Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001426.1 Hibiscus syriacus cultivar Beakdansim tig00002771_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: 202343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4629 original size:2 final size:2
Alignment explanation
Indices: 4622--4668 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4612 CAATGCAGTA
4622 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
4664 AT AT A
1 AT AT A
4669 GATGACATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5429 original size:18 final size:18
Alignment explanation
Indices: 5406--5440 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5396 TCTAAAATTA
5406 TTATATATTTTATATTTT
1 TTATATATTTTATATTTT
*
5424 TTATATATTTTTTATTT
1 TTATATATTTTATATTT
5441 AAAATTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATATATTTTATATTTT
Found at i:6004 original size:14 final size:14
Alignment explanation
Indices: 5985--6029 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
5975 CTACGAAAAC
5985 ATTATATTATTATT
1 ATTATATTATTATT
5999 ATTATATTATTATT
1 ATTATATTATTATT
*
6013 -TTTTATTAATTA-T
1 ATTATATT-ATTATT
6026 ATTA
1 ATTA
6030 ATGATTTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATATTATTATT
Found at i:6011 original size:22 final size:22
Alignment explanation
Indices: 5985--6029 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5975 CTACGAAAAC
5985 ATTATATTATTATT-ATTATATT
1 ATTAT-TTATTATTAATTATATT
*
6007 ATTATTTTTTATTAATTATATT
1 ATTATTTATTATTAATTATATT
6029 A
1 A
6030 ATGATTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTATTTATTATTAATTATATT
Found at i:6037 original size:22 final size:21
Alignment explanation
Indices: 5994--6037 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
5984 CATTATATTA
*
5994 TTATTATTATATTATTATTTT
1 TTATTATTATATTATGATTTT
6015 TTATTAATTATATTAATGATTTT
1 TTATT-ATTATATT-ATGATTTT
6038 GCAGGCCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTATTATTATATTATGATTTT
Found at i:7337 original size:21 final size:20
Alignment explanation
Indices: 7299--7337 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
7289 TATTTTAACA
*
7299 TTTTTTCTCTTAATTTATAT
1 TTTTTTCTCTTAAGTTATAT
*
7319 TTTTTTCCTCTTTAGTTAT
1 TTTTTT-CTCTTAAGTTAT
7338 TTAGTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.15, C:0.13, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTTTCTCTTAAGTTATAT
Found at i:10343 original size:12 final size:12
Alignment explanation
Indices: 10321--10386 Score: 71
Period size: 12 Copynumber: 5.2 Consensus size: 12
10311 TAAGAAGCAA
10321 AAAAGGAAAAAAG
1 AAAA-GAAAAAAG
10334 AAAAGAAAAAAG
1 AAAAGAAAAAAG
10346 AAAAGAAACAAA-
1 AAAAGAAA-AAAG
* *
10358 AAAGGAAAAAAAAC
1 AAA--AGAAAAAAG
10372 AAAAGAAAAAAG
1 AAAAGAAAAAAG
10384 AAA
1 AAA
10387 GAGCAAAGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
12 29 0.63
13 10 0.22
14 7 0.15
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:10359 original size:36 final size:37
Alignment explanation
Indices: 10312--10386 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 37
10302 AAGATTCAAT
* *
10312 AAGAAGCAAAAAAGG-AAAAAAGAAAAGAAAAAAGAA
1 AAGAAACAAAAAAGGAAAAAAACAAAAGAAAAAAGAA
10348 AAGAAACAAAAAAGGAAAAAAAACAAAAGAAAAAAGAA
1 AAGAAACAAAAAAGG-AAAAAAACAAAAGAAAAAAGAA
10386 A
1 A
10387 GAGCAAAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 14 0.40
38 21 0.60
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (37 bp):
AAGAAACAAAAAAGGAAAAAAACAAAAGAAAAAAGAA
Found at i:11347 original size:3 final size:3
Alignment explanation
Indices: 11335--11384 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
11325 CTACGAAAAC
* *
11335 ATT A-T ATT ATT ATT ATT ATT A-T ATT ATT TTT ATT TTT ATT AATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
11379 A-T ATT A
1 ATT ATT A
11385 ATGATTTTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 6 0.15
3 30 0.77
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12693 original size:19 final size:19
Alignment explanation
Indices: 12652--12693 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12642 ATATTTTAAC
*
12652 ATTTTTTCTCTTAATTTAT
1 ATTTTTTCTCTTAAGTTAT
*
12671 ATTTTTTCCTCTTTAGTTA-
1 ATTTTTT-CTCTTAAGTTAT
12690 ATTT
1 ATTT
12694 AGTATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTTCTCTTAAGTTAT
Found at i:15619 original size:18 final size:18
Alignment explanation
Indices: 15576--15613 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
15566 GTGAAGTATG
*
15576 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
15594 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
15612 AA
1 AA
15614 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:21460 original size:19 final size:19
Alignment explanation
Indices: 21424--21461 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21414 CCCTCTTTAA
*
21424 ACTTTTTTTTTTCTTTTTG
1 ACTTTTTTTTTTCATTTTG
*
21443 ACTTTTTTTTTTGATTTTG
1 ACTTTTTTTTTTCATTTTG
21462 TACTGACCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (19 bp):
ACTTTTTTTTTTCATTTTG
Found at i:25075 original size:19 final size:17
Alignment explanation
Indices: 25042--25076 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
25032 ACAACAAATT
25042 AATTTTTCTATTTTATA
1 AATTTTTCTATTTTATA
25059 AATTTTATCTAATTTTAT
1 AATTTT-TCT-ATTTTAT
25077 TATATTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (17 bp):
AATTTTTCTATTTTATA
Found at i:26654 original size:21 final size:22
Alignment explanation
Indices: 26630--26682 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
26620 GCCCCCCGTC
*
26630 GGGGTC-GTTTCC-AGTTGTTTT
1 GGGGTCTG-TTCCTAGTTATTTT
26651 GGGG-CTGTTCCTAGTTATTTT
1 GGGGTCTGTTCCTAGTTATTTT
26672 GGGGT-TGTTCC
1 GGGGTCTGTTCC
26683 CCTATTCCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.06, C:0.15, G:0.34, T:0.45
Consensus pattern (22 bp):
GGGGTCTGTTCCTAGTTATTTT
Found at i:27042 original size:10 final size:10
Alignment explanation
Indices: 27023--27081 Score: 79
Period size: 10 Copynumber: 6.1 Consensus size: 10
27013 AAATAAATTA
27023 ATAA-ATAAT
1 ATAATATAAT
27032 ATAATATAAT
1 ATAATATAAT
27042 ATAATATAAT
1 ATAATATAAT
27052 ATAATATAAT
1 ATAATATAAT
*
27062 A-ATATATACT
1 ATA-ATATAAT
27072 A-AATATAAT
1 ATAATATAAT
27081 A
1 A
27082 ATAAAAACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
9 12 0.26
10 34 0.74
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (10 bp):
ATAATATAAT
Found at i:27045 original size:15 final size:15
Alignment explanation
Indices: 27023--27081 Score: 79
Period size: 15 Copynumber: 4.1 Consensus size: 15
27013 AAATAAATTA
27023 ATAA-ATAATATAAT
1 ATAATATAATATAAT
27037 ATAATATAATATAAT
1 ATAATATAATATAAT
27052 ATAATATAATA-ATAT
1 ATAATATAATATA-AT
*
27067 ATACTA-AATATAAT
1 ATAATATAATATAAT
27081 A
1 A
27082 ATAAAAACTA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
14 12 0.29
15 29 0.71
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAATATAATATAAT
Found at i:27091 original size:19 final size:19
Alignment explanation
Indices: 27054--27091 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
27044 AATATAATAT
* *
27054 AATATAATAATATATACTA
1 AATATAATAATAAAAACTA
27073 AATATAATAATAAAAACTA
1 AATATAATAATAAAAACTA
27092 TATAATACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
AATATAATAATAAAAACTA
Found at i:27141 original size:22 final size:22
Alignment explanation
Indices: 27113--27175 Score: 126
Period size: 22 Copynumber: 2.9 Consensus size: 22
27103 ATTTTCAAAA
27113 ATATGTTTTCAAAAATCATATT
1 ATATGTTTTCAAAAATCATATT
27135 ATATGTTTTCAAAAATCATATT
1 ATATGTTTTCAAAAATCATATT
27157 ATATGTTTTCAAAAATCAT
1 ATATGTTTTCAAAAATCAT
27176 TTTTATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (22 bp):
ATATGTTTTCAAAAATCATATT
Found at i:27295 original size:35 final size:35
Alignment explanation
Indices: 27152--27565 Score: 422
Period size: 35 Copynumber: 11.5 Consensus size: 35
27142 TTCAAAAATC
* * *
27152 ATATTATATGTTTTCAAAAATCATTTTTATAAAA-AAT
1 ATATTATACGTTTTCAAAACT-A-TTTTA-AAAACTAT
*
27189 ATATTATACGTTTTCAAAACCATTTTTAAAAACTAT
1 ATATTATACGTTTTCAAAACTA-TTTTAAAAACTAT
* *
27225 ATACTATATGTTTTCAAAACCGCT-TTTTAAAAACTAT
1 ATATTATACGTTTTCAAAA---CTATTTTAAAAACTAT
* * *
27262 ATATTATACATTTTTAAAATTATTTTAAAAAC--T
1 ATATTATACGTTTTCAAAACTATTTTAAAAACTAT
*
27295 ATATTATACGTTTTCAAAATTATTTTAAAAACTAT
1 ATATTATACGTTTTCAAAACTATTTTAAAAACTAT
* * ** *
27330 ATACTATATGTTTTCAAAACCGTTTTCAAAACTAT
1 ATATTATACGTTTTCAAAACTATTTTAAAAACTAT
* * **
27365 ATACTATATGTTTTCAAAACCGTTTTAAAAACTAT
1 ATATTATACGTTTTCAAAACTATTTTAAAAACTAT
* *
27400 TTATTATACGTTTTCAAAACTATTTTTAAAAAATTAT
