Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001043.1 Hibiscus syriacus cultivar Beakdansim tig00002071_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: 144579
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:510 original size:28 final size:29
Alignment explanation
Indices: 451--512 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
441 GATTATTATT
* *
451 TTTTAATAACAGTTAATAATGTTTATTCA
1 TTTTAATAACAATTAATAATGTATATTCA
*
480 TTTTAATAA-AATTAA-AATGTAATATTTA
1 TTTTAATAACAATTAATAATGT-ATATTCA
508 TTTTA
1 TTTTA
513 TATTTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 15 0.52
29 9 0.31
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (29 bp):
TTTTAATAACAATTAATAATGTATATTCA
Found at i:601 original size:20 final size:20
Alignment explanation
Indices: 577--633 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
567 AGCTTACATT
577 ATTTTTTTTTTTTTTTTT-C
1 ATTTTTTTTTTTTTTTTTGC
** *
596 ATTTTTAATTTTTTTATTGC
1 ATTTTTTTTTTTTTTTTTGC
616 ATTTTTATTTATTTTTTT
1 ATTTTT-TTT-TTTTTTT
634 AAAAAATGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 15 0.52
20 7 0.24
21 1 0.03
22 6 0.21
ACGTcount: A:0.14, C:0.04, G:0.02, T:0.81
Consensus pattern (20 bp):
ATTTTTTTTTTTTTTTTTGC
Found at i:1269 original size:20 final size:21
Alignment explanation
Indices: 1244--1282 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1234 ATAATATTGA
1244 AAGTGAGAAT-ATCGATACAC
1 AAGTGAGAATGATCGATACAC
*
1264 AAGTGATAATGATCGATAC
1 AAGTGAGAATGATCGATAC
1283 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.23
Consensus pattern (21 bp):
AAGTGAGAATGATCGATACAC
Found at i:1545 original size:71 final size:73
Alignment explanation
Indices: 1393--1558 Score: 176
Period size: 71 Copynumber: 2.3 Consensus size: 73
1383 TAATAATAGT
* * * * * *
1393 ATCGATACTTTTAAATATCGAAAAAGTTGAAGATAAGATCGAAAGTTAAGATATCGATACTTATG
1 ATCGATACTTTTAAAAATTGAAAAAGTTGAAGATAAGATCAAAACTCAAGATATCCATACTTATG
1458 CGATAATG
66 CGATAATG
* * * *
1466 ATGGATACTTTTAAAAATTGAAAACGTTGATA-A-AATATCAAAACTCAA-ATATCCATACTTTT
1 ATCGATACTTTTAAAAATTGAAAAAGTTGA-AGATAAGATCAAAACTCAAGATATCCATACTTAT
* *
1528 TCGATGATG
65 GCGATAATG
* *
1537 ATCGATACTTTTAGACATTGAA
1 ATCGATACTTTTAAAAATTGAA
1559 CAAGATGATA
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
71 38 0.49
72 11 0.14
73 27 0.35
74 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (73 bp):
ATCGATACTTTTAAAAATTGAAAAAGTTGAAGATAAGATCAAAACTCAAGATATCCATACTTATG
CGATAATG
Found at i:4581 original size:24 final size:22
Alignment explanation
Indices: 4541--4617 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
4531 ATGCAATTAA
4541 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
4560 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
4583 ATGCATCGATACACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
4604 TGCATCGATGCACT
1 TGCATCGATGCACT
4618 TCAAGGGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:6188 original size:23 final size:23
Alignment explanation
Indices: 6162--6224 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
6152 AACCTTATAT
* *
6162 GGCACTTCGTTGCATTTTTATGC
1 GGCACTTCGGTGCATTTCTATGC
* *
6185 GGCACTACGGTGCAATTCTATGC
1 GGCACTTCGGTGCATTTCTATGC
6208 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
6225 ATACGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTATGC
Found at i:7170 original size:32 final size:32
Alignment explanation
Indices: 7102--7216 Score: 162
Period size: 31 Copynumber: 3.7 Consensus size: 32
7092 ATGACCTATT
* *
7102 CATATGTTCCGAAGAACATAGGTAA-CCTGTC
1 CATATGTCCCGAAGGACATAGGTAATCCTGTC
7133 CATATGTCCCGAAGGACATAGGTAATCCTGTC
1 CATATGTCCCGAAGGACATAGGTAATCCTGTC
* **
7165 TATATGTCCTAAAGGACATAGGTAAT-CTGTC
1 CATATGTCCCGAAGGACATAGGTAATCCTGTC
*
7196 CATATGTCCCCAAGGACATAG
1 CATATGTCCCGAAGGACATAG
7217 TAAACCCTCG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
31 46 0.61
32 29 0.39
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (32 bp):
CATATGTCCCGAAGGACATAGGTAATCCTGTC
Found at i:11890 original size:11 final size:11
Alignment explanation
Indices: 11869--11915 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
11859 CATTTAAATC
*
11869 TTTTTTAAATAC
1 TTTTTT-AATAA
11881 TTTTTTAAT-A
1 TTTTTTAATAA
11891 -TTTTTAATAA
1 TTTTTTAATAA
*
11901 ATTTTTAATAA
1 TTTTTTAATAA
11912 TTTT
1 TTTT
11916 CAAACGATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 8 0.26
10 1 0.03
11 16 0.52
12 6 0.19
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTTTAATAA
Found at i:11894 original size:20 final size:21
Alignment explanation
Indices: 11871--11915 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
11861 TTTAAATCTT
**
11871 TTTTAAATACTTTTTTAAT-A
1 TTTTAAATAAATTTTTAATAA
*
11891 TTTTTAATAAATTTTTAATAA
1 TTTTAAATAAATTTTTAATAA
11912 TTTT
1 TTTT
11916 CAAACGATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAAATAAATTTTTAATAA
Found at i:12480 original size:18 final size:19
Alignment explanation
Indices: 12459--12502 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
12449 TTATTTTAAA
*
12459 ATAATTATATA-TTTTTTT
1 ATAATTATAAATTTTTTTT
*
12477 ATAATTTTTAAATTTTTTTT
1 ATAA-TTATAAATTTTTTTT
12497 ATAATT
1 ATAATT
12503 TTAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 7 0.32
20 11 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATAATTATAAATTTTTTTT
Found at i:15263 original size:20 final size:22
Alignment explanation
Indices: 15238--15289 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 22
15228 ATCAAACGTG
15238 ATATTTGT-T-TCACTCGTATT
1 ATATTTGTGTGTCACTCGTATT
15258 ATATTTGGTGGGTGTCACTCGTATT
