Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002303.1 Hibiscus syriacus cultivar Beakdansim tig00004691_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: 105541
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:206 original size:26 final size:26
Alignment explanation
Indices: 172--432 Score: 213
Period size: 26 Copynumber: 10.7 Consensus size: 26
162 ATTTTCATGC
*
172 TTATGGCATCCTTTCATGCATTTCAT
1 TTATTGCATCCTTTCATGCATTTCAT
198 TTATTGCATCCTTTCATGCATTTCAT
1 TTATTGCATCCTTTCATGCATTTCAT
*
224 TTA-CGACATCCTTTCATGCATTTCAT
1 TTATTG-CATCCTTTCATGCATTTCAT
*
250 TTA-AGACATCCTTTCATGCATTTCAT
1 TTATTG-CATCCTTTCATGCATTTCAT
*
276 TTATGGCATCCTTTCATGC----C--
1 TTATTGCATCCTTTCATGCATTTCAT
* *
296 TTAATGCATCATTTCATGCATTTCAT
1 TTATTGCATCCTTTCATGCATTTCAT
*
322 TTATGGCATCCTTTCATGC----C--
1 TTATTGCATCCTTTCATGCATTTCAT
* *
342 TTAATGCATCATTTCATGCATTTCAT
1 TTATTGCATCCTTTCATGCATTTCAT
*
368 TTA-TGTCATCCTTTCAT--A----AC
1 TTATTG-CATCCTTTCATGCATTTCAT
* **
388 TTAATGCATATTTTCATGCATTTCAT
1 TTATTGCATCCTTTCATGCATTTCAT
* *
414 TTATGGCATACTTTCATGC
1 TTATTGCATCCTTTCATGC
433 CTTAATACAT
Statistics
Matches: 192, Mismatches: 21, Indels: 44
0.75 0.08 0.17
Matches are distributed among these distances:
20 45 0.23
21 2 0.01
22 3 0.02
24 3 0.02
25 3 0.02
26 135 0.70
27 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (26 bp):
TTATTGCATCCTTTCATGCATTTCAT
Found at i:310 original size:20 final size:20
Alignment explanation
Indices: 281--360 Score: 79
Period size: 20 Copynumber: 3.7 Consensus size: 20
271 TTCATTTATG
*
281 GCATCCTTTCATGCCTTAAT
1 GCATCATTTCATGCCTTAAT
*
301 GCATCATTTCATGCATTTCATTTAT
1 GCATCATTTCATGC----C-TTAAT
*
326 GGCATCCTTTCATGCCTTAAT
1 -GCATCATTTCATGCCTTAAT
347 GCATCATTTCATGC
1 GCATCATTTCATGC
361 ATTTCATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 26 0.53
21 4 0.08
22 1 0.02
24 1 0.02
25 4 0.08
26 13 0.27
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATCATTTCATGCCTTAAT
Found at i:312 original size:46 final size:47
Alignment explanation
Indices: 172--667 Score: 477
Period size: 46 Copynumber: 10.6 Consensus size: 47
162 ATTTTCATGC
* *
172 TTATGGCATCCTTTCATGCATTTCATTTATTGCATCCTTTCATGCATTTCAT
1 TTATGGCATCCTTTCATGC----CA-TTAATGCATCATTTCATGCATTTCAT
* * *
224 TTACGACATCCTTTCATGCATTTCATTTAA-GACATCCTTTCATGCATTTCAT
1 TTATGGCATCCTTTCATGC----CA-TTAATG-CATCATTTCATGCATTTCAT
276 TTATGGCATCCTTTCATGCC-TTAATGCATCATTTCATGCATTTCAT
1 TTATGGCATCCTTTCATGCCATTAATGCATCATTTCATGCATTTCAT
322 TTATGGCATCCTTTCATGCC-TTAATGCATCATTTCATGCATTTCAT
1 TTATGGCATCCTTTCATGCCATTAATGCATCATTTCATGCATTTCAT
* **
368 TTATGTCATCCTTTCATAAC-TTAATGCAT-ATTTTCATGCATTTCAT
1 TTATGGCATCCTTTCATGCCATTAATGCATCA-TTTCATGCATTTCAT
* * * * *
414 TTATGGCATACTTTCATGCC-TTAATACATCACTTAATTCATTTCAT
1 TTATGGCATCCTTTCATGCCATTAATGCATCATTTCATGCATTTCAT
* * * *
460 TTATGACATCTTTTCATGCC-TTAATGTAT-TTTTCATGCATTTCAT
1 TTATGGCATCCTTTCATGCCATTAATGCATCATTTCATGCATTTCAT
* * *
505 TTATGGCATCCTTTCATGCCAATAATGCACCCA--T-ATGCATTTCAA
1 TTATGGCATCCTTTCATGCCATTAATGCA-TCATTTCATGCATTTCAT
* * * * *
550 TTATGGCATCTTTTCATGCCAATAATGCACCCATGT-A--CATTTCAA
1 TTATGGCATCCTTTCATGCCATTAATGCA-TCATTTCATGCATTTCAT
* * * *
595 TTATGGCATCCTTTCATGCCAATAATGCACCA--T-GTGCATTTCAA
1 TTATGGCATCCTTTCATGCCATTAATGCATCATTTCATGCATTTCAT
*
639 TTATGGCATCCTTTCATGCCAATAATGCA
1 TTATGGCATCCTTTCATGCCATTAATGCA
668 CGCATATGCA
Statistics
Matches: 397, Mismatches: 36, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
42 1 0.00
44 40 0.10
45 109 0.27
46 177 0.45
47 4 0.01
48 1 0.00
51 1 0.00
52 64 0.16
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (47 bp):
TTATGGCATCCTTTCATGCCATTAATGCATCATTTCATGCATTTCAT
Found at i:383 original size:72 final size:73
Alignment explanation
Indices: 178--384 Score: 203
Period size: 72 Copynumber: 2.8 Consensus size: 73
168 ATGCTTATGG
* *
178 CATCCTTTCATGCATTTCATTTATTGCATCCTTTCATGCATTTCATTTACGACATCCTTTCATGC
1 CATCCTTTCATGC---TCA-TTAATGCATCCTTTCATGCATTTCATTTATG-CATCCTTTCATGC
243 ATTTCATTTAAGA
61 ATTTCATTTAAGA
* * *
256 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGC----C-TTAATGCATCATTTCATGCA
1 CATCCTTTCATGC---TCATTAAT-GCATCCTTTCATGCATTTCATTTATGCATCCTTTCATGCA
* *
316 TTTCATTTATGG
62 TTTCATTTAAGA
*
328 CATCCTTTCATGC-C-TTAATGCATCATTTCATGCATTTCATTTATGTCATCCTTTCAT
1 CATCCTTTCATGCTCATTAATGCATCCTTTCATGCATTTCATTTATG-CATCCTTTCAT
385 AACTTAATGC
Statistics
Matches: 111, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
66 13 0.12
67 4 0.04
68 1 0.01
70 1 0.01
71 5 0.05
72 46 0.41
73 4 0.04
74 1 0.01
77 3 0.03
78 33 0.30
ACGTcount: A:0.22, C:0.25, G:0.09, T:0.45
Consensus pattern (73 bp):
CATCCTTTCATGCTCATTAATGCATCCTTTCATGCATTTCATTTATGCATCCTTTCATGCATTTC
ATTTAAGA
Found at i:1116 original size:20 final size:22
Alignment explanation
Indices: 1091--1142 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1081 TGACTCAAAA
*
1091 GTATCGATAC-CCT-TACCATG
1 GTATCGATACAACTATACCATG
* *
1111 GTATCGAAACAACTATACTATG
1 GTATCGATACAACTATACCATG
1133 GTATCGATAC
1 GTATCGATAC
