Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009580.1 Hibiscus syriacus cultivar Beakdansim tig00116954_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: 1633873
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 6
Found at i:224 original size:19 final size:19
Alignment explanation
Indices: 184--310 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
174 TAGTTTACTT
* *
184 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
204 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
223 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
242 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
256 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
275 TCGCAA--CG--A-C--AA
1 TCGCAACGCGAAACCAAAA
287 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
306 TCGCA
1 TCGCA
311 TTGATTTTCA
Statistics
Matches: 88, Mismatches: 7, Indels: 25
0.73 0.06 0.21
Matches are distributed among these distances:
12 8 0.09
14 12 0.14
15 2 0.02
16 3 0.03
17 5 0.06
18 1 0.01
19 44 0.50
20 13 0.15
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:292 original size:31 final size:32
Alignment explanation
Indices: 220--310 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 32
210 CGCGAAACCA
**
220 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
252 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
285 -AATCGCAACGCGAAACCAAAATCGCA
1 AAATCGCAACGCGAAACCAAAATCGCA
311 TTGATTTTCA
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
31 26 0.46
32 1 0.02
33 29 0.52
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:345 original size:14 final size:14
Alignment explanation
Indices: 326--384 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
316 TTTCATTTCG
326 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
* *
340 CGTTGCGTTTTCATT
1 CGTTGCG-ATTCTTT
*
355 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
371 CGTTGCGATT-TTT
1 CGTTGCGATTCTTT
384 C
1 C
385 ATTTCGCGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
13 3 0.08
14 15 0.42
15 7 0.19
16 6 0.17
17 5 0.14
ACGTcount: A:0.08, C:0.22, G:0.22, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:363 original size:31 final size:33
Alignment explanation
Indices: 313--401 Score: 119
Period size: 31 Copynumber: 2.7 Consensus size: 33
303 AAATCGCATT
* *
313 GATTTTCATTTCGCGTTGCGATTCTTTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTGTCGTTGC
346 G-TTTTCA-TTCGCATTGCGATTCTGTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTGTCGTTGC
*
377 GATTTTTCATTTCGCGTTTGCGATT
1 GA-TTTTCATTTCGC-ATTGCGATT
402 TTGGTTTCGC
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
31 23 0.47
32 6 0.12
33 7 0.14
34 5 0.10
35 8 0.16
ACGTcount: A:0.10, C:0.20, G:0.21, T:0.48
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTCTGTCGTTGC
Found at i:403 original size:20 final size:19
Alignment explanation
Indices: 313--438 Score: 87
Period size: 20 Copynumber: 7.1 Consensus size: 19
303 AAATCGCATT
313 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
332 GA--TTC-TTT--CGTTGC
1 GATTTTCATTTCGCGTTGC
*
346 G-TTTTCA-TTCGCATTGC
1 GATTTTCATTTCGCGTTGC
*
363 GA--TTC-TGT--CGTTGC
1 GATTTTCATTTCGCGTTGC
377 GATTTTTCATTTCGCGTTTGC
1 GA-TTTTCATTTCGCG-TTGC
**
398 GATTTTGGTTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
* *
417 GATTTTAAGTTTCGTGTTGC
1 GATTTTCA-TTTCGCGTTGC
437 GA
1 GA
439 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 9, Indels: 29
0.69 0.07 0.24
Matches are distributed among these distances:
14 14 0.17
15 5 0.06
16 7 0.08
17 12 0.14
18 2 0.02
19 12 0.14
20 25 0.30
21 6 0.07
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:2313 original size:14 final size:14
Alignment explanation
Indices: 2294--2329 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2284 ATTGTTTAAT
2294 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2308 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2322 TGATTTGT
1 TGATTTGT
2330 GTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2502 original size:20 final size:19
Alignment explanation
Indices: 2434--2516 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
2424 AAAAATGACT
2434 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2453 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2467 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2486 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2506 ATCGCAATGCG
1 ATCGCAATGCG
2517 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2569 original size:19 final size:19
Alignment explanation
Indices: 2545--2818 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
2535 GATTATCTCG
2545 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2564 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2583 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2597 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2616 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2635 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2654 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2673 TTGCGATGTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2692 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2706 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2725 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2744 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2758 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2778 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2792 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2811 TTGCGATT
1 TTGCGATT
2819 GTATTTTCCG
Statistics
Matches: 225, Mismatches: 9, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 21 0.09
18 3 0.01
19 136 0.60
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2585 original size:52 final size:52
Alignment explanation
Indices: 2523--2790 Score: 446
Period size: 52 Copynumber: 5.0 Consensus size: 52
2513 TGCGTTTATA
*
2523 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2575 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
2627 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATGTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
2684 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2736 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
2789 AT
1 AT
2791 GTTGGGATTT
Statistics
Matches: 205, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 130 0.63
53 19 0.09
54 5 0.02
55 6 0.03
56 2 0.01
57 43 0.21
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2674 original size:109 final size:105
Alignment explanation
Indices: 2523--2790 Score: 450
Period size: 109 Copynumber: 2.5 Consensus size: 105
2513 TGCGTTTATA
2523 ATTTCGCATTGCGATT-ATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
*
2587 GATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
2627 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATGTTCATTTCGCA
1 ATTTCGCATTGCGA-TT-CATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
2692 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
62 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2736 ATTTCGCATTGCGATTC-TCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
2791 GTTGGGATTT
Statistics
Matches: 153, Mismatches: 5, Indels: 11
0.91 0.03 0.07
Matches are distributed among these distances:
104 29 0.19
105 18 0.12
106 4 0.03
107 6 0.04
108 2 0.01
109 94 0.61
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (105 bp):
ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:5095 original size:12 final size:12
Alignment explanation
Indices: 5078--5102 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5068 TCTTCGGGGA
5078 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5090 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5102 C
1 C
5103 AGGATATATG
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:6015 original size:20 final size:20
Alignment explanation
Indices: 5987--6373 Score: 439
Period size: 20 Copynumber: 19.4 Consensus size: 20
5977 AAATTTCAGT
* * * *
5987 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6007 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
6027 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6047 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6067 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6087 GTTGCGATTTACGGAT---C
1 GTTGCGATTTACGGATACGC
6104 G-TGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6123 GTTGCGATTTACGGATACCGC
1 GTTGCGATTTACGGATA-CGC
*
6144 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6164 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
6184 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
6204 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
6225 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6245 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
6265 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
6285 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
6305 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
6325 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
6345 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
6365 GTTGCGATT
1 GTTGCGATT
6374 ATTGAAAATC
Statistics
Matches: 319, Mismatches: 34, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
16 14 0.04
17 2 0.01
19 7 0.02
20 258 0.81
21 36 0.11
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:12888 original size:14 final size:14
Alignment explanation
Indices: 12869--12915 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
12859 GCAAAACAAA
12869 TCTCTTTTCAGCTG
1 TCTCTTTTCAGCTG
*
12883 TCTCTTTTCGGCTG
1 TCTCTTTTCAGCTG
12897 TCTCTTTTCAGCTG
1 TCTCTTTTCAGCTG
12911 TCTCT
1 TCTCT
