Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009295.1 Hibiscus syriacus cultivar Beakdansim tig00113004_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: 136815
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2450 original size:20 final size:21
Alignment explanation
Indices: 2425--2476 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2415 TTTTCCCAAT
*
2425 TCGCAATGCGAA-T-AAGTAAA
1 TCGCAATGCGAATTGAA-AAAA
*
2445 TCGCAACGCGAATTGAAAAAA
1 TCGCAATGCGAATTGAAAAAA
2466 TCGCAATGCGA
1 TCGCAATGCGA
2477 TACTGACTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.41
21 14 0.52
22 2 0.07
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTGAAAAAA
Found at i:2490 original size:20 final size:20
Alignment explanation
Indices: 2465--2578 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
2455 AATTGAAAAA
2465 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
2485 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
2505 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
2526 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
2546 TTCGCAATGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
2566 TTCGCAACGCGAT
1 ATCGCAATGCGAT
2579 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2493 original size:61 final size:62
Alignment explanation
Indices: 2425--2557 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 62
2415 TTTTCCCAAT
* * *
2425 TCGCAATGCGAATAAGTA-AATCGCAACGCGA-ATTGAAAAAATCGCAATGCGATACTGACTA
1 TCGCAATGCGAATAAGTACAATCGCAACGCGATAAT-AAAAAATCGCAACGAGATACTGACTA
** * * * *
2486 TCGCAATGCG-ATACTTACTATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTT
1 TCGCAATGCGAATAAGTACAATCGCAACGCGATAATAAAAAATCGCAACGAGATACTGACTA
2547 TCGCAATGCGA
1 TCGCAATGCGA
2558 TTCTGACTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
60 5 0.08
61 53 0.88
62 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (62 bp):
TCGCAATGCGAATAAGTACAATCGCAACGCGATAATAAAAAATCGCAACGAGATACTGACTA
Found at i:2558 original size:61 final size:61
Alignment explanation
Indices: 2444--2578 Score: 173
Period size: 61 Copynumber: 2.2 Consensus size: 61
2434 GAATAAGTAA
* * * * *
2444 ATCGCAACGCGA-ATTGAAAAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACT
1 ATCGCAACGCGATAAT-ACAAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACT
* * *
2505 ATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTTTCGCAATGCGATTCTGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACT
*
2566 TTCGCAACGCGAT
1 ATCGCAACGCGAT
2579 TTACATAGCG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 61 0.97
62 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (61 bp):
ATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACT
Found at i:3137 original size:19 final size:20
Alignment explanation
Indices: 3092--3139 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3082 TTCGAGAATG
*
3092 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGCGGAAACA
**
3112 ACTATCGCAACGC-GAAACA
1 AAAATCGCAACGCGGAAACA
3131 AAAATCGCA
1 AAAATCGCA
3140 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.48, C:0.25, G:0.17, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCGGAAACA
Found at i:3157 original size:19 final size:19
Alignment explanation
Indices: 3135--3318 Score: 172
Period size: 19 Copynumber: 10.1 Consensus size: 19
3125 GAAACAAAAA
*
3135 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3154 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3173 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
3192 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3211 TTGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
3225 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
3244 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
3258 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
3277 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
3297 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3317 TC
1 TC
3319 AACCAAAAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
14 18 0.13
16 4 0.03
17 5 0.04
19 76 0.56
20 31 0.23
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3193 original size:38 final size:38
Alignment explanation
Indices: 3135--3318 Score: 172
Period size: 33 Copynumber: 5.1 Consensus size: 38
3125 GAAACAAAAA
*
3135 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
3173 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * * **
3211 TTGCGTTGCGA--TTC---TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
3244 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
3277 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
3317 TC
1 TC
3319 AACCAAAAGA
Statistics
Matches: 126, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
33 47 0.37
34 10 0.08
36 4 0.03
38 46 0.37
39 1 0.01
40 18 0.14
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:5385 original size:42 final size:42
Alignment explanation
Indices: 5309--5397 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
5299 GACTCGCCTG
* * *
5309 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
5351 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
5393 TCATC
1 TCATC
5398 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:6796 original size:14 final size:14
Alignment explanation
Indices: 6777--6812 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6767 ATTGTTTAAT
6777 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
6791 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
6805 TGATTTGT
1 TGATTTGT
6813 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:6943 original size:19 final size:19
Alignment explanation
Indices: 6919--6965 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
6909 AAAAAGTACT
* *
6919 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATAAAA
6938 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAATAAAA
6957 ATCGCAACG
1 ATCGCAACG
6966 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATAAAA
Found at i:7018 original size:19 final size:19
Alignment explanation
Indices: 6996--7120 Score: 73
Period size: 19 Copynumber: 7.4 Consensus size: 19
6986 TAAATTTGCG
6996 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
7015 TTGCGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
*
7029 TTGAGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
7048 TTGCGA-----AATTAGCG
1 TTGCGATTTTCATTTCGCA
7062 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
7081 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
*
7095 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
7114 TTGCGAT
1 TTGCGAT
7121 AGTAATTTCC
Statistics
Matches: 76, Mismatches: 15, Indels: 30
0.63 0.12 0.25
Matches are distributed among these distances:
14 26 0.34
16 8 0.11
17 9 0.12
19 33 0.43
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:7037 original size:33 final size:32
Alignment explanation
Indices: 6994--7120 Score: 166
Period size: 33 Copynumber: 3.9 Consensus size: 32
6984 ATTAAATTTG
6994 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
7027 CGTTGAGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
7060 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
* *
7093 CATTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
7121 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.04
33 76 0.93
35 3 0.04
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:7077 original size:66 final size:66
Alignment explanation
Indices: 6987--7119 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
6977 ACGCGAAATT
* *
6987 AAATTTGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGAGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGAGATTTTCATTTCGCATTGC
7052 G
66 G
* * *
7053 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTTTTATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGAGATTTTCATTTCGCATTGC
7118 G
66 G
7119 A
1 A
7120 TAGTAATTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGAGATTTTCATTTCGCATTGC
G
Found at i:9429 original size:12 final size:12
Alignment explanation
Indices: 9412--9436 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9402 TCTTCGGGGA
9412 CTTTTTCTTCTT
1 CTTTTTCTTCTT
9424 CTTTTTCTTCTT
1 CTTTTTCTTCTT
9436 C
1 C
9437 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:9645 original size:24 final size:24
Alignment explanation
Indices: 9611--9664 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
9601 CTGAAACATC
* *
9611 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
9635 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
9659 ATCAAA
1 ATCAAA
9665 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:10270 original size:20 final size:20
Alignment explanation
Indices: 10245--10285 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
10235 ATTCATTTGA
10245 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
10265 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
10285 C
1 C
10286 AATGCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.24, T:0.15
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:10342 original size:19 final size:19
Alignment explanation
Indices: 10301--10368 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
10291 AAAATGAAAA
10301 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
10317 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
10334 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
10353 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
10369 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:10388 original size:20 final size:20
Alignment explanation
Indices: 10363--10400 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10353 TCGCATTGCG
*
10363 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
10383 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
10401 TCTGTTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:10505 original size:14 final size:14
Alignment explanation
Indices: 10486--10522 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
10476 CATCAATTAA
10486 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
10500 ACAAATCATCTTTT
1 ACAAATCAACATTT
10514 ACAAATCAA
1 ACAAATCAA
10523 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:12410 original size:20 final size:19
Alignment explanation
Indices: 12387--12454 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
12377 GAAACTTAAA
12387 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
12407 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
12427 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
12446 ATCGCAACG
1 ATCGCAACG
12455 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:12462 original size:14 final size:14
Alignment explanation
Indices: 12443--12498 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
12433 ATGCGAAATG
12443 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
12457 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
12473 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
12489 AAAATCGCAA
1 AAAATCGCAA
12499 TGCGAAACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:12485 original size:32 final size:33
Alignment explanation
Indices: 12427--12505 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
12417 GGAAATGGCT
12427 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
12460 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
12492 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
12506 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:12553 original size:14 final size:14
Alignment explanation
Indices: 12534--12591 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
12524 TTTCATTTCG
12534 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
12548 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
12564 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
12580 CGTTGCGATTTT
1 CGTTGCGATTTT
12592 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:12598 original size:33 final size:33