1143 TCCATCATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 9 0.35
21 2 0.08
22 15 0.58
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (22 bp):
GTATCGATACAACTATACCATG
Found at i:1222 original size:20 final size:20
Alignment explanation
Indices: 1186--1235 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1176 GTTAACAATG
*
1186 GTATCGATACCCTCCTCATA
1 GTATCGATACACTCCTCATA
* *
1206 GTATCGATACGAC-CCTCTTG
1 GTATCGATAC-ACTCCTCATA
1226 GTATCGATAC
1 GTATCGATAC
1236 TGCTTGCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACACTCCTCATA
Found at i:5168 original size:57 final size:57
Alignment explanation
Indices: 5100--5889 Score: 1377
Period size: 57 Copynumber: 13.9 Consensus size: 57
5090 ACATATAGTT
*
5100 CCCATACGGAAATTCATACACTTAGTATGAATCTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
5157 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* *
5214 CCCATATGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAATG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
*
5271 CCCATATGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
*
5328 CCCATATGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
5385 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* *
5442 CCCATACAGAAATTCATACACATAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
*
5499 CCCATAC-GAAATTCATACACTTAGTATGAATTTCTTAACATTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* *
5555 -CCATACGGAAATTCATACACTTAGTATAAATTTCTTAACTTTTTGCATACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* *
5611 CCCATACGGAAATTTATACACTTAGTATGAATTTCTTAAATTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* *
5668 CCCATACGAAAATTCATACACTTAGTATAAATTTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* * *
5725 CCTATACGGAAATTCATACACTTAGTATGTATTTCTTAACTTTTTGTACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* *
5782 CTCATACAGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* *
5839 CCCATACAGAAATTCATACACTTAGTATGTATTTCTTAACTTTTTGCACAC
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACAC
5890 CAAATGCTAT
Statistics
Matches: 699, Mismatches: 32, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
55 6 0.01
56 93 0.13
57 600 0.86
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (57 bp):
CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
Found at i:8711 original size:57 final size:57
Alignment explanation
Indices: 8567--8961 Score: 541
Period size: 57 Copynumber: 7.0 Consensus size: 57
8557 ACATATAGTT
* * * * *
8567 CCCATACGAAAATTTATACACTTAGTAAGAATCTCTTAACTTTTTGCTCACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* *
8624 CCCATAAGG-AA---A-ACACTTAGTATGAATTTCTTAACTATTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* * * *
8676 CCAATACGAAAATTCATACACTTAGTATGAATTTCTTAACTTTTTACAGACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
*
8733 TCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* * * *
8790 CCCATAGGGAAATTTATACACTTAGTATGAATTTCTTAACTTTTTGCACAAAAAGTT
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* * * * *
8847 CCCATACGGAAATTCATACACTTTGTATGAATTTTTTATCTTTTTACAAACAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
* *
8904 CCCATAC-GAAATTCAAACACTTAGTATGAATTTCTTAACTTTTTGCACACCAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
8960 CC
1 CC
8962 ATTTGGTAAT
Statistics
Matches: 295, Mismatches: 38, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
52 42 0.14
53 3 0.01
56 47 0.16
57 203 0.69
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.34
Consensus pattern (57 bp):
CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
Found at i:9414 original size:20 final size:20
Alignment explanation
Indices: 9368--9418 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
9358 TCTGTTTTAA
*
9368 TGGTATCGATACCTTCCTCG
1 TGGTATCGATACCTCCCTCG
**
9388 TATTATCGATACCTCCCTC-
1 TGGTATCGATACCTCCCTCG
9407 TCGGTATCGATA
1 T-GGTATCGATA
9419 TTGGTTGCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (20 bp):
TGGTATCGATACCTCCCTCG
Found at i:10579 original size:81 final size:81
Alignment explanation
Indices: 10449--10860 Score: 556
Period size: 81 Copynumber: 5.1 Consensus size: 81
10439 ATTCCTTTAG
* * * ** * * * * * *
10449 TCTTTTACCCAAAGGCATTTAGTCTTTCATCCAACTTGCGTGATTGACACTTTTCTACCAAATGC
1 TCTTTTACTCAAAGGTAGTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
10514 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * *
10530 TCTTTTACTGAAAGATAGTTAACCTTTCATCTAATTGGCATAATTGACACCTTTCAGCCAAATGT
1 TCTTTTACTCAAAGGTAGTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
10595 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
10611 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTTTGCAAAATGC
1 TCTTTTACTCAAAGGTAGTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
10676 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
10692 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACAGACATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTAGTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