1 ATATTT-GT--GTGTCACTCGTATT
15283 ATATTTG
1 ATATTTG
15290 GTGGGAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 6 0.22
21 2 0.07
24 2 0.07
25 17 0.63
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (22 bp):
ATATTTGTGTGTCACTCGTATT
Found at i:15281 original size:25 final size:25
Alignment explanation
Indices: 15247--15294 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
15237 GATATTTGTT
15247 TCACTCGTATTATATTTGGTGGGTG
1 TCACTCGTATTATATTTGGTGGGTG
15272 TCACTCGTATTATATTTGGTGGG
1 TCACTCGTATTATATTTGGTGGG
15295 AGTTACTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.17, C:0.12, G:0.27, T:0.44
Consensus pattern (25 bp):
TCACTCGTATTATATTTGGTGGGTG
Found at i:15302 original size:25 final size:25
Alignment explanation
Indices: 15247--15302 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
15237 GATATTTGTT
*
15247 TCACTCGTATTATATTTGGTGGGTG
1 TCACTCGTATTATATTTGGTGGGAG
15272 TCACTCGTATTATATTTGGTGGGAG
1 TCACTCGTATTATATTTGGTGGGAG
*
15297 TTACTC
1 TCACTC
15303 CTCTAACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (25 bp):
TCACTCGTATTATATTTGGTGGGAG
Found at i:16191 original size:20 final size:20
Alignment explanation
Indices: 16166--16203 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16156 CATATGTTAA
*
16166 AGAATGCATCGATGCACTGT
1 AGAATGCACCGATGCACTGT
*
16186 AGAATGTACCGATGCACT
1 AGAATGCACCGATGCACT
16204 TTAATGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCACCGATGCACTGT
Found at i:16600 original size:19 final size:20
Alignment explanation
Indices: 16576--16613 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16566 CTATGTTATG
16576 ATGAT-ATAAACCATATGAT
1 ATGATAATAAACCATATGAT
*
16595 ATGATAATAAATCATATGA
1 ATGATAATAAACCATATGA
16614 ATATAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (20 bp):
ATGATAATAAACCATATGAT
Found at i:17657 original size:23 final size:23
Alignment explanation
Indices: 17589--17643 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
17579 ACATCTTATA
17589 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
17612 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
17635 TGGCACTTC
1 TGGCACTTC
17644 AGTGTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:19292 original size:15 final size:15
Alignment explanation
Indices: 19269--19316 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
19259 TGAGACATTA
19269 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
*
19284 CCCGTCCCGCATCCG
1 CCCGCCCCGCATCCG
*
19299 CCCGCCCCACATCCG
1 CCCGCCCCGCATCCG
19314 CCC
1 CCC
19317 ACCCAGCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.08, C:0.67, G:0.17, T:0.08
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:22382 original size:50 final size:50
Alignment explanation
Indices: 22328--22450 Score: 156
Period size: 50 Copynumber: 2.5 Consensus size: 50
22318 GCAGTAAAGA
* * *
22328 GCGCCCCCTGAACTGCGCTATATGCTGATTTGGCACCACGTGGGTATAGC
1 GCGCCCCCTGAACCGCGCTATACGCTGATCTGGCACCACGTGGGTATAGC
* ** * * *
22378 GCGCCCTCTGTCCCGCGATATACGGTGATCTGGCGCCACGTGGGTATAGC
1 GCGCCCCCTGAACCGCGCTATACGCTGATCTGGCACCACGTGGGTATAGC
*
22428 GCGCCCCCTGATCCGCGCTATAC
1 GCGCCCCCTGAACCGCGCTATAC
22451 CTGGGTATCT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.22
Consensus pattern (50 bp):
GCGCCCCCTGAACCGCGCTATACGCTGATCTGGCACCACGTGGGTATAGC
Found at i:22930 original size:111 final size:111
Alignment explanation
Indices: 22736--23060 Score: 589
Period size: 111 Copynumber: 2.9 Consensus size: 111
22726 ATATATCTCT
*
22736 ACACTTTGCTGATACGGTAACATTTTAGA-GTTTTAATTTAATTTAAATTATTAGTAATATTTAG
1 ACACTTTGCTGATACGGTAACATTTTA-ACGTTTTAATTTAATTTAAATTATTAGTAATAATTAG
22800 TTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATAACTCG
65 TTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATAACTCG
22847 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
22912 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATAACTCG
22958 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
* * *
23023 TGATTTATTTAATGCATGATTTTTAGAGTAGGAATTAA
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
23061 TTTTTGTAAT
Statistics
Matches: 208, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
110 1 0.00
111 207 1.00
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (111 bp):
ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATAACTCG
Found at i:24564 original size:51 final size:50
Alignment explanation
Indices: 24459--24578 Score: 118
Period size: 51 Copynumber: 2.4 Consensus size: 50
24449 CTACGTGGCG
* **
24459 TATAGCGCGG-AGCAGGGGGCGCTCTACACCCCACGTGTAACCCAATCAGTA
1 TATAGCGCGGTA-CAGGGGGCGCACTACACCCCACGTG-AACCCAATCAACA
* *
24510 TATAGCGCGGTACAGGGGGCGCACTATACTCCACGTG-ACGCCAAATCAACA
1 TATAGCGCGGTACAGGGGGCGCACTACACCCCACGTGAAC-CC-AATCAACA
* * *
24561 TATAACGCGATTCAGGGG
1 TATAGCGCGGTACAGGGG
24579 ACAAGCTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
49 2 0.03
50 2 0.03
51 53 0.91
52 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (50 bp):
TATAGCGCGGTACAGGGGGCGCACTACACCCCACGTGAACCCAATCAACA
Found at i:31532 original size:37 final size:37
Alignment explanation
Indices: 31482--31554 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
31472 GTTAACTACC
31482 CTTTCATATTTGGATAGGACTCAAACTTGAGTGTTAT
1 CTTTCATATTTGGATAGGACTCAAACTTGAGTGTTAT
* * *
31519 CTTTCATATTTGGATCGGAGTCAAACTTGGGTGTTA
1 CTTTCATATTTGGATAGGACTCAAACTTGAGTGTTA
31555 CAAGCTACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.40
Consensus pattern (37 bp):
CTTTCATATTTGGATAGGACTCAAACTTGAGTGTTAT
Found at i:32216 original size:202 final size:202
