Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009573.1 Hibiscus syriacus cultivar Beakdansim tig00116938_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: 1247605
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:2862 original size:14 final size:14
Alignment explanation
Indices: 2843--2878 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2833 ATTGTTTAAT
2843 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2857 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2871 TGATTTGT
1 TGATTTGT
2879 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3079 original size:19 final size:19
Alignment explanation
Indices: 3057--3174 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
3047 CGAAATTAAA
3057 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3076 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
3091 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3109 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
3124 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
3142 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
3161 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
3175 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:3103 original size:33 final size:33
Alignment explanation
Indices: 3061--3154 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
3051 ATTAAATTCG
3061 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
3094 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
3127 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3155 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:5452 original size:12 final size:12
Alignment explanation
Indices: 5435--5459 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5425 TCTTCGGGGA
5435 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5447 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5459 C
1 C
5460 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:7121 original size:20 final size:20
Alignment explanation
Indices: 7096--7146 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
7086 ATTCATTTGA
*
7096 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
7116 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
7136 TTATCGCAACG
1 CTATCGCAACG
7147 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:7199 original size:14 final size:15
Alignment explanation
Indices: 7180--7248 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 15
7170 AATCGCATTA
7180 CGATTTTCTCG-TTG
1 CGATTTTCTCGATTG
7194 CGATTTTCATTTCGCATTG
1 CGATTTTC---TCG-ATTG
*
7213 CGATTTCATTTCGCATTG
1 CGATTT--TCTCG-ATTG
7231 CGATTTTCTCG-TTG
1 CGATTTTCTCGATTG
7245 CGAT
1 CGAT
7249 AGCCATTTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
14 15 0.33
16 4 0.09
17 3 0.07
18 14 0.30
19 9 0.20
21 1 0.02
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (15 bp):
CGATTTTCTCGATTG
Found at i:7213 original size:19 final size:19
Alignment explanation
Indices: 7191--7238 Score: 89
Period size: 18 Copynumber: 2.6 Consensus size: 19
7181 GATTTTCTCG
7191 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
7210 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
7228 TTGCGATTTTC
1 TTGCGATTTTC
7239 TCGTTGCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:7374 original size:14 final size:14
Alignment explanation
Indices: 7355--7391 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
7345 CATCAATTAA
7355 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
7369 ACAAATCATCTTTT
1 ACAAATCAACATTT
7383 ACAAATCAA
1 ACAAATCAA
7392 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:8876 original size:42 final size:43
Alignment explanation
Indices: 8796--8878 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
8786 TTCAACGATG
* * *
8796 ATAGTGGCCTCTTGAACGGTGGGGGGGGGAATCTTGAGGGAGA
1 ATAGGGGCCTCTTGAACGATGGGGAGGGGAATCTTGAGGGAGA
* *
8839 ATAGGGGCCTCTTGAACGAT-TGGAGGGGACTCTTGAGGGA
1 ATAGGGGCCTCTTGAACGATGGGGAGGGGAATCTTGAGGGA
8879 TGACCGGTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 17 0.49
43 18 0.51
ACGTcount: A:0.22, C:0.13, G:0.43, T:0.22
Consensus pattern (43 bp):
ATAGGGGCCTCTTGAACGATGGGGAGGGGAATCTTGAGGGAGA
Found at i:9321 original size:14 final size:14
Alignment explanation
Indices: 9302--9359 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
9292 ATGCGAAATG
9302 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
9316 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
9332 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
9348 AAAATCGCAACG
1 AAAATCGCAACG
9360 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:9344 original size:32 final size:33
Alignment explanation
Indices: 9286--9376 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
9276 GGAAATGGCT
*
9286 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
9319 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
9351 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
9377 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:9370 original size:19 final size:19
Alignment explanation
Indices: 9228--9381 Score: 114
Period size: 19 Copynumber: 8.6 Consensus size: 19
9218 TAGTTTACTT
* *
9228 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
9248 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
9267 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
9287 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
9306 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
9320 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
9338 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
9352 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
9371 TCGCAATGCGA
1 TCGCAACGCGA
9382 TTTGTGTTTC
Statistics
Matches: 108, Mismatches: 14, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
14 20 0.19
15 1 0.01
16 6 0.06
17 2 0.02
18 11 0.10
19 39 0.36
20 29 0.27
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:9412 original size:14 final size:14
Alignment explanation
Indices: 9393--9450 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
9383 TTGTGTTTCG
9393 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
9407 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
9423 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
9439 CGTTGCGATTTT
1 CGTTGCGATTTT
9451 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:9427 original size:32 final size:33
Alignment explanation
Indices: 9388--9466 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
9378 GCGATTTGTG
9388 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
9420 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
9453 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
9467 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:9465 original size:19 final size:17
Alignment explanation
Indices: 9388--9466 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 17
9378 GCGATTTGTG
9388 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
9404 TGTCG-TTGCGATTTCA
1 TTTCGCTTGCGATTTCA
9420 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
9436 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGA-TTTCA
9453 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
9467 AGCCATTTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
14 15 0.30
15 3 0.06
16 12 0.24
17 4 0.08
18 10 0.20
19 6 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTCGCTTGCGATTTCA
Found at i:9485 original size:20 final size:19
Alignment explanation
Indices: 9451--9505 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
9441 TTGCGATTTT
*
9451 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
9470 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
9490 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
9506 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:11371 original size:20 final size:20
Alignment explanation
Indices: 11346--11383 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11336 AATAGTTTCT
11346 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
11366 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
11384 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:11672 original size:22 final size:22
Alignment explanation
Indices: 11647--11690 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11637 GATTTAGATA
11647 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
11669 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
11691 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:11973 original size:20 final size:20
Alignment explanation
Indices: 11879--11973 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
11869 GATTATGTAT
*
11879 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
11899 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
11919 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
11940 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
11960 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
11974 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:11992 original size:41 final size:41
Alignment explanation
Indices: 11901--12035 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
11891 AAAGTCAGTA
* * * ** *
11901 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
11941 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
11983 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
12024 TCGCGTTGCGAT
1 TCGCGTTGCGAT
12036 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:12006 original size:20 final size:20
Alignment explanation
Indices: 11962--12054 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
11952 ATAGTCAGTA
* **
