Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008089.1 Hibiscus syriacus cultivar Beakdansim tig00110599_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: 419803
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:800 original size:12 final size:12
Alignment explanation
Indices: 783--807 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
773 TGAGCGTTAT
783 TATTTTAATTTA
1 TATTTTAATTTA
795 TATTTTAATTTA
1 TATTTTAATTTA
807 T
1 T
808 TATAAAAAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTTAATTTA
Found at i:3450 original size:23 final size:25
Alignment explanation
Indices: 3416--3475 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
3406 TTAAGGTATA
3416 TTTTATTATATTTAA-TATTTT-AT
1 TTTTATTATATTTAAGTATTTTAAT
3439 TTTTAATT-TATTTAAGTATTTTAAT
1 TTTT-ATTATATTTAAGTATTTTAAT
*
3464 TTTT-TAATATTT
1 TTTTATTATATTT
3476 TATTTAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
23 12 0.38
24 14 0.44
25 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (25 bp):
TTTTATTATATTTAAGTATTTTAAT
Found at i:3461 original size:9 final size:8
Alignment explanation
Indices: 3413--3477 Score: 62
Period size: 8 Copynumber: 8.0 Consensus size: 8
3403 TGTTTAAGGT
3413 ATATTTTA
1 ATATTTTA
*
3421 TTATATTTA
1 ATAT-TTTA
3430 ATATTTT-
1 ATATTTTA
3437 AT-TTTTA
1 ATATTTTA
*
3444 ATTTATTTA
1 ATAT-TTTA
3453 AGTATTTTA
1 A-TATTTTA
*
3462 ATTTTTTA
1 ATATTTTA
3470 ATATTTTA
1 ATATTTTA
3478 TTTAATTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
6 4 0.09
7 4 0.09
8 20 0.43
9 17 0.36
10 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (8 bp):
ATATTTTA
Found at i:3468 original size:8 final size:8
Alignment explanation
Indices: 3426--3492 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
3416 TTTTATTATA
*
3426 TTTAATAT
1 TTTAATTT
3434 TTT-A-TT
1 TTTAATTT
3440 TTTAATTT
1 TTTAATTT
*
3448 ATTTAAGTAT
1 -TTTAA-TTT
3458 TTTAATTT
1 TTTAATTT
*
3466 TTTAATAT
1 TTTAATTT
3474 TTT-ATTT
1 TTTAATTT
*
3481 AATTAATTT
1 -TTTAATTT
3490 TTT
1 TTT
3493 TTACAGATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
6 4 0.09
7 5 0.11
8 21 0.46
9 14 0.30
10 2 0.04
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (8 bp):
TTTAATTT
Found at i:3483 original size:12 final size:12
Alignment explanation
Indices: 3419--3483 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
3409 AGGTATATTT
*
3419 TATTATATTTAA
1 TATTTTATTTAA
*
3431 TATTTTATTT-T
1 TATTTTATTTAA
*
3442 TAATTTATTTAA
1 TATTTTATTTAA
3454 GTATTTTAATTTTTTAA
1 -TATTTT-A---TTTAA
3471 TATTTTATTTAA
1 TATTTTATTTAA
3483 T
1 T
3484 TAATTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
11 9 0.21
12 15 0.36
13 5 0.12
14 1 0.02
15 1 0.02
16 6 0.14
17 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:8297 original size:19 final size:19
Alignment explanation
Indices: 8273--8312 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
8263 GTTTGGTGAA
8273 GTGCATTGTGATAATATTG
1 GTGCATTGTGATAATATTG
8292 GTGCATTGTGATAATATTG
1 GTGCATTGTGATAATATTG
8311 GT
1 GT
8313 CTGTTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.05, G:0.28, T:0.42
Consensus pattern (19 bp):
GTGCATTGTGATAATATTG
Found at i:18668 original size:20 final size:22
Alignment explanation
Indices: 18643--18700 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
18633 TTCCCCTTGA
18643 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
18663 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
18686 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
18701 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:20445 original size:64 final size:63
Alignment explanation
Indices: 20336--20478 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 63
20326 TCTTTAACAT
*
20336 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCA-CTTCGATGTTTCCATTTTTAA-GGG
* * * * *
20400 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAACTGCA-TTCGATGTTTCCATTTTTTATG
1 GTGCATCGATGCACTACC-CATGCATCGATACAC-AAAT-CACTTCGATGTTTCCATTTTTAAGG
20463 G
63 G
20464 GTGCATCGATGCACT
1 GTGCATCGATGCACT
20479 TCCTGTACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
63 2 0.03
64 57 0.83
65 8 0.12
66 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACTTCGATGTTTCCATTTTTAAGGG
Found at i:23415 original size:21 final size:21
Alignment explanation
Indices: 23390--23429 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
23380 AGTATGTTCA
* *
23390 GGGGGTATCAATTTCCCCTGG
1 GGGGGAATCAATTCCCCCTGG
*
23411 GGGGGAATCGATTCCCCCT
1 GGGGGAATCAATTCCCCCT
23430 AAAGGAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.28, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCAATTCCCCCTGG
Found at i:24055 original size:15 final size:15
Alignment explanation
Indices: 24037--24066 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24027 CGAGGGTATT
*
24037 GTAGTCCTTCGGGAC
1 GTAGTCCTTCAGGAC
24052 GTAGTCCTTCAGGAC
1 GTAGTCCTTCAGGAC
24067 ATATATAGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (15 bp):
GTAGTCCTTCAGGAC
Found at i:29059 original size:23 final size:23
Alignment explanation
Indices: 29029--29112 Score: 107
Period size: 23 Copynumber: 3.6 Consensus size: 23
29019 CGAACGGATG
*
29029 TAAACGAACATAAATGAACACAA
1 TAAACGAACTTAAATGAACACAA
29052 TAAACGAACGTTAAA-GAACACAA
1 TAAACGAAC-TTAAATGAACACAA
* *
29075 AAGAACGAACGTAAATGAACACAA
1 TA-AACGAACTTAAATGAACACAA
*
29099 TAAATGAACTTAAA
1 TAAACGAACTTAAA
29113 CAAACATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
23 32 0.62
24 20 0.38
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.14
Consensus pattern (23 bp):
TAAACGAACTTAAATGAACACAA
Found at i:30512 original size:10 final size:10
Alignment explanation
Indices: 30497--30571 Score: 69
Period size: 10 Copynumber: 6.9 Consensus size: 10
30487 TTTTTTGTGT
30497 TGTTCGTTTA
1 TGTTCGTTTA
30507 TGTTCGTTTA
1 TGTTCGTTTA
*
30517 TTGTGTTCATTTA
1 ---TGTTCGTTTA
*
30530 TATTCGTTTA
1 TGTTCGTTTA
*
30540 TGTTCATTTATTA
1 TGTTC--GT-TTA
30553 TGTTCGTTTA
1 TGTTCGTTTA
30563 TGTTCGTTT
1 TGTTCGTTT
30572 GCTTGTGTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 34 0.64
11 1 0.02
12 1 0.02
13 17 0.32
ACGTcount: A:0.13, C:0.09, G:0.16, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:30529 original size:23 final size:23
Alignment explanation
Indices: 30497--30540 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
30487 TTTTTTGTGT
* *
30497 TGTTCGTTTATGTTCGTTTATTG
1 TGTTCATTTATATTCGTTTATTG
30520 TGTTCATTTATATTCGTTTAT
1 TGTTCATTTATATTCGTTTAT
30541 GTTCATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.61
Consensus pattern (23 bp):
TGTTCATTTATATTCGTTTATTG
Found at i:30537 original size:33 final size:33
Alignment explanation
Indices: 30499--30571 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
30489 TTTTGTGTTG
* *
30499 TTCGTTTATGTTCGTTTATTGTGTTCATTTATA
1 TTCGTTTATGTTCATTTATTATGTTCATTTATA
* *
30532 TTCGTTTATGTTCATTTATTATGTTCGTTTATG
1 TTCGTTTATGTTCATTTATTATGTTCATTTATA
30565 TTCGTTT
1 TTCGTTT
30572 GCTTGTGTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.14, C:0.10, G:0.15, T:0.62
Consensus pattern (33 bp):
TTCGTTTATGTTCATTTATTATGTTCATTTATA
Found at i:30585 original size:24 final size:23
Alignment explanation
Indices: 30504--30597 Score: 93
Period size: 23 Copynumber: 4.0 Consensus size: 23
30494 TGTTGTTCGT
*
30504 TTATGTTCGTTTAT-TGT-GTTCA
1 TTATGTTCGTTTATGT-TCGTTTA
* *
30526 TTTATATTCGTTTATGTTCATTTA
1 -TTATGTTCGTTTATGTTCGTTTA
*
30550 TTATGTTCGTTTATGTTCGTTTGC
1 TTATGTTCGTTTATGTTCGTTT-A
* *
30574 TTGTGTTCGTTTACGTTCGTTTA
1 TTATGTTCGTTTATGTTCGTTTA
30597 T
1 T
30598 CATTTAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
23 35 0.59
24 24 0.41
ACGTcount: A:0.13, C:0.11, G:0.17, T:0.60
Consensus pattern (23 bp):
TTATGTTCGTTTATGTTCGTTTA
Found at i:31648 original size:2 final size:2
Alignment explanation
Indices: 31641--31665 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31631 AGAAAATTAA
31641 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 A
31666 CACACACGAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35107 original size:15 final size:15
Alignment explanation
Indices: 35084--35117 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35074 ATATTTAACT
* *
35084 GGGCGGGCGGATGTG
1 GGGCAGGCGGATGCG
35099 GGGCAGGCGGATGCG
1 GGGCAGGCGGATGCG
35114 GGGC
1 GGGC
35118 GGGTAAGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.18, G:0.65, T:0.09
Consensus pattern (15 bp):
GGGCAGGCGGATGCG
Found at i:37558 original size:28 final size:29
Alignment explanation
Indices: 37505--37564 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
37495 ATCTTATATC
*
37505 TGATTTACTGTACATTTTTATGTGATCTA
1 TGATTTACTGTACATTTTTATCTGATCTA
* *
37534 TGATTT-CTGTA-TTTTTGTATCTGATTTA
1 TGATTTACTGTACATTTT-TATCTGATCTA
37562 TGA
1 TGA
37565 GTATGAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 17 0.63
29 6 0.22
ACGTcount: A:0.22, C:0.08, G:0.15, T:0.55
Consensus pattern (29 bp):
TGATTTACTGTACATTTTTATCTGATCTA
Found at i:42476 original size:18 final size:19
Alignment explanation
Indices: 42437--42486 Score: 84
Period size: 18 Copynumber: 2.7 Consensus size: 19
42427 ATAGGATTTC
*
42437 TGCATCGATGCATGAGGAG
1 TGCATCGATGCATGAAGAG
42456 TGCATCGATGCAT-AAGAG
1 TGCATCGATGCATGAAGAG
42474 TGCATCGATGCAT
1 TGCATCGATGCAT
42487 CCCCATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCATGAAGAG
Found at i:42476 original size:82 final size:83