12916 AACAGTCCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.04, C:0.30, G:0.15, T:0.51
Consensus pattern (14 bp):
TCTCTTTTCAGCTG
Found at i:13509 original size:17 final size:18
Alignment explanation
Indices: 13483--13522 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
13473 ATTATATGGA
13483 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
13499 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
13517 TATTAT
1 TATTAT
13523 ACGTGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:13773 original size:2 final size:2
Alignment explanation
Indices: 13768--13792 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13758 CTTATAACTT
13768 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 T
13793 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13984 original size:2 final size:2
Alignment explanation
Indices: 13977--14005 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13967 ATATTTGTTG
13977 TA 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 TA T
14006 TTCCTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15067 original size:10 final size:10
Alignment explanation
Indices: 15052--15080 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
15042 TTTCCATTAT
15052 TTTTTATTTA
1 TTTTTATTTA
15062 TTTTTATTTA
1 TTTTTATTTA
15072 TTTTTATTT
1 TTTTTATTT
15081 TACTAACTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:18557 original size:18 final size:16
Alignment explanation
Indices: 18529--18584 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 16
18519 AATCAAGAAT
*
18529 AAAAAAGAAAAGAAGC
1 AAAAAAGAAAACAAGC
18545 AAAAAAGGAAAAACAAGAAC
1 AAAAAA-G-AAAACAAG--C
*
18565 AAAAAAGAAAATAAGC
1 AAAAAAGAAAACAAGC
18581 AAAA
1 AAAA
18585 TTAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 11 0.32
17 1 0.03
18 14 0.41
19 1 0.03
20 7 0.21
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAACAAGC
Found at i:18569 original size:20 final size:20
Alignment explanation
Indices: 18538--18575 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18528 TAAAAAAGAA
18538 AAGAAGCAAAAAAGGAAAAAC
1 AAGAAGCAAAAAA-GAAAAAC
18559 AAGAA-CAAAAAAGAAAA
1 AAGAAGCAAAAAAGAAAA
18576 TAAGCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (20 bp):
AAGAAGCAAAAAAGAAAAAC
Found at i:19636 original size:18 final size:18
Alignment explanation
Indices: 19613--19648 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19603 TCAATATCAA
*
19613 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
19631 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
19649 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:20182 original size:36 final size:38
Alignment explanation
Indices: 20135--20211 Score: 131
Period size: 36 Copynumber: 2.1 Consensus size: 38
20125 GTGCTCACCA
*
20135 TTGTCTCTCTTGAGACAGTTTCCCTT-GAAACAAA-CT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACCT
20171 TTGTCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACCT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACCT
20209 TTG
1 TTG
20212 AAATTGTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 26 0.68
37 7 0.18
38 5 0.13
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (38 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACCT
Found at i:20453 original size:37 final size:37
Alignment explanation
Indices: 20383--20454 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
20373 TGGAACTAAG
* *
20383 TTTTGTCTCTCTTGAGACAGATTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGATTTTCATAAAACAAAA
* *
20420 TTTTGTCTCCCTTGAGACTG-TTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGATTT-TCATAAAACAA
20455 CAGATATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 3 0.10
37 27 0.90
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGATTTTCATAAAACAAAA
Found at i:21207 original size:106 final size:106
Alignment explanation
Indices: 20971--21939 Score: 1356
Period size: 106 Copynumber: 9.0 Consensus size: 106
20961 ATATCGCGCC
* *
20971 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGG-CGGCTGGTTGTCAACAAACCACTTT-
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAA-GGGACGGCTGGTTGTCAACAAA-CAATTTC
* *
21034 TCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
64 CCAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
21081 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCATTACCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
21146 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
21187 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAAACAAACCACTTT-
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC-AACAAA-CAATTTC
* * *
21251 TCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGG
64 CCAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
21298 ACTCAAGACAACACAAGTTTAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAAACAATTTCT
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCC
21363 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
21405 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAACAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCC
* *
21470 CAGTTTCAGAGCCAATTTTAACTTTACAGCGAAGGATATTGG
65 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
21512 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAATAAACCACTTT-T
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCC
*
21576 CAGTTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
65 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
21618 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAGCAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * *
21683 AATTTCAGAG-CATATTTCAACTTCACAACGAATGATATTGG
66 AGTTTCAGAGCCA-ATTTCAACTTCACAGCGAAGGATATTGG
* *
21724 ACTCAAGACGACACAAGTTCAAATTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
21789 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
66 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * * *
21830 ACTTGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* **
21895 AGTTTCGGAGCCAATTTCAACTTCAC-GATAGAGGATATTGG
66 AGTTTCAGAGCCAATTTCAACTTCACAGCGA-AGGATATTGG
21936 ACTC
1 ACTC
21940 GGAATAATAC
Statistics
Matches: 781, Mismatches: 63, Indels: 34
0.89 0.07 0.04
Matches are distributed among these distances:
105 9 0.01
106 407 0.52
107 202 0.26
108 4 0.01
109 8 0.01
110 61 0.08
111 90 0.12
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:21979 original size:431 final size:427
Alignment explanation
Indices: 20971--21940 Score: 1386
Period size: 431 Copynumber: 2.3 Consensus size: 427
20961 ATATCGCGCC
* * *
20971 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGGCGGCTGGTTGTCAACAAACCACTTT-T
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGGCGGCTGGTTGTCAACAAA-CAATTTCC
* *
21035 CAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTT
65 CAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGA-AAAACACAAGTT
21100 CAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCATTACCCAATTTCAGAGCCAATTTCA
125 CAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCATTACCCAATTTCAGAGCCAATTTCA
*
21165 ACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACT
190 ACTTCACATCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACT
* * * *
21230 GGTTGTCAAACAAACCACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATAT
255 GGTTGTCAAACAAACCAATTTCCAG-AT-ATTCAGAGTCAATTTCAACTTCACAACGAAGGATAT
* *
21295 TGGACTCAAGACAACACAAGTTTAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAAACAATT
318 TGGACTCAAGACAACACAAGTTCAAATTCACAACGAAGGGACAGCTGGTTGTCAACAAAACAATT
* * *
21360 TCTCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
383 TCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
* * *
21405 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGGCGGCTGGTTGTCAAC-AAACAATTTCC
* *
21470 CAGTTTCAGAGCCAATTTTAACTTTACAGCGAAGGATATTGGACTC-AAGACAACACAAGTTCAA
65 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAA-A-AACACAAGTTCAA
** * ** *
21534 CTTCACAACGAAGGGACGGTTGGTTGTCAATAAACCACTT-TTCAGTTTCAGAGCCAATTTCAAC
128 CTTCACAACGAAGGGACGACTGGTTGTCAACAAACCA-TTACCCAATTTCAGAGCCAATTTCAAC
*
21598 TTCACAGT-GAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTG
192 TTCACA-TCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTG
* *
21662 GTTGTC-AGCAAA-CAATTTCCCA-AT-TTCAGAG-CATATTTCAACTTCACAACGAATGATATT
256 GTTGTCAAACAAACCAATTT-CCAGATATTCAGAGTCA-ATTTCAACTTCACAACGAAGGATATT
* *
21722 GGACTCAAGACGACACAAGTTCAAATTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTT
319 GGACTCAAGACAACACAAGTTCAAATTCACAACGAAGGGACAGCTGGTTGTCAACAAAACAATTT
21786 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
384 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
* * *
21830 ACTTGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGGCGGCTGGTTGTCAACAAACAATTTCCC
* **
21895 AGTTTCGGAGCCAATTTCAACTTCAC-GATAGAGGATATTGGACTCG
66 AGTTTCAGAGCCAATTTCAACTTCACAGCGA-AGGATATTGGACTCG
21941 GAATAATACT
Statistics
Matches: 484, Mismatches: 42, Indels: 29
0.87 0.08 0.05
Matches are distributed among these distances:
423 2 0.00
424 49 0.10
425 99 0.20
426 82 0.17
428 1 0.00
429 6 0.01
430 8 0.02
431 173 0.36
432 3 0.01
433 1 0.00
434 54 0.11
435 6 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (427 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGGCGGCTGGTTGTCAACAAACAATTTCCC
AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAAAAACACAAGTTCAACTT
CACAACGAAGGGACGACTGGTTGTCAACAAACCATTACCCAATTTCAGAGCCAATTTCAACTTCA
CATCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGT
CAAACAAACCAATTTCCAGATATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCA
AGACAACACAAGTTCAAATTCACAACGAAGGGACAGCTGGTTGTCAACAAAACAATTTCCCAATT
TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