11962 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
11983 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
12003 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
12024 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
12044 TCGCATTGCGA
1 TCGCATTGCGA
12055 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:12036 original size:41 final size:41
Alignment explanation
Indices: 11962--12057 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
11952 ATAGTCAGTA
*
11962 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
12003 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
12044 TCGCATTGCGAATT
1 TCGCATTGCGAATT
12058 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:15659 original size:2 final size:2
Alignment explanation
Indices: 15652--15698 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
15642 AATACTGACC
15652 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15694 TA TA T
1 TA TA T
15699 TATGAAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18570 original size:73 final size:73
Alignment explanation
Indices: 18484--18628 Score: 254
Period size: 73 Copynumber: 2.0 Consensus size: 73
18474 AGAGATCAAT
* *
18484 TGATGGAAAATATGTGAAAATGTTCAACTCCCCCTTTTTCATTAAGAGATTGAATTTTTCAAACC
1 TGATGAAAAATATGTGAAAATGTTCAACTCCCCATTTTTCATTAAGAGATTGAATTTTTCAAACC
18549 ATACTTCA
66 ATACTTCA
* *
18557 TGATGAAAAATATGTGAAAATGTTCAGCTCCCCATTTTTCATTAAGAGATTGATTTTTTCAAACC
1 TGATGAAAAATATGTGAAAATGTTCAACTCCCCATTTTTCATTAAGAGATTGAATTTTTCAAACC
18622 ATACTTC
66 ATACTTC
18629 TCCCCCTCTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (73 bp):
TGATGAAAAATATGTGAAAATGTTCAACTCCCCATTTTTCATTAAGAGATTGAATTTTTCAAACC
ATACTTCA
Found at i:19636 original size:21 final size:21
Alignment explanation
Indices: 19611--19689 Score: 54
Period size: 20 Copynumber: 3.8 Consensus size: 21
19601 TTAAATTAAA
19611 AATTTCTTTTTCAAAACTTTC
1 AATTTCTTTTTCAAAACTTTC
* * *
19632 AATTTTCATTTTTGAAAGCTCT-
1 AA-TTTC-TTTTTCAAAACTTTC
* *
19654 AAATCCTTTTTCAAAA-TTTC
1 AATTTCTTTTTCAAAACTTTC
* **
19674 ATTTTGGTTTTCAAAA
1 AATTTCTTTTTCAAAA
19690 TCCATTTTAG
Statistics
Matches: 42, Mismatches: 13, Indels: 7
0.68 0.21 0.11
Matches are distributed among these distances:
19 2 0.05
20 19 0.45
21 4 0.10
22 6 0.14
23 11 0.26
ACGTcount: A:0.30, C:0.15, G:0.05, T:0.49
Consensus pattern (21 bp):
AATTTCTTTTTCAAAACTTTC
Found at i:19697 original size:19 final size:20
Alignment explanation
Indices: 19661--19707 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
19651 TCTAAATCCT
* *
19661 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTAG
19681 TTTTCAAAA-TCCATTTTAG
1 TTTTCAAAATTCCATTTTAG
*
19700 CTTTCAAA
1 TTTTCAAA
19708 GGAAAATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAG
Found at i:21010 original size:24 final size:24
Alignment explanation
Indices: 20963--21027 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
20953 AACCGGCCCA
**
20963 ACCCGACCTGAAC-CCTTGACCTG
1 ACCCGACCTGAACTGTTTGACCTG
20986 ACCCGACCTGAACTGTTTGACCTG
1 ACCCGACCTGAACTGTTTGACCTG
* *
21010 ACCCAACCAGAACTGTTT
1 ACCCGACCTGAACTGTTT
21028 TACCCGACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 13 0.35
24 24 0.65
ACGTcount: A:0.25, C:0.37, G:0.17, T:0.22
Consensus pattern (24 bp):
ACCCGACCTGAACTGTTTGACCTG
Found at i:23158 original size:15 final size:15
Alignment explanation
Indices: 23138--23169 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23128 GACTAAGGCC
*
23138 GAGGATTGGCTTAGT
1 GAGGATTAGCTTAGT
23153 GAGGATTAGCTTAGT
1 GAGGATTAGCTTAGT
23168 GA
1 GA
23170 TACTGAGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.38, T:0.31
Consensus pattern (15 bp):
GAGGATTAGCTTAGT
Found at i:24449 original size:15 final size:16
Alignment explanation
Indices: 24429--24469 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
24419 GTTTACTTTA
*
24429 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
24444 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
24460 GAATGATTCA
1 GAATGATTCA
24470 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:25621 original size:17 final size:17
Alignment explanation
Indices: 25599--25631 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25589 GACTTTGGCC
25599 CGAAAAGTCAAATTTTT
1 CGAAAAGTCAAATTTTT
*
25616 CGAAAAGTCATATTTT
1 CGAAAAGTCAAATTTT
25632 ATGTTTTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
CGAAAAGTCAAATTTTT
Found at i:38878 original size:2 final size:2
Alignment explanation
Indices: 38871--38896 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38861 GTAATTATGT
38871 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
38897 AACAGTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40485 original size:24 final size:22
Alignment explanation
Indices: 40464--40504 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40454 AAATATATAT
*
40464 TATA-TATAATTTTTGAAAATA
1 TATAGTATATTTTTTGAAAATA
40485 TATAGTATATTTTTTGAAAA
1 TATAGTATATTTTTTGAAAA
40505 CATGTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (22 bp):
TATAGTATATTTTTTGAAAATA
Found at i:40514 original size:14 final size:14
Alignment explanation
Indices: 40495--40521 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40485 TATAGTATAT
40495 TTTTTGAAAACATG
1 TTTTTGAAAACATG
40509 TTTTTGAAAACAT
1 TTTTTGAAAACAT
40522 ATAATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (14 bp):
TTTTTGAAAACATG
Found at i:40585 original size:40 final size:40
Alignment explanation
Indices: 40482--40587 Score: 128
Period size: 40 Copynumber: 2.6 Consensus size: 40
40472 ATTTTTGAAA
* *
40482 ATATATAGTATATTTTTTGAAAACATGTTTTTGAAAACAT
1 ATATATAATATAGTTTTTGAAAACATGTTTTTGAAAACAT
* *
40522 ATA-AT-ATATAGTTTTCTTAAAA-ACTGTTTTTTGGAAACAT
1 ATATATAATATAGTTTT-TGAAAACA-TG-TTTTTGAAAACAT
40562 ATATATAATATAGTTTTTGAAAACAT
1 ATATATAATATAGTTTTTGAAAACAT
40588 ATAATATAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
38 9 0.16
39 9 0.16
40 18 0.33
41 8 0.15
42 11 0.20
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (40 bp):
ATATATAATATAGTTTTTGAAAACATGTTTTTGAAAACAT
Found at i:40592 original size:22 final size:21
Alignment explanation
Indices: 40564--40605 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
40554 GGAAACATAT
40564 ATATAATATAGTTTTTGAAAAC
1 ATATAATATAGTTTTT-AAAAC
40586 ATATAATATAGTTTTTAAAA
1 ATATAATATAGTTTTTAAAA
40606 TATTTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (21 bp):
ATATAATATAGTTTTTAAAAC
Found at i:40608 original size:36 final size:37
Alignment explanation
Indices: 40571--40737 Score: 173
Period size: 36 Copynumber: 4.5 Consensus size: 37
40561 TATATATAAT
40571 ATAGTTTTTGAAAACATAT-A-ATATAGTTTTT-AAA
1 ATAGTTTTTGAAAACATATAATATATAGTTTTTAAAA
* *
40605 ATA-TTTTTGAAAACATATAATATATAATTTTTTAAA
1 ATAGTTTTTGAAAACATATAATATATAGTTTTTAAAA
* * * * *
40641 ATA-TTTTTTAAAACTTATATTATATAGTTTTTTACA
1 ATAGTTTTTGAAAACATATAATATATAGTTTTTAAAA
*
40677 ATGGTTTTTGAAAACATATAATATATAGTTTTTTTAAAAAA
1 ATAGTTTTTGAAAACATATAATATATAG--TTTTT--AAAA
*
40718 ATGGTTTTTGGAAAACATAT
1 ATAGTTTTT-GAAAACATAT
40738 TTTTCAAAAT
Statistics
Matches: 112, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
33 15 0.13
34 4 0.04
35 10 0.09
36 36 0.32
37 21 0.19
39 5 0.04
41 11 0.10
42 10 0.09
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (37 bp):
ATAGTTTTTGAAAACATATAATATATAGTTTTTAAAA
Found at i:40673 original size:37 final size:36
Alignment explanation
Indices: 40575--40715 Score: 189
Period size: 36 Copynumber: 3.9 Consensus size: 36
40565 TATAATATAG
40575 TTTTTGAAAACATAT-A-ATATAG-TTTTTAAAATA
1 TTTTTGAAAACATATAATATATAGTTTTTTAAAATA
*
40608 TTTTTGAAAACATATAATATATAATTTTTTAAAATA
1 TTTTTGAAAACATATAATATATAGTTTTTTAAAATA
* * * * *
40644 TTTTTTAAAACTTATATTATATAGTTTTTTACAATGG
1 TTTTTGAAAACATATAATATATAGTTTTTTAAAAT-A
40681 TTTTTGAAAACATATAATATATAGTTTTTTTAAAA
1 TTTTTGAAAACATATAATATATAG-TTTTTTAAAA
40716 AAATGGTTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
33 15 0.16
34 1 0.01
35 5 0.05
36 41 0.45
37 21 0.23
38 9 0.10
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (36 bp):
TTTTTGAAAACATATAATATATAGTTTTTTAAAATA
Found at i:40780 original size:5 final size:5
Alignment explanation
Indices: 40770--40820 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
40760 TTATTACTAG
*
40770 TATTT TATTT TCCATTT TATTT TATTT TA-TT TATTC T-TTT TATTT TATTT
1 TATTT TATTT T--ATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
40820 T
1 T
40821 TCGGTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 7 0.17
5 28 0.70
7 5 0.12
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:40795 original size:22 final size:23
Alignment explanation
Indices: 40770--40820 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
40760 TTATTACTAG
40770 TATTTTATTT-TCCATTTTATTT
1 TATTTTATTTATCCATTTTATTT
* *
40792 TATTTTATTTATTCTTTTTATTT
1 TATTTTATTTATCCATTTTATTT
40815 TATTTT
1 TATTTT
40821 TCGGTCCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (23 bp):
TATTTTATTTATCCATTTTATTT
Found at i:59285 original size:13 final size:13
Alignment explanation
Indices: 59264--59300 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
59254 CTTTACTAAG
*
59264 AATTTTTATTTTT
1 AATTATTATTTTT
*
59277 CATTATTATTTTT
1 AATTATTATTTTT
59290 AATTATTATTT
1 AATTATTATTT
59301 CTACTTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
AATTATTATTTTT
Found at i:65046 original size:2 final size:2
Alignment explanation
Indices: 65039--65117 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
65029 GTCAATCACA
65039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65081 AT 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 AT A
65118 ATTTACGAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65229 original size:13 final size:13
