Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007468.1 Hibiscus syriacus cultivar Beakdansim tig00020502_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: 67321
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1200 original size:65 final size:64
Alignment explanation
Indices: 1042--1208 Score: 196
Period size: 65 Copynumber: 2.6 Consensus size: 64
1032 TGATGCATCG
* ** *
1042 ATGCACCGATGCAC-CATGAATTAAATTAAACATCGAATGCATTTCATGCATCGATGCACATACC
1 ATGCACCGATGCACTCA-GGATTTTATGAAACATCGAATGCATTTCATGCATCGATGCACATACC
* *
1106 ATGCACCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCA-AC
1 ATGCACCGATGCACTCAGGATTTTATG-AAACATCGAATGCATTTCATGCATCGATGCA-CATAC
1170 C
64 C
* * *
1171 ATGCATCGATGCACTCTGGCTATTT-TGAAACATCGAAT
1 ATGCACCGATGCACTCAGGAT-TTTATGAAACATCGAAT
1209 ACACTCTGGC
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
64 31 0.35
65 53 0.60
66 5 0.06
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (64 bp):
ATGCACCGATGCACTCAGGATTTTATGAAACATCGAATGCATTTCATGCATCGATGCACATACC
Found at i:1215 original size:28 final size:28
Alignment explanation
Indices: 1174--1269 Score: 176
Period size: 28 Copynumber: 3.5 Consensus size: 28
1164 ACCAACCATG
1174 CATCG-ATGCACTCTGGCTATTTTGAAA
1 CATCGAATGCACTCTGGCTATTTTGAAA
*
1201 CATCGAATACACTCTGGCTATTTTGAAA
1 CATCGAATGCACTCTGGCTATTTTGAAA
1229 CATCGAATGCACTCTGGCTATTTTGAAA
1 CATCGAATGCACTCTGGCTATTTTGAAA
1257 CATCGAATGCACT
1 CATCGAATGCACT
1270 TGATGCATCG
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 5 0.08
28 61 0.92
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (28 bp):
CATCGAATGCACTCTGGCTATTTTGAAA
Found at i:8025 original size:22 final size:21
Alignment explanation
Indices: 7998--8080 Score: 78
Period size: 23 Copynumber: 3.8 Consensus size: 21
7988 TTTAGTGCAG
7998 AGGGAATCGATACCCCCTTGA
1 AGGGAATCGATACCCCCTTGA
* *
8019 AGGGGAACCGATTCCCCCTTTGA
1 A-GGGAATCGATACCCCC-TTGA
* * *
8042 ATGGGAATCGATTCCCTCATT-T
1 A-GGGAATCGATACCC-CCTTGA
8064 AGGGAATCGATACCCCC
1 AGGGAATCGATACCCCC
8081 ATGAGTTCTG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 1 0.02
21 14 0.27
22 15 0.29
23 20 0.39
24 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCCTTGA
Found at i:8041 original size:23 final size:22
Alignment explanation
Indices: 7999--8057 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 22
7989 TTAGTGCAGA
*
7999 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATTCCCCCTTGAAG
* *
8021 GGGAACCGATTCCCCCTTTGAAT
1 GGGAATCGATTCCCCC-TTGAAG
8044 GGGAATCGATTCCC
1 GGGAATCGATTCCC
8058 TCATTTAGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (22 bp):
GGGAATCGATTCCCCCTTGAAG
Found at i:9945 original size:23 final size:23
Alignment explanation
Indices: 9913--9959 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
9903 ATTTAAACTT
9913 AAAATAATTTCAAAACAATTTTAA
1 AAAATAATTTC-AAACAATTTTAA
* *
9937 AAAAT-ATTTCGAACCATTTTAA
1 AAAATAATTTCAAACAATTTTAA
9959 A
1 A
9960 GCCAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 5 0.24
24 5 0.24
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAATAATTTCAAACAATTTTAA
Found at i:10965 original size:14 final size:14
Alignment explanation
Indices: 10948--10978 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10938 TTTTTATTTA
*
10948 CATTTTCATTTTTG
1 CATTTTCATCTTTG
10962 CATTTTCATCTTTG
1 CATTTTCATCTTTG
10976 CAT
1 CAT
10979 AATTACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.06, T:0.58
Consensus pattern (14 bp):
CATTTTCATCTTTG
Found at i:13275 original size:23 final size:22
Alignment explanation
Indices: 13233--13276 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
13223 ATACTTATTC
*
13233 AAAAAAAAAAGATGAAAAAAGG
1 AAAAAAAAAAGATAAAAAAAGG
*
13255 AAAAAAGAAAAGAAAAGAAAAA
1 AAAAAA-AAAAGATAA-AAAAA
13277 AAATTAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 7 0.39
24 5 0.28
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAGATAAAAAAAGG
Found at i:13278 original size:18 final size:18
Alignment explanation
Indices: 13236--13278 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
13226 CTTATTCAAA
*
13236 AAAAAAAGATGAAAAAAG
1 AAAAAAAGATAAAAAAAG
*
13254 GAAAAAAGA-AAAGAAAAG
1 AAAAAAAGATAAA-AAAAG
13272 AAAAAAA
1 AAAAAAA
13279 ATTAAATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAAAAAGATAAAAAAAG
Found at i:15739 original size:74 final size:74
Alignment explanation
Indices: 15645--15846 Score: 287
Period size: 75 Copynumber: 2.7 Consensus size: 74
15635 ATCATTTTGA
*
15645 ATGTATTTTTGAACGTTTGTATCAGCAAATGTTGGGCATGCTGAAAGCCCATTTCAATCATAATC
1 ATGTA-TTTTGAACGTTTGTATCAGCAAATGTTGGGCATGCTGAAAGCCCATTTCAATCAGAATC
*
15710 AGGAATATTG
65 AGAAATATTG
* * *
15720 ATGTATTTCGAACGTTTGTATCAGCAAATACTGGGGCATGCTGAAAGCCCATTTCAATCAGAATC
1 ATGTATTTTGAACGTTTGTATCAGCAAAT-GTTGGGCATGCTGAAAGCCCATTTCAATCAGAATC
*
15785 AGAAATGTTG
65 AGAAATATTG
* * * *
15795 ACGCATTTTGAACGCTTGTATCAGCAAATGTTGGGGCATGCTGAAGGCCCAT
1 ATGTATTTTGAACGTTTGTATCAGCAAATGTT-GGGCATGCTGAAAGCCCAT