Alignment explanation
Indices: 12517--12607 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
12507 ACAAATCGCA
*
12517 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
12550 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
12582 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
12608 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:12626 original size:20 final size:19
Alignment explanation
Indices: 12592--12646 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
12582 TTGCGATTTT
*
12592 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
12611 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
12631 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
12647 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:13105 original size:18 final size:18
Alignment explanation
Indices: 13079--13123 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
13069 GTCAATCAGA
*
13079 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGAGAGG
*
13097 TGATAGCTCTGGGAGAGG
1 TGATGGCTCTGGGAGAGG
13115 TGATGGCTC
1 TGATGGCTC
13124 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:0.16, C:0.13, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGAGAGG
Found at i:14487 original size:20 final size:20
Alignment explanation
Indices: 14439--14497 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
14429 AATAGTTTCT
** *
14439 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
14459 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
14479 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
14498 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:14778 original size:22 final size:22
Alignment explanation
Indices: 14751--14794 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
14741 GATGGAGATA
14751 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
**
14773 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
14795 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:15010 original size:20 final size:20
Alignment explanation
Indices: 14982--15034 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
14972 GATTATGTAT
*
14982 TATCACGTTGCGAAAGTCAG
1 TATCACGTTGCGAAAGTAAG
*
15002 TATCGCGTTGCGAAAGTAAG
1 TATCACGTTGCGAAAGTAAG
*
15022 TATCTCGTTGCGA
1 TATCACGTTGCGA
15035 TTTTGTATTA
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:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
TATCACGTTGCGAAAGTAAG
Found at i:15047 original size:41 final size:41
Alignment explanation
Indices: 15002--15079 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
14992 CGAAAGTCAG
* ** *
15002 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCGAAAGTAAGTATAGCATTGCGATTTTGTAT
* *
15043 TATCGCATTGCGATAGTCAGTATAGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATAGCATTGCGATTTT
15080 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATAGCATTGCGATTTTGTAT
Found at i:15095 original size:41 final size:41
Alignment explanation
Indices: 15065--15157 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 41
15055 ATAGTCAGTA
* *
15065 TAGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TAGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * * *
15106 TCGTATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TAGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
*
15147 TCGCATTGCGA
1 TAGCATTGCGA
15158 ATTGGGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TAGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:15096 original size:21 final size:21
Alignment explanation
Indices: 15070--15140 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
15060 CAGTATAGCA
15070 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** **
15091 TTGCGA-TTTACTTATTCGTA
1 TTGCGATTTTCCCAATTCGCG
15111 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
15132 TTGCGATTT
1 TTGCGATTT
15141 ACTTATTCGC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:15114 original size:20 final size:20
Alignment explanation
Indices: 15084--15157 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
15074 GATTTTCCCA
*
15084 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* * **
15104 ATTCGTATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
15125 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
15145 ATTCGCATTGCGA
1 ATTCGCATTGCGA
15158 ATTGGGAAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:16182 original size:6 final size:6
Alignment explanation
Indices: 16171--16200 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
16161 CTTCTCTTCC
16171 TACATT TACATT TACATT TACATT TACATT
1 TACATT TACATT TACATT TACATT TACATT
16201 AGTTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TACATT
Found at i:19951 original size:108 final size:108
Alignment explanation
Indices: 19623--19914 Score: 466
Period size: 108 Copynumber: 2.7 Consensus size: 108
19613 TGATCACGAC
* * * * *
19623 GATAATGATGATAATGGCTTCTCTT-ATTCTCTAGAGGAAGG-TGGTCGTCA-CATACATGCTGG
1 GATAATGATGATAACGGCTTCT-TTAATTCTCCAGAGG-AGGATGGTC-ACAGTAGACATGCTGG
*
19685 GGGATCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGAGCAG
63 GGGATCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGGGCAG
19731 GATAATGATGATAACGGCTTCTTTAATTCTCCAGAGGAGGATGGTCACAGTAGACATGCTGGGGG
1 GATAATGATGATAACGGCTTCTTTAATTCTCCAGAGGAGGATGGTCACAGTAGACATGCTGGGGG
19796 ATCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGGGCAG
66 ATCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGGGCAG
19839 GATAATGATGATAACGGCTTCTTTAATTCTCCAGAGGAGGATGGTCACAGTAGACATGCT-GGGG
1 GATAATGATGATAACGGCTTCTTTAATTCTCCAGAGGAGGATGGTCACAGTAGACATGCTGGGGG
19903 ATTCTTCATCTG
66 A-TCTTCATCTG
19915 GCTCAGACGC
Statistics
Matches: 174, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
107 12 0.07
108 162 0.93
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (108 bp):
GATAATGATGATAACGGCTTCTTTAATTCTCCAGAGGAGGATGGTCACAGTAGACATGCTGGGGG
ATCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGGGCAG
Found at i:23128 original size:31 final size:31