10757 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
10773 T-TGTTTACTCAAAGTTAGTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATG
1 TCT-TTTACTCAAAGGTAGTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATG
* *
10837 TATAGCTAGGCCATTAA
65 CACAGCTAGGCCATTAA
10854 TCTTTTA
1 TCTTTTA
10861 TTTTAGAACA
Statistics
Matches: 293, Mismatches: 36, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
80 1 0.00
81 291 0.99
82 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTAGTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
ACAGCTAGGCCATTAA
Found at i:11242 original size:20 final size:20
Alignment explanation
Indices: 11214--11293 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 20
11204 TTCATTTATG
11214 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
11234 GCATGCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
*
11259 GGCATCCTTTCATACCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
11280 ACATGCTTTCATGC
1 GCATCCTTTCATGC
11294 ATTTCATTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
20 24 0.52
21 4 0.09
22 1 0.02
24 1 0.02
25 4 0.09
26 12 0.26
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:11253 original size:46 final size:46
Alignment explanation
Indices: 11202--11493 Score: 388
Period size: 46 Copynumber: 6.5 Consensus size: 46
11192 TTATTCGTTA
*
11202 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATGCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
11248 ATTTCATTTATGGCATCCTTTCATACCTTAATACATGCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
11294 ATTTCATTTATGGCAT-CTATTCATGCCTTAAGGGATCCTTTGATGC
1 ATTTCATTTATGGCATCCT-TTCATGCCTTAATGCATCCTTTCATGC
* * * *
11340 ATTTCATTTGTGGTATCATTTCATGCTTTAATG--------CA-GC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
11377 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
11423 ATTTCATTTATGGTATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
11469 ATTTCATTTATAGCATCCTTTCATG
1 ATTTCATTTATGGCATCCTTTCATG
11494 TAATTTATTT
Statistics
Matches: 214, Mismatches: 21, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
37 31 0.14
38 1 0.00
45 4 0.02
46 177 0.83
47 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.44
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:11379 original size:37 final size:37
Alignment explanation
Indices: 11338--11420 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
11328 ATCCTTTGAT
* * *
11338 GCATTTCATTTGTGGTATCATTTCATGCTTTAATGCA
1 GCATTTCATTTATGGCATCATTTCATGCCTTAATGCA
*
11375 GCATTTCATTTATGGCATCCTTTCATGCCTTAATGCA
1 GCATTTCATTTATGGCATCATTTCATGCCTTAATGCA
* *
11412 TCCTTTCAT
1 GCATTTCAT
11421 GCATTTCATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (37 bp):
GCATTTCATTTATGGCATCATTTCATGCCTTAATGCA
Found at i:11392 original size:83 final size:83
Alignment explanation
Indices: 11292--11466 Score: 262
Period size: 83 Copynumber: 2.1 Consensus size: 83
11282 ATGCTTTCAT
* * *
11292 GCATTTCATTTATGGCAT-CTATTCATGCCTTAAGGGATCCTTTGATGCATTTCATTTGTGGTAT
1 GCATTTCATTTATGGCATCCT-TTCATGCCTTAAGGCATCCTTTCATGCATTTCATTTATGGTAT
*
11356 CATTTCATGCTTTAATGCA
65 CATTTCATGCCTTAATGCA
*
11375 GCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGTATC
1 GCATTTCATTTATGGCATCCTTTCATGCCTTAAGGCATCCTTTCATGCATTTCATTTATGGTATC
*
11440 CTTTCATGCCTTAATGCA
66 ATTTCATGCCTTAATGCA
* *
11458 TCCTTTCAT
1 GCATTTCAT
11467 GCATTTCATT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
83 81 0.98
84 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.44
Consensus pattern (83 bp):
GCATTTCATTTATGGCATCCTTTCATGCCTTAAGGCATCCTTTCATGCATTTCATTTATGGTATC
ATTTCATGCCTTAATGCA
Found at i:11414 original size:20 final size:20
Alignment explanation
Indices: 11389--11468 Score: 88
Period size: 20 Copynumber: 3.7 Consensus size: 20
11379 TTCATTTATG
11389 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
11409 GCATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
*
11434 GGTATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
11455 GCATCCTTTCATGC
1 GCATCCTTTCATGC
11469 ATTTCATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 27 0.54
21 4 0.08
22 1 0.02
24 1 0.02
25 4 0.08
26 13 0.26
ACGTcount: A:0.19, C:0.28, G:0.11, T:0.42
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:11491 original size:129 final size:129
Alignment explanation
Indices: 11246--11493 Score: 381
Period size: 129 Copynumber: 1.9 Consensus size: 129
11236 ATGCTTTCAT
*
11246 GCATTTCATTTATGGCATCCTTTCATACCTTAATACATGCTTTCATGCATTTCATTTATGGCATC
1 GCATTTCATTTATGGCATCCTTTCATACCTTAATACATCCTTTCATGCATTTCATTTATGGCATC
* * * * *
11311 TATTCATGCCTTAAGGGATCCTTTGATGCATTTCATTTGTGGTATCATTTCATGCTTTAATGCA
66 TATTCATGCCTTAAGGCATCCTTTCATGCATTTCATTTATAGCATCATTTCATGCTTTAATGCA
* * *
11375 GCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGTATC
1 GCATTTCATTTATGGCATCCTTTCATACCTTAATACATCCTTTCATGCATTTCATTTATGGCAT-
* *
11440 CT-TTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATAGCATCCTTTCATG
65 CTATTCATGCCTTAAGGCATCCTTTCATGCATTTCATTTATAGCATCATTTCATG