Alignment explanation
Indices: 42372--42552 Score: 244
Period size: 82 Copynumber: 2.2 Consensus size: 83
42362 ATTGTTTAAG
* *
42372 GTGCATCGATGCATATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTT
1 GTGCATCGATGCATAAGCAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTT
*
42436 CTGCATCGATGCATGAG-G-A
64 ATGCATCGATGCATG-GTGTA
* * *
42455 GTGCATCGATGCATAAG-AGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 GTGCATCGATGCATAAGCAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
42519 TGCATCGATGCATGGTGTA
65 TGCATCGATGCATGGTGTA
42538 GTGCATCGATGCATA
1 GTGCATCGATGCATA
42553 CCTCCATTAA
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
81 1 0.01
82 48 0.55
83 38 0.43
84 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (83 bp):
GTGCATCGATGCATAAGCAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTAT
GCATCGATGCATGGTGTA
Found at i:43175 original size:23 final size:23
Alignment explanation
Indices: 43142--43204 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
43132 ATTATTATAT
43142 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
43165 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
43188 GGCATTTA-GGTGCAATT
1 GGCA-CTACGGTGCAATT
43205 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:55066 original size:18 final size:18
Alignment explanation
Indices: 55043--55089 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
55033 AAATTGTCAT
*
55043 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
55061 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
55078 TATTTATATATT
1 TA-TTATATATT
55090 CTTTAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.42
18 12 0.50
19 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:64564 original size:16 final size:16
Alignment explanation
Indices: 64543--64573 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64533 GTTATGACCC
*
64543 AAGAGAATCGGAGAAG
1 AAGAGAATCGAAGAAG
64559 AAGAGAATCGAAGAA
1 AAGAGAATCGAAGAA
64574 ATAAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAGAATCGAAGAAG
Found at i:68298 original size:16 final size:16
Alignment explanation
Indices: 68277--68307 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
68267 GTTATGACCC
*
68277 AAGAGAATCGGAGAAG
1 AAGAGAATCGAAGAAG
68293 AAGAGAATCGAAGAA
1 AAGAGAATCGAAGAA
68308 ATAGAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAGAATCGAAGAAG
Found at i:70141 original size:20 final size:21
Alignment explanation
Indices: 70118--70158 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
70108 TTTAATTGAG
70118 TATATATAT-AT-T-TTAAAA
1 TATATATATAATCTCTTAAAA
70136 TATATATATAATCTCTTAAAA
1 TATATATATAATCTCTTAAAA
70157 TA
1 TA
70159 AACTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 1 0.05
21 8 0.40
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
TATATATATAATCTCTTAAAA
Found at i:77002 original size:14 final size:14
Alignment explanation
Indices: 76985--77012 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
76975 TGATCAACGA
76985 TCGGGTCGGGTCAG
1 TCGGGTCGGGTCAG
76999 TCGGGTCGGGTCAG
1 TCGGGTCGGGTCAG
77013 ACCGGTCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.50, T:0.21
Consensus pattern (14 bp):
TCGGGTCGGGTCAG
Found at i:77019 original size:9 final size:9
Alignment explanation
Indices: 77007--77069 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
76997 AGTCGGGTCG
77007 GGTCAGACC
1 GGTCAGACC
77016 GGTCAGACC
1 GGTCAGACC
* *
77025 GGTCAAATC
1 GGTCAGACC
77034 GGTTC-GAACC
1 GG-TCAG-ACC
*
77044 GGTCGAAACC
1 GGTC-AGACC
*
77054 GGTCAAACC
1 GGTCAGACC
77063 GGTCAGA
1 GGTCAGA
77070 ATCGGTTGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
9 31 0.70
10 13 0.30
ACGTcount: A:0.27, C:0.29, G:0.30, T:0.14
Consensus pattern (9 bp):
GGTCAGACC
Found at i:77046 original size:19 final size:19
Alignment explanation
Indices: 77022--77076 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
77012 GACCGGTCAG
*
77022 ACCGGTCAAATCGGTTCGA
1 ACCGGTCAAATCGGTTCAA
*
77041 ACCGGTCGAAACCGG-TCAA
1 ACCGGTC-AAATCGGTTCAA
77060 ACCGGTCAGAATCGGTT
1 ACCGGTCA-AATCGGTT
77077 GAAAGTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.03
19 22 0.73
20 7 0.23
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (19 bp):
ACCGGTCAAATCGGTTCAA
Found at i:77075 original size:29 final size:28
Alignment explanation
Indices: 77013--77091 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 28
77003 GTCGGGTCAG
* *
77013 ACCGGTC-AGACCGGTCAAATCGGTTCGA
1 ACCGGTCGAAACCGGTCAAACCGG-TCGA
77041 ACCGGTCGAAACCGGTCAAACCGGTCAGA
1 ACCGGTCGAAACCGGTCAAACCGGTC-GA
* *
77070 ATCGGTTGAAA---GTCAAACCGGT
1 ACCGGTCGAAACCGGTCAAACCGGT
77092 TTCCAGCCCT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 11 0.24
28 9 0.20
29 25 0.56
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.16
Consensus pattern (28 bp):
ACCGGTCGAAACCGGTCAAACCGGTCGA
Found at i:94711 original size:2 final size:2
Alignment explanation
Indices: 94706--94737 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
94696 TTTTTTTAGG
94706 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
94738 CCGTAAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98829 original size:18 final size:18
Alignment explanation
Indices: 98739--98823 Score: 143
Period size: 18 Copynumber: 4.7 Consensus size: 18
98729 AGACAAGCGA
98739 AGCCAAGTGATGTTTGTC
1 AGCCAAGTGATGTTTGTC
98757 AGCCAAGTGATGTTTGTC
1 AGCCAAGTGATGTTTGTC
98775 AGCCAAGTGATGTTTGTC
1 AGCCAAGTGATGTTTGTC
* *
98793 AGCCAAGTGATGTATCTC
1 AGCCAAGTGATGTTTGTC
*
98811 AGCCGAGTGATGT
1 AGCCAAGTGATGT
98824 ATCTCATCCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (18 bp):
AGCCAAGTGATGTTTGTC
Found at i:98989 original size:42 final size:42
Alignment explanation
Indices: 98943--99156 Score: 196
Period size: 42 Copynumber: 4.9 Consensus size: 42
98933 TCATCCTCAC
* * *
98943 CCTCACCCTCACCGCCACCTCCTCCTCCACCTTCACTATCAT
1 CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACCATCAT
* * **
98985 CCTCACCCTCGCCGCCACCTCCTCATTCACCTCCGTCATCAT
1 CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACCATCAT
* * *
99027 CCTCACACTCGCCACCACTTCCTACTCCACCTCCACCTCCACCATCAT
1 CCTCACCCTCGCCGCCA----C--CTCCTCCTCCACCTCCACCATCAT
* * *
99075 CCTCACCCTCACC-CTCACCTCCACCTTCTCCACCTCCACCACCAT
1 CCTCACCCTCGCCGC-CACCT---CCTCCTCCACCTCCACCATCAT
**
99120 CCTCACCCTCGCCGCCACCTCCTCCTCTGCCTCCACC
1 CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACC
99157 TCGACCTCCA
Statistics
Matches: 138, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
42 66 0.48
44 1 0.01
45 36 0.26
46 2 0.01
47 1 0.01
48 32 0.23
ACGTcount: A:0.16, C:0.59, G:0.04, T:0.21
Consensus pattern (42 bp):
CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACCATCAT
Found at i:99154 original size:48 final size:46
Alignment explanation
Indices: 98923--99158 Score: 207
Period size: 48 Copynumber: 5.1 Consensus size: 46
98913 CAAGCACACT
* * * *
98923 ACCTTCACCATCATCCTCACCCTCACCCTCACCGCCACCTCCTCCTCC
1 ACCTCCACCATCATCCTCACCCTCGCCC-CACCTCCTCCT-CTCCTCC
* * *
98971 ACCTTCACTATCATCCTCACCCTCGCCGCCACCTCCT-C-AT--T-C
1 ACCTCCACCATCATCCTCACCCTCGCC-CCACCTCCTCCTCTCCTCC
** * * * *
99013 ACCTCCGTCATCATCCTCACACTCGCCACCACTTCCTACTCCACCTCC
1 ACCTCCACCATCATCCTCACCCTCGCC-CCACCTCCTCCT-CTCCTCC
* *
99061 ACCTCCACCATCATCCTCACCCTCACCCTCACCTCCACCT-T-CTCC
1 ACCTCCACCATCATCCTCACCCTCGCCC-CACCTCCTCCTCTCCTCC
*
99106 ACCTCCACCACCATCCTCACCCTCGCCGCCACCTCCTCCTCTGCCTCC
1 ACCTCCACCATCATCCTCACCCTCGCC-CCACCTCCTCCTCT-CCTCC
99154 ACCTC
1 ACCTC
99159 GACCTCCACT
Statistics
Matches: 151, Mismatches: 25, Indels: 24
0.75 0.12 0.12
Matches are distributed among these distances:
42 31 0.21
43 2 0.01
45 40 0.26
46 2 0.01
47 3 0.02
48 72 0.48
49 1 0.01
ACGTcount: A:0.17, C:0.58, G:0.03, T:0.22
Consensus pattern (46 bp):
ACCTCCACCATCATCCTCACCCTCGCCCCACCTCCTCCTCTCCTCC
Found at i:99591 original size:39 final size:39
Alignment explanation
Indices: 99545--99630 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
99535 TTTTCCACGT
*
99545 TCCCCATCAACACCTTGCAATTTTAGTCATCCTCTTCCC
1 TCCCCATCAAAACCTTGCAATTTTAGTCATCCTCTTCCC
* * *
99584 TCTCCATCAAAACCTTGTAATTTTAGTCATCCTTTTCCC
1 TCCCCATCAAAACCTTGCAATTTTAGTCATCCTCTTCCC
99623 TCCCCATC
1 TCCCCATC
99631 GAAAGAACGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.21, C:0.38, G:0.05, T:0.36
Consensus pattern (39 bp):
TCCCCATCAAAACCTTGCAATTTTAGTCATCCTCTTCCC
Found at i:100065 original size:36 final size:36
Alignment explanation
Indices: 100022--100155 Score: 169
Period size: 36 Copynumber: 3.7 Consensus size: 36
100012 TCCGATGCTG
** * *
100022 CTCCACCTCCAACGTGTAATGCTCCCCCACCCGCTC
1 CTCCACCTCCAACGTCCAATGCTCCTCCACCCCCTC
* * *
100058 CTCCACCTCCAACGTCCGATGCTGCTTCACCCCCTC
1 CTCCACCTCCAACGTCCAATGCTCCTCCACCCCCTC
* *
100094 CTCCACCTCCAACTTCCAATGCTGCTCCACCCCCTC
1 CTCCACCTCCAACGTCCAATGCTCCTCCACCCCCTC
* *
100130 CTCCACGTCCAACGTCAAATGCTCCT
1 CTCCACCTCCAACGTCCAATGCTCCT
100156 TCTCCACTGC
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 84 1.00
ACGTcount: A:0.17, C:0.51, G:0.10, T:0.22
Consensus pattern (36 bp):
CTCCACCTCCAACGTCCAATGCTCCTCCACCCCCTC
Found at i:100327 original size:27 final size:28
Alignment explanation
Indices: 100283--100360 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 28
100273 CCTGGAGGTC
*
100283 GAGCTCTTGGTCCCCCACCTCCA-C-CTG
1 GAGCTCCTGG-CCCCCACCTCCACCACTG
100310 GAGCTCCTGGCCCTCCACCTCCACCAGCTG
1 GAGCTCCTGGCCC-CCACCTCCACCA-CTG
*
