Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007482.1 Hibiscus syriacus cultivar Beakdansim tig00020627_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: 93201
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1185 original size:27 final size:27
Alignment explanation
Indices: 1171--1249 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
1161 ACTTGTTTTC
*
1171 TTTTACTTGACTCCAGTTTTGATTGCT
1 TTTTACTTGACTCCAATTTTGATTGCT
*
1198 TTTTACTTGACTCCACTTTTGATTGCT
1 TTTTACTTGACTCCAATTTTGATTGCT
*
1225 TTTTACTTGACTCCACTTTTGATTG
1 TTTTACTTGACTCCAATTTTGATTG
1250 TTGTGTCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.15, C:0.20, G:0.13, T:0.52
Consensus pattern (27 bp):
TTTTACTTGACTCCAATTTTGATTGCT
Found at i:6244 original size:25 final size:26
Alignment explanation
Indices: 6208--6264 Score: 98
Period size: 25 Copynumber: 2.2 Consensus size: 26
6198 AGTTACCCAC
6208 ACATTAGAAACATTAACTCCTACATT
1 ACATTAGAAACATTAACTCCTACATT
*
6234 ACATTAG-AACATTAACTCCTACGTT
1 ACATTAGAAACATTAACTCCTACATT
6259 ACATTA
1 ACATTA
6265 CAATACAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 23 0.77
26 7 0.23
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (26 bp):
ACATTAGAAACATTAACTCCTACATT
Found at i:9555 original size:30 final size:31
Alignment explanation
Indices: 9503--9566 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
9493 AGCTTTGACT
9503 TTTGGAAGATGATAATGGTTAGGTGTCTTAG
1 TTTGGAAGATGATAATGGTTAGGTGTCTTAG
*
9534 TTTGGAAGATGATAA-GGTTAGGTGTCTTGG
1 TTTGGAAGATGATAATGGTTAGGTGTCTTAG
9564 TTT
1 TTT
9567 AATGGTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.23, C:0.03, G:0.33, T:0.41
Consensus pattern (31 bp):
TTTGGAAGATGATAATGGTTAGGTGTCTTAG
Found at i:9563 original size:25 final size:27
Alignment explanation
Indices: 9503--9561 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 27
9493 AGCTTTGACT
9503 TTTGGAAGATGATAATGGTTAGGTGTC
1 TTTGGAAGATGATAATGGTTAGGTGTC
9530 TTAGTTTGGAAGATGATAA-GGTTAGGTGTC
1 ----TTTGGAAGATGATAATGGTTAGGTGTC
9560 TT
1 TT
9562 GGTTTAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 2 0.07
30 11 0.39
31 15 0.54
ACGTcount: A:0.25, C:0.03, G:0.32, T:0.39
Consensus pattern (27 bp):
TTTGGAAGATGATAATGGTTAGGTGTC
Found at i:20050 original size:24 final size:24
Alignment explanation
Indices: 20018--20072 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
20008 AAGTAAATGG
*
20018 AGTAGATGGATTTTTAGTTGCTCT
1 AGTAGATGGATTTTTAATTGCTCT
20042 AGTAGATGGATTTTTAATTGCTCT
1 AGTAGATGGATTTTTAATTGCTCT
20066 AGTAGAT
1 AGTAGAT
20073 TTCAGATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.44
Consensus pattern (24 bp):
AGTAGATGGATTTTTAATTGCTCT
Found at i:21856 original size:3 final size:3
Alignment explanation
Indices: 21839--21885 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
21829 TATGTAAATA
* *
21839 AAT ATT AAT -AT AAT AAT AAT AAT AAT AAT AAAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
21884 AA
1 AA
21886 GTTAGACCCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:23431 original size:19 final size:21
Alignment explanation
Indices: 23395--23434 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
23385 AATAAATTAA
23395 AAAATTAAAAGTACAATAAAT
1 AAAATTAAAAGTACAATAAAT
*
23416 AAAA-TAAAAG-ATAATAAAT
1 AAAATTAAAAGTACAATAAAT
23435 TTAGTGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 6 0.33
21 4 0.22
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAATTAAAAGTACAATAAAT
Found at i:23683 original size:10 final size:10
Alignment explanation
Indices: 23668--23725 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 10
23658 TTAATTTTGT
23668 AAATTAAAAA
1 AAATTAAAAA
23678 AAATTAGAAAA
1 AAATTA-AAAA
*
23689 AAA-TATAAA
1 AAATTAAAAA
23698 AAATT-AAAA
1 AAATTAAAAA
23707 AAATTACAAAA
1 AAATTA-AAAA
23718 CAAATTAA
1 -AAATTAA
23726 TATGATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
9 14 0.34
10 9 0.22
11 12 0.29
12 6 0.15
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (10 bp):
AAATTAAAAA
Found at i:23709 original size:9 final size:10
Alignment explanation
Indices: 23668--23717 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
23658 TTAATTTTGT
*
23668 AAATTAAAAA
1 AAATTACAAA
*
23678 AAATTAGAAA
1 AAATTACAAA
* *
23688 AAAATATAAA
1 AAATTACAAA
23698 AAATTA-AAA
1 AAATTACAAA
23707 AAATTACAAA
1 AAATTACAAA
23717 A
1 A
23718 CAAATTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 9 0.26
10 26 0.74
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (10 bp):
AAATTACAAA
Found at i:34704 original size:20 final size:20
Alignment explanation
Indices: 34610--34978 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
34600 GATTTTCCAT
* ** *
34610 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
34630 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
34650 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34670 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
34690 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
34710 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34730 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
34750 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
34770 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
34790 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34810 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
34830 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34850 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
