Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008098.1 Hibiscus syriacus cultivar Beakdansim tig00110622_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: 522112
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 3
Found at i:7262 original size:12 final size:12
Alignment explanation
Indices: 7245--7269 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7235 TGAGATGATA
7245 AAAAAGAAGAAG
1 AAAAAGAAGAAG
7257 AAAAAGAAGAAG
1 AAAAAGAAGAAG
7269 A
1 A
7270 GAAGGAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:13031 original size:24 final size:22
Alignment explanation
Indices: 13000--13063 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 22
12990 ATTGTATTCA
13000 TTTATTGTGTTCGTTTACATTCG
1 TTTATTGTGTTCGTTTACATT-G
* *
13023 TTCTTTTGTGTTCCTTTA-A--G
1 TT-TATTGTGTTCGTTTACATTG
13043 TTTATTGTGTTCGTTTACATT
1 TTTATTGTGTTCGTTTACATT
13064 AATTCGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
19 13 0.39
20 4 0.12
23 3 0.09
24 13 0.39
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (22 bp):
TTTATTGTGTTCGTTTACATTG
Found at i:14329 original size:4 final size:4
Alignment explanation
Indices: 14320--14348 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
14310 ATTAGTAATA
14320 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
14349 ATGCATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:19628 original size:46 final size:45
Alignment explanation
Indices: 19535--19660 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 45
19525 GATAAACTGG
* *
19535 AAAATAAGCTTACGAGCTTATGGAAT-AATGGAAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGT
* *
19579 AAAATAAGCTTACAAGCTTATGGGATTAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTATATTGGT
19625 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
19661 AGATTTTATC
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.31
45 12 0.16
46 40 0.53
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGT
Found at i:29603 original size:29 final size:30
Alignment explanation
Indices: 29571--29638 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 30
29561 TTTCAAATAC
*
29571 AAATTTAAGAA-TTATAATTATTTT--TTA
1 AAATTTAAGAATTTAAAATTATTTTGATTA
* *
29598 TAAAATTAACAAATTTAAAATTATTTTGATTA
1 -AAATTTAA-GAATTTAAAATTATTTTGATTA
29630 AAATTTAAG
1 AAATTTAAG
29639 GTATAGACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 7 0.23
29 2 0.06
30 12 0.39
31 7 0.23
32 3 0.10
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (30 bp):
AAATTTAAGAATTTAAAATTATTTTGATTA
Found at i:39280 original size:33 final size:33
Alignment explanation
Indices: 39233--39335 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
39223 ATAAAGTTTA
* *
39233 CGAT-AATTGAAATACTTAAATACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
* *
39265 TGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
39298 CGATAAATTCAAATACTTAAAAAC-TTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
39330 CGATAA
1 CGATAA
39336 TTGAAACAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 16 0.25
33 48 0.75
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.33
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTTCAAGTT
Found at i:39354 original size:21 final size:21
Alignment explanation
Indices: 39330--39371 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
39320 ACTTCAAGTT
*
39330 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAAAAAAGTTTA
39351 CGATAATTGAAAAAAAGTTTA
1 CGATAATTGAAAAAAAGTTTA
39372 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (21 bp):
CGATAATTGAAAAAAAGTTTA
Found at i:47540 original size:38 final size:38
Alignment explanation
Indices: 47489--47575 Score: 165
Period size: 38 Copynumber: 2.3 Consensus size: 38
47479 AATAATTGTT
*
47489 AATTAGTAATTTAACATATTTCTTATTATATACTAGCA
1 AATTAGTAATTTAACATATTTCTTATCATATACTAGCA
47527 AATTAGTAATTTAACATATTTCTTATCATATACTAGCA
1 AATTAGTAATTTAACATATTTCTTATCATATACTAGCA
47565 AATTAGTAATT
1 AATTAGTAATT
47576 ATTAATCAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (38 bp):
AATTAGTAATTTAACATATTTCTTATCATATACTAGCA
Found at i:65158 original size:23 final size:24
Alignment explanation
Indices: 65128--65174 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
65118 TTATTAAATG
*
65128 ATACAATGTGTTG-TGTGTGTGTA
1 ATACAATGCGTTGATGTGTGTGTA
65151 ATACAATGCGTTGAATGTGTGTGT
1 ATACAATGCGTTG-ATGTGTGTGT
65175 GTACGGTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
25 9 0.43
ACGTcount: A:0.23, C:0.06, G:0.30, T:0.40
Consensus pattern (24 bp):
ATACAATGCGTTGATGTGTGTGTA
Found at i:68400 original size:14 final size:14
Alignment explanation
Indices: 68381--68408 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
68371 GAACATTAAC
68381 CTTAAATACATGAA
1 CTTAAATACATGAA
68395 CTTAAATACATGAA
1 CTTAAATACATGAA
68409 AATCTTACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
CTTAAATACATGAA
Found at i:72964 original size:21 final size:21
Alignment explanation
Indices: 72938--72977 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
72928 GGAAATGTTA
* *
72938 AAAAATATTGATGTTTTAGTT
1 AAAAATAATAATGTTTTAGTT
72959 AAAAATAATAATGTTTTAG
1 AAAAATAATAATGTTTTAG
72978 GTAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (21 bp):
AAAAATAATAATGTTTTAGTT
Found at i:75716 original size:35 final size:35
Alignment explanation
Indices: 75651--75720 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
75641 AACTAAAAAT
**
75651 TAAGTATATTCACCAAGTGACATGACTTATTATAA
1 TAAGTATATTCACCAAGTGACACCACTTATTATAA
* *
75686 TAAGTCTATTCACCAAGTGACACCAGTTATTATAA
1 TAAGTATATTCACCAAGTGACACCACTTATTATAA
75721 ATAGTATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (35 bp):
TAAGTATATTCACCAAGTGACACCACTTATTATAA
Found at i:76399 original size:20 final size:21
Alignment explanation
Indices: 76374--76415 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
76364 TAATCATAAC
*
76374 ATTTCAATATG-CATGTATAT
1 ATTTCAATATGACATATATAT
76394 ATTTCAATATGACATATATAT
1 ATTTCAATATGACATATATAT
76415 A
1 A
76416 AATCATGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (21 bp):
ATTTCAATATGACATATATAT
Found at i:76621 original size:38 final size:38
Alignment explanation
Indices: 76569--76664 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 38
76559 CTCGTACAAA
* *
76569 TGTCCTGAAGGACCTATCATCCCGAAGGATGCCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGCAATCTG
* * * *
76607 TGTCCCGAATGACCTGTCATCCTGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGCAATCTG
*
76645 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
76665 ATGTCTTATA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGCAATCTG
Found at i:81085 original size:35 final size:35
Alignment explanation
Indices: 81020--81089 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
81010 AACTAAAAAT
**
81020 TAAGTCCATTCACCAAGTGACATGGCTTATTATAA
1 TAAGTCCATTCACCAAGTGACATAACTTATTATAA
* * *
81055 TAAGTCTATTCACTAAGTGACATAATTTATTATAA
1 TAAGTCCATTCACCAAGTGACATAACTTATTATAA
81090 ATAGCATCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (35 bp):
TAAGTCCATTCACCAAGTGACATAACTTATTATAA
Found at i:82888 original size:22 final size:22
Alignment explanation
Indices: 82863--82904 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
82853 TTAAATATGA
*
82863 ATTCAAGTTAAAATATTATAAT
1 ATTCAACTTAAAATATTATAAT
*
82885 ATTCAACTTAAAATGTTATA
1 ATTCAACTTAAAATATTATA
82905 TAAATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (22 bp):
ATTCAACTTAAAATATTATAAT
Found at i:90332 original size:20 final size:20
Alignment explanation
Indices: 90302--90477 Score: 115
Period size: 20 Copynumber: 8.7 Consensus size: 20
90292 GTTTCCAGAT
*
90302 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
90322 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
**
90342 TTCGCGTTGCGATTTTCTGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
90365 TCACAATGCGAATAT-A-TAA
1 TCGCAATGCGATTCTGACT-A
*
90384 ATCGCAATGCGATTATGACTA
1 -TCGCAATGCGATTCTGACTA
*
90405 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
90425 TCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
* * *
90445 TCACAACGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
*
