGATACTTCTATACTATGGTATCAATACTCCTTTTCAGTA
1 GTATCGATACCT-TACTCATAGTATCGATACTTCTATACTATGGTACCAATACTCCTTTTCAGTA
*
2651641 TCGATGCCATTTCCATATTCTCGATTCATG
65 TCGATACCATTTCCATATTCTCGATTCATG
* *
2651671 GTATCGATACCTTTCTCTTAGTATCGATACTTCTATACTATGGTACCAATACTCCTTTTCAGTAT
1 GTATCGATACCTTACTCATAGTATCGATACTTCTATACTATGGTACCAATACTCCTTTTCAGTAT
** * * * *
2651736 CGATACCATTTCTTTTTTCTGGAATCCCTG
66 CGATACCATTTCCATATTCTCG-ATTCATG
*
2651766 GTATCGATACCTTTA-TCTTAGTATCGATACT
1 GTATCGATACC-TTACTCATAGTATCGATACT
2651797 AATAGCATCA
Statistics
Matches: 110, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
93 2 0.02
94 74 0.67
95 32 0.29
96 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (94 bp):
GTATCGATACCTTACTCATAGTATCGATACTTCTATACTATGGTACCAATACTCCTTTTCAGTAT
CGATACCATTTCCATATTCTCGATTCATG
Found at i:2652679 original size:53 final size:54
Alignment explanation
Indices: 2652615--2652732 Score: 139
Period size: 54 Copynumber: 2.2 Consensus size: 54
2652605 ACTCCTTTTC
* **
2652615 AGTATCAATACCATTTCCACATTCT-GGATCCATGGTATCGATACCTTTCCCTT
1 AGTATCGATACCATTTCCACATTCTAAAATCCATGGTATCGATACCTTTCCCTT
** * * * *
2652668 AGTATCGATACCATTTCTTCCTTCTAAAATCCCTGGTATTGATACCTTTCTCTT
1 AGTATCGATACCATTTCCACATTCTAAAATCCATGGTATCGATACCTTTCCCTT
*
2652722 AGTATTGATAC
1 AGTATCGATAC
2652733 TCCCATCAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
53 21 0.39
54 33 0.61
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (54 bp):
AGTATCGATACCATTTCCACATTCTAAAATCCATGGTATCGATACCTTTCCCTT
Found at i:2653242 original size:81 final size:82
Alignment explanation
Indices: 2653123--2653531 Score: 585
Period size: 81 Copynumber: 5.0 Consensus size: 82
2653113 ATTTAGTATA
* * * * *
2653123 TCATCTAAAGGCAATTAACCTTTCATATAACTTGCATTATTAGCACTA-TTCTGCCAAATGCACT
1 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCACA
*
2653187 GTTAGGCATCTAATCTT
66 GTTAGGCATTTAATCTT
* * * *
2653204 TCATCCAAAGTCATTTAACATTTCATCTAATTTTCATTATTGGCA-TATTTCTGCCAAATGCACA
1 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCACA
2653268 GTTAGGCATTTAATCTT
66 GTTAGGCATTTAATCTT
* * * * *
2653285 TTATCCAAAGGCATTTAACCTTTCATCTAACTTGCAATATTGGCAC-CTTTATGCCAAATGAACA
1 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCACA
2653349 GTTAGGCATTTAATCTT
66 GTTAGGCATTTAATCTT
* *
2653366 TTATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCAC-ATTTCTACCAAATGCACA
1 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCACA
* *
2653430 GTAAGGCATTTAATGTT
66 GTTAGGCATTTAATCTT
* * *
2653447 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCAC-ATTTCTACCAAACGCATA
1 TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCACA
2653511 GTTAGGCATTTAATCTT
66 GTTAGGCATTTAATCTT
2653528 TCAT
1 TCAT
2653532 TTTAAAACAA
Statistics
Matches: 295, Mismatches: 31, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
80 2 0.01
81 293 0.99
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (82 bp):
TCATCCAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTATTTCTGCCAAATGCACA
GTTAGGCATTTAATCTT
Found at i:2653458 original size:22 final size:22
Alignment explanation
Indices: 2653432--2653473 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2653422 AATGCACAGT
**
2653432 AAGGCATTTAATGTTTCATCCA
1 AAGGCATTTAACCTTTCATCCA
2653454 AAGGCATTTAACCTTTCATC
1 AAGGCATTTAACCTTTCATC
2653474 TAACTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (22 bp):
AAGGCATTTAACCTTTCATCCA