Alignment explanation
Indices: 23090--23166 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
23080 AAACTACGAA
23090 TTTAGTACCTAAACTATCAATCTTGATTTAT
1 TTTAGTACCTAAACTATCAATCTTGATTTAT
* *
23121 TTTAGTACCTAAATTATCAATCTTGATTTGT
1 TTTAGTACCTAAACTATCAATCTTGATTTAT
23152 TTTAGTACCTAAACT
1 TTTAGTACCTAAACT
23167 TTTAATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (31 bp):
TTTAGTACCTAAACTATCAATCTTGATTTAT
Found at i:23351 original size:39 final size:38
Alignment explanation
Indices: 23304--23384 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 38
23294 AACTTAACGT
*
23304 TAAA-TTTTAAACGAGT-GTACTAAAATGAAACAAAAAC
1 TAAAGTTTTTAACG-GTGGTACTAAAATGAAACAAAAAC
*
23341 TAAAGTTTTTATCGGTGGGGTACTAAAATGAAACAAAAAC
1 TAAAGTTTTTAACGGT--GGTACTAAAATGAAACAAAAAC
23381 TAAA
1 TAAA
23385 CTTTAGGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
37 6 0.16
38 7 0.18
40 25 0.66
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (38 bp):
TAAAGTTTTTAACGGTGGTACTAAAATGAAACAAAAAC
Found at i:29202 original size:23 final size:23
Alignment explanation
Indices: 29174--29221 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
29164 TATCAAATGA
29174 TTAAGAATATTTAGTAAATATAC
1 TTAAGAATATTTAGTAAATATAC
29197 TTAAGAATATTTAGTAAATATAC
1 TTAAGAATATTTAGTAAATATAC
29220 TT
1 TT
29222 CTTACATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (23 bp):
TTAAGAATATTTAGTAAATATAC
Found at i:36983 original size:16 final size:15
Alignment explanation
Indices: 36962--36996 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
36952 AATATTTTAT
*
36962 ATAAATTAATTAGTTA
1 ATAAATTAAATA-TTA
36978 ATAAATTAAATATTA
1 ATAAATTAAATATTA
36993 ATAA
1 ATAA
36997 GTATATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
ATAAATTAAATATTA
Found at i:38190 original size:20 final size:22
Alignment explanation
Indices: 38151--38196 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
38141 GAAATGAAGG
*
38151 TTTTCAAAGTTTTGGGGTTTT-
1 TTTTCAAAATTTTGGGGTTTTC
*
38172 TTTTCAAAATTTT-GTGTTTTC
1 TTTTCAAAATTTTGGGGTTTTC
38193 TTTT
1 TTTT
38197 TTAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (22 bp):
TTTTCAAAATTTTGGGGTTTTC
Found at i:38364 original size:29 final size:30
Alignment explanation
Indices: 38318--38374 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
38308 TATTTTGAGT
* *
38318 AACGAAATGAAACGATAGGCACAAAACTGA
1 AACGAAATAAAACAATAGGCACAAAACTGA
*
38348 AACGAAA-AAAACAATAGGCACTAAACT
1 AACGAAATAAAACAATAGGCACAAAACT
38375 AAAAAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.56, C:0.18, G:0.16, T:0.11
Consensus pattern (30 bp):
AACGAAATAAAACAATAGGCACAAAACTGA
Found at i:44980 original size:3 final size:3
Alignment explanation
Indices: 44965--45001 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
44955 CTCACGCACA
* *
44965 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT TTT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
45002 ATATGTGGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:47610 original size:38 final size:38
Alignment explanation
Indices: 47554--47645 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
47544 TATAAGACAT
* * *
47554 ATGATAGGTCCTACGGGACACAGATTACATCATTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCATTCAGG
* * *
47592 ATGACAGGTCCTTCGGGACACAGATGACATCCTTTAGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCATTCAGG
*
47630 ATGATAGGTCATTCGG
1 ATGATAGGTCCTTCGG
47646 TCTCCATCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCATTCAGG
Found at i:48203 original size:17 final size:18
Alignment explanation
Indices: 48183--48219 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
48173 ATTCGTAATT
48183 AACACT-TATTACAT-ACC
1 AACACTCTA-TACATAACC
48200 AACACTCTATACATAACC
1 AACACTCTATACATAACC
48218 AA
1 AA
48220 GTACATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (18 bp):
AACACTCTATACATAACC
Found at i:48669 original size:15 final size:15
Alignment explanation
Indices: 48646--48708 Score: 108
Period size: 15 Copynumber: 4.2 Consensus size: 15
48636 CGTAGGACTC
48646 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
48661 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
48676 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
48691 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
48706 CTA
1 CTA
48709 TTATACCCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.14
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:48682 original size:30 final size:30
Alignment explanation
Indices: 48646--48708 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
48636 CGTAGGACTC
48646 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
48676 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
48706 CTA
1 CTA
48709 TTATACCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.14
Consensus pattern (30 bp):
CTACATCCCGAAGGACTACGTCCCGAAGGA
Found at i:48835 original size:29 final size:29
Alignment explanation
Indices: 48793--48866 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
48783 TTTCATATGT
48793 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
48821 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
48850 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
48867 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:48899 original size:12 final size:12
Alignment explanation
Indices: 48882--48917 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
48872 TATCATGTTA
48882 TCATATCACATG
1 TCATATCACATG
*
48894 TCATATCACATA
1 TCATATCACATG
48906 TCATATCACATG
1 TCATATCACATG
48918 AACGTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:61016 original size:43 final size:42
Alignment explanation
Indices: 60926--61063 Score: 138
Period size: 43 Copynumber: 3.2 Consensus size: 42
60916 TAGTATTACT
* ** * *
60926 TTTTATCTTTATAATTGAGACCTGTCGTTTTTTCAATCTCACT
1 TTTTATCTTTATAATTGAGACCTCT-AATTTTTCAATATCACA
* *
60969 TTTTATCTTTATAATTGAGACC-CTTAATTTCTTAAATATCACC
1 TTTTATCTTTATAATTGAGACCTC-TAATTT-TTCAATATCACA
*