11494 TAATTTATTT
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
129 105 0.98
130 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.44
Consensus pattern (129 bp):
GCATTTCATTTATGGCATCCTTTCATACCTTAATACATCCTTTCATGCATTTCATTTATGGCATC
TATTCATGCCTTAAGGCATCCTTTCATGCATTTCATTTATAGCATCATTTCATGCTTTAATGCA
Found at i:11552 original size:45 final size:45
Alignment explanation
Indices: 11502--11720 Score: 334
Period size: 45 Copynumber: 4.9 Consensus size: 45
11492 TGTAATTTAT
* **
11502 TTATGACATCCTTTCATGAAAATAATGCACCCATATGCATTTCAA
1 TTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAA
* * * *
11547 TTATGACATCCTTTCATTCCAATAAAGCACCCATATGGATTTCAA
1 TTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAA
*
11592 TTATGGCATCCTTTCATGCCAATAATGCATCC--ATGCATTTCAA
1 TTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAA
*
11635 TTATGGGATCCTTTCATGCCAATAATGCACCCATATGCATTTCAA
1 TTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAA
*
11680 TTATGGCATCCTTTCATGCCAATAATGCATCCATATGCATT
1 TTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATT
11721 ATTTTAATCA
Statistics
Matches: 158, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
43 40 0.25
45 118 0.75
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (45 bp):
TTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAA
Found at i:11646 original size:88 final size:88
Alignment explanation
Indices: 11502--11713 Score: 325
Period size: 88 Copynumber: 2.4 Consensus size: 88
11492 TGTAATTTAT
* ** * *
11502 TTATGACATCCTTTCATGAAAATAATGCACCCATATGCATTTCAATTATGACATCCTTTCATTCC
1 TTATGGCATCCTTTCATGCCAATAATGCATCC--ATGCATTTCAATTATGACATCCTTTCATGCC
*
11567 AATAAAGCACCCATATGGATTTCAA
64 AATAAAGCACCCATATGCATTTCAA
**
11592 TTATGGCATCCTTTCATGCCAATAATGCATCCATGCATTTCAATTATGGGATCCTTTCATGCCAA
1 TTATGGCATCCTTTCATGCCAATAATGCATCCATGCATTTCAATTATGACATCCTTTCATGCCAA
*
11657 TAATGCACCCATATGCATTTCAA
66 TAAAGCACCCATATGCATTTCAA
11680 TTATGGCATCCTTTCATGCCAATAATGCATCCAT
1 TTATGGCATCCTTTCATGCCAATAATGCATCCAT
11714 ATGCATTATT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 85 0.75
90 28 0.25
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.34
Consensus pattern (88 bp):
TTATGGCATCCTTTCATGCCAATAATGCATCCATGCATTTCAATTATGACATCCTTTCATGCCAA
TAAAGCACCCATATGCATTTCAA
Found at i:11833 original size:17 final size:17
Alignment explanation
Indices: 11780--11835 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
11770 ATATCCTTTC
*
11780 CATACATTAAATGAAAA
1 CATACATTAAATTAAAA
11797 CAT--ATTAACTACTGTAAAA
1 CATACATTAA--A-T-TAAAA
11816 CATACATTAAATTAAAA
1 CATACATTAAATTAAAA
11833 CAT
1 CAT
11836 TTAACTTGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
15 5 0.16
17 12 0.38
18 2 0.06
19 8 0.25
21 5 0.16
ACGTcount: A:0.54, C:0.14, G:0.04, T:0.29
Consensus pattern (17 bp):
CATACATTAAATTAAAA
Found at i:12284 original size:21 final size:21
Alignment explanation
Indices: 12260--12313 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
12250 ACCCCATCTT
*
12260 GGTATCGATATTGCTTGCATC
1 GGTATCGATACTGCTTGCATC
12281 GGTATCGATACTGCTTGCATC
1 GGTATCGATACTGCTTGCATC
12302 GGTATCGATACT
1 GGTATCGATACT
12314 ACTCAACATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
GGTATCGATACTGCTTGCATC
Found at i:14491 original size:2 final size:2
Alignment explanation
Indices: 14484--14508 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14474 AGTAATCATG
14484 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
14509 CGTCCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15780 original size:29 final size:29
Alignment explanation
Indices: 15738--15798 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
15728 TTTACCACTT
15738 AAACTTTCAATACTAAAATTCCAGAATTG
1 AAACTTTCAATACTAAAATTCCAGAATTG
15767 AAACTTTCAATACTAAAATTCCAGAATTG
1 AAACTTTCAATACTAAAATTCCAGAATTG
15796 AAA
1 AAA
15799 GTATTATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.30
Consensus pattern (29 bp):
AAACTTTCAATACTAAAATTCCAGAATTG
Found at i:28437 original size:24 final size:24
Alignment explanation
Indices: 28410--28474 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 24
28400 ATACAAAAGT
28410 ACAC-AATGGTACTAATATGAGAGC
1 ACACAAAT-GTACTAATATGAGAGC
*
28434 ACACAAATGTACTAATATGAGAGTG
1 ACACAAATGTACTAATATGAGAG-C
28459 A-ACAAATGTACTAATA
1 ACACAAATGTACTAATA
28475 CAAGATCGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
24 34 0.89
25 4 0.11
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (24 bp):
ACACAAATGTACTAATATGAGAGC
Found at i:34831 original size:20 final size:20
Alignment explanation
Indices: 34795--34839 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
34785 GATAAAAAGT
*
34795 AAAAGTTAAAAATGAAATAG
1 AAAAGTTAAAAATGAAAGAG
*
34815 AAAAGTTAAGTAA-GAAAGAG
1 AAAAGTTAA-AAATGAAAGAG
34835 AAAAG
1 AAAAG
34840 AAAAAGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAAGTTAAAAATGAAAGAG
Found at i:41495 original size:23 final size:23
Alignment explanation
Indices: 41469--41517 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
