Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004439.1 Hibiscus syriacus cultivar Beakdansim tig00009739_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: 55881
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1223 original size:24 final size:25
Alignment explanation
Indices: 1179--1225 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1169 CGGTACTTTA
* *
1179 TATAGTCACCAAAATATAAGTACTT
1 TATACTCACAAAAATATAAGTACTT
1204 TATACTCACAAAAATA-AAGTAC
1 TATACTCACAAAAATATAAGTAC
1226 CGCAGCAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (25 bp):
TATACTCACAAAAATATAAGTACTT
Found at i:8342 original size:20 final size:20
Alignment explanation
Indices: 8317--8430 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
8307 AATTGGGAAA
*
8317 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
8337 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
8357 ATCGAAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
8378 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
8398 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
8418 TTCGCAACGCGAT
1 ATCGCAACGCGAT
8431 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 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:8430 original size:61 final size:61
Alignment explanation
Indices: 8314--8430 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
8304 GCGAATTGGG
* * * * *
8314 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGAAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGAAACGCGATAATAC
* * * *
8375 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGAAACGCGAT
8431 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGAAACGCGATAATAC
Found at i:9032 original size:19 final size:19
Alignment explanation
Indices: 8987--9026 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
8977 GAGAGAATCA
*
8987 CAACGCGAAATAAAAAACG
1 CAACGCGAAACAAAAAACG
*
9006 CAACGCGAAACAAAAATCG
1 CAACGCGAAACAAAAAACG
9025 CA
1 CA
9027 TTGCGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.25, G:0.15, T:0.05
Consensus pattern (19 bp):
CAACGCGAAACAAAAAACG
Found at i:9044 original size:19 final size:19
Alignment explanation
Indices: 9022--9186 Score: 136
Period size: 19 Copynumber: 9.1 Consensus size: 19
9012 GAAACAAAAA
*
9022 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
9041 TCGCGTTGCGATTTT-ATT
1 TCGCGTTGCGATTTTCATT
9059 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
9079 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
9095 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
9112 TCGCGTTGCGA--TTC-TA
1 TCGCGTTGCGATTTTCATT
**
9128 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
9145 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
9165 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
9185 TC
1 TC
9187 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 13, Indels: 28
0.74 0.08 0.17
Matches are distributed among these distances:
14 18 0.15
15 1 0.01
16 5 0.04
17 5 0.04
18 8 0.07
19 44 0.37
20 37 0.31
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:9111 original size:33 final size:33
Alignment explanation
Indices: 9074--9160 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
9064 GTTGCGATTT
* * *
9074 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTATCGTCGCGATAG
*
9107 TCATTTCGCGTTGCGATTCTATCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTATCGTCGCGATAG
9140 TCATTTCCGCGTTGCGATTCT
1 TCATTT-CGCGTTGCGATTCT
9161 CATTATCTCG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTATCGTCGCGATAG
Found at i:9163 original size:20 final size:20
Alignment explanation
Indices: 9129--9186 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
9119 GCGATTCTAT
**
9129 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
9149 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
9169 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
9187 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:11235 original size:21 final size:21
Alignment explanation
Indices: 11211--11277 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
11201 TCATTCATCG
11211 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
11232 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
11253 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
11274 AGAG
1 AGAG
11278 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:11235 original size:42 final size:42
Alignment explanation
Indices: 11168--11277 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
11158 TTCATCCCTC
* * * * *
11168 AAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCATCG
1 AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCA-TCATCG
* * *
11211 -AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCGTTG
1 AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCATCG
*
11252 AAGAGGT-CCCTCCCACCATTCAAGAG
1 AAGA-GTCCCCTCCCACCGTTCAAGAG
11278 CCCGATTCAC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.07
42 50 0.89
43 2 0.04
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.22
Consensus pattern (42 bp):
AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCATCG
Found at i:12578 original size:14 final size:14
Alignment explanation
Indices: 12559--12594 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
12549 ATTGTTTAAT
12559 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
12573 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
12587 TGATTTGT
1 TGATTTGT
12595 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:12819 original size:33 final size:32
Alignment explanation
Indices: 12777--12903 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
12767 ATTAAATTCA
12777 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
12810 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
12843 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
12876 CGTTGCGATTTTCATTTCGTATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
12904 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:12871 original size:66 final size:66
Alignment explanation
Indices: 12777--12902 Score: 225
Period size: 66 Copynumber: 1.9 Consensus size: 66