Found at i:2653926 original size:20 final size:21
Alignment explanation
Indices: 2653901--2653954 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
2653891 TGGCTCAATA
*
2653901 GTATCGGTAC-CTATACCATG
1 GTATCGATACTCTATACCATG
*
2653921 GTATCGATACTTCTATACTATG
1 GTATCGATAC-TCTATACCATG
*
2653943 GTATCAATACTC
1 GTATCGATACTC
2653955 CTTTTCAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.31
21 2 0.07
22 18 0.62
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (21 bp):
GTATCGATACTCTATACCATG
Found at i:2653938 original size:22 final size:22
Alignment explanation
Indices: 2653911--2653953 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2653901 GTATCGGTAC
*
2653911 CTATACCATGGTATCGATACTT
1 CTATACCATGGTATCAATACTT
*
2653933 CTATACTATGGTATCAATACT
1 CTATACCATGGTATCAATACT
2653954 CCTTTTCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (22 bp):
CTATACCATGGTATCAATACTT
Found at i:2654006 original size:94 final size:94
Alignment explanation
Indices: 2653901--2654119 Score: 260
Period size: 94 Copynumber: 2.3 Consensus size: 94
2653891 TGGCTCAATA
* * *
2653901 GTATCGGTACCTATAC-CATGGTATCGATACTTCTATACTATGGTATCAATACTCCTTTTCAGTA
1 GTATCGATACCT-TACTCATAGTATCGATACTTCTATACTATGGTATCAATACTCATTTTCAGTA
*
2653965 TCAATGCCATTTCCATATTCTCGATTCATG
65 TCAATACCATTTCCATATTCTCGATTCATG
* * *
2653995 GTATCGATACCTTTCTCTTAGTATCGATACTTCTATACTATGGTATCGATACTCATTTTCAGTAT
1 GTATCGATACCTTACTCATAGTATCGATACTTCTATACTATGGTATCAATACTCATTTTCAGTAT
* ** * * * *
2654060 CGATACCATTTCTTTTTTCTGGAATCCCTG
66 CAATACCATTTCCATATTCTCG-ATTCATG
* * *
2654090 GTATCGATACCTTTCTCTTAGTATTGATAC
1 GTATCGATACCTTACTCATAGTATCGATAC
2654120 CTTTCTCTTA
Statistics
Matches: 108, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
93 2 0.02
94 72 0.67
95 34 0.31
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (94 bp):
GTATCGATACCTTACTCATAGTATCGATACTTCTATACTATGGTATCAATACTCATTTTCAGTAT
CAATACCATTTCCATATTCTCGATTCATG
Found at i:2654118 original size:20 final size:20
Alignment explanation
Indices: 2654090--2654139 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2654080 GGAATCCCTG
2654090 GTATCGATACCTTTCTCTTA
1 GTATCGATACCTTTCTCTTA
*
2654110 GTATTGATACCTTTCTCTTA
1 GTATCGATACCTTTCTCTTA
2654130 GTATCGATAC
1 GTATCGATAC
2654140 TAATAGCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (20 bp):
GTATCGATACCTTTCTCTTA
Found at i:2667340 original size:19 final size:20
Alignment explanation
Indices: 2667311--2667353 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2667301 AATAAAATTC
2667311 AAAAAGTTTTATATTGAT-TT
1 AAAAAGTTTTATATT-ATATT
2667331 AAAAAG-TTTATATTATATT
1 AAAAAGTTTTATATTATATT
2667350 AAAA
1 AAAA
2667354 TTAGTTGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.09
19 14 0.64
20 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
AAAAAGTTTTATATTATATT
Found at i:2669154 original size:13 final size:13
Alignment explanation
Indices: 2669138--2669205 Score: 54
Period size: 13 Copynumber: 5.4 Consensus size: 13
2669128 AAAATGTTAG
2669138 ATAAAAATAATAA
1 ATAAAAATAATAA
* **
2669151 ATAAATCA-AAGGA
1 ATAAA-AATAATAA
2669164 A-AAAAATAA-AA
1 ATAAAAATAATAA
*
2669175 TAAAAAAATAATAA
1 -ATAAAAATAATAA
2669189 ATAAAAATAAT-A
1 ATAAAAATAATAA
2669201 ATAAA
1 ATAAA
2669206 TCAAAGGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
11 2 0.05
12 12 0.27
13 27 0.61
14 3 0.07
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (13 bp):
ATAAAAATAATAA