Alignment explanation
Indices: 31863--32272 Score: 777
Period size: 202 Copynumber: 2.0 Consensus size: 202
31853 TTGGTTAGTT
31863 ACATATTTTATTAATAGTGCCTAGCTGAAATTTTATTCAAGTCTACCCCCATTCAAAAAATTTGT
1 ACATATTTTATTAATAGTGCCTAGCTGAAATTTTATTCAAGTCTACCCCCATTCAAAAAATTTGT
*
31928 ATTGCTGACATATGTGTTTCCAGCCTAAAAAATATTTATGTATCTTTCACTGCTTTTTCCTGCTC
66 ATTGCTGACATATGTGTTTCCAGCCTAAAAAATATTTATGTATCTTTCACTACTTTTTCCTGCTC
31993 TTCTCGTTCCTCATCTTCCATAATATTCACTTGCCTTACCTTACATCGATAAGCATGACTAAATT
131 TTCTCGTTCCTCATCTTCCATAATATTCACTTGCCTTACCTTACATCGATAAGCATGACTAAATT
32058 TCTCTCC
196 TCTCTCC
32065 ACATATATTTATTAATAGTGCCTAGCTGAAATTTTATTCAAGTCTA-CCCCATTCAAAAAATTTG
1 ACATAT-TTTATTAATAGTGCCTAGCTGAAATTTTATTCAAGTCTACCCCCATTCAAAAAATTTG
* *
32129 TATTGTTGACATATGTGTTTCCAGCCTAAAAAATATTTCTGTATCTTTCACTACTTTTTCCTGCT
65 TATTGCTGACATATGTGTTTCCAGCCTAAAAAATATTTATGTATCTTTCACTACTTTTTCCTGCT
32194 CTTCTCGTTCCTCATCTTCCATAATATTCACTTGCCTTACCTTACATCGATAAGCATGACTAAAT
130 CTTCTCGTTCCTCATCTTCCATAATATTCACTTGCCTTACCTTACATCGATAAGCATGACTAAAT
32259 TTCTCTCC
195 TTCTCTCC
32267 ACATAT
1 ACATAT
32273 GAAACAAAGG
Statistics
Matches: 204, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
202 165 0.81
203 39 0.19
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.40
Consensus pattern (202 bp):
ACATATTTTATTAATAGTGCCTAGCTGAAATTTTATTCAAGTCTACCCCCATTCAAAAAATTTGT
ATTGCTGACATATGTGTTTCCAGCCTAAAAAATATTTATGTATCTTTCACTACTTTTTCCTGCTC
TTCTCGTTCCTCATCTTCCATAATATTCACTTGCCTTACCTTACATCGATAAGCATGACTAAATT
TCTCTCC
Found at i:33666 original size:3 final size:3
Alignment explanation
Indices: 33658--33684 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
33648 CCACGTTTCT
33658 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
33685 ACTCTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:34252 original size:22 final size:21
Alignment explanation
Indices: 34208--34248 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34198 ATGGAAACAT
*
34208 TTTTCATTTTTACTTTGTTTG
1 TTTTCAGTTTTACTTTGTTTG
34229 TTTTCAGTTTT-CTTTTGTTT
1 TTTTCAGTTTTAC-TTTGTTT
34249 TGTTGAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.07, C:0.10, G:0.10, T:0.73
Consensus pattern (21 bp):
TTTTCAGTTTTACTTTGTTTG
Found at i:34658 original size:41 final size:41
Alignment explanation
Indices: 34613--34773 Score: 205
Period size: 41 Copynumber: 3.9 Consensus size: 41
34603 CATTTGTGTT
* * * * *
34613 TACAAACGCCACTAAAGACTTATACTTTAGTGGCGTTTTTC
1 TACAAACGCCGCTATAGACTTGTACTTTAGTGGCGTTTATA
* *
34654 TACAAAAGCCGCTATAGACTGGTACTTTAGTGGCGTTTATA
1 TACAAACGCCGCTATAGACTTGTACTTTAGTGGCGTTTATA
* **
34695 TACAAACGCCGCTATACACTTGTACTTTAGTGATGTTTATA
1 TACAAACGCCGCTATAGACTTGTACTTTAGTGGCGTTTATA
** *
34736 TACGTACACCGCTATAGACTTGTACTTTAGTGGCGTTT
1 TACAAACGCCGCTATAGACTTGTACTTTAGTGGCGTTT
34774 GTAAACACAA
Statistics
Matches: 102, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 102 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (41 bp):
TACAAACGCCGCTATAGACTTGTACTTTAGTGGCGTTTATA
Found at i:36360 original size:38 final size:37
Alignment explanation
Indices: 36305--36385 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 37
36295 CAAAATTAGA
*
36305 ACTGAAAAATATATGTTCCCTGATTCATTTGTTTATTTT
1 ACTG-AAAATATATGTTCCCTGATTCA-TTATTTATTTT
*
36344 ACTGAAAATATTTGTTCCCTGATTCATTATTTATTTT
1 ACTGAAAATATATGTTCCCTGATTCATTATTTATTTT
36381 ACTGA
1 ACTGA
36386 TCATGAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 15 0.38
38 21 0.52
39 4 0.10
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (37 bp):
ACTGAAAATATATGTTCCCTGATTCATTATTTATTTT
Found at i:41827 original size:9 final size:9
Alignment explanation
Indices: 41813--41856 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
41803 CCAATTTTTT
41813 TTTTTAAAA
1 TTTTTAAAA
41822 TTTTTAAAA
1 TTTTTAAAA
*
41831 TTATATAAAA
1 TT-TTTAAAA
* *
41841 ATTGTAAAA
1 TTTTTAAAA
41850 TTTTTAA
1 TTTTTAA
41857 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:43021 original size:43 final size:42
Alignment explanation
Indices: 42960--43269 Score: 241
Period size: 43 Copynumber: 7.3 Consensus size: 42
42950 ATCATGAGCT
* *
42960 CTTTTGCGGCGTTTATTCCGAAAATGTCGCTATAGATCTCGAC
1 CTTTTGCGGCGTTTATTCC-AAAATGCCGCTATAGATATCGAC
* * * * *
43003 CTTTTACGTCGATTATTCCAAAATCACCGCTATAGAT-TTGAC
1 CTTTTGCGGCGTTTATTCCAAAAT-GCCGCTATAGATATCGAC
* ** * *
43045 ATTTTGCGGCGTTT-TTGGAAACA--CCGCTATATATCTCGAC
1 CTTTTGCGGCGTTTATTCCAAA-ATGCCGCTATAGATATCGAC
* * *
43085 CTTTTGCGACGTTTGTTCCTAAAATGCCGCTATAGATATCGAA
1 CTTTTGCGGCGTTTATTCC-AAAATGCCGCTATAGATATCGAC
* * *
43128 CTTTTGCGGGGTTTGTTCCAAAACGCCGCTATAGATATCGAC
1 CTTTTGCGGCGTTTATTCCAAAATGCCGCTATAGATATCGAC
* * * * *
43170 CTTTTGAGGCATTTGTTCCAAAAACGCCGCGATAGATATCGAC
1 CTTTTGCGGCGTTTATTCC-AAAATGCCGCTATAGATATCGAC
* * * * * * * *
43213 CTTTTACAGCGTTTGTTCTAAAAATGCCACAATAGATCTTGAC
1 CTTTTGCGGCGTTTATTC-CAAAATGCCGCTATAGATATCGAC
* *
43256 CTATTGCGACGTTT
1 CTTTTGCGGCGTTT
43270 TTTGTTCTCA
Statistics
Matches: 215, Mismatches: 43, Indels: 18
0.78 0.16 0.07
Matches are distributed among these distances:
39 10 0.05
40 16 0.07
41 8 0.04
42 60 0.28
43 121 0.56
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (42 bp):
CTTTTGCGGCGTTTATTCCAAAATGCCGCTATAGATATCGAC
Found at i:43171 original size:85 final size:84
Alignment explanation
Indices: 42960--43269 Score: 277
Period size: 85 Copynumber: 3.7 Consensus size: 84
42950 ATCATGAGCT
* * * * * * *
42960 CTTTTGCGGCGTTTATTCCGAAAATGTCGCTATAGATCTCGACCTTTTACGTCGATTATTCCAAA
1 CTTTTGCGGCGTTTGTTCC-AAAACGCCGCTATAGATCTCGACCTTTTGCGACGTTTGTTCCAAA
* *
43025 ATCACCGCTATAGAT-TTG-A