Found at i:23184 original size:17 final size:18
Alignment explanation
Indices: 23158--23197 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
23148 ATTATATAGA
23158 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
23174 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
23192 TATTAT
1 TATTAT
23198 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:23584 original size:41 final size:39
Alignment explanation
Indices: 23539--23616 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 39
23529 AGAGGGCCCA
*
23539 TTTTTTTGTTTTATTTCTAACTAAAGTCTCTCCCACTTTTC
1 TTTTTTTGTCTTATTTCTAACTAAAG-C-CTCCCACTTTTC
*
23580 TTTTTTTGTCTTATTTCTGACTAAAGCCTCCCACTTT
1 TTTTTTTGTCTTATTTCTAACTAAAGCCTCCCACTTT
23617 CGGTGAAGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 10 0.29
40 1 0.03
41 24 0.69
ACGTcount: A:0.17, C:0.23, G:0.06, T:0.54
Consensus pattern (39 bp):
TTTTTTTGTCTTATTTCTAACTAAAGCCTCCCACTTTTC
Found at i:23684 original size:38 final size:40
Alignment explanation
Indices: 23633--23709 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
23623 AGTGAGAGGG
*
23633 TAGCTTTTATATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTATATTTTATAAATACTTTGATGTATATATATA
*
23671 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATAT
1 TAGCTT-TTATATTTTATAAATACTTTGATGTATATATAT
23710 TTATATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 12 0.35
39 7 0.21
40 15 0.44
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (40 bp):
TAGCTTTTATATTTTATAAATACTTTGATGTATATATATA
Found at i:23827 original size:14 final size:14
Alignment explanation
Indices: 23789--23828 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
23779 TATTTATTTA
*
23789 TTTTATTTTTTTCC
1 TTTTATTTTATTCC
*
23803 TTTTATTTTATTCT
1 TTTTATTTTATTCC
*
23817 TTTTATCTTATT
1 TTTTATTTTATT
23829 TGTTTTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTTATTCC
Found at i:23827 original size:19 final size:18
Alignment explanation
Indices: 23776--23829 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
23766 TTTTTCCTTA
23776 TCTTATTTATTTATTTTAT
1 TCTT-TTTATTTATTTTAT
*
23795 T-TTTTTCCTTTTATTTTAT
1 TCTTTTT--ATTTATTTTAT
23814 TCTTTTTATCTTATTT
1 TCTTTTTAT-TTATTT
23830 GTTTTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 18 0.62
20 5 0.17
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (18 bp):
TCTTTTTATTTATTTTAT
Found at i:26624 original size:21 final size:21
Alignment explanation
Indices: 26507--26624 Score: 71
Period size: 21 Copynumber: 5.7 Consensus size: 21
26497 ACGCGAAATA
**
26507 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
26527 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
26547 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
26568 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
26589 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
*
26610 AGAATCGCAACGCGA
1 AAAATCGCAACGCGA
26625 ACACATAAAT
Statistics
Matches: 71, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.34
21 44 0.62
22 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:26637 original size:20 final size:20
Alignment explanation
Indices: 26612--26784 Score: 242
Period size: 20 Copynumber: 8.6 Consensus size: 20
26602 GATTTTCCAG
* *
26612 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
26632 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26652 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
26672 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26692 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26712 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
26732 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
26753 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
26773 AATCGCAACGCG
1 AATCGCAACGCG
26785 ATTTTTAAAG
Statistics
Matches: 137, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
20 118 0.86
21 19 0.14
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:27203 original size:33 final size:33
Alignment explanation
Indices: 27164--27234 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
27154 TTCACTTAGA
*
27164 TTTCATTTCGTGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
27197 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
27230 TTTCA
1 TTTCA
27235 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:27371 original size:19 final size:19
Alignment explanation
Indices: 27347--27391 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
27337 GCAACGAGAG
**
27347 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
27366 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
27385 AATCGCA
1 AATCGCA
27392 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:27409 original size:19 final size:19
Alignment explanation
Indices: 27387--27514 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
27377 GAAACCAAAA
*
27387 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27406 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
27420 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27439 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
27453 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
27473 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
27493 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
27513 TC
1 TC
27515 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:27428 original size:14 final size:14
Alignment explanation
Indices: 27409--27465 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
27399 TTTCATTTCG
27409 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
27423 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
27442 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
27456 CGTTGCGATT
1 CGTTGCGATT
27466 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:27434 original size:33 final size:33
Alignment explanation
Indices: 27392--27514 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
27382 CAAAATCGCA
27392 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
27425 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
27458 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
27499 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
27515 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:27476 original size:21 final size:21
Alignment explanation
Indices: 27450--27514 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
27440 CGCGTTGCGA
27450 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
27471 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
27491 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
27512 TTC
1 TTC
27515 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:29324 original size:93 final size:93
Alignment explanation
Indices: 29165--29534 Score: 731
Period size: 93 Copynumber: 4.0 Consensus size: 93
29155 TCGTGAAATA
29165 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGT
1 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGT
29230 TCGGTTGCTGCCAATTCTGCTAAACTGT
66 TCGGTTGCTGCCAATTCTGCTAAACTGT
29258 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGT
1 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGT
*
29323 TCGGTTGCTGCCAATTCTGCTAAACTAT
66 TCGGTTGCTGCCAATTCTGCTAAACTGT
29351 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGT
1 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGT
29416 TCGGTTGCTGCCAATTCTGCTAAACTGT
66 TCGGTTGCTGCCAATTCTGCTAAACTGT
29444 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGT
1 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGT
29509 TCGGTTGCTGCCAATTCTGCTAAACT
66 TCGGTTGCTGCCAATTCTGCTAAACT
29535 AATACCCTGA
Statistics
Matches: 275, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 275 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGT
TCGGTTGCTGCCAATTCTGCTAAACTGT
Found at i:29669 original size:14 final size:14
Alignment explanation
Indices: 29650--29706 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
29640 CGAAACTTAA
29650 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
29664 AATCGCAACGCAAAATGAA
1 AATCGCAACG----A-GAG
*
29683 AATCGCAACGACAG
1 AATCGCAACGAGAG
29697 AATCGCAACG
1 AATCGCAACG
29707 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 21 0.60
15 1 0.03
18 1 0.03
19 12 0.34
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:29733 original size:32 final size:33
Alignment explanation
Indices: 29632--29753 Score: 149
Period size: 33 Copynumber: 3.7 Consensus size: 33
29622 TAGTTTACTT
* * *
29632 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
* **
29666 TCGCAACGCAAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
29699 TCGCAACGCGAAACCAAAATCGC-ACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
29731 TCGCAACGTGAAACC-AAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
29754 TTGCGACTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
31 7 0.09
32 22 0.29
33 37 0.48
34 11 0.14
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:29776 original size:19 final size:19
Alignment explanation
Indices: 29749--29864 Score: 90
Period size: 19 Copynumber: 6.6 Consensus size: 19
29739 TGAAACCAAA
* *
29749 TCGCATTGCGACTTTCATT
1 TCGCGTTGCGATTTTCATT
29768 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
29782 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
29801 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
29817 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
29834 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
29854 TCGTGTTGCGA
1 TCGCGTTGCGA
29865 AAGTAAACTA
Statistics
Matches: 77, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
14 17 0.22
16 8 0.10
17 8 0.10
19 32 0.42
20 12 0.16
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:29790 original size:14 final size:14