90465 TCGCAATGGGATT
1 TCGCAATGCGATT
90478 TTCAAAGCGC
Statistics
Matches: 123, Mismatches: 24, Indels: 18
0.75 0.15 0.11
Matches are distributed among these distances:
18 1 0.01
19 4 0.03
20 92 0.75
21 12 0.10
22 9 0.07
23 3 0.02
24 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:90428 original size:40 final size:40
Alignment explanation
Indices: 90384--90477 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 40
90374 GAATATATAA
* *
90384 ATCGCAATGCGATTATGACTATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATTATGACTATCACAACGCGATGCTGACT
* **
90424 ATCGCAACGCGATGCTGACTATCACAACGCGATGCTGACT
1 ATCGCAATGCGATTATGACTATCACAACGCGATGCTGACT
*
90464 ATCGCAATGGGATT
1 ATCGCAATGCGATT
90478 TTCAAAGCGC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (40 bp):
ATCGCAATGCGATTATGACTATCACAACGCGATGCTGACT
Found at i:91127 original size:20 final size:20
Alignment explanation
Indices: 91062--91129 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
91052 AGAATCGCAA
* *
91062 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGTGT
**
91081 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
91101 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
91121 TGCGATTTT
1 TGCGATTTT
91130 AAGTTTCAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 7 0.17
20 35 0.83
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.50
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:92884 original size:18 final size:18
Alignment explanation
Indices: 92861--92910 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
92851 TTTACTCGTA
92861 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
92879 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
92897 ATTTCACTTAGATT
1 ATTTCACTTAGATT
92911 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:93028 original size:20 final size:20
Alignment explanation
Indices: 93003--93078 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
92993 TAATTTCATT
**
93003 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
93023 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
**
93043 TTTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
93063 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
93079 CGTGTTGCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:93620 original size:18 final size:19
Alignment explanation
Indices: 93581--93622 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
93571 CTCACATGTC
93581 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
93602 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
93620 ATC
1 ATC
93623 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:93631 original size:21 final size:22
Alignment explanation
Indices: 93607--93667 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
93597 CCCCTATCGT
93607 TCAAGAGGCCCCTATCATCC-C
1 TCAAGAGGCCCCTATCATCCGC
* * *
93628 TCAAGAGTCCCCTCTCA-CCGT
1 TCAAGAGGCCCCTATCATCCGC
* *
93649 TCAAGAGGCCACTGTCATC
1 TCAAGAGGCCCCTATCATC
93668 ATTGAAGAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.21
Consensus pattern (22 bp):
TCAAGAGGCCCCTATCATCCGC
Found at i:95291 original size:20 final size:20
Alignment explanation
Indices: 95253--95291 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
95243 ACACTAAACT
*
95253 CAAAATCGCAATGCAAAAGC
1 CAAAATCGCAACGCAAAAGC
*
95273 CAAAATCGCAACGCGAAAG
1 CAAAATCGCAACGCAAAAG
95292 TCAATTCGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.26, G:0.18, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAACGCAAAAGC
Found at i:95307 original size:19 final size:20
Alignment explanation
Indices: 95285--95327 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
95275 AAATCGCAAC
*
95285 GCGAAAGTC-AATTCGCGTT
1 GCGAAAGTCTAATACGCGTT
* *
95304 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCGTT
95324 GCGA
1 GCGA
95328 TTTTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCGTT
Found at i:95345 original size:34 final size:34
Alignment explanation
Indices: 95300--95436 Score: 139
Period size: 34 Copynumber: 3.9 Consensus size: 34
95290 AGTCAATTCG
* * *
95300 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACCCGTTGCGATTTTCT
* *
95334 CGTTGCAATAGTCAAATACCCGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATACCCGTTGCGAT--T----TTCT
* * * *
95374 CATTGCGATAGTCAAATTCGCATTGCGATTTTCT
1 CGTTGCGATAGTCAAATACCCGTTGCGATTTTCT
95408 CGTTGCGATAGTCAAATACCCGTTGCGAT
1 CGTTGCGATAGTCAAATACCCGTTGCGAT
95437 AATTAAATTC
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
34 53 0.65
36 1 0.01
38 1 0.01
40 27 0.33
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.34
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACCCGTTGCGATTTTCT
Found at i:95359 original size:20 final size:20
Alignment explanation
Indices: 95334--95496 Score: 113
Period size: 20 Copynumber: 8.4 Consensus size: 20
95324 GCGATTTTCT
*
95334 CGTTGCAATAGTCAAATACC
1 CGTTGCGATAGTCAAATACC
* * *
95354 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATACC
* * *
95374 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATACC
* * *
95394 CATTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATACC
95408 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATACC
* * * *
95428 CGTTGCGATAATTAAATTCG
1 CGTTGCGATAGTCAAATACC
* *
95448 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATACC
* * *
95468 CGTTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATACC
95488 CGTTGCGAT
1 CGTTGCGAT
95497 TTTTGCGTTA
Statistics
Matches: 120, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
14 11 0.09
16 1 0.01
18 1 0.01
20 107 0.89
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATACC
Found at i:95384 original size:74 final size:74
Alignment explanation
Indices: 95294--95476 Score: 303
Period size: 74 Copynumber: 2.5 Consensus size: 74
95284 CGCGAAAGTC
* * *
95294 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCAATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTCTCGTTGCAATAGTCAAATACCCGTTG
95359 CGATAATCA
66 CGATAATCA
* *
95368 AATTCGCATTGCGATAGTCAAATTCGCATTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTCTCGTTGCAATAGTCAAATACCCGTTG
*
95433 CGATAATTA
66 CGATAATCA
*
95442 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 AATTCGCGTTGCGATAGTCAAATTCGCATTGCGAT
95477 AGACAAATTC
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 101 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTCTCGTTGCAATAGTCAAATACCCGTTG
CGATAATCA
Found at i:95412 original size:54 final size:54
Alignment explanation
Indices: 95354--95456 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 54
95344 GTCAAATACC
* * *
95354 CGTTGCGATAATCAAATTCGCATTGCGATAGTCAAATTCGCATTGCGATTTTCT
1 CGTTGCGATAATCAAATACCCATTGCGATAATCAAATTCGCATTGCGATTTTCT
* * * *
95408 CGTTGCGATAGTCAAATACCCGTTGCGATAATTAAATTCGCGTTGCGAT
1 CGTTGCGATAATCAAATACCCATTGCGATAATCAAATTCGCATTGCGAT
95457 AGTCAAATTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (54 bp):
CGTTGCGATAATCAAATACCCATTGCGATAATCAAATTCGCATTGCGATTTTCT
Found at i:95432 original size:94 final size:94
Alignment explanation
Indices: 95334--95590 Score: 336
Period size: 94 Copynumber: 2.7 Consensus size: 94
95324 GCGATTTTCT
* * * * *
95334 CGTTGCAATAGTCAAATACCCGTTGCGATAATCAAATTCGCATTGCGATAGTCAAATTCGCATTG
1 CGTTGCGATAGTCAAATTCACGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
*
95399 CGATTTTCT-CGTTGCGATAGTCAAATACC
66 CGATTTT-TGCGTTACGATAGTCAAATACC
* * * * *
95428 CGTTGCGATAATTAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCACGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
* * * *
95493 CGATTTTTGCGTTATGATAGTCATATTCG
66 CGATTTTTGCGTTACGATAGTCAAATACC
* * *
95522 TGTTGCGATAGTCAAATTCACGTTGCAATAATCAAATTCGCGTTGTGATAGTCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCACGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
95587 CGAT
66 CGAT
95591 ATTCAAATGA
Statistics
Matches: 140, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
93 1 0.01
94 139 0.99
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (94 bp):
CGTTGCGATAGTCAAATTCACGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
CGATTTTTGCGTTACGATAGTCAAATACC