12767 ATTAAATTCA
*
12777 CGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTA
1 CGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTA
12842 G
66 G
* *
12843 CGTTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGTATTGCGA
1 CGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGA
12903 TAGTAATTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (66 bp):
CGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTA
G
Found at i:15203 original size:12 final size:12
Alignment explanation
Indices: 15186--15210 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15176 TCTTCGGGGA
15186 CTTTTTCTTCTT
1 CTTTTTCTTCTT
15198 CTTTTTCTTCTT
1 CTTTTTCTTCTT
15210 C
1 C
15211 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:16439 original size:20 final size:20
Alignment explanation
Indices: 16414--16471 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
16404 ATTCATTTGA
*
16414 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
16434 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGAGAAAATGG
16454 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
16472 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:16513 original size:14 final size:14
Alignment explanation
Indices: 16494--16547 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
16484 TGAAATCGCA
16494 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
16508 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
16525 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
16541 TTGCGAT
1 TTGCGAT
16548 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:16526 original size:33 final size:33
Alignment explanation
Indices: 16489--16566 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
16479 CGAAATGAAA
***
16489 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
16522 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
16555 TCGCGTTGCGAT
1 TCGCATTGCGAT
16567 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:16673 original size:14 final size:14
Alignment explanation
Indices: 16654--16690 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
16644 CATCGATTAA
16654 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
16668 ACAAATCATCTTTT
1 ACAAATCAACATTT
16682 ACAAATCAA
1 ACAAATCAA
16691 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:18586 original size:20 final size:19
Alignment explanation
Indices: 18551--18617 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
18541 GAAACTTAAA
18551 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
18570 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
18590 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
18609 ATCGCAACG
1 ATCGCAACG
18618 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:18625 original size:14 final size:14
Alignment explanation
Indices: 18606--18663 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
18596 ATGCGAAATG
18606 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
18620 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
18636 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
18652 AAAATCGCAACG
1 AAAATCGCAACG
18664 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:18648 original size:32 final size:33
Alignment explanation
Indices: 18590--18668 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
18580 GGAAATGGCT
*
18590 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
18623 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
18655 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
18669 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:18725 original size:32 final size:33
Alignment explanation
Indices: 18683--18770 Score: 160
Period size: 32 Copynumber: 2.7 Consensus size: 33
18673 AATCGCATTA
18683 CGATTTTCATTTCGCGTTGCGATTTTGTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTTTGTCGTTG
18716 CGA-TTTCATTTCGCGTTGCGATTTTGTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTTTGTCGTTG
*
18748 CGATTTTCATTTCGCATTGCGAT
1 CGATTTTCATTTCGCGTTGCGAT
18771 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
32 32 0.60
33 21 0.40
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTTTGTCGTTG
Found at i:18769 original size:19 final size:17
Alignment explanation
Indices: 18687--18770 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 17
18677 GCATTACGAT
18687 TTTCATTTCGCGTTGCGA
1 TTTCATTTCGC-TTGCGA
*
18705 TTT--TGTCG-TTGCGA
1 TTTCATTTCGCTTGCGA
18719 TTTCATTTCGCGTTGCGA
1 TTTCATTTCGC-TTGCGA
*
18737 TTT--TGTCG-TTGCGA
1 TTTCATTTCGCTTGCGA
18751 TTTTCATTTCGCATTGCGA
1 -TTTCATTTCGC-TTGCGA
18770 T
1 T
18771 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
14 15 0.28
15 3 0.06
16 12 0.23
17 4 0.08
18 13 0.25
19 6 0.11
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.48
Consensus pattern (17 bp):
TTTCATTTCGCTTGCGA
Found at i:18789 original size:20 final size:19
Alignment explanation
Indices: 18755--18809 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
18745 TTGCGATTTT
*
18755 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
18774 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
18794 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
18810 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:19315 original size:18 final size:18
Alignment explanation
Indices: 19289--19333 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
19279 GTCGATCAGA
*
19289 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
19307 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
19325 TGATGGCTC
1 TGATGGCTC
19334 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:20678 original size:20 final size:20
Alignment explanation
Indices: 20653--20726 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
20643 AATAGTTTCT
*
20653 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
20673 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
20693 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
20713 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
20727 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:21207 original size:20 final size:20
Alignment explanation