1 ATATTATACGTTTTCAAAACTA-TTTT-AAAAACTAT
27437 ATATTATACGTTTTCAAAACTATTTTTTAAAAACTAT
1 ATATTATACGTTTTCAAAACTA--TTTTAAAAACTAT
* *
27474 ATATTATATGTTTTCAAAATTATTTTAAAAACTAT
1 ATATTATACGTTTTCAAAACTATTTTAAAAACTAT
** * *
27509 ATAATACTATATATTTTCAAAATTGTTTTAAAAACTAT
1 AT-AT--TATACGTTTTCAAAACTATTTTAAAAACTAT
*
27547 ATATTATACGTTTTTAAAA
1 ATATTATACGTTTTCAAAA
27566 AAATAAGTTT
Statistics
Matches: 328, Mismatches: 36, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
33 31 0.09
34 1 0.00
35 122 0.37
36 32 0.10
37 105 0.32
38 36 0.11
39 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (35 bp):
ATATTATACGTTTTCAAAACTATTTTAAAAACTAT
Found at i:27468 original size:212 final size:215
Alignment explanation
Indices: 27139--27565 Score: 562
Period size: 212 Copynumber: 2.0 Consensus size: 215
27129 CATATTATAT
* *
27139 GTTTTCAAAAATCATATTATATGTTTTCAAAAATCATTTTTATAAAAAATATATTATACGTTTTC
1 GTTTTCAAAAATCATACTATATGTTTTCAAAAATCAGTTTTATAAAAAATATATTATACGTTTTC
* *
27204 AAAACCATTTTTAAAAACTATATACTATATGTTTTCAAAACCGCTTTTTAAAAACTATATATTAT
66 AAAACCATTTTTAAAAACTATATACTATACGTTTTCAAAACCACTTTTTAAAAACTATATATTAT
* *
27269 ACATTTTTAAAATTATTTTAAAAAC-TAT-AT-TATACGTTTTCAAAATTATTTTAAAAACTATA
131 ACATTTTCAAAATTATTTTAAAAACATATAATATATACATTTTCAAAATTATTTTAAAAACTATA
*
27331 TACTATATGTTTTCAAAACC
196 TACTATACGTTTTCAAAACC
* * *
27351 GTTTTCAAAACTAT-ATACTATATGTTTTC-AAAA-CCGTTTTA-AAAACTATTTATTATACGTT
1 GTTTTCAAAA--ATCATACTATATGTTTTCAAAAATCAGTTTTATAAAA-AATATATTATACGTT
* * * * *
27412 TTCAAAACTATTTTTAAAAAATTATATATTATACGTTTTCAAAACTATTTTTTAAAAACTATATA
63 TTCAAAACCATTTTT-AAAAACTATATACTATACGTTTTCAAAACCACTTTTTAAAAACTATATA
** * *
27477 TTATATGTTTTCAAAATTATTTTAAAAACTATATAATACTATATATTTTCAAAATTGTTTTAAAA
127 TTATACATTTTCAAAATTATTTTAAAAAC-ATATAATA-TATACATTTTCAAAATTATTTTAAAA
* *
27542 ACTATATATTATACGTTTTTAAAA
190 ACTATATACTATACGTTTTCAAAA
27566 AAATAAGTTT
Statistics
Matches: 185, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
210 4 0.02
211 33 0.18
212 83 0.45
213 14 0.08
214 5 0.03
215 2 0.01
217 44 0.24
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (215 bp):
GTTTTCAAAAATCATACTATATGTTTTCAAAAATCAGTTTTATAAAAAATATATTATACGTTTTC
AAAACCATTTTTAAAAACTATATACTATACGTTTTCAAAACCACTTTTTAAAAACTATATATTAT
ACATTTTCAAAATTATTTTAAAAACATATAATATATACATTTTCAAAATTATTTTAAAAACTATA
TACTATACGTTTTCAAAACC
Found at i:27606 original size:38 final size:36
Alignment explanation
Indices: 27152--27606 Score: 257
Period size: 37 Copynumber: 12.6 Consensus size: 36
27142 TTCAAAAATC
* * *
27152 ATATTATATGTTTTCAAAAATCATTTTTATAAAA-AAT
1 ATATTATATATTTTCAAAAAT-AGTTTTA-AAAATTAT
** ** * *
27189 ATATTATACGTTTTCAAAACCATTTTTAAAAACTAT
1 ATATTATATATTTTCAAAAATAGTTTTAAAAATTAT
* * ** *
27225 ATACTATATGTTTTC-AAAACCGCTTTTTAAAAACTAT
1 ATATTATATATTTTCAAAAATAG--TTTTAAAAATTAT
* * * *
27262 ATATTATACATTTTTAAAATTA-TTTTAAAAA--CT
1 ATATTATATATTTTCAAAAATAGTTTTAAAAATTAT
** * *
27295 ATATTATACGTTTTCAAAATTA-TTTTAAAAACTAT
1 ATATTATATATTTTCAAAAATAGTTTTAAAAATTAT
* * ** * *
27330 ATACTATATGTTTTC-AAAACCGTTTTCAAAACTAT
1 ATATTATATATTTTCAAAAATAGTTTTAAAAATTAT
* * ** *
27365 ATACTATATGTTTTC-AAAACCGTTTTAAAAACTAT
1 ATATTATATATTTTCAAAAATAGTTTTAAAAATTAT
* ** * *
27400 TTATTATACGTTTTCAAAACTATTTTTAAAAAATTAT
1 ATATTATATATTTTCAAAAATAGTTTT-AAAAATTAT
** * * *
27437 ATATTATACGTTTTCAAAACTATTTTTTAAAAACTAT
1 ATATTATATATTTTCAAAAATA-GTTTTAAAAATTAT
* *
27474 ATATTATATGTTTTCAAAATTA-TTTTAAAAACTATAT
1 ATATTATATATTTTCAAAAATAGTTTTAAAAA-T-TAT
* * *
27511 AATACTATATATTTTC-AAAATTGTTTTAAAAACTAT
1 -ATATTATATATTTTCAAAAATAGTTTTAAAAATTAT
* *
27547 ATATTATACGT-TTTTAAAAAAATAAGTTTCCAAAAATTAT
1 ATATTATA--TATTTT-CAAAAAT-AGTTT-TAAAAATTAT
27587 ATATTATATATTTTCAAAAA
1 ATATTATATATTTTCAAAAA
27607 CTATATTTGA
Statistics
Matches: 346, Mismatches: 51, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
33 30 0.09
34 3 0.01
35 105 0.30
36 36 0.10
37 107 0.31
38 41 0.12
39 8 0.02
40 16 0.05
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (36 bp):
ATATTATATATTTTCAAAAATAGTTTTAAAAATTAT
Found at i:28218 original size:40 final size:39
Alignment explanation
Indices: 28171--28291 Score: 114
Period size: 40 Copynumber: 3.2 Consensus size: 39
28161 ACTCCTTCAC
28171 CGTGAAGTTAAGTTCATCTCTTGGGCACGATATCCTTCGT
1 CGTGAAGTTAAG-TCATCTCTTGGGCACGATATCCTTCGT
* * * *
28211 CGTGAAGTTGAA---A--TCGTGGG--TGA-CTCCTTCAT
1 CGTGAAGTT-AAGTCATCTCTTGGGCACGATATCCTTCGT
*
28243 CGTGAAGTTAAGTCGATCTCTTGGGCACGATATCATTCGT
1 CGTGAAGTTAAGTC-ATCTCTTGGGCACGATATCCTTCGT
28283 CGTGAAGTT
1 CGTGAAGTT
28292 GAAATCGTGG
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
31 2 0.03
32 16 0.26
33 2 0.03
35 7 0.11
37 7 0.11
39 2 0.03
40 24 0.39
41 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (39 bp):
CGTGAAGTTAAGTCATCTCTTGGGCACGATATCCTTCGT
Found at i:28238 original size:72 final size:72
Alignment explanation
Indices: 28160--28384 Score: 344
Period size: 72 Copynumber: 3.1 Consensus size: 72
28150 TGTTGCAGAC
*
28160 GACTCCTTCACCGTGAAGTTAAGTTC-ATCTCTTGGGCACGATATCCTTCGTCGTGAAGTTGAAA
1 GACTCCTTCATCGTGAAGTTAAG-TCGATCTCTTGGGCACGATATCCTTCGTCGTGAAGTTGAAA
28224 TCGTGGGT
65 TCGTGGGT
*
28232 GACTCCTTCATCGTGAAGTTAAGTCGATCTCTTGGGCACGATATCATTCGTCGTGAAGTTGAAAT
1 GACTCCTTCATCGTGAAGTTAAGTCGATCTCTTGGGCACGATATCCTTCGTCGTGAAGTTGAAAT
28297 CGTGGGT
66 CGTGGGT
** * * * * *
28304 GACTTTTTCTTTGTGAGGTTAAGTCGATCTCTTGGGCATGATATCCATCGTCGTGAAGTTGAAAT
1 GACTCCTTCATCGTGAAGTTAAGTCGATCTCTTGGGCACGATATCCTTCGTCGTGAAGTTGAAAT
*
28369 TGTGGGT
66 CGTGGGT
28376 GACTCCTTC
1 GACTCCTTC
28385 GTCATGATGT
Statistics
Matches: 139, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
71 2 0.01
72 137 0.99
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (72 bp):
GACTCCTTCATCGTGAAGTTAAGTCGATCTCTTGGGCACGATATCCTTCGTCGTGAAGTTGAAAT
CGTGGGT
Found at i:39127 original size:16 final size:17
Alignment explanation
Indices: 39096--39131 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
39086 AAAATAAAAT
*
39096 AATAAAAAGGATATTAA
1 AATAAAAAAGATATTAA
39113 AATAAAAAAGA-ATTAA
1 AATAAAAAAGATATTAA
39129 AAT
1 AAT
39132 TAGGTCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (17 bp):
AATAAAAAAGATATTAA
Found at i:39385 original size:21 final size:21
Alignment explanation
Indices: 39361--39440 Score: 108
Period size: 21 Copynumber: 3.8 Consensus size: 21
39351 TGTTGATGCT
* *
39361 TTGTTTCGGGGCCGTT-TCTAG
1 TTGTTTCGGGGTCGTTCTC-GG
39382 TTGTTTCGGGGTCGTTCTCGG
1 TTGTTTCGGGGTCGTTCTCGG
*
39403 TTGTTTGGGGGTCGTTCTCGG
1 TTGTTTCGGGGTCGTTCTCGG
*
39424 TTGTTTCGGGGTTGTTC
1 TTGTTTCGGGGTCGTTC
39441 CCCCATTTCG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
21 51 0.96
22 2 0.04
ACGTcount: A:0.01, C:0.16, G:0.38, T:0.45
Consensus pattern (21 bp):
TTGTTTCGGGGTCGTTCTCGG
Found at i:39775 original size:5 final size:4
Alignment explanation
Indices: 39762--39834 Score: 51
Period size: 5 Copynumber: 16.8 Consensus size: 4
39752 TTGGACCTGA
39762 AAAT AAAAT GAAAT AAAT AAAT AAAAT AAAT AATAT AATAT AAAT -AAT
1 AAAT -AAAT -AAAT AAAT AAAT -AAAT AAAT AA-AT AA-AT AAAT AAAT
*
39810 AATAT ATACT AAAT ATAAT -AAT AAA
1 AA-AT A-AAT AAAT A-AAT AAAT AAA
39835 AACTATATAA
Statistics
Matches: 58, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 6 0.10
4 22 0.38
5 29 0.50
6 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:39785 original size:18 final size:18
Alignment explanation
Indices: 39762--39815 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
39752 TTGGACCTGA
39762 AAATAAAATGAAATAA-AT
1 AAATAAAAT-AAATAATAT
39780 AAATAAAATAAATAATAT
1 AAATAAAATAAATAATAT
39798 -AATATAAAT-AATAATAT
1 AAATA-AAATAAATAATAT
39815 A
1 A
39816 TACTAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 18 0.55
18 15 0.45
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
AAATAAAATAAATAATAT
Found at i:39788 original size:9 final size:9
Alignment explanation
Indices: 39762--39805 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
39752 TTGGACCTGA
39762 AAATAAAAT
1 AAATAAAAT
39771 GAAAT-AAAT
1 -AAATAAAAT
39780 AAATAAAAT
1 AAATAAAAT
*
39789 AAATAATAT
1 AAATAAAAT
39798 AATATAAA
1 AA-ATAAA
39806 TAATAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 4 0.13
9 18 0.60
10 8 0.27
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (9 bp):
AAATAAAAT
Found at i:39809 original size:14 final size:14
Alignment explanation
Indices: 39774--39846 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 14
39764 ATAAAATGAA
*
39774 ATAAATAA-ATAAA
1 ATAAATAATATAAT
39787 ATAAATAATATAAT
1 ATAAATAATATAAT
39801 ATAAATAATAATATAT
1 ATAAATAAT-ATA-AT
39817 ACTAAAT-ATAATAAT
1 A-TAAATAAT-ATAAT
*
39832 AAAAACT-ATATAAT