34870 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34890 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
34910 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
34930 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
34950 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
34970 AATCACAAC
1 AATCGCAAC
34979 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:35690 original size:24 final size:24
Alignment explanation
Indices: 35651--35697 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
35641 AAATTTGGTC
35651 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
35675 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
35698 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:35888 original size:12 final size:12
Alignment explanation
Indices: 35871--35895 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35861 ATATAATCCT
35871 GAAGAAGAAAAA
1 GAAGAAGAAAAA
35883 GAAGAAGAAAAA
1 GAAGAAGAAAAA
35895 G
1 G
35896 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:38220 original size:19 final size:19
Alignment explanation
Indices: 38198--38504 Score: 358
Period size: 19 Copynumber: 17.4 Consensus size: 19
38188 CGGAAAATAC
*
38198 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
38217 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
38231 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
38251 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
38265 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38284 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
38303 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
38317 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38336 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
38355 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
38369 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
38388 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
38407 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38426 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38445 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
38459 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38478 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
38497 AATCGCAA
1 AATCGCAA
38505 CGAGATAATC
Statistics
Matches: 249, Mismatches: 13, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 16 0.06
17 15 0.06
18 5 0.02
19 151 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:38313 original size:52 final size:53
Alignment explanation
Indices: 38226--38504 Score: 358
Period size: 52 Copynumber: 5.2 Consensus size: 53
38216 AAATCCCAAC
*
38226 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
38279 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
38331 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
38383 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
38440 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
38492 ATGAAAATCGCAA
1 ATGAAAATCGCAA
38505 CGAGATAATC
Statistics
Matches: 212, Mismatches: 8, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
51 2 0.01
52 156 0.74
53 18 0.08
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:38349 original size:71 final size:71
Alignment explanation
Indices: 38265--38504 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
38255 GCAACGAGAG
*
38265 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
38330 AATGAA
66 AATGAA
* * *
38336 AATCGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
*
38396 TACGAAATGAA
61 TGCGAAATGAA
38407 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
38472 AATGAA
66 AATGAA
38478 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
38505 CGAGATAATC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 2 0.01
71 113 0.75
72 2 0.01
73 7 0.05
74 2 0.01
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:38450 original size:142 final size:137
Alignment explanation
Indices: 38198--38536 Score: 497
Period size: 142 Copynumber: 2.4 Consensus size: 137
38188 CGGAAAATAC
* * * *
38198 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAAC-CGAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
38261 AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT
63 AGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAT
38326 GCGAAATGAA
128 GCGAAATGAA
38336 AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACCGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
38401 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 -A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
38466 ATGCGAAATGAA
126 ATGCGAAATGAA
38478 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACCGA-ATAATCGCAATGCGAAATTA-AAATCGCA
38537 TTGCGATTTT
Statistics
Matches: 185, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 33 0.18
139 3 0.02
141 1 0.01
142 123 0.66
143 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGAACCGAATAATCGCAATGCGAAATTAAAATCGCAAACGAGA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:38642 original size:19 final size:19
Alignment explanation
Indices: 38533--38634 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
38523 AAATTATAAA
38533 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
38552 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
38572 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
38588 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