Found at i:95533 original size:20 final size:20
Alignment explanation
Indices: 95508--95598 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 20
95498 TTTGCGTTAT
* *
95508 GATAGTCATATTCGTGTTGC
1 GATAGTCAAATTCGCGTTGC
*
95528 GATAGTCAAATTCACGTTGC
1 GATAGTCAAATTCGCGTTGC
* * *
95548 AATAATCAAATTCGCGTTGT
1 GATAGTCAAATTCGCGTTGC
95568 GATAGTCAAATTCGCGTTGC
1 GATAGTCAAATTCGCGTTGC
*
95588 GATATTCAAAT
1 GATAGTCAAAT
95599 GAATGTGTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (20 bp):
GATAGTCAAATTCGCGTTGC
Found at i:98202 original size:24 final size:24
Alignment explanation
Indices: 98168--98221 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
98158 CTGAAACATC
*
98168 ATCAAAATCCGAGTATTTACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
98192 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
98216 ATCAAA
1 ATCAAA
98222 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:99073 original size:20 final size:20
Alignment explanation
Indices: 99050--99129 Score: 133
Period size: 20 Copynumber: 4.0 Consensus size: 20
99040 GTGTTGCAAC
*
99050 AGTCAGAATCGCGTTGCGAT
1 AGTCAGAATCGCATTGCGAT
*
99070 AGTCAGAATCGCGTTGCGAT
1 AGTCAGAATCGCATTGCGAT
99090 AGTCAGAATCGCATTGCGAT
1 AGTCAGAATCGCATTGCGAT
*
99110 AGTCATAATCGCATTGCGAT
1 AGTCAGAATCGCATTGCGAT
99130 TTACATATTC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (20 bp):
AGTCAGAATCGCATTGCGAT
Found at i:99136 original size:20 final size:20
Alignment explanation
Indices: 99098--99189 Score: 132
Period size: 20 Copynumber: 4.6 Consensus size: 20
99088 ATAGTCAGAA
* *
99098 TCGCATTGCGATAGT-CATAA
1 TCGCATTGCGAT-TTACATAT
99118 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
99138 TCGCATTGGGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
99158 TCGTATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
99178 TCGCATTGCGAT
1 TCGCATTGCGAT
99190 AGTCGGAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 1 0.02
20 64 0.98
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:99142 original size:40 final size:40
Alignment explanation
Indices: 99058--99193 Score: 150
Period size: 40 Copynumber: 3.4 Consensus size: 40
99048 ACAGTCAGAA
* * * * * *
99058 TCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGT-CAGAA
1 TCGCATTGCGATAGTCATAATCGCATTGCGAT-TTACATAT
99098 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
* * * *
99138 TCGCATTGGGAT-TTACATATTCGTATTGCGATTTACATAT
1 TCGCATTGCGATAGT-CATAATCGCATTGCGATTTACATAT
99178 TCGCATTGCGATAGTC
1 TCGCATTGCGATAGTC
99194 GGAAAATCGC
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 78 0.96
41 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
Found at i:103507 original size:15 final size:14
Alignment explanation
Indices: 103464--103522 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
103454 TAAATGAGAA
*
103464 ATAAT-AAAAAATT
1 ATAATAAAAAAAAT
* *
103477 ACAATTAAACAAAAT
1 ATAA-TAAAAAAAAT
103492 A-AAGTAAATAAAAAT
1 ATAA-TAAA-AAAAAT
103507 ATAATAAAAAAAAT
1 ATAATAAAAAAAAT
103521 AT
1 AT
103523 TGATGTATGC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 3 0.08
14 15 0.41
15 17 0.46
16 2 0.05
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (14 bp):
ATAATAAAAAAAAT
Found at i:103518 original size:14 final size:15
Alignment explanation
Indices: 103482--103522 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
103472 AAATTACAAT
*
103482 TAAACAAAATA-AAG
1 TAAAAAAAATATAAG
103496 TAAATAAAAATATAA-
1 TAAA-AAAAATATAAG
103511 TAAAAAAAATAT
1 TAAAAAAAATAT
103523 TGATGTATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.50
15 10 0.42
16 2 0.08
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
TAAAAAAAATATAAG
Found at i:105634 original size:17 final size:17
Alignment explanation
Indices: 105614--105651 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
105604 ATTATATTAG
*
105614 TAAAAT-ATTAAATAAAA
1 TAAAATAATAAAAT-AAA
105631 TAAAATAATAAAATAAA
1 TAAAATAATAAAATAAA
105648 TAAA
1 TAAA
105652 TTAAATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATAATAAAATAAA
Found at i:105657 original size:13 final size:13
Alignment explanation
Indices: 105622--105663 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
105612 AGTAAAATAT
105622 TAAATAAAATAAA
1 TAAATAAAATAAA
105635 -ATAATAAAATAAA
1 TA-AATAAAATAAA
* *
105648 TAAATTAAATACA
1 TAAATAAAATAAA
105661 TAA
1 TAA
105664 TATTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:105717 original size:10 final size:10
Alignment explanation
Indices: 105698--105728 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
105688 CTTAAACAGA
*
105698 GAGAGTATTT
1 GAGAGAATTT
105708 GAGAGAATTT
1 GAGAGAATTT
105718 GAGAGAATTT
1 GAGAGAATTT
105728 G
1 G
105729 GTGTGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:107774 original size:18 final size:19
Alignment explanation
Indices: 107740--107776 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
107730 CACGGAATGT
107740 AAGATTACCAGTGGGAATAA
1 AAGATTACCA-TGGGAATAA
107760 AAGATTACC-TGGGAATA
1 AAGATTACCATGGGAATA
107777 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (19 bp):
AAGATTACCATGGGAATAA
Found at i:111942 original size:2 final size:2
Alignment explanation
Indices: 111935--111979 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
111925 TTTACATTCT
111935 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
111977 TA T
1 TA T
111980 GACCTAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:121805 original size:18 final size:18
Alignment explanation
Indices: 121778--121822 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
121768 TTAAAATTTA
*
121778 ATTT-TTTTATA-TTAAT
1 ATTTATTTTATAGGTAAT
121794 AGTTTATTTTATAGGTAAT
1 A-TTTATTTTATAGGTAAT
121813 ATTTATTTTA
1 ATTTATTTTA
121823 AAATTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 3 0.12
18 16 0.64
19 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (18 bp):
ATTTATTTTATAGGTAAT
Found at i:125399 original size:42 final size:41
Alignment explanation
Indices: 125324--125417 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 41
125314 GAGCCTACAT
* ** *
125324 GGGTATATGCCCAACCACTAGTTCATATGCCACTGTCGCAG
1 GGGTACATGCCCAACCACTAGTTCATATGCCACTACCACAG
125365 GGGTACATGCCCAACCCAAC-AGTTCATATGCCACTACCACAG
1 GGGTACATGCCCAA-CC-ACTAGTTCATATGCCACTACCACAG
*
125407 GGATACATGCC
1 GGGTACATGCC
125418 AAGCCCGCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 13 0.28
42 31 0.67
43 2 0.04
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.20
Consensus pattern (41 bp):
GGGTACATGCCCAACCACTAGTTCATATGCCACTACCACAG
Found at i:125865 original size:46 final size:45
Alignment explanation
Indices: 125815--125909 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 45
125805 TTATGTAATG
* *
125815 TTTTTAATATT-TGTTTATATTTGTTAAATATTTAATGATTTTTTTA
1 TTTTTAAT-TTGTCTTTATAGTTGTTAAATATTTAAT-ATTTTTTTA
* * *
125861 TTTTTAATTTGTCTTTATGGTTGTTAAATGTTTAATTTTTTTTTA
1 TTTTTAATTTGTCTTTATAGTTGTTAAATATTTAATATTTTTTTA
125906 TTTT
1 TTTT
125910 GAAATAAGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
45 14 0.33
46 29 0.67
ACGTcount: A:0.23, C:0.01, G:0.08, T:0.67
Consensus pattern (45 bp):
TTTTTAATTTGTCTTTATAGTTGTTAAATATTTAATATTTTTTTA
Found at i:125940 original size:48 final size:45
Alignment explanation
Indices: 125828--125944 Score: 119
Period size: 46 Copynumber: 2.5 Consensus size: 45
125818 TTAATATTTG
* * * * * *
125828 TTTATATTTGTTAAATATTTAATGATTTTTTTATTTTTAATTTGTC
1 TTTATGTTTGTTAAATGTTTAAT-TTTTTTTTATTTTAAATGTGTA
*
125874 TTTATGGTTGTTAAATGTTTAATTTTTTTTTATTTTGAAATAAGTGTA
1 TTTATGTTTGTTAAATGTTTAATTTTTTTTTATTTT-AAAT--GTGTA
*
125922 TTTGTGTTTGTTAAATG-TTAATT
1 TTTATGTTTGTTAAATGTTTAATT
125945 ATATGATATT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
45 12 0.20
46 23 0.39
47 6 0.10
48 18 0.31
ACGTcount: A:0.26, C:0.01, G:0.12, T:0.62
Consensus pattern (45 bp):
TTTATGTTTGTTAAATGTTTAATTTTTTTTTATTTTAAATGTGTA
Found at i:126050 original size:18 final size:18
Alignment explanation
Indices: 126012--126051 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
126002 CATTGCTCCT
* *
126012 AATTAAAATTTATATTCA
1 AATTAAAATGTACATTCA
*
126030 AATTAAAATGTACATTGA
1 AATTAAAATGTACATTCA