1 ATAAA-TAATATAAT
39846 A
1 A
39847 CTATATTTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
13 8 0.15
14 22 0.42
15 9 0.17
16 9 0.17
17 5 0.09
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAAATAATATAAT
Found at i:39810 original size:17 final size:17
Alignment explanation
Indices: 39777--39829 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
39767 AAATGAAATA
39777 AATA-AATA-AAATAAAT
1 AATATAATATAAAT-AAT
39793 AATATAATATAAATAAT
1 AATATAATATAAATAAT
39810 AATAT-ATACTAAAT-AT
1 AATATAATA-TAAATAAT
39826 AATA
1 AATA
39830 ATAAAAACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.38
17 17 0.50
18 4 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATAATATAAATAAT
Found at i:39816 original size:19 final size:19
Alignment explanation
Indices: 39777--39832 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
39767 AAATGAAATA
*
39777 AATAAATAAAATAAATAATAT
1 AATAAATATAAT-AAT-ATAT
39798 AATATAA-ATAATAATATAT
1 AATA-AATATAATAATATAT
*
39817 ACTAAATATAATAATA
1 AATAAATATAATAATA
39833 AAAACTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 16 0.52
20 3 0.10
21 8 0.26
22 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAAATATAATAATATAT
Found at i:39917 original size:35 final size:35
Alignment explanation
Indices: 39852--40181 Score: 276
Period size: 35 Copynumber: 9.3 Consensus size: 35
39842 TAATACTATA
* *
39852 TTTTCAAAAATATGTTTTCAAAAAT-TATATTATATG
1 TTTTCAAAAATA--TTTTAAAAAATATATATTATACG
* * *
39888 TTTTCAAAAATAATTTAAAAAAAAAATATTATACG
1 TTTTCAAAAATATTTTAAAAAATATATATTATACG
* *
39923 TTTTCAAAACCAT-TTTTAAAAACTATATATTATATATG
1 TTTTCAAAA--ATATTTTAAAAAATATATA-T-TATACG
* * *
39961 TTTTCAAAACCTCTTTTTAAAAACTATATATTATACG
1 TTTTCAAAA-AT-ATTTTAAAAAATATATATTATACG
* *
39998 TTTTTAAAATTATTTT-AAAAA-ATATATTATACG
1 TTTTCAAAAATATTTTAAAAAATATATATTATACG
* * *
40031 TTTTCAAAATTA-TTCAAAAAATTATATACTATACG
1 TTTTCAAAAATATTTTAAAAAA-TATATATTATACG
* *
40066 TTTTCAAAACTATTTTTAAAAAACTATATATTATATG
1 TTTTCAAAAATA-TTTTAAAAAA-TATATATTATACG
* * * **
40103 TTTTCAAAATTATTTTAAAAATTATATACTATATA
1 TTTTCAAAAATATTTTAAAAAATATATATTATACG
* * * *
40138 TTTTCAAAATTGTTTT-TAAACTATATATTATACG
1 TTTTCAAAAATATTTTAAAAAATATATATTATACG
*
40172 TTTTAAAAAA
1 TTTTCAAAAA
40182 ATAAGTTTCC
Statistics
Matches: 246, Mismatches: 36, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
32 2 0.01
33 28 0.11
34 33 0.13
35 70 0.28
36 34 0.14
37 48 0.20
38 15 0.06
39 16 0.07
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (35 bp):
TTTTCAAAAATATTTTAAAAAATATATATTATACG
Found at i:40091 original size:105 final size:103
Alignment explanation
Indices: 39832--40148 Score: 329
Period size: 105 Copynumber: 3.0 Consensus size: 103
39822 ATATAATAAT
* *
39832 AAAAACTATATAATACTATA-TTTTCAAAAATATGTTTTCAAAAA-T-TATATTATATGTTTTCA
1 AAAAAATATAT-ATACTATAGTTTTCAAAACTAT-TTTT-AAAAACTATATATTATATGTTTT-A
* * * *
39894 AAAATAATTTAAAAAAAAAATATTATACGTTTTCAAAACCATTTTT
62 AAAATTATTT-TAAAAAATATATTATACGTTTTC-AAA--ATTTTC
* * * *
39940 AAAAACTATATATTA-TATATGTTTTCAAAACCTCTTTTTAAAAACTATATATTATACGTTTTTA
1 AAAAAATATATA-TACTATA-GTTTTCAAAA-CTATTTTTAAAAACTATATATTATATGTTTTAA
40004 AAATTATTTTAAAAAATATATTATACGTTTTCAAAATTATTC
63 AAATTATTTTAAAAAATATATTATACGTTTTCAAAATT-TTC
*
40046 AAAAAAT-TATATACTATACGTTTTCAAAACTATTTTTAAAAAACTATATATTATATGTTTTCAA
1 AAAAAATATATATACTATA-GTTTTCAAAACTATTTTT-AAAAACTATATATTATATGTTTTAAA
* **
40110 AATTATTTTAAAAATTATATACTATATATTTTCAAAATT
64 AATTATTTTAAAAA--ATATATTATACGTTTTCAAAATT
40149 GTTTTTAAAC
Statistics
Matches: 182, Mismatches: 16, Indels: 23
0.82 0.07 0.10
Matches are distributed among these distances:
104 9 0.05
105 59 0.32
106 8 0.04
107 28 0.15
108 39 0.21
109 23 0.13
110 16 0.09
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (103 bp):
AAAAAATATATATACTATAGTTTTCAAAACTATTTTTAAAAACTATATATTATATGTTTTAAAAA
TTATTTTAAAAAATATATTATACGTTTTCAAAATTTTC
Found at i:40123 original size:72 final size:71
Alignment explanation
Indices: 39844--40180 Score: 343
Period size: 72 Copynumber: 4.8 Consensus size: 71
39834 AAACTATATA
* * *
39844 ATACTATA--TTTTCAAAAATATGTTTTCAAAAA-T-TATATTATATGTTTTCAAAAATAATTTA
1 ATACTATACGTTTTCAAAACTAT-TTTT-AAAAACTATATATTATATGTTTTCAAAATTATTTTA
** *
39905 AAAAAAAA
64 AAAATTAT
* *
39913 ATATTATACGTTTTCAAAACCATTTTTAAAAACTATATATTATATATGTTTTCAAAACCTCT-TT
1 ATACTATACGTTTTCAAAACTATTTTTAAAAACTATATA-T-TATATGTTTTCAAAA--T-TATT
*
39977 TTAAAAACTAT
61 TTAAAAATTAT
* * * * **
39988 ATATTATACGTTTTTAAAATTA-TTTTAAAAA--ATATATTATACGTTTTCAAAATTATTCAAAA
1 ATACTATACGTTTTCAAAACTATTTTTAAAAACTATATATTATATGTTTTCAAAATTATTTTAAA
40050 AATTAT
66 AATTAT
40056 ATACTATACGTTTTCAAAACTATTTTTAAAAAACTATATATTATATGTTTTCAAAATTATTTTAA
1 ATACTATACGTTTTCAAAACTATTTTT-AAAAACTATATATTATATGTTTTCAAAATTATTTTAA
40121 AAATTAT
65 AAATTAT
** * * * *
40128 ATACTATATATTTTCAAAATTGTTTTT--AAACTATATATTATACGTTTTAAAAA
1 ATACTATACGTTTTCAAAACTATTTTTAAAAACTATATATTATATGTTTTCAAAA
40181 AATAAGTTTC
Statistics
Matches: 227, Mismatches: 27, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
67 1 0.00
68 30 0.13
69 40 0.18
70 24 0.11
71 16 0.07
72 63 0.28
73 15 0.07
74 9 0.04
75 28 0.12
76 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (71 bp):
ATACTATACGTTTTCAAAACTATTTTTAAAAACTATATATTATATGTTTTCAAAATTATTTTAAA
AATTAT
Found at i:41123 original size:12 final size:10
Alignment explanation
Indices: 41097--41154 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
41087 TCACTTTTTT
41097 AAAATAAATA
1 AAAATAAATA
41107 AAAATACAATAA
1 AAAATA-AAT-A
*
41119 AAAATAATTA
1 AAAATAAATA
*
41129 AAAATGAATA
1 AAAATAAATA
* *
41139 AAATTTAATA
1 AAAATAAATA
41149 AAAATA
1 AAAATA
41155 TAATGTAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 27 0.69
11 5 0.13
12 7 0.18
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (10 bp):
AAAATAAATA
Found at i:41147 original size:21 final size:21
Alignment explanation
Indices: 41097--41154 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
41087 TCACTTTTTT
41097 AAAATAAATAAAAATACAATAA
1 AAAAT-AATAAAAATACAATAA
*
41119 AAAATAATTAAAAAT-GAATAA
1 AAAATAA-TAAAAATACAATAA
**
41140 AATTTAATAAAAATA
1 AAAATAATAAAAATA
41155 TAATGTAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 7 0.23
21 12 0.39
22 12 0.39
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAATAATAAAAATACAATAA
Found at i:41158 original size:11 final size:11
Alignment explanation
Indices: 41097--41158 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
41087 TCACTTTTTT
41097 AAAATA-AATA
1 AAAATATAATA
*
41107 AAAATACAATA
1 AAAATATAATA
41118 AAAA-ATAATTA
1 AAAATATAA-TA
*
41129 AAAAT-GAAT-
1 AAAATATAATA
*
41138 AAAATTTAATA
1 AAAATATAATA
41149 AAAATATAAT
1 AAAATATAAT
41159 GTAAAGCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
9 5 0.12
10 13 0.30
11 25 0.58
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (11 bp):
AAAATATAATA
Found at i:41273 original size:29 final size:30
Alignment explanation
Indices: 41224--41286 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
41214 TAAAAAATAT
41224 AAAATAAATATAAAATTTTAATT-TTATTA
1 AAAATAAATATAAAATTTTAATTATTATTA
* * *
41253 AAAATGAATAT-ACATTATTAATTATTGTTA
1 AAAATAAATATAAAATT-TTAATTATTATTA
41283 AAAA
1 AAAA
41287 ATAATAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 4 0.14
29 16 0.55
30 9 0.31
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAATAAATATAAAATTTTAATTATTATTA
Found at i:42331 original size:31 final size:32
Alignment explanation
Indices: 42283--42351 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
42273 ATTTTTTAGC
42283 TTTACATTCTATTTTTATTGAATGTTATTGATT
1 TTTA-ATTCTATTTTTATTGAATGTTATTGATT
* * *
42316 TTTAATTC-ATTTTTATTGCATTTTATTTATT
1 TTTAATTCTATTTTTATTGAATGTTATTGATT
42347 TTTAA
1 TTTAA
42352 AAAATGAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 25 0.76
32 4 0.12
33 4 0.12
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (32 bp):
TTTAATTCTATTTTTATTGAATGTTATTGATT
Found at i:42340 original size:21 final size:20
Alignment explanation
Indices: 42293--42350 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
42283 TTTACATTCT
* * *
42293 ATTTTTATTGAATGTTATTG
1 ATTTTTATTCATTTTTATTG
42313 ATTTTTAATTCATTTTTATTG
1 ATTTTT-ATTCATTTTTATTG
*
42334 CA-TTTTATTTATTTTTA
1 -ATTTTTATTCATTTTTA
42351 AAAAATGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 16 0.50
21 15 0.47
22 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.07, T:0.66
Consensus pattern (20 bp):
ATTTTTATTCATTTTTATTG
Found at i:44549 original size:11 final size:12
Alignment explanation
Indices: 44495--44551 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