41459 ATAAAGAACC
*
41469 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
41492 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
41515 AAA
1 AAA
41518 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:42975 original size:2 final size:2
Alignment explanation
Indices: 42970--42994 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42960 ACACACACAC
42970 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
42995 GGTAAGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50940 original size:20 final size:20
Alignment explanation
Indices: 50856--50940 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
50846 GACAAACTAT
*
50856 TATCCATA-CCAAAGGATTGG
1 TATCCATATCGAAA-GATTGG
* * *
50876 TATCCATATCGGATGAGTTTG
1 TATCCATATCGAAAGA-TTGG
*
50897 TATCCATA-CCAAAGATTGG
1 TATCCATATCGAAAGATTGG
* *
50916 CTATCCATATCGAACGCTTGG
1 -TATCCATATCGAAAGATTGG
50937 TATC
1 TATC
50941 AATACCCAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
19 3 0.06
20 26 0.52
21 21 0.42
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (20 bp):
TATCCATATCGAAAGATTGG
Found at i:53645 original size:37 final size:37
Alignment explanation
Indices: 53604--53681 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
53594 CCATACCTCT
53604 CATATCAT-ATAAATTAGTATTGATACCCCTTGGTATC
1 CATATC-TGATAAATTAGTATTGATACCCCTTGGTATC
53641 CATATCTGATAAATTAGTATTGATACCCCTTGGTATC
1 CATATCTGATAAATTAGTATTGATACCCCTTGGTATC
53678 CATA
1 CATA
53682 CCAGAGGATC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 1 0.03
37 39 0.98
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (37 bp):
CATATCTGATAAATTAGTATTGATACCCCTTGGTATC
Found at i:57142 original size:23 final size:24
Alignment explanation
Indices: 57110--57159 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
57100 TAATAAGGAA
57110 TGCATTGCACCATGTACTATATTG
1 TGCATTGCACCATGTACTATATTG
* *
57134 TGCA-TGCACCATGTACTGTGTTG
1 TGCATTGCACCATGTACTATATTG
57157 TGC
1 TGC
57160 CATATAACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (24 bp):
TGCATTGCACCATGTACTATATTG
Found at i:65021 original size:19 final size:19
Alignment explanation
Indices: 64999--65061 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
64989 CACTAAACTT
*
64999 TGATATATGTTCTGATCTC
1 TGATATATATTCTGATCTC
* * *
65018 TGATTTCTATTATGATCTC
1 TGATATATATTCTGATCTC
* * *
65037 TGATATGTACTCTGATTTC
1 TGATATATATTCTGATCTC
65056 TGATAT
1 TGATAT
65062 CTCTATTTAC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (19 bp):
TGATATATATTCTGATCTC
Found at i:70362 original size:108 final size:107
Alignment explanation
Indices: 70240--70824 Score: 528
Period size: 108 Copynumber: 5.4 Consensus size: 107
70230 TGGGTTCGCT
* * *
70240 CCCTATTTCTTCAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTT-GTCTGCCCCCTATTT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAAC-GA-TTCGTCTGCCCCCTATTT
*
70303 CTTCAGAGAGTATAAGACCCATAATCTTCATCAATCGCATCTGCC
63 CTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATCTGCC
* *
70348 CCCTATTTCTTCAGAGAGTATAAGA-TCCGAACAATCTTCAATGATTGCGTCTGCCCCCTTTTTC
1 CCCTATTTCTTCAGAGAGTATAAGACT-CGAACAATCTTCAACGATT-CGTCTGCCCCCTATTTC
70412 TTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATCTGCC
64 TTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATCTGCC
* *
70456 CCCTATTTCTTCAGAGAGTATAAGACACGAACAATCTTCAACGATTGCGTATGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATT-CGTCTGCCCCCTATTTCT
* * **
70521 TCAGAGAGTATAAGACCCGAACAATCTTCAACTATTACATCTGCC
65 TCAGAGAGTATAAGACCC--ACAATCTTCATCAATCGCATCTGCC
* * ** *
70566 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAAC-AATCGGGT-TCGTTCCCTCTTT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTC--GTCT-GCCCCCTATTT
* * * * * * * ** * *
70627 CTCCAGGGAGTAT-AGAACTCGAAAATCTT-TTGAAAACGTGTATGCT
63 CTTCAGAGAGTATAAG-AC-CCACAATCTTCAT-CAATCGCATCTGCC
* * * * *
70673 CCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAAC-AATCGTGTCTACTCCCTA-TTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTC--GTCTGCCCCCTATTTC
* * * * * ** *
70736 TTTCATAGAGTATGAGACTCGAATAATCTTCAACAATCGTGTCTGCT
64 -TTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCATCTGCC
*
70783 CCCTA-TTCTTTCAGAGAGTATAAGACTCGAACAAACTTCAAC
1 CCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAAC
70825 AATCGGGTCT
Statistics
Matches: 402, Mismatches: 54, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
106 3 0.01
107 44 0.11
108 210 0.52
109 41 0.10
110 104 0.26
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (107 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTCGTCTGCCCCCTATTTCTT
CAGAGAGTATAAGACCCACAATCTTCATCAATCGCATCTGCC
Found at i:70517 original size:163 final size:160
Alignment explanation
Indices: 70273--70825 Score: 546
Period size: 163 Copynumber: 3.4 Consensus size: 160
70263 GACTTGAATC
* ** * * *
70273 ATCTTCAACAAACTTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CATAATCTTCATCA
1 ATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-