Found at i:2669187 original size:16 final size:16
Alignment explanation
Indices: 2669163--2669205 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
2669153 AAATCAAAGG
2669163 AAAAA-AATAAAATAA
1 AAAAATAATAAAATAA
2669178 AAAAATAAT-AAATAA
1 AAAAATAATAAAATAA
2669193 AAATAATAATAAA
1 AAA-AATAATAAA
2669206 TCAAAGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 14 0.56
16 9 0.36
17 2 0.08
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAATAATAAAATAA
Found at i:2669217 original size:27 final size:26
Alignment explanation
Indices: 2669138--2669234 Score: 96
Period size: 25 Copynumber: 3.8 Consensus size: 26
2669128 AAAATGTTAG
2669138 ATAAAAATAATAAATAAATCAAAGG--A
1 ATAAAAAT-A-AAATAAATCAAAGGAAA
* **
2669164 A-AAAAATAAAATAAA-AAAATAATAA
1 ATAAAAATAAAATAAATCAAAGGA-AA
2669189 ATAAAAATAATAATAAATCAAAGGAAA
1 ATAAAAATAA-AATAAATCAAAGGAAA
2669216 ATAAAAAT-AAATAAATCAA
1 ATAAAAATAAAATAAATCAA
2669235 TCAATCAAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
22 3 0.05
23 7 0.12
24 1 0.02
25 18 0.31
26 10 0.17
27 16 0.27
28 4 0.07
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (26 bp):
ATAAAAATAAAATAAATCAAAGGAAA
Found at i:2669217 original size:34 final size:34
Alignment explanation
Indices: 2669179--2669261 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 34
2669169 ATAAAATAAA
2669179 AAAATAATAAATAAAAATAAT-AATAAATCAAAGG
1 AAAATAATAAATAAAAA-AATCAATAAATCAAAGG
* *
2669213 AAAATAA-AAATAAATAAATCAATCAATCAAAGG
1 AAAATAATAAATAAAAAAATCAATAAATCAAAGG
*
2669246 GAAA-AATAAAATAAAA
1 AAAATAAT-AAATAAAA
2669262 GAGTTAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
32 5 0.12
33 23 0.55
34 14 0.33
ACGTcount: A:0.71, C:0.05, G:0.06, T:0.18
Consensus pattern (34 bp):
AAAATAATAAATAAAAAAATCAATAAATCAAAGG
Found at i:2669226 original size:33 final size:34
Alignment explanation
Indices: 2669179--2669261 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 34
2669169 ATAAAATAAA
2669179 AAAATAATAAATAAAAATAAT-AATAAATCAAA-GG
1 AAAATAA-AAATAAAAA-AATCAATAAATCAAAGGG
* *
2669213 AAAATAAAAATAAATAAATCAATCAATCAAAGGG
1 AAAATAAAAATAAAAAAATCAATAAATCAAAGGG
2669247 AAAA-ATAAAATAAAA
1 AAAATA-AAAATAAAA
2669262 GAGTTAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
32 3 0.07
33 19 0.44
34 21 0.49
ACGTcount: A:0.71, C:0.05, G:0.06, T:0.18
Consensus pattern (34 bp):
AAAATAAAAATAAAAAAATCAATAAATCAAAGGG
Found at i:2669254 original size:50 final size:50
Alignment explanation
Indices: 2669138--2669255 Score: 123
Period size: 50 Copynumber: 2.3 Consensus size: 50
2669128 AAAATGTTAG
*
2669138 ATAAAAATAATAAATAAATCAAAGGAAAAAAATAAAATAAAAAAATAATAA
1 ATAAAAAGAA-AAATAAATCAAAGGAAAAAAATAAAATAAAAAAATAATAA
* * * * *
2669189 ATAAAAATAATAATAAATCAAAGG-AAAATA-AAAATAAATAAATCAATCA
1 ATAAAAAGAAAAATAAATCAAAGGAAAAAAATAAAATAAAAAAAT-AATAA
**
2669238 ATCAAAGGGAAAAATAAA
1 AT-AAAAAGAAAAATAAA
2669256 ATAAAAGAGT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
48 12 0.21
49 11 0.19
50 24 0.42
51 10 0.18
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (50 bp):
ATAAAAAGAAAAATAAATCAAAGGAAAAAAATAAAATAAAAAAATAATAA
Found at i:2670633 original size:36 final size:37
Alignment explanation
Indices: 2670582--2671090 Score: 593
Period size: 36 Copynumber: 13.8 Consensus size: 37
2670572 AATATTTTCA
*
2670582 AAAAACTATA-A-TATATGTA-TTTTCAAAAT-TATTT
1 AAAAACTATATATTATATATAGTTTTCAAAATGT-TTT
* ** * *
2670616 AAAAACTCTATATTATATATTTTTTTAAAAACGTTTT