Alignment explanation
Indices: 29771--29827 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
29761 TTTCATTTCG
29771 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
29785 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
29802 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
29818 CGTTGCGATT
1 CGTTGCGATT
29828 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:29798 original size:33 final size:33
Alignment explanation
Indices: 29754--29846 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
29744 CCAAATCGCA
*
29754 TTGCGACTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
29787 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
29820 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
29847 TTAAGTTTCG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:30490 original size:33 final size:33
Alignment explanation
Indices: 30448--30694 Score: 230
Period size: 33 Copynumber: 7.1 Consensus size: 33
30438 GGACATAATG
*
30448 GATTTTCATTTCGCATTGCGATTCTCTCGTTAC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
* *
30481 GATTTTCATTTCGCATTGCGATT-T-TCATTTC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
* * ** * *
30512 GCATTGTGATTCTATCGTTGCGATTTTCATTTCGCATTGC
1 G-ATTTTCATT-TCGCATTGCGA--TTC-TCTCG--TTGC
30552 GATTTTCATTTCCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTT-CGCATTGCGATTCTCTCGTTGC
*
30586 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGC
* *
30624 GATTTTCATTTCCGCATTGCGATTTTCAT-GTTGG
1 GATTTTCATTT-CGCATTGCGATTCTC-TCGTTGC
30658 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
30691 GATT
1 GATT
30695 GTAATTTCCG
Statistics
Matches: 175, Mismatches: 21, Indels: 36
0.75 0.09 0.16
Matches are distributed among these distances:
31 6 0.03
32 9 0.05
33 63 0.36
34 29 0.17
35 5 0.03
36 10 0.06
37 7 0.04
38 18 0.10
39 24 0.14
40 4 0.02
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTCTCTCGTTGC
Found at i:30530 original size:52 final size:52
Alignment explanation
Indices: 30448--30694 Score: 351
Period size: 53 Copynumber: 4.7 Consensus size: 52
30438 GGACATAATG
*
30448 GATTTTCATTTCGCATTGCGATTCTCTCGTTACGATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
* *
30500 GATTTTCATTTCGCATTGTGATTCTATCGTTGCGATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
30552 GATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 GATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
* *
30605 GATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--T-G--TTGG
1 GATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATTTCGCATTGC
30658 GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
30695 GTAATTTCCG
Statistics
Matches: 180, Mismatches: 8, Indels: 19
0.87 0.04 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.02
52 70 0.39
53 74 0.41
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.07
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
GATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
Found at i:30605 original size:72 final size:71
Alignment explanation
Indices: 30448--30680 Score: 275
Period size: 72 Copynumber: 3.3 Consensus size: 71
30438 GGACATAATG
* *
30448 GATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTACGATTTTCATTT-CGCATTGCGATTT-T
1 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTCT
* *
30506 CATTTC
66 CGTTGC
* * ** *
30512 GCATTGTGATTCTATCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTC
1 G-ATTTTCATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT-
30577 TCTCGTTGC
63 TCTCGTTGC
30586 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTT-T
1 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTCT
*
30650 CATGTTGG
66 C--GTTGC
30658 GATTTTCATTTCGCATTGCGATT
1 GATTTTCATTTCGCATTGCGATT
30681 CTCTCGTTGC
Statistics
Matches: 142, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
64 1 0.01
65 7 0.05
66 8 0.06
68 3 0.02
69 4 0.03
70 2 0.01
71 15 0.11
72 88 0.62
73 8 0.06
74 6 0.04
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (71 bp):
GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTCT
CGTTGC
Found at i:30702 original size:105 final size:102
Alignment explanation
Indices: 30447--30694 Score: 358
Period size: 105 Copynumber: 2.4 Consensus size: 102
30437 CGGACATAAT
*
30447 GGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATTTTCATTTCGCATTGCGATTTTCATTTC
1 GGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTC
*
30512 GCATTGTGATTCTATCGTTGCGATTTTCATTTCGCATTG
66 GCATTGCGATTCTATCGTTGCGATTTTCA-TTCG-ATTG
*
30551 CGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 GGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
*
30616 CGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA-T-G-TTG
65 CGCATTGCGA--TTC-TAT-CG--TTGCGATTTTCATTCGATTG
30657 GGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 GGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
30695 GTAATTTCCG
Statistics
Matches: 132, Mismatches: 5, Indels: 13
0.88 0.03 0.09
Matches are distributed among these distances:
104 11 0.08
105 86 0.65
106 14 0.11
107 3 0.02
108 3 0.02
109 3 0.02
111 12 0.09
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (102 bp):
GGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTC
GCATTGCGATTCTATCGTTGCGATTTTCATTCGATTG
Found at i:32979 original size:12 final size:12
Alignment explanation
Indices: 32962--32986 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32952 TCTTCGGGGA
32962 CTTTTTCTTCTT
1 CTTTTTCTTCTT
32974 CTTTTTCTTCTT
1 CTTTTTCTTCTT
32986 C
1 C
32987 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:33195 original size:24 final size:24
Alignment explanation
Indices: 33161--33207 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
33151 CTGAAACATC
33161 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
33185 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
33208 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:33924 original size:20 final size:20
Alignment explanation
Indices: 33896--34124 Score: 244
Period size: 20 Copynumber: 11.4 Consensus size: 20
33886 AAATTTCAGT
* * *
33896 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
33916 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
33936 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
33956 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
33976 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
33996 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
34016 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
34036 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
34056 GTTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATTCGC
*
34076 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
34096 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
34116 GTTGCGATT
1 GTTGCGATT
34125 CTGGAAAATC
Statistics
Matches: 183, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 182 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:35466 original size:3 final size:3
Alignment explanation
Indices: 35458--35510 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
35448 CTCTAAAGGT
*
35458 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35506 ATA AT
1 ATA AT
35511 TATATTAAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39466 original size:33 final size:33
Alignment explanation
Indices: 39413--39511 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
39403 TTTGTTTCAA
39413 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
39445 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
39478 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
39511 T
1 T
39512 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:39540 original size:13 final size:13
Alignment explanation
Indices: 39497--39551 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
39487 TTGGAAGTAT
39497 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
39510 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
39524 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
39537 TTAAGTATTTGAA
1 TTAAGTATTTCAA
39550 TT
1 TT
39552 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:39774 original size:21 final size:21
Alignment explanation
Indices: 39748--39804 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
39738 TGGAGCGTGG
*
39748 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
39769 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
39790 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
39805 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:40111 original size:15 final size:17
Alignment explanation
Indices: 40085--40116 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40075 TTCTATGAGA
40085 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
40101 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
40117 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:49962 original size:2 final size:2
Alignment explanation
Indices: 49955--49984 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49945 ATCTAATAAA
49955 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
49985 TGGAACAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54093 original size:2 final size:2
Alignment explanation
Indices: 54086--54124 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
54076 TCGATATCAG
*
54086 AT AT AT AT AT ACT CT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
54125 TATTTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 33 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54417 original size:29 final size:28
Alignment explanation
Indices: 54375--54429 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
54365 TGTTGCATGA
*