Alignment explanation
Indices: 65211--65255 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
65201 CGCAATGAGC
*
65211 GTCATAAATACGT
1 GTCATAAATGCGT
*
65224 GTCATAAATGTGT
1 GTCATAAATGCGT
65237 GTCATAAATGCGT
1 GTCATAAATGCGT
*
65250 ATCATA
1 GTCATA
65256 GATTTATGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:66149 original size:3 final size:3
Alignment explanation
Indices: 66141--66177 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
66131 ATAAAAAATG
66141 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
66178 CAACGGGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:67160 original size:20 final size:21
Alignment explanation
Indices: 67130--67169 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
67120 TTAACCTAAA
67130 TTAAGGGTTTAGTGATTAGAT
1 TTAAGGGTTTAGTGATTAGAT
67151 TTAA-GGTTTAGTGATTAGA
1 TTAAGGGTTTAGTGATTAGA
67170 GGTTATGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (21 bp):
TTAAGGGTTTAGTGATTAGAT
Found at i:72191 original size:21 final size:19
Alignment explanation
Indices: 72166--72211 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
72156 TTTTTTTCTT
72166 AAAATATGTATTTTTAAATA
1 AAAATAT-TATTTTTAAATA
72186 ATAAATTATTATTTTTAAATA
1 A-AAA-TATTATTTTTAAATA
72207 AAAAT
1 AAAAT
72212 TGTGTGTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 16 0.67
22 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
AAAATATTATTTTTAAATA
Found at i:72710 original size:60 final size:61
Alignment explanation
Indices: 72531--72715 Score: 220
Period size: 60 Copynumber: 3.1 Consensus size: 61
72521 TCATATGTCT
* *
72531 TCAAACTATAAGTCTCATTTTAAATTGGTCCTTAAACTTTTGAATATTT-TAATTTCAT-CC
1 TCAAACTATAACTCTCATTCTAAATTGGTCCTTAAACTTTTGAAT-TTTCTAATTTCATCCC
* * * ** *
72591 TCAAATTATAACTCTCATTCTAAATTAGTTCTTAAACTTTTGAACATTCTAATTCCATCCC
1 TCAAACTATAACTCTCATTCTAAATTGGTCCTTAAACTTTTGAATTTTCTAATTTCATCCC
*
72652 T-AAACTATGAACT-TCATTCTAAATTGGTCCCTAAACTTTTGAATTTTCCT-ATTTCATCCC
1 TCAAACTAT-AACTCTCATTCTAAATTGGTCCTTAAACTTTTGAATTTT-CTAATTTCATCCC
72712 -CAAA
1 TCAAA
72716 TTCTTCCAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
59 2 0.02
60 94 0.90
61 9 0.09
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (61 bp):
TCAAACTATAACTCTCATTCTAAATTGGTCCTTAAACTTTTGAATTTTCTAATTTCATCCC
Found at i:73003 original size:60 final size:57
Alignment explanation
Indices: 72838--73003 Score: 163
Period size: 59 Copynumber: 2.8 Consensus size: 57
72828 GTATATAAGT
* * *
72838 ATAGTTTGGATGAAATTGGAATTTTAAAAAGTTTAGGGACTAATTTAGTATGAAGGTA
1 ATAGTTTGGATGAAATTGGAATATT-AAAAGTTTAGGGACTAATTTAGAATGAAGATA
* * * * * * *
72896 ATAGTTTGGGGATGAAACTGCAATGTTAGAAGTTCAAGGACTAATTTAGAATGATA-ATC
1 ATAGTTT--GGATGAAATTGGAATATTAAAAGTTTAGGGACTAATTTAGAATGA-AGATA
*
72955 ATAGTTTAAGGATAAAATTGGAATATTGAAAAGTTTAGGGACTAATTTA
1 ATAGTTT--GGATGAAATTGGAATATT-AAAAGTTTAGGGACTAATTTA
73004 AAAAGATGGT
Statistics
Matches: 86, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
58 7 0.08
59 45 0.52
60 34 0.40
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (57 bp):
ATAGTTTGGATGAAATTGGAATATTAAAAGTTTAGGGACTAATTTAGAATGAAGATA
Found at i:73017 original size:60 final size:57
Alignment explanation
Indices: 72838--73022 Score: 172
Period size: 60 Copynumber: 3.1 Consensus size: 57
72828 GTATATAAGT
* * * *
72838 ATAGTTTGGATGAAATTGGAATTTTAAAAAGTTTAGGGACTAATTTAGTATGAAGGTA
1 ATAGTTTGGATGAAATTGGAATATT-AAAAGTTTAGGGACTAATTTAGAATGATGGTC
* * * * * * **
72896 ATAGTTTGGGGATGAAACTGCAATGTTAGAAGTTCAAGGACTAATTTAGAATGATAATC
1 ATAGTTT--GGATGAAATTGGAATATTAAAAGTTTAGGGACTAATTTAGAATGATGGTC
* * *
72955 ATAGTTTAAGGATAAAATTGGAATATTGAAAAGTTTAGGGACTAATTTAAAAAGATGGTC
1 ATAGTTT--GGATGAAATTGGAATATT-AAAAGTTTAGGGACTAATTTAGAATGATGGTC
*
73015 ATACTTTG
1 ATAGTTTG
73023 AAGACATATG
Statistics
Matches: 99, Mismatches: 25, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
58 8 0.08
59 45 0.45
60 46 0.46
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.34
Consensus pattern (57 bp):
ATAGTTTGGATGAAATTGGAATATTAAAAGTTTAGGGACTAATTTAGAATGATGGTC
Found at i:74105 original size:122 final size:122
Alignment explanation
Indices: 73888--74129 Score: 466
Period size: 122 Copynumber: 2.0 Consensus size: 122
73878 TAGGACATGG
* *
73888 ATGATCTTTTAATTAAGATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTATTGGAC
1 ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTAATGGAC
73953 AATTTTGATCTTGAAATATTTGTTTAGTTGGCAATTATATATAATAATAATTTGAAA
66 AATTTTGATCTTGAAATATTTGTTTAGTTGGCAATTATATATAATAATAATTTGAAA
74010 ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTAATGGAC
1 ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTAATGGAC
74075 AATTTTGATCTTGAAATATTTGTTTAGTTGGCAATTATATATAATAATAATTTGA
66 AATTTTGATCTTGAAATATTTGTTTAGTTGGCAATTATATATAATAATAATTTGA
74130 CTGTCCCAAA
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 118 1.00
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (122 bp):
ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTAATGGAC
AATTTTGATCTTGAAATATTTGTTTAGTTGGCAATTATATATAATAATAATTTGAAA
Found at i:78186 original size:122 final size:122
Alignment explanation
Indices: 77969--78210 Score: 430
Period size: 122 Copynumber: 2.0 Consensus size: 122
77959 TAGGACATGG
* *
77969 ATGATCTTTTAATTAAGATGTTCTACAACTAGAAAATGAGAACCACTGAGTCAGATTTATTGGAC
1 ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAACCACTAAGTCAGATTTATTGGAC
* *
78034 AATTTTGATCTTGGAATATTTGTTTAGTTGGCAATTATATATAATAATAACTTGAAA
66 AATTTTGATCTTGAAATATTTGTCTAGTTGGCAATTATATATAATAATAACTTGAAA
*
78091 ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTATTGGAC
1 ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAACCACTAAGTCAGATTTATTGGAC
*
78156 AATTTTGATCTTGAAATATTTGTCTAGTTGGCAATTATATATAATAATAATTTGA
66 AATTTTGATCTTGAAATATTTGTCTAGTTGGCAATTATATATAATAATAACTTGA
78211 TTGTCCCACA
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
122 114 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (122 bp):
ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAACCACTAAGTCAGATTTATTGGAC
AATTTTGATCTTGAAATATTTGTCTAGTTGGCAATTATATATAATAATAACTTGAAA
Found at i:84367 original size:122 final size:122
Alignment explanation
Indices: 84150--84513 Score: 674
Period size: 122 Copynumber: 3.0 Consensus size: 122
84140 TAGGACATGG
* * *
84150 ATGATCTTTTAATTAAGATGTTCTACAACTAGAAAATGAGAACCACTGAGTCAGATTTATTGGAC
1 ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTATTGGAC
*
84215 AATTTTGATCTTGGAATATTTGTTTAGTTGGCAATTATATATAATAATAATTTGAAA
66 AATTTTGATCTTGAAATATTTGTTTAGTTGGCAATTATATATAATAATAATTTGAAA
*
84272 ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTAATGGAC
1 ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTATTGGAC
*
84337 AATTTTGATCTTGAAATATTTGCTTAGTTGGCAATTATATATAATAATAATTTGAAA
66 AATTTTGATCTTGAAATATTTGTTTAGTTGGCAATTATATATAATAATAATTTGAAA
84394 ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTATTGGAC
1 ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTATTGGAC
84459 AATTTTGATCTTGAAATATTTGTTTAGTTGGCAATTATATATAATAATAATTTGA
66 AATTTTGATCTTGAAATATTTGTTTAGTTGGCAATTATATATAATAATAATTTGA
84514 TTGTCCCACA
Statistics
Matches: 234, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 234 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (122 bp):
ATGATCTTTTAATTAAAATGTTCTACAACTAGAAAATGAGAGCCACTAAGTCAGATTTATTGGAC
AATTTTGATCTTGAAATATTTGTTTAGTTGGCAATTATATATAATAATAATTTGAAA
Found at i:87453 original size:11 final size:11
Alignment explanation
Indices: 87432--87470 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
87422 AACGGTCAAA
87432 CGGGT-CGGGT
1 CGGGTACGGGT
87442 CGGGTACGGGT
1 CGGGTACGGGT
*
87453 CGGGTCAAGGGT
1 CGGGT-ACGGGT
87465 CGGGTA
1 CGGGTA
87471 AACGGGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 5 0.19
11 11 0.42
12 10 0.38
ACGTcount: A:0.10, C:0.18, G:0.54, T:0.18
Consensus pattern (11 bp):
CGGGTACGGGT
Found at i:91683 original size:26 final size:26
Alignment explanation
Indices: 91654--91705 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
91644 AATGCAGGTT
91654 GTCTGGCCTCAGATCTGATTGGACCC
1 GTCTGGCCTCAGATCTGATTGGACCC
91680 GTCTGGCCTCAGATCTGATTGGACCC
1 GTCTGGCCTCAGATCTGATTGGACCC
91706 CTACTCTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.31, G:0.27, T:0.27
Consensus pattern (26 bp):
GTCTGGCCTCAGATCTGATTGGACCC
Found at i:93768 original size:24 final size:24
Alignment explanation
Indices: 93736--93799 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
93726 AGAGTCCATG
* *
93736 TCAAGTATCATATAAAAATTCAGA
1 TCAAATATCATATAAAAATCCAGA
* * *
93760 TCAAATATCATATCAGAATCCAGG
1 TCAAATATCATATAAAAATCCAGA
* *
93784 TCAAAAATCAGATAAA
1 TCAAATATCATATAAA
93800 CTATTTATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (24 bp):
TCAAATATCATATAAAAATCCAGA
Found at i:98303 original size:18 final size:16
Alignment explanation
Indices: 98271--98301 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
98261 AATATTGAAA
98271 CTTGAACTCAAAAAAG
1 CTTGAACTCAAAAAAG
98287 CTTGAACTCAAAAAA
1 CTTGAACTCAAAAAA
98302 AATTTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTCAAAAAAG
Found at i:98748 original size:22 final size:21
Alignment explanation
Indices: 98723--98763 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
98713 ATATAAAAAT
98723 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
98745 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
98764 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:100602 original size:12 final size:12
Alignment explanation
Indices: 100585--100609 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
100575 CTGTCAGCTA
100585 TCAAACCCCTTT
1 TCAAACCCCTTT
100597 TCAAACCCCTTT
1 TCAAACCCCTTT
100609 T
1 T