Indices: 21181--21294 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
21171 GATTATGTAT
21181 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
21201 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
21221 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
21241 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
21262 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
21282 TATCGCATTGCGA
1 TATCGCGTTGCGA
21295 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.79
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:21298 original size:41 final size:41
Alignment explanation
Indices: 21161--21296 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
21151 CGCTTTGAAA
*
21161 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
21202 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
21242 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
21283 ATCGCATTGCGATT
1 ATCGCATTGCGATT
21297 TTCCCAATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 42 0.54
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:21314 original size:41 final size:41
Alignment explanation
Indices: 21161--21316 Score: 109
Period size: 41 Copynumber: 3.8 Consensus size: 41
21151 CGCTTTGAAA
* ** * * * *
21161 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* *** * *
21202 ATCGCGTTGCGAAAGT-CAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* * ** * * *
21242 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
21283 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
21317 TTACTTATTC
Statistics
Matches: 90, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
40 32 0.36
41 56 0.62
42 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
Found at i:30026 original size:35 final size:35
Alignment explanation
Indices: 29980--30055 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
29970 AAAACAGTCC
* *
29980 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * *
30015 TCAATTTCATTCTCAACCCTAAATTCCAAAATAGT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
30050 TCAATT
1 TCAATT
30056 AAATTCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:30607 original size:130 final size:130
Alignment explanation
Indices: 30454--30701 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
30444 TATTTATATA
* ** *
30454 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
30519 TTAGCACATGATCATGACACGTGTCATTGGTGACGCATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
*
30584 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGTATCTGACATATG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* * *
30649 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
30702 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:30732 original size:130 final size:129
Alignment explanation
Indices: 30468--30732 Score: 282
Period size: 130 Copynumber: 2.0 Consensus size: 129
30458 ATTTGGTCCT
* ** * *
30468 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * *** * * **** *
30533 TGACACGTGTCATTGGTGACGCATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
30598 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGTATCTGACATATGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * * *
30663 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
30727 -A
128 CA
30728 AAATT
1 AAATT
30733 TGGGTCTTGG
Statistics
Matches: 110, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
130 97 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:31067 original size:30 final size:27
Alignment explanation
Indices: 31043--31093 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
31033 ATTTTAAAAG
31043 AATAAATTTAAGATTTATATATTTTAA
1 AATAAATTTAAGATTTATATATTTTAA
* *
31070 ACTAAATTTAATATTTATAT-TTTT
1 AATAAATTTAAGATTTATATATTTT
31094 CATATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
AATAAATTTAAGATTTATATATTTTAA
Found at i:31193 original size:16 final size:18
Alignment explanation
Indices: 31172--31205 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
31162 ATTTCTTATT
31172 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
31188 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
31206 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:43888 original size:229 final size:227
Alignment explanation
Indices: 43487--43929 Score: 771
Period size: 229 Copynumber: 1.9 Consensus size: 227
43477 TATCTATCCA
* *
43487 TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGTTAATAT
1 TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAATAT
*
43552 TGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTA
66 TGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTTTGTGTA
*
43617 AATGAAATTATTAAATTAATATTGTAGGTGGAAAATATGAAACACTATTAAAAAAATTAAAACAT
131 AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTAAAACAT
43682 AAATTACATAACTTTCAAAAAAATATATATCAT
196 AAATTACATAACTTT-AAAAAAATATATATCAT
*
43715 TTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGGTTAATA
1 TTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAGTTAATA
*
43780 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAATTTTGTG
65 TTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-ATTTTGTG
* * *
43844 TAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTGAAAC
129 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTAAAAC
43909 ATAAATTACATAACTTTAAAA
194 ATAAATTACATAACTTTAAAA
43930 GCAGTTTTAA
Statistics
Matches: 204, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
228 37 0.18
229 167 0.82
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (227 bp):
TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAATAT
TGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTTTGTGTA
AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTAAAACAT
AAATTACATAACTTTAAAAAAATATATATCAT
Found at i:44018 original size:20 final size:19
Alignment explanation
Indices: 43995--44040 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
43985 CGATATACCA
43995 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
44015 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
44035 GGTAAA
1 GGTAAA