54375 ACTCGAAATCTTTAGGGAGAATAATACTC
1 ACTCGAAATCTTTA-GAAGAATAATACTC
54404 ACTCGAAATCTTTAGAAGAATAATAC
1 ACTCGAAATCTTTAGAAGAATAATAC
54430 GCACATTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (28 bp):
ACTCGAAATCTTTAGAAGAATAATACTC
Found at i:55704 original size:2 final size:2
Alignment explanation
Indices: 55699--55758 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
55689 TCTCTCCAAC
55699 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
55741 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
55759 TTCCCCTCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62255 original size:22 final size:23
Alignment explanation
Indices: 62230--62272 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
62220 TATCTAATTC
62230 TGCGCTTAATTT-TATTTGTTAA
1 TGCGCTTAATTTCTATTTGTTAA
* *
62252 TGCGTTTAATTTCTTTTTGTT
1 TGCGCTTAATTTCTATTTGTT
62273 TGTAGGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.60
Consensus pattern (23 bp):
TGCGCTTAATTTCTATTTGTTAA
Found at i:63195 original size:2 final size:2
Alignment explanation
Indices: 63188--63218 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
63178 GTATGGGCTC
63188 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 A
63219 CAAGTATGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65670 original size:20 final size:21
Alignment explanation
Indices: 65645--65737 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
65635 TTTTCCCAAT
*
65645 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
65665 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
65686 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
65706 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
65727 TCGCAATGCGA
1 TCGCAATGCGA
65738 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:65690 original size:41 final size:41
Alignment explanation
Indices: 65645--65737 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
65635 TTTTCCCAAT
65645 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
65686 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
65727 TCGCAATGCGA
1 TCGCAATGCGA
65738 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:65750 original size:41 final size:41
Alignment explanation
Indices: 65664--65798 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
65654 GAATAAGTAA
* *
65664 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
65705 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
65746 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
65787 TTCGCAACGCGA
1 ATCGCAACGCGA
65799 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:65751 original size:20 final size:20
Alignment explanation
Indices: 65726--65819 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
65716 AATTGGGAAA
*
65726 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
65746 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
65767 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
65787 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
65807 TTCGCAACGCGAT
1 ATCGCAACGCGAT
65820 TTACATAACG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:66396 original size:19 final size:19
Alignment explanation
Indices: 66336--66416 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
66326 TTCGAGAATG
66336 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
66356 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
66372 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
66389 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
66408 AAAATCGCA
1 AAAATCGCA
66417 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:66458 original size:20 final size:19
Alignment explanation
Indices: 66412--66577 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
66402 GAAACCAAAA
*
66412 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
66431 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
66450 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
66470 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
66486 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
66503 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
66517 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
66536 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
66556 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
66576 TC
1 TC
66578 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.34
20 49 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:66493 original size:39 final size:39
Alignment explanation
Indices: 66417--66493 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
66407 CAAAATCGCA
* **
66417 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
66456 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
66494 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:66502 original size:33 final size:33
Alignment explanation
Indices: 66465--66552 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
66455 GTTGCGATTT
* *
66465 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
66498 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
66531 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
66553 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:68637 original size:42 final size:42
Alignment explanation
Indices: 68577--68699 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
68567 GCCCGACTCG
* * *
68577 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
68619 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
68661 ACTGTCATCGTTGAAGAGATCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGAG-TCCACTCCCACCGTTCAAGAG
68700 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 63 0.95
43 3 0.05
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:68657 original size:21 final size:21
Alignment explanation
Indices: 68633--68699 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
68623 TCATTCCTCG
68633 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
68654 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
68675 AGAGAT-CCCTCCCACCATTCA
1 AGAG-TCCCCTCCCACCGTTCA
68696 AGAG
1 AGAG
68700 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:70077 original size:14 final size:14
Alignment explanation
Indices: 70058--70093 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
70048 ATTGTTTAAT
70058 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
70072 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
70086 TGATTTGT
1 TGATTTGT
70094 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:70295 original size:19 final size:19
Alignment explanation
Indices: 70273--70390 Score: 67
Period size: 19 Copynumber: 6.7 Consensus size: 19
70263 CGAAATTAAA
70273 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
70292 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
70307 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
70325 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
70340 -TCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
* ** *
70358 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
70377 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
70391 GGACATTAAG
Statistics
Matches: 72, Mismatches: 16, Indels: 21
0.66 0.15 0.19
Matches are distributed among these distances:
14 17 0.24
16 5 0.07
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:70319 original size:33 final size:33
Alignment explanation
Indices: 70277--70370 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
70267 ATTAAATTCG
70277 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
70310 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
70343 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
70371 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:72633 original size:12 final size:12
Alignment explanation
Indices: 72616--72640 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
72606 TCTTCGGGGA
72616 CTTTTTCTTCTT
1 CTTTTTCTTCTT
72628 CTTTTTCTTCTT
1 CTTTTTCTTCTT
72640 C
1 C
72641 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:72849 original size:24 final size:24
Alignment explanation
Indices: 72815--72868 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
72805 CTGAAACATC
* *
72815 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
72839 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
72863 ATCAAA
1 ATCAAA
72869 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:74019 original size:19 final size:19
Alignment explanation
Indices: 73978--74045 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
73968 GAAATGAAAA
73978 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
73994 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
74011 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
74030 TCGAATTACGATTTTC
1 TCGCATTGCGATTTTC
74046 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 28 0.62
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:76099 original size:20 final size:19
Alignment explanation
Indices: 76064--76130 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
76054 GAAACTTAAA
76064 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
76083 ATCGTAACGCAGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
76103 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
76122 ATCGCAACG
1 ATCGCAACG
76131 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:76138 original size:14 final size:14
Alignment explanation
Indices: 76119--76176 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
76109 ATGCGAAATG
76119 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
76133 AAAATCGCAACACGAA
1 AAAATCGC-A-ACGAC
76149 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
76165 AAAATCGCAACG
1 AAAATCGCAACG