100610 TGTAGGGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (12 bp):
TCAAACCCCTTT
Found at i:124776 original size:13 final size:13
Alignment explanation
Indices: 124758--124857 Score: 70
Period size: 13 Copynumber: 7.9 Consensus size: 13
124748 AAGAATGAAT
124758 GAATGAAAAGAAA
1 GAATGAAAAGAAA
124771 GAATGAAAAGAAA
1 GAATGAAAAGAAA
* *
124784 -AAAGAGAAGAAA
1 GAATGAAAAGAAA
*
124796 -AAT-AGAAGAAA
1 GAATGAAAAGAAA
*
124807 -AATAGAGAAGAAA
1 GAAT-GAAAAGAAA
*
124820 AAATGAAAAGAGAA
1 GAATGAAAAGA-AA
124834 GAA-GAAGAAG-AA
1 GAATGAA-AAGAAA
124846 GAA-GAAATAGAA
1 GAATGAAA-AGAA
124858 CATATTAAGT
Statistics
Matches: 75, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
11 12 0.16
12 22 0.29
13 31 0.41
14 10 0.13
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (13 bp):
GAATGAAAAGAAA
Found at i:124807 original size:21 final size:21
Alignment explanation
Indices: 124717--124848 Score: 89
Period size: 21 Copynumber: 6.2 Consensus size: 21
124707 AAGACCAAGA
*
124717 AAGAAAAGAGAA-AATATAGAAA
1 AAGAAAAGAGAAGAATA-A-AAG
* *
124739 AAGAAAAGA-AAGAATGAATG
1 AAGAAAAGAGAAGAATAAAAG
124759 AATGAAAAGA-AAGAATGAAAAG
1 AA-GAAAAGAGAAGAAT-AAAAG
124781 AA-AAAAGAGAAGAA-AAATAG
1 AAGAAAAGAGAAGAATAAA-AG
* *
124801 AAGAAAA-ATAGAGAAGAAAA-
1 AAGAAAAGAGA-AGAATAAAAG
*
124821 AATGAAAAGAGAAGAAGAAGAAG
1 AA-GAAAAGAGAAGAATAA-AAG
124844 AAGAA
1 AAGAA
124849 GAAATAGAAC
Statistics
Matches: 91, Mismatches: 7, Indels: 24
0.75 0.06 0.20
Matches are distributed among these distances:
19 3 0.03
20 17 0.19
21 42 0.46
22 27 0.30
23 2 0.02
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (21 bp):
AAGAAAAGAGAAGAATAAAAG
Found at i:124839 original size:24 final size:24
Alignment explanation
Indices: 124765--124845 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 24
124755 AATGAATGAA
*
124765 AAGAAAGAATGAAAAGAAAAAAGAG
1 AAGAAAAAATGAAAAG-AAAAAGAG
*
124790 AAG-AAAAATAGAAGAA-AAATAGAG
1 AAGAAAAAAT-GAA-AAGAAAAAGAG
124814 AAGAAAAAATGAAAAGAGAAGAAGAAG
1 AAGAAAAAATGAAAAGA-AA-AAG-AG
124841 AAGAA
1 AAGAA
124846 GAAGAAATAG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
23 2 0.04
24 19 0.41
25 14 0.30
26 4 0.09
27 7 0.15
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (24 bp):
AAGAAAAAATGAAAAGAAAAAGAG
Found at i:124857 original size:12 final size:11
Alignment explanation
Indices: 124782--124857 Score: 54
Period size: 11 Copynumber: 6.9 Consensus size: 11
124772 AATGAAAAGA
*
124782 AAAAAGAGAAG
1 AAAAATAGAAG
124793 AAAAATAGAAG
1 AAAAATAGAAG
124804 AAAAATAG-AG
1 AAAAATAGAAG
124814 AAGAAA-A-AATG
1 AA-AAATAGAA-G
*
124825 -AAAAGAGAAG
1 AAAAATAGAAG
124835 AAGAAGA-AGAAG
1 AA-AA-ATAGAAG
124847 AAGAAATAGAA
1 AA-AAATAGAA
124858 CATATTAAGT
Statistics
Matches: 55, Mismatches: 1, Indels: 17
0.75 0.01 0.23
Matches are distributed among these distances:
9 3 0.05
10 9 0.16
11 26 0.47
12 16 0.29
13 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (11 bp):
AAAAATAGAAG
Found at i:126423 original size:45 final size:45
Alignment explanation
Indices: 126351--126892 Score: 577
Period size: 45 Copynumber: 12.0 Consensus size: 45
126341 TAAATCTCAA
* * * *
126351 CTTGCCTTTCTCGTGAATAGGGGTCAATCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* ** * * *
126396 CTTGACTTTCTCGTGAAGAGGAATCAATATTTCAGTG-TTTCAAT
1 CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * * * *
126440 CTTGAATTTCTCGTGAAGAGGAGTCAATCTTTCAGTGTTATCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * * *
126485 CTTGACTTTCTCGTGAAGAGGAGTTAATCTTTTAGCGTTGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * * * * * * *
126530 CTTAACTTTCTAGTGAAGAAGAGTCAATC-TTTCGATGTTTTCCTT
1 CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAG-TGATGTCATT
* * * *
126575 CTTGACTTTCTCGCGAAAAGGAGTAAACC-TTTAATGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
** * *
126619 CTTGACTTTCTCGCAAAGAGGATTCAACCTTTTAGTGATGTAATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* *
126664 CTTGACTTTATCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* *
126709 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTAATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* ** *
126754 CATGACTTTCTCACGAAGATGAGTCAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * * * *
126799 CTTGACTTCCTCGTGTGAAGATGAGTCAACCTTTTAGTTATATGATT
1 CTTGACTTTCTC--GTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * *
126846 CTTGACTTTCTCGGGAAGATGAGTAAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
126891 CT
1 CT
126893 CAACTTGACT
Statistics
Matches: 425, Mismatches: 67, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
44 75 0.18
45 311 0.73
47 39 0.09
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.39
Consensus pattern (45 bp):
CTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATT
Found at i:126684 original size:179 final size:179
Alignment explanation
Indices: 126439--126898 Score: 528
Period size: 179 Copynumber: 2.6 Consensus size: 179
126429 AGTGTTTCAA
* * * * * *
126439 TCTTGAATTTCTCGTGAAGAGGAGTCAATCTTTCAGTGTTATCATTCTTGACTTTCTCGTGAAGA
1 TCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATATAATTCTTGACTTTCTCGCGAAGA
* * * * * *
126504 GGAGTTAATCTTTTAGCGTTGTCATTCTTAACTTTCTAGTGAAGAAGAGTCAATCTTTCGATGT-
66 GGAGTAAACCTTTTAGTGATGTCATTCTTAACTTTCTAGCGAAGAAGAGTCAACCTTT-GA-GTA
* * * *
126568 TTTCCTTCTTGACTTTCTCGCGAAAAGGAGTAAACC-TTTAATGATGTCAT
129 TGTCATTCATGACTTTCTCACGAAAAGGAGTAAACCTTTTAATGATGTCAT
** * * *
126618 TCTTGACTTTCTCGCAAAGAGGATTCAACCTTTTAGTGATGTAATTCTTGACTTTATCGCGAAGA
1 TCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATATAATTCTTGACTTTCTCGCGAAGA
* * * * *
126683 GGAGTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTAAT
66 GGAGTAAACCTTTTAGTGATGTCATTCTTAACTTTCTAGCGAAGAAGAGTCAACCTTTGAGT-AT
* * * *
126748 GTCATTCATGACTTTCTCACGAAGATGAGTCAACCTTTTAGTGATGTCAT
130 GTCATTCATGACTTTCTCACGAAAAGGAGTAAACCTTTTAATGATGTCAT
* * * * *
126798 TCTTGACTTCCTCGTGTGAAGATGAGTCAACCTTTTAGTTATATGATTCTTGACTTTCTCGGGAA
1 TCTTGACTTTCTC--GTGAAGAGGAGTCAACCTTTTAGTGATATAATTCTTGACTTTCTCGCGAA
* *
126863 GATGAGTAAACCTTTTAGTGATGTCATTCTCAACTT
64 GAGGAGTAAACCTTTTAGTGATGTCATTCTTAACTT
126899 GACTTTCTCG
Statistics
Matches: 233, Mismatches: 43, Indels: 7
0.82 0.15 0.02
Matches are distributed among these distances:
177 2 0.01
178 1 0.00
179 132 0.57
180 25 0.11
182 73 0.31
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (179 bp):
TCTTGACTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATATAATTCTTGACTTTCTCGCGAAGA
GGAGTAAACCTTTTAGTGATGTCATTCTTAACTTTCTAGCGAAGAAGAGTCAACCTTTGAGTATG
TCATTCATGACTTTCTCACGAAAAGGAGTAAACCTTTTAATGATGTCAT
Found at i:126940 original size:50 final size:51
Alignment explanation
Indices: 126664--126947 Score: 138
Period size: 45 Copynumber: 6.0 Consensus size: 51
126654 TGATGTAATT
* * * * *
126664 CTTGACTTTATCGCGAAGAGGAGTCAACCTTTTAGTGATGTCA---TT---
1 CTTGACTTTCTCGAGAAGATGAGTAAACCTTTTAGTGATATCATTCTTCAA
* * * * *
126709 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTAATGTCA---TTC-A
1 CTTGACTTTCTCGAGAAGATGAGTAAACCTTTTAGTGATATCATTCTTCAA
* * *
126756 --TGACTTTCTC-ACGAAGATGAGTCAACCTTTTAGTGATGTCATTCTT-GA
1 CTTGACTTTCTCGA-GAAGATGAGTAAACCTTTTAGTGATATCATTCTTCAA
* * * **
126804 CTT--C-CTCGT-GTGAAGATGAGTCAACCTTTTAGT--TAT-ATGATT---
1 CTTGACTTTC-TCGAGAAGATGAGTAAACCTTTTAGTGATATCATTCTTCAA
* *
126846 CTTGACTTTCTCGGGAAGATGAGTAAACCTTTTAGTGATGTCATTC-TCAA
1 CTTGACTTTCTCGAGAAGATGAGTAAACCTTTTAGTGATATCATTCTTCAA
*
126896 CTTGACTTTCTCGCAG-AGATGAGTCAA-CTTTTCAGT-AGTATCATTCTTCAA
1 CTTGACTTTCTCG-AGAAGATGAGTAAACCTTTT-AGTGA-TATCATTCTTCAA
126947 C
1 C
126948 CTAACGTTTT
Statistics
Matches: 195, Mismatches: 19, Indels: 44
0.76 0.07 0.17
Matches are distributed among these distances:
42 3 0.02
44 6 0.03
45 106 0.54
47 27 0.14
48 7 0.04
49 6 0.03
50 34 0.17
51 6 0.03
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (51 bp):
CTTGACTTTCTCGAGAAGATGAGTAAACCTTTTAGTGATATCATTCTTCAA
Found at i:128415 original size:129 final size:129
Alignment explanation
Indices: 128161--128424 Score: 338
Period size: 129 Copynumber: 2.0 Consensus size: 129
128151 TTCATATATG
* * * * *
128161 ATCTTCCCTGAAGAGCAGTGAAGCAAATCTACCTCGATTCAATCTTCCCTGAAGAACAGTGAAGT
1 ATCTTCCCTAAAGAGCAGAGAAGCAAATCAACCTCGATTCAATCTTACCTAAAGAACAGTGAAGT
* * * *
128226 GAATCAAAGTTTCCAGATTGATCTACCCTGAAAAGTAGTGGATCATATACCTTTTGTAGATTTA
66 GAATCAAAGTTTCCAAATTGATCTACCCTGAAAAGCAGTAGAGCATATACCTTTTGTAGATTTA
* * *
128290 ATCTTCCCTAAAGAGCAGAGAAGCAAATCAACC-CTGATTTAATCTTATCTAAAGAGCAGTGAAG
1 ATCTTCCCTAAAGAGCAGAGAAGCAAATCAACCTC-GATTCAATCTTACCTAAAGAACAGTGAAG
*
128354 TGAATCAAAGTTTCCAAATCTGATCTACCCTGAAAAGCA-TCAGAGC-T-TACCTATTTTTAGAT
65 TGAATCAAAGTTTCCAAAT-TGATCTACCCTGAAAAGCAGT-AGAGCATATACCT-TTTGTAGAT
*
128416 TTG
127 TTA
128419 ATCTTC
1 ATCTTC
128425 AAGAATCTCT
Statistics
Matches: 117, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
128 6 0.05
129 90 0.77
130 21 0.18
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (129 bp):
ATCTTCCCTAAAGAGCAGAGAAGCAAATCAACCTCGATTCAATCTTACCTAAAGAACAGTGAAGT
GAATCAAAGTTTCCAAATTGATCTACCCTGAAAAGCAGTAGAGCATATACCTTTTGTAGATTTA
Found at i:128609 original size:3 final size:3
Alignment explanation
Indices: 128601--128640 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
128591 TGAAACCATT
128601 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
128641 TTACAGATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:130949 original size:44 final size:45
Alignment explanation
Indices: 130892--130980 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
130882 GAAAAGTTTA
130892 GGTTTCACGTGGTTTTG-TTTTAAGTTAAAATATTAGTCTTTAGT
1 GGTTTCACGTGGTTTTGTTTTTAAGTTAAAATATTAGTCTTTAGT
130936 GGTTTCACGTGGTTTTGTTTTTAAGTTAAAATATTAGTCTTTAGT
1 GGTTTCACGTGGTTTTGTTTTTAAGTTAAAATATTAGTCTTTAGT