15847 ATCATCTTAT
Statistics
Matches: 112, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
74 24 0.21
75 88 0.79
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (74 bp):
ATGTATTTTGAACGTTTGTATCAGCAAATGTTGGGCATGCTGAAAGCCCATTTCAATCAGAATCA
GAAATATTG
Found at i:16730 original size:54 final size:54
Alignment explanation
Indices: 16660--16818 Score: 221
Period size: 54 Copynumber: 2.9 Consensus size: 54
16650 ATGAGAAATA
* * *
16660 TGGGCATAAGCGACAGGAAAGGATGAATATGTTGTCAAATGTTTTACGAACATC
1 TGGGCAAAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATC
* *
16714 TGGGCAAAAGCCACAGGAAAGGATGAATGTGTTATCAAATGTTTTATGAACATC
1 TGGGCAAAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATC
* * * *
16768 TGAGCAGAAA-CCACATGAAAGAATGAATGTATTGTCAAATGTTTTACGAAC
1 TGGGCA-AAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
16819 CAATTATTAT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 90 0.97
55 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (54 bp):
TGGGCAAAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATC
Found at i:17943 original size:45 final size:45
Alignment explanation
Indices: 17879--18371 Score: 736
Period size: 45 Copynumber: 10.9 Consensus size: 45
17869 CTATTTCCTA
*
17879 CATCTGTAAGCCCTTCAGTGCAT-ACTGTTTTCAAAACCTTCGGGC
1 CATCTGTAAGCCCTTCAGTGCATGA-TGTTTTCAAAACCTTCGGGT
*
17924 CATCTGTAAGCCCTTCAGTGCATGATGATTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
17969 CATCTGTAAGCCCTTCAGTGTATGATGTTTTCAAAGCCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
18014 CATCTGTAAGCCCTTCGGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * * *
18059 TATCTATAATCCCTTCAGTGCATGATATTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* ** **
18104 CATCTGTAAGCCCTTCAGTGCATAATAATTTCAAAATATTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
18149 CATCTGTCAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
18194 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
18239 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * * *
18284 CATCTGTAAGCCCTTTAGTGCATAATATTTTCAAAACATTCGGGC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
18329 CATATGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCCTTCG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA-CCTTCG
18372 AGAGCTTTTT
Statistics
Matches: 405, Mismatches: 41, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
45 399 0.99
46 6 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:18437 original size:45 final size:45
Alignment explanation
Indices: 18381--18475 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
18371 GAGAGCTTTT
* * * * * * *
18381 TGATATTTTCAAAGTCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCAGATCATCTATAAGACCTACAGTGCA
18426 TGATGTTTTCAAAGCCTTCAGATCATCTATAAGACCTACAGTGCA
1 TGATGTTTTCAAAGCCTTCAGATCATCTATAAGACCTACAGTGCA
*
18471 AGATG
1 TGATG
18476 ATAAGACCTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCAGATCATCTATAAGACCTACAGTGCA
Found at i:18658 original size:3 final size:3
Alignment explanation
Indices: 18650--18685 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
18640 TATTTTACTT
18650 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18686 AATATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21194 original size:42 final size:42
Alignment explanation
Indices: 21118--21199 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
21108 ATGGATGAAC
* *
21118 CTATTGCGGCGTTTGTATAAAAACACTGCTAAAG-TACTACT
1 CTATTGCGACGTTTGTATAAAAACACTGCCAAAGTTACTACT
**
21159 CTATTGCGACGTTTTGTATAAAAATGCTGCCAAAGTTACTA
1 CTATTGCGACG-TTTGTATAAAAACACTGCCAAAGTTACTA
21200 TTTTGTGGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 10 0.29
42 20 0.57
43 5 0.14
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (42 bp):
CTATTGCGACGTTTGTATAAAAACACTGCCAAAGTTACTACT
Found at i:21328 original size:34 final size:35
Alignment explanation
Indices: 21290--21515 Score: 135
Period size: 37 Copynumber: 6.2 Consensus size: 35
21280 CGGAGTTTTA
*
21290 AATATATA-TTTTAATATA-ATTTTTGAACAA-ATAT
1 AATATATACTTTTAA-AAACATTTTTGAA-AACATAT
*
21324 AATATATAGTTTTTAGAAAACATTTTTGAAAACATAT
1 AATATATA-CTTTTA-AAAACATTTTTGAAAACATAT
21361 AATATATACTTTTAAAAAAACTGATTTTTG-AAA-ATAT
1 AATATATACTTTT--AAAAAC--ATTTTTGAAAACATAT
* * **
21398 -ATATATAGTTTTGAAAACGATTTTTG-AAGTATAT
1 AATATATACTTTTAAAAAC-ATTTTTGAAAACATAT
* * * *
21432 ATTATATAGTTTTGAAATCAATTTTTGAAAACATAT
1 AATATATACTTTTAAAAAC-ATTTTTGAAAACATAT
* * *
21468 AAATTATATAGTTTCGAAAATA-ATTTTTGAAAATATAT
1 -AA-TATATACTTT-TAAAA-ACATTTTTGAAAACATAT
21506 ACATACTATA
1 A-ATA-TATA
21516 TAGTTTTAAA
Statistics
Matches: 159, Mismatches: 15, Indels: 32
0.77 0.07 0.16
Matches are distributed among these distances:
33 10 0.06
34 17 0.11
35 23 0.14
36 30 0.19
37 35 0.22
38 34 0.21
39 10 0.06
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (35 bp):
AATATATACTTTTAAAAACATTTTTGAAAACATAT
Found at i:21361 original size:37 final size:35
Alignment explanation