* *
70336 ATCGCATCTGCCCCCTATTTCTTCAGAGAGTATAAGATCCGAACAATCTTCAATGATTGCGTCTG
65 ATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGA-CCGAACAATCTTCAAT-ATTGCGTCTG
70401 CCCCCTTTTTCTTCAGAGAGTATAAGACCCACA
128 CCCCCTTTTTCTTCAGAGAGTATAAGACCCACA
* * *
70434 ATCTTCATCAATCGCATCTGCCCCCTATTTCTTCAGAGAGTATAAGACACGAACAATCTTCAACG
1 ATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-
* * *
70499 ATTGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACTATTACATCTG
65 ATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGA-CCGAACAATCTTCAA-TATTGCGTCTG
*
70564 CCCCCTATTTCTTCAGAGAGTATAAGACCCACA
128 CCCCCTTTTTCTTCAGAGAGTATAAGACCCACA
* ** * * * *
70597 ATCTTCAACAATCGGGT-TCGTTCCCTCTTTCTCCAGGGAGTAT-AGAACTCGAA-AATCTTTTG
1 ATCTTCAACAATCGCGTCT-GCCCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATC--TTC
* * * * * * * *
70659 AA-AACGTGTATGCTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGT
62 AACATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGAC-CGAACAATCTTCAA-TATTGCGT
* * * * * * *
70723 CTACTCCC-TATTCTTTCATAGAGTATGAGACTCGAATA
125 CTGCCCCCTTTTTC-TTCAGAGAGTATAAGAC-C-CACA
* * *
70761 ATCTTCAACAATCGTGTCTGCTCCCTA-TTCTTTCAGAGAGTATAAGACTCGAACAAACTTCAAC
1 ATCTTCAACAATCGCGTCTGCCCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAAC
70825 A
65 A
70826 ATCGGGTCTA
Statistics
Matches: 324, Mismatches: 52, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
161 47 0.15
162 78 0.24
163 146 0.45
164 47 0.15
165 6 0.02
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (160 bp):
ATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
TCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACCGAACAATCTTCAATATTGCGTCTGCCC
CCTTTTTCTTCAGAGAGTATAAGACCCACA
Found at i:70730 original size:55 final size:55
Alignment explanation
Indices: 70240--70847 Score: 589
Period size: 55 Copynumber: 11.2 Consensus size: 55
70230 TGGGTTCGCT
* * * **
70240 CCCTATTTCTTCAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAACAATCGCGTCTGCC
* * * *
70295 CCCTATTTCTTCAGAGAGTATAAGAC-C-CATAATCTTCATCAATCGCATCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
** *
70348 CCCTATTTCTTCAGAGAGTATAAGA-TCCGAACAATCTTCAATGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACT-CGAACAATCTTCAACAATCGCGTCTGCC
* * * *
70403 CCCTTTTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCATCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * * *
70456 CCCTATTTCTTCAGAGAGTATAAGACACGAACAATCTTCAACGATTGCGTATGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * ** *
70511 CCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACTATTACATCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * **
70566 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGGGT-TCGTT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT-GCC
* * * * * * *
70619 CCCTCTTTCTCCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-AA-CGTGTATGCT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATC--TTCAACAATCGCGTCTGCC
* * * * *
70673 CCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTACT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * * * *
70728 CCCTA-TTCTTTCATAGAGTATGAGACTCGAATAATCTTCAACAATCGTGTCTGCT
1 CCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * * *
70783 CCCTA-TTCTTTCAGAGAGTATAAGACTCGAACAAACTTCAACAATCGGGTCTACT
1 CCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
70838 CCCTATTTCT
1 CCCTATTTCT
70848 CTAGGGATTA
Statistics
Matches: 466, Mismatches: 67, Indels: 40
0.81 0.12 0.07
Matches are distributed among these distances:
52 3 0.01
53 128 0.27
54 43 0.09
55 285 0.61
56 7 0.02
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
Found at i:71115 original size:55 final size:54
Alignment explanation
Indices: 70836--71507 Score: 540
Period size: 51 Copynumber: 12.6 Consensus size: 54
70826 ATCGGGTCTA
* * * * ** *
70836 CTCCCTATTTC-TCTAGGGATTATGGAACTCGAACATCTTCTTCTTACAGGTTCG
1 CTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAGATCTTCTTCAAACGGGTTCG
* * * **
70890 CTCCCTCTTTC-TCTAGGGAGTATAGAACTTGAATAATCTTCTGT-AAGC-GAAT--
1 CTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAA-GATCTTCT-TCAAACGGGTTCG
* * * * * *
70942 -TCCCTTTTTCTTTAAGGAGTATAGAACTCGAATAATCTT-TTGGAAACGGGTTTG
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-GATCTTCTT-CAAACGGGTTCG
* ** *
70996 CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATGATCTTCTAAAAACGGGCTCG
1 CTCCCTCTTTC-TTCAGGGAGTATAGAACTCGAA-GATCTTCTTCAAACGGGTTCG
**
71052 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAGATCTTCTTCTTACGGGTTCG
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAGATCTTCTTCAAACGGGTTCG
* * * ** * *
71106 CTTCGCTCTTTCTCCAGGAAGTATAGAACTCGAATGATCTTCTGAAAATGGGCTCG
1 C-TCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-GATCTTCTTCAAACGGGTTCG
**
71162 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAGATCTTCTTCTTACGGGTTCG
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAGATCTTCTTCAAACGGGTTCG
* * * * ** *