1 AAAAACTATATATTATATATAGTTTTCAAAATGTTTT
*
2670653 CAAAACTATATA-T-TATATAGTTTTCAAAATGTTTT
1 AAAAACTATATATTATATATAGTTTTCAAAATGTTTT
*
2670688 AAAAATTATATATTATATATA-TTTTCAAAATGTTTTTTT
1 AAAAACTATATATTATATATAGTTTTCAAAATG---TTTT
*
2670727 AAAAACCATATATTATATA-AGTTTTCAAAATGTCTTTT
1 AAAAACTATATATTATATATAGTTTTCAAAATG--TTTT
2670765 AAAAA-TCATATATTATATA-AGTTTTCAAAATGTTTT
1 AAAAACT-ATATATTATATATAGTTTTCAAAATGTTTT
*
2670801 AAAAACTATGTATTATATATAAGTTTTCAAAATGTTTT
1 AAAAACTATATATTATATAT-AGTTTTCAAAATGTTTT
*
2670839 -AAAACTATATATTATATATATTTTTTCAAAATGTTTT
1 AAAAACTATATATTATATATA-GTTTTCAAAATGTTTT
*
2670876 AAAAATTATATATTATATATA-TAGTTTCAAAATGTTTT
1 AAAAACTATATATTATATATAGT--TTTCAAAATGTTTT
* * *
2670914 AAAAACTATATATTATATATATTTTTTTTAAAATATTTT
1 AAAAACTATATATTATATATA--GTTTTCAAAATGTTTT
* * *
2670953 AAAAATTCTATATTATATATA-TTTTTAAAATGTTTT
1 AAAAACTATATATTATATATAGTTTTCAAAATGTTTT
**
2670989 AAAAACTATATATTATATA-AGTTTTCAAAACATTTT
1 AAAAACTATATATTATATATAGTTTTCAAAATGTTTT
2671025 AAAAACTATATATTATATATA-TTTTCAAAATGTTTT
1 AAAAACTATATATTATATATAGTTTTCAAAATGTTTT
2671061 AAAATA-TATATATTATATAT-GTTTTCAAAA
1 AAAA-ACTATATATTATATATAGTTTTCAAAA
2671091 ACGATTTTTT
Statistics
Matches: 416, Mismatches: 34, Indels: 48
0.84 0.07 0.10
Matches are distributed among these distances:
34 9 0.02
35 30 0.07
36 143 0.34
37 63 0.15
38 107 0.26
39 63 0.15
41 1 0.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (37 bp):
AAAAACTATATATTATATATAGTTTTCAAAATGTTTT
Found at i:2670803 original size:113 final size:110
Alignment explanation
Indices: 2670582--2671090 Score: 566
Period size: 113 Copynumber: 4.6 Consensus size: 110
2670572 AATATTTTCA
* * ** *
2670582 AAAAACTATA-A-TATATGTATTTTCAAAAT-TATTTAAAAACTC-TATATTATATATTTTTTTA
1 AAAAACTATATATTATATATATTTTCAAAATGTTTTTAAAAAC-CATATATTATATATAGTTTTC
* *
2670643 AAAACGTTTTCAAAA-CTATATATTATAT-AGTTTTCAAAATGTTTT
65 AAAATGTTTTAAAAATC-ATATATTATATAAGTTTTCAAAATGTTTT
*
2670688 AAAAATTATATATTATATATATTTTCAAAATGTTTTTTTAAAAACCATATATTATATA-AGTTTT
1 AAAAACTATATATTATATATATTTTCAAAATG--TTTTTAAAAACCATATATTATATATAGTTTT
2670752 CAAAATGTCTTTTAAAAATCATATATTATATAAGTTTTCAAAATGTTTT
64 CAAAATG--TTTTAAAAATCATATATTATATAAGTTTTCAAAATGTTTT
* * *
2670801 AAAAACTATGTATTATATATAAGTTTTCAAAATG-TTTT-AAAACTATATATTATATATATTTTT
1 AAAAACTATATATTATATAT-A-TTTTCAAAATGTTTTTAAAAACCATATATTATATATA-GTTT
*
2670864 TCAAAATGTTTTAAAAATTATATATTATATATA-TAGTTTCAAAATGTTTT
63 TCAAAATGTTTTAAAAATCATATATTATATA-AGT--TTTCAAAATGTTTT
* * *
2670914 AAAAACTATATATTATATATATTTTTTTTAAAAT-ATTTTAAAAATTC-TATATTATATATA-TT
1 AAAAACTATATATTATATATA---TTTTCAAAATGTTTTTAAAAA-CCATATATTATATATAGTT
* **
2670976 TTTAAAATGTTTTAAAAA-CTATATATTATATAAGTTTTCAAAACATTTT
62 TTCAAAATGTTTTAAAAATC-ATATATTATATAAGTTTTCAAAATGTTTT
*
2671025 AAAAACTATATATTATATATATTTTCAAAATG-TTTTAAAATA-TATATATTATATAT-GTTTTC
1 AAAAACTATATATTATATATATTTTCAAAATGTTTTTAAAA-ACCATATATTATATATAGTTTTC
2671087 AAAA
65 AAAA
2671091 ACGATTTTTT
Statistics
Matches: 350, Mismatches: 25, Indels: 54
0.82 0.06 0.13
Matches are distributed among these distances:
106 9 0.03
107 1 0.00
108 54 0.15
109 1 0.00
110 10 0.03
111 94 0.27
112 27 0.08
113 112 0.32
114 14 0.04
115 28 0.08
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (110 bp):
AAAAACTATATATTATATATATTTTCAAAATGTTTTTAAAAACCATATATTATATATAGTTTTCA
AAATGTTTTAAAAATCATATATTATATAAGTTTTCAAAATGTTTT
Found at i:2672391 original size:5 final size:5
Alignment explanation