100340 GAGCTCGTGG--CCCACCTCCAC
1 GAGCTCCTGGCCCCCACCTCCAC
100361 TAGGTGCCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
26 3 0.07
27 28 0.62
28 2 0.04
30 12 0.27
ACGTcount: A:0.13, C:0.49, G:0.21, T:0.18
Consensus pattern (28 bp):
GAGCTCCTGGCCCCCACCTCCACCACTG
Found at i:102181 original size:31 final size:31
Alignment explanation
Indices: 102118--102186 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
102108 TCTTAGGGGC
* * *
102118 CAATTTGATCAAACTTGTCAAGTTTAGGGGT
1 CAATTTGATCAAACTTATCAAGTTCAGAGGT
102149 CAATTTGATCAAACTTATCATA-TTCAGAGGT
1 CAATTTGATCAAACTTATCA-AGTTCAGAGGT
*
102180 CATTTTG
1 CAATTTG
102187 TGTTTGAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (31 bp):
CAATTTGATCAAACTTATCAAGTTCAGAGGT
Found at i:108120 original size:30 final size:30
Alignment explanation
Indices: 108080--108149 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
108070 TTTAATTGTT
* *
108080 TTCCAATTTGGTGCCCAACCTTTGTCTCGG
1 TTCCAGTTTGGTGCCCAACATTTGTCTCGG
* *
108110 TTCCAGTTTGGTGCCTAACATTTGTCTTGG
1 TTCCAGTTTGGTGCCCAACATTTGTCTCGG
*
108140 GTCCAGTTTG
1 TTCCAGTTTG
108150 ATGTCCAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.13, C:0.24, G:0.23, T:0.40
Consensus pattern (30 bp):
TTCCAGTTTGGTGCCCAACATTTGTCTCGG
Found at i:110643 original size:40 final size:40
Alignment explanation
Indices: 110599--110678 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
110589 ATGGTGTACA
* *
110599 AGGTGAGTAAAACAT-GACCTCAGCACTACGGTGCATTATT
1 AGGTGAGCAAAAC-TCGACCTCAGCACTACGGTGCAATATT
** *
110639 AGGTGAGCAATGCTCGACCTCAGCACTTCGGTGCAATATT
1 AGGTGAGCAAAACTCGACCTCAGCACTACGGTGCAATATT
110679 TGACTCCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (40 bp):
AGGTGAGCAAAACTCGACCTCAGCACTACGGTGCAATATT
Found at i:110817 original size:45 final size:45
Alignment explanation
Indices: 110753--110876 Score: 194
Period size: 45 Copynumber: 2.8 Consensus size: 45
110743 GTAACCATGC
*
110753 AAATAAGCTTACGAGCTTATGGAATCAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
110798 AAATAAGCTTATGAGCTTATGAAATAAATGGTAAGTATGTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
110843 AAATAAGCTTACAAGCTTATGGGATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA
110877 ATATTTTGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:111245 original size:2 final size:2
Alignment explanation
Indices: 111238--111291 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
111228 TATTGAAGAA
111238 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
111280 AT AT AT AT AT AT
1 AT AT AT AT AT AT
111292 TTTGAAGTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112549 original size:23 final size:23
Alignment explanation
Indices: 112513--112581 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
112503 CACCATAGCT
* * *
112513 CGTATAAATACACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
112536 CGTAGAATTGCACCGAAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
*
112559 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
112582 TATAAAATTT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:113003 original size:14 final size:14
Alignment explanation
Indices: 112984--113016 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
112974 TGTGTATGTA
*
112984 ATCATATAATTTGT
1 ATCATATAATTTAT
112998 ATCATATAATTTAT
1 ATCATATAATTTAT
113012 ATCAT
1 ATCAT
113017 TTCTCATGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.48
Consensus pattern (14 bp):
ATCATATAATTTAT
Found at i:115753 original size:21 final size:21
Alignment explanation
Indices: 115727--115771 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
115717 AAGCAAGATT
* * *
115727 GCCAAATCTTCTCATCAACAG
1 GCCAAAACTTCCCATCAAAAG
115748 GCCAAAACTTCCCATCAAAAG
1 GCCAAAACTTCCCATCAAAAG
115769 GCC
1 GCC
115772 TTTCCCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.36, G:0.11, T:0.18
Consensus pattern (21 bp):
GCCAAAACTTCCCATCAAAAG
Found at i:118252 original size:17 final size:15
Alignment explanation
Indices: 118216--118254 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
118206 TTTATATACG
118216 TTATTATATATAATA
1 TTATTATATATAATA
*
118231 ATATTATAGTAGTAATA
1 TTATTATA-TA-TAATA
118248 TTATTAT
1 TTATTAT
118255 TTACAAGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 7 0.35
16 2 0.10
17 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
TTATTATATATAATA
Found at i:119554 original size:18 final size:17
Alignment explanation
Indices: 119522--119564 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
119512 ATTTCATCAT
* *
119522 TAATTATTATTTTAAGA
1 TAATTATAATATTAAGA
*
119539 CTAATTATAATATTAATA
1 -TAATTATAATATTAAGA
119557 TAATTATA
1 TAATTATA
119565 TATGTTATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TAATTATAATATTAAGA
Found at i:121152 original size:2 final size:2
Alignment explanation
Indices: 121145--121179 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
121135 GTTTTTATCA
121145 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
121180 AGTGCATGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:128491 original size:129 final size:130
Alignment explanation
Indices: 128268--128514 Score: 415
Period size: 129 Copynumber: 1.9 Consensus size: 130
128258 TATTTATATA
*
128268 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
128333 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
128398 ATCAATTTGGTCCTAAATTAAATAAAATTTAAT-AATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
128462 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
128515 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
129 76 0.70
130 33 0.30
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:128545 original size:129 final size:129
Alignment explanation
Indices: 128282--128545 Score: 300
Period size: 129 Copynumber: 2.0 Consensus size: 129
128272 ATTTGGTCCT
* *
128282 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
128347 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
128412 AAATTAAATAAAATTTAAT-AATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
128476 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
128540 -A
128 CA
128541 AAATT
1 AAATT
128546 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
129 80 0.71
130 19 0.17
131 8 0.07
132 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:128991 original size:16 final size:18
Alignment explanation
Indices: 128970--129003 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
128960 ATTTCTTATT
128970 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
128986 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
129004 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:129150 original size:21 final size:21
Alignment explanation
Indices: 129126--129168 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
129116 TATTACCTTA
129126 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
129147 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
129168 A
1 A
129169 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:129186 original size:35 final size:35
Alignment explanation
Indices: 129137--129222 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
129127 ATTGAAGTAT
** * * *
129137 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAATACTTTAGAAATTAGGG
* *
129172 TTTAGAATAAAATTGAAATACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAATACTTTAGAAATTAGGG
*
129207 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
129223 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.40
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAATACTTTAGAAATTAGGG
Found at i:129923 original size:22 final size:22
Alignment explanation
Indices: 129898--129951 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
129888 ACATGCTCCT
*
129898 CCATGGCCAAACTCAAGCAACA
1 CCATGCCCAAACTCAAGCAACA
129920 CCATGCCCAAACTCAAGCAACA
1 CCATGCCCAAACTCAAGCAACA
129942 CCATGCCCAA
1 CCATGCCCAA
129952 CTCTTCAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.39, C:0.41, G:0.11, T:0.09
Consensus pattern (22 bp):
CCATGCCCAAACTCAAGCAACA
Found at i:137481 original size:32 final size:32
Alignment explanation
Indices: 137445--137514 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
137435 TAAGGATCAC
* *
137445 TTTGTAGCAGTTTGATACGTTTTAACAACCAT
1 TTTGTAGCAGTTAGATAAGTTTTAACAACCAT
*
137477 TTTGTAGCAGTTAGATAAGTTTTAACGACCAT
1 TTTGTAGCAGTTAGATAAGTTTTAACAACCAT
137509 TTTGTA
1 TTTGTA
137515 ATAGCTTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (32 bp):
TTTGTAGCAGTTAGATAAGTTTTAACAACCAT
Found at i:137526 original size:32 final size:31
Alignment explanation
Indices: 137456--137547 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 31
137446 TTGTAGCAGT
* * **
137456 TTGATACGTTTTAACAACCATTTTGTAGCAG
1 TTGATAAGTTTTAACGACCATTTTGTAATAG
137487 TTAGATAAGTTTTAACGACCATTTTGTAATAG
1 TT-GATAAGTTTTAACGACCATTTTGTAATAG
* *
137519 CTTGATAAG-TTTAATGACTATTTTGTAAT
1 -TTGATAAGTTTTAACGACCATTTTGTAAT
137548 TTGTGAAACT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
31 20 0.38
32 31 0.58
33 2 0.04
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (31 bp):
TTGATAAGTTTTAACGACCATTTTGTAATAG
Found at i:139205 original size:2 final size:2
Alignment explanation
Indices: 139198--139222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
139188 AATTAAATTT
139198 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
139223 TTATTTTTAT