61012 TTTTACCTTTATAATTGA-AGCCTCTAATTTTATCAATATCACA
1 TTTTATCTTTATAATTGAGA-CCTCTAATTTT-TCAATATCACA
61055 TTTTA-CTTT
1 TTTTATCTTT
61064 TATCAATAAG
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
42 9 0.11
43 71 0.88
44 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (42 bp):
TTTTATCTTTATAATTGAGACCTCTAATTTTTCAATATCACA
Found at i:61082 original size:43 final size:43
Alignment explanation
Indices: 60953--61084 Score: 119
Period size: 43 Copynumber: 3.1 Consensus size: 43
60943 AGACCTGTCG
* * * * *
60953 TTTTTTCAATCTCACTTTTTATCTTTATAATTG-AGACCCTTAA
1 TTTTATCAATATCACATTTTACCTTTATAATTGAAG-CCCCTAA
* * *
60996 TTTCT-TAAATATCACCTTTTACCTTTATAATTGAAGCCTCTAA
1 TTT-TATCAATATCACATTTTACCTTTATAATTGAAGCCCCTAA
*
61039 TTTTATCAATATCACATTTTACTTTTATCAA-T-AAGCCCCCTAA
1 TTTTATCAATATCACATTTTACCTTTAT-AATTGAAG-CCCCTAA
61082 TTT
1 TTT
61085 AAGCAAATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
42 4 0.05
43 65 0.88
44 5 0.07
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (43 bp):
TTTTATCAATATCACATTTTACCTTTATAATTGAAGCCCCTAA
Found at i:61817 original size:42 final size:43
Alignment explanation
Indices: 61737--61875 Score: 123
Period size: 42 Copynumber: 3.4 Consensus size: 43
61727 AAAATAAATT
* * *
61737 TATTATAAATTGTATTTATTTATTTATTAAAATGATAATAATA
1 TATTATAAATTATATTTAATTATTTATTAAAATAATAATAATA
* **
61780 TATTATTAATTATA-TTAATTATTTATTAACGTAATAAT-AT-
1 TATTATAAATTATATTTAATTATTTATTAAAATAATAATAATA
* * * *
61820 TATTAAAATATTAAATTTAA--A-TTATTAAAATAAGAATATTA
1 TATTATAA-ATTATATTTAATTATTTATTAAAATAATAATAATA
61861 TATTAT--ATTATATTT
1 TATTATAAATTATATTT
61876 TAAAGAGTAT
Statistics
Matches: 77, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
38 8 0.10
39 13 0.17
40 8 0.10
41 12 0.16
42 24 0.31
43 12 0.16
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (43 bp):
TATTATAAATTATATTTAATTATTTATTAAAATAATAATAATA
Found at i:61865 original size:22 final size:21
Alignment explanation
Indices: 61816--61866 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
61806 TAACGTAATA
61816 ATATTATTAAAATATTAAATTT
1 ATATTATTAAAATA-TAAATTT
*
61838 AAATTATTAAAATA-AGAATATT
1 ATATTATTAAAATATA-AAT-TT
61860 ATATTAT
1 ATATTAT
61867 ATTATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 3 0.12
22 21 0.84
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
ATATTATTAAAATATAAATTT
Found at i:61878 original size:39 final size:39
Alignment explanation
Indices: 61760--61879 Score: 100
Period size: 39 Copynumber: 3.0 Consensus size: 39
61750 ATTTATTTAT
* * *
61760 TTATTAAAATGATAATAATATATTATTAATTATATTAATT-AT
1 TTATTAAAATAATAATATTATATTA-T-ATTATATT--TTAAA
** ** *
61802 TTATTAACGTAATAATATTATTAAAATATTA-AATTTAAA
1 TTATTAAAATAATAATATTA-TATTATATTATATTTTAAA
*
61841 TTATTAAAATAAGAATATTATATTATATTATATTTTAAA
1 TTATTAAAATAATAATATTATATTATATTATATTTTAAA
61880 GAGTATTTAT
Statistics
Matches: 61, Mismatches: 14, Indels: 9
0.73 0.17 0.11
Matches are distributed among these distances:
38 10 0.16
39 25 0.41
40 2 0.03
41 4 0.07
42 17 0.28
43 3 0.05
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (39 bp):
TTATTAAAATAATAATATTATATTATATTATATTTTAAA
Found at i:61971 original size:23 final size:22
Alignment explanation
Indices: 61927--62013 Score: 58
Period size: 23 Copynumber: 4.0 Consensus size: 22
61917 TTTTTATGAA
** *
61927 ATTAATAAATAATTTATTATAT
1 ATTAATAAATAAAGTATAATAT
61949 ATTAATAAAATAAAGTATAATATT
1 ATTAAT-AAATAAAGTATAATA-T
*
61973 ATATATTATAAT-AA-TATAAT-T
1 AT-TAATA-AATAAAGTATAATAT
*
61994 A-TAA-CAATAAAGTATAATAT
1 ATTAATAAATAAAGTATAATAT
62014 TATATTATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
17 3 0.06
18 2 0.04
19 8 0.15
20 1 0.02
21 2 0.04
22 6 0.12
23 18 0.35
24 6 0.12
25 6 0.12
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (22 bp):
ATTAATAAATAAAGTATAATAT
Found at i:61974 original size:28 final size:29
Alignment explanation
Indices: 61941--61997 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
61931 ATAAATAATT
61941 TATTATATATTAATAA-AATA-AAGTATAA
1 TATTATATATT-ATAATAATATAAGTATAA
*
61969 TATTATATATTATAATAATATAATTATAA
1 TATTATATATTATAATAATATAAGTATAA
61998 CAATAAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
28 15 0.58
29 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (29 bp):
TATTATATATTATAATAATATAAGTATAA
Found at i:61978 original size:30 final size:30
Alignment explanation
Indices: 61935--61991 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
61925 AAATTAATAA
61935 ATAATTTATTATA-TATTAATAAAATAAAGT
1 ATAATTTATTATATTA-TAATAAAATAAAGT
*
61965 ATAATATTA-TATATTATAATAATATAA
1 ATAAT-TTATTATATTATAATAAAATAA
61992 TTATAACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
ATAATTTATTATATTATAATAAAATAAAGT
Found at i:62016 original size:21 final size:20
Alignment explanation
Indices: 61947--62017 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 20
61937 AATTTATTAT
61947 ATATTAATAAAATAAAGTATA
1 ATATT-ATAAAATAAAGTATA
* *
61968 ATATTATATATTATAA-TA-A
1 ATATTATAAAATA-AAGTATA
61987 TATAATTATAACAATAAAGTATA
1 -AT-ATTATAA-AATAAAGTATA
62010 ATATTATA
1 ATATTATA
62018 TTATTAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
19 1 0.03
20 10 0.25
21 21 0.52
22 7 0.17
23 1 0.03
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (20 bp):
ATATTATAAAATAAAGTATA
Found at i:62025 original size:21 final size:20
Alignment explanation
Indices: 61959--62035 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 20
61949 ATTAATAAAA
61959 TAAAGTATAATATTATATAT
1 TAAAGTATAATATTATATAT
* *
61979 TATAA-TA-ATATAATTATAACAA
1 TA-AAGTATA-AT-ATTAT-ATAT
62001 TAAAGTATAATATTATATTAT
1 TAAAGTATAATATTATA-TAT
62022 TAAAAGTATCAATA
1 T-AAAGTAT-AATA
62036 AATATAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
19 1 0.02
20 7 0.16
21 16 0.36
22 15 0.34
23 5 0.11
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (20 bp):
TAAAGTATAATATTATATAT
Found at i:66955 original size:21 final size:19
Alignment explanation
Indices: 66923--66961 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