44485 CATTATATAT
44495 ATATATTAAAAT-
1 ATAT-TTAAAATA
*
44507 ATATTTAATATA
1 ATATTTAAAATA
*
44519 ATATTTAAATTA
1 ATATTTAAAATA
44531 ATATTTTAAAATA
1 ATA-TTTAAAATA
44544 AT-TTTAAA
1 ATATTTAAA
44552 GATTAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
11 12 0.31
12 17 0.44
13 10 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATTTAAAATA
Found at i:44557 original size:26 final size:26
Alignment explanation
Indices: 44504--44551 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
44494 TATATATTAA
*
44504 AATATATTTAATATAATATTTAAATT
1 AATATATTTAAAATAATATTTAAATT
44530 AATAT-TTTAAAATAAT-TTTAAA
1 AATATATTTAAAATAATATTTAAA
44552 GATTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 10 0.48
26 5 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATATTTAAAATAATATTTAAATT
Found at i:46342 original size:18 final size:16
Alignment explanation
Indices: 46310--46347 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
46300 ATAATTCTTG
46310 ATAAATATTAAAAATT
1 ATAAATATTAAAAATT
46326 ATAAATATATAATAAATT
1 ATAAATAT-TAA-AAATT
46344 ATAA
1 ATAA
46348 TTTAATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 3 0.15
18 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAATATTAAAAATT
Found at i:47512 original size:13 final size:14
Alignment explanation
Indices: 47484--47518 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
47474 TTAATTATTG
47484 TTTTATAAATATAT
1 TTTTATAAATATAT
47498 TTTTATAAATA-AT
1 TTTTATAAATATAT
*
47511 TTATATAA
1 TTTTATAA
47519 TTATTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTATAAATATAT
Found at i:50463 original size:15 final size:15
Alignment explanation
Indices: 50443--50486 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
50433 CTTGGTAAAA
50443 TGGCATCTTCATGGG
1 TGGCATCTTCATGGG
50458 TGGCATCTTCATGGG
1 TGGCATCTTCATGGG
**
50473 AAGCATCATTCATG
1 TGGCATC-TTCATG
50487 AAAGGTCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (15 bp):
TGGCATCTTCATGGG
Found at i:51905 original size:19 final size:19
Alignment explanation
Indices: 51883--51923 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
51873 AATGAATATT
51883 GATTGGTAAAGCAATCATG
1 GATTGGTAAAGCAATCATG
51902 GATTGGTAAAGCAATCATG
1 GATTGGTAAAGCAATCATG
51921 GAT
1 GAT
51924 AGTCCTCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (19 bp):
GATTGGTAAAGCAATCATG
Found at i:53936 original size:21 final size:20
Alignment explanation
Indices: 53912--53972 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 20
53902 TCGGAAATTC
*
53912 TTCTTTTTCTTT-TCTTCTTTT
1 TTCTTTTT-TTTGTCTT-TTCT
53933 TTCTTATTTTTTGTCTTTTCT
1 TTCTT-TTTTTTGTCTTTTCT
53954 TTCTTTCTTTCTT-TCTTTT
1 TTCTTT-TTT-TTGTCTTTT
53973 GTACTTTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 1 0.03
21 25 0.71
22 9 0.26
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (20 bp):
TTCTTTTTTTTGTCTTTTCT
Found at i:53942 original size:8 final size:7
Alignment explanation
Indices: 53915--53972 Score: 53
Period size: 8 Copynumber: 7.4 Consensus size: 7
53905 GAAATTCTTC
53915 TTTTTCT
1 TTTTTCT
53922 TTTCTTCT
1 TTT-TTCT
53930 TTTTTCT
1 TTTTTCT
*
53937 TATTTTTT
1 T-TTTTCT
53945 GTCTTTTCT
1 -T-TTTTCT
53954 TTCTTTCT
1 TT-TTTCT
53962 TTCTTTCT
1 TT-TTTCT
53970 TTT
1 TTT
53973 GTACTTTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
7 10 0.23
8 28 0.64
9 6 0.14
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTTTCT
Found at i:55200 original size:16 final size:16
Alignment explanation
Indices: 55175--55216 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
55165 GGTGAAAGGG
*
55175 CATC-TTCATGGGTAA
1 CATCATTCATGGGCAA
55190 CATCATTCATGGGCAA
1 CATCATTCATGGGCAA
55206 CATCATTCATG
1 CATCATTCATG
55217 AATGGTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (16 bp):
CATCATTCATGGGCAA
Found at i:55774 original size:2 final size:2
Alignment explanation
Indices: 55767--55806 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
55757 TCATAATAAC
55767 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
55807 ACATATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56216 original size:14 final size:14
Alignment explanation
Indices: 56199--56228 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56189 TTGATTTGAA
56199 AAATTCAATTTCTT
1 AAATTCAATTTCTT
56213 AAATTCAATTTCTT
1 AAATTCAATTTCTT
56227 AA
1 AA
56229 TGAAAAAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTCAATTTCTT
Found at i:56289 original size:18 final size:19
Alignment explanation
Indices: 56266--56322 Score: 89
Period size: 18 Copynumber: 2.9 Consensus size: 19
56256 TATATTTTGC
56266 AACAATTGGTATCTTTTT-
1 AACAATTGGTATCTTTTTA
56284 AACAATTGGTATACTTTTGTA
1 AACAATTGGTAT-CTTTT-TA
56305 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
56323 CATTAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 12 0.33
19 6 0.17
20 6 0.17
21 12 0.33
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (19 bp):
AACAATTGGTATCTTTTTA
Found at i:56545 original size:21 final size:20
Alignment explanation
Indices: 56520--56594 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 20
56510 CAAAAAAGCA
*
56520 AAAGGGTATCGATATCCCTTC
1 AAAGGGTATCCATA-CCCTTC
56541 AAAGGGTATCCATACCC-T-
1 AAAGGGTATCCATACCCTTC
56559 ---GGGTA-CCGATATCCCTTC
1 AAAGGGTATCC-ATA-CCCTTC
56577 AAAGGGTATCCATACCCT
1 AAAGGGTATCCATACCCT
56595 GGGTACCGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
14 2 0.04
15 8 0.18
16 3 0.07
17 1 0.02
19 1 0.02
20 7 0.16
21 21 0.47
22 2 0.04
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
AAAGGGTATCCATACCCTTC
Found at i:56569 original size:36 final size:36
Alignment explanation
Indices: 56523--56612 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
56513 AAAAGCAAAA
*
56523 GGGTATCGATATCCCTTCAAAGGGTATCCATACCCT
1 GGGTACCGATATCCCTTCAAAGGGTATCCATACCCT
56559 GGGTACCGATATCCCTTCAAAGGGTATCCATACCCT
1 GGGTACCGATATCCCTTCAAAGGGTATCCATACCCT
*
56595 GGGTACCGATACCCCTTC
1 GGGTACCGATATCCCTTC
56613 CTGGGTATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (36 bp):
GGGTACCGATATCCCTTCAAAGGGTATCCATACCCT
Found at i:56617 original size:20 final size:20
Alignment explanation
Indices: 56592--56630 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56582 GTATCCATAC
*
56592 CCTGGGTACCGATACCCCTT
1 CCTGGGTACCAATACCCCTT
*
56612 CCTGGGTATCAATACCCCT
1 CCTGGGTACCAATACCCCT
56631 ATGACTGCTG
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:0.18, C:0.38, G:0.18, T:0.26
Consensus pattern (20 bp):
CCTGGGTACCAATACCCCTT
Found at i:56679 original size:15 final size:15
Alignment explanation
Indices: 56659--56688 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56649 AATGCAAAAA
56659 GGGTACCGATACCCC
1 GGGTACCGATACCCC
*
56674 GGGTACTGATACCCC
1 GGGTACCGATACCCC
56689 TGCCAAGGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.37, G:0.27, T:0.17
Consensus pattern (15 bp):
GGGTACCGATACCCC
Found at i:56789 original size:21 final size:21
Alignment explanation
Indices: 56760--56816 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
56750 AACAAACGTA
56760 GTACCGATACCCCTTGAAGGG
1 GTACCGATACCCCTTGAAGGG
* *
56781 GTACTGATACCCCTTGAAGTG
1 GTACCGATACCCCTTGAAGGG
56802 GTACCGATATCCCCT
1 GTACCGATA-CCCCT
56817 GTTATGGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 27 0.84
22 5 0.16
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (21 bp):
GTACCGATACCCCTTGAAGGG
Found at i:60993 original size:64 final size:60
Alignment explanation
Indices: 60923--61112 Score: 193
Period size: 64 Copynumber: 3.0 Consensus size: 60
60913 GGTAAACTAA
* * *
60923 GAGTGCATCGATGCATGAAGTGCGTTCGATGTTTGAA-AAATAGCCTGGTGCATCGATGCATG
1 GAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAAT--CATAGTGCATCGATGCATG
* *
60985 GATGGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCATAGTGCATCGATGCATG
1 GA--GTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATCATAGTGCATCGATGCATG
* * * * *
61049 GAGTGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATTGATGCATCGATGCATG
1 GAGTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATCATAG-TGCATCGATGCATG
61112 G
1 G
61113 TATTGATGCA
Statistics
Matches: 110, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
62 41 0.37
63 15 0.14
64 48 0.44
65 2 0.02
66 4 0.04
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (60 bp):
GAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCATAGTGCATCGATGCATG
Found at i:61055 original size:17 final size:17
Alignment explanation
Indices: 61033--61079 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
61023 ATTAAATCAT
61033 AGTGCATCGATGCATGG