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:142865 original size:72 final size:72
Alignment explanation
Indices: 142748--142899 Score: 205
Period size: 72 Copynumber: 2.1 Consensus size: 72
142738 GATGAGCATT
* * * * *
142748 TGCAGCCTGAAGGTATCAAGCTCCACCACAATTCCATCCAAAGAATTTAGGAGAACCATCTCAGA
1 TGCAGCCCGAAGGTAACAACCTCCACCACAACTCCATCCAAAGAATTTACGAGAACCATCTCAGA
142813 AAAAGTG
66 AAAAGTG
* * * *
142820 TGCAGCCCGAAGTTAACAACCTCCACCACTACTCCATCCAAAGAATTTACGAGAACCATGTCGGA
1 TGCAGCCCGAAGGTAACAACCTCCACCACAACTCCATCCAAAGAATTTACGAGAACCATCTCAGA
*
142885 AAAGGTG
66 AAAAGTG
*
142892 TACAGCCC
1 TGCAGCCC
142900 CAGAGTATGC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (72 bp):
TGCAGCCCGAAGGTAACAACCTCCACCACAACTCCATCCAAAGAATTTACGAGAACCATCTCAGA
AAAAGTG
Found at i:148955 original size:9 final size:9
Alignment explanation
Indices: 148933--148966 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
148923 AAAGAGAGAA
148933 AAAT-AAAT
1 AAATAAAAT
148941 AAATAAAAT
1 AAATAAAAT
*
148950 AGATAAAAT
1 AAATAAAAT
148959 AAATAAAA
1 AAATAAAA
148967 CAAAGGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:148981 original size:22 final size:20
Alignment explanation
Indices: 148894--148982 Score: 52
Period size: 22 Copynumber: 3.9 Consensus size: 20
148884 CGTATTAACA
*
148894 AAAAAAATGTAAAAAATAAAAAT
1 AAAAAAA-GGAAAAAAT--AAAT
148917 AAAAATAAAGAGAGAAAAATAAAT
1 -AAAA-AAAG-GA-AAAAATAAAT
* *
148941 AAATAAAATAGATAAAATAAAT
1 AAA-AAAA-GGAAAAAATAAAT
148963 AAAACAAAGGAAAATAATAA
1 AAAA-AAAGGAAAA-AATAA
148983 TAATGATAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
21 5 0.09
22 20 0.38
23 8 0.15
24 10 0.19
25 4 0.08
26 6 0.11
ACGTcount: A:0.75, C:0.01, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAAAAAGGAAAAAATAAAT
Found at i:149424 original size:2 final size:2
Alignment explanation
Indices: 149417--149447 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
149407 AATAGAAATA
149417 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
149448 ACGTAAAAAT
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:151238 original size:37 final size:36
Alignment explanation
Indices: 151188--151635 Score: 257
Period size: 36 Copynumber: 12.9 Consensus size: 36
151178 TGTTTCAAGG
**
151188 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTT-GTTTTAAAA
* * * *
151225 GAAACTGTCTCAAGGGAGACGAAATTTG-TTTCAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
* * * *
151260 GAAAACATAT-TC-----AG--AAATTTTGTTTCAAGA
1 G-AAAC-TGTCTCAAGAGAGACAAAATTTGTTTTAAAA
**
151290 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
* *
151326 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTT-GTTTTAAAA
* * *
151363 GAAATTGTCTCAAGAGAGACGAAATTTG-TTTAAAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
* * * **
151398 GAAAACAGAT-TC-A-A-AG----ATTTTGTTTCAAGG
1 G-AAACTG-TCTCAAGAGAGACAAAATTTGTTTTAAAA
**
151428 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTACGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
* *
151464 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTT-GTTTTAAAA
* * *
151501 GAAACTGTCTCAAGAGATACAAAACTTTG-TTTCAAG
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTTAAAA
* ** ** * **
151537 GAAA-----AC-A-A-ATTCAATGTTTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAA--AATTTGTTTTAAAA
* *
151567 GAAACCGTCTCAAGAGAGACAAAATTTGCTTTAAAA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
151603 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTT
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTT
151636 GAGTAAATTA
Statistics
Matches: 312, Mismatches: 62, Indels: 74
0.70 0.14 0.17
Matches are distributed among these distances:
28 8 0.03
29 29 0.09
30 20 0.06
31 4 0.01
32 2 0.01
33 2 0.01
34 3 0.01
35 12 0.04
36 129 0.41
37 96 0.31
38 7 0.02
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.27
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAAA
Found at i:151248 original size:102 final size:101
Alignment explanation
Indices: 151118--151352 Score: 330
Period size: 102 Copynumber: 2.3 Consensus size: 101
151108 GAAACTGTCT
* * *
151118 CAAAAGAAATTGTCTCGAGTGAGACGAAATTTGTTT-AATGGAAAACATATTCA-AAGATTTTGT
1 CAAAAGAAAATGTCTCAAGAGAGACGAAATTTGTTTCAA-GGAAAACATATTCAGAA-ATTTTGT
*
151181 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAGTTC
64 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT-GTTC
* *
151220 CAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAACATATTCAGAAATTTTGTTT
1 CAAAAGAAAATGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACATATTCAGAAATTTTGTTT
*
151285 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
66 CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTC
* ** *
151321 TACGAGAAAATGTCTCAAGAGAGACAAAATTT
1 CAAAAGAAAATGTCTCAAGAGAGACGAAATTT
151353 AGTTCTAAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
101 29 0.24
102 87 0.73
103 4 0.03
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (101 bp):
CAAAAGAAAATGTCTCAAGAGAGACGAAATTTGTTTCAAGGAAAACATATTCAGAAATTTTGTTT
CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTC
Found at i:151328 original size:36 final size:36
Alignment explanation
Indices: 151278--151635 Score: 266
Period size: 36 Copynumber: 10.2 Consensus size: 36
151268 ATTCAGAAAT
*
151278 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
151314 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
151350 TTTAGTTCTAAAAGAAATTGTCTCAAGAGAGACGAAA
1 TTT-GTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
151387 TTTGTTTAAAG-GAAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTTAAGAG-AAACTG-TCTCAAGAGAGACAAAA
* *
151416 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
151452 TTTGTTTTACGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
151488 TTTAGTTCTAAAAGAAACTGTCTCAAGAGATACAAAA
1 TTT-GTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * ** **
151525 CTTTGTTTCAAG-GAAA-----AC-A-A-ATTCAATGTT
1 -TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAA--AA
* * *
151555 TTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
151591 TTTGCTTTAAAAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
151627 CTTTGTTTT
1 -TTTGTTTT
151636 GAGTAAATTA
Statistics
Matches: 252, Mismatches: 44, Indels: 51
0.73 0.13 0.15
Matches are distributed among these distances:
28 6 0.02
29 30 0.12
30 7 0.03
31 2 0.01
32 2 0.01
33 2 0.01
34 1 0.00
35 3 0.01
36 119 0.47
37 73 0.29
38 7 0.03
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (36 bp):
TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:151424 original size:138 final size:138
Alignment explanation
Indices: 151188--151626 Score: 700
Period size: 138 Copynumber: 3.2 Consensus size: 138
151178 TGTTTCAAGG
* * *
151188 GAAACTGTCTCAAGAGAGACAAAATTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTG
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACGAAATTTG
* *
151253 TTTCAAGGAAAACATATTCAGAA-ATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
66 TTTCAAGGAAAACAAATTCA-AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
151317 GTTTTACGA
130 GTTTTACGA
*
151326 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAATTGTCTCAAGAGAGACGAAATTTG
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACGAAATTTG
* *
151391 TTTAAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
66 TTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
151456 TTTTACGA
131 TTTTACGA
* *
151464 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGATACAAAACTTT
1 GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACGAAA-TTT
* * *
151529 GTTTCAAGGAAAACAAATTCAATGTTTTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTT
65 GTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* **
151594 GCTTTAAAA
130 GTTTTACGA
*
151603 GAAACTGTCTCAAGAGAGACAAAA
1 GAAAATGTCTCAAGAGAGACAAAA
151627 CTTTGTTTTG
Statistics
Matches: 280, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
137 2 0.01
138 186 0.66
139 92 0.33
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (138 bp):
GAAAATGTCTCAAGAGAGACAAAATTTAGTTCTAAAAGAAACTGTCTCAAGAGAGACGAAATTTG
TTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
TTTTACGA
Found at i:153142 original size:95 final size:94
Alignment explanation
Indices: 152966--153161 Score: 277
Period size: 95 Copynumber: 2.1 Consensus size: 94
152956 GGATAACTCA
* * * * * * *
152966 ATATGTAAATACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCTGGGGTGTTTAACCAATTG
1 ATATATAATTACCTGTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG
* *
153031 CCTTATACGGATAACTCAAGCTTTATTGT
66 CCTTAGACGGACAACTCAAGCTTTATTGT
153060 ATAGTATAATTACCTGTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATT
1 ATA-TATAATTACCTGTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATT
*
153125 G-CTCTAGAGGGACAACTCAAGCTTTATTGT
65 GCCT-TAGACGGACAACTCAAGCTTTATTGT
153155 ATATATA
1 ATATATA
153162 TAATATTATA
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
94 9 0.10
95 81 0.90
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (94 bp):
ATATATAATTACCTGTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG
CCTTAGACGGACAACTCAAGCTTTATTGT
Found at i:159764 original size:216 final size:217
Alignment explanation
Indices: 159382--159897 Score: 710
Period size: 216 Copynumber: 2.4 Consensus size: 217
159372 TGACGAGTCT
* * * *
159382 GCTCCCTATTCCTTCAGA-AGTATA-AGGCTCGAACAATATTCATAAAATGTGTATGCTCTCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAGCAATCTTCATAAAATGTGTCTGCTCTCTAT