126048 AATT
1 AATT
126052 GACATTACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (18 bp):
AATTAAAATGTACATTCA
Found at i:126812 original size:33 final size:34
Alignment explanation
Indices: 126769--126846 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
126759 GGGAAGTGAT
* *
126769 GACCACAAACAAAATGA-GAATTTTGAAAGTT-A
1 GACCAGAAACAAAATGAGGAATTTAGAAAGTTAA
* *
126801 GAACCAGAAACACAATGAGGACTTTAGAAAGTTAA
1 G-ACCAGAAACAAAATGAGGAATTTAGAAAGTTAA
126836 GACCAGAAACA
1 GACCAGAAACA
126847 TAATCTTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 1 0.03
33 14 0.36
34 22 0.56
35 2 0.05
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (34 bp):
GACCAGAAACAAAATGAGGAATTTAGAAAGTTAA
Found at i:126874 original size:2 final size:2
Alignment explanation
Indices: 126869--126954 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
126859 TATATATATA
126869 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
126911 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
126953 TG
1 TG
126955 GAAACTCTTC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:129009 original size:53 final size:53
Alignment explanation
Indices: 128941--129073 Score: 148
Period size: 53 Copynumber: 2.5 Consensus size: 53
128931 TTTCTATACT
* * *
128941 TGTGCTTTTCTAATATTTCAATATTGTACGTG-TT-TTTCTACTATTTTAATGT-A
1 TGTGTTTTTCTAATATTTC-A-A-TGTACGTGCTTGTTTCTAATATTTCAATGTAA
*
128994 TGTGTTTTTCTAATATTTCAATGTATGTGCTTGTTTCTAATATTTCAATGTAA
1 TGTGTTTTTCTAATATTTCAATGTACGTGCTTGTTTCTAATATTTCAATGTAA
129047 T-TGTATTTTCTAATATTTTTCAATGTA
1 TGTGT-TTTTCTAATA--TTTCAATGTA
129074 TGTGTATTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
50 7 0.10
51 3 0.04
52 20 0.29
53 30 0.43
55 10 0.14
ACGTcount: A:0.24, C:0.10, G:0.11, T:0.55
Consensus pattern (53 bp):
TGTGTTTTTCTAATATTTCAATGTACGTGCTTGTTTCTAATATTTCAATGTAA
Found at i:129079 original size:28 final size:25
Alignment explanation
Indices: 128941--129087 Score: 161
Period size: 28 Copynumber: 5.5 Consensus size: 25
128931 TTTCTATACT
*
128941 TGTGCTTTTCTAATATTTCAATATTGTA
1 TGTGTTTTTCTAATATTTC-A-A-TGTA
* * *
128969 CGTGTTTTTCTACTATTTTAATGTA
1 TGTGTTTTTCTAATATTTCAATGTA
128994 TGTGTTTTTCTAATATTTCAATGTA
1 TGTGTTTTTCTAATATTTCAATGTA
129019 TGTGCTTGTTTCTAATATTTCAATGTAA
1 TGTG-TT-TTTCTAATATTTCAATGT-A
129047 T-TGTATTTTCTAATATTTTTCAATGTA
1 TGTGT-TTTTCTAATA--TTTCAATGTA
129074 TGTGTATTTTCTAA
1 TGTGT-TTTTCTAA
129088 AAAAAATTGC
Statistics
Matches: 105, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
25 30 0.29
26 13 0.12
27 24 0.23
28 38 0.36
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.55
Consensus pattern (25 bp):
TGTGTTTTTCTAATATTTCAATGTA
Found at i:129164 original size:23 final size:23
Alignment explanation
Indices: 129138--129206 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
129128 TTCATTTTAA
129138 TTTAACCTTAAACCCAAAACCAC
1 TTTAACCTTAAACCCAAAACCAC
*
129161 TTTATCC-TAAACCCCAAAACCAC
1 TTTAACCTTAAA-CCCAAAACCAC
* *
129184 TTTAACCTAAAAACCCTAAACCA
1 TTTAACCT-TAAACCCAAAACCA
129207 TAGTAACCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
22 4 0.10
23 23 0.59
24 9 0.23
25 3 0.08
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (23 bp):
TTTAACCTTAAACCCAAAACCAC
Found at i:129171 original size:22 final size:23
Alignment explanation
Indices: 129138--129194 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
129128 TTCATTTTAA
129138 TTTAACCTTAAA-CCCAAAACCAC
1 TTTAACC-TAAACCCCAAAACCAC
*
129161 TTTATCCTAAACCCCAAAACCAC
1 TTTAACCTAAACCCCAAAACCAC
129184 TTTAACCTAAA
1 TTTAACCTAAA
129195 AACCCTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 4 0.13
23 27 0.87
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (23 bp):
TTTAACCTAAACCCCAAAACCAC
Found at i:129230 original size:25 final size:25
Alignment explanation
Indices: 129177--129295 Score: 125
Period size: 25 Copynumber: 4.8 Consensus size: 25
129167 CTAAACCCCA
*
129177 AAACCACTTTAACCTAAAA-ACCCT
1 AAACCACTCTAACCTAAAAGACCCT
*
129201 AAACCA-TAGTAACCTAAAAGACCCT
1 AAACCACT-CTAACCTAAAAGACCCT
*
129226 AAACCACTCTCACCTAAAAGACCCT
1 AAACCACTCTAACCTAAAAGACCCT
* * * *
129251 AAACCACTTTAACATAAAAAAACCTT
1 AAACCACTCTAACCT-AAAAGACCCT
* *
129277 AAATCACTCCAACCTAAAA
1 AAACCACTCTAACCTAAAA
129296 AACATTAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
23 1 0.01
24 16 0.20
25 42 0.53
26 20 0.25
ACGTcount: A:0.48, C:0.31, G:0.03, T:0.18
Consensus pattern (25 bp):
AAACCACTCTAACCTAAAAGACCCT
Found at i:129269 original size:50 final size:50
Alignment explanation
Indices: 129177--129296 Score: 129
Period size: 51 Copynumber: 2.4 Consensus size: 50
129167 CTAAACCCCA
* * * *
129177 AAACCACTTTAACCTAAAAACCCTAAACCATAGTAACCT-AAAAGACCCT
1 AAACCACTCTCACCTAAAAACCCTAAACCATAGTAACATAAAAAAACCCT
* *
129226 AAACCACTCTCACCTAAAAGACCCTAAACCACT-TTAACATAAAAAAACCTT
1 AAACCACTCTCACCTAAAA-ACCCTAAACCA-TAGTAACATAAAAAAACCCT
*
129277 AAATCACTC-CAACCTAAAAA
1 AAACCACTCTC-ACCTAAAAA
129297 ACATTAAAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
49 17 0.28
50 18 0.30
51 25 0.42
ACGTcount: A:0.48, C:0.31, G:0.03, T:0.18
Consensus pattern (50 bp):
AAACCACTCTCACCTAAAAACCCTAAACCATAGTAACATAAAAAAACCCT
Found at i:132328 original size:43 final size:43
Alignment explanation
Indices: 132279--132363 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
132269 AAGAAGTTAA
132279 AAAATCAAAACTAGAATC-TTTAACATACAAGAATCAGATGTCC
1 AAAATCAAAACTAGAA-CATTTAACATACAAGAATCAGATGTCC
* *
132322 AAAATCAAGACTAGAACATTTAACTTACAAGAATCAGATGTC
1 AAAATCAAAACTAGAACATTTAACATACAAGAATCAGATGTC
132364 AAGAATTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 38 0.97
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.24
Consensus pattern (43 bp):
AAAATCAAAACTAGAACATTTAACATACAAGAATCAGATGTCC
Found at i:138769 original size:33 final size:33
Alignment explanation
Indices: 138727--138792 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
138717 ATAGTAAAAG
*
138727 GATCAAACAAAGCATATTTGTGTCTCCAGCATA
1 GATCAAACAAAGAATATTTGTGTCTCCAGCATA
*
138760 GATCAAACAAAGAATATTTGTGTCTTCAGCATA
1 GATCAAACAAAGAATATTTGTGTCTCCAGCATA
138793 CGCTGAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (33 bp):
GATCAAACAAAGAATATTTGTGTCTCCAGCATA
Found at i:144512 original size:21 final size:21
Alignment explanation
Indices: 144488--144527 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
144478 TTTATTTTAT
144488 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
144509 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
144528 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:144575 original size:33 final size:33
Alignment explanation
Indices: 144522--144620 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
144512 TTTGTTTCAA
144522 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
144554 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
144587 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
144620 T
1 T
144621 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:144649 original size:13 final size:13
Alignment explanation
Indices: 144606--144660 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
144596 TTGGAAGTAT
144606 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
144619 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
144633 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
144646 TTAAGTATTTGAA
1 TTAAGTATTTCAA
144659 TT
1 TT
144661 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:144882 original size:21 final size:21
Alignment explanation
Indices: 144856--144912 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
144846 TGGAGCGTGG
*
144856 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
144877 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
144898 AGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
144913 AAGTGTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:145103 original size:15 final size:15
Alignment explanation
Indices: 145078--145116 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
145068 ATCTGGAATA
*
145078 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
145093 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
145108 TTAAAACCG