1 AGTGCATCGATGCATGG
*
61050 AGTGCATCGGTGCATGG
1 AGTGCATCGATGCATGG
*
61067 AATGCATTCGATG
1 AGTGCA-TCGATG
61080 TTTCAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (17 bp):
AGTGCATCGATGCATGG
Found at i:61117 original size:21 final size:21
Alignment explanation
Indices: 61093--61132 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
61083 CAATTTATTC
61093 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
* *
61114 ATTGATGCATTGGTGCATG
1 ATTGATGCATCGATGCATG
61133 CCTTTGAAAA
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:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:64080 original size:64 final size:60
Alignment explanation
Indices: 64010--64199 Score: 193
Period size: 64 Copynumber: 3.0 Consensus size: 60
64000 GGTAAACTAA
* * *
64010 GAGTGCATCGATGCATGAAGTGCGTTCGATGTTTGAA-AAATAGCCTGGTGCATCGATGCATG
1 GAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAAT--CATAGTGCATCGATGCATG
* *
64072 GATGGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCATAGTGCATCGATGCATG
1 GA--GTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATCATAGTGCATCGATGCATG
* * * * *
64136 GAGTGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATTGATGCATCGATGCATG
1 GAGTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATCATAG-TGCATCGATGCATG
64199 G
1 G
64200 TATTGATGCA
Statistics
Matches: 110, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
62 41 0.37
63 15 0.14
64 48 0.44
65 2 0.02
66 4 0.04
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (60 bp):
GAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCATAGTGCATCGATGCATG
Found at i:64142 original size:17 final size:17
Alignment explanation
Indices: 64120--64166 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
64110 ATTAAATCAT
64120 AGTGCATCGATGCATGG
1 AGTGCATCGATGCATGG
*
64137 AGTGCATCGGTGCATGG
1 AGTGCATCGATGCATGG
*
64154 AATGCATTCGATG
1 AGTGCA-TCGATG
64167 TTTCAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (17 bp):
AGTGCATCGATGCATGG
Found at i:64204 original size:21 final size:21
Alignment explanation
Indices: 64180--64219 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
64170 CAATTTATTC
64180 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
* *
64201 ATTGATGCATTGGTGCATG
1 ATTGATGCATCGATGCATG
64220 CCTTTGAAAA
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:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:67190 original size:64 final size:63
Alignment explanation
Indices: 67083--67293 Score: 201
Period size: 64 Copynumber: 3.3 Consensus size: 63
67073 ATTGGACTCC
* * * * *
67083 TAGTGCATCGGTGCACT-AAGAGTGCAACGATGCATGAAGTGCATTTGATGTTTGAA-AAATAGC
1 TAGTGCATCGATGCA-TGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAT--C
*
67146 C
63 A
* ** * *
67147 TGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCA
1 TAGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-TAAATCA
* * * * *
67211 TAGTGCATCGATGCATGGAGAGTGCATCGGTGAATGAAATGCATTCGATGTTTCAATTTATTCA
1 TAGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-TAAATCA
*
67275 TTGATGCATCGATGCATGG
1 TAG-TGCATCGATGCATGG
67294 TATTGATGCA
Statistics
Matches: 122, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
63 1 0.01
64 102 0.84
65 15 0.12
66 4 0.03
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.31
Consensus pattern (63 bp):
TAGTGCATCGATGCATGGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAATCA
Found at i:67298 original size:21 final size:21
Alignment explanation
Indices: 67274--67313 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
67264 CAATTTATTC
67274 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
67295 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
67314 CCTTTGAAAA
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:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:69910 original size:24 final size:23
Alignment explanation
Indices: 69839--69918 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
69829 CATGATCTTG
*
69839 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* * *
69862 TGCATCGGTG--CA-TCATGCGGT
1 TGCATCGATGCACATTCAAG-GGA
69883 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
69907 TGCATCGATGCA
1 TGCATCGATGCA
69919 TTGTTAAGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.27
23 11 0.24
24 16 0.36
25 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:69931 original size:44 final size:42
Alignment explanation
Indices: 69817--69938 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 42
69807 AAACCCGACC
*
69817 GATGCATCGATGCA-TGATCTTGTGCATCGATGCACATTCAAGG
1 GATGCATCGATGCATTG-T-TAGTGCATCGATGCACATTCAAGG
* * **
69860 CATGCATCGGTGCATCATG-CGGTTGCATCGATGCACATTCAAAGG
1 GATGCATCGATGCAT--TGTTAG-TGCATCGATGCACATTC-AAGG
*
69905 GATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GATGCATCGATGCATTGTT-AGTGCATCGATGCA
69939 TTAAGCACAA
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
43 15 0.24
44 28 0.44
45 18 0.29
46 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (42 bp):
GATGCATCGATGCATTGTTAGTGCATCGATGCACATTCAAGG
Found at i:75768 original size:18 final size:17
Alignment explanation
Indices: 75714--75762 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
75704 TTGGACTCCT
* *
75714 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
75732 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
75750 AGTGCATTCGATG
1 AGTGCA-TCGATG
75763 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:75803 original size:64 final size:63
Alignment explanation
Indices: 75713--75923 Score: 212
Period size: 64 Copynumber: 3.3 Consensus size: 63
75703 GTTGGACTCC
* *
75713 TAGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAATAGT
1 TAGTGCATCGATGCA-TGGAGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAA-A-T
75776 C-
62 CA
* ** * * *
75777 TGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCA
1 TAGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATGTTTGAATAAAATCA
* * ** *
75841 TAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCA
1 TAGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATGTTTGAATAAAATCA
*
75905 TTGATGCATCGATGCATGG
1 TAG-TGCATCGATGCATGG
75924 TATTGATACA
Statistics
Matches: 124, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
63 3 0.02
64 102 0.82
65 19 0.15
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.32
Consensus pattern (63 bp):
TAGTGCATCGATGCATGGAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAAATCA
Found at i:75866 original size:19 final size:18
Alignment explanation
Indices: 75842--75890 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
75832 ATTAAATCAT
75842 AGTGCATCGATGCATGGA
1 AGTGCATCGATGCATGGA
*
75860 GAGTGCATCGGTGCATGGA
1 -AGTGCATCGATGCATGGA
75879 A-TGCATTCGATG
1 AGTGCA-TCGATG
75891 TTTCAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 4 0.15
18 6 0.22
19 17 0.63
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.24
Consensus pattern (18 bp):
AGTGCATCGATGCATGGA
Found at i:75928 original size:21 final size:21
Alignment explanation
Indices: 75904--75943 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
75894 CAATTTATTC
*
75904 ATTGATGCATC-GATGCATGGT
1 ATTGATACATCAG-TGCATGGT
75925 ATTGATACATCAGTGCATG
1 ATTGATACATCAGTGCATG
75944 CCTTTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (21 bp):
ATTGATACATCAGTGCATGGT
Found at i:82641 original size:22 final size:21
Alignment explanation
Indices: 82599--82641 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
82589 AATGTCATAG
*
82599 GGGAACCGATTCCCCACAGTA
1 GGGAACCGATTCCCCAAAGTA
82620 GGGAACCGATTCCCCTAAAGTA
1 GGGAACCGATTCCCC-AAAGTA
82642 AAGTTGTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCAAAGTA
Found at i:87797 original size:20 final size:20
Alignment explanation
Indices: 87755--87797 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
87745 TAAATGCTCT
87755 AAACAAAATGTACAACAATGC
1 AAACAAAATG-ACAACAATGC
87776 AAACAAAATG-CAACATATGC
1 AAACAAAATGACAACA-ATGC
87796 AA
1 AA
87798 TAACTAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 6 0.29
21 10 0.48
ACGTcount: A:0.58, C:0.19, G:0.09, T:0.14
Consensus pattern (20 bp):
AAACAAAATGACAACAATGC
Found at i:106019 original size:32 final size:32
Alignment explanation
Indices: 105982--106045 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
105972 CAAACTAGGC
105982 ACAAAATAACAATCCTCTAAATTTAAATTAAG
1 ACAAAATAACAATCCTCTAAATTTAAATTAAG
106014 ACAAAATAACAATCCTCTAAATTTAAATTAAG
1 ACAAAATAACAATCCTCTAAATTTAAATTAAG
106046 CCCACTAGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.28
Consensus pattern (32 bp):