Indices: 21308--21515 Score: 188
Period size: 38 Copynumber: 5.7 Consensus size: 35
21298 TTTTAATATA
21308 ATTTTTGAACAAATATAATATATAGTTTTTAGAAAAC-
1 ATTTTTGAA-AAATATAATATATAG-TTTT-GAAAACG
* *
21345 ATTTTTGAAAACATATAATATATACTTTTAAAAAAACTG
1 ATTTTTGAAAA-ATATAATATATAGTTTT--GAAAAC-G
21384 ATTTTTG-AAAATAT-ATATATAGTTTTGAAAACG
1 ATTTTTGAAAAATATAATATATAGTTTTGAAAACG
** * * *
21417 ATTTTTGAAGTATATATTATATAGTTTTGAAATCA
1 ATTTTTGAAAAATATAATATATAGTTTTGAAAACG
* **
21452 ATTTTTGAAAACATATAAATTATATAGTTTCGAAAATA
1 ATTTTTGAAAA-ATAT-AA-TATATAGTTTTGAAAACG
21490 ATTTTTGAAAATATATACATACTATA
1 ATTTTTGAAAA-ATATA-ATA-TATA
21516 TAGTTTTAAA
Statistics
Matches: 144, Mismatches: 16, Indels: 21
0.80 0.09 0.12
Matches are distributed among these distances:
33 8 0.06
34 10 0.07
35 25 0.17
36 21 0.15
37 35 0.24
38 38 0.26
39 7 0.05
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (35 bp):
ATTTTTGAAAAATATAATATATAGTTTTGAAAACG
Found at i:21368 original size:73 final size:70
Alignment explanation
Indices: 21291--21525 Score: 198
Period size: 73 Copynumber: 3.2 Consensus size: 70
21281 GGAGTTTTAA
21291 ATATATA-TTTTAATATAATTTTTGAACAAATATAATATATAGTTTTTAGAAAACATTTTTGAAA
1 ATATATAGTTTTAA-ATAATTTTTGAA-AAATATAATATATAG-TTTT-GAAAACATTTTTGAAA
*
21355 ACATATAAT
62 ATATATAAT
* *
21364 ATATACT--TTTAAAAAAACTGATTTTTG-AAAATAT-ATATATAGTTTTGAAAACGATTTTTG-
1 ATATA-TAGTTT---TAAA-TAATTTTTGAAAAATATAATATATAGTTTTGAAAAC-ATTTTTGA
*
21424 AAGTATAT-AT
60 AAATATATAAT
* *
21434 -TATATAGTTTTGAAATCAATTTTTGAAAACATATAAATTATATAGTTTCGAAAATAATTTTTGA
1 ATATATAGTTTT-AAAT-AATTTTTGAAAA-ATAT-AA-TATATAGTTTTGAAAA-CATTTTTGA
21498 AAATATATACAT
60 AAATATATA-AT
21510 ACTATATAGTTTTAAA
1 A-TATATAGTTTTAAA
21526 ATTTTTTTTA
Statistics
Matches: 132, Mismatches: 9, Indels: 38
0.74 0.05 0.21
Matches are distributed among these distances:
67 1 0.01
68 11 0.08
69 7 0.05
70 9 0.07
71 12 0.09
72 12 0.09
73 38 0.29
74 14 0.11
75 2 0.02
76 12 0.09
77 3 0.02
78 11 0.08
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (70 bp):
ATATATAGTTTTAAATAATTTTTGAAAAATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
ATAAT
Found at i:21533 original size:38 final size:37
Alignment explanation
Indices: 21288--21543 Score: 150
Period size: 38 Copynumber: 7.0 Consensus size: 37
21278 TCCGGAGTTT
*
21288 TAAA-TATATA-TTTTAATATAATTTTTGAACAA-ATA
1 TAAACTATATAGTTTTAAAATAATTTTTGAA-AACATA
21323 T-AA-TATATAGTTTTTAGAAA-ACATTTTTGAAAACATA
1 TAAACTATATAG-TTTTA-AAATA-ATTTTTGAAAACATA
* *
21360 T-AA-TATATACTTTTAAAAAAACTGATTTTTG-AAA-ATA
1 TAAACTATATAGTTTT---AAAA-TAATTTTTGAAAACATA
** *
21397 T--A-TATATAGTTTTGAAAACGATTTTTG--AA-GTA
1 TAAACTATATAGTTTT-AAAATAATTTTTGAAAACATA
* * *
21429 TATATTATATAGTTTTGAAATCAATTTTTGAAAACATA
1 TAAACTATATAGTTTTAAAAT-AATTTTTGAAAACATA
* * *
21467 TAAATTATATAGTTTCGAAAATAATTTTTGAAAATATA
1 TAAACTATATAGTTT-TAAAATAATTTTTGAAAACATA
* *
21505 TACATACTATATAGTTTTAAAAT-TTTTTTTAAAACATA
1 TA-A-ACTATATAGTTTTAAAATAATTTTTGAAAACATA
21543 T
1 T
21544 TATGTTATTA
Statistics
Matches: 181, Mismatches: 20, Indels: 37
0.76 0.08 0.16
Matches are distributed among these distances:
32 5 0.03
33 8 0.04
34 16 0.09
35 19 0.10
36 23 0.13
37 29 0.16
38 52 0.29
39 18 0.10
40 11 0.06
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (37 bp):
TAAACTATATAGTTTTAAAATAATTTTTGAAAACATA
Found at i:21609 original size:23 final size:22
Alignment explanation
Indices: 21565--21639 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 22
21555 ATGCTTGCAT
21565 ATTATATAGTTATATCT-A-ATTA
1 ATTATATA-TTATAT-TAATATTA
21587 CATTATATATTATATTAATATT-
1 -ATTATATATTATATTAATATTA
21609 ATT-TATATT-TATTAAT-TATA
1 ATTATATATTATATTAATAT-TA
21629 ATTATA-ATTAT
1 ATTATATATTAT
21640 TTATTTATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
18 1 0.02
19 8 0.17
20 12 0.26
21 7 0.15
22 7 0.15
23 11 0.24
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (22 bp):
ATTATATATTATATTAATATTA
Found at i:21621 original size:13 final size:13
Alignment explanation
Indices: 21605--21661 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
21595 ATTATATTAA
21605 TATTATTTATATT
1 TATTATTTATATT
* *
21618 TATTAATTATAAT
1 TATTATTTATATT
* *
21631 TATAATTATTTATT
1 TATTATT-TATATT
21645 TATTTATTTAT-TT
1 TA-TTATTTATATT
21658 TATT
1 TATT
21662 TACTTCTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
12 2 0.06
13 20 0.59
14 8 0.24
15 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTATTTATATT
Found at i:21662 original size:13 final size:13
Alignment explanation
Indices: 21607--21663 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 13
21597 TATATTAATA
21607 TTATTTATATTTAT
1 TTATTTAT-TTTAT
* * *
21621 TAATTATAATTATAA
1 TTATT-T-ATTTTAT
21636 TTATTTA-TTTAT
1 TTATTTATTTTAT
21648 TTATTTATTTTAT
1 TTATTTATTTTAT
21661 TTA
1 TTA
21664 CTTCTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
12 10 0.29
13 9 0.26
14 5 0.15
15 8 0.24
16 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTTATTTTAT
Found at i:24013 original size:14 final size:15