66913 AATATAAATC
*
66923 TTAAAATTTTATTGAATTG
1 TTAAAATTTTATTAAATTG
66942 TTAAATATATTTATTAAATT
1 TTAAA-AT-TTTATTAAATT
66962 TACCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTAAAATTTTATTAAATTG
Found at i:70322 original size:6 final size:6
Alignment explanation
Indices: 70305--70341 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
70295 TGGAGAACGT
70305 GAAGGAG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG
1 GAAGG-G GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG
70342 AGCGAGTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:79655 original size:37 final size:38
Alignment explanation
Indices: 79600--79683 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
79590 TGGTAACCAA
79600 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
79637 CTTTGAAAAATA-GTTTTTCAAAGTTTTGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
79674 -GTTGAAAAAT
1 CTTTGAAAAAT
79684 GATAATGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.21
37 32 0.76
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:81188 original size:119 final size:118
Alignment explanation
Indices: 81054--81401 Score: 595
Period size: 119 Copynumber: 3.0 Consensus size: 118
81044 CTGTCCACGT
81054 TAAAAAAATAAATATCATTAATATTAACATAAAAATTAATACAATAATAATATTATAATGATAAT
1 TAAAAAAATAAATATCATTAATATTAACATAAAAATTAATACAATAATAATA-TATAATGATAAT
81119 TAGTTTTATTATAATTCAAACTCAACTGTTTAGAGTGATCAAAAACACCCATCA
65 TAGTTTTATTATAATTCAAACTCAACTGTTTAGAGTGATCAAAAACACCCATCA
**
81173 TAAAAAAATAAATATCATTAACGTTAACATAAAAATTAATACAATAATAATAATATAATGATAAT
1 TAAAAAAATAAATATCATTAATATTAACATAAAAATTAATACAATAATAAT-ATATAATGATAAT
*
81238 TAGTTTTATTATAATTCAAACTCAACTGTTTAGAGTGATCAAAAACACCTATCA
65 TAGTTTTATTATAATTCAAACTCAACTGTTTAGAGTGATCAAAAACACCCATCA
81292 TAAAAAAATAAATATCATTAATATTAACATAAAAATTAATAC------AATA-ATAATGATAATT
1 TAAAAAAATAAATATCATTAATATTAACATAAAAATTAATACAATAATAATATATAATGATAATT
81350 AGTTTTATTATAATTCAAACTCAACTGTTTAGAGTGATCAAAAACA-CCATCA
66 AGTTTTATTATAATTCAAACTCAACTGTTTAGAGTGATCAAAAACACCCATCA
81402 ATATGAGTGA
Statistics
Matches: 222, Mismatches: 6, Indels: 11
0.93 0.03 0.05
Matches are distributed among these distances:
110 5 0.02
111 58 0.26
112 1 0.00
113 3 0.01
119 154 0.69
120 1 0.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (118 bp):
TAAAAAAATAAATATCATTAATATTAACATAAAAATTAATACAATAATAATATATAATGATAATT
AGTTTTATTATAATTCAAACTCAACTGTTTAGAGTGATCAAAAACACCCATCA
Found at i:91599 original size:76 final size:75
Alignment explanation
Indices: 91491--91655 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 75
91481 TTAAACTCAA
*
91491 ATTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAAGAGGTTTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAAGAGG-TTTTAGTA
91556 TTTTAATTAAG
65 TTTTAATTAAG
* * * * *
91567 TTTTAGGATATTATTTT-TATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAAGAGGTTTTAGTA
*
91631 TTTTAATTAGG
65 TTTTAATTAAG
*
91642 ATTTAGAATATTAT
1 ATTTAGGATATTAT
91656 ATTGTTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 37 0.47
76 42 0.53
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAAGAGGTTTTAGTAT
TTTAATTAAG
Found at i:91860 original size:29 final size:30
Alignment explanation
Indices: 91789--91848 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
91779 CAATTTAAGG
91789 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
91820 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
91849 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:91982 original size:20 final size:21
Alignment explanation
Indices: 91938--92003 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
91928 TTCAAGATTG
* *
91938 CCCAGGGGGTATAGATTCCCCCC
1 CCCAGGGGGTACAGA-T-ACCCC
91961 CCCA-GGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
91981 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
92002 CC
1 CC
92004 TGCAGGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.20
21 19 0.47
22 9 0.22
23 4 0.10
ACGTcount: A:0.21, C:0.41, G:0.26, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:91982 original size:21 final size:22
Alignment explanation
Indices: 91938--92003 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
91928 TTCAAGATTG
* *
91938 CCCAGGGGGTATAGATTCCCCCC
1 CCCAGGGGGTACAGA-TACCCCC
91961 CCCA-GGGGTACAGATA-CCCC
1 CCCAGGGGGTACAGATACCCCC
91981 CCCAGGGGGTACAGATACCCCC
1 CCCAGGGGGTACAGATACCCCC
92003 C
1 C
92004 TGCAGGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.21
21 13 0.33
22 14 0.36
23 4 0.10
ACGTcount: A:0.21, C:0.41, G:0.26, T:0.12
Consensus pattern (22 bp):
CCCAGGGGGTACAGATACCCCC
Found at i:92120 original size:21 final size:21
Alignment explanation
Indices: 92094--92136 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
92084 ATTTGAATAT
*
92094 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
92115 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
92136 T
1 T
92137 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:92202 original size:20 final size:22
Alignment explanation
Indices: 92164--92203 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
92154 TTTGAGTATA
92164 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
92186 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
92204 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:95163 original size:29 final size:30
Alignment explanation
Indices: 95092--95151 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
95082 CAATTTAAGG
95092 CAAAATGGTTTTTGGACTTAAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTAAATTGAATTTA
*
95123 CAAAATGTTTTTGGAC-TCAATTGAATTTA
1 CAAAATGTTTTTGGACTTAAATTGAATTTA
95152 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 12 0.43
30 10 0.36
31 6 0.21
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTAAATTGAATTTA
Found at i:95278 original size:22 final size:23
Alignment explanation
Indices: 95241--95283 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
95231 TTCAAGATTG
* *
95241 CCCAGGGGGTATAGATTCCCCCC
1 CCCAGGGGGTACAGATACCCCCC