1 TTAAAACCG
145117 AAACCGGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:150499 original size:19 final size:21
Alignment explanation
Indices: 150452--150500 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
150442 CACTAACAAA
150452 CTAACTAATTAACAACAGCAAT
1 CTAACTAATTAACAACAGC-AT
*
150474 CTAACTAATTACCAACAGC-T
1 CTAACTAATTAACAACAGCAT
150494 -TAACTAA
1 CTAACTAA
150501 CTAAATATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 1 0.04
22 18 0.69
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.24
Consensus pattern (21 bp):
CTAACTAATTAACAACAGCAT
Found at i:151340 original size:132 final size:132
Alignment explanation
Indices: 151087--151325 Score: 313
Period size: 132 Copynumber: 1.8 Consensus size: 132
151077 TAAACATAAA
* * *
151087 TAAGATATTTACTTATTTAGAAATATCAGAAAAGAACTTCTAGGTGCTTTAAGACAGCTCTTTTC
1 TAAGATATTTACTTATTTAAAAATATCAGAAAAGAACTTCTAGGTACCTTAAGACAGCTCTTTTC
* * * ** *
151152 TTTGATATTAAAAAATAAATAAATTACTAAAACATTTTCTTGAGATAAAAAAATTATTTTAATAT
66 TTCGATATTAAAAAAAAAATAAATTACTAAAACATTATAATAAGATAAAAAAATTATTTTAATAT
151217 AG
131 AG
* ** *
151219 TAAGATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGGTACCTTAAGATAGCTCTTTTC
1 TAAGATATTTACTTATTTAAAAATATCAGAAAAGAACTTCTAGGTACCTTAAGACAGCTCTTTTC
*
151284 TTCGATATTAATAAATAAAAATAAA-TATTAAAA-A-TATAATAA
66 TTCGATATTAA-AAA-AAAAATAAATTACTAAAACATTATAATAA
151326 TTTAAATTAA
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
131 4 0.04
132 69 0.76
133 10 0.11
134 8 0.09
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (132 bp):
TAAGATATTTACTTATTTAAAAATATCAGAAAAGAACTTCTAGGTACCTTAAGACAGCTCTTTTC
TTCGATATTAAAAAAAAAATAAATTACTAAAACATTATAATAAGATAAAAAAATTATTTTAATAT
AG
Found at i:151528 original size:16 final size:16
Alignment explanation
Indices: 151509--151541 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
151499 AATAACAAAT
151509 TAATA-TTATAAATAAA
1 TAATATTTA-AAATAAA
151525 TAATATTTAAAATAAA
1 TAATATTTAAAATAAA
151541 T
1 T
151542 TTAAAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATTTAAAATAAA
Found at i:152779 original size:3 final size:3
Alignment explanation
Indices: 152763--152828 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
152753 TTTGGGCTTG
* *
152763 TAA TAA TTA T-A TAA TAA T-A TAA TAA TAA TAA TATT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
**
152807 TAA TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
152829 TTAAGTAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 4 0.08
3 47 0.89
4 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:152787 original size:19 final size:17
Alignment explanation
Indices: 152763--152828 Score: 71
Period size: 16 Copynumber: 3.8 Consensus size: 17
152753 TTTGGGCTTG
152763 TAATAATTATATAATAATA
1 TAATAA-TA-ATAATAATA
*
152782 TAATAATAATAAT-ATT
1 TAATAATAATAATAATA
152798 TAATAATAATAATAATAA
1 TAATAATAATAATAAT-A
**
152816 TTTTAATAATAAT
1 TAATAATAATAAT
152829 TTAAGTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 15 0.37
17 7 0.17
18 13 0.32
19 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATAATAATAATAATA
Found at i:152801 original size:16 final size:14
Alignment explanation
Indices: 152773--152816 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
152763 TAATAATTAT
152773 ATAATAATATAATA
1 ATAATAATATAATA
*
152787 ATAATAATAT-TTA
1 ATAATAATATAATA
152800 ATAATAATAATAATA
1 ATAATAAT-ATAATA
152815 AT
1 AT
152817 TTTAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 10 0.38
14 12 0.46
15 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAATAATATAATA
Found at i:153084 original size:76 final size:76
Alignment explanation
Indices: 152986--153843 Score: 1467
Period size: 75 Copynumber: 11.3 Consensus size: 76
152976 TCTTAAAAAT
*
152986 ATCATGCACTGCATGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
153051 TTTTTGGAAAC
66 TTTTTGGAAAC
*
153062 ATCATGCACTGCAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAAGCTCCCGAAGG
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAAGCTCCCGAAGG
153127 CTTTTTGGAAAC
65 CTTTTTGGAAAC
153139 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
153204 TTTTTGGAAAC
66 TTTTTGGAAAC
*
153215 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGTTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
153280 TTTTTGGAAAC
66 TTTTTGGAAAC
*
153291 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCTCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
153356 TTTTTGGAAAC
66 TTTTTGGAAAC
* * * *
153367 ATCATGCACTGTAGGAATTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGT
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
153432 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
153443 ATCATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCTCTCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
153507 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
153518 ATTATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
153582 TTTTTGGAAAC
66 TTTTTGGAAAC
* *
153593 ATCATGCACTGCAGGACTTACACATGACCCGAAGGC-TTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
153657 TTTTTGGAAAC
66 TTTTTGGAAAC
*
153668 ATCATGCACTGTAGGACTTACAGATGA-CCTGAAGGC-TTGAAAACATCAAAAAGCTCCCGAAGG
1 ATCATGCACTGCAGGACTTACAGATGACCCT-AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGG
153731 CTTTTTGGAAAC
65 CTTTTTGGAAAC
* * *
153743 ATCATGCACTGCAGGACTTATAGATGACACGAAGGC-TTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
153807 TTTTTGGAAAC
66 TTTTTGGAAAC
*
153818 ATCATGCACTACAGGACTTACAGATG
1 ATCATGCACTGCAGGACTTACAGATG
153844 TAGGAAATAG
Statistics
Matches: 749, Mismatches: 30, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
74 2 0.00
75 343 0.46
76 329 0.44
77 75 0.10
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
TTTTTGGAAAC
Found at i:154544 original size:22 final size:22
Alignment explanation
Indices: 154519--154595 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
154509 AATAAAGCTT
*
154519 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATCTA
*
154541 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
154563 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
154585 TCATCTTTGAA
1 TCATCTTTGAA
154596 GAGTGTAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:155093 original size:54 final size:54
Alignment explanation
Indices: 155025--155173 Score: 271
Period size: 54 Copynumber: 2.8 Consensus size: 54
155015 TGTAAAATAC
*
155025 TTGACAACATATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAGCAT
1 TTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAGCAT
* *
155079 TTGACAACACATTCATCCTTTTCTGTGGCTTTTGCTTAGATGTTCGTAAAGCAT
1 TTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAGCAT
155133 TTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
1 TTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
155174 TTCTCAATCA
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 90 1.00
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (54 bp):
TTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAGCAT
Found at i:156957 original size:30 final size:30
Alignment explanation
Indices: 156921--156992 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
156911 CCCGCAGGAC
**
156921 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGACAA
156951 CTATCCAGAGGTCATAAAGATCCTCGACAA
1 CTATCCAGAGGTCATAAAGATCCTCGACAA
*
156981 CTATCCATAGGT
1 CTATCCAGAGGT
156993 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGACAA
Found at i:157052 original size:31 final size:31
Alignment explanation
Indices: 157017--157103 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 31
157007 GTGAACTATA
*
157017 CATATGTTCCTTAGAACATAGGTATACTGTC
1 CATATGTTCCATAGAACATAGGTATACTGTC
* * *
157048 CATATGTCTCGAAAG-ACATAGGTAATTCTGTC
1 CATATGT-TCCATAGAACATAGGT-ATACTGTC
*
157080 CATATGTTCCGTAGAACATAGGTA
1 CATATGTTCCATAGAACATAGGTA
157104 CCCTTGACTC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
31 20 0.43
32 26 0.57
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (31 bp):
CATATGTTCCATAGAACATAGGTATACTGTC
Found at i:157099 original size:32 final size:32
Alignment explanation
Indices: 156984--157103 Score: 113