130981 TGGTATATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 17 0.39
45 27 0.61
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.51
Consensus pattern (45 bp):
GGTTTCACGTGGTTTTGTTTTTAAGTTAAAATATTAGTCTTTAGT
Found at i:132150 original size:17 final size:17
Alignment explanation
Indices: 132124--132185 Score: 115
Period size: 17 Copynumber: 3.6 Consensus size: 17
132114 CAATTTGTTG
*
132124 TTTTAATTAAAATTAAT
1 TTTTATTTAAAATTAAT
132141 TTTTATTTAAAATTAAT
1 TTTTATTTAAAATTAAT
132158 TTTTATTTAAAATTAAT
1 TTTTATTTAAAATTAAT
132175 TTTTATTTAAA
1 TTTTATTTAAA
132186 TGACAATGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATTTAAAATTAAT
Found at i:138361 original size:192 final size:191
Alignment explanation
Indices: 138036--138420 Score: 736
Period size: 192 Copynumber: 2.0 Consensus size: 191
138026 ACCTTGTTAT
138036 AGTTAATTTTACACGAACACTCAGAATTTCATTTTTAGATCGATATTTCTGCACGCCTTGGTTAG
1 AGTTAATTTTACACGAACACTCAGAATTTCATTTTTAGATCGATATTTCTGCACGCCTTGGTTAG
138101 AGAAGTCTACGAAGTTCGAACAAATAGAAGATTTCAGAGAATTGAAATAGAAGTGTTCTAGAGAG
66 AGAAGTCTACGAAGTTCGAACAAATAGAAGATTTCAGAGAATTGAAATAGAAGTGTTCTAGAGAG
138166 TCTAGTAA-GGATTATGCTAGTTGCGGTATTTTGTCCGCATCCGATTAAAATACCAAGCCA
131 TCTAGTAATGGATTATGCTAGTTGCGGTATTTTGTCCGCATCCGATTAAAATACCAAGCCA
*
138226 AGTTAATTTTACACGAACACTCAGAAATTTCATTTTTAGATCGATATTTCTGCATTGCCTTGGTT
1 AGTTAATTTTACACGAACACTCAG-AATTTCATTTTTAGATCGATATTTCTGCA-CGCCTTGGTT
138291 AGAGAAGTCTACGAAGTTCGAACAAATAGAAGATTTCAGAGAATTGAAATAGAAGTGTTCTAGAG
64 AGAGAAGTCTACGAAGTTCGAACAAATAGAAGATTTCAGAGAATTGAAATAGAAGTGTTCTAGAG
138356 AGTCTAGTAATGGATTATGCTAGTTGCGGTATTTTGTCCGCATCCGATTAAAATACCAAGCCA
129 AGTCTAGTAATGGATTATGCTAGTTGCGGTATTTTGTCCGCATCCGATTAAAATACCAAGCCA
138419 AG
1 AG
138421 AAAGAAGGGC
Statistics
Matches: 191, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
190 24 0.13
191 29 0.15
192 84 0.44
193 54 0.28
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (191 bp):
AGTTAATTTTACACGAACACTCAGAATTTCATTTTTAGATCGATATTTCTGCACGCCTTGGTTAG
AGAAGTCTACGAAGTTCGAACAAATAGAAGATTTCAGAGAATTGAAATAGAAGTGTTCTAGAGAG
TCTAGTAATGGATTATGCTAGTTGCGGTATTTTGTCCGCATCCGATTAAAATACCAAGCCA
Found at i:140080 original size:36 final size:36
Alignment explanation
Indices: 139966--140103 Score: 215
Period size: 36 Copynumber: 3.8 Consensus size: 36
139956 AGCAAAGTCA
* * *
139966 ATCTTAAGCCTTCACCGAAAAGGAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCAAAAAGGAGTGAAG-AAAACC
*
140003 ATCTTAAGCCTTCACCAAAGAGGAGTGAAG-AAACC
1 ATCTTAAGCCTTCACCAAAAAGGAGTGAAGAAAACC
140038 ATCTTAAGCCTTCACCAAAAAGGAGTGAAGAAAACC
1 ATCTTAAGCCTTCACCAAAAAGGAGTGAAGAAAACC
*
140074 ATCTTAAGCCTTCACCAAAAAGGAGGGAAG
1 ATCTTAAGCCTTCACCAAAAAGGAGTGAAG
140104 CAAATCAATT
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
35 32 0.34
36 34 0.36
37 28 0.30
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCAAAAAGGAGTGAAGAAAACC
Found at i:140181 original size:108 final size:108
Alignment explanation
Indices: 139966--140160 Score: 293
Period size: 108 Copynumber: 1.8 Consensus size: 108
139956 AGCAAAGTCA
* *
139966 ATCTTAAGCCTTCACCGAAAAGGAGTGAAGCAAATCAATCTTAAGCCTTCACCAAAGAGGAGTGA
1 ATCTTAAGCCTTCACCAAAAAGGAGGGAAGCAAATCAATCTTAAGCCTTCACCAAAGAGGAGTGA
*
140031 AGAAACCATCTTAAGCCTTCACCAAAAAGGAGTGAAGAAAACC
66 AGAAACCACCTTAAGCCTTCACCAAAAAGGAGTGAAGAAAACC
* * * *
140074 ATCTTAAGCCTTCACCAAAAAGGAGGGAAGCAAATCAATTTGTAAGCCTTCATCGAAGAGTAGTG
1 ATCTTAAGCCTTCACCAAAAAGGAGGGAAGCAAATCAATCT-TAAGCCTTCACCAAAGAGGAGTG
* *
140139 AAG-CACCACCTTGAGCCTTCAC
65 AAGAAACCACCTTAAGCCTTCAC
140161 AGAAGAATAG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
108 54 0.70
109 23 0.30
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (108 bp):
ATCTTAAGCCTTCACCAAAAAGGAGGGAAGCAAATCAATCTTAAGCCTTCACCAAAGAGGAGTGA
AGAAACCACCTTAAGCCTTCACCAAAAAGGAGTGAAGAAAACC
Found at i:140657 original size:214 final size:214
Alignment explanation
Indices: 140181--141159 Score: 1503
Period size: 214 Copynumber: 4.5 Consensus size: 214
140171 TGAAGCAAAC
*
140181 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGACATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * *
140246 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGAGTTGGATGTTTTCACATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* * *
140311 TGAAAAAAATGATGTTTTAAGAAGATGTAATTTTTTAAAACGAAGAATGCGATTTTCAAAATTTC
131 TG--AAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTC
*
140376 ACAATTTATAAGTCCTTCAGG
194 ACAATTTATAAGTCCTTCGGG
* * *
140397 CCATCAGTAAGTCTTTTGAGCATGATGCTTAAAACCTTCAGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
*
140462 GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
140527 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCAC
131 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCAC
*
140592 AATTTATAAGTCATTCGGG
196 AATTTATAAGTCCTTCGGG
* *
140611 CCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGGGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* *
140676 GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAAGATGTTTTCACATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* *
140741 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAAATAAGAATGTGATTTTCAAAATTTCAC
131 TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCAC
140806 AATTTATAAGTCCTTCGGG
196 AATTTATAAGTCCTTCGGG
*
140825 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATTTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
140890 GATGATAAGTCCTTCGGGCCATCCATAAGACC-TCTGGGTAGGATGTTTTCACATGAATTTGAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTC-GGGTAGGATGTTTTCACATGAA-TT----
* * * *
140954 ATGAAAATGAGAAAATGATGTTTGAAGATGATGAAATTTTTGGAAACTAAGAATGCGATTTCCAA
125 -TGAAAATGA-AAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAA
* *
141019 AATTTCAC-ACTTAGTAAGTCCTTCGAG
188 AATTTCACAATTTA-TAAGTCCTTCGGG
* * * * * * * *
141046 CCATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATTTGTGAGTCTCTCGAGAAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * * *
141111 GATGATAAATCCTTCGGGCCATCCATAAGATCTTCAGGCAGGATGTTTT
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTT
141160 TCACCAAGAT
Statistics
Matches: 705, Mismatches: 48, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
213 2 0.00
214 394 0.56
215 2 0.00
216 124 0.18
220 13 0.02
221 168 0.24
222 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (214 bp):
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
TGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCAC
AATTTATAAGTCCTTCGGG
Found at i:140877 original size:42 final size:41
Alignment explanation
Indices: 140811--140912 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
140801 TTCACAATTT
* * * *
140811 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * **
140852 CTTAAATCCTTCGGGTCATTTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
*
140894 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
140913 CATAAGACCT
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
41 15 0.31
42 33 0.69
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:143732 original size:17 final size:17
Alignment explanation
Indices: 143707--143752 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
143697 AATTTGTTAT
*
143707 TTTAATTAAAATTAAAA
1 TTTATTTAAAATTAAAA
**
143724 TTTATTTAAAATTAATT
1 TTTATTTAAAATTAAAA
143741 TTTATTTAAAAT
1 TTTATTTAAAAT
143753 GACAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTATTTAAAATTAAAA
Found at i:144749 original size:32 final size:32
Alignment explanation
Indices: 144708--144772 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
144698 AAAATGAGTT
*
144708 ACAACTTCTCTCGATT-TAACAAGGAGAAAACAA
1 ACAACTTCTCTC--TTATAAAAAGGAGAAAACAA
144741 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTCTT-ATAAAAAGGAGAAAACAA
144773 CTTAATAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 2 0.07
32 23 0.79
33 4 0.14
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (32 bp):
ACAACTTCTCTCTTATAAAAAGGAGAAAACAA
Found at i:146173 original size:37 final size:36
Alignment explanation
Indices: 146126--146236 Score: 113
Period size: 36 Copynumber: 3.0 Consensus size: 36
146116 TGCTGAACCT
146126 ATATAAGGAATTACTAGCTTGATCAGAACTAAACCTGC
1 ATATAAGGAATTAC-AGCTTGATCA-AACTAAACCTGC
* *
146164 A-ATAAGGAATTACCA-ATTGATCAATGCTAAACCT--
1 ATATAAGGAATTA-CAGCTTGATCAA-ACTAAACCTGC
*
146198 ATATAAGGAATTACATGCTTGATCATAACTGAACCTGC
1 ATATAAGGAATTACA-GCTTGATCA-AACTAAACCTGC
146236 A
1 A
146237 GAGACTTCAC
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
34 3 0.05
35 12 0.20
36 29 0.48
37 13 0.22
38 3 0.05
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (36 bp):
ATATAAGGAATTACAGCTTGATCAAACTAAACCTGC
Found at i:146211 original size:35 final size:35
Alignment explanation
Indices: 146096--146211 Score: 110
Period size: 36 Copynumber: 3.3 Consensus size: 35
146086 AAGGTCCATT
* * ** *
146096 AGGAATTACCAACTAATCGGTGCTGAACCTATATA
1 AGGAATTACCAATTGATCAATGCTAAACCTATATA
* * *
146131 AGGAATTACTAGCTTGATCAGA-ACTAAACCTGCA-ATA
1 AGGAATTACCA-ATTGATCA-ATGCTAAACCT--ATATA
146168 AGGAATTACCAATTGATCAATGCTAAACCTATATA
1 AGGAATTACCAATTGATCAATGCTAAACCTATATA
146203 AGGAATTAC
1 AGGAATTAC
146212 ATGCTTGATC
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
34 1 0.02
35 23 0.36
36 26 0.41
37 13 0.20
38 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.26
Consensus pattern (35 bp):
AGGAATTACCAATTGATCAATGCTAAACCTATATA
Found at i:146218 original size:72 final size:72
Alignment explanation
Indices: 146096--146236 Score: 203
Period size: 72 Copynumber: 2.0 Consensus size: 72
146086 AAGGTCCATT
** *
146096 AGGAATTACCAACTAATCGGTGCTGAACCTATATAAGGAATTACTAGCTTGATCAGAACTAAACC