65 AT-GCCGCTATAGATATCGAA
** * *
43044 CATTTTGCGGCGTTT-TT-GGAAACACCGCTATATATCTCGACCTTTTGCGACGTTTGTTCCTAA
1 C-TTTTGCGGCGTTTGTTCCAAAACGCCGCTATAGATCTCGACCTTTTGCGACGTTTGTTCC-AA
43107 AATGCCGCTATAGATATCGAA
64 AATGCCGCTATAGATATCGAA
* * * * *
43128 CTTTTGCGGGGTTTGTTCCAAAACGCCGCTATAGATATCGACCTTTTGAGGCATTTGTTCCAAAA
1 CTTTTGCGGCGTTTGTTCCAAAACGCCGCTATAGATCTCGACCTTTTGCGACGTTTGTTCC-AAA
* * *
43193 ACGCCGCGATAGATATCGAC
65 ATGCCGCTATAGATATCGAA
* * * * * * * *
43213 CTTTTACAGCGTTTGTTCTAAAAATGCCACAATAGATCTTGACCTATTGCGACGTTT
1 CTTTTGCGGCGTTTGTTC-CAAAACGCCGCTATAGATCTCGACCTTTTGCGACGTTT
43270 TTTGTTCTCA
Statistics
Matches: 181, Mismatches: 38, Indels: 12
0.78 0.16 0.05
Matches are distributed among these distances:
82 44 0.24
83 19 0.10
84 7 0.04
85 83 0.46
86 28 0.15
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (84 bp):
CTTTTGCGGCGTTTGTTCCAAAACGCCGCTATAGATCTCGACCTTTTGCGACGTTTGTTCCAAAA
TGCCGCTATAGATATCGAA
Found at i:46456 original size:21 final size:18
Alignment explanation
Indices: 46432--46479 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 18
46422 TAATTTTAGT
46432 TTTTAAAATTTCAAATATAAA
1 TTTTAAAATTT---ATATAAA
46453 TTTTAAAATTTATATAAA
1 TTTTAAAATTTATATAAA
46471 TTTATAAAA
1 TTT-TAAAA
46480 GAATCAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.38
19 5 0.19
21 11 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTAAAATTTATATAAA
Found at i:49708 original size:19 final size:20
Alignment explanation
Indices: 49670--49713 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
49660 ATATTTTTAA
* *
49670 ATTAAGTTAATAATAAATAT
1 ATTAACTTAATAACAAATAT
49690 ATTAACTTAA-AACAAATAT
1 ATTAACTTAATAACAAATAT
49709 ATTAA
1 ATTAA
49714 AATTAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (20 bp):
ATTAACTTAATAACAAATAT
Found at i:49721 original size:20 final size:19
Alignment explanation
Indices: 49670--49721 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
49660 ATATTTTTAA
* *
49670 ATTAAGTTAATAATAAATAT
1 ATTAAATTAA-AACAAATAT
*
49690 ATTAACTTAAAACAAATAT
1 ATTAAATTAAAACAAATAT
49709 ATTAAAATTAAAA
1 ATT-AAATTAAAA
49722 TCAGTCCTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
ATTAAATTAAAACAAATAT
Found at i:52262 original size:16 final size:17
Alignment explanation
Indices: 52241--52313 Score: 80
Period size: 16 Copynumber: 4.4 Consensus size: 17
52231 TAAGAGTCTC
52241 AGGGGTGACACTT-TTG
1 AGGGGTGACACTTGTTG
*
52257 AGGGGTGGCACTT-TTG
1 AGGGGTGACACTTGTTG
*
52273 AGGAGTGACACTTGGATT-
1 AGGGGTGACACTT-G-TTG
*
52291 AGGGGTGACACTTGTGG
1 AGGGGTGACACTTGTTG
52308 AGGGGT
1 AGGGGT
52314 TGCTTGGGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
16 27 0.56
17 7 0.15
18 12 0.25
19 2 0.04
ACGTcount: A:0.19, C:0.11, G:0.42, T:0.27
Consensus pattern (17 bp):
AGGGGTGACACTTGTTG
Found at i:52362 original size:49 final size:49
Alignment explanation
Indices: 52307--52401 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
52297 GACACTTGTG
** *
52307 GAGGGGTTGCTTGGGATATCCAGAGCACCATGGAGGTCCACCCCTGGAT
1 GAGGGGTTGCCCGGGATACCCAGAGCACCATGGAGGTCCACCCCTGGAT
* * * *
52356 GAGGGGTTGCCCGGGATACCCTGGGCTCCATGGAGGTCCGCCCCTG
1 GAGGGGTTGCCCGGGATACCCAGAGCACCATGGAGGTCCACCCCTG
52402 TAGGCAACTC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.16, C:0.28, G:0.37, T:0.19
Consensus pattern (49 bp):
GAGGGGTTGCCCGGGATACCCAGAGCACCATGGAGGTCCACCCCTGGAT
Found at i:53138 original size:59 final size:59
Alignment explanation
Indices: 52977--53140 Score: 147
Period size: 60 Copynumber: 2.7 Consensus size: 59
52967 AATTTGAGGC
* * * **
52977 TGAAATTGGAATATTCAAAAGTTT-GAAATCTAATTTAGAAA-GAGGGTCATAGTTTAGGGA
1 TGAAATTGAAATATT-AAAATTTTAAAAATC-AATTTA-AAATGAGGGTCATAGCCTAGGGA
* * * * * *
53037 TGAAATTAGAAAT-TTTAATTATTTAAGGACTC-ATTTAGAATGAGGGTCATAGCCTGGGGA
1 TGAAATT-GAAATATTAAAAT-TTTAA-AAATCAATTTAAAATGAGGGTCATAGCCTAGGGA
53097 TGAAATTGAAATATTAAAATTTTAAAAATCAATTTAAAATGAGG
1 TGAAATTGAAATATTAAAATTTTAAAAATCAATTTAAAATGAGG
53141 ATTATAGTTT
Statistics
Matches: 81, Mismatches: 16, Indels: 15
0.72 0.14 0.13
Matches are distributed among these distances:
58 3 0.04
59 26 0.32
60 45 0.56
61 4 0.05
62 3 0.04
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.33
Consensus pattern (59 bp):
TGAAATTGAAATATTAAAATTTTAAAAATCAATTTAAAATGAGGGTCATAGCCTAGGGA
Found at i:56058 original size:29 final size:29
Alignment explanation
Indices: 56015--56083 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
56005 CGATCAACAA
*
56015 TCAAAGTCAACTGGTGGTCAACGGTTAGG
1 TCAAAGTCAACTGGTGGTCAACAGTTAGG
* * *
56044 TTAAAGTTAATTGGTGGTCAACAGTTAGG
1 TCAAAGTCAACTGGTGGTCAACAGTTAGG
56073 TCAAAGTCAAC
1 TCAAAGTCAAC
56084 GGTTTGGTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (29 bp):
TCAAAGTCAACTGGTGGTCAACAGTTAGG
Found at i:56081 original size:18 final size:18
Alignment explanation
Indices: 56060--56100 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
56050 TTAATTGGTG
56060 GTCAACAGTTAGGTCAAA
1 GTCAACAGTTAGGTCAAA
* * *
56078 GTCAACGGTTTGGTCAAT
1 GTCAACAGTTAGGTCAAA
56096 GTCAA
1 GTCAA
56101 TAGGTCAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (18 bp):
GTCAACAGTTAGGTCAAA
Found at i:65623 original size:17 final size:17
Alignment explanation
Indices: 65603--65637 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
65593 AACAAAAACA
65603 AAAACAAAAATAAAAAT
1 AAAACAAAAATAAAAAT
*
65620 AAAATAAAAATAAAAAT
1 AAAACAAAAATAAAAAT
65637 A
1 A
65638 TAGCAGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAACAAAAATAAAAAT
Found at i:65629 original size:6 final size:6
Alignment explanation