ACAAAATAACAATCCTCTAAATTTAAATTAAG
Found at i:111560 original size:22 final size:20
Alignment explanation
Indices: 111509--111578 Score: 54
Period size: 22 Copynumber: 3.5 Consensus size: 20
111499 TGCAAAAATG
* * *
111509 GTATTGATATCATAATAGG-
1 GTATCGATACCATAGTAGGA
111528 GTATC-AGTACCATAGTATGGTA
1 GTATCGA-TACCATAGTA-GG-A
* *
111550 GTATCGATACCATGGTAGGG
1 GTATCGATACCATAGTAGGA
111570 GTATCGATA
1 GTATCGATA
111579 TTGAGGAGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 1 0.02
19 12 0.29
20 11 0.27
21 2 0.05
22 14 0.34
23 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (20 bp):
GTATCGATACCATAGTAGGA
Found at i:112037 original size:45 final size:44
Alignment explanation
Indices: 111987--112282 Score: 364
Period size: 45 Copynumber: 6.6 Consensus size: 44
111977 AACGAATGAA
*
111987 CAAAAGAATAATGCATATGGGTTCATTATTGGCATGAAAGGATG
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATG
*
112031 ACAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAGGATG
1 -CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATG
* * *
112076 CCAAAATAATAATGCATATGGGTGCATTATTTGCATAAAAGGATG
1 -CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATG
*
112121 CCAAAAGAATAATGCATAT-GGTGCATTATTGGCATGAAAGGACG
1 -CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATG
* * * * *
112165 CCATAG-CTGAAATGCATATGGGTGCATTATTTGCATAAAAGGATG
1 CAAAAGAAT--AATGCATATGGGTGCATTATTGGCATGAAAGGATG
*
112210 CTAAAAGAATAATGCATATGGGTTCATTATTGGCATGAAAGGATG
1 C-AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATG
* * *
112255 CCATAG-CTGAAATGCATATGGGTGCATT
1 CAAAAGAAT--AATGCATATGGGTGCATT
112283 TTCAACATAA
Statistics
Matches: 217, Mismatches: 27, Indels: 14
0.84 0.10 0.05
Matches are distributed among these distances:
42 1 0.00
43 5 0.02
44 34 0.16
45 173 0.80
46 3 0.01
47 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (44 bp):
CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATG
Found at i:112179 original size:134 final size:135
Alignment explanation
Indices: 111987--112282 Score: 386
Period size: 134 Copynumber: 2.2 Consensus size: 135
111977 AACGAATGAA
* *
111987 CAAAAGAATAATGCATATGGGTTCATTATTGGCATGAAAGGATGACAAAAGAATAATGCATATGA
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGACGACAAAAGAATAATGCATATGA
* * *
112052 GTGCATTATTGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTTGCATAAAAG
66 GTGCATTATTGGCATAAAAGGATGCCAAAAGAATAATGCATATGGGTGCATTATTGGCATAAAAG
112117 GATGC
131 GATGC
* * *
112122 CAAAAGAATAATGCATAT-GGTGCATTATTGGCATGAAAGGACG-CCATAG-CTGAAATGCATAT
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGACGACAAAAGAAT--AATGCATAT
* * * * *
112184 GGGTGCATTATTTGCATAAAAGGATGCTAAAAGAATAATGCATATGGGTTCATTATTGGCATGAA
64 GAGTGCATTATTGGCATAAAAGGATGCCAAAAGAATAATGCATATGGGTGCATTATTGGCATAAA
112249 AGGATGC
129 AGGATGC
* *
112256 C-ATAG-CTGAAATGCATATGGGTGCATT
1 CAAAAGAAT--AATGCATATGGGTGCATT
112283 TTCAACATAA
Statistics
Matches: 141, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
132 2 0.01
133 7 0.05
134 106 0.75
135 26 0.18
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (135 bp):
CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGACGACAAAAGAATAATGCATATGA
GTGCATTATTGGCATAAAAGGATGCCAAAAGAATAATGCATATGGGTGCATTATTGGCATAAAAG
GATGC
Found at i:112295 original size:90 final size:89
Alignment explanation
Indices: 111996--112282 Score: 443
Period size: 90 Copynumber: 3.2 Consensus size: 89
111986 ACAAAAGAAT
* * * *
111996 AATGCATATGGGTTCATTATTGGCATGAAAGGATGACAAAAGAATAATGCATATGAGTGCATTAT
1 AATGCATATGGGTGCATTATTTGCATAAAAGGATG-CAAAAGAATAATGCATATGGGTGCATTAT
** *
112061 TGGCATGAAAGGATGCCA-AAATAA
65 TGGCATGAAAGGATGCCATAGCTGA
112085 TAATGCATATGGGTGCATTATTTGCATAAAAGGATGCCAAAAGAATAATGCATAT-GGTGCATTA
1 -AATGCATATGGGTGCATTATTTGCATAAAAGGATG-CAAAAGAATAATGCATATGGGTGCATTA
*
112149 TTGGCATGAAAGGACGCCATAGCTGA
64 TTGGCATGAAAGGATGCCATAGCTGA
*
112175 AATGCATATGGGTGCATTATTTGCATAAAAGGATGCTAAAAGAATAATGCATATGGGTTCATTAT
1 AATGCATATGGGTGCATTATTTGCATAAAAGGATGC-AAAAGAATAATGCATATGGGTGCATTAT
112240 TGGCATGAAAGGATGCCATAGCTGA
65 TGGCATGAAAGGATGCCATAGCTGA
112265 AATGCATATGGGTGCATT
1 AATGCATATGGGTGCATT
112283 TTCAACATAA
Statistics
Matches: 183, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
88 1 0.01
89 78 0.43
90 104 0.57
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (89 bp):
AATGCATATGGGTGCATTATTTGCATAAAAGGATGCAAAAGAATAATGCATATGGGTGCATTATT
GGCATGAAAGGATGCCATAGCTGA
Found at i:118690 original size:26 final size:26
Alignment explanation
Indices: 118654--118732 Score: 140
Period size: 26 Copynumber: 3.0 Consensus size: 26
118644 GAGAGGCAAG
*
118654 TAAGTCGATCTTGTACTCTTTAAAAC
1 TAAGCCGATCTTGTACTCTTTAAAAC
118680 TAAGCCGATCTTGTACTCTTTAAAAC
1 TAAGCCGATCTTGTACTCTTTAAAAC
*
118706 TAAGCCAATCTTGTACTCTTTAAAAC
1 TAAGCCGATCTTGTACTCTTTAAAAC
118732 T
1 T
118733 CACTTTACTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (26 bp):
TAAGCCGATCTTGTACTCTTTAAAAC
Found at i:119921 original size:27 final size:26
Alignment explanation
Indices: 119864--119921 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
119854 AAGATTATAA
119864 CAAAATAAATAAAAGATAAAGAAATT
1 CAAAATAAATAAAAGATAAAGAAATT
*
119890 GAAAATAAAATAAGATA-ATAAAGAAA-T
1 CAAAAT-AAATAA-A-AGATAAAGAAATT
119917 CAAAA
1 CAAAA
119922 GATCTCCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 5 0.19
27 11 0.41
28 10 0.37
29 1 0.04
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (26 bp):
CAAAATAAATAAAAGATAAAGAAATT
Found at i:130422 original size:16 final size:16
Alignment explanation
Indices: 130401--130433 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
130391 TGATATATAT
130401 GCTTAAGGAAGGATTA
1 GCTTAAGGAAGGATTA
130417 GCTTAAGGAAGGATTA
1 GCTTAAGGAAGGATTA
130433 G
1 G
130434 ATGGGATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (16 bp):
GCTTAAGGAAGGATTA
Found at i:130994 original size:22 final size:20
Alignment explanation
Indices: 130943--131012 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
130933 TGCAAAAATG
*
130943 GTATCGATACCATAATAGGT
1 GTATCGATACCATAGTAGGT
*
130963 -TATCGGTACCATAGTATGGT
1 GTATCGATACCATAGTA-GGT
*
130983 AGTATCGATACCATGGTAGG-
1 -GTATCGATACCATAGTAGGT
131003 GTATCGATAC
1 GTATCGATAC
131013 TGAGGAGCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 24 0.56
20 3 0.07
21 2 0.05
22 14 0.33
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (20 bp):
GTATCGATACCATAGTAGGT
Found at i:131484 original size:45 final size:45
Alignment explanation
Indices: 131420--131668 Score: 389
Period size: 45 Copynumber: 5.6 Consensus size: 45
131410 AACGAATAAA
131420 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
* *
131465 CAAAAGAATATTGCATAT-GGAGCATTATTGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
**
131509 CAAAAGAATAATGCATATGGGTTTATTATTGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
131554 CAAAAGAATAATGCATATGGGTGCATTATTGG-AT-AAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
* *
131597 CAAAAGAATAATGCATATAGGTGCATTATTGGCATGAAAGGATGT
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
* *
131642 C-ATAGTAAAAATGCATATGGGTGCATT
1 CAAAAG-AATAATGCATATGGGTGCATT
131669 TCCAGCATAA
Statistics
Matches: 187, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
43 40 0.21
44 49 0.26
45 98 0.52
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.27
Consensus pattern (45 bp):
CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
Found at i:131633 original size:88 final size:90
Alignment explanation
Indices: 131420--131668 Score: 389
Period size: 88 Copynumber: 2.8 Consensus size: 90
131410 AACGAATAAA
*
131420 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAAGAATATTGCATAT-G
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAAGAATAATGCATATGG
*
131484 GAGCATTATTGGCATGAAAGGATGC
66 GTGCATTATTGGCATGAAAGGATGC
**
131509 CAAAAGAATAATGCATATGGGTTTATTATTGGCATGAAAGGATGCCAAAAGAATAATGCATATGG
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAAGAATAATGCATATGG
131574 GTGCATTATTGG-AT-AAAGGATGC
66 GTGCATTATTGGCATGAAAGGATGC
* * * *
131597 CAAAAGAATAATGCATATAGGTGCATTATTGGCATGAAAGGATGTC-ATAGTAAAAATGCATATG
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAAG-AATAATGCATATG
131661 GGTGCATT
65 GGTGCATT
131669 TCCAGCATAA
Statistics
Matches: 148, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
87 3 0.02
88 71 0.48
89 62 0.42
90 12 0.08
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.27
Consensus pattern (90 bp):
CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAAGAATAATGCATATGG
GTGCATTATTGGCATGAAAGGATGC
Found at i:133718 original size:20 final size:20