1 AGGAATTACCAACTAATCAATGCTAAACCTATATAAGGAATTACTAGCTTGATCAGAACTAAACC
146161 TGCAATA
66 TGCAATA
* * * *
146168 AGGAATTACCAATTGATCAATGCTAAACCTATATAAGGAATTAC-ATGCTTGATCATAACTGAAC
1 AGGAATTACCAACTAATCAATGCTAAACCTATATAAGGAATTACTA-GCTTGATCAGAACTAAAC
146232 CTGCA
65 CTGCA
146237 GAGACTTCAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 1 0.02
72 60 0.98
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (72 bp):
AGGAATTACCAACTAATCAATGCTAAACCTATATAAGGAATTACTAGCTTGATCAGAACTAAACC
TGCAATA
Found at i:146519 original size:11 final size:11
Alignment explanation
Indices: 146498--146533 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
146488 ATGGTGCTTG
146498 AATAAAATATT
1 AATAAAATATT
146509 AA-AATAATATT
1 AATAA-AATATT
146520 AATAAAATATT
1 AATAAAATATT
146531 AAT
1 AAT
146534 TAATTCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.09
11 19 0.83
12 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATAAAATATT
Found at i:161030 original size:32 final size:32
Alignment explanation
Indices: 160989--161050 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
160979 TACCATATTC
*
160989 AATTCGAGTCTATCAATAATTAACTCTATGAA
1 AATTCGAGTCCATCAATAATTAACTCTATGAA
161021 AATTCGAGTCCATCAATAATTAACTCTATG
1 AATTCGAGTCCATCAATAATTAACTCTATG
161051 TATTTAACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (32 bp):
AATTCGAGTCCATCAATAATTAACTCTATGAA
Found at i:174907 original size:24 final size:24
Alignment explanation
Indices: 174880--174939 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
174870 CTGATTTGAT
174880 TTCTGTTATGATACATGACCTGGA
1 TTCTGTTATGATACATGACCTGGA
* *
174904 TTCTGATCA-GATACTTGACCTGGA
1 TTCTG-TTATGATACATGACCTGGA
* *
174928 TTATGTTTTGAT
1 TTCTGTTATGAT
174940 TTTTAATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 1 0.03
24 26 0.90
25 2 0.07
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (24 bp):
TTCTGTTATGATACATGACCTGGA
Found at i:179709 original size:24 final size:24
Alignment explanation
Indices: 179620--179696 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
179610 CTGATTTGAT
* *
179620 TTATGTTATGATACCTGACCTGGA
1 TTATGATATGATACTTGACCTGGA
*
179644 TTCTGATCAT-ATACTTGACCTGGA
1 TTATGAT-ATGATACTTGACCTGGA
*
179668 TTTTGATATGATACTTGACCTGGA
1 TTATGATATGATACTTGACCTGGA
179692 TTATG
1 TTATG
179697 TTTTGATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 2 0.04
24 42 0.91
25 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (24 bp):
TTATGATATGATACTTGACCTGGA
Found at i:181908 original size:31 final size:31
Alignment explanation
Indices: 181870--181929 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
181860 GAGTCGAGGG
181870 TTACCTATGTTCTACGGAACATATGGACAAT
1 TTACCTATGTTCTACGGAACATATGGACAAT
*
181901 TTACCTATGTTCTTCGGAACATATGGACA
1 TTACCTATGTTCTACGGAACATATGGACA
181930 GTTACATAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGACAAT
Found at i:184194 original size:8 final size:8
Alignment explanation
Indices: 184181--184207 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
184171 GTATTTGGAT
184181 TATATAGA
1 TATATAGA
184189 TATATAGA
1 TATATAGA
184197 TATATAGA
1 TATATAGA
184205 TAT
1 TAT
184208 GATGAATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (8 bp):
TATATAGA
Found at i:186043 original size:31 final size:31
Alignment explanation
Indices: 186005--186063 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
185995 GAGTCGAGGG
186005 TTACCTATGTTCTACGGAACATATGGACAAT
1 TTACCTATGTTCTACGGAACATATGGACAAT
** *
186036 TTACCTATGTTCTTTGGAATATATGGAC
1 TTACCTATGTTCTACGGAACATATGGAC
186064 TGTTACATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGACAAT
Found at i:189382 original size:29 final size:29
Alignment explanation
Indices: 189340--189407 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
189330 AATAATGTGA
189340 TTAGATTTTCCTTTAGTACTTTTCTTTTC
1 TTAGATTTTCCTTTAGTACTTTTCTTTTC
189369 TTAGATTTTCCTTTAGTACTTTTCTTTTC
1 TTAGATTTTCCTTTAGTACTTTTCTTTTC
189398 TTAGATTTTC
1 TTAGATTTTC
189408 TTACTTACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.15, C:0.16, G:0.07, T:0.62
Consensus pattern (29 bp):
TTAGATTTTCCTTTAGTACTTTTCTTTTC
Found at i:189408 original size:15 final size:15
Alignment explanation
Indices: 189359--189409 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
189349 CCTTTAGTAC
189359 TTTTCTTTTCTTAGA
1 TTTTCTTTTCTTAGA
* ** *
189374 TTTTCCTTTAGTA-C
1 TTTTCTTTTCTTAGA
189388 TTTTCTTTTCTTAGA
1 TTTTCTTTTCTTAGA
189403 TTTTCTT
1 TTTTCTT
189410 ACTTACTAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.12, C:0.16, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTCTTTTCTTAGA
Found at i:195462 original size:2 final size:2
Alignment explanation
Indices: 195455--195499 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
195445 CATAATATTC
195455 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
195497 AT A
1 AT A
195500 CAAACGAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:207970 original size:106 final size:106
Alignment explanation
Indices: 207480--208250 Score: 1138
Period size: 105 Copynumber: 7.4 Consensus size: 106
207470 AGGTTTTACC
*
207480 CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
207545 ACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
**
207585 CAGAGCCAATTTTGACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
207650 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
207690 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
207755 ACGAAGTGACCGCTGGTTGCCAACAAA-AATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
207795 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
207860 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
*
207901 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
207966 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
*
208007 CAGAGCCAA--T----TT--CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
208064 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTC-CTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTC-AATTT
* * * * * ** * * *
208105 CGGATCCAATTTCAACTTCACAGCGAAGGACATTAGACTTGAGACAGCACAAGCTCAACTTCAC-
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * ** * *
208169 AGCGAAGGGGCGGCTGACTGTCAACAAACAATTTC-CCAGTT
66 A-CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
* * *
208210 CTAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
208251 AGAACAATAC
Statistics
Matches: 612, Mismatches: 41, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
97 1 0.00
98 87 0.14
100 3 0.00
104 3 0.00
105 295 0.48
106 223 0.36
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTT
Found at i:208093 original size:98 final size:98
Alignment explanation
Indices: 207815--208120 Score: 479
Period size: 98 Copynumber: 3.0 Consensus size: 98
207805 TTCAACTTCA
207815 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
207880 CAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTT
66 CAACAAACAACTTCTCAATTTCAGAGCCAA--T----TT
207919 CACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
1 CA-A-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
207984 GTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
64 GTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
*
208019 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGT
1 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* * * *
208084 CAATAAACAATTTC-CTAATTTCGGATCCAATTT
66 CAACAAACAACTTCTC-AATTTCAGAGCCAATTT
208117 CAAC
1 CAAC
208121 TTCACAGCGA
Statistics
Matches: 194, Mismatches: 5, Indels: 12
0.92 0.02 0.06
Matches are distributed among these distances:
97 1 0.01
98 92 0.47
99 1 0.01
100 4 0.02
104 3 0.02
105 1 0.01
106 92 0.47
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (98 bp):
CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
CAACAAACAACTTCTCAATTTCAGAGCCAATTT
Found at i:209868 original size:21 final size:20
Alignment explanation
Indices: 209844--209899 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
209834 TTTTGTCTTC
209844 ATTATATATATTTTTATTATT
1 ATTATATATA-TTTTATTATT
* *
209865 ATTATAGATATATTATATATT
1 ATTATATATATTTTAT-TATT
209886 ATT-T-TATATTTTAT
1 ATTATATATATTTTAT
209900 ATTTTTAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 8 0.27
20 6 0.20
21 16 0.53
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTATATATATTTTATTATT
Found at i:209892 original size:23 final size:23
Alignment explanation
Indices: 209849--209893 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
209839 TCTTCATTAT
*
209849 ATATATTTTTATTATTATTATAG
1 ATATATTTATATTATTATTATAG
209872 ATATATTATATATTATT-TTATA
1 ATATATT-TATATTATTATTATA
209894 TTTTATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATATATTTATATTATTATTATAG
Found at i:215695 original size:14 final size:14
Alignment explanation
Indices: 215676--215703 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
215666 AACAATCAAA
215676 ACTGAAATTTTGAT
1 ACTGAAATTTTGAT
215690 ACTGAAATTTTGAT
1 ACTGAAATTTTGAT
215704 CAAACTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
ACTGAAATTTTGAT
Found at i:216180 original size:31 final size:31
Alignment explanation
Indices: 216139--216198 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
216129 TCATCTCAAG
* * *
216139 ATAAATATC-AATATTCAAATTTGATATTTTT
1 ATAAAAATCAAATA-TCAAAATTGAAATTTTT
216170 ATAAAAATCAAATATCAAAATTGAAATTT
1 ATAAAAATCAAATATCAAAATTGAAATTT
216199 CTAATTGCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (31 bp):
ATAAAAATCAAATATCAAAATTGAAATTTTT
Found at i:220358 original size:23 final size:22
Alignment explanation
Indices: 220332--220395 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
220322 TAACTCATAT
220332 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACC-AAGTGCCACGTAG