Alignment explanation
Indices: 23986--24018 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
23976 GTAGGACTTT
23986 TTATTTTCATTATTA
1 TTATTTTCATTATTA
*
24001 TTATTTT-ATTATTC
1 TTATTTTCATTATTA
24015 TTAT
1 TTAT
24019 CTCATTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTTTCATTATTA
Found at i:24057 original size:12 final size:13
Alignment explanation
Indices: 24028--24057 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
24018 TCTCATTAAC
24028 TTTTTTCCTTTCA
1 TTTTTTCCTTTCA
*
24041 TTTTTTCCTTTTA
1 TTTTTTCCTTTCA
24054 TTTT
1 TTTT
24058 ATTTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTCCTTTCA
Found at i:27346 original size:85 final size:85
Alignment explanation
Indices: 27197--27352 Score: 231
Period size: 85 Copynumber: 1.8 Consensus size: 85
27187 ATCTTCCAGC
* * *
27197 CAAAGTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCTTCAAGTTCGATTC
1 CAAAGTTACAGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACAAAAACCTTCAAGTTCGATTC
27262 CATTCAACTCAAGGGCATAT
66 CATTCAACTCAAGGGCATAT
* * * * * *
27282 CAAATTTACAGTATAACTTAAGGTGAAAAGGGTTATCTGTCAACAAAAACCTTCGAGTTTGATTC
1 CAAAGTTACAGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACAAAAACCTTCAAGTTCGATTC
27347 CATTCA
66 CATTCA
27353 GTTTGATGAC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 62 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (85 bp):
CAAAGTTACAGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACAAAAACCTTCAAGTTCGATTC
CATTCAACTCAAGGGCATAT
Found at i:27633 original size:285 final size:284
Alignment explanation
Indices: 27005--28002 Score: 1261
Period size: 285 Copynumber: 3.5 Consensus size: 284
26995 AACTGTTTGT
* * * * *
27005 AGCATAGCTCAAGGCGAGAAAGGCTATTTGTCAACAAAAACTTTCGAGTTTGATTCCATTCAACT
1 AGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTTGATTCCATTCAGCT
* * *** * * * * *
27070 TAAGGGTGTATCAACCGTATGATAGCAGTGAGAAACTACTTTCCGGTTGAATTTTAAATCGAGGT
66 CAATGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGT
*
27135 CTTTAAGTCAAGAAGAAGACCTGGGTTGGCTGTA-ATTTAGCAACAATGAACTATCTTCCAGCCA
131 CTTTAAGTCAAGAAGAAGACCTGGGTTGGC--TACATTTAGCAACAAGGAACTATC-TCCAGCCA
* * *
27199 AAGTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAAACCTTCAAGTTCGATTCCA
193 AATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCA
* *
27264 TTCAACTCAAGGGCATATCAAATTTAC
258 TTCAGCTTAAGGGCATATCAAATTTAC
* * * * * *
27291 AGTATAACTTAAGGTGAAAAGGGTTATCTGTCAACAAAAACCTTCGAGTTTGATTCCATTCAGTT
1 AGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTTGATTCCATTCAGCT
** * * *
27356 TGATGACATATCAACTGCATGGTAGCAGCGAGGAGCTACTTTCCGGTTGAATTTTAAACTGAGGT
66 CAATGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGT
* *
27421 CTTTAAGTCAAGAAGAAGACATGGGTTGGCTACATTTTAGCAACAA-AAACTATCTCCAAGCCAA
131 CTTTAAGTCAAGAAGAAGACCTGGGTTGGCTACA-TTTAGCAACAAGGAACTATCTCC-AGCCAA
** * * * *
27485 ATTTACAATATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCAATTCCGT
194 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCAT
27550 TCAGCTTAAGGGCATATCAAATTTAC
259 TCAGCTTAAGGGCATATCAAATTTAC
* * * * *
27576 AGCATAACTCAAGGCGAGAATGGCTATATATCAACAAAAACCTTCGAGTTCGATTCCATTAAGCT
1 AGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTTGATTCCATTCAGCT
* * *
27641 CGATGACATATCAACCGCATGGTAGTAGTGA-GAACTACTTTCCGGTTGAATTTTAAACCGAGGT
66 CAATGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGT
* * *
27705 CTTTAAGTCAAGAAGAA-ATCCTGGGTTGGCTTCGATTTAGTAACAAGGAACTATCTCTCATCCA
131 CTTTAAGTCAAGAAGAAGA-CCTGGGTTGGCTAC-ATTTAGCAACAAGGAACTATCTC-CAGCCA
* ** * *
27769 AATTTATAGCATAGCTCAAGGCGAGAAGGGCCATATGTCAACAAAAACCTTCGAGTTTGATTCCA
193 AATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCA
* *
27834 TTAAGCTTAAGGGCATATCGAATTTAC
258 TTCAGCTTAAGGGCATATCAAATTTAC
* * * * *
27861 AACATAGCTTAAGGCGAGAAGGGCTATCTGT-AA-AAAAACTTTCGAGTTTGATTCCTTTCAGCT
1 AGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTTGATTCCATTCAGCT
* * * * *
27924 CAATAACATATCAACCGCATGGTAGTAGCCAAGAACTACTTTCCGGTTGAAGTTTAAACCGAGGT
66 CAATGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGT
*
27989 CTTTAAGTTAAGAA
131 CTTTAAGTCAAGAA
28003 AAACATCTTG
Statistics
Matches: 616, Mismatches: 88, Indels: 18
0.85 0.12 0.02
Matches are distributed among these distances:
283 54 0.09
284 122 0.20
285 293 0.48
286 147 0.24
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (284 bp):
AGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTTGATTCCATTCAGCT
CAATGACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGT
CTTTAAGTCAAGAAGAAGACCTGGGTTGGCTACATTTAGCAACAAGGAACTATCTCCAGCCAAAT
TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTC
AGCTTAAGGGCATATCAAATTTAC
Found at i:27651 original size:85 final size:85
Alignment explanation
Indices: 27482--27654 Score: 220
Period size: 85 Copynumber: 2.0 Consensus size: 85
27472 ATCTCCAAGC
* * * * *
27482 CAAATTTACAATATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCAATTC
1 CAAATTTACAACATAACTCAAGGCGAGAAGGGCTATATATCAACAAAAACCTTCGAGTTCAATTC