76177 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 19 0.50
15 1 0.03
16 10 0.26
17 1 0.03
18 7 0.18
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:76161 original size:32 final size:33
Alignment explanation
Indices: 76103--76181 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
76093 AGAAATGGCT
*
76103 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
76136 ATCGCAACACGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
76168 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
76182 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 29 0.67
33 14 0.33
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:76229 original size:14 final size:14
Alignment explanation
Indices: 76210--76267 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
76200 TTTCATTTCG
76210 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
76224 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
76240 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
76256 CATTGCGATTTT
1 CGTTGCGATTTT
76268 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:76274 original size:33 final size:33
Alignment explanation
Indices: 76191--76283 Score: 161
Period size: 32 Copynumber: 2.8 Consensus size: 33
76181 ACACAAATCG
*
76191 CATTGCGATTTTCATTTCGCGTTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
*
76224 CGTTGCGA-TTTCATTTCGCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
76256 CATTGCGATTTTCATTTCGCATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
76284 AGCCATTTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.54
33 26 0.46
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.46
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:76319 original size:20 final size:20
Alignment explanation
Indices: 76270--76322 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
76260 GCGATTTTCA
*
76270 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
76290 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
76310 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
76323 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:76820 original size:18 final size:18
Alignment explanation
Indices: 76794--76838 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
76784 GTCGATCAGA
*
76794 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
76812 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
76830 TGATGGCTC
1 TGATGGCTC
76839 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:78182 original size:20 final size:20
Alignment explanation
Indices: 78157--78194 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
78147 AATAGTTTCT
78157 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
78177 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
78195 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:78483 original size:22 final size:22
Alignment explanation
Indices: 78458--78501 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
78448 GATTTAGATA
78458 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
78480 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
78502 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:78714 original size:20 final size:20
Alignment explanation
Indices: 78689--78741 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
78679 GATTATGTAT
*
78689 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
78709 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
78729 TATCTCGTTGCGA
1 TATCGCGTTGCGA
78742 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:78796 original size:20 final size:20
Alignment explanation
Indices: 78752--78844 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
78742 TTTTTTATTA
* **
78752 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
78773 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
78793 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
78814 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
78834 TCGCATTGCGA
1 TCGCATTGCGA
78845 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:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:78797 original size:41 final size:41
Alignment explanation
Indices: 78734--78844 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
78724 GTAAGTATCT
*
78734 CGTTGCGATTT-TTTATTATCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTA-T-TCGCATTGCGATTTTCCCAATTCG
78776 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
78817 CGTTGCGATTTACTTATTCGCATTGCGA
1 CGTTGCGATTTACTTATTCGCATTGCGA
78845 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
41 52 0.78
42 12 0.18
43 3 0.04
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (41 bp):
CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
Found at i:92935 original size:2 final size:2
Alignment explanation
Indices: 92913--92970 Score: 75
Period size: 2 Copynumber: 29.0 Consensus size: 2
92903 TAAAGATTCG
*
92913 AT AT A- AT AT AT AGT -T AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92954 AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT -AT AT
92971 TTAAATTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
1 2 0.04
2 45 0.90
3 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:98006 original size:2 final size:2
Alignment explanation
Indices: 97999--98074 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
97989 ATATGAAGAA
97999 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
98041 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
98075 CTTATATGGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:100526 original size:23 final size:23
Alignment explanation
Indices: 100468--100531 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
100458 CATTATTATA
* *
100468 TGGCACTACGATGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
100491 CGGCAC-TCTGGTGCAATTCTACG
1 TGGCACTTC-GGTGCAATTCTACG
*
100514 TGGCACTTCGGTGTAATT
1 TGGCACTTCGGTGCAATT
100532 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.91
24 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:107310 original size:103 final size:103
Alignment explanation
Indices: 107128--107351 Score: 378
Period size: 103 Copynumber: 2.2 Consensus size: 103
107118 AGAGGGTATG
*
107128 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* **
107193 GATCCTTGGCATATGTATATGATTCTTAAGGAATGATA
66 GATCCCTAACATATGTATATGATTCTTAAGGAATGATA
*
107231 TGTGGTCCTTCAGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
107296 GATCCCTAATATATGTATATGATTCTTAAGGAATGATA
66 GATCCCTAACATATGTATATGATTCTTAAGGAATGATA
107334 TGTGGTCCTT-ATGGACAT
1 TGTGGTCCTTCA-GGACAT
107352 TATTAATGGC
Statistics
Matches: 114, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
102 1 0.01
103 113 0.99
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAACATATGTATATGATTCTTAAGGAATGATA
Found at i:107393 original size:23 final size:23
Alignment explanation
Indices: 107358--107421 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
107348 ACATTATTAA
107358 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
107381 TGGCACT-CTGGTGCAATTCTACG
1 TGGCACTAC-GGTGCAATTCTACG
* *
107404 TGGCACTTCGGTGTAATT
1 TGGCACTACGGTGCAATT
107422 ATATGAGCTG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:108359 original size:13 final size:13
Alignment explanation
Indices: 108314--108373 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
108304 GAATATATTA
*
108314 ATATTTTAA-AAT
1 ATATTATAATAAT
*
108326 A-ATTAAAATAAT
1 ATATTATAATAAT
108338 ATATTTTATAATAAT
1 ATA--TTATAATAAT
*
108353 ATATTATAATTAT
1 ATATTATAATAAT
*
108366 TTATTATA
1 ATATTATA
108374 TTTTAAAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 5 0.13
12 5 0.13
13 17 0.44
15 12 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATTATAATAAT
Found at i:114240 original size:47 final size:47
Alignment explanation
Indices: 114182--114276 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 47
114172 GATTGTGTTG
*
114182 CAGCTAAGTGGTATCCCGAGATGGCTA-ATATAAGGTTCTGGTAGTTT
1 CAGCTAAGTGGTATCCCGAGATGGCTAGA-ATAAGATTCTGGTAGTTT
* * * * *
114229 CAGCTATGTGGTTTCCGGAGATGGTTAGAATAAGATTCTGGTTGTTT
1 CAGCTAAGTGGTATCCCGAGATGGCTAGAATAAGATTCTGGTAGTTT
114276 C
1 C
114277 TTGGTCACTG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 40 0.98
48 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (47 bp):
CAGCTAAGTGGTATCCCGAGATGGCTAGAATAAGATTCTGGTAGTTT
Found at i:122603 original size:57 final size:57
Alignment explanation
Indices: 122460--122644 Score: 194
Period size: 57 Copynumber: 3.2 Consensus size: 57
122450 ATAATTCAAA
* * *
122460 AGTTTG-GGATAAAATTGGAATATTCAAAAGTTTAGGGACTAATTTA-AAATGAGAGTGAT
1 AGTTTGAGGATAAATTTGGAATATTCAAAAGTTT-GGGACCAATTTAGAAA--A-AGTCAT
* * *
122519 AGTTTGAGGATAGATTTTGAATATTCAAAAGTTTGGGACCAATTTAGAAAAAATCAT
1 AGTTTGAGGATAAATTTGGAATATTCAAAAGTTTGGGACCAATTTAGAAAAAGTCAT
* * * * *
122576 AGTTTGAGGATACATTTGGAATGTTCAAAAGTATGGGGATCAATTTAGAATAAGTCAT
1 AGTTTGAGGATAAATTTGGAATATTCAAAAGT-TTGGGACCAATTTAGAAAAAGTCAT
* *
122634 AATTTGGGGAT
1 AGTTTGAGGAT
122645 CGTGTAGTAC
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
57 33 0.31
58 31 0.29
59 17 0.16
60 27 0.25
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (57 bp):
AGTTTGAGGATAAATTTGGAATATTCAAAAGTTTGGGACCAATTTAGAAAAAGTCAT
Found at i:124970 original size:198 final size:198
Alignment explanation
Indices: 124475--125631 Score: 2140
Period size: 198 Copynumber: 5.9 Consensus size: 198
124465 TGTCGATCCC
* *
124475 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
124540 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
124605 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTATTTCCAGAATGA
124670 ATGGAA
193 ATGGAA
124676 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