Period size: 31 Copynumber: 3.8 Consensus size: 32
156974 TCGACAACTA
* * * * *
156984 TCCATAGGTTCCGAAGAACCTAGGTGA-ACTA
1 TCCATATGTTCCGTAGAACATAGGTAATACTG
* *
157015 TACATATGTTCCTTAGAACATAGGT-ATACTG
1 TCCATATGTTCCGTAGAACATAGGTAATACTG
* *
157046 TCCATATG-TCTCG-AAAGACATAGGTAATTCTG
1 TCCATATGTTC-CGTAGA-ACATAGGTAATACTG
157078 TCCATATGTTCCGTAGAACATAGGTA
1 TCCATATGTTCCGTAGAACATAGGTA
157104 CCCTTGACTC
Statistics
Matches: 72, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
30 5 0.07
31 39 0.54
32 24 0.33
33 4 0.06
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (32 bp):
TCCATATGTTCCGTAGAACATAGGTAATACTG
Found at i:159672 original size:31 final size:31
Alignment explanation
Indices: 159637--159699 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
159627 AGAGATGTGG
159637 TCTGAATTCATCAATTGCAGAGTTGACAGAT
1 TCTGAATTCATCAATTGCAGAGTTGACAGAT
159668 TCTGAATTCATCAATTGCAGAGTTGACAGAT
1 TCTGAATTCATCAATTGCAGAGTTGACAGAT
159699 T
1 T
159700 TTATATGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (31 bp):
TCTGAATTCATCAATTGCAGAGTTGACAGAT
Found at i:160077 original size:114 final size:114
Alignment explanation
Indices: 159877--160204 Score: 539
Period size: 114 Copynumber: 2.9 Consensus size: 114
159867 GATCATGCAG
* * * * * * *
159877 TTCATCTTTCAATTCCAATGATTGGTTATGGGGTTCCTACCGAACCAGATCAGATAACTCAAATA
1 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
159942 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATATTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATATTATGAGCAAA
*
159991 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATTAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
160056 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTATTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATATTATGAGCAAA
* * *
160105 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTCCATATCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
160170 ACACTTCCAGAAGATGCTATTGGGTCTCTTTATTT
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTT
160205 CTACTACAAG
Statistics
Matches: 200, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 200 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATATTATGAGCAAA
Found at i:167585 original size:2 final size:2
Alignment explanation
Indices: 167578--167605 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
167568 TTATTATTTA
167578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
167606 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:168644 original size:22 final size:22
Alignment explanation
Indices: 168601--168653 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
168591 TTATTAATAA
168601 TAAT-ATAATATAATAATATTT
1 TAATAATAATATAATAATATTT
168622 TAATAATAATAATAATAAT-TTT
1 TAATAATAAT-ATAATAATATTT
168644 TAATAATAAT
1 TAATAATAAT
168654 TTAAGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.13
22 18 0.60
23 8 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATAATAATATAATAATATTT
Found at i:168648 original size:33 final size:30
Alignment explanation
Indices: 168586--168657 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 30
168576 TTTGGGCTTG
*
168586 TAATATTATTAATAATAATATAATATAATAA
1 TAAT-TTAATAATAATAATATAATATAATAA
* *
168617 TATTTTAATAATAATAATAATAATTTTTAATAA
1 TAATTTAATAATAATAAT-ATAA--TATAATAA
168650 TAATTTAA
1 TAATTTAA
168658 GTAAAATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 13 0.38
31 7 0.21
33 14 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TAATTTAATAATAATAATATAATATAATAA
Found at i:168653 original size:3 final size:3
Alignment explanation
Indices: 168595--168640 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
168585 GTAATATTAT
**
168595 TAA TAA TAA T-A TAA T-A TAA TAA T-A TTT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
168640 T
1 T
168641 TTTTAATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
2 6 0.16
3 31 0.84
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:173041 original size:19 final size:21
Alignment explanation
Indices: 172994--173042 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
172984 CACTAACAAA
172994 CTAACTAATTAACAACAGCAAT
1 CTAACTAATTAACAACAGC-AT
*
173016 CTAACTAATTATCAACAGC-T
1 CTAACTAATTAACAACAGCAT
173036 -TAACTAA
1 CTAACTAA
173043 CTAAATATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 1 0.04
22 18 0.69
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (21 bp):
CTAACTAATTAACAACAGCAT
Found at i:181042 original size:27 final size:29
Alignment explanation
Indices: 181012--181065 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
181002 AACAAAAGAA
181012 AATAATAATAAAAAATAT-TA-ATATAAT
1 AATAATAATAAAAAATATATATATATAAT
* *
181039 AATATTAATAAAATATATATATATATA
1 AATAATAATAAAAAATATATATATATA
181066 TATATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
28 2 0.09
29 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AATAATAATAAAAAATATATATATATAAT
Found at i:181054 original size:11 final size:13
Alignment explanation
Indices: 181010--181048 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
181000 TAAACAAAAG
* *
181010 AAAATAATAATAA
1 AAAATATTAATAT
181023 AAAATATTAATAT
1 AAAATATTAATAT
181036 AATAATATTAATA
1 AA-AATATTAATA
181049 AAATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAATATTAATAT
Found at i:181058 original size:2 final size:2
Alignment explanation
Indices: 181051--181081 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
181041 TATTAATAAA
181051 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
181082 ACAATGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:181070 original size:27 final size:27
Alignment explanation
Indices: 181012--181074 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 27
181002 AACAAAAGAA
*
181012 AATAATAATAAAAAATATTAATATAAT
1 AATATTAATAAAAAATATTAATATAAT
*
181039 AATATTAATAAAATATATATATATATATAT
1 AATATTAATAAAAAATAT-TA-ATATA-AT
181069 ATATAT
1 A-ATAT
181075 ATATATAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 16 0.53
28 2 0.07
29 5 0.17
30 3 0.10
31 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AATATTAATAAAAAATATTAATATAAT
Found at i:181520 original size:33 final size:33
Alignment explanation
Indices: 181439--181520 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
181429 AGTCATACTT
*
181439 GGACTCAAATGC-TTCAGTTTTAGTGTTTCAATA
1 GGACTCAAATGCGTT-GGTTTTAGTGTTTCAATA
*
181472 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATGCGTTGGTTTTAGTGTTTCAATA
*
181505 TGACTCAAATGCGTTG
1 GGACTCAAATGCGTTG
181521 ATTTATTTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 42 0.95
34 2 0.05
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (33 bp):
GGACTCAAATGCGTTGGTTTTAGTGTTTCAATA
Found at i:181603 original size:24 final size:25
Alignment explanation
Indices: 181574--181621 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
181564 GGCCTACAAA
*
181574 AATAAAAAAAATATTAT-TAATAAT
1 AATAAAAAAAATATAATATAATAAT
*
181598 AATAAATAAAATATAATATAATAA
1 AATAAAAAAAATATAATATAATAA
181622 ATTTTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AATAAAAAAAATATAATATAATAAT
Found at i:182151 original size:83 final size:82
Alignment explanation
Indices: 181969--182226 Score: 331
Period size: 83 Copynumber: 3.1 Consensus size: 82
181959 AATGGAATCA
* * * *
181969 AACTCGAAGGTCTTTG--GCAGATATCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGGTGCCT
1 AACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGAT-GTGCCT
* * *
182032 TTGAGCTGAGTGGAGTCG
65 TGGAGCTGAGCGTAGTCG
* *
182050 AACTCGGAGGTCATTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCT
1 AACTCGAAGGTCTTTGTTG-CAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCT
182115 TGGAGCTGAGCGTAGTCG
65 TGGAGCTGAGCGTAGTCG
* * * *
182133 AACTCCAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATTATGTGCAT
1 AACTCGAAGGTCTTTGTT-GCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCT
* * *
182198 TGAAGTTGAGCGTAGTCA
65 TGGAGCTGAGCGTAGTCG
182216 AACTCGAAGGT
1 AACTCGAAGGT
182227 TTGATGTTTC
Statistics
Matches: 154, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
81 14 0.09
83 104 0.68
84 36 0.23
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (82 bp):
AACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCTT
GGAGCTGAGCGTAGTCG
Found at i:182306 original size:36 final size:36
Alignment explanation
Indices: 182259--182375 Score: 180
Period size: 36 Copynumber: 3.2 Consensus size: 36
182249 TTCAAAGGTT
182259 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
182295 TTTGTATCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
182331 TTTGTTTCAAGAGAAACTGTCTCAAAAGAGATAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGA-CAAAA
182368 CTTTGTTT
1 -TTTGTTT
182376 TGAGTAAATT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
36 63 0.85
37 4 0.05
38 7 0.09
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:182342 original size:21 final size:21
Alignment explanation
Indices: 182280--182344 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
182270 GGAAACTGTC
182280 TCAAGAGAGACAAAATTTGTA
1 TCAAGAGAGACAAAATTTGTA
* *
182301 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTA
*
182316 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTA
182337 TCAAGAGA
1 TCAAGAGA
182345 AACTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 16 0.47
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTA
Found at i:183218 original size:110 final size:110
Alignment explanation
Indices: 183084--183409 Score: 485
Period size: 110 Copynumber: 3.0 Consensus size: 110
183074 ATGTATCGTT
* **
183084 TCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATT-AGCTCTGAATGAAACTGTGAAGTTGTTTG
1 TCAAGTCCAATATCCTTCGATGTGAAGTTGAAATTGA-CTCTGAATGAAACTGAAAAGTTGTTTG
*
183148 TTGATAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
65 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
** * * *
183194 TCGTGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAAC-AAAAATGTTGTTTG
1 TCAAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAA-GTTGTTTG
183258 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
65 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
183304 TCAAGTCCAATATCCTTCGATGTGAAGTTAAAATTGACTCTGAATGAAATTGAAAAGTTATTTGT
1 TCAAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * *
183369 TAACAGTCAGTCACCCCTTCGTTGTGAAGTTGAGCTTGTGT
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGT
183410 CATCAATTTC
Statistics
Matches: 194, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
109 2 0.01
110 187 0.96
111 5 0.03
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (110 bp):
TCAAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:187141 original size:14 final size:13
Alignment explanation
Indices: 187113--187147 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
187103 GAGAAAAGAA
187113 TAATAAAATATAT
1 TAATAAAATATAT
*
187126 TAATATAATAATAT
1 TAATAAAAT-ATAT
187140 TAATAAAA
1 TAATAAAA
187148 AATAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAATAAAATATAT
Found at i:187151 original size:13 final size:13
Alignment explanation
Indices: 187113--187151 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
187103 GAGAAAAGAA
*
187113 TAATAAAATATAT
1 TAATAAAAAATAT
*
187126 TAATATAATAATAT
1 TAATA-AAAAATAT
187140 TAATAAAAAATA
1 TAATAAAAAATA
187152 AATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAAAAAATAT
Found at i:187562 original size:33 final size:33
Alignment explanation
Indices: 187525--187602 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
187515 AGTCATACTT
*
187525 GGACTCAAATGC-TTCAGTTTTAGTGTTTTAATA
1 GGACTCAAATGCGTT-AGTTTTAGTGTTTCAATA
* *
187558 GGACTCAAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAATGCGTTAGTTTTAGTGTTTCAATA
*
187591 TGACTCAAATGC
1 GGACTCAAATGC
187603 ATTGATTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 37 0.95
34 2 0.05
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.38
Consensus pattern (33 bp):
GGACTCAAATGCGTTAGTTTTAGTGTTTCAATA
Found at i:192603 original size:30 final size:29
Alignment explanation
Indices: 192569--192625 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
192559 TATAGATAAA
192569 TTATTAAAATTATATAATTATAATTTAAGT
1 TTATTAAAATTATAT-ATTATAATTTAAGT
* **
192599 TTATTTATTTTATATATTATAATTTAA
1 TTATTAAAATTATATATTATAATTTAA
192626 ATATTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (29 bp):
TTATTAAAATTATATATTATAATTTAAGT
Found at i:192625 original size:29 final size:31
Alignment explanation
Indices: 192578--192635 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
192568 ATTATTAAAA
*
192578 TTATATAATTATAATTTAAGT-TTATTTATT
1 TTATATAATTATAATTTAAATATTATTTATT
192608 TTATAT-ATTATAATTTAAATATTATTTA
1 TTATATAATTATAATTTAAATATTATTTA
192636 AACACATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (31 bp):
TTATATAATTATAATTTAAATATTATTTATT
Found at i:206173 original size:15 final size:15
Alignment explanation
Indices: 206153--206182 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
206143 TATCACAATC
206153 GCGCAGGATTTCGGG
1 GCGCAGGATTTCGGG
206168 GCGCAGGATTTCGGG
1 GCGCAGGATTTCGGG
206183 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.47, T:0.20
Consensus pattern (15 bp):
GCGCAGGATTTCGGG
Found at i:211139 original size:15 final size:15
Alignment explanation
Indices: 211119--211148 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
211109 TATCACAATC
211119 GCGCAGGATTTCGGG
1 GCGCAGGATTTCGGG
211134 GCGCAGGATTTCGGG
1 GCGCAGGATTTCGGG
211149 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.47, T:0.20
Consensus pattern (15 bp):
GCGCAGGATTTCGGG
Found at i:217060 original size:5 final size:5
Alignment explanation
Indices: 217050--217076 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
217040 CGGGAACAAC
217050 CAAAA CAAAA CAAAA CAAAA CAAAA CA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CA
217077 GAATGCAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:220935 original size:20 final size:19
Alignment explanation
Indices: 220897--220934 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
220887 ATGCAGTAAT
220897 TTGGTTTTGAGCAAAAAAA
1 TTGGTTTTGAGCAAAAAAA
220916 TTGGTTTTGAGCAAAAAAA
1 TTGGTTTTGAGCAAAAAAA
220935 AAAGTAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (19 bp):
TTGGTTTTGAGCAAAAAAA
Found at i:221403 original size:11 final size:11
Alignment explanation
Indices: 221366--221408 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
221356 TTTTTCCCCT
221366 TTTTGTGTTAA
1 TTTTGTGTTAA
*
221377 TTTCTG-GTTGAT
1 TTT-TGTGTT-AA
221389 TTTTGTGTTAA
1 TTTTGTGTTAA
221400 TTTTGTGTT
1 TTTTGTGTT
221409 TTAATATTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.12, C:0.02, G:0.21, T:0.65
Consensus pattern (11 bp):
TTTTGTGTTAA
Found at i:224056 original size:33 final size:33
Alignment explanation
Indices: 224018--224100 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
224008 CCCGAACCCG
*
224018 AAAATATTTTATATATAATTAATAAAAAAATAT
1 AAAATATTATATATATAATTAATAAAAAAATAT
*
224051 AAAATATTATATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATAAAAAAATAT
*
224084 AAAAAATTATATATATA
1 AAAATATTATATATATA
224101 TATATAATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATAAAAAAATAT
Found at i:231425 original size:23 final size:23
Alignment explanation
Indices: 231357--231425 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
231347 CAACCTTATA
231357 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
231380 TGGCACTACGTTGTAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
231403 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
231426 AGTTATGGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:238316 original size:23 final size:22
Alignment explanation
Indices: 238277--238321 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
238267 TTATTATATT
*
238277 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
238300 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
238322 ATATTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:238328 original size:17 final size:18
Alignment explanation
Indices: 238291--238329 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
238281 ATATTTTGTA
238291 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
238309 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