* * * *
27547 CGTTCAGCTTAAGGGCATAT
66 CATTAAGCTCAAGGACATAT
* * *
27567 CAAATTTACAGCATAACTCAAGGCGAGAATGGCTATATATCAACAAAAACCTTCGAGTTCGATTC
1 CAAATTTACAACATAACTCAAGGCGAGAAGGGCTATATATCAACAAAAACCTTCGAGTTCAATTC
* *
27632 CATTAAGCTCGATGACATAT
66 CATTAAGCTCAAGGACATAT
27652 CAA
1 CAA
27655 CCGCATGGTA
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 74 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (85 bp):
CAAATTTACAACATAACTCAAGGCGAGAAGGGCTATATATCAACAAAAACCTTCGAGTTCAATTC
CATTAAGCTCAAGGACATAT
Found at i:27935 original size:83 final size:85
Alignment explanation
Indices: 27769--27935 Score: 212
Period size: 83 Copynumber: 2.0 Consensus size: 85
27759 CTCTCATCCA
* *
27769 AATTTATAGCATAGCTCAAGGCGAGAAGGGCCATATGTCAACAAAAACCTTCGAGTTTGATTCCA
1 AATTTACAACATAGCTCAAGGCGAGAAGGGCCATATGTCAACAAAAACCTTCGAGTTTGATTCCA
* **
27834 TTAAGCTTAAGGGCATATCG
66 TTAAGCTCAAGAACATATCG
* * * * *
27854 AATTTACAACATAGCTTAAGGCGAGAAGGGCTATCTGT-AA-AAAAACTTTCGAGTTTGATTCCT
1 AATTTACAACATAGCTCAAGGCGAGAAGGGCCATATGTCAACAAAAACCTTCGAGTTTGATTCCA
* *
27917 TTCAGCTCAATAACATATC
66 TTAAGCTCAAGAACATATC
27936 AACCGCATGG
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
83 35 0.50
84 2 0.03
85 33 0.47
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (85 bp):
AATTTACAACATAGCTCAAGGCGAGAAGGGCCATATGTCAACAAAAACCTTCGAGTTTGATTCCA
TTAAGCTCAAGAACATATCG
Found at i:28568 original size:37 final size:39
Alignment explanation
Indices: 28524--28632 Score: 138
Period size: 37 Copynumber: 2.9 Consensus size: 39
28514 ATTTTTATAT
*
28524 AGTTTTTGAACAAATATAATATATAGTTTTT-AGAAAA-C
1 AGTTTTTGAA-AAATATAATATATAGTTTTTAAAAAAATC
*
28562 A-TTTTTGAAAACATATAATATATACTTTTTAAAAAAATC
1 AGTTTTTGAAAA-ATATAATATATAGTTTTTAAAAAAATC
*
28601 AGTTTTTG-AAAATAT-ATATATAGTTTTGAAAA
1 AGTTTTTGAAAAATATAATATATAGTTTTTAAAA
28633 TGATTTCTGA
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
36 2 0.03
37 40 0.63
38 10 0.16
39 5 0.08
40 6 0.10
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (39 bp):
AGTTTTTGAAAAATATAATATATAGTTTTTAAAAAAATC
Found at i:38748 original size:25 final size:25
Alignment explanation
Indices: 38717--38841 Score: 250
Period size: 25 Copynumber: 5.0 Consensus size: 25
38707 ATTTAGGGGA
38717 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
38742 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
38767 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
38792 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
38817 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
38842 GGGTTGATTG
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 100 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:38917 original size:3 final size:3
Alignment explanation
Indices: 38909--38945 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
38899 ATTAATAAAC
38909 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
38946 CGATAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:39202 original size:40 final size:40
Alignment explanation
Indices: 39158--39386 Score: 176
Period size: 40 Copynumber: 5.5 Consensus size: 40
39148 ACATGGTTCC
*
39158 TACGTGATGAGGACATCTGGTCGGGGAATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
* * * * * *
39198 TACGTGATGAAGAGTTCTGGCCATCTAAAGGTG-ATAACACGGTTCC
1 TACGTGATGAGGAGATCTGG---TC----GGGGAATGACACGGCTCA
* ** * * *
39244 TACGTGATGAGGACG-GCTGGTTATCTATGG-TTGACATGGCTCC
1 TACGTGATGAGGA-GATCTGG---TC-GGGGAATGACACGGCTCA
39287 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
* *
39327 TACGTGATGAAGAGTTCTGGTCGGGGAATGACACGGCTCA
1 TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
* *
39367 TACGTGATGAAGAGTTCTGG
1 TACGTGATGAGGAGATCTGG
39387 CCATCTAAAG
Statistics
Matches: 152, Mismatches: 27, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
39 2 0.01
40 87 0.57
42 1 0.01
43 29 0.19
46 29 0.19
47 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (40 bp):
TACGTGATGAGGAGATCTGGTCGGGGAATGACACGGCTCA
Found at i:39248 original size:46 final size:42
Alignment explanation
Indices: 39104--39419 Score: 158
Period size: 40 Copynumber: 7.4 Consensus size: 42
39094 TGTTGGGGAC
*
39104 GACACTGCTCATACGTGATGAAGAGTTCTTGTCG-TCTAAGG-G-T
1 GACACGGCTCATACGTGATGAAGAGTTC-TG--GATCT-AGGTGAT
* * * * ** *
39147 GACATGGTTCCTACGTGATGAGGACATCTGG-TC--GGGGAAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGATCTAGGTG-AT
39187 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGG--ATCT--AGGTGAT
* * * * *
39233 AACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--T
1 GACACGGCTCATACGTGATGAAGA-GTTCTGG--ATCTA-GGTGAT
* * * * *
39276 GACATGGCTCCTACGTGATGAGGAGATCTGG-TC--GGGGAAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGATCTAGGTG-AT
*
39316 GACACGGCTCATACGTGATGAAGAGTTCTGG-TC--GGGGAAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGATCTAGGTG-AT
39356 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGG--ATCT--AGGTGAT
* * *
39402 AACACGGTTCCTACGTGA
1 GACACGGCTCATACGTGA