** *
159445 TTATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGGGTCCGCTCTCTATTCCTTCAG
65 TCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAATAAAACGGGTCCGCTCTCTATTCCTTCAG
* *
159509 AGAGTATAGAACTTGGAAAATCTTTAATAAACAGGTCCGCTCCCTATTCTTTCAGAGAGTATAGG
129 AGAGTATAGAACTTCGAAAATCTTTAATAAACAGGTCCGCTCCCTATTCATTCAGAGAGTATAGG
* * *
159574 ACTTAATCTTTAACAAACGTGTTC
194 ACTCAATCTTTAACAAACATGTCC
* *
159598 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCTGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAATGTGTCTGCTCTCTATT
* *
159663 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-CAAACGTGTCCGCTCTCTATTCCTTCAGAG
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAACGGGTCCGCTCTCTATTCCTTCAGAG
* * *
159727 AGTATAGAAC-TCGAACAATC-TTCATACAACGGGTCCGCTCTCTATTCATTCAGAGAGTATAGG
131 AGTATAGAACTTCGAA-AATCTTTAATA-AACAGGTCCGCTCCCTATTCATTCAGAGAGTATAGG
159790 ACTCAATCTTTAACAAACATGTCC
194 ACTCAATCTTTAACAAACATGTCC
* * * *
159814 GCTCCCTATTCTTTCAGAGAGTATAGGACTC--G--ATCTTTATAAAATGTGTCTGCTCCCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAATGTGTCTGCTCTCTATT
*
159875 CCTTCAGAGAGTATAGTACTCGA
66 CCTTCAGAGAGTATAGAACTCGA
159898 TCTTCATAAA
Statistics
Matches: 269, Mismatches: 26, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
212 47 0.17
214 1 0.00
215 9 0.03
216 143 0.53
217 67 0.25
218 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (217 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAATGTGTCTGCTCTCTATT
CCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAACGGGTCCGCTCTCTATTCCTTCAGAG
AGTATAGAACTTCGAAAATCTTTAATAAACAGGTCCGCTCCCTATTCATTCAGAGAGTATAGGAC
TCAATCTTTAACAAACATGTCC
Found at i:159909 original size:51 final size:52
Alignment explanation
Indices: 159382--159908 Score: 421
Period size: 55 Copynumber: 9.9 Consensus size: 52
159372 TGACGAGTCT
* * * **
159382 GCTCCCTATTCCTTCAGA-AGTATA-AGGCTCGAACAATATTCATAAAATGTGTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCG---AATCTTCATAAAACGTGTCC
* ** * *
159436 GCTCTCTATTTATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCG---AATCTTC-ATAAAACGTGTCC
* * *
159492 GCTCTCTATTCCTTCAGAGAGTATAGAACTTGGAAAATCTTTA-ATAAACAG-GTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAAC-TCG--AATCTTCATA-AAAC-GTGTCC
* * * * *
159547 GCTCCCTATTCTTTCAGAGAGTATAGGACT-TAATCTTTA-ACAAACGTGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAATCTTCATA-AAACGTGTCC
* *
159598 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC--G-AATCTTCATAAAACGTGTCC
*
159653 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCG---AATCTTCATA-AAACGTGTCC
* * *
159708 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATACAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCG---AATCTTCATAAAACGTGTCC
* * * * *
159763 GCTCTCTATTCATTCAGAGAGTATAGGACTC-AATCTTTA-ACAAACATGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAATCTTCATA-AAACGTGTCC
* * * * *
159814 GCTCCCTATTCTTTCAGAGAGTATAGGACTCG-ATCTTTATAAAATGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAATCTTCATAAAACGTGTCC
*
159865 GCTCCCTATTCCTTCAGAGAGTATAGTACTCG-ATCTTCATAAAA
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAATCTTCATAAAA
159909 TAAGTTTGCT
Statistics
Matches: 407, Mismatches: 47, Indels: 41
0.82 0.09 0.08
Matches are distributed among these distances:
50 2 0.00
51 142 0.35
52 1 0.00
53 1 0.00
54 18 0.04
55 196 0.48
56 44 0.11
57 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (52 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAATCTTCATAAAACGTGTCC
Found at i:161292 original size:16 final size:15
Alignment explanation
Indices: 161272--161442 Score: 102
Period size: 16 Copynumber: 10.9 Consensus size: 15
161262 TTATTTCTCT
161272 TTTTTTTCATTTTTC
1 TTTTTTTCATTTTTC
161287 TCTTTTTTCATTTTTC
1 T-TTTTTTCATTTTTC
161303 ATTTTTTCTTC-TATTTTC
1 --TTTTT-TTCAT-TTTTC
** *
161321 CATTTTTC--TCTTC
1 TTTTTTTCATTTTTC
161334 TTTTTTT--TCTTTTC
1 TTTTTTTCAT-TTTTC
*
161348 GTTTTTCCATCATTTTTC
1 -TTTTT--TTCATTTTTC
161366 TTTTTTCTCATTTTTC
1 TTTTTT-TCATTTTTC
* *
161382 TTTTCTTC-TTTTAC
1 TTTTTTTCATTTTTC
* *
161396 TTTTTCTCATTTTTA
1 TTTTTTTCATTTTTC
161411 TTATTTTTCATTTTTTTC
1 TT-TTTTTCA--TTTTTC
*
161429 ATTTTTTCATTTTT
1 TTTTTTTCATTTTT
161443 TCTATTTTAT
Statistics
Matches: 122, Mismatches: 17, Indels: 34
0.71 0.10 0.20
Matches are distributed among these distances:
13 9 0.07
14 15 0.12
15 22 0.18
16 37 0.30
17 18 0.15
18 20 0.16
19 1 0.01
ACGTcount: A:0.09, C:0.17, G:0.01, T:0.74
Consensus pattern (15 bp):
TTTTTTTCATTTTTC
Found at i:161324 original size:19 final size:20
Alignment explanation
Indices: 161265--161338 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 20
161255 CCTCCTTTTA
*
161265 TTTCTCTT-T-TTTTTCATT
1 TTTCTCTTCTATTTTCCATT
* *
161283 TTTCTCTTTTTTCATTTTTCATT
1 TTTCTC--TTCT-ATTTTCCATT
161306 TTT-TCTTCTATTTTCCATT
1 TTTCTCTTCTATTTTCCATT
161325 TTTCTCTTCT-TTTT
1 TTTCTCTTCTATTTT
161339 TTTCTTTTCG
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
18 6 0.12
19 16 0.33
20 11 0.23
21 1 0.02
22 2 0.04
23 12 0.25
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTCTCTTCTATTTTCCATT
Found at i:161353 original size:45 final size:45
Alignment explanation
Indices: 161284--161442 Score: 107
Period size: 45 Copynumber: 3.5 Consensus size: 45
161274 TTTTTCATTT
* * *
161284 TTCTCTTTTTTCATTTTTCATTTTTTCTTCTATTTTCCATTTTTCTC-
1 TTCTTTTTTTTC--TTTTCATTTTTCCATC-ATTTTCCATTTTTCTCA
* * *
161331 TTCTTTTTTTTCTTTTCGTTTTTCCATCATTTTTCTTTTTTCTCA
1 TTCTTTTTTTTCTTTTCATTTTTCCATCATTTTCCATTTTTCTCA
* * *
161376 TTTTTCTTTTCTTCTTTT-ACTTTTT-C-TCATTTT-TATTATTTTTCA
1 TTCTT-TTTT-TTCTTTTCA-TTTTTCCATCATTTTCCATT-TTTCTCA
*
161421 TT-TTTTTCATT-TTTTCATTTTT
1 TTCTTTTT-TTTCTTTTCATTTTT
161443 TCTATTTTAT
Statistics
Matches: 93, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
42 9 0.10
43 6 0.06
44 18 0.19
45 32 0.34
46 5 0.05
47 23 0.25
ACGTcount: A:0.09, C:0.18, G:0.01, T:0.73
Consensus pattern (45 bp):
TTCTTTTTTTTCTTTTCATTTTTCCATCATTTTCCATTTTTCTCA
Found at i:161418 original size:10 final size:9
Alignment explanation
Indices: 161405--161443 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
161395 CTTTTTCTCA
161405 TTTTT-ATT
1 TTTTTCATT
161413 ATTTTTCATT
1 -TTTTTCATT
161423 TTTTTCA-T
1 TTTTTCATT
161431 TTTTTCATT
1 TTTTTCATT
161440 TTTT
1 TTTT
161444 CTATTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.29
9 17 0.61
10 3 0.11
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTCATT
Found at i:161427 original size:47 final size:47
Alignment explanation
Indices: 161336--161441 Score: 114
Period size: 47 Copynumber: 2.2 Consensus size: 47
161326 TTCTCTTCTT
*
161336 TTTTTTCTTTTCGTTTTTCCATCATTTTTCTTTTTTCTCATTTTTC-
1 TTTTTTCTTTTCGTTTTTCCATCATTTTTATTTTTTCTCATTTTTCA
161382 TTTTCTTCTTTTAC-TTTTT-C-TCATTTTTATTATTTT-TCATTTTTTTCA
1 TTTT-TTCTTTT-CGTTTTTCCATCATTTTTATT-TTTTCTCA--TTTTTCA
161430 TTTTTTCATTTT
1 TTTTTTC-TTTT
161442 TTCTATTTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
45 13 0.25
46 9 0.17
47 21 0.40
48 9 0.17
ACGTcount: A:0.09, C:0.16, G:0.01, T:0.74
Consensus pattern (47 bp):
TTTTTTCTTTTCGTTTTTCCATCATTTTTATTTTTTCTCATTTTTCA
Found at i:161442 original size:8 final size:8
Alignment explanation
Indices: 161273--161450 Score: 86
Period size: 8 Copynumber: 21.5 Consensus size: 8
161263 TATTTCTCTT
161273 TTTTTTCA
1 TTTTTTCA
161281 TTTTTCTC-
1 TTTTT-TCA
161289 TTTTTTCA
1 TTTTTTCA
161297 -TTTTTCA
1 TTTTTTCA
*
161304 TTTTTTCT
1 TTTTTTCA
161312 TCTATTTTCCA
1 T-T-TTTT-CA
161323 TTTTTCTC-
1 TTTTT-TCA
**
161331 TTCTTTTTT
1 TT-TTTTCA
*
161340 TTCTTTTCG
1 TT-TTTTCA
*
161349 TTTTTCCA
1 TTTTTTCA
*
161357 TCATTTTTCT
1 T--TTTTTCA
161367 TTTTTCTCA
1 TTTTT-TCA
161376 -TTTTTC-
1 TTTTTTCA
161382 TTTTCTTC-
1 TTTT-TTCA
*
161390 -TTTTAC-
1 TTTTTTCA
161396 TTTTTCTCA
1 TTTTT-TCA
*
161405 TTTTTATTA
1 TTTTT-TCA
161414 -TTTTTCA
1 TTTTTTCA
161421 TTTTTTTCA
1 -TTTTTTCA
161430 TTTTTTCA
1 TTTTTTCA
161438 TTTTTTCTA
1 TTTTTTC-A
161447 TTTT
1 TTTT
161451 ATTTCTTGTT
Statistics
Matches: 135, Mismatches: 15, Indels: 39
0.71 0.08 0.21
Matches are distributed among these distances:
6 2 0.01
7 23 0.17
8 56 0.41
9 40 0.30
10 12 0.09
11 2 0.01
ACGTcount: A:0.09, C:0.17, G:0.01, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:171162 original size:45 final size:45
Alignment explanation
Indices: 171095--171228 Score: 196
Period size: 45 Copynumber: 2.9 Consensus size: 45
171085 CCATGCTTTG
* *
171095 TTATTCACAAAAATAAGTCCTAACCGCATGATATCTAATTCGCATAC
1 TTATTCA-AAAAATAA-ACCTAACCGCATGATATCTAGTTCGCATAC
* *
171142 TTATTCAAAAAATAAACCTAACCACATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATAC
* *
171187 TTGTTCGAAAAATAAACCTAACCGCATGATATCTAGTTCGCA
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCA
171229 AGCATTTATT
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 65 0.81
46 8 0.10
47 7 0.09
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.29
Consensus pattern (45 bp):
TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATAC
Found at i:174676 original size:9 final size:9
Alignment explanation
Indices: 174634--174687 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
174624 AAAATTTTAA
174634 AAATAAAAAT
1 AAAT-AAAAT
*
174644 AAAAATAAAT
1 AAATA-AAAT
174654 AAAT-AAAT
1 AAATAAAAT
174662 AAATAAAAT
1 AAATAAAAT
* *
174671 AGATAAAAC
1 AAATAAAAT
174680 AAATAAAA