71216 CTTCGCTCTTTCTCCAGGAAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTTG
1 C-TCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-GATCTTCTTCAAACGGGTTCG
* *
71272 CTCCCTCTTTCTTCAGGGAGTATGGAACTC-AGACATC-TCTTCAAACGGGTTCG
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGA-AGATCTTCTTCAAACGGGTTCG
* * * * *
71325 CTCCTTCTTTCTTTAAGGAGTATGGAACTCG-A-A-CATCTTCAAACGGGTTCG
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAGATCTTCTTCAAACGGGTTCG
* * * * * *
71376 CTCCTTCTTTCTTTAAGGAGTATAGAACTCG--CAT-ATCTTCACACGGGTTCG
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAGATCTTCTTCAAACGGGTTCG
* * *
71427 CTCCTTCTTTC-TCTAGGGAGTATGGAACTCG--GA-CATCTTCAAACGGGTTCG
1 CTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAAGATCTTCTTCAAACGGGTTCG
* *
71478 CTCCCTCTCTC-TCTAGGGAGTATGGAACTC
1 CTCCCTCTTTCTTC-AGGGAGTATAGAACTC
71508 AAATAATCTT
Statistics
Matches: 517, Mismatches: 79, Indels: 47
0.80 0.12 0.07
Matches are distributed among these distances:
49 1 0.00
50 3 0.01
51 171 0.33
52 4 0.01
53 40 0.08
54 68 0.13
55 151 0.29
56 78 0.15
57 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (54 bp):
CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAGATCTTCTTCAAACGGGTTCG
Found at i:71143 original size:110 final size:108
Alignment explanation
Indices: 70836--71507 Score: 612
Period size: 110 Copynumber: 6.3 Consensus size: 108
70826 ATCGGGTCTA
* * * *
70836 CTCCCTATTTC-TCTAGGGATTATGGAACTCGAACATCTTCTTCTTACAGGTTCGCTCCCTCTTT
1 CTCCCTCTTTCTTC-AGGGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCT-CCTCTTT
* * * * * **
70900 CTCTAGGGAGTATAGAACTTGAATAATCTTCTGTAAGC-GAAT--
64 CTCCAGGAAGTATAGAACTCGAATAATCTTCTGAAAACGGGTTCG
* * * * *** *
70942 -TCCCTTTTTCTTTAAGGAGTATAGAACTCGAATAATCTT-TTGGAAACGGGTTTGCTCCCTCTT
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAA-CATCTTCTT-CTTACGGGTTCGCT-CCTCTT
* * * *
71005 TCTTTCAGGAAGTATAGAACTCGAATGATCTTCTAAAAACGGGCTCG
63 TC-TCCAGGAAGTATAGAACTCGAATAATCTTCTGAAAACGGGTTCG
*
71052 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAGATCTTCTTCTTACGGGTTCGCTTCGCTCTTT
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGC-TC-CTCTTT
* * *
71117 CTCCAGGAAGTATAGAACTCGAATGATCTTCTGAAAATGGGCTCG
64 CTCCAGGAAGTATAGAACTCGAATAATCTTCTGAAAACGGGTTCG
*
71162 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAGATCTTCTTCTTACGGGTTCGCTTCGCTCTTT
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGC-TC-CTCTTT
* *
71227 CTCCAGGAAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTTG
64 CTCCAGGAAGTATAGAACTCGAATAATCTTCTGAAAACGGGTTCG
* **
71272 CTCCCTCTTTCTTCAGGGAGTATGGAACTC-AGACATC-TCTTCAAACGGGTTCGCTCCTTCTTT
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGA-ACATCTTCTTCTTACGGGTTCGCTCC-TCTTT
** * *
71335 CTTTAAGG-AGTATGGAACTCGAA-CATCTTC---AAACGGGTTCG
64 C-TCCAGGAAGTATAGAACTCGAATAATCTTCTGAAAACGGGTTCG
* * * * **
71376 CTCCTTCTTTCTTTAAGGAGTATAGAACTCG--CAT-ATCTTCACACGGGTTCGCTCCTTCTTTC
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCC-TCTTTC
* * * * *
71438 TCTAGGGAGTATGGAACTCGGA-CATCTTC---AAACGGGTTCG
65 TCCAGGAAGTATAGAACTCGAATAATCTTCTGAAAACGGGTTCG
* *
71478 CTCCCTCTCTC-TCTAGGGAGTATGGAACTC
1 CTCCCTCTTTCTTC-AGGGAGTATAGAACTC
71508 AAATAATCTT
Statistics
Matches: 489, Mismatches: 59, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
101 5 0.01
102 84 0.17
104 36 0.07
105 27 0.06
106 24 0.05
107 36 0.07
108 24 0.05
109 20 0.04
110 194 0.40
111 39 0.08
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (108 bp):
CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCTCTTTCT
CCAGGAAGTATAGAACTCGAATAATCTTCTGAAAACGGGTTCG
Found at i:71762 original size:36 final size:36
Alignment explanation
Indices: 71738--71893 Score: 222
Period size: 36 Copynumber: 4.3 Consensus size: 36
71728 ACTACTTTTT
* *
71738 GGTGAAGACTTAAGATGGTTTGCTTCACTACTCTCT
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
*
71774 GGTGAAGACTTATGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
* * * *
71810 GGTGAAGGCTTCAGATTGATTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
* *
71846 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
*
71882 GGTGAAGGCTTA
1 GGTGAAGACTTA
71894 GGATTGACTT
Statistics
Matches: 109, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 109 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (36 bp):
GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
Found at i:77718 original size:12 final size:12
Alignment explanation
Indices: 77701--77727 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
77691 TTTATTTGTT
77701 AATTAAAACGCA
1 AATTAAAACGCA
77713 AATTAAAACGCA
1 AATTAAAACGCA
77725 AAT
1 AAT
77728 CAGGGATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.15, G:0.07, T:0.19
Consensus pattern (12 bp):
AATTAAAACGCA
Found at i:86764 original size:26 final size:26
Alignment explanation
Indices: 86686--86764 Score: 61
Period size: 29 Copynumber: 2.9 Consensus size: 26
86676 ATTTTTTTGG
* * *
86686 AATTTTGATATATTTTTAAAATTAAT
1 AATTATGATATATTTTAAAAATTAAA
* * *
86712 CATAATTATA-ATTTCATAAATAGATTAAA