39420 CGAGGACGGC
Statistics
Matches: 216, Mismatches: 34, Indels: 43
0.74 0.12 0.15
Matches are distributed among these distances:
37 4 0.02
38 1 0.00
40 99 0.46
42 3 0.01
43 51 0.24
44 1 0.00
45 3 0.01
46 47 0.22
47 7 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (42 bp):
GACACGGCTCATACGTGATGAAGAGTTCTGGATCTAGGTGAT
Found at i:39997 original size:15 final size:15
Alignment explanation
Indices: 39973--40016 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
39963 AAGATGATCT
*
39973 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
39988 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
40003 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
40017 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:40560 original size:66 final size:67
Alignment explanation
Indices: 40472--40669 Score: 229
Period size: 67 Copynumber: 3.0 Consensus size: 67
40462 AAAGATTTAC
* ** * * * * *
40472 TTCAAGAGAAACGGTCTCAAGAGATACAAAATTCAATTT-AAGAGAAACAGATTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
40536 GT
66 GT
* ***
40538 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
40603 GT
66 GT
*** *
40605 TTCAAAAGAAACTATCTTAAGAGAGA-AAGAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAA-AATTCAATTTCAAAAGAAACAAACTCAAAGATTTT
40669 T
65 T
40670 TCGCAAAATT
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
66 32 0.28
67 84 0.72
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (67 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTCAATTTCAAAAGAAACAAACTCAAAGATTTTT
GT
Found at i:40573 original size:37 final size:36
Alignment explanation
Indices: 40532--40653 Score: 130
Period size: 37 Copynumber: 3.5 Consensus size: 36
40522 ATTCAAAGAT
*
40532 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAAA
* * * *
40569 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG---AT
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
40599 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAGAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAA-AA
*
40636 TTTTGTTTCCAAAGAAAC
1 TTTTGTTTCAAAAGAAAC
40654 AAACTCAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
30 21 0.31
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 2 0.03
37 37 0.54
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (36 bp):
TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
Found at i:40607 original size:67 final size:67
Alignment explanation
Indices: 40514--40669 Score: 260
Period size: 67 Copynumber: 2.3 Consensus size: 67
40504 TCAATTTAAG
* * *
40514 AGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAA-AATTTTGTTTC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAGAATTTTGTTTC
40578 AAA
65 AAA
*
40581 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAGAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAGAATTTTGTTTCA
40646 AA
66 AA
40648 AGAAACAAACTCAAAGATTTTT
1 AGAAACAAACTCAAAGATTTTT
40670 TCGCAAAATT
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
66 2 0.02
67 82 0.98
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAGAATTTTGTTTCA
AA
Found at i:40735 original size:52 final size:53
Alignment explanation
Indices: 40656--40759 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 53
40646 AAAGAAACAA
* *
40656 ACTCAAAGATTTTTTCGCAAAATTGTCTCAAGAGATACAAAACTTTGTTTCAG
1 ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
*
40709 ACTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
40760 AAATAAATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 39 0.81
53 9 0.19
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (53 bp):
ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
Found at i:40784 original size:26 final size:27
Alignment explanation
Indices: 40755--40876 Score: 92
Period size: 29 Copynumber: 4.4 Consensus size: 27
40745 CAAAACTTTG
*
40755 TTTCAAAATAAATAGACTCAAAG-T-TT
1 TTTCAAAAGAAA-AGACTCAAAGATATT
*
40781 TTTCAAAAGAAACGACTCAAAGATATT
1 TTTCAAAAGAAAAGACTCAAAGATATT
* * *
40808 TATTCAAAAGGAACCA-ACTCCAAGATTTT
1 T-TTCAAAA-GAA-AAGACTCAAAGATATT
40837 TATTCAAAAGGAACAA-ACTCAAAGAT-TT
1 T-TTCAAAA-GAA-AAGACTCAAAGATATT
*
40865 TTTCAAGAGAAA
1 TTTCAAAAGAAA
40877 CTGTCTCAAG
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
25 10 0.12
26 15 0.18
27 9 0.11
28 10 0.12
29 38 0.46
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.28
Consensus pattern (27 bp):
TTTCAAAAGAAAAGACTCAAAGATATT
Found at i:40832 original size:29 final size:28
Alignment explanation
Indices: 40770--40870 Score: 120
Period size: 29 Copynumber: 3.7 Consensus size: 28
40760 AAATAAATAG
* *
40770 ACTCAAAG-TTTT-TTCAAAA-GAAACG
1 ACTCAAAGATTTTATTCAAAAGGAACCA
40795 ACTCAAAGATATTTATTCAAAAGGAACCA
1 ACTCAAAGAT-TTTATTCAAAAGGAACCA
* *
40824 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTTATTCAAAAGGAACCA
40853 ACTCAAAGATTTT-TTCAA
1 ACTCAAAGATTTTATTCAA
40871 GAGAAACTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.12
26 1 0.02
27 8 0.12
28 11 0.17