1 AAATAAAA
174688 CAAAGGAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
8 8 0.22
9 19 0.51
10 10 0.27
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:174683 original size:13 final size:13
Alignment explanation
Indices: 174634--174686 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
174624 AAAATTTTAA
174634 AAATAAA-AATAA-
1 AAATAAATAA-AAT
174646 AAATAAAT-AAAT
1 AAATAAATAAAAT
174658 AAATAAATAAAAT
1 AAATAAATAAAAT
*
174671 AGATAAA-ACAAAT
1 AAATAAATA-AAAT
174684 AAA
1 AAA
174687 ACAAAGGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 2 0.06
12 17 0.49
13 16 0.46
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:174683 original size:22 final size:22
Alignment explanation
Indices: 174640--174686 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
174630 TTAAAAATAA
*
174640 AAATAAAAATAAATAAATAAAT
1 AAATAAAAATAAATAAACAAAT
*
174662 AAAT-AAAATAGATAAAACAAAT
1 AAATAAAAATAAAT-AAACAAAT
174684 AAA
1 AAA
174687 ACAAAGGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATAAAAATAAATAAACAAAT
Found at i:174788 original size:25 final size:23
Alignment explanation
Indices: 174752--174805 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
174742 AAAAATAAGT
174752 AAATAAATAAAA-ATAAATAAATAA
1 AAATAAATAAAATA-AAAT-AATAA
*
174776 AATATAAGTAAAATAAAATAATAA
1 AA-ATAAATAAAATAAAATAATAA
174800 AAATAA
1 AAATAA
174806 TATATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.15
24 9 0.33
25 13 0.48
26 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (23 bp):
AAATAAATAAAATAAAATAATAA
Found at i:174796 original size:14 final size:15
Alignment explanation
Indices: 174737--174801 Score: 64
Period size: 18 Copynumber: 4.3 Consensus size: 15
174727 CAACAAGAAG
174737 AAAATAAAAATAAGT
1 AAAATAAAAATAAGT
*
174752 AAATAAATAAAAATAAAT
1 --A-AAATAAAAATAAGT
174770 -AAATAAAATATAAGT
1 AAAATAAAA-ATAAGT
174785 AAAAT-AAAATAA-T
1 AAAATAAAAATAAGT
174798 AAAA
1 AAAA
174802 ATAATATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
13 5 0.12
14 12 0.28
15 8 0.19
16 4 0.09
17 1 0.02
18 13 0.30
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (15 bp):
AAAATAAAAATAAGT
Found at i:174802 original size:9 final size:9
Alignment explanation
Indices: 174739--174837 Score: 55
Period size: 9 Copynumber: 10.9 Consensus size: 9
174729 ACAAGAAGAA
174739 AATAAAAAT
1 AATAAAAAT
*
174748 AAGTAAATA-
1 AA-TAAAAAT
174757 AATAAAAAT
1 AATAAAAAT
174766 AAATAAATAA-
1 -AATAAA-AAT
* *
174776 AATATAAGT
1 AATAAAAAT
*
174785 AAAATAAAAT
1 AATA-AAAAT
174795 AATAAAAAT
1 AATAAAAAT
* *
174804 AATATATAT
1 AATAAAAAT
174813 -ATACAAAAT
1 AATA-AAAAT
174822 AA-AAGAAAT
1 AATAA-AAAT
174831 AA-AAAAA
1 AATAAAAA
174838 GATCAAAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
8 13 0.19
9 36 0.52
10 18 0.26
11 2 0.03
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (9 bp):
AATAAAAAT
Found at i:177477 original size:60 final size:60
Alignment explanation
Indices: 177376--177517 Score: 198
Period size: 60 Copynumber: 2.4 Consensus size: 60
177366 TATATATGTG
* *
177376 TAGTTTGGGATGAAATTGGAATGTTAAAAGAGTTTGGGGACTAATTTAGAATGA-AGGTCA
1 TAGTTTGGGATGAAATTGAAATGTTAAAAGAGTTTGAGGACTAATTTAGAATGATA-GTCA
*
177436 TAGTTTGGGGATGAAATTGAAATGTTTAAA-AGTTTGAGGACTAATTTAGAATGATAGTCA
1 TAGTTT-GGGATGAAATTGAAATGTTAAAAGAGTTTGAGGACTAATTTAGAATGATAGTCA
* *
177496 TAGTTTAAGGATAAAATTGAAA
1 TAGTTT-GGGATGAAATTGAAA
177518 CACCCAAAAG
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
60 52 0.70
61 22 0.30
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (60 bp):
TAGTTTGGGATGAAATTGAAATGTTAAAAGAGTTTGAGGACTAATTTAGAATGATAGTCA
Found at i:177501 original size:31 final size:31
Alignment explanation
Indices: 177406--177506 Score: 77
Period size: 31 Copynumber: 3.3 Consensus size: 31
177396 ATGTTAAAAG
*
177406 AGTTTGGGGACTAATTTAGAATGA-AGGTCAT
1 AGTTTGAGGACTAATTTAGAATGATA-GTCAT
* * * * *
177437 AGTTTGGGGA-TGAAATT-GAAATG-T-TTAAA
1 AGTTTGAGGACT-AATTTAG-AATGATAGTCAT
177466 AGTTTGAGGACTAATTTAGAATGATAGTCAT
1 AGTTTGAGGACTAATTTAGAATGATAGTCAT
*
177497 AGTTTAAGGA
1 AGTTTGAGGA
177507 TAAAATTGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
29 19 0.36
30 5 0.09
31 29 0.55
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.34
Consensus pattern (31 bp):
AGTTTGAGGACTAATTTAGAATGATAGTCAT
Found at i:177527 original size:60 final size:60
Alignment explanation
Indices: 177406--177530 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
177396 ATGTTAAAAG
* ** * *****
177406 AGTTTGGGGACTAATTTAGAATGAAGGTCATAGTTTGGGGATGAAATTGAAATGTTTAAA
1 AGTTTGAGGACTAATTTAGAATGAAGGTCATAGTTTAAGGATAAAATTGAAACACCCAAA
177466 AGTTTGAGGACTAATTTAGAATGATA-GTCATAGTTTAAGGATAAAATTGAAACACCCAAA
1 AGTTTGAGGACTAATTTAGAATGA-AGGTCATAGTTTAAGGATAAAATTGAAACACCCAAA
177526 AGTTT
1 AGTTT
177531 AGGGAGCGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (60 bp):
AGTTTGAGGACTAATTTAGAATGAAGGTCATAGTTTAAGGATAAAATTGAAACACCCAAA
Found at i:187218 original size:31 final size:31
Alignment explanation
Indices: 187180--187242 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
187170 TACTTATATC
187180 ATTGTTGGAACTTGGACGGTGACAAGATTGA
1 ATTGTTGGAACTTGGACGGTGACAAGATTGA
* *
187211 ATTGTTGGAACTTGGATGGTGTCAAGATTGA
1 ATTGTTGGAACTTGGACGGTGACAAGATTGA
187242 A
1 A
187243 GAGGCCAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.08, G:0.32, T:0.32
Consensus pattern (31 bp):
ATTGTTGGAACTTGGACGGTGACAAGATTGA
Found at i:196731 original size:37 final size:37
Alignment explanation
Indices: 196678--196782 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
196668 CCTTTTCGTC
*
196678 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * *
196715 TTGCTAGGATTTAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
196752 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
196783 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:197725 original size:2 final size:2
Alignment explanation
Indices: 197718--197746 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
197708 TTACCATTAT
197718 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
197747 TCTACACAAA
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:198011 original size:35 final size:34
Alignment explanation
Indices: 197977--198049 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
197967 TCATCATTTA
*
197977 ATTTATTA-AT-T-TATATATATT-TACTTTTTT
1 ATTTATTATATATATATATATATTCTACTTTGTT
198007 ATTTATTATATATATATATATATTCGTACTTTGTT
1 ATTTATTATATATATATATATATTC-TACTTTGTT
198042 A-TTATTAT
1 ATTTATTAT
198050 TTTGTTTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 8 0.22
31 2 0.05
32 1 0.03
33 10 0.27
34 7 0.19
35 9 0.24
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (34 bp):
ATTTATTATATATATATATATATTCTACTTTGTT
Found at i:198059 original size:20 final size:20
Alignment explanation
Indices: 198036--198083 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
198026 ATATTCGTAC
*
198036 TTTGTTATTA-TTATTTTGTT
1 TTTGTT-TTATTTATTTTCTT
198056 TTTGTTTTATTTATTTTCTT
1 TTTGTTTTATTTATTTTCTT
*
198076 TTTCTTTT
1 TTTGTTTT
198084 TTATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.79
Consensus pattern (20 bp):
TTTGTTTTATTTATTTTCTT
Found at i:199294 original size:19 final size:19
Alignment explanation
Indices: 199270--199306 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
199260 ACCTTACTAA
199270 CTCTTTTCATTTT-TTTCCG
1 CTCTTTT-ATTTTATTTCCG
199289 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
199307 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.03, T:0.65
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCG
Found at i:202705 original size:13 final size:15
Alignment explanation
Indices: 202687--202718 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
202677 GAAAATAAGC
202687 AAAAAAG-AAGAA-A
1 AAAAAAGAAAGAACA
202700 AAAAAAGAAAGAACA
1 AAAAAAGAAAGAACA
202715 AAAA
1 AAAA
202719 TCAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAGAACA
Found at i:203410 original size:22 final size:22
Alignment explanation
Indices: 203336--203412 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
203326 GCTACCCCAT
*
203336 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* *
203358 CAAACCTATGAGCATCACATGC
1 CAAACCTTTGAGCATCAAATGC
203380 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
203402 CAAACCTTTGA
1 CAAACCTTTGA
203413 CCAAACATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:204456 original size:106 final size:106
Alignment explanation
Indices: 204240--205720 Score: 2081
Period size: 106 Copynumber: 14.0 Consensus size: 106
204230 ATATCGTGCC
* * * * * *
204240 ACTCAAGACAACACAAGTTCAACTTAACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
204304 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
204345 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCGGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
204410 AATTTCATATCTAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
204451 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTT-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCC
* *
204515 TAATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
204557 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
204622 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
204663 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
204728 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