38605 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
38624 CGCATTGCGAT
1 CGCATTGCGAT
38635 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:38760 original size:14 final size:14
Alignment explanation
Indices: 38741--38777 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
38731 CATCAATTAC
38741 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
38755 ACAAATCATCTTTT
1 ACAAATCAACTTTT
38769 ACAAATCAA
1 ACAAATCAA
38778 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:38789 original size:12 final size:12
Alignment explanation
Indices: 38772--38844 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
38762 ATCTTTTACA
38772 AATCAATTAAAC
1 AATCAATTAAAC
*
38784 AATCAA--AAATTG
1 AATCAATTAAA--C
**
38796 AATCAACTTTTAC
1 AATCAA-TTAAAC
38809 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
38822 AATCAA-AAAAC
1 AATCAATTAAAC
38833 AATCAATTAAAC
1 AATCAATTAAAC
38845 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:38806 original size:38 final size:38
Alignment explanation
Indices: 38758--38830 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
38748 AACTTTTACA
*
38758 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
38796 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
38831 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:40720 original size:14 final size:14
Alignment explanation
Indices: 40701--40757 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
40691 CGCGAAATGA
*
40701 AATCGCAACGACAG
1 AATCGCAACGAAAG
40715 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
40732 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
40748 AATCGCAACG
1 AATCGCAACG
40758 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:40739 original size:19 final size:19
Alignment explanation
Indices: 40646--40779 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
40636 TAGTTTACTT
* *
40646 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
40666 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
40685 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
40703 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
40717 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
40736 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
40750 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
40769 TCGCAATGCGA
1 TCGCAACGCGA
40780 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.17
15 1 0.01
16 14 0.15
17 7 0.07
18 9 0.09
19 37 0.39
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:40740 original size:51 final size:47
Alignment explanation
Indices: 40664--40757 Score: 125
Period size: 51 Copynumber: 1.9 Consensus size: 47
40654 CGAAACTTAA
40664 AATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAATCGCAACGACAG
1 AATCGCAACGCGAAACCAAAATCGCAA--CGAAA-G-AATCGCAACGACAG
* **
40715 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAACG
1 AATCGCAACGCGAAACCAAAATCGCAACGAAAGAATCGCAACG
40758 CGAAATGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
47 10 0.25
48 1 0.03
49 5 0.12
51 24 0.60
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (47 bp):
AATCGCAACGCGAAACCAAAATCGCAACGAAAGAATCGCAACGACAG
Found at i:40742 original size:33 final size:33
Alignment explanation
Indices: 40683--40774 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
40673 GCGAAACCAA
*
40683 AATCGCAACGCGAAATG-AAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
40715 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
40748 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
40775 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 16 0.29
33 40 0.71
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:40797 original size:19 final size:19
Alignment explanation
Indices: 40775--40903 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
40765 AAAATCGCAA
40775 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
40794 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
40808 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
40827 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
40841 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
40860 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
40879 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
40899 TGCGA
1 TGCGA
40904 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:40817 original size:33 final size:33
Alignment explanation
Indices: 40775--40866 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
40765 AAAATCGCAA
40775 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
40808 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
40841 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
40867 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:41104 original size:93 final size:93
Alignment explanation
Indices: 40945--41322 Score: 740
Period size: 93 Copynumber: 4.1 Consensus size: 93
40935 ACTTGAATGG
40945 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
41010 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
41038 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
41103 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
*
41131 ATTTACTTTCGACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
41195 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
41223 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
41288 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
41316 ATTTACT
1 ATTTACT
41323 AAGCAATCTA