Indices: 2672353--2673073 Score: 1251
Period size: 5 Copynumber: 146.6 Consensus size: 5
2672343 GATGGTAATG
* * *
2672353 ATGTT AATGTT CTGTT ATTTT ATAGAT ATG-T ATGTT ATGTT ATGTT ATGTT
1 ATGTT -ATGTT ATGTT ATGTT AT-GTT ATGTT ATGTT ATGTT ATGTT ATGTT
2672404 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
2672454 ATGTT ATGTT ATGTT ATGTT A-GTT ATGTT ATG-T ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
2672502 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
2672552 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
2672602 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
2672652 ATGTT ATG-T -TGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT A--TGTT ATGTT
2672702 ATGTT ATG-T ATGTT ATG-T ATGTT ATGTT ATGTT ATGTT ATG-T ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
2672749 ATGTT ATGTT ATG-T ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
2672798 ATG-T ATGTT ATGTT A-GTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
2672846 ATGTT ATGTT ATGTT ATGTT ATG-T ATGTT ATGTT ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
2672895 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT -TGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
2672944 ATGTT ATGTT ATGTT ATGTT ATG-T -TGTT ATGTT ATGTTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATG-TT ATGTT ATGTT
2672993 ATG-T -TGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT
2673041 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATG
1 ATGTT ATGTT ATGTT ATGTT ATGTT ATGTT ATG
2673074 ATAAGGGTTT
Statistics
Matches: 689, Mismatches: 5, Indels: 43
0.93 0.01 0.06
Matches are distributed among these distances:
3 6 0.01
4 50 0.07
5 615 0.89
6 13 0.02
7 5 0.01
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.59
Consensus pattern (5 bp):
ATGTT
Found at i:2673218 original size:19 final size:19
Alignment explanation
Indices: 2673194--2673239 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2673184 CTGTTTGACA
* *
2673194 CAAAATATGTTCAACCTCT
1 CAAAATAAGTGCAACCTCT
2673213 CAAAATAAGTGCAACCTCT
1 CAAAATAAGTGCAACCTCT
2673232 CAAAATAA
1 CAAAATAA
2673240 CAACCTTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.24
Consensus pattern (19 bp):
CAAAATAAGTGCAACCTCT
Found at i:2673245 original size:16 final size:17
Alignment explanation
Indices: 2673205--2673245 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
2673195 AAAATATGTT
2673205 CAACCTCTCAAAATAAGTG
1 CAACCTCTCAAAATAA--G
2673224 CAACCTCTCAAAATAA-
1 CAACCTCTCAAAATAAG
2673240 CAACCT
1 CAACCT
2673246 TCGATCCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.27
19 16 0.73
ACGTcount: A:0.44, C:0.32, G:0.05, T:0.20
Consensus pattern (17 bp):
CAACCTCTCAAAATAAG
Found at i:2676247 original size:24 final size:24
Alignment explanation
Indices: 2676220--2676276 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
2676210 CATTTTCAGG
*
2676220 ATTGGTTTTAGTATGTTCAACAAC
1 ATTGGTTTCAGTATGTTCAACAAC
*
2676244 ATTGGTTTCAGTATGTTCAACAAT
1 ATTGGTTTCAGTATGTTCAACAAC
2676268 ATTGGTTTC
1 ATTGGTTTC
2676277 CACAACTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (24 bp):
ATTGGTTTCAGTATGTTCAACAAC
Found at i:2677523 original size:13 final size:12
Alignment explanation
Indices: 2677505--2677562 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
2677495 ATTTCAGAAC
*
2677505 TTTCATATTTTAT
1 TTTCATA-TTCAT
*
2677518 TTTCATCATTCAC