1 AATTATGATATATTT--TAAA-A-ATTAAA
86741 AATTATGATATATTTTAAAAATTA
1 AATTATGATATATTTTAAAAATTA
86765 CATGATATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
25 4 0.10
26 10 0.26
27 4 0.10
28 5 0.13
29 12 0.31
30 4 0.10
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.46
Consensus pattern (26 bp):
AATTATGATATATTTTAAAAATTAAA
Found at i:86771 original size:21 final size:20
Alignment explanation
Indices: 86736--86777 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 20
86726 CATAAATAGA
86736 TTAAAAATTATGATA-TATT
1 TTAAAAATTATGATATTATT
86755 TTAAAAATTACATGATATTATT
1 TTAAAAATT--ATGATATTATT
86777 T
1 T
86778 CTATAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
21 6 0.30
22 5 0.25
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
TTAAAAATTATGATATTATT
Found at i:87829 original size:15 final size:15
Alignment explanation
Indices: 87809--87849 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
87799 TGTATTCTAC
87809 ATTTTAATATATTTA
1 ATTTTAATATATTTA
87824 ATTTTAATAT-TTTA
1 ATTTTAATATATTTA
*
87838 ATATTTTATATA
1 AT-TTTAATATA
87850 AGGAAATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTAATATATTTA
Found at i:87837 original size:8 final size:8
Alignment explanation
Indices: 87809--87845 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
87799 TGTATTCTAC
87809 ATTTTAAT
1 ATTTTAAT
87817 ATATTT-A-
1 AT-TTTAAT
87824 ATTTTAAT
1 ATTTTAAT
87832 ATTTTAAT
1 ATTTTAAT
87840 ATTTTA
1 ATTTTA
87846 TATAAGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 3 0.12
7 3 0.12
8 17 0.65
9 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTTAAT
Found at i:89542 original size:18 final size:18
Alignment explanation
Indices: 89519--89637 Score: 120
Period size: 18 Copynumber: 6.7 Consensus size: 18
89509 AATCTACGTT
*
89519 TGATAATTGTAAAACATC
1 TGATAACTGTAAAACATC
89537 TGATAACTGT-AAACATC
1 TGATAACTGTAAAACATC
*
89554 TGATGACTG-AAAATCATC
1 TGATAACTGTAAAA-CATC
*
89572 TGATAACTGT-AAATATC
1 TGATAACTGTAAAACATC
*
89589 TGATAACT-AAAAATCATC
1 TGATAACTGTAAAA-CATC
* ** *
89607 TGATAACTGTGAAATGTA
1 TGATAACTGTAAAACATC
89625 TGATAACTGTAAA
1 TGATAACTGTAAA
89638 CATTTAGAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
17 32 0.39
18 48 0.58
19 3 0.04
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (18 bp):
TGATAACTGTAAAACATC
Found at i:89579 original size:35 final size:35
Alignment explanation
Indices: 89529--89616 Score: 142
Period size: 35 Copynumber: 2.5 Consensus size: 35
89519 TGATAATTGT
* *
89529 AAAA-CATCTGATAACTGTAAACATCTGATGACTG
1 AAAATCATCTGATAACTGTAAACATCTGATAACTA
*
89563 AAAATCATCTGATAACTGTAAATATCTGATAACTA
1 AAAATCATCTGATAACTGTAAACATCTGATAACTA
89598 AAAATCATCTGATAACTGT
1 AAAATCATCTGATAACTGT
89617 GAAATGTATG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
34 4 0.08
35 46 0.92
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (35 bp):
AAAATCATCTGATAACTGTAAACATCTGATAACTA
Found at i:89607 original size:53 final size:52
Alignment explanation
Indices: 89519--89640 Score: 138
Period size: 53 Copynumber: 2.3 Consensus size: 52
89509 AATCTACGTT
* ** * *
89519 TGATAATTGTAAAACATCTGATAACTGTAAACATCTGATGACTG-AAAATCATC
1 TGATAACTGT-AAACATCTGATAACTAAAAACATCTGATAACTGTAAAAT-ATA
* * *
89572 TGATAACTGTAAATATCTGATAACTAAAAATCATCTGATAACTGTGAAATGTA
1 TGATAACTGTAAACATCTGATAACTAAAAA-CATCTGATAACTGTAAAATATA
89625 TGATAACTGTAAACAT
1 TGATAACTGTAAACAT
89641 TTAGAATTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
52 17 0.29
53 37 0.64
54 4 0.07
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (52 bp):
TGATAACTGTAAACATCTGATAACTAAAAACATCTGATAACTGTAAAATATA
Found at i:96108 original size:19 final size:20
Alignment explanation
Indices: 96084--96144 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 20
96074 AACGGTCAAC
*
96084 TCAGGTCAAAGTTC-ATGTG
1 TCAGGTCAAAGTTCAATGGG
96103 TCAGGTCAAAG-TCAATGGG
1 TCAGGTCAAAGTTCAATGGG
* *
96122 TCGGGTCAAAGTT-AACGGG
1 TCAGGTCAAAGTTCAATGGG
96141 TCAG
1 TCAG
96145 ACCGGTTCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.06
19 33 0.92
20 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (20 bp):
TCAGGTCAAAGTTCAATGGG
Found at i:96177 original size:20 final size:20
Alignment explanation
Indices: 96154--96223 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
96144 GACCGGTTCA
96154 GGTTGACTCAGATCAGATCG
1 GGTTGACTCAGATCAGATCG
*
96174 GGTTGACTCAGATCAGATCA
1 GGTTGACTCAGATCAGATCG
96194 GGTTGACTCAGATCAGATCG
1 GGTTGACTCAGATCAGATCG
*
96214 AGTTGACTCA
1 GGTTGACTCA
96224 TTTCGATCTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (20 bp):
GGTTGACTCAGATCAGATCG
Found at i:98607 original size:12 final size:14
Alignment explanation
Indices: 98590--98621 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
98580 TGGACGGTTC
98590 TATTTT-AA-ATTA
1 TATTTTAAATATTA
98602 TATTTTAAATATTA
1 TATTTTAAATATTA
98616 TATTTT
1 TATTTT
98622 GATTTTACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 2 0.11
14 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTTAAATATTA
Done.