95264 CCCA-GGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
95284 GGGTACAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.21, C:0.40, G:0.26, T:0.14
Consensus pattern (23 bp):
CCCAGGGGGTACAGATACCCCCC
Found at i:95289 original size:15 final size:15
Alignment explanation
Indices: 95269--95298 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
95259 CCCCCCCCAG
95269 GGGTACAGATACCCC
1 GGGTACAGATACCCC
95284 GGGTACAGATACCCC
1 GGGTACAGATACCCC
95299 CTGCAGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:95417 original size:21 final size:21
Alignment explanation
Indices: 95391--95433 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
95381 ATTTGAATAT
*
95391 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
95412 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
95433 T
1 T
95434 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:95754 original size:34 final size:32
Alignment explanation
Indices: 95715--95784 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
95705 TTTTGTAAAG
* *
95715 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
95749 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
95781 GGGA
1 GGGA
95785 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:96687 original size:9 final size:9
Alignment explanation
Indices: 96675--96705 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
96665 ATATTTATTA
96675 TATTATTTT
1 TATTATTTT
96684 TATTATTTT
1 TATTATTTT
96693 TATTATTTT
1 TATTATTTT
96702 TATT
1 TATT
96706 TTAATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TATTATTTT
Found at i:96687 original size:18 final size:18
Alignment explanation
Indices: 96666--96718 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
96656 TTACTATTAA
96666 TATTTATTATATTATTTT
1 TATTTATTATATTATTTT
*
96684 TA-TTATTTTTATTATTTT
1 TATTTA-TTATATTATTTT
*
96702 TATTT-TAATA-TATTTT
1 TATTTATTATATTATTTT
96718 T
1 T
96719 TCAACTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 7 0.23
17 6 0.20
18 15 0.50
19 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTATTATATTATTTT
Found at i:96695 original size:15 final size:15
Alignment explanation
Indices: 96677--96718 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
96667 ATTTATTATA
96677 TTATT-TTTATTATTT
1 TTATTATTT-TTATTT
96692 TTATTATTTTTATTT
1 TTATTATTTTTATTT
*
96707 TAATATATTTTT
1 TTAT-TATTTTT
96719 TCAACTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTATTTTTATTT
Found at i:96698 original size:23 final size:25
Alignment explanation
Indices: 96668--96718 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
96658 ACTATTAATA
*
96668 TTTATTA-TATTATTTTTAT-TATT
1 TTTATTATTATTATTTTAATATATT
*
96691 TTTATTATTTTTATTTTAATATATT
1 TTTATTATTATTATTTTAATATATT
96716 TTT
1 TTT
96719 TCAACTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.29
24 10 0.42
25 7 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTATTATTATTATTTTAATATATT
Found at i:98329 original size:15 final size:15
Alignment explanation
Indices: 98309--98342 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
98299 CCAGCAGAAA
98309 AAGACGCACATCAGG
1 AAGACGCACATCAGG
98324 AAGACGCACATCAGG
1 AAGACGCACATCAGG
98339 AAGA
1 AAGA
98343 ACAAGAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.24, G:0.26, T:0.06
Consensus pattern (15 bp):
AAGACGCACATCAGG
Found at i:102276 original size:20 final size:21
Alignment explanation
Indices: 102244--102283 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
102234 CATTTCGTTA
102244 TATTTTTGTTTTTATTTTTTT
1 TATTTTTGTTTTTATTTTTTT
102265 TATTTTTG-TTTTATTTTTT
1 TATTTTTGTTTTTATTTTTT
102284 AGCGAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.10, C:0.00, G:0.05, T:0.85
Consensus pattern (21 bp):
TATTTTTGTTTTTATTTTTTT
Found at i:104315 original size:65 final size:70
Alignment explanation
Indices: 104154--104346 Score: 200
Period size: 65 Copynumber: 2.7 Consensus size: 70
104144 AACATTATAT
** * *
104154 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAAGATATTATTTT
1 TTTATCTAGGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAAGATTT---ATATTATTAT
104219 TATATTTTATC
62 TATA-TTTA-C
** *
104230 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTATTTTA-TATTATA
1 TTTATCTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTATATTATTATTATA
104294 -TTA-
66 TTTAC
* *
104297 TTT-T-TAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 TTTATCTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTTA
104347 ATATGTTTTA
Statistics
Matches: 109, Mismatches: 7, Indels: 13
0.84 0.05 0.10
Matches are distributed among these distances:
64 5 0.05
65 36 0.33
66 1 0.01
67 3 0.03
69 3 0.03
71 6 0.06
72 5 0.05
75 22 0.20
76 28 0.26
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (70 bp):
TTTATCTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTATATTATTATTATA
TTTAC
Found at i:104366 original size:65 final size:65
Alignment explanation
Indices: 104239--104374 Score: 168
Period size: 65 Copynumber: 2.1 Consensus size: 65
104229 CTTTATCTTT
* * *
104239 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTATTTTATATTATATTATTTTTAG
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAATATATATTAGATTATTTTTAG
* * * * * *
104304 GTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTAATATGTTTTAGCTTGTTTTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTTAATATATATTAGATTATTTTTA
104368 G
65 G
104369 G-ATTTT
1 GTATTTT
104375 GAAGGCTATA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 10 0.16
65 51 0.84
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (65 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAATATATATTAGATTATTTTTAG
Found at i:105034 original size:16 final size:16
Alignment explanation
Indices: 104995--105046 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
104985 CCCTTTTATA
104995 TTTATTACTATTAATATTT
1 TTTATTA-TATT-AT-TTT
*
105014 ATTATTATATTATTTT
1 TTTATTATATTATTTT
105030 TTTATT-TATTTATTTT
1 TTTATTATA-TTATTTT
105046 T
1 T