1 TTTCAT-ATTCAT
* *
2677531 TTTCACATTCCT
1 TTTCATATTCAT
2677543 TTTCATATTTCAT
1 TTTCATA-TTCAT
2677556 TTTCATA
1 TTTCATA
2677563 ATCAATACTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
12 10 0.28
13 25 0.69
14 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTCATATTCAT
Found at i:2680961 original size:13 final size:12
Alignment explanation
Indices: 2680940--2680969 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
2680930 AATACACACT
2680940 ATAAAATATGCA
1 ATAAAATATGCA
2680952 ATAAATATATGCA
1 ATAAA-ATATGCA
2680965 ATAAA
1 ATAAA
2680970 CATTTAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (12 bp):
ATAAAATATGCA
Found at i:2682896 original size:23 final size:23
Alignment explanation
Indices: 2682843--2682907 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
2682833 TTAGTTGCCT
*
2682843 AACATTAAAAGTACATGATCACG
1 AACATTAAAAGAACATGATCACG
* * *
2682866 AACGTTAAATGAACATGATCGCG
1 AACATTAAAAGAACATGATCACG
* *
2682889 GACATTAAACGAACATGAT
1 AACATTAAAAGAACATGAT
2682908 TCATTATAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.22
Consensus pattern (23 bp):
AACATTAAAAGAACATGATCACG
Found at i:2687747 original size:20 final size:19
Alignment explanation
Indices: 2687724--2687769 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
2687714 CGATATACCA
2687724 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
2687744 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
2687764 GGTAAA
1 GGTAAA
2687770 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2687912 original size:20 final size:19
Alignment explanation
Indices: 2687889--2687935 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2687879 CGATATAACA
2687889 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
2687909 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
2687929 GGTAAAA
1 GGTAAAA
2687936 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2687937 original size:17 final size:19
Alignment explanation
Indices: 2687898--2687940 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2687888 AGGTAAAAAT
2687898 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
2687918 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
2687935 ATGATA
1 ATGATA
2687941 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:2690215 original size:21 final size:21
Alignment explanation
Indices: 2690168--2690231 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
2690158 AAGACAATCA
* *
2690168 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
2690190 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
2690210 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
2690231 A
1 A
2690232 TGCTGAGGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.28, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:2690312 original size:33 final size:33
Alignment explanation
Indices: 2690265--2690330 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2690255 AAATAGATGG
* *
2690265 AGTGGTGAATGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
2690298 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2690331 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.48, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2692149 original size:19 final size:19
Alignment explanation
Indices: 2692125--2692173 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2692115 AATGTAGGGT