Statistics
Matches: 282, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 91 0.32
93 191 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
TTTAGCAGAATTGGCAGCAACCGAACAA
Found at i:41258 original size:185 final size:186
Alignment explanation
Indices: 40945--41322 Score: 740
Period size: 185 Copynumber: 2.0 Consensus size: 186
40935 ACTTGAATGG
40945 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
41010 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
66 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
41075 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
131 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
*
41131 ATTTACTTTCGACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
41195 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
66 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
41260 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
131 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
41316 ATTTACT
1 ATTTACT
41323 AAGCAATCTA
Statistics
Matches: 191, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
185 155 0.81
186 36 0.19
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
Found at i:43044 original size:14 final size:14
Alignment explanation
Indices: 43025--43081 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
43015 TTGAAATGAA
43025 AATCGCAACGAGAG
1 AATCGCAACGAGAG
43039 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
43056 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
43072 AATCGCAACG
1 AATCGCAACG
43082 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
16 6 0.16
17 6 0.16
19 8 0.21
ACGTcount: A:0.40, C:0.25, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:43062 original size:33 final size:33
Alignment explanation
Indices: 43017--43103 Score: 156
Period size: 33 Copynumber: 2.6 Consensus size: 33
43007 TCTTTTGGTT
43017 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
43050 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
43083 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
43104 CATTCTCTCG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:43063 original size:19 final size:18
Alignment explanation
Indices: 43024--43100 Score: 71
Period size: 19 Copynumber: 4.6 Consensus size: 18
43014 GTTGAAATGA
43024 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
43039 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
43056 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
43072 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
43089 AAAATCGCAACG
1 -AAATCGCAACG
43101 AGACATTCTC
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
14 16 0.31
16 10 0.20
17 7 0.14
19 18 0.35
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:43179 original size:20 final size:20
Alignment explanation
Indices: 43104--43193 Score: 68
Period size: 20 Copynumber: 4.8 Consensus size: 20
43094 CGCAACGAGA
*
43104 CATTCTCTCGTTGCGATTTC
1 CATTCTCTCGTTGCGATTTT
*
43124 CATT-TCGCGTTGCG-----
1 CATTCTCTCGTTGCGATTTT
***
43138 -ATTCTCTCGTTGCGACAGT
1 CATTCTCTCGTTGCGATTTT
43157 CATTCTCTCGTTGCGATTTT
1 CATTCTCTCGTTGCGATTTT
*
43177 CATTTATCTCGTTGCGA
1 CA-TTCTCTCGTTGCGA
43194 CTCTTCTGCA
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 22 0.39
21 13 0.23
ACGTcount: A:0.12, C:0.27, G:0.19, T:0.42
Consensus pattern (20 bp):
CATTCTCTCGTTGCGATTTT
Found at i:43315 original size:33 final size:33
Alignment explanation
Indices: 43273--43343 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
43263 AATACTAACT
*
43273 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
43306 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
43339 TGAAA
1 TGAAA
43344 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:43576 original size:22 final size:22
Alignment explanation
Indices: 43524--43578 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
43514 TGGTTGTGAG
**
43524 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
43546 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
43568 GGATTTCTTCG
1 GGATTTCTTCG
43579 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:43749 original size:20 final size:20
Alignment explanation
Indices: 43724--43897 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
43714 CTTTAAATAT
43724 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
43744 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
43766 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
43785 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
43805 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
43825 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
43845 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
43865 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
43885 CGCGTTGCGATTT
1 CGCGTTGCGATTT
43898 TAATATTCGC
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 113 0.86
21 15 0.11
22 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:43889 original size:60 final size:60
Alignment explanation
Indices: 43726--43897 Score: 245
Period size: 60 Copynumber: 2.9 Consensus size: 60
43716 TTAAATATCG
** *
43726 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
43787 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
43847 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
43898 TAATATTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:43906 original size:20 final size:21
Alignment explanation