204769 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
204834 AATTTCAGAGCAAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
204875 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
204940 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
204981 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGATCGCTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
205046 AATTTCAGAGCCAATTTCAACTTTACAGCGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
205087 ACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
205152 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
205193 ACTCCATACAACGCAAGTTCAACTTCAAGACGAAGGGACCGCTGGTTGTCAACAAACAACTTT-T
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCC
*
205257 CAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
205299 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGGCCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
205364 AATTTCAGAGCCAATTTCAATTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
205405 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * * * * *
205470 AATTTTAGAGCCAATTTCAACATCTCAGCGAAGGATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
205511 AC-CCAAGGCAACACAAGCTCAACTTTACGATGAAGAGG-CGGCTGATTGTCAAC-AA-AATTT-
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG-GGACCGCTGGTTGTCAACAAACAATTTC
* *
205571 -C-A-TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTAG
64 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
205611 ACTCGAGACAACACAAGTTC-ACTTTCACAATGAAGGGA-CGACTGGTTGTCAACAAACAATTTC
1 ACTCCAGACAACGCAAGTTCAAC-TTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTC
* * ** *
205674 CCAGTTCCAGAGCCAATTAAAACTTCA-AGACGGAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACA-ACGAAGGATATTGG
205717 ACTC
1 ACTC
205721 AGAACAATGC
Statistics
Matches: 1235, Mismatches: 123, Indels: 35
0.89 0.09 0.03
Matches are distributed among these distances:
99 5 0.00
100 66 0.05
101 4 0.00
102 6 0.00
104 5 0.00
105 55 0.04
106 1087 0.88
107 7 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:206502 original size:37 final size:37
Alignment explanation
Indices: 206449--206545 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
206439 CCTTTTCGTC
*
206449 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATATGATAGAATT
* * * *
206486 TTGCTAGGATTTAAACTCCAAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATATGATAGAATT
*
206523 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTTAAACTCCTAAA
206546 GATAGGATCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATATGATAGAATT
Found at i:207185 original size:25 final size:25
Alignment explanation
Indices: 207157--207211 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
207147 TATATTTTCC
207157 TTTTAT-TCTAATTATATATGTATATT
1 TTTTATATCTAATTAT-TAT-TATATT
* *
207183 TTTTATATTTTATTATTATTATATT
1 TTTTATATCTAATTATTATTATATT
207208 TTTT
1 TTTT
207212 CTTTCTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.38
26 9 0.35
27 7 0.27
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTATATCTAATTATTATTATATT
Found at i:226581 original size:30 final size:30
Alignment explanation
Indices: 226547--226607 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
226537 TTCGATATAA
*
226547 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
226577 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
226607 C
1 C
226608 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:235196 original size:30 final size:30
Alignment explanation
Indices: 235162--235222 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
235152 TTCGATATAA
*
235162 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
235192 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
235222 C
1 C
235223 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:243081 original size:28 final size:29
Alignment explanation
Indices: 243026--243093 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 29
243016 AAATTATACG
* * * *
243026 TTTAATATTTTAAATTATCATATTTAAAC
1 TTTAATTTTTTAAATAATAATACTTAAAC
*
243055 TTTAATTTTTTAAA-AATAATACTTAAAG
1 TTTAATTTTTTAAATAATAATACTTAAAC
243083 TTTAATTTTTT
1 TTTAATTTTTT
243094 TTCTTTTCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (29 bp):
TTTAATTTTTTAAATAATAATACTTAAAC
Found at i:245093 original size:15 final size:15
Alignment explanation
Indices: 245073--245119 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
245063 GGATTTCATA
245073 TAAAATATATGAAAT
1 TAAAATATATGAAAT
*
245088 TAAAATA-ATCAAAT
1 TAAAATATATGAAAT
245102 T----TATATGAAAT
1 TAAAATATATGAAAT
245113 TAAAATA
1 TAAAATA
245120 ATCAAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
10 2 0.08
11 7 0.28
14 7 0.28
15 9 0.36
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (15 bp):
TAAAATATATGAAAT
Found at i:245107 original size:25 final size:25
Alignment explanation
Indices: 245078--245132 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
245068 TCATATAAAA
245078 TATATGAAATTAAAATAATCAAATT
1 TATATGAAATTAAAATAATCAAATT
245103 TATATGAAATTAAAATAATCAAATT
1 TATATGAAATTAAAATAATCAAATT
245128 TATAT
1 TATAT
245133 AATATATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (25 bp):
TATATGAAATTAAAATAATCAAATT
Found at i:281879 original size:30 final size:30
Alignment explanation
Indices: 281836--281915 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
281826 TCCTCCGCCA
*
281836 GGGTATGGTTACCCGCCTCCACAACAG-CC
1 GGGTATGGGTACCCGCCTCCACAACAGCCC
* * *
281865 GGGATATGGGTACCCGCCGCCGCAGCAGCCC
1 GGG-TATGGGTACCCGCCTCCACAACAGCCC
* *
281896 GGGTATGGGTATCCTCCTCC
1 GGGTATGGGTACCCGCCTCC
281916 CGGGGGATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 3 0.07
30 34 0.81
31 5 0.12
ACGTcount: A:0.16, C:0.36, G:0.30, T:0.17
Consensus pattern (30 bp):
GGGTATGGGTACCCGCCTCCACAACAGCCC
Found at i:287622 original size:90 final size:90
Alignment explanation
Indices: 287464--287645 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 90
287454 TCTGATTCGC
* *
287464 CACTGGCTGCAGCCTTCAAAAGAGCAGCCAATGCAGCAGAACTAAGTAGCTCTTCCGCTTGATAT
1 CACTGGCTGCAGCCTTCAAAAGAGCAGCCAATGCAGCAGAACTAAGTAGCTCTTCAGCTTCATAT
*
287529 TCCCTCTCAACTTCCGCTTCTTCAT
66 TCCCTCTCAACTTCAGCTTCTTCAT
* * * * *
287554 CACTTGCTGCAGCTTTCAAAAGAGCAGTCAATGCAGCAGAATCT-TGTAGCTCTTTAGCTTCATA
1 CACTGGCTGCAGCCTTCAAAAGAGCAGCCAATGCAGCAGAA-CTAAGTAGCTCTTCAGCTTCATA
*
287618 TTCCCTCTCAGCTTCAGCTTCTTCAT
65 TTCCCTCTCAACTTCAGCTTCTTCAT
287644 CA
1 CA
287646 GAGTCTACGA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 80 0.98
91 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (90 bp):
CACTGGCTGCAGCCTTCAAAAGAGCAGCCAATGCAGCAGAACTAAGTAGCTCTTCAGCTTCATAT
TCCCTCTCAACTTCAGCTTCTTCAT
Found at i:288639 original size:183 final size:182
Alignment explanation
Indices: 288326--288686 Score: 641
Period size: 183 Copynumber: 2.0 Consensus size: 182
288316 CTTTCCAAAC
*
288326 CAGACCCCTTATCTTCACCTACAAAATCCTCCAACACCTCCTCGTCTTCAACCCCGAGGCCACCT
1 CAGACCCCTTATCTTCACCTACAAAATCCTCCAACACCTCCTCGTCTTCAACCCCGAAGCCACCT
* *
288391 TTAATCTAGGTGAACTTTCAACACTACCAGCAACGTTAACCACACCAGAGAACCCACCATCTTCA
66 TTAATCTAGGTGAACTTTCAACACCACCAGCAACCTTAACCACACCAGAGAACCCACCATCTTCA
*
288456 ACTCCGCCCACCGTTTCATCCTCACTCGACATTTCATCAAACACTTCAAAAT
131 ACTCCGCCCACCGTTTCATCCACACTCGACATTTCATCAAACACTTCAAAAT
288508 CAGACCCCTTATCTTCACCTACAAAATCCTCCAACACCTCCTCGTCTTCAACCCCCGAAGCCACC
1 CAGACCCCTTATCTTCACCTACAAAATCCTCCAACACCTCCTCGTCTTCAA-CCCCGAAGCCACC
* *
288573 TTTAATCTAGGTGAACTTTCAACACCACCAGCAACCTTAACCACACCAGAGAACTCACCCTCTTC
65 TTTAATCTAGGTGAACTTTCAACACCACCAGCAACCTTAACCACACCAGAGAACCCACCATCTTC
* *
288638 AACTCCGGCCACCGTTTCATCCACACTCGACATTTCATCAGACACTTCA
130 AACTCCGCCCACCGTTTCATCCACACTCGACATTTCATCAAACACTTCA
288687 TCATCCATCG
Statistics
Matches: 170, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
182 51 0.30
183 119 0.70
ACGTcount: A:0.29, C:0.40, G:0.08, T:0.23
Consensus pattern (182 bp):
CAGACCCCTTATCTTCACCTACAAAATCCTCCAACACCTCCTCGTCTTCAACCCCGAAGCCACCT
TTAATCTAGGTGAACTTTCAACACCACCAGCAACCTTAACCACACCAGAGAACCCACCATCTTCA
ACTCCGCCCACCGTTTCATCCACACTCGACATTTCATCAAACACTTCAAAAT
Found at i:300703 original size:7 final size:7
Alignment explanation
Indices: 300691--300758 Score: 55
Period size: 7 Copynumber: 9.7 Consensus size: 7
300681 TTGTTAAAAT
300691 CCTAAAC
1 CCTAAAC
300698 CCTAAAC
1 CCTAAAC
*
300705 ACTAAAC
1 CCTAAAC
**
300712 TATAAAC
1 CCTAAAC
300719 CCTAAAC
1 CCTAAAC
*
300726 TCTAAAC
1 CCTAAAC
**
300733 ATTAAAC
1 CCTAAAC
*
300740 TCTAAAC
1 CCTAAAC
**
300747 ATTAAAC
1 CCTAAAC
300754 CCTAA
1 CCTAA
300759 CCATTCTCCC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (7 bp):
CCTAAAC
Found at i:300711 original size:14 final size:14
Alignment explanation
Indices: 300692--300758 Score: 80
Period size: 14 Copynumber: 4.8 Consensus size: 14
300682 TGTTAAAATC
*
300692 CTAAACCCTAAACA
1 CTAAACTCTAAACA
* *
300706 CTAAACTATAAACC
1 CTAAACTCTAAACA
300720 CTAAACTCTAAACA
1 CTAAACTCTAAACA
*
300734 TTAAACTCTAAACA
1 CTAAACTCTAAACA
* *
300748 TTAAACCCTAA
1 CTAAACTCTAA
300759 CCATTCTCCC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.22
Consensus pattern (14 bp):
CTAAACTCTAAACA
Found at i:300717 original size:21 final size:21
Alignment explanation
Indices: 300693--300753 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
300683 GTTAAAATCC
300693 TAAACCCTAAACACTAAAC-T
1 TAAACCCTAAACACTAAACAT
*
300713 ATAAACCCTAAACTCTAAACAT
1 -TAAACCCTAAACACTAAACAT
* *