Indices: 65596--65637 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
65586 CTGACGAAAC
* *
65596 AAAAAC AAAAAC AAAAAT AAAAAT -AAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
65638 TAGCAGAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.83, C:0.05, G:0.00, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:65629 original size:11 final size:11
Alignment explanation
Indices: 65609--65634 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
65599 AACAAAAACA
65609 AAAATAAAAAT
1 AAAATAAAAAT
65620 AAAATAAAAAT
1 AAAATAAAAAT
65631 AAAA
1 AAAA
65635 ATATAGCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:68275 original size:21 final size:21
Alignment explanation
Indices: 68249--68296 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
68239 ACCCATTTGC
68249 TATCTGAAATTGGATATATAA
1 TATCTGAAATTGGATATATAA
68270 TATCTGAAATTGGATATATAA
1 TATCTGAAATTGGATATATAA
68291 TATCTG
1 TATCTG
68297 CATCTAGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (21 bp):
TATCTGAAATTGGATATATAA
Found at i:71152 original size:18 final size:19
Alignment explanation
Indices: 71126--71166 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
71116 ATTTAAGTAG
*
71126 TAAAGAAAAACGA-TTAAA
1 TAAAGAAAAACAATTTAAA
*
71144 TAAATAAAAACAATTTAAA
1 TAAAGAAAAACAATTTAAA
71163 TAAA
1 TAAA
71167 AATAAGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (19 bp):
TAAAGAAAAACAATTTAAA
Found at i:73453 original size:45 final size:45
Alignment explanation
Indices: 73362--73569 Score: 201
Period size: 45 Copynumber: 4.7 Consensus size: 45
73352 CATCTTTTAG
* * * * *
73362 GTTGATAATGCACTCATATGCATTTCAAC-GT-ATAT--TTTTAT
1 GTTGATAATGTACCCATATACATTTCAACTCTAATATACTTTTCT
* * *
73403 GTTGATGATGTACCCCTATACATCTCAAC-CATAATATACTTTTCT
1 GTTGATAATGTACCCATATACATTTCAACTC-TAATATACTTTTCT
**
73448 GTTGATAATGTACCCATATACATTTCAACTCTAGCATACTTTTCT
1 GTTGATAATGTACCCATATACATTTCAACTCTAATATACTTTTCT
* * * ** * *
73493 GTTGATAATGCACCCATATGCATTTCAACGCTAGCATGCTTTTTT
1 GTTGATAATGTACCCATATACATTTCAACTCTAATATACTTTTCT
* *
73538 GTTGATAATGCACCCATATGCATTTCAACTCT
1 GTTGATAATGTACCCATATACATTTCAACTCT
73570 GACATCCTTT
Statistics
Matches: 143, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
41 23 0.16
42 1 0.01
43 4 0.03
45 114 0.80
46 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.39
Consensus pattern (45 bp):
GTTGATAATGTACCCATATACATTTCAACTCTAATATACTTTTCT
Found at i:73543 original size:90 final size:90
Alignment explanation
Indices: 73441--73685 Score: 237
Period size: 79 Copynumber: 2.8 Consensus size: 90
73431 CCATAATATA
* * ***
73441 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCT-AGCATACTTTTC-TGTTGATAATGC
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTCTGA-CAT-CCTTTCATGCCAATAATGC
73504 ACCCATATGCATTTCAACGCTAGCATG
64 ACCCATATGCATTTCAACGCTAGCATG
* *
73531 CTTTTTTGTTGATAATGCACCCATATGCATTTCAACTCTGACATCCTTTCATGCCAATAATGCAC
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTCTGACATCCTTTCATGCCAATAATGCAC
**
73596 CCATATGCA-TT--A-TTTA--A--
66 CCATATGCATTTCAACGCTAGCATG
* * * * * *
73613 ---TTATGTTGATAATGTACCCATATACATTTCATCTATGGCATCATTTCATGCCAATAATGCAC
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTCTGACATCCTTTCATGCCAATAATGCAC
*
73675 ACATATGCATT
66 CCATATGCATT
73686 ATTCTTTTAC
Statistics
Matches: 135, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
79 63 0.47
80 1 0.01
84 1 0.01
86 2 0.01
87 1 0.01
89 7 0.05
90 59 0.44
91 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (90 bp):
CTTTTCTGTTGATAATGCACCCATATACATTTCAACTCTGACATCCTTTCATGCCAATAATGCAC
CCATATGCATTTCAACGCTAGCATG
Found at i:73591 original size:45 final size:44
Alignment explanation
Indices: 73443--73606 Score: 204
Period size: 45 Copynumber: 3.7 Consensus size: 44
73433 ATAATATACT
* * *
73443 TTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATACT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCAT-CC
* *
73488 TTTCTGTTGATAATGCACCCATATGCATTTCAACGCTAGCATGCT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCAT-CC
*
73533 TTTTTGTTGATAATGCACCCATATGCATTTCAACTCT-GACATCC
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAG-CATCC
***
73577 TTTCATGCCAATAATGCACCCATATGCATT
1 TTTC-TGTTGATAATGCACCCATATGCATT
73607 ATTTAATTAT
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
44 5 0.05
45 101 0.95
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (44 bp):
TTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCC
Found at i:73668 original size:79 final size:79
Alignment explanation
Indices: 73537--73688 Score: 241
Period size: 79 Copynumber: 1.9 Consensus size: 79
73527 CATGCTTTTT
* * * *
73537 TGTTGATAATGCACCCATATGCATTTCAACTCTGACATCCTTTCATGCCAATAATGCACCCATAT
1 TGTTGATAATGCACCCATATACATTTCAACTATGACATCATTTCATGCCAATAATGCACACATAT
73602 GCATTATTTAATTA
66 GCATTATTTAATTA
* * *
73616 TGTTGATAATGTACCCATATACATTTCATCTATGGCATCATTTCATGCCAATAATGCACACATAT
1 TGTTGATAATGCACCCATATACATTTCAACTATGACATCATTTCATGCCAATAATGCACACATAT
73681 GCATTATT
66 GCATTATT
73689 CTTTTACGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (79 bp):
TGTTGATAATGCACCCATATACATTTCAACTATGACATCATTTCATGCCAATAATGCACACATAT
GCATTATTTAATTA
Found at i:74146 original size:19 final size:20
Alignment explanation
Indices: 74102--74151 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
74092 GGCCCTTAGA
74102 TATCGATACCCCTACTTATGG
1 TATCGATACCCC-ACTTATGG
74123 TATCGATACCCC-CTTCAT-G
1 TATCGATACCCCACTT-ATGG
74142 TATCGATACC
1 TATCGATACC
74152 AGAATTAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 14 0.50
20 2 0.07
21 12 0.43
ACGTcount: A:0.24, C:0.32, G:0.12, T:0.32