Indices: 43865--43918 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
43855 TTTACGGATA
* *
43865 CGCGTTGCGA-TTTATGTGTT
1 CGCGTTGCGATTTTATATATT
43885 CGCGTTGCGATTTTA-ATATT
1 CGCGTTGCGATTTTATATATT
43905 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
43919 GGAAAATCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.13, C:0.17, G:0.26, T:0.44
Consensus pattern (21 bp):
CGCGTTGCGATTTTATATATT
Found at i:43911 original size:60 final size:60
Alignment explanation
Indices: 43724--43917 Score: 237
Period size: 60 Copynumber: 3.2 Consensus size: 60
43714 CTTTAAATAT
** *
43724 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACAGATA
* * *** * *
43785 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
* * * *
43845 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTA-ATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGA-TTTACAGATA
43905 CGCGTTGCGATTT
1 CGCGTTGCGATTT
43918 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
60 80 0.71
61 32 0.29
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:43934 original size:21 final size:20
Alignment explanation
Indices: 43910--43986 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
43900 ATATTCGCGT
43910 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
43931 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
43951 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
43973 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
43987 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:43977 original size:42 final size:43
Alignment explanation
Indices: 43884--43982 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 43
43874 ATTTATGTGT
* * *
43884 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATCGCGATTTTGCAAAA
** *
43925 TCGCAATGCGAATTTGTACTA-TCGCATCGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATCGCGATTTTGCAA-AA
*
43967 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
43983 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 10 0.22
42 32 0.70
43 4 0.09
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATCGCGATTTTGCAAAA
Found at i:43997 original size:20 final size:20
Alignment explanation
Indices: 43972--44023 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
43962 AAGAATCGCG
*
43972 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
43992 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
44012 TTGCGATTCTGG
1 TTGCGATTCTGG
44024 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:51107 original size:20 final size:22
Alignment explanation
Indices: 51082--51139 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
51072 TTCCCCTTGA
51082 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
51102 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
51125 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
51140 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:51205 original size:64 final size:63
Alignment explanation
Indices: 51127--51267 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
51117 TCTTTAACAT
* * *
51127 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
51190 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
51254 GTGCATCGATGCAC
1 GTGCATCGATGCAC
51268 ATTGAATATG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 21 0.31
64 46 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:59417 original size:16 final size:16
Alignment explanation
Indices: 59396--59428 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
59386 AGTACGAGCA
*
59396 TCACGAGTAGCATTGT
1 TCACGAGCAGCATTGT
59412 TCACGAGCAGCATTGT
1 TCACGAGCAGCATTGT
59428 T
1 T
59429 ACTGACTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (16 bp):
TCACGAGCAGCATTGT
Found at i:63528 original size:23 final size:23
Alignment explanation
Indices: 63498--63546 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
63488 TGGTGGTTGG
63498 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATGTTT-AACTTTAT
*
63521 TTTAATGGTATGTTTAAGTTTAT
1 TTTAATGGTATGTTTAACTTTAT
63544 TTT
1 TTT
63547 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATGTTTAACTTTAT
Found at i:69172 original size:24 final size:24
Alignment explanation
Indices: 69127--69176 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
69117 TGGTGGTTGG
69127 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
69151 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
69175 TT
1 TT
69177 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:78760 original size:26 final size:26
Alignment explanation
Indices: 78726--78776 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
78716 AATACTAAGG
**
78726 GTTATTCTGGTCATTTTTGAGTTCAT
1 GTTATTCTGACCATTTTTGAGTTCAT
*
78752 GTTATTCTGACCATTTTTGGGTTCA
1 GTTATTCTGACCATTTTTGAGTTCA
78777 AGGGCAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.51
Consensus pattern (26 bp):
GTTATTCTGACCATTTTTGAGTTCAT
Found at i:93117 original size:28 final size:31
Alignment explanation
Indices: 93086--93145 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 31
93076 TTATTTCATG
* *
93086 AGAC-TAAAATGAAAGAAA-GCA-GAAAATA
1 AGACATAAAATAAAAAAAATGCATGAAAATA
*
93114 AGACATAAATTAAAAAAAATGCATGAAAATA
1 AGACATAAAATAAAAAAAATGCATGAAAATA
93145 A
1 A
93146 ATACTGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 11 0.42
30 3 0.12
31 8 0.31
ACGTcount: A:0.65, C:0.07, G:0.13, T:0.15
Consensus pattern (31 bp):
AGACATAAAATAAAAAAAATGCATGAAAATA
Done.