124741 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
124806 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATG
124871 GAA
196 GAA
124874 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
124939 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTT-T-----
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
124997 -ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATG
125061 GAA
196 GAA
125064 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA-C
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
125128 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
125193 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATG
125258 GAA
196 GAA
125261 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
125326 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
125391 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATG
125456 GAA
196 GAA
125459 AACA-GGTGCACCCATAAAGTGTCGATCCATATAT-AAAA-TGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
125521 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
125586 AATATGTCTAAATAATGTGTCGACACTAATAGAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
125632 CTAATTTAAA
Statistics
Matches: 938, Mismatches: 9, Indels: 24
0.97 0.01 0.02
Matches are distributed among these distances:
189 55 0.06
190 132 0.14
191 1 0.00
195 133 0.14
196 5 0.01
197 162 0.17
198 277 0.30
199 114 0.12
200 24 0.03
201 35 0.04
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATG
GAA
Found at i:125213 original size:387 final size:391
Alignment explanation
Indices: 124475--125631 Score: 2103
Period size: 387 Copynumber: 2.9 Consensus size: 391
124465 TGTCGATCCC
* *
124475 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
124540 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT---
124605 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
126 --AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGA
124670 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
188 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
124735 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
253 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
124800 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAA
318 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAA
124865 TGAATGGAA
383 TGAATGGAA
124874 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
124939 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTT-T-ATAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATAATAT
125001 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAA
131 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAA
125066 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA-CCA
196 CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
125130 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
261 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
125195 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGA
326 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGA
125260 A
391 A
125261 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
125326 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA--T---
*
125391 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATG
126 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
125456 GAAAACA-GGTGCACCCATAAAGTGTCGATCCATATAT-AAAA-TGTCGATCCCAAAATCATCGA
191 GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
125518 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
256 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
*
125583 GAGAATATGTCTAAATAATGTGTCGACACTAATAGAGTTTGTGTCGATA
321 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
125632 CTAATTTAAA
Statistics
Matches: 744, Mismatches: 5, Indels: 24
0.96 0.01 0.03
Matches are distributed among these distances:
387 253 0.34
388 88 0.12
389 45 0.06
391 1 0.00
392 22 0.03
393 115 0.15
394 30 0.04
395 71 0.10
396 3 0.00
397 57 0.08
398 24 0.03
399 35 0.05
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (391 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATAATAT
GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAA
CAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGA
A
Found at i:127359 original size:25 final size:25
Alignment explanation
Indices: 127325--127389 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
127315 TTATCATTAA
127325 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
127350 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
127375 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
127390 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:127761 original size:23 final size:23
Alignment explanation
Indices: 127730--127793 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
127720 ATAGGTAAAC
*
127730 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
127753 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
127776 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
127794 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:127800 original size:23 final size:23
Alignment explanation
Indices: 127730--127802 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
127720 ATAGGTAAAC
* **
127730 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
127753 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
127776 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
127799 ATAT
1 ATAT
127803 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:128450 original size:334 final size:330
Alignment explanation
Indices: 127845--128509 Score: 1249
Period size: 334 Copynumber: 2.0 Consensus size: 330
127835 CATACTTTTT
*
127845 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAAT
127910 TATAGGCGTCTAATGATTTATTTTTTACATTACGATATATTATTATTAAATTAAAAATTCTAAAT
66 TATAGGCGTCTAATGATTTATTTTTTACATTACGATATATTATTATTAAATTAAAAATTCTAAAT
*
127975 ATTATTTTATAAAATATCAAAAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATT
131 AATATTTTATAAAATATCAAAAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATT
*
128040 GTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAG
196 GTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAA
128105 TATCGATCATTTTTATAAAAAGTATGAACACTTTCAATATAATATAATGTAATAGGTAAATTTGC
261 TATCGATCATTTTTATAAAAAGTATGAACACTTTCAATATAATATAATGTAATAGGTAAATTTGC
128170 AATGC
326 AATGC
128175 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAAT
1 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAAT
*
128240 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAA
66 TATAGGCGTCTAATGATTTATTTTTTACATTACG--ATATATTATTATTAAATTAAAAATTCTAA
128305 ATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
129 ATAATATTTTATAAAATATC-AAA-AATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
128370 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAA
192 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAA
*
128435 GAAATATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAATATAATGTAATAGGTAAAT
257 GAAATATCGATCATTTTTATAAAAAGTATGAACACTTTCAATATAATATAATGTAATAGGTAAAT
128500 TTGCAATGC
322 TTGCAATGC
128509 T
1 T
128510 ATCGGTATAA
Statistics
Matches: 326, Mismatches: 5, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
330 97 0.30
332 48 0.15
333 3 0.01
334 178 0.55
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (330 bp):
TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAATAAT
TATAGGCGTCTAATGATTTATTTTTTACATTACGATATATTATTATTAAATTAAAAATTCTAAAT
AATATTTTATAAAATATCAAAAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATT
GTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAA
TATCGATCATTTTTATAAAAAGTATGAACACTTTCAATATAATATAATGTAATAGGTAAATTTGC
AATGC
Found at i:131556 original size:20 final size:20
Alignment explanation
Indices: 131531--131590 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
131521 TCTTTTAGTT
*
131531 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
* *
131551 ATTAGATAGAATCAATTTTT
1 ATTAGATAGAATCAGTTTTA
131571 ATTAGATAGAATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
131591 TTTTGTTGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:134643 original size:16 final size:18
Alignment explanation
Indices: 134611--134645 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
134601 ATATAAAAAC
134611 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
134629 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
134645 A
1 A
134646 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:136164 original size:79 final size:79
Alignment explanation
Indices: 136033--136189 Score: 296
Period size: 79 Copynumber: 2.0 Consensus size: 79
136023 GAATGAAATT
*
136033 TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCT
1 TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCT
136098 TCGTTGGGAAGTTG
66 TCGTTGGGAAGTTG
136112 TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCT
1 TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCT
*
136177 TCGTTGTGAAGTT
66 TCGTTGGGAAGTT
136190 AAAATTGGCT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.34
Consensus pattern (79 bp):
TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCT
TCGTTGGGAAGTTG
Found at i:136221 original size:105 final size:105
Alignment explanation
Indices: 136105--136679 Score: 944
Period size: 105 Copynumber: 5.5 Consensus size: 105
136095 CCTTCGTTGG
* *
136105 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
1 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
* ** *
136170 ATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGCGATTGG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
136210 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
1 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