29 37 0.56
30 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.29
Consensus pattern (28 bp):
ACTCAAAGATTTTATTCAAAAGGAACCA
Found at i:41198 original size:36 final size:36
Alignment explanation
Indices: 41114--41217 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
41104 GAGAAAATGA
* * *
41114 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
41148 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
41184 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
41218 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:41245 original size:36 final size:36
Alignment explanation
Indices: 41115--41233 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
41105 AGAAAATGAT
* * * *
41115 GTCTCAAGCGAGACGAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
41149 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
41185 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
41220 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
41234 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.17
36 38 0.55
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:41365 original size:105 final size:102
Alignment explanation
Indices: 41185--41422 Score: 268
Period size: 105 Copynumber: 2.3 Consensus size: 102
41175 TAGAGAAATT
* *
41185 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATG
* *
41250 TGAAACAAATTCGAAATTTGGATCTCAAAGG-GAAAAG
65 TGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAG
* *
41287 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTGTTT
* * * * *
41351 -TTAGTGAATCAAATTTAAAATTTGTATCTCAAAGGAAAAAAT
61 AAT-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAG
**
41393 GTCTCAAGCGAGACGCAATTTGTTTT-AGAA
1 GTCTCAAGCGAGACAAAATTTGTTTTGAGAA
41423 TTCTCAAAAT
Statistics
Matches: 116, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
101 5 0.04
102 23 0.20
103 4 0.03
104 5 0.04
105 51 0.44
106 28 0.24
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (102 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAG
Found at i:41878 original size:4 final size:4
Alignment explanation
Indices: 41869--41918 Score: 68
Period size: 4 Copynumber: 13.0 Consensus size: 4
41859 TTTATGTATC
* *
41869 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT AAGT TTGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
41915 ATGT
1 ATGT
41919 GTATACTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
4 38 0.95
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:43114 original size:11 final size:11
Alignment explanation
Indices: 43098--43138 Score: 73
Period size: 11 Copynumber: 3.6 Consensus size: 11
43088 CTCTTCTTTT
43098 TTTTTCTTTGA
1 TTTTTCTTTGA
43109 TTTTTCTTTGA
1 TTTTTCTTTGA
43120 TTTTTGCTTTGA
1 TTTTT-CTTTGA
43132 TTTTTCT
1 TTTTTCT
43139 CTTTGCTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 18 0.62
12 11 0.38
ACGTcount: A:0.07, C:0.10, G:0.10, T:0.73
Consensus pattern (11 bp):
TTTTTCTTTGA
Found at i:43124 original size:12 final size:12
Alignment explanation
Indices: 43097--43143 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
43087 TCTCTTCTTT
43097 TTTTTTCTTTGA
1 TTTTTTCTTTGA
43109 -TTTTTCTTTGA
1 TTTTTTCTTTGA
*
43120 TTTTTGCTTTGA
1 TTTTTTCTTTGA
43132 TTTTTCTCTTTG
1 TTTTT-TCTTTG
43144 CTCTTTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 11 0.35
12 15 0.48
13 5 0.16
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:43143 original size:18 final size:17
Alignment explanation
Indices: 43122--43168 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
43112 TTCTTTGATT
43122 TTTGCTTTGATTTTTCTC
1 TTTGCTTTGATTTTT-TC
43140 TTTGCTCTTTG-TTTTTTC
1 TTTG--CTTTGATTTTTTC
*
43158 TTTGGTTTGAT
1 TTTGCTTTGAT
43169 CTTTGCACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.16
17 1 0.04
18 10 0.40
19 5 0.20
20 5 0.20
ACGTcount: A:0.04, C:0.13, G:0.15, T:0.68
Consensus pattern (17 bp):
TTTGCTTTGATTTTTTC
Found at i:43161 original size:11 final size:11
Alignment explanation
Indices: 43091--43161 Score: 58
Period size: 11 Copynumber: 6.6 Consensus size: 11
43081 CCACTTTCTC
43091 TTCTTT-TTTT
1 TTCTTTGTTTT
*
43101 TTCTTTGATTT
1 TTCTTTGTTTT
43112 TTCTTTGATTTT
1 TTCTTTG-TTTT
* *
43124 TGCTTTGATTT
1 TTCTTTGTTTT
* *
43135 TTC--TCTTTG
1 TTCTTTGTTTT
*
43144 CTCTTTGTTTT
1 TTCTTTGTTTT
43155 TTCTTTG
1 TTCTTTG
43162 GTTTGATCTT
Statistics
Matches: 45, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
9 5 0.11
10 6 0.13
11 25 0.56
12 9 0.20
ACGTcount: A:0.04, C:0.13, G:0.10, T:0.73
Consensus pattern (11 bp):
TTCTTTGTTTT
Found at i:45338 original size:31 final size:32
Alignment explanation
Indices: 45282--45343 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
45272 TGACAAAATG
45282 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
45314 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
45344 CATGTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:49534 original size:25 final size:25
Alignment explanation