44041 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:44185 original size:29 final size:29
Alignment explanation
Indices: 44152--44211 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
44142 CGATCCACAA
44152 CGATATAACAGGTAAAAATATGATAAAAC
1 CGATATAACAGGTAAAAATATGATAAAAC
44181 CGATATAACAGGTAAAAATATGATAAAAC
1 CGATATAACAGGTAAAAATATGATAAAAC
44210 CG
1 CG
44212 GTAACAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.53, C:0.12, G:0.15, T:0.20
Consensus pattern (29 bp):
CGATATAACAGGTAAAAATATGATAAAAC
Found at i:44214 original size:20 final size:19
Alignment explanation
Indices: 44191--44237 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
44181 CGATATAACA
44191 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
44211 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
44231 GGTAAAA
1 GGTAAAA
44238 TGATACAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:44239 original size:17 final size:18
Alignment explanation
Indices: 44195--44242 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
44185 ATAACAGGTA
44195 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
44214 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
44234 -AAAATGATA
1 AAAAATGATA
44243 CAGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:46517 original size:21 final size:21
Alignment explanation
Indices: 46470--46534 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
46460 AAGACAATCA
* *
46470 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
46492 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
46512 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
46533 AG
1 AG
46535 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:46610 original size:33 final size:33
Alignment explanation
Indices: 46568--46633 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
46558 AAATAGATGG
*
46568 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
46601 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
46634 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:48449 original size:19 final size:19
Alignment explanation
Indices: 48425--48473 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
48415 AATGTCGACT
48425 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
48444 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
48463 TATTTTTGTAT
1 TAATTTTGTAT
48474 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:48936 original size:198 final size:198
Alignment explanation
Indices: 48592--50205 Score: 3176
Period size: 198 Copynumber: 8.1 Consensus size: 198
48582 CAATATGGCC
* *
48592 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
48657 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
48722 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
48787 TGGA
195 TGGA
48791 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
48856 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
48921 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
48986 GGA
196 GGA
*
48989 AACAAGGTGCACTCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
49054 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
49119 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
49184 GGA
196 GGA
49187 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
49252 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
49317 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
49382 GGA
196 GGA
49385 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
49450 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
49515 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
49580 GGA
196 GGA
49583 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
49648 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
49713 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
49778 GGA
196 GGA
49781 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
49846 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
49911 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
49976 GGA
196 GGA
49979 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
50043 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
50108 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
50173 GGAA
196 GG-A
50177 AACAAGGTGCACCCATAAAGTGTCGATCC
1 AACAAGGTGCACCCATAAAGTGTCGATCC
50206 CAAAATCATC
Statistics
Matches: 1410, Mismatches: 4, Indels: 3
1.00 0.00 0.00
Matches are distributed among these distances:
197 161 0.11
198 1215 0.86
199 34 0.02
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGA
Found at i:51811 original size:3 final size:3
Alignment explanation
Indices: 51803--51877 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
51793 TGAAGCTGAC
* * * ** * *
51803 GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
51851 GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
51878 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:53278 original size:87 final size:86
Alignment explanation
Indices: 53131--53310 Score: 290
Period size: 87 Copynumber: 2.1 Consensus size: 86
53121 AAATGTGTCG
53131 ATACCATTTAAAAAAGTGTCGATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAAT
1 ATACCATTTAAAAAAGTGTCGATT--AAAAACATCGGAACCCAGATTTATAATGTAATAGATAAT
*
53196 TTTGTAATATAACCGGTATAAAT
64 TTTGTAATATAACCGGTATAAAA
* *
53219 ATACCATTTAAAAAAGTGTCGACATT-TACACATCGGAACCCAGATTTATAATGTAATAGATAAT
1 ATACCATTTAAAAAAGTGTCG--ATTAAAAACATCGGAACCCAGATTTATAATGTAATAGATAAT
53283 TTTGTAATATAACCGGTATAAAA
64 TTTGTAATATAACCGGTATAAAA
53306 ATACC
1 ATACC
53311 GGTTTTATGA
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
87 63 0.72
88 21 0.24
90 3 0.03
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (86 bp):
ATACCATTTAAAAAAGTGTCGATTAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTT
TGTAATATAACCGGTATAAAA
Found at i:53519 original size:22 final size:23
Alignment explanation
Indices: 53486--53528 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
53476 AACCGGTATA
53486 AAAATGTGTCGATACCTTTTTAT
1 AAAATGTGTCGATACCTTTTTAT
*
53509 AAAA-GTGTCGATACTTTTTT
1 AAAATGTGTCGATACCTTTTT
53529 CACTGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (23 bp):
AAAATGTGTCGATACCTTTTTAT
Done.