2692125 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2692144 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
2692163 TATTTTTGTAT
1 TAATTTTGTAT
2692174 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2692634 original size:198 final size:198
Alignment explanation
Indices: 2692292--2693041 Score: 1410
Period size: 198 Copynumber: 3.8 Consensus size: 198
2692282 CAATATGGCC
*
2692292 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATTGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
**
2692357 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTTATTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGATTTTATGAGAG
*
2692422 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
2692487 GAA
196 GAA
2692490 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
2692555 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGATTTTATGAGAG
*
2692620 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCAGAATGAATG
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
2692685 GAA
196 GAA
2692688 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
**
2692753 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACTTATTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGATTTTATGAGAG
*
2692818 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
2692883 GAA
196 GAA
2692886 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
2692951 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGATTTTATGAGAG
2693016 AATATGTATAAATAATGTGTCGACAC
131 AATATGTATAAATAATGTGTCGACAC
2693042 AATTATACCG
Statistics
Matches: 537, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
198 537 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGATTTTATGAGAG
AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:2695225 original size:25 final size:25
Alignment explanation
Indices: 2695191--2695255 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
2695181 TTATCATTAA
2695191 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
2695216 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
2695241 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
2695256 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:2695633 original size:23 final size:23
Alignment explanation
Indices: 2695602--2695665 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2695592 ATAGGTAAAC
*
2695602 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
2695625 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
2695648 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
2695666 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:2695672 original size:23 final size:23
Alignment explanation
Indices: 2695602--2695674 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
2695592 ATAGGTAAAC
* **
2695602 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
2695625 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
2695648 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
2695671 ATAT
1 ATAT
2695675 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:2695977 original size:25 final size:25
Alignment explanation
Indices: 2695943--2695993 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
2695933 ACAACAAATC
*
2695943 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
2695968 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
2695993 A
1 A
2695994 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Done.