105047 AATATATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.07
16 16 0.53
17 2 0.07
18 4 0.13
19 6 0.20
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATTATATTATTTT
Found at i:110146 original size:18 final size:19
Alignment explanation
Indices: 110105--110147 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
110095 TATCTTTCAA
110105 CTTTTCTCTCTCTACGTCT
1 CTTTTCTCTCTCTACGTCT
110124 C-TTTCTCTCTC-AC-TCAT
1 CTTTTCTCTCTCTACGTC-T
110141 CTTTTCT
1 CTTTTCT
110148 ATCTAGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.09
17 4 0.18
18 15 0.68
19 1 0.05
ACGTcount: A:0.07, C:0.37, G:0.02, T:0.53
Consensus pattern (19 bp):
CTTTTCTCTCTCTACGTCT
Found at i:121676 original size:13 final size:13
Alignment explanation
Indices: 121628--121681 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
121618 AAGTTCGTTC
* *
121628 TTTTCTTTTCAAG
1 TTTTATTTTTAAG
121641 TTTTCATTTTT-A-
1 TTTT-ATTTTTAAG
121653 TTTTA-TTTTAAG
1 TTTTATTTTTAAG
121665 TTTTATTTTTAAG
1 TTTTATTTTTAAG
121678 TTTT
1 TTTT
121682 TAAGTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 4 0.11
11 2 0.06
12 9 0.26
13 16 0.46
14 4 0.11
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.70
Consensus pattern (13 bp):
TTTTATTTTTAAG
Found at i:121684 original size:21 final size:22
Alignment explanation
Indices: 121658--121702 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
121648 TTTTATTTTA
121658 TTTTAAGTTTTATTT-TTAAGT
1 TTTTAAGTTTTATTTGTTAAGT
*
121679 TTTTAAGTTTTATTTGTTATGT
1 TTTTAAGTTTTATTTGTTAAGT
121701 TT
1 TT
121703 AACTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (22 bp):
TTTTAAGTTTTATTTGTTAAGT
Found at i:128830 original size:3 final size:3
Alignment explanation
Indices: 128824--128891 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
128814 ATTTTTTATT
* * *
128824 TAA TAA TAA TAA TAA TAA TAC TAA TAT TAA TAA AAA TTAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
* *
128869 TAA -AA CAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
128892 AAAAATTAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 4 0.07
3 48 0.89
4 2 0.04
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:128880 original size:20 final size:20
Alignment explanation
Indices: 128824--128893 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
128814 ATTTTTTATT
* * *
128824 TAATAATAATAATAATAATAC
1 TAATAATAA-AACAAAAATAA
* * *
128845 TAATATTAATA-AAAATTAA
1 TAATAATAAAACAAAAATAA
128864 -AATAATAAAACAAAAATAA
1 TAATAATAAAACAAAAATAA
128883 TAATAATAAAA
1 TAATAATAAAA
128894 AAATTAATGT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 8 0.21
19 12 0.31
20 11 0.28
21 8 0.21
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
TAATAATAAAACAAAAATAA
Found at i:129172 original size:76 final size:76
Alignment explanation
Indices: 129065--129954 Score: 1575
Period size: 76 Copynumber: 11.7 Consensus size: 76
129055 AAACATAAAA
* * *
129065 AAAAAACTCCTGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
*
129130 TTAAAAACATC
66 TTGAAAACATC
*
129141 AAAAAGCTCCCGAAGGCTTTTTGGAAGCATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
129206 TTGAAAACATC
66 TTGAAAACATC
*
129217 AAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
129282 TTGAAAACATC
66 TTGAAAACATC
*
129293 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCT
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
129358 TTGAAAACATC
66 TTGAAAACATC
* * *
129369 AAAAAGATCCCGAAGGCTTTTTGGAAGCATCATGCACTGAAGGACTTACAGATGACCCTAAGGCT
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
129434 TTGAAAACATC
66 TTGAAAACATC
* *
129445 AAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCT
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
129510 TTGAAAACATC
66 TTGAAAACATC
* *
129521 AAAAAGATCCCGAAGGCTTTTTGGAAGCATCATGCACTGAAGGACTTACAGATGACCCGAA-GCT
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
129585 TCTGAAAACATC
66 T-TGAAAACATC
*
129597 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCT
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
129662 TTGAAAACATC
66 TTGAAAACATC
*
129673 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCT
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
129738 TTGAAAACATC
66 TTGAAAACATC
* * *
129749 AAAAAGCTCACGAAGGATTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCT
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
129814 TTGAAAACATC
66 TTGAAAACATC
*
129825 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCT
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
129890 TTGAAAACATC
66 TTGAAAACATC
*
129901 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
129955 TGAGAAATAG
Statistics
Matches: 785, Mismatches: 27, Indels: 4
0.96 0.03 0.00
Matches are distributed among these distances:
75 4 0.01
76 777 0.99
77 4 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCT
TTGAAAACATC
Found at i:133475 original size:81 final size:81
Alignment explanation
Indices: 133285--133576 Score: 523
Period size: 81 Copynumber: 3.6 Consensus size: 81
133275 GGTTTTATAT
* *
133285 CAAACCAAATCAGATAACTCAAAGAACACTTTCAGAAGATGCTATGATCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATC--TCAAA
133350 TTCAATGATTGGTTTTAC
64 TTCAATGATTGGTTTTAC
133368 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTCAAATT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTCAAATT
133433 CAATGATTGGTTTTAC
66 CAATGATTGGTTTTAC
*
133449 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTCAAATT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTCAAATT
133514 CAATGATTGGTTTTAC
66 CAATGATTGGTTTTAC
*
133530 CAAACCAGATCATATAACTC-AAGAACACTTCCAGAAGATGCTATGAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAT
133577 ATATGCATTT
Statistics
Matches: 204, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
80 26 0.13
81 122 0.60
83 56 0.27
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (81 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGATCACATTCATCTCAAATT
CAATGATTGGTTTTAC
Done.