* *
220355 AATTGCACCGAAGTTCCGCGTAG
1 AATTGCACC-AAGTGCCACGTAG
220378 AATTGCACCATAGTGCCA
1 AATTGCACCA-AGTGCCA
220396 TATAATAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (22 bp):
AATTGCACCAAGTGCCACGTAG
Found at i:220579 original size:102 final size:103
Alignment explanation
Indices: 220411--220627 Score: 409
Period size: 102 Copynumber: 2.1 Consensus size: 103
220401 TAATGTCCAT
*
220411 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
220476 GA-CTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
220513 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
220578 GACCTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
220616 AAGGACCACATA
1 AAGGACCACATA
220628 GACCCTCTAC
Statistics
Matches: 112, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
102 66 0.59
103 46 0.41
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:221192 original size:21 final size:21
Alignment explanation
Indices: 221168--221210 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
221158 TCATATTCGT
*
221168 TTGAGGGGGAATCGATTCCCC
1 TTGAAGGGGAATCGATTCCCC
* *
221189 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGAATCGATTCCCC
221210 T
1 T
221211 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGAATCGATTCCCC
Found at i:227275 original size:22 final size:23
Alignment explanation
Indices: 227250--227304 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
227240 CAGCTCATAT
* *
227250 AATTGCACCTAAGT-GCACGTAG
1 AATTGCACCGAAGTACCACGTAG
* *
227272 AATTGCACCGACGTACCGCGTAG
1 AATTGCACCGAAGTACCACGTAG
227295 AATTGCACCG
1 AATTGCACCG
227305 TTGTGCCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTACCACGTAG
Found at i:228085 original size:21 final size:21
Alignment explanation
Indices: 228061--228101 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
228051 TCATATTCGT
*
228061 TTGAGGGGGAATCGATTCCCA
1 TTGAAGGGGAATCGATTCCCA
* *
228082 TTGAATGGGTATCGATTCCC
1 TTGAAGGGGAATCGATTCCC
228102 CTAGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGAATCGATTCCCA
Found at i:229474 original size:65 final size:65
Alignment explanation
Indices: 229370--229554 Score: 316
Period size: 65 Copynumber: 2.8 Consensus size: 65
229360 AGGCTATGGT
* *
229370 ATGAGGTGGAGTGATAATTGAATATAATACATATCACTCATATGACTCATGTACCTTTGTTGTGC
1 ATGAGGTGGAGTGATAATTGAATATAATACAAATCACTCATATGACTCATGTACCTTTGTGGTGC
*
229435 ATGAGGTGGAGTGATAATTGAATATAATACAAATCACTCATACGACTCATGTACCTTTGTGGTGC
1 ATGAGGTGGAGTGATAATTGAATATAATACAAATCACTCATATGACTCATGTACCTTTGTGGTGC
* * *
229500 ATGAGGTGGAGTGATAATTGTATATAGTACAGATCACTCATATGACTCATGTACC
1 ATGAGGTGGAGTGATAATTGAATATAATACAAATCACTCATATGACTCATGTACC
229555 CATGTCAAAA
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 113 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (65 bp):
ATGAGGTGGAGTGATAATTGAATATAATACAAATCACTCATATGACTCATGTACCTTTGTGGTGC
Found at i:231722 original size:95 final size:96
Alignment explanation
Indices: 231576--231784 Score: 307
Period size: 95 Copynumber: 2.2 Consensus size: 96
231566 ACAGACAAGG
* *
231576 TAGTATCGATACCATGATAAGGGTATCGATACCAAGCAACAACGAATCTAATTTTGGTATCGATA
1 TAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACAACGAACCTAATTTTGGTATCGATA
*
231641 CCGGAAGGGGGTATCGATACCA-TAGTAT-GA
66 CCCGAAGGGGGTATCGATACCACT-GTATAGA
* * * *
231671 TAGTATCAATACCATGGTAAGGGTATCGATACCAGGTAACATCGAACCTAATTTTGGTATCGATA
1 TAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACAACGAACCTAATTTTGGTATCGATA
*
231736 CCCGAAGGGGGTATCGGTACCACTGTATAGA
66 CCCGAAGGGGGTATCGATACCACTGTATAGA
*
231767 -AGTATCGGTACCATGGTA
1 TAGTATCGATACCATGGTA
231785 GTATTATCGA
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
95 99 0.97
96 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (96 bp):
TAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACAACGAACCTAATTTTGGTATCGATA
CCCGAAGGGGGTATCGATACCACTGTATAGA
Found at i:232220 original size:55 final size:55
Alignment explanation
Indices: 232131--232612 Score: 553
Period size: 55 Copynumber: 8.8 Consensus size: 55
232121 GTACTACGTA
* * * *
232131 CACTTTGTGTGCATATCCATGGAATTCATCATGGGTTGATGAATCACCATACATG
1 CACTTTGTGTGCAAATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATG
* * * * * *
232186 CACTTTGTGTGCATATACACGAAATTCATAATGGGTGGATGAATCATCGTACAAG
1 CACTTTGTGTGCAAATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATG
* * * * *
232241 CAGTTTGTGTGCAAATTCACGGAATTCAGCATGGGTTGACGAATCACCGTACATG
1 CACTTTGTGTGCAAATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATG
* *
232296 CACTTTGTGTGCATAA-CCAC-ATAATTCATCATGGGTTGACGAATCACCGTACAAG
1 CACTTTGTGTGCA-AATCCACGA-AATTCATCATGGGTTGATGAATCACCGTACATG
* * * * *
232351 CACTTTGTATGCATATCCATGGAATTCATCATGGGTTGATTAATCACCGTACATG
1 CACTTTGTGTGCAAATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATG
* *
232406 CACTTTGTGTTCAAATCCAC-AGAATTCATCATGGGTTGATGAATTACCGTACATG
1 CACTTTGTGTGCAAATCCACGA-AATTCATCATGGGTTGATGAATCACCGTACATG
* * * *
232461 CACTTTGTGTACAAATCCAC-AGAATTCATCAT-GGTTGATGATTCACCGTATAAG
1 CACTTTGTGTGCAAATCCACGA-AATTCATCATGGGTTGATGAATCACCGTACATG
* * **
232515 CACTTTGTGTGCAAATCCATGGAATTCATCATTAGTTGATGAATCACCGTACATG
1 CACTTTGTGTGCAAATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATG
* * * **
232570 CACTATGTGTGC-AACCCATGAAATTCATCATGATTTGATGAAT
1 CACTTTGTGTGCAAATCCACGAAATTCATCATGGGTTGATGAAT
232613 TTCTGTATAG
Statistics
Matches: 366, Mismatches: 54, Indels: 15
0.84 0.12 0.03
Matches are distributed among these distances:
54 74 0.20
55 290 0.79
56 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (55 bp):
CACTTTGTGTGCAAATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATG
Found at i:232415 original size:165 final size:165
Alignment explanation
Indices: 232131--232583 Score: 613
Period size: 165 Copynumber: 2.8 Consensus size: 165
232121 GTACTACGTA
* ** * *
232131 CACTTTGTGTGCATATCCATGGAATTCATCATGGGTTGATGAATCACCATACATGCACTTTGTGT
1 CACTTTGTGTGCATAACCACAGAATTCATCATGGGTTGATGAATCACCGTACAAGCACTTTGTGT
* * * * * * * * *
232196 GCATATACACGAAATTCATAATGGGTGGATGAATCATCGTACAAGCAGTTTGTGTGCAAATTCAC
66 GCATATCCATGGAATTCATCATGGGTTGATGAATCACCGTACATGCACTTTGTGTGCAAATCCAC
*
232261 GGAATTCAGCATGGGTTGACGAATCACCGTACATG
131 AGAATTCAGCATGGGTTGACGAATCACCGTACATG
* * *
232296 CACTTTGTGTGCATAACCACATAATTCATCATGGGTTGACGAATCACCGTACAAGCACTTTGTAT
1 CACTTTGTGTGCATAACCACAGAATTCATCATGGGTTGATGAATCACCGTACAAGCACTTTGTGT
* *
232361 GCATATCCATGGAATTCATCATGGGTTGATTAATCACCGTACATGCACTTTGTGTTCAAATCCAC
66 GCATATCCATGGAATTCATCATGGGTTGATGAATCACCGTACATGCACTTTGTGTGCAAATCCAC
* * *
232426 AGAATTCATCATGGGTTGATGAATTACCGTACATG
131 AGAATTCAGCATGGGTTGACGAATCACCGTACATG
* * *
232461 CACTTTGTGTACA-AATCCACAGAATTCATCAT-GGTTGATGATTCACCGTATAAGCACTTTGTG
1 CACTTTGTGTGCATAA-CCACAGAATTCATCATGGGTTGATGAATCACCGTACAAGCACTTTGTG
* ** *
232524 TGCAAATCCATGGAATTCATCATTAGTTGATGAATCACCGTACATGCACTATGTGTGCAA
65 TGCATATCCATGGAATTCATCATGGGTTGATGAATCACCGTACATGCACTTTGTGTGCAA
232584 CCCATGAAAT
Statistics
Matches: 252, Mismatches: 35, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
164 83 0.33
165 169 0.67
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (165 bp):
CACTTTGTGTGCATAACCACAGAATTCATCATGGGTTGATGAATCACCGTACAAGCACTTTGTGT
GCATATCCATGGAATTCATCATGGGTTGATGAATCACCGTACATGCACTTTGTGTGCAAATCCAC
AGAATTCAGCATGGGTTGACGAATCACCGTACATG
Found at i:234473 original size:6 final size:6
Alignment explanation
Indices: 234464--234490 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
234454 AAGTAGAAGT
234464 AGAGGA AGAGGA AGAGGA AGAGGA AGA
1 AGAGGA AGAGGA AGAGGA AGAGGA AGA
234491 TCAGGAGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:245914 original size:55 final size:55
Alignment explanation
Indices: 245828--246076 Score: 338
Period size: 55 Copynumber: 4.5 Consensus size: 55
245818 ATGGGTTGAT
* *
245828 ATCCACAGAATTTATCATGGGTTGATTAATCACCGTACATGCACTTTGTGTGCAA
1 ATCCACAGAATTCATCATGGGTTGATGAATCACCGTACATGCACTTTGTGTGCAA
*
245883 ATCCACAGAATTCATCATGGGTTGATGAATCACCGTACAAGCACTTTGTGTGCAA
1 ATCCACAGAATTCATCATGGGTTGATGAATCACCGTACATGCACTTTGTGTGCAA
* *
245938 ATCCACGGAATTCATCATGGGTTGATAAATCACCGTACATGCACTTTGTGTGCAA
1 ATCCACAGAATTCATCATGGGTTGATGAATCACCGTACATGCACTTTGTGTGCAA
* * * * * * * *
245993 ATCAACGGAATGCTTCATGAGTTGATGAATCACCATACATTCACTATGTGTGC-A
1 ATCCACAGAATTCATCATGGGTTGATGAATCACCGTACATGCACTTTGTGTGCAA
* * * *
246047 ACCCACTGAATGCATCATGAGTTGATGAAT
1 ATCCACAGAATTCATCATGGGTTGATGAAT
246077 TTCTGTATAG
Statistics
Matches: 176, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
54 27 0.15
55 149 0.85
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (55 bp):
ATCCACAGAATTCATCATGGGTTGATGAATCACCGTACATGCACTTTGTGTGCAA
Found at i:246954 original size:22 final size:20
Alignment explanation
Indices: 246917--246979 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
246907 TAAAACACTA
246917 ATTTATTTAATT-TTTAAAAT
1 ATTTATTT-ATTATTTAAAAT
*
246937 CATATTATTTATTATTTATAAT
1 -AT-TTATTTATTATTTAAAAT
* *
246959 ATTATAATAATTATTTAAAAT
1 ATT-TATTTATTATTTAAAAT
246980 TAAATAGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 1 0.03
21 21 0.60
22 13 0.37
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTATTTATTATTTAAAAT
Found at i:247056 original size:21 final size:21
Alignment explanation
Indices: 247030--247072 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
247020 GTAATTATTA
247030 AGTTTAGTATAATAAAAAATT
1 AGTTTAGTATAATAAAAAATT
247051 AGTTTAGTATAATAAAAAATT
1 AGTTTAGTATAATAAAAAATT
247072 A
1 A
247073 AGTAATGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (21 bp):
AGTTTAGTATAATAAAAAATT
Found at i:247144 original size:21 final size:22
Alignment explanation
Indices: 247088--247155 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 22
247078 TGTTTTAAAA