Alignment explanation
Indices: 133693--133735 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
133683 ATCGTGTATC
*
133693 AGTTTAAGCACAAATAACAA
1 AGTTTAAGCAAAAATAACAA
*
133713 AGTTTAAGCAAAAATAACCA
1 AGTTTAAGCAAAAATAACAA
133733 AGT
1 AGT
133736 CCTAGCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.21
Consensus pattern (20 bp):
AGTTTAAGCAAAAATAACAA
Found at i:138374 original size:27 final size:27
Alignment explanation
Indices: 138344--138409 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
138334 AAACACTAGA
* * * *
138344 TATCATTTAGTACTAACATAGACCATG
1 TATCCTTTAGTACTAACACACACCAGG
138371 TATCCTTTAGTACTAACACACACCAGG
1 TATCCTTTAGTACTAACACACACCAGG
138398 TATCCTTTAGTA
1 TATCCTTTAGTA
138410 TGGTCTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (27 bp):
TATCCTTTAGTACTAACACACACCAGG
Found at i:156244 original size:6 final size:5
Alignment explanation
Indices: 156198--156255 Score: 59
Period size: 5 Copynumber: 11.4 Consensus size: 5
156188 TACTTTGATA
156198 TCATT TC-TT TCCATT TCATT TCATT TCATT TC-TT ATCAATT TCAATT
1 TCATT TCATT T-CATT TCATT TCATT TCATT TCATT -TC-ATT TC-ATT
156245 TC-TT TCATT TC
1 TCATT TCATT TC
156256 TTATTTCCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
4 9 0.19
5 25 0.53
6 11 0.23
7 2 0.04
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (5 bp):
TCATT
Found at i:156250 original size:26 final size:26
Alignment explanation
Indices: 156198--156259 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
156188 TACTTTGATA
*
156198 TCATTTCTT-TCCATTTCATTTCATT
1 TCATTTCTTATCAATTTCATTTCATT
156223 TCATTTCTTATCAATTTCAATTTC-TT
1 TCATTTCTTATCAATTTC-ATTTCATT
156249 TCATTTCTTAT
1 TCATTTCTTAT
156260 TTCCAATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 9 0.26
26 20 0.59
27 5 0.15
ACGTcount: A:0.19, C:0.21, G:0.00, T:0.60
Consensus pattern (26 bp):
TCATTTCTTATCAATTTCATTTCATT
Found at i:159875 original size:10 final size:10
Alignment explanation
Indices: 159848--159881 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
159838 AAAAAAACAA
*
159848 AAAAAAAGGC
1 AAAAAAAGCC
159858 AAAAAAAGCC
1 AAAAAAAGCC
159868 AAAAAAAGCC
1 AAAAAAAGCC
159878 AAAA
1 AAAA
159882 TTTCAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.74, C:0.15, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCC
Found at i:170842 original size:12 final size:14
Alignment explanation
Indices: 170815--170846 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
170805 ACGTAAAATC
170815 AAAATATAATATTT
1 AAAATATAATATTT
170829 AAAATAT-A-ATTT
1 AAAATATAATATTT
170841 AAAATA
1 AAAATA
170847 GAACCGTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATATAATATTT
Found at i:172361 original size:10 final size:11
Alignment explanation
Indices: 172334--172359 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
172324 GTCAAACCCC
172334 AAAAATTATTT
1 AAAAATTATTT
172345 AAAAATTATTT
1 AAAAATTATTT
172356 AAAA
1 AAAA
172360 TTGATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATTATTT
Found at i:173306 original size:25 final size:23
Alignment explanation
Indices: 173238--173307 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 23
173228 GTCAACTCGA
173238 TCTGATCTGAGTCAACCTGA---
1 TCTGATCTGAGTCAACCTGACCG
*
173258 TCTGATCTGAGTCAACCCGA---
1 TCTGATCTGAGTCAACCTGACCG
173278 TCTGATCTGAGTCAACCTGAACCGG
1 TCTGATCTGAGTCAACCTG-ACC-G
173303 TCTGA
1 TCTGA
173308 CCCGTTAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 37 0.86
21 1 0.02
25 5 0.12
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (23 bp):
TCTGATCTGAGTCAACCTGACCG
Found at i:173307 original size:20 final size:20
Alignment explanation
Indices: 173225--173297 Score: 121
Period size: 20 Copynumber: 3.6 Consensus size: 20
173215 CAGATCGAAA
173225 TGAGTCAA-CTCGATCTGATC
1 TGAGTCAACCT-GATCTGATC
173245 TGAGTCAACCTGATCTGATC
1 TGAGTCAACCTGATCTGATC
*
173265 TGAGTCAACCCGATCTGATC
1 TGAGTCAACCTGATCTGATC
173285 TGAGTCAACCTGA
1 TGAGTCAACCTGA
173298 ACCGGTCTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 48 0.96
21 2 0.04
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (20 bp):
TGAGTCAACCTGATCTGATC
Found at i:173307 original size:40 final size:40
Alignment explanation
Indices: 173225--173307 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
173215 CAGATCGAAA
* * *
173225 TGAGTCAACTCGATCTGATCTGAGTCAACCTGATCTGATC
1 TGAGTCAACCCGATCTGATCTGAGTCAACCTGAACCGATC
*
173265 TGAGTCAACCCGATCTGATCTGAGTCAACCTGAACCGGTC
1 TGAGTCAACCCGATCTGATCTGAGTCAACCTGAACCGATC
173305 TGA
1 TGA
173308 CCCGTTAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
TGAGTCAACCCGATCTGATCTGAGTCAACCTGAACCGATC
Found at i:173362 original size:19 final size:20
Alignment explanation
Indices: 173314--173364 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
173304 CTGACCCGTT
* *
173314 AACTTTGACCCGACCCATTG
1 AACTTTGACCTGACACATTG
173334 -ACTTTGACCTGACACA-TG
1 AACTTTGACCTGACACATTG
173352 AACTTTGACCTGA
1 AACTTTGACCTGA
173365 GTTGACCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (20 bp):
AACTTTGACCTGACACATTG
Found at i:179884 original size:18 final size:18
Alignment explanation
Indices: 179862--179958 Score: 119
Period size: 18 Copynumber: 5.5 Consensus size: 18
179852 ATACATTTCA
179862 CAGTTATCAGATGATTTT
1 CAGTTATCAGATGATTTT
* *
179880 TAGTTATCAGAT-ATTTA
1 CAGTTATCAGATGATTTT
179897 CAGTTATCAGATGATTTT
1 CAGTTATCAGATGATTTT
* *
179915 CAGTCATCAGATG-TTTA
1 CAGTTATCAGATGATTTT
179932 CAGTTATCAGATG-TTTT
1 CAGTTATCAGATGATTTT
*
179949 ACAATTATCA
1 -CAGTTATCA
179959 AACGTAGATT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
17 33 0.49
18 35 0.51
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (18 bp):
CAGTTATCAGATGATTTT
Found at i:179903 original size:35 final size:35
Alignment explanation
Indices: 179844--179958 Score: 151
Period size: 35 Copynumber: 3.3 Consensus size: 35
179834 TAAATGTTTA
* *
179844 CAGTTATCATACATTTCACAGTTATCAGATGATTTT
1 CAGTTATCAGATATTT-ACAGTTATCAGATGATTTT
*
179880 TAGTTATCAGATATTTACAGTTATCAGATGATTTT
1 CAGTTATCAGATATTTACAGTTATCAGATGATTTT
* *
179915 CAGTCATCAGATGTTTACAGTTATCAGATG-TTTT
1 CAGTTATCAGATATTTACAGTTATCAGATGATTTT
*
179949 ACAATTATCA
1 -CAGTTATCA
179959 AACGTAGATT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
34 4 0.06
35 53 0.76
36 13 0.19
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (35 bp):
CAGTTATCAGATATTTACAGTTATCAGATGATTTT
Found at i:179903 original size:53 final size:53
Alignment explanation
Indices: 179840--179958 Score: 134
Period size: 53 Copynumber: 2.2 Consensus size: 53
179830 ATTCTAAATG
* * **
179840 TTTACAGTTATCATA-CATTTCACAGTTATCAGATGATTTTTAGTTATCAGAT-A
1 TTTACAGTTATCAGATCATTT-ACAGTCATCAGATG-TTTACAGTTATCAGATGA
* * *
179893 TTTACAGTTATCAGATGATTTTCAGTCATCAGATGTTTACAGTTATCAGATGT
1 TTTACAGTTATCAGATCATTTACAGTCATCAGATGTTTACAGTTATCAGATGA
*
179946 TTTACAATTATCA
1 TTTACAGTTATCA
179959 AACGTAGATT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
52 14 0.25
53 38 0.68
54 4 0.07
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (53 bp):
TTTACAGTTATCAGATCATTTACAGTCATCAGATGTTTACAGTTATCAGATGA
Found at i:181650 original size:8 final size:8
Alignment explanation
Indices: 181637--181675 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 8
181627 TTTCCTTATA
181637 TAAAATAT
1 TAAAATAT
181645 TAAAATATT
1 TAAAATA-T
181654 TAAAA-AT
1 TAAAATAT
181661 TAAATATAT
1 TAAA-ATAT
181670 TAAAAT
1 TAAAAT
181676 GTAGAATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 5 0.18
8 11 0.39
9 12 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TAAAATAT
Found at i:181664 original size:16 final size:17
Alignment explanation
Indices: 181633--181675 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
181623 TGAATTTCCT
181633 TATA-TAAAATATTAAA
1 TATATTAAAATATTAAA
181649 -ATATTTAAAA-ATTAAA
1 TATA-TTAAAATATTAAA
181665 TATATTAAAAT
1 TATATTAAAAT
181676 GTAGAATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 3 0.13
16 12 0.52
17 8 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATATTAAAATATTAAA
Found at i:182736 original size:21 final size:20
Alignment explanation
Indices: 182706--182747 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 20
182696 AAACTTATAG
182706 AAATAATATCATGTAATTTTTA
1 AAATAATATCA--TAATTTTTA
182728 AAAT-ATATCATAATTTTTA
1 AAATAATATCATAATTTTTA
182747 A
1 A
182748 TCTATTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.50
21 6 0.30
22 4 0.20
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (20 bp):
AAATAATATCATAATTTTTA
Found at i:191751 original size:12 final size:12
Alignment explanation