Consensus pattern (20 bp):
TATCGATACCCCACTTATGG
Found at i:74243 original size:19 final size:20
Alignment explanation
Indices: 74193--74246 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
74183 ACCCTCACCA
74193 AGGTATTGATACCCCTATGCTTT
1 AGGTATTGATACCCC--T-CTTT
*
74216 -GGTACTGATACCCC-CTTT
1 AGGTATTGATACCCCTCTTT
74234 AGGTATTGATACC
1 AGGTATTGATACC
74247 TATAATAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 4 0.14
19 11 0.39
22 13 0.46
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (20 bp):
AGGTATTGATACCCCTCTTT
Found at i:78655 original size:19 final size:20
Alignment explanation
Indices: 78617--78660 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
78607 ATACTTTTAA
* *
78617 ATTAAGTTAATAATAAATAT
1 ATTAACTTAATAACAAATAT
78637 ATTAACTTAA-AACAAATAT
1 ATTAACTTAATAACAAATAT
78656 ATTAA
1 ATTAA
78661 AATTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (20 bp):
ATTAACTTAATAACAAATAT
Found at i:78668 original size:20 final size:19
Alignment explanation
Indices: 78617--78668 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
78607 ATACTTTTAA
* *
78617 ATTAAGTTAATAATAAATAT
1 ATTAAATTAA-AACAAATAT
*
78637 ATTAACTTAAAACAAATAT
1 ATTAAATTAAAACAAATAT
78656 ATTAAAATTAAAA
1 ATT-AAATTAAAA
78669 TTAGTCCTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
ATTAAATTAAAACAAATAT
Found at i:80205 original size:20 final size:20
Alignment explanation
Indices: 80182--80289 Score: 144
Period size: 20 Copynumber: 5.4 Consensus size: 20
80172 TGCGATTTTC
* *
80182 CAAATTCGCAACACAGATGT
1 CAAATTCGCAACACAAAAGT
** *
80202 CAAATTCGCAACATGATAGT
1 CAAATTCGCAACACAAAAGT
*
80222 CAAATCCGCAACACAAAAGT
1 CAAATTCGCAACACAAAAGT
*
80242 TAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACAAAAGT
*
80262 CAAATTCGCAACACAAAGGT
1 CAAATTCGCAACACAAAAGT
80282 CAAATTCG
1 CAAATTCG
80290 ACGTCTTGGT
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.44, C:0.24, G:0.13, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACACAAAAGT
Found at i:81433 original size:69 final size:68
Alignment explanation
Indices: 81360--81536 Score: 240
Period size: 68 Copynumber: 2.6 Consensus size: 68
81350 TGGGATACAT
81360 TTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAA-TTGATGAGGAAATAA
1 TTTTTTGCTTGTTTAATTGAATTTGT--A---AAAGTTGATTTGTTTAATTTGATGAGGAAATAA
81423 G-A-ATTA
61 GAATATTA
* *
81429 TTTTTTGCTTGTTTAATTG-ATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAA-T
81493 ATTA
65 ATTA
81497 TTTTTTGCTTGTTTAATTG-ATTTGTAAAAGTTGATTTGTT
1 TTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTT
81537 GTTTTAAGAA
Statistics
Matches: 101, Mismatches: 2, Indels: 11
0.89 0.02 0.10
Matches are distributed among these distances:
64 17 0.17
65 14 0.14
66 1 0.01
67 1 0.01
68 48 0.48
69 20 0.20
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (68 bp):
TTTTTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATA
TTA
Found at i:81660 original size:20 final size:20
Alignment explanation
Indices: 81612--81660 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
81602 CGCGAAATAA
*
81612 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGAAAGTCAAATTC
***
81632 GCAACGCGAAAGTCAAATTC
1 GCGTTGCGAAAGTCAAATTC
81652 GCGTTGCGA
1 GCGTTGCGA
81661 TTTTCGGTTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (20 bp):
GCGTTGCGAAAGTCAAATTC
Found at i:81733 original size:20 final size:19
Alignment explanation
Indices: 81708--81758 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
81698 CGCAACACTT
*
81708 ATTTCGCGTTGCGAATTTGA
1 ATTTCGCGTTGCAAATTT-A
*
81728 ATTTCGCATTGCAAATTTA
1 ATTTCGCGTTGCAAATTTA
81747 ACTTTCGCGTTG
1 A-TTTCGCGTTG
81759 ATCGCAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (19 bp):
ATTTCGCGTTGCAAATTTA
Found at i:85337 original size:19 final size:18
Alignment explanation
Indices: 85294--85340 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
85284 AAAAACATTT
85294 GTGTTGCGAAATTAAAAC
1 GTGTTGCGAAATTAAAAC
* *
85312 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAATTAAA-AC
85331 GTGTTGCGAA
1 GTGTTGCGAA
85341 TTCGAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (18 bp):
GTGTTGCGAAATTAAAAC
Found at i:85342 original size:18 final size:19
Alignment explanation
Indices: 85313--85403 Score: 69
Period size: 20 Copynumber: 4.6 Consensus size: 19
85303 AATTAAAACC
85313 TGTTGCGAAATT-AAATTCG
1 TGTTGCG-AATTGAAATTCG
*
85332 TGTTGCGAATTCGAAAATC-
1 TGTTGCGAATT-GAAATTCG
85351 TAGTTGCGAATTTGAAATTCTG
1 T-GTTGCGAA-TTGAAATTC-G
* ** *
85373 CGTTGCGAATTTGACTTTTG
1 TGTTGCGAA-TTGAAATTCG
85393 TGTTGCGAATT
1 TGTTGCGAATT
85404 TGACTTCTGT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.07
19 10 0.17
20 28 0.47
21 17 0.29
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (19 bp):
TGTTGCGAATTGAAATTCG
Found at i:85399 original size:20 final size:20
Alignment explanation
Indices: 85353--85420 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
85343 CGAAAATCTA
* *
85353 GTTGCGAATTTGAAATTCTGC
1 GTTGCGAATTTG-ACTTCTGT
*
85374 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
85394 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
85414 GTTGCGA
1 GTTGCGA
85421 TTTACAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 31 0.72
21 12 0.28
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:85525 original size:20 final size:21
Alignment explanation
Indices: 85472--85525 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
85462 TGATTTACAG
85472 ATTCGCGTTGCGAAATTGAAA
1 ATTCGCGTTGCGAAATTGAAA
* * *
85493 ATT-GGGTTACGAAATTG-GA