247088 ATTTTAAAAATTAAATAATACT
1 ATTTTAAAAATTAAATAATACT
* *
247110 ATTTCAAAATAAATAAATAATA-T
1 ATTT-TAAA-AATTAAATAATACT
*
247133 GATTTTAAAAATTAAAAAATACT
1 -ATTTTAAAAATTAAATAATACT
247156 TTAAAATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 14 0.38
23 8 0.22
24 15 0.41
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (22 bp):
ATTTTAAAAATTAAATAATACT
Found at i:250078 original size:22 final size:22
Alignment explanation
Indices: 250053--250094 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
250043 TCGTTTTCAC
* *
250053 ATAAGTCAATTTTTTTTTTGAA
1 ATAAATCAATTTTATTTTTGAA
*
250075 ATAAATCAGTTTTATTTTTG
1 ATAAATCAATTTTATTTTTG
250095 TCTTTTAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.55
Consensus pattern (22 bp):
ATAAATCAATTTTATTTTTGAA
Found at i:257450 original size:14 final size:14
Alignment explanation
Indices: 257431--257476 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
257421 TCTTCGCATT
* *
257431 TTTACACCGTGTTC
1 TTTACACCATATTC
257445 TTTACACCATATTC
1 TTTACACCATATTC
**
257459 TTTATTCCATATTC
1 TTTACACCATATTC
257473 TTTA
1 TTTA
257477 TTCTTTACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.22, C:0.24, G:0.04, T:0.50
Consensus pattern (14 bp):
TTTACACCATATTC
Found at i:257477 original size:14 final size:14
Alignment explanation
Indices: 257451--257479 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
257441 GTTCTTTACA
257451 CCATATTCTTTATT
1 CCATATTCTTTATT
257465 CCATATTCTTTATT
1 CCATATTCTTTATT
257479 C
1 C
257480 TTTACATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (14 bp):
CCATATTCTTTATT
Found at i:260631 original size:15 final size:15
Alignment explanation
Indices: 260541--260624 Score: 51
Period size: 15 Copynumber: 5.3 Consensus size: 15
260531 TATTATGCTT
*
260541 AGAAAAAAACAAAAA
1 AGAAAAAAAAAAAAA
260556 AGAAAAAACTAAAAAAA
1 AGAAAAAA--AAAAAAA
*
260573 GAGAAATTAATAAAAAAA
1 -AGAAA--AAAAAAAAAA
** * * **
260591 TTAGAGAGGAAAAAA
1 AGAAAAAAAAAAAAA
260606 AGAAAAAAAAAAAAA
1 AGAAAAAAAAAAAAA
260621 AGAA
1 AGAA
260625 GGAAAAAGTG
Statistics
Matches: 50, Mismatches: 14, Indels: 10
0.68 0.19 0.14
Matches are distributed among these distances:
15 28 0.56
17 8 0.16
18 12 0.24
20 2 0.04
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (15 bp):
AGAAAAAAAAAAAAA
Found at i:261292 original size:78 final size:78
Alignment explanation
Indices: 261163--261318 Score: 240
Period size: 78 Copynumber: 2.0 Consensus size: 78
261153 AGCAAGTGGT
* *
261163 TGACAGAAGGTAACACGAGAGATGTCAATAACATGAATGAAAAAATGAATAATGAAATGACTATA
1 TGACAGAAGGTAACACGAGAGATGTCAATAACACGAATGAAAAAATAAATAATGAAATGACTATA
* *
261228 ACATAGTTTGTTC
66 ACACAGTTCGTTC
* * * *
261241 TGACAGAAGGTGACACGAGAGATTTCAATAACCCGAATGACAAAATAAATAATGAAATGACTATA
1 TGACAGAAGGTAACACGAGAGATGTCAATAACACGAATGAAAAAATAAATAATGAAATGACTATA
261306 ACACAGTTCGTTC
66 ACACAGTTCGTTC
261319 CAAGGCATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (78 bp):
TGACAGAAGGTAACACGAGAGATGTCAATAACACGAATGAAAAAATAAATAATGAAATGACTATA
ACACAGTTCGTTC
Found at i:262965 original size:41 final size:40
Alignment explanation
Indices: 262881--262958 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
262871 TGTAGTGACT
* * * *
262881 TTTTTATACAAACACCGTATAAACTTATACTTTAATAACG
1 TTTTGATACAAAAACCGTATAAACTCATACTTTAACAACG
*
262921 TTTTGATACAAAAATCGCTATAAACTCATACTTTAACA
1 TTTTGATACAAAAACCG-TATAAACTCATACTTTAACA
262959 GTGTTTTACA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 14 0.44
41 18 0.56
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (40 bp):
TTTTGATACAAAAACCGTATAAACTCATACTTTAACAACG
Found at i:266339 original size:27 final size:28
Alignment explanation
Indices: 266283--266339 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
266273 GTTGTAAACA
*
266283 CCATTTTTCAACACCAACACCCACCCTC
1 CCATTTTTCAACACCAACACCCACCATC
* *
266311 CCATTTTTCAACACTAAC-CCCATCATC
1 CCATTTTTCAACACCAACACCCACCATC
266338 CC
1 CC
266340 TTGTTCCGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.28, C:0.47, G:0.00, T:0.25
Consensus pattern (28 bp):
CCATTTTTCAACACCAACACCCACCATC
Found at i:272884 original size:99 final size:99
Alignment explanation
Indices: 272713--272911 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
272703 CACTAAGGTT
272713 TACACCAGACCCTTCACATCCTCCTGGTTTCACCCCAGTGCACATTTCTGTTAGATCGCAAGCTT
1 TACACCAGACCCTTCACATCCTCCTGGTTTCACCCCAGTGCACATTTCTGTTAGATCGCAAGCTT
272778 TGCAGGAAGCTCGCCTAGGAGTTTACATGGAAAA
66 TGCAGGAAGCTCGCCTAGGAGTTTACATGGAAAA
272812 TACACCAGACCCTTCACATCCTCCTGGTTTCACCCCAGTGCACATTTCTGTTAGATCGCAAGCTT
1 TACACCAGACCCTTCACATCCTCCTGGTTTCACCCCAGTGCACATTTCTGTTAGATCGCAAGCTT
272877 TGCAGGAAGCTCGCCTAGGAGTTTACATGGAAAA
66 TGCAGGAAGCTCGCCTAGGAGTTTACATGGAAAA
272911 T
1 T
272912 CAACAGAATC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (99 bp):
TACACCAGACCCTTCACATCCTCCTGGTTTCACCCCAGTGCACATTTCTGTTAGATCGCAAGCTT
TGCAGGAAGCTCGCCTAGGAGTTTACATGGAAAA
Found at i:273955 original size:21 final size:21
Alignment explanation
Indices: 273929--273978 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
273919 CCACCTTACC
*
273929 CTCACTGGTATAATGCCAATG
1 CTCACTGCTATAATGCCAATG
273950 CTCACTGCTATAATGCCAATG
1 CTCACTGCTATAATGCCAATG
273971 CTCACTGC
1 CTCACTGC
273979 GAATACCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (21 bp):
CTCACTGCTATAATGCCAATG
Found at i:280630 original size:33 final size:33
Alignment explanation
Indices: 280540--280908 Score: 452
Period size: 33 Copynumber: 11.1 Consensus size: 33
280530 ATTTTCATTT
*
280540 CATTCAAATTCATCACAGAAAGAGGTGGATCGA
1 CATTCAAATCCATCACAGAAAGAGGTGGATCGA
* * * *
280573 CATTTTAAATTCATTACAGAAAGAGATGGATCGA
1 CA-TTCAAATCCATCACAGAAAGAGGTGGATCGA
280607 CATTCAAATCCATCACAGAAAGAGGTGGATCGA
1 CATTCAAATCCATCACAGAAAGAGGTGGATCGA
* * *
280640 CATTCAAATCCATCATAAAAAGGGGTGGATCGA
1 CATTCAAATCCATCACAGAAAGAGGTGGATCGA
* *
280673 CATTTTAAATCCATTACAGAAAGAGGTGGATCGA
1 CA-TTCAAATCCATCACAGAAAGAGGTGGATCGA
*
280707 CATTCAAATCCATCATAGAAAGAGGTGGATCGA
1 CATTCAAATCCATCACAGAAAGAGGTGGATCGA
*** * *
280740 CATTTTGATCCATCACAGAAAGAGATGGATCAA
1 CATTCAAATCCATCACAGAAAGAGGTGGATCGA
*
280773 CATTCAAATCCATCACAGAAAGAGGTTGATCGA
1 CATTCAAATCCATCACAGAAAGAGGTGGATCGA
****
280806 CATTTCAAATCCATCACAGAAAGAGACATATCGA
1 CA-TTCAAATCCATCACAGAAAGAGGTGGATCGA
*
280840 CATTCAAATTCATCACAGAAAGAGGTGGATCGA
1 CATTCAAATCCATCACAGAAAGAGGTGGATCGA
* * * * *
280873 CA-TCTTAATCTATCACAGAAGGAGTTGGATCAA
1 CATTC-AAATCCATCACAGAAAGAGGTGGATCGA
280906 CAT
1 CAT
280909 CAACTTTTTG
Statistics
Matches: 286, Mismatches: 45, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
32 2 0.01
33 197 0.69
34 87 0.30
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (33 bp):
CATTCAAATCCATCACAGAAAGAGGTGGATCGA
Found at i:280713 original size:100 final size:100
Alignment explanation
Indices: 280540--280908 Score: 481
Period size: 100 Copynumber: 3.7 Consensus size: 100
280530 ATTTTCATTT
* * * *
280540 CATTCAAATTCATCACAGAAAGAGGTGGATCGACATTTTAAATTCATTACAGAAAGAGATGGATC
1 CATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTTAAATCCATCACAGAAAGAGGTGGATC
280605 GACATTCAAATCCATCACAGAAAGAGGTGGATCGA
66 GACATTCAAATCCATCACAGAAAGAGGTGGATCGA
* * * *
280640 CATTCAAATCCATCATAAAAAGGGGTGGATCGACATTTTAAATCCATTACAGAAAGAGGTGGATC
1 CATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTTAAATCCATCACAGAAAGAGGTGGATC
*
280705 GACATTCAAATCCATCATAGAAAGAGGTGGATCGA
66 GACATTCAAATCCATCACAGAAAGAGGTGGATCGA
*** * * * *
280740 CATTTTGATCCATCACAGAAAGAGATGGATCAACA-TTCAAATCCATCACAGAAAGAGGTTGATC
1 CATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTTAAATCCATCACAGAAAGAGGTGGATC
****
280804 GACATTTCAAATCCATCACAGAAAGAGACATATCGA
66 GACA-TTCAAATCCATCACAGAAAGAGGTGGATCGA
* * * * *
280840 CATTCAAATTCATCACAGAAAGAGGTGGATCGACATCTT-AATCTATCACAGAAGGAGTTGGATC
1 CATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTTAAATCCATCACAGAAAGAGGTGGATC
*
280904 AACAT
66 GACAT
280909 CAACTTTTTG
Statistics
Matches: 231, Mismatches: 36, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
99 31 0.13
100 199 0.86
101 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (100 bp):
CATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTTAAATCCATCACAGAAAGAGGTGGATC
GACATTCAAATCCATCACAGAAAGAGGTGGATCGA
Found at i:280751 original size:133 final size:133
Alignment explanation
Indices: 280542--280908 Score: 500
Period size: 133 Copynumber: 2.8 Consensus size: 133
280532 TTTCATTTCA
* * * *
280542 TTCAAATTCATCACAGAAAGAGGTGGATCGACATTTTAAATTCATTACAGAAAGAGATGGATCGA
1 TTCAAATCCATCACAGAAAGAGGTGGATCGACA-TTCAAATTCATCACAGAAAGAGGTGGATCGA
** * * * *
280607 CATTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATCCATCATAAAAAGGGGTGGATCG
65 CATTTTAATCCATCACAGAAAGAGATGGATCAACATTCAAATCCATCACAAAAAGAGGTGGATCG
280672 ACAT
130 ACAT
* * * *
280676 TTTAAATCCATTACAGAAAGAGGTGGATCGACATTCAAATCCATCATAGAAAGAGGTGGATCGAC
1 TTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATTCATCACAGAAAGAGGTGGATCGAC
* * *
280741 ATTTTGATCCATCACAGAAAGAGATGGATCAACATTCAAATCCATCACAGAAAGAGGTTGATCGA
66 ATTTTAATCCATCACAGAAAGAGATGGATCAACATTCAAATCCATCACAAAAAGAGGTGGATCGA
280806 CAT
131 CAT
****
280809 TTCAAATCCATCACAGAAAGAGACATATCGACATTCAAATTCATCACAGAAAGAGGTGGATCGAC
1 TTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATTCATCACAGAAAGAGGTGGATCGAC
* * * *
280874 ATCTTAATCTATCACAGAAGGAGTTGGATCAACAT
66 ATTTTAATCCATCACAGAAAGAGATGGATCAACAT
280909 CAACTTTTTG
Statistics
Matches: 203, Mismatches: 30, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
133 173 0.85
134 30 0.15
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (133 bp):
TTCAAATCCATCACAGAAAGAGGTGGATCGACATTCAAATTCATCACAGAAAGAGGTGGATCGAC
ATTTTAATCCATCACAGAAAGAGATGGATCAACATTCAAATCCATCACAAAAAGAGGTGGATCGA
CAT
Done.