136275 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
136315 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
1 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
* *
136380 ATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
136420 GAA----TTATTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCC-
1 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
*
136480 ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* *
136520 GAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
136585 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
* ** * *
136625 GAAGTTGTTTGTTGACAACCAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
1 GAAGTTG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
136680 CCTCGAGTGC
Statistics
Matches: 444, Mismatches: 20, Indels: 11
0.93 0.04 0.02
Matches are distributed among these distances:
100 42 0.09
101 55 0.12
104 55 0.12
105 251 0.57
106 41 0.09
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
Found at i:136567 original size:310 final size:312
Alignment explanation
Indices: 136115--136679 Score: 981
Period size: 310 Copynumber: 1.8 Consensus size: 312
136105 GAAGTTGTTG
* *
136115 TTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCG
1 TTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCCAATATCCTTCA
** *
136180 TTGTGAAGTTAAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCG
66 TTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCG
136245 TGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
131 TGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
*
136310 ATTGAGAAGTTG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
196 ATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
136374 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAATTA
261 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAATTA
* *
136426 TTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCC-ATATCCTTCA
1 TTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCCAATATCCTTCA
* *
136490 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCG
66 TTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCG
*
136555 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
131 TGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
** * *
136620 ATTGAGAAGTTGTTTGTTGACAACCAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
196 ATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
136680 CCTCGAGTGC
Statistics
Matches: 238, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
310 145 0.61
311 93 0.39
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (312 bp):
TTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGAAGTCCAATATCCTTCA
TTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCG
TGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
ATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAATTA
Found at i:136570 original size:205 final size:207
Alignment explanation
Indices: 136105--136679 Score: 911
Period size: 205 Copynumber: 2.8 Consensus size: 207
136095 CCTTCGTTGG
*
136105 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
1 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* ** * *
136170 ATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAGCAGCGGT
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---GTTATTGACAAGCAGCGGT
*
136235 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
128 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAAT
136300 TGGCTCTGAAATTGA
193 TGGCTCTGAAATTGA
*
136315 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCA
1 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * *
136380 ATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA-TTATTGACAGGCAGCGGTCCC
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTGACAAGCAGCGGTCCC
136444 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCC-ATATCCTTCATTGTGAAGTTGAAATTGG
131 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGG
136508 CTCTGAAATTGA
196 CTCTGAAATTGA
*
136520 GAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * **
136585 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGTTG
66 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---G-TTATTGACAAGCAGCGG
* *
136650 TCCCTTCGTTGTGAAGTTGAACTTGTGTTG
127 TCCCTTCGTCGTGAAGTTGAACTTGCGTTG
136680 CCTCGAGTGC
Statistics
Matches: 338, Mismatches: 22, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
205 143 0.42
206 55 0.16
210 140 0.41
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (207 bp):
GAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTGACAAGCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGG
CTCTGAAATTGA
Found at i:137462 original size:62 final size:68
Alignment explanation
Indices: 137318--137469 Score: 181
Period size: 68 Copynumber: 2.3 Consensus size: 68
137308 AGATATCTGT
* * ** *
137318 TTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATTTT
1 TTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAGTTT
137383 GTG
66 GTG
* * *
137386 TTTCAAGAGTAACTGTCTCAAGGGAGA-AAAATT-TGTTTT-AGGGGAA-AAATTCAAAG-GTTT
1 TTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAGTTT
137446 -TG
66 GTG
*
137448 TTTCAAGGGAAACTGTCTCAAG
1 TTTCAAGAGAAACTGTCTCAAG
137470 ATAGACGAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
62 22 0.30
63 3 0.04
64 8 0.11
65 6 0.08
66 6 0.08
67 6 0.08
68 23 0.31
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (68 bp):
TTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAGTTT
GTG
Found at i:137496 original size:36 final size:36
Alignment explanation
Indices: 137445--137568 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
137435 TTCAAAGGTT
*
137445 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
* *
137481 TTGTTTCAAGAGAAACTGTCTTAAGAGAGAC-AAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
* * *
137516 CTTAGTTCCAAGGGAAACTATCTCAAGAGAGACGAAAT
1 -TT-GTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
*
137554 TTATTTCAAGGGAAA
1 TTGTTTCAAGGGAAA
137569 TGTTTTCAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
Found at i:138570 original size:22 final size:22
Alignment explanation
Indices: 138529--138572 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
138519 CATTTTTGTT
*
138529 CATTTGATGCTAAATGGTTTGA
1 CATTTGATGCTAAATAGTTTGA
138551 CATTTGATGCTCAAA-AGTTTGA
1 CATTTGATGCT-AAATAGTTTGA
138573 TGGGGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTAAATAGTTTGA
Found at i:139247 original size:23 final size:23
Alignment explanation
Indices: 139203--139246 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
139193 TTTGTTCTTA
*
139203 TTTTTTCCTTTTTGCTTCTTTTC
1 TTTTTTCCTTTTTGCCTCTTTTC
*
139226 TTTTTTTCTTTTTGCC-CTTTT
1 TTTTTTCCTTTTTGCCTCTTTT
139247 TGTTCTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (23 bp):
TTTTTTCCTTTTTGCCTCTTTTC
Found at i:140449 original size:8 final size:8
Alignment explanation
Indices: 140433--140471 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
140423 ATTGTAGATG
140433 AAAATGCA
1 AAAATGCA
*
140441 AAAAGGCA
1 AAAATGCA
140449 AAAATGC-
1 AAAATGCA
140456 AAAATGCA
1 AAAATGCA
*
140464 AGAATGCA
1 AAAATGCA
140472 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:140459 original size:15 final size:15
Alignment explanation
Indices: 140433--140471 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
140423 ATTGTAGATG
140433 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
140449 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
140464 AGAATGCA
1 AAAATGCA
140472 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:143136 original size:16 final size:18
Alignment explanation
Indices: 143104--143138 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
143094 ATATAAAAAC
143104 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
143122 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
143138 A
1 A
143139 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:143196 original size:25 final size:24
Alignment explanation
Indices: 143149--143207 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
143139 AATGAGTAAA
*
143149 ATATATAAAAAGTAAAAGCATAAT
1 ATATATAAAAAGTAAAAGAATAAT
* *
143173 ATATATATATAAGTAAAATAATAAT
1 ATATATA-AAAAGTAAAAGAATAAT
*
143198 A-ATAAAAAAA
1 ATATATAAAAA
143208 AAGAAAATCA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.10
24 11 0.38
25 15 0.52
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (24 bp):
ATATATAAAAAGTAAAAGAATAAT
Found at i:145919 original size:20 final size:20
Alignment explanation
Indices: 145894--145953 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
145884 TCTGTTAGTT
145894 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
*
145914 ATTAGATATGATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
*
145934 ATTAGATAGAATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
145954 TTATGTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.42
Consensus pattern (20 bp):
ATTAGATAGGATCAGTTTTA
Found at i:153026 original size:16 final size:16
Alignment explanation
Indices: 153005--153036 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
152995 TGTTCACCCC
153005 CTTTCCCTTCCTCTTT
1 CTTTCCCTTCCTCTTT
*
153021 CTTTCCCTTTCTCTTT
1 CTTTCCCTTCCTCTTT
153037 TTCCCAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (16 bp):
CTTTCCCTTCCTCTTT
Found at i:153225 original size:21 final size:21
Alignment explanation
Indices: 153184--153225 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
153174 TAATTGATAT
* *
153184 AATTATACTCTTTAATTTTTA
1 AATTATACTATTTAATATTTA
153205 AATTATACATATTTAA-ATTTA
1 AATTATAC-TATTTAATATTTA
153226 TAATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTATACTATTTAATATTTA
Done.