Indices: 191736--191762 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
191726 TTGATCCCTG
191736 ATTTGCGTTTTA
1 ATTTGCGTTTTA
191748 ATTTGCGTTTTA
1 ATTTGCGTTTTA
191760 ATT
1 ATT
191763 AACAAATAAA
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:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (12 bp):
ATTTGCGTTTTA
Found at i:197567 original size:36 final size:36
Alignment explanation
Indices: 197513--197665 Score: 213
Period size: 36 Copynumber: 4.3 Consensus size: 36
197503 AGTCAATCCT
197513 AAGCCTTCA-CGGAGAATAGTGAAGCAAACCATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
* *
197548 AAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
197584 AAG-CTTCACCGGAGAATAGTGAAGCAAACCATCAT-
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATC-TG
* * * *
197619 AAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCTT
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
*
197655 AAGTCTTCACC
1 AAGCCTTCACC
197666 AAAAAGTAGT
Statistics
Matches: 108, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
35 41 0.38
36 67 0.62
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (36 bp):
AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
Found at i:197627 original size:71 final size:72
Alignment explanation
Indices: 197517--197665 Score: 214
Period size: 71 Copynumber: 2.1 Consensus size: 72
197507 AATCCTAAGC
* *
197517 CTTCA-CGGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAATCAAT
1 CTTCACCGGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCAGAGAATAGTGAAGCAAACAAT
197581 CTGAAG-
66 CTGAAGT
* * *
197587 CTTCACCGGAGAATAGTGAAGCAAACCATCAT-AAGTCTTCACCAGAGAGTAGTGAAGCAAACCA
1 CTTCACCGGAGAATAGTGAAGCAAACCATC-TGAAGCCTTCACCAGAGAATAGTGAAGCAAACAA
*
197651 TCTTAAGT
65 TCTGAAGT
197659 CTTCACC
1 CTTCACC
197666 AAAAAGTAGT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
70 5 0.07
71 57 0.81
72 8 0.11
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (72 bp):
CTTCACCGGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCAGAGAATAGTGAAGCAAACAAT
CTGAAGT
Found at i:197666 original size:36 final size:36
Alignment explanation
Indices: 197524--197681 Score: 205
Period size: 36 Copynumber: 4.4 Consensus size: 36
197514 AGCCTTCACG
* *
197524 GAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCG
1 GAGAATAGTGAAGCAAACCATCTGAAGTCTTCACCA
* * *
197560 GAGAATAGTGAAGCAATCAATCTGAAG-CTTCACCG
1 GAGAATAGTGAAGCAAACCATCTGAAGTCTTCACCA
197595 GAGAATAGTGAAGCAAACCATCAT-AAGTCTTCACCA
1 GAGAATAGTGAAGCAAACCATC-TGAAGTCTTCACCA
* *
197631 GAGAGTAGTGAAGCAAACCATCTTAAGTCTTCACCA
1 GAGAATAGTGAAGCAAACCATCTGAAGTCTTCACCA
*
197667 -AAAAGTAGTGAAGCA
1 GAGAA-TAGTGAAGCA
197682 GATCAATTTT
Statistics
Matches: 110, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
35 34 0.31
36 76 0.69
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (36 bp):
GAGAATAGTGAAGCAAACCATCTGAAGTCTTCACCA
Found at i:197988 original size:51 final size:51
Alignment explanation
Indices: 197896--198137 Score: 298
Period size: 51 Copynumber: 4.8 Consensus size: 51
197886 AAGATTATTT
* *
197896 GAGTTCCATACT-CCTAGAGAGAG-AGG-GCGAACCCGTTTGAAGATGTCC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * * *
197944 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * * *
197995 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAA-CCGTTTGAAGCTGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* *
198045 GAGTTCCATACT-CTTAAAGAAAGAAGGAGCGAA-CCGTTTGAAGAGATGTCT
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTCC
* *
198096 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTG
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG
198138 TTGAAGATTG
Statistics
Matches: 169, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
48 12 0.07
49 38 0.22
50 27 0.16
51 67 0.40
52 19 0.11
53 6 0.04
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (51 bp):
GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
Found at i:198100 original size:101 final size:101
Alignment explanation
Indices: 197895--198131 Score: 313
Period size: 101 Copynumber: 2.4 Consensus size: 101
197885 GAAGATTATT
* *
197895 TGAGTTCCATACTCCTAGAGAGAG-AGG-GCGAACCCGTTTGAAGATGTCCGAGTTCCATACTCC
1 TGAGTTCCATACTCCTAAAGAAAGAAGGAGCGAA-CCGTTTGAAGATGTCCGAGTTCCATACTCC
* *
197958 CTAGAGAAAGAAGGAGCGAACCCGTGTGAAGATATGC
65 CTAAAGAAAGAAGGAGCGAACCCGTGTGAAGAGATGC
* * *
197995 -GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCGTTTGAAGCTGTTCGAGTTCCATACT-C
1 TGAGTTCCATACTCC-TAAAGAAAGAAGGAGCGAACCGTTTGAAGATGTCCGAGTTCCATACTCC
* *
198058 TTAAAGAAAGAAGGAGCGAA-CCGTTTGAAGAGATGTC
65 CTAAAGAAAGAAGGAGCGAACCCGTGTGAAGAGATG-C
*
198095 TGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACC
1 TGAGTTCCATACT-CCTAAAGAAAGAAGGAGCGAACC
198132 CATTTGTTGA
Statistics
Matches: 120, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
99 26 0.22
100 27 0.22
101 60 0.50
102 7 0.06
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (101 bp):
TGAGTTCCATACTCCTAAAGAAAGAAGGAGCGAACCGTTTGAAGATGTCCGAGTTCCATACTCCC
TAAAGAAAGAAGGAGCGAACCCGTGTGAAGAGATGC
Found at i:198342 original size:108 final size:108
Alignment explanation
Indices: 198137--198554 Score: 646
Period size: 108 Copynumber: 3.9 Consensus size: 108
198127 GAACCCATTT
* *
198137 GTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGGG-AGACGCGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
*
198201 GTGGGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGCAATC
66 GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
198244 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
* * * *
198309 GTGGGTCTTATACTCTCTGAACATATAGGGGGCAGACGCGATT
66 GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
*
198352 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
*
198417 GTGGGTCTTATACTCTCTGAAGAAACA-GGGGCAGACGCAATC
66 GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * *
198459 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGCAGACAAGTTTGTTGAAGA-T
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
** *
198522 GATTCAAGTCTTATACCCTCTGAAGAAATAGGG
66 G--T-GGGTCTTATACTCTCTGAAGAAATAGGG
198555 AGCGAACCCA
Statistics
Matches: 285, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
105 2 0.01
106 19 0.07
107 96 0.34
108 166 0.58
109 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (108 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT
GTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
Found at i:198367 original size:215 final size:214
Alignment explanation
Indices: 198135--198521 Score: 695
Period size: 215 Copynumber: 1.8 Consensus size: 214
198125 GCGAACCCAT
198135 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGGG-AGACGCGATTGATGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGCGATTGATGAAGA
*
198199 TTGTGGGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCT
66 TTGTGGGTCTTATACTCTCTAAAGAAACA-GGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCT
*
198264 TATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGGGTCTTATACTCTCTGA
130 TATACTCTCTGAAGAAATA-GGGGCAGACAAGATTGATGAAGATTGTGGGTCTTATACTCTCTGA
198329 ACATATAGGGGGCAGACGCGA
194 ACATATAGGGGGCAGACGCGA
*
198350 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGCGATTGATGAAGA
*
198415 TTGTGGGTCTTATACTCTCTGAAGAAACAGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTT
66 TTGTGGGTCTTATACTCTCTAAAGAAACAGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTT
* *
198480 ATACTCTCTGAAGAAATAGGGGCAGACAAGTTTGTTGAAGAT
131 ATACTCTCTGAAGAAATAGGGGCAGACAAGATTGATGAAGAT
198522 GATTCAAGTC
Statistics
Matches: 165, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
214 21 0.13
215 99 0.60
216 45 0.27
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.28
Consensus pattern (214 bp):
TTGTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGCGATTGATGAAGA
TTGTGGGTCTTATACTCTCTAAAGAAACAGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTT
ATACTCTCTGAAGAAATAGGGGCAGACAAGATTGATGAAGATTGTGGGTCTTATACTCTCTGAAC
ATATAGGGGGCAGACGCGA
Found at i:199408 original size:28 final size:28
Alignment explanation
Indices: 199361--199432 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
199351 TCACGTGAGC
*
199361 TCACCATTTTC-ACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
199388 TCACCATTTCCAACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
199416 TCACCATTTCCAACCCG
1 TCACCATTTCCAACCCG
199433 GGCTTACCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 10 0.23
28 33 0.77
ACGTcount: A:0.18, C:0.43, G:0.12, T:0.26
Consensus pattern (28 bp):
TCACCATTTCCAACCCGTGCCAGTGCCT
Done.