1 ATTCGCGTTGCGAAATTGAAA
*
85512 GTTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
85526 TTTGTTGGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 3 0.12
20 20 0.77
21 3 0.12
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTGAAA
Found at i:89878 original size:19 final size:18
Alignment explanation
Indices: 89836--89879 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
89826 GTCAACTGGT
89836 AGGTCAACGGTTAAGTCA
1 AGGTCAACGGTTAAGTCA
* **
89854 AAGTCAACGGTTTGGGTCA
1 AGGTCAACGG-TTAAGTCA
89873 AGGTCAA
1 AGGTCAA
89880 TAGGTCAGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGTCAACGGTTAAGTCA
Found at i:91703 original size:13 final size:13
Alignment explanation
Indices: 91685--91710 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
91675 GCATAAATCA
91685 TTTGGTGTTTTGG
1 TTTGGTGTTTTGG
91698 TTTGGTGTTTTGG
1 TTTGGTGTTTTGG
91711 AAAACGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (13 bp):
TTTGGTGTTTTGG
Found at i:94839 original size:17 final size:17
Alignment explanation
Indices: 94817--94849 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
94807 TGTGAATGAT
94817 TAAAATA-AATTGATTGG
1 TAAAATATAA-TGATTGG
94834 TAAAATATAATGATTG
1 TAAAATATAATGATTG
94850 CCTTATCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
TAAAATATAATGATTGG
Found at i:101085 original size:21 final size:21
Alignment explanation
Indices: 101061--101101 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
101051 AAATTTAAAA
101061 CATTCATCAT-TATACGTTTAC
1 CATTCA-CATATATACGTTTAC
*
101082 CATTTACATATATACGTTTA
1 CATTCACATATATACGTTTA
101102 AAACATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.44
Consensus pattern (21 bp):
CATTCACATATATACGTTTAC
Found at i:107368 original size:22 final size:21
Alignment explanation
Indices: 107343--107385 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
107333 ATTGTCATAG
*
107343 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGA-TACCCTGCTACA
*
107365 GGGAACTGATACCCTGCTACA
1 GGGAACCGATACCCTGCTACA
107386 ATACTGCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.19
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTACA
Found at i:107467 original size:2 final size:2
Alignment explanation
Indices: 107460--107490 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
107450 GTTTACCATT
107460 TA 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 TA T
107491 GTTTAAAACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:112003 original size:75 final size:74
Alignment explanation
Indices: 111911--112195 Score: 365
Period size: 75 Copynumber: 3.8 Consensus size: 74
111901 ATAGGTTTTA
* * * * * * **
111911 TCTCTCTTGAGATAGTTTCACTTGAAACGAA-AGATTTTATCTCACTTGAGATTGTTTTTCTTAA
1 TCTCGCTTGAGACAGTTTTACTTGAAA-GAAGACATTTCATTTCACTCAAGATTGTTTTTCTTAA
*
111975 AACATACTTTG
65 AACA-AATTTG
*
111986 TCTCGCTTGAGACAGTTTTACTCGAAAGAAGACATTTCATTTCACTCAAGATTGTTTTTCTTAAA
1 TCTCGCTTGAGACAGTTTTACTTGAAAGAAGACATTTCATTTCACTCAAGATTGTTTTTCTTAAA
112051 ACAAATTTTG
66 ACAAA-TTTG
*
112061 TCTCGCTTGAGACAGTTTTACTTGAAAGAAGACATTTCATTTCACGCAAGATTGTTTTTCTTAAA
1 TCTCGCTTGAGACAGTTTTACTTGAAAGAAGACATTTCATTTCACTCAAGATTGTTTTTCTTAAA
112126 ACAAGATTTG
66 ACAA-ATTTG
** * * * *
112136 TCTCGCTTGAGACAGTTTTTACTCAAAAGAAAACATTTCACTTCACTCAATAGTGTTTTT
1 TCTCGCTTGAGACAG-TTTTACTTGAAAGAAGACATTTCATTTCACTCAAGATTGTTTTT
112196 AAAGAAGATT
Statistics
Matches: 187, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
74 4 0.02
75 145 0.78
76 38 0.20
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (74 bp):
TCTCGCTTGAGACAGTTTTACTTGAAAGAAGACATTTCATTTCACTCAAGATTGTTTTTCTTAAA
ACAAATTTG
Found at i:112079 original size:36 final size:37
Alignment explanation
Indices: 111944--112155 Score: 98
Period size: 36 Copynumber: 5.7 Consensus size: 37
111934 GAAACGAAAG
* * **
111944 ATTTTATCTCACTTGAGATTGTTTTTCTTAAAACATAC
1 ATTTTGTCTCGCTTGAGACAGTTTTTCTTAAAACA-AC
* *
111982 --TTTGTCTCGCTTGAGACAGTTTTACTCGAAAGA-AGAC
1 ATTTTGTCTCGCTTGAGACAGTTTTTCT-TAAA-ACA-AC
** * * ** **
112019 ATTTCATTTCACTCAAGATTGTTTTTCTTAAAACAA-
1 ATTTTGTCTCGCTTGAGACAGTTTTTCTTAAAACAAC
*
112055 ATTTTGTCTCGCTTGAGACAGTTTTACTTGAAAGA-AGAC
1 ATTTTGTCTCGCTTGAGACAGTTTTTCTT-AAA-ACA-AC
* * * ** *
112094 ATTTCATTTCACGC--AAGATTGTTTTTCTTAAAACAAG
1 ATTT--TGTCTCGCTTGAGACAGTTTTTCTTAAAACAAC
112131 A-TTTGTCTCGCTTGAGACAGTTTTT
1 ATTTTGTCTCGCTTGAGACAGTTTTT
112156 ACTCAAAAGA
Statistics
Matches: 122, Mismatches: 38, Indels: 30
0.64 0.20 0.16
Matches are distributed among these distances:
34 6 0.05
36 52 0.43
37 15 0.12
38 11 0.09
39 32 0.26
41 6 0.05
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (37 bp):
ATTTTGTCTCGCTTGAGACAGTTTTTCTTAAAACAAC
Found at i:112241 original size:150 final size:152
Alignment explanation
Indices: 111909--112242 Score: 398
Period size: 150 Copynumber: 2.2 Consensus size: 152
111899 AAATAGGTTT
* * * ***
111909 TATCTCTCTTGAGATAGTTTCACTTGAAAC-GAA-AGATTTTATCTCACTTGAGATTGTTTTTCT
1 TATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGACATTTCATCTCACGCAAGATTGTTTTTCT
* * * *
111972 TAAAACATACTTTGTCTCGCTTGAGACAGTTTTACTCGAAAGAAGACATTTCATTTCACTCAAGA
66 TAAAACATAATTTGTCTCGCTTGAGACAGTTTTACTCAAAAGAAAACATTTCACTTCACTCAAGA
* * *
112037 TTGTTTTTCTTAAAACAAATTT
131 TAGTGTTTCTTAAAACAAATTG
* * * *
112059 TGTCTCGCTTGAGACAGTTTTACTTG-AA-AGAAGACATTTCATTTCACGCAAGATTGTTTTTCT
1 TATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGACATTTCATCTCACGCAAGATTGTTTTTCT
112122 TAAAACA-AGATTTGTCTCGCTTGAGACAGTTTTTACTCAAAAGAAAACATTTCACTTCACTC-A
66 TAAAACATA-ATTTGTCTCGCTTGAGACAG-TTTTACTCAAAAGAAAACATTTCACTTCACTCAA
*