300735 TAAACTCTAAACATTAAAC
1 TAAACCCTAAACACTAAAC
300754 CCTAACCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 34 0.97
22 1 0.03
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCCTAAACACTAAACAT
Found at i:301431 original size:20 final size:19
Alignment explanation
Indices: 301402--301442 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
301392 AAATTCAACT
301402 ATTTATAAATT-TGATTTAA
1 ATTTATAAATTCT-ATTTAA
301421 ATTTAATAAATTCTATTTAA
1 ATTT-ATAAATTCTATTTAA
301441 AT
1 AT
301443 ATTTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 15 0.75
21 1 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTATAAATTCTATTTAA
Found at i:330546 original size:20 final size:20
Alignment explanation
Indices: 330510--330547 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
330500 AGGCACTCAC
*
330510 TTTAAAATTATTTATTTTCT
1 TTTAAAATTATTAATTTTCT
330530 TTTAAAA-TATATAATTTT
1 TTTAAAATTAT-TAATTTT
330548 TGCTTAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAAAATTATTAATTTTCT
Found at i:337990 original size:16 final size:16
Alignment explanation
Indices: 337969--338006 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
337959 ATCAAGGAAA
337969 GGTTTGTCTAGATTCT
1 GGTTTGTCTAGATTCT
337985 GGTTTGTCTAGATTCT
1 GGTTTGTCTAGATTCT
338001 GGTTTG
1 GGTTTG
338007 AAATGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.11, C:0.11, G:0.29, T:0.50
Consensus pattern (16 bp):
GGTTTGTCTAGATTCT
Found at i:342259 original size:2 final size:2
Alignment explanation
Indices: 342246--342288 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
342236 ATATCGTCCG
*
342246 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
342288 C
1 C
342289 ACAGGTGCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:344020 original size:51 final size:50
Alignment explanation
Indices: 343877--344029 Score: 270
Period size: 50 Copynumber: 3.0 Consensus size: 50
343867 GAAAGAGACT
*
343877 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
*
343927 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
*
343977 AATAGCATCTTCTGGAAGTTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AATAGCATCTTCTGGAAG-TGTTCTTTGAGTTATCTGATCTGGTTTGACAG
344028 AA
1 AA
344030 CCAATCATTG
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
50 66 0.67
51 32 0.33
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
Found at i:344844 original size:41 final size:42
Alignment explanation
Indices: 344779--344885 Score: 168
Period size: 41 Copynumber: 2.6 Consensus size: 42
344769 ATTCTTTTCC
*
344779 AGAG-GAAGAGTTCATAATGAGAAGAACTTATCTGAAG-AGGA
1 AGAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
344820 AGAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 AGAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
344862 AGA-AG-AAGTTCATAATGAGAAGAA
1 AGAGAGAAAGTTCATAATGAGAAGAA
344886 TTTGTTCAAC
Statistics
Matches: 63, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
40 19 0.30
41 34 0.54
42 10 0.16
ACGTcount: A:0.48, C:0.07, G:0.27, T:0.18
Consensus pattern (42 bp):
AGAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:345244 original size:117 final size:118
Alignment explanation
Indices: 344820--345432 Score: 1089
Period size: 118 Copynumber: 5.2 Consensus size: 118
344810 CTGAAGAGGA
344820 AGAGAGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 AGAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
*
344881 AAGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
65 AAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
344935 AGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 AGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
345000 AGAATTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
66 AGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
345053 AGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 AGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
345118 AGAAC-TGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
66 AGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
345170 AGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC-GAAGAAGGAAGAAGAAGTTCATAATGAGA
1 AGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
345234 AGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
66 AGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
345287 AGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 AGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * **
345352 AGAACTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGAACATCATCCCC
66 AGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
*
345405 AGCA-GAA-AGTTCGTAATGAGAAGAACTC
1 AG-AGGAAGAGTTCATAATGAGAAGAACTC
345433 ATCTGGAGAA
Statistics
Matches: 485, Mismatches: 6, Indels: 12
0.96 0.01 0.02
Matches are distributed among these distances:
114 3 0.01
115 22 0.05
116 34 0.07
117 185 0.38
118 240 0.49
119 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (118 bp):
AGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
Found at i:345593 original size:3 final size:3
Alignment explanation
Indices: 345585--345669 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
345575 TTTTTATCCA
*
345585 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
345633 TTT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
345670 AATATATTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 2 0.03
3 75 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:352212 original size:12 final size:12
Alignment explanation
Indices: 352197--352242 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
352187 ACGGTTTTTT
*
352197 ACCGGATAAAAA
1 ACCGGTTAAAAA
352209 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
352224 ACCGGTTAAAAA
1 ACCGGTTAAAAA
352236 ACCGGTT
1 ACCGGTT
352243 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:352224 original size:15 final size:13
Alignment explanation
Indices: 352203--352243 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
352193 TTTTACCGGA
352203 TAAAAAACCGGTT
1 TAAAAAACCGGTT
352216 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
352230 TAAAAAACCGGTT
1 TAAAAAACCGGTT
352243 T
1 T
352244 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:354151 original size:17 final size:17
Alignment explanation
Indices: 354131--354172 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
354121 ATATATACAT
*
354131 ATAATAATAATACATGA
1 ATAATAATAATAAATGA
*
354148 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
354165 ATAA-AATA
1 ATAATAATA
354173 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:354609 original size:37 final size:37
Alignment explanation
Indices: 354527--354630 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
354517 GTGCTTGTGG
* * * * * *
354527 ATCATATCTTTAAGAATTTAAATCTTAGTAGAACTCT
1 ATCATATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
* * *
354564 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTTT
1 ATCATATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
354601 ATCATATTTTTAGGAGTTTGAATCCTAGTA
1 ATCATATTTTTAGGAGTTTGAATCCTAGTA
354631 GGACGAAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:355478 original size:105 final size:105
Alignment explanation
Indices: 355174--355699 Score: 776
Period size: 105 Copynumber: 5.0 Consensus size: 105
355164 GCATTGTTCC
* * * *
355174 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
355238 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
355280 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A---CGAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
355340 CAGAGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
355380 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
355445 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
355485 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
355550 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
355590 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
355655 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
355696 GAGT
1 GAGT
355700 GTCACGATAT
Statistics
Matches: 386, Mismatches: 27, Indels: 14
0.90 0.06 0.03
Matches are distributed among these distances:
100 83 0.22
101 1 0.00
102 6 0.02
104 5 0.01
105 206 0.53
106 85 0.22
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:355959 original size:36 final size:36
Alignment explanation
Indices: 355904--355973 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
355894 GGAGAGAAAT
* *
355904 TGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAGC
1 TGTCTCAAGCGAGACAAAATTCATTTCAAGGGAAGC
*
355940 TGTCTCAAGCGAGATAAAATTCATTTCAAGGGAA
1 TGTCTCAAGCGAGACAAAATTCATTTCAAGGGAA
355974 ATGTTTATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTCATTTCAAGGGAAGC
Found at i:356023 original size:39 final size:40
Alignment explanation
Indices: 355972--356053 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 40
355962 ATTTCAAGGG
* * *
355972 AAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACA
1 AAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAA
* *
356012 AAAT-TTTATGTTTCGAGGGAAACTATCTCAAGAGAGAAA
1 AAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAA
356051 AAA
1 AAA
356054 ATCATTTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 33 0.89
40 4 0.11
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (40 bp):
AAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAAA
Done.