Indices: 49503--49602 Score: 200
Period size: 25 Copynumber: 4.0 Consensus size: 25
49493 ATTTAGGGGA
49503 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
49528 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
49553 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
49578 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
49603 GGGTTGATTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 75 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:49678 original size:3 final size:3
Alignment explanation
Indices: 49670--49709 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
49660 ATTAATAAAC
49670 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
49710 CGATAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:49695 original size:22 final size:22
Alignment explanation
Indices: 49662--49705 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
49652 AATATGTAAT
49662 TAATAAACATAATAATAATAAA
1 TAATAAACATAATAATAATAAA
49684 TAATAATA-ATAATAATAATAAA
1 TAATAA-ACATAATAATAATAAA
49706 ATAACGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAAACATAATAATAATAAA
Found at i:55549 original size:32 final size:35
Alignment explanation
Indices: 55510--55580 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
55500 TTGATTACAT
* *
55510 TTAT-ATAAGTCATATCATTTGATGAATGGACTTA
1 TTATAATAAGTCATATAATTTGATGAATAGACTTA
*
55544 TTATAATAAGTCATGTAATTTGATGAATAGACTTA
1 TTATAATAAGTCATATAATTTGATGAATAGACTTA
55579 TT
1 TT
55581 TTTTAGTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 4 0.12
35 29 0.88
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (35 bp):
TTATAATAAGTCATATAATTTGATGAATAGACTTA
Found at i:57457 original size:35 final size:35
Alignment explanation
Indices: 57386--57454 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
57376 TTGATGCTAT
* *
57386 TTATATAAGTCATGTCACTTGGTGAATGGACTTTA
1 TTATATAAGTCATGTCACTTGATGAATAGACTTTA
*
57421 TTATAATAAGTCATGTCATTTGATGAATAGACTT
1 TTAT-ATAAGTCATGTCACTTGATGAATAGACTT
57455 ATTTTTTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (35 bp):
TTATATAAGTCATGTCACTTGATGAATAGACTTTA
Found at i:63860 original size:34 final size:34
Alignment explanation
Indices: 63810--63891 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
63800 GCCATTTCAT
* *
63810 CGATACACACCTATTTCGAATACAATTTATGCAC
1 CGATGCACACCCATTTCGAATACAATTTATGCAC
63844 CGATGCACACCCATTTCGAATACAATTTATGCAC
1 CGATGCACACCCATTTCGAATACAATTTATGCAC
*
63878 CGATGCACAACCAT
1 CGATGCACACCCAT
63892 GCATCGATGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (34 bp):
CGATGCACACCCATTTCGAATACAATTTATGCAC
Found at i:63942 original size:62 final size:64
Alignment explanation
Indices: 63869--63989 Score: 194
Period size: 63 Copynumber: 1.9 Consensus size: 64
63859 TCGAATACAA
63869 TTTATGCACCGATGCACA-ACCATGCATCGATGCACTCTA-AAT-TTATGAAACATCGAATTGGT
1 TTTATGCACCGATGCACACACCATGCATCGATGCACTCTAGAATATT-TGAAACATCGAATTGGT
* *
63931 TTTATGTACCGATGCACACACCATGCATCGATGCACTCTAGACTATTTGAAACATCGAA
1 TTTATGCACCGATGCACACACCATGCATCGATGCACTCTAGAATATTTGAAACATCGAA
63990 GCAAATTTGT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
62 17 0.31
63 21 0.39
64 14 0.26
65 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (64 bp):
TTTATGCACCGATGCACACACCATGCATCGATGCACTCTAGAATATTTGAAACATCGAATTGGT
Found at i:64012 original size:63 final size:63
Alignment explanation
Indices: 63867--64012 Score: 172
Period size: 63 Copynumber: 2.3 Consensus size: 63
63857 TTTCGAATAC
***
63867 AATTTATGCACCGATGCACA-ACCATGCATCGATGCACTCTAAATTTATGAAACATCGAATTG
1 AATTTATGCACCGATGCACACACCATGCATCGATGCACTCTAAATTTATGAAACATCGAAGCA
** * *
63929 GTTTTATGTACCGATGCACACACCATGCATCGATGCACTCTAGACTATT-TGAAACATCGAAGCA
1 AATTTATGCACCGATGCACACACCATGCATCGATGCACTCTA-AAT-TTATGAAACATCGAAGCA
* *
63993 AATTTGTGCA-CGATACACAC
1 AATTTATGCACCGATGCACAC
64013 CCTAGTGTAC
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
62 17 0.25
63 30 0.43
64 20 0.29
65 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (63 bp):
AATTTATGCACCGATGCACACACCATGCATCGATGCACTCTAAATTTATGAAACATCGAAGCA
Found at i:65901 original size:21 final size:20
Alignment explanation
Indices: 65877--65919 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 20
65867 GGCTTCTGAT
65877 TATAAGAAAT-TATTTCTAAAA
1 TATAA-AAATATATTTC-AAAA
65898 TATAAAAATGATATTTCAAAA
1 TATAAAAAT-ATATTTCAAAA
65919 T
1 T
65920 TGAAAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.20
21 10 0.50
22 6 0.30
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
TATAAAAATATATTTCAAAA
Found at i:65925 original size:21 final size:22
Alignment explanation
Indices: 65887--65929 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
65877 TATAAGAAAT
65887 TATTTCTAAAATATAAAAATGA
1 TATTTCTAAAATATAAAAATGA
65909 TATTTC-AAAAT-TGAAAAATGA
1 TATTTCTAAAATAT-AAAAATGA
65930 AAATAATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.65
22 6 0.30
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (22 bp):
TATTTCTAAAATATAAAAATGA
Done.