112185 -ATAGTGTTT-TTAAAGA-AGATTG
129 GATAGTGTTTCTTAAA-ACAAATTG
* *
112207 TATCTCGCTTGAGGTAGTTTCCCTTGAAACAGAAGA
1 TATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGA
112243 TTGTATCTCA
Statistics
Matches: 154, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
148 30 0.19
149 16 0.10
150 79 0.51
151 29 0.19
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (152 bp):
TATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGACATTTCATCTCACGCAAGATTGTTTTTCT
TAAAACATAATTTGTCTCGCTTGAGACAGTTTTACTCAAAAGAAAACATTTCACTTCACTCAAGA
TAGTGTTTCTTAAAACAAATTG
Found at i:112257 original size:39 final size:39
Alignment explanation
Indices: 112198--112599 Score: 502
Period size: 39 Copynumber: 10.3 Consensus size: 39
112188 GTGTTTTTAA
* * *
112198 AGAAGATTGTATCTCGCTTGAGGTAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
112237 AGAAGATTGTATCTCACTTGAGATAGTTTCACTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * * *
112276 AAAAGATTGTATTTTGCTTGAGATAGTTTCACTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
112315 AGAAGATTTTGTCTCACTTGAGATAGTTTCCCTCGAAATT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAA-C
* *
112355 A-AAGATTTTATCTCGCTTGAGATTGTTTCCCTCGATAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
112393 AGGAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
112432 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
112471 AGAAGACTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * * *
112510 AAAAGATTTT-TCCTCACTTAAGATAGTTTCTCTCAAAAC
1 AGAAGATTTTAT-CTCGCTTGAGATAGTTTCCCTCGAAAC
* **
112549 AGAAGATTTTATCTTGCTTGAGATAGTTTCTATCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
112588 AAAAGATTTTAT
1 AGAAGATTTTAT
112600 AAGAAACTAA
Statistics
Matches: 319, Mismatches: 40, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
38 2 0.01
39 314 0.98
40 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:113173 original size:132 final size:132
Alignment explanation
Indices: 112936--113310 Score: 490
Period size: 132 Copynumber: 2.8 Consensus size: 132
112926 TCGACATTTT
** * * * * **
112936 AATCCATCACAGAAGGAGTTGGATCA-ACATTAACTTTTCGCTCGATTCTATCACATAATTAGGT
1 AATCCATCGTAGAAGGAGTTGGATCATA-ATCAACTTTTAGCTCGATTCTATCATAGAAAGAGGT
* * *
113000 AGATCAGCACCGACATCTCATTCGATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTT-G
65 AGATCAACA-CAACATCTCATTCGATTTCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCG
113064 CTCA
129 CTCA
113068 AATCCATCGTAGAAGGAGTTGGATCATAATCAACTTTGT-GCTCGATTCTATCATAGAAAGAGGT
1 AATCCATCGTAGAAGGAGTTGGATCATAATCAACTTT-TAGCTCGATTCTATCATAGAAAGAGGT
*
113132 AGATTAACATCAACATCTCATTCGATTTCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCG
65 AGATCAACA-CAACATCTCATTCGATTTCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCG
113197 CTCA
129 CTCA
* *
113201 AATCCATCGTAGAAGGAGTTGGATCAGT-GTCAACTTTTAACTCGATTCTATCATAGAAAGAGGT
1 AATCCATCGTAGAAGGAGTTGGATCA-TAATCAACTTTTAGCTCGATTCTATCATAGAAAGAGGT
* * *
113265 AGATCATCACACACATCTCGTTTCGA-TTCAATCATAGAAGGAGGTG
65 AGATCAACACA-ACATCTC-ATTCGATTTC-ATCACAGAAGGAGGTG
113311 AATTGTCATT
Statistics
Matches: 217, Mismatches: 18, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
132 114 0.53
133 82 0.38
134 21 0.10
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (132 bp):
AATCCATCGTAGAAGGAGTTGGATCATAATCAACTTTTAGCTCGATTCTATCATAGAAAGAGGTA
GATCAACACAACATCTCATTCGATTTCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCT
CA
Found at i:116671 original size:21 final size:21
Alignment explanation
Indices: 116647--116696 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
116637 ATCATAATGA
116647 AGTTTAAATTTTGAAACTCGT
1 AGTTTAAATTTTGAAACTCGT
116668 AGTTTAAATTTTGAAACTCGT
1 AGTTTAAATTTTGAAACTCGT
116689 AGTTTAAA
1 AGTTTAAA
116697 ACCTTCTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (21 bp):
AGTTTAAATTTTGAAACTCGT
Found at i:125016 original size:23 final size:23
Alignment explanation
Indices: 124990--125049 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
124980 AATACAGAGA
*
124990 AAATGTGCCACAAATGTATAGAT
1 AAATGTGCCACAAAAGTATAGAT
125013 AAATGTGCCACAAAAGTATAGAT
1 AAATGTGCCACAAAAGTATAGAT
* *
125036 AAACGTGTCACAAA
1 AAATGTGCCACAAA
125050 GACAAACTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.22
Consensus pattern (23 bp):
AAATGTGCCACAAAAGTATAGAT
Found at i:132226 original size:20 final size:19
Alignment explanation
Indices: 132197--132248 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
132187 TCATGAAATG
*
132197 GGTATTGATATTG-TAGATGT
1 GGTATCGATATTGCTAG--GT
*
132217 GGTATCGATACTCGCTAGGT
1 GGTATCGATA-TTGCTAGGT
132237 GGTATCGATATT
1 GGTATCGATATT
132249 AGTTTACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.78
21 2 0.07
22 3 0.11
ACGTcount: A:0.23, C:0.10, G:0.29, T:0.38
Consensus pattern (19 bp):
GGTATCGATATTGCTAGGT
Found at i:132541 original size:2 final size:2
Alignment explanation
Indices: 132536--132585 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
132526 ATGCATACTA
*
132536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
132578 TT AT AT AT
1 AT AT AT AT
132586 GTGTTGTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:140358 original size:24 final size:25
Alignment explanation
Indices: 140331--140378 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
140321 AGATATATAT
* *
140331 TGTTTTCTCTATTACTATT-TTAAG
1 TGTTTACTCGATTACTATTGTTAAG
*
140355 TGTTTAGTCGATTACTATTGTTAA
1 TGTTTACTCGATTACTATTGTTAA
140379 AAAAAATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.54
Consensus pattern (25 bp):
TGTTTACTCGATTACTATTGTTAAG
Done.