238326 TTTA
1 TTTA
238330 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:244350 original size:49 final size:48
Alignment explanation
Indices: 244234--244350 Score: 137
Period size: 49 Copynumber: 2.4 Consensus size: 48
244224 AGGCGCAGTA
* * * *
244234 CCTGCACCGCGCCTTATATAATTATATCAGTTAAAGGTATGGTGCGGCC
1 CCTGCCCCGCGTC-TATATAATTATATCAGTTAAAGGTAAGGCGCGGCC
* *
244283 CCTGCCCCGTGTTATATATAATTATATCAGAATTAAAGGTAAGGCGCGGCC
1 CCTGCCCCGCG-TCTATATAATTATATCAG--TTAAAGGTAAGGCGCGGCC
244334 CCTGCCCCGCG-CTATAT
1 CCTGCCCCGCGTCTATAT
244351 CCCTACGTGG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
49 30 0.53
51 27 0.47
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (48 bp):
CCTGCCCCGCGTCTATATAATTATATCAGTTAAAGGTAAGGCGCGGCC
Found at i:244350 original size:51 final size:49
Alignment explanation
Indices: 244234--244350 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 49
244224 AGGCGCAGTA
* * *
244234 CCTGCACCGCGCCT-TATATAATTATATCAGTTAAAGGTATGGTGCGGCC
1 CCTGCCCCGCG-CTATATATAATTATATCAGTTAAAGGTAAGGCGCGGCC
* *
244283 CCTGCCCCGTGTTATATATAATTATATCAGAATTAAAGGTAAGGCGCGGCC
1 CCTGCCCCGCGCTATATATAATTATATCAG--TTAAAGGTAAGGCGCGGCC
244334 CCTGCCCCGCGCTATAT
1 CCTGCCCCGCGCTATAT
244351 CCCTACGTGG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 1 0.02
49 25 0.43
51 32 0.55
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (49 bp):
CCTGCCCCGCGCTATATATAATTATATCAGTTAAAGGTAAGGCGCGGCC
Found at i:250015 original size:61 final size:61
Alignment explanation
Indices: 249917--250036 Score: 186
Period size: 61 Copynumber: 2.0 Consensus size: 61
249907 CAATCTCTCG
* * **
249917 AAAACAAATGCAATCCGCATGGCAATTTGCGACCTAAATGAACAATATAATAATTTAAACA
1 AAAACAAATGCAATCCACATAGCAATTCACGACCTAAATGAACAATATAATAATTTAAACA
* *
249978 AAAACAAATGCAATCCACATAGCAATTCATGATCTAAATGAACAATATAATAATTTAAA
1 AAAACAAATGCAATCCACATAGCAATTCACGACCTAAATGAACAATATAATAATTTAAA
250037 AGGCGTAGGA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (61 bp):
AAAACAAATGCAATCCACATAGCAATTCACGACCTAAATGAACAATATAATAATTTAAACA
Found at i:252504 original size:98 final size:100
Alignment explanation
Indices: 252330--252526 Score: 353
Period size: 99 Copynumber: 2.0 Consensus size: 100
252320 GGATAAAACT
** *
252330 TTAACCACAGCCGGACAGCACTTTACAAATCCTATGGAAAACAACTCAAATTACAAACCATGATG
1 TTAACCACAGCCGGACAGCACTCAACAAATCCTATGGAAAACAACTCAAATTACAAACAATGATG
252395 CTATAATCC-AAAAACAGAAACCACTGTTTATTTC
66 CTATAATCCAAAAAACAGAAACCACTGTTTATTTC
252429 TTAACCACAGCCGGACAGCACTCAACAAATCCTATGG-AAACAACTCAAATTACAAACAATGATG
1 TTAACCACAGCCGGACAGCACTCAACAAATCCTATGGAAAACAACTCAAATTACAAACAATGATG
252493 CTATAATCCAAAAAACAGAAACCACTGTTTATTT
66 CTATAATCCAAAAAACAGAAACCACTGTTTATTT
252527 TCTTCTGTCA
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
98 35 0.37
99 59 0.63
ACGTcount: A:0.43, C:0.25, G:0.10, T:0.22
Consensus pattern (100 bp):
TTAACCACAGCCGGACAGCACTCAACAAATCCTATGGAAAACAACTCAAATTACAAACAATGATG
CTATAATCCAAAAAACAGAAACCACTGTTTATTTC
Found at i:263352 original size:20 final size:20
Alignment explanation
Indices: 263323--263360 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
263313 CCCCTTCAAA
*
263323 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
263343 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
263361 TGCACCAAAA
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:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:281372 original size:17 final size:16
Alignment explanation
Indices: 281350--281384 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
281340 TTTCCATACT
*
281350 ATCCAATTCCAAATAAA
1 ATCCAATT-CAAACAAA
281367 ATCCAATTCAAACAAA
1 ATCCAATTCAAACAAA
281383 AT
1 AT
281385 ATTCTTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (16 bp):
ATCCAATTCAAACAAA
Found at i:287396 original size:2 final size:2
Alignment explanation
Indices: 287389--287415 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
287379 AATTATTTGA
287389 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
287416 ATAATAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:288722 original size:3 final size:3
Alignment explanation
Indices: 288716--288773 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
288706 TTTTTTTAAT
* * *
288716 TTA TTA TT- TTA TT- TTA TTA GTA TTA TTA TTA TTA TTA TTA GTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
288762 TTA TTA TTA TTA
1 TTA TTA TTA TTA
288774 ATTTACATGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:290381 original size:30 final size:30
Alignment explanation
Indices: 290314--290382 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
290304 CCCCTAGGTT
* * **
290314 TTCTGTTTTTGTTATTTGGATCCTTTAATT
1 TTCTGTTTTTGTCATTTAGATCCTTTAAAC
*
290344 TTATGTTTTTGTCATTTTAG-TCCTTTAAAC
1 TTCTGTTTTTGTCA-TTTAGATCCTTTAAAC
290374 TTCTGTTTT
1 TTCTGTTTT
290383 AGTTTTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.62
Consensus pattern (30 bp):
TTCTGTTTTTGTCATTTAGATCCTTTAAAC
Found at i:293506 original size:20 final size:20
Alignment explanation
Indices: 293481--293541 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
293471 ACATTCCCTC
293481 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
293501 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
*
293521 TCTTT-ACGGCCTTGAAACAT
1 TCTTTGA-GACCTTGAAACAT
293541 T
1 T
293542 GCATTTATCC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
TCTTTGAGACCTTGAAACAT
Found at i:294163 original size:16 final size:14
Alignment explanation
Indices: 294151--294214 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
294141 TAAAGAAAAT
294151 CAAAGAGAAAGAAA
1 CAAAGAGAAAGAAA
*
294165 CAAAGAGAAAAACAA
1 CAAAGAGAAAGA-AA
*
294180 GCAGAAAGAAAAAGAAA
1 -C--AAAGAGAAAGAAA
*
294197 -AAAGA-AAAAAAA
1 CAAAGAGAAAGAAA
294209 CAAAGA
1 CAAAGA
294215 AAAAAGAGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
12 6 0.15
13 10 0.24
14 11 0.27
15 2 0.05
16 1 0.02
17 2 0.05
18 9 0.22
ACGTcount: A:0.75, C:0.08, G:0.17, T:0.00
Consensus pattern (14 bp):
CAAAGAGAAAGAAA
Found at i:294205 original size:8 final size:7
Alignment explanation
Indices: 294184--294221 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
294174 AAACAAGCAG
294184 AAAG-AA
1 AAAGAAA
294190 AAAGAAA
1 AAAGAAA
294197 AAAGAAA
1 AAAGAAA
*
294204 AAA-AAC
1 AAAGAAA
294210 AAAGAAA
1 AAAGAAA
294217 AAAGA
1 AAAGA
294222 GGACAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 9 0.32
7 19 0.68
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:294213 original size:26 final size:28
Alignment explanation
Indices: 294146--294218 Score: 78
Period size: 32 Copynumber: 2.5 Consensus size: 28
294136 AAGAATAAAG
* *
294146 AAAATCAAAGAGAAAGAAACAAAGAGAA
1 AAAAACAAAGAAAAAGAAACAAAGAGAA
294174 AAACAAGCAGAAAGAAAAAGAAA-AAAGA-AA
1 AAA-AA-C--AAAGAAAAAGAAACAAAGAGAA
294204 AAAAACAAAGAAAAA
1 AAAAACAAAGAAAAA
294219 AGAGGACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 9 0.23
28 4 0.10
29 3 0.08
30 6 0.15
31 5 0.13
32 12 0.31
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (28 bp):
AAAAACAAAGAAAAAGAAACAAAGAGAA
Found at i:294230 original size:16 final size:13
Alignment explanation
Indices: 294146--294219 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 13
294136 AAGAATAAAG
*
294146 AAAATCAAAGAGAA
1 AAAAACAAAGA-AA
*
294160 AGAAACAAAGAGAA
1 AAAAACAAAGA-AA
294174 AAACAAGCAGAAAGAAA
1 AAA-AA-C--AAAGAAA
294191 AAGAAA-AAAGAAA
1 AA-AAACAAAGAAA
294204 AAAAACAAAGAAA
1 AAAAACAAAGAAA
294217 AAA
1 AAA
294220 GAGGACAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
12 3 0.06
13 19 0.37
14 14 0.27
15 2 0.04
16 1 0.02
17 6 0.12
18 6 0.12
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (13 bp):
AAAAACAAAGAAA
Found at i:295418 original size:2 final size:2
Alignment explanation
Indices: 295411--295507 Score: 194
Period size: 2 Copynumber: 48.5 Consensus size: 2
295401 TTAAGATAAG
295411 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
295453 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
295495 CA CA CA CA CA CA C
1 CA CA CA CA CA CA C
295508 GTACGTTAAA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 95 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.